From 1c7aeaa9f2051821191e37712f13ec3fce363149 Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Fri, 22 Mar 2019 01:07:28 +0000
Subject: [PATCH 001/258] Initial generation of blacklight OAI

---
 hyrax/Gemfile                               |  1 +
 hyrax/Gemfile.lock                          | 11 +++++++++++
 hyrax/app/controllers/catalog_controller.rb |  1 +
 hyrax/app/models/solr_document.rb           |  1 +
 hyrax/config/routes.rb                      |  2 ++
 5 files changed, 16 insertions(+)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 8c665020..1c937175 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -79,3 +79,4 @@ group :production do
 end
 
 gem 'willow_sword', git: 'https://github.com/CottageLabs/willow_sword.git', :branch => 'feature/prep_for_new_release'
+gem 'blacklight_oai_provider'
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index 3a0a592f..fdae4575 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -127,6 +127,10 @@ GEM
       bootstrap-sass (~> 3.0)
       openseadragon (>= 0.2.0)
       rails
+    blacklight_oai_provider (6.0.0)
+      blacklight (~> 6.0)
+      oai (~> 0.4)
+      rails (>= 4.2, < 6)
     bootstrap-datepicker-rails (1.8.0.1)
       railties (>= 3.0)
     bootstrap-sass (3.4.1)
@@ -250,6 +254,8 @@ GEM
       multipart-post (>= 1.2, < 3)
     faraday-encoding (0.0.4)
       faraday
+    faraday_middleware (0.13.1)
+      faraday (>= 0.7.4, < 1.0)
     fcrepo_wrapper (0.9.0)
       ruby-progressbar
     ffi (1.11.1)
@@ -511,6 +517,10 @@ GEM
       mini_portile2 (~> 2.4.0)
     nokogumbo (1.5.0)
       nokogiri
+    oai (0.4.0)
+      builder (>= 3.1.0)
+      faraday
+      faraday_middleware
     oauth (0.5.4)
     oauth2 (1.4.1)
       faraday (>= 0.8, < 0.16.0)
@@ -785,6 +795,7 @@ PLATFORMS
 
 DEPENDENCIES
   airbrake (~> 5.0)
+  blacklight_oai_provider
   bootstrap-datepicker-rails
   byebug
   coffee-rails (~> 4.2)
diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index cc194e36..c922f0d6 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -1,6 +1,7 @@
 class CatalogController < ApplicationController
   include Hydra::Catalog
   include Hydra::Controller::ControllerBehavior
+  include BlacklightOaiProvider::Controller
 
   # This filter applies the hydra access controls
   before_action :enforce_show_permissions, only: :show
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 5cea143e..db2414df 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -2,6 +2,7 @@
 class SolrDocument
   include Blacklight::Solr::Document
   include Blacklight::Gallery::OpenseadragonSolrDocument
+  include BlacklightOaiProvider::SolrDocument
 
   # Adds Hyrax behaviors to the SolrDocument.
   include Hyrax::SolrDocumentBehavior
diff --git a/hyrax/config/routes.rb b/hyrax/config/routes.rb
index ad5c159b..eaa4391b 100644
--- a/hyrax/config/routes.rb
+++ b/hyrax/config/routes.rb
@@ -17,6 +17,7 @@
 
   concern :exportable, Blacklight::Routes::Exportable.new
   concern :searchable, Blacklight::Routes::Searchable.new
+  concern :oai_provider, BlacklightOaiProvider::Routes.new
 
   curation_concerns_basic_routes
 
@@ -28,6 +29,7 @@
   end
 
   resource :catalog, only: [:index], as: 'catalog', path: '/catalog', controller: 'catalog' do
+    concerns :oai_provider
     concerns :searchable
   end
 

From 524ca7feac79706d0fa1d10b3c0af673d6f09b8e Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Wed, 24 Apr 2019 12:46:14 +0100
Subject: [PATCH 002/258] Added blacklight oai configuration

---
 hyrax/app/controllers/catalog_controller.rb | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index c922f0d6..2049caf4 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -30,6 +30,22 @@ def self.modified_field
     config.view.gallery.partials = [:index_header, :index]
     config.view.slideshow.partials = [:index]
 
+    config.oai = {
+      provider: {
+        repository_name: 'NIMS NGDR',
+        repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
+        record_prefix: 'oai:ngdrdemo',
+        admin_email: 'nims.ngdr@gmail.com',
+        sample_id: '9e9f5e08-8905-44bc-8d85-5bfc691a7e3c'
+      },
+      document: {
+        limit: 25,            # number of records returned with each request, default: 15
+        set_fields: nil #[        # ability to define ListSets, optional, default: nil
+            #{ label: 'language', solr_field: 'language_facet' }
+        #]
+      }
+    }
+
     ## Default parameters to send to solr for all search-like requests. See also SolrHelper#solr_search_params
     config.default_solr_params = {
       qt: "search",

From 78ed3edfaf38131ca817fc5b77113bf820ce4e91 Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Wed, 1 May 2019 14:28:17 +0100
Subject: [PATCH 003/258] tests for oai

---
 hyrax/spec/features/oai_pmh_spec.rb | 37 +++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 hyrax/spec/features/oai_pmh_spec.rb

diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
new file mode 100644
index 00000000..bace525e
--- /dev/null
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -0,0 +1,37 @@
+# From Samvera Hyku
+
+RSpec.describe "OAI PMH Support", type: :feature do
+  let(:user) { create(:user) }
+  let(:work) { create(:work, user: user) }
+  let(:identifier) { work.id }
+
+  before do
+    login_as(user, scope: :user)
+    work
+  end
+
+  context 'oai interface with works present' do
+    it 'lists metadata prefixess' do
+      visit oai_catalog_path(verb: 'ListMetadataFormats')
+      expect(page).to have_content('oai_dc')
+    end
+
+    it 'retrieves a list of records' do
+      visit oai_catalog_path(verb: 'ListRecords', metadataPrefix: 'oai_dc')
+      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).to have_content(work.title.first)
+    end
+
+    it 'retrieves a single record' do
+      visit oai_catalog_path(verb: 'GetRecord', metadataPrefix: 'oai_dc', identifier: identifier)
+      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).to have_content(work.title.first)
+    end
+
+    it 'retrieves a list of identifiers' do
+      visit oai_catalog_path(verb: 'ListIdentifiers', metadataPrefix: 'oai_dc')
+      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).not_to have_content(work.title.first)
+    end
+  end
+end
\ No newline at end of file

From 9921757668bdd6f36fa5c36cf9316e38e454e41a Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Wed, 1 May 2019 16:37:48 +0100
Subject: [PATCH 004/258] Change configuration for OAI

---
 hyrax/app/controllers/catalog_controller.rb | 2 +-
 hyrax/app/models/solr_document.rb           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index 2049caf4..1d41c9ad 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -34,7 +34,7 @@ def self.modified_field
       provider: {
         repository_name: 'NIMS NGDR',
         repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
-        record_prefix: 'oai:ngdrdemo',
+        record_prefix: 'ngdrdemo',
         admin_email: 'nims.ngdr@gmail.com',
         sample_id: '9e9f5e08-8905-44bc-8d85-5bfc691a7e3c'
       },
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index db2414df..317e4d49 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -1,8 +1,8 @@
 # frozen_string_literal: true
 class SolrDocument
   include Blacklight::Solr::Document
-  include Blacklight::Gallery::OpenseadragonSolrDocument
   include BlacklightOaiProvider::SolrDocument
+  include Blacklight::Gallery::OpenseadragonSolrDocument
 
   # Adds Hyrax behaviors to the SolrDocument.
   include Hyrax::SolrDocumentBehavior

From 4802a5e4c22546fdb25d33766a449434241e499a Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Mon, 13 May 2019 12:35:05 +0100
Subject: [PATCH 005/258] Replaced Blacklight OAI plugin for CL modified
 version

---
 hyrax/Gemfile          | 2 +-
 hyrax/config/routes.rb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 1c937175..fbcc9503 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -79,4 +79,4 @@ group :production do
 end
 
 gem 'willow_sword', git: 'https://github.com/CottageLabs/willow_sword.git', :branch => 'feature/prep_for_new_release'
-gem 'blacklight_oai_provider'
+gem 'blacklight_oai_provider', git: 'https://github.com/CottageLabs/blacklight_oai_provider.git', branch: 'master'
diff --git a/hyrax/config/routes.rb b/hyrax/config/routes.rb
index eaa4391b..57159bf0 100644
--- a/hyrax/config/routes.rb
+++ b/hyrax/config/routes.rb
@@ -17,7 +17,7 @@
 
   concern :exportable, Blacklight::Routes::Exportable.new
   concern :searchable, Blacklight::Routes::Searchable.new
-  concern :oai_provider, BlacklightOaiProvider::Routes.new
+  concern :oai_provider, BlacklightOaiProvider::Routes::Provider.new
 
   curation_concerns_basic_routes
 

From e5bdb7dd9e66b8a95e4083cf80c520d4a1b6d913 Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Mon, 13 May 2019 19:14:37 +0100
Subject: [PATCH 006/258] Updates pertaining to the older version of blacklight
 oai

---
 hyrax/app/controllers/catalog_controller.rb | 4 ++--
 hyrax/app/models/solr_document.rb           | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index 1d41c9ad..dd4bd263 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -1,7 +1,7 @@
 class CatalogController < ApplicationController
   include Hydra::Catalog
   include Hydra::Controller::ControllerBehavior
-  include BlacklightOaiProvider::Controller
+  include BlacklightOaiProvider::CatalogControllerBehavior
 
   # This filter applies the hydra access controls
   before_action :enforce_show_permissions, only: :show
@@ -36,7 +36,7 @@ def self.modified_field
         repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
         record_prefix: 'ngdrdemo',
         admin_email: 'nims.ngdr@gmail.com',
-        sample_id: '9e9f5e08-8905-44bc-8d85-5bfc691a7e3c'
+        sample_id: 'x059c7329'
       },
       document: {
         limit: 25,            # number of records returned with each request, default: 15
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 317e4d49..f149bbf5 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 class SolrDocument
   include Blacklight::Solr::Document
-  include BlacklightOaiProvider::SolrDocument
+  include BlacklightOaiProvider::SolrDocumentBehavior
   include Blacklight::Gallery::OpenseadragonSolrDocument
 
   # Adds Hyrax behaviors to the SolrDocument.

From cea6a7371855f6ac0cbd53d6b4c708b814368db6 Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Thu, 6 Jun 2019 20:02:46 +0100
Subject: [PATCH 007/258] Efforts to introduce jpcoar metadata format.

---
 hyrax/Gemfile.lock                          | 16 ++--
 hyrax/app/controllers/catalog_controller.rb |  5 +-
 hyrax/app/models/formats/jpcoar.rb          | 90 +++++++++++++++++++++
 hyrax/app/models/formats/oai_dc.rb          | 65 +++++++++++++++
 hyrax/app/models/metadata/jpcoar.rb         | 10 +++
 hyrax/app/models/solr_document.rb           | 41 ++++++++++
 6 files changed, 221 insertions(+), 6 deletions(-)
 create mode 100644 hyrax/app/models/formats/jpcoar.rb
 create mode 100644 hyrax/app/models/formats/oai_dc.rb
 create mode 100644 hyrax/app/models/metadata/jpcoar.rb

diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index fdae4575..ea2ac894 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -1,3 +1,13 @@
+GIT
+  remote: https://github.com/CottageLabs/blacklight_oai_provider.git
+  revision: 73d5f34315e313fb22084cfc52939d71e3c0728a
+  branch: master
+  specs:
+    blacklight_oai_provider (1.4.1)
+      blacklight (>= 6.1)
+      oai (~> 0.4.0)
+      rails (>= 4.2)
+
 GIT
   remote: https://github.com/CottageLabs/willow_sword.git
   revision: ab456d99eaa4d07ed12d0510330be07909981204
@@ -127,10 +137,6 @@ GEM
       bootstrap-sass (~> 3.0)
       openseadragon (>= 0.2.0)
       rails
-    blacklight_oai_provider (6.0.0)
-      blacklight (~> 6.0)
-      oai (~> 0.4)
-      rails (>= 4.2, < 6)
     bootstrap-datepicker-rails (1.8.0.1)
       railties (>= 3.0)
     bootstrap-sass (3.4.1)
@@ -795,7 +801,7 @@ PLATFORMS
 
 DEPENDENCIES
   airbrake (~> 5.0)
-  blacklight_oai_provider
+  blacklight_oai_provider!
   bootstrap-datepicker-rails
   byebug
   coffee-rails (~> 4.2)
diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index dd4bd263..566e2f08 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -33,7 +33,8 @@ def self.modified_field
     config.oai = {
       provider: {
         repository_name: 'NIMS NGDR',
-        repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
+        #repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
+        repository_url: 'http://localhost:3000/catalog/oai',
         record_prefix: 'ngdrdemo',
         admin_email: 'nims.ngdr@gmail.com',
         sample_id: 'x059c7329'
@@ -46,6 +47,8 @@ def self.modified_field
       }
     }
 
+    BlacklightOaiProvider::SolrDocumentProvider.register_format(Metadata::Jpcoar.instance)
+
     ## Default parameters to send to solr for all search-like requests. See also SolrHelper#solr_search_params
     config.default_solr_params = {
       qt: "search",
diff --git a/hyrax/app/models/formats/jpcoar.rb b/hyrax/app/models/formats/jpcoar.rb
new file mode 100644
index 00000000..6da1dcf1
--- /dev/null
+++ b/hyrax/app/models/formats/jpcoar.rb
@@ -0,0 +1,90 @@
+require 'builder'
+
+# This module provide JPCOAR export
+module Formats
+  module Jpcoar
+
+    FORMAT_JPCOAR = {
+        'tag': {
+            'name': 'jpcoar',
+            'attributes': {
+                'xmlns:xs' => "http://www.w3.org/2001/XMLSchema",
+                'xmlns:dc' => "http://purl.org/dc/elements/1.1/",
+                'xmlns:dcterms' => "http://purl.org/dc/terms/",
+                'xmlns:rioxxterms' => "http://www.rioxx.net/schema/v2.0/rioxxterms/",
+                'xmlns:datacite' => "https://schema.datacite.org/meta/kernel-4/",
+                'xmlns:oaire' => "http://namespace.openaire.eu/schema/oaire/",
+                'xmlns:dcndl' => "http://ndl.go.jp/dcndl/terms/",
+                'xmlns:jpcoar' => "https://github.com/JPCOAR/schema/blob/master/1.0/",
+                'xsi:schemaLocation' => "https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd"
+            }
+        },
+        'fields': {
+            'dc:title': 'title_tesim',
+            'dcterms:alternative': 'alternative_title_tesim',
+            'jpcoar:creator': {'function': 'creator'},
+            'jpcoar:contributor': {'function': 'contributor'},      # looks very similar to creator
+            'dcterms:accessRights': '',
+            'rioxxterms:apc': '',
+            'dc:rights': {'function': 'complex_rights'},
+            'jpcoar:rightsHolder': {'function': 'rightsHolder'},
+            'jpcoar:subject': 'subject_sim',
+            'datacite:description': '',
+            'dc:publisher': '',
+            'datacite:date': '',
+            'dc:language': '',
+            'dc:type': '',
+            'datacite:version': '',
+            'oaire:version': '',
+            'jpcoar:identifier': '',
+            'jpcoar:identifierRegistration': '',
+            'jpcoar:relation': '',
+            'dcterms:temporal': '',
+            'datacite:geoLocation': '',
+            'jpcoar:fundingReference': '',
+            'jpcoar:sourceIdentifier': '',
+            'jpcoar:sourceTitle': '',
+            'jpcoar:volume': '',
+            'jpcoar:issue': '',
+            'jpcoar:numPages': '',
+            'jpcoar:pageStart': '',
+            'jpcoar:pageEnd': '',
+            'dcndl:dissertationNumber': '',
+            'dcndl:degreeName': '',
+            'dcndl:dateGranted': '',
+            'jpcoar:degreeGrantor': '',
+            'jpcoar:conference': '',
+            'jpcoar:file': '',
+        }
+    }
+    # 'dcterms:isReferencedBy': {'function': 'full_resource_uri'}
+
+    def export_as_jpcoar_xml
+      xml = Builder::XmlMarkup.new
+      format = FORMAT_JPCOAR
+
+      xml.tag!(format[:'tag'][:'name'], format[:'tag'][:'attributes']) do
+        format[:'fields'].each do |field, mapping|
+          process_mapping(xml, field, mapping)
+        end
+      end
+      xml.target!
+    end
+
+    def to_jpcoar
+      export_as('jpcoar_xml')
+    end
+
+    def format(field, xml)
+      if mime_types.present?
+        Array.wrap(mime_types).each do |mime_type|
+          xml.tag!(field, mime_type, 'xsi:type' => 'dcterms:IMT')
+        end
+      end
+    end
+
+    def mime_types
+      self['content_mime_type_ssm']
+    end
+  end
+end
diff --git a/hyrax/app/models/formats/oai_dc.rb b/hyrax/app/models/formats/oai_dc.rb
new file mode 100644
index 00000000..7a839422
--- /dev/null
+++ b/hyrax/app/models/formats/oai_dc.rb
@@ -0,0 +1,65 @@
+module Formats
+  module OaiDc
+
+    FORMAT_OAI_DC = {
+      'tag': {
+        'name': 'oai_dc:dc',
+        'attributes': {
+          'xmlns:oai_dc': "http://www.openarchives.org/OAI/2.0/oai_dc/DERP",
+          'xmlns:dc': "http://purl.org/dc/elements/1.1/DERP",
+          'xmlns:xsi': "http://www.w3.org/2001/XMLSchema-instanceDERP",
+          'xsi:schemaLocation': "http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"
+        }
+      },
+      'fields': {
+        'dc:title': Solrizer.solr_name('title', :displayable),
+        'dc:creator': Solrizer.solr_name('creator', :displayable),
+        'dc:subject': Solrizer.solr_name('subject', :displayable),
+        'dc:description': Solrizer.solr_name('description', :displayable),
+        'dc:publisher': Solrizer.solr_name('publisher', :displayable),
+        'dc:contributor': Solrizer.solr_name('contributor', :displayable),
+        'dc:date': Solrizer.solr_name('date_uploaded', :displayable),
+        'dc:type': Solrizer.solr_name('resource_type', :displayable),
+        'dc:format': Solrizer.solr_name('format', :displayable),
+        'dc:identifier': Solrizer.solr_name('id', :displayable),
+        'dc:source': Solrizer.solr_name('', :displayable),
+        'dc:language': Solrizer.solr_name('language', :displayable),
+        'dc:relation': Solrizer.solr_name('', :displayable),
+        'dc:coverage': Solrizer.solr_name('', :displayable),
+        'dc:rights': Solrizer.solr_name('rights_statement', :displayable)
+      }
+=begin
+      'fields': {
+        'dc:title': 'title_tesim',
+        'dc:creator': '',
+        'dc:subject': 'subject_topic_ssm',
+        'dc:description': 'description_ssm',
+        'dc:publisher': 'publisher_ssm',
+        'dc:contributor': '',
+        'dc:date': 'date_issued_ssm',
+        'dc:type': 'type_of_resource_ssm',
+        'dc:format': 'content_format_ssm',
+        'dc:identifier': 'id',
+        'dc:source': '',
+        'dc:language': 'language_text_ssm',
+        'dc:relation': '',
+        'dc:coverage': '',
+        'dc:rights': 'rights_ssm'
+    }
+=end
+    }
+
+    def export_as_oai_dc_xml
+      xml = Builder::XmlMarkup.new
+      format = FORMAT_OAI_DC
+
+      xml.tag!(format[:'tag'][:'name'], format[:'tag'][:'attributes']) do
+        format[:'fields'].each do |field, mapping|
+          process_mapping(xml, field, mapping)
+        end
+      end
+      xml.target!
+    end
+
+  end
+end
diff --git a/hyrax/app/models/metadata/jpcoar.rb b/hyrax/app/models/metadata/jpcoar.rb
new file mode 100644
index 00000000..73386a71
--- /dev/null
+++ b/hyrax/app/models/metadata/jpcoar.rb
@@ -0,0 +1,10 @@
+# The JPCOAR metadata format for MDR
+class Metadata::Jpcoar < OAI::Provider::Metadata::Format
+
+  def initialize
+    @prefix = 'jpcoar'
+    @schema = 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
+    @namespace = 'https://github.com/JPCOAR/schema/blob/master/1.0/'
+  end
+
+end
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index f149bbf5..26e43a79 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -26,6 +26,47 @@ class SolrDocument
 
   use_extension( Hydra::ContentNegotiation )
 
+  include Formats::OaiDc
+  include Formats::Jpcoar
+
+  def process_mapping(xml, field, mapping)
+    if mapping.present?
+      if mapping.is_a?(Array)
+        mapping.each do |mapping_item|
+          # recurse and process each item in the array
+          process_mapping(xml, field, mapping_item)
+        end
+
+      elsif mapping.is_a?(Hash)
+        if mapping[:field].present?
+          Array.wrap(self[mapping[:field]]).each do |unparsed_value|
+            value = self.send(mapping[:'function'], unparsed_value, mapping[:'argument'] || '.')
+            xml.tag! field, value if value.present?
+          end
+        elsif mapping[:function].present?
+          value = self.send(mapping[:'function'], field, xml)
+        else
+          puts "WARNING: mapping #{mapping.inspect} is ignored"
+        end
+
+      elsif mapping.is_a?(String)
+        Array.wrap(self[mapping]).each do |value|
+          xml.tag! field, value
+        end
+      end
+
+    end
+  end
+
+  def xml_parse_and_select(unparsed_value, xpath_select)
+    # using some caching to avoid re-parsing the same content
+    key = unparsed_value.hash
+    @parsed_xml ||= {}
+    @parsed_xml[key] ||=  Nokogiri::XML(JSON.parse(unparsed_value).to_xml(root: 'root'))
+
+    @parsed_xml[key].xpath(xpath_select)
+  end
+
   def alternative_title
     self[Solrizer.solr_name('alternative_title', :stored_searchable)]
   end

From 9e61324128060032db95a2b52b0c3ab4065b1b25 Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Fri, 7 Jun 2019 14:20:29 +0100
Subject: [PATCH 008/258] Trying out new solr fields for oai

---
 hyrax/app/models/formats/jpcoar.rb | 26 +++++++++++++++++++-------
 hyrax/app/models/formats/oai_dc.rb |  3 ++-
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/hyrax/app/models/formats/jpcoar.rb b/hyrax/app/models/formats/jpcoar.rb
index 6da1dcf1..6c2e9b6e 100644
--- a/hyrax/app/models/formats/jpcoar.rb
+++ b/hyrax/app/models/formats/jpcoar.rb
@@ -20,20 +20,20 @@ module Jpcoar
             }
         },
         'fields': {
-            'dc:title': 'title_tesim',
-            'dcterms:alternative': 'alternative_title_tesim',
+            'dc:title': Solrizer.solr_name('title', :displayable),
+            'dcterms:alternative': Solrizer.solr_name('alternative_title', :displayable),
             'jpcoar:creator': {'function': 'creator'},
             'jpcoar:contributor': {'function': 'contributor'},      # looks very similar to creator
             'dcterms:accessRights': '',
             'rioxxterms:apc': '',
-            'dc:rights': {'function': 'complex_rights'},
-            'jpcoar:rightsHolder': {'function': 'rightsHolder'},
+            'dc:rights': Solrizer.solr_name('rights_statement', :displayable),
+            'jpcoar:rightsHolder': {'function': 'rights_holder'},
             'jpcoar:subject': 'subject_sim',
             'datacite:description': '',
-            'dc:publisher': '',
+            'dc:publisher': Solrizer.solr_name('publisher', :displayable),
             'datacite:date': '',
-            'dc:language': '',
-            'dc:type': '',
+            'dc:language': Solrizer.solr_name('language', :displayable),
+            'dc:type': Solrizer.solr_name('resource_type', :displayable),
             'datacite:version': '',
             'oaire:version': '',
             'jpcoar:identifier': '',
@@ -86,5 +86,17 @@ def format(field, xml)
     def mime_types
       self['content_mime_type_ssm']
     end
+
+    def creator
+    end
+
+    def contributor
+    end
+
+    def rights_holder
+    end
+
+
+
   end
 end
diff --git a/hyrax/app/models/formats/oai_dc.rb b/hyrax/app/models/formats/oai_dc.rb
index 7a839422..ef4ffee3 100644
--- a/hyrax/app/models/formats/oai_dc.rb
+++ b/hyrax/app/models/formats/oai_dc.rb
@@ -28,6 +28,8 @@ module OaiDc
         'dc:coverage': Solrizer.solr_name('', :displayable),
         'dc:rights': Solrizer.solr_name('rights_statement', :displayable)
       }
+    }
+
 =begin
       'fields': {
         'dc:title': 'title_tesim',
@@ -47,7 +49,6 @@ module OaiDc
         'dc:rights': 'rights_ssm'
     }
 =end
-    }
 
     def export_as_oai_dc_xml
       xml = Builder::XmlMarkup.new

From a9900eba65026b689ac8c9d39681ec3c7b105e4f Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 9 Aug 2019 13:39:24 +0100
Subject: [PATCH 009/258] wip - working dc (needs more fields mapping), some
 way to jpcoar

---
 hyrax/app/models/document/jpcoar.rb |  83 +++++++++++++++++++++
 hyrax/app/models/metadata/jpcoar.rb |  50 ++++++++++++-
 hyrax/app/models/solr_document.rb   | 109 ++++++++++++++++++----------
 3 files changed, 201 insertions(+), 41 deletions(-)
 create mode 100644 hyrax/app/models/document/jpcoar.rb

diff --git a/hyrax/app/models/document/jpcoar.rb b/hyrax/app/models/document/jpcoar.rb
new file mode 100644
index 00000000..e967d8e3
--- /dev/null
+++ b/hyrax/app/models/document/jpcoar.rb
@@ -0,0 +1,83 @@
+# frozen_string_literal: true
+
+require 'builder'
+
+# This module provide Jpcoar export based on the document's semantic values
+module Document::Jpcoar
+  def self.extended(document)
+    # Register our exportable formats
+    Document::Jpcoar.register_export_formats(document)
+  end
+
+  def self.register_export_formats(document)
+    document.will_export_as(:jpcoar_xml, 'text/xml')
+  end
+
+  # JA - these are taken from formats/jpcoar (although there are two 'version' (datacite and openaire) so I've just used datacite)
+  # JA - I've done these as hashes so we can map field name to the field with the correct namespace / name
+  # JA - the namespace bit might be wrong, we may just want them all to be jpcoar?
+  def jpcoar_field_names
+    { title: 'dc:title',
+      alternative: 'dcterms:alternative',
+      creator: 'jpcoar:creator',
+      contributor: 'jpcoar:contributor',
+      access_rights: 'dcterms:accessRights',
+      apc: 'rioxxterms:apc',
+      rights: 'dc:rights',
+      rights_older: 'jpcoar:rightsHolder',
+      subject: 'jpcoar:subject',
+      description: 'datacite:description',
+      publisher: 'dc:publisher',
+      date: 'datacite:date',
+      language: 'dc:language',
+      type: 'dc:type',
+      version: 'datacite:version',
+      identifier: 'jpcoar:identifier',
+      identifier_registration: 'jpcoar:identifierRegistration',
+      relation: 'jpcoar:relation',
+      temporal: 'dcterms:temporal',
+      geo_location: 'datacite:geoLocation',
+      funding_reference: 'jpcoar:fundingReference',
+      source_identifier: 'jpcoar:sourceIdentifier',
+      source_title: 'jpcoar:sourceTitle',
+      volume: 'jpcoar:volume',
+      issue: 'jpcoar:issue',
+      num_pages: 'jpcoar:numPages',
+      page_start: 'jpcoar:pageStart',
+      page_end: 'jpcoar:pageEnd',
+      dissertation_number: 'dcndl:dissertationNumber',
+      degree_name: 'dcndl:degreeName',
+      dateGranted: 'dcndl:dateGranted',
+      degree_grantor: 'jpcoar:degreeGrantor',
+      conference: 'jpcoar:conference',
+      file: 'jpcoar:file' }
+  end
+
+  # jpcoar elements are mapped against the #jpcoar_field_names whitelist.
+  # JA - I think jpcoar is a nested xml so this will need to be refactored
+  def export_as_jpcoar_xml
+    xml = Builder::XmlMarkup.new
+    xml.tag!('jpcoar',
+             'xmlns:dc' => 'http://purl.org/dc/elements/1.1/',
+             'xmlns:dcterms' => 'http://purl.org/dc/terms/',
+             'xmlns:rioxxterms' => 'http://www.rioxx.net/schema/v2.0/rioxxterms/',
+             'xmlns:datacite' => 'https://schema.datacite.org/meta/kernel-4/',
+             'xmlns:openaire' => 'http://namespace.openaire.eu/schema/oaire/',
+             'xmlns:dcndl' => 'http://ndl.go.jp/dcndl/terms/',
+             'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
+             'xsi:schemaLocation ' => 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd') do
+      to_semantic_values.select { |field, _values| jpcoar_field_name? field }.each do |field, values|
+        Array.wrap(values).each do |v|
+          xml.tag! jpcoar_field_names[field], v
+        end
+      end
+    end
+    xml.target!
+  end
+
+  private
+
+  def jpcoar_field_name?(field)
+    jpcoar_field_names.keys.include? field.to_sym
+  end
+end
diff --git a/hyrax/app/models/metadata/jpcoar.rb b/hyrax/app/models/metadata/jpcoar.rb
index 73386a71..cafe0c3d 100644
--- a/hyrax/app/models/metadata/jpcoar.rb
+++ b/hyrax/app/models/metadata/jpcoar.rb
@@ -1,10 +1,58 @@
 # The JPCOAR metadata format for MDR
 class Metadata::Jpcoar < OAI::Provider::Metadata::Format
-
+  
   def initialize
     @prefix = 'jpcoar'
     @schema = 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
     @namespace = 'https://github.com/JPCOAR/schema/blob/master/1.0/'
+    @element_namespace = 'jpcoar'
+    @fields = %i[title
+                 alternative
+                 creator
+                 contributor
+                 accessRights
+                 apc
+                 rights
+                 rightsHolder
+                 subject
+                 description
+                 publisher
+                 date
+                 language
+                 type
+                 version
+                 version
+                 identifier
+                 identifierRegistration
+                 relation
+                 temporal
+                 geoLocation
+                 fundingReference
+                 sourceIdentifier
+                 sourceTitle
+                 volume
+                 issue
+                 numPages
+                 pageStart
+                 pageEnd
+                 dissertationNumber
+                 degreeName
+                 dateGranted
+                 degreeGrantor
+                 conference
+                 file]
   end
 
+  def header_specification
+    {
+      'xmlns:dc' => 'http://purl.org/dc/elements/1.1/',
+      'xmlns:dcterms' => 'http://purl.org/dc/terms/',
+      'xmlns:rioxxterms' => 'http://www.rioxx.net/schema/v2.0/rioxxterms/',
+      'xmlns:datacite' => 'https://schema.datacite.org/meta/kernel-4/',
+      'xmlns:openaire' => 'http://namespace.openaire.eu/schema/oaire/',
+      'xmlns:dcndl' => 'http://ndl.go.jp/dcndl/terms/',
+      'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
+      'xsi:schemaLocation ' => 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
+    }
+  end
 end
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 26e43a79..6403facb 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -21,51 +21,80 @@ class SolrDocument
   # and Blacklight::Document::SemanticFields#to_semantic_values
   # Recommendation: Use field names from Dublin Core
   use_extension(Blacklight::Document::DublinCore)
+  # JA - add blacklight document for jpcoar
+  use_extension(Document::Jpcoar)
+
+  # JA - add field_semantics for oai_dc
+  field_semantics.merge!(
+    contributor: '', # @todo - extract anything other than author from complex person, may need new solr field
+    creator: 'complex_person_author_tesim',
+    date: 'date_tesim',
+    description: 'description_tesim',
+    identifier: 'complex_identifier_tesim', # @todo
+    language: 'language_tesim',
+    publisher: 'publisher_tesim',
+    relation: '', # @todo have a think about what to map here
+    rights: 'rights_tesim',
+    subject: 'subject_tesim',
+    title: 'title_tesim',
+    type: 'resource_type_tesim'
+    # todo add jpcoar fields
+  )
+
+  # JA - to_jpcoar
+  def to_jpcoar
+    export_as('jpcoar_xml')
+  end
 
   # Do content negotiation for AF models.
 
   use_extension( Hydra::ContentNegotiation )
 
-  include Formats::OaiDc
-  include Formats::Jpcoar
-
-  def process_mapping(xml, field, mapping)
-    if mapping.present?
-      if mapping.is_a?(Array)
-        mapping.each do |mapping_item|
-          # recurse and process each item in the array
-          process_mapping(xml, field, mapping_item)
-        end
-
-      elsif mapping.is_a?(Hash)
-        if mapping[:field].present?
-          Array.wrap(self[mapping[:field]]).each do |unparsed_value|
-            value = self.send(mapping[:'function'], unparsed_value, mapping[:'argument'] || '.')
-            xml.tag! field, value if value.present?
-          end
-        elsif mapping[:function].present?
-          value = self.send(mapping[:'function'], field, xml)
-        else
-          puts "WARNING: mapping #{mapping.inspect} is ignored"
-        end
-
-      elsif mapping.is_a?(String)
-        Array.wrap(self[mapping]).each do |value|
-          xml.tag! field, value
-        end
-      end
-
-    end
-  end
-
-  def xml_parse_and_select(unparsed_value, xpath_select)
-    # using some caching to avoid re-parsing the same content
-    key = unparsed_value.hash
-    @parsed_xml ||= {}
-    @parsed_xml[key] ||=  Nokogiri::XML(JSON.parse(unparsed_value).to_xml(root: 'root'))
-
-    @parsed_xml[key].xpath(xpath_select)
-  end
+  # JA - I wasn't sure whether the OaiDc was needed as I think Blacklight::Document::DublinCore is doing this already, when used with field_semantics I added
+  # include Formats::OaiDc
+
+  # I think my Document::Jpcoar above is doing the same as Jpcoar here, but needs additional processing
+  # include Formats::Jpcoar
+
+  # JA - commented out during testing Document::Jpcoar
+  #  I think this can be moved into Document::Jpcoar and used for building the xml there
+  # def process_mapping(xml, field, mapping)
+  #   if mapping.present?
+  #     if mapping.is_a?(Array)
+  #       mapping.each do |mapping_item|
+  #         # recurse and process each item in the array
+  #         process_mapping(xml, field, mapping_item)
+  #       end
+
+  #     elsif mapping.is_a?(Hash)
+  #       if mapping[:field].present?
+  #         Array.wrap(self[mapping[:field]]).each do |unparsed_value|
+  #           value = self.send(mapping[:'function'], unparsed_value, mapping[:'argument'] || '.')
+  #           xml.tag! field, value if value.present?
+  #         end
+  #       elsif mapping[:function].present?
+  #         value = self.send(mapping[:'function'], field, xml)
+  #       else
+  #         puts "WARNING: mapping #{mapping.inspect} is ignored"
+  #       end
+
+  #     elsif mapping.is_a?(String)
+  #       Array.wrap(self[mapping]).each do |value|
+  #         xml.tag! field, value
+  #       end
+  #     end
+
+  #   end
+  # end
+
+  # def xml_parse_and_select(unparsed_value, xpath_select)
+  #   # using some caching to avoid re-parsing the same content
+  #   key = unparsed_value.hash
+  #   @parsed_xml ||= {}
+  #   @parsed_xml[key] ||=  Nokogiri::XML(JSON.parse(unparsed_value).to_xml(root: 'root'))
+
+  #   @parsed_xml[key].xpath(xpath_select)
+  # end
 
   def alternative_title
     self[Solrizer.solr_name('alternative_title', :stored_searchable)]

From 0b7bf9ed37a62bf61bd0e63264e506444c73ac97 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 2 Oct 2019 00:18:15 +0900
Subject: [PATCH 010/258] add "readonly" option to disable name and email

---
 .../app/views/hyrax/contact_form/new.html.erb | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/contact_form/new.html.erb

diff --git a/hyrax/app/views/hyrax/contact_form/new.html.erb b/hyrax/app/views/hyrax/contact_form/new.html.erb
new file mode 100644
index 00000000..c9076662
--- /dev/null
+++ b/hyrax/app/views/hyrax/contact_form/new.html.erb
@@ -0,0 +1,50 @@
+<div class="alert alert-info">
+  <%= render 'directions' %>
+</div>
+
+<h1>
+    <%= t('hyrax.contact_form.header') %>
+</h1>
+
+<% if user_signed_in? %>
+  <% nm = current_user.name %>
+  <% em = current_user.email %>
+<% else %>
+  <% nm = '' %>
+  <% em = '' %>
+<% end %>
+
+<%= form_for @contact_form, url: hyrax.contact_form_index_path,
+                            html: { class: 'form-horizontal' } do |f| %>
+  <%= f.text_field :contact_method, class: 'hide' %>
+  <div class="form-group">
+    <%= f.label :category, t('hyrax.contact_form.type_label'), class: "col-sm-2 control-label" %>
+    <% issue_types = Hyrax::ContactForm.issue_types_for_locale.dup %>
+    <% issue_types.unshift([t('hyrax.contact_form.select_type'), nil]) %>
+    <div class="col-sm-10">
+      <%= f.select 'category', options_for_select(issue_types), {}, {class: 'form-control', required: true } %>
+    </div>
+  </div>
+
+  <div class="form-group">
+    <%= f.label :name, t('hyrax.contact_form.name_label'), class: "col-sm-2 control-label" %>
+    <div class="col-sm-10"><%= f.text_field :name, value: nm, class: 'form-control', required: true, readonly: user_signed_in? %></div>
+  </div>
+
+  <div class="form-group">
+    <%= f.label :email, t('hyrax.contact_form.email_label'), class: "col-sm-2 control-label" %>
+    <div class="col-sm-10"><%= f.text_field :email, value: em, class: 'form-control', required: true, readonly: user_signed_in? %></div>
+  </div>
+
+  <div class="form-group">
+    <%= f.label :subject, t('hyrax.contact_form.subject_label'), class: "col-sm-2 control-label" %>
+    <div class="col-sm-10"><%= f.text_field :subject, class: 'form-control', required: true %></div>
+  </div>
+
+  <div class="form-group">
+    <%= f.label :message, t('hyrax.contact_form.message_label'), class: "col-sm-2 control-label" %>
+    <div class="col-sm-10"><%= f.text_area :message, rows: 4, class: 'form-control', required: true %></div>
+  </div>
+
+  <%= f.submit value: t('hyrax.contact_form.button_label'), class: "btn btn-primary" %>
+<% end %>

From 9aeaaf4be9bcd4aed76cc164db347ca1da89c16b Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 12 Oct 2019 20:30:03 +0900
Subject: [PATCH 011/258] add feature spec file for the contact form

---
 hyrax/db/schema.rb                       |  3 ++-
 hyrax/spec/features/contact_form_spec.rb | 27 ++++++++++++++++++++++++
 2 files changed, 29 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/spec/features/contact_form_spec.rb

diff --git a/hyrax/db/schema.rb b/hyrax/db/schema.rb
index 51741bd8..e959d543 100644
--- a/hyrax/db/schema.rb
+++ b/hyrax/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20190822033353) do
+ActiveRecord::Schema.define(version: 20190930025332) do
 
   create_table "bookmarks", force: :cascade do |t|
     t.integer "user_id", null: false
@@ -547,6 +547,7 @@
     t.integer "failed_attempts", default: 0, null: false
     t.string "unlock_token"
     t.datetime "locked_at"
+    t.string "remember_token"
     t.index ["email"], name: "index_users_on_email"
     t.index ["reset_password_token"], name: "index_users_on_reset_password_token", unique: true
     t.index ["username"], name: "index_users_on_username", unique: true
diff --git a/hyrax/spec/features/contact_form_spec.rb b/hyrax/spec/features/contact_form_spec.rb
new file mode 100644
index 00000000..8ad793fc
--- /dev/null
+++ b/hyrax/spec/features/contact_form_spec.rb
@@ -0,0 +1,27 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+# NOTE: If you generated more than one work, you have to set "js: true"
+RSpec.feature 'Show Contact form', js: false do
+  context 'a logged in user' do
+    let(:user_attributes) do
+      { email: 'test@example.com' }
+    end
+    let(:user) do
+      User.new(user_attributes) { |u| u.save(validate: false) }
+    end
+
+    before do
+      login_as user
+    end
+
+    scenario do
+      visit '/contact'
+
+      it "should display contact form" do
+        expect(page).to have_field 'Your Name', with: user.username, readonly: true
+        expect(page).to have_field 'Your Email', with: user.email, readonly: true
+      end
+    end
+  end
+end

From 747affc59efc9d449d6d57f3dc736e5767fa9e98 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Thu, 17 Oct 2019 08:54:55 +0100
Subject: [PATCH 012/258] Removed JPCOAR OAI format so we can get OAI:DC out of
 the door

---
 hyrax/app/controllers/catalog_controller.rb |   2 -
 hyrax/app/models/document/jpcoar.rb         |  83 ----------------
 hyrax/app/models/formats/jpcoar.rb          | 102 --------------------
 hyrax/app/models/formats/oai_dc.rb          |  66 -------------
 hyrax/app/models/metadata/jpcoar.rb         |  58 -----------
 hyrax/app/models/solr_document.rb           |  55 +----------
 6 files changed, 1 insertion(+), 365 deletions(-)
 delete mode 100644 hyrax/app/models/document/jpcoar.rb
 delete mode 100644 hyrax/app/models/formats/jpcoar.rb
 delete mode 100644 hyrax/app/models/formats/oai_dc.rb
 delete mode 100644 hyrax/app/models/metadata/jpcoar.rb

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index eca1e7e3..f5939e4b 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -47,8 +47,6 @@ def self.modified_field
       }
     }
 
-    BlacklightOaiProvider::SolrDocumentProvider.register_format(Metadata::Jpcoar.instance)
-
     ## Default parameters to send to solr for all search-like requests. See also SolrHelper#solr_search_params
     config.default_solr_params = {
       qt: "search",
diff --git a/hyrax/app/models/document/jpcoar.rb b/hyrax/app/models/document/jpcoar.rb
deleted file mode 100644
index e967d8e3..00000000
--- a/hyrax/app/models/document/jpcoar.rb
+++ /dev/null
@@ -1,83 +0,0 @@
-# frozen_string_literal: true
-
-require 'builder'
-
-# This module provide Jpcoar export based on the document's semantic values
-module Document::Jpcoar
-  def self.extended(document)
-    # Register our exportable formats
-    Document::Jpcoar.register_export_formats(document)
-  end
-
-  def self.register_export_formats(document)
-    document.will_export_as(:jpcoar_xml, 'text/xml')
-  end
-
-  # JA - these are taken from formats/jpcoar (although there are two 'version' (datacite and openaire) so I've just used datacite)
-  # JA - I've done these as hashes so we can map field name to the field with the correct namespace / name
-  # JA - the namespace bit might be wrong, we may just want them all to be jpcoar?
-  def jpcoar_field_names
-    { title: 'dc:title',
-      alternative: 'dcterms:alternative',
-      creator: 'jpcoar:creator',
-      contributor: 'jpcoar:contributor',
-      access_rights: 'dcterms:accessRights',
-      apc: 'rioxxterms:apc',
-      rights: 'dc:rights',
-      rights_older: 'jpcoar:rightsHolder',
-      subject: 'jpcoar:subject',
-      description: 'datacite:description',
-      publisher: 'dc:publisher',
-      date: 'datacite:date',
-      language: 'dc:language',
-      type: 'dc:type',
-      version: 'datacite:version',
-      identifier: 'jpcoar:identifier',
-      identifier_registration: 'jpcoar:identifierRegistration',
-      relation: 'jpcoar:relation',
-      temporal: 'dcterms:temporal',
-      geo_location: 'datacite:geoLocation',
-      funding_reference: 'jpcoar:fundingReference',
-      source_identifier: 'jpcoar:sourceIdentifier',
-      source_title: 'jpcoar:sourceTitle',
-      volume: 'jpcoar:volume',
-      issue: 'jpcoar:issue',
-      num_pages: 'jpcoar:numPages',
-      page_start: 'jpcoar:pageStart',
-      page_end: 'jpcoar:pageEnd',
-      dissertation_number: 'dcndl:dissertationNumber',
-      degree_name: 'dcndl:degreeName',
-      dateGranted: 'dcndl:dateGranted',
-      degree_grantor: 'jpcoar:degreeGrantor',
-      conference: 'jpcoar:conference',
-      file: 'jpcoar:file' }
-  end
-
-  # jpcoar elements are mapped against the #jpcoar_field_names whitelist.
-  # JA - I think jpcoar is a nested xml so this will need to be refactored
-  def export_as_jpcoar_xml
-    xml = Builder::XmlMarkup.new
-    xml.tag!('jpcoar',
-             'xmlns:dc' => 'http://purl.org/dc/elements/1.1/',
-             'xmlns:dcterms' => 'http://purl.org/dc/terms/',
-             'xmlns:rioxxterms' => 'http://www.rioxx.net/schema/v2.0/rioxxterms/',
-             'xmlns:datacite' => 'https://schema.datacite.org/meta/kernel-4/',
-             'xmlns:openaire' => 'http://namespace.openaire.eu/schema/oaire/',
-             'xmlns:dcndl' => 'http://ndl.go.jp/dcndl/terms/',
-             'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
-             'xsi:schemaLocation ' => 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd') do
-      to_semantic_values.select { |field, _values| jpcoar_field_name? field }.each do |field, values|
-        Array.wrap(values).each do |v|
-          xml.tag! jpcoar_field_names[field], v
-        end
-      end
-    end
-    xml.target!
-  end
-
-  private
-
-  def jpcoar_field_name?(field)
-    jpcoar_field_names.keys.include? field.to_sym
-  end
-end
diff --git a/hyrax/app/models/formats/jpcoar.rb b/hyrax/app/models/formats/jpcoar.rb
deleted file mode 100644
index 6c2e9b6e..00000000
--- a/hyrax/app/models/formats/jpcoar.rb
+++ /dev/null
@@ -1,102 +0,0 @@
-require 'builder'
-
-# This module provide JPCOAR export
-module Formats
-  module Jpcoar
-
-    FORMAT_JPCOAR = {
-        'tag': {
-            'name': 'jpcoar',
-            'attributes': {
-                'xmlns:xs' => "http://www.w3.org/2001/XMLSchema",
-                'xmlns:dc' => "http://purl.org/dc/elements/1.1/",
-                'xmlns:dcterms' => "http://purl.org/dc/terms/",
-                'xmlns:rioxxterms' => "http://www.rioxx.net/schema/v2.0/rioxxterms/",
-                'xmlns:datacite' => "https://schema.datacite.org/meta/kernel-4/",
-                'xmlns:oaire' => "http://namespace.openaire.eu/schema/oaire/",
-                'xmlns:dcndl' => "http://ndl.go.jp/dcndl/terms/",
-                'xmlns:jpcoar' => "https://github.com/JPCOAR/schema/blob/master/1.0/",
-                'xsi:schemaLocation' => "https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd"
-            }
-        },
-        'fields': {
-            'dc:title': Solrizer.solr_name('title', :displayable),
-            'dcterms:alternative': Solrizer.solr_name('alternative_title', :displayable),
-            'jpcoar:creator': {'function': 'creator'},
-            'jpcoar:contributor': {'function': 'contributor'},      # looks very similar to creator
-            'dcterms:accessRights': '',
-            'rioxxterms:apc': '',
-            'dc:rights': Solrizer.solr_name('rights_statement', :displayable),
-            'jpcoar:rightsHolder': {'function': 'rights_holder'},
-            'jpcoar:subject': 'subject_sim',
-            'datacite:description': '',
-            'dc:publisher': Solrizer.solr_name('publisher', :displayable),
-            'datacite:date': '',
-            'dc:language': Solrizer.solr_name('language', :displayable),
-            'dc:type': Solrizer.solr_name('resource_type', :displayable),
-            'datacite:version': '',
-            'oaire:version': '',
-            'jpcoar:identifier': '',
-            'jpcoar:identifierRegistration': '',
-            'jpcoar:relation': '',
-            'dcterms:temporal': '',
-            'datacite:geoLocation': '',
-            'jpcoar:fundingReference': '',
-            'jpcoar:sourceIdentifier': '',
-            'jpcoar:sourceTitle': '',
-            'jpcoar:volume': '',
-            'jpcoar:issue': '',
-            'jpcoar:numPages': '',
-            'jpcoar:pageStart': '',
-            'jpcoar:pageEnd': '',
-            'dcndl:dissertationNumber': '',
-            'dcndl:degreeName': '',
-            'dcndl:dateGranted': '',
-            'jpcoar:degreeGrantor': '',
-            'jpcoar:conference': '',
-            'jpcoar:file': '',
-        }
-    }
-    # 'dcterms:isReferencedBy': {'function': 'full_resource_uri'}
-
-    def export_as_jpcoar_xml
-      xml = Builder::XmlMarkup.new
-      format = FORMAT_JPCOAR
-
-      xml.tag!(format[:'tag'][:'name'], format[:'tag'][:'attributes']) do
-        format[:'fields'].each do |field, mapping|
-          process_mapping(xml, field, mapping)
-        end
-      end
-      xml.target!
-    end
-
-    def to_jpcoar
-      export_as('jpcoar_xml')
-    end
-
-    def format(field, xml)
-      if mime_types.present?
-        Array.wrap(mime_types).each do |mime_type|
-          xml.tag!(field, mime_type, 'xsi:type' => 'dcterms:IMT')
-        end
-      end
-    end
-
-    def mime_types
-      self['content_mime_type_ssm']
-    end
-
-    def creator
-    end
-
-    def contributor
-    end
-
-    def rights_holder
-    end
-
-
-
-  end
-end
diff --git a/hyrax/app/models/formats/oai_dc.rb b/hyrax/app/models/formats/oai_dc.rb
deleted file mode 100644
index ef4ffee3..00000000
--- a/hyrax/app/models/formats/oai_dc.rb
+++ /dev/null
@@ -1,66 +0,0 @@
-module Formats
-  module OaiDc
-
-    FORMAT_OAI_DC = {
-      'tag': {
-        'name': 'oai_dc:dc',
-        'attributes': {
-          'xmlns:oai_dc': "http://www.openarchives.org/OAI/2.0/oai_dc/DERP",
-          'xmlns:dc': "http://purl.org/dc/elements/1.1/DERP",
-          'xmlns:xsi': "http://www.w3.org/2001/XMLSchema-instanceDERP",
-          'xsi:schemaLocation': "http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"
-        }
-      },
-      'fields': {
-        'dc:title': Solrizer.solr_name('title', :displayable),
-        'dc:creator': Solrizer.solr_name('creator', :displayable),
-        'dc:subject': Solrizer.solr_name('subject', :displayable),
-        'dc:description': Solrizer.solr_name('description', :displayable),
-        'dc:publisher': Solrizer.solr_name('publisher', :displayable),
-        'dc:contributor': Solrizer.solr_name('contributor', :displayable),
-        'dc:date': Solrizer.solr_name('date_uploaded', :displayable),
-        'dc:type': Solrizer.solr_name('resource_type', :displayable),
-        'dc:format': Solrizer.solr_name('format', :displayable),
-        'dc:identifier': Solrizer.solr_name('id', :displayable),
-        'dc:source': Solrizer.solr_name('', :displayable),
-        'dc:language': Solrizer.solr_name('language', :displayable),
-        'dc:relation': Solrizer.solr_name('', :displayable),
-        'dc:coverage': Solrizer.solr_name('', :displayable),
-        'dc:rights': Solrizer.solr_name('rights_statement', :displayable)
-      }
-    }
-
-=begin
-      'fields': {
-        'dc:title': 'title_tesim',
-        'dc:creator': '',
-        'dc:subject': 'subject_topic_ssm',
-        'dc:description': 'description_ssm',
-        'dc:publisher': 'publisher_ssm',
-        'dc:contributor': '',
-        'dc:date': 'date_issued_ssm',
-        'dc:type': 'type_of_resource_ssm',
-        'dc:format': 'content_format_ssm',
-        'dc:identifier': 'id',
-        'dc:source': '',
-        'dc:language': 'language_text_ssm',
-        'dc:relation': '',
-        'dc:coverage': '',
-        'dc:rights': 'rights_ssm'
-    }
-=end
-
-    def export_as_oai_dc_xml
-      xml = Builder::XmlMarkup.new
-      format = FORMAT_OAI_DC
-
-      xml.tag!(format[:'tag'][:'name'], format[:'tag'][:'attributes']) do
-        format[:'fields'].each do |field, mapping|
-          process_mapping(xml, field, mapping)
-        end
-      end
-      xml.target!
-    end
-
-  end
-end
diff --git a/hyrax/app/models/metadata/jpcoar.rb b/hyrax/app/models/metadata/jpcoar.rb
deleted file mode 100644
index cafe0c3d..00000000
--- a/hyrax/app/models/metadata/jpcoar.rb
+++ /dev/null
@@ -1,58 +0,0 @@
-# The JPCOAR metadata format for MDR
-class Metadata::Jpcoar < OAI::Provider::Metadata::Format
-  
-  def initialize
-    @prefix = 'jpcoar'
-    @schema = 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
-    @namespace = 'https://github.com/JPCOAR/schema/blob/master/1.0/'
-    @element_namespace = 'jpcoar'
-    @fields = %i[title
-                 alternative
-                 creator
-                 contributor
-                 accessRights
-                 apc
-                 rights
-                 rightsHolder
-                 subject
-                 description
-                 publisher
-                 date
-                 language
-                 type
-                 version
-                 version
-                 identifier
-                 identifierRegistration
-                 relation
-                 temporal
-                 geoLocation
-                 fundingReference
-                 sourceIdentifier
-                 sourceTitle
-                 volume
-                 issue
-                 numPages
-                 pageStart
-                 pageEnd
-                 dissertationNumber
-                 degreeName
-                 dateGranted
-                 degreeGrantor
-                 conference
-                 file]
-  end
-
-  def header_specification
-    {
-      'xmlns:dc' => 'http://purl.org/dc/elements/1.1/',
-      'xmlns:dcterms' => 'http://purl.org/dc/terms/',
-      'xmlns:rioxxterms' => 'http://www.rioxx.net/schema/v2.0/rioxxterms/',
-      'xmlns:datacite' => 'https://schema.datacite.org/meta/kernel-4/',
-      'xmlns:openaire' => 'http://namespace.openaire.eu/schema/oaire/',
-      'xmlns:dcndl' => 'http://ndl.go.jp/dcndl/terms/',
-      'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
-      'xsi:schemaLocation ' => 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
-    }
-  end
-end
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 6403facb..13444b29 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -21,10 +21,8 @@ class SolrDocument
   # and Blacklight::Document::SemanticFields#to_semantic_values
   # Recommendation: Use field names from Dublin Core
   use_extension(Blacklight::Document::DublinCore)
-  # JA - add blacklight document for jpcoar
-  use_extension(Document::Jpcoar)
 
-  # JA - add field_semantics for oai_dc
+  # Add field_semantics for oai_dc
   field_semantics.merge!(
     contributor: '', # @todo - extract anything other than author from complex person, may need new solr field
     creator: 'complex_person_author_tesim',
@@ -38,64 +36,13 @@ class SolrDocument
     subject: 'subject_tesim',
     title: 'title_tesim',
     type: 'resource_type_tesim'
-    # todo add jpcoar fields
   )
 
-  # JA - to_jpcoar
-  def to_jpcoar
-    export_as('jpcoar_xml')
-  end
 
   # Do content negotiation for AF models.
 
   use_extension( Hydra::ContentNegotiation )
 
-  # JA - I wasn't sure whether the OaiDc was needed as I think Blacklight::Document::DublinCore is doing this already, when used with field_semantics I added
-  # include Formats::OaiDc
-
-  # I think my Document::Jpcoar above is doing the same as Jpcoar here, but needs additional processing
-  # include Formats::Jpcoar
-
-  # JA - commented out during testing Document::Jpcoar
-  #  I think this can be moved into Document::Jpcoar and used for building the xml there
-  # def process_mapping(xml, field, mapping)
-  #   if mapping.present?
-  #     if mapping.is_a?(Array)
-  #       mapping.each do |mapping_item|
-  #         # recurse and process each item in the array
-  #         process_mapping(xml, field, mapping_item)
-  #       end
-
-  #     elsif mapping.is_a?(Hash)
-  #       if mapping[:field].present?
-  #         Array.wrap(self[mapping[:field]]).each do |unparsed_value|
-  #           value = self.send(mapping[:'function'], unparsed_value, mapping[:'argument'] || '.')
-  #           xml.tag! field, value if value.present?
-  #         end
-  #       elsif mapping[:function].present?
-  #         value = self.send(mapping[:'function'], field, xml)
-  #       else
-  #         puts "WARNING: mapping #{mapping.inspect} is ignored"
-  #       end
-
-  #     elsif mapping.is_a?(String)
-  #       Array.wrap(self[mapping]).each do |value|
-  #         xml.tag! field, value
-  #       end
-  #     end
-
-  #   end
-  # end
-
-  # def xml_parse_and_select(unparsed_value, xpath_select)
-  #   # using some caching to avoid re-parsing the same content
-  #   key = unparsed_value.hash
-  #   @parsed_xml ||= {}
-  #   @parsed_xml[key] ||=  Nokogiri::XML(JSON.parse(unparsed_value).to_xml(root: 'root'))
-
-  #   @parsed_xml[key].xpath(xpath_select)
-  # end
-
   def alternative_title
     self[Solrizer.solr_name('alternative_title', :stored_searchable)]
   end

From f39273181ab512a89fe3d80a72c02fa7fea56343 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Thu, 17 Oct 2019 09:04:21 +0100
Subject: [PATCH 013/258] Field semantics for contributor

---
 hyrax/app/models/solr_document.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 13444b29..98e28210 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -24,11 +24,11 @@ class SolrDocument
 
   # Add field_semantics for oai_dc
   field_semantics.merge!(
-    contributor: '', # @todo - extract anything other than author from complex person, may need new solr field
+    contributor: 'complex_person_other_tesim', # @todo - extract anything other than author from complex person, may need new solr field
     creator: 'complex_person_author_tesim',
     date: 'date_tesim',
     description: 'description_tesim',
-    identifier: 'complex_identifier_tesim', # @todo
+    identifier: 'complex_identifier_tesim',
     language: 'language_tesim',
     publisher: 'publisher_tesim',
     relation: '', # @todo have a think about what to map here

From 0f5f4eceefc6e567da17aabd3acdcba5bbcf703b Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Wed, 23 Oct 2019 14:18:21 +0100
Subject: [PATCH 014/258] Moved OAI configuration, added to .env.template

---
 .env.template                               |  6 ++++++
 hyrax/app/controllers/catalog_controller.rb | 17 +----------------
 hyrax/config/initializers/oai_config.rb     | 13 +++++++++++++
 3 files changed, 20 insertions(+), 16 deletions(-)
 create mode 100644 hyrax/config/initializers/oai_config.rb

diff --git a/.env.template b/.env.template
index 8824ece8..99d6563c 100644
--- a/.env.template
+++ b/.env.template
@@ -94,3 +94,9 @@ LDAP_SSL=false
 
 SMTP_HOST=
 SMTP_PORT=
+
+# OAI config used in config/initializers/oai_config.rb
+OAI_REPOSTIORY_NAME='NIMS MDR'
+OAI_REPOSITORY_URL=http://localhost:3000/catalog/oai
+OAI_RECORD_PREFIX=nims_mdr
+OAI_ADMIN_EMAIL=***REMOVED***
\ No newline at end of file
diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index f5939e4b..54a10488 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -30,22 +30,7 @@ def self.modified_field
     config.view.gallery.partials = [:index_header, :index]
     config.view.slideshow.partials = [:index]
 
-    config.oai = {
-      provider: {
-        repository_name: 'NIMS NGDR',
-        #repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
-        repository_url: 'http://localhost:3000/catalog/oai',
-        record_prefix: 'ngdrdemo',
-        admin_email: 'nims.ngdr@gmail.com',
-        sample_id: 'x059c7329'
-      },
-      document: {
-        limit: 25,            # number of records returned with each request, default: 15
-        set_fields: nil #[        # ability to define ListSets, optional, default: nil
-            #{ label: 'language', solr_field: 'language_facet' }
-        #]
-      }
-    }
+    config.oai = OAI_CONFIG
 
     ## Default parameters to send to solr for all search-like requests. See also SolrHelper#solr_search_params
     config.default_solr_params = {
diff --git a/hyrax/config/initializers/oai_config.rb b/hyrax/config/initializers/oai_config.rb
new file mode 100644
index 00000000..c17a7595
--- /dev/null
+++ b/hyrax/config/initializers/oai_config.rb
@@ -0,0 +1,13 @@
+OAI_CONFIG =
+    {
+        provider: {
+            repository_name: ENV['OAI_REPOSTIORY_NAME'],
+            repository_url: ENV['OAI_REPOSITORY_URL'],     # todo: can we get this from the other places that use the base url?
+            record_prefix: ENV['OAI_RECORD_PREFIX'],
+            admin_email: ENV['OAI_ADMIN_EMAIL'],
+            sample_id: 'x059c7329'
+        },
+        document: {
+            limit: 25,            # number of records returned with each request, default: 15
+        }
+    }
\ No newline at end of file

From ab853c2286269ca4afb77d1eb559d0c9ffa6742c Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Fri, 22 Mar 2019 01:07:28 +0000
Subject: [PATCH 015/258] Initial generation of blacklight OAI

---
 hyrax/Gemfile                               |  1 +
 hyrax/Gemfile.lock                          | 11 +++++++++++
 hyrax/app/controllers/catalog_controller.rb |  1 +
 hyrax/app/models/solr_document.rb           |  1 +
 hyrax/config/routes.rb                      |  2 ++
 5 files changed, 16 insertions(+)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 1badfed0..3122da75 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -87,3 +87,4 @@ group :test do
 end
 
 gem 'coveralls', require: false
+gem 'blacklight_oai_provider'
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index 0767fa62..d1a863c1 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -127,6 +127,10 @@ GEM
       bootstrap-sass (~> 3.0)
       openseadragon (>= 0.2.0)
       rails
+    blacklight_oai_provider (6.0.0)
+      blacklight (~> 6.0)
+      oai (~> 0.4)
+      rails (>= 4.2, < 6)
     bootstrap-datepicker-rails (1.8.0.1)
       railties (>= 3.0)
     bootstrap-sass (3.4.1)
@@ -270,6 +274,8 @@ GEM
       multipart-post (>= 1.2, < 3)
     faraday-encoding (0.0.4)
       faraday
+    faraday_middleware (0.13.1)
+      faraday (>= 0.7.4, < 1.0)
     fcrepo_wrapper (0.9.0)
       ruby-progressbar
     ffi (1.11.1)
@@ -535,6 +541,10 @@ GEM
       mini_portile2 (~> 2.4.0)
     nokogumbo (1.5.0)
       nokogiri
+    oai (0.4.0)
+      builder (>= 3.1.0)
+      faraday
+      faraday_middleware
     oauth (0.5.4)
     oauth2 (1.4.2)
       faraday (>= 0.8, < 2.0)
@@ -833,6 +843,7 @@ PLATFORMS
 
 DEPENDENCIES
   airbrake (~> 5.0)
+  blacklight_oai_provider
   bootstrap-datepicker-rails
   byebug
   capybara
diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index cea6e987..e103ca3f 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -1,6 +1,7 @@
 class CatalogController < ApplicationController
   include Hydra::Catalog
   include Hydra::Controller::ControllerBehavior
+  include BlacklightOaiProvider::Controller
 
   # This filter applies the hydra access controls
   before_action :enforce_show_permissions, only: :show
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 3aab625c..431226f9 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -2,6 +2,7 @@
 class SolrDocument
   include Blacklight::Solr::Document
   include Blacklight::Gallery::OpenseadragonSolrDocument
+  include BlacklightOaiProvider::SolrDocument
 
   # Adds Hyrax behaviors to the SolrDocument.
   include Hyrax::SolrDocumentBehavior
diff --git a/hyrax/config/routes.rb b/hyrax/config/routes.rb
index ad5c159b..eaa4391b 100644
--- a/hyrax/config/routes.rb
+++ b/hyrax/config/routes.rb
@@ -17,6 +17,7 @@
 
   concern :exportable, Blacklight::Routes::Exportable.new
   concern :searchable, Blacklight::Routes::Searchable.new
+  concern :oai_provider, BlacklightOaiProvider::Routes.new
 
   curation_concerns_basic_routes
 
@@ -28,6 +29,7 @@
   end
 
   resource :catalog, only: [:index], as: 'catalog', path: '/catalog', controller: 'catalog' do
+    concerns :oai_provider
     concerns :searchable
   end
 

From d0e12eafc5bcc5acd0046485407a6c2e47ceeef8 Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Wed, 24 Apr 2019 12:46:14 +0100
Subject: [PATCH 016/258] Added blacklight oai configuration

---
 hyrax/app/controllers/catalog_controller.rb | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index e103ca3f..cdc809b8 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -30,6 +30,22 @@ def self.modified_field
     config.view.gallery.partials = [:index_header, :index]
     config.view.slideshow.partials = [:index]
 
+    config.oai = {
+      provider: {
+        repository_name: 'NIMS NGDR',
+        repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
+        record_prefix: 'oai:ngdrdemo',
+        admin_email: 'nims.ngdr@gmail.com',
+        sample_id: '9e9f5e08-8905-44bc-8d85-5bfc691a7e3c'
+      },
+      document: {
+        limit: 25,            # number of records returned with each request, default: 15
+        set_fields: nil #[        # ability to define ListSets, optional, default: nil
+            #{ label: 'language', solr_field: 'language_facet' }
+        #]
+      }
+    }
+
     ## Default parameters to send to solr for all search-like requests. See also SolrHelper#solr_search_params
     config.default_solr_params = {
       qt: "search",

From 514dbc3e1ab327cc540d227b7316d17e998b3779 Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Wed, 1 May 2019 14:28:17 +0100
Subject: [PATCH 017/258] tests for oai

---
 hyrax/spec/features/oai_pmh_spec.rb | 37 +++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 hyrax/spec/features/oai_pmh_spec.rb

diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
new file mode 100644
index 00000000..bace525e
--- /dev/null
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -0,0 +1,37 @@
+# From Samvera Hyku
+
+RSpec.describe "OAI PMH Support", type: :feature do
+  let(:user) { create(:user) }
+  let(:work) { create(:work, user: user) }
+  let(:identifier) { work.id }
+
+  before do
+    login_as(user, scope: :user)
+    work
+  end
+
+  context 'oai interface with works present' do
+    it 'lists metadata prefixess' do
+      visit oai_catalog_path(verb: 'ListMetadataFormats')
+      expect(page).to have_content('oai_dc')
+    end
+
+    it 'retrieves a list of records' do
+      visit oai_catalog_path(verb: 'ListRecords', metadataPrefix: 'oai_dc')
+      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).to have_content(work.title.first)
+    end
+
+    it 'retrieves a single record' do
+      visit oai_catalog_path(verb: 'GetRecord', metadataPrefix: 'oai_dc', identifier: identifier)
+      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).to have_content(work.title.first)
+    end
+
+    it 'retrieves a list of identifiers' do
+      visit oai_catalog_path(verb: 'ListIdentifiers', metadataPrefix: 'oai_dc')
+      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).not_to have_content(work.title.first)
+    end
+  end
+end
\ No newline at end of file

From 649640ea8f26131b24a7d53563567f4ef90268df Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Wed, 1 May 2019 16:37:48 +0100
Subject: [PATCH 018/258] Change configuration for OAI

---
 hyrax/app/controllers/catalog_controller.rb | 2 +-
 hyrax/app/models/solr_document.rb           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index cdc809b8..f2ecd7ba 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -34,7 +34,7 @@ def self.modified_field
       provider: {
         repository_name: 'NIMS NGDR',
         repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
-        record_prefix: 'oai:ngdrdemo',
+        record_prefix: 'ngdrdemo',
         admin_email: 'nims.ngdr@gmail.com',
         sample_id: '9e9f5e08-8905-44bc-8d85-5bfc691a7e3c'
       },
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 431226f9..01746d80 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -1,8 +1,8 @@
 # frozen_string_literal: true
 class SolrDocument
   include Blacklight::Solr::Document
-  include Blacklight::Gallery::OpenseadragonSolrDocument
   include BlacklightOaiProvider::SolrDocument
+  include Blacklight::Gallery::OpenseadragonSolrDocument
 
   # Adds Hyrax behaviors to the SolrDocument.
   include Hyrax::SolrDocumentBehavior

From e8b112193793643cc05e53ba6beaf6da997ab48a Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Mon, 13 May 2019 12:35:05 +0100
Subject: [PATCH 019/258] Replaced Blacklight OAI plugin for CL modified
 version

---
 hyrax/Gemfile          |  2 +-
 hyrax/Gemfile.lock     | 16 +++++++++++-----
 hyrax/config/routes.rb |  2 +-
 3 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 3122da75..914c7660 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -87,4 +87,4 @@ group :test do
 end
 
 gem 'coveralls', require: false
-gem 'blacklight_oai_provider'
+gem 'blacklight_oai_provider', git: 'https://github.com/CottageLabs/blacklight_oai_provider.git', branch: 'master'
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index d1a863c1..9d7b6af5 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -1,3 +1,13 @@
+GIT
+  remote: https://github.com/CottageLabs/blacklight_oai_provider.git
+  revision: 73d5f34315e313fb22084cfc52939d71e3c0728a
+  branch: master
+  specs:
+    blacklight_oai_provider (1.4.1)
+      blacklight (>= 6.1)
+      oai (~> 0.4.0)
+      rails (>= 4.2)
+
 GIT
   remote: https://github.com/CottageLabs/willow_sword.git
   revision: ab456d99eaa4d07ed12d0510330be07909981204
@@ -127,10 +137,6 @@ GEM
       bootstrap-sass (~> 3.0)
       openseadragon (>= 0.2.0)
       rails
-    blacklight_oai_provider (6.0.0)
-      blacklight (~> 6.0)
-      oai (~> 0.4)
-      rails (>= 4.2, < 6)
     bootstrap-datepicker-rails (1.8.0.1)
       railties (>= 3.0)
     bootstrap-sass (3.4.1)
@@ -843,7 +849,7 @@ PLATFORMS
 
 DEPENDENCIES
   airbrake (~> 5.0)
-  blacklight_oai_provider
+  blacklight_oai_provider!
   bootstrap-datepicker-rails
   byebug
   capybara
diff --git a/hyrax/config/routes.rb b/hyrax/config/routes.rb
index eaa4391b..57159bf0 100644
--- a/hyrax/config/routes.rb
+++ b/hyrax/config/routes.rb
@@ -17,7 +17,7 @@
 
   concern :exportable, Blacklight::Routes::Exportable.new
   concern :searchable, Blacklight::Routes::Searchable.new
-  concern :oai_provider, BlacklightOaiProvider::Routes.new
+  concern :oai_provider, BlacklightOaiProvider::Routes::Provider.new
 
   curation_concerns_basic_routes
 

From 9affcbf0d542cb054e7c71e82c4d2c1e03b4f78c Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Mon, 13 May 2019 19:14:37 +0100
Subject: [PATCH 020/258] Updates pertaining to the older version of blacklight
 oai

---
 hyrax/app/controllers/catalog_controller.rb | 4 ++--
 hyrax/app/models/solr_document.rb           | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index f2ecd7ba..46e6fe19 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -1,7 +1,7 @@
 class CatalogController < ApplicationController
   include Hydra::Catalog
   include Hydra::Controller::ControllerBehavior
-  include BlacklightOaiProvider::Controller
+  include BlacklightOaiProvider::CatalogControllerBehavior
 
   # This filter applies the hydra access controls
   before_action :enforce_show_permissions, only: :show
@@ -36,7 +36,7 @@ def self.modified_field
         repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
         record_prefix: 'ngdrdemo',
         admin_email: 'nims.ngdr@gmail.com',
-        sample_id: '9e9f5e08-8905-44bc-8d85-5bfc691a7e3c'
+        sample_id: 'x059c7329'
       },
       document: {
         limit: 25,            # number of records returned with each request, default: 15
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 01746d80..e8fcf3d2 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 class SolrDocument
   include Blacklight::Solr::Document
-  include BlacklightOaiProvider::SolrDocument
+  include BlacklightOaiProvider::SolrDocumentBehavior
   include Blacklight::Gallery::OpenseadragonSolrDocument
 
   # Adds Hyrax behaviors to the SolrDocument.

From 8dccd69735a3936ccaf22d8ad1f09d33f355dc9a Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Thu, 6 Jun 2019 20:02:46 +0100
Subject: [PATCH 021/258] Efforts to introduce jpcoar metadata format.

---
 hyrax/app/controllers/catalog_controller.rb |  5 +-
 hyrax/app/models/formats/jpcoar.rb          | 90 +++++++++++++++++++++
 hyrax/app/models/formats/oai_dc.rb          | 65 +++++++++++++++
 hyrax/app/models/metadata/jpcoar.rb         | 10 +++
 hyrax/app/models/solr_document.rb           | 41 ++++++++++
 5 files changed, 210 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/app/models/formats/jpcoar.rb
 create mode 100644 hyrax/app/models/formats/oai_dc.rb
 create mode 100644 hyrax/app/models/metadata/jpcoar.rb

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index 46e6fe19..eca1e7e3 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -33,7 +33,8 @@ def self.modified_field
     config.oai = {
       provider: {
         repository_name: 'NIMS NGDR',
-        repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
+        #repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
+        repository_url: 'http://localhost:3000/catalog/oai',
         record_prefix: 'ngdrdemo',
         admin_email: 'nims.ngdr@gmail.com',
         sample_id: 'x059c7329'
@@ -46,6 +47,8 @@ def self.modified_field
       }
     }
 
+    BlacklightOaiProvider::SolrDocumentProvider.register_format(Metadata::Jpcoar.instance)
+
     ## Default parameters to send to solr for all search-like requests. See also SolrHelper#solr_search_params
     config.default_solr_params = {
       qt: "search",
diff --git a/hyrax/app/models/formats/jpcoar.rb b/hyrax/app/models/formats/jpcoar.rb
new file mode 100644
index 00000000..6da1dcf1
--- /dev/null
+++ b/hyrax/app/models/formats/jpcoar.rb
@@ -0,0 +1,90 @@
+require 'builder'
+
+# This module provide JPCOAR export
+module Formats
+  module Jpcoar
+
+    FORMAT_JPCOAR = {
+        'tag': {
+            'name': 'jpcoar',
+            'attributes': {
+                'xmlns:xs' => "http://www.w3.org/2001/XMLSchema",
+                'xmlns:dc' => "http://purl.org/dc/elements/1.1/",
+                'xmlns:dcterms' => "http://purl.org/dc/terms/",
+                'xmlns:rioxxterms' => "http://www.rioxx.net/schema/v2.0/rioxxterms/",
+                'xmlns:datacite' => "https://schema.datacite.org/meta/kernel-4/",
+                'xmlns:oaire' => "http://namespace.openaire.eu/schema/oaire/",
+                'xmlns:dcndl' => "http://ndl.go.jp/dcndl/terms/",
+                'xmlns:jpcoar' => "https://github.com/JPCOAR/schema/blob/master/1.0/",
+                'xsi:schemaLocation' => "https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd"
+            }
+        },
+        'fields': {
+            'dc:title': 'title_tesim',
+            'dcterms:alternative': 'alternative_title_tesim',
+            'jpcoar:creator': {'function': 'creator'},
+            'jpcoar:contributor': {'function': 'contributor'},      # looks very similar to creator
+            'dcterms:accessRights': '',
+            'rioxxterms:apc': '',
+            'dc:rights': {'function': 'complex_rights'},
+            'jpcoar:rightsHolder': {'function': 'rightsHolder'},
+            'jpcoar:subject': 'subject_sim',
+            'datacite:description': '',
+            'dc:publisher': '',
+            'datacite:date': '',
+            'dc:language': '',
+            'dc:type': '',
+            'datacite:version': '',
+            'oaire:version': '',
+            'jpcoar:identifier': '',
+            'jpcoar:identifierRegistration': '',
+            'jpcoar:relation': '',
+            'dcterms:temporal': '',
+            'datacite:geoLocation': '',
+            'jpcoar:fundingReference': '',
+            'jpcoar:sourceIdentifier': '',
+            'jpcoar:sourceTitle': '',
+            'jpcoar:volume': '',
+            'jpcoar:issue': '',
+            'jpcoar:numPages': '',
+            'jpcoar:pageStart': '',
+            'jpcoar:pageEnd': '',
+            'dcndl:dissertationNumber': '',
+            'dcndl:degreeName': '',
+            'dcndl:dateGranted': '',
+            'jpcoar:degreeGrantor': '',
+            'jpcoar:conference': '',
+            'jpcoar:file': '',
+        }
+    }
+    # 'dcterms:isReferencedBy': {'function': 'full_resource_uri'}
+
+    def export_as_jpcoar_xml
+      xml = Builder::XmlMarkup.new
+      format = FORMAT_JPCOAR
+
+      xml.tag!(format[:'tag'][:'name'], format[:'tag'][:'attributes']) do
+        format[:'fields'].each do |field, mapping|
+          process_mapping(xml, field, mapping)
+        end
+      end
+      xml.target!
+    end
+
+    def to_jpcoar
+      export_as('jpcoar_xml')
+    end
+
+    def format(field, xml)
+      if mime_types.present?
+        Array.wrap(mime_types).each do |mime_type|
+          xml.tag!(field, mime_type, 'xsi:type' => 'dcterms:IMT')
+        end
+      end
+    end
+
+    def mime_types
+      self['content_mime_type_ssm']
+    end
+  end
+end
diff --git a/hyrax/app/models/formats/oai_dc.rb b/hyrax/app/models/formats/oai_dc.rb
new file mode 100644
index 00000000..7a839422
--- /dev/null
+++ b/hyrax/app/models/formats/oai_dc.rb
@@ -0,0 +1,65 @@
+module Formats
+  module OaiDc
+
+    FORMAT_OAI_DC = {
+      'tag': {
+        'name': 'oai_dc:dc',
+        'attributes': {
+          'xmlns:oai_dc': "http://www.openarchives.org/OAI/2.0/oai_dc/DERP",
+          'xmlns:dc': "http://purl.org/dc/elements/1.1/DERP",
+          'xmlns:xsi': "http://www.w3.org/2001/XMLSchema-instanceDERP",
+          'xsi:schemaLocation': "http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"
+        }
+      },
+      'fields': {
+        'dc:title': Solrizer.solr_name('title', :displayable),
+        'dc:creator': Solrizer.solr_name('creator', :displayable),
+        'dc:subject': Solrizer.solr_name('subject', :displayable),
+        'dc:description': Solrizer.solr_name('description', :displayable),
+        'dc:publisher': Solrizer.solr_name('publisher', :displayable),
+        'dc:contributor': Solrizer.solr_name('contributor', :displayable),
+        'dc:date': Solrizer.solr_name('date_uploaded', :displayable),
+        'dc:type': Solrizer.solr_name('resource_type', :displayable),
+        'dc:format': Solrizer.solr_name('format', :displayable),
+        'dc:identifier': Solrizer.solr_name('id', :displayable),
+        'dc:source': Solrizer.solr_name('', :displayable),
+        'dc:language': Solrizer.solr_name('language', :displayable),
+        'dc:relation': Solrizer.solr_name('', :displayable),
+        'dc:coverage': Solrizer.solr_name('', :displayable),
+        'dc:rights': Solrizer.solr_name('rights_statement', :displayable)
+      }
+=begin
+      'fields': {
+        'dc:title': 'title_tesim',
+        'dc:creator': '',
+        'dc:subject': 'subject_topic_ssm',
+        'dc:description': 'description_ssm',
+        'dc:publisher': 'publisher_ssm',
+        'dc:contributor': '',
+        'dc:date': 'date_issued_ssm',
+        'dc:type': 'type_of_resource_ssm',
+        'dc:format': 'content_format_ssm',
+        'dc:identifier': 'id',
+        'dc:source': '',
+        'dc:language': 'language_text_ssm',
+        'dc:relation': '',
+        'dc:coverage': '',
+        'dc:rights': 'rights_ssm'
+    }
+=end
+    }
+
+    def export_as_oai_dc_xml
+      xml = Builder::XmlMarkup.new
+      format = FORMAT_OAI_DC
+
+      xml.tag!(format[:'tag'][:'name'], format[:'tag'][:'attributes']) do
+        format[:'fields'].each do |field, mapping|
+          process_mapping(xml, field, mapping)
+        end
+      end
+      xml.target!
+    end
+
+  end
+end
diff --git a/hyrax/app/models/metadata/jpcoar.rb b/hyrax/app/models/metadata/jpcoar.rb
new file mode 100644
index 00000000..73386a71
--- /dev/null
+++ b/hyrax/app/models/metadata/jpcoar.rb
@@ -0,0 +1,10 @@
+# The JPCOAR metadata format for MDR
+class Metadata::Jpcoar < OAI::Provider::Metadata::Format
+
+  def initialize
+    @prefix = 'jpcoar'
+    @schema = 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
+    @namespace = 'https://github.com/JPCOAR/schema/blob/master/1.0/'
+  end
+
+end
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index e8fcf3d2..5a310995 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -27,6 +27,47 @@ class SolrDocument
 
   use_extension( Hydra::ContentNegotiation )
 
+  include Formats::OaiDc
+  include Formats::Jpcoar
+
+  def process_mapping(xml, field, mapping)
+    if mapping.present?
+      if mapping.is_a?(Array)
+        mapping.each do |mapping_item|
+          # recurse and process each item in the array
+          process_mapping(xml, field, mapping_item)
+        end
+
+      elsif mapping.is_a?(Hash)
+        if mapping[:field].present?
+          Array.wrap(self[mapping[:field]]).each do |unparsed_value|
+            value = self.send(mapping[:'function'], unparsed_value, mapping[:'argument'] || '.')
+            xml.tag! field, value if value.present?
+          end
+        elsif mapping[:function].present?
+          value = self.send(mapping[:'function'], field, xml)
+        else
+          puts "WARNING: mapping #{mapping.inspect} is ignored"
+        end
+
+      elsif mapping.is_a?(String)
+        Array.wrap(self[mapping]).each do |value|
+          xml.tag! field, value
+        end
+      end
+
+    end
+  end
+
+  def xml_parse_and_select(unparsed_value, xpath_select)
+    # using some caching to avoid re-parsing the same content
+    key = unparsed_value.hash
+    @parsed_xml ||= {}
+    @parsed_xml[key] ||=  Nokogiri::XML(JSON.parse(unparsed_value).to_xml(root: 'root'))
+
+    @parsed_xml[key].xpath(xpath_select)
+  end
+
   def alternative_title
     self[Solrizer.solr_name('alternative_title', :stored_searchable)]
   end

From 515d656294eb30f2575de45d0f6a6e3505ae9f7f Mon Sep 17 00:00:00 2001
From: Steven Eardley <steve@eardley.xyz>
Date: Fri, 7 Jun 2019 14:20:29 +0100
Subject: [PATCH 022/258] Trying out new solr fields for oai

---
 hyrax/app/models/formats/jpcoar.rb | 26 +++++++++++++++++++-------
 hyrax/app/models/formats/oai_dc.rb |  3 ++-
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/hyrax/app/models/formats/jpcoar.rb b/hyrax/app/models/formats/jpcoar.rb
index 6da1dcf1..6c2e9b6e 100644
--- a/hyrax/app/models/formats/jpcoar.rb
+++ b/hyrax/app/models/formats/jpcoar.rb
@@ -20,20 +20,20 @@ module Jpcoar
             }
         },
         'fields': {
-            'dc:title': 'title_tesim',
-            'dcterms:alternative': 'alternative_title_tesim',
+            'dc:title': Solrizer.solr_name('title', :displayable),
+            'dcterms:alternative': Solrizer.solr_name('alternative_title', :displayable),
             'jpcoar:creator': {'function': 'creator'},
             'jpcoar:contributor': {'function': 'contributor'},      # looks very similar to creator
             'dcterms:accessRights': '',
             'rioxxterms:apc': '',
-            'dc:rights': {'function': 'complex_rights'},
-            'jpcoar:rightsHolder': {'function': 'rightsHolder'},
+            'dc:rights': Solrizer.solr_name('rights_statement', :displayable),
+            'jpcoar:rightsHolder': {'function': 'rights_holder'},
             'jpcoar:subject': 'subject_sim',
             'datacite:description': '',
-            'dc:publisher': '',
+            'dc:publisher': Solrizer.solr_name('publisher', :displayable),
             'datacite:date': '',
-            'dc:language': '',
-            'dc:type': '',
+            'dc:language': Solrizer.solr_name('language', :displayable),
+            'dc:type': Solrizer.solr_name('resource_type', :displayable),
             'datacite:version': '',
             'oaire:version': '',
             'jpcoar:identifier': '',
@@ -86,5 +86,17 @@ def format(field, xml)
     def mime_types
       self['content_mime_type_ssm']
     end
+
+    def creator
+    end
+
+    def contributor
+    end
+
+    def rights_holder
+    end
+
+
+
   end
 end
diff --git a/hyrax/app/models/formats/oai_dc.rb b/hyrax/app/models/formats/oai_dc.rb
index 7a839422..ef4ffee3 100644
--- a/hyrax/app/models/formats/oai_dc.rb
+++ b/hyrax/app/models/formats/oai_dc.rb
@@ -28,6 +28,8 @@ module OaiDc
         'dc:coverage': Solrizer.solr_name('', :displayable),
         'dc:rights': Solrizer.solr_name('rights_statement', :displayable)
       }
+    }
+
 =begin
       'fields': {
         'dc:title': 'title_tesim',
@@ -47,7 +49,6 @@ module OaiDc
         'dc:rights': 'rights_ssm'
     }
 =end
-    }
 
     def export_as_oai_dc_xml
       xml = Builder::XmlMarkup.new

From 45948c7147c7b5d82361a75173d946ce297380a3 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 9 Aug 2019 13:39:24 +0100
Subject: [PATCH 023/258] wip - working dc (needs more fields mapping), some
 way to jpcoar

---
 hyrax/app/models/document/jpcoar.rb |  83 +++++++++++++++++++++
 hyrax/app/models/metadata/jpcoar.rb |  50 ++++++++++++-
 hyrax/app/models/solr_document.rb   | 109 ++++++++++++++++++----------
 3 files changed, 201 insertions(+), 41 deletions(-)
 create mode 100644 hyrax/app/models/document/jpcoar.rb

diff --git a/hyrax/app/models/document/jpcoar.rb b/hyrax/app/models/document/jpcoar.rb
new file mode 100644
index 00000000..e967d8e3
--- /dev/null
+++ b/hyrax/app/models/document/jpcoar.rb
@@ -0,0 +1,83 @@
+# frozen_string_literal: true
+
+require 'builder'
+
+# This module provide Jpcoar export based on the document's semantic values
+module Document::Jpcoar
+  def self.extended(document)
+    # Register our exportable formats
+    Document::Jpcoar.register_export_formats(document)
+  end
+
+  def self.register_export_formats(document)
+    document.will_export_as(:jpcoar_xml, 'text/xml')
+  end
+
+  # JA - these are taken from formats/jpcoar (although there are two 'version' (datacite and openaire) so I've just used datacite)
+  # JA - I've done these as hashes so we can map field name to the field with the correct namespace / name
+  # JA - the namespace bit might be wrong, we may just want them all to be jpcoar?
+  def jpcoar_field_names
+    { title: 'dc:title',
+      alternative: 'dcterms:alternative',
+      creator: 'jpcoar:creator',
+      contributor: 'jpcoar:contributor',
+      access_rights: 'dcterms:accessRights',
+      apc: 'rioxxterms:apc',
+      rights: 'dc:rights',
+      rights_older: 'jpcoar:rightsHolder',
+      subject: 'jpcoar:subject',
+      description: 'datacite:description',
+      publisher: 'dc:publisher',
+      date: 'datacite:date',
+      language: 'dc:language',
+      type: 'dc:type',
+      version: 'datacite:version',
+      identifier: 'jpcoar:identifier',
+      identifier_registration: 'jpcoar:identifierRegistration',
+      relation: 'jpcoar:relation',
+      temporal: 'dcterms:temporal',
+      geo_location: 'datacite:geoLocation',
+      funding_reference: 'jpcoar:fundingReference',
+      source_identifier: 'jpcoar:sourceIdentifier',
+      source_title: 'jpcoar:sourceTitle',
+      volume: 'jpcoar:volume',
+      issue: 'jpcoar:issue',
+      num_pages: 'jpcoar:numPages',
+      page_start: 'jpcoar:pageStart',
+      page_end: 'jpcoar:pageEnd',
+      dissertation_number: 'dcndl:dissertationNumber',
+      degree_name: 'dcndl:degreeName',
+      dateGranted: 'dcndl:dateGranted',
+      degree_grantor: 'jpcoar:degreeGrantor',
+      conference: 'jpcoar:conference',
+      file: 'jpcoar:file' }
+  end
+
+  # jpcoar elements are mapped against the #jpcoar_field_names whitelist.
+  # JA - I think jpcoar is a nested xml so this will need to be refactored
+  def export_as_jpcoar_xml
+    xml = Builder::XmlMarkup.new
+    xml.tag!('jpcoar',
+             'xmlns:dc' => 'http://purl.org/dc/elements/1.1/',
+             'xmlns:dcterms' => 'http://purl.org/dc/terms/',
+             'xmlns:rioxxterms' => 'http://www.rioxx.net/schema/v2.0/rioxxterms/',
+             'xmlns:datacite' => 'https://schema.datacite.org/meta/kernel-4/',
+             'xmlns:openaire' => 'http://namespace.openaire.eu/schema/oaire/',
+             'xmlns:dcndl' => 'http://ndl.go.jp/dcndl/terms/',
+             'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
+             'xsi:schemaLocation ' => 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd') do
+      to_semantic_values.select { |field, _values| jpcoar_field_name? field }.each do |field, values|
+        Array.wrap(values).each do |v|
+          xml.tag! jpcoar_field_names[field], v
+        end
+      end
+    end
+    xml.target!
+  end
+
+  private
+
+  def jpcoar_field_name?(field)
+    jpcoar_field_names.keys.include? field.to_sym
+  end
+end
diff --git a/hyrax/app/models/metadata/jpcoar.rb b/hyrax/app/models/metadata/jpcoar.rb
index 73386a71..cafe0c3d 100644
--- a/hyrax/app/models/metadata/jpcoar.rb
+++ b/hyrax/app/models/metadata/jpcoar.rb
@@ -1,10 +1,58 @@
 # The JPCOAR metadata format for MDR
 class Metadata::Jpcoar < OAI::Provider::Metadata::Format
-
+  
   def initialize
     @prefix = 'jpcoar'
     @schema = 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
     @namespace = 'https://github.com/JPCOAR/schema/blob/master/1.0/'
+    @element_namespace = 'jpcoar'
+    @fields = %i[title
+                 alternative
+                 creator
+                 contributor
+                 accessRights
+                 apc
+                 rights
+                 rightsHolder
+                 subject
+                 description
+                 publisher
+                 date
+                 language
+                 type
+                 version
+                 version
+                 identifier
+                 identifierRegistration
+                 relation
+                 temporal
+                 geoLocation
+                 fundingReference
+                 sourceIdentifier
+                 sourceTitle
+                 volume
+                 issue
+                 numPages
+                 pageStart
+                 pageEnd
+                 dissertationNumber
+                 degreeName
+                 dateGranted
+                 degreeGrantor
+                 conference
+                 file]
   end
 
+  def header_specification
+    {
+      'xmlns:dc' => 'http://purl.org/dc/elements/1.1/',
+      'xmlns:dcterms' => 'http://purl.org/dc/terms/',
+      'xmlns:rioxxterms' => 'http://www.rioxx.net/schema/v2.0/rioxxterms/',
+      'xmlns:datacite' => 'https://schema.datacite.org/meta/kernel-4/',
+      'xmlns:openaire' => 'http://namespace.openaire.eu/schema/oaire/',
+      'xmlns:dcndl' => 'http://ndl.go.jp/dcndl/terms/',
+      'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
+      'xsi:schemaLocation ' => 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
+    }
+  end
 end
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 5a310995..a256a8fd 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -22,51 +22,80 @@ class SolrDocument
   # and Blacklight::Document::SemanticFields#to_semantic_values
   # Recommendation: Use field names from Dublin Core
   use_extension(Blacklight::Document::DublinCore)
+  # JA - add blacklight document for jpcoar
+  use_extension(Document::Jpcoar)
+
+  # JA - add field_semantics for oai_dc
+  field_semantics.merge!(
+    contributor: '', # @todo - extract anything other than author from complex person, may need new solr field
+    creator: 'complex_person_author_tesim',
+    date: 'date_tesim',
+    description: 'description_tesim',
+    identifier: 'complex_identifier_tesim', # @todo
+    language: 'language_tesim',
+    publisher: 'publisher_tesim',
+    relation: '', # @todo have a think about what to map here
+    rights: 'rights_tesim',
+    subject: 'subject_tesim',
+    title: 'title_tesim',
+    type: 'resource_type_tesim'
+    # todo add jpcoar fields
+  )
+
+  # JA - to_jpcoar
+  def to_jpcoar
+    export_as('jpcoar_xml')
+  end
 
   # Do content negotiation for AF models.
 
   use_extension( Hydra::ContentNegotiation )
 
-  include Formats::OaiDc
-  include Formats::Jpcoar
-
-  def process_mapping(xml, field, mapping)
-    if mapping.present?
-      if mapping.is_a?(Array)
-        mapping.each do |mapping_item|
-          # recurse and process each item in the array
-          process_mapping(xml, field, mapping_item)
-        end
-
-      elsif mapping.is_a?(Hash)
-        if mapping[:field].present?
-          Array.wrap(self[mapping[:field]]).each do |unparsed_value|
-            value = self.send(mapping[:'function'], unparsed_value, mapping[:'argument'] || '.')
-            xml.tag! field, value if value.present?
-          end
-        elsif mapping[:function].present?
-          value = self.send(mapping[:'function'], field, xml)
-        else
-          puts "WARNING: mapping #{mapping.inspect} is ignored"
-        end
-
-      elsif mapping.is_a?(String)
-        Array.wrap(self[mapping]).each do |value|
-          xml.tag! field, value
-        end
-      end
-
-    end
-  end
-
-  def xml_parse_and_select(unparsed_value, xpath_select)
-    # using some caching to avoid re-parsing the same content
-    key = unparsed_value.hash
-    @parsed_xml ||= {}
-    @parsed_xml[key] ||=  Nokogiri::XML(JSON.parse(unparsed_value).to_xml(root: 'root'))
-
-    @parsed_xml[key].xpath(xpath_select)
-  end
+  # JA - I wasn't sure whether the OaiDc was needed as I think Blacklight::Document::DublinCore is doing this already, when used with field_semantics I added
+  # include Formats::OaiDc
+
+  # I think my Document::Jpcoar above is doing the same as Jpcoar here, but needs additional processing
+  # include Formats::Jpcoar
+
+  # JA - commented out during testing Document::Jpcoar
+  #  I think this can be moved into Document::Jpcoar and used for building the xml there
+  # def process_mapping(xml, field, mapping)
+  #   if mapping.present?
+  #     if mapping.is_a?(Array)
+  #       mapping.each do |mapping_item|
+  #         # recurse and process each item in the array
+  #         process_mapping(xml, field, mapping_item)
+  #       end
+
+  #     elsif mapping.is_a?(Hash)
+  #       if mapping[:field].present?
+  #         Array.wrap(self[mapping[:field]]).each do |unparsed_value|
+  #           value = self.send(mapping[:'function'], unparsed_value, mapping[:'argument'] || '.')
+  #           xml.tag! field, value if value.present?
+  #         end
+  #       elsif mapping[:function].present?
+  #         value = self.send(mapping[:'function'], field, xml)
+  #       else
+  #         puts "WARNING: mapping #{mapping.inspect} is ignored"
+  #       end
+
+  #     elsif mapping.is_a?(String)
+  #       Array.wrap(self[mapping]).each do |value|
+  #         xml.tag! field, value
+  #       end
+  #     end
+
+  #   end
+  # end
+
+  # def xml_parse_and_select(unparsed_value, xpath_select)
+  #   # using some caching to avoid re-parsing the same content
+  #   key = unparsed_value.hash
+  #   @parsed_xml ||= {}
+  #   @parsed_xml[key] ||=  Nokogiri::XML(JSON.parse(unparsed_value).to_xml(root: 'root'))
+
+  #   @parsed_xml[key].xpath(xpath_select)
+  # end
 
   def alternative_title
     self[Solrizer.solr_name('alternative_title', :stored_searchable)]

From 95d2ba5d3ba46aa47896665a7b960856ae606403 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Thu, 17 Oct 2019 08:54:55 +0100
Subject: [PATCH 024/258] Removed JPCOAR OAI format so we can get OAI:DC out of
 the door

---
 hyrax/app/controllers/catalog_controller.rb |   2 -
 hyrax/app/models/document/jpcoar.rb         |  83 ----------------
 hyrax/app/models/formats/jpcoar.rb          | 102 --------------------
 hyrax/app/models/formats/oai_dc.rb          |  66 -------------
 hyrax/app/models/metadata/jpcoar.rb         |  58 -----------
 hyrax/app/models/solr_document.rb           |  55 +----------
 6 files changed, 1 insertion(+), 365 deletions(-)
 delete mode 100644 hyrax/app/models/document/jpcoar.rb
 delete mode 100644 hyrax/app/models/formats/jpcoar.rb
 delete mode 100644 hyrax/app/models/formats/oai_dc.rb
 delete mode 100644 hyrax/app/models/metadata/jpcoar.rb

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index eca1e7e3..f5939e4b 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -47,8 +47,6 @@ def self.modified_field
       }
     }
 
-    BlacklightOaiProvider::SolrDocumentProvider.register_format(Metadata::Jpcoar.instance)
-
     ## Default parameters to send to solr for all search-like requests. See also SolrHelper#solr_search_params
     config.default_solr_params = {
       qt: "search",
diff --git a/hyrax/app/models/document/jpcoar.rb b/hyrax/app/models/document/jpcoar.rb
deleted file mode 100644
index e967d8e3..00000000
--- a/hyrax/app/models/document/jpcoar.rb
+++ /dev/null
@@ -1,83 +0,0 @@
-# frozen_string_literal: true
-
-require 'builder'
-
-# This module provide Jpcoar export based on the document's semantic values
-module Document::Jpcoar
-  def self.extended(document)
-    # Register our exportable formats
-    Document::Jpcoar.register_export_formats(document)
-  end
-
-  def self.register_export_formats(document)
-    document.will_export_as(:jpcoar_xml, 'text/xml')
-  end
-
-  # JA - these are taken from formats/jpcoar (although there are two 'version' (datacite and openaire) so I've just used datacite)
-  # JA - I've done these as hashes so we can map field name to the field with the correct namespace / name
-  # JA - the namespace bit might be wrong, we may just want them all to be jpcoar?
-  def jpcoar_field_names
-    { title: 'dc:title',
-      alternative: 'dcterms:alternative',
-      creator: 'jpcoar:creator',
-      contributor: 'jpcoar:contributor',
-      access_rights: 'dcterms:accessRights',
-      apc: 'rioxxterms:apc',
-      rights: 'dc:rights',
-      rights_older: 'jpcoar:rightsHolder',
-      subject: 'jpcoar:subject',
-      description: 'datacite:description',
-      publisher: 'dc:publisher',
-      date: 'datacite:date',
-      language: 'dc:language',
-      type: 'dc:type',
-      version: 'datacite:version',
-      identifier: 'jpcoar:identifier',
-      identifier_registration: 'jpcoar:identifierRegistration',
-      relation: 'jpcoar:relation',
-      temporal: 'dcterms:temporal',
-      geo_location: 'datacite:geoLocation',
-      funding_reference: 'jpcoar:fundingReference',
-      source_identifier: 'jpcoar:sourceIdentifier',
-      source_title: 'jpcoar:sourceTitle',
-      volume: 'jpcoar:volume',
-      issue: 'jpcoar:issue',
-      num_pages: 'jpcoar:numPages',
-      page_start: 'jpcoar:pageStart',
-      page_end: 'jpcoar:pageEnd',
-      dissertation_number: 'dcndl:dissertationNumber',
-      degree_name: 'dcndl:degreeName',
-      dateGranted: 'dcndl:dateGranted',
-      degree_grantor: 'jpcoar:degreeGrantor',
-      conference: 'jpcoar:conference',
-      file: 'jpcoar:file' }
-  end
-
-  # jpcoar elements are mapped against the #jpcoar_field_names whitelist.
-  # JA - I think jpcoar is a nested xml so this will need to be refactored
-  def export_as_jpcoar_xml
-    xml = Builder::XmlMarkup.new
-    xml.tag!('jpcoar',
-             'xmlns:dc' => 'http://purl.org/dc/elements/1.1/',
-             'xmlns:dcterms' => 'http://purl.org/dc/terms/',
-             'xmlns:rioxxterms' => 'http://www.rioxx.net/schema/v2.0/rioxxterms/',
-             'xmlns:datacite' => 'https://schema.datacite.org/meta/kernel-4/',
-             'xmlns:openaire' => 'http://namespace.openaire.eu/schema/oaire/',
-             'xmlns:dcndl' => 'http://ndl.go.jp/dcndl/terms/',
-             'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
-             'xsi:schemaLocation ' => 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd') do
-      to_semantic_values.select { |field, _values| jpcoar_field_name? field }.each do |field, values|
-        Array.wrap(values).each do |v|
-          xml.tag! jpcoar_field_names[field], v
-        end
-      end
-    end
-    xml.target!
-  end
-
-  private
-
-  def jpcoar_field_name?(field)
-    jpcoar_field_names.keys.include? field.to_sym
-  end
-end
diff --git a/hyrax/app/models/formats/jpcoar.rb b/hyrax/app/models/formats/jpcoar.rb
deleted file mode 100644
index 6c2e9b6e..00000000
--- a/hyrax/app/models/formats/jpcoar.rb
+++ /dev/null
@@ -1,102 +0,0 @@
-require 'builder'
-
-# This module provide JPCOAR export
-module Formats
-  module Jpcoar
-
-    FORMAT_JPCOAR = {
-        'tag': {
-            'name': 'jpcoar',
-            'attributes': {
-                'xmlns:xs' => "http://www.w3.org/2001/XMLSchema",
-                'xmlns:dc' => "http://purl.org/dc/elements/1.1/",
-                'xmlns:dcterms' => "http://purl.org/dc/terms/",
-                'xmlns:rioxxterms' => "http://www.rioxx.net/schema/v2.0/rioxxterms/",
-                'xmlns:datacite' => "https://schema.datacite.org/meta/kernel-4/",
-                'xmlns:oaire' => "http://namespace.openaire.eu/schema/oaire/",
-                'xmlns:dcndl' => "http://ndl.go.jp/dcndl/terms/",
-                'xmlns:jpcoar' => "https://github.com/JPCOAR/schema/blob/master/1.0/",
-                'xsi:schemaLocation' => "https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd"
-            }
-        },
-        'fields': {
-            'dc:title': Solrizer.solr_name('title', :displayable),
-            'dcterms:alternative': Solrizer.solr_name('alternative_title', :displayable),
-            'jpcoar:creator': {'function': 'creator'},
-            'jpcoar:contributor': {'function': 'contributor'},      # looks very similar to creator
-            'dcterms:accessRights': '',
-            'rioxxterms:apc': '',
-            'dc:rights': Solrizer.solr_name('rights_statement', :displayable),
-            'jpcoar:rightsHolder': {'function': 'rights_holder'},
-            'jpcoar:subject': 'subject_sim',
-            'datacite:description': '',
-            'dc:publisher': Solrizer.solr_name('publisher', :displayable),
-            'datacite:date': '',
-            'dc:language': Solrizer.solr_name('language', :displayable),
-            'dc:type': Solrizer.solr_name('resource_type', :displayable),
-            'datacite:version': '',
-            'oaire:version': '',
-            'jpcoar:identifier': '',
-            'jpcoar:identifierRegistration': '',
-            'jpcoar:relation': '',
-            'dcterms:temporal': '',
-            'datacite:geoLocation': '',
-            'jpcoar:fundingReference': '',
-            'jpcoar:sourceIdentifier': '',
-            'jpcoar:sourceTitle': '',
-            'jpcoar:volume': '',
-            'jpcoar:issue': '',
-            'jpcoar:numPages': '',
-            'jpcoar:pageStart': '',
-            'jpcoar:pageEnd': '',
-            'dcndl:dissertationNumber': '',
-            'dcndl:degreeName': '',
-            'dcndl:dateGranted': '',
-            'jpcoar:degreeGrantor': '',
-            'jpcoar:conference': '',
-            'jpcoar:file': '',
-        }
-    }
-    # 'dcterms:isReferencedBy': {'function': 'full_resource_uri'}
-
-    def export_as_jpcoar_xml
-      xml = Builder::XmlMarkup.new
-      format = FORMAT_JPCOAR
-
-      xml.tag!(format[:'tag'][:'name'], format[:'tag'][:'attributes']) do
-        format[:'fields'].each do |field, mapping|
-          process_mapping(xml, field, mapping)
-        end
-      end
-      xml.target!
-    end
-
-    def to_jpcoar
-      export_as('jpcoar_xml')
-    end
-
-    def format(field, xml)
-      if mime_types.present?
-        Array.wrap(mime_types).each do |mime_type|
-          xml.tag!(field, mime_type, 'xsi:type' => 'dcterms:IMT')
-        end
-      end
-    end
-
-    def mime_types
-      self['content_mime_type_ssm']
-    end
-
-    def creator
-    end
-
-    def contributor
-    end
-
-    def rights_holder
-    end
-
-
-
-  end
-end
diff --git a/hyrax/app/models/formats/oai_dc.rb b/hyrax/app/models/formats/oai_dc.rb
deleted file mode 100644
index ef4ffee3..00000000
--- a/hyrax/app/models/formats/oai_dc.rb
+++ /dev/null
@@ -1,66 +0,0 @@
-module Formats
-  module OaiDc
-
-    FORMAT_OAI_DC = {
-      'tag': {
-        'name': 'oai_dc:dc',
-        'attributes': {
-          'xmlns:oai_dc': "http://www.openarchives.org/OAI/2.0/oai_dc/DERP",
-          'xmlns:dc': "http://purl.org/dc/elements/1.1/DERP",
-          'xmlns:xsi': "http://www.w3.org/2001/XMLSchema-instanceDERP",
-          'xsi:schemaLocation': "http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"
-        }
-      },
-      'fields': {
-        'dc:title': Solrizer.solr_name('title', :displayable),
-        'dc:creator': Solrizer.solr_name('creator', :displayable),
-        'dc:subject': Solrizer.solr_name('subject', :displayable),
-        'dc:description': Solrizer.solr_name('description', :displayable),
-        'dc:publisher': Solrizer.solr_name('publisher', :displayable),
-        'dc:contributor': Solrizer.solr_name('contributor', :displayable),
-        'dc:date': Solrizer.solr_name('date_uploaded', :displayable),
-        'dc:type': Solrizer.solr_name('resource_type', :displayable),
-        'dc:format': Solrizer.solr_name('format', :displayable),
-        'dc:identifier': Solrizer.solr_name('id', :displayable),
-        'dc:source': Solrizer.solr_name('', :displayable),
-        'dc:language': Solrizer.solr_name('language', :displayable),
-        'dc:relation': Solrizer.solr_name('', :displayable),
-        'dc:coverage': Solrizer.solr_name('', :displayable),
-        'dc:rights': Solrizer.solr_name('rights_statement', :displayable)
-      }
-    }
-
-=begin
-      'fields': {
-        'dc:title': 'title_tesim',
-        'dc:creator': '',
-        'dc:subject': 'subject_topic_ssm',
-        'dc:description': 'description_ssm',
-        'dc:publisher': 'publisher_ssm',
-        'dc:contributor': '',
-        'dc:date': 'date_issued_ssm',
-        'dc:type': 'type_of_resource_ssm',
-        'dc:format': 'content_format_ssm',
-        'dc:identifier': 'id',
-        'dc:source': '',
-        'dc:language': 'language_text_ssm',
-        'dc:relation': '',
-        'dc:coverage': '',
-        'dc:rights': 'rights_ssm'
-    }
-=end
-
-    def export_as_oai_dc_xml
-      xml = Builder::XmlMarkup.new
-      format = FORMAT_OAI_DC
-
-      xml.tag!(format[:'tag'][:'name'], format[:'tag'][:'attributes']) do
-        format[:'fields'].each do |field, mapping|
-          process_mapping(xml, field, mapping)
-        end
-      end
-      xml.target!
-    end
-
-  end
-end
diff --git a/hyrax/app/models/metadata/jpcoar.rb b/hyrax/app/models/metadata/jpcoar.rb
deleted file mode 100644
index cafe0c3d..00000000
--- a/hyrax/app/models/metadata/jpcoar.rb
+++ /dev/null
@@ -1,58 +0,0 @@
-# The JPCOAR metadata format for MDR
-class Metadata::Jpcoar < OAI::Provider::Metadata::Format
-  
-  def initialize
-    @prefix = 'jpcoar'
-    @schema = 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
-    @namespace = 'https://github.com/JPCOAR/schema/blob/master/1.0/'
-    @element_namespace = 'jpcoar'
-    @fields = %i[title
-                 alternative
-                 creator
-                 contributor
-                 accessRights
-                 apc
-                 rights
-                 rightsHolder
-                 subject
-                 description
-                 publisher
-                 date
-                 language
-                 type
-                 version
-                 version
-                 identifier
-                 identifierRegistration
-                 relation
-                 temporal
-                 geoLocation
-                 fundingReference
-                 sourceIdentifier
-                 sourceTitle
-                 volume
-                 issue
-                 numPages
-                 pageStart
-                 pageEnd
-                 dissertationNumber
-                 degreeName
-                 dateGranted
-                 degreeGrantor
-                 conference
-                 file]
-  end
-
-  def header_specification
-    {
-      'xmlns:dc' => 'http://purl.org/dc/elements/1.1/',
-      'xmlns:dcterms' => 'http://purl.org/dc/terms/',
-      'xmlns:rioxxterms' => 'http://www.rioxx.net/schema/v2.0/rioxxterms/',
-      'xmlns:datacite' => 'https://schema.datacite.org/meta/kernel-4/',
-      'xmlns:openaire' => 'http://namespace.openaire.eu/schema/oaire/',
-      'xmlns:dcndl' => 'http://ndl.go.jp/dcndl/terms/',
-      'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
-      'xsi:schemaLocation ' => 'https://github.com/JPCOAR/schema/blob/master/1.0/jpcoar_scm.xsd'
-    }
-  end
-end
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index a256a8fd..47e6782d 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -22,10 +22,8 @@ class SolrDocument
   # and Blacklight::Document::SemanticFields#to_semantic_values
   # Recommendation: Use field names from Dublin Core
   use_extension(Blacklight::Document::DublinCore)
-  # JA - add blacklight document for jpcoar
-  use_extension(Document::Jpcoar)
 
-  # JA - add field_semantics for oai_dc
+  # Add field_semantics for oai_dc
   field_semantics.merge!(
     contributor: '', # @todo - extract anything other than author from complex person, may need new solr field
     creator: 'complex_person_author_tesim',
@@ -39,64 +37,13 @@ class SolrDocument
     subject: 'subject_tesim',
     title: 'title_tesim',
     type: 'resource_type_tesim'
-    # todo add jpcoar fields
   )
 
-  # JA - to_jpcoar
-  def to_jpcoar
-    export_as('jpcoar_xml')
-  end
 
   # Do content negotiation for AF models.
 
   use_extension( Hydra::ContentNegotiation )
 
-  # JA - I wasn't sure whether the OaiDc was needed as I think Blacklight::Document::DublinCore is doing this already, when used with field_semantics I added
-  # include Formats::OaiDc
-
-  # I think my Document::Jpcoar above is doing the same as Jpcoar here, but needs additional processing
-  # include Formats::Jpcoar
-
-  # JA - commented out during testing Document::Jpcoar
-  #  I think this can be moved into Document::Jpcoar and used for building the xml there
-  # def process_mapping(xml, field, mapping)
-  #   if mapping.present?
-  #     if mapping.is_a?(Array)
-  #       mapping.each do |mapping_item|
-  #         # recurse and process each item in the array
-  #         process_mapping(xml, field, mapping_item)
-  #       end
-
-  #     elsif mapping.is_a?(Hash)
-  #       if mapping[:field].present?
-  #         Array.wrap(self[mapping[:field]]).each do |unparsed_value|
-  #           value = self.send(mapping[:'function'], unparsed_value, mapping[:'argument'] || '.')
-  #           xml.tag! field, value if value.present?
-  #         end
-  #       elsif mapping[:function].present?
-  #         value = self.send(mapping[:'function'], field, xml)
-  #       else
-  #         puts "WARNING: mapping #{mapping.inspect} is ignored"
-  #       end
-
-  #     elsif mapping.is_a?(String)
-  #       Array.wrap(self[mapping]).each do |value|
-  #         xml.tag! field, value
-  #       end
-  #     end
-
-  #   end
-  # end
-
-  # def xml_parse_and_select(unparsed_value, xpath_select)
-  #   # using some caching to avoid re-parsing the same content
-  #   key = unparsed_value.hash
-  #   @parsed_xml ||= {}
-  #   @parsed_xml[key] ||=  Nokogiri::XML(JSON.parse(unparsed_value).to_xml(root: 'root'))
-
-  #   @parsed_xml[key].xpath(xpath_select)
-  # end
-
   def alternative_title
     self[Solrizer.solr_name('alternative_title', :stored_searchable)]
   end

From ced4e4cc72ff3133b1491fa526c994bedecdcc63 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Thu, 17 Oct 2019 09:04:21 +0100
Subject: [PATCH 025/258] Field semantics for contributor

---
 hyrax/app/models/solr_document.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 47e6782d..9745e68f 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -25,11 +25,11 @@ class SolrDocument
 
   # Add field_semantics for oai_dc
   field_semantics.merge!(
-    contributor: '', # @todo - extract anything other than author from complex person, may need new solr field
+    contributor: 'complex_person_other_tesim', # @todo - extract anything other than author from complex person, may need new solr field
     creator: 'complex_person_author_tesim',
     date: 'date_tesim',
     description: 'description_tesim',
-    identifier: 'complex_identifier_tesim', # @todo
+    identifier: 'complex_identifier_tesim',
     language: 'language_tesim',
     publisher: 'publisher_tesim',
     relation: '', # @todo have a think about what to map here

From 46ead03ae40b6950967190ab9a73d75c04ff0f4d Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Wed, 23 Oct 2019 14:18:21 +0100
Subject: [PATCH 026/258] Moved OAI configuration, added to .env.template

---
 .env.template                               |  6 ++++++
 hyrax/app/controllers/catalog_controller.rb | 17 +----------------
 hyrax/config/initializers/oai_config.rb     | 13 +++++++++++++
 3 files changed, 20 insertions(+), 16 deletions(-)
 create mode 100644 hyrax/config/initializers/oai_config.rb

diff --git a/.env.template b/.env.template
index c2f25243..fc8b9d6c 100644
--- a/.env.template
+++ b/.env.template
@@ -98,3 +98,9 @@ SMTP_HOST=
 SMTP_PORT=
 
 MDR_HOST=
+
+# OAI config used in config/initializers/oai_config.rb
+OAI_REPOSTIORY_NAME='NIMS MDR'
+OAI_REPOSITORY_URL=http://localhost:3000/catalog/oai
+OAI_RECORD_PREFIX=nims_mdr
+OAI_ADMIN_EMAIL=***REMOVED***
diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index f5939e4b..54a10488 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -30,22 +30,7 @@ def self.modified_field
     config.view.gallery.partials = [:index_header, :index]
     config.view.slideshow.partials = [:index]
 
-    config.oai = {
-      provider: {
-        repository_name: 'NIMS NGDR',
-        #repository_url: 'https://ngdrdemo.cottagelabs.com/catalog/oai',
-        repository_url: 'http://localhost:3000/catalog/oai',
-        record_prefix: 'ngdrdemo',
-        admin_email: 'nims.ngdr@gmail.com',
-        sample_id: 'x059c7329'
-      },
-      document: {
-        limit: 25,            # number of records returned with each request, default: 15
-        set_fields: nil #[        # ability to define ListSets, optional, default: nil
-            #{ label: 'language', solr_field: 'language_facet' }
-        #]
-      }
-    }
+    config.oai = OAI_CONFIG
 
     ## Default parameters to send to solr for all search-like requests. See also SolrHelper#solr_search_params
     config.default_solr_params = {
diff --git a/hyrax/config/initializers/oai_config.rb b/hyrax/config/initializers/oai_config.rb
new file mode 100644
index 00000000..c17a7595
--- /dev/null
+++ b/hyrax/config/initializers/oai_config.rb
@@ -0,0 +1,13 @@
+OAI_CONFIG =
+    {
+        provider: {
+            repository_name: ENV['OAI_REPOSTIORY_NAME'],
+            repository_url: ENV['OAI_REPOSITORY_URL'],     # todo: can we get this from the other places that use the base url?
+            record_prefix: ENV['OAI_RECORD_PREFIX'],
+            admin_email: ENV['OAI_ADMIN_EMAIL'],
+            sample_id: 'x059c7329'
+        },
+        document: {
+            limit: 25,            # number of records returned with each request, default: 15
+        }
+    }
\ No newline at end of file

From 78365c884065524dac959fc9e9d8b8deb41c16cb Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 31 Oct 2019 11:53:40 +0900
Subject: [PATCH 027/258] user -> depositor

---
 hyrax/spec/features/oai_pmh_spec.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
index bace525e..40fe4232 100644
--- a/hyrax/spec/features/oai_pmh_spec.rb
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -2,7 +2,7 @@
 
 RSpec.describe "OAI PMH Support", type: :feature do
   let(:user) { create(:user) }
-  let(:work) { create(:work, user: user) }
+  let(:work) { create(:work, depositor: user) }
   let(:identifier) { work.id }
 
   before do
@@ -34,4 +34,4 @@
       expect(page).not_to have_content(work.title.first)
     end
   end
-end
\ No newline at end of file
+end

From a8a7de4c1110ab34e391898d4e814a6fedede074 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 31 Oct 2019 12:12:39 +0900
Subject: [PATCH 028/258] fix route to oai_provider, use email as depositor

---
 hyrax/spec/features/oai_pmh_spec.rb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
index 40fe4232..5b751d92 100644
--- a/hyrax/spec/features/oai_pmh_spec.rb
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -2,7 +2,7 @@
 
 RSpec.describe "OAI PMH Support", type: :feature do
   let(:user) { create(:user) }
-  let(:work) { create(:work, depositor: user) }
+  let(:work) { create(:work, depositor: user.email) }
   let(:identifier) { work.id }
 
   before do
@@ -12,24 +12,24 @@
 
   context 'oai interface with works present' do
     it 'lists metadata prefixess' do
-      visit oai_catalog_path(verb: 'ListMetadataFormats')
+      visit oai_provider_catalog_path(verb: 'ListMetadataFormats')
       expect(page).to have_content('oai_dc')
     end
 
     it 'retrieves a list of records' do
-      visit oai_catalog_path(verb: 'ListRecords', metadataPrefix: 'oai_dc')
+      visit oai_provider_catalog_path(verb: 'ListRecords', metadataPrefix: 'oai_dc')
       expect(page).to have_content("oai:ngdrdemo:#{identifier}")
       expect(page).to have_content(work.title.first)
     end
 
     it 'retrieves a single record' do
-      visit oai_catalog_path(verb: 'GetRecord', metadataPrefix: 'oai_dc', identifier: identifier)
+      visit oai_provider_catalog_path(verb: 'GetRecord', metadataPrefix: 'oai_dc', identifier: identifier)
       expect(page).to have_content("oai:ngdrdemo:#{identifier}")
       expect(page).to have_content(work.title.first)
     end
 
     it 'retrieves a list of identifiers' do
-      visit oai_catalog_path(verb: 'ListIdentifiers', metadataPrefix: 'oai_dc')
+      visit oai_provider_catalog_path(verb: 'ListIdentifiers', metadataPrefix: 'oai_dc')
       expect(page).to have_content("oai:ngdrdemo:#{identifier}")
       expect(page).not_to have_content(work.title.first)
     end

From 13ffc96db57d27f745d9e31bd5cb880fddc38f1f Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Wed, 6 Nov 2019 20:24:23 +0000
Subject: [PATCH 029/258] Removed duplicate blacklight OAI

---
 hyrax/Gemfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index da1cef62..5a5c8b40 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -92,4 +92,3 @@ group :test do
 end
 
 gem 'coveralls', require: false
-gem 'blacklight_oai_provider', git: 'https://github.com/CottageLabs/blacklight_oai_provider.git', branch: 'master'

From b3baebca865da0d3f093a3b6a3e2626de8fc9f30 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Thu, 7 Nov 2019 19:43:20 +0900
Subject: [PATCH 030/258] Add favicons

---
 hyrax/public/apple-touch-icon-precomposed.png | Bin 0 -> 5975 bytes
 hyrax/public/apple-touch-icon.png             | Bin 0 -> 5401 bytes
 hyrax/public/favicon.ico                      | Bin 0 -> 15086 bytes
 3 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/hyrax/public/apple-touch-icon-precomposed.png b/hyrax/public/apple-touch-icon-precomposed.png
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..cf6370f9e93774bcc78dec15d6c7ede791524bb6 100644
GIT binary patch
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From 0d1cfa097fc1799f5cfad1c9fd3cd1afb117bab3 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 8 Nov 2019 11:02:01 +0000
Subject: [PATCH 031/258] extend text extraction support to text/csv and
 text/tab-separated-values

---
 hyrax/app/models/file_set.rb       | 22 +++++++++++++---------
 hyrax/spec/models/file_set_spec.rb |  6 ++++++
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/hyrax/app/models/file_set.rb b/hyrax/app/models/file_set.rb
index 794ad065..7e4e3816 100644
--- a/hyrax/app/models/file_set.rb
+++ b/hyrax/app/models/file_set.rb
@@ -10,14 +10,18 @@ class FileSet < ActiveFedora::Base
   # override method in lib/hydra/works/models/concerns/file_set/mime_types.rb
     #   add text/plain
   def self.office_document_mime_types
-    ['text/plain',
-     'text/rtf',
-     'application/msword',
-     'application/vnd.openxmlformats-officedocument.wordprocessingml.document',
-     'application/vnd.oasis.opendocument.text',
-     'application/vnd.ms-excel',
-     'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
-     'application/vnd.ms-powerpoint',
-     'application/vnd.openxmlformats-officedocument.presentationml.presentation']
+    [
+      'text/plain',
+      'text/csv',
+      'text/tab-separated-values',
+      'text/rtf',
+      'application/msword',
+      'application/vnd.openxmlformats-officedocument.wordprocessingml.document',
+      'application/vnd.oasis.opendocument.text',
+      'application/vnd.ms-excel',
+      'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
+      'application/vnd.ms-powerpoint',
+      'application/vnd.openxmlformats-officedocument.presentationml.presentation'
+    ]
   end
 end
diff --git a/hyrax/spec/models/file_set_spec.rb b/hyrax/spec/models/file_set_spec.rb
index 663018e0..5d0647e7 100644
--- a/hyrax/spec/models/file_set_spec.rb
+++ b/hyrax/spec/models/file_set_spec.rb
@@ -4,4 +4,10 @@
   it "adds plain text to office_document_mime_types" do
     expect(described_class.office_document_mime_types).to include('text/plain')
   end
+  it "adds csv to office_document_mime_types" do
+    expect(described_class.office_document_mime_types).to include('text/csv')
+  end
+  it "adds tsv to office_document_mime_types" do
+    expect(described_class.office_document_mime_types).to include('text/tab-separated-values')
+  end
 end

From 10ada7bf67ee09bbbde350eb23da129d9f00477a Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 11 Nov 2019 18:25:12 +0000
Subject: [PATCH 032/258] wip - now authenticating with local cas server

---
 .env.template                                 |  3 +
 hyrax/Gemfile                                 |  1 +
 hyrax/Gemfile.lock                            |  6 ++
 hyrax/app/models/user.rb                      | 21 ++++++-
 hyrax/config/initializers/devise.rb           | 57 +++++++++++++++++++
 ..._local_authority_entries_on_lower_label.rb | 16 ++++++
 hyrax/db/schema.rb                            |  3 +-
 7 files changed, 105 insertions(+), 2 deletions(-)
 create mode 100644 hyrax/db/migrate/20191111115624_index_qa_local_authority_entries_on_lower_label.rb

diff --git a/.env.template b/.env.template
index b9ec1580..1998c5df 100644
--- a/.env.template
+++ b/.env.template
@@ -87,6 +87,7 @@ BOX_CLIENT_SECRET=
 # (database_authenticatable is pre-configured and useful for a development environment)
 MDR_DEVISE_AUTH_MODULE=ldap_authenticatable
 # MDR_DEVISE_AUTH_MODULE=database_authenticatable
+# MDR_DEVISE_AUTH_MODULE=cas_authenticatable
 
 LDAP_HOST=***REMOVED***
 LDAP_PORT=443
@@ -100,3 +101,5 @@ SMTP_HOST=
 SMTP_PORT=
 
 MDR_HOST=
+
+CAS_BASE_URL=https://cas.nims.go.jp/
diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 233d9240..f0016995 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -72,6 +72,7 @@ gem 'hydra-role-management'
 gem 'bootstrap-datepicker-rails'
 gem 'pg'
 gem 'devise_ldap_authenticatable'
+gem 'devise_cas_authenticatable'
 
 gem 'riiif', '~> 2.0'
 
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index 499e6da0..01ab3398 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -218,6 +218,9 @@ GEM
       warden (~> 1.2.3)
     devise-guests (0.7.0)
       devise
+    devise_cas_authenticatable (1.10.4)
+      devise (>= 1.2.0)
+      rubycas-client (>= 2.2.1)
     devise_ldap_authenticatable (0.8.6)
       devise (>= 3.4.1)
       net-ldap (>= 0.16.0)
@@ -731,6 +734,8 @@ GEM
       multipart-post
       oauth2
     ruby-progressbar (1.10.1)
+    rubycas-client (2.3.9)
+      activesupport
     rubyzip (2.0.0)
     samvera-nesting_indexer (2.0.0)
       dry-equalizer
@@ -878,6 +883,7 @@ DEPENDENCIES
   database_cleaner
   devise
   devise-guests (~> 0.6)
+  devise_cas_authenticatable
   devise_ldap_authenticatable
   factory_bot_rails
   fcrepo_wrapper
diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 50b9dc25..da5af59b 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -18,7 +18,8 @@ class User < ApplicationRecord
   # Include default devise modules. Others available are:
   # :registerable, :confirmable, :lockable, :timeoutable and :omniauthable
   devise ENV.fetch('MDR_DEVISE_AUTH_MODULE', 'database_authenticatable').to_sym,
-         :rememberable, :trackable, :validatable, :lockable
+         :rememberable, :trackable, :lockable
+         # NB: the :validatable module is not compatible with CAS authentication
 
   # Method added by Blacklight; Blacklight uses #to_s on your
   # user class to get a user-displayable login/identifier for
@@ -36,4 +37,22 @@ def ldap_before_save
     self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
     self.password = Devise.friendly_token[0, 20]
   end
+
+  def cas_extra_attributes=(extra_attributes)
+    extra_attributes.each do |name, value|
+      case name.to_sym
+      # TODO: change these mappings to match NIMS CAS schema
+      when :mail
+        self.email = value
+      when :eduPersonNickname
+        self.display_name = value
+      when :cn
+        self.email = value
+      # when :fullname
+      #   self.fullname = value
+      # when :email
+      #   self.email = value
+      end
+    end
+  end
 end
diff --git a/hyrax/config/initializers/devise.rb b/hyrax/config/initializers/devise.rb
index 5356780b..42c372f8 100644
--- a/hyrax/config/initializers/devise.rb
+++ b/hyrax/config/initializers/devise.rb
@@ -293,4 +293,61 @@
   # When using OmniAuth, Devise cannot automatically set OmniAuth path,
   # so you need to do it manually. For the users scope, it would be:
   # config.omniauth_path_prefix = '/my_engine/users/auth'
+
+  # CAS (Central Authentication Service) setup
+  config.cas_base_url = ENV['CAS_BASE_URL'] || 'https://cas.nims.go.jp/'
+
+  # you can override these if you need to, but cas_base_url is usually enough
+  # config.cas_login_url = "https://cas.myorganization.com/login"
+  # config.cas_logout_url = "https://cas.myorganization.com/logout"
+  # config.cas_validate_url = "https://cas.myorganization.com/serviceValidate"
+  config.cas_validate_url = "https://castest:8443/cas/serviceValidate" # TODO: FIXME!
+
+  # The CAS specification allows for the passing of a follow URL to be displayed when
+  # a user logs out on the CAS server. RubyCAS-Server also supports redirecting to a
+  # URL via the destination param. Set either of these urls and specify either nil,
+  # 'destination' or 'follow' as the logout_url_param. If the urls are blank but
+  # logout_url_param is set, a default will be detected for the service.
+  # config.cas_destination_url = 'https://cas.myorganization.com'
+  # config.cas_follow_url = 'https://cas.myorganization.com'
+  # config.cas_logout_url_param = nil
+
+  # You can specify the name of the destination argument with the following option.
+  # e.g. the following option will change it from 'destination' to 'url'
+  # config.cas_destination_logout_param_name = 'url'
+
+  # By default, devise_cas_authenticatable will create users.  If you would rather
+  # require user records to already exist locally before they can authenticate via
+  # CAS, uncomment the following line.
+  # config.cas_create_user = false
+
+  # You can enable Single Sign Out, which by default is disabled.
+  config.cas_enable_single_sign_out = true
+
+  # If you don't want to use the username returned from your CAS server as the unique
+  # identifier, but some other field passed in cas_extra_attributes, you can specify
+  # the field name here.
+  # config.cas_user_identifier = nil
+
+  # If you want to use the Devise Timeoutable module with single sign out,
+  # uncommenting this will redirect timeouts to the logout url, so that the CAS can
+  # take care of signing out the other serviced applocations. Note that each
+  # application manages timeouts independently, so one application timing out will
+  # kill the session on all applications serviced by the CAS.
+  # config.warden do |manager|
+  #   manager.failure_app = DeviseCasAuthenticatable::SingleSignOut::WardenFailureApp
+  # end
+
+  # You can also set another single sign out strategy so that you won't be attached to rails_cache.
+  # Be aware that to do so you also need to set the session_store.
+  # Example for setting redis_cache.
+  # There are some gems the help with it. One of them is called redis-rails and it can easily be set like this:
+  # Rails.application.config.session_store :redis_store, servers: ["redis://localhost:6379/0/session"]
+  # This is specially useful when you need to share session id accross apps (i.e. in a distributed environment)
+  # config.cas_single_sign_out_mapping_strategy = :redis_cache
+
+  # If you need to specify some extra configs for rubycas-client, you can do this via:
+  # config.cas_client_config_options = {
+  #     logger: Rails.logger
+  # }
 end
diff --git a/hyrax/db/migrate/20191111115624_index_qa_local_authority_entries_on_lower_label.rb b/hyrax/db/migrate/20191111115624_index_qa_local_authority_entries_on_lower_label.rb
new file mode 100644
index 00000000..6f1363c0
--- /dev/null
+++ b/hyrax/db/migrate/20191111115624_index_qa_local_authority_entries_on_lower_label.rb
@@ -0,0 +1,16 @@
+class IndexQaLocalAuthorityEntriesOnLowerLabel < ActiveRecord::Migration[5.1]
+
+  # ActiveRecord doesn't support functional indexes, so we need to add this the old fashioned way. Note the different
+  # syntax for sqlite vs postgres
+  def up
+    if ActiveRecord::Base.connection.adapter_name.downcase.start_with? 'sqlite'
+      execute 'CREATE INDEX "index_qa_local_authority_entries_on_lower_label" ON "qa_local_authority_entries" (local_authority_id, label collate nocase);'
+    else
+      execute 'CREATE INDEX "index_qa_local_authority_entries_on_lower_label" ON "qa_local_authority_entries" (local_authority_id, lower(label));'
+    end
+  end
+
+  def down
+    execute "DROP INDEX index_qa_local_authority_entries_on_lower_label;"
+  end
+end
diff --git a/hyrax/db/schema.rb b/hyrax/db/schema.rb
index e959d543..8fcb5120 100644
--- a/hyrax/db/schema.rb
+++ b/hyrax/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20190930025332) do
+ActiveRecord::Schema.define(version: 20191111115624) do
 
   create_table "bookmarks", force: :cascade do |t|
     t.integer "user_id", null: false
@@ -279,6 +279,7 @@
     t.string "uri"
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
+    t.index ["local_authority_id", "label"], name: "index_qa_local_authority_entries_on_lower_label"
     t.index ["local_authority_id"], name: "index_qa_local_authority_entries_on_local_authority_id"
     t.index ["uri"], name: "index_qa_local_authority_entries_on_uri", unique: true
   end

From 2cd41a60bf53d9d53822715908f6d1f9669fc983 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 13 Nov 2019 10:30:53 +0000
Subject: [PATCH 033/258] wip

---
 .env.template                       |  2 ++
 cas/Dockerfile                      | 10 ++++++++++
 cas/cas.properties                  | 15 +++++++++++++++
 docker-compose.override.yml         | 12 +++++++++++-
 hyrax/Dockerfile                    |  2 +-
 hyrax/config/initializers/devise.rb |  4 +++-
 6 files changed, 42 insertions(+), 3 deletions(-)
 create mode 100644 cas/Dockerfile
 create mode 100644 cas/cas.properties

diff --git a/.env.template b/.env.template
index 1998c5df..af26eae7 100644
--- a/.env.template
+++ b/.env.template
@@ -103,3 +103,5 @@ SMTP_PORT=
 MDR_HOST=
 
 CAS_BASE_URL=https://cas.nims.go.jp/
+# CAS_VALIDATE_URL may need to be set depending on how MDR is configured
+# CAS_VALIDATE_URL=https://cas:8443/cas/serviceValidate
diff --git a/cas/Dockerfile b/cas/Dockerfile
new file mode 100644
index 00000000..ad1b64d9
--- /dev/null
+++ b/cas/Dockerfile
@@ -0,0 +1,10 @@
+FROM apereo/cas:v5.3.10
+RUN keytool -genkeypair -alias cas -keyalg RSA -keypass changeit \
+            -storepass changeit -keystore /cas-overlay/etc/cas/thekeystore \
+            -dname "CN=cas.example.org,OU=Example,OU=Org,C=AU" \
+            -ext SAN="dns:example.org,dns:localhost,ip:127.0.0.1"
+COPY cas.properties /cas-overlay/etc/cas/config/cas.properties
+# COPY users.json /cas-overlay/etc/cas/users.json
+
+RUN build.sh package \
+  && build.sh copy
diff --git a/cas/cas.properties b/cas/cas.properties
new file mode 100644
index 00000000..635bebe5
--- /dev/null
+++ b/cas/cas.properties
@@ -0,0 +1,15 @@
+# Required CAS settings
+cas.server.name: https://cas.example.org:8443
+cas.server.prefix: https://cas.example.org:8443/cas
+
+cas.adminPagesSecurity.ip=127\.0\.0\.1
+
+logging.config: file:/etc/cas/config/log4j2.xml
+
+# Disable authentication with a static list of credentials
+# cas.authn.accept.users=
+
+# Use JSON file for authentication
+# cas.authn.json.name=
+# cas.authn.json.location=file:///etc/cas/users.json
+# cas.authn.json.passwordPolicy=
diff --git a/docker-compose.override.yml b/docker-compose.override.yml
index 9e71affd..03374cc5 100644
--- a/docker-compose.override.yml
+++ b/docker-compose.override.yml
@@ -37,9 +37,19 @@ services:
   web:
     ports:
       - 3000:3000
+    depends_on:
+      - cas
     environment:
-    - RAILS_FORCE_SSL=false
+      - RAILS_FORCE_SSL=false
 
   redis:
     volumes:
       - redis:/data
+
+  cas:
+    build:
+      context: cas
+    networks:
+      internal:
+    ports:
+      - 8443:8443
diff --git a/hyrax/Dockerfile b/hyrax/Dockerfile
index b6572ade..c24807c4 100644
--- a/hyrax/Dockerfile
+++ b/hyrax/Dockerfile
@@ -61,7 +61,7 @@ RUN cd $APP_PRODUCTION && \
     && if [ "$RAILS_ENV" = "production" ]; then \
             bundle install --without test:development; \
         else \
-            bundle install --without production --no-deployment; \
+            bundle install --no-deployment; \
         fi \
     && mv Gemfile.lock Gemfile.lock.built_by_docker
 
diff --git a/hyrax/config/initializers/devise.rb b/hyrax/config/initializers/devise.rb
index 42c372f8..84da8b7b 100644
--- a/hyrax/config/initializers/devise.rb
+++ b/hyrax/config/initializers/devise.rb
@@ -301,7 +301,9 @@
   # config.cas_login_url = "https://cas.myorganization.com/login"
   # config.cas_logout_url = "https://cas.myorganization.com/logout"
   # config.cas_validate_url = "https://cas.myorganization.com/serviceValidate"
-  config.cas_validate_url = "https://castest:8443/cas/serviceValidate" # TODO: FIXME!
+  if ENV['CAS_VALIDATE_URL'].present?
+    config.cas_validate_url = ENV['CAS_VALIDATE_URL']
+  end
 
   # The CAS specification allows for the passing of a follow URL to be displayed when
   # a user logs out on the CAS server. RubyCAS-Server also supports redirecting to a

From d750312aa33c41c07b43d8f18d2d5991de308faf Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 13 Nov 2019 18:04:39 +0000
Subject: [PATCH 034/258] custom cas server, fix password issue

---
 cas/Dockerfile                           |   6 +-
 cas/{ => etc/cas/config}/cas.properties  |  10 +-
 cas/etc/cas/services/NIMS-CAStest-1.json |   6 +
 cas/etc/cas/users.json                   |  14 ++
 cas/pom.xml                              | 230 +++++++++++++++++++++++
 hyrax/app/models/user.rb                 |   9 +
 6 files changed, 270 insertions(+), 5 deletions(-)
 rename cas/{ => etc/cas/config}/cas.properties (61%)
 create mode 100644 cas/etc/cas/services/NIMS-CAStest-1.json
 create mode 100644 cas/etc/cas/users.json
 create mode 100644 cas/pom.xml

diff --git a/cas/Dockerfile b/cas/Dockerfile
index ad1b64d9..f0c40858 100644
--- a/cas/Dockerfile
+++ b/cas/Dockerfile
@@ -3,8 +3,10 @@ RUN keytool -genkeypair -alias cas -keyalg RSA -keypass changeit \
             -storepass changeit -keystore /cas-overlay/etc/cas/thekeystore \
             -dname "CN=cas.example.org,OU=Example,OU=Org,C=AU" \
             -ext SAN="dns:example.org,dns:localhost,ip:127.0.0.1"
-COPY cas.properties /cas-overlay/etc/cas/config/cas.properties
-# COPY users.json /cas-overlay/etc/cas/users.json
+COPY etc/cas/config/* /cas-overlay/etc/cas/config/
+COPY etc/cas/services/* /cas-overlay/etc/cas/services/
+COPY etc/cas/users.json /cas-overlay/etc/cas/
+COPY pom.xml /cas-overlay/
 
 RUN build.sh package \
   && build.sh copy
diff --git a/cas/cas.properties b/cas/etc/cas/config/cas.properties
similarity index 61%
rename from cas/cas.properties
rename to cas/etc/cas/config/cas.properties
index 635bebe5..282cdcbe 100644
--- a/cas/cas.properties
+++ b/cas/etc/cas/config/cas.properties
@@ -6,10 +6,14 @@ cas.adminPagesSecurity.ip=127\.0\.0\.1
 
 logging.config: file:/etc/cas/config/log4j2.xml
 
+# Service Registry
+cas.serviceRegistry.initFromJson: false
+cas.serviceRegistry.json.location: file:/etc/cas/services
+
 # Disable authentication with a static list of credentials
-# cas.authn.accept.users=
+cas.authn.accept.users=
 
 # Use JSON file for authentication
-# cas.authn.json.name=
-# cas.authn.json.location=file:///etc/cas/users.json
+cas.authn.json.location=file:///etc/cas/users.json
+cas.authn.json.name=
 # cas.authn.json.passwordPolicy=
diff --git a/cas/etc/cas/services/NIMS-CAStest-1.json b/cas/etc/cas/services/NIMS-CAStest-1.json
new file mode 100644
index 00000000..eb0d9256
--- /dev/null
+++ b/cas/etc/cas/services/NIMS-CAStest-1.json
@@ -0,0 +1,6 @@
+{
+  "@class" : "org.apereo.cas.services.RegexRegisteredService",
+  "serviceId" :  "^(https|http)://.*",
+  "name" : "NIMS-CAStest",
+  "id" : 1
+}
diff --git a/cas/etc/cas/users.json b/cas/etc/cas/users.json
new file mode 100644
index 00000000..9500f4e1
--- /dev/null
+++ b/cas/etc/cas/users.json
@@ -0,0 +1,14 @@
+{
+  "@class" : "java.util.LinkedHashMap",
+  "casuser" : {
+    "@class" : "org.apereo.cas.adaptors.generic.CasUserAccount",
+    "password" : "Mellon2",
+    "attributes" : {
+      "@class" : "java.util.LinkedHashMap",
+      "firstName" : "Apereo",
+      "lastName" : "CAS"
+    },
+    "status" : "OK",
+    "expirationDate" : "2022-01-19"
+  }
+}
diff --git a/cas/pom.xml b/cas/pom.xml
new file mode 100644
index 00000000..867a86be
--- /dev/null
+++ b/cas/pom.xml
@@ -0,0 +1,230 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd ">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.apereo.cas</groupId>
+  <artifactId>cas-overlay</artifactId>
+  <packaging>war</packaging>
+  <version>1.0</version>
+
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>com.rimerosolutions.maven.plugins</groupId>
+        <artifactId>wrapper-maven-plugin</artifactId>
+        <version>0.0.5</version>
+        <configuration>
+          <verifyDownload>true</verifyDownload>
+          <checksumAlgorithm>MD5</checksumAlgorithm>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.springframework.boot</groupId>
+        <artifactId>spring-boot-maven-plugin</artifactId>
+        <version>${springboot.version}</version>
+        <configuration>
+          <mainClass>${mainClassName}</mainClass>
+          <addResources>true</addResources>
+          <executable>${isExecutable}</executable>
+          <layout>WAR</layout>
+        </configuration>
+        <executions>
+          <execution>
+            <goals>
+              <goal>repackage</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-war-plugin</artifactId>
+        <version>2.6</version>
+        <configuration>
+          <warName>cas</warName>
+          <failOnMissingWebXml>false</failOnMissingWebXml>
+          <recompressZippedFiles>false</recompressZippedFiles>
+          <archive>
+            <compress>false</compress>
+            <manifestFile>${manifestFileToUse}</manifestFile>
+          </archive>
+          <overlays>
+            <overlay>
+              <groupId>org.apereo.cas</groupId>
+              <artifactId>cas-server-webapp${app.server}</artifactId>
+            </overlay>
+          </overlays>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.3</version>
+      </plugin>
+    </plugins>
+    <finalName>cas</finalName>
+  </build>
+
+  <dependencies>
+    <dependency>
+      <groupId>org.apereo.cas</groupId>
+      <artifactId>cas-server-support-json-service-registry</artifactId>
+      <version>${cas.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apereo.cas</groupId>
+      <artifactId>cas-server-support-generic</artifactId>
+      <version>${cas.version}</version>
+    </dependency>
+  </dependencies>
+
+  <properties>
+    <cas.version>5.3.9</cas.version>
+    <springboot.version>1.5.18.RELEASE</springboot.version>
+    <!-- app.server could be -jetty, -undertow, -tomcat, or blank if you plan to provide appserver -->
+    <app.server>-tomcat</app.server>
+
+    <mainClassName>org.springframework.boot.loader.WarLauncher</mainClassName>
+    <isExecutable>false</isExecutable>
+    <manifestFileToUse>
+      ${project.build.directory}/war/work/org.apereo.cas/cas-server-webapp${app.server}/META-INF/MANIFEST.MF
+    </manifestFileToUse>
+
+    <maven.compiler.source>1.8</maven.compiler.source>
+    <maven.compiler.target>1.8</maven.compiler.target>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+
+  <repositories>
+    <repository>
+      <id>sonatype-releases</id>
+      <url>http://oss.sonatype.org/content/repositories/releases/</url>
+      <snapshots>
+        <enabled>false</enabled>
+      </snapshots>
+      <releases>
+        <enabled>true</enabled>
+      </releases>
+    </repository>
+    <repository>
+      <id>sonatype-snapshots</id>
+      <url>https://oss.sonatype.org/content/repositories/snapshots/</url>
+      <snapshots>
+        <enabled>true</enabled>
+      </snapshots>
+      <releases>
+        <enabled>false</enabled>
+      </releases>
+    </repository>
+    <repository>
+      <id>shibboleth-releases</id>
+      <url>https://build.shibboleth.net/nexus/content/repositories/releases</url>
+    </repository>
+  </repositories>
+
+  <profiles>
+    <profile>
+      <activation>
+        <activeByDefault>true</activeByDefault>
+      </activation>
+      <id>default</id>
+      <dependencies>
+        <dependency>
+          <groupId>org.apereo.cas</groupId>
+          <artifactId>cas-server-webapp${app.server}</artifactId>
+          <version>${cas.version}</version>
+          <type>war</type>
+          <scope>runtime</scope>
+        </dependency>
+        <!--
+        ...Additional dependencies may be placed here...
+        -->
+      </dependencies>
+    </profile>
+
+    <profile>
+      <activation>
+        <activeByDefault>false</activeByDefault>
+      </activation>
+      <id>exec</id>
+      <properties>
+        <mainClassName>org.apereo.cas.web.CasWebApplication</mainClassName>
+        <isExecutable>true</isExecutable>
+        <manifestFileToUse></manifestFileToUse>
+      </properties>
+      <build>
+        <plugins>
+          <plugin>
+            <groupId>com.soebes.maven.plugins</groupId>
+            <artifactId>echo-maven-plugin</artifactId>
+            <version>0.3.0</version>
+            <executions>
+              <execution>
+                <phase>prepare-package</phase>
+                <goals>
+                  <goal>echo</goal>
+                </goals>
+              </execution>
+            </executions>
+            <configuration>
+              <echos>
+                <echo>Executable profile to make the generated CAS web application executable.</echo>
+              </echos>
+            </configuration>
+          </plugin>
+        </plugins>
+      </build>
+    </profile>
+
+    <profile>
+      <activation>
+        <activeByDefault>false</activeByDefault>
+      </activation>
+      <id>bootiful</id>
+      <properties>
+        <app.server>-tomcat</app.server>
+        <isExecutable>false</isExecutable>
+      </properties>
+      <dependencies>
+        <dependency>
+          <groupId>org.apereo.cas</groupId>
+          <artifactId>cas-server-webapp${app.server}</artifactId>
+          <version>${cas.version}</version>
+          <type>war</type>
+          <scope>runtime</scope>
+        </dependency>
+      </dependencies>
+    </profile>
+
+    <profile>
+      <activation>
+        <activeByDefault>false</activeByDefault>
+      </activation>
+      <id>pgp</id>
+      <build>
+        <plugins>
+          <plugin>
+            <groupId>com.github.s4u.plugins</groupId>
+            <artifactId>pgpverify-maven-plugin</artifactId>
+            <version>1.1.0</version>
+            <executions>
+              <execution>
+                <goals>
+                  <goal>check</goal>
+                </goals>
+              </execution>
+            </executions>
+            <configuration>
+              <pgpKeyServer>hkp://pool.sks-keyservers.net</pgpKeyServer>
+              <pgpKeysCachePath>${settings.localRepository}/pgpkeys-cache</pgpKeysCachePath>
+              <scope>test</scope>
+              <verifyPomFiles>true</verifyPomFiles>
+              <failNoSignature>false</failNoSignature>
+            </configuration>
+          </plugin>
+        </plugins>
+      </build>
+    </profile>
+  </profiles>
+</project>
diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index da5af59b..683b3837 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -21,6 +21,15 @@ class User < ApplicationRecord
          :rememberable, :trackable, :lockable
          # NB: the :validatable module is not compatible with CAS authentication
 
+  # hack to ignore setting password when using CAS authentication
+  if ENV['MDR_DEVISE_AUTH_MODULE'] == 'cas_authenticatable'
+    attr_reader :password
+    def password=(new_password)
+      @password = new_password
+      self.encrypted_password = ''
+    end
+  end
+
   # Method added by Blacklight; Blacklight uses #to_s on your
   # user class to get a user-displayable login/identifier for
   # the account.

From 5f7bcf1c250f7b91ab131a4a3bc1cd4564590a80 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 14 Nov 2019 10:49:03 +0000
Subject: [PATCH 035/258] more efficient cas building

---
 cas/Dockerfile         | 7 ++++---
 cas/etc/cas/users.json | 4 ++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/cas/Dockerfile b/cas/Dockerfile
index f0c40858..a0c24470 100644
--- a/cas/Dockerfile
+++ b/cas/Dockerfile
@@ -1,4 +1,7 @@
 FROM apereo/cas:v5.3.10
+COPY pom.xml /cas-overlay/
+RUN build.sh package
+
 RUN keytool -genkeypair -alias cas -keyalg RSA -keypass changeit \
             -storepass changeit -keystore /cas-overlay/etc/cas/thekeystore \
             -dname "CN=cas.example.org,OU=Example,OU=Org,C=AU" \
@@ -7,6 +10,4 @@ COPY etc/cas/config/* /cas-overlay/etc/cas/config/
 COPY etc/cas/services/* /cas-overlay/etc/cas/services/
 COPY etc/cas/users.json /cas-overlay/etc/cas/
 COPY pom.xml /cas-overlay/
-
-RUN build.sh package \
-  && build.sh copy
+RUN build.sh copy
diff --git a/cas/etc/cas/users.json b/cas/etc/cas/users.json
index 9500f4e1..45a1ec2c 100644
--- a/cas/etc/cas/users.json
+++ b/cas/etc/cas/users.json
@@ -1,8 +1,8 @@
 {
   "@class" : "java.util.LinkedHashMap",
-  "casuser" : {
+  "user1" : {
     "@class" : "org.apereo.cas.adaptors.generic.CasUserAccount",
-    "password" : "Mellon2",
+    "password" : "password",
     "attributes" : {
       "@class" : "java.util.LinkedHashMap",
       "firstName" : "Apereo",

From 8874e31fd23b6be8b30649726e11e91f3fbfc349 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 8 Nov 2019 15:37:15 +0000
Subject: [PATCH 036/258] i212 - search links not working

---
 .../complex_field/instrument_indexer.rb       | 33 +++++++++++++++++++
 .../complex_field/purchase_record_indexer.rb  |  6 ++++
 hyrax/app/indexers/dataset_indexer.rb         |  3 +-
 hyrax/app/models/dataset.rb                   |  2 +-
 .../nested_affiliation_attribute_renderer.rb  |  2 +-
 .../renderers/nested_attribute_renderer.rb    | 24 ++++++++++++--
 .../nested_desc_id_attribute_renderer.rb      |  2 +-
 .../nested_instrument_attribute_renderer.rb   | 13 ++++----
 ...nested_material_type_attribute_renderer.rb |  2 +-
 .../nested_organization_attribute_renderer.rb |  2 +-
 .../nested_person_attribute_renderer.rb       |  4 +--
 ...sted_purchase_record_attribute_renderer.rb | 11 ++++---
 .../nested_relation_attribute_renderer.rb     |  2 +-
 .../nested_source_attribute_renderer.rb       |  4 +--
 ...nested_specimen_type_attribute_renderer.rb | 16 ++++-----
 ...d_structural_feature_attribute_renderer.rb |  2 +-
 hyrax/config/locales/hyrax.en.yml             |  1 +
 hyrax/spec/indexers/dataset_indexer_spec.rb   | 33 +++++++++++++++++--
 18 files changed, 127 insertions(+), 35 deletions(-)

diff --git a/hyrax/app/indexers/complex_field/instrument_indexer.rb b/hyrax/app/indexers/complex_field/instrument_indexer.rb
index 0cd8b5a3..806510bd 100644
--- a/hyrax/app/indexers/complex_field/instrument_indexer.rb
+++ b/hyrax/app/indexers/complex_field/instrument_indexer.rb
@@ -9,6 +9,15 @@ def generate_solr_document
     def index_instrument(solr_doc)
       solr_doc[Solrizer.solr_name('complex_instrument', :displayable)] = object.complex_instrument.to_json
       solr_doc[Solrizer.solr_name('instrument_title', :stored_searchable)] = object.complex_instrument.map { |i| i.title.reject(&:blank?) }.flatten!
+      # use the instrument title for the complex_instrument_sim facet
+      solr_doc[Solrizer.solr_name('complex_instrument', :facetable)] = object.complex_instrument.map { |i| i.title.reject(&:blank?) }.flatten!
+      
+      fld_name = Solrizer.solr_name('instrument_title', :facetable)
+      solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
+      vals = object.complex_instrument.map { |i| i.title.reject(&:blank?) }
+      solr_doc[fld_name] << vals
+      solr_doc[fld_name].flatten!
+      
       solr_doc[Solrizer.solr_name('instrument_alternative_title', :stored_searchable)] = object.complex_instrument.map { |i| i.alternative_title.reject(&:blank?) }.flatten!
       solr_doc[Solrizer.solr_name('instrument_description', :stored_searchable)] = object.complex_instrument.map { |i| i.description.reject(&:blank?) }.flatten!
       solr_doc[Solrizer.solr_name('instrument_model_number', :stored_searchable)] = object.complex_instrument.map { |i| i.model_number.reject(&:blank?) }.flatten!
@@ -70,6 +79,29 @@ def index_instrument(solr_doc)
           solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
           solr_doc[fld_name] << person_name
           solr_doc[fld_name].flatten!
+          # Affiliation
+          pn.complex_affiliation.each do |ca|
+            ca.complex_organization.each do |co|
+              vals = co.organization.reject(&:blank?)
+              fld_name = Solrizer.solr_name("complex_person_#{label}_organization", :stored_searchable)
+              solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
+              solr_doc[fld_name] << vals
+              solr_doc[fld_name] = solr_doc[fld_name].flatten.uniq
+              fld_name = Solrizer.solr_name("complex_person_#{label}_organization", :facetable)
+              solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
+              solr_doc[fld_name] << vals
+              solr_doc[fld_name] = solr_doc[fld_name].flatten.uniq
+              vals = co.sub_organization.reject(&:blank?)
+              fld_name = Solrizer.solr_name("complex_person_#{label}_sub_organization", :stored_searchable)
+              solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
+              solr_doc[fld_name] << vals
+              solr_doc[fld_name] = solr_doc[fld_name].flatten.uniq
+              fld_name = Solrizer.solr_name("complex_person_#{label}_sub_organization", :facetable)
+              solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
+              solr_doc[fld_name] << vals
+              solr_doc[fld_name] = solr_doc[fld_name].flatten.uniq
+            end
+          end
         end
         i.managing_organization.each do |org|
           fld_name = Solrizer.solr_name('instrument_managing_organization', :stored_searchable)
@@ -95,6 +127,7 @@ def index_instrument(solr_doc)
     def self.instrument_facet_fields
       # solr fields that will be treated as facets
       fields = []
+      #fields << Solrizer.solr_name('instrument_title', :facetable)
       fields << Solrizer.solr_name('instrument_manufacturer', :facetable)
       fields << Solrizer.solr_name('instrument_manufacturer_sub_organization', :facetable)
       fields << Solrizer.solr_name('instrument_model_number', :facetable)
diff --git a/hyrax/app/indexers/complex_field/purchase_record_indexer.rb b/hyrax/app/indexers/complex_field/purchase_record_indexer.rb
index e63f5038..3b28c0f5 100644
--- a/hyrax/app/indexers/complex_field/purchase_record_indexer.rb
+++ b/hyrax/app/indexers/complex_field/purchase_record_indexer.rb
@@ -20,6 +20,11 @@ def index_purchase_record(solr_doc)
         vals = st.complex_purchase_record.map { |i| i.title.reject(&:blank?) }
         solr_doc[fld_name] << vals
         solr_doc[fld_name].flatten!
+        fld_name = Solrizer.solr_name('complex_purchase_record_title', :facetable)
+        solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
+        vals = st.complex_purchase_record.map { |i| i.title.reject(&:blank?) }
+        solr_doc[fld_name] << vals
+        solr_doc[fld_name].flatten!
         st.complex_purchase_record.each do |i|
           # date
           dates = i.date.reject(&:blank?)
@@ -87,6 +92,7 @@ def index_purchase_record(solr_doc)
     def self.purchase_record_facet_fields
       # solr fields that will be treated as facets
       fields = []
+      # fields << Solrizer.solr_name('complex_purchase_record_title', :facetable)
       fields << Solrizer.solr_name('complex_purchase_record_manufacturer', :facetable)
       fields << Solrizer.solr_name('complex_purchase_record_manufacturer_sub_organization', :facetable)
       fields << Solrizer.solr_name('complex_purchase_record_supplier', :facetable)
diff --git a/hyrax/app/indexers/dataset_indexer.rb b/hyrax/app/indexers/dataset_indexer.rb
index e2fb44d3..f74fb02a 100644
--- a/hyrax/app/indexers/dataset_indexer.rb
+++ b/hyrax/app/indexers/dataset_indexer.rb
@@ -27,7 +27,8 @@ def self.facet_fields
         'computational_methods',
         'data_origin',
         'properties_addressed',
-        'synthesis_and_processing'
+        'synthesis_and_processing',
+        'characterization_methods'
       ]
       dataset_facet_fields.each do |fld|
         fields << Solrizer.solr_name(fld, :facetable)
diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index c905a9f5..05303a8d 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -52,7 +52,7 @@ class Dataset < ActiveFedora::Base
   property :complex_organization, predicate: ::RDF::Vocab::ORG.organization, class_name:"ComplexOrganization"
 
   property :characterization_methods, predicate: ::RDF::Vocab::NimsRdp['characterization-methods'], multiple: false do |index|
-    index.as :stored_searchable
+    index.as :stored_searchable, :facetable
   end
 
   property :computational_methods, predicate: ::RDF::Vocab::NimsRdp['computational-methods'], multiple: false do |index|
diff --git a/hyrax/app/renderers/nested_affiliation_attribute_renderer.rb b/hyrax/app/renderers/nested_affiliation_attribute_renderer.rb
index 6798c5b3..851c73cc 100644
--- a/hyrax/app/renderers/nested_affiliation_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_affiliation_attribute_renderer.rb
@@ -13,7 +13,7 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_organization').blank?
         label = 'Organization'
         renderer_class = NestedOrganizationAttributeRenderer
-        each_html += get_nested_output(label, v['complex_organization'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_organization'], renderer_class, false)
       end
       html += get_inner_html(each_html)
     end
diff --git a/hyrax/app/renderers/nested_attribute_renderer.rb b/hyrax/app/renderers/nested_attribute_renderer.rb
index 25deb227..ad2b3f9a 100644
--- a/hyrax/app/renderers/nested_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_attribute_renderer.rb
@@ -48,12 +48,12 @@ def get_label_row(label)
     row
   end
 
-  def get_nested_output(label, nested_value, renderer_class, display_label=false)
+  def get_nested_output(field, label, nested_value, renderer_class, display_label=false)
     output_html = ''
     unless nested_value.kind_of?(Array)
       nested_value = [nested_value]
     end
-    renderer = renderer_class.new(label, nested_value)
+    renderer = renderer_class.new(get_field(field, label), nested_value)
     nested_value.each do |val|
       inner_html = renderer.attribute_value_to_html(val)
       unless inner_html.blank?
@@ -83,4 +83,24 @@ def get_ouput_html(html)
     end
     html_out
   end
+
+  # map the field/label pair to the correct facet search link
+  def get_field(field, label)
+    case
+    when field == :complex_person && label == 'Organization'
+      :complex_person_organization
+    when field == :complex_instrument && label == 'Manufacturer'
+      :instrument_manufacturer
+    when field == :complex_instrument && label == 'Operator'
+      :complex_person_operator
+    when field == :complex_instrument && label == 'Managing organization'
+      :instrument_managing_organization
+    when field == :complex_specimen_type && label == 'Supplier'
+      :complex_purchase_record_supplier
+    when field == :complex_specimen_type && label == 'Manufacturer'
+      :complex_purchase_record_manufacturer
+    else
+      field
+    end
+  end
 end
diff --git a/hyrax/app/renderers/nested_desc_id_attribute_renderer.rb b/hyrax/app/renderers/nested_desc_id_attribute_renderer.rb
index 8e23a1cd..ec195731 100644
--- a/hyrax/app/renderers/nested_desc_id_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_desc_id_attribute_renderer.rb
@@ -13,7 +13,7 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       html += get_inner_html(each_html)
     end
diff --git a/hyrax/app/renderers/nested_instrument_attribute_renderer.rb b/hyrax/app/renderers/nested_instrument_attribute_renderer.rb
index 549112ec..1212b47c 100644
--- a/hyrax/app/renderers/nested_instrument_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_instrument_attribute_renderer.rb
@@ -8,6 +8,7 @@ def attribute_value_to_html(input_value)
       # title
       if v.dig('title').present? and v['title'][0].present?
         label ="Title"
+        # @todo - fixme
         val = link_to(ERB::Util.h(v['title'][0]), search_path(v['title'][0]))
         each_html += get_row(label, val)
       end
@@ -21,7 +22,7 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_date').blank?
         label = 'Date'
         renderer_class = NestedDateAttributeRenderer
-        each_html += get_nested_output(label, v['complex_date'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_date'], renderer_class, false)
       end
       # description
       unless v.dig('description').blank?
@@ -33,19 +34,19 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       # instrument function
       unless v.dig('instrument_function').blank?
         label = 'Instrument function'
         renderer_class = NestedInstrumentFunctionAttributeRenderer
-        each_html += get_nested_output(label, v['instrument_function'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['instrument_function'], renderer_class, true)
       end
       # manufacturer
       unless v.dig('manufacturer').blank?
         label = 'Manufacturer'
         renderer_class = NestedOrganizationAttributeRenderer
-        each_html += get_nested_output(label, v['manufacturer'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['manufacturer'], renderer_class, true)
       end
       # model_number
       unless v.dig('model_number').blank?
@@ -57,13 +58,13 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_person').blank?
         label = 'Operator'
         renderer_class = NestedPersonAttributeRenderer
-        each_html += get_nested_output(label, v['complex_person'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_person'], renderer_class, true)
       end
       # managing_organization
       unless v.dig('managing_organization').blank?
         label = 'Managing organization'
         renderer_class = NestedOrganizationAttributeRenderer
-        each_html += get_nested_output(label, v['managing_organization'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['managing_organization'], renderer_class, true)
       end
       html += get_inner_html(each_html)
     end
diff --git a/hyrax/app/renderers/nested_material_type_attribute_renderer.rb b/hyrax/app/renderers/nested_material_type_attribute_renderer.rb
index bbb90574..fa1ad7cf 100644
--- a/hyrax/app/renderers/nested_material_type_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_material_type_attribute_renderer.rb
@@ -19,7 +19,7 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       # description
       unless v.dig('description').blank?
diff --git a/hyrax/app/renderers/nested_organization_attribute_renderer.rb b/hyrax/app/renderers/nested_organization_attribute_renderer.rb
index 031d9762..6680ed1d 100644
--- a/hyrax/app/renderers/nested_organization_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_organization_attribute_renderer.rb
@@ -23,7 +23,7 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       html += get_inner_html(each_html)
     end
diff --git a/hyrax/app/renderers/nested_person_attribute_renderer.rb b/hyrax/app/renderers/nested_person_attribute_renderer.rb
index c17603aa..5f4bcff9 100644
--- a/hyrax/app/renderers/nested_person_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_person_attribute_renderer.rb
@@ -29,13 +29,13 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       # complex_affiliation
       unless v.dig('complex_affiliation').blank?
         label = 'Affiliation'
         renderer_class = NestedAffiliationAttributeRenderer
-        each_html += get_nested_output(label, v['complex_affiliation'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_affiliation'], renderer_class, true)
       end
       # role
       unless v.dig('role').blank?
diff --git a/hyrax/app/renderers/nested_purchase_record_attribute_renderer.rb b/hyrax/app/renderers/nested_purchase_record_attribute_renderer.rb
index fde1b838..d6e6b2c6 100644
--- a/hyrax/app/renderers/nested_purchase_record_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_purchase_record_attribute_renderer.rb
@@ -8,7 +8,10 @@ def attribute_value_to_html(input_value)
       # title
       if v.dig('title').present? and v['title'][0].present?
         label ="Title"
-        val = link_to(ERB::Util.h(v['title'][0]), search_path(v['title'][0]))
+        # call search_catalog_path directly to get correct search link
+        val = link_to(ERB::Util.h(v['title'][0]),
+          Rails.application.routes.url_helpers.search_catalog_path(:"f[complex_purchase_record_title_sim][]" => v['title'][0], locale: I18n.locale)
+        )
         each_html += get_row(label, val)
       end
       # date
@@ -19,19 +22,19 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       # supplier
       unless v.dig('supplier').blank?
         label = 'Supplier'
         renderer_class = NestedOrganizationAttributeRenderer
-        each_html += get_nested_output(label, v['supplier'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['supplier'], renderer_class, true)
       end
       # manufacturer
       unless v.dig('manufacturer').blank?
         label = 'Manufacturer'
         renderer_class = NestedOrganizationAttributeRenderer
-        each_html += get_nested_output(label, v['manufacturer'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['manufacturer'], renderer_class, true)
       end
       # purchase_record_item
       unless v.dig('purchase_record_item').blank?
diff --git a/hyrax/app/renderers/nested_relation_attribute_renderer.rb b/hyrax/app/renderers/nested_relation_attribute_renderer.rb
index 315c1a38..3b10df0d 100644
--- a/hyrax/app/renderers/nested_relation_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_relation_attribute_renderer.rb
@@ -19,7 +19,7 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       # Relationship
       unless v.dig('relationship').blank?
diff --git a/hyrax/app/renderers/nested_source_attribute_renderer.rb b/hyrax/app/renderers/nested_source_attribute_renderer.rb
index 2f0eaa7c..985546d8 100644
--- a/hyrax/app/renderers/nested_source_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_source_attribute_renderer.rb
@@ -19,12 +19,12 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_person').blank?
         label = 'Contributor'
         renderer_class = NestedPersonAttributeRenderer
-        each_html += get_nested_output(label, v['complex_person'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_person'], renderer_class, true)
       end
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       unless v.dig('issue').blank?
         label = 'Issue'
diff --git a/hyrax/app/renderers/nested_specimen_type_attribute_renderer.rb b/hyrax/app/renderers/nested_specimen_type_attribute_renderer.rb
index 03eaa862..0571b56f 100644
--- a/hyrax/app/renderers/nested_specimen_type_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_specimen_type_attribute_renderer.rb
@@ -15,13 +15,13 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_chemical_composition').blank?
         label = 'Chemical composition'
         renderer_class = NestedDescIdAttributeRenderer
-        each_html += get_nested_output(label, v['complex_chemical_composition'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_chemical_composition'], renderer_class, true)
       end
       # complex_crystallographic_structure
       unless v.dig('complex_crystallographic_structure').blank?
         label = 'Crystallographic structure'
         renderer_class = NestedDescIdAttributeRenderer
-        each_html += get_nested_output(label, v['complex_crystallographic_structure'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_crystallographic_structure'], renderer_class, true)
       end
       # description
       unless v.dig('description').blank?
@@ -33,37 +33,37 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       # complex_material_type
       unless v.dig('complex_material_type').blank?
         label = 'Material type'
         renderer_class = NestedMaterialTypeAttributeRenderer
-        each_html += get_nested_output(label, v['complex_material_type'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_material_type'], renderer_class, true)
       end
       # complex_purchase_record
       unless v.dig('complex_purchase_record').blank?
         label = 'Purchase record'
         renderer_class = NestedPurchaseRecordAttributeRenderer
-        each_html += get_nested_output(label, v['complex_purchase_record'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_purchase_record'], renderer_class, true)
       end
       # complex_shape
       unless v.dig('complex_shape').blank?
         label = 'Shape'
         renderer_class = NestedDescIdAttributeRenderer
-        each_html += get_nested_output(label, v['complex_shape'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_shape'], renderer_class, true)
       end
       # complex_state_of_matter
       unless v.dig('complex_state_of_matter').blank?
         label = 'State of matter'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_state_of_matter'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_state_of_matter'], renderer_class, true)
       end
       # complex_structural_feature
       unless v.dig('complex_structural_feature').blank?
         label = 'Structural feature'
         renderer_class = NestedStructuralFeatureAttributeRenderer
-        each_html += get_nested_output(label, v['complex_structural_feature'], renderer_class, true)
+        each_html += get_nested_output(field, label, v['complex_structural_feature'], renderer_class, true)
       end
       html += get_inner_html(each_html)
     end
diff --git a/hyrax/app/renderers/nested_structural_feature_attribute_renderer.rb b/hyrax/app/renderers/nested_structural_feature_attribute_renderer.rb
index 367c021c..e55ee92c 100644
--- a/hyrax/app/renderers/nested_structural_feature_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_structural_feature_attribute_renderer.rb
@@ -27,7 +27,7 @@ def attribute_value_to_html(input_value)
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'
         renderer_class = NestedIdentifierAttributeRenderer
-        each_html += get_nested_output(label, v['complex_identifier'], renderer_class, false)
+        each_html += get_nested_output(field, label, v['complex_identifier'], renderer_class, false)
       end
       html += get_inner_html(each_html)
     end
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index a46d352d..2ce9daf2 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -6,6 +6,7 @@ en:
         facet:
           based_near_label_sim: Location
           creator_sim: Creator
+          characterization_methods_sim: Characterization methods
           complex_date_dtsim: Date
           complex_date_accepted_dtsim: Date accepted
           complex_date_available_dtsim: Date available
diff --git a/hyrax/spec/indexers/dataset_indexer_spec.rb b/hyrax/spec/indexers/dataset_indexer_spec.rb
index d6cf3e1b..a1e1b555 100644
--- a/hyrax/spec/indexers/dataset_indexer_spec.rb
+++ b/hyrax/spec/indexers/dataset_indexer_spec.rb
@@ -337,7 +337,14 @@
         model_number: '123xfty',
         complex_person_attributes: [{
           name: ['Name of operator'],
-          role: ['Operator']
+          role: ['Operator'],
+          complex_affiliation_attributes: [{
+            job_title: 'Technician',
+            complex_organization_attributes: [{
+              organization: 'Org 1',
+              sub_organization: 'Sub org 1'
+            }]
+          }]
         }],
         managing_organization_attributes: [{
           organization: 'FooFoo',
@@ -378,7 +385,14 @@
         model_number: 'ABC12E',
         complex_person_attributes: [{
           name: ['Name of operator 2'],
-          role: ['Operator']
+          role: ['Operator'],
+          complex_affiliation_attributes: [{
+            job_title: 'Technician',
+            complex_organization_attributes: [{
+              organization: 'Org 2',
+              sub_organization: 'Sub org 2'
+            }]
+          }]
         }],
         managing_organization_attributes: [{
           organization: 'BigBig',
@@ -398,6 +412,9 @@
       expect(@solr_document).to include('complex_instrument_ssm')
       expect(JSON.parse(@solr_document['complex_instrument_ssm'])).not_to be_empty
     end
+    it 'indexes title as facetable to complex_instrument_sim' do
+      expect(@solr_document['complex_instrument_sim']).to match_array(['Instrument title', 'Instrument title 2'])
+    end
     it 'indexes title as stored searchable' do
       expect(@solr_document['instrument_title_tesim']).to match_array(['Instrument title', 'Instrument title 2'])
     end
@@ -437,9 +454,15 @@
     it 'indexes person by role as stored searchable' do
       expect(@solr_document['complex_person_operator_tesim']).to match_array(['Name of operator', 'Name of operator 2'])
     end
-    it 'imdexes person by role as facetable' do
+    it 'indexes person by role as facetable' do
       expect(@solr_document['complex_person_operator_sim']).to match_array(['Name of operator', 'Name of operator 2'])
     end
+    it 'indexes person affiliation by role as stored searchable' do
+      expect(@solr_document['complex_person_operator_organization_tesim']).to match_array(["Org 1", "Org 2"])
+    end
+    it 'indexes person affiliation by role as facetable' do
+      expect(@solr_document['complex_person_operator_organization_sim']).to match_array(["Org 1", "Org 2"])
+    end
     it 'indexes managing organization as stored searchable' do
       expect(@solr_document['instrument_managing_organization_tesim']).to match_array(['FooFoo', 'BigBig'])
     end
@@ -797,6 +820,10 @@
       expect(@solr_document['complex_purchase_record_title_tesim']).to match_array(
         ['Purchase record title', 'Purchase record title 2', 'Purchase record title 3'])
     end
+    it 'indexes purchase record title as facetable' do
+      expect(@solr_document['complex_purchase_record_title_sim']).to match_array(
+        ['Purchase record title', 'Purchase record title 2', 'Purchase record title 3'])
+    end
     it 'indexes purchase record date as dateable' do
       expect(@solr_document['complex_date_purchased_dtsim']).to match_array(
         ["2018-02-14T00:00:00Z", "2019-02-14T00:00:00Z", "2019-03-14T00:00:00Z"])

From d942f0c27e60a6b550adb2db9ccc40759f96e843 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 18 Nov 2019 11:08:09 +0000
Subject: [PATCH 037/258] wip

wip - new view test for links
---
 hyrax/features/datasets/search_links.feature  | 27 +++++++++++++++++++
 .../step_definitions/dataset_steps.rb         | 10 +++++++
 2 files changed, 37 insertions(+)
 create mode 100644 hyrax/features/datasets/search_links.feature

diff --git a/hyrax/features/datasets/search_links.feature b/hyrax/features/datasets/search_links.feature
new file mode 100644
index 00000000..b163ecf1
--- /dev/null
+++ b/hyrax/features/datasets/search_links.feature
@@ -0,0 +1,27 @@
+Feature: Search links on a dataset
+  Background:
+    Given an initialised sysem with a default admin set, permission template and workflow
+    And there is a dataset with:
+      | TRAIT                                   |
+      | open                                    |
+      | with_complex_person                     |
+      | with_complex_author                     |
+      | with_complex_chemical_composition       |
+      | with_complex_crystallographic_structure |
+      | with_custom_property                    |
+      | with_complex_date                       |
+      | with_complex_identifier                 |
+      | with_complex_instrument                 |
+      | with_complex_specimen_type              |
+      | with_complex_relation                   |
+      | with_complex_rights                     |
+      | with_complex_version                    |
+
+
+  Scenario: search links find the dataset
+    Given I am on dataset page
+    Then I see the following links:
+      | LABEL            | HREF                                                             |
+      | Anamika          | /catalog?f%5Bcomplex_person_sim%5D%5B%5D=Anamika                 |
+      | University       | /catalog?f%5Bcomplex_person_organization_sim%5D%5B%5D=University |
+      | Instrument title | /catalog?f%5Bcomplex_instrument_sim%5D%5B%5D=Instrument+title    |
diff --git a/hyrax/features/step_definitions/dataset_steps.rb b/hyrax/features/step_definitions/dataset_steps.rb
index 7c4d41c8..8c93b276 100644
--- a/hyrax/features/step_definitions/dataset_steps.rb
+++ b/hyrax/features/step_definitions/dataset_steps.rb
@@ -6,6 +6,16 @@
   ActiveFedora::SolrService.commit
 end
 
+Given(/^there is a dataset with:$/) do |table|
+  @dataset = FactoryBot.create(:dataset, *table.rows.flatten.map(&:to_sym))
+  ActiveFedora::SolrService.add(@dataset.to_solr)
+  ActiveFedora::SolrService.commit
+end
+
+Given(/^I am on dataset page$/) do
+  visit hyrax_dataset_path(@dataset)
+end
+
 When(/^I navigate to the new dataset page$/) do
   visit '/dashboard'
   click_link "Works"

From 7efc7b817d6b6b8c387d3c1b829a0b5d3d7f25f9 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 19 Nov 2019 11:05:59 +0000
Subject: [PATCH 038/258] complete view test

---
 hyrax/features/datasets/search_links.feature  | 21 ++++++++++++-------
 .../step_definitions/dataset_steps.rb         |  8 ++++++-
 hyrax/spec/factories/dataset.rb               |  2 +-
 hyrax/spec/indexers/dataset_indexer_spec.rb   |  6 +++---
 .../inputs/nested_instrument_input_spec.rb    |  2 +-
 .../concerns/complex_instrument_spec.rb       |  4 ++--
 hyrax/spec/models/dataset_spec.rb             |  2 +-
 ...sted_instrument_attribute_renderer_spec.rb |  2 +-
 8 files changed, 30 insertions(+), 17 deletions(-)

diff --git a/hyrax/features/datasets/search_links.feature b/hyrax/features/datasets/search_links.feature
index b163ecf1..798e423d 100644
--- a/hyrax/features/datasets/search_links.feature
+++ b/hyrax/features/datasets/search_links.feature
@@ -18,10 +18,17 @@ Feature: Search links on a dataset
       | with_complex_version                    |
 
 
-  Scenario: search links find the dataset
-    Given I am on dataset page
-    Then I see the following links:
-      | LABEL            | HREF                                                             |
-      | Anamika          | /catalog?f%5Bcomplex_person_sim%5D%5B%5D=Anamika                 |
-      | University       | /catalog?f%5Bcomplex_person_organization_sim%5D%5B%5D=University |
-      | Instrument title | /catalog?f%5Bcomplex_instrument_sim%5D%5B%5D=Instrument+title    |
+  Scenario: Search links are generated correctly
+    Given I am on the dataset page
+    Then I should see the following links:
+      | LABEL                      | HREF                                                                                  |
+      | Anamika                    | /catalog?f%5Bcomplex_person_sim%5D%5B%5D=Anamika                                      |
+      | University                 | /catalog?f%5Bcomplex_person_organization_sim%5D%5B%5D=University                      |
+      | Instrument title           | /catalog?f%5Bcomplex_instrument_sim%5D%5B%5D=Instrument+title                         |
+      | Foo                        | /catalog?f%5Binstrument_manufacturer_sim%5D%5B%5D=Foo                                 |
+      | Name of operator           | /catalog?f%5Bcomplex_person_operator_sim%5D%5B%5D=Name+of+operator                    |
+      | University                 | /catalog?f%5Bcomplex_person_operator_sim%5D%5B%5D=University                          |
+      | Managing organization name | /catalog?f%5Binstrument_managing_organization_sim%5D%5B%5D=Managing+organization+name |
+      | Purchase record title      | /catalog?f%5Bcomplex_purchase_record_title_sim%5D%5B%5D=Purchase+record+title         |
+      | Fooss                      | /catalog?f%5Bcomplex_purchase_record_supplier_sim%5D%5B%5D=Fooss                      |
+      | Foo                        | /catalog?f%5Bcomplex_purchase_record_manufacturer_sim%5D%5B%5D=Foo                    |
diff --git a/hyrax/features/step_definitions/dataset_steps.rb b/hyrax/features/step_definitions/dataset_steps.rb
index 8c93b276..64947c08 100644
--- a/hyrax/features/step_definitions/dataset_steps.rb
+++ b/hyrax/features/step_definitions/dataset_steps.rb
@@ -12,7 +12,7 @@
   ActiveFedora::SolrService.commit
 end
 
-Given(/^I am on dataset page$/) do
+Given(/^I am on the dataset page$/) do
   visit hyrax_dataset_path(@dataset)
 end
 
@@ -92,3 +92,9 @@
     expect(page).to_not have_link(dataset.title.first, href: Regexp.new(hyrax_dataset_path(dataset)))
   end
 end
+
+Then(/^I should see the following links:$/) do |table|
+  table.symbolic_hashes.each do |row|
+    expect(page).to have_link(row[:label], href: Regexp.new(Regexp.quote(row[:href])))
+  end
+end
diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 0cfbf9d1..9f28edde 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -173,7 +173,7 @@
              }]
           }],
           managing_organization_attributes: [{
-            organization: 'FooFoo',
+            organization: 'Managing organization name',
             sub_organization: 'BarBar',
             purpose: 'Managing organization',
             complex_identifier_attributes: [{
diff --git a/hyrax/spec/indexers/dataset_indexer_spec.rb b/hyrax/spec/indexers/dataset_indexer_spec.rb
index a1e1b555..41ec450b 100644
--- a/hyrax/spec/indexers/dataset_indexer_spec.rb
+++ b/hyrax/spec/indexers/dataset_indexer_spec.rb
@@ -347,7 +347,7 @@
           }]
         }],
         managing_organization_attributes: [{
-          organization: 'FooFoo',
+          organization: 'Managing organization name',
           sub_organization: 'BarBar',
           purpose: 'Managing organization',
           complex_identifier_attributes: [{
@@ -464,10 +464,10 @@
       expect(@solr_document['complex_person_operator_organization_sim']).to match_array(["Org 1", "Org 2"])
     end
     it 'indexes managing organization as stored searchable' do
-      expect(@solr_document['instrument_managing_organization_tesim']).to match_array(['FooFoo', 'BigBig'])
+      expect(@solr_document['instrument_managing_organization_tesim']).to match_array(['Managing organization name', 'BigBig'])
     end
     it 'indexes managing organization as facetable' do
-      expect(@solr_document['instrument_managing_organization_sim']).to match_array(['FooFoo', 'BigBig'])
+      expect(@solr_document['instrument_managing_organization_sim']).to match_array(['Managing organization name', 'BigBig'])
     end
     it 'indexes managing sub organization as stored searchable' do
       expect(@solr_document['instrument_managing_sub_organization_tesim']).to match_array(['BarBar', 'BazBaz'])
diff --git a/hyrax/spec/inputs/nested_instrument_input_spec.rb b/hyrax/spec/inputs/nested_instrument_input_spec.rb
index d8e2f455..6bc07d8e 100644
--- a/hyrax/spec/inputs/nested_instrument_input_spec.rb
+++ b/hyrax/spec/inputs/nested_instrument_input_spec.rb
@@ -46,7 +46,7 @@
     is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_sub_organization', type: :text, with: 'Department')
     is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_purpose', type: :text, with: 'Research')
 
-    is_expected.to have_field('dataset[instrument_attributes][0]_managing_organization_attributes_0_organization', type: :text, with: 'FooFoo')
+    is_expected.to have_field('dataset[instrument_attributes][0]_managing_organization_attributes_0_organization', type: :text, with: 'Managing organization name')
     is_expected.to have_field('dataset[instrument_attributes][0]_managing_organization_attributes_0_sub_organization', type: :text, with: 'BarBar')
     is_expected.to have_field('dataset[instrument_attributes][0]_managing_organization_attributes_0_purpose', type: :text, with: 'Managing organization')
   end
diff --git a/hyrax/spec/models/concerns/complex_instrument_spec.rb b/hyrax/spec/models/concerns/complex_instrument_spec.rb
index 2fc5e1ba..0de03df0 100644
--- a/hyrax/spec/models/concerns/complex_instrument_spec.rb
+++ b/hyrax/spec/models/concerns/complex_instrument_spec.rb
@@ -90,7 +90,7 @@ class ExampleWork < ActiveFedora::Base
               role: ['Operator']
             }],
             managing_organization_attributes: [{
-              organization: 'FooFoo',
+              organization: 'Managing organization name',
               sub_organization: 'BarBar',
               purpose: 'Managing organization',
               complex_identifier_attributes: [{
@@ -126,7 +126,7 @@ class ExampleWork < ActiveFedora::Base
         expect(subject.complex_person.first.name).to eq ['Name of operator']
         expect(subject.complex_person.first.role).to eq ['Operator']
         expect(subject.managing_organization.first).to be_kind_of ActiveTriples::Resource
-        expect(subject.managing_organization.first.organization).to eq ['FooFoo']
+        expect(subject.managing_organization.first.organization).to eq ['Managing organization name']
         expect(subject.managing_organization.first.sub_organization).to eq ['BarBar']
         expect(subject.managing_organization.first.purpose).to eq ['Managing organization']
         expect(subject.managing_organization.first.complex_identifier.first.identifier).to eq ['123456789mo']
diff --git a/hyrax/spec/models/dataset_spec.rb b/hyrax/spec/models/dataset_spec.rb
index e1458703..12bec99f 100644
--- a/hyrax/spec/models/dataset_spec.rb
+++ b/hyrax/spec/models/dataset_spec.rb
@@ -484,7 +484,7 @@
       expect(@obj.complex_instrument.first.complex_person.first.name).to eq ['Name of operator']
       expect(@obj.complex_instrument.first.complex_person.first.role).to eq ['operator']
       expect(@obj.complex_instrument.first.managing_organization.first).to be_kind_of ActiveTriples::Resource
-      expect(@obj.complex_instrument.first.managing_organization.first.organization).to eq ['FooFoo']
+      expect(@obj.complex_instrument.first.managing_organization.first.organization).to eq ['Managing organization name']
       expect(@obj.complex_instrument.first.managing_organization.first.sub_organization).to eq ['BarBar']
       expect(@obj.complex_instrument.first.managing_organization.first.purpose).to eq ['Managing organization']
       expect(@obj.complex_instrument.first.managing_organization.first.complex_identifier.first.identifier).to eq ['123456789mo']
diff --git a/hyrax/spec/renderers/nested_instrument_attribute_renderer_spec.rb b/hyrax/spec/renderers/nested_instrument_attribute_renderer_spec.rb
index fc5791ba..6c2c5ea5 100644
--- a/hyrax/spec/renderers/nested_instrument_attribute_renderer_spec.rb
+++ b/hyrax/spec/renderers/nested_instrument_attribute_renderer_spec.rb
@@ -75,7 +75,7 @@
 
     is_expected.to have_css('div.row label', text: 'Managing organization')
     is_expected.to have_css('div.row label', text: 'Organization')
-    is_expected.to have_css('div.row a', text: 'FooFoo')
+    is_expected.to have_css('div.row a', text: 'Managing organization name')
 
     is_expected.to have_css('div.row label', text: 'Sub organization')
     is_expected.to have_css('div.row', text: 'BarBar')

From 278294bb661ea6c4bacebd18b1846d6c604e3104 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 19 Nov 2019 11:42:47 +0000
Subject: [PATCH 039/258] disable HSTS for localhost cas

---
 cas/etc/cas/config/cas.properties | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cas/etc/cas/config/cas.properties b/cas/etc/cas/config/cas.properties
index 282cdcbe..76c6058f 100644
--- a/cas/etc/cas/config/cas.properties
+++ b/cas/etc/cas/config/cas.properties
@@ -2,6 +2,7 @@
 cas.server.name: https://cas.example.org:8443
 cas.server.prefix: https://cas.example.org:8443/cas
 
+cas.httpWebRequest.header.hsts=false
 cas.adminPagesSecurity.ip=127\.0\.0\.1
 
 logging.config: file:/etc/cas/config/log4j2.xml

From 812ba91a95c18a0bdb95bc99bf8c8c04a5ae1aff Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 19 Nov 2019 16:51:24 +0000
Subject: [PATCH 040/258] single sign out with local cas

---
 cas/etc/cas/config/cas.properties                          | 2 ++
 .../cas/services/{NIMS-CAStest-1.json => castest-1.json}   | 3 ++-
 hyrax/app/views/_user_util_links.html.erb                  | 7 +++++--
 hyrax/config/initializers/errbit.rb                        | 7 +++++++
 4 files changed, 16 insertions(+), 3 deletions(-)
 rename cas/etc/cas/services/{NIMS-CAStest-1.json => castest-1.json} (75%)

diff --git a/cas/etc/cas/config/cas.properties b/cas/etc/cas/config/cas.properties
index 76c6058f..08220718 100644
--- a/cas/etc/cas/config/cas.properties
+++ b/cas/etc/cas/config/cas.properties
@@ -4,6 +4,8 @@ cas.server.prefix: https://cas.example.org:8443/cas
 
 cas.httpWebRequest.header.hsts=false
 cas.adminPagesSecurity.ip=127\.0\.0\.1
+cas.logout.followServiceRedirects=true
+cas.logout.redirectParameter=service
 
 logging.config: file:/etc/cas/config/log4j2.xml
 
diff --git a/cas/etc/cas/services/NIMS-CAStest-1.json b/cas/etc/cas/services/castest-1.json
similarity index 75%
rename from cas/etc/cas/services/NIMS-CAStest-1.json
rename to cas/etc/cas/services/castest-1.json
index eb0d9256..3a431aa9 100644
--- a/cas/etc/cas/services/NIMS-CAStest-1.json
+++ b/cas/etc/cas/services/castest-1.json
@@ -2,5 +2,6 @@
   "@class" : "org.apereo.cas.services.RegexRegisteredService",
   "serviceId" :  "^(https|http)://.*",
   "name" : "NIMS-CAStest",
-  "id" : 1
+  "id" : 1,
+  "logoutType" : "BACK_CHANNEL"
 }
diff --git a/hyrax/app/views/_user_util_links.html.erb b/hyrax/app/views/_user_util_links.html.erb
index 69193bf3..54674744 100644
--- a/hyrax/app/views/_user_util_links.html.erb
+++ b/hyrax/app/views/_user_util_links.html.erb
@@ -24,9 +24,12 @@
       <% end %>
       <ul id="user-util-links" class="dropdown-menu dropdown-menu-right" role="menu">
         <li><%= link_to t("hyrax.toolbar.dashboard.menu"), hyrax.dashboard_path %></li>
-
         <li class="divider"></li>
-        <li><%= link_to t("hyrax.toolbar.profile.logout"), main_app.destroy_user_session_path %></li>
+        <% if ENV['MDR_DEVISE_AUTH_MODULE'] == 'cas_authenticatable' %>
+          <li><%= link_to t("hyrax.toolbar.profile.logout"), "#{::Devise.cas_base_url}logout?#{{service: main_app.destroy_user_session_url}.to_query}" %></li>
+        <% else %>
+          <li><%= link_to t("hyrax.toolbar.profile.logout"), main_app.destroy_user_session_path %></li>
+        <% end %>
       </ul>
     </li><!-- /.btn-group -->
   <% else %>
diff --git a/hyrax/config/initializers/errbit.rb b/hyrax/config/initializers/errbit.rb
index 7f2dad46..96d2c51b 100644
--- a/hyrax/config/initializers/errbit.rb
+++ b/hyrax/config/initializers/errbit.rb
@@ -9,4 +9,11 @@
     config.environment = Rails.env
     config.ignore_environments = %w(development test)
   end
+else
+  # disable Airbrake if the env vars are not present
+  puts 'Disabling Airbrake because the required env vars are not set'
+  Airbrake.configure do |c|
+    c.environment = Rails.env
+    c.ignore_environments = %w(development test production)
+  end
 end

From 25c5d4957a69a64b084af9e3f0061c201a9b2936 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 20 Nov 2019 16:44:58 +0000
Subject: [PATCH 041/258] wip

---
 hyrax/Gemfile               |  2 +-
 hyrax/Gemfile.lock          |  1 +
 hyrax/app/models/ability.rb | 26 ++++++++++++++++++++++++++
 hyrax/app/models/user.rb    | 28 ++++++++++++++++++++++++++++
 4 files changed, 56 insertions(+), 1 deletion(-)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 5a5c8b40..0014981d 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -72,7 +72,7 @@ gem 'hydra-role-management'
 gem 'bootstrap-datepicker-rails'
 gem 'pg'
 gem 'devise_ldap_authenticatable'
-
+gem 'cancancan', '~> 1.17' # NB: locked to an older version because of hyrax > hydra-editor
 gem 'riiif', '~> 2.0'
 
 group :production do
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index e189343d..dbbb0ee1 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -888,6 +888,7 @@ DEPENDENCIES
   blacklight_oai_provider!
   bootstrap-datepicker-rails
   byebug
+  cancancan (~> 1.17)
   capybara
   coffee-rails (~> 4.2)
   coveralls
diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index b9bc6f37..2b12602d 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -4,6 +4,7 @@ class Ability
 
   # Registered user can only create datasets and publications
   self.ability_logic += [
+    :read_metadata,
     :everyone_can_create_dataset,
     :everyone_can_create_publication
   ]
@@ -36,4 +37,29 @@ def everyone_can_create_publication
     return unless registered_user?
     can :create, [::Publication]
   end
+
+  def read_metadata
+    can :read_abstract, [::Dataset, ::Image, ::Publication] if current_user.authenticated?
+    can :read_alternative_title, [::Dataset, ::Image, ::Publication]
+    # NB: no users can :read_application_number
+    can :read_creator, [::Dataset, ::Image, ::Publication]
+    can :read_date, [::Dataset, ::Image, ::Publication]
+    can :read_event, [::Publication]
+    can :read_identifier, [::Dataset, ::Image, ::Publication]
+    can :read_issue, [::Publication]
+    can :read_table_of_contents, [::Publication]
+    can :read_keyword, [::Dataset, ::Image, ::Publication]
+    can :read_language, [::Dataset, ::Image, ::Publication]
+    can :read_location, [::Publication]
+    can :read_number_of_pages, [::Publication]
+    can :read_organization, [::Dataset, ::Publication]
+    can :read_publisher, [::Dataset, ::Image, ::Publication]
+    can :read_related, [::Dataset, ::Publication]
+    can :read_resource_type, [::Image, ::Publication]
+    can :read_rights, [::Dataset, ::Image, ::Publication]
+    can :read_source, [::Publication]
+    can :read_subject, [::Dataset, ::Publication]
+    can :read_title, [::Dataset, ::Image, ::Publication]
+    can :read_version, [::Dataset, ::Image, ::Publication]
+  end
 end
diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 50b9dc25..9689fbc1 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -36,4 +36,32 @@ def ldap_before_save
     self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
     self.password = Devise.friendly_token[0, 20]
   end
+
+  def authenticated_nims_researcher?
+    # Coming in Phase 2 (Feb 2020)
+    # TODO: look at LDAP/CAS properties or user role?
+    registered_user?
+  end
+
+  def authenticated_nims_other?
+    # Coming in Phase 2 (Feb 2020)
+    # TODO: look at LDAP/CAS properties or user role?
+    false
+  end
+
+  def authenticated_nims?
+    authenticated_nims_researcher? || authenticated_nims_other?
+  end
+
+  def authenticated_external?
+    # Coming in Phase 3 (June 2020)
+    # TODO: look at LDAP/CAS properties or user role?
+    false
+  end
+
+  def authenticated?
+    authenticated_nims? || authenticated_external?
+  end
+
+  alias_method :unauthenticated?, :guest?
 end

From c1cde814634d74babbcfdaa9a195131615898ef2 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 22 Nov 2019 18:00:53 +0000
Subject: [PATCH 042/258] presenter.complex_identifier is an array

---
 .../hyrax/citations_behaviors/publication_behavior.rb      | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
index 4c0b6109..ddc97214 100644
--- a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
+++ b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
@@ -7,8 +7,11 @@ module PublicationBehavior
 
       # nims override to add doi
       def setup_doi(presenter)
-        return '' if presenter.complex_identifier == ["[]"]
-        JSON.parse(presenter.complex_identifier).
+        ci = presenter.complex_identifier
+        if presenter.complex_identifier.is_a?(Array)
+          ci = presenter.complex_identifier.first
+        end
+        JSON.parse(ci).
             select{|i| i["scheme"].any?{|s| s =~/doi/i} }.
             pluck('identifier').
             flatten.

From 7a16fa802ca8ad75c0d99740450037e398d1ed33 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 26 Nov 2019 10:44:45 +0000
Subject: [PATCH 043/258] wip - added employee_type_code

---
 hyrax/app/models/nims_roles.rb                | 36 ++++++++++++++++
 hyrax/app/models/user.rb                      | 42 ++++++-------------
 ...5140832_add_employee_type_code_to_users.rb |  6 +++
 hyrax/db/schema.rb                            |  5 ++-
 4 files changed, 58 insertions(+), 31 deletions(-)
 create mode 100644 hyrax/app/models/nims_roles.rb
 create mode 100644 hyrax/db/migrate/20191125140832_add_employee_type_code_to_users.rb

diff --git a/hyrax/app/models/nims_roles.rb b/hyrax/app/models/nims_roles.rb
new file mode 100644
index 00000000..7ef9c30b
--- /dev/null
+++ b/hyrax/app/models/nims_roles.rb
@@ -0,0 +1,36 @@
+module NIMSRoles
+  def authenticated_nims_researcher?
+    unless defined?(@authenticated_nims_researcher)
+      if !guest? && employee_type_code.present? && employee_type_code =~ /^(A|G|L|Q|R|S)/i
+        @authenticated_nims_researcher = true
+      else
+        @authenticated_nims_researcher = false
+      end
+    end
+    @authenticated_nims_researcher
+  end
+
+  def authenticated_nims_other?
+    unless defined?(@authenticated_nims_other)
+      if !guest? && employee_type_code.present? && employee_type_code =~ /^(T|Z)/i
+        @authenticated_nims_other = true
+      else
+        @authenticated_nims_other = false
+      end
+    end
+    @authenticated_nims_other
+  end
+
+  def authenticated_nims?
+    authenticated_nims_researcher? || authenticated_nims_other?
+  end
+
+  def authenticated_external?
+    # Coming in Phase 3 (June 2020)
+    false
+  end
+
+  def authenticated?
+    authenticated_nims? || authenticated_external?
+  end
+end
diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 9689fbc1..13fdeb0c 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -3,13 +3,12 @@ class User < ApplicationRecord
   include Hydra::User
   # Connects this user object to Role-management behaviors.
   include Hydra::RoleManagement::UserRoles
-
+  include NIMSRoles
 
   # Connects this user object to Hyrax behaviors.
   include Hyrax::User
   include Hyrax::UserUsageStats
 
-
   if Blacklight::Utils.needs_attr_accessible?
     attr_accessible :username, :email, :password, :password_confirmation
   end
@@ -32,36 +31,19 @@ def self.find_or_create_system_user(user_key)
     User.find_by('email' => user_key) || User.create!(username: username, email: user_key, password: Devise.friendly_token[0, 20])
   end
 
+  def after_ldap_authentication
+    # runs after the password is authenticated; synchronises the employeeType
+    Devise::LDAP::Adapter.get_ldap_param(self.username, "employeeType").tap do |employee_type|
+      if employee_type.present? && employee_type.first.present?
+        self.employee_type_code = employee_type.first.first
+      else
+        self.employee_type_code = nil
+      end
+    end
+  end
+
   def ldap_before_save
     self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
     self.password = Devise.friendly_token[0, 20]
   end
-
-  def authenticated_nims_researcher?
-    # Coming in Phase 2 (Feb 2020)
-    # TODO: look at LDAP/CAS properties or user role?
-    registered_user?
-  end
-
-  def authenticated_nims_other?
-    # Coming in Phase 2 (Feb 2020)
-    # TODO: look at LDAP/CAS properties or user role?
-    false
-  end
-
-  def authenticated_nims?
-    authenticated_nims_researcher? || authenticated_nims_other?
-  end
-
-  def authenticated_external?
-    # Coming in Phase 3 (June 2020)
-    # TODO: look at LDAP/CAS properties or user role?
-    false
-  end
-
-  def authenticated?
-    authenticated_nims? || authenticated_external?
-  end
-
-  alias_method :unauthenticated?, :guest?
 end
diff --git a/hyrax/db/migrate/20191125140832_add_employee_type_code_to_users.rb b/hyrax/db/migrate/20191125140832_add_employee_type_code_to_users.rb
new file mode 100644
index 00000000..97f82dcf
--- /dev/null
+++ b/hyrax/db/migrate/20191125140832_add_employee_type_code_to_users.rb
@@ -0,0 +1,6 @@
+class AddEmployeeTypeCodeToUsers < ActiveRecord::Migration[5.1]
+  def change
+    add_column :users, :employee_type_code, :string
+    add_index :users, :employee_type_code
+  end
+end
diff --git a/hyrax/db/schema.rb b/hyrax/db/schema.rb
index e959d543..6f7f370a 100644
--- a/hyrax/db/schema.rb
+++ b/hyrax/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20190930025332) do
+ActiveRecord::Schema.define(version: 20191125140832) do
 
   create_table "bookmarks", force: :cascade do |t|
     t.integer "user_id", null: false
@@ -279,6 +279,7 @@
     t.string "uri"
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
+    t.index ["local_authority_id", "label"], name: "index_qa_local_authority_entries_on_lower_label"
     t.index ["local_authority_id"], name: "index_qa_local_authority_entries_on_local_authority_id"
     t.index ["uri"], name: "index_qa_local_authority_entries_on_uri", unique: true
   end
@@ -548,7 +549,9 @@
     t.string "unlock_token"
     t.datetime "locked_at"
     t.string "remember_token"
+    t.string "employee_type_code"
     t.index ["email"], name: "index_users_on_email"
+    t.index ["employee_type_code"], name: "index_users_on_employee_type_code"
     t.index ["reset_password_token"], name: "index_users_on_reset_password_token", unique: true
     t.index ["username"], name: "index_users_on_username", unique: true
   end

From 80972da719dadcb4d61453c3a8441e829603c8b4 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 26 Nov 2019 12:12:41 +0000
Subject: [PATCH 044/258] Update user_spec.rb

new nims_roles specs
---
 hyrax/spec/models/user_spec.rb | 61 +++++++++++++++++++++++++++++++++-
 1 file changed, 60 insertions(+), 1 deletion(-)

diff --git a/hyrax/spec/models/user_spec.rb b/hyrax/spec/models/user_spec.rb
index 52aef32d..6e4d62d7 100644
--- a/hyrax/spec/models/user_spec.rb
+++ b/hyrax/spec/models/user_spec.rb
@@ -10,7 +10,7 @@
 
   describe '#ldap_before_save' do
     before do
-      allow(Devise::LDAP::Adapter).to receive(:get_ldap_param) { ['email@example.com'] }
+      allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'mail') { ['email@example.com'] }
       allow(Devise).to receive(:friendly_token) { 'password' }
       user.ldap_before_save
     end
@@ -50,4 +50,63 @@
       end
     end
   end
+
+  describe '#after_ldap_authentication' do
+    context 'researcher' do
+      before do
+        allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'employeeType') { ['G1234'] }
+        user.after_ldap_authentication
+      end
+
+      it 'has an employee_type_code' do
+        expect(user.employee_type_code).to eql('G')
+      end
+
+      it 'is a researcher' do
+        expect(user.authenticated_nims_researcher?).to be true
+      end
+
+      it 'is not a non-researcher' do
+        expect(user.authenticated_nims_other?).to be false
+      end
+    end
+
+    context 'non-researcher' do
+      before do
+        allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'employeeType') { ['T4567'] }
+        user.after_ldap_authentication
+      end
+
+      it 'has an employee_type_code' do
+        expect(user.employee_type_code).to eql('T')
+      end
+
+      it 'is not a researcher' do
+        expect(user.authenticated_nims_researcher?).to be false
+      end
+
+      it 'is a non-researcher' do
+        expect(user.authenticated_nims_other?).to be true
+      end
+    end
+
+    context 'unknown' do
+      before do
+        allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'employeeType') { ['????'] }
+        user.after_ldap_authentication
+      end
+
+      it 'has an employee_type_code' do
+        expect(user.employee_type_code).to eql('?')
+      end
+
+      it 'is not a researcher' do
+        expect(user.authenticated_nims_researcher?).to be false
+      end
+
+      it 'is not a non-researcher' do
+        expect(user.authenticated_nims_other?).to be false
+      end
+    end
+  end
 end

From be3a70527e243ab0f0c0d5b5c0a8870c315f9b06 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 26 Nov 2019 18:33:25 +0000
Subject: [PATCH 045/258] new view permissions applied to templates

---
 hyrax/app/models/ability.rb                   |   4 +-
 hyrax/app/views/hyrax/base/show.html.erb      |   4 +-
 .../hyrax/datasets/_attribute_rows.html.erb   | 183 ++++++++----------
 .../hyrax/images/_attribute_rows.html.erb     |  62 ++++--
 .../publications/_attribute_rows.html.erb     |  93 +++++++--
 5 files changed, 206 insertions(+), 140 deletions(-)

diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index 2b12602d..bc01122c 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -58,8 +58,8 @@ def read_metadata
     can :read_resource_type, [::Image, ::Publication]
     can :read_rights, [::Dataset, ::Image, ::Publication]
     can :read_source, [::Publication]
-    can :read_subject, [::Dataset, ::Publication]
-    can :read_title, [::Dataset, ::Image, ::Publication]
+    can :read_subject, [::Dataset, ::Publication, ::Image]  # NB: added Image to list
+    can :read_title, [::Dataset, ::Image, ::Publication]    # NB: not used in Publication
     can :read_version, [::Dataset, ::Image, ::Publication]
   end
 end
diff --git a/hyrax/app/views/hyrax/base/show.html.erb b/hyrax/app/views/hyrax/base/show.html.erb
index 99e5440b..cc51fae5 100644
--- a/hyrax/app/views/hyrax/base/show.html.erb
+++ b/hyrax/app/views/hyrax/base/show.html.erb
@@ -26,7 +26,9 @@
             <%#= render 'social_media' %> <!-- No social media buttons -->
           </div>
           <div class="col-sm-9">
-            <%= render 'work_description', presenter: @presenter %>
+            <% if can? :read_abstract, @presenter.model_name.name.constantize %>
+              <%= render 'work_description', presenter: @presenter %>
+            <% end %>
             <%= render 'metadata', presenter: @presenter %>
           </div>
           <div class="col-sm-12">
diff --git a/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb b/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
index 73e2d815..e90ff3a0 100644
--- a/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
@@ -12,74 +12,73 @@
     <!-- Accordion body -->
     <div id="description" class="panel-collapse collapse in">
       <div class="panel-body">
-        <%= presenter.attribute_to_html(:alternative_title,
-          label: t('ngdr.fields.alternative_title'),
-          html_dl: true) %>
-        <%#=
-        <!-- This is displayed above the attributes row -->
-        # presenter.attribute_to_html(:description, html_dl: true)
-        %>
-        <%= presenter.attribute_to_html(:complex_person,
-          render_as: :nested_person,
-          label: t('ngdr.fields.complex_person'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:complex_organization,
-          render_as: :nested_organization,
-          label: t('ngdr.fields.complex_organization'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:keyword,
-          render_as: :faceted,
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:subject,
-          render_as: :faceted,
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:language,
-          render_as: :faceted,
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:publisher,
-          render_as: :faceted,
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:complex_date,
-          render_as: :nested_date,
-          label: t('ngdr.fields.complex_date'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:complex_identifier,
-          render_as: :nested_identifier,
-          label: t('ngdr.fields.complex_identifier'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:license,
-          render_as: :license,
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:complex_rights,
-          render_as: :nested_rights,
-          label: t('ngdr.fields.complex_rights'),
-          html_dl: true) %>
-        <%#= # presenter.attribute_to_html(:rights_statement,
-          render_as: :rights_statement,
-          html_dl: true) %>
-        <%#= # presenter.attribute_to_html(:rights_notes,
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:complex_version,
-          render_as: :nested_version,
-          label: t('ngdr.fields.complex_version'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:resource_type,
-          render_as: :faceted,
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:complex_relation,
-          render_as: :nested_relation,
-          label: t('ngdr.fields.complex_relation'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:source,
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:date_created,
-          render_as: :linked, search_field: 'date_created_tesim',
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:date_modified,
-          label: t('hyrax.base.show.last_modified'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:access_right,
-          html_dl: true) %>
+        <% if can? :read_alternative_title, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:alternative_title, label: t('ngdr.fields.alternative_title'), html_dl: true) %>
+        <% end %>
+
+        <!-- Description is displayed above the attributes row -->
+
+        <% if can? :read_creator, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:complex_person, render_as: :nested_person, label: t('ngdr.fields.complex_person'), html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_organization, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:complex_organization, render_as: :nested_organization, label: t('ngdr.fields.complex_organization'), html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_keyword, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:keyword, render_as: :faceted, html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_subject, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:subject, render_as: :faceted, html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_language, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:language, render_as: :faceted, html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_publisher, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:publisher, render_as: :faceted, html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_date, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:complex_date, render_as: :nested_date, label: t('ngdr.fields.complex_date'), html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_identifier, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:complex_identifier, render_as: :nested_identifier, label: t('ngdr.fields.complex_identifier'), html_dl: true) %>
+        <% end %>
+
+        <!-- no defined permission for license -->
+        <%= presenter.attribute_to_html(:license, render_as: :license, html_dl: true) %>
+
+        <% if can? :read_rights, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:complex_rights, render_as: :nested_rights, label: t('ngdr.fields.complex_rights'), html_dl: true) %>
+          <%#= # presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
+          <%#= # presenter.attribute_to_html(:rights_notes, html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_version, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:complex_version, render_as: :nested_version, label: t('ngdr.fields.complex_version'), html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_resource_type, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:resource_type, render_as: :faceted, html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_related, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:complex_relation, render_as: :nested_relation, label: t('ngdr.fields.complex_relation'), html_dl: true) %>
+        <% end %>
+
+        <% if can? :read_source, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:source, html_dl: true) %>
+        <% end %>
+
+        <!-- no defined permissions for date_created, date_modified, access_right -->
+        <%= presenter.attribute_to_html(:date_created, render_as: :linked, search_field: 'date_created_tesim', html_dl: true) %>
+        <%= presenter.attribute_to_html(:date_modified, label: t('hyrax.base.show.last_modified'), html_dl: true) %>
+        <%= presenter.attribute_to_html(:access_right, html_dl: true) %>
       </div> <!-- panel body -->
     </div> <!-- Accordion body -->
   </div> <!-- Description accordion -->
@@ -95,36 +94,14 @@
     <!-- Accordion body -->
     <div id="experimentalMethod" class="panel-collapse collapse in">
       <div class="panel-body">
-        <%= presenter.attribute_to_html(:characterization_methods,
-          render_as: :faceted,
-          label: t('ngdr.fields.characterization_methods'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:computational_methods,
-          render_as: :faceted,
-          label: t('ngdr.fields.computational_methods'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:data_origin,
-          render_as: :faceted,
-          label: t('ngdr.fields.data_origin'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:origin_system_provenance,
-          label: t('ngdr.fields.origin_system_provenance'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:properties_addressed,
-          render_as: :faceted,
-          label: t('ngdr.fields.properties_addressed'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:specimen_set,
-          label: t('ngdr.fields.specimen_set'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:synthesis_and_processing,
-          render_as: :faceted,
-          label: t('ngdr.fields.synthesis_and_processing'),
-          html_dl: true) %>
-        <%= presenter.attribute_to_html(:custom_property,
-          render_as: :nested_custom_property,
-          label: t('ngdr.fields.custom_property'),
-          html_dl: true) %>
+        <%= presenter.attribute_to_html(:characterization_methods, render_as: :faceted, label: t('ngdr.fields.characterization_methods'), html_dl: true) %>
+        <%= presenter.attribute_to_html(:computational_methods, render_as: :faceted, label: t('ngdr.fields.computational_methods'), html_dl: true) %>
+        <%= presenter.attribute_to_html(:data_origin, render_as: :faceted, label: t('ngdr.fields.data_origin'), html_dl: true) %>
+        <%= presenter.attribute_to_html(:origin_system_provenance, label: t('ngdr.fields.origin_system_provenance'), html_dl: true) %>
+        <%= presenter.attribute_to_html(:properties_addressed, render_as: :faceted, label: t('ngdr.fields.properties_addressed'), html_dl: true) %>
+        <%= presenter.attribute_to_html(:specimen_set, label: t('ngdr.fields.specimen_set'), html_dl: true) %>
+        <%= presenter.attribute_to_html(:synthesis_and_processing, render_as: :faceted, label: t('ngdr.fields.synthesis_and_processing'), html_dl: true) %>
+        <%= presenter.attribute_to_html(:custom_property, render_as: :nested_custom_property, label: t('ngdr.fields.custom_property'), html_dl: true) %>
       </div> <!-- panel body -->
     </div> <!-- Accordion body -->
   </div> <!-- Method accordion -->
@@ -140,10 +117,7 @@
     <!-- Accordion body -->
     <div id="instrument" class="panel-collapse collapse in">
       <div class="panel-body">
-        <%= presenter.attribute_to_html(:complex_instrument,
-          render_as: :nested_instrument,
-          label: t('ngdr.fields.instrument'),
-          html_dl: true) %>
+        <%= presenter.attribute_to_html(:complex_instrument, render_as: :nested_instrument, label: t('ngdr.fields.instrument'), html_dl: true) %>
       </div> <!-- panel body -->
     </div> <!-- Accordion body -->
   </div> <!-- Instruments accordion -->
@@ -159,10 +133,7 @@
     <!-- Accordion body -->
     <div id="specimenType" class="panel-collapse collapse in">
       <div class="panel-body">
-        <%= presenter.attribute_to_html(:complex_specimen_type,
-          render_as: :nested_specimen_type,
-          label: t('ngdr.fields.complex_specimen_type'),
-          html_dl: true) %>
+        <%= presenter.attribute_to_html(:complex_specimen_type, render_as: :nested_specimen_type, label: t('ngdr.fields.complex_specimen_type'), html_dl: true) %>
       </div> <!-- panel body -->
     </div> <!-- Accordion body -->
   </div> <!-- Specimen details accordion -->
diff --git a/hyrax/app/views/hyrax/images/_attribute_rows.html.erb b/hyrax/app/views/hyrax/images/_attribute_rows.html.erb
index 6bbdb00c..e84e2e30 100644
--- a/hyrax/app/views/hyrax/images/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/images/_attribute_rows.html.erb
@@ -1,17 +1,55 @@
 <%= presenter.attribute_to_html(:date_modified, label: t('hyrax.base.show.last_modified'), html_dl: true) %>
-<%= presenter.attribute_to_html(:alternative_title, label: t('ngdr.fields.alternative_title'), html_dl: true) %>
-<%= presenter.attribute_to_html(:subject, render_as: :faceted, html_dl: true) %>
-<%= presenter.attribute_to_html(:publisher, render_as: :faceted, html_dl: true) %>
-<%= presenter.attribute_to_html(:language, render_as: :faceted, html_dl: true) %>
-<%= presenter.attribute_to_html(:keyword, render_as: :faceted, html_dl: true) %>
+
+<% if can? :read_alternative_title, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:alternative_title, label: t('ngdr.fields.alternative_title'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_subject, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:subject, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_publisher, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:publisher, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_language, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:language, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_keyword, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:keyword, render_as: :faceted, html_dl: true) %>
+<% end %>
+
 <%= presenter.attribute_to_html(:date_created, render_as: :linked, search_field: 'date_created_tesim', html_dl: true) %>
-<%= presenter.attribute_to_html(:resource_type, render_as: :faceted, html_dl: true) %>
-<%= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_date, render_as: :nested_date, label: t('ngdr.fields.complex_date'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_identifier, render_as: :nested_identifier, label: t('ngdr.fields.complex_identifier'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_person, render_as: :nested_person, label: t('ngdr.fields.complex_person'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_rights, render_as: :nested_rights, label: t('ngdr.fields.complex_rights'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_version, render_as: :nested_version, label: t('ngdr.fields.complex_version'), html_dl: true) %>
+
+<% if can? :read_resource_type, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:resource_type, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_rights, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
+<% end %>
+
+<% if can? :read_date, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_date, render_as: :nested_date, label: t('ngdr.fields.complex_date'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_identifier, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_identifier, render_as: :nested_identifier, label: t('ngdr.fields.complex_identifier'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_creator, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_person, render_as: :nested_person, label: t('ngdr.fields.complex_person'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_rights, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_rights, render_as: :nested_rights, label: t('ngdr.fields.complex_rights'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_version, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_version, render_as: :nested_version, label: t('ngdr.fields.complex_version'), html_dl: true) %>
+<% end %>
+
 <%= presenter.attribute_to_html(:status, render_as: :faceted, label: "Status", html_dl: true) %>
 <%= presenter.attribute_to_html(:instrument, render_as: :faceted, html_dl: true) %>
 <%= presenter.attribute_to_html(:specimen_set, render_as: :faceted, label: t('ngdr.fields.specimen_set'), html_dl: true) %>
diff --git a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
index aeae5a39..607d3768 100644
--- a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
@@ -1,21 +1,76 @@
 <%= presenter.attribute_to_html(:date_modified, label: t('hyrax.base.show.last_modified'), html_dl: true) %>
-<%= presenter.attribute_to_html(:alternative_title, label: t('ngdr.fields.alternative_title'), html_dl: true) %>
-<%= presenter.attribute_to_html(:subject, render_as: :faceted, html_dl: true) %>
-<%= presenter.attribute_to_html(:publisher, render_as: :faceted, html_dl: true) %>
-<%= presenter.attribute_to_html(:language, render_as: :faceted, html_dl: true) %>
-<%= presenter.attribute_to_html(:keyword, render_as: :faceted, html_dl: true) %>
+
+<% if can? :read_alternative_title, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:alternative_title, label: t('ngdr.fields.alternative_title'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_subject, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:subject, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_publisher, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:publisher, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_language, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:language, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_keyword, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:keyword, render_as: :faceted, html_dl: true) %>
+<% end %>
+
 <%= presenter.attribute_to_html(:date_created, render_as: :linked, search_field: 'date_created_tesim', html_dl: true) %>
-<%= presenter.attribute_to_html(:resource_type, render_as: :faceted, html_dl: true) %>
-<%= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_date, render_as: :nested_date, label: t('ngdr.fields.complex_date'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_identifier, render_as: :nested_identifier, label: t('ngdr.fields.complex_identifier'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_person, render_as: :nested_person, label: t('ngdr.fields.complex_person'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_rights, render_as: :nested_rights, label: t('ngdr.fields.complex_rights'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_version, render_as: :nested_version, label: t('ngdr.fields.complex_version'), html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_event, render_as: :nested_event, label: "Event", html_dl: true) %>
-<%= presenter.attribute_to_html(:issue, label: "Issue", html_dl: true) %>
-<%= presenter.attribute_to_html(:place, render_as: :faceted, label: "Location", html_dl: true) %>
-<%= presenter.attribute_to_html(:table_of_contents, label: "Table of contents", html_dl: true) %>
-<%= presenter.attribute_to_html(:total_number_of_pages, label: "Number of pages", html_dl: true) %>
-<%= presenter.attribute_to_html(:source, label: "Source", html_dl: true) %>
-<%= presenter.attribute_to_html(:complex_source, render_as: :nested_source, label: t('ngdr.fields.complex_source'), html_dl: true) %>
+
+<% if can? :read_resource_type, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:resource_type, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_rights, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
+<% end %>
+
+<% if can? :read_date, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_date, render_as: :nested_date, label: t('ngdr.fields.complex_date'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_identifier, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_identifier, render_as: :nested_identifier, label: t('ngdr.fields.complex_identifier'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_creator, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_person, render_as: :nested_person, label: t('ngdr.fields.complex_person'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_rights, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_rights, render_as: :nested_rights, label: t('ngdr.fields.complex_rights'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_version, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_version, render_as: :nested_version, label: t('ngdr.fields.complex_version'), html_dl: true) %>
+<% end %>
+
+<% if can? :read_event, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_event, render_as: :nested_event, label: "Event", html_dl: true) %>
+<% end %>
+
+<% if can? :read_issue, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:issue, label: "Issue", html_dl: true) %>
+<% end %>
+
+<% if can? :read_location, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:place, render_as: :faceted, label: "Location", html_dl: true) %>
+<% end %>
+
+<% if can? :read_table_of_contents, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:table_of_contents, label: "Table of contents", html_dl: true) %>
+<% end %>
+
+<% if can? :read_number_of_pages, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:total_number_of_pages, label: "Number of pages", html_dl: true) %>
+<% end %>
+
+<% if can? :read_source, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:source, label: "Source", html_dl: true) %>
+  <%= presenter.attribute_to_html(:complex_source, render_as: :nested_source, label: t('ngdr.fields.complex_source'), html_dl: true) %>
+<% end %>

From 8c4bb22e2f44802815d59d9f0cd749bf495032af Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 27 Nov 2019 11:18:49 +0900
Subject: [PATCH 046/258] fix indexing invalid date such as "2019-01"

---
 hyrax/app/indexers/complex_field/date_indexer.rb | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/indexers/complex_field/date_indexer.rb b/hyrax/app/indexers/complex_field/date_indexer.rb
index 8593b0a9..ce562267 100644
--- a/hyrax/app/indexers/complex_field/date_indexer.rb
+++ b/hyrax/app/indexers/complex_field/date_indexer.rb
@@ -13,7 +13,11 @@ def index_date(solr_doc)
       # date as complex_date searchable
       dates = object.complex_date.map { |d| d.date.reject(&:blank?) }.flatten
       # cope with just a year being supplied
-      dates_utc = dates.map { |d| d.length <= 4 ? DateTime.strptime(d, '%Y').utc.iso8601 : DateTime.parse(d).utc.iso8601 } unless dates.blank?
+      begin
+        dates_utc = dates.map{|d| d.tr('０-９ａ-ｚＡ-Ｚ','0-9a-zA-Z')}.map { |d| d.length <= 4 ? DateTime.strptime(d, '%Y').utc.iso8601 : DateTime.parse(d).utc.iso8601 } unless dates.blank?
+      rescue ArgumentError
+        dates_utc = dates.map{|d| d.tr('０-９ａ-ｚＡ-Ｚ','0-9a-zA-Z')}.map { |d| DateTime.parse("#{d}-01").utc.iso8601 } unless dates.blank?
+      end
       solr_doc[Solrizer.solr_name('complex_date', :stored_searchable, type: :date)] = dates_utc unless dates.blank?
       solr_doc[Solrizer.solr_name('complex_date', :dateable)] = dates_utc unless dates.blank?
       object.complex_date.each do |d|
@@ -34,7 +38,11 @@ def index_date(solr_doc)
         vals = d.date.reject(&:blank?)
         fld_name = Solrizer.solr_name("complex_date_#{label}", :dateable)
         solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
-        solr_doc[fld_name] << vals.map { |dt| dt.length <= 4 ? DateTime.strptime(dt, '%Y').utc.iso8601 : DateTime.parse(dt).utc.iso8601 }
+        begin
+          solr_doc[fld_name] << vals.map{|d| d.tr('０-９ａ-ｚＡ-Ｚ','0-9a-zA-Z')}.map { |dt| dt.length <= 4 ? DateTime.strptime(dt, '%Y').utc.iso8601 : DateTime.parse(dt).utc.iso8601 }
+        rescue ArgumentError
+          solr_doc[fld_name] << vals.map{|d| d.tr('０-９ａ-ｚＡ-Ｚ','0-9a-zA-Z')}.map { |dt| DateTime.parse("#{dt}-01").utc.iso8601 }
+        end
         solr_doc[fld_name].flatten!
         # date as complex_date_type displayable
         fld_name = Solrizer.solr_name("complex_date_#{label}", :displayable)

From 90fb2052db2a17ff4641e7767480a3a4ab601a1f Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 28 Nov 2019 18:13:55 +0000
Subject: [PATCH 047/258] wip - service to update user authorisation details

---
 hyrax/app/models/user.rb                      | 22 +++++-----
 .../services/user_authorisation_service.rb    | 42 +++++++++++++++++++
 hyrax/config/initializers/devise.rb           |  8 ++--
 3 files changed, 56 insertions(+), 16 deletions(-)
 create mode 100644 hyrax/app/services/user_authorisation_service.rb

diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 13fdeb0c..2ad181cd 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -31,19 +31,17 @@ def self.find_or_create_system_user(user_key)
     User.find_by('email' => user_key) || User.create!(username: username, email: user_key, password: Devise.friendly_token[0, 20])
   end
 
-  def after_ldap_authentication
-    # runs after the password is authenticated; synchronises the employeeType
-    Devise::LDAP::Adapter.get_ldap_param(self.username, "employeeType").tap do |employee_type|
-      if employee_type.present? && employee_type.first.present?
-        self.employee_type_code = employee_type.first.first
-      else
-        self.employee_type_code = nil
-      end
-    end
-  end
+  # def after_database_authentication
+  #   puts "AFTER DATABASE AUTHENTICATION"
+  # end
+  #
+  # def after_ldap_authentication
+  #   puts "AFTER LDAP AUTHENTICATION"
+  # end
 
   def ldap_before_save
-    self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
-    self.password = Devise.friendly_token[0, 20]
+    puts "LDAP BEFORE SAVE"
+    # self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
+    # self.password = Devise.friendly_token[0, 20]
   end
 end
diff --git a/hyrax/app/services/user_authorisation_service.rb b/hyrax/app/services/user_authorisation_service.rb
new file mode 100644
index 00000000..6ab67759
--- /dev/null
+++ b/hyrax/app/services/user_authorisation_service.rb
@@ -0,0 +1,42 @@
+require 'net/ldap'
+class UserAuthorisationService
+  # This service is called immediately after authentication (see config/initializers/devise.rb). It updates the user's
+  # authorisation attributes from an LDAP source (USER_AUTHORISATION_LDAP_HOST). This is necessary as the CAS server
+  # does not provide employeeType/email etc.
+  # NB: In the future, this service may query a TSV file on a network drive rather than an LDAP server.
+
+  def initialize(user)
+    @user = user
+  end
+
+  def enabled?
+    ENV['USER_AUTHORISATION_LDAP_HOST'].present? &&
+        ENV['USER_AUTHORISATION_LDAP_BASE'].present? &&
+        ENV['USER_AUTHORISATION_LDAP_ATTRIBUTE'].present?
+  end
+
+  def update_attributes
+    success = false
+    if enabled? && records.length == 1
+      records.first.tap do |record|
+        @user.update(email: record[:mail]&.first,
+                     display_name: record[:cn]&.first,
+                     employee_type_code: record[:employeeType]&.first&.first)
+        success = true
+      end
+    else
+      puts "ERROR: UserAuthorisationService failed to retrieve user attributes, check USER_AUTHORISATION_LDAP_HOST, USER_AUTHORISATION_LDAP_BASE, USER_AUTHORISATION_LDAP_ATTRIBUTE env vars"
+    end
+    success
+  end
+
+  private
+
+  def server
+    @server ||= Net::LDAP.new(host: ENV['USER_AUTHORISATION_LDAP_HOST'], port: ENV.fetch('USER_AUTHORISATION_LDAP_PORT', 389))
+  end
+
+  def records
+    @records ||= server.search(base: ENV['USER_AUTHORISATION_LDAP_BASE'], filter: Net::LDAP::Filter.eq(ENV['USER_AUTHORISATION_LDAP_ATTRIBUTE'], @user.username))
+  end
+end
diff --git a/hyrax/config/initializers/devise.rb b/hyrax/config/initializers/devise.rb
index 5356780b..6bcea4c2 100644
--- a/hyrax/config/initializers/devise.rb
+++ b/hyrax/config/initializers/devise.rb
@@ -275,10 +275,10 @@
   # If you want to use other strategies, that are not supported by Devise, or
   # change the failure app, you can configure them inside the config.warden block.
   #
-  # config.warden do |manager|
-  #   manager.intercept_401 = false
-  #   manager.default_strategies(scope: :user).unshift :some_external_strategy
-  # end
+  Warden::Manager.after_authentication do |user,auth,opts|
+    # call the service to update the user's attributes (used for authorisation) after authentication
+    UserAuthorisationService.new(user).update_attributes
+  end
 
   # ==> Mountable engine configurations
   # When using Devise inside an engine, let's call it `MyEngine`, and this engine

From 32a166f80f7540955b8a38bea87b11679fc32d1f Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 29 Nov 2019 11:43:11 +0000
Subject: [PATCH 048/258] changes to airbrake config, default in .env.template
 to db auth

---
 .env.template                       |  4 ++--
 hyrax/config/initializers/errbit.rb | 24 +++++++++++++-----------
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/.env.template b/.env.template
index 0853ccc4..c79c0361 100644
--- a/.env.template
+++ b/.env.template
@@ -85,8 +85,8 @@ BOX_CLIENT_SECRET=
 
 # Choose one of the following authentication methods.
 # (database_authenticatable is pre-configured and useful for a development environment)
-MDR_DEVISE_AUTH_MODULE=ldap_authenticatable
-# MDR_DEVISE_AUTH_MODULE=database_authenticatable
+# MDR_DEVISE_AUTH_MODULE=ldap_authenticatable
+MDR_DEVISE_AUTH_MODULE=database_authenticatable
 
 LDAP_HOST=***REMOVED***
 LDAP_PORT=443
diff --git a/hyrax/config/initializers/errbit.rb b/hyrax/config/initializers/errbit.rb
index 7f2dad46..f262b8f5 100644
--- a/hyrax/config/initializers/errbit.rb
+++ b/hyrax/config/initializers/errbit.rb
@@ -1,12 +1,14 @@
-if ENV.fetch('AIRBRAKE_HOST', nil).present? and
-  ENV.fetch('AIRBRAKE_PROJECT_ID', nil).present? and
-  ENV.fetch('AIRBRAKE_PROJECT_KEY', nil).present?
-  Airbrake.configure do |config|
-    config.host = ENV['AIRBRAKE_HOST']
-    config.project_id = ENV['AIRBRAKE_PROJECT_ID']
-    config.project_key = ENV['AIRBRAKE_PROJECT_KEY']
-    # setting for the rails app
-    config.environment = Rails.env
-    config.ignore_environments = %w(development test)
-  end
+# frozen_string_literal: true
+
+Airbrake.configure do |config|
+  # setting for the rails app
+  config.environment = Rails.env
+  config.ignore_environments = %w[development test]
+  # ignore production if the environment variables aren't set
+  config.ignore_environments << 'production' if ENV.fetch('AIRBRAKE_HOST', nil).blank? &&
+                                                ENV.fetch('AIRBRAKE_PROJECT_ID', nil).blank? &&
+                                                ENV.fetch('AIRBRAKE_PROJECT_KEY', nil).blank?
+  config.host = ENV['AIRBRAKE_HOST']
+  config.project_id = ENV['AIRBRAKE_PROJECT_ID']
+  config.project_key = ENV['AIRBRAKE_PROJECT_KEY']
 end

From e6998499fa15855e359dfd6a27398f441d9e356b Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 29 Nov 2019 11:57:37 +0000
Subject: [PATCH 049/258] foo

---
 hyrax/Gemfile | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 5a5c8b40..fbfa5a49 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -75,9 +75,7 @@ gem 'devise_ldap_authenticatable'
 
 gem 'riiif', '~> 2.0'
 
-group :production do
-  gem 'airbrake', '~> 5.0'
-end
+gem 'airbrake', '~> 5.0'
 
 gem 'willow_sword', git: 'https://github.com/CottageLabs/willow_sword.git', :branch => 'feature/prep_for_new_release'
 gem 'blacklight_oai_provider', git: 'https://github.com/CottageLabs/blacklight_oai_provider.git', branch: 'master'

From 8dc5458e3ff9bd6165c7110760c6a6a564d39d72 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 29 Nov 2019 12:50:58 +0000
Subject: [PATCH 050/258] Create a Hyrax::UploadedFile for new versions.

---
 .../controllers/hyrax/file_sets_controller.rb | 191 ++++++++++++++++++
 .../hyrax/file_sets_controller_spec.rb        |  42 ++++
 hyrax/spec/factories/file_sets.rb             |  25 +++
 3 files changed, 258 insertions(+)
 create mode 100644 hyrax/app/controllers/hyrax/file_sets_controller.rb
 create mode 100644 hyrax/spec/controllers/hyrax/file_sets_controller_spec.rb
 create mode 100644 hyrax/spec/factories/file_sets.rb

diff --git a/hyrax/app/controllers/hyrax/file_sets_controller.rb b/hyrax/app/controllers/hyrax/file_sets_controller.rb
new file mode 100644
index 00000000..4c69d286
--- /dev/null
+++ b/hyrax/app/controllers/hyrax/file_sets_controller.rb
@@ -0,0 +1,191 @@
+module Hyrax
+  class FileSetsController < ApplicationController
+    include Blacklight::Base
+    include Blacklight::AccessControls::Catalog
+    include Hyrax::Breadcrumbs
+
+    before_action :authenticate_user!, except: [:show, :citation, :stats]
+    load_and_authorize_resource class: ::FileSet, except: :show
+    before_action :build_breadcrumbs, only: [:show, :edit, :stats]
+
+    # provides the help_text view method
+    helper PermissionsHelper
+
+    helper_method :curation_concern
+    copy_blacklight_config_from(::CatalogController)
+
+    class_attribute :show_presenter, :form_class
+    self.show_presenter = Hyrax::FileSetPresenter
+    self.form_class = Hyrax::Forms::FileSetEditForm
+
+    # A little bit of explanation, CanCan(Can) sets the @file_set via the .load_and_authorize_resource
+    # method. However the interface for various CurationConcern modules leverages the #curation_concern method
+    # Thus we have file_set and curation_concern that are aliases for each other.
+    attr_accessor :file_set
+    alias curation_concern file_set
+    private :file_set=
+    alias curation_concern= file_set=
+    private :curation_concern=
+    helper_method :file_set
+
+    layout :decide_layout
+
+    # GET /concern/file_sets/:id
+    def edit
+      initialize_edit_form
+    end
+
+    # GET /concern/parent/:parent_id/file_sets/:id
+    def show
+      respond_to do |wants|
+        wants.html { presenter }
+        wants.json { presenter }
+        additional_response_formats(wants)
+      end
+    end
+
+    # DELETE /concern/file_sets/:id
+    def destroy
+      parent = curation_concern.parent
+      actor.destroy
+      redirect_to [main_app, parent], notice: 'The file has been deleted.'
+    end
+
+    # PATCH /concern/file_sets/:id
+    def update
+      if attempt_update
+        after_update_response
+      else
+        after_update_failure_response
+      end
+    rescue RSolr::Error::Http => error
+      flash[:error] = error.message
+      logger.error "FileSetsController::update rescued #{error.class}\n\t#{error.message}\n #{error.backtrace.join("\n")}\n\n"
+      render action: 'edit'
+    end
+
+    # GET /files/:id/stats
+    def stats
+      @stats = FileUsage.new(params[:id])
+    end
+
+    # GET /files/:id/citation
+    def citation; end
+
+    private
+
+      # this is provided so that implementing application can override this behavior and map params to different attributes
+      def update_metadata
+        file_attributes = form_class.model_attributes(attributes)
+        actor.update_metadata(file_attributes)
+      end
+
+      # Override Hyrax 2.6.0 - pass Hyrax::UploadedFile to actor.update_content
+      def attempt_update
+        if wants_to_revert?
+          actor.revert_content(params[:revision])
+        elsif params.key?(:file_set)
+          if params[:file_set].key?(:files)
+            actor.update_content(uploaded_file_from_path)
+          else
+            update_metadata
+          end
+        end
+      end
+  
+      # Override Hyrax 2.6.0 - create an Hyrax::UploadedFile from the file upload
+      def uploaded_file_from_path
+        uploaded_file = CarrierWave::SanitizedFile.new(params[:file_set][:files].first)
+        Hyrax::UploadedFile.create(user_id: current_user.id, file: uploaded_file)
+      end
+
+      def after_update_response
+        respond_to do |wants|
+          wants.html do
+            redirect_to [main_app, curation_concern], notice: "The file #{view_context.link_to(curation_concern, [main_app, curation_concern])} has been updated."
+          end
+          wants.json do
+            @presenter = show_presenter.new(curation_concern, current_ability)
+            render :show, status: :ok, location: polymorphic_path([main_app, curation_concern])
+          end
+        end
+      end
+
+      def after_update_failure_response
+        respond_to do |wants|
+          wants.html do
+            initialize_edit_form
+            flash[:error] = "There was a problem processing your request."
+            render 'edit', status: :unprocessable_entity
+          end
+          wants.json { render_json_response(response_type: :unprocessable_entity, options: { errors: curation_concern.errors }) }
+        end
+      end
+
+      def add_breadcrumb_for_controller
+        add_breadcrumb I18n.t('hyrax.dashboard.my.works'), hyrax.my_works_path
+      end
+
+      def add_breadcrumb_for_action
+        case action_name
+        when 'edit'.freeze
+          add_breadcrumb I18n.t("hyrax.file_set.browse_view"), main_app.hyrax_file_set_path(params["id"])
+        when 'show'.freeze
+          add_breadcrumb presenter.parent.to_s, main_app.polymorphic_path(presenter.parent)
+          add_breadcrumb presenter.to_s, main_app.polymorphic_path(presenter)
+        end
+      end
+
+      # Override of Blacklight::RequestBuilders
+      def search_builder_class
+        Hyrax::FileSetSearchBuilder
+      end
+
+      def initialize_edit_form
+        @parent = @file_set.in_objects.first
+        original = @file_set.original_file
+        @version_list = Hyrax::VersionListPresenter.new(original ? original.versions.all : [])
+        @groups = current_user.groups
+      end
+
+      def actor
+        @actor ||= Hyrax::Actors::FileSetActor.new(@file_set, current_user)
+      end
+
+      def attributes
+        params.fetch(:file_set, {}).except(:files).permit!.dup # use a copy of the hash so that original params stays untouched when interpret_visibility modifies things
+      end
+
+      def presenter
+        @presenter ||= begin
+          _, document_list = search_results(params)
+          curation_concern = document_list.first
+          raise CanCan::AccessDenied unless curation_concern
+          show_presenter.new(curation_concern, current_ability, request)
+        end
+      end
+
+      def wants_to_revert?
+        params.key?(:revision) && params[:revision] != curation_concern.latest_content_version.label
+      end
+
+      # Override this method to add additional response formats to your local app
+      def additional_response_formats(_); end
+
+      # This allows us to use the unauthorized and form_permission template in hyrax/base,
+      # while prefering our local paths. Thus we are unable to just override `self.local_prefixes`
+      def _prefixes
+        @_prefixes ||= super + ['hyrax/base']
+      end
+
+      def decide_layout
+        layout = case action_name
+                 when 'show'
+                   '1_column'
+                 else
+                   'dashboard'
+                 end
+        File.join(theme, layout)
+      end
+  end
+end
diff --git a/hyrax/spec/controllers/hyrax/file_sets_controller_spec.rb b/hyrax/spec/controllers/hyrax/file_sets_controller_spec.rb
new file mode 100644
index 00000000..292bf4b7
--- /dev/null
+++ b/hyrax/spec/controllers/hyrax/file_sets_controller_spec.rb
@@ -0,0 +1,42 @@
+require 'rails_helper'
+require 'devise'
+
+RSpec.describe Hyrax::FileSetsController do
+  include Devise::Test::ControllerHelpers
+
+  routes { Rails.application.routes }
+  let(:user) { create(:user) }
+  let(:actor) { controller.send(:actor) }
+
+  context 'when signed in' do
+    before do
+      sign_in user
+    end
+
+    describe '#update' do
+      let(:file_set) do
+        create(:file_set, user: user)
+      end
+
+      context 'when updating the attached file version' do
+        before do
+          allow(Hyrax::Actors::FileActor).to receive(:new).and_return(actor)
+        end
+
+        it 'returns a Hyrax::UploadedFile' do
+          expect(actor).to receive(:update_content).with(
+            instance_of(Hyrax::UploadedFile)
+          ).and_return(true)
+          file = fixture_file_upload('/xml/other.txt', 'text/plain')
+          post :update, params: {
+            id: file_set,
+            file_set: {
+              files: [file],
+              permissions_attributes: [{ type: 'person', name: user.username, access: 'edit' }]
+            }
+          }
+        end
+      end
+    end
+  end
+end
diff --git a/hyrax/spec/factories/file_sets.rb b/hyrax/spec/factories/file_sets.rb
new file mode 100644
index 00000000..a801b6c2
--- /dev/null
+++ b/hyrax/spec/factories/file_sets.rb
@@ -0,0 +1,25 @@
+FactoryBot.define do
+  factory :file_set do
+    transient do
+      user { create(:user) }
+      content { nil }
+    end
+    after(:build) do |fs, evaluator|
+      fs.apply_depositor_metadata evaluator.user.user_key
+    end
+
+    after(:create) do |file, evaluator|
+      Hydra::Works::UploadFileToFileSet.call(file, evaluator.content) if evaluator.content
+    end
+
+    factory :file_with_work do
+      after(:build) do |file, _evaluator|
+        file.title = ['testfile']
+      end
+      after(:create) do |file, evaluator|
+        Hydra::Works::UploadFileToFileSet.call(file, evaluator.content) if evaluator.content
+        create(:work, user: evaluator.user).members << file
+      end
+    end
+  end
+end

From 6d9f463cb3ba5defc60c0d88ff0bf34feaa65649 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 29 Nov 2019 16:35:08 +0000
Subject: [PATCH 051/258] revert to skipping airbrake in anything other than
 production

---
 hyrax/Gemfile                       |  4 +++-
 hyrax/config/initializers/errbit.rb | 25 +++++++++++++------------
 2 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index fbfa5a49..5a5c8b40 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -75,7 +75,9 @@ gem 'devise_ldap_authenticatable'
 
 gem 'riiif', '~> 2.0'
 
-gem 'airbrake', '~> 5.0'
+group :production do
+  gem 'airbrake', '~> 5.0'
+end
 
 gem 'willow_sword', git: 'https://github.com/CottageLabs/willow_sword.git', :branch => 'feature/prep_for_new_release'
 gem 'blacklight_oai_provider', git: 'https://github.com/CottageLabs/blacklight_oai_provider.git', branch: 'master'
diff --git a/hyrax/config/initializers/errbit.rb b/hyrax/config/initializers/errbit.rb
index f262b8f5..512f3859 100644
--- a/hyrax/config/initializers/errbit.rb
+++ b/hyrax/config/initializers/errbit.rb
@@ -1,14 +1,15 @@
 # frozen_string_literal: true
-
-Airbrake.configure do |config|
-  # setting for the rails app
-  config.environment = Rails.env
-  config.ignore_environments = %w[development test]
-  # ignore production if the environment variables aren't set
-  config.ignore_environments << 'production' if ENV.fetch('AIRBRAKE_HOST', nil).blank? &&
-                                                ENV.fetch('AIRBRAKE_PROJECT_ID', nil).blank? &&
-                                                ENV.fetch('AIRBRAKE_PROJECT_KEY', nil).blank?
-  config.host = ENV['AIRBRAKE_HOST']
-  config.project_id = ENV['AIRBRAKE_PROJECT_ID']
-  config.project_key = ENV['AIRBRAKE_PROJECT_KEY']
+if Rails.env == 'production'
+  Airbrake.configure do |config|
+    # setting for the rails app
+    config.environment = Rails.env
+    config.ignore_environments = %w[development test]
+    # ignore production if the environment variables aren't set
+    config.ignore_environments << 'production' if ENV.fetch('AIRBRAKE_HOST', nil).blank? &&
+                                                  ENV.fetch('AIRBRAKE_PROJECT_ID', nil).blank? &&
+                                                  ENV.fetch('AIRBRAKE_PROJECT_KEY', nil).blank?
+    config.host = ENV['AIRBRAKE_HOST']
+    config.project_id = ENV['AIRBRAKE_PROJECT_ID']
+    config.project_key = ENV['AIRBRAKE_PROJECT_KEY']
+  end
 end

From abb871d362beb6a39d928aabb35aa6f94706d69c Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 29 Nov 2019 17:28:12 +0000
Subject: [PATCH 052/258] index identifier by scheme

---
 hyrax/app/indexers/complex_field/identifier_indexer.rb | 4 ++--
 hyrax/spec/indexers/dataset_indexer_spec.rb            | 9 ++++-----
 hyrax/spec/indexers/image_indexer_spec.rb              | 9 ++++-----
 hyrax/spec/indexers/publication_indexer_spec.rb        | 9 ++++-----
 4 files changed, 14 insertions(+), 17 deletions(-)

diff --git a/hyrax/app/indexers/complex_field/identifier_indexer.rb b/hyrax/app/indexers/complex_field/identifier_indexer.rb
index ea71ee87..16878528 100644
--- a/hyrax/app/indexers/complex_field/identifier_indexer.rb
+++ b/hyrax/app/indexers/complex_field/identifier_indexer.rb
@@ -10,8 +10,8 @@ def index_identifier(solr_doc)
       solr_doc[Solrizer.solr_name('complex_identifier', :symbol)] = object.complex_identifier.map { |i| i.identifier.reject(&:blank?).first }
       solr_doc[Solrizer.solr_name('complex_identifier', :displayable)] = object.complex_identifier.to_json
       object.complex_identifier.each do |i|
-        unless i.label.blank? || i.identifier.blank?
-          fld_name = Solrizer.solr_name("complex_identifier_#{i.label.reject(&:blank?).first.downcase.tr(' ', '_')}", :symbol)
+        unless i.scheme.blank? || i.identifier.blank?
+          fld_name = Solrizer.solr_name("complex_identifier_#{i.scheme.reject(&:blank?).first.downcase.tr(' ', '_')}", :symbol)
           solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
           solr_doc[fld_name] << i.identifier.reject(&:blank?)
           solr_doc[fld_name].flatten!
diff --git a/hyrax/spec/indexers/dataset_indexer_spec.rb b/hyrax/spec/indexers/dataset_indexer_spec.rb
index d6cf3e1b..d0f55b12 100644
--- a/hyrax/spec/indexers/dataset_indexer_spec.rb
+++ b/hyrax/spec/indexers/dataset_indexer_spec.rb
@@ -49,14 +49,13 @@
       ids = [
         {
           identifier: '0000-0000-0000-0000',
-          scheme: 'uri_of_ORCID_scheme',
-          label: 'ORCID'
+          scheme: 'ORCID'
         }, {
           identifier: '1234',
-          label: 'Local ID'
+          scheme: 'identifier local'
         }, {
           identifier: '12345345234',
-          label: 'Orcid'
+          scheme: 'Orcid'
         }
       ]
       obj = build(:dataset, complex_identifier_attributes: ids)
@@ -71,7 +70,7 @@
     end
     it 'indexes each type as symbol' do
       expect(@solr_document['complex_identifier_orcid_ssim']).to match_array(['0000-0000-0000-0000', '12345345234'])
-      expect(@solr_document['complex_identifier_local_id_ssim']).to match_array(['1234'])
+      expect(@solr_document['complex_identifier_identifier_local_ssim']).to match_array(['1234'])
     end
   end
 
diff --git a/hyrax/spec/indexers/image_indexer_spec.rb b/hyrax/spec/indexers/image_indexer_spec.rb
index 57db711d..8ab75a73 100644
--- a/hyrax/spec/indexers/image_indexer_spec.rb
+++ b/hyrax/spec/indexers/image_indexer_spec.rb
@@ -49,14 +49,13 @@
       ids = [
         {
           identifier: '0000-0000-0000-0000',
-          scheme: 'uri_of_ORCID_scheme',
-          label: 'ORCID'
+          scheme: 'ORCID'
         }, {
           identifier: '1234',
-          label: 'Local ID'
+          scheme: 'identifier local'
         }, {
           identifier: '12345345234',
-          label: 'Orcid'
+          scheme: 'Orcid'
         }
       ]
       obj = build(:image, complex_identifier_attributes: ids)
@@ -71,7 +70,7 @@
     end
     it 'indexes each type as symbol' do
       expect(@solr_document['complex_identifier_orcid_ssim']).to match_array(['0000-0000-0000-0000', '12345345234'])
-      expect(@solr_document['complex_identifier_local_id_ssim']).to match_array(['1234'])
+      expect(@solr_document['complex_identifier_identifier_local_ssim']).to match_array(['1234'])
     end
   end
 
diff --git a/hyrax/spec/indexers/publication_indexer_spec.rb b/hyrax/spec/indexers/publication_indexer_spec.rb
index 586cb8de..5e523fb2 100644
--- a/hyrax/spec/indexers/publication_indexer_spec.rb
+++ b/hyrax/spec/indexers/publication_indexer_spec.rb
@@ -49,14 +49,13 @@
       ids = [
         {
           identifier: '0000-0000-0000-0000',
-          scheme: 'uri_of_ORCID_scheme',
-          label: 'ORCID'
+          scheme: 'ORCID'
         }, {
           identifier: '1234',
-          label: 'Local ID'
+          scheme: 'identifier local'
         }, {
           identifier: '12345345234',
-          label: 'Orcid'
+          scheme: 'Orcid'
         }
       ]
       obj = build(:publication, complex_identifier_attributes: ids)
@@ -71,7 +70,7 @@
     end
     it 'indexes each type as symbol' do
       expect(@solr_document['complex_identifier_orcid_ssim']).to match_array(['0000-0000-0000-0000', '12345345234'])
-      expect(@solr_document['complex_identifier_local_id_ssim']).to match_array(['1234'])
+      expect(@solr_document['complex_identifier_identifier_local_ssim']).to match_array(['1234'])
     end
   end
 

From ff6363e991abcf4a0bc55c54c950f0e981a4e945 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 2 Dec 2019 14:56:32 +0000
Subject: [PATCH 053/258] fix oai-pmh rspec

---
 hyrax/spec/features/oai_pmh_spec.rb | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
index 5b751d92..2ae999b3 100644
--- a/hyrax/spec/features/oai_pmh_spec.rb
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -1,14 +1,11 @@
 # From Samvera Hyku
+require 'rails_helper'
 
 RSpec.describe "OAI PMH Support", type: :feature do
-  let(:user) { create(:user) }
-  let(:work) { create(:work, depositor: user.email) }
+  let(:work) { create(:dataset, :open) }
   let(:identifier) { work.id }
 
-  before do
-    login_as(user, scope: :user)
-    work
-  end
+  before { work }
 
   context 'oai interface with works present' do
     it 'lists metadata prefixess' do
@@ -18,19 +15,19 @@
 
     it 'retrieves a list of records' do
       visit oai_provider_catalog_path(verb: 'ListRecords', metadataPrefix: 'oai_dc')
-      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).to have_content("#{ENV['OAI_RECORD_PREFIX']}:#{identifier}")
       expect(page).to have_content(work.title.first)
     end
 
     it 'retrieves a single record' do
       visit oai_provider_catalog_path(verb: 'GetRecord', metadataPrefix: 'oai_dc', identifier: identifier)
-      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).to have_content("#{ENV['OAI_RECORD_PREFIX']}:#{identifier}")
       expect(page).to have_content(work.title.first)
     end
 
     it 'retrieves a list of identifiers' do
       visit oai_provider_catalog_path(verb: 'ListIdentifiers', metadataPrefix: 'oai_dc')
-      expect(page).to have_content("oai:ngdrdemo:#{identifier}")
+      expect(page).to have_content("#{ENV['OAI_RECORD_PREFIX']}:#{identifier}")
       expect(page).not_to have_content(work.title.first)
     end
   end

From c4e2c8f011c8c378da0c9aa3a28b9f507c08e41b Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 2 Dec 2019 16:40:25 +0000
Subject: [PATCH 054/258] Create user_authorisation_service_spec.rb

---
 .../user_authorisation_service_spec.rb        | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 hyrax/spec/services/user_authorisation_service_spec.rb

diff --git a/hyrax/spec/services/user_authorisation_service_spec.rb b/hyrax/spec/services/user_authorisation_service_spec.rb
new file mode 100644
index 00000000..993b655e
--- /dev/null
+++ b/hyrax/spec/services/user_authorisation_service_spec.rb
@@ -0,0 +1,37 @@
+require 'rails_helper'
+
+RSpec.describe UserAuthorisationService do
+  let(:user) { create(:user) }
+  let(:service) { described_class.new(user) }
+
+  context 'without env vars' do
+    before do
+      allow(ENV).to receive(:[]).with('USER_AUTHORISATION_LDAP_HOST').and_return(nil)
+      allow(ENV).to receive(:[]).with('USER_AUTHORISATION_LDAP_BASE').and_return(nil)
+      allow(ENV).to receive(:[]).with('USER_AUTHORISATION_LDAP_ATTRIBUTE').and_return(nil)
+    end
+    it { expect(service.enabled?).to be false }
+    it { expect(service.update_attributes).to be false }
+  end
+
+  context 'with env vars' do
+    before do
+      allow(ENV).to receive(:[]).with('USER_AUTHORISATION_LDAP_HOST').and_return('localhost')
+      allow(ENV).to receive(:[]).with('USER_AUTHORISATION_LDAP_BASE').and_return('ou=people,dc=test,dc=com')
+      allow(ENV).to receive(:[]).with('USER_AUTHORISATION_LDAP_ATTRIBUTE').and_return('uid')
+    end
+    it { expect(service.enabled?).to be true }
+
+    describe '#update_attributes' do
+      let(:entry) { Net::LDAP::Entry.from_single_ldif_string( "dn: user1234\ncn: Alice Bloggs\nmail: newmail@example.com\nemployeeType: Z1234") }
+      before do
+        allow_any_instance_of(Net::LDAP).to receive(:search).with(base: 'ou=people,dc=test,dc=com', filter: Net::LDAP::Filter.eq('uid', user.username)).and_return([entry])
+        service.update_attributes
+      end
+      it { expect(user.email).to eql('newmail@example.com') }
+      it { expect(user.display_name).to eql('Alice Bloggs') }
+      it { expect(user.employee_type_code).to eql('Z') }
+      it { expect(service.update_attributes).to be true }
+    end
+  end
+end

From 4497c42df710cfc4e3ac2dfa17c70355eba0ee77 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 2 Dec 2019 17:09:41 +0000
Subject: [PATCH 055/258] more tests

---
 hyrax/app/models/user.rb       |  16 ++----
 hyrax/spec/models/user_spec.rb | 100 ++++++++++++++++++++++-----------
 2 files changed, 72 insertions(+), 44 deletions(-)

diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 2ad181cd..291b7e54 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -9,6 +9,8 @@ class User < ApplicationRecord
   include Hyrax::User
   include Hyrax::UserUsageStats
 
+  has_many :uploaded_files, class_name: 'Hyrax::UploadedFile', dependent: :nullify
+
   if Blacklight::Utils.needs_attr_accessible?
     attr_accessible :username, :email, :password, :password_confirmation
   end
@@ -31,17 +33,9 @@ def self.find_or_create_system_user(user_key)
     User.find_by('email' => user_key) || User.create!(username: username, email: user_key, password: Devise.friendly_token[0, 20])
   end
 
-  # def after_database_authentication
-  #   puts "AFTER DATABASE AUTHENTICATION"
-  # end
-  #
-  # def after_ldap_authentication
-  #   puts "AFTER LDAP AUTHENTICATION"
-  # end
-
   def ldap_before_save
-    puts "LDAP BEFORE SAVE"
-    # self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
-    # self.password = Devise.friendly_token[0, 20]
+    # Runs before saving a new user record in the database via LDAP Authentication
+    self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
+    self.password = Devise.friendly_token[0, 20]
   end
 end
diff --git a/hyrax/spec/models/user_spec.rb b/hyrax/spec/models/user_spec.rb
index 6e4d62d7..f67d5780 100644
--- a/hyrax/spec/models/user_spec.rb
+++ b/hyrax/spec/models/user_spec.rb
@@ -51,62 +51,96 @@
     end
   end
 
-  describe '#after_ldap_authentication' do
-    context 'researcher' do
-      before do
-        allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'employeeType') { ['G1234'] }
-        user.after_ldap_authentication
-      end
+  describe 'NIMS Roles' do
+    let(:user) { described_class.new(employee_type_code: employee_type_code) }
+
+    describe '#authenticated_nims_researcher?' do
+      subject { user.authenticated_nims_researcher? }
 
-      it 'has an employee_type_code' do
-        expect(user.employee_type_code).to eql('G')
+      context 'employee_type A' do
+        let(:employee_type_code) { 'A' }
+        it { is_expected.to be true }
       end
 
-      it 'is a researcher' do
-        expect(user.authenticated_nims_researcher?).to be true
+      context 'employee_type G' do
+        let(:employee_type_code) { 'G' }
+        it { is_expected.to be true }
       end
 
-      it 'is not a non-researcher' do
-        expect(user.authenticated_nims_other?).to be false
+      context 'employee_type L' do
+        let(:employee_type_code) { 'L' }
+        it { is_expected.to be true }
       end
-    end
 
-    context 'non-researcher' do
-      before do
-        allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'employeeType') { ['T4567'] }
-        user.after_ldap_authentication
+      context 'employee_type Q' do
+        let(:employee_type_code) { 'Q' }
+        it { is_expected.to be true }
       end
 
-      it 'has an employee_type_code' do
-        expect(user.employee_type_code).to eql('T')
+      context 'employee_type R' do
+        let(:employee_type_code) { 'R' }
+        it { is_expected.to be true }
       end
 
-      it 'is not a researcher' do
-        expect(user.authenticated_nims_researcher?).to be false
+      context 'employee_type S' do
+        let(:employee_type_code) { 'S' }
+        it { is_expected.to be true }
       end
 
-      it 'is a non-researcher' do
-        expect(user.authenticated_nims_other?).to be true
+      context 'employee_type X' do
+        let(:employee_type_code) { 'X' }
+        it { is_expected.to be false }
       end
     end
 
-    context 'unknown' do
-      before do
-        allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'employeeType') { ['????'] }
-        user.after_ldap_authentication
+    describe '#authenticated_nims_other?' do
+      subject { user.authenticated_nims_other? }
+
+      context 'employee_type T' do
+        let(:employee_type_code) { 'T' }
+        it { is_expected.to be true }
+      end
+
+      context 'employee_type Z' do
+        let(:employee_type_code) { 'Z' }
+        it { is_expected.to be true }
+      end
+
+      context 'employee_type X' do
+        let(:employee_type_code) { 'X' }
+        it { is_expected.to be false }
       end
+    end
 
-      it 'has an employee_type_code' do
-        expect(user.employee_type_code).to eql('?')
+    describe '#authenticated_nims?' do
+      subject { user.authenticated_nims? }
+
+      context 'employee_type A' do
+        let(:employee_type_code) { 'A' }
+        it { is_expected.to be true }
       end
 
-      it 'is not a researcher' do
-        expect(user.authenticated_nims_researcher?).to be false
+      context 'employee_type T' do
+        let(:employee_type_code) { 'T' }
+        it { is_expected.to be true }
       end
 
-      it 'is not a non-researcher' do
-        expect(user.authenticated_nims_other?).to be false
+      context 'employee_type X' do
+        let(:employee_type_code) { 'X' }
+        it { is_expected.to be false }
       end
     end
+
+    describe '#authenticated_external?' do
+      let(:employee_type_code) { nil }
+      subject { user.authenticated_external? }
+      it { is_expected.to be false }
+    end
+
+    describe '#authenticated?' do
+      let(:employee_type_code) { 'A' }
+      subject { user.authenticated? }
+      it { is_expected.to be true }
+    end
   end
 end

From b1d25d88fe99a79cc17b8c25cb358676b4d30ea0 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 2 Dec 2019 17:12:43 +0000
Subject: [PATCH 056/258] warning not error

---
 hyrax/app/services/user_authorisation_service.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/services/user_authorisation_service.rb b/hyrax/app/services/user_authorisation_service.rb
index 6ab67759..f32a8ef8 100644
--- a/hyrax/app/services/user_authorisation_service.rb
+++ b/hyrax/app/services/user_authorisation_service.rb
@@ -25,7 +25,7 @@ def update_attributes
         success = true
       end
     else
-      puts "ERROR: UserAuthorisationService failed to retrieve user attributes, check USER_AUTHORISATION_LDAP_HOST, USER_AUTHORISATION_LDAP_BASE, USER_AUTHORISATION_LDAP_ATTRIBUTE env vars"
+      puts "WARNING: UserAuthorisationService failed to retrieve user attributes, check USER_AUTHORISATION_LDAP_HOST, USER_AUTHORISATION_LDAP_BASE, USER_AUTHORISATION_LDAP_ATTRIBUTE env vars"
     end
     success
   end

From 26cc2ee5a416e583d725510e82d5e534f75afdd2 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 3 Dec 2019 16:23:42 +0000
Subject: [PATCH 057/258] new view spec for dataset metadata attributes

---
 hyrax/app/models/ability.rb                   |  4 +-
 hyrax/spec/factories/dataset.rb               | 30 +++++++++-
 hyrax/spec/factories/users.rb                 | 12 ++++
 hyrax/spec/rails_helper.rb                    |  2 +
 .../datasets/_attribute_rows.html_spec.rb     | 59 +++++++++++++++++++
 5 files changed, 104 insertions(+), 3 deletions(-)
 create mode 100644 hyrax/spec/views/datasets/_attribute_rows.html_spec.rb

diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index bc01122c..6a8aab7b 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -55,9 +55,9 @@ def read_metadata
     can :read_organization, [::Dataset, ::Publication]
     can :read_publisher, [::Dataset, ::Image, ::Publication]
     can :read_related, [::Dataset, ::Publication]
-    can :read_resource_type, [::Image, ::Publication]
+    can :read_resource_type, [::Dataset, ::Image, ::Publication] #NB: added Dataset to list
     can :read_rights, [::Dataset, ::Image, ::Publication]
-    can :read_source, [::Publication]
+    can :read_source, [::Dataset, ::Publication] #NB: added Dataset to the list
     can :read_subject, [::Dataset, ::Publication, ::Image]  # NB: added Image to list
     can :read_title, [::Dataset, ::Image, ::Publication]    # NB: not used in Publication
     can :read_version, [::Dataset, ::Image, ::Publication]
diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 0cfbf9d1..5df8bb89 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -26,7 +26,35 @@
 
     trait :restricted do
       visibility { 'restricted' }
-      title { ["Resstricted Dataset"] }
+      title { ["Restricted Dataset"] }
+    end
+
+    trait :with_alternative_title do
+      alternative_title { 'Dataset Alternative Title' }
+    end
+
+    trait :with_keyword do
+      keyword { ['Keyword123'] }
+    end
+
+    trait :with_subject do
+      subject { ['Subject123'] }
+    end
+
+    trait :with_language do
+      language { ['Faroese'] }
+    end
+
+    trait :with_publisher do
+      publisher { ['Publisher123'] }
+    end
+
+    trait :with_resource_type do
+      resource_type { ['ResourceType123'] }
+    end
+
+    trait :with_source do
+      source { ['Source123'] }
     end
 
     trait :with_complex_person do
diff --git a/hyrax/spec/factories/users.rb b/hyrax/spec/factories/users.rb
index 592e4cea..13e2fab8 100644
--- a/hyrax/spec/factories/users.rb
+++ b/hyrax/spec/factories/users.rb
@@ -3,6 +3,7 @@
   factory :user do
     sequence(:email) { |n| "user#{n}@example.com" }
     sequence(:username) { |n| "user#{n}" }
+    sequence(:display_name) { |n| "User #{n}"}
     password { 'password' }
 
     transient do
@@ -37,5 +38,16 @@
       roles { build_list :role, 1, :admin }
     end
 
+    trait :nims_researcher do
+      sequence(:display_name) { |n| "Researcher #{n}"}
+      guest { false }
+      employee_type_code { 'A' }
+    end
+
+    trait :nims_other do
+      sequence(:display_name) { |n| "Non-Researcher #{n}"}
+      guest { false }
+      employee_type_code { 'T' }
+    end
   end
 end
diff --git a/hyrax/spec/rails_helper.rb b/hyrax/spec/rails_helper.rb
index 954ebeb3..fac43a21 100644
--- a/hyrax/spec/rails_helper.rb
+++ b/hyrax/spec/rails_helper.rb
@@ -32,6 +32,8 @@
 ActiveRecord::Migration.maintain_test_schema!
 
 RSpec.configure do |config|
+  config.include Devise::Test::ControllerHelpers, type: :view
+
   # Remove this line if you're not using ActiveRecord or ActiveRecord fixtures
   config.fixture_path = "#{::Rails.root}/spec/fixtures"
 
diff --git a/hyrax/spec/views/datasets/_attribute_rows.html_spec.rb b/hyrax/spec/views/datasets/_attribute_rows.html_spec.rb
new file mode 100644
index 00000000..ee5eeae0
--- /dev/null
+++ b/hyrax/spec/views/datasets/_attribute_rows.html_spec.rb
@@ -0,0 +1,59 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'hyrax/datasets/_attribute_rows' do
+  let(:partial) { 'hyrax/datasets/attribute_rows' }
+  let(:dataset) { build(:dataset, :with_alternative_title, :with_complex_person, :with_keyword, :with_subject, :with_language,
+                        :with_publisher, :with_complex_date, :with_complex_identifier, :with_complex_rights,
+                        :with_complex_version, :with_resource_type, :with_complex_relation, :with_source) }
+  let(:presenter) { Hyrax::DatasetPresenter.new(SolrDocument.new(dataset.to_solr), Ability.new(user)) }
+
+  before do
+    allow(controller).to receive(:current_user).and_return(user)
+    login_as user if user.present?
+    render partial: partial, locals: { presenter: presenter }
+  end
+
+  # NB: the visibility of individual metadata components is set in app/models/ability.rb
+  # This test confirms the current expected behaviour (which is most metadata is visible)
+
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Dataset Alternative Title')
+      expect(rendered).to have_content('Anamika')
+      expect(rendered).to have_content('University')
+      expect(rendered).to have_content('Keyword123')
+      expect(rendered).to have_content('Subject123')
+      expect(rendered).to have_content('Faroese')
+      expect(rendered).to have_content('Publisher123')
+      expect(rendered).to have_content('1978-10-28')
+      expect(rendered).to have_content('10.0.1111')
+      expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
+      expect(rendered).to have_content('Creating the first version')
+      expect(rendered).to have_content('ResourceType123')
+      expect(rendered).to have_content('A relation label')
+      expect(rendered).to have_content('Source123')
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { create(:user, :nims_researcher) }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Dataset Alternative Title')
+      expect(rendered).to have_content('Anamika')
+      expect(rendered).to have_content('University')
+      expect(rendered).to have_content('Keyword123')
+      expect(rendered).to have_content('Subject123')
+      expect(rendered).to have_content('Faroese')
+      expect(rendered).to have_content('Publisher123')
+      expect(rendered).to have_content('1978-10-28')
+      expect(rendered).to have_content('10.0.1111')
+      expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
+      expect(rendered).to have_content('Creating the first version')
+      expect(rendered).to have_content('ResourceType123')
+      expect(rendered).to have_content('A relation label')
+      expect(rendered).to have_content('Source123')
+    end
+  end
+end

From 3614aadf1a258ac5698023be8d2707a9bade87ff Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 3 Dec 2019 17:50:07 +0000
Subject: [PATCH 058/258] wip

extending view test to publications, small tweaks
---
 hyrax/spec/factories/dataset.rb               | 10 +--
 hyrax/spec/factories/publication.rb           | 70 +++++++++++++++++--
 .../publication_behavior_helper_spec.rb       | 12 ++--
 hyrax/spec/inputs/nested_event_input_spec.rb  |  4 +-
 .../nested_event_attribute_renderer_spec.rb   |  4 +-
 .../datasets/_attribute_rows.html_spec.rb     | 22 +++---
 .../publications/_attribute_rows.html_spec.rb | 70 +++++++++++++++++++
 7 files changed, 161 insertions(+), 31 deletions(-)
 rename hyrax/spec/views/{ => hyrax}/datasets/_attribute_rows.html_spec.rb (79%)
 create mode 100644 hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb

diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 5df8bb89..beb6e2af 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -34,11 +34,11 @@
     end
 
     trait :with_keyword do
-      keyword { ['Keyword123'] }
+      keyword { ['Keyword-123'] }
     end
 
     trait :with_subject do
-      subject { ['Subject123'] }
+      subject { ['Subject-123'] }
     end
 
     trait :with_language do
@@ -46,15 +46,15 @@
     end
 
     trait :with_publisher do
-      publisher { ['Publisher123'] }
+      publisher { ['Publisher-123'] }
     end
 
     trait :with_resource_type do
-      resource_type { ['ResourceType123'] }
+      resource_type { ['Resource-Type-123'] }
     end
 
     trait :with_source do
-      source { ['Source123'] }
+      source { ['Source-123'] }
     end
 
     trait :with_complex_person do
diff --git a/hyrax/spec/factories/publication.rb b/hyrax/spec/factories/publication.rb
index f1f3fd52..8b64de98 100644
--- a/hyrax/spec/factories/publication.rb
+++ b/hyrax/spec/factories/publication.rb
@@ -29,6 +29,46 @@
       }
     end
 
+    trait :with_alternative_title do
+      alternative_title { 'Publication Alternative Title' }
+    end
+
+    trait :with_keyword do
+      keyword { ['Keyword-123'] }
+    end
+
+    trait :with_subject do
+      subject { ['Subject-123'] }
+    end
+
+    trait :with_language do
+      language { ['Faroese'] }
+    end
+
+    trait :with_resource_type do
+      resource_type { ['Resource-Type-123'] }
+    end
+
+    trait :with_source do
+      source { ['Source-123'] }
+    end
+
+    trait :with_rights_statement do
+      rights_statement { ['Rights-Statement-123'] }
+    end
+
+    trait :with_issue do
+      issue { 'Issue-123' }
+    end
+
+    trait :with_table_of_contents do
+      table_of_contents { 'Table-of-Contents-123' }
+    end
+
+    trait :with_number_of_pages do
+      total_number_of_pages { 'Number-of-Pages-123' }
+    end
+
     trait :with_complex_identifier do
       complex_identifier_attributes {
         [
@@ -43,24 +83,24 @@
       solr_document { {} }
     end
 
-    trait :with_date do
+    trait :with_complex_date do
       complex_date_attributes { [{ date: '2019-05-28',  description: 'Published' }] }
     end
 
     trait :with_place do
-      place { '221B Baker Street' }
+      place { '221B Baker Street Place' }
     end
 
     trait :with_publisher do
-      publisher { ['Foo Publisher'] }
+      publisher { ['Publisher-123'] }
     end
 
     trait :with_complex_event do
       complex_event_attributes {
         [{
-             title: 'A Title',
+             title: 'Event-Title-123',
              invitation_status: true,
-             place: '221B Baker Street',
+             place: 'New Scotland Yard',
              start_date: '2018-12-25',
              end_date: '2019-01-01'
         }]
@@ -89,5 +129,25 @@
         }]
       }
     end
+
+    trait :with_complex_rights do
+      complex_rights_attributes {
+        [{
+           date: '1980-10-10',
+           rights: 'http://creativecommons.org/publicdomain/zero/1.0/'
+         }]
+      }
+    end
+
+    trait :with_complex_version do
+      complex_version_attributes {
+        [{
+           date: '1990-12-12',
+           description: 'Creating the first version',
+           identifier: 'id1',
+           version: '1.0'
+         }]
+      }
+    end
   end
 end
diff --git a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
index d7c47ed8..dc3df793 100644
--- a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
+++ b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
@@ -18,7 +18,7 @@
   end
 
   describe '#setup_pub_date' do
-    let(:publication) { build(:publication, :with_date) }
+    let(:publication) { build(:publication, :with_complex_date) }
     subject { helper.setup_pub_date(presenter) }
     it { is_expected.to eql('0528') }
   end
@@ -27,7 +27,7 @@
     context 'with publication' do
       let(:publication) { build(:publication, :with_place) }
       subject { helper.setup_pub_place(presenter) }
-      it { is_expected.to eql('221B Baker Street') }
+      it { is_expected.to eql('221B Baker Street Place') }
     end
     context 'with dataset' do
       let(:publication) { build(:dataset) }
@@ -39,21 +39,21 @@
   describe '#setup_pub_publisher' do
     let(:publication) { build(:publication, :with_publisher) }
     subject { helper.setup_pub_publisher(presenter) }
-    it { is_expected.to eql('Foo Publisher') }
+    it { is_expected.to eql('Publisher-123') }
   end
 
   describe '#setup_pub_info' do
-    let(:publication) { build(:publication, :with_complex_identifier, :with_date, :with_place, :with_publisher) }
+    let(:publication) { build(:publication, :with_complex_identifier, :with_complex_date, :with_place, :with_publisher) }
     subject { helper.setup_pub_info(presenter, include_date) }
 
     context 'without date' do
       let(:include_date) { false }
-      it { is_expected.to eql('221B Baker Street: Foo Publisher. 10.0.1111. 10.0.2222') }
+      it { is_expected.to eql('221B Baker Street Place: Publisher-123. 10.0.1111. 10.0.2222') }
     end
 
     context 'with date' do
       let(:include_date) { true }
-      it { is_expected.to eql('221B Baker Street: Foo Publisher, 0528. 10.0.1111. 10.0.2222') }
+      it { is_expected.to eql('221B Baker Street Place: Publisher-123, 0528. 10.0.1111. 10.0.2222') }
     end
   end
 
diff --git a/hyrax/spec/inputs/nested_event_input_spec.rb b/hyrax/spec/inputs/nested_event_input_spec.rb
index 09f34f37..c75b61a1 100644
--- a/hyrax/spec/inputs/nested_event_input_spec.rb
+++ b/hyrax/spec/inputs/nested_event_input_spec.rb
@@ -15,8 +15,8 @@
   subject { Capybara.string(html) }
 
   it 'generates the correct fields' do
-    is_expected.to have_field('publication_complex_event_attributes_0_title', type: :text, with: 'A Title')
-    is_expected.to have_field('publication_complex_event_attributes_0_place', type: :text, with: '221B Baker Street')
+    is_expected.to have_field('publication_complex_event_attributes_0_title', type: :text, with: 'Event-Title-123')
+    is_expected.to have_field('publication_complex_event_attributes_0_place', type: :text, with: 'New Scotland Yard')
     is_expected.to have_field('publication_complex_event_attributes_0_start_date', type: :text, with: '2018-12-25')
     is_expected.to have_field('publication_complex_event_attributes_0_end_date', type: :text, with: '2019-01-01')
     is_expected.to have_field('publication_complex_event_attributes_0_invitation_status', type: :text, with: 'true')
diff --git a/hyrax/spec/renderers/nested_event_attribute_renderer_spec.rb b/hyrax/spec/renderers/nested_event_attribute_renderer_spec.rb
index 1c09fe2f..46c8428d 100644
--- a/hyrax/spec/renderers/nested_event_attribute_renderer_spec.rb
+++ b/hyrax/spec/renderers/nested_event_attribute_renderer_spec.rb
@@ -7,10 +7,10 @@
   it 'generates the correct fields' do
     is_expected.to have_css('th', text: 'Event')
     is_expected.to have_css('div.row label', text: 'Title')
-    is_expected.to have_css('div.row', text: 'A Title')
+    is_expected.to have_css('div.row', text: 'Event-Title-123')
 
     is_expected.to have_css('div.row label', text: 'Location')
-    is_expected.to have_css('div.row', text: '221B Baker Street')
+    is_expected.to have_css('div.row', text: 'New Scotland Yard')
 
     is_expected.to have_css('div.row label', text: 'Start date')
     is_expected.to have_css('div.row', text: '2018-12-25')
diff --git a/hyrax/spec/views/datasets/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
similarity index 79%
rename from hyrax/spec/views/datasets/_attribute_rows.html_spec.rb
rename to hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
index ee5eeae0..e2b520c4 100644
--- a/hyrax/spec/views/datasets/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
@@ -15,7 +15,7 @@
   end
 
   # NB: the visibility of individual metadata components is set in app/models/ability.rb
-  # This test confirms the current expected behaviour (which is most metadata is visible)
+  # This test confirms the current expected behaviour (which is that most metadata is visible)
 
   context 'unauthenticated user' do
     let(:user) { nil }
@@ -23,17 +23,17 @@
       expect(rendered).to have_content('Dataset Alternative Title')
       expect(rendered).to have_content('Anamika')
       expect(rendered).to have_content('University')
-      expect(rendered).to have_content('Keyword123')
-      expect(rendered).to have_content('Subject123')
+      expect(rendered).to have_content('Keyword-123')
+      expect(rendered).to have_content('Subject-123')
       expect(rendered).to have_content('Faroese')
-      expect(rendered).to have_content('Publisher123')
+      expect(rendered).to have_content('Publisher-123')
       expect(rendered).to have_content('1978-10-28')
       expect(rendered).to have_content('10.0.1111')
       expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
       expect(rendered).to have_content('Creating the first version')
-      expect(rendered).to have_content('ResourceType123')
+      expect(rendered).to have_content('Resource-Type-123')
       expect(rendered).to have_content('A relation label')
-      expect(rendered).to have_content('Source123')
+      expect(rendered).to have_content('Source-123')
     end
   end
 
@@ -43,17 +43,17 @@
       expect(rendered).to have_content('Dataset Alternative Title')
       expect(rendered).to have_content('Anamika')
       expect(rendered).to have_content('University')
-      expect(rendered).to have_content('Keyword123')
-      expect(rendered).to have_content('Subject123')
+      expect(rendered).to have_content('Keyword-123')
+      expect(rendered).to have_content('Subject-123')
       expect(rendered).to have_content('Faroese')
-      expect(rendered).to have_content('Publisher123')
+      expect(rendered).to have_content('Publisher-123')
       expect(rendered).to have_content('1978-10-28')
       expect(rendered).to have_content('10.0.1111')
       expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
       expect(rendered).to have_content('Creating the first version')
-      expect(rendered).to have_content('ResourceType123')
+      expect(rendered).to have_content('Resource-Type-123')
       expect(rendered).to have_content('A relation label')
-      expect(rendered).to have_content('Source123')
+      expect(rendered).to have_content('Source-123')
     end
   end
 end
diff --git a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
new file mode 100644
index 00000000..c6a169a8
--- /dev/null
+++ b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
@@ -0,0 +1,70 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'hyrax/publications/_attribute_rows' do
+  let(:partial) { 'hyrax/publications/attribute_rows' }
+  let(:publication) { build(:publication, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
+                        :with_publisher, :with_complex_date, :with_complex_identifier, :with_rights_statement, :with_complex_rights,
+                        :with_complex_version, :with_resource_type, :with_source, :with_issue, :with_complex_source, :with_complex_event,
+                        :with_place, :with_table_of_contents, :with_number_of_pages) }
+  let(:presenter) { Hyrax::PublicationPresenter.new(SolrDocument.new(publication.to_solr), Ability.new(user)) }
+
+  before do
+    allow(controller).to receive(:current_user).and_return(user)
+    login_as user if user.present?
+    render partial: partial, locals: { presenter: presenter }
+  end
+
+  # NB: the visibility of individual metadata components is set in app/models/ability.rb
+  # This test confirms the current expected behaviour (which is that most metadata is visible)
+
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Publication Alternative Title')
+      expect(rendered).to have_content('Subject-123')
+      expect(rendered).to have_content('Publisher-123')
+      expect(rendered).to have_content('Faroese')
+      expect(rendered).to have_content('Keyword-123')
+      expect(rendered).to have_content('Resource-Type-123')
+      expect(rendered).to have_content('Rights-Statement-123')
+      expect(rendered).to have_content('28/05/2019') # NB: complex date is reformatted to dd/mm/yyyy
+      expect(rendered).to have_content('10.0.1111')
+      expect(rendered).to have_content('Big Baz')
+      expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
+      expect(rendered).to have_content('Creating the first version')
+      expect(rendered).to have_content('Event-Title-123')
+      expect(rendered).to have_content('Issue-123')
+      expect(rendered).to have_content('221B Baker Street Place')
+      expect(rendered).to have_content('Table-of-Contents-123')
+      expect(rendered).to have_content('Number-of-Pages-123')
+      expect(rendered).to have_content('Source-123')
+      expect(rendered).to have_content('Test journal')
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { create(:user, :nims_researcher) }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Publication Alternative Title')
+      expect(rendered).to have_content('Subject-123')
+      expect(rendered).to have_content('Publisher-123')
+      expect(rendered).to have_content('Faroese')
+      expect(rendered).to have_content('Keyword-123')
+      expect(rendered).to have_content('Resource-Type-123')
+      expect(rendered).to have_content('Rights-Statement-123')
+      expect(rendered).to have_content('28/05/2019') # NB: complex date is reformatted to dd/mm/yyyy
+      expect(rendered).to have_content('10.0.1111')
+      expect(rendered).to have_content('Big Baz')
+      expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
+      expect(rendered).to have_content('Creating the first version')
+      expect(rendered).to have_content('Event-Title-123')
+      expect(rendered).to have_content('Issue-123')
+      expect(rendered).to have_content('221B Baker Street Place')
+      expect(rendered).to have_content('Table-of-Contents-123')
+      expect(rendered).to have_content('Number-of-Pages-123')
+      expect(rendered).to have_content('Source-123')
+      expect(rendered).to have_content('Test journal')
+    end
+  end
+end

From 54bd6a984eee5fe01f3f391819415318de74ef33 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 4 Dec 2019 10:32:04 +0000
Subject: [PATCH 059/258] image view tests

---
 hyrax/spec/factories/dataset.rb               |  2 +-
 hyrax/spec/factories/image.rb                 | 75 +++++++++++++++++++
 hyrax/spec/factories/publication.rb           |  2 +-
 .../datasets/_attribute_rows.html_spec.rb     |  4 +-
 .../hyrax/images/_attribute_rows.html_spec.rb | 56 ++++++++++++++
 .../publications/_attribute_rows.html_spec.rb |  4 +-
 6 files changed, 137 insertions(+), 6 deletions(-)
 create mode 100644 hyrax/spec/views/hyrax/images/_attribute_rows.html_spec.rb

diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index beb6e2af..2d144877 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -30,7 +30,7 @@
     end
 
     trait :with_alternative_title do
-      alternative_title { 'Dataset Alternative Title' }
+      alternative_title { 'Alternative-Title-123' }
     end
 
     trait :with_keyword do
diff --git a/hyrax/spec/factories/image.rb b/hyrax/spec/factories/image.rb
index b746ef1a..fa5bfdda 100644
--- a/hyrax/spec/factories/image.rb
+++ b/hyrax/spec/factories/image.rb
@@ -7,4 +7,79 @@
     override_new_record
   end
 
+  trait :with_alternative_title do
+    alternative_title { 'Alternative-Title-123' }
+  end
+
+  trait :with_subject do
+    subject { ['Subject-123'] }
+  end
+
+  trait :with_publisher do
+    publisher { ['Publisher-123'] }
+  end
+
+  trait :with_language do
+    language { ['Faroese'] }
+  end
+
+  trait :with_keyword do
+    keyword { ['Keyword-123'] }
+  end
+
+  trait :with_resource_type do
+    resource_type { ['Resource-Type-123'] }
+  end
+
+  trait :with_rights_statement do
+    rights_statement { ['Rights-Statement-123'] }
+  end
+
+  trait :with_complex_date do
+    complex_date_attributes {
+      [{
+         date: '2019-05-28',
+         description: 'Published'
+       }]
+    }
+  end
+
+  trait :with_complex_identifier do
+    complex_identifier_attributes {
+      [
+        { identifier: '10.0.1111', scheme: 'http://dx.doi.org', label: 'DOI' },
+        { identifier: '10.0.2222', scheme: 'HTTPS://DX.DOI.ORG', label: 'DOI' },
+        { identifier: '3333', label: 'Local ID' }
+      ]
+    }
+  end
+
+  trait :with_complex_person do
+    complex_person_attributes {
+      [{
+         name: 'Complex-Person-123',
+         role: ['operator']
+       }]
+    }
+  end
+
+  trait :with_complex_rights do
+    complex_rights_attributes {
+      [{
+         date: '1978-10-28',
+         rights: 'http://creativecommons.org/publicdomain/zero/1.0/'
+       }]
+    }
+  end
+
+  trait :with_complex_version do
+    complex_version_attributes {
+      [{
+         date: '1978-10-28',
+         description: 'Complex-Version-123',
+         identifier: 'id1',
+         version: '1.0'
+       }]
+    }
+  end
 end
diff --git a/hyrax/spec/factories/publication.rb b/hyrax/spec/factories/publication.rb
index 8b64de98..ce334458 100644
--- a/hyrax/spec/factories/publication.rb
+++ b/hyrax/spec/factories/publication.rb
@@ -30,7 +30,7 @@
     end
 
     trait :with_alternative_title do
-      alternative_title { 'Publication Alternative Title' }
+      alternative_title { 'Alternative-Title-123' }
     end
 
     trait :with_keyword do
diff --git a/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
index e2b520c4..974a23e6 100644
--- a/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
@@ -20,7 +20,7 @@
   context 'unauthenticated user' do
     let(:user) { nil }
     it 'shows the correct metadata' do
-      expect(rendered).to have_content('Dataset Alternative Title')
+      expect(rendered).to have_content('Alternative-Title-123')
       expect(rendered).to have_content('Anamika')
       expect(rendered).to have_content('University')
       expect(rendered).to have_content('Keyword-123')
@@ -40,7 +40,7 @@
   context 'authenticated NIMS Researcher' do
     let(:user) { create(:user, :nims_researcher) }
     it 'shows the correct metadata' do
-      expect(rendered).to have_content('Dataset Alternative Title')
+      expect(rendered).to have_content('Alternative-Title-123')
       expect(rendered).to have_content('Anamika')
       expect(rendered).to have_content('University')
       expect(rendered).to have_content('Keyword-123')
diff --git a/hyrax/spec/views/hyrax/images/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/images/_attribute_rows.html_spec.rb
new file mode 100644
index 00000000..4dc57d44
--- /dev/null
+++ b/hyrax/spec/views/hyrax/images/_attribute_rows.html_spec.rb
@@ -0,0 +1,56 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'hyrax/images/_attribute_rows' do
+  let(:partial) { 'hyrax/images/attribute_rows' }
+  let(:image) { build(:image, :with_alternative_title, :with_subject, :with_publisher, :with_language,
+                            :with_keyword, :with_resource_type, :with_rights_statement, :with_complex_date,
+                            :with_complex_identifier, :with_complex_person, :with_complex_rights,
+                            :with_complex_version) }
+  let(:presenter) { Hyrax::ImagePresenter.new(SolrDocument.new(image.to_solr), Ability.new(user)) }
+
+  before do
+    allow(controller).to receive(:current_user).and_return(user)
+    login_as user if user.present?
+    render partial: partial, locals: { presenter: presenter }
+  end
+
+  # NB: the visibility of individual metadata components is set in app/models/ability.rb
+  # This test confirms the current expected behaviour (which is that most metadata is visible)
+
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Alternative-Title-123')
+      expect(rendered).to have_content('Subject-123')
+      expect(rendered).to have_content('Publisher-123')
+      expect(rendered).to have_content('Faroese')
+      expect(rendered).to have_content('Keyword-123')
+      expect(rendered).to have_content('Resource-Type-123')
+      expect(rendered).to have_content('Rights-Statement-123')
+      expect(rendered).to have_content('28/05/2019') # NB: complex date is reformatted to dd/mm/yyyy
+      expect(rendered).to have_content('10.0.1111')
+      expect(rendered).to have_content('Complex-Person-123')
+      expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
+      expect(rendered).to have_content('Complex-Version-123')
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { create(:user, :nims_researcher) }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Alternative-Title-123')
+      expect(rendered).to have_content('Subject-123')
+      expect(rendered).to have_content('Publisher-123')
+      expect(rendered).to have_content('Faroese')
+      expect(rendered).to have_content('Keyword-123')
+      expect(rendered).to have_content('Resource-Type-123')
+      expect(rendered).to have_content('Rights-Statement-123')
+      expect(rendered).to have_content('28/05/2019') # NB: complex date is reformatted to dd/mm/yyyy
+      expect(rendered).to have_content('10.0.1111')
+      expect(rendered).to have_content('Complex-Person-123')
+      expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
+      expect(rendered).to have_content('Complex-Version-123')
+    end
+  end
+end
diff --git a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
index c6a169a8..ce701fc2 100644
--- a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
@@ -21,7 +21,7 @@
   context 'unauthenticated user' do
     let(:user) { nil }
     it 'shows the correct metadata' do
-      expect(rendered).to have_content('Publication Alternative Title')
+      expect(rendered).to have_content('Alternative-Title-123')
       expect(rendered).to have_content('Subject-123')
       expect(rendered).to have_content('Publisher-123')
       expect(rendered).to have_content('Faroese')
@@ -46,7 +46,7 @@
   context 'authenticated NIMS Researcher' do
     let(:user) { create(:user, :nims_researcher) }
     it 'shows the correct metadata' do
-      expect(rendered).to have_content('Publication Alternative Title')
+      expect(rendered).to have_content('Alternative-Title-123')
       expect(rendered).to have_content('Subject-123')
       expect(rendered).to have_content('Publisher-123')
       expect(rendered).to have_content('Faroese')

From cca3f3ed3d410d2fd5461dfc82a11bdbeaa12f4e Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 4 Dec 2019 11:36:41 +0000
Subject: [PATCH 060/258] Update ability_spec.rb

---
 hyrax/spec/models/ability_spec.rb | 210 ++++++++++++++++++++++++++++--
 1 file changed, 196 insertions(+), 14 deletions(-)

diff --git a/hyrax/spec/models/ability_spec.rb b/hyrax/spec/models/ability_spec.rb
index 6450d5e1..4b2fa66d 100644
--- a/hyrax/spec/models/ability_spec.rb
+++ b/hyrax/spec/models/ability_spec.rb
@@ -3,41 +3,223 @@
 RSpec.describe Ability do
   let(:ability) { Ability.new(user) }
 
-  describe 'everyone_can_create_dataset' do
-    subject { ability.everyone_can_create_dataset }
+  describe '#everyone_can_create_dataset' do
+    subject { ability.can?(:create, ::Dataset) }
 
     context 'guest user' do
-      let(:user) { create(:user, :guest) }
-      it { is_expected.to be_nil }
+      let(:user) { build(:user, :guest) }
+      it { is_expected.to be false }
     end
 
     context 'general user' do
       let(:user) { create(:user) }
-      it { is_expected.to eql [::Dataset] }
+      it { is_expected.to be true }
     end
 
     context 'admin user' do
-      let(:user) { create(:user, :admin )}
-      it { is_expected.to eql [::Dataset] }
+      let(:user) { build(:user, :admin )}
+      it { is_expected.to be true }
     end
   end
 
-  describe 'everyone_can_create_publication' do
-    subject { ability.everyone_can_create_publication }
+  describe '#everyone_can_create_publication' do
+    subject { ability.can?(:create, ::Publication) }
 
     context 'guest user' do
-      let(:user) { create(:user, :guest) }
-      it { is_expected.to be_nil }
+      let(:user) { build(:user, :guest) }
+      it { is_expected.to be false }
     end
 
     context 'general user' do
       let(:user) { create(:user) }
-      it { is_expected.to eql [::Publication] }
+      it { is_expected.to be true }
     end
 
     context 'admin user' do
-      let(:user) { create(:user, :admin )}
-      it { is_expected.to eql [::Publication] }
+      let(:user) { build(:user, :admin )}
+      it { is_expected.to be true }
+    end
+  end
+
+  describe '#read_metadata' do
+    let(:read_abstract) { ability.can?(:read_abstract, model) }
+    let(:read_alternative_title) { ability.can?(:read_alternative_title, model) }
+    let(:read_creator) { ability.can?(:read_creator, model) }
+    let(:read_date) { ability.can?(:read_date, model) }
+    let(:read_event) { ability.can?(:read_event, model) }
+    let(:read_identifier) { ability.can?(:read_identifier, model) }
+    let(:read_issue) { ability.can?(:read_issue, model) }
+    let(:read_table_of_contents) { ability.can?(:read_table_of_contents, model) }
+    let(:read_keyword) { ability.can?(:read_keyword, model) }
+    let(:read_language) { ability.can?(:read_language, model) }
+    let(:read_location) { ability.can?(:read_location, model) }
+    let(:read_number_of_pages) { ability.can?(:read_number_of_pages, model) }
+    let(:read_organization) { ability.can?(:read_organization, model) }
+    let(:read_publisher) { ability.can?(:read_publisher, model) }
+    let(:read_related) { ability.can?(:read_related, model) }
+    let(:read_resource_type) { ability.can?(:read_resource_type, model) }
+    let(:read_rights) { ability.can?(:read_rights, model) }
+    let(:read_source) { ability.can?(:read_source, model) }
+    let(:read_subject) { ability.can?(:read_subject, model) }
+    let(:read_title) { ability.can?(:read_title, model) }
+    let(:read_version) { ability.can?(:read_version, model) }
+
+    context 'unauthenticated user' do
+      let(:user) { build(:user, :guest) }
+
+      context 'dataset' do
+        let(:model) { ::Dataset}
+        it { expect(read_abstract).to be false }
+        it { expect(read_alternative_title).to be true }
+        it { expect(read_creator).to be true }
+        it { expect(read_date).to be true }
+        it { expect(read_event).to be false }
+        it { expect(read_identifier).to be true }
+        it { expect(read_issue).to be false }
+        it { expect(read_table_of_contents).to be false }
+        it { expect(read_keyword).to be true }
+        it { expect(read_language).to be true }
+        it { expect(read_location).to be false }
+        it { expect(read_number_of_pages).to be false }
+        it { expect(read_organization).to be true }
+        it { expect(read_publisher).to be true }
+        it { expect(read_related).to be true }
+        it { expect(read_resource_type).to be true }
+        it { expect(read_rights).to be true }
+        it { expect(read_source).to be true }
+        it { expect(read_subject).to be true }
+        it { expect(read_title).to be true }
+        it { expect(read_version).to be true }
+      end
+
+      context 'image' do
+        let(:model) { ::Image}
+        it { expect(read_abstract).to be false }
+        it { expect(read_alternative_title).to be true }
+        it { expect(read_creator).to be true }
+        it { expect(read_date).to be true }
+        it { expect(read_event).to be false }
+        it { expect(read_identifier).to be true }
+        it { expect(read_issue).to be false }
+        it { expect(read_table_of_contents).to be false }
+        it { expect(read_keyword).to be true }
+        it { expect(read_language).to be true }
+        it { expect(read_location).to be false }
+        it { expect(read_number_of_pages).to be false }
+        it { expect(read_organization).to be false }
+        it { expect(read_publisher).to be true }
+        it { expect(read_related).to be false }
+        it { expect(read_resource_type).to be true }
+        it { expect(read_rights).to be true }
+        it { expect(read_source).to be false }
+        it { expect(read_subject).to be true }
+        it { expect(read_title).to be true }
+        it { expect(read_version).to be true }
+      end
+
+      context 'publication' do
+        let(:model) { ::Publication}
+        it { expect(read_abstract).to be false }
+        it { expect(read_alternative_title).to be true }
+        it { expect(read_creator).to be true }
+        it { expect(read_date).to be true }
+        it { expect(read_event).to be true }
+        it { expect(read_identifier).to be true }
+        it { expect(read_issue).to be true }
+        it { expect(read_table_of_contents).to be true }
+        it { expect(read_keyword).to be true }
+        it { expect(read_language).to be true }
+        it { expect(read_location).to be true }
+        it { expect(read_number_of_pages).to be true }
+        it { expect(read_organization).to be true }
+        it { expect(read_publisher).to be true }
+        it { expect(read_related).to be true }
+        it { expect(read_resource_type).to be true }
+        it { expect(read_rights).to be true }
+        it { expect(read_source).to be true }
+        it { expect(read_subject).to be true }
+        it { expect(read_title).to be true }
+        it { expect(read_version).to be true }
+      end
+    end
+
+    context 'authenticated NIMS Researcher' do
+      let(:user) { build(:user, :nims_researcher) }
+
+      context 'dataset' do
+        let(:model) { ::Dataset}
+        it { expect(read_abstract).to be true }
+        it { expect(read_alternative_title).to be true }
+        it { expect(read_creator).to be true }
+        it { expect(read_date).to be true }
+        it { expect(read_event).to be false }
+        it { expect(read_identifier).to be true }
+        it { expect(read_issue).to be false }
+        it { expect(read_table_of_contents).to be false }
+        it { expect(read_keyword).to be true }
+        it { expect(read_language).to be true }
+        it { expect(read_location).to be false }
+        it { expect(read_number_of_pages).to be false }
+        it { expect(read_organization).to be true }
+        it { expect(read_publisher).to be true }
+        it { expect(read_related).to be true }
+        it { expect(read_resource_type).to be true }
+        it { expect(read_rights).to be true }
+        it { expect(read_source).to be true }
+        it { expect(read_subject).to be true }
+        it { expect(read_title).to be true }
+        it { expect(read_version).to be true }
+      end
+
+      context 'image' do
+        let(:model) { ::Image}
+        it { expect(read_abstract).to be true }
+        it { expect(read_alternative_title).to be true }
+        it { expect(read_creator).to be true }
+        it { expect(read_date).to be true }
+        it { expect(read_event).to be false }
+        it { expect(read_identifier).to be true }
+        it { expect(read_issue).to be false }
+        it { expect(read_table_of_contents).to be false }
+        it { expect(read_keyword).to be true }
+        it { expect(read_language).to be true }
+        it { expect(read_location).to be false }
+        it { expect(read_number_of_pages).to be false }
+        it { expect(read_organization).to be false }
+        it { expect(read_publisher).to be true }
+        it { expect(read_related).to be false }
+        it { expect(read_resource_type).to be true }
+        it { expect(read_rights).to be true }
+        it { expect(read_source).to be false }
+        it { expect(read_subject).to be true }
+        it { expect(read_title).to be true }
+        it { expect(read_version).to be true }
+      end
+
+      context 'publication' do
+        let(:model) { ::Publication}
+        it { expect(read_abstract).to be true }
+        it { expect(read_alternative_title).to be true }
+        it { expect(read_creator).to be true }
+        it { expect(read_date).to be true }
+        it { expect(read_event).to be true }
+        it { expect(read_identifier).to be true }
+        it { expect(read_issue).to be true }
+        it { expect(read_table_of_contents).to be true }
+        it { expect(read_keyword).to be true }
+        it { expect(read_language).to be true }
+        it { expect(read_location).to be true }
+        it { expect(read_number_of_pages).to be true }
+        it { expect(read_organization).to be true }
+        it { expect(read_publisher).to be true }
+        it { expect(read_related).to be true }
+        it { expect(read_resource_type).to be true }
+        it { expect(read_rights).to be true }
+        it { expect(read_source).to be true }
+        it { expect(read_subject).to be true }
+        it { expect(read_title).to be true }
+        it { expect(read_version).to be true }
+      end
     end
   end
 end

From b2657a1b7398f164bae1054ad6670dd78b76bbb3 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 4 Dec 2019 12:07:34 +0000
Subject: [PATCH 061/258] additional ability specs

---
 hyrax/app/models/ability.rb       |  2 +-
 hyrax/spec/models/ability_spec.rb | 52 +++++++++++++++++++++++++++++--
 2 files changed, 51 insertions(+), 3 deletions(-)

diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index 6a8aab7b..dd940267 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -1,6 +1,6 @@
 class Ability
   include Hydra::Ability
-  include Hyrax::Ability
+  include Hyrax::Ability # NB: not the same as the line above!
 
   # Registered user can only create datasets and publications
   self.ability_logic += [
diff --git a/hyrax/spec/models/ability_spec.rb b/hyrax/spec/models/ability_spec.rb
index 4b2fa66d..965ad4db 100644
--- a/hyrax/spec/models/ability_spec.rb
+++ b/hyrax/spec/models/ability_spec.rb
@@ -7,7 +7,7 @@
     subject { ability.can?(:create, ::Dataset) }
 
     context 'guest user' do
-      let(:user) { build(:user, :guest) }
+      let(:user) { create(:user, :guest) }
       it { is_expected.to be false }
     end
 
@@ -26,7 +26,7 @@
     subject { ability.can?(:create, ::Publication) }
 
     context 'guest user' do
-      let(:user) { build(:user, :guest) }
+      let(:user) { create(:user, :guest) }
       it { is_expected.to be false }
     end
 
@@ -41,6 +41,54 @@
     end
   end
 
+  describe '#custom_permissions' do
+    let(:role_create) { ability.can?(:create, Role) }
+    let(:role_show) { ability.can?(:show, Role) }
+    let(:role_add_user) { ability.can?(:add_user, Role) }
+    let(:role_remove_user) { ability.can?(:remove_user, Role) }
+    let(:role_index) { ability.can?(:index, Role) }
+    let(:role_edit) { ability.can?(:edit, Role) }
+    let(:role_update) { ability.can?(:update, Role) }
+    let(:role_destroy) { ability.can?(:destroy, Role) }
+
+    let(:create_dataset) { ability.can?(:create, Dataset) }
+    let(:create_image) { ability.can?(:create, Image) }
+    let(:create_publication) { ability.can?(:create, Publication) }
+    let(:create_work) { ability.can?(:create, Work) }
+
+    context 'admin user' do
+      let(:user) { create(:user, :admin) }
+      it { expect(role_create).to be true }
+      it { expect(role_show).to be true }
+      it { expect(role_add_user).to be true }
+      it { expect(role_remove_user).to be true }
+      it { expect(role_index).to be true }
+      it { expect(role_edit).to be true }
+      it { expect(role_update).to be true }
+      it { expect(role_destroy).to be true }
+      it { expect(create_dataset).to be true }
+      it { expect(create_image).to be true }
+      it { expect(create_publication).to be true }
+      it { expect(create_work).to be true }
+    end
+
+    context 'guest user' do
+      let(:user) { create(:user, :guest) }
+      it { expect(role_create).to be false }
+      it { expect(role_show).to be false }
+      it { expect(role_add_user).to be false }
+      it { expect(role_remove_user).to be false }
+      it { expect(role_index).to be false }
+      it { expect(role_edit).to be false }
+      it { expect(role_update).to be false }
+      it { expect(role_destroy).to be false }
+      it { expect(create_dataset).to be false }
+      it { expect(create_image).to be false }
+      it { expect(create_publication).to be false }
+      it { expect(create_work).to be false }
+    end
+  end
+
   describe '#read_metadata' do
     let(:read_abstract) { ability.can?(:read_abstract, model) }
     let(:read_alternative_title) { ability.can?(:read_alternative_title, model) }

From b13636b83e50ec426289b09f5e633dcac9e18fe0 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 4 Dec 2019 12:32:27 +0000
Subject: [PATCH 062/258] Update .env.template

---
 .env.template | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.env.template b/.env.template
index 0853ccc4..671ef283 100644
--- a/.env.template
+++ b/.env.template
@@ -106,3 +106,9 @@ OAI_REPOSTIORY_NAME='NIMS MDR'
 OAI_REPOSITORY_URL=http://localhost:3000/catalog/oai
 OAI_RECORD_PREFIX=nims_mdr
 OAI_ADMIN_EMAIL=***REMOVED***
+
+# User Authorisation LDAP (runs after database / LDAP / CAS authentication)
+USER_AUTHORISATION_LDAP_HOST=
+USER_AUTHORISATION_LDAP_PORT=389
+USER_AUTHORISATION_LDAP_ATTRIBUTE=uid
+USER_AUTHORISATION_LDAP_BASE=

From 538e40f59af739e781f8f3f5406ae9c818b6a110 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 4 Dec 2019 14:47:29 +0000
Subject: [PATCH 063/258] Update Gemfile

---
 hyrax/Gemfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index db24ad6e..9a220d02 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -76,7 +76,7 @@ gem 'devise_cas_authenticatable'
 
 gem 'riiif', '~> 2.0'
 
-group :production do
+group :production, :development do
   gem 'airbrake', '~> 5.0'
 end
 

From 2c6cd4e5839ede4e1f5ab33018e3fcaa3c0da87d Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 4 Dec 2019 16:46:10 +0000
Subject: [PATCH 064/258] ensure only nims researchers can create content

---
 hyrax/app/models/ability.rb                   | 14 +---
 hyrax/features/datasets/create.feature        | 10 ++-
 hyrax/features/datasets/index.feature         | 11 ++-
 .../step_definitions/dataset_steps.rb         |  4 +
 hyrax/features/step_definitions/user_steps.rb |  4 +-
 hyrax/features/step_definitions/work_steps.rb |  4 +
 hyrax/spec/factories/users.rb                 |  4 -
 hyrax/spec/models/ability_spec.rb             | 78 ++++++++++---------
 8 files changed, 71 insertions(+), 58 deletions(-)

diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index dd940267..74cd7684 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -5,8 +5,7 @@ class Ability
   # Registered user can only create datasets and publications
   self.ability_logic += [
     :read_metadata,
-    :everyone_can_create_dataset,
-    :everyone_can_create_publication
+    :create_content
   ]
 
   # Define any customized permissions here.
@@ -28,14 +27,9 @@ def custom_permissions
     # end
   end
 
-  def everyone_can_create_dataset
-    return unless registered_user?
-    can :create, [::Dataset]
-  end
-
-  def everyone_can_create_publication
-    return unless registered_user?
-    can :create, [::Publication]
+  def create_content
+    # only NIMS Researchers may upload new content
+    can :create, [::Dataset, ::Publication, ::Image] if current_user.authenticated_nims_researcher?
   end
 
   def read_metadata
diff --git a/hyrax/features/datasets/create.feature b/hyrax/features/datasets/create.feature
index d3c4e70f..2e4fbe8c 100644
--- a/hyrax/features/datasets/create.feature
+++ b/hyrax/features/datasets/create.feature
@@ -3,8 +3,14 @@ Feature: Create a dataset
   Background:
     Given an initialised sysem with a default admin set, permission template and workflow
 
-  Scenario: Create a dataset as a general user
-    Given I am logged in as a general user
+  Scenario: Cannot create a dataset as a Non-Researcher user
+    Given I am logged in as a nims_other user
+    And I have permission to deposit
+    When I try to navigate to the new dataset page
+    Then I should not be authorized to access the page
+
+  Scenario: Create a dataset as a NIMS Researcher user
+    Given I am logged in as a nims_researcher user
     And I have permission to deposit
     When I navigate to the new dataset page
     And I create the dataset with:
diff --git a/hyrax/features/datasets/index.feature b/hyrax/features/datasets/index.feature
index 77aa30a2..a80cbcde 100644
--- a/hyrax/features/datasets/index.feature
+++ b/hyrax/features/datasets/index.feature
@@ -13,8 +13,15 @@ Feature: Datasets catalog index
     But I should not see the authenticated datasets
     And I should not see the restricted dataset
 
-  Scenario: General user can view open and authenticated datasets
-    Given I am logged in as a general user
+  Scenario: Non-researcher user can view open and authenticated datasets
+    Given I am logged in as a nims_other user
+    When I navigate to the dataset catalog page
+    Then I should see the open datasets
+    And I should see the authenticated datasets
+    But I should not see the restricted dataset
+
+  Scenario: Researcher user can view open and authenticated datasets
+    Given I am logged in as a nims_researcher user
     When I navigate to the dataset catalog page
     Then I should see the open datasets
     And I should see the authenticated datasets
diff --git a/hyrax/features/step_definitions/dataset_steps.rb b/hyrax/features/step_definitions/dataset_steps.rb
index 7c4d41c8..27282fc6 100644
--- a/hyrax/features/step_definitions/dataset_steps.rb
+++ b/hyrax/features/step_definitions/dataset_steps.rb
@@ -19,6 +19,10 @@
   visit new_hyrax_dataset_path
 end
 
+When /^I try to navigate to the new dataset page$/ do
+  visit new_hyrax_dataset_path
+end
+
 When(/^I navigate to the dataset catalog page$/) do
   visit root_path
   click_link 'Browse all datasets'
diff --git a/hyrax/features/step_definitions/user_steps.rb b/hyrax/features/step_definitions/user_steps.rb
index ad71c8ae..a491da0b 100644
--- a/hyrax/features/step_definitions/user_steps.rb
+++ b/hyrax/features/step_definitions/user_steps.rb
@@ -1,6 +1,6 @@
 include Warden::Test::Helpers
 
-Given(/^an? (general|admin) user$/) do |user_type|
+Given(/^an? (guest|nims_other|nims_researcher|admin) user$/) do |user_type|
   @user = FactoryBot.create(:user, user_type.to_sym)
 end
 
@@ -8,7 +8,7 @@
   login_as @user
 end
 
-Given(/^I am logged in as an? (general|admin) user$/) do |user_type|
+Given(/^I am logged in as an? (guest|nims_other|nims_researcher|admin) user$/) do |user_type|
   step "a #{user_type} user"
   step 'I am logged in'
 end
diff --git a/hyrax/features/step_definitions/work_steps.rb b/hyrax/features/step_definitions/work_steps.rb
index 0f5b4d56..edd0a271 100644
--- a/hyrax/features/step_definitions/work_steps.rb
+++ b/hyrax/features/step_definitions/work_steps.rb
@@ -5,3 +5,7 @@
 Then(/^I should see no results found$/) do
   expect(page).to have_content 'No results found for your search'
 end
+
+Then(/^I should not be authorized to access the page$/) do
+  expect(page).to have_content "You are not authorized to access this page."
+end
diff --git a/hyrax/spec/factories/users.rb b/hyrax/spec/factories/users.rb
index 13e2fab8..bd06127e 100644
--- a/hyrax/spec/factories/users.rb
+++ b/hyrax/spec/factories/users.rb
@@ -26,10 +26,6 @@
       end
     end
 
-    trait :general do
-      guest { false }
-    end
-
     trait :guest do
       guest { true }
     end
diff --git a/hyrax/spec/models/ability_spec.rb b/hyrax/spec/models/ability_spec.rb
index 965ad4db..84e61eaf 100644
--- a/hyrax/spec/models/ability_spec.rb
+++ b/hyrax/spec/models/ability_spec.rb
@@ -3,44 +3,6 @@
 RSpec.describe Ability do
   let(:ability) { Ability.new(user) }
 
-  describe '#everyone_can_create_dataset' do
-    subject { ability.can?(:create, ::Dataset) }
-
-    context 'guest user' do
-      let(:user) { create(:user, :guest) }
-      it { is_expected.to be false }
-    end
-
-    context 'general user' do
-      let(:user) { create(:user) }
-      it { is_expected.to be true }
-    end
-
-    context 'admin user' do
-      let(:user) { build(:user, :admin )}
-      it { is_expected.to be true }
-    end
-  end
-
-  describe '#everyone_can_create_publication' do
-    subject { ability.can?(:create, ::Publication) }
-
-    context 'guest user' do
-      let(:user) { create(:user, :guest) }
-      it { is_expected.to be false }
-    end
-
-    context 'general user' do
-      let(:user) { create(:user) }
-      it { is_expected.to be true }
-    end
-
-    context 'admin user' do
-      let(:user) { build(:user, :admin )}
-      it { is_expected.to be true }
-    end
-  end
-
   describe '#custom_permissions' do
     let(:role_create) { ability.can?(:create, Role) }
     let(:role_show) { ability.can?(:show, Role) }
@@ -89,6 +51,46 @@
     end
   end
 
+  describe '#create_content' do
+    let(:models) { [::Dataset, ::Image, ::Publication] }
+
+    context 'unauthenticated user' do
+      let(:user) { build(:user, :guest) }
+      it 'cannot create content' do
+        models.each do |model|
+          expect(ability.can?(:create, model)).to be false
+        end
+      end
+    end
+
+    context 'authenticated NIMS non-Researcher' do
+      let(:user) { build(:user, :nims_other) }
+      it 'cannot create content' do
+        models.each do |model|
+          expect(ability.can?(:create, model)).to be false
+        end
+      end
+    end
+
+    context 'authenticated NIMS Researcher' do
+      let(:user) { build(:user, :nims_researcher) }
+      it 'can create content' do
+        models.each do |model|
+          expect(ability.can?(:create, model)).to be true
+        end
+      end
+    end
+
+    context 'admin user' do
+      let(:user) { build(:user, :admin) }
+      it 'can create content' do
+        models.each do |model|
+          expect(ability.can?(:create, model)).to be true
+        end
+      end
+    end
+  end
+
   describe '#read_metadata' do
     let(:read_abstract) { ability.can?(:read_abstract, model) }
     let(:read_alternative_title) { ability.can?(:read_alternative_title, model) }

From c5fb56af0d8644de91f270f5e27923d680f0447b Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 5 Dec 2019 12:36:57 +0000
Subject: [PATCH 065/258] disable turbolinks, remove unused extra attributes

---
 hyrax/app/models/user.rb                  | 19 +------------------
 hyrax/app/views/_user_util_links.html.erb |  8 ++------
 2 files changed, 3 insertions(+), 24 deletions(-)

diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 683b3837..caca0b29 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -43,25 +43,8 @@ def self.find_or_create_system_user(user_key)
   end
 
   def ldap_before_save
+    # Runs before saving a new user record in the database via LDAP Authentication
     self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
     self.password = Devise.friendly_token[0, 20]
   end
-
-  def cas_extra_attributes=(extra_attributes)
-    extra_attributes.each do |name, value|
-      case name.to_sym
-      # TODO: change these mappings to match NIMS CAS schema
-      when :mail
-        self.email = value
-      when :eduPersonNickname
-        self.display_name = value
-      when :cn
-        self.email = value
-      # when :fullname
-      #   self.fullname = value
-      # when :email
-      #   self.email = value
-      end
-    end
-  end
 end
diff --git a/hyrax/app/views/_user_util_links.html.erb b/hyrax/app/views/_user_util_links.html.erb
index 54674744..76ae8aad 100644
--- a/hyrax/app/views/_user_util_links.html.erb
+++ b/hyrax/app/views/_user_util_links.html.erb
@@ -25,16 +25,12 @@
       <ul id="user-util-links" class="dropdown-menu dropdown-menu-right" role="menu">
         <li><%= link_to t("hyrax.toolbar.dashboard.menu"), hyrax.dashboard_path %></li>
         <li class="divider"></li>
-        <% if ENV['MDR_DEVISE_AUTH_MODULE'] == 'cas_authenticatable' %>
-          <li><%= link_to t("hyrax.toolbar.profile.logout"), "#{::Devise.cas_base_url}logout?#{{service: main_app.destroy_user_session_url}.to_query}" %></li>
-        <% else %>
-          <li><%= link_to t("hyrax.toolbar.profile.logout"), main_app.destroy_user_session_path %></li>
-        <% end %>
+        <li><%= link_to t("hyrax.toolbar.profile.logout"), main_app.destroy_user_session_path, 'data-turbolinks': 'false' %></li>
       </ul>
     </li><!-- /.btn-group -->
   <% else %>
     <li>
-      <%= link_to main_app.new_user_session_path do %>
+      <%= link_to main_app.new_user_session_path, 'data-turbolinks': 'false' do %>
         <span class="glyphicon glyphicon-log-in" aria-hidden="true"></span> <%= t("hyrax.toolbar.profile.login") %>
       <% end %>
     </li>

From 404fe817ba31460566f5205f0cb3591b27ad79dd Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 5 Dec 2019 15:39:31 +0000
Subject: [PATCH 066/258] Update devise.rb

better support for single-sign-out
---
 hyrax/config/initializers/devise.rb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/hyrax/config/initializers/devise.rb b/hyrax/config/initializers/devise.rb
index 84da8b7b..08e46d1c 100644
--- a/hyrax/config/initializers/devise.rb
+++ b/hyrax/config/initializers/devise.rb
@@ -318,6 +318,10 @@
   # e.g. the following option will change it from 'destination' to 'url'
   # config.cas_destination_logout_param_name = 'url'
 
+  # NB: these two parameters are necessary for single-sign-out to work correctly on the NIMS CAS server (Apereo CAS 6)
+  config.cas_logout_url_param = 'destination'
+  config.cas_destination_logout_param_name = 'service'
+
   # By default, devise_cas_authenticatable will create users.  If you would rather
   # require user records to already exist locally before they can authenticate via
   # CAS, uncomment the following line.

From 474bf64ee4179612c6481b61c05a836f48f597e6 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 5 Dec 2019 16:33:52 +0000
Subject: [PATCH 067/258] final tweaks

---
 hyrax/Dockerfile                    | 2 +-
 hyrax/Gemfile                       | 2 +-
 hyrax/app/models/user.rb            | 9 ---------
 hyrax/config/initializers/errbit.rb | 2 +-
 4 files changed, 3 insertions(+), 12 deletions(-)

diff --git a/hyrax/Dockerfile b/hyrax/Dockerfile
index c24807c4..b6572ade 100644
--- a/hyrax/Dockerfile
+++ b/hyrax/Dockerfile
@@ -61,7 +61,7 @@ RUN cd $APP_PRODUCTION && \
     && if [ "$RAILS_ENV" = "production" ]; then \
             bundle install --without test:development; \
         else \
-            bundle install --no-deployment; \
+            bundle install --without production --no-deployment; \
         fi \
     && mv Gemfile.lock Gemfile.lock.built_by_docker
 
diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 9a220d02..db24ad6e 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -76,7 +76,7 @@ gem 'devise_cas_authenticatable'
 
 gem 'riiif', '~> 2.0'
 
-group :production, :development do
+group :production do
   gem 'airbrake', '~> 5.0'
 end
 
diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index caca0b29..ca85e4cd 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -21,15 +21,6 @@ class User < ApplicationRecord
          :rememberable, :trackable, :lockable
          # NB: the :validatable module is not compatible with CAS authentication
 
-  # hack to ignore setting password when using CAS authentication
-  if ENV['MDR_DEVISE_AUTH_MODULE'] == 'cas_authenticatable'
-    attr_reader :password
-    def password=(new_password)
-      @password = new_password
-      self.encrypted_password = ''
-    end
-  end
-
   # Method added by Blacklight; Blacklight uses #to_s on your
   # user class to get a user-displayable login/identifier for
   # the account.
diff --git a/hyrax/config/initializers/errbit.rb b/hyrax/config/initializers/errbit.rb
index 96d2c51b..0416bff3 100644
--- a/hyrax/config/initializers/errbit.rb
+++ b/hyrax/config/initializers/errbit.rb
@@ -9,7 +9,7 @@
     config.environment = Rails.env
     config.ignore_environments = %w(development test)
   end
-else
+elsif defined?(Airbrake)
   # disable Airbrake if the env vars are not present
   puts 'Disabling Airbrake because the required env vars are not set'
   Airbrake.configure do |c|

From 67196fc5eb94c9f242f8316ab27e17322bf8045c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 6 Dec 2019 08:26:22 +0000
Subject: [PATCH 068/258] Bump puma from 3.12.1 to 3.12.2 in /hyrax

Bumps [puma](https://github.com/puma/puma) from 3.12.1 to 3.12.2.
- [Release notes](https://github.com/puma/puma/releases)
- [Changelog](https://github.com/puma/puma/blob/master/History.md)
- [Commits](https://github.com/puma/puma/compare/v3.12.1...v3.12.2)

Signed-off-by: dependabot[bot] <support@github.com>
---
 hyrax/Gemfile      | 2 +-
 hyrax/Gemfile.lock | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 5a5c8b40..1da0a2ea 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -9,7 +9,7 @@ end
 # Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
 gem 'rails', '>= 5.0.6'
 # Use Puma as the app server
-gem 'puma', '~> 3.0'
+gem 'puma', '~> 3.12'
 # Use SCSS for stylesheets
 gem 'sass-rails', '~> 5.0'
 # Use Uglifier as compressor for JavaScript assets
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index e189343d..50482af9 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -599,7 +599,7 @@ GEM
       method_source (~> 0.9.0)
     public_suffix (4.0.1)
     pul_uv_rails (2.0.1)
-    puma (3.12.1)
+    puma (3.12.2)
     qa (2.2.0)
       activerecord-import
       deprecation
@@ -906,7 +906,7 @@ DEPENDENCIES
   listen (~> 3.0.5)
   pg
   pry
-  puma (~> 3.0)
+  puma (~> 3.12)
   rails (>= 5.0.6)
   redis (~> 3.0)
   riiif (~> 2.0)

From 4ab7cebd826de0461e36dfb720863bdec5bc0fff Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 9 Dec 2019 16:40:28 +0000
Subject: [PATCH 069/258] conditional search fields

---
 hyrax/app/controllers/catalog_controller.rb | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index 54a10488..b7f0d4a8 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -66,9 +66,9 @@ def self.modified_field
     # solr fields to be displayed in the index (search results) view
     #   The ordering of the field names is the order of the display
     config.add_index_field solr_name('title', :stored_searchable), label: 'Title', itemprop: 'name', if: false
-    config.add_index_field solr_name('description', :stored_searchable), itemprop: 'description', helper_method: :iconify_auto_link
-    config.add_index_field solr_name('keyword', :stored_searchable), itemprop: 'keywords', link_to_search: solr_name('keyword', :facetable)
-    config.add_index_field solr_name('subject', :stored_searchable), itemprop: 'about', link_to_search: solr_name('subject', :facetable)
+    config.add_index_field solr_name('description', :stored_searchable), itemprop: 'description', helper_method: :iconify_auto_link, if: lambda { |context, field_config, document| context.can?(:read_abstract, document.hydra_model) }
+    config.add_index_field solr_name('keyword', :stored_searchable), itemprop: 'keywords', link_to_search: solr_name('keyword', :facetable), if: lambda { |context, field_config, document| context.can?(:read_keyword, document.hydra_model) }
+    config.add_index_field solr_name('subject', :stored_searchable), itemprop: 'about', link_to_search: solr_name('subject', :facetable), if: lambda { |context, field_config, document| context.can?(:read_subject, document.hydra_model) }
     # config.add_index_field solr_name('creator', :stored_searchable), itemprop: 'creator', link_to_search: solr_name('creator', :facetable)
     # config.add_index_field solr_name('contributor', :stored_searchable), itemprop: 'contributor', link_to_search: solr_name('contributor', :facetable)
     config.add_index_field solr_name('complex_person_other', :stored_searchable), itemprop: 'creator or contributor', link_to_search: solr_name('complex_person_other', :facetable)
@@ -80,15 +80,15 @@ def self.modified_field
     config.add_index_field solr_name('complex_person_operator', :stored_searchable), itemprop: 'operator', link_to_search: solr_name('complex_person_operator', :facetable)
     config.add_index_field solr_name('proxy_depositor', :symbol), label: 'Depositor', helper_method: :link_to_profile
     config.add_index_field solr_name('depositor'), label: 'Owner', helper_method: :link_to_profile
-    config.add_index_field solr_name('publisher', :stored_searchable), itemprop: 'publisher', link_to_search: solr_name('publisher', :facetable)
+    config.add_index_field solr_name('publisher', :stored_searchable), itemprop: 'publisher', link_to_search: solr_name('publisher', :facetable), if: lambda { |context, field_config, document| context.can?(:read_publisher, document.hydra_model) }
     # config.add_index_field solr_name('based_near_label', :stored_searchable), itemprop: 'contentLocation', link_to_search: solr_name('based_near_label', :facetable)
-    config.add_index_field solr_name('language', :stored_searchable), itemprop: 'inLanguage', link_to_search: solr_name('language', :facetable)
+    config.add_index_field solr_name('language', :stored_searchable), itemprop: 'inLanguage', link_to_search: solr_name('language', :facetable), if: lambda { |context, field_config, document| context.can?(:read_language, document.hydra_model) }
     config.add_index_field solr_name('date_uploaded', :stored_sortable, type: :date), itemprop: 'datePublished', helper_method: :human_readable_date
     config.add_index_field solr_name('date_modified', :stored_sortable, type: :date), itemprop: 'dateModified', helper_method: :human_readable_date
     config.add_index_field solr_name('date_created', :stored_searchable), itemprop: 'dateCreated'
-    config.add_index_field solr_name('rights_statement', :stored_searchable), helper_method: :rights_statement_links
+    config.add_index_field solr_name('rights_statement', :stored_searchable), helper_method: :rights_statement_links, if: lambda { |context, field_config, document| context.can?(:read_rights, document.hydra_model) }
     config.add_index_field solr_name('license', :stored_searchable), helper_method: :license_links
-    config.add_index_field solr_name('resource_type', :stored_searchable), label: 'Resource Type', link_to_search: solr_name('resource_type', :facetable)
+    config.add_index_field solr_name('resource_type', :stored_searchable), label: 'Resource Type', link_to_search: solr_name('resource_type', :facetable), if: lambda { |context, field_config, document| context.can?(:read_resource_type, document.hydra_model) }
     config.add_index_field solr_name('file_format', :stored_searchable), link_to_search: solr_name('file_format', :facetable)
     config.add_index_field solr_name('identifier', :stored_searchable), helper_method: :index_field_link, field_name: 'identifier'
     config.add_index_field solr_name('embargo_release_date', :stored_sortable, type: :date), label: 'Embargo release date', helper_method: :human_readable_date

From f38586535a062b0964b0dce39675f436b8bbfcb3 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 9 Dec 2019 18:25:05 +0000
Subject: [PATCH 070/258] new cucumber tests to verify metadata visibility

---
 .../{index.feature => catalog.feature}        | 10 ++++-
 hyrax/features/datasets/create.feature        |  2 +-
 .../step_definitions/dataset_steps.rb         | 38 ++++++++++++++++---
 .../step_definitions/initial_steps.rb         |  2 +-
 hyrax/spec/factories/dataset.rb               | 12 ++++++
 5 files changed, 56 insertions(+), 8 deletions(-)
 rename hyrax/features/datasets/{index.feature => catalog.feature} (74%)

diff --git a/hyrax/features/datasets/index.feature b/hyrax/features/datasets/catalog.feature
similarity index 74%
rename from hyrax/features/datasets/index.feature
rename to hyrax/features/datasets/catalog.feature
index a80cbcde..d822488f 100644
--- a/hyrax/features/datasets/index.feature
+++ b/hyrax/features/datasets/catalog.feature
@@ -1,7 +1,7 @@
 Feature: Datasets catalog index
 
   Background:
-    Given an initialised sysem with a default admin set, permission template and workflow
+    Given an initialised system with a default admin set, permission template and workflow
     And there is 1 open dataset
     And there are 2 authenticated datasets
     And there is 1 restricted dataset
@@ -10,6 +10,7 @@ Feature: Datasets catalog index
   Scenario: Unauthenticated user can only view open datasets
     When I navigate to the dataset catalog page
     Then I should see the open datasets
+    And I should see only the public metadata of the open datasets
     But I should not see the authenticated datasets
     And I should not see the restricted dataset
 
@@ -18,6 +19,8 @@ Feature: Datasets catalog index
     When I navigate to the dataset catalog page
     Then I should see the open datasets
     And I should see the authenticated datasets
+    And I should see both the public and restricted metadata of the open datasets
+    And I should see both the public and restricted metadata of the authenticated datasets
     But I should not see the restricted dataset
 
   Scenario: Researcher user can view open and authenticated datasets
@@ -25,6 +28,8 @@ Feature: Datasets catalog index
     When I navigate to the dataset catalog page
     Then I should see the open datasets
     And I should see the authenticated datasets
+    And I should see both the public and restricted metadata of the open datasets
+    And I should see both the public and restricted metadata of the authenticated datasets
     But I should not see the restricted dataset
 
   Scenario: Admin user can view open, authenticated and restricted datasets
@@ -33,6 +38,9 @@ Feature: Datasets catalog index
     Then I should see the open datasets
     And I should see the authenticated datasets
     And I should see the restricted dataset
+    And I should see both the public and restricted metadata of the open datasets
+    And I should see both the public and restricted metadata of the authenticated datasets
+    And I should see both the public and restricted metadata of the restricted datasets
 
 #Feature: データセット一覧を参照する
 #  現在登録されているユーザを確認するため
diff --git a/hyrax/features/datasets/create.feature b/hyrax/features/datasets/create.feature
index 2e4fbe8c..8e9fe8da 100644
--- a/hyrax/features/datasets/create.feature
+++ b/hyrax/features/datasets/create.feature
@@ -1,7 +1,7 @@
 Feature: Create a dataset
 
   Background:
-    Given an initialised sysem with a default admin set, permission template and workflow
+    Given an initialised system with a default admin set, permission template and workflow
 
   Scenario: Cannot create a dataset as a Non-Researcher user
     Given I am logged in as a nims_other user
diff --git a/hyrax/features/step_definitions/dataset_steps.rb b/hyrax/features/step_definitions/dataset_steps.rb
index 27282fc6..16308460 100644
--- a/hyrax/features/step_definitions/dataset_steps.rb
+++ b/hyrax/features/step_definitions/dataset_steps.rb
@@ -1,6 +1,6 @@
 Given(/^there (?:are|is) (\d+) (open|authenticated|embargo|lease|restricted) datasets?$/) do |number, access|
   @datasets ||= {}
-  @datasets[access] = FactoryBot.create_list(:dataset, number, access.to_sym).each do |obj|
+  @datasets[access] = FactoryBot.create_list(:dataset, number, access.to_sym, :with_description_seq, :with_keyword_seq, :with_subject_seq).each do |obj|
     ActiveFedora::SolrService.add(obj.to_solr)
   end
   ActiveFedora::SolrService.commit
@@ -65,9 +65,7 @@
 
 Then(/^I should see the (open|authenticated|embargo|lease|restricted) datasets?$/) do |access|
   # first, verify @datasets is present and has some data
-  expect(@datasets).to be_present
   expect(@datasets[access]).to be_present
-  expect(@datasets[access].length).to_not be_zero
 
   # next, verify there is a link to each dataset (using a regular expression to allow for the locale parameter)
   @datasets[access].each do |dataset|
@@ -77,12 +75,42 @@
 
 Then(/^I should not see the (open|authenticated|embargo|lease|restricted) datasets?$/) do |access|
   # first, verify @datasets is present and has some data
-  expect(@datasets).to be_present
   expect(@datasets[access]).to be_present
-  expect(@datasets[access].length).to_not be_zero
 
   # next, verify there is a link to each dataset (using a regular expression to allow for the locale parameter)
   @datasets[access].each do |dataset|
     expect(page).to_not have_link(dataset.title.first, href: Regexp.new(hyrax_dataset_path(dataset)))
   end
 end
+
+Then(/^I should see only the public metadata of the (open|authenticated|embargo|lease|restricted) datasets?$/) do |access|
+  # first, verify @datasets is present and has some data
+  expect(@datasets[access]).to be_present
+
+  @datasets[access].each do |dataset|
+    # check public metadata is visible
+    [:subject, :keyword].each do |field|
+      expect(page).to have_css('div.metadata dl dt', text: Regexp.new(field.to_s, Regexp::IGNORECASE))
+      expect(page).to have_css('div.metadata dl dd', text: dataset.send(field).first)
+    end
+
+    # check restricted metadata is not visible
+    [:description].each do |field|
+      expect(page).not_to have_css('div.metadata dl dt', text: Regexp.new(field.to_s, Regexp::IGNORECASE))
+      expect(page).not_to have_css('div.metadata dl dd', text: dataset.send(field).first)
+    end
+  end
+end
+
+Then(/^I should see both the public and restricted metadata of the (open|authenticated|embargo|lease|restricted) datasets?$/) do |access|
+  # first, verify @datasets is present and has some data
+  expect(@datasets[access]).to be_present
+
+  @datasets[access].each do |dataset|
+    # check public and restricted metadata is visible
+    [:description, :subject, :keyword].each do |field|
+      expect(page).to have_css('div.metadata dl dt', text: Regexp.new(field.to_s, Regexp::IGNORECASE))
+      expect(page).to have_css('div.metadata dl dd', text: dataset.send(field).first)
+    end
+  end
+end
diff --git a/hyrax/features/step_definitions/initial_steps.rb b/hyrax/features/step_definitions/initial_steps.rb
index 61b3db90..a0f6ebf2 100644
--- a/hyrax/features/step_definitions/initial_steps.rb
+++ b/hyrax/features/step_definitions/initial_steps.rb
@@ -1,4 +1,4 @@
-Given(/^an initialised sysem with a default admin set, permission template and workflow$/) do
+Given(/^an initialised system with a default admin set, permission template and workflow$/) do
   @admin_set_id = AdminSet.find_or_create_default_admin_set_id
   @permission_template =  Hyrax::PermissionTemplate.find_or_create_by!(source_id: @admin_set_id)
   @workflow = Sipity::Workflow.create!(active: true, name: 'test-workflow', permission_template: @permission_template)
diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 2d144877..9ffd2e3b 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -29,6 +29,10 @@
       title { ["Restricted Dataset"] }
     end
 
+    trait :with_description_seq do
+      sequence(:description) { |n| ["Abstract-Description-#{n}"] }
+    end
+
     trait :with_alternative_title do
       alternative_title { 'Alternative-Title-123' }
     end
@@ -37,10 +41,18 @@
       keyword { ['Keyword-123'] }
     end
 
+    trait :with_keyword_seq do
+      sequence(:keyword) { |n| ["Keyword-#{n}"] }
+    end
+
     trait :with_subject do
       subject { ['Subject-123'] }
     end
 
+    trait :with_subject_seq do
+      sequence(:subject) { |n| ["Subject-#{n}"] }
+    end
+
     trait :with_language do
       language { ['Faroese'] }
     end

From 88085aec3d5dacc6c6ccaf743764cea37558e652 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 10 Dec 2019 12:20:30 +0000
Subject: [PATCH 071/258] new view test for abstract

---
 hyrax/spec/factories/image.rb                 |  5 +++
 hyrax/spec/factories/publication.rb           |  5 +++
 hyrax/spec/views/hyrax/base/show.html_spec.rb | 39 +++++++++++++++++++
 .../datasets/_attribute_rows.html_spec.rb     |  6 +--
 .../hyrax/images/_attribute_rows.html_spec.rb |  4 +-
 .../publications/_attribute_rows.html_spec.rb |  4 +-
 6 files changed, 56 insertions(+), 7 deletions(-)
 create mode 100644 hyrax/spec/views/hyrax/base/show.html_spec.rb

diff --git a/hyrax/spec/factories/image.rb b/hyrax/spec/factories/image.rb
index fa5bfdda..9510b9fc 100644
--- a/hyrax/spec/factories/image.rb
+++ b/hyrax/spec/factories/image.rb
@@ -7,6 +7,11 @@
     override_new_record
   end
 
+  trait :open do
+    visibility { 'open' }
+    title { ["Open Image"] }
+  end
+
   trait :with_alternative_title do
     alternative_title { 'Alternative-Title-123' }
   end
diff --git a/hyrax/spec/factories/publication.rb b/hyrax/spec/factories/publication.rb
index ce334458..972ecd57 100644
--- a/hyrax/spec/factories/publication.rb
+++ b/hyrax/spec/factories/publication.rb
@@ -6,6 +6,11 @@
     skip_create
     override_new_record
 
+    trait :open do
+      visibility { 'open' }
+      title { ["Open Publication"] }
+    end
+
     trait :with_people do
       complex_person_attributes {
         [
diff --git a/hyrax/spec/views/hyrax/base/show.html_spec.rb b/hyrax/spec/views/hyrax/base/show.html_spec.rb
new file mode 100644
index 00000000..37fb0011
--- /dev/null
+++ b/hyrax/spec/views/hyrax/base/show.html_spec.rb
@@ -0,0 +1,39 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'hyrax/base/show' do
+  let(:dataset) { create(:dataset, :open, :with_description_seq) }
+  let(:presenter) { Hyrax::DatasetPresenter.new(SolrDocument.new(dataset.to_solr), Ability.new(user), controller.request) }
+
+  before do
+    allow(controller).to receive(:current_user).and_return(user)
+    login_as user if user.present?
+    assign(:presenter, presenter)
+    render
+  end
+
+  # This test confirms the abstract is only visible if you are logged in
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'does not show the abstract' do
+      expect(rendered).to have_css('h2', text: dataset.title.first)
+      expect(rendered).not_to have_css('p.work_description', text: dataset.description.first)
+    end
+  end
+
+  context 'authenticated non-researcher' do
+    let(:user) { build(:user, :nims_other) }
+    it 'shows the abstract' do
+      expect(rendered).to have_css('h2', text: dataset.title.first)
+      expect(rendered).to have_css('p.work_description', text: dataset.description.first)
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { build(:user, :nims_researcher) }
+    it 'shows the abstract' do
+      expect(rendered).to have_css('h2', text: dataset.title.first)
+      expect(rendered).to have_css('p.work_description', text: dataset.description.first)
+    end
+  end
+end
diff --git a/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
index 974a23e6..05353887 100644
--- a/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
@@ -3,10 +3,10 @@
 
 RSpec.describe 'hyrax/datasets/_attribute_rows' do
   let(:partial) { 'hyrax/datasets/attribute_rows' }
-  let(:dataset) { build(:dataset, :with_alternative_title, :with_complex_person, :with_keyword, :with_subject, :with_language,
-                        :with_publisher, :with_complex_date, :with_complex_identifier, :with_complex_rights,
+  let(:dataset) { build(:dataset, :open, :with_alternative_title, :with_complex_person, :with_keyword, :with_subject,
+                        :with_language, :with_publisher, :with_complex_date, :with_complex_identifier, :with_complex_rights,
                         :with_complex_version, :with_resource_type, :with_complex_relation, :with_source) }
-  let(:presenter) { Hyrax::DatasetPresenter.new(SolrDocument.new(dataset.to_solr), Ability.new(user)) }
+  let(:presenter) { Hyrax::DatasetPresenter.new(SolrDocument.new(dataset.to_solr), Ability.new(user), controller.request) }
 
   before do
     allow(controller).to receive(:current_user).and_return(user)
diff --git a/hyrax/spec/views/hyrax/images/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/images/_attribute_rows.html_spec.rb
index 4dc57d44..ffeca685 100644
--- a/hyrax/spec/views/hyrax/images/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/images/_attribute_rows.html_spec.rb
@@ -3,11 +3,11 @@
 
 RSpec.describe 'hyrax/images/_attribute_rows' do
   let(:partial) { 'hyrax/images/attribute_rows' }
-  let(:image) { build(:image, :with_alternative_title, :with_subject, :with_publisher, :with_language,
+  let(:image) { build(:image, :open, :with_alternative_title, :with_subject, :with_publisher, :with_language,
                             :with_keyword, :with_resource_type, :with_rights_statement, :with_complex_date,
                             :with_complex_identifier, :with_complex_person, :with_complex_rights,
                             :with_complex_version) }
-  let(:presenter) { Hyrax::ImagePresenter.new(SolrDocument.new(image.to_solr), Ability.new(user)) }
+  let(:presenter) { Hyrax::ImagePresenter.new(SolrDocument.new(image.to_solr), Ability.new(user), controller.request) }
 
   before do
     allow(controller).to receive(:current_user).and_return(user)
diff --git a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
index ce701fc2..bfe0a036 100644
--- a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
@@ -3,11 +3,11 @@
 
 RSpec.describe 'hyrax/publications/_attribute_rows' do
   let(:partial) { 'hyrax/publications/attribute_rows' }
-  let(:publication) { build(:publication, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
+  let(:publication) { build(:publication, :open, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
                         :with_publisher, :with_complex_date, :with_complex_identifier, :with_rights_statement, :with_complex_rights,
                         :with_complex_version, :with_resource_type, :with_source, :with_issue, :with_complex_source, :with_complex_event,
                         :with_place, :with_table_of_contents, :with_number_of_pages) }
-  let(:presenter) { Hyrax::PublicationPresenter.new(SolrDocument.new(publication.to_solr), Ability.new(user)) }
+  let(:presenter) { Hyrax::PublicationPresenter.new(SolrDocument.new(publication.to_solr), Ability.new(user), controller.request) }
 
   before do
     allow(controller).to receive(:current_user).and_return(user)

From 64d7550c15e51b9e235ec86416fd84fc86632147 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 10 Dec 2019 13:24:57 +0000
Subject: [PATCH 072/258] override and extra test to confirm zotero open url
 formatter

---
 .../formatters/open_url_formatter.rb          | 41 +++++++++++++++++++
 hyrax/spec/views/hyrax/base/show.html_spec.rb |  3 ++
 2 files changed, 44 insertions(+)
 create mode 100644 hyrax/app/helpers/hyrax/citations_behaviors/formatters/open_url_formatter.rb

diff --git a/hyrax/app/helpers/hyrax/citations_behaviors/formatters/open_url_formatter.rb b/hyrax/app/helpers/hyrax/citations_behaviors/formatters/open_url_formatter.rb
new file mode 100644
index 00000000..879dca32
--- /dev/null
+++ b/hyrax/app/helpers/hyrax/citations_behaviors/formatters/open_url_formatter.rb
@@ -0,0 +1,41 @@
+# override - hyrax-2.6.0
+
+module Hyrax
+  module CitationsBehaviors
+    module Formatters
+      class OpenUrlFormatter < BaseFormatter
+        def format(work)
+          export_text = []
+          export_text << "url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2Fblacklight.rubyforge.org%3Agenerator"
+          FIELD_MAP.each do |element, kev|
+            next unless work.respond_to?(element)
+            # ensure the abstract is not visible unless the user is authorised to view it
+            next if element == :description && view_context.cannot?(:read_abstract, work.model_name.name.constantize)
+            values = work.send(element)
+            Array.wrap(values).each do |value|
+              next if value.blank?
+              export_text << "rft.#{kev}=#{CGI.escape(value.to_s)}"
+            end
+          end
+          export_text.join('&') if export_text.present?
+        end
+
+        FIELD_MAP = {
+            title: 'title',
+            creator: 'creator',
+            subject: 'subject',
+            description: 'description',
+            publisher: 'publisher',
+            contributor: 'contributor',
+            date_created: 'date',
+            resource_type: 'format',
+            identifier: 'identifier',
+            language: 'language',
+            keyword: 'relation',
+            based_near: 'coverage',
+            license: 'license'
+        }.freeze
+      end
+    end
+  end
+end
diff --git a/hyrax/spec/views/hyrax/base/show.html_spec.rb b/hyrax/spec/views/hyrax/base/show.html_spec.rb
index 37fb0011..d84dfdb8 100644
--- a/hyrax/spec/views/hyrax/base/show.html_spec.rb
+++ b/hyrax/spec/views/hyrax/base/show.html_spec.rb
@@ -18,6 +18,7 @@
     it 'does not show the abstract' do
       expect(rendered).to have_css('h2', text: dataset.title.first)
       expect(rendered).not_to have_css('p.work_description', text: dataset.description.first)
+      expect(rendered).not_to have_css("span.Z3988[title*='rft.description=#{CGI.escape(dataset.description.first)}']")
     end
   end
 
@@ -26,6 +27,7 @@
     it 'shows the abstract' do
       expect(rendered).to have_css('h2', text: dataset.title.first)
       expect(rendered).to have_css('p.work_description', text: dataset.description.first)
+      expect(rendered).to have_css("span.Z3988[title*='rft.description=#{CGI.escape(dataset.description.first)}']")
     end
   end
 
@@ -34,6 +36,7 @@
     it 'shows the abstract' do
       expect(rendered).to have_css('h2', text: dataset.title.first)
       expect(rendered).to have_css('p.work_description', text: dataset.description.first)
+      expect(rendered).to have_css("span.Z3988[title*='rft.description=#{CGI.escape(dataset.description.first)}']")
     end
   end
 end

From 70685239172dcc3a7e251a61a729d5ba0f1eee73 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 10 Dec 2019 15:55:03 +0000
Subject: [PATCH 073/258] ensure twitter card does not include abstract if
 unauthenticated

---
 hyrax/app/views/shared/_citations.html.erb    | 36 +++++++++++++++++
 .../datasets/_attribute_rows.html_spec.rb     |  2 +-
 .../spec/views/shared/_citations.html_spec.rb | 39 +++++++++++++++++++
 3 files changed, 76 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/app/views/shared/_citations.html.erb
 create mode 100644 hyrax/spec/views/shared/_citations.html_spec.rb

diff --git a/hyrax/app/views/shared/_citations.html.erb b/hyrax/app/views/shared/_citations.html.erb
new file mode 100644
index 00000000..4fa1a342
--- /dev/null
+++ b/hyrax/app/views/shared/_citations.html.erb
@@ -0,0 +1,36 @@
+<% content_for(:twitter_meta) do %>
+  <meta name="twitter:card" content="product" />
+  <meta name="twitter:site" content="<%= t('hyrax.product_twitter_handle') %>" />
+  <meta name="twitter:creator" content="<%= @presenter.tweeter %>" />
+  <meta property="og:site_name" content="<%= application_name %>" />
+  <meta property="og:type" content="object" />
+  <meta property="og:title" content="<%= @presenter.title.first %>" />
+  <% if can? :read_abstract, @presenter.model_name.name.constantize %>
+  <meta property="og:description" content="<%= @presenter.description.first.truncate(200) rescue @presenter.title.first %>" />
+  <% else %>
+  <meta property="og:description" content="<%= @presenter.title.first %>" />
+  <% end %>
+  <meta property="og:image" content="<%= @presenter.download_url %>" />
+  <meta property="og:url" content="<%= polymorphic_url([main_app, @presenter]) %>" />
+  <meta name="twitter:data1" content="<%= @presenter.keyword.join(', ') %>" />
+  <meta name="twitter:label1" content="Keywords" />
+  <meta name="twitter:data2" content="<%= @presenter.rights_statement.first %>" />
+  <meta name="twitter:label2" content="Rights Statement" />
+<% end %>
+
+<% content_for(:gscholar_meta) do %>
+  <meta name="citation_title" content="<%= @presenter.title.first %>" />
+  <% @presenter.creator.each do |creator| %>
+    <meta name="citation_author" content="<%= creator %>" />
+  <% end %>
+  <meta name="citation_publication_date" content="<%= @presenter.date_created.first %>" />
+  <meta name="citation_pdf_url" content="<%= @presenter.download_url %>" />
+  <!-- Hyrax does not yet support these metadata -->
+  <!--
+    <meta name="citation_journal_title" content=""/>
+    <meta name="citation_volume" content=""/>
+    <meta name="citation_issue" content=""/>
+    <meta name="citation_firstpage" content=""/>
+    <meta name="citation_lastpage" content=""/>
+  -->
+<% end %>
diff --git a/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
index 05353887..3e558c3b 100644
--- a/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
@@ -3,7 +3,7 @@
 
 RSpec.describe 'hyrax/datasets/_attribute_rows' do
   let(:partial) { 'hyrax/datasets/attribute_rows' }
-  let(:dataset) { build(:dataset, :open, :with_alternative_title, :with_complex_person, :with_keyword, :with_subject,
+  let(:dataset) { create(:dataset, :open, :with_alternative_title, :with_complex_person, :with_keyword, :with_subject,
                         :with_language, :with_publisher, :with_complex_date, :with_complex_identifier, :with_complex_rights,
                         :with_complex_version, :with_resource_type, :with_complex_relation, :with_source) }
   let(:presenter) { Hyrax::DatasetPresenter.new(SolrDocument.new(dataset.to_solr), Ability.new(user), controller.request) }
diff --git a/hyrax/spec/views/shared/_citations.html_spec.rb b/hyrax/spec/views/shared/_citations.html_spec.rb
new file mode 100644
index 00000000..6e2739c2
--- /dev/null
+++ b/hyrax/spec/views/shared/_citations.html_spec.rb
@@ -0,0 +1,39 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'shared/_citations' do
+  let(:dataset) { create(:dataset, :open, :with_description_seq) }
+  let(:presenter) { Hyrax::DatasetPresenter.new(SolrDocument.new(dataset.to_solr), Ability.new(user), controller.request) }
+
+  before do
+    allow(controller).to receive(:current_user).and_return(user)
+    login_as user if user.present?
+    assign(:presenter, presenter)
+    render
+    render inline: '<%= yield :twitter_meta %>'
+  end
+
+  # This test confirms the abstract is only visible if you are logged in
+  describe 'og:description' do
+    context 'unauthenticated user' do
+      let(:user) { nil }
+      it 'does not show the abstract and shows the title instead' do
+        expect(rendered).to have_css("meta[property='og:description'][content='#{dataset.title.first}']", visible: false)
+      end
+    end
+
+    context 'authenticated non-researcher' do
+      let(:user) { build(:user, :nims_other) }
+      it 'shows the abstract' do
+        expect(rendered).to have_css("meta[property='og:description'][content='#{dataset.description.first}']", visible: false)
+      end
+    end
+
+    context 'authenticated NIMS Researcher' do
+      let(:user) { create(:user, :nims_researcher) }
+      it 'shows the abstract' do
+        expect(rendered).to have_css("meta[property='og:description'][content='#{dataset.description.first}']", visible: false)
+      end
+    end
+  end
+end

From 9615c1a7d936c84c758d993361eae054f16c5d6a Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 10 Dec 2019 18:56:10 +0000
Subject: [PATCH 074/258] users cucumber

---
 .../step_definitions/dataset_steps.rb         |  2 +-
 hyrax/features/step_definitions/user_steps.rb | 33 +++++++++++++++
 hyrax/features/users/index.feature            | 40 +++++++++++++++++++
 3 files changed, 74 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/features/users/index.feature

diff --git a/hyrax/features/step_definitions/dataset_steps.rb b/hyrax/features/step_definitions/dataset_steps.rb
index 7c4d41c8..3ad67f73 100644
--- a/hyrax/features/step_definitions/dataset_steps.rb
+++ b/hyrax/features/step_definitions/dataset_steps.rb
@@ -7,7 +7,7 @@
 end
 
 When(/^I navigate to the new dataset page$/) do
-  visit '/dashboard'
+  visit hyrax.dashboard_path  # /dashboard
   click_link "Works"
   click_link "Add new work"
 
diff --git a/hyrax/features/step_definitions/user_steps.rb b/hyrax/features/step_definitions/user_steps.rb
index ad71c8ae..d90406b1 100644
--- a/hyrax/features/step_definitions/user_steps.rb
+++ b/hyrax/features/step_definitions/user_steps.rb
@@ -12,3 +12,36 @@
   step "a #{user_type} user"
   step 'I am logged in'
 end
+
+Given(/^there (?:are|is) (\d+) (general|admin) users?$/) do |number, user_type|
+  @users ||= {}
+  @users[user_type] = FactoryBot.create_list(:user, number, user_type.to_sym)
+end
+
+When(/^I navigate to the users list$/) do
+  visit hyrax.users_path
+end
+
+Then(/^I should see the (general|admin) users?$/) do |user_type|
+  # first, verify @users is present and has some data
+  expect(@users[user_type]).to be_present
+
+  # next, verify there is a link to each dataset (using a regular expression to allow for the locale parameter)
+  @users[user_type].each do |user|
+    expect(page).to have_link(user.username, href: Regexp.new(hyrax.user_path(user)))
+  end
+end
+
+Then(/^I should not see the (general|admin) users?$/) do |user_type|
+  # first, verify @users is present and has some data
+  expect(@users[user_type]).to be_present
+
+  # next, verify there is a link to each dataset (using a regular expression to allow for the locale parameter)
+  @users[user_type].each do |user|
+    expect(page).to_not have_link(user.username, href: Regexp.new(hyrax.user_path(user)))
+  end
+end
+
+Then(/^I should be redirected to the login page$/) do
+  expect(current_path).to eql(new_user_session_path)
+end
diff --git a/hyrax/features/users/index.feature b/hyrax/features/users/index.feature
new file mode 100644
index 00000000..a36046a6
--- /dev/null
+++ b/hyrax/features/users/index.feature
@@ -0,0 +1,40 @@
+Feature: Users index page
+
+  Background:
+    Given there are 3 general users
+
+  Scenario: Unauthenticated user cannot view users
+    When I navigate to the users list
+    Then I should not see the general users
+    And I should be redirected to the login page
+
+  Scenario: General user can view users
+    Given I am logged in as an general user
+    When I navigate to the users list
+    Then I should see the general users
+
+  Scenario: Admin user can view users
+    Given I am logged in as an admin user
+    When I navigate to the users list
+    Then I should see the general users
+
+#Feature: ユーザ一覧を参照する
+#現在登録されているユーザを確認するため
+#
+#  Scenario: 非ログインユーザがユーザ一覧を表示する
+#    Given ログインしない
+#    Given ユーザが5件登録されている
+#    When ユーザ一覧画面を開く
+#    Then ユーザが5件とも表示されない
+#
+#  Scenario: 一般ユーザがユーザ一覧を表示する
+#    Given 一般ユーザでログインする
+#    Given ユーザが5件登録されている
+#    When ユーザ一覧画面を開く
+#    Then ユーザが5件表示される
+#
+#  Scenario: 管理者ユーザがユーザ一覧を表示する
+#    Given 管理者でログインする
+#    Given ユーザが5件登録されている
+#    When ユーザ一覧画面を開く
+#    Then ユーザが5件表示される

From ef983e86704de182fc6a3af1314d281b7dbccedc Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Wed, 11 Dec 2019 12:28:51 +0900
Subject: [PATCH 075/258] hide user list from general users

---
 .../app/controllers/hyrax/users_controller.rb |  9 +++++++++
 hyrax/app/models/ability.rb                   | 12 ++++++++++-
 .../features/step_definitions/users_steps.rb  | 20 +++++++++++++++++++
 hyrax/features/users/index.feature            | 20 +++++++++++++++++++
 4 files changed, 60 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/app/controllers/hyrax/users_controller.rb
 create mode 100644 hyrax/features/step_definitions/users_steps.rb
 create mode 100644 hyrax/features/users/index.feature

diff --git a/hyrax/app/controllers/hyrax/users_controller.rb b/hyrax/app/controllers/hyrax/users_controller.rb
new file mode 100644
index 00000000..737f0ec6
--- /dev/null
+++ b/hyrax/app/controllers/hyrax/users_controller.rb
@@ -0,0 +1,9 @@
+require_dependency Hyrax::Engine.config.root.join('app', 'controllers', 'hyrax', 'users_controller.rb').to_s
+
+class Hyrax::UsersController
+  def index
+    authenticate_user! if Flipflop.hide_users_list?
+    authorize! :index, ::User
+    @users = search(params[:uq])
+  end
+end
diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index b9bc6f37..bb18849e 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -3,9 +3,11 @@ class Ability
   include Hyrax::Ability
 
   # Registered user can only create datasets and publications
+  # Only admin can view the user list
   self.ability_logic += [
     :everyone_can_create_dataset,
-    :everyone_can_create_publication
+    :everyone_can_create_publication,
+    :only_admin_can_view_user_list
   ]
 
   # Define any customized permissions here.
@@ -36,4 +38,12 @@ def everyone_can_create_publication
     return unless registered_user?
     can :create, [::Publication]
   end
+
+  def only_admin_can_view_user_list
+    if current_user.admin?
+      can :index, ::User
+    else
+      cannot :index, ::User
+    end
+  end
 end
diff --git a/hyrax/features/step_definitions/users_steps.rb b/hyrax/features/step_definitions/users_steps.rb
new file mode 100644
index 00000000..22a91e44
--- /dev/null
+++ b/hyrax/features/step_definitions/users_steps.rb
@@ -0,0 +1,20 @@
+When("I navigate to the user list page") do
+  visit '/users'
+end
+
+Then("I should not see the user list") do
+  expect(page).not_to have_content 'Search Users'
+end
+
+Then("I should get 'need to sign in'") do
+  expect(page).to have_content 'You need to sign in or sign up before continuing.'
+end
+
+Then("I should get 'not authorized'") do
+  expect(page).to have_content 'You are not authorized to access this page.'
+end
+
+Then("I should see the user list") do
+  expect(@user.admin?).to be_truthy
+  expect(page).to have_content 'Search Users'
+end
diff --git a/hyrax/features/users/index.feature b/hyrax/features/users/index.feature
new file mode 100644
index 00000000..fd67b96d
--- /dev/null
+++ b/hyrax/features/users/index.feature
@@ -0,0 +1,20 @@
+Feature: Users index
+
+  Background:
+    Given an initialised sysem with a default admin set, permission template and workflow
+
+  Scenario: Unauthenticated user can not view the user list
+    When I navigate to the user list page
+    Then I should not see the user list
+    And I should get 'need to sign in'
+
+  Scenario: General user can not view the user list
+    Given I am logged in as a general user
+    When I navigate to the user list page
+    Then I should not see the user list
+    And I should get 'not authorized'
+
+  Scenario: Admin user can view the user list
+    Given I am logged in as an admin user
+    When I navigate to the user list page
+    Then I should see the user list

From 4ef0925e55df667f2fbad4ce4bb7866808670786 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 2 Oct 2019 00:18:15 +0900
Subject: [PATCH 076/258] add "readonly" option to disable name and email

---
 .../app/views/hyrax/contact_form/new.html.erb | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/contact_form/new.html.erb

diff --git a/hyrax/app/views/hyrax/contact_form/new.html.erb b/hyrax/app/views/hyrax/contact_form/new.html.erb
new file mode 100644
index 00000000..c9076662
--- /dev/null
+++ b/hyrax/app/views/hyrax/contact_form/new.html.erb
@@ -0,0 +1,50 @@
+<div class="alert alert-info">
+  <%= render 'directions' %>
+</div>
+
+<h1>
+    <%= t('hyrax.contact_form.header') %>
+</h1>
+
+<% if user_signed_in? %>
+  <% nm = current_user.name %>
+  <% em = current_user.email %>
+<% else %>
+  <% nm = '' %>
+  <% em = '' %>
+<% end %>
+
+<%= form_for @contact_form, url: hyrax.contact_form_index_path,
+                            html: { class: 'form-horizontal' } do |f| %>
+  <%= f.text_field :contact_method, class: 'hide' %>
+  <div class="form-group">
+    <%= f.label :category, t('hyrax.contact_form.type_label'), class: "col-sm-2 control-label" %>
+    <% issue_types = Hyrax::ContactForm.issue_types_for_locale.dup %>
+    <% issue_types.unshift([t('hyrax.contact_form.select_type'), nil]) %>
+    <div class="col-sm-10">
+      <%= f.select 'category', options_for_select(issue_types), {}, {class: 'form-control', required: true } %>
+    </div>
+  </div>
+
+  <div class="form-group">
+    <%= f.label :name, t('hyrax.contact_form.name_label'), class: "col-sm-2 control-label" %>
+    <div class="col-sm-10"><%= f.text_field :name, value: nm, class: 'form-control', required: true, readonly: user_signed_in? %></div>
+  </div>
+
+  <div class="form-group">
+    <%= f.label :email, t('hyrax.contact_form.email_label'), class: "col-sm-2 control-label" %>
+    <div class="col-sm-10"><%= f.text_field :email, value: em, class: 'form-control', required: true, readonly: user_signed_in? %></div>
+  </div>
+
+  <div class="form-group">
+    <%= f.label :subject, t('hyrax.contact_form.subject_label'), class: "col-sm-2 control-label" %>
+    <div class="col-sm-10"><%= f.text_field :subject, class: 'form-control', required: true %></div>
+  </div>
+
+  <div class="form-group">
+    <%= f.label :message, t('hyrax.contact_form.message_label'), class: "col-sm-2 control-label" %>
+    <div class="col-sm-10"><%= f.text_area :message, rows: 4, class: 'form-control', required: true %></div>
+  </div>
+
+  <%= f.submit value: t('hyrax.contact_form.button_label'), class: "btn btn-primary" %>
+<% end %>

From 67b9c00942f8147b3f14ce5005f91edbac895af2 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 12 Oct 2019 20:30:03 +0900
Subject: [PATCH 077/258] add feature spec file for the contact form

---
 hyrax/spec/features/contact_form_spec.rb | 27 ++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 hyrax/spec/features/contact_form_spec.rb

diff --git a/hyrax/spec/features/contact_form_spec.rb b/hyrax/spec/features/contact_form_spec.rb
new file mode 100644
index 00000000..8ad793fc
--- /dev/null
+++ b/hyrax/spec/features/contact_form_spec.rb
@@ -0,0 +1,27 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+# NOTE: If you generated more than one work, you have to set "js: true"
+RSpec.feature 'Show Contact form', js: false do
+  context 'a logged in user' do
+    let(:user_attributes) do
+      { email: 'test@example.com' }
+    end
+    let(:user) do
+      User.new(user_attributes) { |u| u.save(validate: false) }
+    end
+
+    before do
+      login_as user
+    end
+
+    scenario do
+      visit '/contact'
+
+      it "should display contact form" do
+        expect(page).to have_field 'Your Name', with: user.username, readonly: true
+        expect(page).to have_field 'Your Email', with: user.email, readonly: true
+      end
+    end
+  end
+end

From f132c104c6cf7a9bcbe2a4c707f68d02bf6e6930 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 12 Dec 2019 15:20:18 +0900
Subject: [PATCH 078/258] add feature files

---
 hyrax/features/contact/contact.feature        | 24 +++++++++++++++++++
 .../step_definitions/contact_steps.rb         | 23 ++++++++++++++++++
 2 files changed, 47 insertions(+)
 create mode 100644 hyrax/features/contact/contact.feature
 create mode 100644 hyrax/features/step_definitions/contact_steps.rb

diff --git a/hyrax/features/contact/contact.feature b/hyrax/features/contact/contact.feature
new file mode 100644
index 00000000..3de62266
--- /dev/null
+++ b/hyrax/features/contact/contact.feature
@@ -0,0 +1,24 @@
+Feature: Contact form
+
+  Background:
+    Given an initialised sysem with a default admin set, permission template and workflow
+
+  Scenario: Unauthenticated user can edit name and email in the contact form
+    When I navigate to the contact form
+    Then I should see the contact form
+    And Name field is not readonly
+    And Email field is not readonly
+
+  Scenario: General user cannot edit name and email in the contact form
+    Given I am logged in as a general user
+    When I navigate to the contact form
+    Then I should see the contact form
+    But Name field is readonly
+    And Email field is readonly
+
+  Scenario: Admin user cannot edit name and email in the contact form
+    Given I am logged in as an admin user
+    When I navigate to the contact form
+    Then I should see the contact form
+    But Name field is readonly
+    And Email field is readonly
diff --git a/hyrax/features/step_definitions/contact_steps.rb b/hyrax/features/step_definitions/contact_steps.rb
new file mode 100644
index 00000000..c69be310
--- /dev/null
+++ b/hyrax/features/step_definitions/contact_steps.rb
@@ -0,0 +1,23 @@
+When("I navigate to the contact form") do
+  visit '/contact'
+end
+
+Then("I should see the contact form") do
+  expect(page).to have_content('Contact Form')
+end
+
+Then("Name field is not readonly") do
+  expect(page).to have_field('Your Name', type: 'text', readonly: false)
+end
+
+Then("Email field is not readonly") do
+  expect(page).to have_field('Your Email', type: 'text', readonly: false)
+end
+
+Then("Name field is readonly") do
+  expect(page).to have_field('Your Email', type: 'text', readonly: true)
+end
+
+Then("Email field is readonly") do
+  expect(page).to have_field('Your Email', type: 'text', readonly: true)
+end

From 0ec2d8df6eb75bebd2cc2cef666f372675dc9e3a Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Thu, 12 Dec 2019 10:17:35 +0000
Subject: [PATCH 079/258] fixes operator organization link

---
 hyrax/app/renderers/nested_attribute_renderer.rb | 2 ++
 hyrax/features/datasets/search_links.feature     | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/renderers/nested_attribute_renderer.rb b/hyrax/app/renderers/nested_attribute_renderer.rb
index ad2b3f9a..bf62cbca 100644
--- a/hyrax/app/renderers/nested_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_attribute_renderer.rb
@@ -99,6 +99,8 @@ def get_field(field, label)
       :complex_purchase_record_supplier
     when field == :complex_specimen_type && label == 'Manufacturer'
       :complex_purchase_record_manufacturer
+    when field == :complex_person_operator && label == 'Organization'
+      :complex_person_operator_organization
     else
       field
     end
diff --git a/hyrax/features/datasets/search_links.feature b/hyrax/features/datasets/search_links.feature
index 798e423d..5c879717 100644
--- a/hyrax/features/datasets/search_links.feature
+++ b/hyrax/features/datasets/search_links.feature
@@ -27,7 +27,7 @@ Feature: Search links on a dataset
       | Instrument title           | /catalog?f%5Bcomplex_instrument_sim%5D%5B%5D=Instrument+title                         |
       | Foo                        | /catalog?f%5Binstrument_manufacturer_sim%5D%5B%5D=Foo                                 |
       | Name of operator           | /catalog?f%5Bcomplex_person_operator_sim%5D%5B%5D=Name+of+operator                    |
-      | University                 | /catalog?f%5Bcomplex_person_operator_sim%5D%5B%5D=University                          |
+      | University                 | /catalog?f%5Bcomplex_person_operator_organization_sim%5D%5B%5D=University             |
       | Managing organization name | /catalog?f%5Binstrument_managing_organization_sim%5D%5B%5D=Managing+organization+name |
       | Purchase record title      | /catalog?f%5Bcomplex_purchase_record_title_sim%5D%5B%5D=Purchase+record+title         |
       | Fooss                      | /catalog?f%5Bcomplex_purchase_record_supplier_sim%5D%5B%5D=Fooss                      |

From 09b2f0614ff7c5613ff8a561fdaa72927b39e04b Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Thu, 12 Dec 2019 11:11:45 +0000
Subject: [PATCH 080/258] override file_set_actor to retain japanese characters

---
 .../initializers/file_set_actor_override.rb     | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 hyrax/config/initializers/file_set_actor_override.rb

diff --git a/hyrax/config/initializers/file_set_actor_override.rb b/hyrax/config/initializers/file_set_actor_override.rb
new file mode 100644
index 00000000..499313e9
--- /dev/null
+++ b/hyrax/config/initializers/file_set_actor_override.rb
@@ -0,0 +1,17 @@
+# Override Hyrax 2.6 to support Japanese characters in filenames
+# Use Addressable::URI.unencode rather than Addressable::URI.parse
+# PR to Hyrax 3.x https://github.com/samvera/hyrax/pull/4172
+Hyrax::Actors::FileSetActor.class_eval do
+  def label_for(file)
+    if file.is_a?(Hyrax::UploadedFile) # filename not present for uncached remote file!
+      file.uploader.filename.present? ? file.uploader.filename : File.basename(Addressable::URI.unencode(file.file_url))
+    elsif file.respond_to?(:original_name) # e.g. Hydra::Derivatives::IoDecorator
+      file.original_name
+    elsif file_set.import_url.present?
+      # This path is taken when file is a Tempfile (e.g. from ImportUrlJob)
+      File.basename(Addressable::URI.unencode(file.file_url))
+    else
+      File.basename(file)
+    end
+  end
+end
\ No newline at end of file

From aa2cb874b331f05c6ddf7929fe766b97f3588146 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 12 Dec 2019 13:37:44 +0000
Subject: [PATCH 081/258] work in progress

need model tests, also still to consider handles
---
 hyrax/app/models/doi.rb                       | 32 +++++++++++++++++++
 .../renderers/nested_attribute_renderer.rb    | 11 ++++++-
 hyrax/spec/models/doi_spec.rb                 |  5 +++
 ...sted_identifier_attribute_renderer_spec.rb |  2 +-
 4 files changed, 48 insertions(+), 2 deletions(-)
 create mode 100644 hyrax/app/models/doi.rb
 create mode 100644 hyrax/spec/models/doi_spec.rb

diff --git a/hyrax/app/models/doi.rb b/hyrax/app/models/doi.rb
new file mode 100644
index 00000000..84b35d53
--- /dev/null
+++ b/hyrax/app/models/doi.rb
@@ -0,0 +1,32 @@
+class DOI
+  attr_reader :identifier
+
+  DOI_URL_REGEXP = /^https?\:\/\/(?:dx\.)?doi\.org\/(.+)$/i
+  DOI_PREFIX_REGEXP = /^doi\:(?:\s*)(.+)$/i
+
+  def initialize(value)
+    # Example valid DOIs which should be parsed:
+    # * 10.5555/12345678
+    # * doi:10.5555/12345678
+    # * http://dx.doi.org/10.5555/12345678
+    # * https://doi.org/10.5555/12345678
+    # * 10/hvx
+    # * doi:10/hvx
+    # * http://doi.org/hvx
+
+    if match = value.match(DOI_URL_REGEXP) || value.match(DOI_PREFIX_REGEXP)
+      @identifier = match.captures.first
+    else
+      # the value is not a URL or prefixed with doi:, so just assume it is a raw doi
+      @identifier = value
+    end
+  end
+
+  def url
+    "https://doi.org/#{@identifier}"
+  end
+
+  def label
+    "doi:#{@identifier}"
+  end
+end
diff --git a/hyrax/app/renderers/nested_attribute_renderer.rb b/hyrax/app/renderers/nested_attribute_renderer.rb
index 25deb227..f87dbcd3 100644
--- a/hyrax/app/renderers/nested_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_attribute_renderer.rb
@@ -35,7 +35,11 @@ def get_row(label, val)
     return row if val.blank?
     row += '<div class="row">'
     row += "<div class=\"col-md-3\"><label>#{label}</label></div>"
-    row += "<div class=\"col-md-9\">#{val}</div>"
+    if label =~ /^doi$/i
+      row += "<div class=\"col-md-9\">#{get_doi_hyperlink(val)}</div>"
+    else
+      row += "<div class=\"col-md-9\">#{val}</div>"
+    end
     row += "</div>"
     row
   end
@@ -48,6 +52,11 @@ def get_label_row(label)
     row
   end
 
+  def get_doi_hyperlink(val)
+    doi = DOI.new(val)
+    link_to(doi.label, doi.url, target: '_blank')
+  end
+
   def get_nested_output(label, nested_value, renderer_class, display_label=false)
     output_html = ''
     unless nested_value.kind_of?(Array)
diff --git a/hyrax/spec/models/doi_spec.rb b/hyrax/spec/models/doi_spec.rb
new file mode 100644
index 00000000..edb0bf51
--- /dev/null
+++ b/hyrax/spec/models/doi_spec.rb
@@ -0,0 +1,5 @@
+require 'rails_helper'
+
+RSpec.describe DOI do
+  pending 'work in progress'
+end
diff --git a/hyrax/spec/renderers/nested_identifier_attribute_renderer_spec.rb b/hyrax/spec/renderers/nested_identifier_attribute_renderer_spec.rb
index a96d113b..9f1ca06f 100644
--- a/hyrax/spec/renderers/nested_identifier_attribute_renderer_spec.rb
+++ b/hyrax/spec/renderers/nested_identifier_attribute_renderer_spec.rb
@@ -7,6 +7,6 @@
   it 'generates the correct fields' do
     is_expected.to have_css('th', text: 'Identifier')
     is_expected.to have_css('div.row label', text: 'DOI')
-    is_expected.to have_css('div.row', text: '10.0.1111')
+    is_expected.to have_css('div.row a[href="https://doi.org/10.0.1111"]', text: 'doi:10.0.1111')
   end
 end

From 66670cd6b6f8de842202bef44b03b892324073e9 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 16 Dec 2019 10:38:56 +0000
Subject: [PATCH 082/258] Update doi_spec.rb

---
 hyrax/spec/models/doi_spec.rb | 52 ++++++++++++++++++++++++++++++++++-
 1 file changed, 51 insertions(+), 1 deletion(-)

diff --git a/hyrax/spec/models/doi_spec.rb b/hyrax/spec/models/doi_spec.rb
index edb0bf51..c38ffee0 100644
--- a/hyrax/spec/models/doi_spec.rb
+++ b/hyrax/spec/models/doi_spec.rb
@@ -1,5 +1,55 @@
 require 'rails_helper'
 
 RSpec.describe DOI do
-  pending 'work in progress'
+  let(:doi) { described_class.new(value) }
+
+  shared_examples 'doi' do
+    context 'url' do
+      subject { doi.url }
+      it { is_expected.to eql('https://doi.org/10.5555/12345678') }
+    end
+
+    context 'label' do
+      subject { doi.label }
+      it { is_expected.to eql('doi:10.5555/12345678') }
+    end
+  end
+
+  context 'http:// prefix' do
+    context 'with dx.' do
+      let(:value) { 'http://dx.doi.org/10.5555/12345678' }
+      it_behaves_like 'doi'
+    end
+    context 'without dx.' do
+      let(:value) { 'http://doi.org/10.5555/12345678' }
+      it_behaves_like 'doi'
+    end
+  end
+
+  context 'https:// prefix' do
+    context 'with dx.' do
+      let(:value) { 'https://dx.doi.org/10.5555/12345678' }
+      it_behaves_like 'doi'
+    end
+    context 'without dx.' do
+      let(:value) { 'https://doi.org/10.5555/12345678' }
+      it_behaves_like 'doi'
+    end
+  end
+
+  context 'doi: prefix' do
+    context 'with whitespace' do
+      let(:value) { 'doi: 10.5555/12345678' }
+      it_behaves_like 'doi'
+    end
+    context 'without whitespace' do
+      let(:value) { 'doi:10.5555/12345678' }
+      it_behaves_like 'doi'
+    end
+  end
+
+  context 'no prefix' do
+    let(:value) { '10.5555/12345678' }
+    it_behaves_like 'doi'
+  end
 end

From f030018ad9e0573a6a87d6f90ed30a91b7e7fb60 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 16 Dec 2019 13:04:25 +0000
Subject: [PATCH 083/258] handle handler

---
 hyrax/app/models/doi.rb                       | 12 +++-
 hyrax/app/models/handle.rb                    | 37 ++++++++++++
 .../renderers/nested_attribute_renderer.rb    |  9 ++-
 hyrax/spec/factories/dataset.rb               |  2 +-
 hyrax/spec/models/doi_spec.rb                 | 16 +++++
 hyrax/spec/models/handle_spec.rb              | 59 +++++++++++++++++++
 ...sted_identifier_attribute_renderer_spec.rb | 25 ++++++--
 ...nested_relation_attribute_renderer_spec.rb |  2 +-
 8 files changed, 151 insertions(+), 11 deletions(-)
 create mode 100644 hyrax/app/models/handle.rb
 create mode 100644 hyrax/spec/models/handle_spec.rb

diff --git a/hyrax/app/models/doi.rb b/hyrax/app/models/doi.rb
index 84b35d53..7d78764e 100644
--- a/hyrax/app/models/doi.rb
+++ b/hyrax/app/models/doi.rb
@@ -3,21 +3,24 @@ class DOI
 
   DOI_URL_REGEXP = /^https?\:\/\/(?:dx\.)?doi\.org\/(.+)$/i
   DOI_PREFIX_REGEXP = /^doi\:(?:\s*)(.+)$/i
+  INFO_DOI_PREFIX_REGEXP = /^info\:(?:\s*)doi\/(.+)$/i
 
   def initialize(value)
     # Example valid DOIs which should be parsed:
     # * 10.5555/12345678
     # * doi:10.5555/12345678
+    # * info:doi/10.5555/12345678       # from RFC4452
     # * http://dx.doi.org/10.5555/12345678
     # * https://doi.org/10.5555/12345678
     # * 10/hvx
     # * doi:10/hvx
     # * http://doi.org/hvx
 
-    if match = value.match(DOI_URL_REGEXP) || value.match(DOI_PREFIX_REGEXP)
+    # check if the value has a doi: or url prefix, and if so, extract the raw doi
+    if (match = DOI.match_doi_prefix(value))
       @identifier = match.captures.first
     else
-      # the value is not a URL or prefixed with doi:, so just assume it is a raw doi
+      # the value is not a doi URL or prefixed with doi: or info:doi/, so just assume it is a raw doi
       @identifier = value
     end
   end
@@ -29,4 +32,9 @@ def url
   def label
     "doi:#{@identifier}"
   end
+
+  def self.match_doi_prefix(value)
+    return nil unless value.is_a?(String) && value.present?
+    value.match(DOI_URL_REGEXP) || value.match(DOI_PREFIX_REGEXP) || value.match(INFO_DOI_PREFIX_REGEXP)
+  end
 end
diff --git a/hyrax/app/models/handle.rb b/hyrax/app/models/handle.rb
new file mode 100644
index 00000000..a8751836
--- /dev/null
+++ b/hyrax/app/models/handle.rb
@@ -0,0 +1,37 @@
+class Handle
+  attr_reader :identifier
+
+  HDL_URL_REGEXP = /^https?\:\/\/(?:hdl\.)?handle\.net\/(.+)$/i
+  HDL_PREFIX_REGEXP = /^hdl\:(?:\s*)(.+)$/i
+  INFO_HDL_PREFIX_REGEXP = /^info\:(?:\s*)hdl\/(.+)$/i
+
+  def initialize(value)
+    # Example valid Handles which should be parsed:
+    # * 4263537/400
+    # * hdl:4263537/400
+    # * info:hdl/4263537/400       # from RFC4452
+    # * http://hdl.handle.net/4263537/400
+    # * https://hdl.handle.net/4263537/400
+
+    # check if the value has a hdl: or url prefix, and if so, extract the raw handle
+    if (match = Handle.match_hdl_prefix(value))
+      @identifier = match.captures.first
+    else
+      # the value is not a handle URL or prefixed with hdl: or info:hdl/, so just assume it is a raw handle
+      @identifier = value
+    end
+  end
+
+  def url
+    "https://hdl.handle.net/#{@identifier}"
+  end
+
+  def label
+    "hdl:#{@identifier}"
+  end
+
+  def self.match_hdl_prefix(value)
+    return nil unless value.is_a?(String) && value.present?
+    value.match(HDL_URL_REGEXP) || value.match(HDL_PREFIX_REGEXP) || value.match(INFO_HDL_PREFIX_REGEXP)
+  end
+end
diff --git a/hyrax/app/renderers/nested_attribute_renderer.rb b/hyrax/app/renderers/nested_attribute_renderer.rb
index f87dbcd3..1b22474e 100644
--- a/hyrax/app/renderers/nested_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_attribute_renderer.rb
@@ -35,8 +35,10 @@ def get_row(label, val)
     return row if val.blank?
     row += '<div class="row">'
     row += "<div class=\"col-md-3\"><label>#{label}</label></div>"
-    if label =~ /^doi$/i
+    if label =~ /^doi$/i || DOI.match_doi_prefix(val)
       row += "<div class=\"col-md-9\">#{get_doi_hyperlink(val)}</div>"
+    elsif Handle.match_hdl_prefix(val)
+      row += "<div class=\"col-md-9\">#{get_handle_hyperlink(val)}</div>"
     else
       row += "<div class=\"col-md-9\">#{val}</div>"
     end
@@ -57,6 +59,11 @@ def get_doi_hyperlink(val)
     link_to(doi.label, doi.url, target: '_blank')
   end
 
+  def get_handle_hyperlink(val)
+    handle = Handle.new(val)
+    link_to(handle.label, handle.url, target: '_blank')
+  end
+
   def get_nested_output(label, nested_value, renderer_class, display_label=false)
     output_html = ''
     unless nested_value.kind_of?(Array)
diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 0cfbf9d1..1119190a 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -285,7 +285,7 @@
           title: 'A relation label',
           url: 'http://example.com/relation',
           complex_identifier_attributes: [{
-            identifier: ['123456'],
+            identifier: ['info:hdl/4263537/400'],
             scheme: 'identifier persistent'
           }],
           relationship: 'isNewVersionOf'
diff --git a/hyrax/spec/models/doi_spec.rb b/hyrax/spec/models/doi_spec.rb
index c38ffee0..0c1bea2a 100644
--- a/hyrax/spec/models/doi_spec.rb
+++ b/hyrax/spec/models/doi_spec.rb
@@ -13,6 +13,11 @@
       subject { doi.label }
       it { is_expected.to eql('doi:10.5555/12345678') }
     end
+
+    context 'identifier' do
+      subject { doi.identifier }
+      it { is_expected.to eql('10.5555/12345678') }
+    end
   end
 
   context 'http:// prefix' do
@@ -48,6 +53,17 @@
     end
   end
 
+  context 'info:doi/ prefix' do
+    context 'with whitespace' do
+      let(:value) { 'info: doi/10.5555/12345678' }
+      it_behaves_like 'doi'
+    end
+    context 'without whitespace' do
+      let(:value) { 'info:doi/10.5555/12345678' }
+      it_behaves_like 'doi'
+    end
+  end
+
   context 'no prefix' do
     let(:value) { '10.5555/12345678' }
     it_behaves_like 'doi'
diff --git a/hyrax/spec/models/handle_spec.rb b/hyrax/spec/models/handle_spec.rb
new file mode 100644
index 00000000..6ae629ff
--- /dev/null
+++ b/hyrax/spec/models/handle_spec.rb
@@ -0,0 +1,59 @@
+require 'rails_helper'
+
+RSpec.describe Handle do
+  let(:handle) { described_class.new(value) }
+
+  shared_examples 'handle' do
+    context 'url' do
+      subject { handle.url }
+      it { is_expected.to eql('https://hdl.handle.net/4263537/400') }
+    end
+
+    context 'label' do
+      subject { handle.label }
+      it { is_expected.to eql('hdl:4263537/400') }
+    end
+
+    context 'identifier' do
+      subject { handle.identifier }
+      it { is_expected.to eql('4263537/400') }
+    end
+  end
+
+  context 'http:// prefix' do
+    let(:value) { 'http://hdl.handle.net/4263537/400' }
+    it_behaves_like 'handle'
+  end
+
+  context 'https:// prefix' do
+    let(:value) { 'https://hdl.handle.net/4263537/400' }
+    it_behaves_like 'handle'
+  end
+
+  context 'hdl: prefix' do
+    context 'with whitespace' do
+      let(:value) { 'hdl: 4263537/400' }
+      it_behaves_like 'handle'
+    end
+    context 'without whitespace' do
+      let(:value) { 'hdl:4263537/400' }
+      it_behaves_like 'handle'
+    end
+  end
+
+  context 'info:hdl/ prefix' do
+    context 'with whitespace' do
+      let(:value) { 'info: hdl/4263537/400' }
+      it_behaves_like 'handle'
+    end
+    context 'without whitespace' do
+      let(:value) { 'info:hdl/4263537/400' }
+      it_behaves_like 'handle'
+    end
+  end
+
+  context 'no prefix' do
+    let(:value) { '4263537/400' }
+    it_behaves_like 'handle'
+  end
+end
diff --git a/hyrax/spec/renderers/nested_identifier_attribute_renderer_spec.rb b/hyrax/spec/renderers/nested_identifier_attribute_renderer_spec.rb
index 9f1ca06f..64425b32 100644
--- a/hyrax/spec/renderers/nested_identifier_attribute_renderer_spec.rb
+++ b/hyrax/spec/renderers/nested_identifier_attribute_renderer_spec.rb
@@ -2,11 +2,24 @@
 
 RSpec.describe NestedIdentifierAttributeRenderer do
   let(:html) { described_class.new('Identifier', nested_value.to_json).render }
-  let(:nested_value) { build(:dataset, :with_complex_identifier).complex_identifier.first }
-  subject { Capybara.string(html) }
-  it 'generates the correct fields' do
-    is_expected.to have_css('th', text: 'Identifier')
-    is_expected.to have_css('div.row label', text: 'DOI')
-    is_expected.to have_css('div.row a[href="https://doi.org/10.0.1111"]', text: 'doi:10.0.1111')
+
+  context 'doi' do
+    let(:nested_value) { build(:dataset, :with_complex_identifier).complex_identifier.first }
+    subject { Capybara.string(html) }
+    it 'generates the correct fields' do
+      is_expected.to have_css('th', text: 'Identifier')
+      is_expected.to have_css('div.row label', text: 'DOI')
+      is_expected.to have_css('div.row a[href="https://doi.org/10.0.1111"]', text: 'doi:10.0.1111')
+    end
+  end
+
+  context 'handle' do
+    let(:nested_value) { build(:dataset, :with_complex_relation).complex_relation.first.complex_identifier.first }
+    subject { Capybara.string(html) }
+    it 'generates the correct fields' do
+      is_expected.to have_css('th', text: 'Identifier')
+      is_expected.to have_css('div.row label', text: 'Identifier - Persistent')
+      is_expected.to have_css('div.row a[href="https://hdl.handle.net/4263537/400"]', text: 'hdl:4263537/400')
+    end
   end
 end
diff --git a/hyrax/spec/renderers/nested_relation_attribute_renderer_spec.rb b/hyrax/spec/renderers/nested_relation_attribute_renderer_spec.rb
index cd67863a..64eb22f3 100644
--- a/hyrax/spec/renderers/nested_relation_attribute_renderer_spec.rb
+++ b/hyrax/spec/renderers/nested_relation_attribute_renderer_spec.rb
@@ -12,7 +12,7 @@
     is_expected.to have_link("A relation label", href: 'http://example.com/relation')
 
     is_expected.to have_css('div.row label', text: 'Identifier - Persistent')
-    is_expected.to have_css('div.row', text: '123456')
+    is_expected.to have_css('div.row a[href="https://hdl.handle.net/4263537/400"]', text: 'hdl:4263537/400')
 
     is_expected.to have_css('div.row label', text: 'Relationship')
     is_expected.to have_css('div.row', text: 'is new version of')

From 9b3593798070857e0005338ef031cf258e8274bd Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 16 Dec 2019 16:39:49 +0000
Subject: [PATCH 084/258] detect csv file types

---
 .../controllers/hyrax/citations_controller.rb |  2 +-
 .../controllers/hyrax/file_sets_controller.rb |  2 +-
 hyrax/app/helpers/hyrax/file_set_helper.rb    | 35 +++++++++++++++++++
 hyrax/app/presenters/file_set_presenter.rb    | 11 ++++++
 .../file_sets/media_display/_csv.html.erb     |  1 +
 5 files changed, 49 insertions(+), 2 deletions(-)
 create mode 100644 hyrax/app/helpers/hyrax/file_set_helper.rb
 create mode 100644 hyrax/app/presenters/file_set_presenter.rb
 create mode 100644 hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb

diff --git a/hyrax/app/controllers/hyrax/citations_controller.rb b/hyrax/app/controllers/hyrax/citations_controller.rb
index 1887e93b..ded7bba4 100644
--- a/hyrax/app/controllers/hyrax/citations_controller.rb
+++ b/hyrax/app/controllers/hyrax/citations_controller.rb
@@ -18,7 +18,7 @@ def file
       # which is intended to find works (not files)
       solr_file = ::SolrDocument.find(params[:id])
       authorize! :show, solr_file
-      @presenter = FileSetPresenter.new(solr_file, current_ability, request)
+      @presenter = ::FileSetPresenter.new(solr_file, current_ability, request)
       show
     end
 
diff --git a/hyrax/app/controllers/hyrax/file_sets_controller.rb b/hyrax/app/controllers/hyrax/file_sets_controller.rb
index 4c69d286..25019a70 100644
--- a/hyrax/app/controllers/hyrax/file_sets_controller.rb
+++ b/hyrax/app/controllers/hyrax/file_sets_controller.rb
@@ -15,7 +15,7 @@ class FileSetsController < ApplicationController
     copy_blacklight_config_from(::CatalogController)
 
     class_attribute :show_presenter, :form_class
-    self.show_presenter = Hyrax::FileSetPresenter
+    self.show_presenter = ::FileSetPresenter
     self.form_class = Hyrax::Forms::FileSetEditForm
 
     # A little bit of explanation, CanCan(Can) sets the @file_set via the .load_and_authorize_resource
diff --git a/hyrax/app/helpers/hyrax/file_set_helper.rb b/hyrax/app/helpers/hyrax/file_set_helper.rb
new file mode 100644
index 00000000..4c952b26
--- /dev/null
+++ b/hyrax/app/helpers/hyrax/file_set_helper.rb
@@ -0,0 +1,35 @@
+# Hyrax override 2.6.0
+
+module Hyrax::FileSetHelper
+  def parent_path(parent)
+    if parent.is_a?(::Collection)
+      main_app.collection_path(parent)
+    else
+      polymorphic_path([main_app, parent])
+    end
+  end
+
+  def media_display(presenter, locals = {})
+    render media_display_partial(presenter),
+           locals.merge(file_set: presenter)
+  end
+
+  def media_display_partial(file_set)
+    'hyrax/file_sets/media_display/' +
+        if file_set.image?
+          'image'
+        elsif file_set.video?
+          'video'
+        elsif file_set.audio?
+          'audio'
+        elsif file_set.pdf?
+          'pdf'
+        elsif file_set.office_document?
+          'office_document'
+        elsif file_set.csv?
+          'csv'
+        else
+          'default'
+        end
+  end
+end
diff --git a/hyrax/app/presenters/file_set_presenter.rb b/hyrax/app/presenters/file_set_presenter.rb
new file mode 100644
index 00000000..b4674c14
--- /dev/null
+++ b/hyrax/app/presenters/file_set_presenter.rb
@@ -0,0 +1,11 @@
+# special adaptation of the default hyrax fileset presenter to cater for CSV files
+class FileSetPresenter < Hyrax::FileSetPresenter
+
+  def mime_type
+    solr_document.present? && solr_document.respond_to?(:mime_type) && solr_document.mime_type
+  end
+
+  def csv?
+    mime_type.present? && mime_type =~ /^(?:text|application)\/csv$/i
+  end
+end
diff --git a/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb b/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
new file mode 100644
index 00000000..592196f3
--- /dev/null
+++ b/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
@@ -0,0 +1 @@
+<b>Work in progress: CSV preview here</b>

From b07a372436f0f87136abc1ed3559f199eb408714 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 16 Dec 2019 16:52:03 +0000
Subject: [PATCH 085/258] Create file_set_presenter_spec.rb

---
 hyrax/spec/presenters/file_set_presenter_spec.rb | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 hyrax/spec/presenters/file_set_presenter_spec.rb

diff --git a/hyrax/spec/presenters/file_set_presenter_spec.rb b/hyrax/spec/presenters/file_set_presenter_spec.rb
new file mode 100644
index 00000000..7e599fd6
--- /dev/null
+++ b/hyrax/spec/presenters/file_set_presenter_spec.rb
@@ -0,0 +1,5 @@
+require 'rails_helper'
+
+RSpec.describe FileSetPresenter do
+  pending 'add tests here'
+end

From 473dae47b64229bcd5ba7ebb86c67b398863fa0b Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Wed, 18 Dec 2019 17:47:04 +0900
Subject: [PATCH 086/258] add rake task to fetch a synonym file from Wikibase

---
 hyrax/lib/tasks/wikibase.rake | 39 +++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 hyrax/lib/tasks/wikibase.rake

diff --git a/hyrax/lib/tasks/wikibase.rake b/hyrax/lib/tasks/wikibase.rake
new file mode 100644
index 00000000..953a7cd7
--- /dev/null
+++ b/hyrax/lib/tasks/wikibase.rake
@@ -0,0 +1,39 @@
+require 'csv'
+
+namespace :wikibase do
+  desc 'Fetch Wikibase TSV'
+  task :fetch_synonym, ['filename'] => :environment do |task, args|
+    Rails.logger.formatter = ::Logger::Formatter.new
+    Rails.logger.info("Started Wikibase import task")
+
+    url = ENV.fetch('WIKIBASE_BASE_URL')
+    filename = args['filename']
+    raise 'Please specify filename.' unless filename
+
+    conn = Faraday.new(url: url) do |req|
+      req.use FaradayMiddleware::FollowRedirects
+      req.headers['Accept'] = 'application/sparql-results+json'
+      req.adapter :net_http
+    end
+
+    res = conn.get ENV.fetch('WIKIBASE_SPARQL_QUERY_SYNONYM')
+
+    json = JSON.parse(res.body.force_encoding('UTF-8'))
+    File.open(filename, 'wb'){|file|
+      json['results']['bindings'].each do |row|
+        file.write row['synonyms']['value'].split("\t").to_csv
+      end
+    }
+
+    Rails.logger.info("Completed Wikibase import task")
+  end
+
+  task :reload_solr_core do |task|
+    response = Net::HTTP.get_response(URI("http://#{ENV.fetch('SOLR_HOST')}:#{ENV.fetch('SOLR_PORT')}/solr/admin/cores?action=RELOAD&core=#{ENV.fetch('SOLR_CORE')}"))
+    if response.message == 'OK'
+      puts response.message
+    else
+      raise 'Failed to reload Solr core'
+    end
+  end
+end

From f937c90f44cfcb52598cdaaba7ed15bc3b1980fb Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Wed, 18 Dec 2019 17:52:22 +0900
Subject: [PATCH 087/258] add ENV entries for Wikibase

---
 .env.template | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.env.template b/.env.template
index c79c0361..2ac68789 100644
--- a/.env.template
+++ b/.env.template
@@ -106,3 +106,6 @@ OAI_REPOSTIORY_NAME='NIMS MDR'
 OAI_REPOSITORY_URL=http://localhost:3000/catalog/oai
 OAI_RECORD_PREFIX=nims_mdr
 OAI_ADMIN_EMAIL=***REMOVED***
+
+WIKIBASE_BASE_URL=https://wikibase.example.jp
+WIKIBASE_SPARQL_QUERY_SYNONYM=/query/example?query=some_sparql_query

From dae22713eb868a0b4b4f2bfca3e4ebdf2ad1b072 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Wed, 11 Dec 2019 19:08:56 +0000
Subject: [PATCH 088/258] hide collections from users

---
 .../app/views/hyrax/base/_guts4form.html.erb  | 56 +++++++++++++++++++
 .../sidebar/_repository_content.html.erb      | 14 +++++
 .../views/hyrax/datasets/_guts4form.html.erb  |  3 +-
 3 files changed, 72 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/app/views/hyrax/base/_guts4form.html.erb
 create mode 100644 hyrax/app/views/hyrax/dashboard/sidebar/_repository_content.html.erb

diff --git a/hyrax/app/views/hyrax/base/_guts4form.html.erb b/hyrax/app/views/hyrax/base/_guts4form.html.erb
new file mode 100644
index 00000000..80066b14
--- /dev/null
+++ b/hyrax/app/views/hyrax/base/_guts4form.html.erb
@@ -0,0 +1,56 @@
+<% # we will yield to content_for for each tab, e.g. :files_tab %>
+<% # Override Hyrax 2.6 - remove relationships tab from here %>
+<% tabs ||= %w[metadata files] # default tab order %>
+<div class="row">
+  <div class="col-xs-12 col-sm-8">
+    <div class="panel panel-default tabs" role="main">
+      <!-- Nav tabs -->
+      <ul class="nav nav-tabs" role="tablist">
+        <% tabs.each_with_index do | tab, i | %>
+          <% if i == 0 %>
+            <li role="presentation" class="active">
+          <% else %>
+            <li role="presentation">
+          <% end %>
+              <a href="#<%= tab %>" aria-controls="<%= tab %>" role="tab" data-toggle="tab">
+                <%= t("hyrax.works.form.tab.#{tab}") %>
+              </a>
+            </li>
+        <% end %>
+
+        <li role="presentation" id="tab-share" class="hidden">
+          <a href="#share" aria-controls="share" role="tab" data-toggle="tab">
+            <%= t("hyrax.works.form.tab.share") %>
+          </a>
+        </li>
+      </ul>
+
+      <!-- Tab panes -->
+      <div class="tab-content">
+        <% (tabs - ['share']).each_with_index do | tab, i | %>
+          <% if i == 0 %>
+            <div role="tabpanel" class="tab-pane active" id="<%= tab %>">
+          <% else %>
+            <div role="tabpanel" class="tab-pane" id="<%= tab %>">
+          <% end %>
+            <div class="form-tab-content">
+              <% # metadata_tab is sometimes provided %>
+              <%= yield "#{tab}_tab".to_sym if content_for? "#{tab}_tab".to_sym %>
+              <%= render "form_#{tab}", f: f %>
+            </div>
+          </div>
+        <% end %>
+
+        <div role="tabpanel" class="tab-pane" id="share" data-param-key="<%= f.object.model_name.param_key %>">
+            <div class="form-tab-content">
+              <%= render "form_share", f: f %>
+            </div>
+        </div>
+      </div>
+    </div>
+  </div>
+
+  <div id="savewidget" class="col-xs-12 col-sm-4 fixedsticky" role="complementary">
+    <%= render 'form_progress', f: f %>
+  </div>
+</div>
diff --git a/hyrax/app/views/hyrax/dashboard/sidebar/_repository_content.html.erb b/hyrax/app/views/hyrax/dashboard/sidebar/_repository_content.html.erb
new file mode 100644
index 00000000..fcf7df0e
--- /dev/null
+++ b/hyrax/app/views/hyrax/dashboard/sidebar/_repository_content.html.erb
@@ -0,0 +1,14 @@
+<li class="h5"><%= t('hyrax.admin.sidebar.repository_objects') %></li>
+
+  <% # Override Hyrax 2.6 - restrict collections to admins %>
+  <% if can? :read, :admin_dashboard %>
+    <%= menu.nav_link(hyrax.my_collections_path,
+                      also_active_for: hyrax.dashboard_collections_path) do %>
+      <span class="fa fa-folder-open" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.collections') %></span>
+    <% end %>
+  <% end %>
+
+  <%= menu.nav_link(hyrax.my_works_path,
+                    also_active_for: hyrax.dashboard_works_path) do %>
+    <span class="fa fa-file" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.works') %></span>
+  <% end %>
\ No newline at end of file
diff --git a/hyrax/app/views/hyrax/datasets/_guts4form.html.erb b/hyrax/app/views/hyrax/datasets/_guts4form.html.erb
index 54eefe74..73fc103a 100644
--- a/hyrax/app/views/hyrax/datasets/_guts4form.html.erb
+++ b/hyrax/app/views/hyrax/datasets/_guts4form.html.erb
@@ -1,5 +1,6 @@
 <% # we will yield to content_for for each tab, e.g. :files_tab %>
-<% tabs ||= %w[metadata method instrument specimen files relationships] # default tab order %>
+<% # Override Hyrax 2.6 - remove relationships tab from here %>
+<% tabs ||= %w[metadata method instrument specimen files] # default tab order %>
 <div class="row">
   <div class="col-xs-12 col-sm-8">
     <div class="panel panel-default tabs" role="main">

From c2f03579b5543c0da38375e0113fde232bf55ac4 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Wed, 11 Dec 2019 19:13:04 +0000
Subject: [PATCH 089/258] and batch upload form

---
 .../views/hyrax/batch_uploads/_form.html.erb  | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/batch_uploads/_form.html.erb

diff --git a/hyrax/app/views/hyrax/batch_uploads/_form.html.erb b/hyrax/app/views/hyrax/batch_uploads/_form.html.erb
new file mode 100644
index 00000000..5aa3b86b
--- /dev/null
+++ b/hyrax/app/views/hyrax/batch_uploads/_form.html.erb
@@ -0,0 +1,22 @@
+<%= simple_form_for [hyrax, @form],
+                    html: {
+                      data: { behavior: 'work-form',
+                              'param-key' => @form.model_name.param_key },
+                      multipart: true
+                    } do |f| %>
+  <% provide :files_tab do %>
+    <p class="instructions"><%= t("hyrax.batch_uploads.files.instructions") %></p>
+    <p class="switch-upload-type"><%= t("hyrax.batch_uploads.files.upload_type_instructions") %>
+      <%= link_to t("hyrax.batch_uploads.files.button_label"), [main_app, :new, Hyrax.primary_work_type.model_name.singular_route_key] %>
+    </p>
+  <% end %>
+	<% # Override Hyrax 2.6 - remove relationships tab from here %>
+  <%= render 'hyrax/base/guts4form', f: f, tabs: %w[files metadata] %>
+  <%= f.hidden_field :payload_concern, value: @form.payload_concern %>
+<% end %>
+
+<script type="text/javascript">
+  Blacklight.onLoad(function() {
+    $("#fileupload").fileupload('option', 'downloadTemplateId', 'batch-template-download')
+  });
+</script>

From c459ca872c401642492fac9e67f260b7d3ef4a70 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Wed, 11 Dec 2019 19:23:24 +0000
Subject: [PATCH 090/258] remove add to collection button

---
 .../views/hyrax/base/_show_actions.html.erb   | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/base/_show_actions.html.erb

diff --git a/hyrax/app/views/hyrax/base/_show_actions.html.erb b/hyrax/app/views/hyrax/base/_show_actions.html.erb
new file mode 100644
index 00000000..1940d0af
--- /dev/null
+++ b/hyrax/app/views/hyrax/base/_show_actions.html.erb
@@ -0,0 +1,50 @@
+<div class="show-actions">
+  <% if Hyrax.config.analytics? %>
+    <%= link_to "Analytics", presenter.stats_path, id: 'stats', class: 'btn btn-default' %>
+  <% end %>
+  <% if presenter.editor? %>
+      <%= link_to "Edit", edit_polymorphic_path([main_app, presenter]), class: 'btn btn-default' %>
+      <%= link_to "Delete", [main_app, presenter], class: 'btn btn-danger', data: { confirm: "Delete this #{presenter.human_readable_type}?" }, method: :delete %>
+      <% if presenter.member_presenters.size > 1 %>
+          <%= link_to t("hyrax.file_manager.link_text"), polymorphic_path([main_app, :file_manager, presenter]), class: 'btn btn-default' %>
+      <% end %>
+      <% if presenter.valid_child_concerns.length > 0 %>
+        <div class="btn-group">
+          <button type="button" class="btn btn-default dropdown-toggle" type="button" id="dropdown-menu" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+            Attach Child <span class="caret"></span></button>
+            <ul class="dropdown-menu">
+              <% presenter.valid_child_concerns.each do |concern| %>
+                <li>
+                  <%= link_to "Attach #{concern.human_readable_type}", polymorphic_path([main_app, :new, :hyrax, :parent, concern.model_name.singular], parent_id: presenter.id) %>
+                </li>
+              <% end %>
+            </ul>
+        </div>
+      <% end %>
+  <% end %>
+	<% # Override Hyrax 2.6 - remove add to collection button %>
+  <%
+=begin%>
+ <% if presenter.show_deposit_for?(collections: @user_collections) %>
+      <input type="checkbox"  style="display:none" name="batch_document_ids[]" id="batch_document_<%= presenter.id %>" value="<%= presenter.id %>" class="batch_document_selector" checked="checked" />
+      <%= button_tag t('hyrax.dashboard.my.action.add_to_collection'),
+                     class: 'btn btn-default submits-batches submits-batches-add',
+                     data: { toggle: "modal", target: "#collection-list-container" } %>
+  <% end %> 
+<%
+=end%>
+  <% if presenter.work_featurable? %>
+      <%= link_to "Feature", hyrax.featured_work_path(presenter, format: :json),
+          data: { behavior: 'feature' },
+          class: presenter.display_unfeature_link? ? 'btn btn-default collapse' : 'btn btn-default' %>
+
+      <%= link_to "Unfeature", hyrax.featured_work_path(presenter, format: :json),
+          data: { behavior: 'unfeature' },
+          class: presenter.display_feature_link? ? 'btn btn-default collapse' : 'btn btn-default' %>
+  <% end %>
+</div>
+
+<!-- COinS hook for Zotero -->
+  <span class="Z3988" title="<%= export_as_openurl_ctx_kev(presenter) %>"></span>
+<!-- Render Modals -->
+  <%= render 'hyrax/dashboard/collections/form_for_select_collection', user_collections: @user_collections %>

From dbb244225990712604fae69c70c9ba948b07cffc Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Thu, 2 Jan 2020 15:35:06 +0000
Subject: [PATCH 091/258] added tests

---
 .../views/hyrax/base/_form.html.erb_spec.rb   | 28 ++++++++++++
 .../hyrax/base/_show_actions.html.erb_spec.rb | 27 ++++++++++++
 .../batch_uploads/_form.html.erb_spec.rb      | 28 ++++++++++++
 .../hyrax/dashboard/_sidebar.html.erb_spec.rb | 44 +++++++++++++++++++
 .../hyrax/datasets/_form.html.erb_spec.rb     | 29 ++++++++++++
 5 files changed, 156 insertions(+)
 create mode 100644 hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
 create mode 100644 hyrax/spec/views/hyrax/base/_show_actions.html.erb_spec.rb
 create mode 100644 hyrax/spec/views/hyrax/batch_uploads/_form.html.erb_spec.rb
 create mode 100644 hyrax/spec/views/hyrax/dashboard/_sidebar.html.erb_spec.rb
 create mode 100644 hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb

diff --git a/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb b/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
new file mode 100644
index 00000000..7eb4d477
--- /dev/null
+++ b/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe 'hyrax/base/_form.html.erb', type: :view do
+  let(:work) { Publication.new }
+  let(:ability) { double }
+  let(:user) { FactoryBot.build(:user) }
+
+  let(:form) do
+    Hyrax::PublicationForm.new(work, ability, controller)
+  end
+
+  before do
+    allow(controller).to receive(:current_user).and_return(user)
+    assign(:form, form)
+  end
+
+  describe 'tabs' do
+    it 'does not show the relationships tab' do
+      render
+      expect(rendered).not_to have_selector('#relationships[role="tabpanel"]')
+      expect(rendered).to have_selector('#metadata[role="tabpanel"]')
+      expect(rendered).to have_selector('#files[role="tabpanel"]')
+      expect(rendered).to have_selector('#share[data-param-key="publication"]')
+    end
+  end
+end
diff --git a/hyrax/spec/views/hyrax/base/_show_actions.html.erb_spec.rb b/hyrax/spec/views/hyrax/base/_show_actions.html.erb_spec.rb
new file mode 100644
index 00000000..73a9411f
--- /dev/null
+++ b/hyrax/spec/views/hyrax/base/_show_actions.html.erb_spec.rb
@@ -0,0 +1,27 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe 'hyrax/base/_show_actions.html.erb', type: :view do
+  let(:presenter) { Hyrax::WorkShowPresenter.new(solr_document, ability) }
+  let(:solr_document) { SolrDocument.new(attributes) }
+  let(:attributes) { { 'has_model_ssim' => ['Publication'], :id => '0r967372b' } }
+  let(:ability) { double }
+
+  before do
+    allow(ability).to receive(:can?).with(:create, FeaturedWork).and_return(false)
+    allow(presenter).to receive(:show_deposit_for?).with(anything).and_return(true)
+    allow(presenter).to receive(:editor?).and_return(true)
+  end
+
+  context 'as a registered user' do
+    it 'shows edit / delete / Add to collection links' do
+      render 'hyrax/base/show_actions', presenter: presenter
+
+      expect(rendered).to have_link 'Edit'
+      expect(rendered).to have_link 'Delete'
+      expect(rendered).not_to have_link 'Add to collection'
+      expect(rendered).not_to have_button 'Add to collection'
+    end
+  end
+end
diff --git a/hyrax/spec/views/hyrax/batch_uploads/_form.html.erb_spec.rb b/hyrax/spec/views/hyrax/batch_uploads/_form.html.erb_spec.rb
new file mode 100644
index 00000000..b73bfca1
--- /dev/null
+++ b/hyrax/spec/views/hyrax/batch_uploads/_form.html.erb_spec.rb
@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe 'hyrax/batch_uploads/_form.html.erb', type: :view do
+  let(:work) { Publication.new }
+  let(:ability) { double('ability', current_user: user) }
+  let(:user) { FactoryBot.build(:user) }
+
+  let(:form) do
+    Hyrax::Forms::BatchUploadForm.new(work, ability, controller)
+  end
+
+  before do
+    view.lookup_context.prefixes += ['hyrax/base']
+    allow(controller).to receive(:current_user).and_return(user)
+    assign(:form, form)
+  end
+
+  describe 'tabs' do
+    it 'does not show the relationships tab' do
+      render
+      expect(rendered).not_to have_selector('#relationships[role="tabpanel"]')
+      expect(rendered).to have_selector('#metadata[role="tabpanel"]')
+      expect(rendered).to have_selector('#files[role="tabpanel"]')
+    end
+  end
+end
diff --git a/hyrax/spec/views/hyrax/dashboard/_sidebar.html.erb_spec.rb b/hyrax/spec/views/hyrax/dashboard/_sidebar.html.erb_spec.rb
new file mode 100644
index 00000000..7fb380de
--- /dev/null
+++ b/hyrax/spec/views/hyrax/dashboard/_sidebar.html.erb_spec.rb
@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe 'hyrax/dashboard/_sidebar.html.erb', type: :view do
+  let(:user) { FactoryBot.build(:user) }
+  let(:can_result) { false }
+
+  before do
+    allow(view).to receive(:signed_in?).and_return(true)
+    allow(view).to receive(:current_user).and_return(user)
+    assign(:user, user)
+    allow(view).to receive(:can?).with(:read, :admin_dashboard).and_return(can_result)
+    allow(view).to receive(:can?).with(:manage_any, AdminSet).and_return(can_result)
+    allow(view).to receive(:can?).with(:review, :submissions).and_return(can_result)
+    allow(view).to receive(:can?).with(:manage, User).and_return(can_result)
+    allow(view).to receive(:can?).with(:update, :appearance).and_return(can_result)
+    allow(view).to receive(:can?).with(:manage, Hyrax::Feature).and_return(can_result)
+    allow(view).to receive(:can?).with(:manage, Sipity::WorkflowResponsibility).and_return(can_result)
+    allow(view).to receive(:can?).with(:manage, :collection_types).and_return(can_result)
+  end
+
+  context 'with any user' do
+    before do
+      render
+    end
+    subject { rendered }
+
+    it { is_expected.not_to have_link t('hyrax.admin.sidebar.collections') }
+    it { is_expected.to have_link t('hyrax.admin.sidebar.works') }
+  end
+
+  context 'with a user who can read the admin dashboard' do
+    let(:can_result) { true }
+
+    before do
+      render
+    end
+    subject { rendered }
+
+    it { is_expected.to have_link t('hyrax.admin.sidebar.collections') }
+    it { is_expected.to have_link t('hyrax.admin.sidebar.works') }
+  end
+end
diff --git a/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb b/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb
new file mode 100644
index 00000000..ccb17bcb
--- /dev/null
+++ b/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb
@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe 'hyrax/datasets/_form.html.erb', type: :view do
+  let(:work) { Dataset.new }
+  let(:ability) { double }
+  let(:user) { FactoryBot.build(:user) }
+
+  let(:form) do
+    Hyrax::DatasetForm.new(work, ability, controller)
+  end
+
+  before do
+    view.lookup_context.prefixes += ['hyrax/base']
+    allow(controller).to receive(:current_user).and_return(user)
+    assign(:form, form)
+  end
+
+  describe 'tabs' do
+    it 'does not show the relationships tab' do
+      render
+      expect(rendered).not_to have_selector('#relationships[role="tabpanel"]')
+      expect(rendered).to have_selector('#metadata[role="tabpanel"]')
+      expect(rendered).to have_selector('#files[role="tabpanel"]')
+      expect(rendered).to have_selector('#share[data-param-key="dataset"]')
+    end
+  end
+end

From ac59c2096d297225feb1062efc5e7359e101eee0 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Thu, 2 Jan 2020 16:20:34 +0000
Subject: [PATCH 092/258] search results display changes

---
 hyrax/app/controllers/catalog_controller.rb | 17 ++++++++++-------
 hyrax/config/locales/hyrax.en.yml           |  9 ++++++---
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index 54a10488..90064eca 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -21,7 +21,6 @@ def self.modified_field
     config.view.masonry.partials = [:index]
     config.view.slideshow.partials = [:index]
 
-
     config.show.tile_source_field = :content_metadata_image_iiif_info_ssm
     config.show.partials.insert(1, :openseadragon)
     config.search_builder_class = Hyrax::CatalogSearchBuilder
@@ -71,18 +70,22 @@ def self.modified_field
     config.add_index_field solr_name('subject', :stored_searchable), itemprop: 'about', link_to_search: solr_name('subject', :facetable)
     # config.add_index_field solr_name('creator', :stored_searchable), itemprop: 'creator', link_to_search: solr_name('creator', :facetable)
     # config.add_index_field solr_name('contributor', :stored_searchable), itemprop: 'contributor', link_to_search: solr_name('contributor', :facetable)
-    config.add_index_field solr_name('complex_person_other', :stored_searchable), itemprop: 'creator or contributor', link_to_search: solr_name('complex_person_other', :facetable)
     config.add_index_field solr_name('complex_person_author', :stored_searchable), itemprop: 'author', link_to_search: solr_name('complex_person_author', :facetable)
-    config.add_index_field solr_name('complex_person_editor', :stored_searchable), itemprop: 'editor', link_to_search: solr_name('complex_person_editor', :facetable)
-    config.add_index_field solr_name('complex_person_translator', :stored_searchable), itemprop: 'translator', link_to_search: solr_name('complex_person_translator', :facetable)
+    # config.add_index_field solr_name('complex_person_editor', :stored_searchable), itemprop: 'editor', link_to_search: solr_name('complex_person_editor', :facetable)
+    # config.add_index_field solr_name('complex_person_translator', :stored_searchable), itemprop: 'translator', link_to_search: solr_name('complex_person_translator', :facetable)
     config.add_index_field solr_name('complex_person_data_depositor', :stored_searchable), itemprop: 'data depositor', link_to_search: solr_name('complex_person_data_depositor', :facetable)
     config.add_index_field solr_name('complex_person_data_curator', :stored_searchable), itemprop: 'data curator', link_to_search: solr_name('complex_person_data_curator', :facetable)
     config.add_index_field solr_name('complex_person_operator', :stored_searchable), itemprop: 'operator', link_to_search: solr_name('complex_person_operator', :facetable)
-    config.add_index_field solr_name('proxy_depositor', :symbol), label: 'Depositor', helper_method: :link_to_profile
-    config.add_index_field solr_name('depositor'), label: 'Owner', helper_method: :link_to_profile
+    config.add_index_field solr_name('complex_person_other', :stored_searchable), itemprop: 'creator or contributor', link_to_search: solr_name('complex_person_other', :facetable)
+    # config.add_index_field solr_name('proxy_depositor', :symbol), label: 'Depositor', helper_method: :link_to_profile
+    #  config.add_index_field solr_name('depositor'), label: 'Owner', helper_method: :link_to_profile
+    config.add_index_field solr_name('data_origin', :stored_searchable), itemprop: 'data_origin', link_to_search: solr_name('data_origin', :facetable)
+    config.add_index_field solr_name('complex_specimen_type', :stored_searchable), itemprop: 'specimen'
+    config.add_index_field solr_name('complex_source_title', :stored_searchable), itemprop: 'journal'
+    config.add_index_field solr_name('complex_date_published', :stored_searchable, type: :date), itemprop: 'datePublished', helper_method: :human_readable_date
     config.add_index_field solr_name('publisher', :stored_searchable), itemprop: 'publisher', link_to_search: solr_name('publisher', :facetable)
     # config.add_index_field solr_name('based_near_label', :stored_searchable), itemprop: 'contentLocation', link_to_search: solr_name('based_near_label', :facetable)
-    config.add_index_field solr_name('language', :stored_searchable), itemprop: 'inLanguage', link_to_search: solr_name('language', :facetable)
+    # config.add_index_field solr_name('language', :stored_searchable), itemprop: 'inLanguage', link_to_search: solr_name('language', :facetable)
     config.add_index_field solr_name('date_uploaded', :stored_sortable, type: :date), itemprop: 'datePublished', helper_method: :human_readable_date
     config.add_index_field solr_name('date_modified', :stored_sortable, type: :date), itemprop: 'dateModified', helper_method: :human_readable_date
     config.add_index_field solr_name('date_created', :stored_searchable), itemprop: 'dateCreated'
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index a46d352d..d94ce9df 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -96,10 +96,12 @@ en:
           complex_identifier_orcid_ssim: Orcid
           complex_identifier_local_id_ssim: Local identifier
           complex_person_other_tesim: Creator
-          complex_person_author_tesim: Author
+          # use Creator for label in search results - see i131  (was Author)
+          complex_person_author_tesim: Creator
           complex_person_editor_tesim: Editor
           complex_person_translator_tesim: Translator
-          complex_person_data_depositor_tesim: Data depositor
+          # use Creator for label - see i131 (was Data depositor)
+          complex_person_data_depositor_tesim: Creator
           complex_person_data_curator_tesim: Data curator
           complex_person_operator_tesim: Operator
           complex_person_organization_tesim: Organization
@@ -114,6 +116,7 @@ en:
           complex_relation_title_tesim: Title of related item
           complex_shape_tesim: Shape
           complex_shape_identifier_ssim: Shape identifier
+          complex_source_title_tesim: Journal
           complex_specimen_type_tesim: Specimen type
           complex_specimen_type_description_tesim: Specimen description
           complex_specimen_type_identifier_ssim: Specimen identifier
@@ -210,7 +213,7 @@ en:
           properties_addressed_tesim: Properties processed
           publisher_tesim: Publisher
           rights_statement_tesim: Rights Statement
-          specimen_set_tesim: Specimen
+          specimen_type_tesim: Specimen
           subject_tesim: Subject
           synthesis_and_processing_tesim: Synthesis and processing
           table_of_contents_tesim: Table of contents

From df39d3f143cb30b9a03ec2d47f71eecb6a9d6979 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Sun, 5 Jan 2020 18:31:59 +0000
Subject: [PATCH 093/258] wip - now displaying csv previews

---
 hyrax/app/assets/javascripts/application.js   |  2 +-
 hyrax/app/assets/javascripts/csv_preview.js   | 26 +++++++++++++
 hyrax/app/assets/stylesheets/ngdr.scss        |  4 ++
 hyrax/app/controllers/exports_controller.rb   | 32 ++++++++++++++++
 .../controllers/hyrax/citations_controller.rb |  2 +-
 .../controllers/hyrax/file_sets_controller.rb |  2 +-
 hyrax/app/helpers/hyrax/file_set_helper.rb    | 35 -----------------
 .../app/helpers/hyrax/nims_file_set_helper.rb | 30 +++++++++++++++
 hyrax/app/presenters/file_set_presenter.rb    | 11 ------
 .../app/presenters/hyrax/dataset_presenter.rb |  2 +
 hyrax/app/presenters/hyrax/image_presenter.rb |  2 +
 .../hyrax/nims_file_set_presenter.rb          | 18 +++++++++
 .../presenters/hyrax/publication_presenter.rb |  2 +
 hyrax/app/presenters/hyrax/work_presenter.rb  |  1 +
 .../hyrax/base/_representative_media.html.erb |  4 +-
 hyrax/app/views/hyrax/base/show.html.erb      |  2 +
 .../file_sets/media_display/_csv.html.erb     | 24 +++++++++++-
 hyrax/config/routes.rb                        |  6 +++
 .../presenters/file_set_presenter_spec.rb     |  5 ---
 .../hyrax/nims_file_set_presenter_spec.rb     | 38 +++++++++++++++++++
 20 files changed, 191 insertions(+), 57 deletions(-)
 create mode 100644 hyrax/app/assets/javascripts/csv_preview.js
 create mode 100644 hyrax/app/controllers/exports_controller.rb
 delete mode 100644 hyrax/app/helpers/hyrax/file_set_helper.rb
 create mode 100644 hyrax/app/helpers/hyrax/nims_file_set_helper.rb
 delete mode 100644 hyrax/app/presenters/file_set_presenter.rb
 create mode 100644 hyrax/app/presenters/hyrax/nims_file_set_presenter.rb
 delete mode 100644 hyrax/spec/presenters/file_set_presenter_spec.rb
 create mode 100644 hyrax/spec/presenters/hyrax/nims_file_set_presenter_spec.rb

diff --git a/hyrax/app/assets/javascripts/application.js b/hyrax/app/assets/javascripts/application.js
index 1337ca2f..358c0e80 100644
--- a/hyrax/app/assets/javascripts/application.js
+++ b/hyrax/app/assets/javascripts/application.js
@@ -17,10 +17,10 @@
 //= require dataTables/jquery.dataTables
 //= require dataTables/bootstrap/3/jquery.dataTables.bootstrap
 //= require bootstrap-datepicker
+//= require csv_preview
 //
 // Required by Blacklight
 //= require blacklight/blacklight
 
 //= require_tree .
 //= require hyrax
-
diff --git a/hyrax/app/assets/javascripts/csv_preview.js b/hyrax/app/assets/javascripts/csv_preview.js
new file mode 100644
index 00000000..a09b1cc0
--- /dev/null
+++ b/hyrax/app/assets/javascripts/csv_preview.js
@@ -0,0 +1,26 @@
+$( document ).on('turbolinks:load', function() {
+    $('.csv-preview').each(function() {
+        var preview = $(this);
+        $.ajax({
+            url: preview.data('url'),
+            success: function (data) {
+                preview.find('.csv-preview-error').hide();
+                preview.find('.csv-preview-datatable').DataTable({
+                    data: data.data,
+                    columns: data.columns.map(function (name) {
+                        return {title: name}
+                    })
+                });
+                preview.find('.csv-preview-title').text('Preview: ' + data.file_name);
+                if (data.total_rows > data.maximum_rows) {
+                    preview.find('.csv-preview-size').text('preview is limited to the first ' + data.maximum_rows + ' records, the full file contains ' + data.total_rows + ' records').show();
+                } else {
+                    preview.find('.csv-preview-size').hide();
+                }
+            },
+            error: function() {
+                preview.find('.csv-preview-error').show();
+            }
+        });
+    });
+} );
diff --git a/hyrax/app/assets/stylesheets/ngdr.scss b/hyrax/app/assets/stylesheets/ngdr.scss
index 50f072d7..4c7abdd4 100644
--- a/hyrax/app/assets/stylesheets/ngdr.scss
+++ b/hyrax/app/assets/stylesheets/ngdr.scss
@@ -118,3 +118,7 @@ div#announcement {
   font-size: 1em;
   background-color: #1E2022;
 }
+
+.csv-preview-size {
+  text-align: right;
+}
diff --git a/hyrax/app/controllers/exports_controller.rb b/hyrax/app/controllers/exports_controller.rb
new file mode 100644
index 00000000..6ad04a92
--- /dev/null
+++ b/hyrax/app/controllers/exports_controller.rb
@@ -0,0 +1,32 @@
+require 'csv'
+require 'json'
+
+class ExportsController < Hyrax::DownloadsController
+  MAXIMUM_ROWS = 100
+
+  def export
+    if file.present? && file.mime_type.present? && file.mime_type =~ /^(?:text|application)\/csv$/i
+      render json: csv_as_datatable
+    else
+      render :json => { error: 'Unknown or unsupported file type' }, :status => :bad_request
+    end
+  end
+
+  private
+
+  def csv_as_datatable
+    # CSV files come in many different flavours (character encodings), e.g. ASCII-8BIT, UTF-8, ISO-8859-1 or Windows-1252.
+    # It is not possible to detect the character encoding of a file with 100% accuracy. So we will assume files are in UTF-8
+    # (as the world is moving that way) and scrub out any characters which do not conform to UTF-8. This "lossy" approach
+    # should be ok as this export is merely used to provide a preview of the file, rather than the actual file itself.
+    content = file.content.force_encoding(Encoding::UTF_8).scrub
+    csv = CSV.parse(content, headers: true)
+    {
+        columns: csv.headers,
+        data: csv.take(MAXIMUM_ROWS).map(&:values_at),
+        total_rows: csv.size,
+        maximum_rows: MAXIMUM_ROWS,
+        file_name: file_name
+    }
+  end
+end
diff --git a/hyrax/app/controllers/hyrax/citations_controller.rb b/hyrax/app/controllers/hyrax/citations_controller.rb
index ded7bba4..48adbc68 100644
--- a/hyrax/app/controllers/hyrax/citations_controller.rb
+++ b/hyrax/app/controllers/hyrax/citations_controller.rb
@@ -18,7 +18,7 @@ def file
       # which is intended to find works (not files)
       solr_file = ::SolrDocument.find(params[:id])
       authorize! :show, solr_file
-      @presenter = ::FileSetPresenter.new(solr_file, current_ability, request)
+      @presenter = NimsFileSetPresenter.new(solr_file, current_ability, request)
       show
     end
 
diff --git a/hyrax/app/controllers/hyrax/file_sets_controller.rb b/hyrax/app/controllers/hyrax/file_sets_controller.rb
index 25019a70..a03ef83d 100644
--- a/hyrax/app/controllers/hyrax/file_sets_controller.rb
+++ b/hyrax/app/controllers/hyrax/file_sets_controller.rb
@@ -15,7 +15,7 @@ class FileSetsController < ApplicationController
     copy_blacklight_config_from(::CatalogController)
 
     class_attribute :show_presenter, :form_class
-    self.show_presenter = ::FileSetPresenter
+    self.show_presenter = NimsFileSetPresenter
     self.form_class = Hyrax::Forms::FileSetEditForm
 
     # A little bit of explanation, CanCan(Can) sets the @file_set via the .load_and_authorize_resource
diff --git a/hyrax/app/helpers/hyrax/file_set_helper.rb b/hyrax/app/helpers/hyrax/file_set_helper.rb
deleted file mode 100644
index 4c952b26..00000000
--- a/hyrax/app/helpers/hyrax/file_set_helper.rb
+++ /dev/null
@@ -1,35 +0,0 @@
-# Hyrax override 2.6.0
-
-module Hyrax::FileSetHelper
-  def parent_path(parent)
-    if parent.is_a?(::Collection)
-      main_app.collection_path(parent)
-    else
-      polymorphic_path([main_app, parent])
-    end
-  end
-
-  def media_display(presenter, locals = {})
-    render media_display_partial(presenter),
-           locals.merge(file_set: presenter)
-  end
-
-  def media_display_partial(file_set)
-    'hyrax/file_sets/media_display/' +
-        if file_set.image?
-          'image'
-        elsif file_set.video?
-          'video'
-        elsif file_set.audio?
-          'audio'
-        elsif file_set.pdf?
-          'pdf'
-        elsif file_set.office_document?
-          'office_document'
-        elsif file_set.csv?
-          'csv'
-        else
-          'default'
-        end
-  end
-end
diff --git a/hyrax/app/helpers/hyrax/nims_file_set_helper.rb b/hyrax/app/helpers/hyrax/nims_file_set_helper.rb
new file mode 100644
index 00000000..d0186061
--- /dev/null
+++ b/hyrax/app/helpers/hyrax/nims_file_set_helper.rb
@@ -0,0 +1,30 @@
+# special extension of the default FileSetHelper to cater for CSV files
+module Hyrax
+  module NimsFileSetHelper
+    include Hyrax::FileSetHelper
+
+    def nims_media_display(presenter, locals = {})
+      render nims_media_display_partial(presenter),
+             locals.merge(file_set: presenter)
+    end
+
+    def nims_media_display_partial(file_set)
+      'hyrax/file_sets/media_display/' +
+          if file_set.image?
+            'image'
+          elsif file_set.video?
+            'video'
+          elsif file_set.audio?
+            'audio'
+          elsif file_set.pdf?
+            'pdf'
+          elsif file_set.office_document?
+            'office_document'
+          elsif file_set.csv?
+            'csv'
+          else
+            'default'
+          end
+    end
+  end
+end
diff --git a/hyrax/app/presenters/file_set_presenter.rb b/hyrax/app/presenters/file_set_presenter.rb
deleted file mode 100644
index b4674c14..00000000
--- a/hyrax/app/presenters/file_set_presenter.rb
+++ /dev/null
@@ -1,11 +0,0 @@
-# special adaptation of the default hyrax fileset presenter to cater for CSV files
-class FileSetPresenter < Hyrax::FileSetPresenter
-
-  def mime_type
-    solr_document.present? && solr_document.respond_to?(:mime_type) && solr_document.mime_type
-  end
-
-  def csv?
-    mime_type.present? && mime_type =~ /^(?:text|application)\/csv$/i
-  end
-end
diff --git a/hyrax/app/presenters/hyrax/dataset_presenter.rb b/hyrax/app/presenters/hyrax/dataset_presenter.rb
index 9f0ca20e..ffca8c9f 100644
--- a/hyrax/app/presenters/hyrax/dataset_presenter.rb
+++ b/hyrax/app/presenters/hyrax/dataset_presenter.rb
@@ -8,5 +8,7 @@ class DatasetPresenter < Hyrax::WorkShowPresenter
       :complex_instrument, :origin_system_provenance, :properties_addressed,
       :complex_relation, :specimen_set, :complex_specimen_type,
       :synthesis_and_processing, :custom_property, to: :solr_document
+
+    Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
 end
diff --git a/hyrax/app/presenters/hyrax/image_presenter.rb b/hyrax/app/presenters/hyrax/image_presenter.rb
index 4c195468..dbf70f16 100644
--- a/hyrax/app/presenters/hyrax/image_presenter.rb
+++ b/hyrax/app/presenters/hyrax/image_presenter.rb
@@ -5,5 +5,7 @@ class ImagePresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
       :complex_rights, :complex_version, :status, :specimen_set, :instrument,
       :complex_relation, :custom_property, to: :solr_document
+
+    Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
 end
diff --git a/hyrax/app/presenters/hyrax/nims_file_set_presenter.rb b/hyrax/app/presenters/hyrax/nims_file_set_presenter.rb
new file mode 100644
index 00000000..2abc83a6
--- /dev/null
+++ b/hyrax/app/presenters/hyrax/nims_file_set_presenter.rb
@@ -0,0 +1,18 @@
+# special extension of the default FileSetPresenter to cater for CSV files
+module Hyrax
+  class NimsFileSetPresenter < FileSetPresenter
+
+    def mime_type
+      solr_document.mime_type if solr_document.present? && solr_document.respond_to?(:mime_type)
+    end
+
+    def csv?
+      if mime_type.present? && mime_type =~ /^(?:text|application)\/csv$/i
+        true
+      else
+        false
+      end
+    end
+
+  end
+end
diff --git a/hyrax/app/presenters/hyrax/publication_presenter.rb b/hyrax/app/presenters/hyrax/publication_presenter.rb
index 17f2885b..0d37cbad 100644
--- a/hyrax/app/presenters/hyrax/publication_presenter.rb
+++ b/hyrax/app/presenters/hyrax/publication_presenter.rb
@@ -5,5 +5,7 @@ class PublicationPresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
              :complex_rights, :complex_version, :complex_event, :issue, :place,
              :table_of_contents, :total_number_of_pages, :complex_source, to: :solr_document
+
+    Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
 end
diff --git a/hyrax/app/presenters/hyrax/work_presenter.rb b/hyrax/app/presenters/hyrax/work_presenter.rb
index 71535ec2..21150234 100644
--- a/hyrax/app/presenters/hyrax/work_presenter.rb
+++ b/hyrax/app/presenters/hyrax/work_presenter.rb
@@ -2,5 +2,6 @@
 #  `rails generate hyrax:work Work`
 module Hyrax
   class WorkPresenter < Hyrax::WorkShowPresenter
+    Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
 end
diff --git a/hyrax/app/views/hyrax/base/_representative_media.html.erb b/hyrax/app/views/hyrax/base/_representative_media.html.erb
index 6e6609f5..48b67405 100644
--- a/hyrax/app/views/hyrax/base/_representative_media.html.erb
+++ b/hyrax/app/views/hyrax/base/_representative_media.html.erb
@@ -3,8 +3,8 @@
   <% if defined?(viewer) && viewer %>
     <%= iiif_viewer_display presenter %>
   <% else %>
-    <%= media_display presenter.representative_presenter %>
+    <%= nims_media_display presenter.representative_presenter %>
   <% end %>
 <% else %>
   <%= image_tag 'default.png', class: "canonical-image" %>
-<% end %>
\ No newline at end of file
+<% end %>
diff --git a/hyrax/app/views/hyrax/base/show.html.erb b/hyrax/app/views/hyrax/base/show.html.erb
index 99e5440b..91cad687 100644
--- a/hyrax/app/views/hyrax/base/show.html.erb
+++ b/hyrax/app/views/hyrax/base/show.html.erb
@@ -28,7 +28,9 @@
           <div class="col-sm-9">
             <%= render 'work_description', presenter: @presenter %>
             <%= render 'metadata', presenter: @presenter %>
+            <%= nims_media_display(@presenter.representative_presenter, datatable: true) if @presenter&.representative_presenter&.respond_to?(:csv?) && @presenter&.representative_presenter&.csv? %>
           </div>
+
           <div class="col-sm-12">
             <%= render 'relationships', presenter: @presenter %>
             <%= render 'items', presenter: @presenter %>
diff --git a/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb b/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
index 592196f3..ae409c8c 100644
--- a/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
+++ b/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
@@ -1 +1,23 @@
-<b>Work in progress: CSV preview here</b>
+<% if local_assigns[:datatable] %>
+  <div class="csv-preview panel panel-default" data-url="<%= main_app.export_file_path(file_set)%>">
+    <a name="csv-preview-panel-<%= file_set.id %>"></a>
+    <div class="panel-heading" data-toggle="collapse" data-target="#csv-preview-<%= file_set.id %>">
+      <h4 class="panel-title">
+        <a class="csv-preview-title accordion-toggle">Preview: <%= file_set.link_name %></a>
+      </h4>
+    </div>
+    <div id="csv-preview-<%= file_set.id %>" class="panel-collapse collapse in">
+      <div class="panel-body">
+        <div class="csv-preview-error" style="display: none;">There was an error generating the CSV preview; please download the file instead.</div>
+        <table class="csv-preview-datatable display full-width"></table>
+      </div>
+      <div class="panel-footer csv-preview-size" style="display: none;">
+        <!-- size -->
+      </div>
+    </div>
+  </div>
+<% else %>
+  <div>
+    <a data-turbolinks="false" href="#csv-preview-panel-<%= file_set.id %>">Preview</a>
+  </div>
+<% end %>
diff --git a/hyrax/config/routes.rb b/hyrax/config/routes.rb
index 57159bf0..1e2dc7b2 100644
--- a/hyrax/config/routes.rb
+++ b/hyrax/config/routes.rb
@@ -37,6 +37,12 @@
     concerns :exportable
   end
 
+  resources :files, only: [] do
+    member do
+      get :export, controller: :exports
+    end
+  end
+
   resources :welcome, only: 'index'
   root 'hyrax/homepage#index'
 
diff --git a/hyrax/spec/presenters/file_set_presenter_spec.rb b/hyrax/spec/presenters/file_set_presenter_spec.rb
deleted file mode 100644
index 7e599fd6..00000000
--- a/hyrax/spec/presenters/file_set_presenter_spec.rb
+++ /dev/null
@@ -1,5 +0,0 @@
-require 'rails_helper'
-
-RSpec.describe FileSetPresenter do
-  pending 'add tests here'
-end
diff --git a/hyrax/spec/presenters/hyrax/nims_file_set_presenter_spec.rb b/hyrax/spec/presenters/hyrax/nims_file_set_presenter_spec.rb
new file mode 100644
index 00000000..2c92880d
--- /dev/null
+++ b/hyrax/spec/presenters/hyrax/nims_file_set_presenter_spec.rb
@@ -0,0 +1,38 @@
+require 'rails_helper'
+
+RSpec.describe Hyrax::NimsFileSetPresenter do
+  let(:presenter) { described_class.new(solr_document, nil) }
+  let(:solr_document) { double(mime_type: mime_type) }
+
+  describe 'mime_type' do
+    subject { presenter.mime_type }
+    context 'some/mime_type' do
+      let(:mime_type) { 'some/mime_type' }
+      it { is_expected.to eql('some/mime_type') }
+    end
+    context 'no mime type' do
+      let(:mime_type) { nil }
+      it { is_expected.to be_nil }
+    end
+  end
+
+  describe 'csv?' do
+    subject { presenter.csv? }
+    context 'text/csv' do
+      let(:mime_type) { 'text/csv' }
+      it { is_expected.to be true }
+    end
+    context 'APPLICATION/CSV' do
+      let(:mime_type) { 'APPLICATION/CSV' }
+      it { is_expected.to be true }
+    end
+    context 'some/mime_type' do
+      let(:mime_type) { 'some/mime_type' }
+      it { is_expected.to be false }
+    end
+    context 'no mime type' do
+      let(:mime_type) { nil }
+      it { is_expected.to be false }
+    end
+  end
+end

From 219407dc856f525c9a7442f12712048b16d59dc8 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 6 Jan 2020 13:08:16 +0000
Subject: [PATCH 094/258] new helper spec

---
 .../app/helpers/hyrax/nims_file_set_helper.rb | 14 ++---
 .../hyrax/nims_file_set_helper_spec.rb        | 51 +++++++++++++++++++
 2 files changed, 58 insertions(+), 7 deletions(-)
 create mode 100644 hyrax/spec/helpers/hyrax/nims_file_set_helper_spec.rb

diff --git a/hyrax/app/helpers/hyrax/nims_file_set_helper.rb b/hyrax/app/helpers/hyrax/nims_file_set_helper.rb
index d0186061..07419026 100644
--- a/hyrax/app/helpers/hyrax/nims_file_set_helper.rb
+++ b/hyrax/app/helpers/hyrax/nims_file_set_helper.rb
@@ -8,19 +8,19 @@ def nims_media_display(presenter, locals = {})
              locals.merge(file_set: presenter)
     end
 
-    def nims_media_display_partial(file_set)
+    def nims_media_display_partial(presenter)
       'hyrax/file_sets/media_display/' +
-          if file_set.image?
+          if presenter.image?
             'image'
-          elsif file_set.video?
+          elsif presenter.video?
             'video'
-          elsif file_set.audio?
+          elsif presenter.audio?
             'audio'
-          elsif file_set.pdf?
+          elsif presenter.pdf?
             'pdf'
-          elsif file_set.office_document?
+          elsif presenter.office_document?
             'office_document'
-          elsif file_set.csv?
+          elsif presenter.csv?
             'csv'
           else
             'default'
diff --git a/hyrax/spec/helpers/hyrax/nims_file_set_helper_spec.rb b/hyrax/spec/helpers/hyrax/nims_file_set_helper_spec.rb
new file mode 100644
index 00000000..30eff18e
--- /dev/null
+++ b/hyrax/spec/helpers/hyrax/nims_file_set_helper_spec.rb
@@ -0,0 +1,51 @@
+require 'rails_helper'
+
+RSpec.describe Hyrax::NimsFileSetHelper, type: :helper do
+  let(:presenter) { Hyrax::NimsFileSetPresenter.new(solr_document, nil) }
+  let(:solr_document) { SolrDocument.new(mime_type_ssi: mime_type) }
+
+  describe '#nims_media_display' do
+    let(:mime_type) { 'text/csv' }
+    subject { helper.nims_media_display(presenter) }
+    it { is_expected.to have_css('a', text: 'Preview') }
+  end
+
+  describe '#nims_media_display_partial' do
+    subject { helper.nims_media_display_partial(presenter) }
+
+    context 'image' do
+      let(:mime_type) { 'image/tiff' }
+      it { is_expected.to eql 'hyrax/file_sets/media_display/image' }
+    end
+
+    context 'video' do
+      let(:mime_type) { 'video/mpeg' }
+      it { is_expected.to eql 'hyrax/file_sets/media_display/video' }
+    end
+
+    context 'audio' do
+      let(:mime_type) { 'audio/ogg' }
+      it { is_expected.to eql 'hyrax/file_sets/media_display/audio' }
+    end
+
+    context 'pdf' do
+      let(:mime_type) { 'application/pdf' }
+      it { is_expected.to eql 'hyrax/file_sets/media_display/pdf' }
+    end
+
+    context 'office_document' do
+      let(:mime_type) { 'application/vnd.ms-powerpoint' }
+      it { is_expected.to eql 'hyrax/file_sets/media_display/office_document' }
+    end
+
+    context 'csv' do
+      let(:mime_type) { 'text/csv' }
+      it { is_expected.to eql 'hyrax/file_sets/media_display/csv' }
+    end
+
+    context 'anything else' do
+      let(:mime_type) { 'foo/bar' }
+      it { is_expected.to eql 'hyrax/file_sets/media_display/default' }
+    end
+  end
+end

From 3ff6069bbba79549f1739270c89de7f267e3e4d6 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 6 Jan 2020 17:19:35 +0000
Subject: [PATCH 095/258] exports controller spec

---
 .../hyrax/exports_controller_spec.rb          | 71 +++++++++++++++++++
 hyrax/spec/factories/file_sets.rb             | 31 +++++---
 hyrax/spec/fixtures/csv/example.csv           |  8 +++
 3 files changed, 102 insertions(+), 8 deletions(-)
 create mode 100644 hyrax/spec/controllers/hyrax/exports_controller_spec.rb
 create mode 100644 hyrax/spec/fixtures/csv/example.csv

diff --git a/hyrax/spec/controllers/hyrax/exports_controller_spec.rb b/hyrax/spec/controllers/hyrax/exports_controller_spec.rb
new file mode 100644
index 00000000..9000f2fd
--- /dev/null
+++ b/hyrax/spec/controllers/hyrax/exports_controller_spec.rb
@@ -0,0 +1,71 @@
+require 'rails_helper'
+require 'devise'
+
+RSpec.describe ExportsController do
+  include Devise::Test::ControllerHelpers
+
+  describe '#export' do
+    let(:response) { get :export, params: {id: file_set.id} }
+    let(:status) { response.status }
+    let(:json) { JSON.parse(response.body) }
+
+    context 'no file' do
+      let(:file_set) { create(:file_set, :open) }
+      it 'should return an error' do
+        expect(status).to eql(400)
+        expect(json['error']).to eql('Unknown or unsupported file type')
+      end
+    end
+
+    context 'non-csv' do
+      let(:file_set) { create(:file_set, :open, content: File.open(fixture_path + '/xml/other.txt')) }
+      it 'should return an error' do
+        expect(status).to eql(400)
+        expect(json['error']).to eql('Unknown or unsupported file type')
+      end
+    end
+
+    context 'csv' do
+      context 'open' do
+        let(:file_set) { create(:file_set, :open, content: File.open(fixture_path + '/csv/example.csv')) }
+        it 'should return a json export of the CSV file' do
+          expect(status).to eql(200)
+          expect(json['columns']).to match_array(["Code", "Study_participation", "Census_usually_resident_population_count"])
+          expect(json['data']).to match_array([
+                                                  ["1", "Full-time study", "1000911"],
+                                                  ["2", "Part-time study", "149919"],
+                                                  ["4", "Not studying", "3548922"],
+                                                  ["7", "Response not identifiable", "0"],
+                                                  ["9", "Not stated", "0"],
+                                                  ["TotalStated", "Total stated", "4699755"],
+                                                  ["Total", "Total", "4699755"]
+                                              ])
+          expect(json['total_rows']).to eql(7)
+          expect(json['maximum_rows']).to eql(100)
+          expect(json['file_name']).to eql("example.csv")
+        end
+      end
+
+      describe 'authentication' do
+        let(:file_set) { create(:file_set, :authenticated, content: File.open(fixture_path + '/csv/example.csv')) }
+
+        context 'unauthenticated' do
+          it 'should return an unauthenticated error' do
+            expect(status).to eql(401)
+          end
+        end
+
+        context 'authenticated' do
+          let(:user) { create(:user) }
+          before do
+            sign_in user
+          end
+
+          it 'should return success' do
+            expect(status).to eql(200)
+          end
+        end
+      end
+    end
+  end
+end
diff --git a/hyrax/spec/factories/file_sets.rb b/hyrax/spec/factories/file_sets.rb
index a801b6c2..0debbd1d 100644
--- a/hyrax/spec/factories/file_sets.rb
+++ b/hyrax/spec/factories/file_sets.rb
@@ -12,14 +12,29 @@
       Hydra::Works::UploadFileToFileSet.call(file, evaluator.content) if evaluator.content
     end
 
-    factory :file_with_work do
-      after(:build) do |file, _evaluator|
-        file.title = ['testfile']
-      end
-      after(:create) do |file, evaluator|
-        Hydra::Works::UploadFileToFileSet.call(file, evaluator.content) if evaluator.content
-        create(:work, user: evaluator.user).members << file
-      end
+    trait :open do
+      visibility { 'open' }
+      title { ["Open File Set"] }
+    end
+
+    trait :authenticated do
+      visibility { 'authenticated' }
+      title { ["Authenticated File Set"] }
+    end
+
+    trait :embargo do
+      visibility { 'embargo' }
+      title { ["Embargo File Set"] }
+    end
+
+    trait :lease do
+      visibility { 'lease' }
+      title { ["Leased File Set"] }
+    end
+
+    trait :restricted do
+      visibility { 'restricted' }
+      title { ["Resstricted File Set"] }
     end
   end
 end
diff --git a/hyrax/spec/fixtures/csv/example.csv b/hyrax/spec/fixtures/csv/example.csv
new file mode 100644
index 00000000..59232a80
--- /dev/null
+++ b/hyrax/spec/fixtures/csv/example.csv
@@ -0,0 +1,8 @@
+"Code","Study_participation","Census_usually_resident_population_count"
+"1","Full-time study",1000911
+"2","Part-time study",149919
+"4","Not studying",3548922
+"7","Response not identifiable",0
+"9","Not stated",0
+"TotalStated","Total stated",4699755
+"Total","Total",4699755
\ No newline at end of file

From 5b24ea7b163976b9947572c86e5b98e5bed67256 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Wed, 8 Jan 2020 21:08:37 +0900
Subject: [PATCH 096/258] use user_identifier instead of username in a profile
 URL

---
 hyrax/app/helpers/hyrax_helper.rb                   | 13 +++++++++++++
 hyrax/app/models/user.rb                            |  7 ++++++-
 .../20200108111832_add_user_identifier_to_users.rb  |  6 ++++++
 hyrax/db/schema.rb                                  |  4 +++-
 hyrax/spec/models/user_spec.rb                      |  4 ++--
 5 files changed, 30 insertions(+), 4 deletions(-)
 create mode 100644 hyrax/db/migrate/20200108111832_add_user_identifier_to_users.rb

diff --git a/hyrax/app/helpers/hyrax_helper.rb b/hyrax/app/helpers/hyrax_helper.rb
index 7cdb90bd..dd571241 100644
--- a/hyrax/app/helpers/hyrax_helper.rb
+++ b/hyrax/app/helpers/hyrax_helper.rb
@@ -14,4 +14,17 @@ def available_translations
       # 'zh' => '中文'
     }
   end
+
+  def link_to_profile(args)
+    user_or_key = args.is_a?(Hash) ? args[:value].first : args
+    user = case user_or_key
+           when User
+             user_or_key
+           when String
+             ::User.find_by_user_key(user_or_key)
+           end
+    return user_or_key if user.nil?
+    text = user.respond_to?(:name) ? user.name : user_or_key
+    link_to text, Hyrax::Engine.routes.url_helpers.user_path(user.user_identifier)
+  end
 end
diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 50b9dc25..ae9e6d14 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -24,7 +24,7 @@ class User < ApplicationRecord
   # user class to get a user-displayable login/identifier for
   # the account.
   def to_s
-    username
+    display_name
   end
 
   def self.find_or_create_system_user(user_key)
@@ -35,5 +35,10 @@ def self.find_or_create_system_user(user_key)
   def ldap_before_save
     self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
     self.password = Devise.friendly_token[0, 20]
+    self.user_identifier = Noid::Rails::Service.new.mint
+  end
+
+  def self.from_url_component(component)
+    User.find_by(user_identifier: component) || User.find_by_user_key(component.gsub(/-dot-/, '.'))
   end
 end
diff --git a/hyrax/db/migrate/20200108111832_add_user_identifier_to_users.rb b/hyrax/db/migrate/20200108111832_add_user_identifier_to_users.rb
new file mode 100644
index 00000000..7c07d463
--- /dev/null
+++ b/hyrax/db/migrate/20200108111832_add_user_identifier_to_users.rb
@@ -0,0 +1,6 @@
+class AddUserIdentifierToUsers < ActiveRecord::Migration[5.1]
+  def change
+    add_column :users, :user_identifier, :string
+    add_index :users, :user_identifier
+  end
+end
diff --git a/hyrax/db/schema.rb b/hyrax/db/schema.rb
index e959d543..467c7d8e 100644
--- a/hyrax/db/schema.rb
+++ b/hyrax/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20190930025332) do
+ActiveRecord::Schema.define(version: 20200108111832) do
 
   create_table "bookmarks", force: :cascade do |t|
     t.integer "user_id", null: false
@@ -548,8 +548,10 @@
     t.string "unlock_token"
     t.datetime "locked_at"
     t.string "remember_token"
+    t.string "user_identifier"
     t.index ["email"], name: "index_users_on_email"
     t.index ["reset_password_token"], name: "index_users_on_reset_password_token", unique: true
+    t.index ["user_identifier"], name: "index_users_on_user_identifier"
     t.index ["username"], name: "index_users_on_username", unique: true
   end
 
diff --git a/hyrax/spec/models/user_spec.rb b/hyrax/spec/models/user_spec.rb
index 52aef32d..7c622ea9 100644
--- a/hyrax/spec/models/user_spec.rb
+++ b/hyrax/spec/models/user_spec.rb
@@ -1,11 +1,11 @@
 require 'rails_helper'
 
 RSpec.describe ::User do
-  let(:user) { described_class.new(username: 'username') }
+  let(:user) { described_class.new(username: 'username', display_name: 'Test user') }
 
   describe '#to_s' do
     subject { user.to_s }
-    it { is_expected.to eql 'username'}
+    it { is_expected.to eql 'Test user'}
   end
 
   describe '#ldap_before_save' do

From cfba5e086745e280b05e55f23f87f9e140b33faf Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 8 Jan 2020 12:19:52 +0000
Subject: [PATCH 097/258] Final tweaks

now displays preview on fileset page, add link to download file
---
 hyrax/app/assets/javascripts/csv_preview.js   |  2 +-
 .../file_sets/media_display/_csv.html.erb     |  9 ++++++--
 hyrax/app/views/hyrax/file_sets/show.html.erb | 21 +++++++++++++++++++
 .../hyrax/nims_file_set_helper_spec.rb        |  3 ++-
 4 files changed, 31 insertions(+), 4 deletions(-)
 create mode 100644 hyrax/app/views/hyrax/file_sets/show.html.erb

diff --git a/hyrax/app/assets/javascripts/csv_preview.js b/hyrax/app/assets/javascripts/csv_preview.js
index a09b1cc0..f89f8100 100644
--- a/hyrax/app/assets/javascripts/csv_preview.js
+++ b/hyrax/app/assets/javascripts/csv_preview.js
@@ -8,7 +8,7 @@ $( document ).on('turbolinks:load', function() {
                 preview.find('.csv-preview-datatable').DataTable({
                     data: data.data,
                     columns: data.columns.map(function (name) {
-                        return {title: name}
+                        return { title: name.replace(/[\_\-]/g, ' ') };
                     })
                 });
                 preview.find('.csv-preview-title').text('Preview: ' + data.file_name);
diff --git a/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb b/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
index ae409c8c..b30611de 100644
--- a/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
+++ b/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
@@ -1,5 +1,5 @@
 <% if local_assigns[:datatable] %>
-  <div class="csv-preview panel panel-default" data-url="<%= main_app.export_file_path(file_set)%>">
+  <div class="csv-preview panel panel-default" data-url="<%= main_app.export_file_path(file_set.id)%>">
     <a name="csv-preview-panel-<%= file_set.id %>"></a>
     <div class="panel-heading" data-toggle="collapse" data-target="#csv-preview-<%= file_set.id %>">
       <h4 class="panel-title">
@@ -9,7 +9,7 @@
     <div id="csv-preview-<%= file_set.id %>" class="panel-collapse collapse in">
       <div class="panel-body">
         <div class="csv-preview-error" style="display: none;">There was an error generating the CSV preview; please download the file instead.</div>
-        <table class="csv-preview-datatable display full-width"></table>
+        <table class="csv-preview-datatable display full-width" style="width:100%"></table>
       </div>
       <div class="panel-footer csv-preview-size" style="display: none;">
         <!-- size -->
@@ -20,4 +20,9 @@
   <div>
     <a data-turbolinks="false" href="#csv-preview-panel-<%= file_set.id %>">Preview</a>
   </div>
+  <% if Hyrax.config.display_media_download_link? %>
+    <div>
+      <%= link_to t('hyrax.file_set.show.download'), hyrax.download_path(file_set.id), id: "file_download", data: { label: file_set.id }, target: "_new" %>
+    </div>
+  <% end %>
 <% end %>
diff --git a/hyrax/app/views/hyrax/file_sets/show.html.erb b/hyrax/app/views/hyrax/file_sets/show.html.erb
new file mode 100644
index 00000000..c93941f3
--- /dev/null
+++ b/hyrax/app/views/hyrax/file_sets/show.html.erb
@@ -0,0 +1,21 @@
+<% provide :page_title, @presenter.page_title %>
+<div class="container-fluid">
+  <div class="row">
+    <div class="col-xs-12 col-sm-4">
+      <%= nims_media_display @presenter %>
+      <%= render 'show_actions', presenter: @presenter %>
+      <%= render 'single_use_links', presenter: @presenter if @presenter.editor? %>
+    </div>
+    <div itemscope itemtype="<%= @presenter.itemtype %>" class="col-xs-12 col-sm-8">
+      <header>
+        <%= render 'file_set_title', presenter: @presenter %>
+      </header>
+
+      <%# TODO: render 'show_descriptions' See https://github.com/samvera/hyrax/issues/1481 %>
+      <%= render 'show_details' %>
+
+      <%= nims_media_display(@presenter, datatable: true) if @presenter.respond_to?(:csv?) && @presenter.csv? %>
+      <%= render 'hyrax/users/activity_log', events: @presenter.events %>
+    </div><!-- /columns second -->
+  </div> <!-- /.row -->
+</div><!-- /.container-fluid -->
diff --git a/hyrax/spec/helpers/hyrax/nims_file_set_helper_spec.rb b/hyrax/spec/helpers/hyrax/nims_file_set_helper_spec.rb
index 30eff18e..716c241a 100644
--- a/hyrax/spec/helpers/hyrax/nims_file_set_helper_spec.rb
+++ b/hyrax/spec/helpers/hyrax/nims_file_set_helper_spec.rb
@@ -2,12 +2,13 @@
 
 RSpec.describe Hyrax::NimsFileSetHelper, type: :helper do
   let(:presenter) { Hyrax::NimsFileSetPresenter.new(solr_document, nil) }
-  let(:solr_document) { SolrDocument.new(mime_type_ssi: mime_type) }
+  let(:solr_document) { SolrDocument.new(mime_type_ssi: mime_type, id: '12345') }
 
   describe '#nims_media_display' do
     let(:mime_type) { 'text/csv' }
     subject { helper.nims_media_display(presenter) }
     it { is_expected.to have_css('a', text: 'Preview') }
+    it { is_expected.to have_css('a', text: 'Download the file') }
   end
 
   describe '#nims_media_display_partial' do

From 83f3c8a1b695add127ac0ee934819bd09297bfdb Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 9 Jan 2020 09:57:10 +0000
Subject: [PATCH 098/258] test fixes

---
 hyrax/features/step_definitions/user_steps.rb |  4 ++++
 hyrax/spec/features/contact_form_spec.rb      | 16 ++++------------
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/hyrax/features/step_definitions/user_steps.rb b/hyrax/features/step_definitions/user_steps.rb
index d90406b1..eb176d53 100644
--- a/hyrax/features/step_definitions/user_steps.rb
+++ b/hyrax/features/step_definitions/user_steps.rb
@@ -45,3 +45,7 @@
 Then(/^I should be redirected to the login page$/) do
   expect(current_path).to eql(new_user_session_path)
 end
+
+Then(/^I should be redirected to the home page$/) do
+  expect(current_path).to eql(root_path)
+end
diff --git a/hyrax/spec/features/contact_form_spec.rb b/hyrax/spec/features/contact_form_spec.rb
index 8ad793fc..1ba9fc93 100644
--- a/hyrax/spec/features/contact_form_spec.rb
+++ b/hyrax/spec/features/contact_form_spec.rb
@@ -4,24 +4,16 @@
 # NOTE: If you generated more than one work, you have to set "js: true"
 RSpec.feature 'Show Contact form', js: false do
   context 'a logged in user' do
-    let(:user_attributes) do
-      { email: 'test@example.com' }
-    end
-    let(:user) do
-      User.new(user_attributes) { |u| u.save(validate: false) }
-    end
+    let(:user) { build(:user) }
 
     before do
       login_as user
     end
 
-    scenario do
+    scenario "should display contact form" do
       visit '/contact'
-
-      it "should display contact form" do
-        expect(page).to have_field 'Your Name', with: user.username, readonly: true
-        expect(page).to have_field 'Your Email', with: user.email, readonly: true
-      end
+      expect(page).to have_field 'Your Name', with: user.username, readonly: true
+      expect(page).to have_field 'Your Email', with: user.email, readonly: true
     end
   end
 end

From a8acbb7a50126716da1bc08c5f4fb26f50ce477d Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 9 Jan 2020 11:34:09 +0000
Subject: [PATCH 099/258] Update contact_form_spec.rb

test fix
---
 hyrax/spec/features/contact_form_spec.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/spec/features/contact_form_spec.rb b/hyrax/spec/features/contact_form_spec.rb
index 1ba9fc93..fb3d51d4 100644
--- a/hyrax/spec/features/contact_form_spec.rb
+++ b/hyrax/spec/features/contact_form_spec.rb
@@ -12,7 +12,7 @@
 
     scenario "should display contact form" do
       visit '/contact'
-      expect(page).to have_field 'Your Name', with: user.username, readonly: true
+      expect(page).to have_field 'Your Name', with: user.display_name, readonly: true
       expect(page).to have_field 'Your Email', with: user.email, readonly: true
     end
   end

From c906ee7348f843a1f7f99daedd7f240980f1d6e7 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Fri, 10 Jan 2020 11:58:44 +0900
Subject: [PATCH 100/258] add Handle identifier to the authority file

---
 hyrax/config/authorities/identifiers.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/hyrax/config/authorities/identifiers.yml b/hyrax/config/authorities/identifiers.yml
index 83e90334..a85f2687 100644
--- a/hyrax/config/authorities/identifiers.yml
+++ b/hyrax/config/authorities/identifiers.yml
@@ -8,6 +8,9 @@ terms:
   - id: DOI
     term: DOI
     active: true
+  - id: handle identifier
+    term: Handle identifier
+    active: true
   - id: edu person principal name
     term: eduPersonPrincipalName
     active: true

From fd7f603d881a857f54798b22b1232d4eefc67ad2 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 15 Jan 2020 15:52:38 +0000
Subject: [PATCH 101/258] single sign-out patches

---
 .env.template                                 |  8 ++++
 README.md                                     | 48 +++++++++++++++++++
 cas/Dockerfile                                |  5 +-
 cas/etc/cas/config/cas.properties             |  4 +-
 cas/etc/cas/services/casmdrnimstest-1.json    |  8 ++++
 cas/etc/cas/services/castest-1.json           |  7 ---
 docker-compose.override.yml                   |  9 ++++
 hyrax/Gemfile                                 |  3 ++
 hyrax/Gemfile.lock                            |  4 ++
 hyrax/config/initializers/session_store.rb    | 15 +++++-
 .../single_sign_out/single_sign_out.rb        | 23 +++++++++
 11 files changed, 122 insertions(+), 12 deletions(-)
 create mode 100644 cas/etc/cas/services/casmdrnimstest-1.json
 delete mode 100644 cas/etc/cas/services/castest-1.json
 create mode 100644 hyrax/lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out.rb

diff --git a/.env.template b/.env.template
index a14fbd0b..20c209c7 100644
--- a/.env.template
+++ b/.env.template
@@ -103,6 +103,14 @@ SMTP_PORT=
 MDR_HOST=
 
 CAS_BASE_URL=https://cas.nims.go.jp/
+
+# For local docker-based setup for development, use:
+# CAS_BASE_URL=https://cas.mdr.nims.test:8443/cas/
+# and add the following two localhost pointers to your system's /etc/hosts file:
+# 127.0.0.1       mdr.nims.test         # <-- MDR website
+# 127.0.0.1       cas.mdr.nims.test     # <-- CAS server
+# and also trust the SSL certificate for cas.mdr.nims.test
+
 # CAS_VALIDATE_URL may need to be set depending on how MDR is configured
 # CAS_VALIDATE_URL=https://cas:8443/cas/serviceValidate
 
diff --git a/README.md b/README.md
index 0819f337..db4ef2f1 100644
--- a/README.md
+++ b/README.md
@@ -212,6 +212,54 @@ $ curl -L https://github.com/docker/compose/releases/download/[INSERT_DESIRED_DO
 4. Open a console and try running `docker -h` and `docker-compose -h` to verify they are both accessible.
 
 
+### Using a local Docker-based CAS server for Single Sign-On and Single Sign-Off
+
+If you would like to use a local Docker-based CAS server for single sign-on and sign off, a little more configuration is 
+required. Note that these steps are optional: you could use database authentication or LDAP authentication, or a remote 
+CAS server instead.
+
+1. In your system's `/etc/hosts` file, add the following two entries which will redirect the specified hostnames to localhost:
+
+    ```
+    127.0.0.1       mdr.nims.test
+    127.0.0.1       cas.mdr.nims.test
+    ``` 
+
+2. In your `.env` file, set the following variables:
+
+    ```
+    MDR_DEVISE_AUTH_MODULE=cas_authenticatable
+    CAS_BASE_URL=https://cas.mdr.nims.test:8443/cas/
+    ```
+
+3. Now build and run the `web` and `cas` containers:
+
+    ```bash
+    docker-compose build web cas
+    docker-compose up web cas
+    ```
+
+4. Open a browser and goto the MDR website: http://mdr.nims.test:3000/
+    Click on Login and you should be directed to https://cas.mdr.nims.test:8443/cas/
+
+    At this point your web browser will likely complain that the SSL certificate is invalid / untrusted. Grant the 
+    certificate `cas.mdr.nims.test` full trust:
+ 
+    * In Chrome, view the certificate and export it (or drag it) to your desktop
+    * Next, double-click on the certificate file (`cas.mdr.nims.test.cer`) and mark it as Always Trust (see: https://support.apple.com/en-gb/guide/keychain-access/kyca11871/mac)
+    * Check that reloading https://cas.mdr.nims.test:8443/cas/ should now present the valid CAS website without any certificate warnings or other errors
+
+5. To test single sign-on, open a browser window and go to to the MDR website: http://mdr.nims.test:3000/
+    
+    * Click on "login" and you will be redirected to the CAS website. 
+    * Log in as `user1` / `password`.
+    * After completing the login on the CAS website you will be redirected back to the MDR website and now logged in as `user1`
+    
+6. To test single sign-off, after logging in as `user1` on MDR (see previous step), open an extra browser window and navigate directly to the CAS website: https://cas.mdr.nims.test:8443/cas
+    
+    * Logout of the CAS system (by clicking on "log out" in "please log out and exit your web browser")
+    * Then reload the *other* browser window which had the user logged in to MDR and verify that they are now logged out.
+
 ## Backups
 
 There is [docker documentation](https://docs.docker.com/storage/volumes/#backup-restore-or-migrate-data-volumes) advising how to back up volumes and their data.
diff --git a/cas/Dockerfile b/cas/Dockerfile
index a0c24470..d5dfbe9d 100644
--- a/cas/Dockerfile
+++ b/cas/Dockerfile
@@ -4,8 +4,9 @@ RUN build.sh package
 
 RUN keytool -genkeypair -alias cas -keyalg RSA -keypass changeit \
             -storepass changeit -keystore /cas-overlay/etc/cas/thekeystore \
-            -dname "CN=cas.example.org,OU=Example,OU=Org,C=AU" \
-            -ext SAN="dns:example.org,dns:localhost,ip:127.0.0.1"
+            -dname "CN=cas.mdr.nims.test,OU=MDR,OU=NIMS,OU=Test,C=JP" \
+            -ext SAN="dns:cas.mdr.nims.test,dns:localhost,ip:127.0.0.1" \
+            -validity 365
 COPY etc/cas/config/* /cas-overlay/etc/cas/config/
 COPY etc/cas/services/* /cas-overlay/etc/cas/services/
 COPY etc/cas/users.json /cas-overlay/etc/cas/
diff --git a/cas/etc/cas/config/cas.properties b/cas/etc/cas/config/cas.properties
index 08220718..e2ced10c 100644
--- a/cas/etc/cas/config/cas.properties
+++ b/cas/etc/cas/config/cas.properties
@@ -1,6 +1,6 @@
 # Required CAS settings
-cas.server.name: https://cas.example.org:8443
-cas.server.prefix: https://cas.example.org:8443/cas
+cas.server.name: https://cas.mdr.nims.test:8443
+cas.server.prefix: https://cas.mdr.nims.test:8443/cas
 
 cas.httpWebRequest.header.hsts=false
 cas.adminPagesSecurity.ip=127\.0\.0\.1
diff --git a/cas/etc/cas/services/casmdrnimstest-1.json b/cas/etc/cas/services/casmdrnimstest-1.json
new file mode 100644
index 00000000..2a88c349
--- /dev/null
+++ b/cas/etc/cas/services/casmdrnimstest-1.json
@@ -0,0 +1,8 @@
+{
+  "@class" : "org.apereo.cas.services.RegexRegisteredService",
+  "serviceId" :  "^(https|http)://.*",
+  "name" : "cas.mdr.nims.test",
+  "id" : 1,
+  "logoutType" : "BACK_CHANNEL",
+  "logoutUrl" : "http://mdr.nims.test:3000/users/service"
+}
diff --git a/cas/etc/cas/services/castest-1.json b/cas/etc/cas/services/castest-1.json
deleted file mode 100644
index 3a431aa9..00000000
--- a/cas/etc/cas/services/castest-1.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-  "@class" : "org.apereo.cas.services.RegexRegisteredService",
-  "serviceId" :  "^(https|http)://.*",
-  "name" : "NIMS-CAStest",
-  "id" : 1,
-  "logoutType" : "BACK_CHANNEL"
-}
diff --git a/docker-compose.override.yml b/docker-compose.override.yml
index 03374cc5..4edb97b8 100644
--- a/docker-compose.override.yml
+++ b/docker-compose.override.yml
@@ -41,6 +41,11 @@ services:
       - cas
     environment:
       - RAILS_FORCE_SSL=false
+    networks:
+      internal:
+        aliases:
+          - web
+          - mdr.nims.test
 
   redis:
     volumes:
@@ -51,5 +56,9 @@ services:
       context: cas
     networks:
       internal:
+        aliases:
+          - cas
+          - cas.mdr.nims.test
+
     ports:
       - 8443:8443
diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index cfda50e3..a13263e5 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -27,6 +27,9 @@ gem 'turbolinks', '~> 5'
 gem 'jbuilder', '~> 2.5'
 # Use Redis adapter to run Action Cable in production
 gem 'redis', '~> 3.0'
+# Using redis to store sessions in the redis cache (rather than cookies) - this is to support single sign out
+# NB: Once we upgrade to rails >= 5.2 the gem can probably be removed as redis sessions are built in
+gem 'redis-session-store', '~> 0.11.1'
 # Use ActiveModel has_secure_password
 # gem 'bcrypt', '~> 3.1.7'
 
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index 20f7cbc5..be356c6d 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -704,6 +704,9 @@ GEM
     redis (3.3.5)
     redis-namespace (1.6.0)
       redis (>= 3.0.4)
+    redis-session-store (0.11.1)
+      actionpack (>= 3)
+      redis (>= 3, < 5)
     redlock (1.0.1)
       redis (>= 3.0.0, < 5.0)
     regexp_parser (1.6.0)
@@ -915,6 +918,7 @@ DEPENDENCIES
   puma (~> 3.12)
   rails (>= 5.0.6)
   redis (~> 3.0)
+  redis-session-store (~> 0.11.1)
   riiif (~> 2.0)
   rsolr (>= 1.0)
   rspec-rails
diff --git a/hyrax/config/initializers/session_store.rb b/hyrax/config/initializers/session_store.rb
index 65463958..e15473c4 100644
--- a/hyrax/config/initializers/session_store.rb
+++ b/hyrax/config/initializers/session_store.rb
@@ -1,3 +1,16 @@
 # Be sure to restart your server when you modify this file.
 
-Rails.application.config.session_store :cookie_store, key: '_hyrax_session'
+# NB the cookie session store is not compatible with single sign out - so we shall use a Redis-based session store instead (redis-session-store gem)
+redis_config = YAML.safe_load(ERB.new(IO.read(Rails.root.join('config', 'redis.yml'))).result)[Rails.env].with_indifferent_access
+Rails.application.config.session_store :redis_session_store, {
+    key: '_hyrax_session',
+    redis: {
+        expire_after: 90.minutes,  # cookie expiration
+        ttl: 90.minutes,           # Redis expiration, defaults to 'expire_after'
+        key_prefix: 'hyrax:session:',
+        url: "redis://#{redis_config[:host]}:#{redis_config[:port]}/0",
+    }
+}
+
+# monkey patch single sign out method
+require_relative '../../lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out'
diff --git a/hyrax/lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out.rb b/hyrax/lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out.rb
new file mode 100644
index 00000000..858ecdf6
--- /dev/null
+++ b/hyrax/lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out.rb
@@ -0,0 +1,23 @@
+# Monkey Patch to DeviseCasAuthenticatable::SingleSignOut::DestroySession#destroy_session_by_id to fix env issue
+
+module Extensions
+  module DeviseCasAuthenticatable
+    module SingleSignOut
+      module DestroySession
+        def destroy_session_by_id(sid)
+          logger.debug "Single Sign Out from session store: #{current_session_store.class}"
+          if session_store_class.name =~ /RedisSessionStore/
+            current_session_store.send(:destroy_session, {}, sid, drop: true)
+            true
+          else
+            logger.error "Unsupported session store: #{session_store_class.name}"
+            false
+          end
+        end
+      end
+    end
+  end
+end
+
+# monkey patch DestroySession
+::DeviseCasAuthenticatable::SingleSignOut::DestroySession.include Extensions::DeviseCasAuthenticatable::SingleSignOut::DestroySession

From 163dd528e3de739aa1ac0e1c6d317ed9eefcc272 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 15 Jan 2020 15:53:03 +0000
Subject: [PATCH 102/258] Create log4j2.xml

debug logging for CAS server
---
 cas/etc/cas/config/log4j2.xml | 117 ++++++++++++++++++++++++++++++++++
 1 file changed, 117 insertions(+)
 create mode 100644 cas/etc/cas/config/log4j2.xml

diff --git a/cas/etc/cas/config/log4j2.xml b/cas/etc/cas/config/log4j2.xml
new file mode 100644
index 00000000..36a22845
--- /dev/null
+++ b/cas/etc/cas/config/log4j2.xml
@@ -0,0 +1,117 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<!-- Specify the refresh internal in seconds. -->
+<Configuration monitorInterval="5" packages="org.apereo.cas.logging">
+  <Properties>
+    <!--
+    Default log directory is the current directory but that can be overridden with -Dcas.log.dir=<logdir>
+    Or you can change this property to a new default
+    -->
+    <Property name="cas.log.dir" >.</Property>
+    <!-- To see more CAS specific logging, adjust this property to info or debug or run server with -Dcas.log.leve=debug -->
+    <Property name="cas.log.level" >debug</Property>
+  </Properties>
+  <Appenders>
+    <Console name="console" target="SYSTEM_OUT">
+      <PatternLayout pattern="%d %p [%c] - &lt;%m&gt;%n"/>
+    </Console>
+    <RollingFile name="file" fileName="${sys:cas.log.dir}/cas.log" append="true"
+                 filePattern="${sys:cas.log.dir}/cas-%d{yyyy-MM-dd-HH}-%i.log">
+      <PatternLayout pattern="%d %p [%c] - &lt;%m&gt;%n"/>
+      <Policies>
+        <OnStartupTriggeringPolicy />
+        <SizeBasedTriggeringPolicy size="10 MB"/>
+        <TimeBasedTriggeringPolicy />
+      </Policies>
+    </RollingFile>
+    <RollingFile name="auditlogfile" fileName="${sys:cas.log.dir}/cas_audit.log" append="true"
+                 filePattern="${sys:cas.log.dir}/cas_audit-%d{yyyy-MM-dd-HH}-%i.log">
+      <PatternLayout pattern="%d %p [%c] - %m%n"/>
+      <Policies>
+        <OnStartupTriggeringPolicy />
+        <SizeBasedTriggeringPolicy size="10 MB"/>
+        <TimeBasedTriggeringPolicy />
+      </Policies>
+    </RollingFile>
+
+    <RollingFile name="perfFileAppender" fileName="${sys:cas.log.dir}/perfStats.log" append="true"
+                 filePattern="${sys:cas.log.dir}/perfStats-%d{yyyy-MM-dd-HH}-%i.log">
+      <PatternLayout pattern="%m%n"/>
+      <Policies>
+        <OnStartupTriggeringPolicy />
+        <SizeBasedTriggeringPolicy size="10 MB"/>
+        <TimeBasedTriggeringPolicy />
+      </Policies>
+    </RollingFile>
+
+    <CasAppender name="casAudit">
+      <AppenderRef ref="auditlogfile" />
+    </CasAppender>
+    <CasAppender name="casFile">
+      <AppenderRef ref="file" />
+    </CasAppender>
+    <CasAppender name="casConsole">
+      <AppenderRef ref="console" />
+    </CasAppender>
+    <CasAppender name="casPerf">
+      <AppenderRef ref="perfFileAppender" />
+    </CasAppender>
+  </Appenders>
+  <Loggers>
+    <!-- If adding a Logger with level set higher than warn, make category as selective as possible -->
+    <!-- Loggers inherit appenders from Root Logger unless additivity is false -->
+    <AsyncLogger name="org.apereo" level="${sys:cas.log.level}" includeLocation="true"/>
+    <AsyncLogger name="org.apereo.services.persondir" level="${sys:cas.log.level}" includeLocation="true"/>
+    <AsyncLogger name="org.apereo.cas.web.flow" level="info" includeLocation="true"/>
+    <AsyncLogger name="org.apache" level="warn" />
+    <AsyncLogger name="org.apache.http" level="error" />
+    <AsyncLogger name="org.springframework" level="warn" />
+    <AsyncLogger name="org.springframework.cloud.server" level="warn" />
+    <AsyncLogger name="org.springframework.cloud.client" level="warn" />
+    <AsyncLogger name="org.springframework.cloud.bus" level="warn" />
+    <AsyncLogger name="org.springframework.aop" level="warn" />
+    <AsyncLogger name="org.springframework.boot" level="warn" />
+    <AsyncLogger name="org.springframework.boot.actuate.autoconfigure" level="warn" />
+    <AsyncLogger name="org.springframework.webflow" level="warn" />
+    <AsyncLogger name="org.springframework.session" level="warn" />
+    <AsyncLogger name="org.springframework.amqp" level="error" />
+    <AsyncLogger name="org.springframework.integration" level="warn" />
+    <AsyncLogger name="org.springframework.messaging" level="warn" />
+    <AsyncLogger name="org.springframework.web" level="warn" />
+    <AsyncLogger name="org.springframework.orm.jpa" level="warn" />
+    <AsyncLogger name="org.springframework.scheduling" level="warn" />
+    <AsyncLogger name="org.springframework.context.annotation" level="error" />
+    <AsyncLogger name="org.springframework.boot.devtools" level="error" />
+    <AsyncLogger name="org.springframework.web.socket" level="warn" />
+    <AsyncLogger name="org.thymeleaf" level="warn" />
+    <AsyncLogger name="org.pac4j" level="warn" />
+    <AsyncLogger name="org.opensaml" level="warn"/>
+    <AsyncLogger name="net.sf.ehcache" level="warn" />
+    <AsyncLogger name="com.couchbase" level="warn" includeLocation="true"/>
+    <AsyncLogger name="com.ryantenney.metrics" level="warn" />
+    <AsyncLogger name="net.jradius" level="warn" />
+    <AsyncLogger name="org.openid4java" level="warn" />
+    <AsyncLogger name="org.ldaptive" level="warn" />
+    <AsyncLogger name="com.hazelcast" level="warn" />
+    <AsyncLogger name="org.apereo.spring" level="warn" />
+
+    <!-- Log perf stats only to perfStats.log -->
+    <AsyncLogger name="perfStatsLogger" level="info" additivity="false" includeLocation="true">
+      <AppenderRef ref="casPerf"/>
+    </AsyncLogger>
+
+    <!-- Log audit to all root appenders, and also to audit log (additivity is not false) -->
+    <AsyncLogger name="org.apereo.inspektr.audit.support" level="info" includeLocation="true" >
+      <AppenderRef ref="casAudit"/>
+    </AsyncLogger>
+
+    <!-- All Loggers inherit appenders specified here, unless additivity="false" on the Logger -->
+    <AsyncRoot level="warn">
+      <AppenderRef ref="casFile"/>
+      <!--
+           For deployment to an application server running as service,
+           delete the casConsole appender below
+      -->
+      <AppenderRef ref="casConsole"/>
+    </AsyncRoot>
+  </Loggers>
+</Configuration>

From 54143ce1a8ce9e46e57784f8f022053b66c78701 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 15 Jan 2020 18:56:03 +0000
Subject: [PATCH 103/258] monkey patch fix

---
 .../single_sign_out/destroy_session.rb        | 18 +++++++++++++++
 hyrax/config/initializers/session_store.rb    |  3 ---
 .../single_sign_out/single_sign_out.rb        | 23 -------------------
 3 files changed, 18 insertions(+), 26 deletions(-)
 create mode 100644 hyrax/app/patches/devise_cas_authenticatable/single_sign_out/destroy_session.rb
 delete mode 100644 hyrax/lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out.rb

diff --git a/hyrax/app/patches/devise_cas_authenticatable/single_sign_out/destroy_session.rb b/hyrax/app/patches/devise_cas_authenticatable/single_sign_out/destroy_session.rb
new file mode 100644
index 00000000..c57c772a
--- /dev/null
+++ b/hyrax/app/patches/devise_cas_authenticatable/single_sign_out/destroy_session.rb
@@ -0,0 +1,18 @@
+# Monkey Patch to DeviseCasAuthenticatable::SingleSignOut::DestroySession#destroy_session_by_id to fix env issue
+
+module DeviseCasAuthenticatable
+  module SingleSignOut
+    module DestroySession
+      def destroy_session_by_id(sid)
+        logger.debug "Single Sign Out from session store: #{current_session_store.class}"
+        if session_store_class.name =~ /RedisSessionStore/
+          current_session_store.send(:destroy_session, {}, sid, drop: true)
+          true
+        else
+          logger.error "Unsupported session store: #{session_store_class.name}"
+          false
+        end
+      end
+    end
+  end
+end
diff --git a/hyrax/config/initializers/session_store.rb b/hyrax/config/initializers/session_store.rb
index e15473c4..688ba657 100644
--- a/hyrax/config/initializers/session_store.rb
+++ b/hyrax/config/initializers/session_store.rb
@@ -11,6 +11,3 @@
         url: "redis://#{redis_config[:host]}:#{redis_config[:port]}/0",
     }
 }
-
-# monkey patch single sign out method
-require_relative '../../lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out'
diff --git a/hyrax/lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out.rb b/hyrax/lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out.rb
deleted file mode 100644
index 858ecdf6..00000000
--- a/hyrax/lib/extensions/devise_cas_authenticatable/single_sign_out/single_sign_out.rb
+++ /dev/null
@@ -1,23 +0,0 @@
-# Monkey Patch to DeviseCasAuthenticatable::SingleSignOut::DestroySession#destroy_session_by_id to fix env issue
-
-module Extensions
-  module DeviseCasAuthenticatable
-    module SingleSignOut
-      module DestroySession
-        def destroy_session_by_id(sid)
-          logger.debug "Single Sign Out from session store: #{current_session_store.class}"
-          if session_store_class.name =~ /RedisSessionStore/
-            current_session_store.send(:destroy_session, {}, sid, drop: true)
-            true
-          else
-            logger.error "Unsupported session store: #{session_store_class.name}"
-            false
-          end
-        end
-      end
-    end
-  end
-end
-
-# monkey patch DestroySession
-::DeviseCasAuthenticatable::SingleSignOut::DestroySession.include Extensions::DeviseCasAuthenticatable::SingleSignOut::DestroySession

From b201af80990f0974169a2270d120939818e1ac14 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Fri, 17 Jan 2020 10:50:49 +0000
Subject: [PATCH 104/258] temporarily disable apis

see issue #241
---
 hyrax/app/controllers/catalog_controller.rb   |  1 +
 .../concerns/disable_api_behavior.rb          | 19 +++++++++++++++++++
 .../controllers/hyrax/citations_controller.rb |  1 +
 .../controllers/hyrax/datasets_controller.rb  |  2 ++
 .../controllers/hyrax/file_sets_controller.rb |  1 +
 .../controllers/hyrax/images_controller.rb    |  2 ++
 .../hyrax/publications_controller.rb          |  2 ++
 .../app/controllers/hyrax/users_controller.rb |  2 ++
 .../app/controllers/hyrax/works_controller.rb |  2 ++
 hyrax/config/routes.rb                        |  4 ++--
 hyrax/spec/features/oai_pmh_spec.rb           |  4 +++-
 11 files changed, 37 insertions(+), 3 deletions(-)
 create mode 100644 hyrax/app/controllers/concerns/disable_api_behavior.rb

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index 54a10488..b4a55dec 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -2,6 +2,7 @@ class CatalogController < ApplicationController
   include Hydra::Catalog
   include Hydra::Controller::ControllerBehavior
   include BlacklightOaiProvider::CatalogControllerBehavior
+  include DisableApiBehavior
 
   # This filter applies the hydra access controls
   before_action :enforce_show_permissions, only: :show
diff --git a/hyrax/app/controllers/concerns/disable_api_behavior.rb b/hyrax/app/controllers/concerns/disable_api_behavior.rb
new file mode 100644
index 00000000..6bf87048
--- /dev/null
+++ b/hyrax/app/controllers/concerns/disable_api_behavior.rb
@@ -0,0 +1,19 @@
+# Temporarily disable API behaviour, see https://github.com/antleaf/nims-mdr-development/issues/241
+
+module DisableApiBehavior
+  def show
+    respond_to do |format|
+      format.html { super }
+      format.json { render json: { error: 'API is currently unavailable' }, status: 400 }
+      format.any { render plain: 'API is currently unavailable', content_type: 'text/plain', status: 400}
+    end
+  end
+
+  def index
+    respond_to do |format|
+      format.html { super }
+      format.json { render json: { error: 'API is currently unavailable' }, status: 400 }
+      format.any { render plain: 'API is currently unavailable', content_type: 'text/plain', status: 400}
+    end
+  end
+end
diff --git a/hyrax/app/controllers/hyrax/citations_controller.rb b/hyrax/app/controllers/hyrax/citations_controller.rb
index 1887e93b..6849b06b 100644
--- a/hyrax/app/controllers/hyrax/citations_controller.rb
+++ b/hyrax/app/controllers/hyrax/citations_controller.rb
@@ -3,6 +3,7 @@ class CitationsController < ApplicationController
     include WorksControllerBehavior
     include Breadcrumbs
     include SingularSubresourceController
+    prepend ::DisableApiBehavior
 
     # Overrides decide_layout from WorksControllerBehavior
     with_themed_layout '1_column'
diff --git a/hyrax/app/controllers/hyrax/datasets_controller.rb b/hyrax/app/controllers/hyrax/datasets_controller.rb
index 7aac5208..76353387 100644
--- a/hyrax/app/controllers/hyrax/datasets_controller.rb
+++ b/hyrax/app/controllers/hyrax/datasets_controller.rb
@@ -7,6 +7,8 @@ class DatasetsController < ApplicationController
     include Hyrax::WorksControllerBehavior
     include Hyrax::BreadcrumbsForWorks
     include ::ComplexFieldsBehavior
+    prepend ::DisableApiBehavior
+
     self.curation_concern_type = ::Dataset
 
     # Use this line if you want to use a custom presenter
diff --git a/hyrax/app/controllers/hyrax/file_sets_controller.rb b/hyrax/app/controllers/hyrax/file_sets_controller.rb
index 4c69d286..32e2809f 100644
--- a/hyrax/app/controllers/hyrax/file_sets_controller.rb
+++ b/hyrax/app/controllers/hyrax/file_sets_controller.rb
@@ -3,6 +3,7 @@ class FileSetsController < ApplicationController
     include Blacklight::Base
     include Blacklight::AccessControls::Catalog
     include Hyrax::Breadcrumbs
+    prepend ::DisableApiBehavior
 
     before_action :authenticate_user!, except: [:show, :citation, :stats]
     load_and_authorize_resource class: ::FileSet, except: :show
diff --git a/hyrax/app/controllers/hyrax/images_controller.rb b/hyrax/app/controllers/hyrax/images_controller.rb
index 56eb837b..c0a19b33 100644
--- a/hyrax/app/controllers/hyrax/images_controller.rb
+++ b/hyrax/app/controllers/hyrax/images_controller.rb
@@ -6,6 +6,8 @@ class ImagesController < ApplicationController
     # Adds Hyrax behaviors to the controller.
     include Hyrax::WorksControllerBehavior
     include Hyrax::BreadcrumbsForWorks
+    prepend ::DisableApiBehavior
+
     self.curation_concern_type = ::Image
 
     # Use this line if you want to use a custom presenter
diff --git a/hyrax/app/controllers/hyrax/publications_controller.rb b/hyrax/app/controllers/hyrax/publications_controller.rb
index 69035d55..eceeaeeb 100644
--- a/hyrax/app/controllers/hyrax/publications_controller.rb
+++ b/hyrax/app/controllers/hyrax/publications_controller.rb
@@ -7,6 +7,8 @@ class PublicationsController < ApplicationController
     include Hyrax::WorksControllerBehavior
     include Hyrax::BreadcrumbsForWorks
     include ::ComplexFieldsBehavior
+    prepend ::DisableApiBehavior
+
     self.curation_concern_type = ::Publication
 
     # Use this line if you want to use a custom presenter
diff --git a/hyrax/app/controllers/hyrax/users_controller.rb b/hyrax/app/controllers/hyrax/users_controller.rb
index 737f0ec6..92783ed1 100644
--- a/hyrax/app/controllers/hyrax/users_controller.rb
+++ b/hyrax/app/controllers/hyrax/users_controller.rb
@@ -1,6 +1,8 @@
 require_dependency Hyrax::Engine.config.root.join('app', 'controllers', 'hyrax', 'users_controller.rb').to_s
 
 class Hyrax::UsersController
+  prepend ::DisableApiBehavior
+
   def index
     authenticate_user! if Flipflop.hide_users_list?
     authorize! :index, ::User
diff --git a/hyrax/app/controllers/hyrax/works_controller.rb b/hyrax/app/controllers/hyrax/works_controller.rb
index 0753b1ed..5c8aa577 100644
--- a/hyrax/app/controllers/hyrax/works_controller.rb
+++ b/hyrax/app/controllers/hyrax/works_controller.rb
@@ -6,6 +6,8 @@ class WorksController < ApplicationController
     # Adds Hyrax behaviors to the controller.
     include Hyrax::WorksControllerBehavior
     include Hyrax::BreadcrumbsForWorks
+    prepend ::DisableApiBehavior
+
     self.curation_concern_type = ::Work
 
     # Use this line if you want to use a custom presenter
diff --git a/hyrax/config/routes.rb b/hyrax/config/routes.rb
index 57159bf0..f2b46c73 100644
--- a/hyrax/config/routes.rb
+++ b/hyrax/config/routes.rb
@@ -17,7 +17,7 @@
 
   concern :exportable, Blacklight::Routes::Exportable.new
   concern :searchable, Blacklight::Routes::Searchable.new
-  concern :oai_provider, BlacklightOaiProvider::Routes::Provider.new
+  #concern :oai_provider, BlacklightOaiProvider::Routes::Provider.new # Temporarily disable API behaviour, see https://github.com/antleaf/nims-mdr-development/issues/241
 
   curation_concerns_basic_routes
 
@@ -29,7 +29,7 @@
   end
 
   resource :catalog, only: [:index], as: 'catalog', path: '/catalog', controller: 'catalog' do
-    concerns :oai_provider
+    #concerns :oai_provider # Temporarily disable API behaviour, see https://github.com/antleaf/nims-mdr-development/issues/241
     concerns :searchable
   end
 
diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
index 2ae999b3..7e35b140 100644
--- a/hyrax/spec/features/oai_pmh_spec.rb
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -7,7 +7,9 @@
 
   before { work }
 
-  context 'oai interface with works present' do
+  scenario 'oai interface with works present' do
+    skip 'Temporarily disable API behaviour, see https://github.com/antleaf/nims-mdr-development/issues/241'
+
     it 'lists metadata prefixess' do
       visit oai_provider_catalog_path(verb: 'ListMetadataFormats')
       expect(page).to have_content('oai_dc')

From 30c845358c0c5f81bfaa6f7957a9bb2a3143069f Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 17 Jan 2020 11:21:44 +0000
Subject: [PATCH 105/258] Use loofah to sanitize incoming form data

---
 .../concerns/complex_fields_behavior.rb       | 104 ++++++++++++------
 hyrax/db/schema.rb                            |   1 -
 2 files changed, 69 insertions(+), 36 deletions(-)

diff --git a/hyrax/app/controllers/concerns/complex_fields_behavior.rb b/hyrax/app/controllers/concerns/complex_fields_behavior.rb
index 5f1a657c..f1513d9a 100644
--- a/hyrax/app/controllers/concerns/complex_fields_behavior.rb
+++ b/hyrax/app/controllers/concerns/complex_fields_behavior.rb
@@ -1,62 +1,61 @@
 module ComplexFieldsBehavior
-
   private
 
   def is_complex?(attribute_name)
-    complex_prefixes = [
-      'complex',
-      'instrument_function',
-      'manufacturer',
-      'managing_organization',
-      'supplier',
-      'manufacturer',
-      'custom_property'
+    complex_prefixes = %w[
+      complex
+      instrument_function
+      manufacturer
+      managing_organization
+      supplier
+      manufacturer
+      custom_property
     ]
     complex_prefixes.each { |prefix| return true if attribute_name.to_s.start_with? prefix }
     false
   end
 
   def hash_is_blank?(hash_param)
-    other_keys = hash_param.keys - ['id', '_destroy']
+    other_keys = hash_param.keys - %w[id _destroy]
     return false unless other_keys.blank?
-    if hash_param.fetch('id', nil) and hash_param.fetch('_destroy', nil)
-      return false if hash_param['_destroy'] == "true"
+    if hash_param.fetch('id', nil) && hash_param.fetch('_destroy', nil)
+      return false if hash_param['_destroy'] == 'true'
     end
     true
   end
 
-  # Delete person/organization from instrument and specimen_type where the record contains 
+  # Delete person/organization from instrument and specimen_type where the record contains
   #   only role=operator (person) or purpose=manufacturer/supplier (organization)
   #   this happens because we are validating nothing on instrument or speciment_type
   # This is temporary until proper validation is in place
   def cleanup_instrument_and_specimen_type(attribute)
     # complex_instrument
-    attribute['complex_instrument_attributes'].each_with_index do | complex_instrument, index |
-      complex_instrument['complex_person_attributes'].each_with_index do | complex_person, i |
+    attribute['complex_instrument_attributes'].each_with_index do |complex_instrument, index|
+      complex_instrument['complex_person_attributes'].each_with_index do |complex_person, i|
         if complex_person['name'].blank? && complex_person['role'].include?('operator')
           attribute['complex_instrument_attributes'][index]['complex_person_attributes'].delete_at(i)
         end
       end
-      complex_instrument['manufacturer_attributes'].each_with_index do | manufacturer, i |
+      complex_instrument['manufacturer_attributes'].each_with_index do |manufacturer, i|
         if manufacturer['organization'].blank? && manufacturer['purpose'].include?('Manufacturer')
           attribute['complex_instrument_attributes'][index]['manufacturer_attributes'].delete_at(i)
         end
       end
-      complex_instrument['managing_organization_attributes'].each_with_index do | managing_organization, i |
+      complex_instrument['managing_organization_attributes'].each_with_index do |managing_organization, i|
         if managing_organization['organization'].blank? && managing_organization['purpose'].include?('Managing organization')
           attribute['complex_instrument_attributes'][index]['managing_organization_attributes'].delete_at(i)
         end
       end
     end
     # complex_specimen_type
-    attribute['complex_specimen_type_attributes'].each_with_index do | complex_specimen_type, index |
-      complex_specimen_type['complex_purchase_record_attributes'].each_with_index do | complex_purchase_record, i |
-        complex_purchase_record['supplier_attributes'].each_with_index do | supplier, ii |
+    attribute['complex_specimen_type_attributes'].each_with_index do |complex_specimen_type, index|
+      complex_specimen_type['complex_purchase_record_attributes'].each_with_index do |complex_purchase_record, i|
+        complex_purchase_record['supplier_attributes'].each_with_index do |supplier, ii|
           if supplier['organization'].blank? && supplier['purpose'].include?('Supplier')
             attribute['complex_specimen_type_attributes'][index]['complex_purchase_record_attributes'][i]['supplier_attributes'].delete_at(ii)
           end
         end
-        complex_purchase_record['manufacturer_attributes'].each_with_index do | manufacturer, ii |
+        complex_purchase_record['manufacturer_attributes'].each_with_index do |manufacturer, ii|
           if manufacturer['organization'].blank? && manufacturer['purpose'].include?('Manufacturer')
             attribute['complex_specimen_type_attributes'][index]['complex_purchase_record_attributes'][i]['manufacturer_attributes'].delete_at(ii)
           end
@@ -67,28 +66,27 @@ def cleanup_instrument_and_specimen_type(attribute)
   end
 
   def cleanup_params(attribute)
-    if attribute.kind_of? Hash and attribute.keys.all? {|k| k !~ /\D/ }
+    if attribute.is_a?(Hash) && attribute.keys.all? { |k| k !~ /\D/ }
       # removes hashes with integer keys
       attribute = cleanup_params(attribute.values)
-    elsif attribute.kind_of? Hash
+    elsif attribute.is_a? Hash
       new_attribute = {}
       attribute.each do |k, v|
         v = cleanup_params(v) if is_complex?(k)
-        v = cleanup_params(v) if v.kind_of? Array
-        unless v.blank?
-          new_attribute[k] = v
-        end
-      end
-      unless hash_is_blank?(new_attribute)
-        new_attribute.compact
-      else
-        nil
+        v = cleanup_params(v) if v.is_a? Array
+        next if v.blank?
+        new_attribute[k] = if skip_controlled.include?(k) || k.end_with?('_attributes')
+                             v
+                           else
+                             sanitize_value(v)
+                           end
       end
-    elsif attribute.kind_of? Array
+      new_attribute.compact unless hash_is_blank?(new_attribute)
+    elsif attribute.is_a? Array
       new_attr = []
       attribute.reject(&:blank?).each do |v|
-        v = cleanup_params(v) if v.kind_of? Hash
-        new_attr << v unless v.blank?
+        v = cleanup_params(v) if v.is_a? Hash
+        new_attr << sanitize_value(v) unless v.blank?
       end
       new_attr.reject(&:blank?)
     elsif attribute.blank?
@@ -97,4 +95,40 @@ def cleanup_params(attribute)
       attribute
     end
   end
+
+  def sanitize_value(value)
+    if value.is_a? Array
+      value.map do |v|
+        if v.is_a? String
+          Loofah.fragment(v).scrub!(:strip).to_s
+        else
+          v
+        end
+      end
+    elsif value.is_a? String
+      Loofah.fragment(value).scrub!(:strip).to_s
+    else
+      value
+    end
+  end
+
+  # Don't scrub controlled fields
+  def skip_controlled
+    %w[
+      representative_id
+      thumbnail_id
+      visibility_during_embargo
+      visibility_after_embargo
+      visibility_during_lease
+      visibility_after_lease
+      visibility
+      admin_set_id
+      data_origin
+      version
+      _destroy
+      id
+      purpose
+      role
+    ]
+  end
 end
diff --git a/hyrax/db/schema.rb b/hyrax/db/schema.rb
index 6f7f370a..85bb24b8 100644
--- a/hyrax/db/schema.rb
+++ b/hyrax/db/schema.rb
@@ -279,7 +279,6 @@
     t.string "uri"
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
-    t.index ["local_authority_id", "label"], name: "index_qa_local_authority_entries_on_lower_label"
     t.index ["local_authority_id"], name: "index_qa_local_authority_entries_on_local_authority_id"
     t.index ["uri"], name: "index_qa_local_authority_entries_on_uri", unique: true
   end

From 960815b99d4ee2c2a85dd786d1657e5470f36d51 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 18 Jan 2020 00:11:21 +0900
Subject: [PATCH 106/258] require faraday_middleware

---
 hyrax/Gemfile      | 1 +
 hyrax/Gemfile.lock | 1 +
 2 files changed, 2 insertions(+)

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index 1da0a2ea..8718aeb8 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -72,6 +72,7 @@ gem 'hydra-role-management'
 gem 'bootstrap-datepicker-rails'
 gem 'pg'
 gem 'devise_ldap_authenticatable'
+gem 'faraday_middleware'
 
 gem 'riiif', '~> 2.0'
 
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index 50482af9..a8f6f113 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -897,6 +897,7 @@ DEPENDENCIES
   devise-guests (~> 0.6)
   devise_ldap_authenticatable
   factory_bot_rails
+  faraday_middleware
   fcrepo_wrapper
   hydra-role-management
   hyrax (~> 2.6)

From 6c99eb390921699de69bf1b675f3ff992c024843 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Wed, 22 Jan 2020 16:34:55 +0900
Subject: [PATCH 107/258] make characterization-methods, computational_methods
 and synthesis_and_processing supporting multi-value

---
 hyrax/app/models/dataset.rb                          |  6 +++---
 .../edit_fields/_characterization_methods.html.erb   |  2 +-
 .../edit_fields/_computational_methods.html.erb      |  2 +-
 .../edit_fields/_synthesis_and_processing.html.erb   |  2 +-
 hyrax/spec/indexers/dataset_indexer_spec.rb          |  6 +++---
 hyrax/spec/models/dataset_spec.rb                    | 12 ++++++------
 hyrax/spec/models/solr_document_spec.rb              |  6 +++---
 7 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index 05303a8d..b025ecb1 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -51,11 +51,11 @@ class Dataset < ActiveFedora::Base
 
   property :complex_organization, predicate: ::RDF::Vocab::ORG.organization, class_name:"ComplexOrganization"
 
-  property :characterization_methods, predicate: ::RDF::Vocab::NimsRdp['characterization-methods'], multiple: false do |index|
+  property :characterization_methods, predicate: ::RDF::Vocab::NimsRdp['characterization-methods'] do |index|
     index.as :stored_searchable, :facetable
   end
 
-  property :computational_methods, predicate: ::RDF::Vocab::NimsRdp['computational-methods'], multiple: false do |index|
+  property :computational_methods, predicate: ::RDF::Vocab::NimsRdp['computational-methods'] do |index|
     index.as :stored_searchable, :facetable
   end
 
@@ -93,7 +93,7 @@ class Dataset < ActiveFedora::Base
   property :complex_specimen_type, predicate: ::RDF::Vocab::NimsRdp['specimen-type'],
   class_name: "ComplexSpecimenType"
 
-  property :synthesis_and_processing, predicate: ::RDF::Vocab::NimsRdp['synthesis-and-processing'], multiple: false do |index|
+  property :synthesis_and_processing, predicate: ::RDF::Vocab::NimsRdp['synthesis-and-processing'] do |index|
     index.as :stored_searchable, :facetable
   end
 
diff --git a/hyrax/app/views/records/edit_fields/_characterization_methods.html.erb b/hyrax/app/views/records/edit_fields/_characterization_methods.html.erb
index c7f05b51..25cc2b2b 100644
--- a/hyrax/app/views/records/edit_fields/_characterization_methods.html.erb
+++ b/hyrax/app/views/records/edit_fields/_characterization_methods.html.erb
@@ -1,5 +1,5 @@
 <% service = CharacterizationMethodService.new %>
-<%= f.input :characterization_methods, as: :select,
+<%= f.input :characterization_methods, as: :multi_value_select,
     collection: service.select_active_options,
     include_blank: true,
     item_helper: service.method(:include_current_value),
diff --git a/hyrax/app/views/records/edit_fields/_computational_methods.html.erb b/hyrax/app/views/records/edit_fields/_computational_methods.html.erb
index cced795e..c7ee5cea 100644
--- a/hyrax/app/views/records/edit_fields/_computational_methods.html.erb
+++ b/hyrax/app/views/records/edit_fields/_computational_methods.html.erb
@@ -1,5 +1,5 @@
 <% service = ComputationalMethodService.new %>
-<%= f.input :computational_methods, as: :select,
+<%= f.input :computational_methods, as: :multi_value_select,
     collection: service.select_active_options,
     include_blank: true,
     item_helper: service.method(:include_current_value),
diff --git a/hyrax/app/views/records/edit_fields/_synthesis_and_processing.html.erb b/hyrax/app/views/records/edit_fields/_synthesis_and_processing.html.erb
index d3e05393..2963503f 100644
--- a/hyrax/app/views/records/edit_fields/_synthesis_and_processing.html.erb
+++ b/hyrax/app/views/records/edit_fields/_synthesis_and_processing.html.erb
@@ -1,5 +1,5 @@
 <% service = SynthesisAndProcessingService.new %>
-<%= f.input :synthesis_and_processing, as: :select,
+<%= f.input :synthesis_and_processing, as: :multi_value_select,
     collection: service.select_active_options,
     include_blank: true,
     item_helper: service.method(:include_current_value),
diff --git a/hyrax/spec/indexers/dataset_indexer_spec.rb b/hyrax/spec/indexers/dataset_indexer_spec.rb
index 34af4e7a..184879e5 100644
--- a/hyrax/spec/indexers/dataset_indexer_spec.rb
+++ b/hyrax/spec/indexers/dataset_indexer_spec.rb
@@ -272,7 +272,7 @@
 
   describe 'indexes characterization methods' do
     before do
-      obj = build(:dataset, characterization_methods: 'Method D')
+      obj = build(:dataset, characterization_methods: ['Method D'])
       @solr_document = obj.to_solr
     end
     it 'indexes as stored searchable' do
@@ -282,7 +282,7 @@
 
   describe 'indexes computational methods' do
     before do
-      obj = build(:dataset, computational_methods: 'Method D')
+      obj = build(:dataset, computational_methods: ['Method D'])
       @solr_document = obj.to_solr
     end
     it 'indexes as stored searchable' do
@@ -911,7 +911,7 @@
 
   describe 'indexes synthesis and processing' do
     before do
-      obj = build(:dataset, synthesis_and_processing: 'synthesis A')
+      obj = build(:dataset, synthesis_and_processing: ['synthesis A'])
       @solr_document = obj.to_solr
     end
     it 'indexes as stored searchable' do
diff --git a/hyrax/spec/models/dataset_spec.rb b/hyrax/spec/models/dataset_spec.rb
index 12bec99f..744ac464 100644
--- a/hyrax/spec/models/dataset_spec.rb
+++ b/hyrax/spec/models/dataset_spec.rb
@@ -437,15 +437,15 @@
 
   describe 'characterization_methods' do
     it 'has characterization_methods' do
-      @obj = build(:dataset, characterization_methods: 'Characterization methods')
-      expect(@obj.characterization_methods).to eq 'Characterization methods'
+      @obj = build(:dataset, characterization_methods: ['Characterization methods'])
+      expect(@obj.characterization_methods).to eq ['Characterization methods']
     end
   end
 
   describe 'computational_methods' do
     it 'has computational_methods' do
-      @obj = build(:dataset, computational_methods: 'computational methods')
-      expect(@obj.computational_methods).to eq 'computational methods'
+      @obj = build(:dataset, computational_methods: ['computational methods'])
+      expect(@obj.computational_methods).to eq ['computational methods']
     end
   end
 
@@ -851,8 +851,8 @@
 
   describe 'synthesis_and_processing' do
     it 'has synthesis_and_processing' do
-      @obj = build(:dataset, synthesis_and_processing: 'Synthesis and processing methods')
-      expect(@obj.synthesis_and_processing).to eq 'Synthesis and processing methods'
+      @obj = build(:dataset, synthesis_and_processing: ['Synthesis and processing methods'])
+      expect(@obj.synthesis_and_processing).to eq ['Synthesis and processing methods']
     end
   end
 
diff --git a/hyrax/spec/models/solr_document_spec.rb b/hyrax/spec/models/solr_document_spec.rb
index ff1464aa..9298f762 100644
--- a/hyrax/spec/models/solr_document_spec.rb
+++ b/hyrax/spec/models/solr_document_spec.rb
@@ -23,8 +23,8 @@
             complex_chemical_composition_attributes: [{ description: 'chemical composition 1' }]
           }],
           complex_version_attributes: [{ version: '1.0' }],
-          characterization_methods: 'Characterization methods',
-          computational_methods: 'computational methods',
+          characterization_methods: ['Characterization methods'],
+          computational_methods: ['computational methods'],
           data_origin: ['data origin'],
           origin_system_provenance: 'Origin A',
           properties_addressed: ['Properties Addressed'],
@@ -35,7 +35,7 @@
             relationship: 'IsPartOf'
           }],
           specimen_set: 'Specimen Set',
-          synthesis_and_processing: 'Synthesis and processing methods',
+          synthesis_and_processing: ['Synthesis and processing methods'],
           custom_property_attributes: [{ label: 'Full name', description: 'My full name is' }]
     )
   end

From 2b1b5f6055e0ea818eeb6c55bcc3b196837091a0 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Wed, 22 Jan 2020 19:28:58 +0900
Subject: [PATCH 108/258] use loofah :escape option to sanitize incoming data

---
 hyrax/app/controllers/concerns/complex_fields_behavior.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/controllers/concerns/complex_fields_behavior.rb b/hyrax/app/controllers/concerns/complex_fields_behavior.rb
index f1513d9a..2dec6e83 100644
--- a/hyrax/app/controllers/concerns/complex_fields_behavior.rb
+++ b/hyrax/app/controllers/concerns/complex_fields_behavior.rb
@@ -100,13 +100,13 @@ def sanitize_value(value)
     if value.is_a? Array
       value.map do |v|
         if v.is_a? String
-          Loofah.fragment(v).scrub!(:strip).to_s
+          Loofah.fragment(v).scrub!(:escape).to_s
         else
           v
         end
       end
     elsif value.is_a? String
-      Loofah.fragment(value).scrub!(:strip).to_s
+      Loofah.fragment(value).scrub!(:escape).to_s
     else
       value
     end

From 50ddfed3aa0aa181b5fede6a99a9ebc9fc8c489f Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 22 Jan 2020 22:30:31 +0000
Subject: [PATCH 109/258] cucumber fixes

---
 hyrax/features/contact/contact.feature        | 13 ++++++++++---
 hyrax/features/datasets/search_links.feature  |  2 +-
 hyrax/features/step_definitions/user_steps.rb |  6 +++---
 hyrax/features/users/index.feature            | 18 ++++++++++++------
 4 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/hyrax/features/contact/contact.feature b/hyrax/features/contact/contact.feature
index 3de62266..7861b76c 100644
--- a/hyrax/features/contact/contact.feature
+++ b/hyrax/features/contact/contact.feature
@@ -1,7 +1,7 @@
 Feature: Contact form
 
   Background:
-    Given an initialised sysem with a default admin set, permission template and workflow
+    Given an initialised system with a default admin set, permission template and workflow
 
   Scenario: Unauthenticated user can edit name and email in the contact form
     When I navigate to the contact form
@@ -9,8 +9,15 @@ Feature: Contact form
     And Name field is not readonly
     And Email field is not readonly
 
-  Scenario: General user cannot edit name and email in the contact form
-    Given I am logged in as a general user
+  Scenario: nims_other user cannot edit name and email in the contact form
+    Given I am logged in as a nims_other user
+    When I navigate to the contact form
+    Then I should see the contact form
+    But Name field is readonly
+    And Email field is readonly
+
+  Scenario: nims_researcher user cannot edit name and email in the contact form
+    Given I am logged in as a nims_researcher user
     When I navigate to the contact form
     Then I should see the contact form
     But Name field is readonly
diff --git a/hyrax/features/datasets/search_links.feature b/hyrax/features/datasets/search_links.feature
index 5c879717..f33cde97 100644
--- a/hyrax/features/datasets/search_links.feature
+++ b/hyrax/features/datasets/search_links.feature
@@ -1,6 +1,6 @@
 Feature: Search links on a dataset
   Background:
-    Given an initialised sysem with a default admin set, permission template and workflow
+    Given an initialised system with a default admin set, permission template and workflow
     And there is a dataset with:
       | TRAIT                                   |
       | open                                    |
diff --git a/hyrax/features/step_definitions/user_steps.rb b/hyrax/features/step_definitions/user_steps.rb
index ea2d4ab8..cc043756 100644
--- a/hyrax/features/step_definitions/user_steps.rb
+++ b/hyrax/features/step_definitions/user_steps.rb
@@ -13,7 +13,7 @@
   step 'I am logged in'
 end
 
-Given(/^there (?:are|is) (\d+) (general|admin) users?$/) do |number, user_type|
+Given(/^there (?:are|is) (\d+) (guest|nims_other|nims_researcher|admin) users?$/) do |number, user_type|
   @users ||= {}
   @users[user_type] = FactoryBot.create_list(:user, number, user_type.to_sym)
 end
@@ -22,7 +22,7 @@
   visit hyrax.users_path
 end
 
-Then(/^I should see the (general|admin) users?$/) do |user_type|
+Then(/^I should see the (guest|nims_other|nims_researcher|admin) users?$/) do |user_type|
   # first, verify @users is present and has some data
   expect(@users[user_type]).to be_present
 
@@ -32,7 +32,7 @@
   end
 end
 
-Then(/^I should not see the (general|admin) users?$/) do |user_type|
+Then(/^I should not see the (guest|nims_other|nims_researcher|admin) users?$/) do |user_type|
   # first, verify @users is present and has some data
   expect(@users[user_type]).to be_present
 
diff --git a/hyrax/features/users/index.feature b/hyrax/features/users/index.feature
index 1c1f78f8..c73df8bb 100644
--- a/hyrax/features/users/index.feature
+++ b/hyrax/features/users/index.feature
@@ -1,23 +1,29 @@
 Feature: Users index page
 
   Background:
-    Given there are 3 general users
+    Given there are 3 nims_researcher users
 
   Scenario: Unauthenticated user cannot view users
     When I navigate to the users list
-    Then I should not see the general users
+    Then I should not see the nims_researcher users
     And I should be redirected to the login page
 
-  Scenario: General user cannot view users
-    Given I am logged in as an general user
+  Scenario: nims_other user cannot view users
+    Given I am logged in as an nims_other user
     When I navigate to the users list
-    Then I should not see the general users
+    Then I should not see the nims_researcher users
+    And I should be redirected to the home page
+
+  Scenario: nims_researcher user cannot view users
+    Given I am logged in as an nims_researcher user
+    When I navigate to the users list
+    Then I should not see the nims_researcher users
     And I should be redirected to the home page
 
   Scenario: Admin user can view users
     Given I am logged in as an admin user
     When I navigate to the users list
-    Then I should see the general users
+    Then I should see the nims_researcher users
 
 #Feature: ユーザ一覧を参照する
 #現在登録されているユーザを確認するため

From 8ca00584642ef420b7871882b352b5c02a16bb8b Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 27 Jan 2020 20:15:22 +0000
Subject: [PATCH 110/258] wip - initial filtering version

---
 .../app/presenters/concerns/filtered_graph.rb  | 18 ++++++++++++++++++
 .../app/presenters/hyrax/dataset_presenter.rb  |  2 ++
 hyrax/app/presenters/hyrax/image_presenter.rb  |  2 ++
 .../presenters/hyrax/publication_presenter.rb  |  2 ++
 hyrax/app/presenters/hyrax/work_presenter.rb   |  1 +
 5 files changed, 25 insertions(+)
 create mode 100644 hyrax/app/presenters/concerns/filtered_graph.rb

diff --git a/hyrax/app/presenters/concerns/filtered_graph.rb b/hyrax/app/presenters/concerns/filtered_graph.rb
new file mode 100644
index 00000000..29e5c43e
--- /dev/null
+++ b/hyrax/app/presenters/concerns/filtered_graph.rb
@@ -0,0 +1,18 @@
+# Filters the RDF graph to remove some statements (abstract, supervisor) for ttl, nt and jsonld APIs (though not used by html or json)
+
+module FilteredGraph
+  private
+
+  def graph
+    RDF::Graph.new.insert(*unfiltered_graph.each_statement.to_a.reject { |statement| exclude?(statement) })
+  end
+
+  def unfiltered_graph
+    Hyrax::GraphExporter.new(solr_document, request).fetch
+  end
+
+  def exclude?(statement)
+    (statement.predicate.ends_with?('purl.org/dc/elements/1.1/description') && @current_ability.cannot?(:read_abstract, model_name.name.constantize)) ||
+        (statement.predicate.ends_with?('www.nims.go.jp/vocabs/ngdr/supervisor-approval'))
+  end
+end
diff --git a/hyrax/app/presenters/hyrax/dataset_presenter.rb b/hyrax/app/presenters/hyrax/dataset_presenter.rb
index 9f0ca20e..afafd5dd 100644
--- a/hyrax/app/presenters/hyrax/dataset_presenter.rb
+++ b/hyrax/app/presenters/hyrax/dataset_presenter.rb
@@ -8,5 +8,7 @@ class DatasetPresenter < Hyrax::WorkShowPresenter
       :complex_instrument, :origin_system_provenance, :properties_addressed,
       :complex_relation, :specimen_set, :complex_specimen_type,
       :synthesis_and_processing, :custom_property, to: :solr_document
+
+    prepend ::FilteredGraph
   end
 end
diff --git a/hyrax/app/presenters/hyrax/image_presenter.rb b/hyrax/app/presenters/hyrax/image_presenter.rb
index 4c195468..f7a3c5c1 100644
--- a/hyrax/app/presenters/hyrax/image_presenter.rb
+++ b/hyrax/app/presenters/hyrax/image_presenter.rb
@@ -5,5 +5,7 @@ class ImagePresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
       :complex_rights, :complex_version, :status, :specimen_set, :instrument,
       :complex_relation, :custom_property, to: :solr_document
+
+    prepend ::FilteredGraph
   end
 end
diff --git a/hyrax/app/presenters/hyrax/publication_presenter.rb b/hyrax/app/presenters/hyrax/publication_presenter.rb
index 17f2885b..4f3aed6f 100644
--- a/hyrax/app/presenters/hyrax/publication_presenter.rb
+++ b/hyrax/app/presenters/hyrax/publication_presenter.rb
@@ -5,5 +5,7 @@ class PublicationPresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
              :complex_rights, :complex_version, :complex_event, :issue, :place,
              :table_of_contents, :total_number_of_pages, :complex_source, to: :solr_document
+
+    prepend ::FilteredGraph
   end
 end
diff --git a/hyrax/app/presenters/hyrax/work_presenter.rb b/hyrax/app/presenters/hyrax/work_presenter.rb
index 71535ec2..b49e5b2e 100644
--- a/hyrax/app/presenters/hyrax/work_presenter.rb
+++ b/hyrax/app/presenters/hyrax/work_presenter.rb
@@ -2,5 +2,6 @@
 #  `rails generate hyrax:work Work`
 module Hyrax
   class WorkPresenter < Hyrax::WorkShowPresenter
+    prepend ::FilteredGraph
   end
 end

From 2fbab527b25ab0954a1997c5c8defe85562ed7f3 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Fri, 31 Jan 2020 20:35:10 +0000
Subject: [PATCH 111/258] fix for empty instruments and specimens

---
 hyrax/app/controllers/concerns/complex_fields_behavior.rb | 7 ++++++-
 hyrax/app/controllers/hyrax/datasets_controller.rb        | 6 ++++--
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/hyrax/app/controllers/concerns/complex_fields_behavior.rb b/hyrax/app/controllers/concerns/complex_fields_behavior.rb
index 2dec6e83..c93aa441 100644
--- a/hyrax/app/controllers/concerns/complex_fields_behavior.rb
+++ b/hyrax/app/controllers/concerns/complex_fields_behavior.rb
@@ -19,7 +19,7 @@ def hash_is_blank?(hash_param)
     other_keys = hash_param.keys - %w[id _destroy]
     return false unless other_keys.blank?
     if hash_param.fetch('id', nil) && hash_param.fetch('_destroy', nil)
-      return false if hash_param['_destroy'] == 'true'
+      return false if ['true', '1', true, 1].include? hash_param['_destroy']
     end
     true
   end
@@ -46,6 +46,11 @@ def cleanup_instrument_and_specimen_type(attribute)
           attribute['complex_instrument_attributes'][index]['managing_organization_attributes'].delete_at(i)
         end
       end
+      complex_instrument['complex_date_attributes'].each_with_index do |complex_date, i|
+        if complex_date['date'].blank? && complex_date['description'].include?('Processed')
+          attribute['complex_instrument_attributes'][index]['complex_date_attributes'].delete_at(i)
+        end
+      end
     end
     # complex_specimen_type
     attribute['complex_specimen_type_attributes'].each_with_index do |complex_specimen_type, index|
diff --git a/hyrax/app/controllers/hyrax/datasets_controller.rb b/hyrax/app/controllers/hyrax/datasets_controller.rb
index 7aac5208..2a2d0aea 100644
--- a/hyrax/app/controllers/hyrax/datasets_controller.rb
+++ b/hyrax/app/controllers/hyrax/datasets_controller.rb
@@ -14,13 +14,15 @@ class DatasetsController < ApplicationController
 
     def create
       safe_dataset_params = params['dataset'].permit(::Hyrax::DatasetForm.build_permitted_params)
-      params['dataset'] = cleanup_instrument_and_specimen_type(cleanup_params(safe_dataset_params.to_h))
+      # NB: need to cleanup twice
+      params['dataset'] = cleanup_params(cleanup_instrument_and_specimen_type(cleanup_params(safe_dataset_params.to_h)))
       super
     end
 
     def update
       safe_dataset_params = params['dataset'].permit(::Hyrax::DatasetForm.build_permitted_params)
-      params['dataset'] = cleanup_instrument_and_specimen_type(cleanup_params(safe_dataset_params.to_h))
+      # NB: need to cleanup twice
+      params['dataset'] = cleanup_params(cleanup_instrument_and_specimen_type(cleanup_params(safe_dataset_params.to_h)))
       super
     end
 

From 85adc5eafa14e67fcf4f42cbbe3957e5f27ae8a1 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Tue, 4 Feb 2020 11:49:01 +0900
Subject: [PATCH 112/258] add CAS_DESTINATION_URL

---
 .env.template                       | 1 +
 hyrax/config/initializers/devise.rb | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.env.template b/.env.template
index 458e3871..d1c3b815 100644
--- a/.env.template
+++ b/.env.template
@@ -113,6 +113,7 @@ CAS_BASE_URL=https://cas.nims.go.jp/
 
 # CAS_VALIDATE_URL may need to be set depending on how MDR is configured
 # CAS_VALIDATE_URL=https://cas:8443/cas/serviceValidate
+# CAS_DESTINATION_URL=https://portal.nims.test/
 
 # OAI config used in config/initializers/oai_config.rb
 OAI_REPOSTIORY_NAME='NIMS MDR'
diff --git a/hyrax/config/initializers/devise.rb b/hyrax/config/initializers/devise.rb
index 889c8510..852da1f5 100644
--- a/hyrax/config/initializers/devise.rb
+++ b/hyrax/config/initializers/devise.rb
@@ -310,7 +310,7 @@
   # URL via the destination param. Set either of these urls and specify either nil,
   # 'destination' or 'follow' as the logout_url_param. If the urls are blank but
   # logout_url_param is set, a default will be detected for the service.
-  # config.cas_destination_url = 'https://cas.myorganization.com'
+  config.cas_destination_url = ENV['CAS_DESTINATION_URL']
   # config.cas_follow_url = 'https://cas.myorganization.com'
   # config.cas_logout_url_param = nil
 

From 76d4554d6e17e780d8963a159f505937af55bf9d Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Wed, 5 Feb 2020 11:38:35 +0000
Subject: [PATCH 113/258] Fix issue with search for works user profile

---
 hyrax/app/views/hyrax/users/_vitals.html.erb | 21 ++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/users/_vitals.html.erb

diff --git a/hyrax/app/views/hyrax/users/_vitals.html.erb b/hyrax/app/views/hyrax/users/_vitals.html.erb
new file mode 100644
index 00000000..843b42f6
--- /dev/null
+++ b/hyrax/app/views/hyrax/users/_vitals.html.erb
@@ -0,0 +1,21 @@
+<%# Override Hyrax - fix bug with number of works search %>
+<div class="list-group-item">
+  <span class="glyphicon glyphicon-time" aria-hidden="true"></span> <%= t("hyrax.dashboard.stats.joined_on") %> <%= user.created_at.to_date.strftime("%b %d, %Y") %>
+</div>
+
+<div class="list-group-item">
+  <span class="badge"><%= number_of_collections(user) %></span>
+  <span class="glyphicon glyphicon-folder-open" aria-hidden="true"></span> 
+	<%= link_to t("hyrax.dashboard.stats.works"), main_app.search_catalog_path(f: {generic_type_sim: ['Collection'], depositor_ssim: [user.to_s]}) %>
+</div>
+
+<div class="list-group-item">
+  <span class="badge"><%= number_of_works(user) %></span>
+  <span class="glyphicon glyphicon-upload" aria-hidden="true"></span> 
+	<%= link_to t("hyrax.dashboard.stats.works"), main_app.search_catalog_path(f: {generic_type_sim: ['Work'], depositor_ssim: [user.to_s]}) %>
+
+  <ul class="views-downloads-dashboard list-unstyled">
+      <li><span class="badge badge-optional"><%= user.total_file_views %></span> <%= t("hyrax.dashboard.stats.file_views").pluralize(user.total_file_views) %></li>
+      <li><span class="badge badge-optional"><%= user.total_file_downloads %></span> <%= t("hyrax.dashboard.stats.file_downloads").pluralize(user.total_file_downloads) %></li>
+  </ul>
+</div>

From 5e37d994edc7ce3cb101406c445fdcacb7baf8c5 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Wed, 5 Feb 2020 13:03:27 +0000
Subject: [PATCH 114/258] use the default thumbnail for text file_sets; do not
 generate a thumbnail for them

---
 hyrax/app/models/file_set.rb                     | 11 ++++++++---
 .../file_set_derivatives_service_override.rb     | 16 ++++++++++++++++
 .../thumbnail_path_service_override.rb           |  7 +++++++
 3 files changed, 31 insertions(+), 3 deletions(-)
 create mode 100644 hyrax/config/initializers/file_set_derivatives_service_override.rb
 create mode 100644 hyrax/config/initializers/thumbnail_path_service_override.rb

diff --git a/hyrax/app/models/file_set.rb b/hyrax/app/models/file_set.rb
index 7e4e3816..1cb99abe 100644
--- a/hyrax/app/models/file_set.rb
+++ b/hyrax/app/models/file_set.rb
@@ -1,14 +1,13 @@
 # Generated by hyrax:models:install
 class FileSet < ActiveFedora::Base
-
   property :date_copyrighted, predicate: ::RDF::Vocab::DC.dateCopyrighted do |index|
     index.as :stored_searchable, type: :date
   end
 
   include ::Hyrax::FileSetBehavior
-  
+
   # override method in lib/hydra/works/models/concerns/file_set/mime_types.rb
-    #   add text/plain
+  #   add text/plain
   def self.office_document_mime_types
     [
       'text/plain',
@@ -24,4 +23,10 @@ def self.office_document_mime_types
       'application/vnd.openxmlformats-officedocument.presentationml.presentation'
     ]
   end
+
+  def text?
+    ['text/plain',
+     'text/csv',
+     'text/tab-separated-values'].include? mime_type
+  end
 end
diff --git a/hyrax/config/initializers/file_set_derivatives_service_override.rb b/hyrax/config/initializers/file_set_derivatives_service_override.rb
new file mode 100644
index 00000000..febc9cc2
--- /dev/null
+++ b/hyrax/config/initializers/file_set_derivatives_service_override.rb
@@ -0,0 +1,16 @@
+# Override Hyrax 2.6 to skip thumbnail creation for text files
+Hyrax::FileSetDerivativesService.class_eval do
+  def create_office_document_derivatives(filename)
+    # Don't create thumbnails for 'text/plain','text/csv','text/tab-separated-values','text/rtf'
+    unless file_set.text?
+      Hydra::Derivatives::DocumentDerivatives.create(filename,
+                                                     outputs: [{
+                                                       label: :thumbnail, format: 'jpg',
+                                                       size: '200x150>',
+                                                       url: derivative_url('thumbnail'),
+                                                       layer: 0
+                                                     }])
+    end
+    extract_full_text(filename, uri)
+  end
+end
diff --git a/hyrax/config/initializers/thumbnail_path_service_override.rb b/hyrax/config/initializers/thumbnail_path_service_override.rb
new file mode 100644
index 00000000..e8f9cb79
--- /dev/null
+++ b/hyrax/config/initializers/thumbnail_path_service_override.rb
@@ -0,0 +1,7 @@
+# Override Hyrax 2.6 to return default thumbnail for text
+Hyrax::ThumbnailPathService.class_eval do
+  def call(object)
+    return default_image if object.file_set? && object.text?
+    super
+  end
+end

From ce7e4afaea32a7cbbf1d896c41caf5826f5cb93c Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Wed, 5 Feb 2020 17:05:43 +0000
Subject: [PATCH 115/258] Expanded 'temporary' validation on complex fields to
 fix duplication issues

---
 .../concerns/complex_fields_behavior.rb       | 56 ++++++++++++-------
 1 file changed, 35 insertions(+), 21 deletions(-)

diff --git a/hyrax/app/controllers/concerns/complex_fields_behavior.rb b/hyrax/app/controllers/concerns/complex_fields_behavior.rb
index c93aa441..610e60e6 100644
--- a/hyrax/app/controllers/concerns/complex_fields_behavior.rb
+++ b/hyrax/app/controllers/concerns/complex_fields_behavior.rb
@@ -31,38 +31,52 @@ def hash_is_blank?(hash_param)
   def cleanup_instrument_and_specimen_type(attribute)
     # complex_instrument
     attribute['complex_instrument_attributes'].each_with_index do |complex_instrument, index|
-      complex_instrument['complex_person_attributes'].each_with_index do |complex_person, i|
-        if complex_person['name'].blank? && complex_person['role'].include?('operator')
-          attribute['complex_instrument_attributes'][index]['complex_person_attributes'].delete_at(i)
+      if complex_instrument['complex_person_attributes'].present?
+        complex_instrument['complex_person_attributes'].each_with_index do |complex_person, i|
+          if complex_person['name'].blank? && complex_person['role'].include?('operator')
+            attribute['complex_instrument_attributes'][index]['complex_person_attributes'].delete_at(i)
+          end
         end
       end
-      complex_instrument['manufacturer_attributes'].each_with_index do |manufacturer, i|
-        if manufacturer['organization'].blank? && manufacturer['purpose'].include?('Manufacturer')
-          attribute['complex_instrument_attributes'][index]['manufacturer_attributes'].delete_at(i)
+      if complex_instrument['manufacturer_attributes'].present?
+        complex_instrument['manufacturer_attributes'].each_with_index do |manufacturer, i|
+          if manufacturer['organization'].blank? && manufacturer['purpose'].include?('Manufacturer')
+            attribute['complex_instrument_attributes'][index]['manufacturer_attributes'].delete_at(i)
+          end
         end
       end
-      complex_instrument['managing_organization_attributes'].each_with_index do |managing_organization, i|
-        if managing_organization['organization'].blank? && managing_organization['purpose'].include?('Managing organization')
-          attribute['complex_instrument_attributes'][index]['managing_organization_attributes'].delete_at(i)
+      if complex_instrument['managing_organization_attributes'].present?
+        complex_instrument['managing_organization_attributes'].each_with_index do |managing_organization, i|
+          if managing_organization['organization'].blank? && managing_organization['purpose'].include?('Managing organization')
+            attribute['complex_instrument_attributes'][index]['managing_organization_attributes'].delete_at(i)
+          end
         end
       end
-      complex_instrument['complex_date_attributes'].each_with_index do |complex_date, i|
-        if complex_date['date'].blank? && complex_date['description'].include?('Processed')
-          attribute['complex_instrument_attributes'][index]['complex_date_attributes'].delete_at(i)
+      if complex_instrument['complex_date_attributes'].present?
+        complex_instrument['complex_date_attributes'].each_with_index do |complex_date, i|
+          if complex_date.present?
+            if complex_date['date'].blank? && complex_date['description'].include?('Processed')
+              attribute['complex_instrument_attributes'][index]['complex_date_attributes'].delete_at(i)
+            end
+          end
         end
       end
     end
     # complex_specimen_type
     attribute['complex_specimen_type_attributes'].each_with_index do |complex_specimen_type, index|
-      complex_specimen_type['complex_purchase_record_attributes'].each_with_index do |complex_purchase_record, i|
-        complex_purchase_record['supplier_attributes'].each_with_index do |supplier, ii|
-          if supplier['organization'].blank? && supplier['purpose'].include?('Supplier')
-            attribute['complex_specimen_type_attributes'][index]['complex_purchase_record_attributes'][i]['supplier_attributes'].delete_at(ii)
+      if complex_specimen_type['complex_purchase_record_attributes'].present?
+        complex_specimen_type['complex_purchase_record_attributes'].each_with_index do |complex_purchase_record, i|
+          if complex_purchase_record['supplier_attributes'].present?
+            complex_purchase_record['supplier_attributes'].each_with_index do |supplier, ii|
+              if supplier['organization'].blank? && supplier['purpose'].include?('Supplier')
+                attribute['complex_specimen_type_attributes'][index]['complex_purchase_record_attributes'][i]['supplier_attributes'].delete_at(ii)
+              end
+            end
           end
-        end
-        complex_purchase_record['manufacturer_attributes'].each_with_index do |manufacturer, ii|
-          if manufacturer['organization'].blank? && manufacturer['purpose'].include?('Manufacturer')
-            attribute['complex_specimen_type_attributes'][index]['complex_purchase_record_attributes'][i]['manufacturer_attributes'].delete_at(ii)
+          complex_purchase_record['manufacturer_attributes'].each_with_index do |manufacturer, ii|
+            if manufacturer['organization'].blank? && manufacturer['purpose'].include?('Manufacturer')
+              attribute['complex_specimen_type_attributes'][index]['complex_purchase_record_attributes'][i]['manufacturer_attributes'].delete_at(ii)
+            end
           end
         end
       end
@@ -73,7 +87,7 @@ def cleanup_instrument_and_specimen_type(attribute)
   def cleanup_params(attribute)
     if attribute.is_a?(Hash) && attribute.keys.all? { |k| k !~ /\D/ }
       # removes hashes with integer keys
-      attribute = cleanup_params(attribute.values)
+      cleanup_params(attribute.values)
     elsif attribute.is_a? Hash
       new_attribute = {}
       attribute.each do |k, v|

From f0e4f113533dc755dfa08f7cc69f4a53acf5a3c6 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Tue, 11 Feb 2020 20:45:03 +0000
Subject: [PATCH 116/258] small fix for i239 app reload bug

---
 hyrax/config/initializers/work_form_override.rb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/hyrax/config/initializers/work_form_override.rb b/hyrax/config/initializers/work_form_override.rb
index fab08cf1..174cb570 100644
--- a/hyrax/config/initializers/work_form_override.rb
+++ b/hyrax/config/initializers/work_form_override.rb
@@ -1,10 +1,10 @@
 # Overriding changes introduced to the initialize_field method in Hyrax commit 
 # https://github.com/samvera/hyrax/commit/89ffdb757a7ae545e303919d2277901237a5fd30
 # To solve issue https://github.com/CottageLabs/willow-hyrax/issues/6
-Hyrax::Forms::WorkForm.class_eval do
-  def initialize_field(key)
-    super unless [:embargo_release_date, :lease_expiration_date].include?(key)
+Rails.configuration.to_prepare do
+  Hyrax::Forms::WorkForm.class_eval do
+    def initialize_field(key)
+      super unless [:embargo_release_date, :lease_expiration_date].include?(key)
+    end
   end
 end
-
-

From 41bc5ca8cd557023cbbd18ac708cdc7bbad47550 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 12 Feb 2020 19:39:32 +0000
Subject: [PATCH 117/258] new ttl dataset export test

---
 hyrax/spec/factories/dataset.rb               |  4 +
 .../hyrax/dataset_presenter_spec.rb           | 77 ++++++++++++++++++-
 2 files changed, 77 insertions(+), 4 deletions(-)

diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 76296b42..7b8ff310 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -29,6 +29,10 @@
       title { ["Restricted Dataset"] }
     end
 
+    trait :with_description_abstract do
+      description { ["Abstract-Description-123"] }
+    end
+
     trait :with_description_seq do
       sequence(:description) { |n| ["Abstract-Description-#{n}"] }
     end
diff --git a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
index 1d69ff0f..cf203064 100644
--- a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
@@ -1,9 +1,78 @@
-# Generated via
-#  `rails generate hyrax:work Dataset`
 require 'rails_helper'
 
 RSpec.describe Hyrax::DatasetPresenter do
-  it "has tests" do
-    skip "Add your tests here"
+  let(:dataset) { create(:dataset, :open, :with_alternative_title, :with_description_abstract) }
+  let(:solr_document) { SolrDocument.new(dataset.to_solr) }
+  let(:host) { double(host: 'http://example.org/') }
+
+  let(:presenter) { described_class.new(solr_document, Ability.new(user), host) }
+
+  let(:ttl_regex) {
+    [
+      %r(<http://example.org//concern/datasets/#{dataset.id}> a),
+      %r(<http://projecthydra.org/works/models#Work>),
+      %r(<http://pcdm.org/models#Object>),
+      %r(<http://purl.org/dc/terms/title> "Open Dataset";),
+      %r(<http://purl.org/dc/terms/alternative> "Alternative-Title-123";),
+      %r(<http://www.w3.org/ns/auth/acl#accessControl> <http://example.org//catalog/([a-f0-9\\-]*)+>;),
+      %r(<info:fedora/fedora-system:def/model#hasModel> "Dataset" .)
+    ]
+  }
+  let(:ttl_regex_abstract) { %r(<http://purl.org/dc/elements/1.1/description> "Abstract-Description-123";) }
+
+  describe '#export_as_ttl' do
+    subject { presenter.export_as_ttl }
+    let(:user) { nil }
+    it 'generates ttl' do
+      ttl_regex.each do |regex|
+        expect(subject).to match(regex)
+      end
+    end
+
+    context 'anonymous user' do
+      it { is_expected.not_to match(ttl_regex_abstract) }
+    end
+
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to match(ttl_regex_abstract) }
+    end
   end
+
+
+
+
+
+
+  # # let(:graph) { Hyrax::GraphExporter.new(solr_document, host).fetch }
+  #
+  # let(:ttl) { graph.dump(:ttl) }
+  # let(:dmp) {  graph.each_statement {|s| puts "SUBJ: #{s.subject}\tPRED:#{s.predicate}\tOBJ: #{s.object}" } }
+  #
+  # # let(:replacer) { ->(id, _graph) {
+  # #     puts "id: #{id.inspect}\n _graph: #{_graph.inspect}"
+  # #   }
+  # # }
+  #
+  #
+  # #let(:connection) { Hyrax::CleanConnection.new(ActiveFedora.fedora.connection) }
+  # #let(:clean_graph_repository) { Hydra::ContentNegotiation::CleanGraphRepository.new(connection, replacer) }
+  # #let(:clean_graph) { clean_graph_repository.find(solr_document.id) }
+  #
+  # let(:clean_graph) {
+  #   RDF::Graph.new.insert(*graph.each_statement.to_a.reject { |statement| statement.predicate == 'http://purl.org/dc/elements/1.1/description' })
+  # }
+  #
+  # let(:clean_ttl) { clean_graph.dump(:ttl) }
+  # let(:clean_dmp) {  clean_graph.each_statement {|s| puts "SUBJ: #{s.subject}\tPRED:#{s.predicate}\tOBJ: #{s.object}" } }
+  #
+  #
+  # it "filters abstract for anonymous users" do
+  #   # puts graph.inspect
+  #   require 'byebug'
+  #   byebug
+  #
+  #
+  #
+  # end
 end

From c1ad22f1c153d8439c6466b6fa75db5f7b69f2fb Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 12 Feb 2020 23:51:02 +0000
Subject: [PATCH 118/258] more dataset presenter tests

now checks ttl, nt and jsonld
---
 hyrax/spec/factories/dataset.rb               |   4 +
 .../hyrax/dataset_presenter_spec.rb           | 135 +++++++++++-------
 2 files changed, 87 insertions(+), 52 deletions(-)

diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 7b8ff310..6179baf1 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -356,5 +356,9 @@
         }]
       }
     end
+
+    trait :with_supervisor_approval do
+      supervisor_approval { ['Professor Supervisor Approval'] }
+    end
   end
 end
diff --git a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
index cf203064..a8d06cdd 100644
--- a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
@@ -1,78 +1,109 @@
 require 'rails_helper'
 
 RSpec.describe Hyrax::DatasetPresenter do
-  let(:dataset) { create(:dataset, :open, :with_alternative_title, :with_description_abstract) }
+  let(:dataset) { create(:dataset, :open, :with_alternative_title, :with_description_abstract, :with_supervisor_approval) }
   let(:solr_document) { SolrDocument.new(dataset.to_solr) }
-  let(:host) { double(host: 'http://example.org/') }
-
+  let(:host) { double(host: 'http://example.org') }
+  let(:user) { nil }
   let(:presenter) { described_class.new(solr_document, Ability.new(user), host) }
 
-  let(:ttl_regex) {
-    [
-      %r(<http://example.org//concern/datasets/#{dataset.id}> a),
-      %r(<http://projecthydra.org/works/models#Work>),
-      %r(<http://pcdm.org/models#Object>),
-      %r(<http://purl.org/dc/terms/title> "Open Dataset";),
-      %r(<http://purl.org/dc/terms/alternative> "Alternative-Title-123";),
-      %r(<http://www.w3.org/ns/auth/acl#accessControl> <http://example.org//catalog/([a-f0-9\\-]*)+>;),
-      %r(<info:fedora/fedora-system:def/model#hasModel> "Dataset" .)
-    ]
-  }
-  let(:ttl_regex_abstract) { %r(<http://purl.org/dc/elements/1.1/description> "Abstract-Description-123";) }
-
   describe '#export_as_ttl' do
     subject { presenter.export_as_ttl }
-    let(:user) { nil }
-    it 'generates ttl' do
-      ttl_regex.each do |regex|
+    let(:export_regex) {
+      [
+        %r(<http://example.org/concern/datasets/#{dataset.id}> a),
+        %r(<http://projecthydra.org/works/models#Work>),
+        %r(<http://pcdm.org/models#Object>),
+        %r(<http://purl.org/dc/terms/title> "Open Dataset";),
+        %r(<http://purl.org/dc/terms/alternative> "Alternative-Title-123";),
+        %r(<http://www.w3.org/ns/auth/acl#accessControl> <http://example.org/catalog/([a-f0-9\\-]*)+>;),
+        %r(<info:fedora/fedora-system:def/model#hasModel> "Dataset" .)
+      ]
+    }
+    let(:abstract_regex) { %r(<http://purl.org/dc/elements/1.1/description> "Abstract-Description-123";) }
+    let(:supervisor_regex) { %r(<http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor Supervisor Approval";) }
+
+    it 'exports' do
+      export_regex.each do |regex|
         expect(subject).to match(regex)
       end
     end
 
     context 'anonymous user' do
-      it { is_expected.not_to match(ttl_regex_abstract) }
+      it { is_expected.not_to match(abstract_regex) }
+      it { is_expected.not_to match(supervisor_regex) }
     end
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to match(ttl_regex_abstract) }
+      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(supervisor_regex) }
     end
   end
 
+  describe '#export_as_nt' do
+    subject { presenter.export_as_nt }
+    let(:export_regex) {
+      [
+        %r(<http://example.org/concern/datasets/#{dataset.id}> <http://www.w3.org/ns/auth/acl#accessControl> <http://example.org/catalog/([a-f0-9\\-]*)+>),
+        %r(<http://example.org/concern/datasets/#{dataset.id}> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://projecthydra.org/works/models#Work>),
+        %r(<http://example.org/concern/datasets/#{dataset.id}> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://pcdm.org/models#Object>),
+        %r(<http://example.org/concern/datasets/#{dataset.id}> <info:fedora/fedora-system:def/model#hasModel> "Dataset"),
+        %r(<http://example.org/concern/datasets/#{dataset.id}> <http://purl.org/dc/terms/alternative> "Alternative-Title-123"),
+        %r(<http://example.org/concern/datasets/#{dataset.id}> <http://purl.org/dc/terms/title> "Open Dataset")
+      ]
+    }
+    let(:abstract_regex) { %r(<http://example.org/concern/datasets/#{dataset.id}> <http://purl.org/dc/elements/1.1/description> "Abstract-Description-123") }
+    let(:supervisor_regex) { %r(<http://example.org/concern/datasets/#{dataset.id}> <http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor Supervisor Approval") }
 
+    it 'exports' do
+      export_regex.each do |regex|
+        expect(subject).to match(regex)
+      end
+    end
 
+    context 'anonymous user' do
+      it { is_expected.not_to match(abstract_regex) }
+      it { is_expected.not_to match(supervisor_regex) }
+    end
 
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(supervisor_regex) }
+    end
+  end
+
+  describe '#export_as_jsonld' do
+    subject { JSON.parse(presenter.export_as_jsonld) }
+    # NB: it is important to use => rather than a colon: - otherwise the strings get symbolised
 
+    it 'exports' do
+      expect(subject["@context"]).to include(
+        "pcdmterms" => "http://pcdm.org/models#",
+        "worksterms" => "http://projecthydra.org/works/models#",
+        "dc" => "http://purl.org/dc/terms/",
+        "acl" => "http://www.w3.org/ns/auth/acl#",
+        "system" => "info:fedora/fedora-system:",
+        "model" => "system:def/model#"
+      )
+      expect(subject["@id"]).to eql "http://example.org/concern/datasets/#{dataset.id}"
+      expect(subject["dc:title"]).to eql "Open Dataset"
+      expect(subject["dc:alternative"]).to eql "Alternative-Title-123"
+      expect(subject["model:hasModel"]).to eql "Dataset"
+      expect(subject["acl:accessControl"]).to include("@id")
+      expect(subject["@type"]).to match_array %w(pcdmterms:Object worksterms:Work)
+    end
+
+    context 'anonymous user' do
+      it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
+      it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor Supervisor Approval") }
+    end
 
-  # # let(:graph) { Hyrax::GraphExporter.new(solr_document, host).fetch }
-  #
-  # let(:ttl) { graph.dump(:ttl) }
-  # let(:dmp) {  graph.each_statement {|s| puts "SUBJ: #{s.subject}\tPRED:#{s.predicate}\tOBJ: #{s.object}" } }
-  #
-  # # let(:replacer) { ->(id, _graph) {
-  # #     puts "id: #{id.inspect}\n _graph: #{_graph.inspect}"
-  # #   }
-  # # }
-  #
-  #
-  # #let(:connection) { Hyrax::CleanConnection.new(ActiveFedora.fedora.connection) }
-  # #let(:clean_graph_repository) { Hydra::ContentNegotiation::CleanGraphRepository.new(connection, replacer) }
-  # #let(:clean_graph) { clean_graph_repository.find(solr_document.id) }
-  #
-  # let(:clean_graph) {
-  #   RDF::Graph.new.insert(*graph.each_statement.to_a.reject { |statement| statement.predicate == 'http://purl.org/dc/elements/1.1/description' })
-  # }
-  #
-  # let(:clean_ttl) { clean_graph.dump(:ttl) }
-  # let(:clean_dmp) {  clean_graph.each_statement {|s| puts "SUBJ: #{s.subject}\tPRED:#{s.predicate}\tOBJ: #{s.object}" } }
-  #
-  #
-  # it "filters abstract for anonymous users" do
-  #   # puts graph.inspect
-  #   require 'byebug'
-  #   byebug
-  #
-  #
-  #
-  # end
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
+      it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor Supervisor Approval") }
+    end
+  end
 end

From be51551ae333377e3018e6bf9e65d3c25a818fb2 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 13 Feb 2020 16:58:22 +0000
Subject: [PATCH 119/258] add filtering to json builder

---
 hyrax/app/models/ability.rb                   |   2 +
 .../app/presenters/concerns/filtered_graph.rb |   6 +-
 hyrax/app/views/hyrax/base/show.json.jbuilder |   8 +
 hyrax/spec/factories/dataset.rb               |   2 +-
 hyrax/spec/factories/image.rb                 | 146 +++++++++---------
 hyrax/spec/features/oai_pmh_spec.rb           |  10 ++
 .../hyrax/dataset_presenter_spec.rb           |   8 +-
 .../presenters/hyrax/image_presenter_spec.rb  | 100 +++++++++++-
 .../datasets/_attribute_rows.html_spec.rb     |   7 +-
 9 files changed, 207 insertions(+), 82 deletions(-)
 create mode 100644 hyrax/app/views/hyrax/base/show.json.jbuilder

diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index 58f899ac..aed95c93 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -38,6 +38,8 @@ def read_metadata
     can :read_abstract, [::Dataset, ::Image, ::Publication] if current_user.authenticated?
     can :read_alternative_title, [::Dataset, ::Image, ::Publication]
     # NB: no users can :read_application_number
+    # NB: no users can :read_supervisor_approval (though it is visible on the edit form to users with permission to edit)
+    cannot :read_supervisor_approval, [::Dataset, ::Image, ::Publication]
     can :read_creator, [::Dataset, ::Image, ::Publication]
     can :read_date, [::Dataset, ::Image, ::Publication]
     can :read_event, [::Publication]
diff --git a/hyrax/app/presenters/concerns/filtered_graph.rb b/hyrax/app/presenters/concerns/filtered_graph.rb
index 29e5c43e..64da5156 100644
--- a/hyrax/app/presenters/concerns/filtered_graph.rb
+++ b/hyrax/app/presenters/concerns/filtered_graph.rb
@@ -12,7 +12,9 @@ def unfiltered_graph
   end
 
   def exclude?(statement)
-    (statement.predicate.ends_with?('purl.org/dc/elements/1.1/description') && @current_ability.cannot?(:read_abstract, model_name.name.constantize)) ||
-        (statement.predicate.ends_with?('www.nims.go.jp/vocabs/ngdr/supervisor-approval'))
+    # Returns true if the statement should be filtered out of the graph
+    model = model_name.name.constantize
+    (statement.predicate.ends_with?('purl.org/dc/elements/1.1/description') && @current_ability.cannot?(:read_abstract, model)) ||
+      (statement.predicate.ends_with?('www.nims.go.jp/vocabs/ngdr/supervisor-approval') && @current_ability.cannot?(:read_supervisor_approval, model))
   end
 end
diff --git a/hyrax/app/views/hyrax/base/show.json.jbuilder b/hyrax/app/views/hyrax/base/show.json.jbuilder
new file mode 100644
index 00000000..5087735c
--- /dev/null
+++ b/hyrax/app/views/hyrax/base/show.json.jbuilder
@@ -0,0 +1,8 @@
+model = @curation_concern.class
+fields = @curation_concern.class.fields
+             .reject { |f| [:has_model].include? f }
+             .reject { |f| f == :description && current_ability.cannot?(:read_abstract, model) }
+             .reject { |f| f == :supervisor_approval && current_ability.cannot?(:read_supervisor_approval, model) }
+
+j = json.extract! @curation_concern, *[:id] + fields
+json.version @curation_concern.etag
diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 6179baf1..1fea9f06 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -358,7 +358,7 @@
     end
 
     trait :with_supervisor_approval do
-      supervisor_approval { ['Professor Supervisor Approval'] }
+      supervisor_approval { ['Professor-Supervisor-Approval'] }
     end
   end
 end
diff --git a/hyrax/spec/factories/image.rb b/hyrax/spec/factories/image.rb
index 9510b9fc..a3de1a2d 100644
--- a/hyrax/spec/factories/image.rb
+++ b/hyrax/spec/factories/image.rb
@@ -3,88 +3,94 @@
   factory :image do
     title { ["Image"] }
     access_control
-    skip_create
-    override_new_record
-  end
+    # skip_create
+    # override_new_record
 
-  trait :open do
-    visibility { 'open' }
-    title { ["Open Image"] }
-  end
 
-  trait :with_alternative_title do
-    alternative_title { 'Alternative-Title-123' }
-  end
+    trait :open do
+      visibility { 'open' }
+      title { ["Open Image"] }
+    end
 
-  trait :with_subject do
-    subject { ['Subject-123'] }
-  end
+    trait :with_alternative_title do
+      alternative_title { 'Alternative-Title-123' }
+    end
 
-  trait :with_publisher do
-    publisher { ['Publisher-123'] }
-  end
+    trait :with_subject do
+      subject { ['Subject-123'] }
+    end
 
-  trait :with_language do
-    language { ['Faroese'] }
-  end
+    trait :with_publisher do
+      publisher { ['Publisher-123'] }
+    end
 
-  trait :with_keyword do
-    keyword { ['Keyword-123'] }
-  end
+    trait :with_language do
+      language { ['Faroese'] }
+    end
 
-  trait :with_resource_type do
-    resource_type { ['Resource-Type-123'] }
-  end
+    trait :with_keyword do
+      keyword { ['Keyword-123'] }
+    end
 
-  trait :with_rights_statement do
-    rights_statement { ['Rights-Statement-123'] }
-  end
+    trait :with_resource_type do
+      resource_type { ['Resource-Type-123'] }
+    end
 
-  trait :with_complex_date do
-    complex_date_attributes {
-      [{
-         date: '2019-05-28',
-         description: 'Published'
-       }]
-    }
-  end
+    trait :with_rights_statement do
+      rights_statement { ['Rights-Statement-123'] }
+    end
 
-  trait :with_complex_identifier do
-    complex_identifier_attributes {
-      [
-        { identifier: '10.0.1111', scheme: 'http://dx.doi.org', label: 'DOI' },
-        { identifier: '10.0.2222', scheme: 'HTTPS://DX.DOI.ORG', label: 'DOI' },
-        { identifier: '3333', label: 'Local ID' }
-      ]
-    }
-  end
+    trait :with_complex_date do
+      complex_date_attributes {
+        [{
+           date: '2019-05-28',
+           description: 'Published'
+         }]
+      }
+    end
 
-  trait :with_complex_person do
-    complex_person_attributes {
-      [{
-         name: 'Complex-Person-123',
-         role: ['operator']
-       }]
-    }
-  end
+    trait :with_complex_identifier do
+      complex_identifier_attributes {
+        [
+          { identifier: '10.0.1111', scheme: 'http://dx.doi.org', label: 'DOI' },
+          { identifier: '10.0.2222', scheme: 'HTTPS://DX.DOI.ORG', label: 'DOI' },
+          { identifier: '3333', label: 'Local ID' }
+        ]
+      }
+    end
 
-  trait :with_complex_rights do
-    complex_rights_attributes {
-      [{
-         date: '1978-10-28',
-         rights: 'http://creativecommons.org/publicdomain/zero/1.0/'
-       }]
-    }
-  end
+    trait :with_complex_person do
+      complex_person_attributes {
+        [{
+           name: 'Complex-Person-123',
+           role: ['operator']
+         }]
+      }
+    end
+
+    trait :with_complex_rights do
+      complex_rights_attributes {
+        [{
+           date: '1978-10-28',
+           rights: 'http://creativecommons.org/publicdomain/zero/1.0/'
+         }]
+      }
+    end
 
-  trait :with_complex_version do
-    complex_version_attributes {
-      [{
-         date: '1978-10-28',
-         description: 'Complex-Version-123',
-         identifier: 'id1',
-         version: '1.0'
-       }]
-    }
+    trait :with_complex_version do
+      complex_version_attributes {
+        [{
+           date: '1978-10-28',
+           description: 'Complex-Version-123',
+           identifier: 'id1',
+           version: '1.0'
+         }]
+      }
+    end
+
+    trait :with_description_abstract do
+      description { ["Abstract-Description-123"] }
+    end
   end
 end
+
diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
index 2ae999b3..9f85a4bd 100644
--- a/hyrax/spec/features/oai_pmh_spec.rb
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -15,6 +15,16 @@
 
     it 'retrieves a list of records' do
       visit oai_provider_catalog_path(verb: 'ListRecords', metadataPrefix: 'oai_dc')
+
+      puts "----------"
+      puts "#{ENV['OAI_RECORD_PREFIX']}:#{identifier}"
+      puts page.body.inspect
+
+      # require 'byebug'
+      # byebug
+
+
+
       expect(page).to have_content("#{ENV['OAI_RECORD_PREFIX']}:#{identifier}")
       expect(page).to have_content(work.title.first)
     end
diff --git a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
index a8d06cdd..12a956cf 100644
--- a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
@@ -21,7 +21,7 @@
       ]
     }
     let(:abstract_regex) { %r(<http://purl.org/dc/elements/1.1/description> "Abstract-Description-123";) }
-    let(:supervisor_regex) { %r(<http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor Supervisor Approval";) }
+    let(:supervisor_regex) { %r(<http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor-Supervisor-Approval";) }
 
     it 'exports' do
       export_regex.each do |regex|
@@ -54,7 +54,7 @@
       ]
     }
     let(:abstract_regex) { %r(<http://example.org/concern/datasets/#{dataset.id}> <http://purl.org/dc/elements/1.1/description> "Abstract-Description-123") }
-    let(:supervisor_regex) { %r(<http://example.org/concern/datasets/#{dataset.id}> <http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor Supervisor Approval") }
+    let(:supervisor_regex) { %r(<http://example.org/concern/datasets/#{dataset.id}> <http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor-Supervisor-Approval") }
 
     it 'exports' do
       export_regex.each do |regex|
@@ -97,13 +97,13 @@
 
     context 'anonymous user' do
       it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
-      it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor Supervisor Approval") }
+      it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
     end
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
       it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
-      it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor Supervisor Approval") }
+      it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
     end
   end
 end
diff --git a/hyrax/spec/presenters/hyrax/image_presenter_spec.rb b/hyrax/spec/presenters/hyrax/image_presenter_spec.rb
index fc371feb..8edd2253 100644
--- a/hyrax/spec/presenters/hyrax/image_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/image_presenter_spec.rb
@@ -1,9 +1,101 @@
-# Generated via
-#  `rails generate hyrax:work Image`
 require 'rails_helper'
 
 RSpec.describe Hyrax::ImagePresenter do
-  it "has tests" do
-    skip "Add your tests here"
+  let(:image) { create(:image, :open, :with_alternative_title, :with_description_abstract) }
+  let(:solr_document) { SolrDocument.new(image.to_solr) }
+  let(:host) { double(host: 'http://example.org') }
+  let(:user) { nil }
+  let(:presenter) { described_class.new(solr_document, Ability.new(user), host) }
+
+  describe '#export_as_ttl' do
+    subject { presenter.export_as_ttl }
+    let(:export_regex) {
+      [
+          %r(<http://example.org/concern/images/#{image.id}> a),
+          %r(<http://projecthydra.org/works/models#Work>),
+          %r(<http://pcdm.org/models#Object>),
+          %r(<http://purl.org/dc/terms/title> "Open Image";),
+          %r(<http://purl.org/dc/terms/alternative> "Alternative-Title-123";),
+          %r(<http://www.w3.org/ns/auth/acl#accessControl> <http://example.org/catalog/([a-f0-9\\-]*)+>;),
+          %r(<info:fedora/fedora-system:def/model#hasModel> "Image" .)
+      ]
+    }
+    let(:abstract_regex) { %r(<http://purl.org/dc/elements/1.1/description> "Abstract-Description-123";) }
+
+    it 'exports' do
+      export_regex.each do |regex|
+        expect(subject).to match(regex)
+      end
+    end
+
+    context 'anonymous user' do
+      it { is_expected.not_to match(abstract_regex) }
+    end
+
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to match(abstract_regex) }
+    end
+  end
+
+  describe '#export_as_nt' do
+    subject { presenter.export_as_nt }
+    let(:export_regex) {
+      [
+          %r(<http://example.org/concern/images/#{image.id}> <http://www.w3.org/ns/auth/acl#accessControl> <http://example.org/catalog/([a-f0-9\\-]*)+>),
+          %r(<http://example.org/concern/images/#{image.id}> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://projecthydra.org/works/models#Work>),
+          %r(<http://example.org/concern/images/#{image.id}> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://pcdm.org/models#Object>),
+          %r(<http://example.org/concern/images/#{image.id}> <info:fedora/fedora-system:def/model#hasModel> "Image"),
+          %r(<http://example.org/concern/images/#{image.id}> <http://purl.org/dc/terms/alternative> "Alternative-Title-123"),
+          %r(<http://example.org/concern/images/#{image.id}> <http://purl.org/dc/terms/title> "Open Image")
+      ]
+    }
+    let(:abstract_regex) { %r(<http://example.org/concern/images/#{image.id}> <http://purl.org/dc/elements/1.1/description> "Abstract-Description-123") }
+
+    it 'exports' do
+      export_regex.each do |regex|
+        expect(subject).to match(regex)
+      end
+    end
+
+    context 'anonymous user' do
+      it { is_expected.not_to match(abstract_regex) }
+    end
+
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to match(abstract_regex) }
+    end
+  end
+
+  describe '#export_as_jsonld' do
+    subject { JSON.parse(presenter.export_as_jsonld) }
+    # NB: it is important to use => rather than a colon: - otherwise the strings get symbolised
+
+    it 'exports' do
+      expect(subject["@context"]).to include(
+                                         "pcdmterms" => "http://pcdm.org/models#",
+                                         "worksterms" => "http://projecthydra.org/works/models#",
+                                         "dc" => "http://purl.org/dc/terms/",
+                                         "acl" => "http://www.w3.org/ns/auth/acl#",
+                                         "system" => "info:fedora/fedora-system:",
+                                         "model" => "system:def/model#"
+                                     )
+      expect(subject["@id"]).to eql "http://example.org/concern/images/#{image.id}"
+      expect(subject["dc:title"]).to eql "Open Image"
+      expect(subject["dc:alternative"]).to eql "Alternative-Title-123"
+      expect(subject["model:hasModel"]).to eql "Image"
+      expect(subject["acl:accessControl"]).to include("@id")
+      expect(subject["@type"]).to match_array %w(pcdmterms:Object worksterms:Work)
+    end
+
+    context 'anonymous user' do
+      it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
+    end
+
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
+    end
   end
 end
diff --git a/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
index 3e558c3b..c58a676d 100644
--- a/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/datasets/_attribute_rows.html_spec.rb
@@ -5,7 +5,8 @@
   let(:partial) { 'hyrax/datasets/attribute_rows' }
   let(:dataset) { create(:dataset, :open, :with_alternative_title, :with_complex_person, :with_keyword, :with_subject,
                         :with_language, :with_publisher, :with_complex_date, :with_complex_identifier, :with_complex_rights,
-                        :with_complex_version, :with_resource_type, :with_complex_relation, :with_source) }
+                        :with_complex_version, :with_resource_type, :with_complex_relation, :with_source,
+                        :with_description_abstract, :with_supervisor_approval) }
   let(:presenter) { Hyrax::DatasetPresenter.new(SolrDocument.new(dataset.to_solr), Ability.new(user), controller.request) }
 
   before do
@@ -34,6 +35,8 @@
       expect(rendered).to have_content('Resource-Type-123')
       expect(rendered).to have_content('A relation label')
       expect(rendered).to have_content('Source-123')
+      expect(rendered).not_to have_content('Abstract-Description-123') # Abstract/Description is not displayed in this table partial
+      expect(rendered).not_to have_content('Professor-Supervisor-Approval')
     end
   end
 
@@ -54,6 +57,8 @@
       expect(rendered).to have_content('Resource-Type-123')
       expect(rendered).to have_content('A relation label')
       expect(rendered).to have_content('Source-123')
+      expect(rendered).not_to have_content('Abstract-Description-123') # Abstract/Description is not displayed in this table partial
+      expect(rendered).not_to have_content('Professor-Supervisor-Approval')
     end
   end
 end

From b871095c31f505c03712c2cc53e70522d424b93c Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 13 Feb 2020 20:59:59 +0000
Subject: [PATCH 120/258] publication presenter specs

---
 hyrax/spec/factories/publication.rb           |  10 +-
 .../hyrax/publication_presenter_spec.rb       | 108 +++++++++++++++++-
 2 files changed, 112 insertions(+), 6 deletions(-)

diff --git a/hyrax/spec/factories/publication.rb b/hyrax/spec/factories/publication.rb
index 972ecd57..077b5ec2 100644
--- a/hyrax/spec/factories/publication.rb
+++ b/hyrax/spec/factories/publication.rb
@@ -3,8 +3,6 @@
   factory :publication do
     title { ["Publication"] }
     access_control
-    skip_create
-    override_new_record
 
     trait :open do
       visibility { 'open' }
@@ -154,5 +152,13 @@
          }]
       }
     end
+
+    trait :with_description_abstract do
+      description { ["Abstract-Description-123"] }
+    end
+
+    trait :with_supervisor_approval do
+      supervisor_approval { ['Professor-Supervisor-Approval'] }
+    end
   end
 end
diff --git a/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb b/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
index 6653f7e6..1294e0ba 100644
--- a/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
@@ -1,9 +1,109 @@
-# Generated via
-#  `rails generate hyrax:work Publication`
 require 'rails_helper'
 
 RSpec.describe Hyrax::PublicationPresenter do
-  it "has tests" do
-    skip "Add your tests here"
+  let(:publication) { create(:publication, :open, :with_alternative_title, :with_description_abstract, :with_supervisor_approval) }
+  let(:solr_document) { SolrDocument.new(publication.to_solr) }
+  let(:host) { double(host: 'http://example.org') }
+  let(:user) { nil }
+  let(:presenter) { described_class.new(solr_document, Ability.new(user), host) }
+
+  describe '#export_as_ttl' do
+    subject { presenter.export_as_ttl }
+    let(:export_regex) {
+      [
+          %r(<http://example.org/concern/publications/#{publication.id}> a),
+          %r(<http://projecthydra.org/works/models#Work>),
+          %r(<http://pcdm.org/models#Object>),
+          %r(<http://purl.org/dc/terms/title> "Open Publication";),
+          %r(<http://purl.org/dc/terms/alternative> "Alternative-Title-123";),
+          %r(<http://www.w3.org/ns/auth/acl#accessControl> <http://example.org/catalog/([a-f0-9\\-]*)+>;),
+          %r(<info:fedora/fedora-system:def/model#hasModel> "Publication" .)
+      ]
+    }
+    let(:abstract_regex) { %r(<http://purl.org/dc/elements/1.1/description> "Abstract-Description-123";) }
+    let(:supervisor_regex) { %r(<http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor-Supervisor-Approval";) }
+
+    it 'exports' do
+      export_regex.each do |regex|
+        expect(subject).to match(regex)
+      end
+    end
+
+    context 'anonymous user' do
+      it { is_expected.not_to match(abstract_regex) }
+      it { is_expected.not_to match(supervisor_regex) }
+    end
+
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(supervisor_regex) }
+    end
+  end
+
+  describe '#export_as_nt' do
+    subject { presenter.export_as_nt }
+    let(:export_regex) {
+      [
+          %r(<http://example.org/concern/publications/#{publication.id}> <http://www.w3.org/ns/auth/acl#accessControl> <http://example.org/catalog/([a-f0-9\\-]*)+>),
+          %r(<http://example.org/concern/publications/#{publication.id}> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://projecthydra.org/works/models#Work>),
+          %r(<http://example.org/concern/publications/#{publication.id}> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://pcdm.org/models#Object>),
+          %r(<http://example.org/concern/publications/#{publication.id}> <info:fedora/fedora-system:def/model#hasModel> "Publication"),
+          %r(<http://example.org/concern/publications/#{publication.id}> <http://purl.org/dc/terms/alternative> "Alternative-Title-123"),
+          %r(<http://example.org/concern/publications/#{publication.id}> <http://purl.org/dc/terms/title> "Open Publication")
+      ]
+    }
+    let(:abstract_regex) { %r(<http://example.org/concern/publications/#{publication.id}> <http://purl.org/dc/elements/1.1/description> "Abstract-Description-123") }
+    let(:supervisor_regex) { %r(<http://example.org/concern/publications/#{publication.id}> <http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor-Supervisor-Approval") }
+
+    it 'exports' do
+      export_regex.each do |regex|
+        expect(subject).to match(regex)
+      end
+    end
+
+    context 'anonymous user' do
+      it { is_expected.not_to match(abstract_regex) }
+      it { is_expected.not_to match(supervisor_regex) }
+    end
+
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(supervisor_regex) }
+    end
+  end
+
+  describe '#export_as_jsonld' do
+    subject { JSON.parse(presenter.export_as_jsonld) }
+    # NB: it is important to use => rather than a colon: - otherwise the strings get symbolised
+
+    it 'exports' do
+      expect(subject["@context"]).to include(
+                                         "pcdmterms" => "http://pcdm.org/models#",
+                                         "worksterms" => "http://projecthydra.org/works/models#",
+                                         "dc" => "http://purl.org/dc/terms/",
+                                         "acl" => "http://www.w3.org/ns/auth/acl#",
+                                         "system" => "info:fedora/fedora-system:",
+                                         "model" => "system:def/model#"
+                                     )
+      expect(subject["@id"]).to eql "http://example.org/concern/publications/#{publication.id}"
+      expect(subject["dc:title"]).to eql "Open Publication"
+      expect(subject["dc:alternative"]).to eql "Alternative-Title-123"
+      expect(subject["model:hasModel"]).to eql "Publication"
+      expect(subject["acl:accessControl"]).to include("@id")
+      expect(subject["@type"]).to match_array %w(pcdmterms:Object worksterms:Work)
+    end
+
+    context 'anonymous user' do
+      it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
+      it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
+    end
+
+    context 'authenticated user' do
+      let(:user) { create(:user, :nims_other) }
+      it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
+      it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
+    end
   end
 end

From f185803aa122431bd106fe6432850536e7bb1a36 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Fri, 14 Feb 2020 12:08:29 +0000
Subject: [PATCH 121/258] hide description on OAI-PMH feed

---
 hyrax/app/models/solr_document.rb   |  2 +-
 hyrax/spec/features/oai_pmh_spec.rb | 10 ----------
 2 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 9745e68f..da74863f 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -28,7 +28,7 @@ class SolrDocument
     contributor: 'complex_person_other_tesim', # @todo - extract anything other than author from complex person, may need new solr field
     creator: 'complex_person_author_tesim',
     date: 'date_tesim',
-    description: 'description_tesim',
+    # description: 'description_tesim', # hide description/abstract field for OAI-PMH feed
     identifier: 'complex_identifier_tesim',
     language: 'language_tesim',
     publisher: 'publisher_tesim',
diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
index 797ec7c6..7e35b140 100644
--- a/hyrax/spec/features/oai_pmh_spec.rb
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -17,16 +17,6 @@
 
     it 'retrieves a list of records' do
       visit oai_provider_catalog_path(verb: 'ListRecords', metadataPrefix: 'oai_dc')
-
-      puts "----------"
-      puts "#{ENV['OAI_RECORD_PREFIX']}:#{identifier}"
-      puts page.body.inspect
-
-      # require 'byebug'
-      # byebug
-
-
-
       expect(page).to have_content("#{ENV['OAI_RECORD_PREFIX']}:#{identifier}")
       expect(page).to have_content(work.title.first)
     end

From 477b01ab47834a92723f9661e8cee8117308ad85 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Fri, 14 Feb 2020 12:09:36 +0000
Subject: [PATCH 122/258] Revert "temporarily disable apis"

This reverts commit b201af80990f0974169a2270d120939818e1ac14.
---
 hyrax/app/controllers/catalog_controller.rb   |  1 -
 .../concerns/disable_api_behavior.rb          | 19 -------------------
 .../controllers/hyrax/citations_controller.rb |  1 -
 .../controllers/hyrax/datasets_controller.rb  |  2 --
 .../controllers/hyrax/file_sets_controller.rb |  1 -
 .../controllers/hyrax/images_controller.rb    |  2 --
 .../hyrax/publications_controller.rb          |  2 --
 .../app/controllers/hyrax/users_controller.rb |  2 --
 .../app/controllers/hyrax/works_controller.rb |  2 --
 hyrax/config/routes.rb                        |  4 ++--
 hyrax/spec/features/oai_pmh_spec.rb           |  4 +---
 11 files changed, 3 insertions(+), 37 deletions(-)
 delete mode 100644 hyrax/app/controllers/concerns/disable_api_behavior.rb

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index 91e52625..25858d67 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -2,7 +2,6 @@ class CatalogController < ApplicationController
   include Hydra::Catalog
   include Hydra::Controller::ControllerBehavior
   include BlacklightOaiProvider::CatalogControllerBehavior
-  include DisableApiBehavior
 
   # This filter applies the hydra access controls
   before_action :enforce_show_permissions, only: :show
diff --git a/hyrax/app/controllers/concerns/disable_api_behavior.rb b/hyrax/app/controllers/concerns/disable_api_behavior.rb
deleted file mode 100644
index 6bf87048..00000000
--- a/hyrax/app/controllers/concerns/disable_api_behavior.rb
+++ /dev/null
@@ -1,19 +0,0 @@
-# Temporarily disable API behaviour, see https://github.com/antleaf/nims-mdr-development/issues/241
-
-module DisableApiBehavior
-  def show
-    respond_to do |format|
-      format.html { super }
-      format.json { render json: { error: 'API is currently unavailable' }, status: 400 }
-      format.any { render plain: 'API is currently unavailable', content_type: 'text/plain', status: 400}
-    end
-  end
-
-  def index
-    respond_to do |format|
-      format.html { super }
-      format.json { render json: { error: 'API is currently unavailable' }, status: 400 }
-      format.any { render plain: 'API is currently unavailable', content_type: 'text/plain', status: 400}
-    end
-  end
-end
diff --git a/hyrax/app/controllers/hyrax/citations_controller.rb b/hyrax/app/controllers/hyrax/citations_controller.rb
index 6849b06b..1887e93b 100644
--- a/hyrax/app/controllers/hyrax/citations_controller.rb
+++ b/hyrax/app/controllers/hyrax/citations_controller.rb
@@ -3,7 +3,6 @@ class CitationsController < ApplicationController
     include WorksControllerBehavior
     include Breadcrumbs
     include SingularSubresourceController
-    prepend ::DisableApiBehavior
 
     # Overrides decide_layout from WorksControllerBehavior
     with_themed_layout '1_column'
diff --git a/hyrax/app/controllers/hyrax/datasets_controller.rb b/hyrax/app/controllers/hyrax/datasets_controller.rb
index 76353387..7aac5208 100644
--- a/hyrax/app/controllers/hyrax/datasets_controller.rb
+++ b/hyrax/app/controllers/hyrax/datasets_controller.rb
@@ -7,8 +7,6 @@ class DatasetsController < ApplicationController
     include Hyrax::WorksControllerBehavior
     include Hyrax::BreadcrumbsForWorks
     include ::ComplexFieldsBehavior
-    prepend ::DisableApiBehavior
-
     self.curation_concern_type = ::Dataset
 
     # Use this line if you want to use a custom presenter
diff --git a/hyrax/app/controllers/hyrax/file_sets_controller.rb b/hyrax/app/controllers/hyrax/file_sets_controller.rb
index 32e2809f..4c69d286 100644
--- a/hyrax/app/controllers/hyrax/file_sets_controller.rb
+++ b/hyrax/app/controllers/hyrax/file_sets_controller.rb
@@ -3,7 +3,6 @@ class FileSetsController < ApplicationController
     include Blacklight::Base
     include Blacklight::AccessControls::Catalog
     include Hyrax::Breadcrumbs
-    prepend ::DisableApiBehavior
 
     before_action :authenticate_user!, except: [:show, :citation, :stats]
     load_and_authorize_resource class: ::FileSet, except: :show
diff --git a/hyrax/app/controllers/hyrax/images_controller.rb b/hyrax/app/controllers/hyrax/images_controller.rb
index c0a19b33..56eb837b 100644
--- a/hyrax/app/controllers/hyrax/images_controller.rb
+++ b/hyrax/app/controllers/hyrax/images_controller.rb
@@ -6,8 +6,6 @@ class ImagesController < ApplicationController
     # Adds Hyrax behaviors to the controller.
     include Hyrax::WorksControllerBehavior
     include Hyrax::BreadcrumbsForWorks
-    prepend ::DisableApiBehavior
-
     self.curation_concern_type = ::Image
 
     # Use this line if you want to use a custom presenter
diff --git a/hyrax/app/controllers/hyrax/publications_controller.rb b/hyrax/app/controllers/hyrax/publications_controller.rb
index eceeaeeb..69035d55 100644
--- a/hyrax/app/controllers/hyrax/publications_controller.rb
+++ b/hyrax/app/controllers/hyrax/publications_controller.rb
@@ -7,8 +7,6 @@ class PublicationsController < ApplicationController
     include Hyrax::WorksControllerBehavior
     include Hyrax::BreadcrumbsForWorks
     include ::ComplexFieldsBehavior
-    prepend ::DisableApiBehavior
-
     self.curation_concern_type = ::Publication
 
     # Use this line if you want to use a custom presenter
diff --git a/hyrax/app/controllers/hyrax/users_controller.rb b/hyrax/app/controllers/hyrax/users_controller.rb
index 92783ed1..737f0ec6 100644
--- a/hyrax/app/controllers/hyrax/users_controller.rb
+++ b/hyrax/app/controllers/hyrax/users_controller.rb
@@ -1,8 +1,6 @@
 require_dependency Hyrax::Engine.config.root.join('app', 'controllers', 'hyrax', 'users_controller.rb').to_s
 
 class Hyrax::UsersController
-  prepend ::DisableApiBehavior
-
   def index
     authenticate_user! if Flipflop.hide_users_list?
     authorize! :index, ::User
diff --git a/hyrax/app/controllers/hyrax/works_controller.rb b/hyrax/app/controllers/hyrax/works_controller.rb
index 5c8aa577..0753b1ed 100644
--- a/hyrax/app/controllers/hyrax/works_controller.rb
+++ b/hyrax/app/controllers/hyrax/works_controller.rb
@@ -6,8 +6,6 @@ class WorksController < ApplicationController
     # Adds Hyrax behaviors to the controller.
     include Hyrax::WorksControllerBehavior
     include Hyrax::BreadcrumbsForWorks
-    prepend ::DisableApiBehavior
-
     self.curation_concern_type = ::Work
 
     # Use this line if you want to use a custom presenter
diff --git a/hyrax/config/routes.rb b/hyrax/config/routes.rb
index f2b46c73..57159bf0 100644
--- a/hyrax/config/routes.rb
+++ b/hyrax/config/routes.rb
@@ -17,7 +17,7 @@
 
   concern :exportable, Blacklight::Routes::Exportable.new
   concern :searchable, Blacklight::Routes::Searchable.new
-  #concern :oai_provider, BlacklightOaiProvider::Routes::Provider.new # Temporarily disable API behaviour, see https://github.com/antleaf/nims-mdr-development/issues/241
+  concern :oai_provider, BlacklightOaiProvider::Routes::Provider.new
 
   curation_concerns_basic_routes
 
@@ -29,7 +29,7 @@
   end
 
   resource :catalog, only: [:index], as: 'catalog', path: '/catalog', controller: 'catalog' do
-    #concerns :oai_provider # Temporarily disable API behaviour, see https://github.com/antleaf/nims-mdr-development/issues/241
+    concerns :oai_provider
     concerns :searchable
   end
 
diff --git a/hyrax/spec/features/oai_pmh_spec.rb b/hyrax/spec/features/oai_pmh_spec.rb
index 7e35b140..2ae999b3 100644
--- a/hyrax/spec/features/oai_pmh_spec.rb
+++ b/hyrax/spec/features/oai_pmh_spec.rb
@@ -7,9 +7,7 @@
 
   before { work }
 
-  scenario 'oai interface with works present' do
-    skip 'Temporarily disable API behaviour, see https://github.com/antleaf/nims-mdr-development/issues/241'
-
+  context 'oai interface with works present' do
     it 'lists metadata prefixess' do
       visit oai_provider_catalog_path(verb: 'ListMetadataFormats')
       expect(page).to have_content('oai_dc')

From d5b255c0a5faf01ecb72bc929a870df6cf9057aa Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 17 Feb 2020 10:48:44 +0900
Subject: [PATCH 123/258] add unique index to user_identifier, add PIDs to
 default users

---
 hyrax/app/models/user.rb                                 | 3 ++-
 .../20200108111832_add_user_identifier_to_users.rb       | 4 ++--
 hyrax/seed/setup.json                                    | 9 ++++++---
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index ae9e6d14..0b355c5a 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -29,12 +29,13 @@ def to_s
 
   def self.find_or_create_system_user(user_key)
     username = user_key.split('@')[0]
-    User.find_by('email' => user_key) || User.create!(username: username, email: user_key, password: Devise.friendly_token[0, 20])
+    User.find_by('email' => user_key) || User.create!(username: username, email: user_key, password: Devise.friendly_token[0, 20], user_identifier: Noid::Rails::Service.new.mint)
   end
 
   def ldap_before_save
     self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
     self.password = Devise.friendly_token[0, 20]
+    # TODO: This will be replaced by NIMS PID when the CAS server is online
     self.user_identifier = Noid::Rails::Service.new.mint
   end
 
diff --git a/hyrax/db/migrate/20200108111832_add_user_identifier_to_users.rb b/hyrax/db/migrate/20200108111832_add_user_identifier_to_users.rb
index 7c07d463..83545c86 100644
--- a/hyrax/db/migrate/20200108111832_add_user_identifier_to_users.rb
+++ b/hyrax/db/migrate/20200108111832_add_user_identifier_to_users.rb
@@ -1,6 +1,6 @@
 class AddUserIdentifierToUsers < ActiveRecord::Migration[5.1]
   def change
-    add_column :users, :user_identifier, :string
-    add_index :users, :user_identifier
+    add_column :users, :user_identifier, :string #, null: false
+    add_index :users, :user_identifier, unique: true
   end
 end
diff --git a/hyrax/seed/setup.json b/hyrax/seed/setup.json
index 4c93f69e..e8ddfc25 100644
--- a/hyrax/seed/setup.json
+++ b/hyrax/seed/setup.json
@@ -4,7 +4,8 @@
       "username": "admin_hyrax",
       "password": "password",
       "name": "hyrax Admin",
-      "role": "admin"
+      "role": "admin",
+      "user_identifier": "urn:USER_IDENTIFIER.dpfc.nims.go.jp:8c5f864c-c315-49c0-a49d-609895a8925d"
     },
     {
       "email": "user@hyrax",
@@ -12,14 +13,16 @@
       "password": "demouser",
       "name": "Demo User",
       "role": "user",
-      "depositor": true
+      "depositor": true,
+      "user_identifier": "urn:USER_IDENTIFIER.dpfc.nims.go.jp:ebb7db80-27ef-4d3c-896d-e5956ee22ca5"
     },
     {
       "email": "workflow@hyrax",
       "username": "workflow_hyrax",
       "password": "workflow",
       "name": "Workflow Admin",
-      "role": "admin"
+      "role": "admin",
+      "user_identifier": "urn:USER_IDENTIFIER.dpfc.nims.go.jp:5a882edb-377f-4f35-85b1-a0963293c261"
     }
   ]
 }

From 8a0124f7ec517cc8b881fd109624a111f3e32bf2 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 17 Feb 2020 10:53:55 +0900
Subject: [PATCH 124/258] update schema.rb

---
 hyrax/db/schema.rb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/hyrax/db/schema.rb b/hyrax/db/schema.rb
index 467c7d8e..176801ff 100644
--- a/hyrax/db/schema.rb
+++ b/hyrax/db/schema.rb
@@ -279,6 +279,7 @@
     t.string "uri"
     t.datetime "created_at", null: false
     t.datetime "updated_at", null: false
+    t.index ["local_authority_id", "label"], name: "index_qa_local_authority_entries_on_lower_label"
     t.index ["local_authority_id"], name: "index_qa_local_authority_entries_on_local_authority_id"
     t.index ["uri"], name: "index_qa_local_authority_entries_on_uri", unique: true
   end
@@ -548,10 +549,12 @@
     t.string "unlock_token"
     t.datetime "locked_at"
     t.string "remember_token"
+    t.string "employee_type_code"
     t.string "user_identifier"
     t.index ["email"], name: "index_users_on_email"
+    t.index ["employee_type_code"], name: "index_users_on_employee_type_code"
     t.index ["reset_password_token"], name: "index_users_on_reset_password_token", unique: true
-    t.index ["user_identifier"], name: "index_users_on_user_identifier"
+    t.index ["user_identifier"], name: "index_users_on_user_identifier", unique: true
     t.index ["username"], name: "index_users_on_username", unique: true
   end
 

From be985a74710f799121f301118252b3d8d85d7287 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 20 Feb 2020 10:32:25 +0900
Subject: [PATCH 125/258] add .mvn directory to store local jvm.config

---
 cas/.mvn/.keep | 0
 cas/Dockerfile | 1 +
 2 files changed, 1 insertion(+)
 create mode 100644 cas/.mvn/.keep

diff --git a/cas/.mvn/.keep b/cas/.mvn/.keep
new file mode 100644
index 00000000..e69de29b
diff --git a/cas/Dockerfile b/cas/Dockerfile
index d5dfbe9d..8e31a121 100644
--- a/cas/Dockerfile
+++ b/cas/Dockerfile
@@ -1,5 +1,6 @@
 FROM apereo/cas:v5.3.10
 COPY pom.xml /cas-overlay/
+COPY .mvn/ /cas-overlay/.mvn/
 RUN build.sh package
 
 RUN keytool -genkeypair -alias cas -keyalg RSA -keypass changeit \

From f5fe5a2cb4bb5a611c42c05e22c4fbe85c959d00 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 20 Feb 2020 10:41:48 +0900
Subject: [PATCH 126/258] add jvm.config to .gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 752f2dc5..402e4001 100644
--- a/.gitignore
+++ b/.gitignore
@@ -351,3 +351,4 @@ $RECYCLE.BIN/
 .env
 /hyrax/.fedora-test.pid
 /hyrax/.solr-test.pid
+cas/.mvn/jvm.config

From b6842e1ebc110038904833ad2762ae9d7049d040 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 20 Feb 2020 13:43:11 +0000
Subject: [PATCH 127/258] now handles null title and formats table in
 scrollable area

---
 hyrax/app/assets/javascripts/csv_preview.js                 | 6 +++++-
 hyrax/app/assets/stylesheets/csv_preview.scss               | 3 +++
 hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb | 2 +-
 3 files changed, 9 insertions(+), 2 deletions(-)
 create mode 100644 hyrax/app/assets/stylesheets/csv_preview.scss

diff --git a/hyrax/app/assets/javascripts/csv_preview.js b/hyrax/app/assets/javascripts/csv_preview.js
index f89f8100..3a66c121 100644
--- a/hyrax/app/assets/javascripts/csv_preview.js
+++ b/hyrax/app/assets/javascripts/csv_preview.js
@@ -8,7 +8,11 @@ $( document ).on('turbolinks:load', function() {
                 preview.find('.csv-preview-datatable').DataTable({
                     data: data.data,
                     columns: data.columns.map(function (name) {
-                        return { title: name.replace(/[\_\-]/g, ' ') };
+                        if (name === null) {
+                            return { title: '' };
+                        } else {
+                            return {title: name.replace(/[\_\-]/g, ' ')};
+                        }
                     })
                 });
                 preview.find('.csv-preview-title').text('Preview: ' + data.file_name);
diff --git a/hyrax/app/assets/stylesheets/csv_preview.scss b/hyrax/app/assets/stylesheets/csv_preview.scss
new file mode 100644
index 00000000..9fc68902
--- /dev/null
+++ b/hyrax/app/assets/stylesheets/csv_preview.scss
@@ -0,0 +1,3 @@
+.overflow-scroll {
+  overflow: scroll;
+}
diff --git a/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb b/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
index b30611de..732ec072 100644
--- a/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
+++ b/hyrax/app/views/hyrax/file_sets/media_display/_csv.html.erb
@@ -7,7 +7,7 @@
       </h4>
     </div>
     <div id="csv-preview-<%= file_set.id %>" class="panel-collapse collapse in">
-      <div class="panel-body">
+      <div class="panel-body overflow-scroll">
         <div class="csv-preview-error" style="display: none;">There was an error generating the CSV preview; please download the file instead.</div>
         <table class="csv-preview-datatable display full-width" style="width:100%"></table>
       </div>

From 653703c2e4da8f269f6d605e7489474ce4f361b7 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 21 Feb 2020 17:16:59 +0000
Subject: [PATCH 128/258] add facetable _year_ fields for all dates, and a year
 field for searching on complex_date

---
 .../indexers/complex_field/date_indexer.rb    | 43 ++++++++++++-------
 hyrax/config/locales/hyrax.en.yml             | 13 ++++++
 2 files changed, 41 insertions(+), 15 deletions(-)

diff --git a/hyrax/app/indexers/complex_field/date_indexer.rb b/hyrax/app/indexers/complex_field/date_indexer.rb
index ce562267..f97dd7d1 100644
--- a/hyrax/app/indexers/complex_field/date_indexer.rb
+++ b/hyrax/app/indexers/complex_field/date_indexer.rb
@@ -20,6 +20,10 @@ def index_date(solr_doc)
       end
       solr_doc[Solrizer.solr_name('complex_date', :stored_searchable, type: :date)] = dates_utc unless dates.blank?
       solr_doc[Solrizer.solr_name('complex_date', :dateable)] = dates_utc unless dates.blank?
+      # add year
+      years = dates_utc.map {|d| DateTime.parse(d).strftime("%Y")} 
+      solr_doc[Solrizer.solr_name('complex_year', :stored_searchable)] = years unless dates.blank?
+      solr_doc[Solrizer.solr_name('complex_', :facetable)] = years unless dates.blank?
       object.complex_date.each do |d|
         next if d.date.reject(&:blank?).blank?
         label = 'other'
@@ -39,11 +43,18 @@ def index_date(solr_doc)
         fld_name = Solrizer.solr_name("complex_date_#{label}", :dateable)
         solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
         begin
-          solr_doc[fld_name] << vals.map{|d| d.tr('０-９ａ-ｚＡ-Ｚ','0-9a-zA-Z')}.map { |dt| dt.length <= 4 ? DateTime.strptime(dt, '%Y').utc.iso8601 : DateTime.parse(dt).utc.iso8601 }
+          dates_utc = vals.map{|d| d.tr('０-９ａ-ｚＡ-Ｚ','0-9a-zA-Z')}.map { |d| d.length <= 4 ? DateTime.strptime(d, '%Y').utc.iso8601 : DateTime.parse(d).utc.iso8601 } unless dates.blank?
         rescue ArgumentError
-          solr_doc[fld_name] << vals.map{|d| d.tr('０-９ａ-ｚＡ-Ｚ','0-9a-zA-Z')}.map { |dt| DateTime.parse("#{dt}-01").utc.iso8601 }
+          dates_utc = vals.map{|d| d.tr('０-９ａ-ｚＡ-Ｚ','0-9a-zA-Z')}.map { |d| DateTime.parse("#{d}-01").utc.iso8601 } unless dates.blank?
         end
+        solr_doc[fld_name] << dates_utc unless dates_utc.blank?
         solr_doc[fld_name].flatten!
+        # Add years
+        year_fld = Solrizer.solr_name("complex_year_#{label}", :facetable)
+        years = dates_utc.map {|d| DateTime.parse(d).strftime("%Y")}
+        solr_doc[year_fld] = [] unless solr_doc.include?(year_fld)
+        solr_doc[year_fld] << years unless years.blank?
+        solr_doc[year_fld].flatten!
         # date as complex_date_type displayable
         fld_name = Solrizer.solr_name("complex_date_#{label}", :displayable)
         solr_doc[fld_name] = [] unless solr_doc.include?(fld_name)
@@ -55,19 +66,20 @@ def index_date(solr_doc)
     def self.date_facet_fields
       # solr fields that will be treated as facets
       fields = []
-      fields << Solrizer.solr_name('complex_date_accepted', :dateable)
-      fields << Solrizer.solr_name('complex_date_available', :dateable)
-      fields << Solrizer.solr_name('complex_date_copyrighted', :dateable)
-      fields << Solrizer.solr_name('complex_date_collected', :dateable)
-      fields << Solrizer.solr_name('complex_date_created', :dateable)
-      fields << Solrizer.solr_name('complex_date_issued', :dateable)
-      fields << Solrizer.solr_name('complex_date_published', :dateable)
-      fields << Solrizer.solr_name('complex_date_submitted', :dateable)
-      fields << Solrizer.solr_name('complex_date_updated', :dateable)
-      fields << Solrizer.solr_name('complex_date_valid', :dateable)
-      fields << Solrizer.solr_name('complex_date_processed', :dateable)
-      fields << Solrizer.solr_name('complex_date_purchased', :dateable)
-      fields << Solrizer.solr_name('complex_date_other', :dateable)
+      # change all dates to years
+      fields << Solrizer.solr_name('complex_year_accepted', :facetable)
+      fields << Solrizer.solr_name('complex_year_available', :facetable)
+      fields << Solrizer.solr_name('complex_year_copyrighted', :facetable)
+      fields << Solrizer.solr_name('complex_year_collected', :facetable)
+      fields << Solrizer.solr_name('complex_year_created', :facetable)
+      fields << Solrizer.solr_name('complex_year_issued', :facetable)
+      fields << Solrizer.solr_name('complex_year_published', :facetable)
+      fields << Solrizer.solr_name('complex_year_submitted', :facetable)
+      fields << Solrizer.solr_name('complex_year_updated', :facetable)
+      fields << Solrizer.solr_name('complex_year_valid', :facetable)
+      fields << Solrizer.solr_name('complex_year_processed', :facetable)
+      fields << Solrizer.solr_name('complex_year_purchased', :facetable)
+      fields << Solrizer.solr_name('complex_year_other', :facetable)
       fields
     end
 
@@ -75,6 +87,7 @@ def self.date_search_fields
       # solr fields that will be used for a search
       fields = []
       fields << Solrizer.solr_name('complex_date', :stored_searchable, type: :date)
+      fields << Solrizer.solr_name('complex_year', :stored_searchable)
       fields
     end
 
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index e1b7e034..beea6fec 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -9,18 +9,31 @@ en:
           characterization_methods_sim: Characterization methods
           complex_date_dtsim: Date
           complex_date_accepted_dtsim: Date accepted
+          complex_year_accepted_sim: Date accepted
           complex_date_available_dtsim: Date available
+          complex_year_available_sim: Date available
           complex_date_copyrighted_dtsim: Date copyrighted
+          complex_year_copyrighted_sim: Date copyrighted
           complex_date_collected_dtsim: Date collected
+          complex_year_collected_sim: Date collected
           complex_date_created_dtsim: Date created
+          complex_year_created_sim: Date created
           complex_date_issued_dtsim: Date issued
+          complex_year_issued_sim: Date issued
           complex_date_published_dtsim: Date published
+          complex_year_published_sim: Date published
           complex_date_submitted_dtsim: Date submitted
+          complex_year_submitted_sim: Date submitted
           complex_date_updated_dtsim: Date updated
+          complex_year_updated_sim: Date updated
           complex_date_valid_dtsim: Date valid
+          complex_year_valid_sim: Date valid
           complex_date_processed_dtsim: Date processed
+          complex_year_processed_sim: Date processed
           complex_date_purchased_dtsim: Date purchased
+          complex_year_purchased_sim: Date purchased
           complex_date_other_dtsim: Date
+          complex_year_other_sim: Date
           complex_event_sim: Event
           complex_material_sub_type_sim: Material sub type
           complex_material_type_sim: Material type

From 6d1ca9bd31d9601741fd6399e6f9b3a2e2ee07fe Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Mon, 24 Feb 2020 14:55:11 +0000
Subject: [PATCH 129/258] add spec

---
 hyrax/app/indexers/complex_field/date_indexer.rb | 2 +-
 hyrax/spec/indexers/dataset_indexer_spec.rb      | 7 +++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/indexers/complex_field/date_indexer.rb b/hyrax/app/indexers/complex_field/date_indexer.rb
index f97dd7d1..e2c6c8cb 100644
--- a/hyrax/app/indexers/complex_field/date_indexer.rb
+++ b/hyrax/app/indexers/complex_field/date_indexer.rb
@@ -23,7 +23,7 @@ def index_date(solr_doc)
       # add year
       years = dates_utc.map {|d| DateTime.parse(d).strftime("%Y")} 
       solr_doc[Solrizer.solr_name('complex_year', :stored_searchable)] = years unless dates.blank?
-      solr_doc[Solrizer.solr_name('complex_', :facetable)] = years unless dates.blank?
+      solr_doc[Solrizer.solr_name('complex_year', :facetable)] = years unless dates.blank?
       object.complex_date.each do |d|
         next if d.date.reject(&:blank?).blank?
         label = 'other'
diff --git a/hyrax/spec/indexers/dataset_indexer_spec.rb b/hyrax/spec/indexers/dataset_indexer_spec.rb
index 184879e5..1351a6ad 100644
--- a/hyrax/spec/indexers/dataset_indexer_spec.rb
+++ b/hyrax/spec/indexers/dataset_indexer_spec.rb
@@ -32,6 +32,10 @@
       expect(@solr_document['complex_date_dtsim']).to match_array(
         ["1988-10-28T00:00:00Z", "2018-01-01T00:00:00Z"])
     end
+    it 'indexes year as facetable' do
+      expect(@solr_document['complex_year_sim']).to match_array(
+        ["1988", "2018"])
+    end
     it 'indexes each type as sortable' do
       skip 'this cannot be multi-valued'
       expect(@solr_document['complex_date_submitted_dtsi']).to match_array("1988-10-28T00:00:00Z")
@@ -42,6 +46,9 @@
     it 'indexes each type as displayable' do
       expect(@solr_document['complex_date_submitted_ssm']).to match_array(["1988-10-28"])
     end
+    it 'indexes each year as facetable' do
+      expect(@solr_document['complex_year_submitted_sim']).to match_array(["1988"])
+    end
   end
 
   describe 'indexes an identifier active triple resource with all the attributes' do

From ddb705843537bcdb43a7903f20ffffafba1877d5 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Thu, 27 Feb 2020 15:26:28 +0000
Subject: [PATCH 130/258] Create index.json.jbuilder

now observes field visibility
---
 hyrax/app/views/catalog/index.json.jbuilder | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 hyrax/app/views/catalog/index.json.jbuilder

diff --git a/hyrax/app/views/catalog/index.json.jbuilder b/hyrax/app/views/catalog/index.json.jbuilder
new file mode 100644
index 00000000..9ab17e88
--- /dev/null
+++ b/hyrax/app/views/catalog/index.json.jbuilder
@@ -0,0 +1,13 @@
+json.response do
+  json.docs do
+    json.array! @presenter.documents do |document|
+      index_fields(document).each do |field_name, field|
+        if should_render_index_field? document, field
+          json.set! field_name, document[field_name]
+        end
+      end
+    end
+  end
+  json.facets @presenter.search_facets_as_json
+  json.pages @presenter.pagination_info
+end

From d3583e229c3be9ee5ff32ec845f93319be202b4d Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Fri, 28 Feb 2020 14:41:59 +0000
Subject: [PATCH 131/258] now filtering catalog index and show in all formats

---
 hyrax/app/controllers/catalog_controller.rb   | 11 +++++
 .../solr_document/content_negotiation.rb      | 42 +++++++++++++++++++
 hyrax/app/models/solr_document.rb             |  6 +--
 .../app/presenters/concerns/filtered_graph.rb |  4 +-
 hyrax/app/views/catalog/index.json.jbuilder   |  1 +
 hyrax/app/views/catalog/show.json.jbuilder    | 12 ++++++
 6 files changed, 70 insertions(+), 6 deletions(-)
 create mode 100644 hyrax/app/models/concerns/hyrax/solr_document/content_negotiation.rb
 create mode 100644 hyrax/app/views/catalog/show.json.jbuilder

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index 25858d67..eb5ecf09 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -280,4 +280,15 @@ def self.modified_field
   def render_bookmarks_control?
     false
   end
+
+  def show
+    @response, @document = fetch params[:id]
+    respond_to do |format|
+      format.html { setup_next_and_previous_documents }
+      format.json do
+        @presenter = Blacklight::JsonPresenter.new(@response, @document, facets_from_request, blacklight_config)
+      end
+      additional_export_formats(@document, format)
+    end
+  end
 end
diff --git a/hyrax/app/models/concerns/hyrax/solr_document/content_negotiation.rb b/hyrax/app/models/concerns/hyrax/solr_document/content_negotiation.rb
new file mode 100644
index 00000000..aff6c636
--- /dev/null
+++ b/hyrax/app/models/concerns/hyrax/solr_document/content_negotiation.rb
@@ -0,0 +1,42 @@
+module Hyrax
+  module SolrDocument
+    module ContentNegotiation
+      include FilteredGraph
+      def self.extended(document)
+        document.will_export_as(:nt, "application/n-triples")
+        document.will_export_as(:jsonld, "application/ld+json")
+        document.will_export_as(:ttl, "text/turtle")
+      end
+
+      def export_as_nt
+        graph.dump(:ntriples)
+      end
+
+      def export_as_jsonld
+        graph.dump(:jsonld, :standard_prefixes => true)
+      end
+
+      def export_as_ttl
+        graph.dump(:ttl)
+      end
+
+      private
+
+      def current_ability
+        ::Ability.new(nil) # public user for exports
+      end
+
+      def unfiltered_graph
+        @unfiltered_graph ||= unfiltered_graph_repository.find(id)
+      end
+
+      def unfiltered_graph_repository
+        Hydra::ContentNegotiation::CleanGraphRepository.new(connection)
+      end
+
+      def connection
+        ActiveFedora.fedora.clean_connection
+      end
+    end
+  end
+end
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index da74863f..6ce19ee3 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -39,10 +39,8 @@ class SolrDocument
     type: 'resource_type_tesim'
   )
 
-
-  # Do content negotiation for AF models.
-
-  use_extension( Hydra::ContentNegotiation )
+  # Using custom extension for content negotiation for ActiveFedora models
+  use_extension( ::Hyrax::SolrDocument::ContentNegotiation )
 
   def alternative_title
     self[Solrizer.solr_name('alternative_title', :stored_searchable)]
diff --git a/hyrax/app/presenters/concerns/filtered_graph.rb b/hyrax/app/presenters/concerns/filtered_graph.rb
index 64da5156..35840866 100644
--- a/hyrax/app/presenters/concerns/filtered_graph.rb
+++ b/hyrax/app/presenters/concerns/filtered_graph.rb
@@ -14,7 +14,7 @@ def unfiltered_graph
   def exclude?(statement)
     # Returns true if the statement should be filtered out of the graph
     model = model_name.name.constantize
-    (statement.predicate.ends_with?('purl.org/dc/elements/1.1/description') && @current_ability.cannot?(:read_abstract, model)) ||
-      (statement.predicate.ends_with?('www.nims.go.jp/vocabs/ngdr/supervisor-approval') && @current_ability.cannot?(:read_supervisor_approval, model))
+    (statement.predicate.ends_with?('purl.org/dc/elements/1.1/description') && current_ability.cannot?(:read_abstract, model)) ||
+      (statement.predicate.ends_with?('www.nims.go.jp/vocabs/ngdr/supervisor-approval') && current_ability.cannot?(:read_supervisor_approval, model))
   end
 end
diff --git a/hyrax/app/views/catalog/index.json.jbuilder b/hyrax/app/views/catalog/index.json.jbuilder
index 9ab17e88..b38459d3 100644
--- a/hyrax/app/views/catalog/index.json.jbuilder
+++ b/hyrax/app/views/catalog/index.json.jbuilder
@@ -1,6 +1,7 @@
 json.response do
   json.docs do
     json.array! @presenter.documents do |document|
+      json.id document.id
       index_fields(document).each do |field_name, field|
         if should_render_index_field? document, field
           json.set! field_name, document[field_name]
diff --git a/hyrax/app/views/catalog/show.json.jbuilder b/hyrax/app/views/catalog/show.json.jbuilder
new file mode 100644
index 00000000..3c26424f
--- /dev/null
+++ b/hyrax/app/views/catalog/show.json.jbuilder
@@ -0,0 +1,12 @@
+json.response do
+  json.document do
+    @presenter.documents.tap do |document|
+      json.id document.id
+      index_fields(document).each do |field_name, field|
+        if should_render_index_field? document, field
+          json.set! field_name, document[field_name]
+        end
+      end
+    end
+  end
+end

From ca1671831afe5e898f9cb618c3e79c41b641bd93 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Fri, 28 Feb 2020 15:16:13 +0000
Subject: [PATCH 132/258] Update image.rb

---
 hyrax/spec/factories/image.rb | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/hyrax/spec/factories/image.rb b/hyrax/spec/factories/image.rb
index a3de1a2d..8afd61d5 100644
--- a/hyrax/spec/factories/image.rb
+++ b/hyrax/spec/factories/image.rb
@@ -3,9 +3,6 @@
   factory :image do
     title { ["Image"] }
     access_control
-    # skip_create
-    # override_new_record
-
 
     trait :open do
       visibility { 'open' }

From 619faa5ee6357559c1a80427cfff4abaf1782193 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Sun, 8 Mar 2020 22:42:14 +0000
Subject: [PATCH 133/258] Adds a protostype RO-Crate export service and rake
 task

---
 hyrax/Gemfile                                 |   2 +
 hyrax/Gemfile.lock                            |   9 ++
 .../app/assets/images/ro_crate/nims_logo.png  | Bin 0 -> 8533 bytes
 .../hyrax/solr_document/mdr_export.rb         |   8 +-
 hyrax/app/services/ro_crate_export_service.rb |  95 ++++++++++++++++++
 hyrax/app/views/ro_crate/preview.html.erb     |  74 ++++++++++++++
 hyrax/lib/tasks/ro_crate_export.rake          |  13 +++
 7 files changed, 199 insertions(+), 2 deletions(-)
 create mode 100644 hyrax/app/assets/images/ro_crate/nims_logo.png
 create mode 100644 hyrax/app/services/ro_crate_export_service.rb
 create mode 100644 hyrax/app/views/ro_crate/preview.html.erb
 create mode 100644 hyrax/lib/tasks/ro_crate_export.rake

diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index dc8a4cfd..7ba52f66 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -82,6 +82,8 @@ gem 'cancancan', '~> 1.17' # NB: locked to an older version because of hyrax > h
 
 gem 'riiif', '~> 2.0'
 
+gem 'ro-crate-ruby', git: 'https://github.com/fbacall/ro-crate-ruby'
+
 group :production do
   gem 'airbrake', '~> 5.0'
 end
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index a3096e6a..f953f73d 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -19,6 +19,14 @@ GIT
       rails (~> 5.1.6.1)
       rubyzip (>= 1.0.0)
 
+GIT
+  remote: https://github.com/fbacall/ro-crate-ruby
+  revision: 0982279c5e3613e718e34125a6182f1575222306
+  specs:
+    ro-crate-ruby (0.0.3)
+      addressable
+      rubyzip
+
 GEM
   remote: https://rubygems.org/
   specs:
@@ -922,6 +930,7 @@ DEPENDENCIES
   redis (~> 3.0)
   redis-session-store (~> 0.11.1)
   riiif (~> 2.0)
+  ro-crate-ruby!
   rsolr (>= 1.0)
   rspec-rails
   sass-rails (~> 5.0)
diff --git a/hyrax/app/assets/images/ro_crate/nims_logo.png b/hyrax/app/assets/images/ro_crate/nims_logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..e6067d4a6c6509496cb8fc4d0f88c4dc36c152fd
GIT binary patch
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P00000NkvXXu0mjfmg1%r

literal 0
HcmV?d00001

diff --git a/hyrax/app/models/concerns/hyrax/solr_document/mdr_export.rb b/hyrax/app/models/concerns/hyrax/solr_document/mdr_export.rb
index 4eca7b4c..df8df0f5 100644
--- a/hyrax/app/models/concerns/hyrax/solr_document/mdr_export.rb
+++ b/hyrax/app/models/concerns/hyrax/solr_document/mdr_export.rb
@@ -1,8 +1,12 @@
 module Hyrax
   module SolrDocument
     module MdrExport
-      def persistent_url
-        Rails.application.routes.url_helpers.polymorphic_url(self)
+      def persistent_url(host: nil)
+        if host.present?
+          Rails.application.routes.url_helpers.polymorphic_url(self, host: host)
+        else
+          Rails.application.routes.url_helpers.polymorphic_url(self)
+        end
       end
     end
   end
diff --git a/hyrax/app/services/ro_crate_export_service.rb b/hyrax/app/services/ro_crate_export_service.rb
new file mode 100644
index 00000000..a960e9ec
--- /dev/null
+++ b/hyrax/app/services/ro_crate_export_service.rb
@@ -0,0 +1,95 @@
+require 'json'
+require 'tmpdir'
+require 'ro_crate_ruby'
+
+# This service generates an RO-Crate export for the specified work
+# NB: this is a prototype proof-of-concept exporter and has a few rough edges!
+class ROCrateExportService
+  include ActionView::Helpers::NumberHelper
+
+  def initialize(work, hostname = ENV['MDR_HOST'] || 'https://mdr.nims.go.jp')
+    @work = work
+    @hostname = hostname
+    @work_solr = SolrDocument.new(work.to_solr)
+    @presenter = show_presenter.new(
+        @work_solr,
+      Ability.new(nil), # always public
+      Struct.new(:host).new(@hostname)
+    )
+  end
+
+  def export_as_zip(zipfile)
+    # First, generate the MDR metadata
+    metadata = JSON.parse(@presenter.export_as_jsonld)
+
+    # Next, create a new crate and set some basic metadata
+    crate = ROCrate::Crate.new
+    crate.name = @work.title.first
+    crate.url = @work_solr.persistent_url(host: @hostname)
+    crate.author = @work.complex_person.map{|p| p.name.first}.sort.join(', ')
+    crate.license = @work.complex_rights.map{|r| r.rights_ids.first}.sort.join(', ')
+    crate.publisher = @work.publisher.sort.join(', ')
+    crate.add_organization('https://ror.org/026v1ze26', identifier: "https://ror.org/026v1ze26", name: "National Institute for Materials Science")
+    crate.preview.template = File.read('app/views/ro_crate/preview.html.erb')
+
+    # Loop through all associated filesets and add them to the crate
+    Dir.mktmpdir do |tmpdir|
+      filename = get_filename(tmpdir, 'mdr-metadata.json')
+      File.open(File.join(tmpdir, filename), 'w') do |output|
+        output.write(metadata.to_json)
+      end
+      crate.add_file(File.join(tmpdir, filename),
+                     name: 'MDR Metadata (json)',
+                     contentSize: number_to_human_size(File.size(File.join(tmpdir, filename))),
+                     encodingFormat: 'application/ld+json' )
+
+      # Now get a list of all the related filesets and add them to the metadata graph
+      @work.file_sets.each do |file_set|
+        file_set.original_file.tap do |file|
+          filename = get_filename(tmpdir, file.file_name.first)
+
+          File.open(File.join(tmpdir, filename), 'wb') do |output|
+            file.stream.each { |content| output.write(content) }
+          end
+          crate.add_file(File.join(tmpdir, filename), contentSize: number_to_human_size(file.file_size.first), encodingFormat: file.mime_type)
+        end
+      end
+
+      crate.add_file('app/assets/images/ro_crate/nims_logo.png')
+
+      # Warning: there seems to be a bug in the RO-Crate library which does not correctly handle binary files.
+      # Work around this by exporting as a Zip instead of as a folder.
+      ROCrate::Writer.new(crate).write_zip(File.new(zipfile, 'w'))
+    end # deletes tmpdir
+    self
+  end
+
+private
+
+  def show_presenter
+    case @work.class.to_s
+    when 'Dataset'
+      Hyrax::DatasetPresenter
+    when 'Image'
+      Hyrax::ImagePresenter
+    when 'Publication'
+      Hyrax::PublicationPresenter
+    when 'Work'
+      Hyrax::WorkPresenter
+    else
+      Hyrax::WorkShowPresenter
+    end
+  end
+
+  def get_filename(tmpdir, original_filename)
+    counter = 1
+    output_filename = original_filename
+    extension = File.extname(output_filename)
+    basename = File.basename(output_filename, extension)
+    while File.exist?(File.join(tmpdir, output_filename))
+      output_filename = "#{basename}-#{counter}#{extension}"
+      counter += 1
+    end
+    output_filename
+  end
+end
diff --git a/hyrax/app/views/ro_crate/preview.html.erb b/hyrax/app/views/ro_crate/preview.html.erb
new file mode 100644
index 00000000..337219e0
--- /dev/null
+++ b/hyrax/app/views/ro_crate/preview.html.erb
@@ -0,0 +1,74 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <title>
+    <%= name || "RO Crate" %>
+  </title>
+  <script type="application/ld+json"><%= metadata.generate %></script>
+  <meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
+  <meta name="keywords" content="RO Crate">
+  <style>
+    html,body,h1,h2,h3,h4,h5,h6 {font-family: sans-serif;}
+  </style>
+</head>
+<body>
+<h1>
+  <%= name || "RO Crate" %>
+</h1>
+
+<%if url.present? %>
+<p>
+  <a href="<%= url %>" target="_blank"><%= url %></a>
+</p>
+<%end %>
+<p>
+  <%= description %>
+</p>
+<dl>
+  <%if author.present? %>
+    <dt>
+      Creator(s)
+    </dt>
+    <dd>
+      <%= author %>
+    </dd>
+  <%end %>
+  <%if publisher.present? %>
+    <dt>
+      Publisher
+    </dt>
+    <dd>
+      <%= publisher %>
+    </dd>
+  <%end %>
+  <%if license.present? %>
+    <dt>
+      License
+    </dt>
+    <dd>
+      <%= license %>
+    </dd>
+  <%end %>
+</dl>
+<h2>
+  Contents
+</h2>
+<ul>
+  <% data_entities.each do |data_entity| %>
+    <li id="__data_entity_<%= data_entity.id.gsub(/\s/, '-') %>">
+      <strong><a href="<%= data_entity.id %>"><%= data_entity.name || data_entity.id %></a></strong>
+      <% if data_entity.content_size %>
+        <br/>Size: <%= data_entity.content_size %>
+      <% end %>
+      <% if data_entity.encoding_format %>
+        <br/>Format: <%= data_entity.encoding_format %>
+      <% end %>
+    </li>
+  <% end %>
+</ul>
+<hr />
+<div style="text-align: right">
+  <img src="nims_logo.png" title="National Institute for Materials Science" alt="NIMS logo" />
+</div>
+</body>
+</html>
diff --git a/hyrax/lib/tasks/ro_crate_export.rake b/hyrax/lib/tasks/ro_crate_export.rake
new file mode 100644
index 00000000..614ea73a
--- /dev/null
+++ b/hyrax/lib/tasks/ro_crate_export.rake
@@ -0,0 +1,13 @@
+
+desc "Exports an RO-Crate file usage: rake 'ro_crate_export[WORK-ID, path/to/zipfile]'"
+task :"ro_crate_export", [:work_id, :zipfile] => :environment do |task, args|
+  unless args.work_id.present? && args.zipfile.present?
+    puts "Please profile a valid work-id and the output path to the zipfile: rake 'ro_crate_export[WORK-ID, path/to/zipfile]'"
+    puts "e.g.  $ rake 'ro_crate_export[v692t620b, tmp/rocrate-example.zip]'"
+    abort
+  end
+
+  work = ActiveFedora::Base.find(args.work_id)
+  puts "Exporting #{work.title.first} to: #{args.zipfile}"
+  ROCrateExportService.new(work).export_as_zip(args.zipfile)
+end

From ea3e13aa966ec7d88f06b1ba4e8634c0efd5ad74 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Mon, 9 Mar 2020 15:24:30 +0900
Subject: [PATCH 134/258] disable default sort in CSV viewer

---
 hyrax/app/assets/javascripts/csv_preview.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/assets/javascripts/csv_preview.js b/hyrax/app/assets/javascripts/csv_preview.js
index 3a66c121..f28492da 100644
--- a/hyrax/app/assets/javascripts/csv_preview.js
+++ b/hyrax/app/assets/javascripts/csv_preview.js
@@ -13,7 +13,8 @@ $( document ).on('turbolinks:load', function() {
                         } else {
                             return {title: name.replace(/[\_\-]/g, ' ')};
                         }
-                    })
+                    }),
+                    order: []
                 });
                 preview.find('.csv-preview-title').text('Preview: ' + data.file_name);
                 if (data.total_rows > data.maximum_rows) {

From 32240adda9fafa4fc0c3b9b215d6d989f0ebdb53 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Fri, 13 Mar 2020 19:39:57 +0900
Subject: [PATCH 135/258] remove NIMS Person ID from the identifier authority
 file

---
 hyrax/config/authorities/identifiers.yml                    | 3 ---
 hyrax/spec/factories/dataset.rb                             | 6 +++---
 hyrax/spec/inputs/nested_instrument_input_spec.rb           | 2 +-
 hyrax/spec/inputs/nested_person_input_spec.rb               | 2 +-
 .../renderers/nested_instrument_attribute_renderer_spec.rb  | 2 +-
 .../spec/renderers/nested_person_attribute_renderer_spec.rb | 2 +-
 6 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/hyrax/config/authorities/identifiers.yml b/hyrax/config/authorities/identifiers.yml
index a85f2687..b0c81ae5 100644
--- a/hyrax/config/authorities/identifiers.yml
+++ b/hyrax/config/authorities/identifiers.yml
@@ -20,9 +20,6 @@ terms:
   - id: full image url
     term: Full Image URL
     active: true
-  - id: nims person id
-    term: NIMS Person ID
-    active: true
   - id: ORCID
     term: ORCID
     active: true
diff --git a/hyrax/spec/factories/dataset.rb b/hyrax/spec/factories/dataset.rb
index 76296b42..877ff4c2 100644
--- a/hyrax/spec/factories/dataset.rb
+++ b/hyrax/spec/factories/dataset.rb
@@ -76,7 +76,7 @@
           role: ['operator'],
            complex_identifier_attributes: [{
               identifier: '123456',
-              scheme: 'nims person id'
+              scheme: 'identifier local'
             }],
           complex_affiliation_attributes: [{
             job_title: 'Principal Investigator',
@@ -97,7 +97,7 @@
          role: ['author'],
           complex_identifier_attributes: [{
              identifier: '123456',
-             scheme: 'nims person id'
+             scheme: 'identifier local'
            }],
          complex_affiliation_attributes: [{
            job_title: 'Principal Investigator',
@@ -201,7 +201,7 @@
             role: ['operator'],
             complex_identifier_attributes: [{
               identifier: '123456789mo',
-              scheme: 'nims person id'
+              scheme: 'identifier local'
             }],
             complex_affiliation_attributes: [{
               job_title: 'Principal Investigator',
diff --git a/hyrax/spec/inputs/nested_instrument_input_spec.rb b/hyrax/spec/inputs/nested_instrument_input_spec.rb
index 6bc07d8e..10762e8e 100644
--- a/hyrax/spec/inputs/nested_instrument_input_spec.rb
+++ b/hyrax/spec/inputs/nested_instrument_input_spec.rb
@@ -39,7 +39,7 @@
 
     is_expected.to have_field('dataset[instrument_attributes][0]_complex_person_attributes_0_name', type: :text, with: 'Name of operator')
     is_expected.to have_select('dataset[instrument_attributes][0]_complex_person_attributes_0_role', selected: 'operator/データ測定者・計算者')
-    is_expected.to have_select('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'NIMS Person ID')
+    is_expected.to have_select('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'Identifier - Local')
     is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: '123456789mo')
     is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_affiliation_attributes_0_job_title', type: :text, with: 'Principal Investigator')
     is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_organization', type: :text, with: 'University')
diff --git a/hyrax/spec/inputs/nested_person_input_spec.rb b/hyrax/spec/inputs/nested_person_input_spec.rb
index b884da16..5c556337 100644
--- a/hyrax/spec/inputs/nested_person_input_spec.rb
+++ b/hyrax/spec/inputs/nested_person_input_spec.rb
@@ -18,7 +18,7 @@
     is_expected.to have_field('dataset_complex_person_attributes_0_name', type: :text, with: 'Anamika')
     is_expected.to have_select('dataset_complex_person_attributes_0_role', selected: 'operator/データ測定者・計算者')
 
-    is_expected.to have_select('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'NIMS Person ID')
+    is_expected.to have_select('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'Identifier - Local')
     is_expected.to have_field('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: '123456')
 
     is_expected.to have_field('dataset[complex_person_attributes][0]_complex_affiliation_attributes_0_job_title', type: :text, with: 'Principal Investigator')
diff --git a/hyrax/spec/renderers/nested_instrument_attribute_renderer_spec.rb b/hyrax/spec/renderers/nested_instrument_attribute_renderer_spec.rb
index 6c2c5ea5..e4d23553 100644
--- a/hyrax/spec/renderers/nested_instrument_attribute_renderer_spec.rb
+++ b/hyrax/spec/renderers/nested_instrument_attribute_renderer_spec.rb
@@ -54,7 +54,7 @@
     is_expected.to have_css('div.row label', text: 'Name')
     is_expected.to have_css('div.row a', text: 'Name of operator')
 
-    is_expected.to have_css('div.row label', text: 'NIMS Person ID')
+    is_expected.to have_css('div.row label', text: 'Identifier - Local')
     is_expected.to have_css('div.row', text: '123456789mo')
 
     is_expected.to have_css('div.row label', text: 'Affiliation')
diff --git a/hyrax/spec/renderers/nested_person_attribute_renderer_spec.rb b/hyrax/spec/renderers/nested_person_attribute_renderer_spec.rb
index c54b4488..107dcf21 100644
--- a/hyrax/spec/renderers/nested_person_attribute_renderer_spec.rb
+++ b/hyrax/spec/renderers/nested_person_attribute_renderer_spec.rb
@@ -13,7 +13,7 @@
       is_expected.to have_css('div.row label', text: 'Name')
       is_expected.to have_css('div.row a', text: 'Anamika')
 
-      is_expected.to have_css('div.row label', text: 'NIMS Person ID')
+      is_expected.to have_css('div.row label', text: 'Identifier - Local')
       is_expected.to have_css('div.row', text: '123456')
 
       is_expected.to have_css('div.row label', text: 'Affiliation')

From 89fab0a9a3449aa74ca568650f6c23d672f1007c Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 19 Mar 2020 11:35:20 +0900
Subject: [PATCH 136/258] move custom_property section to description

---
 hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb b/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
index e90ff3a0..9a1f3e18 100644
--- a/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
@@ -75,6 +75,8 @@
           <%= presenter.attribute_to_html(:source, html_dl: true) %>
         <% end %>
 
+        <%= presenter.attribute_to_html(:custom_property, render_as: :nested_custom_property, label: t('ngdr.fields.custom_property'), html_dl: true) %>
+
         <!-- no defined permissions for date_created, date_modified, access_right -->
         <%= presenter.attribute_to_html(:date_created, render_as: :linked, search_field: 'date_created_tesim', html_dl: true) %>
         <%= presenter.attribute_to_html(:date_modified, label: t('hyrax.base.show.last_modified'), html_dl: true) %>
@@ -101,7 +103,6 @@
         <%= presenter.attribute_to_html(:properties_addressed, render_as: :faceted, label: t('ngdr.fields.properties_addressed'), html_dl: true) %>
         <%= presenter.attribute_to_html(:specimen_set, label: t('ngdr.fields.specimen_set'), html_dl: true) %>
         <%= presenter.attribute_to_html(:synthesis_and_processing, render_as: :faceted, label: t('ngdr.fields.synthesis_and_processing'), html_dl: true) %>
-        <%= presenter.attribute_to_html(:custom_property, render_as: :nested_custom_property, label: t('ngdr.fields.custom_property'), html_dl: true) %>
       </div> <!-- panel body -->
     </div> <!-- Accordion body -->
   </div> <!-- Method accordion -->

From 116dba5cd9ec759491fdfc8170c8381864bfcf5c Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 19 Mar 2020 11:59:23 +0900
Subject: [PATCH 137/258] send "Referrer-Policy:
 strict-origin-when-cross-origin" in http header

---
 hyrax/config/application.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/hyrax/config/application.rb b/hyrax/config/application.rb
index 9cacc7d3..82b8d38e 100644
--- a/hyrax/config/application.rb
+++ b/hyrax/config/application.rb
@@ -21,5 +21,7 @@ class Application < Rails::Application
     config.action_dispatch.rescue_responses.merge!(
       'I18n::InvalidLocale' => :not_found
     )
+
+    config.action_dispatch.default_headers['Referrer-Policy'] = 'strict-origin-when-cross-origin'
   end
 end

From 9ef7455bedc34b446fb0e8b487c4752104422b95 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 19 Mar 2020 12:43:56 +0900
Subject: [PATCH 138/258] remove social media icons from Item page

---
 .../views/hyrax/file_sets/_show_actions.html.erb  | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/file_sets/_show_actions.html.erb

diff --git a/hyrax/app/views/hyrax/file_sets/_show_actions.html.erb b/hyrax/app/views/hyrax/file_sets/_show_actions.html.erb
new file mode 100644
index 00000000..3a6703ae
--- /dev/null
+++ b/hyrax/app/views/hyrax/file_sets/_show_actions.html.erb
@@ -0,0 +1,15 @@
+<div class="form-actions">
+  <% if Hyrax.config.analytics? %>
+    <%= link_to "Analytics", @presenter.stats_path, id: 'stats', class: 'btn btn-default' %>
+  <% end %>
+
+  <% if @presenter.editor? %>
+      <%= link_to "Edit This #{@presenter.human_readable_type}", edit_polymorphic_path([main_app, @presenter]),
+                  class: 'btn btn-default' %>
+      <%= link_to "Delete This #{@presenter.human_readable_type}", [main_app, @presenter],
+                  class: 'btn btn-danger', data: { confirm: "Delete this #{@presenter.human_readable_type}?" },
+                  method: :delete %>
+  <% end %>
+
+  <%# render 'social_media' %>
+</div>

From 477451628cde9e80a75de504db6afd17fa932231 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 19 Mar 2020 14:23:18 +0900
Subject: [PATCH 139/258] move relationship section to the top of Work page

---
 hyrax/app/views/hyrax/base/show.html.erb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/views/hyrax/base/show.html.erb b/hyrax/app/views/hyrax/base/show.html.erb
index bcc135ba..35568c85 100644
--- a/hyrax/app/views/hyrax/base/show.html.erb
+++ b/hyrax/app/views/hyrax/base/show.html.erb
@@ -26,6 +26,8 @@
             <%#= render 'social_media' %> <!-- No social media buttons -->
           </div>
           <div class="col-sm-9">
+            <%= render 'relationships', presenter: @presenter %>
+
             <% if can? :read_abstract, @presenter.model_name.name.constantize %>
               <%= render 'work_description', presenter: @presenter %>
             <% end %>
@@ -34,7 +36,6 @@
           </div>
 
           <div class="col-sm-12">
-            <%= render 'relationships', presenter: @presenter %>
             <%= render 'items', presenter: @presenter %>
             <%# TODO: we may consider adding these partials in the future %>
             <%# = render 'sharing_with', presenter: @presenter %>

From ee8549061abf4eacef863ec3904c8d9755e51170 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Mon, 23 Mar 2020 11:52:25 +0900
Subject: [PATCH 140/258] set display_name and employee_type_code

---
 hyrax/app/models/user.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index c546b2f8..56f4c76d 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -37,6 +37,8 @@ def self.find_or_create_system_user(user_key)
   def ldap_before_save
     # Runs before saving a new user record in the database via LDAP Authentication
     self.email = Devise::LDAP::Adapter.get_ldap_param(username, "mail").first
+    self.display_name = Devise::LDAP::Adapter.get_ldap_param(username, "cn").first
+    self.employee_type_code = Devise::LDAP::Adapter.get_ldap_param(username, "employeeType").first.try(:first)
     self.password = Devise.friendly_token[0, 20]
     # TODO: This will be replaced by NIMS PID when the CAS server is online
     self.user_identifier = Noid::Rails::Service.new.mint

From 203fbfd3c286a6ba1a771a27824ccd3a2a537153 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 23 Mar 2020 14:35:56 +0900
Subject: [PATCH 141/258] hide user activity log

---
 hyrax/app/views/hyrax/file_sets/show.html.erb      |  2 +-
 hyrax/app/views/hyrax/users/_activity_log.html.erb | 12 ++++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/app/views/hyrax/users/_activity_log.html.erb

diff --git a/hyrax/app/views/hyrax/file_sets/show.html.erb b/hyrax/app/views/hyrax/file_sets/show.html.erb
index c93941f3..92525dc3 100644
--- a/hyrax/app/views/hyrax/file_sets/show.html.erb
+++ b/hyrax/app/views/hyrax/file_sets/show.html.erb
@@ -15,7 +15,7 @@
       <%= render 'show_details' %>
 
       <%= nims_media_display(@presenter, datatable: true) if @presenter.respond_to?(:csv?) && @presenter.csv? %>
-      <%= render 'hyrax/users/activity_log', events: @presenter.events %>
+      <%# render 'hyrax/users/activity_log', events: @presenter.events %>
     </div><!-- /columns second -->
   </div> <!-- /.row -->
 </div><!-- /.container-fluid -->
diff --git a/hyrax/app/views/hyrax/users/_activity_log.html.erb b/hyrax/app/views/hyrax/users/_activity_log.html.erb
new file mode 100644
index 00000000..b4f44e64
--- /dev/null
+++ b/hyrax/app/views/hyrax/users/_activity_log.html.erb
@@ -0,0 +1,12 @@
+User activity log is disabled.
+
+<table id="activity" class="table table-striped table-bordered">
+  <thead>
+    <tr>
+      <th>User Activity</th>
+      <th>Date</th>
+    </tr>
+  </thead>
+  <tbody>
+  </tbody>
+</table>

From 9c9f19bea9d5e5a2dfd9a19b65636b0aba02c78f Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Tue, 31 Mar 2020 17:46:29 +0900
Subject: [PATCH 142/258] fix the version of universalviewer

---
 hyrax/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/package.json b/hyrax/package.json
index 11b941e3..9ae7710d 100644
--- a/hyrax/package.json
+++ b/hyrax/package.json
@@ -3,7 +3,7 @@
   "private": true,
   "repository": "git@github.com:antleaf/nims-hyrax.git",
   "dependencies": {
-  "universalviewer": "^3.0.16"
+  "universalviewer": "3.0.16"
 },
 "scripts": {
   "preinstall": "rm -rf ./public/uv",

From 131f7dc6cacc51ec7cd4890dddebf12d72188c54 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 13 Mar 2020 20:01:02 +0000
Subject: [PATCH 143/258] Download_all

---
 hyrax/.solr_wrapper                           |   2 +-
 .../controllers/download_all_controller.rb    | 110 ++++++++++++++++++
 hyrax/app/helpers/hyrax_helper.rb             |  25 ++++
 .../views/hyrax/base/_download_all.html.erb   |  15 +++
 .../hyrax/base/_representative_media.html.erb |   2 +
 hyrax/config/locales/hyrax.en.yml             |   1 +
 hyrax/config/routes.rb                        |   2 +
 .../download_all_controller_spec.rb           |  49 ++++++++
 hyrax/spec/factories/file_sets.rb             |   4 +-
 9 files changed, 207 insertions(+), 3 deletions(-)
 create mode 100644 hyrax/app/controllers/download_all_controller.rb
 create mode 100644 hyrax/app/views/hyrax/base/_download_all.html.erb
 create mode 100644 hyrax/spec/controllers/download_all_controller_spec.rb

diff --git a/hyrax/.solr_wrapper b/hyrax/.solr_wrapper
index d4186ed6..504d4f8b 100644
--- a/hyrax/.solr_wrapper
+++ b/hyrax/.solr_wrapper
@@ -1,5 +1,5 @@
 # Place any default configuration for solr_wrapper here
-# version: 6.0.0
+version: 7.7.1
 # port: 8983
 instance_dir: tmp/solr-development
 collection:
diff --git a/hyrax/app/controllers/download_all_controller.rb b/hyrax/app/controllers/download_all_controller.rb
new file mode 100644
index 00000000..52ccb2c7
--- /dev/null
+++ b/hyrax/app/controllers/download_all_controller.rb
@@ -0,0 +1,110 @@
+# frozen_string_literal: true
+
+class DownloadAllController < Hyrax::DownloadsController
+  include HyraxHelper
+  include Hydra::Controller::DownloadBehavior
+  include Hyrax::LocalFileDownloadsControllerBehavior
+
+  # GET /download_all/1
+  def show
+    respond_to do |format|
+      format.zip { send_zip }
+      format.any { head :unsupported }
+    end
+  end
+
+  private
+
+  # Override from DownloadsController
+  #
+  # @return [String] path to zip
+  def file
+    @file ||= zip_file
+  end
+
+  # Override from DownloadBehavior
+  def asset
+    @work ||= ActiveFedora::Base.find(params[:id])
+  end
+
+  def send_zip
+    if within_file_size_threshold?(asset.file_set_ids)
+      build_zip
+      # Hyrax::LocalFileDownloadsControllerBehavior#send_local_content
+      send_local_content
+    else
+      head :unsupported
+    end
+  end
+
+  # Extend here to add other files to the zip
+  def build_zip
+    mk_zip_file_path
+    add_metadata
+    add_files
+    zip!
+  end
+
+  # Add :ttl metadata from resource.dump(:ttl) 
+  # Change this method to write a different metadata format
+  def add_metadata
+    File.write(
+      File.join(zip_file_path, 'metadata.ttl'),
+      asset.resource.dump(:ttl),
+      mode: 'wb'
+    )
+  end
+
+  # Add all file_sets
+  def add_files
+    file_sets(asset.file_set_ids).each do |fs|
+      file_set = FileSet.find(fs['id'])
+      next if file_set.blank?
+
+      original = file_set.original_file
+      next if original.blank?
+
+      File.write(
+        File.join(zip_file_path, original.file_name.first),
+        URI.parse(original.uri).open.read,
+        mode: 'wb'
+      )
+    end
+  end
+
+  def mk_zip_file_path
+    FileUtils.mkdir_p(zip_file_path)
+  end
+
+  def zip_file_path
+    @zip_file_path ||= File.join(
+      ENV.fetch('RAILS_TMP', '/tmp'),
+      asset.id.to_s
+    )
+  end
+
+  def zip_file
+    @zip_file ||= "#{zip_file_path}.zip"
+  end
+
+  def zip!
+    WillowSword::ZipPackage.new(
+      zip_file_path, zip_file
+    ).create_zip
+  end
+
+  # Override from LocalFileDownloadsControllerBehavior
+  def local_file_mime_type
+    'application/zip'
+  end
+
+  # Override from LocalFileDownloadsControllerBehavior
+  def local_file_name
+    "#{asset.id}.zip"
+  end
+
+  # Override from LocalFileDownloadsControllerBehavior
+  def local_derivative_download_options
+    super.merge(disposition: 'attachment')
+  end
+end
diff --git a/hyrax/app/helpers/hyrax_helper.rb b/hyrax/app/helpers/hyrax_helper.rb
index dd571241..41ca8863 100644
--- a/hyrax/app/helpers/hyrax_helper.rb
+++ b/hyrax/app/helpers/hyrax_helper.rb
@@ -27,4 +27,29 @@ def link_to_profile(args)
     text = user.respond_to?(:name) ? user.name : user_or_key
     link_to text, Hyrax::Engine.routes.url_helpers.user_path(user.user_identifier)
   end
+  
+  # Gather file_sets ids available to the requesting user
+  def available_file_set_ids(presenter, ability)
+    presenter.file_set_presenters.select do |p|
+      ability.can?(:read, p.id)
+    end.collect(&:id)
+  end
+
+  def within_file_size_threshold?(ids)
+    total_size_file_sets(ids) > 0 && total_size_file_sets(ids) < max_size_file_sets
+  end
+
+  def total_size_file_sets(ids)
+    @total_size_file_sets ||= file_sets(ids).map { |fs| fs['file_size_lts'] }.inject(:+) || 0
+  end
+
+  def file_sets(ids)
+    @file_sets ||= FileSet.search_with_conditions(id: ids)
+  end
+
+  # 100Mb
+  def max_size_file_sets
+    100_000_000
+  end
+
 end
diff --git a/hyrax/app/views/hyrax/base/_download_all.html.erb b/hyrax/app/views/hyrax/base/_download_all.html.erb
new file mode 100644
index 00000000..aaace626
--- /dev/null
+++ b/hyrax/app/views/hyrax/base/_download_all.html.erb
@@ -0,0 +1,15 @@
+
+<%# Only show the download all button if there are file_sets, and the total size is > 0 and < 100Mb %>
+<% if presenter.member_presenters.length > 1 %>
+<% file_set_ids = presenter.member_presenters.map {|fs| fs.id }.compact %>
+  <% if within_file_size_threshold?(file_set_ids) %>
+    <div class="download-all">
+      <%= link_to t(:'hyrax.download_all'),
+        main_app.download_all_path(presenter.id, format: :zip),
+        id: "download-all",
+        class: "btn btn-default",
+        target: "_new"
+        %>
+    </div>
+  <% end %>
+<% end %>
diff --git a/hyrax/app/views/hyrax/base/_representative_media.html.erb b/hyrax/app/views/hyrax/base/_representative_media.html.erb
index 48b67405..86c877c0 100644
--- a/hyrax/app/views/hyrax/base/_representative_media.html.erb
+++ b/hyrax/app/views/hyrax/base/_representative_media.html.erb
@@ -8,3 +8,5 @@
 <% else %>
   <%= image_tag 'default.png', class: "canonical-image" %>
 <% end %>
+
+<%= render 'download_all', presenter: @presenter %>
\ No newline at end of file
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index beea6fec..7f5cf274 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -236,6 +236,7 @@ en:
     account_name: My Institution Account Id
     directory:
       suffix: "@example.org"
+    download_all: Download All Files (Zip)
     footer:
       copyright_html: "Copyright &copy; National Institute for Materials Science"
       service_html: A service of <a href="http://samvera.org/" class="navbar-link" target="_blank">Samvera</a>.
diff --git a/hyrax/config/routes.rb b/hyrax/config/routes.rb
index 2d78725b..8a30fbea 100644
--- a/hyrax/config/routes.rb
+++ b/hyrax/config/routes.rb
@@ -43,6 +43,8 @@
     end
   end
 
+  resources :download_all, only: :show
+
   resources :welcome, only: 'index'
   root 'hyrax/homepage#index'
 
diff --git a/hyrax/spec/controllers/download_all_controller_spec.rb b/hyrax/spec/controllers/download_all_controller_spec.rb
new file mode 100644
index 00000000..9e362568
--- /dev/null
+++ b/hyrax/spec/controllers/download_all_controller_spec.rb
@@ -0,0 +1,49 @@
+require 'rails_helper'
+require 'devise'
+
+RSpec.describe DownloadAllController, type: :controller do
+  include Devise::Test::ControllerHelpers
+  routes { Rails.application.routes }
+
+  describe 'GET #show' do
+    let(:user) { create(:user) } # not used yet!
+    let(:file_set) { create(:file_set) }
+    let(:dataset) { create(:dataset, members: [file_set]) }
+
+    before do
+      allow(subject).to receive(:authorize_download!).and_return(true)
+    end
+
+    context 'with file_sets' do
+      before do
+        CharacterizeJob.perform_now(file_set, file_set.original_file.id)
+      end
+
+      context 'request application/zip' do
+        it 'returns a success response' do
+          get :show, params: { id: dataset.id, format: :zip }
+          expect(response).to be_successful
+          expect(File.exist?('/tmp/test-0151_Dataset.zip')).to be_truthy
+        end
+      end
+
+      context 'request anything other than application/zip' do
+        it 'returns a failed response' do
+          get :show, params: { id: dataset.id, format: :html }
+          expect(response).not_to be_successful
+        end
+      end
+    end
+
+    context 'without file_sets' do
+      let(:dataset) { create(:dataset) }
+
+      context 'request application/zip but without filesets' do
+        it 'returns a failed response' do
+          get :show, params: { id: dataset.id, format: :zip }
+          expect(response).not_to be_successful
+        end
+      end
+    end
+  end
+end
diff --git a/hyrax/spec/factories/file_sets.rb b/hyrax/spec/factories/file_sets.rb
index 0debbd1d..cf132a48 100644
--- a/hyrax/spec/factories/file_sets.rb
+++ b/hyrax/spec/factories/file_sets.rb
@@ -2,7 +2,7 @@
   factory :file_set do
     transient do
       user { create(:user) }
-      content { nil }
+      content { File.open('spec/fixtures/csv/example.csv', 'r') }
     end
     after(:build) do |fs, evaluator|
       fs.apply_depositor_metadata evaluator.user.user_key
@@ -34,7 +34,7 @@
 
     trait :restricted do
       visibility { 'restricted' }
-      title { ["Resstricted File Set"] }
+      title { ["Restricted File Set"] }
     end
   end
 end

From 6e6098afac23c6a595a2c2f8d311de14b253639f Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Wed, 1 Apr 2020 13:57:50 +0100
Subject: [PATCH 144/258] refactor to honour current_ability; cleanup the zip
 folder on download

---
 .../controllers/download_all_controller.rb    | 57 +++++++++++++-----
 .../views/hyrax/base/_download_all.html.erb   |  6 +-
 .../download_all_controller_spec.rb           | 26 +++++---
 hyrax/spec/helpers/hyrax_helper_spec.rb       | 59 +++++++++++++++++--
 4 files changed, 118 insertions(+), 30 deletions(-)

diff --git a/hyrax/app/controllers/download_all_controller.rb b/hyrax/app/controllers/download_all_controller.rb
index 52ccb2c7..be92a02c 100644
--- a/hyrax/app/controllers/download_all_controller.rb
+++ b/hyrax/app/controllers/download_all_controller.rb
@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+# DownloadAllController
 class DownloadAllController < Hyrax::DownloadsController
   include HyraxHelper
   include Hydra::Controller::DownloadBehavior
@@ -22,13 +23,25 @@ def file
     @file ||= zip_file
   end
 
+  def work
+    @work ||= ActiveFedora::Base.find(params[:id])
+  end
+
   # Override from DownloadBehavior
   def asset
-    @work ||= ActiveFedora::Base.find(params[:id])
+    @asset ||= Hyrax::WorkShowPresenter.new(
+      SolrDocument.new(work.to_solr),
+      current_ability,
+      request
+    )
+  end
+
+  def file_set_ids
+    @file_set_ids ||= available_file_set_ids(asset, current_ability)
   end
 
   def send_zip
-    if within_file_size_threshold?(asset.file_set_ids)
+    if within_file_size_threshold?(file_set_ids)
       build_zip
       # Hyrax::LocalFileDownloadsControllerBehavior#send_local_content
       send_local_content
@@ -39,25 +52,29 @@ def send_zip
 
   # Extend here to add other files to the zip
   def build_zip
-    mk_zip_file_path
+    mk_zip_file_dir
     add_metadata
     add_files
     zip!
+    cleanup
   end
 
-  # Add :ttl metadata from resource.dump(:ttl) 
+  # Add :ttl metadata
   # Change this method to write a different metadata format
   def add_metadata
     File.write(
       File.join(zip_file_path, 'metadata.ttl'),
-      asset.resource.dump(:ttl),
+      # This presenter method #export_as_ttl doesn't work, possibly a bug
+      #   so grab the ttl directly from the work
+      # asset.export_as_ttl,
+      work.resource.dump(:ttl),
       mode: 'wb'
     )
   end
 
   # Add all file_sets
   def add_files
-    file_sets(asset.file_set_ids).each do |fs|
+    file_sets(file_set_ids).each do |fs|
       file_set = FileSet.find(fs['id'])
       next if file_set.blank?
 
@@ -72,25 +89,33 @@ def add_files
     end
   end
 
-  def mk_zip_file_path
-    FileUtils.mkdir_p(zip_file_path)
+  def cleanup
+    FileUtils.rm_rf(zip_file_path)
+  end
+
+  def zip!
+    WillowSword::ZipPackage.new(
+      zip_file_path, zip_file
+    ).create_zip
   end
 
   def zip_file_path
-    @zip_file_path ||= File.join(
+    File.join(
       ENV.fetch('RAILS_TMP', '/tmp'),
-      asset.id.to_s
+      file_name
     )
   end
 
   def zip_file
-    @zip_file ||= "#{zip_file_path}.zip"
+    "#{zip_file_path}.zip"
   end
 
-  def zip!
-    WillowSword::ZipPackage.new(
-      zip_file_path, zip_file
-    ).create_zip
+  def mk_zip_file_dir
+    FileUtils.mkdir_p(zip_file_path)
+  end
+
+  def file_name
+    current_user.present? ? "#{asset.id}_user#{current_user.id}" : asset.id.to_s
   end
 
   # Override from LocalFileDownloadsControllerBehavior
@@ -100,7 +125,7 @@ def local_file_mime_type
 
   # Override from LocalFileDownloadsControllerBehavior
   def local_file_name
-    "#{asset.id}.zip"
+    "#{file_name}.zip"
   end
 
   # Override from LocalFileDownloadsControllerBehavior
diff --git a/hyrax/app/views/hyrax/base/_download_all.html.erb b/hyrax/app/views/hyrax/base/_download_all.html.erb
index aaace626..06c886b4 100644
--- a/hyrax/app/views/hyrax/base/_download_all.html.erb
+++ b/hyrax/app/views/hyrax/base/_download_all.html.erb
@@ -1,7 +1,7 @@
 
-<%# Only show the download all button if there are file_sets, and the total size is > 0 and < 100Mb %>
-<% if presenter.member_presenters.length > 1 %>
-<% file_set_ids = presenter.member_presenters.map {|fs| fs.id }.compact %>
+<%# Only show the download all button if there are available file_sets, and the total size is > 0 and < 100Mb %>
+<% file_set_ids = available_file_set_ids(presenter, current_ability)%>
+<% if presenter.member_presenters.length > 0 && file_set_ids.size > 0 %>
   <% if within_file_size_threshold?(file_set_ids) %>
     <div class="download-all">
       <%= link_to t(:'hyrax.download_all'),
diff --git a/hyrax/spec/controllers/download_all_controller_spec.rb b/hyrax/spec/controllers/download_all_controller_spec.rb
index 9e362568..232c1daa 100644
--- a/hyrax/spec/controllers/download_all_controller_spec.rb
+++ b/hyrax/spec/controllers/download_all_controller_spec.rb
@@ -6,16 +6,13 @@
   routes { Rails.application.routes }
 
   describe 'GET #show' do
-    let(:user) { create(:user) } # not used yet!
     let(:file_set) { create(:file_set) }
     let(:dataset) { create(:dataset, members: [file_set]) }
 
-    before do
-      allow(subject).to receive(:authorize_download!).and_return(true)
-    end
-
-    context 'with file_sets' do
+    context 'with public file_set' do
       before do
+        allow(subject).to receive(:authorize_download!).and_return(true)
+        allow(subject).to receive(:available_file_set_ids).and_return([file_set.id])
         CharacterizeJob.perform_now(file_set, file_set.original_file.id)
       end
 
@@ -23,7 +20,6 @@
         it 'returns a success response' do
           get :show, params: { id: dataset.id, format: :zip }
           expect(response).to be_successful
-          expect(File.exist?('/tmp/test-0151_Dataset.zip')).to be_truthy
         end
       end
 
@@ -38,6 +34,10 @@
     context 'without file_sets' do
       let(:dataset) { create(:dataset) }
 
+      before do
+        allow(subject).to receive(:available_file_set_ids).and_return([])
+      end
+
       context 'request application/zip but without filesets' do
         it 'returns a failed response' do
           get :show, params: { id: dataset.id, format: :zip }
@@ -45,5 +45,17 @@
         end
       end
     end
+
+    context 'with restricted file_sets' do
+      let(:file_set) { create(:file_set, :restricted) }
+      let(:dataset) { create(:dataset, members: [file_set]) }
+
+      context 'request application/zip' do
+        it 'returns a failed response' do
+          get :show, params: { id: dataset.id, format: :zip }
+          expect(response).not_to be_successful
+        end
+      end
+    end
   end
 end
diff --git a/hyrax/spec/helpers/hyrax_helper_spec.rb b/hyrax/spec/helpers/hyrax_helper_spec.rb
index 3a655d0e..33f2be3a 100644
--- a/hyrax/spec/helpers/hyrax_helper_spec.rb
+++ b/hyrax/spec/helpers/hyrax_helper_spec.rb
@@ -1,13 +1,64 @@
 require 'rails_helper'
 
-RSpec.describe HyraxHelper, :type => :helper do
+RSpec.describe HyraxHelper, type: :helper do
   describe '#available_translations' do
     it 'returns available translations' do
-      expect(helper.available_translations).to eql({"en"=>"English"})
+      expect(helper.available_translations).to eql('en' => 'English')
     end
   end
 
-  it 'has no singleton methods' do
-    expect(subject.singleton_methods).to be_empty
+  describe '#available_file_set_ids' do
+    let(:file_set) { create(:file_set) }
+    let(:dataset) { create(:dataset, members: [file_set]) }
+    let(:solr_document) { SolrDocument.new(dataset.to_solr) }
+    let(:ability) { Ability.new(create(:user)) }
+    let(:presenter) { Hyrax::WorkShowPresenter.new(solr_document, ability) }
+
+    before do
+      allow(presenter).to receive(:file_set_presenters).and_return([file_set])
+    end
+
+    context 'user can read file_set' do
+      before do
+        allow(ability).to receive(:can?).and_return(true)
+      end
+      it 'returns available_file_set_ids' do
+        expect(helper.available_file_set_ids(presenter, ability)).to eq([file_set.id])
+      end
+    end
+
+    context 'user cannot read file_set' do
+      before do
+        allow(ability).to receive(:can?).and_return(false)
+      end
+
+      it 'returns available_file_set_ids' do
+        expect(helper.available_file_set_ids(presenter, ability)).to eq([])
+      end
+    end
+  end
+
+  describe '#within_file_size_threshold?' do
+    let(:file_set) { create(:file_set) }
+
+    before do
+      CharacterizeJob.perform_now(file_set, file_set.original_file.id)
+    end
+
+    context 'above threshold' do
+      before do
+        allow(helper).to receive(:total_size_file_sets).with([file_set.id]).and_return(100_000_001)
+      end
+
+      it 'returns true' do
+        expect(helper.within_file_size_threshold?([file_set.id])).to eq(false)
+      end
+    end
+
+    context 'below threshold' do
+      it 'returns true' do
+        expect(helper.within_file_size_threshold?([file_set.id])).to eq(true)
+      end
+    end
   end
 end

From 3c2032e548e478ebea15c97670cc24ca4d3b585e Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Tue, 7 Apr 2020 23:52:47 +0900
Subject: [PATCH 145/258] require exception_notification

---
 .env.template                           |  8 --------
 hyrax/Gemfile                           |  3 ++-
 hyrax/Gemfile.lock                      | 12 ++++++++----
 hyrax/config/environments/production.rb | 10 ++++++++++
 hyrax/config/initializers/errbit.rb     | 22 ----------------------
 5 files changed, 20 insertions(+), 35 deletions(-)
 delete mode 100644 hyrax/config/initializers/errbit.rb

diff --git a/.env.template b/.env.template
index d1c3b815..dc7f20f6 100644
--- a/.env.template
+++ b/.env.template
@@ -69,14 +69,6 @@ CONFIG_IIIF_IMAGE_ENDPOINT=
 # If the rails server is configured to serve requests in https, set this to true
 IIIF_TO_SERVE_SSL_URLS=false
 
-# errbit setup
-# Host where errbit server is installed. Start with http or https
-AIRBRAKE_HOST=
-# Any positive integer should work
-AIRBRAKE_PROJECT_ID=
-# The project key to authorize loggint with errbit server
-AIRBRAKE_PROJECT_KEY=
-
 # Browse Everything credentials
 GOOGLE_DRIVE_CLIENT_ID=
 GOOGLE_DRIVE_CLIENT_SECRET=
diff --git a/hyrax/Gemfile b/hyrax/Gemfile
index dc8a4cfd..53c880ba 100644
--- a/hyrax/Gemfile
+++ b/hyrax/Gemfile
@@ -83,7 +83,8 @@ gem 'cancancan', '~> 1.17' # NB: locked to an older version because of hyrax > h
 gem 'riiif', '~> 2.0'
 
 group :production do
-  gem 'airbrake', '~> 5.0'
+  gem 'exception_notification', '~> 4.4'
+  gem 'exception_notification-rake', '~> 0.3.1'
 end
 
 gem 'willow_sword', git: 'https://github.com/CottageLabs/willow_sword.git', :branch => 'feature/prep_for_new_release'
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index a3096e6a..d6335133 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -81,9 +81,6 @@ GEM
       tzinfo (~> 1.1)
     addressable (2.7.0)
       public_suffix (>= 2.0.2, < 5.0)
-    airbrake (5.8.1)
-      airbrake-ruby (~> 1.8)
-    airbrake-ruby (1.8.0)
     almond-rails (0.1.0)
       rails (>= 4.2, < 6)
     arel (8.0.0)
@@ -298,6 +295,12 @@ GEM
     erubi (1.9.0)
     ethon (0.12.0)
       ffi (>= 1.3.0)
+    exception_notification (4.4.0)
+      actionmailer (>= 4.0, < 7)
+      activesupport (>= 4.0, < 7)
+    exception_notification-rake (0.3.1)
+      exception_notification (~> 4.3)
+      rake (>= 0.9.0)
     execjs (2.7.0)
     factory_bot (5.0.2)
       activesupport (>= 4.2.0)
@@ -892,7 +895,6 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  airbrake (~> 5.0)
   blacklight_oai_provider!
   bootstrap-datepicker-rails
   byebug
@@ -906,6 +908,8 @@ DEPENDENCIES
   devise-guests (~> 0.6)
   devise_cas_authenticatable
   devise_ldap_authenticatable
+  exception_notification (~> 4.4)
+  exception_notification-rake (~> 0.3.1)
   factory_bot_rails
   faraday_middleware
   fcrepo_wrapper
diff --git a/hyrax/config/environments/production.rb b/hyrax/config/environments/production.rb
index cbfcd940..75bbf373 100644
--- a/hyrax/config/environments/production.rb
+++ b/hyrax/config/environments/production.rb
@@ -112,4 +112,14 @@
     port: ENV['SMTP_PORT'],
     enable_starttls_auto: false
   }
+
+  config.middleware.use ExceptionNotification::Rack,
+    ignore_if: lambda { |env, exception| !env.nil? },
+    email: {
+      email_prefix: '[MDR] ',
+      sender_address: ENV['NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS'],
+      exception_recipients: [ENV['NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS']]
+    }
+
+  ExceptionNotifier::Rake.configure
 end
diff --git a/hyrax/config/initializers/errbit.rb b/hyrax/config/initializers/errbit.rb
deleted file mode 100644
index a046220e..00000000
--- a/hyrax/config/initializers/errbit.rb
+++ /dev/null
@@ -1,22 +0,0 @@
-# frozen_string_literal: true
-if Rails.env == 'production'
-  Airbrake.configure do |config|
-    # setting for the rails app
-    config.environment = Rails.env
-    config.ignore_environments = %w[development test]
-    # ignore production if the environment variables aren't set
-    config.ignore_environments << 'production' if ENV.fetch('AIRBRAKE_HOST', nil).blank? &&
-                                                  ENV.fetch('AIRBRAKE_PROJECT_ID', nil).blank? &&
-                                                  ENV.fetch('AIRBRAKE_PROJECT_KEY', nil).blank?
-    config.host = ENV['AIRBRAKE_HOST']
-    config.project_id = ENV['AIRBRAKE_PROJECT_ID']
-    config.project_key = ENV['AIRBRAKE_PROJECT_KEY']
-  end
-elsif defined?(Airbrake)
-  # disable Airbrake if the env vars are not present
-  puts 'Disabling Airbrake because the required env vars are not set'
-  Airbrake.configure do |c|
-    c.environment = Rails.env
-    c.ignore_environments = %w(development test production)
-  end
-end

From eff780e9b52c474ac3dfe07d48038a827d3d72b8 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Wed, 8 Apr 2020 00:01:30 +0900
Subject: [PATCH 146/258] add user_identifier to User factory file

---
 hyrax/spec/factories/users.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/hyrax/spec/factories/users.rb b/hyrax/spec/factories/users.rb
index bd06127e..b16ff170 100644
--- a/hyrax/spec/factories/users.rb
+++ b/hyrax/spec/factories/users.rb
@@ -4,6 +4,7 @@
     sequence(:email) { |n| "user#{n}@example.com" }
     sequence(:username) { |n| "user#{n}" }
     sequence(:display_name) { |n| "User #{n}"}
+    sequence(:user_identifier) { |n| "identifier_#{n}" }
     password { 'password' }
 
     transient do

From 58e5bc1647de91443b03f6ef833320e605de5e19 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 1 Aug 2019 21:09:17 +0900
Subject: [PATCH 147/258] add application_number to Dataset and Publication

---
 hyrax/app/forms/hyrax/dataset_form.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/forms/hyrax/dataset_form.rb b/hyrax/app/forms/hyrax/dataset_form.rb
index 3e16bf08..dc790a84 100644
--- a/hyrax/app/forms/hyrax/dataset_form.rb
+++ b/hyrax/app/forms/hyrax/dataset_form.rb
@@ -26,7 +26,8 @@ class DatasetForm < Hyrax::Forms::WorkForm
       :complex_identifier,
       :data_origin, :complex_instrument, :origin_system_provenance,
       :properties_addressed, :complex_relation, :specimen_set,
-      :complex_specimen_type, :synthesis_and_processing, :custom_property
+      :complex_specimen_type, :synthesis_and_processing, :custom_property,
+      :application_number
     ]
 
     self.required_fields -= [

From fc934928cf42a51942bce245554d10438276f909 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Mon, 11 Nov 2019 18:25:12 +0000
Subject: [PATCH 148/258] wip - now authenticating with local cas server

---
 .env.template                         | 15 +++++++++++++++
 hyrax/app/forms/hyrax/dataset_form.rb |  3 +--
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/.env.template b/.env.template
index d1c3b815..b9785121 100644
--- a/.env.template
+++ b/.env.template
@@ -85,8 +85,13 @@ BOX_CLIENT_SECRET=
 
 # Choose one of the following authentication methods.
 # (database_authenticatable is pre-configured and useful for a development environment)
+<<<<<<< HEAD
 MDR_DEVISE_AUTH_MODULE=database_authenticatable
 # MDR_DEVISE_AUTH_MODULE=ldap_authenticatable
+=======
+MDR_DEVISE_AUTH_MODULE=ldap_authenticatable
+# MDR_DEVISE_AUTH_MODULE=database_authenticatable
+>>>>>>> wip - now authenticating with local cas server
 # MDR_DEVISE_AUTH_MODULE=cas_authenticatable
 
 LDAP_HOST=***REMOVED***
@@ -102,6 +107,7 @@ SMTP_PORT=
 
 MDR_HOST=
 
+<<<<<<< HEAD
 CAS_BASE_URL=https://cas.nims.go.jp/
 
 # For local docker-based setup for development, use:
@@ -115,11 +121,15 @@ CAS_BASE_URL=https://cas.nims.go.jp/
 # CAS_VALIDATE_URL=https://cas:8443/cas/serviceValidate
 # CAS_DESTINATION_URL=https://portal.nims.test/
 
+=======
+<<<<<<< HEAD
+>>>>>>> wip - now authenticating with local cas server
 # OAI config used in config/initializers/oai_config.rb
 OAI_REPOSTIORY_NAME='NIMS MDR'
 OAI_REPOSITORY_URL=http://localhost:3000/catalog/oai
 OAI_RECORD_PREFIX=nims_mdr
 OAI_ADMIN_EMAIL=***REMOVED***
+<<<<<<< HEAD
 
 # User Authorisation LDAP (runs after database / LDAP / CAS authentication)
 USER_AUTHORISATION_LDAP_HOST=
@@ -129,3 +139,8 @@ USER_AUTHORISATION_LDAP_BASE=
 
 WIKIBASE_BASE_URL=https://wikibase.example.jp
 WIKIBASE_SPARQL_QUERY_SYNONYM=/query/example?query=some_sparql_query
+=======
+=======
+CAS_BASE_URL=https://cas.nims.go.jp/
+>>>>>>> wip - now authenticating with local cas server
+>>>>>>> wip - now authenticating with local cas server
diff --git a/hyrax/app/forms/hyrax/dataset_form.rb b/hyrax/app/forms/hyrax/dataset_form.rb
index dc790a84..3e16bf08 100644
--- a/hyrax/app/forms/hyrax/dataset_form.rb
+++ b/hyrax/app/forms/hyrax/dataset_form.rb
@@ -26,8 +26,7 @@ class DatasetForm < Hyrax::Forms::WorkForm
       :complex_identifier,
       :data_origin, :complex_instrument, :origin_system_provenance,
       :properties_addressed, :complex_relation, :specimen_set,
-      :complex_specimen_type, :synthesis_and_processing, :custom_property,
-      :application_number
+      :complex_specimen_type, :synthesis_and_processing, :custom_property
     ]
 
     self.required_fields -= [

From f78d8dad0ee9f10e7a029d2c4498ed0a3f1b2804 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 13 Nov 2019 10:30:53 +0000
Subject: [PATCH 149/258] wip

---
 .env.template      |  9 +++++++++
 cas/cas.properties | 15 +++++++++++++++
 2 files changed, 24 insertions(+)
 create mode 100644 cas/cas.properties

diff --git a/.env.template b/.env.template
index b9785121..7086c66b 100644
--- a/.env.template
+++ b/.env.template
@@ -107,6 +107,7 @@ SMTP_PORT=
 
 MDR_HOST=
 
+<<<<<<< HEAD
 <<<<<<< HEAD
 CAS_BASE_URL=https://cas.nims.go.jp/
 
@@ -124,12 +125,15 @@ CAS_BASE_URL=https://cas.nims.go.jp/
 =======
 <<<<<<< HEAD
 >>>>>>> wip - now authenticating with local cas server
+=======
+>>>>>>> wip
 # OAI config used in config/initializers/oai_config.rb
 OAI_REPOSTIORY_NAME='NIMS MDR'
 OAI_REPOSITORY_URL=http://localhost:3000/catalog/oai
 OAI_RECORD_PREFIX=nims_mdr
 OAI_ADMIN_EMAIL=***REMOVED***
 <<<<<<< HEAD
+<<<<<<< HEAD
 
 # User Authorisation LDAP (runs after database / LDAP / CAS authentication)
 USER_AUTHORISATION_LDAP_HOST=
@@ -144,3 +148,8 @@ WIKIBASE_SPARQL_QUERY_SYNONYM=/query/example?query=some_sparql_query
 CAS_BASE_URL=https://cas.nims.go.jp/
 >>>>>>> wip - now authenticating with local cas server
 >>>>>>> wip - now authenticating with local cas server
+=======
+CAS_BASE_URL=https://cas.nims.go.jp/
+# CAS_VALIDATE_URL may need to be set depending on how MDR is configured
+# CAS_VALIDATE_URL=https://cas:8443/cas/serviceValidate
+>>>>>>> wip
diff --git a/cas/cas.properties b/cas/cas.properties
new file mode 100644
index 00000000..635bebe5
--- /dev/null
+++ b/cas/cas.properties
@@ -0,0 +1,15 @@
+# Required CAS settings
+cas.server.name: https://cas.example.org:8443
+cas.server.prefix: https://cas.example.org:8443/cas
+
+cas.adminPagesSecurity.ip=127\.0\.0\.1
+
+logging.config: file:/etc/cas/config/log4j2.xml
+
+# Disable authentication with a static list of credentials
+# cas.authn.accept.users=
+
+# Use JSON file for authentication
+# cas.authn.json.name=
+# cas.authn.json.location=file:///etc/cas/users.json
+# cas.authn.json.passwordPolicy=

From 13de5eaaf02bb52150f3f3cd426109248601afe5 Mon Sep 17 00:00:00 2001
From: Martyn Whitwell <martyn.whitwell@gmail.com>
Date: Wed, 13 Nov 2019 18:04:39 +0000
Subject: [PATCH 150/258] custom cas server, fix password issue

---
 cas/cas.properties                       | 15 ---------------
 cas/etc/cas/services/NIMS-CAStest-1.json |  6 ++++++
 2 files changed, 6 insertions(+), 15 deletions(-)
 delete mode 100644 cas/cas.properties
 create mode 100644 cas/etc/cas/services/NIMS-CAStest-1.json

diff --git a/cas/cas.properties b/cas/cas.properties
deleted file mode 100644
index 635bebe5..00000000
--- a/cas/cas.properties
+++ /dev/null
@@ -1,15 +0,0 @@
-# Required CAS settings
-cas.server.name: https://cas.example.org:8443
-cas.server.prefix: https://cas.example.org:8443/cas
-
-cas.adminPagesSecurity.ip=127\.0\.0\.1
-
-logging.config: file:/etc/cas/config/log4j2.xml
-
-# Disable authentication with a static list of credentials
-# cas.authn.accept.users=
-
-# Use JSON file for authentication
-# cas.authn.json.name=
-# cas.authn.json.location=file:///etc/cas/users.json
-# cas.authn.json.passwordPolicy=
diff --git a/cas/etc/cas/services/NIMS-CAStest-1.json b/cas/etc/cas/services/NIMS-CAStest-1.json
new file mode 100644
index 00000000..eb0d9256
--- /dev/null
+++ b/cas/etc/cas/services/NIMS-CAStest-1.json
@@ -0,0 +1,6 @@
+{
+  "@class" : "org.apereo.cas.services.RegexRegisteredService",
+  "serviceId" :  "^(https|http)://.*",
+  "name" : "NIMS-CAStest",
+  "id" : 1
+}

From c34058eae399b629cf12694f2247ed36fa1302c5 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 23 Mar 2020 11:30:48 +0900
Subject: [PATCH 151/258] add orcid, organization and sub_organization to
 ComplexPerson

---
 hyrax/app/forms/hyrax/dataset_form.rb         |  3 ++
 hyrax/app/inputs/nested_person_input.rb       | 51 +++++++++++++++++++
 hyrax/app/models/concerns/complex_person.rb   |  5 ++
 .../nested_person_attribute_renderer.rb       | 25 +++++++++
 4 files changed, 84 insertions(+)

diff --git a/hyrax/app/forms/hyrax/dataset_form.rb b/hyrax/app/forms/hyrax/dataset_form.rb
index 3e16bf08..a8612a1e 100644
--- a/hyrax/app/forms/hyrax/dataset_form.rb
+++ b/hyrax/app/forms/hyrax/dataset_form.rb
@@ -187,6 +187,9 @@ def self.permitted_person_params
        {
          name: [],
          role: [],
+         orcid: [],
+         organization: [],
+         sub_organization: [],
          complex_affiliation_attributes: permitted_affiliation_params,
          complex_identifier_attributes: permitted_identifier_params,
          uri: []
diff --git a/hyrax/app/inputs/nested_person_input.rb b/hyrax/app/inputs/nested_person_input.rb
index f82784ea..80979768 100644
--- a/hyrax/app/inputs/nested_person_input.rb
+++ b/hyrax/app/inputs/nested_person_input.rb
@@ -52,6 +52,57 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << '  </div>'
     out << '</div>' # row
 
+    # --- orcid
+    field = :orcid
+    field_name = name_for(attribute_name, index, field, parent)
+    field_id = id_for(attribute_name, index, field, parent)
+    field_value = value.send(field).first
+
+    out << "<div class='row'>"
+    out << "  <div class='col-md-3'>"
+    out << template.label_tag(field_name, field.to_s.humanize, required: required)
+    out << '  </div>'
+
+    out << "  <div class='col-md-9'>"
+    out << @builder.text_field(field_name,
+        options.merge(value: field_value, name: field_name, id: field_id, required: required))
+    out << '  </div>'
+    out << '</div>' # row
+
+    # --- organization
+    field = :organization
+    field_name = name_for(attribute_name, index, field, parent)
+    field_id = id_for(attribute_name, index, field, parent)
+    field_value = value.send(field).first
+
+    out << "<div class='row'>"
+    out << "  <div class='col-md-3'>"
+    out << template.label_tag(field_name, field.to_s.humanize, required: required)
+    out << '  </div>'
+
+    out << "  <div class='col-md-9'>"
+    out << @builder.text_field(field_name,
+        options.merge(value: field_value, name: field_name, id: field_id, required: required))
+    out << '  </div>'
+    out << '</div>' # row
+
+    # --- sub_organization
+    field = :sub_organization
+    field_name = name_for(attribute_name, index, field, parent)
+    field_id = id_for(attribute_name, index, field, parent)
+    field_value = value.send(field).first
+
+    out << "<div class='row'>"
+    out << "  <div class='col-md-3'>"
+    out << template.label_tag(field_name, field.to_s.humanize, required: required)
+    out << '  </div>'
+
+    out << "  <div class='col-md-9'>"
+    out << @builder.text_field(field_name,
+        options.merge(value: field_value, name: field_name, id: field_id, required: required))
+    out << '  </div>'
+    out << '</div>' # row
+
     # --- complex_identifier
     field = :complex_identifier
     field_value = value.send(field)
diff --git a/hyrax/app/models/concerns/complex_person.rb b/hyrax/app/models/concerns/complex_person.rb
index 0b998376..e41200b4 100644
--- a/hyrax/app/models/concerns/complex_person.rb
+++ b/hyrax/app/models/concerns/complex_person.rb
@@ -15,6 +15,11 @@ class ComplexPerson < ActiveTriples::Resource
   accepts_nested_attributes_for :complex_identifier
   property :uri, predicate: ::RDF::Vocab::Identifiers.uri
 
+  # Workaround for nested properties
+  property :orcid, predicate: ::RDF::Vocab::DataCite.hasIdentifier
+  property :organization, predicate: ::RDF::Vocab::ORG.organization
+  property :sub_organization, predicate: ::RDF::Vocab::ORG.hasSubOrganization
+
   ## Necessary to get AT to create hash URIs.
   def initialize(uri, parent)
     if uri.try(:node?)
diff --git a/hyrax/app/renderers/nested_person_attribute_renderer.rb b/hyrax/app/renderers/nested_person_attribute_renderer.rb
index 5f4bcff9..d5e29c4b 100644
--- a/hyrax/app/renderers/nested_person_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_person_attribute_renderer.rb
@@ -25,6 +25,31 @@ def attribute_value_to_html(input_value)
           each_html += get_row(label, val)
         end
       end
+
+      # Workaround for nested properties
+      # orcid
+      unless v.dig('orcid').blank?
+        label = 'ORCID'
+        val = v['orcid'][0]
+        each_html += get_row(label, val)
+      end
+
+      # Workaround for nested properties
+      # organization
+      unless v.dig('organization').blank?
+        label = 'Organization'
+        val = v['organization'][0]
+        each_html += get_row(label, val)
+      end
+
+      # Workaround for nested properties
+      # sub_organization
+      unless v.dig('sub_organization').blank?
+        label = 'Sub organization'
+        val = v['sub_organization'][0]
+        each_html += get_row(label, val)
+      end
+
       # complex_identifier
       unless v.dig('complex_identifier').blank?
         label = 'Identifier'

From 0a0eb4c41ef9bbbfdd2c45bf1b648abd75f5a4ca Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Mon, 13 Apr 2020 19:13:09 +0900
Subject: [PATCH 152/258] hide complex_affiliation from creator form

---
 hyrax/app/inputs/nested_person_input.rb | 26 ++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/hyrax/app/inputs/nested_person_input.rb b/hyrax/app/inputs/nested_person_input.rb
index 80979768..d377cd98 100644
--- a/hyrax/app/inputs/nested_person_input.rb
+++ b/hyrax/app/inputs/nested_person_input.rb
@@ -123,23 +123,23 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << "</div>" # row
 
     # --- complex_affiliation
-    field = :complex_affiliation
-    field_value = value.send(field)
-    if field_value.blank?
-      value.complex_affiliation.build
-      field_value = value.send(field)
-    end
-    nested_fields = NestedAffiliationInput.new(@builder, field, nil, :multi_value, {})
-    out << "<div class='inner-nested'>"
-    out << "<div class='form-group'>"
-    out << "  <label class='control-label optional' for='dataset_#{field.to_s}'>Affiliation</label>"
-    out << nested_fields.nested_input({:class=>"form-control", :repeats => false}, field_value, parent_attribute)
-    out << "</div>"
+    #field = :complex_affiliation
+    #field_value = value.send(field)
+    #if field_value.blank?
+    #  value.complex_affiliation.build
+    #  field_value = value.send(field)
+    #end
+    #nested_fields = NestedAffiliationInput.new(@builder, field, nil, :multi_value, {})
+    #out << "<div class='inner-nested'>"
+    #out << "<div class='form-group'>"
+    #out << "  <label class='control-label optional' for='dataset_#{field.to_s}'>Affiliation</label>"
+    #out << nested_fields.nested_input({:class=>"form-control", :repeats => false}, field_value, parent_attribute)
+    #out << "</div>"
     # out << "  <button type='button' class='btn btn-link add'>"
     # out << "    <span class='glyphicon glyphicon-plus'></span>"
     # out << "    <span class='controls-add-text'>Add another affiliation</span>"
     # out << "  </button>"
-    out << "</div>" # row
+    #out << "</div>" # row
 
     # last row
     # --- delete checkbox

From 9a87f4d345ad10a6c320749387c28bcbed7e6e8c Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Mon, 13 Apr 2020 19:20:42 +0900
Subject: [PATCH 153/258] fix .env.template

---
 .env.template | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/.env.template b/.env.template
index 7086c66b..d1c3b815 100644
--- a/.env.template
+++ b/.env.template
@@ -85,13 +85,8 @@ BOX_CLIENT_SECRET=
 
 # Choose one of the following authentication methods.
 # (database_authenticatable is pre-configured and useful for a development environment)
-<<<<<<< HEAD
 MDR_DEVISE_AUTH_MODULE=database_authenticatable
 # MDR_DEVISE_AUTH_MODULE=ldap_authenticatable
-=======
-MDR_DEVISE_AUTH_MODULE=ldap_authenticatable
-# MDR_DEVISE_AUTH_MODULE=database_authenticatable
->>>>>>> wip - now authenticating with local cas server
 # MDR_DEVISE_AUTH_MODULE=cas_authenticatable
 
 LDAP_HOST=***REMOVED***
@@ -107,8 +102,6 @@ SMTP_PORT=
 
 MDR_HOST=
 
-<<<<<<< HEAD
-<<<<<<< HEAD
 CAS_BASE_URL=https://cas.nims.go.jp/
 
 # For local docker-based setup for development, use:
@@ -122,18 +115,11 @@ CAS_BASE_URL=https://cas.nims.go.jp/
 # CAS_VALIDATE_URL=https://cas:8443/cas/serviceValidate
 # CAS_DESTINATION_URL=https://portal.nims.test/
 
-=======
-<<<<<<< HEAD
->>>>>>> wip - now authenticating with local cas server
-=======
->>>>>>> wip
 # OAI config used in config/initializers/oai_config.rb
 OAI_REPOSTIORY_NAME='NIMS MDR'
 OAI_REPOSITORY_URL=http://localhost:3000/catalog/oai
 OAI_RECORD_PREFIX=nims_mdr
 OAI_ADMIN_EMAIL=***REMOVED***
-<<<<<<< HEAD
-<<<<<<< HEAD
 
 # User Authorisation LDAP (runs after database / LDAP / CAS authentication)
 USER_AUTHORISATION_LDAP_HOST=
@@ -143,13 +129,3 @@ USER_AUTHORISATION_LDAP_BASE=
 
 WIKIBASE_BASE_URL=https://wikibase.example.jp
 WIKIBASE_SPARQL_QUERY_SYNONYM=/query/example?query=some_sparql_query
-=======
-=======
-CAS_BASE_URL=https://cas.nims.go.jp/
->>>>>>> wip - now authenticating with local cas server
->>>>>>> wip - now authenticating with local cas server
-=======
-CAS_BASE_URL=https://cas.nims.go.jp/
-# CAS_VALIDATE_URL may need to be set depending on how MDR is configured
-# CAS_VALIDATE_URL=https://cas:8443/cas/serviceValidate
->>>>>>> wip

From c084d9a0f502a36ec1c7a450e1dcd97e8bf2da45 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Mon, 13 Apr 2020 19:28:25 +0900
Subject: [PATCH 154/258] remove dummy CAS json file

---
 cas/etc/cas/services/NIMS-CAStest-1.json | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 cas/etc/cas/services/NIMS-CAStest-1.json

diff --git a/cas/etc/cas/services/NIMS-CAStest-1.json b/cas/etc/cas/services/NIMS-CAStest-1.json
deleted file mode 100644
index eb0d9256..00000000
--- a/cas/etc/cas/services/NIMS-CAStest-1.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-  "@class" : "org.apereo.cas.services.RegexRegisteredService",
-  "serviceId" :  "^(https|http)://.*",
-  "name" : "NIMS-CAStest",
-  "id" : 1
-}

From c614177af5561e55164935f6d54cf4046a9c5c86 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Mon, 13 Apr 2020 20:11:39 +0900
Subject: [PATCH 155/258] update spec files

---
 hyrax/spec/factories/users.rb                     |  1 +
 hyrax/spec/inputs/nested_instrument_input_spec.rb |  8 ++++----
 hyrax/spec/inputs/nested_person_input_spec.rb     | 11 +++++++----
 3 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/hyrax/spec/factories/users.rb b/hyrax/spec/factories/users.rb
index bd06127e..92605d52 100644
--- a/hyrax/spec/factories/users.rb
+++ b/hyrax/spec/factories/users.rb
@@ -4,6 +4,7 @@
     sequence(:email) { |n| "user#{n}@example.com" }
     sequence(:username) { |n| "user#{n}" }
     sequence(:display_name) { |n| "User #{n}"}
+    sequence(:user_identifier) { |n| "identifier#{n}" }
     password { 'password' }
 
     transient do
diff --git a/hyrax/spec/inputs/nested_instrument_input_spec.rb b/hyrax/spec/inputs/nested_instrument_input_spec.rb
index 6bc07d8e..7cb58a58 100644
--- a/hyrax/spec/inputs/nested_instrument_input_spec.rb
+++ b/hyrax/spec/inputs/nested_instrument_input_spec.rb
@@ -41,10 +41,10 @@
     is_expected.to have_select('dataset[instrument_attributes][0]_complex_person_attributes_0_role', selected: 'operator/データ測定者・計算者')
     is_expected.to have_select('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'NIMS Person ID')
     is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: '123456789mo')
-    is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_affiliation_attributes_0_job_title', type: :text, with: 'Principal Investigator')
-    is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_organization', type: :text, with: 'University')
-    is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_sub_organization', type: :text, with: 'Department')
-    is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_purpose', type: :text, with: 'Research')
+    #is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_affiliation_attributes_0_job_title', type: :text, with: 'Principal Investigator')
+    #is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_organization', type: :text, with: 'University')
+    #is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_sub_organization', type: :text, with: 'Department')
+    #is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_purpose', type: :text, with: 'Research')
 
     is_expected.to have_field('dataset[instrument_attributes][0]_managing_organization_attributes_0_organization', type: :text, with: 'Managing organization name')
     is_expected.to have_field('dataset[instrument_attributes][0]_managing_organization_attributes_0_sub_organization', type: :text, with: 'BarBar')
diff --git a/hyrax/spec/inputs/nested_person_input_spec.rb b/hyrax/spec/inputs/nested_person_input_spec.rb
index b884da16..6811c50f 100644
--- a/hyrax/spec/inputs/nested_person_input_spec.rb
+++ b/hyrax/spec/inputs/nested_person_input_spec.rb
@@ -21,9 +21,12 @@
     is_expected.to have_select('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'NIMS Person ID')
     is_expected.to have_field('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: '123456')
 
-    is_expected.to have_field('dataset[complex_person_attributes][0]_complex_affiliation_attributes_0_job_title', type: :text, with: 'Principal Investigator')
-    is_expected.to have_field('dataset[complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_organization', type: :text, with: 'University')
-    is_expected.to have_field('dataset[complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_sub_organization', type: :text, with: 'Department')
-    is_expected.to have_field('dataset[complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_purpose', type: :text, with: 'Research')
+    #is_expected.to have_field('dataset[complex_person_attributes][0]_complex_affiliation_attributes_0_job_title', type: :text, with: 'Principal Investigator')
+    #is_expected.to have_field('dataset[complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_organization', type: :text, with: 'University')
+    #is_expected.to have_field('dataset[complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_sub_organization', type: :text, with: 'Department')
+    #is_expected.to have_field('dataset[complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_purpose', type: :text, with: 'Research')
+    is_expected.to have_field('dataset_complex_person_attributes_0_orcid', type: :text)
+    is_expected.to have_field('dataset_complex_person_attributes_0_organization', type: :text)
+    is_expected.to have_field('dataset_complex_person_attributes_0_sub_organization', type: :text)
   end
 end

From 2133a4f2ff9b3c0bb072898c4462a4004aa608f0 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Mon, 13 Apr 2020 20:58:02 +0900
Subject: [PATCH 156/258] add a workflow message

---
 .../views/hyrax/base/_form_progress.html.erb  | 65 +++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/base/_form_progress.html.erb

diff --git a/hyrax/app/views/hyrax/base/_form_progress.html.erb b/hyrax/app/views/hyrax/base/_form_progress.html.erb
new file mode 100644
index 00000000..f58c98bd
--- /dev/null
+++ b/hyrax/app/views/hyrax/base/_form_progress.html.erb
@@ -0,0 +1,65 @@
+<aside id="form-progress" class="form-progress panel panel-default">
+  <div class="panel-heading">
+    <h3 class="panel-title"><%= t("hyrax.works.progress.header") %></h3>
+  </div>
+  <div class="list-group">
+    <div class="list-group-item">
+      <fieldset>
+        <legend class="legend-save-work"><%= t('.requirements') %></legend>
+        <ul class="requirements">
+          <li class="incomplete" id="required-metadata"><%= t('.required_descriptions') %></li>
+          <% if Hyrax.config.work_requires_files? %>
+            <li class="incomplete" id="required-files"><%= t('.required_files') %></li>
+          <% end %>
+          <% if Flipflop.show_deposit_agreement? && Flipflop.active_deposit_agreement_acceptance? %>
+            <li class="incomplete" id="required-agreement"><%= t('.required_agreement') %></li>
+          <% end %>
+        </ul>
+      </fieldset>
+    </div>
+
+    <div class="set-access-controls list-group-item">
+      <%= render 'form_visibility_component', f: f %>
+    </div>
+    <% if Flipflop.proxy_deposit? && current_user.can_make_deposits_for.any? %>
+        <div class="list-group-item">
+          <%= f.input :on_behalf_of, collection: current_user.can_make_deposits_for.map(&:user_key), prompt: "Yourself" %>
+        </div>
+    <% end %>
+  </div>
+  <div class="panel-footer">
+    Your data will not be made public yet! After you push the button, send the URL of the next screen to <a href="mailto:<%= ENV['CONTACT_EMAIL']%>"><%= ENV['CONTACT_EMAIL'] %></a>.
+  </div>
+  <div class="panel-footer text-center">
+    <% if ::Flipflop.show_deposit_agreement? %>
+      <% if ::Flipflop.active_deposit_agreement_acceptance? %>
+        <label>
+          <%= check_box_tag 'agreement', 1, f.object.agreement_accepted, required: true %>
+          <%= t('hyrax.active_consent_to_agreement') %><br />
+          <%= link_to t('hyrax.pages.tabs.agreement_page'),
+                      hyrax.agreement_path,
+                      target: '_blank' %>
+        </label>
+      <% else %>
+        <%= t('hyrax.passive_consent_to_agreement') %><br />
+        <%= link_to t('hyrax.pages.tabs.agreement_page'),
+                    hyrax.agreement_path,
+                    target: '_blank' %>
+      <% end %>
+    <% end %>
+    <br />
+    <%# TODO: If we start using ActionCable, we could listen for object updates and
+              alert the user that the object has changed by someone else %>
+    <%= f.input Hyrax::Actors::OptimisticLockValidator.version_field, as: :hidden if f.object.persisted? %>
+    <%= f.submit class: 'btn btn-primary', onclick: "confirmation_needed = false;", id: "with_files_submit", name: "save_with_files" %>
+  </div>
+
+  <%# Provide immediate feedback after the form is submitted while the subsequent page is loading %>
+  <div class="panel-footer hidden">
+    <div class="progress">
+      <div class="progress-bar progress-bar-striped progress-bar-complete active">
+        <span id="form-feedback" aria-live="assertive">Saving your work. This may take a few moments</span>
+      </div>
+    </div>
+  </div>
+</aside>

From 1922c1042f984bbdd0f86548e18ecc9b88c23a90 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Fri, 17 Apr 2020 14:29:19 +0900
Subject: [PATCH 157/258] mount /data/public/branding

---
 docker-compose.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker-compose.yml b/docker-compose.yml
index 61ad9ff4..4295af4e 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -95,6 +95,7 @@ services:
       - app:${UPLOADS_PATH}
       - app:${DERIVATIVES_PATH}
       - app:${CACHE_PATH}
+      - app:/data/public/branding
     networks:
       internal:
 

From ed0bbf3dd8c7729cf514ff6f573e37dc9c1ae4c3 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 20 Apr 2020 17:03:41 +0900
Subject: [PATCH 158/258] remove custom template files

---
 hyrax/config/environments/production.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/config/environments/production.rb b/hyrax/config/environments/production.rb
index 75bbf373..d03d2d75 100644
--- a/hyrax/config/environments/production.rb
+++ b/hyrax/config/environments/production.rb
@@ -116,7 +116,7 @@
   config.middleware.use ExceptionNotification::Rack,
     ignore_if: lambda { |env, exception| !env.nil? },
     email: {
-      email_prefix: '[MDR] ',
+      email_prefix: 'MDR [Hyrax] ',
       sender_address: ENV['NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS'],
       exception_recipients: [ENV['NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS']]
     }

From 3b7f52605ade0c7d1a0bc285ad6e7ae2404f14e6 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Wed, 22 Apr 2020 18:18:03 +0900
Subject: [PATCH 159/258] Make the text color of links darker

---
 hyrax/app/assets/stylesheets/theme.scss | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/assets/stylesheets/theme.scss b/hyrax/app/assets/stylesheets/theme.scss
index f55341d7..fd4ed17c 100644
--- a/hyrax/app/assets/stylesheets/theme.scss
+++ b/hyrax/app/assets/stylesheets/theme.scss
@@ -17,6 +17,7 @@ $mdr-grey: #F4F4F4;
 $mdr-black: #1E2022;
 $mdr-green: #AFCA0B;
 $mdr-green-light: #7DB928;
+$mdr-green-dark: #387A06;
 
 //-------------- Fonts -----------------
 body {
@@ -48,7 +49,7 @@ h3, .h3 {
 
 //------------- anchor -----------------
 a, a:focus, a:hover, a:active {
-  color: $mdr-green;
+  color: $mdr-green-dark;
 }
 
 // --------------- buttons -------------

From 68c56a4528677ff010972e6febd54e68b7eadc99 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Thu, 23 Apr 2020 17:04:08 +0900
Subject: [PATCH 160/258] Tweak mdr-green-dark closer to the theme's hue

---
 hyrax/app/assets/stylesheets/theme.scss | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/assets/stylesheets/theme.scss b/hyrax/app/assets/stylesheets/theme.scss
index fd4ed17c..14c7c1f0 100644
--- a/hyrax/app/assets/stylesheets/theme.scss
+++ b/hyrax/app/assets/stylesheets/theme.scss
@@ -17,7 +17,7 @@ $mdr-grey: #F4F4F4;
 $mdr-black: #1E2022;
 $mdr-green: #AFCA0B;
 $mdr-green-light: #7DB928;
-$mdr-green-dark: #387A06;
+$mdr-green-dark: #51791A;
 
 //-------------- Fonts -----------------
 body {

From b90a92dfb45a9ea5316ab613ec0759874ba6dada Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Fri, 24 Apr 2020 15:57:18 +0100
Subject: [PATCH 161/258] remove nil values before calculating total size

---
 hyrax/app/helpers/hyrax_helper.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/helpers/hyrax_helper.rb b/hyrax/app/helpers/hyrax_helper.rb
index 41ca8863..a2f74a43 100644
--- a/hyrax/app/helpers/hyrax_helper.rb
+++ b/hyrax/app/helpers/hyrax_helper.rb
@@ -40,7 +40,7 @@ def within_file_size_threshold?(ids)
   end
 
   def total_size_file_sets(ids)
-    @total_size_file_sets ||= file_sets(ids).map { |fs| fs['file_size_lts'] }.inject(:+) || 0
+    @total_size_file_sets ||= file_sets(ids).map { |fs| fs['file_size_lts'] }.compact.inject(:+) || 0
   end
 
   def file_sets(ids)

From 187841c02e7db219ddb0d706b2ad6991bd7e42f2 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Fri, 24 Apr 2020 17:12:50 +0100
Subject: [PATCH 162/258] Env-ified the brand path volume

---
 .env.template      | 1 +
 docker-compose.yml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.env.template b/.env.template
index d1c3b815..fd7e128b 100644
--- a/.env.template
+++ b/.env.template
@@ -56,6 +56,7 @@ FITS_PATH=/fits/fits-1.3.0/fits.sh
 FITS_VERSION=fits-1.3.0
 UPLOADS_PATH=/shared/uploads/
 CACHE_PATH=/shared/cache/
+BRAND_PATH=/data/public/branding
 DEFAULT_DATE_FORMAT=%d/%m/%Y
 NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS="no-reply@mailboxer.com"
 USER_MANAGEMENT_EMAIL_FROM_ADDRESS=repo-admin@example.org
diff --git a/docker-compose.yml b/docker-compose.yml
index 4295af4e..243ec279 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -95,7 +95,7 @@ services:
       - app:${UPLOADS_PATH}
       - app:${DERIVATIVES_PATH}
       - app:${CACHE_PATH}
-      - app:/data/public/branding
+      - app:${BRAND_PATH}
     networks:
       internal:
 

From 1bde4f92b10952717a91a02d4f749bdf5441bba4 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 27 Apr 2020 15:34:45 +0900
Subject: [PATCH 163/258] use user_identifier as a file name

---
 hyrax/app/controllers/download_all_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/controllers/download_all_controller.rb b/hyrax/app/controllers/download_all_controller.rb
index be92a02c..bcb0811b 100644
--- a/hyrax/app/controllers/download_all_controller.rb
+++ b/hyrax/app/controllers/download_all_controller.rb
@@ -115,7 +115,7 @@ def mk_zip_file_dir
   end
 
   def file_name
-    current_user.present? ? "#{asset.id}_user#{current_user.id}" : asset.id.to_s
+    current_user.present? ? "#{asset.id}_user#{current_user.user_identifier.to_s}" : asset.id.to_s
   end
 
   # Override from LocalFileDownloadsControllerBehavior

From 15a0dba25d2cca3bf6610341194b4c1cc17ba4b6 Mon Sep 17 00:00:00 2001
From: Julie Allinson <julie@notch8.com>
Date: Mon, 27 Apr 2020 15:17:16 +0100
Subject: [PATCH 164/258] add a user_identifier to the development user,
 otherwise creating a new work will error

---
 hyrax/lib/tasks/setup_hyrax.rake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/lib/tasks/setup_hyrax.rake b/hyrax/lib/tasks/setup_hyrax.rake
index 18d6d4d4..71f05f9c 100644
--- a/hyrax/lib/tasks/setup_hyrax.rake
+++ b/hyrax/lib/tasks/setup_hyrax.rake
@@ -22,7 +22,7 @@ namespace :ngdr do
     admin = Role.where(name: "admin").first_or_create!
     seed["users"].each do |user|
       newUser = User.where(username: user["username"]).first_or_create!(password: user["password"], display_name: user["name"], email: user["email"])
-
+      newuser.user_identifier = 'user_identifier'
       if user["role"] == "admin"
         unless admin.users.include?(newUser)
           admin.users << newUser

From 9c4ac39116f29dcb6cec3a6ae376bfd8973813fb Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 7 May 2020 09:16:36 +0900
Subject: [PATCH 165/258] hide complex_identifier field from complex_person
 form

---
 hyrax/app/inputs/nested_person_input.rb | 26 ++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/hyrax/app/inputs/nested_person_input.rb b/hyrax/app/inputs/nested_person_input.rb
index d377cd98..9775014c 100644
--- a/hyrax/app/inputs/nested_person_input.rb
+++ b/hyrax/app/inputs/nested_person_input.rb
@@ -104,23 +104,23 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << '</div>' # row
 
     # --- complex_identifier
-    field = :complex_identifier
-    field_value = value.send(field)
-    if field_value.blank?
-      value.complex_identifier.build
-      field_value = value.send(field)
-    end
-    nested_fields = NestedIdentifierInput.new(@builder, field, nil, :multi_value, {})
-    out << "<div class='inner-nested'>"
-    out << "<div class='form-group'>"
-    out << "  <label class='control-label optional' for='dataset_#{field.to_s}'>Identifier</label>"
-    out << nested_fields.nested_input({:class=>"form-control", :repeats => false}, field_value, parent_attribute)
-    out << "</div>"
+    #field = :complex_identifier
+    #field_value = value.send(field)
+    #if field_value.blank?
+    #  value.complex_identifier.build
+    #  field_value = value.send(field)
+    #end
+    #nested_fields = NestedIdentifierInput.new(@builder, field, nil, :multi_value, {})
+    #out << "<div class='inner-nested'>"
+    #out << "<div class='form-group'>"
+    #out << "  <label class='control-label optional' for='dataset_#{field.to_s}'>Identifier</label>"
+    #out << nested_fields.nested_input({:class=>"form-control", :repeats => false}, field_value, parent_attribute)
+    #out << "</div>"
     # out << "  <button type='button' class='btn btn-link add'>"
     # out << "    <span class='glyphicon glyphicon-plus'></span>"
     # out << "    <span class='controls-add-text'>Add another identifier</span>"
     # out << "  </button>"
-    out << "</div>" # row
+    #out << "</div>" # row
 
     # --- complex_affiliation
     #field = :complex_affiliation

From 9e533aeead559e51f08c69419e2b4b53668eda22 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 7 May 2020 13:14:35 +0900
Subject: [PATCH 166/258] update alert message

---
 hyrax/app/views/hyrax/base/_form_progress.html.erb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/views/hyrax/base/_form_progress.html.erb b/hyrax/app/views/hyrax/base/_form_progress.html.erb
index f58c98bd..55aad96d 100644
--- a/hyrax/app/views/hyrax/base/_form_progress.html.erb
+++ b/hyrax/app/views/hyrax/base/_form_progress.html.erb
@@ -27,8 +27,8 @@
         </div>
     <% end %>
   </div>
-  <div class="panel-footer">
-    Your data will not be made public yet! After you push the button, send the URL of the next screen to <a href="mailto:<%= ENV['CONTACT_EMAIL']%>"><%= ENV['CONTACT_EMAIL'] %></a>.
+  <div class="panel-footer label-warning">
+    <strong>&#x26a0; Your data will not be made public yet! After you push the button, send the URL of the next screen to <a href="mailto:<%= ENV['CONTACT_EMAIL']%>"><%= ENV['CONTACT_EMAIL'] %></a>.</strong>
   </div>
   <div class="panel-footer text-center">
     <% if ::Flipflop.show_deposit_agreement? %>

From 4b26e2aaa9aa492f64e5b29e3bebfdf1ab7b0ffe Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 7 May 2020 15:29:30 +0900
Subject: [PATCH 167/258] hide column_number field from instrument_function
 form

---
 .../nested_instrument_function_input.rb       | 30 +++++++++----------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/hyrax/app/inputs/nested_instrument_function_input.rb b/hyrax/app/inputs/nested_instrument_function_input.rb
index 808b3ac5..be5fd05a 100644
--- a/hyrax/app/inputs/nested_instrument_function_input.rb
+++ b/hyrax/app/inputs/nested_instrument_function_input.rb
@@ -16,21 +16,21 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     repeats = true if repeats.nil?
 
     # --- column_number
-    field = :column_number
-    field_name = name_for(attribute_name, index, field, parent)
-    field_id = id_for(attribute_name, index, field, parent)
-    field_value = value.send(field).first
-
-    out << "<div class='row'>"
-    out << "  <div class='col-md-3'>"
-    out << template.label_tag(field_name, field.to_s.humanize, required: required)
-    out << '  </div>'
-
-    out << "  <div class='col-md-9'>"
-    out << @builder.text_field(field_name,
-        options.merge(value: field_value, name: field_name, id: field_id, required: required))
-    out << '  </div>'
-    out << '</div>' # row
+    #field = :column_number
+    #field_name = name_for(attribute_name, index, field, parent)
+    #field_id = id_for(attribute_name, index, field, parent)
+    #field_value = value.send(field).first
+
+    #out << "<div class='row'>"
+    #out << "  <div class='col-md-3'>"
+    #out << template.label_tag(field_name, field.to_s.humanize, required: required)
+    #out << '  </div>'
+
+    #out << "  <div class='col-md-9'>"
+    #out << @builder.text_field(field_name,
+    #    options.merge(value: field_value, name: field_name, id: field_id, required: required))
+    #out << '  </div>'
+    #out << '</div>' # row
 
     # --- category
     field = :category

From 3af65d60aab02caed4c64cc49fd860049d6e00b7 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 14 May 2020 12:42:47 +0900
Subject: [PATCH 168/258] make abstract and keyword as a required field

---
 hyrax/app/forms/hyrax/dataset_form.rb     | 3 ++-
 hyrax/app/forms/hyrax/publication_form.rb | 3 ++-
 hyrax/app/models/dataset.rb               | 4 ++++
 hyrax/app/models/publication.rb           | 4 ++++
 4 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/forms/hyrax/dataset_form.rb b/hyrax/app/forms/hyrax/dataset_form.rb
index a8612a1e..277a953c 100644
--- a/hyrax/app/forms/hyrax/dataset_form.rb
+++ b/hyrax/app/forms/hyrax/dataset_form.rb
@@ -37,7 +37,8 @@ class DatasetForm < Hyrax::Forms::WorkForm
 
     self.required_fields += [
       # # Adding all required fields in order of display in form
-      :supervisor_approval, :title, :data_origin
+      :supervisor_approval, :title, :data_origin,
+      :description, :keyword
     ]
 
     def metadata_tab_terms
diff --git a/hyrax/app/forms/hyrax/publication_form.rb b/hyrax/app/forms/hyrax/publication_form.rb
index f672a534..151fb711 100644
--- a/hyrax/app/forms/hyrax/publication_form.rb
+++ b/hyrax/app/forms/hyrax/publication_form.rb
@@ -33,7 +33,8 @@ class PublicationForm < Hyrax::Forms::WorkForm
 
     self.required_fields += [
       # Adding all required fields in order of display in form
-      :supervisor_approval, :title, :resource_type
+      :supervisor_approval, :title, :resource_type,
+      :description, :keyword
     ]
 
     NESTED_ASSOCIATIONS = [:complex_date, :complex_identifier,
diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index b025ecb1..19bdd403 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -101,6 +101,10 @@ class Dataset < ActiveFedora::Base
 
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
+  property :doi, predicate: ::RDF::Vocab::Identifiers.doi, multiple: false do |index|
+    index.as :stored_searchable
+  end
+
   # This must be included at the end, because it finalizes the metadata
   # schema (by adding accepts_nested_attributes)
   include ::Hyrax::BasicMetadata
diff --git a/hyrax/app/models/publication.rb b/hyrax/app/models/publication.rb
index c442bff2..21e2f92b 100644
--- a/hyrax/app/models/publication.rb
+++ b/hyrax/app/models/publication.rb
@@ -85,6 +85,10 @@ class Publication < ActiveFedora::Base
 
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
+  property :doi, predicate: ::RDF::Vocab::Identifiers.doi, multiple: false do |index|
+    index.as :stored_searchable
+  end
+
   # This must be included at the end, because it finalizes the metadata
   # schema (by adding accepts_nested_attributes)
   include ::Hyrax::BasicMetadata

From bb30f4ad6f830f850cfe773b1ffacd0e9c294dd1 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 14 May 2020 12:52:40 +0900
Subject: [PATCH 169/258] reverted changes for doi

---
 hyrax/app/models/dataset.rb     | 4 ----
 hyrax/app/models/publication.rb | 4 ----
 2 files changed, 8 deletions(-)

diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index 19bdd403..b025ecb1 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -101,10 +101,6 @@ class Dataset < ActiveFedora::Base
 
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
-  property :doi, predicate: ::RDF::Vocab::Identifiers.doi, multiple: false do |index|
-    index.as :stored_searchable
-  end
-
   # This must be included at the end, because it finalizes the metadata
   # schema (by adding accepts_nested_attributes)
   include ::Hyrax::BasicMetadata
diff --git a/hyrax/app/models/publication.rb b/hyrax/app/models/publication.rb
index 21e2f92b..c442bff2 100644
--- a/hyrax/app/models/publication.rb
+++ b/hyrax/app/models/publication.rb
@@ -85,10 +85,6 @@ class Publication < ActiveFedora::Base
 
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
-  property :doi, predicate: ::RDF::Vocab::Identifiers.doi, multiple: false do |index|
-    index.as :stored_searchable
-  end
-
   # This must be included at the end, because it finalizes the metadata
   # schema (by adding accepts_nested_attributes)
   include ::Hyrax::BasicMetadata

From e6eb972e6709a3f3d037777ba9a9dd90390b3713 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 14 May 2020 12:59:33 +0900
Subject: [PATCH 170/258] add NIMS DOI to Dataset and Publication

---
 hyrax/app/indexers/dataset_indexer.rb                       | 1 +
 hyrax/app/indexers/publication_indexer.rb                   | 1 +
 hyrax/app/models/dataset.rb                                 | 4 ++++
 hyrax/app/models/publication.rb                             | 4 ++++
 hyrax/app/models/solr_document.rb                           | 4 ++++
 hyrax/app/presenters/hyrax/dataset_presenter.rb             | 2 +-
 hyrax/app/presenters/hyrax/publication_presenter.rb         | 3 ++-
 hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb     | 1 +
 hyrax/app/views/hyrax/publications/_attribute_rows.html.erb | 1 +
 9 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/indexers/dataset_indexer.rb b/hyrax/app/indexers/dataset_indexer.rb
index f74fb02a..b41b9dbb 100644
--- a/hyrax/app/indexers/dataset_indexer.rb
+++ b/hyrax/app/indexers/dataset_indexer.rb
@@ -57,6 +57,7 @@ def self.search_fields
         'properties_addressed',
         'specimen_set',
         'synthesis_and_processing',
+        'doi'
       ]
       dataset_search_fields.each do |fld|
         fields << Solrizer.solr_name(fld, :stored_searchable)
diff --git a/hyrax/app/indexers/publication_indexer.rb b/hyrax/app/indexers/publication_indexer.rb
index 04eeddd7..7f134001 100644
--- a/hyrax/app/indexers/publication_indexer.rb
+++ b/hyrax/app/indexers/publication_indexer.rb
@@ -26,6 +26,7 @@ def self.search_fields
       fields << Solrizer.solr_name('issue', :stored_searchable)
       fields << Solrizer.solr_name('place', :stored_searchable)
       fields << Solrizer.solr_name('table_of_contents', :stored_searchable)
+      fields << Solrizer.solr_name('doi', :stored_searchable)
       fields.concat ComplexField::DateIndexer.date_search_fields
       fields.concat ComplexField::IdentifierIndexer.identifier_search_fields
       fields.concat ComplexField::PersonIndexer.person_search_fields
diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index b025ecb1..19bdd403 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -101,6 +101,10 @@ class Dataset < ActiveFedora::Base
 
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
+  property :doi, predicate: ::RDF::Vocab::Identifiers.doi, multiple: false do |index|
+    index.as :stored_searchable
+  end
+
   # This must be included at the end, because it finalizes the metadata
   # schema (by adding accepts_nested_attributes)
   include ::Hyrax::BasicMetadata
diff --git a/hyrax/app/models/publication.rb b/hyrax/app/models/publication.rb
index c442bff2..21e2f92b 100644
--- a/hyrax/app/models/publication.rb
+++ b/hyrax/app/models/publication.rb
@@ -85,6 +85,10 @@ class Publication < ActiveFedora::Base
 
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
+  property :doi, predicate: ::RDF::Vocab::Identifiers.doi, multiple: false do |index|
+    index.as :stored_searchable
+  end
+
   # This must be included at the end, because it finalizes the metadata
   # schema (by adding accepts_nested_attributes)
   include ::Hyrax::BasicMetadata
diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 9745e68f..89625a06 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -147,5 +147,9 @@ def complex_source
   def status
     self[Solrizer.solr_name('status', :stored_searchable)]
   end
+
+  def doi
+    self[Solrizer.solr_name('doi', :stored_searchable)]
+  end
 end
 
diff --git a/hyrax/app/presenters/hyrax/dataset_presenter.rb b/hyrax/app/presenters/hyrax/dataset_presenter.rb
index ffca8c9f..74adf783 100644
--- a/hyrax/app/presenters/hyrax/dataset_presenter.rb
+++ b/hyrax/app/presenters/hyrax/dataset_presenter.rb
@@ -7,7 +7,7 @@ class DatasetPresenter < Hyrax::WorkShowPresenter
       :characterization_methods, :computational_methods, :data_origin,
       :complex_instrument, :origin_system_provenance, :properties_addressed,
       :complex_relation, :specimen_set, :complex_specimen_type,
-      :synthesis_and_processing, :custom_property, to: :solr_document
+      :synthesis_and_processing, :custom_property, :doi, to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
diff --git a/hyrax/app/presenters/hyrax/publication_presenter.rb b/hyrax/app/presenters/hyrax/publication_presenter.rb
index 0d37cbad..9b50bfcb 100644
--- a/hyrax/app/presenters/hyrax/publication_presenter.rb
+++ b/hyrax/app/presenters/hyrax/publication_presenter.rb
@@ -4,7 +4,8 @@ module Hyrax
   class PublicationPresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
              :complex_rights, :complex_version, :complex_event, :issue, :place,
-             :table_of_contents, :total_number_of_pages, :complex_source, to: :solr_document
+             :table_of_contents, :total_number_of_pages, :complex_source, :doi,
+             to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
diff --git a/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb b/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
index 9a1f3e18..17e70208 100644
--- a/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
@@ -47,6 +47,7 @@
         <% end %>
 
         <% if can? :read_identifier, presenter.model_name.name.constantize %>
+          <%= presenter.attribute_to_html(:doi, label: 'DOI', html_dl: true) %>
           <%= presenter.attribute_to_html(:complex_identifier, render_as: :nested_identifier, label: t('ngdr.fields.complex_identifier'), html_dl: true) %>
         <% end %>
 
diff --git a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
index 607d3768..037aaa4d 100644
--- a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
@@ -35,6 +35,7 @@
 <% end %>
 
 <% if can? :read_identifier, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:doi, label: 'DOI', html_dl: true) %>
   <%= presenter.attribute_to_html(:complex_identifier, render_as: :nested_identifier, label: t('ngdr.fields.complex_identifier'), html_dl: true) %>
 <% end %>
 

From 1c14b72b1f2daaa9601870c0ea4478a2da9a0db7 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 14 May 2020 15:26:37 +0900
Subject: [PATCH 171/258] add first_published_url to Dataset and Publication

---
 hyrax/app/forms/hyrax/dataset_form.rb                       | 6 +++---
 hyrax/app/forms/hyrax/publication_form.rb                   | 4 ++--
 hyrax/app/indexers/dataset_indexer.rb                       | 1 +
 hyrax/app/indexers/publication_indexer.rb                   | 1 +
 hyrax/app/models/dataset.rb                                 | 4 ++++
 hyrax/app/models/publication.rb                             | 4 ++++
 hyrax/app/presenters/hyrax/dataset_presenter.rb             | 3 ++-
 hyrax/app/presenters/hyrax/publication_presenter.rb         | 3 ++-
 hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb     | 1 +
 hyrax/app/views/hyrax/publications/_attribute_rows.html.erb | 4 ++++
 hyrax/config/locales/en.yml                                 | 1 +
 11 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/hyrax/app/forms/hyrax/dataset_form.rb b/hyrax/app/forms/hyrax/dataset_form.rb
index a8612a1e..abeda206 100644
--- a/hyrax/app/forms/hyrax/dataset_form.rb
+++ b/hyrax/app/forms/hyrax/dataset_form.rb
@@ -18,7 +18,7 @@ class DatasetForm < Hyrax::Forms::WorkForm
 
     self.terms += [
       # Adding all fields in order of display in form
-      :supervisor_approval,
+      :supervisor_approval, :first_published_url,
       :title, :alternative_title, :description, :keyword, :language,
       :publisher, :complex_rights, :subject, :complex_date, :complex_person,
       :complex_version, :characterization_methods, :computational_methods,
@@ -37,13 +37,13 @@ class DatasetForm < Hyrax::Forms::WorkForm
 
     self.required_fields += [
       # # Adding all required fields in order of display in form
-      :supervisor_approval, :title, :data_origin
+      :supervisor_approval, :first_published_url, :title, :data_origin
     ]
 
     def metadata_tab_terms
       [
         # Description tab order determined here
-        :supervisor_approval,
+        :supervisor_approval, :first_published_url,
         :title, :alternative_title, :data_origin, :description, :keyword,
         :specimen_set, :complex_person, 
         :complex_identifier, # not using this
diff --git a/hyrax/app/forms/hyrax/publication_form.rb b/hyrax/app/forms/hyrax/publication_form.rb
index f672a534..0daa1657 100644
--- a/hyrax/app/forms/hyrax/publication_form.rb
+++ b/hyrax/app/forms/hyrax/publication_form.rb
@@ -18,7 +18,7 @@ class PublicationForm < Hyrax::Forms::WorkForm
 
     self.terms += [
       # Adding all fields in order of display in form
-      :supervisor_approval,
+      :supervisor_approval, :first_published_url,
       :title, :alternative_title, :complex_person, :description, :keyword,
       :publisher, :resource_type, :complex_rights,
       :complex_date, :complex_identifier, :complex_source, :complex_version,
@@ -33,7 +33,7 @@ class PublicationForm < Hyrax::Forms::WorkForm
 
     self.required_fields += [
       # Adding all required fields in order of display in form
-      :supervisor_approval, :title, :resource_type
+      :supervisor_approval, :first_published_url, :title, :resource_type
     ]
 
     NESTED_ASSOCIATIONS = [:complex_date, :complex_identifier,
diff --git a/hyrax/app/indexers/dataset_indexer.rb b/hyrax/app/indexers/dataset_indexer.rb
index f74fb02a..c697f758 100644
--- a/hyrax/app/indexers/dataset_indexer.rb
+++ b/hyrax/app/indexers/dataset_indexer.rb
@@ -57,6 +57,7 @@ def self.search_fields
         'properties_addressed',
         'specimen_set',
         'synthesis_and_processing',
+        'first_published_url'
       ]
       dataset_search_fields.each do |fld|
         fields << Solrizer.solr_name(fld, :stored_searchable)
diff --git a/hyrax/app/indexers/publication_indexer.rb b/hyrax/app/indexers/publication_indexer.rb
index 04eeddd7..0e51aefb 100644
--- a/hyrax/app/indexers/publication_indexer.rb
+++ b/hyrax/app/indexers/publication_indexer.rb
@@ -26,6 +26,7 @@ def self.search_fields
       fields << Solrizer.solr_name('issue', :stored_searchable)
       fields << Solrizer.solr_name('place', :stored_searchable)
       fields << Solrizer.solr_name('table_of_contents', :stored_searchable)
+      fields << Solrizer.solr_name('first_published_url', :stored_searchable)
       fields.concat ComplexField::DateIndexer.date_search_fields
       fields.concat ComplexField::IdentifierIndexer.identifier_search_fields
       fields.concat ComplexField::PersonIndexer.person_search_fields
diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index b025ecb1..a43d3c08 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -101,6 +101,10 @@ class Dataset < ActiveFedora::Base
 
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
+  property :first_published_url, predicate: ::RDF::Vocab::NimsRdp['first_published_url'], multiple: false do |index|
+    index.as :stored_searchable
+  end
+
   # This must be included at the end, because it finalizes the metadata
   # schema (by adding accepts_nested_attributes)
   include ::Hyrax::BasicMetadata
diff --git a/hyrax/app/models/publication.rb b/hyrax/app/models/publication.rb
index c442bff2..9928b2f0 100644
--- a/hyrax/app/models/publication.rb
+++ b/hyrax/app/models/publication.rb
@@ -85,6 +85,10 @@ class Publication < ActiveFedora::Base
 
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
+  property :first_published_url, predicate: ::RDF::Vocab::NimsRdp['first_published_url'], multiple: false do |index|
+    index.as :stored_searchable
+  end
+
   # This must be included at the end, because it finalizes the metadata
   # schema (by adding accepts_nested_attributes)
   include ::Hyrax::BasicMetadata
diff --git a/hyrax/app/presenters/hyrax/dataset_presenter.rb b/hyrax/app/presenters/hyrax/dataset_presenter.rb
index ffca8c9f..d6e7c659 100644
--- a/hyrax/app/presenters/hyrax/dataset_presenter.rb
+++ b/hyrax/app/presenters/hyrax/dataset_presenter.rb
@@ -7,7 +7,8 @@ class DatasetPresenter < Hyrax::WorkShowPresenter
       :characterization_methods, :computational_methods, :data_origin,
       :complex_instrument, :origin_system_provenance, :properties_addressed,
       :complex_relation, :specimen_set, :complex_specimen_type,
-      :synthesis_and_processing, :custom_property, to: :solr_document
+      :synthesis_and_processing, :custom_property, :first_published_url,
+      to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
diff --git a/hyrax/app/presenters/hyrax/publication_presenter.rb b/hyrax/app/presenters/hyrax/publication_presenter.rb
index 0d37cbad..5109c6e5 100644
--- a/hyrax/app/presenters/hyrax/publication_presenter.rb
+++ b/hyrax/app/presenters/hyrax/publication_presenter.rb
@@ -4,7 +4,8 @@ module Hyrax
   class PublicationPresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
              :complex_rights, :complex_version, :complex_event, :issue, :place,
-             :table_of_contents, :total_number_of_pages, :complex_source, to: :solr_document
+             :table_of_contents, :total_number_of_pages, :complex_source,
+             :first_published_url, to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
diff --git a/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb b/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
index 9a1f3e18..5465cf5a 100644
--- a/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/datasets/_attribute_rows.html.erb
@@ -69,6 +69,7 @@
 
         <% if can? :read_related, presenter.model_name.name.constantize %>
           <%= presenter.attribute_to_html(:complex_relation, render_as: :nested_relation, label: t('ngdr.fields.complex_relation'), html_dl: true) %>
+          <%= presenter.attribute_to_html(:first_published_url, label: t('ngdr.fields.first_published_url'), html_dl: true) %>
         <% end %>
 
         <% if can? :read_source, presenter.model_name.name.constantize %>
diff --git a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
index 607d3768..c13d40a2 100644
--- a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
@@ -70,6 +70,10 @@
   <%= presenter.attribute_to_html(:total_number_of_pages, label: "Number of pages", html_dl: true) %>
 <% end %>
 
+<% if can? :read_related, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:first_published_url, label: t('ngdr.fields.first_published_url'), html_dl: true) %>
+<% end %>
+
 <% if can? :read_source, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:source, label: "Source", html_dl: true) %>
   <%= presenter.attribute_to_html(:complex_source, render_as: :nested_source, label: t('ngdr.fields.complex_source'), html_dl: true) %>
diff --git a/hyrax/config/locales/en.yml b/hyrax/config/locales/en.yml
index 44179a6a..b9f96d1d 100644
--- a/hyrax/config/locales/en.yml
+++ b/hyrax/config/locales/en.yml
@@ -54,3 +54,4 @@ en:
       sub_organization:         "Sub organization"
       synthesis_and_processing: "Synthesis and processing"
       total_number_of_pages:    "Number of pages"
+      first_published_url:      "First published at"

From 7c5778154d7dc93d74519bbd4b73e9dd6d2bb2d1 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 14 May 2020 16:00:43 +0900
Subject: [PATCH 172/258] add a help message for title

---
 hyrax/config/locales/en.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/hyrax/config/locales/en.yml b/hyrax/config/locales/en.yml
index 44179a6a..037c02d6 100644
--- a/hyrax/config/locales/en.yml
+++ b/hyrax/config/locales/en.yml
@@ -54,3 +54,7 @@ en:
       sub_organization:         "Sub organization"
       synthesis_and_processing: "Synthesis and processing"
       total_number_of_pages:    "Number of pages"
+  simple_form:
+    hints:
+      defaults:
+        title: A name to aid in identifying a work. English is preferred.

From 5d1301dae57fdc26b1ed7f222e1c90de59feb6ca Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 15 May 2020 17:24:51 +0900
Subject: [PATCH 173/258] update some labels

---
 hyrax/config/locales/en.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/hyrax/config/locales/en.yml b/hyrax/config/locales/en.yml
index 037c02d6..054e924f 100644
--- a/hyrax/config/locales/en.yml
+++ b/hyrax/config/locales/en.yml
@@ -28,11 +28,11 @@ en:
       complex_structural_feature: "Structural feature"
       complex_version:          "Version"
       data_origin:              "Data origin"
-      first_name:               "First name"
+      first_name:               "Given name"
       instrument:               "Instrument"
       issue:                    "Issue"
       instrument_function:      "Instrument function"
-      last_name:                "Last name"
+      last_name:                "Surname"
       managing_organization:    "Managing organization"
       material_sub_type:        "Material sub type"
       material_type:            "Material type"
@@ -54,7 +54,10 @@ en:
       sub_organization:         "Sub organization"
       synthesis_and_processing: "Synthesis and processing"
       total_number_of_pages:    "Number of pages"
+      first_published_url:      "First published at"
   simple_form:
     hints:
       defaults:
         title: A name to aid in identifying a work. English is preferred.
+        publisher: The person or group making the work available.
+        first_published_url: The DOI of the article related to this dataset or the URL where this dataset was first made public.

From fcaaa0da3eff7120d2f189ddb08e2e373bd96c4f Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 15 May 2020 17:32:47 +0900
Subject: [PATCH 174/258] add DOI example

---
 hyrax/config/locales/en.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/config/locales/en.yml b/hyrax/config/locales/en.yml
index 054e924f..cca93376 100644
--- a/hyrax/config/locales/en.yml
+++ b/hyrax/config/locales/en.yml
@@ -60,4 +60,4 @@ en:
       defaults:
         title: A name to aid in identifying a work. English is preferred.
         publisher: The person or group making the work available.
-        first_published_url: The DOI of the article related to this dataset or the URL where this dataset was first made public.
+        first_published_url: The DOI of the article related to this dataset or the URL where this dataset was first made public. DOI example: https://doi.org/10.xxxx/xxxxx

From 21d228a90c2527a29193df8c5a6e59b206e8355c Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 15 May 2020 17:50:31 +0900
Subject: [PATCH 175/258] add quotation marks

---
 hyrax/config/locales/en.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/config/locales/en.yml b/hyrax/config/locales/en.yml
index cca93376..a2ea9430 100644
--- a/hyrax/config/locales/en.yml
+++ b/hyrax/config/locales/en.yml
@@ -60,4 +60,4 @@ en:
       defaults:
         title: A name to aid in identifying a work. English is preferred.
         publisher: The person or group making the work available.
-        first_published_url: The DOI of the article related to this dataset or the URL where this dataset was first made public. DOI example: https://doi.org/10.xxxx/xxxxx
+        first_published_url: "The DOI of the article related to this dataset or the URL where this dataset was first made public. DOI example: https://doi.org/10.xxxx/xxxxx"

From 0afa50b656e647f44bc19557bfbc209c92ab1c57 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Tue, 31 Mar 2020 17:46:29 +0900
Subject: [PATCH 176/258] fix the version of universalviewer

---
 hyrax/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/package.json b/hyrax/package.json
index 11b941e3..9ae7710d 100644
--- a/hyrax/package.json
+++ b/hyrax/package.json
@@ -3,7 +3,7 @@
   "private": true,
   "repository": "git@github.com:antleaf/nims-hyrax.git",
   "dependencies": {
-  "universalviewer": "^3.0.16"
+  "universalviewer": "3.0.16"
 },
 "scripts": {
   "preinstall": "rm -rf ./public/uv",

From 7c1652f1e4169a6881bcb1fd98e7f35819bca773 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Fri, 15 May 2020 22:47:33 +0900
Subject: [PATCH 177/258] remove depositor from JSON and RDF responses

---
 .../app/presenters/concerns/filtered_graph.rb |  3 +-
 hyrax/app/views/catalog/index.json.jbuilder   |  4 +-
 hyrax/app/views/catalog/show.json.jbuilder    |  4 +-
 .../hyrax/dataset_presenter_spec.rb           | 10 +++-
 .../hyrax/publication_presenter_spec.rb       | 10 +++-
 .../views/catalog/index.json.jbuilder_spec.rb | 47 +++++++++++++++++++
 .../views/catalog/show.json.jbuilder_spec.rb  | 38 +++++++++++++++
 7 files changed, 111 insertions(+), 5 deletions(-)
 create mode 100644 hyrax/spec/views/catalog/index.json.jbuilder_spec.rb
 create mode 100644 hyrax/spec/views/catalog/show.json.jbuilder_spec.rb

diff --git a/hyrax/app/presenters/concerns/filtered_graph.rb b/hyrax/app/presenters/concerns/filtered_graph.rb
index 35840866..6134d5ee 100644
--- a/hyrax/app/presenters/concerns/filtered_graph.rb
+++ b/hyrax/app/presenters/concerns/filtered_graph.rb
@@ -15,6 +15,7 @@ def exclude?(statement)
     # Returns true if the statement should be filtered out of the graph
     model = model_name.name.constantize
     (statement.predicate.ends_with?('purl.org/dc/elements/1.1/description') && current_ability.cannot?(:read_abstract, model)) ||
-      (statement.predicate.ends_with?('www.nims.go.jp/vocabs/ngdr/supervisor-approval') && current_ability.cannot?(:read_supervisor_approval, model))
+      (statement.predicate.ends_with?('www.nims.go.jp/vocabs/ngdr/supervisor-approval') && current_ability.cannot?(:read_supervisor_approval, model)) ||
+      (statement.predicate.ends_with?('id.loc.gov/vocabulary/relators/dpt'))
   end
 end
diff --git a/hyrax/app/views/catalog/index.json.jbuilder b/hyrax/app/views/catalog/index.json.jbuilder
index b38459d3..d9cb6dc1 100644
--- a/hyrax/app/views/catalog/index.json.jbuilder
+++ b/hyrax/app/views/catalog/index.json.jbuilder
@@ -4,7 +4,9 @@ json.response do
       json.id document.id
       index_fields(document).each do |field_name, field|
         if should_render_index_field? document, field
-          json.set! field_name, document[field_name]
+          unless field.name == 'depositor'
+            json.set! field_name, document[field_name]
+          end
         end
       end
     end
diff --git a/hyrax/app/views/catalog/show.json.jbuilder b/hyrax/app/views/catalog/show.json.jbuilder
index 3c26424f..9581dbed 100644
--- a/hyrax/app/views/catalog/show.json.jbuilder
+++ b/hyrax/app/views/catalog/show.json.jbuilder
@@ -4,7 +4,9 @@ json.response do
       json.id document.id
       index_fields(document).each do |field_name, field|
         if should_render_index_field? document, field
-          json.set! field_name, document[field_name]
+          unless field.name == 'depositor'
+            json.set! field_name, document[field_name]
+          end
         end
       end
     end
diff --git a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
index 12a956cf..3a378eff 100644
--- a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
@@ -1,7 +1,7 @@
 require 'rails_helper'
 
 RSpec.describe Hyrax::DatasetPresenter do
-  let(:dataset) { create(:dataset, :open, :with_alternative_title, :with_description_abstract, :with_supervisor_approval) }
+  let(:dataset) { create(:dataset, :open, :with_alternative_title, :with_description_abstract, :with_supervisor_approval, depositor: 'despositor') }
   let(:solr_document) { SolrDocument.new(dataset.to_solr) }
   let(:host) { double(host: 'http://example.org') }
   let(:user) { nil }
@@ -22,6 +22,7 @@
     }
     let(:abstract_regex) { %r(<http://purl.org/dc/elements/1.1/description> "Abstract-Description-123";) }
     let(:supervisor_regex) { %r(<http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor-Supervisor-Approval";) }
+    let(:depositor_regex) { %r(<http://example.org/concern/datasets/#{dataset.id}> <http://id.loc.gov/vocabulary/relators/dpt> "depositor") }
 
     it 'exports' do
       export_regex.each do |regex|
@@ -32,12 +33,14 @@
     context 'anonymous user' do
       it { is_expected.not_to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
+      it { is_expected.not_to match(depositor_regex) }
     end
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
       it { is_expected.to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
+      it { is_expected.not_to match(depositor_regex) }
     end
   end
 
@@ -55,6 +58,7 @@
     }
     let(:abstract_regex) { %r(<http://example.org/concern/datasets/#{dataset.id}> <http://purl.org/dc/elements/1.1/description> "Abstract-Description-123") }
     let(:supervisor_regex) { %r(<http://example.org/concern/datasets/#{dataset.id}> <http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor-Supervisor-Approval") }
+    let(:depositor_regex) { %r(<http://example.org/concern/publications/#{dataset.id}> <http://id.loc.gov/vocabulary/relators/dpt> "depositor") }
 
     it 'exports' do
       export_regex.each do |regex|
@@ -65,12 +69,14 @@
     context 'anonymous user' do
       it { is_expected.not_to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
+      it { is_expected.not_to match(depositor_regex) }
     end
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
       it { is_expected.to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
+      it { is_expected.not_to match(depositor_regex) }
     end
   end
 
@@ -98,12 +104,14 @@
     context 'anonymous user' do
       it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
       it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
+      it { is_expected.not_to include("marcrelators:dpt" => "depositor") }
     end
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
       it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
       it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
+      it { is_expected.not_to include("marcrelators:dpt" => "depositor") }
     end
   end
 end
diff --git a/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb b/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
index 1294e0ba..c16e4779 100644
--- a/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
@@ -1,7 +1,7 @@
 require 'rails_helper'
 
 RSpec.describe Hyrax::PublicationPresenter do
-  let(:publication) { create(:publication, :open, :with_alternative_title, :with_description_abstract, :with_supervisor_approval) }
+  let(:publication) { create(:publication, :open, :with_alternative_title, :with_description_abstract, :with_supervisor_approval, depositor: 'depositor') }
   let(:solr_document) { SolrDocument.new(publication.to_solr) }
   let(:host) { double(host: 'http://example.org') }
   let(:user) { nil }
@@ -22,6 +22,7 @@
     }
     let(:abstract_regex) { %r(<http://purl.org/dc/elements/1.1/description> "Abstract-Description-123";) }
     let(:supervisor_regex) { %r(<http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor-Supervisor-Approval";) }
+    let(:depositor_regex) { %r(<http://example.org/concern/publications/#{publication.id}> <http://id.loc.gov/vocabulary/relators/dpt> "depositor") }
 
     it 'exports' do
       export_regex.each do |regex|
@@ -32,12 +33,14 @@
     context 'anonymous user' do
       it { is_expected.not_to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
+      it { is_expected.not_to match(depositor_regex) }
     end
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
       it { is_expected.to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
+      it { is_expected.not_to match(depositor_regex) }
     end
   end
 
@@ -55,6 +58,7 @@
     }
     let(:abstract_regex) { %r(<http://example.org/concern/publications/#{publication.id}> <http://purl.org/dc/elements/1.1/description> "Abstract-Description-123") }
     let(:supervisor_regex) { %r(<http://example.org/concern/publications/#{publication.id}> <http://www.nims.go.jp/vocabs/ngdr/supervisor-approval> "Professor-Supervisor-Approval") }
+    let(:depositor_regex) { %r(<http://example.org/concern/publications/#{publication.id}> <http://id.loc.gov/vocabulary/relators/dpt> "depositor") }
 
     it 'exports' do
       export_regex.each do |regex|
@@ -65,12 +69,14 @@
     context 'anonymous user' do
       it { is_expected.not_to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
+      it { is_expected.not_to match(depositor_regex) }
     end
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
       it { is_expected.to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
+      it { is_expected.not_to match(depositor_regex) }
     end
   end
 
@@ -98,12 +104,14 @@
     context 'anonymous user' do
       it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
       it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
+      it { is_expected.not_to include("marcrelators:dpt" => "depositor") }
     end
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
       it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
       it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
+      it { is_expected.not_to include("marcrelators:dpt" => "depositor") }
     end
   end
 end
diff --git a/hyrax/spec/views/catalog/index.json.jbuilder_spec.rb b/hyrax/spec/views/catalog/index.json.jbuilder_spec.rb
new file mode 100644
index 00000000..e566c2d4
--- /dev/null
+++ b/hyrax/spec/views/catalog/index.json.jbuilder_spec.rb
@@ -0,0 +1,47 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe "catalog/index.json", api: true do
+  let(:response) { instance_double(Blacklight::Solr::Response, documents: docs, prev_page: nil, next_page: 2, total_pages: 3) }
+  let(:docs) do
+    [
+      SolrDocument.new(id: '123', title_tsim: 'Book1', author_tsim: 'Julie', format: 'Book'),
+      SolrDocument.new(id: '456', title_tsim: 'Article1', author_tsim: 'Rosie', format: 'Article')
+    ]
+  end
+  let(:config) do
+    Blacklight::Configuration.new do |config|
+      config.add_index_field 'title', label: 'Title', field: 'title_tsim'
+    end
+  end
+  let(:presenter) { Blacklight::JsonPresenter.new(response, config) }
+
+  let(:hash) do
+    render template: "catalog/index.json", format: :json
+    JSON.parse(rendered).with_indifferent_access
+  end
+
+  # This test confirms the abstract is only visible if you are logged in
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'does not show the abstract' do
+      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+    end
+  end
+
+  context 'authenticated non-researcher' do
+    let(:user) { build(:user, :nims_other) }
+    it 'shows the abstract' do
+      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { build(:user, :nims_researcher) }
+    it 'shows the abstract' do
+      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+    end
+  end
+end
diff --git a/hyrax/spec/views/catalog/show.json.jbuilder_spec.rb b/hyrax/spec/views/catalog/show.json.jbuilder_spec.rb
new file mode 100644
index 00000000..0fe0b7d5
--- /dev/null
+++ b/hyrax/spec/views/catalog/show.json.jbuilder_spec.rb
@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'catalog/show.json.jbuilder' do
+  let(:document) do
+    SolrDocument.new(id: '123', title_tsim: 'Book1', author_tsim: 'Julie', format: 'Book')
+  end
+
+  let(:config) do
+    Blacklight::Configuration.new do |config|
+      config.add_show_field 'title', label: 'Title', field: 'title_tsim'
+    end
+  end
+
+  # This test confirms the abstract is only visible if you are logged in
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'does not show the abstract' do
+      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+    end
+  end
+
+  context 'authenticated non-researcher' do
+    let(:user) { build(:user, :nims_other) }
+    it 'shows the abstract' do
+      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { build(:user, :nims_researcher) }
+    it 'shows the abstract' do
+      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+    end
+  end
+end

From b7f5e0f6d6b8ab30be1f48478384a69b71922da1 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 18 May 2020 19:36:01 +0900
Subject: [PATCH 178/258] update ability file to prevent from creating a new
 image

---
 hyrax/app/models/ability.rb       | 2 +-
 hyrax/spec/models/ability_spec.rb | 6 +++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index 58f899ac..0f781204 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -31,7 +31,7 @@ def custom_permissions
 
   def create_content
     # only NIMS Researchers may upload new content
-    can :create, [::Dataset, ::Publication, ::Image] if current_user.authenticated_nims_researcher?
+    can :create, [::Dataset, ::Publication] if current_user.authenticated_nims_researcher?
   end
 
   def read_metadata
diff --git a/hyrax/spec/models/ability_spec.rb b/hyrax/spec/models/ability_spec.rb
index 84e61eaf..62ae6c45 100644
--- a/hyrax/spec/models/ability_spec.rb
+++ b/hyrax/spec/models/ability_spec.rb
@@ -75,10 +75,14 @@
     context 'authenticated NIMS Researcher' do
       let(:user) { build(:user, :nims_researcher) }
       it 'can create content' do
-        models.each do |model|
+        [::Dataset, ::Publication].each do |model|
           expect(ability.can?(:create, model)).to be true
         end
       end
+
+      it 'cannot create Image' do
+        expect(ability.can?(:create, ::Image)).to be false
+      end
     end
 
     context 'admin user' do

From b506a0f7031a59382267bb5c384b66499bae77dd Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 18 May 2020 20:17:38 +0900
Subject: [PATCH 179/258] update ability file to display description

---
 hyrax/app/models/ability.rb                     | 2 +-
 hyrax/features/datasets/catalog.feature         | 2 +-
 hyrax/spec/models/ability_spec.rb               | 6 +++---
 hyrax/spec/views/hyrax/base/show.html_spec.rb   | 4 ++--
 hyrax/spec/views/shared/_citations.html_spec.rb | 4 ++--
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/hyrax/app/models/ability.rb b/hyrax/app/models/ability.rb
index 0f781204..5974e73a 100644
--- a/hyrax/app/models/ability.rb
+++ b/hyrax/app/models/ability.rb
@@ -35,7 +35,7 @@ def create_content
   end
 
   def read_metadata
-    can :read_abstract, [::Dataset, ::Image, ::Publication] if current_user.authenticated?
+    can :read_abstract, [::Dataset, ::Image, ::Publication]
     can :read_alternative_title, [::Dataset, ::Image, ::Publication]
     # NB: no users can :read_application_number
     can :read_creator, [::Dataset, ::Image, ::Publication]
diff --git a/hyrax/features/datasets/catalog.feature b/hyrax/features/datasets/catalog.feature
index d822488f..d22e2532 100644
--- a/hyrax/features/datasets/catalog.feature
+++ b/hyrax/features/datasets/catalog.feature
@@ -10,7 +10,7 @@ Feature: Datasets catalog index
   Scenario: Unauthenticated user can only view open datasets
     When I navigate to the dataset catalog page
     Then I should see the open datasets
-    And I should see only the public metadata of the open datasets
+    And I should see both the public and restricted metadata of the open datasets
     But I should not see the authenticated datasets
     And I should not see the restricted dataset
 
diff --git a/hyrax/spec/models/ability_spec.rb b/hyrax/spec/models/ability_spec.rb
index 62ae6c45..621d07ef 100644
--- a/hyrax/spec/models/ability_spec.rb
+++ b/hyrax/spec/models/ability_spec.rb
@@ -123,7 +123,7 @@
 
       context 'dataset' do
         let(:model) { ::Dataset}
-        it { expect(read_abstract).to be false }
+        it { expect(read_abstract).to be true }
         it { expect(read_alternative_title).to be true }
         it { expect(read_creator).to be true }
         it { expect(read_date).to be true }
@@ -148,7 +148,7 @@
 
       context 'image' do
         let(:model) { ::Image}
-        it { expect(read_abstract).to be false }
+        it { expect(read_abstract).to be true }
         it { expect(read_alternative_title).to be true }
         it { expect(read_creator).to be true }
         it { expect(read_date).to be true }
@@ -173,7 +173,7 @@
 
       context 'publication' do
         let(:model) { ::Publication}
-        it { expect(read_abstract).to be false }
+        it { expect(read_abstract).to be true }
         it { expect(read_alternative_title).to be true }
         it { expect(read_creator).to be true }
         it { expect(read_date).to be true }
diff --git a/hyrax/spec/views/hyrax/base/show.html_spec.rb b/hyrax/spec/views/hyrax/base/show.html_spec.rb
index d84dfdb8..d854b6c2 100644
--- a/hyrax/spec/views/hyrax/base/show.html_spec.rb
+++ b/hyrax/spec/views/hyrax/base/show.html_spec.rb
@@ -17,8 +17,8 @@
     let(:user) { nil }
     it 'does not show the abstract' do
       expect(rendered).to have_css('h2', text: dataset.title.first)
-      expect(rendered).not_to have_css('p.work_description', text: dataset.description.first)
-      expect(rendered).not_to have_css("span.Z3988[title*='rft.description=#{CGI.escape(dataset.description.first)}']")
+      expect(rendered).to have_css('p.work_description', text: dataset.description.first)
+      expect(rendered).to have_css("span.Z3988[title*='rft.description=#{CGI.escape(dataset.description.first)}']")
     end
   end
 
diff --git a/hyrax/spec/views/shared/_citations.html_spec.rb b/hyrax/spec/views/shared/_citations.html_spec.rb
index 6e2739c2..6929247d 100644
--- a/hyrax/spec/views/shared/_citations.html_spec.rb
+++ b/hyrax/spec/views/shared/_citations.html_spec.rb
@@ -17,8 +17,8 @@
   describe 'og:description' do
     context 'unauthenticated user' do
       let(:user) { nil }
-      it 'does not show the abstract and shows the title instead' do
-        expect(rendered).to have_css("meta[property='og:description'][content='#{dataset.title.first}']", visible: false)
+      it 'shows the abstract' do
+        expect(rendered).to have_css("meta[property='og:description'][content='#{dataset.description.first}']", visible: false)
       end
     end
 

From 6ea7def27cd09dae60a3682f8baa8c14ca6339d8 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 18 May 2020 20:58:37 +0900
Subject: [PATCH 180/258] fix LDAP attributes and complex_identifier errors in
 spec files

---
 hyrax/spec/inputs/nested_instrument_function_input_spec.rb | 2 +-
 hyrax/spec/inputs/nested_instrument_input_spec.rb          | 6 +++---
 hyrax/spec/inputs/nested_person_input_spec.rb              | 4 ++--
 hyrax/spec/models/user_spec.rb                             | 2 ++
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/hyrax/spec/inputs/nested_instrument_function_input_spec.rb b/hyrax/spec/inputs/nested_instrument_function_input_spec.rb
index 06491a09..463e3a2f 100644
--- a/hyrax/spec/inputs/nested_instrument_function_input_spec.rb
+++ b/hyrax/spec/inputs/nested_instrument_function_input_spec.rb
@@ -15,7 +15,7 @@
   subject { Capybara.string(html) }
 
   it 'generates the correct fields' do
-    is_expected.to have_field('dataset_instrument_function_attributes_0_column_number', type: :text, with: '1')
+    is_expected.not_to have_field('dataset_instrument_function_attributes_0_column_number', type: :text, with: '1')
     is_expected.to have_field('dataset_instrument_function_attributes_0_category', type: :text, with: 'some value')
     is_expected.to have_field('dataset_instrument_function_attributes_0_sub_category', type: :text, with: 'some other value')
     is_expected.to have_field('dataset_instrument_function_attributes_0_description', type: :text, with: 'Instrument function description')
diff --git a/hyrax/spec/inputs/nested_instrument_input_spec.rb b/hyrax/spec/inputs/nested_instrument_input_spec.rb
index 18eae95a..37a90e32 100644
--- a/hyrax/spec/inputs/nested_instrument_input_spec.rb
+++ b/hyrax/spec/inputs/nested_instrument_input_spec.rb
@@ -26,7 +26,7 @@
     is_expected.to have_select('dataset[instrument_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'Identifier - Persistent')
     is_expected.to have_field('dataset[instrument_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: 'instrument/27213727')
 
-    is_expected.to have_field('dataset[instrument_attributes][0]_instrument_function_attributes_0_column_number', type: :text, with: '1')
+    is_expected.not_to have_field('dataset[instrument_attributes][0]_instrument_function_attributes_0_column_number', type: :text, with: '1')
     is_expected.to have_field('dataset[instrument_attributes][0]_instrument_function_attributes_0_category', type: :text, with: 'some value')
     is_expected.to have_field('dataset[instrument_attributes][0]_instrument_function_attributes_0_sub_category', type: :text, with: 'some other value')
     is_expected.to have_field('dataset[instrument_attributes][0]_instrument_function_attributes_0_description', type: :text, with: 'Instrument function description')
@@ -39,8 +39,8 @@
 
     is_expected.to have_field('dataset[instrument_attributes][0]_complex_person_attributes_0_name', type: :text, with: 'Name of operator')
     is_expected.to have_select('dataset[instrument_attributes][0]_complex_person_attributes_0_role', selected: 'operator/データ測定者・計算者')
-    is_expected.to have_select('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'Identifier - Local')
-    is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: '123456789mo')
+    is_expected.not_to have_select('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'Identifier - Local')
+    is_expected.not_to have_field('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: '123456789mo')
     #is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0]_complex_affiliation_attributes_0_job_title', type: :text, with: 'Principal Investigator')
     #is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_organization', type: :text, with: 'University')
     #is_expected.to have_field('dataset[instrument_attributes][0][complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_sub_organization', type: :text, with: 'Department')
diff --git a/hyrax/spec/inputs/nested_person_input_spec.rb b/hyrax/spec/inputs/nested_person_input_spec.rb
index c9360cd6..71edc8f8 100644
--- a/hyrax/spec/inputs/nested_person_input_spec.rb
+++ b/hyrax/spec/inputs/nested_person_input_spec.rb
@@ -18,8 +18,8 @@
     is_expected.to have_field('dataset_complex_person_attributes_0_name', type: :text, with: 'Anamika')
     is_expected.to have_select('dataset_complex_person_attributes_0_role', selected: 'operator/データ測定者・計算者')
 
-    is_expected.to have_select('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'Identifier - Local')
-    is_expected.to have_field('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: '123456')
+    is_expected.not_to have_select('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_scheme', selected: 'Identifier - Local')
+    is_expected.not_to have_field('dataset[complex_person_attributes][0]_complex_identifier_attributes_0_identifier', type: :text, with: '123456')
 
     #is_expected.to have_field('dataset[complex_person_attributes][0]_complex_affiliation_attributes_0_job_title', type: :text, with: 'Principal Investigator')
     #is_expected.to have_field('dataset[complex_person_attributes][0][complex_affiliation_attributes][0]_complex_organization_attributes_0_organization', type: :text, with: 'University')
diff --git a/hyrax/spec/models/user_spec.rb b/hyrax/spec/models/user_spec.rb
index d8b5528e..3b227087 100644
--- a/hyrax/spec/models/user_spec.rb
+++ b/hyrax/spec/models/user_spec.rb
@@ -11,6 +11,8 @@
   describe '#ldap_before_save' do
     before do
       allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'mail') { ['email@example.com'] }
+      allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'cn') { ['Example user'] }
+      allow(Devise::LDAP::Adapter).to receive(:get_ldap_param).with(user.username, 'employeeType') { ['A'] }
       allow(Devise).to receive(:friendly_token) { 'password' }
       user.ldap_before_save
     end

From a99170568681ab1f8822f438d264bed1448eaf21 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Tue, 19 May 2020 18:03:07 +0900
Subject: [PATCH 181/258] remove description from JSON responses

---
 .../app/presenters/concerns/filtered_graph.rb |  2 +-
 hyrax/app/views/catalog/index.json.jbuilder   |  2 +-
 hyrax/app/views/catalog/show.json.jbuilder    |  2 +-
 hyrax/app/views/hyrax/base/show.json.jbuilder |  3 +-
 .../hyrax/dataset_presenter_spec.rb           |  6 +--
 .../presenters/hyrax/image_presenter_spec.rb  |  6 +--
 .../hyrax/publication_presenter_spec.rb       |  6 +--
 .../views/catalog/index.json.jbuilder_spec.rb |  9 ++--
 .../views/catalog/show.json.jbuilder_spec.rb  | 21 ++++++----
 .../hyrax/base/show.json.jbuilder_spec.rb     | 41 +++++++++++++++++++
 10 files changed, 75 insertions(+), 23 deletions(-)
 create mode 100644 hyrax/spec/views/hyrax/base/show.json.jbuilder_spec.rb

diff --git a/hyrax/app/presenters/concerns/filtered_graph.rb b/hyrax/app/presenters/concerns/filtered_graph.rb
index 6134d5ee..169ce187 100644
--- a/hyrax/app/presenters/concerns/filtered_graph.rb
+++ b/hyrax/app/presenters/concerns/filtered_graph.rb
@@ -14,7 +14,7 @@ def unfiltered_graph
   def exclude?(statement)
     # Returns true if the statement should be filtered out of the graph
     model = model_name.name.constantize
-    (statement.predicate.ends_with?('purl.org/dc/elements/1.1/description') && current_ability.cannot?(:read_abstract, model)) ||
+    statement.predicate.ends_with?('purl.org/dc/elements/1.1/description') ||
       (statement.predicate.ends_with?('www.nims.go.jp/vocabs/ngdr/supervisor-approval') && current_ability.cannot?(:read_supervisor_approval, model)) ||
       (statement.predicate.ends_with?('id.loc.gov/vocabulary/relators/dpt'))
   end
diff --git a/hyrax/app/views/catalog/index.json.jbuilder b/hyrax/app/views/catalog/index.json.jbuilder
index d9cb6dc1..ab54cf9e 100644
--- a/hyrax/app/views/catalog/index.json.jbuilder
+++ b/hyrax/app/views/catalog/index.json.jbuilder
@@ -4,7 +4,7 @@ json.response do
       json.id document.id
       index_fields(document).each do |field_name, field|
         if should_render_index_field? document, field
-          unless field.name == 'depositor'
+          unless ['description_tesim', 'depositor_ti'].include?(field_name)
             json.set! field_name, document[field_name]
           end
         end
diff --git a/hyrax/app/views/catalog/show.json.jbuilder b/hyrax/app/views/catalog/show.json.jbuilder
index 9581dbed..fb9df6af 100644
--- a/hyrax/app/views/catalog/show.json.jbuilder
+++ b/hyrax/app/views/catalog/show.json.jbuilder
@@ -4,7 +4,7 @@ json.response do
       json.id document.id
       index_fields(document).each do |field_name, field|
         if should_render_index_field? document, field
-          unless field.name == 'depositor'
+          unless ['description_tesim', 'depositor_ti'].include?(field_name)
             json.set! field_name, document[field_name]
           end
         end
diff --git a/hyrax/app/views/hyrax/base/show.json.jbuilder b/hyrax/app/views/hyrax/base/show.json.jbuilder
index 5087735c..3180c339 100644
--- a/hyrax/app/views/hyrax/base/show.json.jbuilder
+++ b/hyrax/app/views/hyrax/base/show.json.jbuilder
@@ -1,7 +1,8 @@
 model = @curation_concern.class
 fields = @curation_concern.class.fields
              .reject { |f| [:has_model].include? f }
-             .reject { |f| f == :description && current_ability.cannot?(:read_abstract, model) }
+             .reject { |f| f == :depositor }
+             .reject { |f| f == :description }
              .reject { |f| f == :supervisor_approval && current_ability.cannot?(:read_supervisor_approval, model) }
 
 j = json.extract! @curation_concern, *[:id] + fields
diff --git a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
index 3a378eff..3b15d2d9 100644
--- a/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/dataset_presenter_spec.rb
@@ -38,7 +38,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
       it { is_expected.not_to match(depositor_regex) }
     end
@@ -74,7 +74,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
       it { is_expected.not_to match(depositor_regex) }
     end
@@ -109,7 +109,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
+      it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
       it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
       it { is_expected.not_to include("marcrelators:dpt" => "depositor") }
     end
diff --git a/hyrax/spec/presenters/hyrax/image_presenter_spec.rb b/hyrax/spec/presenters/hyrax/image_presenter_spec.rb
index 8edd2253..07eab92f 100644
--- a/hyrax/spec/presenters/hyrax/image_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/image_presenter_spec.rb
@@ -34,7 +34,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(abstract_regex) }
     end
   end
 
@@ -64,7 +64,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(abstract_regex) }
     end
   end
 
@@ -95,7 +95,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
+      it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
     end
   end
 end
diff --git a/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb b/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
index c16e4779..df9203b8 100644
--- a/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
+++ b/hyrax/spec/presenters/hyrax/publication_presenter_spec.rb
@@ -38,7 +38,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
       it { is_expected.not_to match(depositor_regex) }
     end
@@ -74,7 +74,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to match(abstract_regex) }
+      it { is_expected.not_to match(abstract_regex) }
       it { is_expected.not_to match(supervisor_regex) }
       it { is_expected.not_to match(depositor_regex) }
     end
@@ -109,7 +109,7 @@
 
     context 'authenticated user' do
       let(:user) { create(:user, :nims_other) }
-      it { is_expected.to include("dc11:description" => "Abstract-Description-123") }
+      it { is_expected.not_to include("dc11:description" => "Abstract-Description-123") }
       it { is_expected.not_to include("nimsrdp:supervisor-approval" => "Professor-Supervisor-Approval") }
       it { is_expected.not_to include("marcrelators:dpt" => "depositor") }
     end
diff --git a/hyrax/spec/views/catalog/index.json.jbuilder_spec.rb b/hyrax/spec/views/catalog/index.json.jbuilder_spec.rb
index e566c2d4..b3ab42d3 100644
--- a/hyrax/spec/views/catalog/index.json.jbuilder_spec.rb
+++ b/hyrax/spec/views/catalog/index.json.jbuilder_spec.rb
@@ -27,21 +27,24 @@
   context 'unauthenticated user' do
     let(:user) { nil }
     it 'does not show the abstract' do
-      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+      expect(rendered).not_to match('depositor_ti')
+      expect(rendered).not_to match('description_tesim')
     end
   end
 
   context 'authenticated non-researcher' do
     let(:user) { build(:user, :nims_other) }
     it 'shows the abstract' do
-      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+      expect(rendered).not_to match('depositor_ti')
+      expect(rendered).not_to match('description_tesim')
     end
   end
 
   context 'authenticated NIMS Researcher' do
     let(:user) { build(:user, :nims_researcher) }
     it 'shows the abstract' do
-      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+      expect(rendered).not_to match('depositor_ti')
+      expect(rendered).not_to match('description_tesim')
     end
   end
 end
diff --git a/hyrax/spec/views/catalog/show.json.jbuilder_spec.rb b/hyrax/spec/views/catalog/show.json.jbuilder_spec.rb
index 0fe0b7d5..9e95dc81 100644
--- a/hyrax/spec/views/catalog/show.json.jbuilder_spec.rb
+++ b/hyrax/spec/views/catalog/show.json.jbuilder_spec.rb
@@ -3,36 +3,43 @@
 require 'rails_helper'
 include Warden::Test::Helpers
 
-RSpec.describe 'catalog/show.json.jbuilder' do
+RSpec.describe "catalog/show.json.jbuilder", api: true do
   let(:document) do
-    SolrDocument.new(id: '123', title_tsim: 'Book1', author_tsim: 'Julie', format: 'Book')
+    SolrDocument.new(id: '123', title_tsim: 'Book1', author_tsim: 'Julie', format: 'Book', description_tesim: 'Description', depositor_ti: '1')
   end
-
   let(:config) do
     Blacklight::Configuration.new do |config|
-      config.add_show_field 'title', label: 'Title', field: 'title_tsim'
+      config.add_index_field 'title', label: 'Title', field: 'title_tsim'
     end
   end
 
+  let(:hash) do
+    render template: "catalog/index.json", format: :json
+    JSON.parse(rendered).with_indifferent_access
+  end
+
   # This test confirms the abstract is only visible if you are logged in
   context 'unauthenticated user' do
     let(:user) { nil }
     it 'does not show the abstract' do
-      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+      expect(rendered).not_to match('depositor_ti')
+      expect(rendered).not_to match('description_tesim')
     end
   end
 
   context 'authenticated non-researcher' do
     let(:user) { build(:user, :nims_other) }
     it 'shows the abstract' do
-      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+      expect(rendered).not_to match('depositor_ti')
+      expect(rendered).not_to match('description_tesim')
     end
   end
 
   context 'authenticated NIMS Researcher' do
     let(:user) { build(:user, :nims_researcher) }
     it 'shows the abstract' do
-      expect(rendered).not_to match('id.loc.gov/vocabulary/relators/dpt')
+      expect(rendered).not_to match('depositor_ti')
+      expect(rendered).not_to match('description_tesim')
     end
   end
 end
diff --git a/hyrax/spec/views/hyrax/base/show.json.jbuilder_spec.rb b/hyrax/spec/views/hyrax/base/show.json.jbuilder_spec.rb
new file mode 100644
index 00000000..52c71ac9
--- /dev/null
+++ b/hyrax/spec/views/hyrax/base/show.json.jbuilder_spec.rb
@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'hyrax/base/show.json.jbuilder' do
+  let(:document) do
+    SolrDocument.new(id: '123', title_tsim: 'Book1', author_tsim: 'Julie', format: 'Book', description_tesim: 'Description', depositor_ti: '1')
+  end
+
+  let(:config) do
+    Blacklight::Configuration.new do |config|
+      config.add_show_field 'title', label: 'Title', field: 'title_tsim'
+    end
+  end
+
+  # This test confirms the abstract is only visible if you are logged in
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'does not show the abstract' do
+      expect(rendered).not_to match('depositor')
+      expect(rendered).not_to match('description')
+    end
+  end
+
+  context 'authenticated non-researcher' do
+    let(:user) { build(:user, :nims_other) }
+    it 'shows the abstract' do
+      expect(rendered).not_to match('depositor')
+      expect(rendered).not_to match('description')
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { build(:user, :nims_researcher) }
+    it 'shows the abstract' do
+      expect(rendered).not_to match('depositor')
+      expect(rendered).not_to match('description')
+    end
+  end
+end

From 625ef1aef75f9fb62c62997be7bca610ffd789b6 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Tue, 19 May 2020 18:14:22 +0900
Subject: [PATCH 182/258] fix variable name "newuser"

---
 hyrax/lib/tasks/setup_hyrax.rake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/lib/tasks/setup_hyrax.rake b/hyrax/lib/tasks/setup_hyrax.rake
index 71f05f9c..73fc7e4e 100644
--- a/hyrax/lib/tasks/setup_hyrax.rake
+++ b/hyrax/lib/tasks/setup_hyrax.rake
@@ -21,7 +21,7 @@ namespace :ngdr do
     depositor = false
     admin = Role.where(name: "admin").first_or_create!
     seed["users"].each do |user|
-      newUser = User.where(username: user["username"]).first_or_create!(password: user["password"], display_name: user["name"], email: user["email"])
+      newuser = User.where(username: user["username"]).first_or_create!(password: user["password"], display_name: user["name"], email: user["email"])
       newuser.user_identifier = 'user_identifier'
       if user["role"] == "admin"
         unless admin.users.include?(newUser)

From f9b25776e68c6e17e7040498c871b0cbe5780fa5 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Tue, 19 May 2020 18:25:48 +0900
Subject: [PATCH 183/258] fix variable name "newuser"

---
 hyrax/lib/tasks/setup_hyrax.rake | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/hyrax/lib/tasks/setup_hyrax.rake b/hyrax/lib/tasks/setup_hyrax.rake
index 73fc7e4e..df9fa02b 100644
--- a/hyrax/lib/tasks/setup_hyrax.rake
+++ b/hyrax/lib/tasks/setup_hyrax.rake
@@ -24,14 +24,14 @@ namespace :ngdr do
       newuser = User.where(username: user["username"]).first_or_create!(password: user["password"], display_name: user["name"], email: user["email"])
       newuser.user_identifier = 'user_identifier'
       if user["role"] == "admin"
-        unless admin.users.include?(newUser)
-          admin.users << newUser
+        unless admin.users.include?(newuser)
+          admin.users << newuser
           admin.save!
         end
       end
 
       if user.has_key?("depositor")
-        depositor = newUser
+        depositor = newuser
       end
     end
 

From a21fe265730c3b39c1b820708e84aa99a7c8b6d3 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 20 May 2020 12:22:29 +0900
Subject: [PATCH 184/258] add last_name and first_name fields to ComplexPerson
 form

---
 hyrax/app/forms/hyrax/dataset_form.rb     |  4 ++-
 hyrax/app/forms/hyrax/publication_form.rb |  5 ++++
 hyrax/app/inputs/nested_person_input.rb   | 34 +++++++++++++++++++++++
 3 files changed, 42 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/forms/hyrax/dataset_form.rb b/hyrax/app/forms/hyrax/dataset_form.rb
index 277a953c..34cf2e96 100644
--- a/hyrax/app/forms/hyrax/dataset_form.rb
+++ b/hyrax/app/forms/hyrax/dataset_form.rb
@@ -82,7 +82,7 @@ def self.permitted_affiliation_params
        :_destroy,
        {
          job_title: [],
-	       complex_organization_attributes: permitted_organization_params,
+         complex_organization_attributes: permitted_organization_params,
        }
       ]
     end
@@ -186,6 +186,8 @@ def self.permitted_person_params
       [:id,
        :_destroy,
        {
+         last_name: [],
+         first_name: [],
          name: [],
          role: [],
          orcid: [],
diff --git a/hyrax/app/forms/hyrax/publication_form.rb b/hyrax/app/forms/hyrax/publication_form.rb
index 151fb711..b38987eb 100644
--- a/hyrax/app/forms/hyrax/publication_form.rb
+++ b/hyrax/app/forms/hyrax/publication_form.rb
@@ -89,8 +89,13 @@ def self.permitted_person_params
       [:id,
        :_destroy,
        {
+         last_name: [],
+         first_name: [],
          name: [],
          role: [],
+         orcid: [],
+         organization: [],
+         sub_organization: [],
          complex_affiliation_attributes: permitted_affiliation_params,
          complex_identifier_attributes: permitted_identifier_params,
          uri: []
diff --git a/hyrax/app/inputs/nested_person_input.rb b/hyrax/app/inputs/nested_person_input.rb
index 9775014c..2d2aaddc 100644
--- a/hyrax/app/inputs/nested_person_input.rb
+++ b/hyrax/app/inputs/nested_person_input.rb
@@ -17,6 +17,40 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
 
     parent_attribute = name_for(attribute_name, index, '', parent)[0..-5]
 
+    # --- last_name
+    field = :last_name
+    field_name = name_for(attribute_name, index, field, parent)
+    field_id = id_for(attribute_name, index, field, parent)
+    field_value = value.send(field).first
+
+    out << "<div class='row'>"
+    out << "  <div class='col-md-3'>"
+    out << template.label_tag(field_name, I18n.t('ngdr.fields.last_name'), required: required)
+    out << '  </div>'
+
+    out << "  <div class='col-md-9'>"
+    out << @builder.text_field(field_name,
+        options.merge(value: field_value, name: field_name, id: field_id, required: required))
+    out << '  </div>'
+    out << '</div>' # row
+
+    # --- first_name
+    field = :first_name
+    field_name = name_for(attribute_name, index, field, parent)
+    field_id = id_for(attribute_name, index, field, parent)
+    field_value = value.send(field).first
+
+    out << "<div class='row'>"
+    out << "  <div class='col-md-3'>"
+    out << template.label_tag(field_name, I18n.t('ngdr.fields.first_name'), required: required)
+    out << '  </div>'
+
+    out << "  <div class='col-md-9'>"
+    out << @builder.text_field(field_name,
+        options.merge(value: field_value, name: field_name, id: field_id, required: required))
+    out << '  </div>'
+    out << '</div>' # row
+
     # --- name
     field = :name
     field_name = name_for(attribute_name, index, field, parent)

From d6492637b063e5bc4974eaf47b88be89511b6bd6 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 20 May 2020 12:28:22 +0900
Subject: [PATCH 185/258] update order of properties in the nested_source form

---
 hyrax/app/inputs/nested_source_input.rb | 34 ++++++++++++-------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/hyrax/app/inputs/nested_source_input.rb b/hyrax/app/inputs/nested_source_input.rb
index cb0b72fd..237c26eb 100644
--- a/hyrax/app/inputs/nested_source_input.rb
+++ b/hyrax/app/inputs/nested_source_input.rb
@@ -45,8 +45,8 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << '  </div>'
     out << '</div>' # row
 
-    # --- start_page
-    field = :start_page
+    # --- volume
+    field = :volume
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -56,14 +56,14 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
     out << '</div>' # row
 
-    # --- end_page
-    field = :end_page
+    # --- issue
+    field = :issue
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -73,14 +73,14 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
     out << '</div>' # row
 
-    # --- issue
-    field = :issue
+    # --- sequence_number
+    field = :sequence_number
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -90,14 +90,14 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
     out << '</div>' # row
 
-    # --- sequence_number
-    field = :sequence_number
+    # --- start_page
+    field = :start_page
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -107,14 +107,14 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
     out << '</div>' # row
 
-    # --- total_number_of_pages
-    field = :total_number_of_pages
+    # --- end_page
+    field = :end_page
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -124,7 +124,7 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
@@ -133,8 +133,8 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     # last row
     out << "<div class='row'>"
 
-    # --- volume
-    field = :volume
+    # --- total_number_of_pages
+    field = :total_number_of_pages
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first

From 7560861feaf87a3768a40ea6a3c403f5d44cb779 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 20 May 2020 12:32:10 +0900
Subject: [PATCH 186/258] update the order of properties in the nested_source
 form

---
 hyrax/app/inputs/nested_source_input.rb | 34 ++++++++++++-------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/hyrax/app/inputs/nested_source_input.rb b/hyrax/app/inputs/nested_source_input.rb
index cb0b72fd..237c26eb 100644
--- a/hyrax/app/inputs/nested_source_input.rb
+++ b/hyrax/app/inputs/nested_source_input.rb
@@ -45,8 +45,8 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << '  </div>'
     out << '</div>' # row
 
-    # --- start_page
-    field = :start_page
+    # --- volume
+    field = :volume
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -56,14 +56,14 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
     out << '</div>' # row
 
-    # --- end_page
-    field = :end_page
+    # --- issue
+    field = :issue
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -73,14 +73,14 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
     out << '</div>' # row
 
-    # --- issue
-    field = :issue
+    # --- sequence_number
+    field = :sequence_number
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -90,14 +90,14 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
     out << '</div>' # row
 
-    # --- sequence_number
-    field = :sequence_number
+    # --- start_page
+    field = :start_page
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -107,14 +107,14 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
     out << '</div>' # row
 
-    # --- total_number_of_pages
-    field = :total_number_of_pages
+    # --- end_page
+    field = :end_page
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first
@@ -124,7 +124,7 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     out << template.label_tag(field_name, field.to_s.humanize, required: false)
     out << '  </div>'
 
-    out << "  <div class='col-md-9'>"
+    out << "  <div class='col-md-6'>"
     out << @builder.text_field(field_name,
         options.merge(value: field_value, name: field_name, id: field_id, required: false))
     out << '  </div>'
@@ -133,8 +133,8 @@ def build_components(attribute_name, value, index, options, parent=@builder.obje
     # last row
     out << "<div class='row'>"
 
-    # --- volume
-    field = :volume
+    # --- total_number_of_pages
+    field = :total_number_of_pages
     field_name = name_for(attribute_name, index, field, parent)
     field_id = id_for(attribute_name, index, field, parent)
     field_value = value.send(field).first

From 0876f1cd96066760ccc84598ea1a6111f603b0eb Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Wed, 20 May 2020 21:43:35 +0100
Subject: [PATCH 187/258] Remove delegate of first published url to the solr
 document - it's in publication & dataset

---
 hyrax/app/presenters/hyrax/dataset_presenter.rb     | 3 +--
 hyrax/app/presenters/hyrax/publication_presenter.rb | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/hyrax/app/presenters/hyrax/dataset_presenter.rb b/hyrax/app/presenters/hyrax/dataset_presenter.rb
index d6e7c659..ffca8c9f 100644
--- a/hyrax/app/presenters/hyrax/dataset_presenter.rb
+++ b/hyrax/app/presenters/hyrax/dataset_presenter.rb
@@ -7,8 +7,7 @@ class DatasetPresenter < Hyrax::WorkShowPresenter
       :characterization_methods, :computational_methods, :data_origin,
       :complex_instrument, :origin_system_provenance, :properties_addressed,
       :complex_relation, :specimen_set, :complex_specimen_type,
-      :synthesis_and_processing, :custom_property, :first_published_url,
-      to: :solr_document
+      :synthesis_and_processing, :custom_property, to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end
diff --git a/hyrax/app/presenters/hyrax/publication_presenter.rb b/hyrax/app/presenters/hyrax/publication_presenter.rb
index 5109c6e5..0d37cbad 100644
--- a/hyrax/app/presenters/hyrax/publication_presenter.rb
+++ b/hyrax/app/presenters/hyrax/publication_presenter.rb
@@ -4,8 +4,7 @@ module Hyrax
   class PublicationPresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
              :complex_rights, :complex_version, :complex_event, :issue, :place,
-             :table_of_contents, :total_number_of_pages, :complex_source,
-             :first_published_url, to: :solr_document
+             :table_of_contents, :total_number_of_pages, :complex_source, to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
   end

From 25a209e0595a92de5cfae399bf5c479f8840525a Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 21 May 2020 19:22:46 +0900
Subject: [PATCH 188/258] revert the relationships tab

---
 hyrax/app/views/hyrax/base/_guts4form.html.erb     | 2 +-
 hyrax/app/views/hyrax/datasets/_guts4form.html.erb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/views/hyrax/base/_guts4form.html.erb b/hyrax/app/views/hyrax/base/_guts4form.html.erb
index 80066b14..dd4def11 100644
--- a/hyrax/app/views/hyrax/base/_guts4form.html.erb
+++ b/hyrax/app/views/hyrax/base/_guts4form.html.erb
@@ -1,6 +1,6 @@
 <% # we will yield to content_for for each tab, e.g. :files_tab %>
 <% # Override Hyrax 2.6 - remove relationships tab from here %>
-<% tabs ||= %w[metadata files] # default tab order %>
+<% tabs ||= %w[metadata files relationships] # default tab order %>
 <div class="row">
   <div class="col-xs-12 col-sm-8">
     <div class="panel panel-default tabs" role="main">
diff --git a/hyrax/app/views/hyrax/datasets/_guts4form.html.erb b/hyrax/app/views/hyrax/datasets/_guts4form.html.erb
index 73fc103a..8ded9fa6 100644
--- a/hyrax/app/views/hyrax/datasets/_guts4form.html.erb
+++ b/hyrax/app/views/hyrax/datasets/_guts4form.html.erb
@@ -1,6 +1,6 @@
 <% # we will yield to content_for for each tab, e.g. :files_tab %>
 <% # Override Hyrax 2.6 - remove relationships tab from here %>
-<% tabs ||= %w[metadata method instrument specimen files] # default tab order %>
+<% tabs ||= %w[metadata method instrument specimen files relationships] # default tab order %>
 <div class="row">
   <div class="col-xs-12 col-sm-8">
     <div class="panel panel-default tabs" role="main">

From c6724028059c8e75ed0c93cb308c97cb8979d906 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 21 May 2020 19:26:20 +0900
Subject: [PATCH 189/258] update spec files

---
 hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb     | 2 +-
 hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb b/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
index 7eb4d477..2c616751 100644
--- a/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
+++ b/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
@@ -19,7 +19,7 @@
   describe 'tabs' do
     it 'does not show the relationships tab' do
       render
-      expect(rendered).not_to have_selector('#relationships[role="tabpanel"]')
+      expect(rendered).to have_selector('#relationships[role="tabpanel"]')
       expect(rendered).to have_selector('#metadata[role="tabpanel"]')
       expect(rendered).to have_selector('#files[role="tabpanel"]')
       expect(rendered).to have_selector('#share[data-param-key="publication"]')
diff --git a/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb b/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb
index ccb17bcb..7ea03c2d 100644
--- a/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb
+++ b/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb
@@ -18,9 +18,9 @@
   end
 
   describe 'tabs' do
-    it 'does not show the relationships tab' do
+    it 'shows the relationships tab' do
       render
-      expect(rendered).not_to have_selector('#relationships[role="tabpanel"]')
+      expect(rendered).to have_selector('#relationships[role="tabpanel"]')
       expect(rendered).to have_selector('#metadata[role="tabpanel"]')
       expect(rendered).to have_selector('#files[role="tabpanel"]')
       expect(rendered).to have_selector('#share[data-param-key="dataset"]')

From cf379578c9e04b8210844301ea84512b372e6313 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Thu, 21 May 2020 21:28:34 +0900
Subject: [PATCH 190/258] Hide some elements in Relationships and Sharing tabs

---
 hyrax/app/assets/stylesheets/ngdr.scss | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/hyrax/app/assets/stylesheets/ngdr.scss b/hyrax/app/assets/stylesheets/ngdr.scss
index 4c7abdd4..d955fc25 100644
--- a/hyrax/app/assets/stylesheets/ngdr.scss
+++ b/hyrax/app/assets/stylesheets/ngdr.scss
@@ -122,3 +122,20 @@ div#announcement {
 .csv-preview-size {
   text-align: right;
 }
+
+// Hiding Relationships and Sharing tab contents from casual users
+// https://github.com/antleaf/nims-mdr-development/issues/292 
+
+#relationships > .form-tab-content::before {
+  content: "Relationships settings are not available.";
+}
+
+#relationships > .form-tab-content > * {
+  visibility: hidden;
+}
+
+#share > .form-tab-content > p,
+#share > .form-tab-content > h2,
+#share > .form-tab-content > fieldset {
+  display: none;
+}

From 0cae1634750653c5d8b9edeae128fc3cd482f35b Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 22 May 2020 09:34:24 +0900
Subject: [PATCH 191/258] first_published_url should be displayed first

---
 hyrax/app/forms/hyrax/dataset_form.rb     | 6 +++---
 hyrax/app/forms/hyrax/publication_form.rb | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/hyrax/app/forms/hyrax/dataset_form.rb b/hyrax/app/forms/hyrax/dataset_form.rb
index c00966fc..ae8d4dc9 100644
--- a/hyrax/app/forms/hyrax/dataset_form.rb
+++ b/hyrax/app/forms/hyrax/dataset_form.rb
@@ -18,7 +18,7 @@ class DatasetForm < Hyrax::Forms::WorkForm
 
     self.terms += [
       # Adding all fields in order of display in form
-      :supervisor_approval, :first_published_url,
+      :first_published_url, :supervisor_approval,
       :title, :alternative_title, :description, :keyword, :language,
       :publisher, :complex_rights, :subject, :complex_date, :complex_person,
       :complex_version, :characterization_methods, :computational_methods,
@@ -37,14 +37,14 @@ class DatasetForm < Hyrax::Forms::WorkForm
 
     self.required_fields += [
       # # Adding all required fields in order of display in form
-      :supervisor_approval, :first_published_url, :title, :data_origin,
+      :first_published_url, :supervisor_approval, :title, :data_origin,
       :description, :keyword
     ]
 
     def metadata_tab_terms
       [
         # Description tab order determined here
-        :supervisor_approval, :first_published_url,
+        :first_published_url, :supervisor_approval,
         :title, :alternative_title, :data_origin, :description, :keyword,
         :specimen_set, :complex_person, 
         :complex_identifier, # not using this
diff --git a/hyrax/app/forms/hyrax/publication_form.rb b/hyrax/app/forms/hyrax/publication_form.rb
index 573e30b7..4706fbdf 100644
--- a/hyrax/app/forms/hyrax/publication_form.rb
+++ b/hyrax/app/forms/hyrax/publication_form.rb
@@ -18,7 +18,7 @@ class PublicationForm < Hyrax::Forms::WorkForm
 
     self.terms += [
       # Adding all fields in order of display in form
-      :supervisor_approval, :first_published_url,
+      :first_published_url, :supervisor_approval,
       :title, :alternative_title, :complex_person, :description, :keyword,
       :publisher, :resource_type, :complex_rights,
       :complex_date, :complex_identifier, :complex_source, :complex_version,
@@ -33,7 +33,7 @@ class PublicationForm < Hyrax::Forms::WorkForm
 
     self.required_fields += [
       # Adding all required fields in order of display in form
-      :supervisor_approval, :first_published_url, :title, :resource_type,
+      :first_published_url, :supervisor_approval, :title, :resource_type,
       :description, :keyword
     ]
 

From debacbcb3e82c046fcbec701b8de7f848a6e7015 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Sat, 23 May 2020 00:26:13 +0900
Subject: [PATCH 192/258] fix broken models

---
 hyrax/app/models/dataset.rb     | 2 ++
 hyrax/app/models/publication.rb | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/hyrax/app/models/dataset.rb b/hyrax/app/models/dataset.rb
index ba081d69..5ac0069c 100644
--- a/hyrax/app/models/dataset.rb
+++ b/hyrax/app/models/dataset.rb
@@ -102,6 +102,8 @@ class Dataset < ActiveFedora::Base
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
   property :first_published_url, predicate: ::RDF::Vocab::NimsRdp['first_published_url'], multiple: false do |index|
+    index.as :stored_searchable
+  end
 
   property :doi, predicate: ::RDF::Vocab::Identifiers.doi, multiple: false do |index|
     index.as :stored_searchable
diff --git a/hyrax/app/models/publication.rb b/hyrax/app/models/publication.rb
index 3200b84f..4504dd3f 100644
--- a/hyrax/app/models/publication.rb
+++ b/hyrax/app/models/publication.rb
@@ -86,6 +86,8 @@ class Publication < ActiveFedora::Base
   property :supervisor_approval, predicate: ::RDF::Vocab::NimsRdp['supervisor-approval']
 
   property :first_published_url, predicate: ::RDF::Vocab::NimsRdp['first_published_url'], multiple: false do |index|
+    index.as :stored_searchable
+  end
 
   property :doi, predicate: ::RDF::Vocab::Identifiers.doi, multiple: false do |index|
     index.as :stored_searchable

From e610ae66f3f3db2d2759628b80eca0d93df8f77a Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Sat, 23 May 2020 00:26:49 +0900
Subject: [PATCH 193/258] update the hint message for supervisor_approval
 https://github.com/antleaf/nims-mdr-development/issues/279#issuecomment-632001601

---
 .../views/records/edit_fields/_supervisor_approval.html.erb  | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/hyrax/app/views/records/edit_fields/_supervisor_approval.html.erb b/hyrax/app/views/records/edit_fields/_supervisor_approval.html.erb
index 19187c23..3a8aa7f1 100644
--- a/hyrax/app/views/records/edit_fields/_supervisor_approval.html.erb
+++ b/hyrax/app/views/records/edit_fields/_supervisor_approval.html.erb
@@ -1,8 +1,5 @@
 <%= f.input :supervisor_approval,
   required: f.object.required?(key),
   as: :multi_value,
-  hint: raw("Fill in the name of your supervisor and the date of approval. If you have already got approval on the NIMS Research Presentation Management System （発表許可申請システム）, please also fill in the application number （申請番号）.
-  The content (Dataset or Publication) submitted here will be published to the public with yours and your supervisor's consent. See <a href='https://komorido.nims.go.jp/mdr/' target='_blank' rel='noopener'>the User's Manual</a> for details.
-<br />
-e.g. Butsuzai, Taro 2019-09-30 2019A00xxxA"),
+  hint: raw("If you entered a DOI above, enter \"approved\". If you entered a non-DOI URL above, fill in the name of your supervisor and the date of their approval. See <a href='https://komorido.nims.go.jp/mdr/' target='_blank' rel='noopener'>the User's Manual</a> for details."),
   input_html: {class: 'form-control'} %>

From 428a16392b88b2c51a9518eb6d8e5558a0d417f5 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 23 May 2020 14:48:41 +0900
Subject: [PATCH 194/258] add first_published_url to SolrDocument and
 presenters

---
 hyrax/app/models/solr_document.rb                   | 4 ++++
 hyrax/app/presenters/hyrax/dataset_presenter.rb     | 3 ++-
 hyrax/app/presenters/hyrax/publication_presenter.rb | 4 ++--
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/hyrax/app/models/solr_document.rb b/hyrax/app/models/solr_document.rb
index 78f67e1e..382e45d0 100644
--- a/hyrax/app/models/solr_document.rb
+++ b/hyrax/app/models/solr_document.rb
@@ -146,6 +146,10 @@ def status
     self[Solrizer.solr_name('status', :stored_searchable)]
   end
 
+  def first_published_url
+    self[Solrizer.solr_name('first_published_url', :stored_searchable)]
+  end
+
   def doi
     self[Solrizer.solr_name('doi', :stored_searchable)]
   end
diff --git a/hyrax/app/presenters/hyrax/dataset_presenter.rb b/hyrax/app/presenters/hyrax/dataset_presenter.rb
index 6525f7e7..f51bcaf2 100644
--- a/hyrax/app/presenters/hyrax/dataset_presenter.rb
+++ b/hyrax/app/presenters/hyrax/dataset_presenter.rb
@@ -7,7 +7,8 @@ class DatasetPresenter < Hyrax::WorkShowPresenter
       :characterization_methods, :computational_methods, :data_origin,
       :complex_instrument, :origin_system_provenance, :properties_addressed,
       :complex_relation, :specimen_set, :complex_specimen_type,
-      :synthesis_and_processing, :custom_property, :doi, to: :solr_document
+      :synthesis_and_processing, :custom_property, :first_published_url, :doi,
+      to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
     prepend ::FilteredGraph
diff --git a/hyrax/app/presenters/hyrax/publication_presenter.rb b/hyrax/app/presenters/hyrax/publication_presenter.rb
index b56b6173..ef872aa2 100644
--- a/hyrax/app/presenters/hyrax/publication_presenter.rb
+++ b/hyrax/app/presenters/hyrax/publication_presenter.rb
@@ -4,8 +4,8 @@ module Hyrax
   class PublicationPresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
              :complex_rights, :complex_version, :complex_event, :issue, :place,
-             :table_of_contents, :total_number_of_pages, :complex_source, :doi,
-             to: :solr_document
+             :table_of_contents, :total_number_of_pages, :complex_source,
+             :first_published_url, :doi, to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
     prepend ::FilteredGraph

From afcab51549860b5c16e42a4bed319379315c3802 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 23 May 2020 16:17:12 +0900
Subject: [PATCH 195/258] add ERROR_NOTIFICATION_RECIPIENT_EMAIL and
 ERROR_NOTIFICATION_SUBJECT_PREFIX

---
 .env.template                           | 4 +++-
 docker-compose.yml                      | 3 ---
 hyrax/config/environments/production.rb | 5 +++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.env.template b/.env.template
index 3044b86b..c5ed7a18 100644
--- a/.env.template
+++ b/.env.template
@@ -58,7 +58,9 @@ UPLOADS_PATH=/shared/uploads/
 CACHE_PATH=/shared/cache/
 BRAND_PATH=/data/public/branding
 DEFAULT_DATE_FORMAT=%d/%m/%Y
-NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS="no-reply@mailboxer.com"
+NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS=no-reply@mailboxer.com
+ERROR_NOTIFICATION_RECIPIENT_EMAIL=error-notification@example.org
+ERROR_NOTIFICATION_SUBJECT_PREFIX=mdr-development
 USER_MANAGEMENT_EMAIL_FROM_ADDRESS=repo-admin@example.org
 CONTACT_FORM_SUBJECT_PREFIX=Hyrax Contact form:
 CONTACT_EMAIL=
diff --git a/docker-compose.yml b/docker-compose.yml
index 243ec279..6a648edf 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -86,9 +86,6 @@ services:
         CACHE_PATH: ${CACHE_PATH}
         FITS_PATH: ${FITS_PATH}
         FITS_VERSION: ${FITS_VERSION}
-        AIRBRAKE_HOST: ${AIRBRAKE_HOST}
-        AIRBRAKE_PROJECT_ID: ${AIRBRAKE_PROJECT_ID}
-        AIRBRAKE_PROJECT_KEY: ${AIRBRAKE_PROJECT_KEY}
     env_file:
       - .env
     volumes:
diff --git a/hyrax/config/environments/production.rb b/hyrax/config/environments/production.rb
index d03d2d75..52daf9e5 100644
--- a/hyrax/config/environments/production.rb
+++ b/hyrax/config/environments/production.rb
@@ -115,10 +115,11 @@
 
   config.middleware.use ExceptionNotification::Rack,
     ignore_if: lambda { |env, exception| !env.nil? },
+    error_grouping: true,
     email: {
-      email_prefix: 'MDR [Hyrax] ',
+      email_prefix: "[MDR #{ENV['ERROR_NOTIFICATION_SUBJECT_PREFIX']}] ",
       sender_address: ENV['NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS'],
-      exception_recipients: [ENV['NOTIFICATIONS_EMAIL_DEFAULT_FROM_ADDRESS']]
+      exception_recipients: [ENV['ERROR_NOTIFICATION_RECIPIENT_EMAIL']]
     }
 
   ExceptionNotifier::Rake.configure

From ee3e4ab9167156e1552f573a58c32cc1785f5c50 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 27 May 2020 20:54:34 +0900
Subject: [PATCH 196/258] display the product's full name in the title

---
 hyrax/app/helpers/hyrax/title_helper.rb       |  5 +++
 hyrax/app/views/hyrax/homepage/index.html.erb |  2 +-
 hyrax/config/locales/hyrax.en.yml             |  1 +
 .../hyrax/homepage/index.html.erb_spec.rb     | 37 +++++++++++++++++++
 4 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/app/helpers/hyrax/title_helper.rb
 create mode 100644 hyrax/spec/views/hyrax/homepage/index.html.erb_spec.rb

diff --git a/hyrax/app/helpers/hyrax/title_helper.rb b/hyrax/app/helpers/hyrax/title_helper.rb
new file mode 100644
index 00000000..15bb4653
--- /dev/null
+++ b/hyrax/app/helpers/hyrax/title_helper.rb
@@ -0,0 +1,5 @@
+module Hyrax::TitleHelper
+  def application_name_full
+    t('hyrax.product_name_full')
+  end
+end
diff --git a/hyrax/app/views/hyrax/homepage/index.html.erb b/hyrax/app/views/hyrax/homepage/index.html.erb
index 31315210..33b2178e 100644
--- a/hyrax/app/views/hyrax/homepage/index.html.erb
+++ b/hyrax/app/views/hyrax/homepage/index.html.erb
@@ -1,4 +1,4 @@
-<% provide :page_title, application_name %>
+<% provide :page_title, application_name_full %>
 
 <div class="homepage-row">
   <%= render 'home_share' %>
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index 7f5cf274..eadcf65b 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -244,6 +244,7 @@ en:
     institution_name: Institution
     institution_name_full: The Institution Name
     product_name: MDR
+    product_name_full: "MDR: NIMS Materials Data Repository"
     product_twitter_handle: "@SamveraRepo"
     works:
       form:
diff --git a/hyrax/spec/views/hyrax/homepage/index.html.erb_spec.rb b/hyrax/spec/views/hyrax/homepage/index.html.erb_spec.rb
new file mode 100644
index 00000000..e555e8a9
--- /dev/null
+++ b/hyrax/spec/views/hyrax/homepage/index.html.erb_spec.rb
@@ -0,0 +1,37 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'hyrax/homepage/index.html.erb', type: :view do
+  let(:search_state) { double(has_facet?: false, add_facet_params_and_redirect: { controller: 'catalog' }) }
+  let(:page) { Capybara::Node::Simple.new(rendered) }
+  let(:presenter) do
+    instance_double(Hyrax::HomepagePresenter,
+                    create_work_presenter: type_presenter,
+                    create_many_work_types?: true,
+                    draw_select_work_modal?: true)
+  end
+  let(:type_presenter) { instance_double(Hyrax::SelectTypeListPresenter) }
+
+  before do
+    allow(view).to receive(:current_search_parameters).and_return(nil)
+    allow(view).to receive(:current_user).and_return(nil)
+    assign(:presenter, presenter)
+    assign(:featured_work_list, [])
+    assign(:featured_researcher, ContentBlock.featured_researcher)
+    stub_template 'shared/_select_work_type_modal.html.erb' => 'modal'
+    stub_template "hyrax/homepage/_marketing.html.erb" => "marketing"
+    stub_template "hyrax/homepage/_home_content.html.erb" => "home content"
+    stub_template "_controls.html.erb" => "controls"
+    stub_template "_masthead.html.erb" => "masthead"
+  end
+
+  it "shows the product's full name" do
+    without_partial_double_verification {
+      allow(view).to receive(:search_state).and_return(search_state)
+      allow(presenter).to receive(:display_share_button?).and_return(true)
+    }
+
+    render template: 'hyrax/homepage/index', layout: 'layouts/homepage'
+    expect(page).to have_title t('hyrax.product_name_full')
+  end
+end

From ea22aeff9e2700f9ead33df075c90ef138573ea4 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 27 May 2020 21:25:00 +0900
Subject: [PATCH 197/258] rename helper module

---
 .../helpers/hyrax/{title_helper.rb => nims_title_helper.rb} | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)
 rename hyrax/app/helpers/hyrax/{title_helper.rb => nims_title_helper.rb} (58%)

diff --git a/hyrax/app/helpers/hyrax/title_helper.rb b/hyrax/app/helpers/hyrax/nims_title_helper.rb
similarity index 58%
rename from hyrax/app/helpers/hyrax/title_helper.rb
rename to hyrax/app/helpers/hyrax/nims_title_helper.rb
index 15bb4653..7af36c89 100644
--- a/hyrax/app/helpers/hyrax/title_helper.rb
+++ b/hyrax/app/helpers/hyrax/nims_title_helper.rb
@@ -1,5 +1,9 @@
-module Hyrax::TitleHelper
+module Hyrax::NimsTitleHelper
   def application_name_full
     t('hyrax.product_name_full')
   end
 end
+
+module Hyrax::TitleHelper
+  include Hyrax::NimsTitleHelper
+end

From 86c3d295082c8431683ee13647bd03e7e0c021a8 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 27 May 2020 23:28:03 +0900
Subject: [PATCH 198/258] add guest_username_authentication_key method

---
 hyrax/app/controllers/application_controller.rb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/hyrax/app/controllers/application_controller.rb b/hyrax/app/controllers/application_controller.rb
index 2669f3f0..62a5aaa9 100644
--- a/hyrax/app/controllers/application_controller.rb
+++ b/hyrax/app/controllers/application_controller.rb
@@ -31,4 +31,8 @@ def after_sign_in_path_for(resource)
     # Trying fix for redirect loop
     stored_path || new_path
   end
+
+  def guest_username_authentication_key(key)
+    "guest_" + guest_user_unique_suffix
+  end
 end

From 363f3438f7ad042ee3dc8e095b06bce28ad96587 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 28 May 2020 00:52:19 +0900
Subject: [PATCH 199/258] hide email from user profile page

---
 .../app/views/hyrax/users/_user_info.html.erb | 85 +++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/users/_user_info.html.erb

diff --git a/hyrax/app/views/hyrax/users/_user_info.html.erb b/hyrax/app/views/hyrax/users/_user_info.html.erb
new file mode 100644
index 00000000..cfb0809f
--- /dev/null
+++ b/hyrax/app/views/hyrax/users/_user_info.html.erb
@@ -0,0 +1,85 @@
+<dl id="user_info">
+
+<% if user.orcid.present? %>
+  <dt><%= orcid_label('profile') %></dt>
+  <dd><%= link_to user.orcid, user.orcid, { target: '_blank' } %></dd>
+<% end %>
+
+<% if Hyrax.config.arkivo_api? && user.zotero_userid.present? %>
+  <dt><%= zotero_label(html_class: 'profile') %></dt>
+  <dd><%= link_to zotero_profile_url(user.zotero_userid), zotero_profile_url(user.zotero_userid), { target: '_blank' } %></dd>
+<% end %>
+
+<% if user.facebook_handle.present? %>
+  <dt><i class="fa fa-facebook" aria-hidden="true"></i> Facebook Handle</dt>
+  <dd><%= link_to user.facebook_handle, "http://facebook.com/#{user.facebook_handle}", {target:'_blank'} %></dd>
+<% end %>
+
+<% if user.twitter_handle.present? %>
+  <dt><i class="fa fa-twitter" aria-hidden="true"></i> Twitter Handle</dt>
+  <dd><%= link_to user.twitter_handle, "http://twitter.com/#{user.twitter_handle}", {target:'_blank'} %></dd>
+<% end %>
+
+<% if user.googleplus_handle.present? %>
+  <dt><i class="fa fa-google-plus" aria-hidden="true"></i> Google+ Handle</dt>
+  <dd><%= link_to user.googleplus_handle, "http://google.com/+#{user.googleplus_handle}", {target:'_blank'} %></dd>
+<% end %>
+
+<% if user.linkedin_handle.present? %>
+  <dt><i class="fa fa-linkedin" aria-hidden="true"></i> LinkedIn</dt>
+  <dd><%= link_to "#{@linkedInUrl}", "#{@linkedInUrl}", { target: '_blank' } %></dd>
+<% end %>
+
+<!--
+  <dt><i class="fa fa-envelope" aria-hidden="true"></i> Email</dt>
+  <dd><%# mail_to user.email %></dd>
+-->
+
+  <% if user.chat_id %>
+    <dt><i class="glyphicon glyphicon-bullhorn" aria-hidden="true"></i> Chat ID</dt>
+    <dd><%# user.chat_id %></dd>
+  <% end %>
+
+  <!-- TODO: add a link to SAMURAI -->
+
+  <% if user.website %>
+    <dt><i class="glyphicon glyphicon-globe" aria-hidden="true"></i> Website(s)</dt>
+    <dd><%= iconify_auto_link(user.website) %></dd>
+  <% end %>
+
+  <% if user.title %>
+    <dt>Title</dt>
+    <dd><%= user.title %></dd>
+  <% end %>
+
+  <% if user.admin_area %>
+    <dt>Administrative Area</dt>
+    <dd><%= user.admin_area %></dd>
+  <% end %>
+
+  <% if user.department %>
+    <dt>Department</dt>
+    <dd><%= user.department %></dd>
+  <% end %>
+
+  <% if user.office %>
+    <dt>Office</dt>
+    <dd><%= user.office %></dd>
+  <% end %>
+
+  <% if user.address %>
+    <dt><i class="glyphicon glyphicon-map-marker" aria-hidden="true"></i> Address</dt>
+    <dd><%= user.address %></dd>
+  <% end %>
+
+  <% if user.affiliation %>
+    <dt>Affiliation</dt>
+    <dd><%= user.affiliation %></dd>
+  <% end %>
+
+  <% if user.telephone %>
+    <dt><i class="glyphicon glyphicon-earphone" aria-hidden="true"></i> Telephone</dt>
+    <dd><%= link_to_telephone(user) %></dd>
+  <% end %>
+
+</dl>

From 0310245352980094ab760d118bb3f6c757573bd4 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 28 May 2020 00:55:02 +0900
Subject: [PATCH 200/258] remove relationships header

---
 hyrax/app/views/hyrax/base/_relationships.html.erb | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/base/_relationships.html.erb

diff --git a/hyrax/app/views/hyrax/base/_relationships.html.erb b/hyrax/app/views/hyrax/base/_relationships.html.erb
new file mode 100644
index 00000000..064471c9
--- /dev/null
+++ b/hyrax/app/views/hyrax/base/_relationships.html.erb
@@ -0,0 +1,3 @@
+<dl class="work-show">
+<%= render 'relationships_parent_rows', presenter: presenter %>
+</dl>

From 00b467d15b1979092747dacc342071c388f94510 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 29 May 2020 10:35:06 +0900
Subject: [PATCH 201/258] Remove row class from announcement div

---
 hyrax/app/views/hyrax/homepage/_announcement.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/views/hyrax/homepage/_announcement.html.erb b/hyrax/app/views/hyrax/homepage/_announcement.html.erb
index fe0c5836..8802a3fa 100644
--- a/hyrax/app/views/hyrax/homepage/_announcement.html.erb
+++ b/hyrax/app/views/hyrax/homepage/_announcement.html.erb
@@ -1,3 +1,3 @@
 <% if display_content_block? @announcement_text %>
-  <%= displayable_content_block @announcement_text, class: 'row', id: 'announcement' %>
+  <%= displayable_content_block @announcement_text, id: 'announcement' %>
 <% end %>

From e58db1cf4e5804f00701765f2d036297dcbda52a Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 29 May 2020 11:43:29 +0900
Subject: [PATCH 202/258] Add footer nav menu with links to terms, privacy,
 library, and platform

---
 hyrax/app/assets/stylesheets/theme.scss |  3 +++
 hyrax/app/views/shared/_footer.html.erb | 17 +++++++++++++++--
 hyrax/config/locales/hyrax.en.yml       | 12 +++++++-----
 3 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/hyrax/app/assets/stylesheets/theme.scss b/hyrax/app/assets/stylesheets/theme.scss
index 14c7c1f0..192b00f4 100644
--- a/hyrax/app/assets/stylesheets/theme.scss
+++ b/hyrax/app/assets/stylesheets/theme.scss
@@ -195,6 +195,9 @@ nav.searchbar {
   padding: 20px;
   background-color: $mdr-black;
   color: #fff;
+}
+
+.site-footer .navbar-nav {
   font-weight: bold;
 }
 
diff --git a/hyrax/app/views/shared/_footer.html.erb b/hyrax/app/views/shared/_footer.html.erb
index 76adc07f..6c97e07f 100644
--- a/hyrax/app/views/shared/_footer.html.erb
+++ b/hyrax/app/views/shared/_footer.html.erb
@@ -1,7 +1,20 @@
-<footer class="navbar site-footer">
+<footer class="navbar navbar-inverse site-footer">
   <div class="row">
     <div class="col-sm-6 text-left">
-        <p><%= t('hyrax.footer.address_html') %></p>
+      <ul class="nav navbar-nav">
+        <li>
+          <a href="/terms"><%= t('hyrax.pages.tabs.terms_page') %></a>
+        </li>
+        <li>
+          <%= t('hyrax.footer.privacy_html') %>
+        </li>
+        <li>
+          <%= t('hyrax.footer.service_html') %>
+        </li>
+        <li>
+          <%= t('hyrax.footer.platform_html') %>
+        </li>
+      </ul>
     </div>
     <div class="col-sm-6 text-right">
       <p><%= t('hyrax.footer.copyright_html') %></p>
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index 7f5cf274..f3de26d7 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -238,13 +238,15 @@ en:
       suffix: "@example.org"
     download_all: Download All Files (Zip)
     footer:
-      copyright_html: "Copyright &copy; National Institute for Materials Science"
-      service_html: A service of <a href="http://samvera.org/" class="navbar-link" target="_blank">Samvera</a>.
+      copyright_html: "&copy; 2020 National Institute for Materials Science<br>Works are available under licenses specified on their page."
+      service_html: <a href="https://library.nims.go.jp/" target="_blank" rel="noopener">NIMS Digital Library</a>
+      platform_html: <a href="https://dice.nims.go.jp/" target="_blank" rel="noopener">DICE</a>
+      privacy_html: <a href="https://www.nims.go.jp/eng/siteinfo/privacy-policy.html" target="_blank" rel="noopener">Privacy Policy</a>
       address_html: National Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 JAPAN
-    institution_name: Institution
-    institution_name_full: The Institution Name
+    institution_name: NIMS
+    institution_name_full: National Institute for Materials Science
     product_name: MDR
-    product_twitter_handle: "@SamveraRepo"
+    product_twitter_handle: "@nims_library"
     works:
       form:
         tab:

From 0968759ef3125acacc2c36fd5c56889a2a086313 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 29 May 2020 13:19:40 +0900
Subject: [PATCH 203/258] Undo fixed site-footer height 60px

---
 hyrax/app/assets/stylesheets/theme.scss | 1 -
 1 file changed, 1 deletion(-)

diff --git a/hyrax/app/assets/stylesheets/theme.scss b/hyrax/app/assets/stylesheets/theme.scss
index 192b00f4..1c60aded 100644
--- a/hyrax/app/assets/stylesheets/theme.scss
+++ b/hyrax/app/assets/stylesheets/theme.scss
@@ -191,7 +191,6 @@ nav.searchbar {
 
 // ------------- footer ----------------
 .site-footer {
-  height: 60px;
   padding: 20px;
   background-color: $mdr-black;
   color: #fff;

From 73e70fee073e15ca573d79179182e59c8d639959 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 29 May 2020 13:43:13 +0900
Subject: [PATCH 204/258] Copy layout of platform site footer

---
 hyrax/app/assets/stylesheets/theme.scss | 11 +++++++++--
 hyrax/app/views/shared/_footer.html.erb | 10 ++++++----
 hyrax/config/locales/hyrax.en.yml       |  6 +++++-
 3 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/hyrax/app/assets/stylesheets/theme.scss b/hyrax/app/assets/stylesheets/theme.scss
index 1c60aded..8c2ce2d4 100644
--- a/hyrax/app/assets/stylesheets/theme.scss
+++ b/hyrax/app/assets/stylesheets/theme.scss
@@ -196,8 +196,15 @@ nav.searchbar {
   color: #fff;
 }
 
-.site-footer .navbar-nav {
-  font-weight: bold;
+.site-footer h2 {
+  margin: 0;
+  color: #fff;
+}
+
+.site-footer a,
+.site-footer a:hover,
+.site-footer a:focus {
+  color: #fff;
 }
 
 // ------------- homepage -----------------
diff --git a/hyrax/app/views/shared/_footer.html.erb b/hyrax/app/views/shared/_footer.html.erb
index 6c97e07f..54ba7025 100644
--- a/hyrax/app/views/shared/_footer.html.erb
+++ b/hyrax/app/views/shared/_footer.html.erb
@@ -1,7 +1,12 @@
 <footer class="navbar navbar-inverse site-footer">
   <div class="row">
     <div class="col-sm-6 text-left">
-      <ul class="nav navbar-nav">
+      <h2><%= t('hyrax.institution_name_full') %></h2>
+      <p><%= t('hyrax.division_name_full') %> (<%= t('hyrax.division_name') %>)<br><%= t('hyrax.center_name') %></p>
+      <small><%= t('hyrax.footer.copyright_html') %></small>
+    </div>
+    <div class="col-sm-6 text-right">
+      <ul class="list-unstyled">
         <li>
           <a href="/terms"><%= t('hyrax.pages.tabs.terms_page') %></a>
         </li>
@@ -16,8 +21,5 @@
         </li>
       </ul>
     </div>
-    <div class="col-sm-6 text-right">
-      <p><%= t('hyrax.footer.copyright_html') %></p>
-    </div>
   </div>
 </footer>
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index f3de26d7..c9544369 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -238,13 +238,17 @@ en:
       suffix: "@example.org"
     download_all: Download All Files (Zip)
     footer:
-      copyright_html: "&copy; 2020 National Institute for Materials Science<br>Works are available under licenses specified on their page."
+      copyright_html: "&copy; 2020 National Institute for Materials Science. Works are available under licenses specified on their pages."
       service_html: <a href="https://library.nims.go.jp/" target="_blank" rel="noopener">NIMS Digital Library</a>
       platform_html: <a href="https://dice.nims.go.jp/" target="_blank" rel="noopener">DICE</a>
       privacy_html: <a href="https://www.nims.go.jp/eng/siteinfo/privacy-policy.html" target="_blank" rel="noopener">Privacy Policy</a>
       address_html: National Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 JAPAN
     institution_name: NIMS
     institution_name_full: National Institute for Materials Science
+    center_name: DPFC
+    center_name_full: Materials Data Platform Center
+    division_name: MaDIS
+    division_name_full: Research and Services Division of Materials Data and Integrated System 
     product_name: MDR
     product_twitter_handle: "@nims_library"
     works:

From 7625c0f284388d7d8112fad0ad3deb5826782e1d Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 29 May 2020 15:26:44 +0900
Subject: [PATCH 205/258] Fix footer height and its left-right balance

---
 hyrax/app/assets/stylesheets/theme.scss | 3 +++
 hyrax/app/views/shared/_footer.html.erb | 6 +++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/hyrax/app/assets/stylesheets/theme.scss b/hyrax/app/assets/stylesheets/theme.scss
index 8c2ce2d4..cbd21f37 100644
--- a/hyrax/app/assets/stylesheets/theme.scss
+++ b/hyrax/app/assets/stylesheets/theme.scss
@@ -12,6 +12,9 @@
   font-style: normal;
 }
 
+//------------ Variables ---------------
+$footer-height: 200px;
+
 //---------- colours to be used --------
 $mdr-grey: #F4F4F4;
 $mdr-black: #1E2022;
diff --git a/hyrax/app/views/shared/_footer.html.erb b/hyrax/app/views/shared/_footer.html.erb
index 54ba7025..db75e3c2 100644
--- a/hyrax/app/views/shared/_footer.html.erb
+++ b/hyrax/app/views/shared/_footer.html.erb
@@ -1,11 +1,11 @@
 <footer class="navbar navbar-inverse site-footer">
   <div class="row">
-    <div class="col-sm-6 text-left">
+    <div class="col-sm-9 text-left">
       <h2><%= t('hyrax.institution_name_full') %></h2>
-      <p><%= t('hyrax.division_name_full') %> (<%= t('hyrax.division_name') %>)<br><%= t('hyrax.center_name') %></p>
+      <p><%= t('hyrax.division_name_full') %> (<%= t('hyrax.division_name') %>)<br><%= t('hyrax.center_name_full') %></p>
       <small><%= t('hyrax.footer.copyright_html') %></small>
     </div>
-    <div class="col-sm-6 text-right">
+    <div class="col-sm-3 text-left">
       <ul class="list-unstyled">
         <li>
           <a href="/terms"><%= t('hyrax.pages.tabs.terms_page') %></a>

From 8fe19ac1601b0202de6a05ff7a0995c8221e766e Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 29 May 2020 20:49:12 +0900
Subject: [PATCH 206/258] Remove dangling comma

---
 hyrax/app/assets/stylesheets/theme.scss | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/assets/stylesheets/theme.scss b/hyrax/app/assets/stylesheets/theme.scss
index cbd21f37..7bd4d6c3 100644
--- a/hyrax/app/assets/stylesheets/theme.scss
+++ b/hyrax/app/assets/stylesheets/theme.scss
@@ -60,8 +60,8 @@ a, a:focus, a:hover, a:active {
   border-radius: 0px;
 }
 
-.btn-primary, .btn-primary:focus, .btn-primary:hover, .btn-primary:active,
- {
+.btn-primary, .btn-primary:focus, .btn-primary:hover, .btn-primary:active
+{
   background-color: $mdr-black;
   border-color: $mdr-black;
   color: $mdr-green;

From 69a224c32dfd3a73731d216ae7a77ae70eaa580f Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 29 May 2020 23:08:07 +0900
Subject: [PATCH 207/258] Import bootstrap in the file to do the same
 arithmetics as the upstream stylesheet

---
 hyrax/app/assets/stylesheets/theme.scss | 28 ++++++++++++++++++++++---
 hyrax/app/views/shared/_footer.html.erb |  2 +-
 2 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/hyrax/app/assets/stylesheets/theme.scss b/hyrax/app/assets/stylesheets/theme.scss
index 7bd4d6c3..86810b75 100644
--- a/hyrax/app/assets/stylesheets/theme.scss
+++ b/hyrax/app/assets/stylesheets/theme.scss
@@ -1,3 +1,7 @@
+@import "bootstrap-sprockets";
+@import "bootstrap-default-overrides";
+@import "bootstrap";
+
 //----------- fonts to be used ---------
 @font-face {
   font-family: "Galano Grotesque";
@@ -12,9 +16,6 @@
   font-style: normal;
 }
 
-//------------ Variables ---------------
-$footer-height: 200px;
-
 //---------- colours to be used --------
 $mdr-grey: #F4F4F4;
 $mdr-black: #1E2022;
@@ -193,10 +194,31 @@ nav.searchbar {
 }
 
 // ------------- footer ----------------
+// Some lines taken from Hyrax's _variables.scss and _footer.scss.
+// Declaring these properties in advance to use a custom footer-height value.
+$footer-top-margin: 3 * $padding-small-vertical;
+$footer-height: 170px;
+
+body {
+  margin-bottom: $footer-height + $footer-top-margin;
+}
+
 .site-footer {
   padding: 20px;
   background-color: $mdr-black;
   color: #fff;
+  position: absolute;
+  bottom: 0;
+  height: $footer-height;
+}
+
+@media (max-width: $screen-sm) {
+  body {
+    margin-bottom: 2 * $footer-height + $footer-top-margin;
+  }
+  .site-footer {
+    height: 2 * $footer-height;
+  }
 }
 
 .site-footer h2 {
diff --git a/hyrax/app/views/shared/_footer.html.erb b/hyrax/app/views/shared/_footer.html.erb
index db75e3c2..4127f879 100644
--- a/hyrax/app/views/shared/_footer.html.erb
+++ b/hyrax/app/views/shared/_footer.html.erb
@@ -1,4 +1,4 @@
-<footer class="navbar navbar-inverse site-footer">
+<footer class="site-footer">
   <div class="row">
     <div class="col-sm-9 text-left">
       <h2><%= t('hyrax.institution_name_full') %></h2>

From 55337598a0b93ca648dbb44fc1665ca042d36b0d Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Tue, 2 Jun 2020 16:37:48 +0900
Subject: [PATCH 208/258] Add links to organizational pages

---
 hyrax/app/views/shared/_footer.html.erb | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/views/shared/_footer.html.erb b/hyrax/app/views/shared/_footer.html.erb
index 4127f879..eed57bad 100644
--- a/hyrax/app/views/shared/_footer.html.erb
+++ b/hyrax/app/views/shared/_footer.html.erb
@@ -1,8 +1,14 @@
 <footer class="site-footer">
   <div class="row">
     <div class="col-sm-9 text-left">
-      <h2><%= t('hyrax.institution_name_full') %></h2>
-      <p><%= t('hyrax.division_name_full') %> (<%= t('hyrax.division_name') %>)<br><%= t('hyrax.center_name_full') %></p>
+      <h2>
+        <a href="https://www.nims.go.jp/eng/" target="_blank" rel="noopener"><%= t('hyrax.institution_name_full') %></a>
+      </h2>
+      <p>
+        <a href="https://www.nims.go.jp/eng/research/MaDIS/" target="_blank" rel="noopener"><%= t('hyrax.division_name_full') %> (<%= t('hyrax.division_name') %>)</a>
+        <br>
+        <a href="https://www.nims.go.jp/eng/research/materials-data-pf/" target="_blank" rel="noopener"><%= t('hyrax.center_name_full') %></a>
+      </p>
       <small><%= t('hyrax.footer.copyright_html') %></small>
     </div>
     <div class="col-sm-3 text-left">

From b7bae0d28148939cd3198db415253a86fce2e1e4 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Tue, 2 Jun 2020 17:52:24 +0900
Subject: [PATCH 209/258] update the order of the services

---
 hyrax/app/views/shared/_footer.html.erb | 4 ++--
 hyrax/config/locales/hyrax.en.yml       | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/hyrax/app/views/shared/_footer.html.erb b/hyrax/app/views/shared/_footer.html.erb
index eed57bad..4052531c 100644
--- a/hyrax/app/views/shared/_footer.html.erb
+++ b/hyrax/app/views/shared/_footer.html.erb
@@ -20,10 +20,10 @@
           <%= t('hyrax.footer.privacy_html') %>
         </li>
         <li>
-          <%= t('hyrax.footer.service_html') %>
+          <%= t('hyrax.footer.platform_html') %>
         </li>
         <li>
-          <%= t('hyrax.footer.platform_html') %>
+          <%= t('hyrax.footer.service_html') %>
         </li>
       </ul>
     </div>
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index 3aaef771..c76ef916 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -240,7 +240,7 @@ en:
     footer:
       copyright_html: "&copy; 2020 National Institute for Materials Science. Works are available under licenses specified on their pages."
       service_html: <a href="https://library.nims.go.jp/" target="_blank" rel="noopener">NIMS Digital Library</a>
-      platform_html: <a href="https://dice.nims.go.jp/" target="_blank" rel="noopener">DICE</a>
+      platform_html: <a href="https://dice.nims.go.jp/" target="_blank" rel="noopener">Data Platform DICE</a>
       privacy_html: <a href="https://www.nims.go.jp/eng/siteinfo/privacy-policy.html" target="_blank" rel="noopener">Privacy Policy</a>
       address_html: National Institute for Materials Science (NIMS) 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 JAPAN
     institution_name: NIMS

From 9168b21126a40d41ea2f7fb1d94097c13953e415 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Tue, 2 Jun 2020 23:55:13 +0900
Subject: [PATCH 210/258] - add setup_pub_source and setup_pub_page helper -
 display Publication#creator on the citation page

---
 .../publication_behavior.rb                   | 44 +++++++++++++++++++
 .../app/presenters/hyrax/dataset_presenter.rb |  2 +-
 .../presenters/hyrax/publication_presenter.rb |  2 +-
 hyrax/app/views/hyrax/citations/work.html.erb | 11 +++++
 .../publication_behavior_helper_spec.rb       | 12 +++++
 5 files changed, 69 insertions(+), 2 deletions(-)
 create mode 100644 hyrax/app/views/hyrax/citations/work.html.erb

diff --git a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
index ddc97214..aeb80ccd 100644
--- a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
+++ b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
@@ -66,6 +66,50 @@ def setup_pub_info(presenter, include_date = false)
         pub_info.strip!
         pub_info.blank? ? nil : pub_info
       end
+
+      def setup_pub_source(presenter)
+        return nil unless presenter.complex_source.first
+        source = JSON.parse(presenter.complex_source).first
+
+        pub_source = ''
+
+        if source['title'].present?
+          pub_source << '"'
+          pub_source << source['title'].first
+          pub_source << '." '
+        end
+
+        if source['volume'].present?
+          pub_source << source['volume'].first
+          pub_source << ', '
+        end
+
+        if source['issue'].present?
+          pub_source << 'no. '
+          pub_source << source['issue'].first
+          pub_source << '. '
+        end
+
+        if source['sequence_number'].present?
+          pub_source << source['sequence_number'].first
+          pub_source << '. '
+        end
+
+        pub_source.blank? ? nil : pub_source.strip
+      end
+
+      def setup_pub_page(presenter)
+        return nil unless presenter.complex_source.first
+        source = JSON.parse(presenter.complex_source).first
+        pub_page = ''
+
+        if source['start_page'].present? && source['end_page'].present?
+          pub_page << "#{source['start_page'].first}-#{source['end_page'].first}"
+          pub_page << '. '
+        end
+
+        pub_page.blank? ? nil : pub_page.strip
+      end
     end
   end
 end
diff --git a/hyrax/app/presenters/hyrax/dataset_presenter.rb b/hyrax/app/presenters/hyrax/dataset_presenter.rb
index f51bcaf2..76a55b8c 100644
--- a/hyrax/app/presenters/hyrax/dataset_presenter.rb
+++ b/hyrax/app/presenters/hyrax/dataset_presenter.rb
@@ -8,7 +8,7 @@ class DatasetPresenter < Hyrax::WorkShowPresenter
       :complex_instrument, :origin_system_provenance, :properties_addressed,
       :complex_relation, :specimen_set, :complex_specimen_type,
       :synthesis_and_processing, :custom_property, :first_published_url, :doi,
-      to: :solr_document
+      :creator,  to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
     prepend ::FilteredGraph
diff --git a/hyrax/app/presenters/hyrax/publication_presenter.rb b/hyrax/app/presenters/hyrax/publication_presenter.rb
index ef872aa2..8349ee76 100644
--- a/hyrax/app/presenters/hyrax/publication_presenter.rb
+++ b/hyrax/app/presenters/hyrax/publication_presenter.rb
@@ -5,7 +5,7 @@ class PublicationPresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
              :complex_rights, :complex_version, :complex_event, :issue, :place,
              :table_of_contents, :total_number_of_pages, :complex_source,
-             :first_published_url, :doi, to: :solr_document
+             :first_published_url, :doi, :creator, to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
     prepend ::FilteredGraph
diff --git a/hyrax/app/views/hyrax/citations/work.html.erb b/hyrax/app/views/hyrax/citations/work.html.erb
new file mode 100644
index 00000000..e29d3d54
--- /dev/null
+++ b/hyrax/app/views/hyrax/citations/work.html.erb
@@ -0,0 +1,11 @@
+<h4>Citation Formats</h4>
+
+<span class="citation">
+<%= @presenter.creator.join(', ') %>.
+<%= @presenter.title.first %>.
+<%= setup_pub_source(@presenter) %>
+(<%= setup_pub_date(@presenter) %>):
+<%= @presenter.doi.first %>
+</span>
+
+<br /><br />
diff --git a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
index dc3df793..5718a63e 100644
--- a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
+++ b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
@@ -60,4 +60,16 @@
   it 'has no singleton methods' do
     expect(subject.singleton_methods).to be_empty
   end
+
+  describe '#setup_pub_source' do
+    let(:publication) { build(:publication, :with_complex_source) }
+    subject { helper.setup_pub_source(presenter) }
+    it { is_expected.to eql('"Test journal." 3, no. 34. 1.2.2.') }
+  end
+
+  describe '#setup_pub_page' do
+    let(:publication) { build(:publication, :with_complex_source) }
+    subject { helper.setup_pub_page(presenter) }
+    it { is_expected.to eql('4-12.') }
+  end
 end

From d0f8a9518ded40e2a7291565ff5428b7c5bee427 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 3 Jun 2020 00:39:28 +0900
Subject: [PATCH 211/258] fixed parsing JSON

---
 .../publication_behavior.rb                   | 20 ++++++++++++-------
 hyrax/app/views/hyrax/citations/work.html.erb |  2 +-
 .../publication_behavior_helper_spec.rb       |  2 +-
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
index aeb80ccd..4b14c202 100644
--- a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
+++ b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
@@ -68,15 +68,17 @@ def setup_pub_info(presenter, include_date = false)
       end
 
       def setup_pub_source(presenter)
-        return nil unless presenter.complex_source.first
-        source = JSON.parse(presenter.complex_source).first
-
+        return if presenter.complex_source.empty?
+        cs = presenter.complex_source
+        if presenter.complex_source.is_a?(Array)
+          cs = presenter.complex_source.first
+        end
+        source = JSON.parse(cs).first
         pub_source = ''
 
         if source['title'].present?
-          pub_source << '"'
           pub_source << source['title'].first
-          pub_source << '." '
+          pub_source << '. '
         end
 
         if source['volume'].present?
@@ -99,8 +101,12 @@ def setup_pub_source(presenter)
       end
 
       def setup_pub_page(presenter)
-        return nil unless presenter.complex_source.first
-        source = JSON.parse(presenter.complex_source).first
+        return if presenter.complex_source.empty?
+        cs = presenter.complex_source
+        if presenter.complex_source.is_a?(Array)
+          cs = presenter.complex_source.first
+        end
+        source = JSON.parse(cs).first
         pub_page = ''
 
         if source['start_page'].present? && source['end_page'].present?
diff --git a/hyrax/app/views/hyrax/citations/work.html.erb b/hyrax/app/views/hyrax/citations/work.html.erb
index e29d3d54..296d16a0 100644
--- a/hyrax/app/views/hyrax/citations/work.html.erb
+++ b/hyrax/app/views/hyrax/citations/work.html.erb
@@ -2,7 +2,7 @@
 
 <span class="citation">
 <%= @presenter.creator.join(', ') %>.
-<%= @presenter.title.first %>.
+"<%= @presenter.title.first %>".
 <%= setup_pub_source(@presenter) %>
 (<%= setup_pub_date(@presenter) %>):
 <%= @presenter.doi.first %>
diff --git a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
index 5718a63e..88e6274c 100644
--- a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
+++ b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
@@ -64,7 +64,7 @@
   describe '#setup_pub_source' do
     let(:publication) { build(:publication, :with_complex_source) }
     subject { helper.setup_pub_source(presenter) }
-    it { is_expected.to eql('"Test journal." 3, no. 34. 1.2.2.') }
+    it { is_expected.to eql('Test journal. 3, no. 34. 1.2.2.') }
   end
 
   describe '#setup_pub_page' do

From 91b0516e7f41ab18eeb6295caa7ba52026b11358 Mon Sep 17 00:00:00 2001
From: Rob Kaufman <rob@notch8.com>
Date: Tue, 2 Jun 2020 22:55:35 -0700
Subject: [PATCH 212/258] update readme to include fits install instructions

---
 hyrax/README.md | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/hyrax/README.md b/hyrax/README.md
index deab187f..a665e969 100644
--- a/hyrax/README.md
+++ b/hyrax/README.md
@@ -8,6 +8,7 @@ The application contains
 Requires:
 * redis
 * Ruby 2.3 - 2.5
+* fits
 
 ### Set up ruby with `rbenv`
 1. Install `rbenv` on your system per the [installation instructions](https://github.com/rbenv/rbenv#installation)
@@ -20,6 +21,17 @@ Requires:
     RBENV_VERSION=2.5.3 gem install bundler
     ```
 
+### Characterization
+(copied with edits from https://github.com/samvera/hyrax/blob/master/README.md#characterization)
+FITS can be installed on OSX using Homebrew by running the command: `brew install fits`
+
+**OR**
+
+1. Go to http://projects.iq.harvard.edu/fits/downloads and download a copy of FITS (see above to pick a known working version) & unpack it somewhere on your machine.
+1. Mark fits.sh as executable: `chmod a+x fits.sh`
+1. Run `fits.sh -h` from the command line and see a help message to ensure FITS is properly installed
+1. Set FITS_PATH in your .env to the installed fits.sh location
+
 ### Steps to install the application 
 1.  Clone this project
 2.  To install, cd to the `hyrax/` directory and
@@ -66,4 +78,4 @@ When the app is set up, from `hyrax/`:
 for all tests, and e.g.
 
     bundle exec rspec spec/models/concerns/complex_date_spec.rb
-for tests in a specific file.
\ No newline at end of file
+for tests in a specific file.

From 3a92c29274e47f0bea4f4032fe23a7af5687106d Mon Sep 17 00:00:00 2001
From: Rob Kaufman <rob@notch8.com>
Date: Tue, 2 Jun 2020 23:47:46 -0700
Subject: [PATCH 213/258] exports controller should not count finding the
 default file as a success

---
 hyrax/app/controllers/exports_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/controllers/exports_controller.rb b/hyrax/app/controllers/exports_controller.rb
index 6ad04a92..b29ef403 100644
--- a/hyrax/app/controllers/exports_controller.rb
+++ b/hyrax/app/controllers/exports_controller.rb
@@ -5,7 +5,7 @@ class ExportsController < Hyrax::DownloadsController
   MAXIMUM_ROWS = 100
 
   def export
-    if file.present? && file.mime_type.present? && file.mime_type =~ /^(?:text|application)\/csv$/i
+    if file.present? && file != default_file && file.mime_type.present? && file.mime_type =~ /^(?:text|application)\/csv$/i
       render json: csv_as_datatable
     else
       render :json => { error: 'Unknown or unsupported file type' }, :status => :bad_request

From 9f0a9992e47f18cf930d3b6d4ad8c1a302387506 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 3 Jun 2020 16:41:03 +0900
Subject: [PATCH 214/258] add a spec file for the author list

---
 hyrax/app/views/hyrax/citations/work.html.erb |  2 +-
 .../hyrax/citations/work.html.erb_spec.rb     | 41 +++++++++++++++++++
 2 files changed, 42 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb

diff --git a/hyrax/app/views/hyrax/citations/work.html.erb b/hyrax/app/views/hyrax/citations/work.html.erb
index 296d16a0..4bacb258 100644
--- a/hyrax/app/views/hyrax/citations/work.html.erb
+++ b/hyrax/app/views/hyrax/citations/work.html.erb
@@ -1,7 +1,7 @@
 <h4>Citation Formats</h4>
 
 <span class="citation">
-<%= @presenter.creator.join(', ') %>.
+<%= @presenter.creator.first %>.
 "<%= @presenter.title.first %>".
 <%= setup_pub_source(@presenter) %>
 (<%= setup_pub_date(@presenter) %>):
diff --git a/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
new file mode 100644
index 00000000..c0a8dcb4
--- /dev/null
+++ b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
@@ -0,0 +1,41 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'hyrax/citations/work' do
+  let(:publication) { build(:publication, :open, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
+                        :with_publisher, :with_complex_date, :with_complex_identifier, :with_rights_statement, :with_complex_rights,
+                        :with_complex_version, :with_resource_type, :with_source, :with_issue, :with_complex_source, :with_complex_event,
+                        :with_place, :with_table_of_contents, :with_number_of_pages,
+                        doi: 'https://doi.org/10.5555/12345678',
+                        creator: ['Asahiko Matsuda, Kosuke Tanabe']) }
+  let(:ability) { double }
+  let(:presenter) { Hyrax::PublicationPresenter.new(SolrDocument.new(publication.to_solr), Ability.new(user), controller.request) }
+
+  before do
+    allow(controller).to receive(:current_user).and_return(user)
+    login_as user if user.present?
+    assign(:presenter, presenter)
+    render
+  end
+
+  # NB: the visibility of individual metadata components is set in app/models/ability.rb
+  # This test confirms the current expected behaviour (which is that most metadata is visible)
+
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Asahiko Matsuda, Kosuke Tanabe.')
+      expect(rendered).to have_content("\"Open Publication\".\nTest journal. 3, no. 34. 1.2.2.\n(0528):")
+      expect(rendered).to have_content('https://doi.org/10.5555/12345678')
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { create(:user, :nims_researcher) }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Asahiko Matsuda, Kosuke Tanabe.')
+      expect(rendered).to have_content("\"Open Publication\".\nTest journal. 3, no. 34. 1.2.2.\n(0528):")
+      expect(rendered).to have_content('https://doi.org/10.5555/12345678')
+    end
+  end
+end

From 4d42be5faab9781d85882b7b3c5d197170e13e52 Mon Sep 17 00:00:00 2001
From: Rob Kaufman <rob@notch8.com>
Date: Wed, 3 Jun 2020 00:45:00 -0700
Subject: [PATCH 215/258] fix export spec to deal with change to file set
 factory

---
 hyrax/app/controllers/exports_controller.rb             | 2 +-
 hyrax/spec/controllers/hyrax/exports_controller_spec.rb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/controllers/exports_controller.rb b/hyrax/app/controllers/exports_controller.rb
index b29ef403..6ad04a92 100644
--- a/hyrax/app/controllers/exports_controller.rb
+++ b/hyrax/app/controllers/exports_controller.rb
@@ -5,7 +5,7 @@ class ExportsController < Hyrax::DownloadsController
   MAXIMUM_ROWS = 100
 
   def export
-    if file.present? && file != default_file && file.mime_type.present? && file.mime_type =~ /^(?:text|application)\/csv$/i
+    if file.present? && file.mime_type.present? && file.mime_type =~ /^(?:text|application)\/csv$/i
       render json: csv_as_datatable
     else
       render :json => { error: 'Unknown or unsupported file type' }, :status => :bad_request
diff --git a/hyrax/spec/controllers/hyrax/exports_controller_spec.rb b/hyrax/spec/controllers/hyrax/exports_controller_spec.rb
index 9000f2fd..4e91a191 100644
--- a/hyrax/spec/controllers/hyrax/exports_controller_spec.rb
+++ b/hyrax/spec/controllers/hyrax/exports_controller_spec.rb
@@ -10,7 +10,7 @@
     let(:json) { JSON.parse(response.body) }
 
     context 'no file' do
-      let(:file_set) { create(:file_set, :open) }
+      let(:file_set) { create(:file_set, :open, content: nil) }
       it 'should return an error' do
         expect(status).to eql(400)
         expect(json['error']).to eql('Unknown or unsupported file type')

From c2b460cab4dbbcd429d9fefa33e0e4d1548e9f08 Mon Sep 17 00:00:00 2001
From: Rob Kaufman <rob@notch8.com>
Date: Wed, 3 Jun 2020 01:01:07 -0700
Subject: [PATCH 216/258] all the current updates before rack

---
 hyrax/Gemfile.lock | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index d6335133..489d2af2 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -482,18 +482,18 @@ GEM
     json-schema (2.8.1)
       addressable (>= 2.4)
     jwt (2.2.1)
-    kaminari (1.1.1)
+    kaminari (1.2.1)
       activesupport (>= 4.1.0)
-      kaminari-actionview (= 1.1.1)
-      kaminari-activerecord (= 1.1.1)
-      kaminari-core (= 1.1.1)
-    kaminari-actionview (1.1.1)
+      kaminari-actionview (= 1.2.1)
+      kaminari-activerecord (= 1.2.1)
+      kaminari-core (= 1.2.1)
+    kaminari-actionview (1.2.1)
       actionview
-      kaminari-core (= 1.1.1)
-    kaminari-activerecord (1.1.1)
+      kaminari-core (= 1.2.1)
+    kaminari-activerecord (1.2.1)
       activerecord
-      kaminari-core (= 1.1.1)
-    kaminari-core (1.1.1)
+      kaminari-core (= 1.2.1)
+    kaminari-core (1.2.1)
     kaminari_route_prefix (0.1.1)
       kaminari (~> 1.0)
     launchy (2.4.3)
@@ -546,7 +546,7 @@ GEM
     listen (3.0.8)
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
-    loofah (2.3.1)
+    loofah (2.5.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     mail (2.7.1)
@@ -562,7 +562,7 @@ GEM
     mini_magick (4.9.5)
     mini_mime (1.0.2)
     mini_portile2 (2.4.0)
-    minitest (5.13.0)
+    minitest (5.14.0)
     multi_json (1.14.1)
     multi_test (0.1.2)
     multi_xml (0.6.0)
@@ -578,7 +578,7 @@ GEM
     noid-rails (3.0.1)
       actionpack (>= 5.0.0, < 6)
       noid (~> 0.9)
-    nokogiri (1.10.4)
+    nokogiri (1.10.9)
       mini_portile2 (~> 2.4.0)
     nokogumbo (1.5.0)
       nokogiri
@@ -605,7 +605,7 @@ GEM
       method_source (~> 0.9.0)
     public_suffix (4.0.1)
     pul_uv_rails (2.0.1)
-    puma (3.12.2)
+    puma (3.12.4)
     qa (2.2.0)
       activerecord-import
       deprecation
@@ -864,7 +864,7 @@ GEM
       railties (>= 3.1)
     typhoeus (1.3.1)
       ethon (>= 0.9.0)
-    tzinfo (1.2.5)
+    tzinfo (1.2.7)
       thread_safe (~> 0.1)
     uber (0.1.0)
     uglifier (4.1.20)

From 83701760979df34317646fc074a30a35f421d0e9 Mon Sep 17 00:00:00 2001
From: Rob Kaufman <rob@notch8.com>
Date: Wed, 3 Jun 2020 01:07:31 -0700
Subject: [PATCH 217/258] bump rack, no oai issues detected

---
 docker-compose.override.yml |  9 +++++++++
 hyrax/Gemfile.lock          |  2 +-
 hyrax/config/blacklight.yml |  2 +-
 hyrax/config/fedora.yml     |  4 ++--
 hyrax/config/ldap.yml       | 14 +++++++-------
 hyrax/config/solr.yml       |  2 +-
 6 files changed, 21 insertions(+), 12 deletions(-)

diff --git a/docker-compose.override.yml b/docker-compose.override.yml
index 4edb97b8..96ae00e2 100644
--- a/docker-compose.override.yml
+++ b/docker-compose.override.yml
@@ -12,6 +12,7 @@ volumes:
   file_uploads:
   derivatives:
   cache:
+  brand:
   fcrepo:
   redis:
 
@@ -32,6 +33,8 @@ services:
       - file_uploads:${UPLOADS_PATH}
       - derivatives:${DERIVATIVES_PATH}
       - cache:${CACHE_PATH}
+      - brand:${BRAND_PATH}
+      - ./hyrax:/data
       - ${HOST_APP_DATA_PATH:-/srv/ngdr/data/}:/data/data
 
   web:
@@ -39,6 +42,12 @@ services:
       - 3000:3000
     depends_on:
       - cas
+    volumes:
+      - file_uploads:${UPLOADS_PATH}
+      - derivatives:${DERIVATIVES_PATH}
+      - cache:${CACHE_PATH}
+      - brand:${BRAND_PATH}
+      - ./hyrax:/data
     environment:
       - RAILS_FORCE_SSL=false
     networks:
diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index 489d2af2..817368a3 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -613,7 +613,7 @@ GEM
       nokogiri (~> 1.6)
       rails (~> 5.0)
       rdf
-    rack (2.0.7)
+    rack (2.0.8)
     rack-protection (2.0.5)
       rack
     rack-test (1.1.0)
diff --git a/hyrax/config/blacklight.yml b/hyrax/config/blacklight.yml
index 5357d8fb..b991dca8 100644
--- a/hyrax/config/blacklight.yml
+++ b/hyrax/config/blacklight.yml
@@ -2,7 +2,7 @@
 
 development:
   adapter: solr
-  url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_PORT'] || '8983' %>/solr/hydra-development
+  url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_PORT'] || '8983' %>/solr/hyrax_production
 test: &test
   adapter: solr
   url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_TEST_PORT'] || '8985' %>/solr/hydra-test
diff --git a/hyrax/config/fedora.yml b/hyrax/config/fedora.yml
index bdebde7c..44988f4f 100644
--- a/hyrax/config/fedora.yml
+++ b/hyrax/config/fedora.yml
@@ -1,12 +1,12 @@
 development:
   user: fedoraAdmin
   password: fedoraAdmin
-  url: <%= ENV['FEDORA_URL_SCHEME'] || 'http' %>://<%= ENV['FEDORA_HOST'] || 'localhost' %>:<%= ENV['FCREPO_DEVELOPMENT_PORT'] || 8984 %>/rest
+  url: <%= ENV['FEDORA_URL_SCHEME'] || 'http' %>://<%= ENV['FEDORA_HOST'] || 'localhost' %>:<%= ENV['FEDORA_PORT'] || 8080 %>/fcrepo/rest
   base_path: /dev
 test:
   user: fedoraAdmin
   password: fedoraAdmin
-  url: <%= ENV['FEDORA_URL_SCHEME'] || 'http' %>://<%= ENV['FEDORA_HOST'] || 'localhost' %>:<%= ENV['FEDORA_TEST_PORT'] || 8986 %>/rest
+  url: <%= ENV['FEDORA_URL_SCHEME'] || 'http' %>://<%= ENV['FEDORA_HOST'] || 'localhost' %>:<%= ENV['FEDORA_PORT'] || 8080 %>/fcrepo/rest
   base_path: /test
 production:
   user: fedoraAdmin
diff --git a/hyrax/config/ldap.yml b/hyrax/config/ldap.yml
index 1397d88d..d470bcc4 100644
--- a/hyrax/config/ldap.yml
+++ b/hyrax/config/ldap.yml
@@ -28,13 +28,13 @@ authorizations: &AUTHORIZATIONS
 ## Environment
 
 development:
-  host: localhost
-  port: 389
-  attribute: cn
-  base: ou=people,dc=test,dc=com
-  admin_user: cn=admin,dc=test,dc=com
-  admin_password: admin_password
-  ssl: false
+  host: <%= ENV['LDAP_HOST'] %>
+  port: <%= ENV['LDAP_PORT'] %>
+  attribute: <%= ENV['LDAP_ATTRIBUTE'] %>
+  base: <%= ENV['LDAP_BASE'] %>
+  admin_user: <%= ENV['LDAP_ADMIN_USER'] %>
+  admin_password: <%= ENV['LDAP_ADMIN_PASSWORD'] %>
+  ssl: <%= ENV['LDAP_SSL'] %>
   # <<: *AUTHORIZATIONS
 
 test:
diff --git a/hyrax/config/solr.yml b/hyrax/config/solr.yml
index f0b152cb..8d26c597 100644
--- a/hyrax/config/solr.yml
+++ b/hyrax/config/solr.yml
@@ -1,7 +1,7 @@
 # NB: the URLs in this file should match those in blacklight.yml
 
 development:
-  url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_PORT'] || '8983' %>/solr/hydra-development
+  url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_PORT'] || '8983' %>/solr/hyrax_production
 test:
   url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_TEST_PORT'] || '8985' %>/solr/hydra-test
 production:

From 6e3442e8c064d4b6f467c51dd9d8f482e7a14f90 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Thu, 4 Jun 2020 17:23:18 +0900
Subject: [PATCH 218/258] Copy from samvera/hyrax 2.x-stable

---
 .../concerns/hyrax/solr_document/export.rb    | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 hyrax/app/models/concerns/hyrax/solr_document/export.rb

diff --git a/hyrax/app/models/concerns/hyrax/solr_document/export.rb b/hyrax/app/models/concerns/hyrax/solr_document/export.rb
new file mode 100644
index 00000000..5e9e0e51
--- /dev/null
+++ b/hyrax/app/models/concerns/hyrax/solr_document/export.rb
@@ -0,0 +1,58 @@
+module Hyrax
+  module SolrDocument
+    module Export
+      # MIME: 'application/x-endnote-refer'
+      def export_as_endnote
+        text = []
+        text << "%0 #{human_readable_type}"
+        end_note_format.each do |endnote_key, mapping|
+          if mapping.is_a? String
+            values = [mapping]
+          else
+            values = send(mapping[0]) if respond_to? mapping[0]
+            values = mapping[1].call(values) if mapping.length == 2
+            values = Array.wrap(values)
+          end
+          next if values.blank? || values.first.nil?
+          spaced_values = values.join("; ")
+          text << "#{endnote_key} #{spaced_values}"
+        end
+        text.join("\n")
+      end
+
+      # Name of the downloaded endnote file
+      # Override this if you want to use a different name
+      def endnote_filename
+        "#{id}.endnote"
+      end
+
+      def persistent_url
+        "#{Hyrax.config.persistent_hostpath}#{id}"
+      end
+
+      def end_note_format
+        {
+          '%T' => [:title],
+          # '%Q' => [:title, ->(x) { x.drop(1) }], # subtitles
+          '%A' => [:creator],
+          '%C' => [:publication_place],
+          '%D' => [:date_created],
+          '%8' => [:date_uploaded],
+          '%E' => [:contributor],
+          '%I' => [:publisher],
+          '%J' => [:series_title],
+          '%@' => [:isbn],
+          '%U' => [:related_url],
+          '%7' => [:edition_statement],
+          '%R' => [:persistent_url],
+          '%X' => [:description],
+          '%G' => [:language],
+          '%[' => [:date_modified],
+          '%9' => [:resource_type],
+          '%~' => I18n.t('hyrax.product_name'),
+          '%W' => Institution.name
+        }
+      end
+    end
+  end
+end
\ No newline at end of file

From 497a852bd87814b9d12e5ba7d00e740cb99c3b33 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Thu, 4 Jun 2020 19:35:06 +0900
Subject: [PATCH 219/258] Re-map EndNote metadata; Change label for Citation
 dropdown

---
 .../app/models/concerns/hyrax/solr_document/export.rb  | 10 ++++++----
 hyrax/config/locales/hyrax.en.yml                      |  3 +++
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/hyrax/app/models/concerns/hyrax/solr_document/export.rb b/hyrax/app/models/concerns/hyrax/solr_document/export.rb
index 5e9e0e51..2828e523 100644
--- a/hyrax/app/models/concerns/hyrax/solr_document/export.rb
+++ b/hyrax/app/models/concerns/hyrax/solr_document/export.rb
@@ -42,15 +42,17 @@ def end_note_format
           '%I' => [:publisher],
           '%J' => [:series_title],
           '%@' => [:isbn],
-          '%U' => [:related_url],
+          '%U' => [:persistent_url],
           '%7' => [:edition_statement],
-          '%R' => [:persistent_url],
+          '%R' => [:doi],
+          '%(' => [:first_published_url],
           '%X' => [:description],
           '%G' => [:language],
           '%[' => [:date_modified],
           '%9' => [:resource_type],
-          '%~' => I18n.t('hyrax.product_name'),
-          '%W' => Institution.name
+          '%K' => [:keyword],
+          '%~' => I18n.t('hyrax.product_name_full'),
+          '%W' => Institution.name_full
         }
       end
     end
diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index c76ef916..028c0b9c 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -234,6 +234,9 @@ en:
           title_tesim: Title
   hyrax:
     account_name: My Institution Account Id
+    base:
+      citations:
+        header: 'Export:'
     directory:
       suffix: "@example.org"
     download_all: Download All Files (Zip)

From f95d93ca584cc1a82481eccf2b8d99692132744e Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 5 Jun 2020 13:34:28 +0900
Subject: [PATCH 220/258] Copy from samvera/hyrax 2.x-stable

---
 hyrax/app/views/hyrax/base/_citations.html.erb | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/base/_citations.html.erb

diff --git a/hyrax/app/views/hyrax/base/_citations.html.erb b/hyrax/app/views/hyrax/base/_citations.html.erb
new file mode 100644
index 00000000..ad75024f
--- /dev/null
+++ b/hyrax/app/views/hyrax/base/_citations.html.erb
@@ -0,0 +1,15 @@
+<div class="citations">
+    <% if Hyrax.config.citations? %>
+      <%= link_to t(".citations"), hyrax.citations_work_path(presenter), id: 'citations', class: 'btn btn-default' %>
+    <% end %>
+    <div class="btn-group">
+      <button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+        <%= t('.header') %> <span class="caret"></span>
+      </button>
+      <ul class="dropdown-menu">
+        <li><%= link_to t('.endnote'), polymorphic_path([main_app, presenter], format: 'endnote') %></li>
+        <li><%= link_to t('.zotero'), hyrax.zotero_path, id: 'zoteroLink', name: 'zotero' %></li>
+        <li><%= link_to t('.mendeley'), hyrax.mendeley_path, id: 'mendeleyLink', name: 'mendeley' %></li>
+      </ul>
+    </div>
+</div>

From f14acb207c747fff3e2523c1f823543226c560e9 Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 5 Jun 2020 13:57:44 +0900
Subject: [PATCH 221/258] Temporarily hide Zotero and Mendeley links

---
 hyrax/app/views/hyrax/base/_citations.html.erb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/hyrax/app/views/hyrax/base/_citations.html.erb b/hyrax/app/views/hyrax/base/_citations.html.erb
index ad75024f..46984732 100644
--- a/hyrax/app/views/hyrax/base/_citations.html.erb
+++ b/hyrax/app/views/hyrax/base/_citations.html.erb
@@ -8,8 +8,10 @@
       </button>
       <ul class="dropdown-menu">
         <li><%= link_to t('.endnote'), polymorphic_path([main_app, presenter], format: 'endnote') %></li>
+        <% =begin %>
         <li><%= link_to t('.zotero'), hyrax.zotero_path, id: 'zoteroLink', name: 'zotero' %></li>
         <li><%= link_to t('.mendeley'), hyrax.mendeley_path, id: 'mendeleyLink', name: 'mendeley' %></li>
+        <% =end %>
       </ul>
     </div>
 </div>

From 2e1865362f475a663192dbed8564ab70dcbb988e Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 5 Jun 2020 22:06:56 +0900
Subject: [PATCH 222/258] =begin and =end must be at the beginning of lines

---
 hyrax/app/views/hyrax/base/_citations.html.erb | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/views/hyrax/base/_citations.html.erb b/hyrax/app/views/hyrax/base/_citations.html.erb
index 46984732..eef6c07c 100644
--- a/hyrax/app/views/hyrax/base/_citations.html.erb
+++ b/hyrax/app/views/hyrax/base/_citations.html.erb
@@ -8,10 +8,14 @@
       </button>
       <ul class="dropdown-menu">
         <li><%= link_to t('.endnote'), polymorphic_path([main_app, presenter], format: 'endnote') %></li>
-        <% =begin %>
+        <% 
+=begin 
+        %>
         <li><%= link_to t('.zotero'), hyrax.zotero_path, id: 'zoteroLink', name: 'zotero' %></li>
         <li><%= link_to t('.mendeley'), hyrax.mendeley_path, id: 'mendeleyLink', name: 'mendeley' %></li>
-        <% =end %>
+        <% 
+=end 
+        %>
       </ul>
     </div>
 </div>

From eba33b30996b7e937a39646d555fa904560a8c3e Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 5 Jun 2020 22:08:32 +0900
Subject: [PATCH 223/258] Rest of the locale messages on the same level are
 required

---
 hyrax/config/locales/hyrax.en.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/hyrax/config/locales/hyrax.en.yml b/hyrax/config/locales/hyrax.en.yml
index 028c0b9c..10e6d457 100644
--- a/hyrax/config/locales/hyrax.en.yml
+++ b/hyrax/config/locales/hyrax.en.yml
@@ -236,7 +236,11 @@ en:
     account_name: My Institution Account Id
     base:
       citations:
+        citations: Citations
+        endnote: EndNote
         header: 'Export:'
+        mendeley: Mendeley
+        zotero: Zotero
     directory:
       suffix: "@example.org"
     download_all: Download All Files (Zip)

From 4f7a238b2c013f130d1a19a3bb93547b20dbdacd Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 6 Jun 2020 04:10:23 +0900
Subject: [PATCH 224/258] update spec files

---
 hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb | 14 +++++++++++++-
 .../views/hyrax/datasets/_form.html.erb_spec.rb    | 12 ++++++++++++
 2 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb b/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
index 2c616751..65e125bf 100644
--- a/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
+++ b/hyrax/spec/views/hyrax/base/_form.html.erb_spec.rb
@@ -10,14 +10,26 @@
   let(:form) do
     Hyrax::PublicationForm.new(work, ability, controller)
   end
+  let(:options_presenter) { double(select_options: []) }
 
   before do
+    allow(Hyrax::AdminSetOptionsPresenter).to receive(:new).and_return(options_presenter)
+    stub_template('hyrax/base/_form_progress.html.erb' => 'Progress')
+    # TODO: stub_model is not stubbing new_record? correctly on ActiveFedora models.
+    allow(work).to receive(:new_record?).and_return(true)
+    allow(work).to receive(:member_ids).and_return([1, 2])
     allow(controller).to receive(:current_user).and_return(user)
     assign(:form, form)
+    allow(controller).to receive(:controller_name).and_return('batch_uploads')
+    allow(controller).to receive(:action_name).and_return('new')
+
+    allow(form).to receive(:permissions).and_return([])
+    allow(form).to receive(:visibility).and_return('public')
+    stub_template 'hyrax/base/_form_files.html.erb' => 'files'
   end
 
   describe 'tabs' do
-    it 'does not show the relationships tab' do
+    it 'shows the relationships tab' do
       render
       expect(rendered).to have_selector('#relationships[role="tabpanel"]')
       expect(rendered).to have_selector('#metadata[role="tabpanel"]')
diff --git a/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb b/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb
index 7ea03c2d..fa9f31e9 100644
--- a/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb
+++ b/hyrax/spec/views/hyrax/datasets/_form.html.erb_spec.rb
@@ -10,11 +10,23 @@
   let(:form) do
     Hyrax::DatasetForm.new(work, ability, controller)
   end
+  let(:options_presenter) { double(select_options: []) }
 
   before do
     view.lookup_context.prefixes += ['hyrax/base']
+    allow(Hyrax::AdminSetOptionsPresenter).to receive(:new).and_return(options_presenter)
+    stub_template('hyrax/base/_form_progress.html.erb' => 'Progress')
+    # TODO: stub_model is not stubbing new_record? correctly on ActiveFedora models.
+    allow(work).to receive(:new_record?).and_return(true)
+    allow(work).to receive(:member_ids).and_return([1, 2])
     allow(controller).to receive(:current_user).and_return(user)
     assign(:form, form)
+    allow(controller).to receive(:controller_name).and_return('batch_uploads')
+    allow(controller).to receive(:action_name).and_return('new')
+
+    allow(form).to receive(:permissions).and_return([])
+    allow(form).to receive(:visibility).and_return('public')
+    stub_template 'hyrax/base/_form_files.html.erb' => 'files'
   end
 
   describe 'tabs' do

From c01876ea27f7555db4b1e3683d1e82547080856e Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Fri, 5 Jun 2020 20:44:14 +0100
Subject: [PATCH 225/258] Changed port for rake server for fcrepo

---
 hyrax/config/fcrepo_wrapper_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/config/fcrepo_wrapper_test.yml b/hyrax/config/fcrepo_wrapper_test.yml
index 75397920..b836a23b 100644
--- a/hyrax/config/fcrepo_wrapper_test.yml
+++ b/hyrax/config/fcrepo_wrapper_test.yml
@@ -1,4 +1,4 @@
-port: 8986
+port: 8080
 verbose: false
 version: '4.7.3' # NB: ideally this should match the version in docker-compose.yml
 instance_dir: 'tmp/fcrepo4-test'

From d08a4a9968e7325e01c87cf97f073a809e187341 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Tue, 26 May 2020 21:26:24 +0900
Subject: [PATCH 226/258] fix link to complex_source_title

---
 hyrax/app/renderers/nested_source_attribute_renderer.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/hyrax/app/renderers/nested_source_attribute_renderer.rb b/hyrax/app/renderers/nested_source_attribute_renderer.rb
index 985546d8..87f84115 100644
--- a/hyrax/app/renderers/nested_source_attribute_renderer.rb
+++ b/hyrax/app/renderers/nested_source_attribute_renderer.rb
@@ -8,7 +8,8 @@ def attribute_value_to_html(input_value)
       # title
       if v.dig('title').present? and v['title'][0].present?
         label = "Title"
-        val = link_to(ERB::Util.h(v['title'][0]), search_path(v['title'][0]))
+        val = link_to(ERB::Util.h(v['title'][0]),
+          Rails.application.routes.url_helpers.search_catalog_path(:"f[complex_source_title_sim][]" => v['title'][0], locale: I18n.locale))
         each_html += get_row(label, val)
       end
       unless v.dig('alternative_title').blank?

From d27c1fd7d4211564a289e2690846d5a28e188927 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 1 Jun 2020 21:36:27 +0900
Subject: [PATCH 227/258] added feature files

---
 hyrax/features/datasets/search_links.feature  |   2 +-
 .../publications/search_links.feature         |  21 +++
 .../step_definitions/dataset_steps.rb         |   2 +-
 .../step_definitions/publication_steps.rb     | 132 ++++++++++++++++++
 hyrax/spec/factories/publication.rb           |  36 +++--
 5 files changed, 172 insertions(+), 21 deletions(-)
 create mode 100644 hyrax/features/publications/search_links.feature
 create mode 100644 hyrax/features/step_definitions/publication_steps.rb

diff --git a/hyrax/features/datasets/search_links.feature b/hyrax/features/datasets/search_links.feature
index f33cde97..3001649e 100644
--- a/hyrax/features/datasets/search_links.feature
+++ b/hyrax/features/datasets/search_links.feature
@@ -20,7 +20,7 @@ Feature: Search links on a dataset
 
   Scenario: Search links are generated correctly
     Given I am on the dataset page
-    Then I should see the following links:
+    Then I should see the following links to datasets:
       | LABEL                      | HREF                                                                                  |
       | Anamika                    | /catalog?f%5Bcomplex_person_sim%5D%5B%5D=Anamika                                      |
       | University                 | /catalog?f%5Bcomplex_person_organization_sim%5D%5B%5D=University                      |
diff --git a/hyrax/features/publications/search_links.feature b/hyrax/features/publications/search_links.feature
new file mode 100644
index 00000000..60153444
--- /dev/null
+++ b/hyrax/features/publications/search_links.feature
@@ -0,0 +1,21 @@
+Feature: Search links on a publication
+  Background:
+    Given an initialised system with a default admin set, permission template and workflow
+    And there is a publication with:
+      | TRAIT                                   |
+      | open                                    |
+      | with_complex_author                     |
+      | with_complex_date                       |
+      | with_complex_identifier                 |
+      | with_complex_rights                     |
+      | with_complex_version                    |
+      | with_complex_source                     |
+
+
+  Scenario: Search links are generated correctly
+    Given I am on the publication page
+    Then I should see the following links to publications:
+      | LABEL                      | HREF                                                                                  |
+      | Anamika                    | /catalog?f%5Bcomplex_person_sim%5D%5B%5D=Anamika                                      |
+      | University                 | /catalog?f%5Bcomplex_person_organization_sim%5D%5B%5D=University                      |
+      | Test journal               | /catalog?f%5Bcomplex_source_title_sim%5D%5B%5D=Test+journal                           |
diff --git a/hyrax/features/step_definitions/dataset_steps.rb b/hyrax/features/step_definitions/dataset_steps.rb
index e375ebf5..3d2d0b07 100644
--- a/hyrax/features/step_definitions/dataset_steps.rb
+++ b/hyrax/features/step_definitions/dataset_steps.rb
@@ -125,7 +125,7 @@
   end
 end
 
-Then(/^I should see the following links:$/) do |table|
+Then(/^I should see the following links to datasets:$/) do |table|
   table.symbolic_hashes.each do |row|
     expect(page).to have_link(row[:label], href: Regexp.new(Regexp.quote(row[:href])))
   end
diff --git a/hyrax/features/step_definitions/publication_steps.rb b/hyrax/features/step_definitions/publication_steps.rb
new file mode 100644
index 00000000..4b1065dd
--- /dev/null
+++ b/hyrax/features/step_definitions/publication_steps.rb
@@ -0,0 +1,132 @@
+Given(/^there (?:are|is) (\d+) (open|authenticated|embargo|lease|restricted) publications?$/) do |number, access|
+  @publications ||= {}
+  @publications[access] = FactoryBot.create_list(:publication, number, access.to_sym, :with_source).each do |obj|
+    ActiveFedora::SolrService.add(obj.to_solr)
+  end
+  ActiveFedora::SolrService.commit
+end
+
+Given(/^there is a publication with:$/) do |table|
+  @publication = FactoryBot.create(:publication, *table.rows.flatten.map(&:to_sym))
+  ActiveFedora::SolrService.add(@publication.to_solr)
+  ActiveFedora::SolrService.commit
+end
+
+Given(/^I am on the publication page$/) do
+  visit hyrax_publication_path(@publication)
+end
+
+When(/^I navigate to the new publication page$/) do
+  visit hyrax.dashboard_path  # /dashboard
+  click_link "Works"
+  click_link "Add new work"
+
+  # If you generate more than one work uncomment these lines
+  choose "payload_concern", option: "Publication"
+  click_button "Create work"
+
+  # small hack to skip to create publication page without requiring javascript
+  visit new_hyrax_publication_path
+end
+
+When /^I try to navigate to the new publication page$/ do
+  visit new_hyrax_publication_path
+end
+
+When(/^I navigate to the publication catalog page$/) do
+  visit root_path
+  click_link 'Browse all publications'
+  # visit search_catalog_path('f[human_readable_type_sim][]' => 'Publication')
+end
+
+When(/^I create the publication with:$/) do |table|
+  values = table.hashes.first # table is a table.hashes.keys # => [:TITLE, :SUPERVISOR, :DATA_ORIGIN, :CREATOR, :KEYWORD]
+
+  expect(page).to have_content /Add New Publication/i
+
+  click_link "Files" # switch tab
+  expect(page).to have_content /Add files/i
+  expect(page).to have_content /Add folder/i
+  within('span#addfiles') do
+    attach_file("files[]", "#{Hyrax::Engine.root}/spec/fixtures/image.jp2", visible: false)
+    attach_file("files[]", "#{Hyrax::Engine.root}/spec/fixtures/jp2_fits.xml", visible: false)
+  end
+
+  click_link "Descriptions" # switch tab
+  fill_in('Title', with: values[:TITLE])
+  fill_in('Supervisor', with: values[:SUPERVISOR])
+  select(values[:DATA_ORIGIN], from: 'Data origin')
+  fill_in('publication[complex_person_attributes][0][name][]', with: values[:CREATOR])
+  fill_in('Keyword', with: values[:KEYWORD])
+  select('Creative Commons BY-SA Attribution-ShareAlike 4.0 International', from: 'publication[complex_rights_attributes][0][rights][]')
+
+  # With selenium and the chrome driver, focus remains on the
+  # select box. Click outside the box so the next line can't find
+  # its element
+  find('body').click
+  choose('publication_visibility_open')
+  expect(page).to have_content('Please note, making something visible to the world (i.e. marking this as Public) may be viewed as publishing which could impact your ability to')
+  check('agreement')
+
+  click_on('Save')
+
+  expect(page).to have_content(values[:TITLE])
+end
+
+Then(/^I should see the (open|authenticated|embargo|lease|restricted) publications?$/) do |access|
+  # first, verify @publications is present and has some data
+  expect(@publications[access]).to be_present
+
+  # next, verify there is a link to each publication (using a regular expression to allow for the locale parameter)
+  @publications[access].each do |publication|
+    expect(page).to have_link(publication.title.first, href: Regexp.new(hyrax_publication_path(publication)))
+  end
+end
+
+Then(/^I should not see the (open|authenticated|embargo|lease|restricted) publications?$/) do |access|
+  # first, verify @publications is present and has some data
+  expect(@publications[access]).to be_present
+
+  # next, verify there is a link to each publication (using a regular expression to allow for the locale parameter)
+  @publications[access].each do |publication|
+    expect(page).to_not have_link(publication.title.first, href: Regexp.new(hyrax_publication_path(publication)))
+  end
+end
+
+Then(/^I should see only the public metadata of the (open|authenticated|embargo|lease|restricted) publications?$/) do |access|
+  # first, verify @publications is present and has some data
+  expect(@publications[access]).to be_present
+
+  @publications[access].each do |publication|
+    # check public metadata is visible
+    [:subject, :keyword].each do |field|
+      expect(page).to have_css('div.metadata dl dt', text: Regexp.new(field.to_s, Regexp::IGNORECASE))
+      expect(page).to have_css('div.metadata dl dd', text: publication.send(field).first)
+    end
+
+    # check restricted metadata is not visible
+    [:description].each do |field|
+      expect(page).not_to have_css('div.metadata dl dt', text: Regexp.new(field.to_s, Regexp::IGNORECASE))
+      expect(page).not_to have_css('div.metadata dl dd', text: publication.send(field).first)
+    end
+  end
+end
+
+Then(/^I should see both the public and restricted metadata of the (open|authenticated|embargo|lease|restricted) publications?$/) do |access|
+  # first, verify @publications is present and has some data
+  expect(@publications[access]).to be_present
+
+  @publications[access].each do |publication|
+    # check public and restricted metadata is visible
+    [:description, :subject, :keyword].each do |field|
+      expect(page).to have_css('div.metadata dl dt', text: Regexp.new(field.to_s, Regexp::IGNORECASE))
+      expect(page).to have_css('div.metadata dl dd', text: publication.send(field).first)
+    end
+  end
+end
+
+Then(/^I should see the following links to publications:$/) do |table|
+  table.symbolic_hashes.each do |row|
+    expect(page).to have_link(row[:label], href: Regexp.new(Regexp.quote(row[:href])))
+  end
+end
diff --git a/hyrax/spec/factories/publication.rb b/hyrax/spec/factories/publication.rb
index 077b5ec2..5a203712 100644
--- a/hyrax/spec/factories/publication.rb
+++ b/hyrax/spec/factories/publication.rb
@@ -9,26 +9,24 @@
       title { ["Open Publication"] }
     end
 
-    trait :with_people do
+    trait :with_complex_author do
       complex_person_attributes {
-        [
-          {
-              first_name: ['Foo'],
-              last_name: 'Bar',
-              role: "author"
-          }, {
-              name: 'Big Baz',
-              role: "editor"
-          }, {
-              name: 'Small Buz',
-              role: "author"
-          }, {
-              first_name: ['Moo'],
-              last_name: 'Milk',
-              name: 'Moo Milk',
-              role: "data depositor"
-          }
-        ]
+        [{
+         name: 'Anamika',
+         role: ['author'],
+          complex_identifier_attributes: [{
+             identifier: '123456',
+             scheme: 'identifier local'
+           }],
+         complex_affiliation_attributes: [{
+           job_title: 'Principal Investigator',
+           complex_organization_attributes: [{
+             organization: 'University',
+             sub_organization: 'Department',
+             purpose: 'Research'
+           }]
+         }]
+       }]
       }
     end
 

From ba06ce3292f9d7ee56dc5a86c6401121b6a7f313 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Fri, 5 Jun 2020 22:31:43 +0100
Subject: [PATCH 228/258] Revert "Changed port for rake server for fcrepo"

This reverts commit c01876ea
---
 hyrax/config/fcrepo_wrapper_test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/config/fcrepo_wrapper_test.yml b/hyrax/config/fcrepo_wrapper_test.yml
index b836a23b..75397920 100644
--- a/hyrax/config/fcrepo_wrapper_test.yml
+++ b/hyrax/config/fcrepo_wrapper_test.yml
@@ -1,4 +1,4 @@
-port: 8080
+port: 8986
 verbose: false
 version: '4.7.3' # NB: ideally this should match the version in docker-compose.yml
 instance_dir: 'tmp/fcrepo4-test'

From dd09513f5c9080454b81ca541bc7fcee42774026 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Fri, 5 Jun 2020 22:49:46 +0100
Subject: [PATCH 229/258] Partial revert of environment changes to cheer up the
 test suite. I'm not sure why, as most of them looked good.

---
 hyrax/config/blacklight.yml |  2 +-
 hyrax/config/fedora.yml     |  4 ++--
 hyrax/config/ldap.yml       | 14 +++++++-------
 hyrax/config/solr.yml       |  2 +-
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/hyrax/config/blacklight.yml b/hyrax/config/blacklight.yml
index b991dca8..5357d8fb 100644
--- a/hyrax/config/blacklight.yml
+++ b/hyrax/config/blacklight.yml
@@ -2,7 +2,7 @@
 
 development:
   adapter: solr
-  url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_PORT'] || '8983' %>/solr/hyrax_production
+  url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_PORT'] || '8983' %>/solr/hydra-development
 test: &test
   adapter: solr
   url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_TEST_PORT'] || '8985' %>/solr/hydra-test
diff --git a/hyrax/config/fedora.yml b/hyrax/config/fedora.yml
index 44988f4f..bdebde7c 100644
--- a/hyrax/config/fedora.yml
+++ b/hyrax/config/fedora.yml
@@ -1,12 +1,12 @@
 development:
   user: fedoraAdmin
   password: fedoraAdmin
-  url: <%= ENV['FEDORA_URL_SCHEME'] || 'http' %>://<%= ENV['FEDORA_HOST'] || 'localhost' %>:<%= ENV['FEDORA_PORT'] || 8080 %>/fcrepo/rest
+  url: <%= ENV['FEDORA_URL_SCHEME'] || 'http' %>://<%= ENV['FEDORA_HOST'] || 'localhost' %>:<%= ENV['FCREPO_DEVELOPMENT_PORT'] || 8984 %>/rest
   base_path: /dev
 test:
   user: fedoraAdmin
   password: fedoraAdmin
-  url: <%= ENV['FEDORA_URL_SCHEME'] || 'http' %>://<%= ENV['FEDORA_HOST'] || 'localhost' %>:<%= ENV['FEDORA_PORT'] || 8080 %>/fcrepo/rest
+  url: <%= ENV['FEDORA_URL_SCHEME'] || 'http' %>://<%= ENV['FEDORA_HOST'] || 'localhost' %>:<%= ENV['FEDORA_TEST_PORT'] || 8986 %>/rest
   base_path: /test
 production:
   user: fedoraAdmin
diff --git a/hyrax/config/ldap.yml b/hyrax/config/ldap.yml
index d470bcc4..1397d88d 100644
--- a/hyrax/config/ldap.yml
+++ b/hyrax/config/ldap.yml
@@ -28,13 +28,13 @@ authorizations: &AUTHORIZATIONS
 ## Environment
 
 development:
-  host: <%= ENV['LDAP_HOST'] %>
-  port: <%= ENV['LDAP_PORT'] %>
-  attribute: <%= ENV['LDAP_ATTRIBUTE'] %>
-  base: <%= ENV['LDAP_BASE'] %>
-  admin_user: <%= ENV['LDAP_ADMIN_USER'] %>
-  admin_password: <%= ENV['LDAP_ADMIN_PASSWORD'] %>
-  ssl: <%= ENV['LDAP_SSL'] %>
+  host: localhost
+  port: 389
+  attribute: cn
+  base: ou=people,dc=test,dc=com
+  admin_user: cn=admin,dc=test,dc=com
+  admin_password: admin_password
+  ssl: false
   # <<: *AUTHORIZATIONS
 
 test:
diff --git a/hyrax/config/solr.yml b/hyrax/config/solr.yml
index 8d26c597..f0b152cb 100644
--- a/hyrax/config/solr.yml
+++ b/hyrax/config/solr.yml
@@ -1,7 +1,7 @@
 # NB: the URLs in this file should match those in blacklight.yml
 
 development:
-  url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_PORT'] || '8983' %>/solr/hyrax_production
+  url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_PORT'] || '8983' %>/solr/hydra-development
 test:
   url: <%= ENV['SOLR_URL_SCHEME'] || 'http' %>://<%= ENV['SOLR_HOST'] || '127.0.0.1' %>:<%= ENV['SOLR_TEST_PORT'] || '8985' %>/solr/hydra-test
 production:

From 1c653bb8ffc4ebdbf5e5e13bcdf5bf7276c12aba Mon Sep 17 00:00:00 2001
From: Asahiko Matsuda <689506+asahiko@users.noreply.github.com>
Date: Fri, 5 Jun 2020 16:41:39 +0900
Subject: [PATCH 230/258] Error pages with MDR-like theme but standalone

---
 hyrax/public/404.html | 284 +++++++++++++++++++++++++++++++++---------
 hyrax/public/422.html | 284 +++++++++++++++++++++++++++++++++---------
 hyrax/public/500.html | 281 ++++++++++++++++++++++++++++++++---------
 3 files changed, 673 insertions(+), 176 deletions(-)

diff --git a/hyrax/public/404.html b/hyrax/public/404.html
index 2be3af26..dd6b95b7 100644
--- a/hyrax/public/404.html
+++ b/hyrax/public/404.html
@@ -1,67 +1,233 @@
 <!DOCTYPE html>
-<html>
+<html lang="en">
 <head>
-  <title>The page you were looking for doesn't exist (404)</title>
-  <meta name="viewport" content="width=device-width,initial-scale=1">
-  <style>
-  .rails-default-error-page {
-    background-color: #EFEFEF;
-    color: #2E2F30;
-    text-align: center;
-    font-family: arial, sans-serif;
-    margin: 0;
-  }
-
-  .rails-default-error-page div.dialog {
-    width: 95%;
-    max-width: 33em;
-    margin: 4em auto 0;
-  }
-
-  .rails-default-error-page div.dialog > div {
-    border: 1px solid #CCC;
-    border-right-color: #999;
-    border-left-color: #999;
-    border-bottom-color: #BBB;
-    border-top: #B00100 solid 4px;
-    border-top-left-radius: 9px;
-    border-top-right-radius: 9px;
-    background-color: white;
-    padding: 7px 12% 0;
-    box-shadow: 0 3px 8px rgba(50, 50, 50, 0.17);
-  }
-
-  .rails-default-error-page h1 {
-    font-size: 100%;
-    color: #730E15;
-    line-height: 1.5em;
-  }
-
-  .rails-default-error-page div.dialog > p {
-    margin: 0 0 1em;
-    padding: 1em;
-    background-color: #F7F7F7;
-    border: 1px solid #CCC;
-    border-right-color: #999;
-    border-left-color: #999;
-    border-bottom-color: #999;
-    border-bottom-left-radius: 4px;
-    border-bottom-right-radius: 4px;
-    border-top-color: #DADADA;
-    color: #666;
-    box-shadow: 0 3px 8px rgba(50, 50, 50, 0.17);
-  }
-  </style>
+<meta charset="utf-8">
+<title>Error | MDR</title>
+<meta name="viewport" content="width=device-width,initial-scale=1">
+<link href="https://fonts.googleapis.com/css2?family=Montserrat:wght@300;500;700&display=swap" rel="stylesheet"> 
+
+<style>
+body {
+  font-family: 'Montserrat', sans-serif;  
+  font-size: 14px;
+  line-height: 1.428571429;
+  color: #1e2022;
+  margin: 0;
+  margin-bottom: 185px;
+  font-weight: 300;
+}
+
+strong {
+  font-weight: 700;
+}
+
+a, a:hover, a:active {
+  text-decoration: none;
+}
+header {
+  color: #afca0b;
+  background-color: #1e2022;
+  margin: 0;
+  min-height: 80px;
+}
+
+.logo {
+  width: 332px;
+  height: 50px;
+  float: left;
+  padding: 15px;
+}
+
+nav {
+  padding: 30px;
+  font-weight: 300;
+}
+header nav a { 
+  color: #dcdcdc;
+  text-decoration: none;  
+  padding: 20px;
+}
+header nav a:hover, header nav a:active {
+  color: white;
+}
+.list-unstyled {
+  list-style-type: none;
+}
+nav ul {
+  float: right;
+  margin: 0;
+}
+nav li {
+  display: block;
+  float: left;
+}
+#content-wrapper {
+  margin: auto;
+  max-width: 700px;
+  padding: 50px; 
+  font-size: 16px;
+}
+
+a {
+  color: #2e74b2;
+  font-weight: 500;
+}
+
+a:hover, a:focus {
+  color: #51791a;
+  text-decoration: underline;
+}
+
+h1 {
+  background-color: #7db928;
+  text-align: center;
+  margin: 0;
+  padding: 15px;
+  font-weight: bold;
+}
+
+.btn {
+  display: inline-block;
+  text-align: center;
+  white-space: nowrap;
+  vertical-align: middle;
+  cursor: pointer;
+  padding: 6px 12px;
+  margin: auto;
+}
+.btn-primary {
+  background-color: #1e2022;
+}
+
+.mainaction {
+  text-align: right;
+}
+
+a.btn-primary, a.btn-primary:focus, a.btn-primary:hover, a.btn-primary:active {
+  color: #afca0b;
+  text-decoration: none;
+}
+
+.site-footer {
+  margin-top: 15px;
+  padding: 20px 0;
+  background-color: #1e2022;
+  color: #ffffff;
+  position: absolute;
+  bottom: 0;
+  height: 170px;
+  width: 100%;
+  font-weight: 300;
+}
+
+.site-footer h2 {
+  margin: 0;
+  color: #fff;
+}
+
+.site-footer a,
+.site-footer a:hover,
+.site-footer a:focus {
+  color: #fff;
+}
+.row div {
+  float: left;
+}
+.col-sm-9 {
+  width: 70%;
+}
+.col-sm-9 > * {
+  padding-left: 5%;
+}
+.col-sm-3 {
+  width: 25%;
+}
+</style>
+
 </head>
 
-<body class="rails-default-error-page">
-  <!-- This file lives in public/404.html -->
-  <div class="dialog">
-    <div>
-      <h1>The page you were looking for doesn't exist.</h1>
-      <p>You may have mistyped the address or the page may have moved.</p>
+<body>
+<header>
+
+<div class="logo">
+<a href="/">
+<img alt="MDR" src="data:image/png;base64,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">
+</a>
+</div>
+
+<nav id="masthead" class="navbar navbar-inverse navbar-static-top" role="navigation">
+  <ul id="user_utility_links" class="nav navbar-nav navbar-right list-unstyled">
+    <li>
+      <a href="/">Home</a>
+    </li>
+    <li>
+      <a href="/about">About</a>
+    </li>
+    <li>
+      <a href="/help">Help</a>
+    </li>
+    <li>
+      <a href="/contact">Contact</a>
+    </li>
+  </ul>
+</nav>
+
+</header>
+
+<h1>Not Found</h1>
+
+<div id="content-wrapper" role="main">
+
+<p><strong>The page you were looking for doesn't exist.</strong></p>
+
+<p>You may have mistyped the address or the page may have moved.</p>
+
+<p>If you are lost, please refer to the <a href="/help">User's manual</a>.</p>
+
+<p>If you arrived here by following a link, please let us know:
+  <ul>
+    <li><a href="/contact">Contact form</a></li>
+    <li>Email: mdr@ml.nims.go.jp</li>
+  </ul>
+</p>
+
+<p class="mainaction">
+  <a class="btn btn-primary" href="javascript:history.back()">GO BACK</a>
+</p>
+
+</div>
+<!--/#content-wrapper-->
+
+<footer class="site-footer">
+  <div class="row">
+    <div class="col-sm-9 text-left">
+      <h2>
+        <a href="https://www.nims.go.jp/eng/" target="_blank" rel="noopener">National Institute for Materials Science</a>
+      </h2>
+      <p>
+        <a href="https://www.nims.go.jp/eng/research/MaDIS/" target="_blank" rel="noopener">Research and Services Division of Materials Data and Integrated System (MaDIS)</a>
+        <br>
+        <a href="https://www.nims.go.jp/eng/research/materials-data-pf/" target="_blank" rel="noopener">Materials Data Platform Center</a>
+      </p>
+      <small>&copy; 2020 National Institute for Materials Science.</small>
+    </div>
+    <div class="col-sm-3 text-left">
+      <ul class="list-unstyled">
+        <li>
+          <a href="/terms">Terms of Use</a>
+        </li>
+        <li>
+          <a href="https://www.nims.go.jp/eng/siteinfo/privacy-policy.html" target="_blank" rel="noopener">Privacy Policy</a>
+        </li>
+        <li>
+          <a href="https://dice.nims.go.jp/" target="_blank" rel="noopener">Data Platform DICE</a>
+        </li>
+        <li>
+          <a href="https://library.nims.go.jp/" target="_blank" rel="noopener">NIMS Digital Library</a>
+        </li>
+      </ul>
     </div>
-    <p>If you are the application owner check the logs for more information.</p>
   </div>
+</footer>
 </body>
 </html>
diff --git a/hyrax/public/422.html b/hyrax/public/422.html
index c08eac0d..837dc1c3 100644
--- a/hyrax/public/422.html
+++ b/hyrax/public/422.html
@@ -1,67 +1,233 @@
 <!DOCTYPE html>
-<html>
+<html lang="en">
 <head>
-  <title>The change you wanted was rejected (422)</title>
-  <meta name="viewport" content="width=device-width,initial-scale=1">
-  <style>
-  .rails-default-error-page {
-    background-color: #EFEFEF;
-    color: #2E2F30;
-    text-align: center;
-    font-family: arial, sans-serif;
-    margin: 0;
-  }
-
-  .rails-default-error-page div.dialog {
-    width: 95%;
-    max-width: 33em;
-    margin: 4em auto 0;
-  }
-
-  .rails-default-error-page div.dialog > div {
-    border: 1px solid #CCC;
-    border-right-color: #999;
-    border-left-color: #999;
-    border-bottom-color: #BBB;
-    border-top: #B00100 solid 4px;
-    border-top-left-radius: 9px;
-    border-top-right-radius: 9px;
-    background-color: white;
-    padding: 7px 12% 0;
-    box-shadow: 0 3px 8px rgba(50, 50, 50, 0.17);
-  }
-
-  .rails-default-error-page h1 {
-    font-size: 100%;
-    color: #730E15;
-    line-height: 1.5em;
-  }
-
-  .rails-default-error-page div.dialog > p {
-    margin: 0 0 1em;
-    padding: 1em;
-    background-color: #F7F7F7;
-    border: 1px solid #CCC;
-    border-right-color: #999;
-    border-left-color: #999;
-    border-bottom-color: #999;
-    border-bottom-left-radius: 4px;
-    border-bottom-right-radius: 4px;
-    border-top-color: #DADADA;
-    color: #666;
-    box-shadow: 0 3px 8px rgba(50, 50, 50, 0.17);
-  }
-  </style>
+<meta charset="utf-8">
+<title>Error | MDR</title>
+<meta name="viewport" content="width=device-width,initial-scale=1">
+<link href="https://fonts.googleapis.com/css2?family=Montserrat:wght@300;500;700&display=swap" rel="stylesheet"> 
+
+<style>
+body {
+  font-family: 'Montserrat', sans-serif;  
+  font-size: 14px;
+  line-height: 1.428571429;
+  color: #1e2022;
+  margin: 0;
+  margin-bottom: 185px;
+  font-weight: 300;
+}
+
+strong {
+  font-weight: 700;
+}
+
+a, a:hover, a:active {
+  text-decoration: none;
+}
+header {
+  color: #afca0b;
+  background-color: #1e2022;
+  margin: 0;
+  min-height: 80px;
+}
+
+.logo {
+  width: 332px;
+  height: 50px;
+  float: left;
+  padding: 15px;
+}
+
+nav {
+  padding: 30px;
+  font-weight: 300;
+}
+header nav a { 
+  color: #dcdcdc;
+  text-decoration: none;  
+  padding: 20px;
+}
+header nav a:hover, header nav a:active {
+  color: white;
+}
+.list-unstyled {
+  list-style-type: none;
+}
+nav ul {
+  float: right;
+  margin: 0;
+}
+nav li {
+  display: block;
+  float: left;
+}
+#content-wrapper {
+  margin: auto;
+  max-width: 700px;
+  padding: 50px; 
+  font-size: 16px;
+}
+
+a {
+  color: #2e74b2;
+  font-weight: 500;
+}
+
+a:hover, a:focus {
+  color: #51791a;
+  text-decoration: underline;
+}
+
+h1 {
+  background-color: #7db928;
+  text-align: center;
+  margin: 0;
+  padding: 15px;
+  font-weight: bold;
+}
+
+.btn {
+  display: inline-block;
+  text-align: center;
+  white-space: nowrap;
+  vertical-align: middle;
+  cursor: pointer;
+  padding: 6px 12px;
+  margin: auto;
+}
+.btn-primary {
+  background-color: #1e2022;
+}
+
+.mainaction {
+  text-align: right;
+}
+
+a.btn-primary, a.btn-primary:focus, a.btn-primary:hover, a.btn-primary:active {
+  color: #afca0b;
+  text-decoration: none;
+}
+
+.site-footer {
+  margin-top: 15px;
+  padding: 20px 0;
+  background-color: #1e2022;
+  color: #ffffff;
+  position: absolute;
+  bottom: 0;
+  height: 170px;
+  width: 100%;
+  font-weight: 300;
+}
+
+.site-footer h2 {
+  margin: 0;
+  color: #fff;
+}
+
+.site-footer a,
+.site-footer a:hover,
+.site-footer a:focus {
+  color: #fff;
+}
+.row div {
+  float: left;
+}
+.col-sm-9 {
+  width: 70%;
+}
+.col-sm-9 > * {
+  padding-left: 5%;
+}
+.col-sm-3 {
+  width: 25%;
+}
+</style>
+
 </head>
 
-<body class="rails-default-error-page">
-  <!-- This file lives in public/422.html -->
-  <div class="dialog">
-    <div>
-      <h1>The change you wanted was rejected.</h1>
-      <p>Maybe you tried to change something you didn't have access to.</p>
+<body>
+<header>
+
+<div class="logo">
+<a href="/">
+<img alt="MDR" src="data:image/png;base64,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">
+</a>
+</div>
+
+<nav id="masthead" class="navbar navbar-inverse navbar-static-top" role="navigation">
+  <ul id="user_utility_links" class="nav navbar-nav navbar-right list-unstyled">
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+      <a href="/contact">Contact</a>
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+</nav>
+
+</header>
+
+<h1>Unprocessable Entity</h1>
+
+<div id="content-wrapper" role="main">
+
+<p><strong>The change you wanted was rejected.</strong></p>
+
+<p>Maybe you tried to change something you didn't have access to.</p>
+
+<p>Information may be available in the <a href="/help">User's manual</a>.</p>
+
+<p>If the problem persists, please let us know:
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+      </h2>
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diff --git a/hyrax/public/500.html b/hyrax/public/500.html
index 78a030af..ce226583 100644
--- a/hyrax/public/500.html
+++ b/hyrax/public/500.html
@@ -1,66 +1,231 @@
 <!DOCTYPE html>
-<html>
+<html lang="en">
 <head>
-  <title>We're sorry, but something went wrong (500)</title>
-  <meta name="viewport" content="width=device-width,initial-scale=1">
-  <style>
-  .rails-default-error-page {
-    background-color: #EFEFEF;
-    color: #2E2F30;
-    text-align: center;
-    font-family: arial, sans-serif;
-    margin: 0;
-  }
-
-  .rails-default-error-page div.dialog {
-    width: 95%;
-    max-width: 33em;
-    margin: 4em auto 0;
-  }
-
-  .rails-default-error-page div.dialog > div {
-    border: 1px solid #CCC;
-    border-right-color: #999;
-    border-left-color: #999;
-    border-bottom-color: #BBB;
-    border-top: #B00100 solid 4px;
-    border-top-left-radius: 9px;
-    border-top-right-radius: 9px;
-    background-color: white;
-    padding: 7px 12% 0;
-    box-shadow: 0 3px 8px rgba(50, 50, 50, 0.17);
-  }
-
-  .rails-default-error-page h1 {
-    font-size: 100%;
-    color: #730E15;
-    line-height: 1.5em;
-  }
-
-  .rails-default-error-page div.dialog > p {
-    margin: 0 0 1em;
-    padding: 1em;
-    background-color: #F7F7F7;
-    border: 1px solid #CCC;
-    border-right-color: #999;
-    border-left-color: #999;
-    border-bottom-color: #999;
-    border-bottom-left-radius: 4px;
-    border-bottom-right-radius: 4px;
-    border-top-color: #DADADA;
-    color: #666;
-    box-shadow: 0 3px 8px rgba(50, 50, 50, 0.17);
-  }
-  </style>
+<meta charset="utf-8">
+<title>Error | MDR</title>
+<meta name="viewport" content="width=device-width,initial-scale=1">
+<link href="https://fonts.googleapis.com/css2?family=Montserrat:wght@300;500;700&display=swap" rel="stylesheet"> 
+
+<style>
+body {
+  font-family: 'Montserrat', sans-serif;  
+  font-size: 14px;
+  line-height: 1.428571429;
+  color: #1e2022;
+  margin: 0;
+  margin-bottom: 185px;
+  font-weight: 300;
+}
+
+strong {
+  font-weight: 700;
+}
+
+a, a:hover, a:active {
+  text-decoration: none;
+}
+header {
+  color: #afca0b;
+  background-color: #1e2022;
+  margin: 0;
+  min-height: 80px;
+}
+
+.logo {
+  width: 332px;
+  height: 50px;
+  float: left;
+  padding: 15px;
+}
+
+nav {
+  padding: 30px;
+  font-weight: 300;
+}
+header nav a { 
+  color: #dcdcdc;
+  text-decoration: none;  
+  padding: 20px;
+}
+header nav a:hover, header nav a:active {
+  color: white;
+}
+.list-unstyled {
+  list-style-type: none;
+}
+nav ul {
+  float: right;
+  margin: 0;
+}
+nav li {
+  display: block;
+  float: left;
+}
+#content-wrapper {
+  margin: auto;
+  max-width: 700px;
+  padding: 50px; 
+  font-size: 16px;
+}
+
+a {
+  color: #2e74b2;
+  font-weight: 500;
+}
+
+a:hover, a:focus {
+  color: #51791a;
+  text-decoration: underline;
+}
+
+h1 {
+  background-color: #7db928;
+  text-align: center;
+  margin: 0;
+  padding: 15px;
+  font-weight: bold;
+}
+
+.btn {
+  display: inline-block;
+  text-align: center;
+  white-space: nowrap;
+  vertical-align: middle;
+  cursor: pointer;
+  padding: 6px 12px;
+  margin: auto;
+}
+.btn-primary {
+  background-color: #1e2022;
+}
+
+.mainaction {
+  text-align: right;
+}
+
+a.btn-primary, a.btn-primary:focus, a.btn-primary:hover, a.btn-primary:active {
+  color: #afca0b;
+  text-decoration: none;
+}
+
+.site-footer {
+  margin-top: 15px;
+  padding: 20px 0;
+  background-color: #1e2022;
+  color: #ffffff;
+  position: absolute;
+  bottom: 0;
+  height: 170px;
+  width: 100%;
+  font-weight: 300;
+}
+
+.site-footer h2 {
+  margin: 0;
+  color: #fff;
+}
+
+.site-footer a,
+.site-footer a:hover,
+.site-footer a:focus {
+  color: #fff;
+}
+.row div {
+  float: left;
+}
+.col-sm-9 {
+  width: 70%;
+}
+.col-sm-9 > * {
+  padding-left: 5%;
+}
+.col-sm-3 {
+  width: 25%;
+}
+</style>
+
 </head>
 
-<body class="rails-default-error-page">
-  <!-- This file lives in public/500.html -->
-  <div class="dialog">
-    <div>
-      <h1>We're sorry, but something went wrong.</h1>
+<body>
+<header>
+
+<div class="logo">
+<a href="/">
+<img alt="MDR" src="data:image/png;base64,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">
+</a>
+</div>
+
+<nav id="masthead" class="navbar navbar-inverse navbar-static-top" role="navigation">
+  <ul id="user_utility_links" class="nav navbar-nav navbar-right list-unstyled">
+    <li>
+      <a href="/">Home</a>
+    </li>
+    <li>
+      <a href="/about">About</a>
+    </li>
+    <li>
+      <a href="/help">Help</a>
+    </li>
+    <li>
+      <a href="/contact">Contact</a>
+    </li>
+  </ul>
+</nav>
+
+</header>
+
+<h1>Internal Server Error</h1>
+
+<div id="content-wrapper" role="main">
+
+<p><strong>We're sorry, but something went wrong.</strong></p>
+
+<p>Information may be available in the <a href="/help">User's manual</a>.</p>
+
+<p>If the problem persists, please let us know:
+  <ul>
+    <li><a href="/contact">Contact form</a></li>
+    <li>Email: mdr@ml.nims.go.jp</li>
+  </ul>
+</p>
+
+<p class="mainaction">
+  <a class="btn btn-primary" href="javascript:history.back()">GO BACK</a>
+</p>
+
+</div>
+<!--/#content-wrapper-->
+
+<footer class="site-footer">
+  <div class="row">
+    <div class="col-sm-9 text-left">
+      <h2>
+        <a href="https://www.nims.go.jp/eng/" target="_blank" rel="noopener">National Institute for Materials Science</a>
+      </h2>
+      <p>
+        <a href="https://www.nims.go.jp/eng/research/MaDIS/" target="_blank" rel="noopener">Research and Services Division of Materials Data and Integrated System (MaDIS)</a>
+        <br>
+        <a href="https://www.nims.go.jp/eng/research/materials-data-pf/" target="_blank" rel="noopener">Materials Data Platform Center</a>
+      </p>
+      <small>&copy; 2020 National Institute for Materials Science.</small>
+    </div>
+    <div class="col-sm-3 text-left">
+      <ul class="list-unstyled">
+        <li>
+          <a href="/terms">Terms of Use</a>
+        </li>
+        <li>
+          <a href="https://www.nims.go.jp/eng/siteinfo/privacy-policy.html" target="_blank" rel="noopener">Privacy Policy</a>
+        </li>
+        <li>
+          <a href="https://dice.nims.go.jp/" target="_blank" rel="noopener">Data Platform DICE</a>
+        </li>
+        <li>
+          <a href="https://library.nims.go.jp/" target="_blank" rel="noopener">NIMS Digital Library</a>
+        </li>
+      </ul>
     </div>
-    <p>If you are the application owner check the logs for more information.</p>
   </div>
+</footer>
 </body>
 </html>

From 462c93b9731e8d79e352c02c6542d3ee61113ac7 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 6 Jun 2020 16:45:06 +0900
Subject: [PATCH 231/258] update spec files

---
 hyrax/spec/factories/publication.rb           | 42 ++++++++++++-------
 .../name_behavior_helper_spec.rb              |  2 +-
 .../publications/_attribute_rows.html_spec.rb | 10 +++--
 3 files changed, 36 insertions(+), 18 deletions(-)

diff --git a/hyrax/spec/factories/publication.rb b/hyrax/spec/factories/publication.rb
index 5a203712..a4ebd386 100644
--- a/hyrax/spec/factories/publication.rb
+++ b/hyrax/spec/factories/publication.rb
@@ -12,21 +12,35 @@
     trait :with_complex_author do
       complex_person_attributes {
         [{
-         name: 'Anamika',
-         role: ['author'],
+          name: ['Foo Bar'],
+          role: ['author'],
+          orcid: ['https://orcid.example.org/0000-1111-2222-3333'],
+          organization: ['National Institute for Materials Science'],
+          sub_organization: ['MaDIS DPFC'],
           complex_identifier_attributes: [{
-             identifier: '123456',
-             scheme: 'identifier local'
-           }],
-         complex_affiliation_attributes: [{
-           job_title: 'Principal Investigator',
-           complex_organization_attributes: [{
-             organization: 'University',
-             sub_organization: 'Department',
-             purpose: 'Research'
-           }]
-         }]
-       }]
+            identifier: '123456',
+            scheme: 'identifier local'
+          }],
+          complex_affiliation_attributes: [{
+            job_title: 'Principal Investigator',
+            complex_organization_attributes: [{
+              organization: 'University',
+              sub_organization: 'Department',
+              purpose: 'Research'
+            }]
+          }
+        ]}, {
+          name: ['Big Buz'],
+          role: ['editor'],
+        }, {
+          name: ['Small Buz'],
+          role: ['author'],
+        }, {
+          first_name: ['Moo'],
+          last_name: ['Milk'],
+          name: ['Moo Milk'],
+          role: ['data depositor']
+        }]
       }
     end
 
diff --git a/hyrax/spec/helpers/hyrax/citations_behaviors/name_behavior_helper_spec.rb b/hyrax/spec/helpers/hyrax/citations_behaviors/name_behavior_helper_spec.rb
index 77c2a0ea..0bcca87c 100644
--- a/hyrax/spec/helpers/hyrax/citations_behaviors/name_behavior_helper_spec.rb
+++ b/hyrax/spec/helpers/hyrax/citations_behaviors/name_behavior_helper_spec.rb
@@ -1,7 +1,7 @@
 require 'rails_helper'
 
 RSpec.describe Hyrax::CitationsBehaviors::NameBehavior, :type => :helper do
-  let(:publication) { build(:publication, :with_people) }
+  let(:publication) { build(:publication, :with_complex_author) }
   let(:presenter) { Hyrax::WorkPresenter.new(SolrDocument.new(publication.to_solr),  Ability.new(nil)) }
 
   describe '#author_list' do
diff --git a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
index bfe0a036..74b78be4 100644
--- a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
@@ -3,7 +3,7 @@
 
 RSpec.describe 'hyrax/publications/_attribute_rows' do
   let(:partial) { 'hyrax/publications/attribute_rows' }
-  let(:publication) { build(:publication, :open, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
+  let(:publication) { build(:publication, :open, :with_alternative_title, :with_complex_author, :with_keyword, :with_subject, :with_language,
                         :with_publisher, :with_complex_date, :with_complex_identifier, :with_rights_statement, :with_complex_rights,
                         :with_complex_version, :with_resource_type, :with_source, :with_issue, :with_complex_source, :with_complex_event,
                         :with_place, :with_table_of_contents, :with_number_of_pages) }
@@ -30,7 +30,9 @@
       expect(rendered).to have_content('Rights-Statement-123')
       expect(rendered).to have_content('28/05/2019') # NB: complex date is reformatted to dd/mm/yyyy
       expect(rendered).to have_content('10.0.1111')
-      expect(rendered).to have_content('Big Baz')
+      expect(rendered).to have_content('Foo Bar')
+      expect(rendered).to have_content('https://orcid.example.org/0000-1111-2222-3333')
+      expect(rendered).to have_content('MaDIS DPFC')
       expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
       expect(rendered).to have_content('Creating the first version')
       expect(rendered).to have_content('Event-Title-123')
@@ -55,7 +57,9 @@
       expect(rendered).to have_content('Rights-Statement-123')
       expect(rendered).to have_content('28/05/2019') # NB: complex date is reformatted to dd/mm/yyyy
       expect(rendered).to have_content('10.0.1111')
-      expect(rendered).to have_content('Big Baz')
+      expect(rendered).to have_content('Foo Bar')
+      expect(rendered).to have_content('https://orcid.example.org/0000-1111-2222-3333')
+      expect(rendered).to have_content('MaDIS DPFC')
       expect(rendered).to have_content('http://creativecommons.org/publicdomain/zero/1.0/')
       expect(rendered).to have_content('Creating the first version')
       expect(rendered).to have_content('Event-Title-123')

From 6fb25da484c5cb3929378283f26323fe2c905d27 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 6 Jun 2020 17:06:19 +0900
Subject: [PATCH 232/258] fix author name in feature files

---
 hyrax/features/publications/search_links.feature     | 2 +-
 hyrax/features/step_definitions/publication_steps.rb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/features/publications/search_links.feature b/hyrax/features/publications/search_links.feature
index 60153444..c8e04214 100644
--- a/hyrax/features/publications/search_links.feature
+++ b/hyrax/features/publications/search_links.feature
@@ -16,6 +16,6 @@ Feature: Search links on a publication
     Given I am on the publication page
     Then I should see the following links to publications:
       | LABEL                      | HREF                                                                                  |
-      | Anamika                    | /catalog?f%5Bcomplex_person_sim%5D%5B%5D=Anamika                                      |
+      | Foo Bar                    | /catalog?f%5Bcomplex_person_sim%5D%5B%5D=Foo+Bar                                      |
       | University                 | /catalog?f%5Bcomplex_person_organization_sim%5D%5B%5D=University                      |
       | Test journal               | /catalog?f%5Bcomplex_source_title_sim%5D%5B%5D=Test+journal                           |
diff --git a/hyrax/features/step_definitions/publication_steps.rb b/hyrax/features/step_definitions/publication_steps.rb
index 4b1065dd..26a2d054 100644
--- a/hyrax/features/step_definitions/publication_steps.rb
+++ b/hyrax/features/step_definitions/publication_steps.rb
@@ -1,6 +1,6 @@
 Given(/^there (?:are|is) (\d+) (open|authenticated|embargo|lease|restricted) publications?$/) do |number, access|
   @publications ||= {}
-  @publications[access] = FactoryBot.create_list(:publication, number, access.to_sym, :with_source).each do |obj|
+  @publications[access] = FactoryBot.create_list(:publication, number, access.to_sym, :with_source, :with_complex_author).each do |obj|
     ActiveFedora::SolrService.add(obj.to_solr)
   end
   ActiveFedora::SolrService.commit

From 498f60848a7cceab5fc325e10d8684f3319b21ad Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sat, 6 Jun 2020 08:12:15 +0000
Subject: [PATCH 233/258] Bump websocket-extensions from 0.1.4 to 0.1.5 in
 /hyrax

Bumps [websocket-extensions](https://github.com/faye/websocket-extensions-ruby) from 0.1.4 to 0.1.5.
- [Release notes](https://github.com/faye/websocket-extensions-ruby/releases)
- [Changelog](https://github.com/faye/websocket-extensions-ruby/blob/master/CHANGELOG.md)
- [Commits](https://github.com/faye/websocket-extensions-ruby/compare/0.1.4...0.1.5)

Signed-off-by: dependabot[bot] <support@github.com>
---
 hyrax/Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index 546e0da6..dde47dd1 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -894,7 +894,7 @@ GEM
       selenium-webdriver (>= 3.0, < 4.0)
     websocket-driver (0.6.5)
       websocket-extensions (>= 0.1.0)
-    websocket-extensions (0.1.4)
+    websocket-extensions (0.1.5)
     xml-simple (1.1.5)
     xpath (3.2.0)
       nokogiri (~> 1.8)

From 1e3b3b41bd444bc73f622763bc39435712cc16fb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sat, 6 Jun 2020 08:57:24 +0000
Subject: [PATCH 234/258] Bump puma from 3.12.2 to 3.12.6 in /hyrax

Bumps [puma](https://github.com/puma/puma) from 3.12.2 to 3.12.6.
- [Release notes](https://github.com/puma/puma/releases)
- [Changelog](https://github.com/puma/puma/blob/master/History.md)
- [Commits](https://github.com/puma/puma/commits)

Signed-off-by: dependabot[bot] <support@github.com>
---
 hyrax/Gemfile.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/Gemfile.lock b/hyrax/Gemfile.lock
index 546e0da6..1081cd02 100644
--- a/hyrax/Gemfile.lock
+++ b/hyrax/Gemfile.lock
@@ -613,7 +613,7 @@ GEM
       method_source (~> 0.9.0)
     public_suffix (4.0.1)
     pul_uv_rails (2.0.1)
-    puma (3.12.4)
+    puma (3.12.6)
     qa (2.2.0)
       activerecord-import
       deprecation

From 3c56daeec018046373b17f49455c4b86264daa28 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Tue, 2 Jun 2020 23:55:13 +0900
Subject: [PATCH 235/258] - add setup_pub_source and setup_pub_page helper -
 display Publication#creator on the citation page

---
 .../publication_behavior.rb                   | 44 +++++++++++++++++++
 .../app/presenters/hyrax/dataset_presenter.rb |  2 +-
 .../presenters/hyrax/publication_presenter.rb |  2 +-
 hyrax/app/views/hyrax/citations/work.html.erb | 11 +++++
 .../publication_behavior_helper_spec.rb       | 12 +++++
 5 files changed, 69 insertions(+), 2 deletions(-)
 create mode 100644 hyrax/app/views/hyrax/citations/work.html.erb

diff --git a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
index ddc97214..aeb80ccd 100644
--- a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
+++ b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
@@ -66,6 +66,50 @@ def setup_pub_info(presenter, include_date = false)
         pub_info.strip!
         pub_info.blank? ? nil : pub_info
       end
+
+      def setup_pub_source(presenter)
+        return nil unless presenter.complex_source.first
+        source = JSON.parse(presenter.complex_source).first
+
+        pub_source = ''
+
+        if source['title'].present?
+          pub_source << '"'
+          pub_source << source['title'].first
+          pub_source << '." '
+        end
+
+        if source['volume'].present?
+          pub_source << source['volume'].first
+          pub_source << ', '
+        end
+
+        if source['issue'].present?
+          pub_source << 'no. '
+          pub_source << source['issue'].first
+          pub_source << '. '
+        end
+
+        if source['sequence_number'].present?
+          pub_source << source['sequence_number'].first
+          pub_source << '. '
+        end
+
+        pub_source.blank? ? nil : pub_source.strip
+      end
+
+      def setup_pub_page(presenter)
+        return nil unless presenter.complex_source.first
+        source = JSON.parse(presenter.complex_source).first
+        pub_page = ''
+
+        if source['start_page'].present? && source['end_page'].present?
+          pub_page << "#{source['start_page'].first}-#{source['end_page'].first}"
+          pub_page << '. '
+        end
+
+        pub_page.blank? ? nil : pub_page.strip
+      end
     end
   end
 end
diff --git a/hyrax/app/presenters/hyrax/dataset_presenter.rb b/hyrax/app/presenters/hyrax/dataset_presenter.rb
index f51bcaf2..76a55b8c 100644
--- a/hyrax/app/presenters/hyrax/dataset_presenter.rb
+++ b/hyrax/app/presenters/hyrax/dataset_presenter.rb
@@ -8,7 +8,7 @@ class DatasetPresenter < Hyrax::WorkShowPresenter
       :complex_instrument, :origin_system_provenance, :properties_addressed,
       :complex_relation, :specimen_set, :complex_specimen_type,
       :synthesis_and_processing, :custom_property, :first_published_url, :doi,
-      to: :solr_document
+      :creator,  to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
     prepend ::FilteredGraph
diff --git a/hyrax/app/presenters/hyrax/publication_presenter.rb b/hyrax/app/presenters/hyrax/publication_presenter.rb
index ef872aa2..8349ee76 100644
--- a/hyrax/app/presenters/hyrax/publication_presenter.rb
+++ b/hyrax/app/presenters/hyrax/publication_presenter.rb
@@ -5,7 +5,7 @@ class PublicationPresenter < Hyrax::WorkShowPresenter
     delegate :alternative_title, :complex_date, :complex_identifier, :complex_person,
              :complex_rights, :complex_version, :complex_event, :issue, :place,
              :table_of_contents, :total_number_of_pages, :complex_source,
-             :first_published_url, :doi, to: :solr_document
+             :first_published_url, :doi, :creator, to: :solr_document
 
     Hyrax::MemberPresenterFactory.file_presenter_class = Hyrax::NimsFileSetPresenter
     prepend ::FilteredGraph
diff --git a/hyrax/app/views/hyrax/citations/work.html.erb b/hyrax/app/views/hyrax/citations/work.html.erb
new file mode 100644
index 00000000..e29d3d54
--- /dev/null
+++ b/hyrax/app/views/hyrax/citations/work.html.erb
@@ -0,0 +1,11 @@
+<h4>Citation Formats</h4>
+
+<span class="citation">
+<%= @presenter.creator.join(', ') %>.
+<%= @presenter.title.first %>.
+<%= setup_pub_source(@presenter) %>
+(<%= setup_pub_date(@presenter) %>):
+<%= @presenter.doi.first %>
+</span>
+
+<br /><br />
diff --git a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
index dc3df793..5718a63e 100644
--- a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
+++ b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
@@ -60,4 +60,16 @@
   it 'has no singleton methods' do
     expect(subject.singleton_methods).to be_empty
   end
+
+  describe '#setup_pub_source' do
+    let(:publication) { build(:publication, :with_complex_source) }
+    subject { helper.setup_pub_source(presenter) }
+    it { is_expected.to eql('"Test journal." 3, no. 34. 1.2.2.') }
+  end
+
+  describe '#setup_pub_page' do
+    let(:publication) { build(:publication, :with_complex_source) }
+    subject { helper.setup_pub_page(presenter) }
+    it { is_expected.to eql('4-12.') }
+  end
 end

From 159bd70f7c84f9eaf801906df9e1919bc0243e3c Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 3 Jun 2020 00:39:28 +0900
Subject: [PATCH 236/258] fixed parsing JSON

---
 .../publication_behavior.rb                   | 20 ++++++++++++-------
 hyrax/app/views/hyrax/citations/work.html.erb |  2 +-
 .../publication_behavior_helper_spec.rb       |  2 +-
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
index aeb80ccd..4b14c202 100644
--- a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
+++ b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
@@ -68,15 +68,17 @@ def setup_pub_info(presenter, include_date = false)
       end
 
       def setup_pub_source(presenter)
-        return nil unless presenter.complex_source.first
-        source = JSON.parse(presenter.complex_source).first
-
+        return if presenter.complex_source.empty?
+        cs = presenter.complex_source
+        if presenter.complex_source.is_a?(Array)
+          cs = presenter.complex_source.first
+        end
+        source = JSON.parse(cs).first
         pub_source = ''
 
         if source['title'].present?
-          pub_source << '"'
           pub_source << source['title'].first
-          pub_source << '." '
+          pub_source << '. '
         end
 
         if source['volume'].present?
@@ -99,8 +101,12 @@ def setup_pub_source(presenter)
       end
 
       def setup_pub_page(presenter)
-        return nil unless presenter.complex_source.first
-        source = JSON.parse(presenter.complex_source).first
+        return if presenter.complex_source.empty?
+        cs = presenter.complex_source
+        if presenter.complex_source.is_a?(Array)
+          cs = presenter.complex_source.first
+        end
+        source = JSON.parse(cs).first
         pub_page = ''
 
         if source['start_page'].present? && source['end_page'].present?
diff --git a/hyrax/app/views/hyrax/citations/work.html.erb b/hyrax/app/views/hyrax/citations/work.html.erb
index e29d3d54..296d16a0 100644
--- a/hyrax/app/views/hyrax/citations/work.html.erb
+++ b/hyrax/app/views/hyrax/citations/work.html.erb
@@ -2,7 +2,7 @@
 
 <span class="citation">
 <%= @presenter.creator.join(', ') %>.
-<%= @presenter.title.first %>.
+"<%= @presenter.title.first %>".
 <%= setup_pub_source(@presenter) %>
 (<%= setup_pub_date(@presenter) %>):
 <%= @presenter.doi.first %>
diff --git a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
index 5718a63e..88e6274c 100644
--- a/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
+++ b/hyrax/spec/helpers/hyrax/citations_behaviors/publication_behavior_helper_spec.rb
@@ -64,7 +64,7 @@
   describe '#setup_pub_source' do
     let(:publication) { build(:publication, :with_complex_source) }
     subject { helper.setup_pub_source(presenter) }
-    it { is_expected.to eql('"Test journal." 3, no. 34. 1.2.2.') }
+    it { is_expected.to eql('Test journal. 3, no. 34. 1.2.2.') }
   end
 
   describe '#setup_pub_page' do

From 56dd8ed1bf82492ecdc3c50c5cf716224f94de6d Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 3 Jun 2020 16:41:03 +0900
Subject: [PATCH 237/258] add a spec file for the author list

---
 hyrax/app/views/hyrax/citations/work.html.erb |  2 +-
 .../hyrax/citations/work.html.erb_spec.rb     | 41 +++++++++++++++++++
 2 files changed, 42 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb

diff --git a/hyrax/app/views/hyrax/citations/work.html.erb b/hyrax/app/views/hyrax/citations/work.html.erb
index 296d16a0..4bacb258 100644
--- a/hyrax/app/views/hyrax/citations/work.html.erb
+++ b/hyrax/app/views/hyrax/citations/work.html.erb
@@ -1,7 +1,7 @@
 <h4>Citation Formats</h4>
 
 <span class="citation">
-<%= @presenter.creator.join(', ') %>.
+<%= @presenter.creator.first %>.
 "<%= @presenter.title.first %>".
 <%= setup_pub_source(@presenter) %>
 (<%= setup_pub_date(@presenter) %>):
diff --git a/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
new file mode 100644
index 00000000..c0a8dcb4
--- /dev/null
+++ b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
@@ -0,0 +1,41 @@
+require 'rails_helper'
+include Warden::Test::Helpers
+
+RSpec.describe 'hyrax/citations/work' do
+  let(:publication) { build(:publication, :open, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
+                        :with_publisher, :with_complex_date, :with_complex_identifier, :with_rights_statement, :with_complex_rights,
+                        :with_complex_version, :with_resource_type, :with_source, :with_issue, :with_complex_source, :with_complex_event,
+                        :with_place, :with_table_of_contents, :with_number_of_pages,
+                        doi: 'https://doi.org/10.5555/12345678',
+                        creator: ['Asahiko Matsuda, Kosuke Tanabe']) }
+  let(:ability) { double }
+  let(:presenter) { Hyrax::PublicationPresenter.new(SolrDocument.new(publication.to_solr), Ability.new(user), controller.request) }
+
+  before do
+    allow(controller).to receive(:current_user).and_return(user)
+    login_as user if user.present?
+    assign(:presenter, presenter)
+    render
+  end
+
+  # NB: the visibility of individual metadata components is set in app/models/ability.rb
+  # This test confirms the current expected behaviour (which is that most metadata is visible)
+
+  context 'unauthenticated user' do
+    let(:user) { nil }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Asahiko Matsuda, Kosuke Tanabe.')
+      expect(rendered).to have_content("\"Open Publication\".\nTest journal. 3, no. 34. 1.2.2.\n(0528):")
+      expect(rendered).to have_content('https://doi.org/10.5555/12345678')
+    end
+  end
+
+  context 'authenticated NIMS Researcher' do
+    let(:user) { create(:user, :nims_researcher) }
+    it 'shows the correct metadata' do
+      expect(rendered).to have_content('Asahiko Matsuda, Kosuke Tanabe.')
+      expect(rendered).to have_content("\"Open Publication\".\nTest journal. 3, no. 34. 1.2.2.\n(0528):")
+      expect(rendered).to have_content('https://doi.org/10.5555/12345678')
+    end
+  end
+end

From 3e022b4716f5410b3cd2ebf656e69fb357b6d600 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Sat, 6 Jun 2020 21:47:58 +0900
Subject: [PATCH 238/258] fix: citation list raises an error if complex_person
 is empty

---
 .../publication_behavior.rb                   |  2 +
 hyrax/app/views/hyrax/citations/work.html.erb |  2 +-
 .../hyrax/citations/work.html.erb_spec.rb     | 80 +++++++++++++------
 3 files changed, 59 insertions(+), 25 deletions(-)

diff --git a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
index 4b14c202..e56f32d1 100644
--- a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
+++ b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
@@ -74,6 +74,8 @@ def setup_pub_source(presenter)
           cs = presenter.complex_source.first
         end
         source = JSON.parse(cs).first
+        return if source.blank?
+
         pub_source = ''
 
         if source['title'].present?
diff --git a/hyrax/app/views/hyrax/citations/work.html.erb b/hyrax/app/views/hyrax/citations/work.html.erb
index 4bacb258..f8b58937 100644
--- a/hyrax/app/views/hyrax/citations/work.html.erb
+++ b/hyrax/app/views/hyrax/citations/work.html.erb
@@ -5,7 +5,7 @@
 "<%= @presenter.title.first %>".
 <%= setup_pub_source(@presenter) %>
 (<%= setup_pub_date(@presenter) %>):
-<%= @presenter.doi.first %>
+<%= @presenter.doi&.first %>
 </span>
 
 <br /><br />
diff --git a/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
index c0a8dcb4..edf8dabe 100644
--- a/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
+++ b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
@@ -2,40 +2,72 @@
 include Warden::Test::Helpers
 
 RSpec.describe 'hyrax/citations/work' do
-  let(:publication) { build(:publication, :open, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
+  context 'publication with creators' do
+    let(:publication) { build(:publication, :open, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
                         :with_publisher, :with_complex_date, :with_complex_identifier, :with_rights_statement, :with_complex_rights,
                         :with_complex_version, :with_resource_type, :with_source, :with_issue, :with_complex_source, :with_complex_event,
                         :with_place, :with_table_of_contents, :with_number_of_pages,
                         doi: 'https://doi.org/10.5555/12345678',
                         creator: ['Asahiko Matsuda, Kosuke Tanabe']) }
-  let(:ability) { double }
-  let(:presenter) { Hyrax::PublicationPresenter.new(SolrDocument.new(publication.to_solr), Ability.new(user), controller.request) }
-
-  before do
-    allow(controller).to receive(:current_user).and_return(user)
-    login_as user if user.present?
-    assign(:presenter, presenter)
-    render
-  end
+    let(:ability) { double }
+    let(:presenter) { Hyrax::PublicationPresenter.new(SolrDocument.new(publication.to_solr), Ability.new(user), controller.request) }
+
+    before do
+      allow(controller).to receive(:current_user).and_return(user)
+      login_as user if user.present?
+      assign(:presenter, presenter)
+      render
+    end
 
-  # NB: the visibility of individual metadata components is set in app/models/ability.rb
-  # This test confirms the current expected behaviour (which is that most metadata is visible)
+    # NB: the visibility of individual metadata components is set in app/models/ability.rb
+    # This test confirms the current expected behaviour (which is that most metadata is visible)
 
-  context 'unauthenticated user' do
-    let(:user) { nil }
-    it 'shows the correct metadata' do
-      expect(rendered).to have_content('Asahiko Matsuda, Kosuke Tanabe.')
-      expect(rendered).to have_content("\"Open Publication\".\nTest journal. 3, no. 34. 1.2.2.\n(0528):")
-      expect(rendered).to have_content('https://doi.org/10.5555/12345678')
+    context 'unauthenticated user' do
+      let(:user) { nil }
+      it 'shows the correct metadata' do
+        expect(rendered).to have_content('Asahiko Matsuda, Kosuke Tanabe.')
+        expect(rendered).to have_content("\"Open Publication\".\nTest journal. 3, no. 34. 1.2.2.\n(0528):")
+        expect(rendered).to have_content('https://doi.org/10.5555/12345678')
+      end
+    end
+
+    context 'authenticated NIMS Researcher' do
+      let(:user) { create(:user, :nims_researcher) }
+      it 'shows the correct metadata' do
+        expect(rendered).to have_content('Asahiko Matsuda, Kosuke Tanabe.')
+        expect(rendered).to have_content("\"Open Publication\".\nTest journal. 3, no. 34. 1.2.2.\n(0528):")
+        expect(rendered).to have_content('https://doi.org/10.5555/12345678')
+      end
     end
   end
 
-  context 'authenticated NIMS Researcher' do
-    let(:user) { create(:user, :nims_researcher) }
-    it 'shows the correct metadata' do
-      expect(rendered).to have_content('Asahiko Matsuda, Kosuke Tanabe.')
-      expect(rendered).to have_content("\"Open Publication\".\nTest journal. 3, no. 34. 1.2.2.\n(0528):")
-      expect(rendered).to have_content('https://doi.org/10.5555/12345678')
+  context 'publication without creators' do
+    let(:publication) { build(:publication, :open) }
+    let(:ability) { double }
+    let(:presenter) { Hyrax::PublicationPresenter.new(SolrDocument.new(publication.to_solr), Ability.new(user), controller.request) }
+
+    before do
+      allow(controller).to receive(:current_user).and_return(user)
+      login_as user if user.present?
+      assign(:presenter, presenter)
+      render
+    end
+
+    # NB: the visibility of individual metadata components is set in app/models/ability.rb
+    # This test confirms the current expected behaviour (which is that most metadata is visible)
+
+    context 'unauthenticated user' do
+      let(:user) { nil }
+      it 'shows the correct metadata' do
+        expect(rendered).to have_content("\"Open Publication\".\n\n():")
+      end
+    end
+
+    context 'authenticated NIMS Researcher' do
+      let(:user) { create(:user, :nims_researcher) }
+      it 'shows the correct metadata' do
+        expect(rendered).to have_content("\"Open Publication\".\n\n():")
+      end
     end
   end
 end

From 300098a7f01764945996d7e761de1f451afa0ff6 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Sun, 7 Jun 2020 15:45:07 +0100
Subject: [PATCH 239/258] Remove branding volume from
 docker-compose.override.yml - it was breaking the CSS.

---
 docker-compose.override.yml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/docker-compose.override.yml b/docker-compose.override.yml
index 96ae00e2..fefa0b08 100644
--- a/docker-compose.override.yml
+++ b/docker-compose.override.yml
@@ -4,7 +4,6 @@
 # - No nginx in front of the app
 # - app accessible on port 3000
 
-# todo: nginx to serve static files
 
 version: '3'
 
@@ -12,7 +11,6 @@ volumes:
   file_uploads:
   derivatives:
   cache:
-  brand:
   fcrepo:
   redis:
 
@@ -33,8 +31,6 @@ services:
       - file_uploads:${UPLOADS_PATH}
       - derivatives:${DERIVATIVES_PATH}
       - cache:${CACHE_PATH}
-      - brand:${BRAND_PATH}
-      - ./hyrax:/data
       - ${HOST_APP_DATA_PATH:-/srv/ngdr/data/}:/data/data
 
   web:
@@ -42,12 +38,6 @@ services:
       - 3000:3000
     depends_on:
       - cas
-    volumes:
-      - file_uploads:${UPLOADS_PATH}
-      - derivatives:${DERIVATIVES_PATH}
-      - cache:${CACHE_PATH}
-      - brand:${BRAND_PATH}
-      - ./hyrax:/data
     environment:
       - RAILS_FORCE_SSL=false
     networks:

From 837ae60b4786e70182ad6b7672cf45fef2f27087 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Mon, 8 Jun 2020 14:50:42 +0900
Subject: [PATCH 240/258] remove "ignore_if" option from exception_notification

---
 hyrax/config/environments/production.rb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/hyrax/config/environments/production.rb b/hyrax/config/environments/production.rb
index 52daf9e5..442ed8fa 100644
--- a/hyrax/config/environments/production.rb
+++ b/hyrax/config/environments/production.rb
@@ -114,7 +114,6 @@
   }
 
   config.middleware.use ExceptionNotification::Rack,
-    ignore_if: lambda { |env, exception| !env.nil? },
     error_grouping: true,
     email: {
       email_prefix: "[MDR #{ENV['ERROR_NOTIFICATION_SUBJECT_PREFIX']}] ",

From be95aa4ee9b129bcc1d0572f334071ee8677e4f1 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Mon, 8 Jun 2020 23:40:53 +0900
Subject: [PATCH 241/258] - disable username in profile URL - use
 link_to_profile helper in the statistics page

---
 hyrax/app/models/user.rb                      |  2 +-
 .../hyrax/admin/stats/_deposits.html.erb      |  9 ++++
 .../hyrax/admin/stats/_new_users.html.erb     | 22 ++++++++
 .../hyrax/admin/stats/show.html.erb_spec.rb   | 54 +++++++++++++++++++
 4 files changed, 86 insertions(+), 1 deletion(-)
 create mode 100644 hyrax/app/views/hyrax/admin/stats/_deposits.html.erb
 create mode 100644 hyrax/app/views/hyrax/admin/stats/_new_users.html.erb
 create mode 100644 hyrax/spec/views/hyrax/admin/stats/show.html.erb_spec.rb

diff --git a/hyrax/app/models/user.rb b/hyrax/app/models/user.rb
index 56f4c76d..6e90c51c 100644
--- a/hyrax/app/models/user.rb
+++ b/hyrax/app/models/user.rb
@@ -45,6 +45,6 @@ def ldap_before_save
   end
 
   def self.from_url_component(component)
-    User.find_by(user_identifier: component) || User.find_by_user_key(component.gsub(/-dot-/, '.'))
+    User.find_by(user_identifier: component)
   end
 end
diff --git a/hyrax/app/views/hyrax/admin/stats/_deposits.html.erb b/hyrax/app/views/hyrax/admin/stats/_deposits.html.erb
new file mode 100644
index 00000000..2bae2cdb
--- /dev/null
+++ b/hyrax/app/views/hyrax/admin/stats/_deposits.html.erb
@@ -0,0 +1,9 @@
+<h3>Deposits By Users (<%= @presenter.date_filter_string %>)</h3>
+<ul>
+  <% @presenter.depositors.each do |usr| %>
+    <li>
+      <%= link_to_profile(usr.name) %>
+      deposited <%= pluralize(usr[:deposits], "file") %>
+    </li>
+  <% end %>
+</ul>
diff --git a/hyrax/app/views/hyrax/admin/stats/_new_users.html.erb b/hyrax/app/views/hyrax/admin/stats/_new_users.html.erb
new file mode 100644
index 00000000..5cf0746a
--- /dev/null
+++ b/hyrax/app/views/hyrax/admin/stats/_new_users.html.erb
@@ -0,0 +1,22 @@
+<h3>Newest Users (<%= @presenter.date_filter_string %>)</h3>
+<h4>
+<%- if !@presenter.start_date.blank? %>
+  Total: <%= @presenter.recent_users.count %></div>
+<%- else %>
+    <%= @presenter.recent_users.count %> most recent users:
+<%- end %>
+</h4>
+<ul>
+  <% @presenter.recent_users.each do |usr| %>
+    <li>
+      <%= link_to_profile(usr.name) %>
+      <%- if usr.department %>
+        of <%= usr.department %>
+      <%- end %>
+      registered
+      <span class="date">
+        <%= usr.created_at.to_time.strftime("%m/%d/%Y") %>
+      </span>
+    </li>
+  <% end %>
+</ul>
diff --git a/hyrax/spec/views/hyrax/admin/stats/show.html.erb_spec.rb b/hyrax/spec/views/hyrax/admin/stats/show.html.erb_spec.rb
new file mode 100644
index 00000000..344a8ec8
--- /dev/null
+++ b/hyrax/spec/views/hyrax/admin/stats/show.html.erb_spec.rb
@@ -0,0 +1,54 @@
+RSpec.describe "hyrax/admin/stats/show.html.erb", type: :view do
+  let(:presenter) do
+    Hyrax::AdminStatsPresenter.new({}, 5)
+  end
+
+  before do
+    assign(:presenter, presenter)
+    allow(presenter).to receive(:top_formats).and_return([])
+    allow(presenter).to receive(:works_count).and_return(total: 0)
+    allow(presenter).to receive(:depositors).and_return([])
+  end
+
+  context 'locales' do
+    before do
+      allow(presenter).to receive(:active_users).and_return([])
+      render
+    end
+    it 'includes a default locale hidden input' do
+      expect(rendered).to have_selector 'input', exact: 'en'
+    end
+  end
+
+  context "default depositors" do
+    let(:top_5_active_users) do
+      (1..5).map { |i| double(label: i.to_s, value: i) }
+    end
+
+    before do
+      allow(presenter).to receive(:active_users).and_return(top_5_active_users)
+      render
+    end
+    it "shows top 5 depositors and option to view more" do
+      expect(rendered).to have_content("(top 5)")
+      expect(rendered).to have_link("View top 20", href: "/admin/stats?limit=20")
+    end
+  end
+
+  context "top 20 depositors" do
+    let(:top_20_active_users) do
+      (1..20).map { |i| double(label: i.to_s, value: i) }
+    end
+
+    before do
+      allow(presenter).to receive(:active_users).and_return(top_20_active_users)
+      allow(presenter).to receive(:limit).and_return(20)
+      render
+    end
+
+    it "shows top 20 depositors, without an option to view more" do
+      expect(rendered).to have_content("(top 20)")
+      expect(rendered).not_to have_content("View top 20")
+    end
+  end
+end

From 9de4fa5d013b5f07d3bce0c589c574e7ade95aab Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Tue, 9 Jun 2020 01:12:29 +0900
Subject: [PATCH 242/258] fix link to profile page

---
 hyrax/app/views/hyrax/admin/stats/_deposits.html.erb  | 2 +-
 hyrax/app/views/hyrax/admin/stats/_new_users.html.erb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/hyrax/app/views/hyrax/admin/stats/_deposits.html.erb b/hyrax/app/views/hyrax/admin/stats/_deposits.html.erb
index 2bae2cdb..a2160ead 100644
--- a/hyrax/app/views/hyrax/admin/stats/_deposits.html.erb
+++ b/hyrax/app/views/hyrax/admin/stats/_deposits.html.erb
@@ -2,7 +2,7 @@
 <ul>
   <% @presenter.depositors.each do |usr| %>
     <li>
-      <%= link_to_profile(usr.name) %>
+      <%= link_to_profile(usr[:user]) %>
       deposited <%= pluralize(usr[:deposits], "file") %>
     </li>
   <% end %>
diff --git a/hyrax/app/views/hyrax/admin/stats/_new_users.html.erb b/hyrax/app/views/hyrax/admin/stats/_new_users.html.erb
index 5cf0746a..05717b84 100644
--- a/hyrax/app/views/hyrax/admin/stats/_new_users.html.erb
+++ b/hyrax/app/views/hyrax/admin/stats/_new_users.html.erb
@@ -9,7 +9,7 @@
 <ul>
   <% @presenter.recent_users.each do |usr| %>
     <li>
-      <%= link_to_profile(usr.name) %>
+      <%= link_to_profile(usr) %>
       <%- if usr.department %>
         of <%= usr.department %>
       <%- end %>

From 2b4c04680d0f17c6f7b58cde72c59f95020c0c8e Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Tue, 9 Jun 2020 02:04:12 +0900
Subject: [PATCH 243/258] hide identifier from index

---
 hyrax/app/controllers/catalog_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/controllers/catalog_controller.rb b/hyrax/app/controllers/catalog_controller.rb
index eb5ecf09..9bb1bf01 100644
--- a/hyrax/app/controllers/catalog_controller.rb
+++ b/hyrax/app/controllers/catalog_controller.rb
@@ -93,7 +93,7 @@ def self.modified_field
     config.add_index_field solr_name('license', :stored_searchable), helper_method: :license_links
     config.add_index_field solr_name('resource_type', :stored_searchable), label: 'Resource Type', link_to_search: solr_name('resource_type', :facetable), if: lambda { |context, field_config, document| context.can?(:read_resource_type, document.hydra_model) }
     config.add_index_field solr_name('file_format', :stored_searchable), link_to_search: solr_name('file_format', :facetable)
-    config.add_index_field solr_name('identifier', :stored_searchable), helper_method: :index_field_link, field_name: 'identifier'
+    #config.add_index_field solr_name('identifier', :stored_searchable), helper_method: :index_field_link, field_name: 'identifier'
     config.add_index_field solr_name('embargo_release_date', :stored_sortable, type: :date), label: 'Embargo release date', helper_method: :human_readable_date
     config.add_index_field solr_name('lease_expiration_date', :stored_sortable, type: :date), label: 'Lease expiration date', helper_method: :human_readable_date
     config.add_index_field solr_name('place', :stored_searchable), itemprop: 'place', link_to_search: solr_name('place', :facetable)

From 9b60b2bd0aa4996832052b340ad64bfc748078e4 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Mon, 8 Jun 2020 20:04:52 +0100
Subject: [PATCH 244/258] Repairing test missing from latest merged PR

---
 hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
index edf8dabe..078ed3b5 100644
--- a/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
+++ b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
@@ -3,7 +3,7 @@
 
 RSpec.describe 'hyrax/citations/work' do
   context 'publication with creators' do
-    let(:publication) { build(:publication, :open, :with_alternative_title, :with_people, :with_keyword, :with_subject, :with_language,
+    let(:publication) { build(:publication, :open, :with_alternative_title, :with_complex_author, :with_keyword, :with_subject, :with_language,
                         :with_publisher, :with_complex_date, :with_complex_identifier, :with_rights_statement, :with_complex_rights,
                         :with_complex_version, :with_resource_type, :with_source, :with_issue, :with_complex_source, :with_complex_event,
                         :with_place, :with_table_of_contents, :with_number_of_pages,

From cfc3bde4524df346e0be2bf5363509bb03c019dc Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Mon, 8 Jun 2020 20:15:16 +0100
Subject: [PATCH 245/258] Moved code status to top of readme (to trigger build)

---
 README.md | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index db4ef2f1..0f9806cb 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,11 @@
 
 [Nims-Hyrax](https://github.com/antleaf/nims-hyrax/) is an implementation of the Hyrax stack by [Cottage Labs](http://cottagelabs.com/) and [AntLeaf](http://antleaf.com/). It is built with Docker containers, which simplify development and deployment onto live services.
 
+## Code Status
+
+[![Codeship Status for antleaf/nims-hyrax](https://app.codeship.com/projects/d4cc8560-e430-0136-fffd-6a7889452552/status?branch=develop)](https://app.codeship.com/projects/319029)
+
+[![Coverage Status](https://coveralls.io/repos/github/antleaf/nims-hyrax/badge.svg?branch=develop)](https://coveralls.io/github/antleaf/nims-hyrax?branch=develop)
 
 ## Getting Started
 
@@ -269,9 +274,3 @@ There is [docker documentation](https://docs.docker.com/storage/volumes/#backup-
 * As mentioned above, there is a `.env` file containing application secrets. This **must not** be checked into version control!
 * The system is configured on start-up using the `docker-entrypoint.sh` script, which configures users in the `seed/setup.json` file.
 * Importers are run manually in the container using the rails console. See [The project wiki](https://github.com/antleaf/nims-hyrax/wiki) for more information.
-
-## Code Status
-
-[![Codeship Status for antleaf/nims-hyrax](https://app.codeship.com/projects/d4cc8560-e430-0136-fffd-6a7889452552/status?branch=develop)](https://app.codeship.com/projects/319029)
-
-[![Coverage Status](https://coveralls.io/repos/github/antleaf/nims-hyrax/badge.svg?branch=develop)](https://coveralls.io/github/antleaf/nims-hyrax?branch=develop)

From 57c4f1d59a501afde465f813c96f66bfc10c2a19 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Wed, 10 Jun 2020 19:06:49 +0900
Subject: [PATCH 246/258] don't call complex_source if the work is Dataset

---
 .../publication_behavior.rb                   |  1 +
 .../hyrax/citations/work.html.erb_spec.rb     | 27 +++++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
index e56f32d1..6b362861 100644
--- a/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
+++ b/hyrax/app/helpers/hyrax/citations_behaviors/publication_behavior.rb
@@ -68,6 +68,7 @@ def setup_pub_info(presenter, include_date = false)
       end
 
       def setup_pub_source(presenter)
+        return unless presenter.respond_to?(:complex_source)
         return if presenter.complex_source.empty?
         cs = presenter.complex_source
         if presenter.complex_source.is_a?(Array)
diff --git a/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
index edf8dabe..7405a67b 100644
--- a/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
+++ b/hyrax/spec/views/hyrax/citations/work.html.erb_spec.rb
@@ -70,4 +70,31 @@
       end
     end
   end
+
+  context 'dataset without creators' do
+    let(:dataset) { build(:dataset, :open) }
+    let(:ability) { double }
+    let(:presenter) { Hyrax::DatasetPresenter.new(SolrDocument.new(dataset.to_solr), Ability.new(user), controller.request) }
+
+    before do
+      allow(controller).to receive(:current_user).and_return(user)
+      login_as user if user.present?
+      assign(:presenter, presenter)
+      render
+    end
+
+    context 'unauthenticated user' do
+      let(:user) { nil }
+      it 'shows the correct metadata' do
+        expect(rendered).to have_content("\"Open Dataset\".\n\n():")
+      end
+    end
+
+    context 'authenticated NIMS Researcher' do
+      let(:user) { create(:user, :nims_researcher) }
+      it 'shows the correct metadata' do
+        expect(rendered).to have_content("\"Open Dataset\".\n\n():")
+      end
+    end
+  end
 end

From 878e7bd6a31a054d8450abf10b3e902dad103ea8 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 11 Jun 2020 02:34:46 +0900
Subject: [PATCH 247/258] update the display order of Publication metadata

---
 .../publications/_attribute_rows.html.erb     | 53 +++++++++----------
 1 file changed, 25 insertions(+), 28 deletions(-)

diff --git a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
index 23cf4d78..7ef2af45 100644
--- a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
@@ -1,33 +1,25 @@
-<%= presenter.attribute_to_html(:date_modified, label: t('hyrax.base.show.last_modified'), html_dl: true) %>
-
 <% if can? :read_alternative_title, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:alternative_title, label: t('ngdr.fields.alternative_title'), html_dl: true) %>
 <% end %>
 
-<% if can? :read_subject, presenter.model_name.name.constantize %>
-  <%= presenter.attribute_to_html(:subject, render_as: :faceted, html_dl: true) %>
-<% end %>
-
-<% if can? :read_publisher, presenter.model_name.name.constantize %>
-  <%= presenter.attribute_to_html(:publisher, render_as: :faceted, html_dl: true) %>
-<% end %>
-
-<% if can? :read_language, presenter.model_name.name.constantize %>
-  <%= presenter.attribute_to_html(:language, render_as: :faceted, html_dl: true) %>
+<% if can? :read_creator, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:complex_person, render_as: :nested_person, label: t('ngdr.fields.complex_person'), html_dl: true) %>
 <% end %>
 
 <% if can? :read_keyword, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:keyword, render_as: :faceted, html_dl: true) %>
 <% end %>
 
-<%= presenter.attribute_to_html(:date_created, render_as: :linked, search_field: 'date_created_tesim', html_dl: true) %>
+<% if can? :read_subject, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:subject, render_as: :faceted, html_dl: true) %>
+<% end %>
 
-<% if can? :read_resource_type, presenter.model_name.name.constantize %>
-  <%= presenter.attribute_to_html(:resource_type, render_as: :faceted, html_dl: true) %>
+<% if can? :read_language, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:language, render_as: :faceted, html_dl: true) %>
 <% end %>
 
-<% if can? :read_rights, presenter.model_name.name.constantize %>
-  <%= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
+<% if can? :read_publisher, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:publisher, render_as: :faceted, html_dl: true) %>
 <% end %>
 
 <% if can? :read_date, presenter.model_name.name.constantize %>
@@ -39,22 +31,32 @@
   <%= presenter.attribute_to_html(:complex_identifier, render_as: :nested_identifier, label: t('ngdr.fields.complex_identifier'), html_dl: true) %>
 <% end %>
 
-<% if can? :read_creator, presenter.model_name.name.constantize %>
-  <%= presenter.attribute_to_html(:complex_person, render_as: :nested_person, label: t('ngdr.fields.complex_person'), html_dl: true) %>
-<% end %>
-
 <% if can? :read_rights, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:complex_rights, render_as: :nested_rights, label: t('ngdr.fields.complex_rights'), html_dl: true) %>
+  <%#= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
 <% end %>
 
 <% if can? :read_version, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:complex_version, render_as: :nested_version, label: t('ngdr.fields.complex_version'), html_dl: true) %>
 <% end %>
 
+<% if can? :read_resource_type, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:resource_type, render_as: :faceted, html_dl: true) %>
+<% end %>
+
+<% if can? :read_related, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:first_published_url, label: t('ngdr.fields.first_published_url'), html_dl: true) %>
+<% end %>
+
 <% if can? :read_event, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:complex_event, render_as: :nested_event, label: "Event", html_dl: true) %>
 <% end %>
 
+<% if can? :read_source, presenter.model_name.name.constantize %>
+  <%= presenter.attribute_to_html(:source, label: "Source", html_dl: true) %>
+  <%= presenter.attribute_to_html(:complex_source, render_as: :nested_source, label: t('ngdr.fields.complex_source'), html_dl: true) %>
+<% end %>
+
 <% if can? :read_issue, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:issue, label: "Issue", html_dl: true) %>
 <% end %>
@@ -71,11 +73,6 @@
   <%= presenter.attribute_to_html(:total_number_of_pages, label: "Number of pages", html_dl: true) %>
 <% end %>
 
-<% if can? :read_related, presenter.model_name.name.constantize %>
-  <%= presenter.attribute_to_html(:first_published_url, label: t('ngdr.fields.first_published_url'), html_dl: true) %>
-<% end %>
+<%= presenter.attribute_to_html(:date_created, render_as: :linked, search_field: 'date_created_tesim', html_dl: true) %>
 
-<% if can? :read_source, presenter.model_name.name.constantize %>
-  <%= presenter.attribute_to_html(:source, label: "Source", html_dl: true) %>
-  <%= presenter.attribute_to_html(:complex_source, render_as: :nested_source, label: t('ngdr.fields.complex_source'), html_dl: true) %>
-<% end %>
+<%= presenter.attribute_to_html(:date_modified, label: t('hyrax.base.show.last_modified'), html_dl: true) %>

From 4d3ff18611b886de5be579b7c84feab1c13e8b78 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 11 Jun 2020 08:08:20 +0900
Subject: [PATCH 248/258] show rights_statement (it is not in the form)

---
 hyrax/app/views/hyrax/publications/_attribute_rows.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
index 7ef2af45..24e1d638 100644
--- a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
@@ -33,7 +33,7 @@
 
 <% if can? :read_rights, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:complex_rights, render_as: :nested_rights, label: t('ngdr.fields.complex_rights'), html_dl: true) %>
-  <%#= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
+  <%= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
 <% end %>
 
 <% if can? :read_version, presenter.model_name.name.constantize %>

From a72e9e142c701a46075f284742dc461c348ada7d Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 11 Jun 2020 10:20:24 +0900
Subject: [PATCH 249/258] use final-icons-01-100.png as a default work
 thumbnail

---
 hyrax/app/services/hyrax/work_thumbnail_path_service.rb | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 hyrax/app/services/hyrax/work_thumbnail_path_service.rb

diff --git a/hyrax/app/services/hyrax/work_thumbnail_path_service.rb b/hyrax/app/services/hyrax/work_thumbnail_path_service.rb
new file mode 100644
index 00000000..da1292f0
--- /dev/null
+++ b/hyrax/app/services/hyrax/work_thumbnail_path_service.rb
@@ -0,0 +1,9 @@
+module Hyrax
+  class WorkThumbnailPathService < Hyrax::ThumbnailPathService
+    class << self
+      def default_image
+        ActionController::Base.helpers.image_path 'final-icons-01-100.png'
+      end
+    end
+  end
+end

From 18f41b010db47627bf87cb7a156c47ed94c52ac8 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <nabeta@fastmail.fm>
Date: Thu, 11 Jun 2020 23:18:00 +0900
Subject: [PATCH 250/258] fix profile url in the sidebar

---
 .../dashboard/sidebar/_activity.html.erb      | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/dashboard/sidebar/_activity.html.erb

diff --git a/hyrax/app/views/hyrax/dashboard/sidebar/_activity.html.erb b/hyrax/app/views/hyrax/dashboard/sidebar/_activity.html.erb
new file mode 100644
index 00000000..aceed9d4
--- /dev/null
+++ b/hyrax/app/views/hyrax/dashboard/sidebar/_activity.html.erb
@@ -0,0 +1,33 @@
+  <li class="h5"><%= t('hyrax.admin.sidebar.activity') %></li>
+
+  <li>
+    <%= menu.collapsable_section t('hyrax.admin.sidebar.user_activity'),
+                                 icon_class: "fa fa-line-chart",
+                                 id: 'collapseUserActivity',
+                                 open: menu.user_activity_section? do %>
+      <%= menu.nav_link(hyrax.dashboard_profile_path(current_user&.user_identifier),
+                        also_active_for: hyrax.edit_dashboard_profile_path(current_user&.user_identifier)) do %>
+        <span class="fa fa-id-card" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.profile') %></span>
+      <% end %>
+
+      <%= menu.nav_link(hyrax.notifications_path) do %>
+        <span class="fa fa-bell" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.notifications') %></span>
+      <% end %>
+
+      <%= menu.nav_link(hyrax.transfers_path) do %>
+        <span class="fa fa-arrows-h" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.transfers') %></span>
+      <% end %>
+
+      <% if Flipflop.proxy_deposit? %>
+        <%= menu.nav_link(hyrax.depositors_path) do %>
+          <span class="fa fa-users" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.dashboard.manage_proxies') %></span>
+        <% end %>
+      <% end %>
+    <% end %>
+  </li>
+
+  <% if can? :read, :admin_dashboard %>
+    <%= menu.nav_link(hyrax.admin_stats_path) do %>
+      <span class="fa fa-bar-chart" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.statistics') %></span>
+    <% end %>
+  <% end %>

From 7af29d6f7b05d1175150bbc9e02ff7b68d865cec Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 11 Jun 2020 23:49:05 +0900
Subject: [PATCH 251/258] add spec file for profile url in the sidebar

---
 .../dashboard/sidebar/_activity.html.erb      | 33 +++++++++++++++++++
 .../sidebar/_activity.html.erb_spec.rb        | 23 +++++++++++++
 2 files changed, 56 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/dashboard/sidebar/_activity.html.erb
 create mode 100644 hyrax/spec/views/hyrax/dashboard/sidebar/_activity.html.erb_spec.rb

diff --git a/hyrax/app/views/hyrax/dashboard/sidebar/_activity.html.erb b/hyrax/app/views/hyrax/dashboard/sidebar/_activity.html.erb
new file mode 100644
index 00000000..aceed9d4
--- /dev/null
+++ b/hyrax/app/views/hyrax/dashboard/sidebar/_activity.html.erb
@@ -0,0 +1,33 @@
+  <li class="h5"><%= t('hyrax.admin.sidebar.activity') %></li>
+
+  <li>
+    <%= menu.collapsable_section t('hyrax.admin.sidebar.user_activity'),
+                                 icon_class: "fa fa-line-chart",
+                                 id: 'collapseUserActivity',
+                                 open: menu.user_activity_section? do %>
+      <%= menu.nav_link(hyrax.dashboard_profile_path(current_user&.user_identifier),
+                        also_active_for: hyrax.edit_dashboard_profile_path(current_user&.user_identifier)) do %>
+        <span class="fa fa-id-card" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.profile') %></span>
+      <% end %>
+
+      <%= menu.nav_link(hyrax.notifications_path) do %>
+        <span class="fa fa-bell" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.notifications') %></span>
+      <% end %>
+
+      <%= menu.nav_link(hyrax.transfers_path) do %>
+        <span class="fa fa-arrows-h" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.transfers') %></span>
+      <% end %>
+
+      <% if Flipflop.proxy_deposit? %>
+        <%= menu.nav_link(hyrax.depositors_path) do %>
+          <span class="fa fa-users" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.dashboard.manage_proxies') %></span>
+        <% end %>
+      <% end %>
+    <% end %>
+  </li>
+
+  <% if can? :read, :admin_dashboard %>
+    <%= menu.nav_link(hyrax.admin_stats_path) do %>
+      <span class="fa fa-bar-chart" aria-hidden="true"></span> <span class="sidebar-action-text"><%= t('hyrax.admin.sidebar.statistics') %></span>
+    <% end %>
+  <% end %>
diff --git a/hyrax/spec/views/hyrax/dashboard/sidebar/_activity.html.erb_spec.rb b/hyrax/spec/views/hyrax/dashboard/sidebar/_activity.html.erb_spec.rb
new file mode 100644
index 00000000..0230b472
--- /dev/null
+++ b/hyrax/spec/views/hyrax/dashboard/sidebar/_activity.html.erb_spec.rb
@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+require 'rails_helper'
+
+RSpec.describe 'hyrax/dashboard/sidebar/_activity.html.erb', type: :view do
+  let(:user) { FactoryBot.build(:user) }
+  let(:can_result) { false }
+
+  before do
+    allow(view).to receive(:signed_in?).and_return(true)
+    allow(view).to receive(:current_user).and_return(user)
+    assign(:user, user)
+  end
+
+  context 'with any user' do
+    before do
+      render partial: 'hyrax/dashboard/sidebar/activity', locals: {menu: Hyrax::MenuPresenter.new(view)}
+    end
+    subject { rendered }
+
+    it { is_expected.to have_link 'Profile', href: "/dashboard/profiles/#{user.user_identifier}" }
+  end
+end

From 431dd4466baab4b86f3f002b3469f712eabe1748 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Thu, 11 Jun 2020 23:57:05 +0900
Subject: [PATCH 252/258] hide rights_statement again

---
 hyrax/app/views/hyrax/publications/_attribute_rows.html.erb   | 2 +-
 .../views/hyrax/publications/_attribute_rows.html_spec.rb     | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
index 24e1d638..7ef2af45 100644
--- a/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
+++ b/hyrax/app/views/hyrax/publications/_attribute_rows.html.erb
@@ -33,7 +33,7 @@
 
 <% if can? :read_rights, presenter.model_name.name.constantize %>
   <%= presenter.attribute_to_html(:complex_rights, render_as: :nested_rights, label: t('ngdr.fields.complex_rights'), html_dl: true) %>
-  <%= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
+  <%#= presenter.attribute_to_html(:rights_statement, render_as: :rights_statement, html_dl: true) %>
 <% end %>
 
 <% if can? :read_version, presenter.model_name.name.constantize %>
diff --git a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
index 74b78be4..49cb4209 100644
--- a/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
+++ b/hyrax/spec/views/hyrax/publications/_attribute_rows.html_spec.rb
@@ -27,7 +27,7 @@
       expect(rendered).to have_content('Faroese')
       expect(rendered).to have_content('Keyword-123')
       expect(rendered).to have_content('Resource-Type-123')
-      expect(rendered).to have_content('Rights-Statement-123')
+      #expect(rendered).to have_content('Rights-Statement-123')
       expect(rendered).to have_content('28/05/2019') # NB: complex date is reformatted to dd/mm/yyyy
       expect(rendered).to have_content('10.0.1111')
       expect(rendered).to have_content('Foo Bar')
@@ -54,7 +54,7 @@
       expect(rendered).to have_content('Faroese')
       expect(rendered).to have_content('Keyword-123')
       expect(rendered).to have_content('Resource-Type-123')
-      expect(rendered).to have_content('Rights-Statement-123')
+      #expect(rendered).to have_content('Rights-Statement-123')
       expect(rendered).to have_content('28/05/2019') # NB: complex date is reformatted to dd/mm/yyyy
       expect(rendered).to have_content('10.0.1111')
       expect(rendered).to have_content('Foo Bar')

From abccf855d2b2d6010a78385172b29de30b27f4e1 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 12 Jun 2020 02:13:03 +0900
Subject: [PATCH 253/258] fix profile url in the dropdown menu

---
 hyrax/app/views/_user_util_links.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hyrax/app/views/_user_util_links.html.erb b/hyrax/app/views/_user_util_links.html.erb
index 76ae8aad..c898bfaa 100644
--- a/hyrax/app/views/_user_util_links.html.erb
+++ b/hyrax/app/views/_user_util_links.html.erb
@@ -15,7 +15,7 @@
       <%= render_notifications(user: current_user) %>
     </li>
     <li class="dropdown">
-      <%= link_to hyrax.dashboard_profile_path(current_user), role: 'button', data: { toggle: 'dropdown' }, aria: { haspopup: true, expanded: false, controls: 'user-util-links' } do %>
+      <%= link_to hyrax.dashboard_profile_path(current_user.user_identifier), role: 'button', data: { toggle: 'dropdown' }, aria: { haspopup: true, expanded: false, controls: 'user-util-links' } do %>
         <span class="sr-only"><%= t("hyrax.toolbar.profile.sr_action") %></span>
         <span class="hidden-xs">&nbsp;<%= current_user.name %></span>
         <span class="sr-only"> <%= t("hyrax.toolbar.profile.sr_target") %></span>

From 32c2d2ac055ef97d330d400c68512e814b1d2435 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 12 Jun 2020 02:17:07 +0900
Subject: [PATCH 254/258] add Hyrax::NimsThumbnailPathService module and
 mdr-default.png

---
 hyrax/app/assets/images/mdr-default.png       | Bin 0 -> 5013 bytes
 .../hyrax/nims_thumbnail_path_service.rb      |  23 ++++++++++++++++++
 .../hyrax/work_thumbnail_path_service.rb      |   9 -------
 .../hyrax/thumbnail_path_service_spec.rb      |  14 +++++++++++
 .../hyrax/work_thumbnail_path_service_spec.rb |  14 +++++++++++
 5 files changed, 51 insertions(+), 9 deletions(-)
 create mode 100644 hyrax/app/assets/images/mdr-default.png
 create mode 100644 hyrax/app/services/hyrax/nims_thumbnail_path_service.rb
 delete mode 100644 hyrax/app/services/hyrax/work_thumbnail_path_service.rb
 create mode 100644 hyrax/spec/services/hyrax/thumbnail_path_service_spec.rb
 create mode 100644 hyrax/spec/services/hyrax/work_thumbnail_path_service_spec.rb

diff --git a/hyrax/app/assets/images/mdr-default.png b/hyrax/app/assets/images/mdr-default.png
new file mode 100644
index 0000000000000000000000000000000000000000..8d6bc9270ee67dd06819400289cb7b455fe5c1ad
GIT binary patch
literal 5013
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z%Iya4mXMH;vpWZOmXMI7ZOblc07>`@JqQf4VdpO2kdWB-Xj>#jfy_<-RE{|79^n#t
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diff --git a/hyrax/app/services/hyrax/nims_thumbnail_path_service.rb b/hyrax/app/services/hyrax/nims_thumbnail_path_service.rb
new file mode 100644
index 00000000..931a5bc2
--- /dev/null
+++ b/hyrax/app/services/hyrax/nims_thumbnail_path_service.rb
@@ -0,0 +1,23 @@
+#require_dependency Rails.root.join('app/services/hyrax/work_thumbnail_path_service')
+
+module Hyrax
+  module NimsThumbnailPathService
+    def default_image
+      ActionController::Base.helpers.image_path 'mdr-default.png'
+    end
+  end
+end
+
+class Hyrax::ThumbnailPathService
+  class << self
+    prepend Hyrax::NimsThumbnailPathService
+  end
+end
+
+class Hyrax::WorkThumbnailPathService
+  class << self
+    prepend Hyrax::NimsThumbnailPathService
+  end
+end
+
+#Hyrax::ThumbnailPathService.singleton_class.prepend Hyrax::NimsThumbnailPathService
diff --git a/hyrax/app/services/hyrax/work_thumbnail_path_service.rb b/hyrax/app/services/hyrax/work_thumbnail_path_service.rb
deleted file mode 100644
index da1292f0..00000000
--- a/hyrax/app/services/hyrax/work_thumbnail_path_service.rb
+++ /dev/null
@@ -1,9 +0,0 @@
-module Hyrax
-  class WorkThumbnailPathService < Hyrax::ThumbnailPathService
-    class << self
-      def default_image
-        ActionController::Base.helpers.image_path 'final-icons-01-100.png'
-      end
-    end
-  end
-end
diff --git a/hyrax/spec/services/hyrax/thumbnail_path_service_spec.rb b/hyrax/spec/services/hyrax/thumbnail_path_service_spec.rb
new file mode 100644
index 00000000..9e13caf2
--- /dev/null
+++ b/hyrax/spec/services/hyrax/thumbnail_path_service_spec.rb
@@ -0,0 +1,14 @@
+require 'rails_helper'
+
+RSpec.describe Hyrax::ThumbnailPathService do
+  let(:service) { described_class }
+  before(:each) do
+    service.prepend Hyrax::NimsThumbnailPathService
+  end
+
+  describe "default_image" do
+    it "returns the path to mdr-default.png" do
+      expect(service.default_image).to eq "/assets/mdr-default-60f9f544d1af015df85c14718210b56b8525e2b8d87787a1d14789c4e1120191.png"
+    end
+  end
+end
diff --git a/hyrax/spec/services/hyrax/work_thumbnail_path_service_spec.rb b/hyrax/spec/services/hyrax/work_thumbnail_path_service_spec.rb
new file mode 100644
index 00000000..42a8ad68
--- /dev/null
+++ b/hyrax/spec/services/hyrax/work_thumbnail_path_service_spec.rb
@@ -0,0 +1,14 @@
+require 'rails_helper'
+
+RSpec.describe Hyrax::WorkThumbnailPathService do
+  let(:service) { described_class }
+  before(:each) do
+    service.prepend Hyrax::NimsThumbnailPathService
+  end
+
+  describe "default_image" do
+    it "returns the path to mdr-default.png" do
+      expect(service.default_image).to eq "/assets/mdr-default-60f9f544d1af015df85c14718210b56b8525e2b8d87787a1d14789c4e1120191.png"
+    end
+  end
+end

From e5bf68ef4b6f4bf491a5f812924b9fb6eca2229e Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 12 Jun 2020 02:47:10 +0900
Subject: [PATCH 255/258] clean up

---
 hyrax/app/services/hyrax/nims_thumbnail_path_service.rb | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/hyrax/app/services/hyrax/nims_thumbnail_path_service.rb b/hyrax/app/services/hyrax/nims_thumbnail_path_service.rb
index 931a5bc2..8ba129a6 100644
--- a/hyrax/app/services/hyrax/nims_thumbnail_path_service.rb
+++ b/hyrax/app/services/hyrax/nims_thumbnail_path_service.rb
@@ -1,5 +1,3 @@
-#require_dependency Rails.root.join('app/services/hyrax/work_thumbnail_path_service')
-
 module Hyrax
   module NimsThumbnailPathService
     def default_image
@@ -19,5 +17,3 @@ class << self
     prepend Hyrax::NimsThumbnailPathService
   end
 end
-
-#Hyrax::ThumbnailPathService.singleton_class.prepend Hyrax::NimsThumbnailPathService

From eff1ea9bd0ac6925aabbeb2b51c83557c7c8a232 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 12 Jun 2020 14:39:46 +0900
Subject: [PATCH 256/258] hide "Edit profile" link

---
 hyrax/app/views/hyrax/users/_user.html.erb | 24 ++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/users/_user.html.erb

diff --git a/hyrax/app/views/hyrax/users/_user.html.erb b/hyrax/app/views/hyrax/users/_user.html.erb
new file mode 100644
index 00000000..428201e0
--- /dev/null
+++ b/hyrax/app/views/hyrax/users/_user.html.erb
@@ -0,0 +1,24 @@
+<div class="panel panel-default panel-user">
+  <div class="panel-heading">
+    <%= image_tag user.avatar.url(:thumb), width: 100 if user.avatar.present? %>
+    <h3>
+      <%= user.name %>
+    </h3>
+  </div>
+
+  <div class="list-group">
+    <%= render "hyrax/users/vitals", user: user %>
+
+    <div class="list-group-item">
+      <%= render 'hyrax/users/user_info', user: user %>
+    </div>
+  </div>
+
+  <div class="panel-footer clearfix">
+    <%# if can? :edit, user %>
+      <%#= link_to hyrax.edit_dashboard_profile_path(user), class: "btn btn-default pull-right" do %>
+        <!-- <i class="glyphicon glyphicon-edit"></i> <%#= t("hyrax.edit_profile") %> -->
+      <%# end %>
+    <%# end %>
+  </div>
+</div>

From 3c966ee3d2a6ea5922c08bcf3474dbfeb5cf6ca2 Mon Sep 17 00:00:00 2001
From: Kosuke Tanabe <TANABE.Kosuke@nims.go.jp>
Date: Fri, 12 Jun 2020 15:04:01 +0900
Subject: [PATCH 257/258] hide "Edit profile" link in the dashboard

---
 .../hyrax/dashboard/profiles/show.html.erb    | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 hyrax/app/views/hyrax/dashboard/profiles/show.html.erb

diff --git a/hyrax/app/views/hyrax/dashboard/profiles/show.html.erb b/hyrax/app/views/hyrax/dashboard/profiles/show.html.erb
new file mode 100644
index 00000000..98251f25
--- /dev/null
+++ b/hyrax/app/views/hyrax/dashboard/profiles/show.html.erb
@@ -0,0 +1,30 @@
+<% provide :page_header do %>
+  <h1><span class="fa fa-id-card" aria-hidden="true"></span> <%= t("hyrax.admin.sidebar.profile") %></h1>
+  <!--
+  <%# if can? :edit, current_user %>
+    <div class="pull-right">
+      <%#= link_to hyrax.edit_dashboard_profile_path(@user), class: "btn btn-primary" do %>
+        <%#= t("hyrax.edit_profile") %>
+      <%# end %>
+    </div>
+  <%# end %>
+  -->
+<% end %>
+
+  <div class="panel panel-default">
+    <div class="panel-body">
+      <div class="list-group col-md-5 col-sm-8">
+        <%= render "hyrax/users/vitals", user: @user %>
+
+        <div class="list-group-item">
+          <%= render 'hyrax/users/user_info', user: @user %>
+        </div>
+
+        <% if @presenter.trophies.any? %>
+          <div class="list-group-item">
+            <%= render 'hyrax/users/contributions', presenter: @presenter %>
+          </div>
+        <% end %>
+      </div>
+    </div>
+  </div>

From ea002912008a94d2fa056e72eaa38060db73a0b6 Mon Sep 17 00:00:00 2001
From: Steve Eardley <steve@eardley.xyz>
Date: Fri, 12 Jun 2020 09:41:55 +0100
Subject: [PATCH 258/258] Updated package.json for public release

---
 hyrax/package.json | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/hyrax/package.json b/hyrax/package.json
index 9ae7710d..98f2e252 100644
--- a/hyrax/package.json
+++ b/hyrax/package.json
@@ -2,16 +2,17 @@
   "name": "nims-hyrax",
   "private": true,
   "repository": "git@github.com:antleaf/nims-hyrax.git",
+  "version": "1.0.0",
   "dependencies": {
-  "universalviewer": "3.0.16"
-},
-"scripts": {
-  "preinstall": "rm -rf ./public/uv",
-  "postinstall": "yarn run uv-install && yarn run uv-config",
-  "uv-install": "shx cp -r ./node_modules/universalviewer/uv ./public/",
-  "uv-config": "shx cp ./config/uv/uv.html ./public/uv/uv.html & shx cp ./config/uv/uv-config.json ./public/uv/"
+    "universalviewer": "3.0.16"
+  },
+  "scripts": {
+    "preinstall": "rm -rf ./public/uv",
+    "postinstall": "yarn run uv-install && yarn run uv-config",
+    "uv-install": "shx cp -r ./node_modules/universalviewer/uv ./public/",
+    "uv-config": "shx cp ./config/uv/uv.html ./public/uv/uv.html & shx cp ./config/uv/uv-config.json ./public/uv/"
   },
   "devDependencies": {
-  "shx": "^0.3.2"
+    "shx": "^0.3.2"
   }
 }