From 8128f109d0dca873247e229cd604f1642dfbf565 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Thu, 13 Jun 2024 12:25:49 -0700
Subject: [PATCH 1/7] Change stop() to nx_report_error() for user permission
 error

---
 server.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/server.R b/server.R
index 8f3ed576..f3cd9472 100644
--- a/server.R
+++ b/server.R
@@ -141,7 +141,13 @@ shinyServer(function(input, output, session) {
       }, 1L)
       asset_views(all_asset_views[has_access == 1])
       
-      if (length(asset_views) == 0) stop("You do not have DOWNLOAD access to any supported Asset Views.")
+      if (length(asset_views) == 0) {
+        nx_report_error(
+          title = "You do not have DOWNLOAD access to any supported Asset Views",
+          message = "Contact your DCC admin for access"
+        )
+        hide(selector = "#NXReportButton") # hide OK button so users can't continue
+      }
       updateSelectInput(session, "dropdown_asset_view",
                         choices = asset_views()
       )

From 32fc4ad457f972914d78774d72f911d30837419d Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 2 Jul 2024 15:21:34 -0700
Subject: [PATCH 2/7] Create function to read DCA config file and explicitly
 check for required variables and set defaults for missing optional ones.

---
 R/read_dca_config.R | 101 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 R/read_dca_config.R

diff --git a/R/read_dca_config.R b/R/read_dca_config.R
new file mode 100644
index 00000000..2bbfe4bf
--- /dev/null
+++ b/R/read_dca_config.R
@@ -0,0 +1,101 @@
+#' @title Read the DCA config file and report issues
+#' @param config URL or filepath to a DCA JSON config file
+read_dca_config <- function(config) {
+  conf <- jsonlite::fromJSON(config)
+  
+  name_check <- function(req, prov) {
+    if (!all(req %in% prov)) {
+      which_miss <- req[which(!req %in% prov)]
+      stop(sprintf("DCA config missing %s", which_miss))
+    }
+  }
+  
+  lvl_1_props_req <- list(
+    "dcc" = list(),
+    "dca" = list(),
+    "schematic" = list()
+  )
+  lvl_1_props_ops <- list() # Placeholder for optional properties
+  lvl_1_props_conf <- names(conf)
+  name_check(names(lvl_1_props_req), lvl_1_props_conf)
+  
+  dca_props_req <- list() # Placeholder for required DCA properties
+  dca_props_ops <- list(
+    "use_compliance_dashboard" = FALSE,
+    "primary_col" = "#2a668d",
+    "secondary_col" = "#184e71",
+    "sidebar_col" = "#191919"
+  )
+  dca_props_conf <- names(conf$dca)
+  name_check(names(dca_props_req), dca_props_conf)
+  
+  if (!"use_compliance_dashboard" %in% dca_props_conf) {
+    conf$dca$use_compliance_dashboard <- FALSE
+  }
+  if (!"primary_col" %in% dca_props_conf) {
+    conf$dca$primary_col <- "#2a668d"
+  }
+  if (!"secondary_col" %in% dca_props_conf) {
+    conf$dca$secondary_col <- "#184e71"
+  }
+  if (!"primary_col" %in% dca_props_conf) {
+    conf$dca$sidebar_col <- "#191919"
+  }
+  
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  schematic_props_req <- list(
+    "manifest_generate" = list(),
+    "model_validate" = list(),
+    "model_submit" = list()
+  )
+  schematic_props_ops <- list(
+    "global" = list()
+  )
+  schematic_props_conf <- names(conf$schematic)
+  name_check(names(schematic_props_req), schematic_props_conf)
+  
+  if (!"global" %in% schematic_props_conf) {
+    conf$schematic$global <- list()
+  }
+  
+  global_ops <- list(
+    "data_model_labels" = "class_label"
+  )
+  global_conf <- names(conf$schematic$global)
+  if (!"data_model_labels" %in% global_conf) {
+    conf$schematic$global$data_model_labels <- "class_label"
+  }
+  
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  mg_props_req <- list(
+    "output_format" = "excel",
+    "use_annotations" = TRUE
+  )
+  mg_props_ops <- list()
+  mg_props_conf <- names(conf$schematic$manifest_generate)
+  name_check(names(mg_props_req), mg_props_conf)
+  
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  mv_props_req <- list(
+    "restrict_rules" = FALSE
+  )
+  mv_props_ops <- list()
+  mv_props_conf <- names(conf$schematic$model_validate)
+  name_check(names(mv_props_req), mv_props_conf)
+  
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  ms_props_req <- list(
+    "table_manipulation" = "replace",
+    "manifest_record_type" = "file_only",
+    "hide_blanks" = FALSE
+  )
+  ms_props_ops <- list()
+  ms_props_conf <- names(conf$schematic$model_submit)
+  
+  conf
+  
+}

From 3887dc10180a18cb7b2797b6666be1af4dc78d73 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 2 Jul 2024 15:23:53 -0700
Subject: [PATCH 3/7] Read DCA config with function

---
 server.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server.R b/server.R
index f3cd9472..fc740883 100644
--- a/server.R
+++ b/server.R
@@ -184,7 +184,7 @@ shinyServer(function(input, output, session) {
     tenant_config_react(tenants_config[tenants_config$synapse_asset_view == selected$master_asset_view(), ])
     if (dca_schematic_api == "offline") tenant_config_react(tenants_config[tenants_config$name == "DCA Demo", ])
 
-    dcc_config_react(read_json(
+    dcc_config_react(read_dca_config(
       file.path(config_dir, tenant_config_react()$config_location)
     ))
 

From fb6466924714054d13e6d950a13ff9c76b999420 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Tue, 2 Jul 2024 15:24:10 -0700
Subject: [PATCH 4/7] Add function to read DCA config file

---
 functions/read_dca_config.R | 101 ++++++++++++++++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 functions/read_dca_config.R

diff --git a/functions/read_dca_config.R b/functions/read_dca_config.R
new file mode 100644
index 00000000..2bbfe4bf
--- /dev/null
+++ b/functions/read_dca_config.R
@@ -0,0 +1,101 @@
+#' @title Read the DCA config file and report issues
+#' @param config URL or filepath to a DCA JSON config file
+read_dca_config <- function(config) {
+  conf <- jsonlite::fromJSON(config)
+  
+  name_check <- function(req, prov) {
+    if (!all(req %in% prov)) {
+      which_miss <- req[which(!req %in% prov)]
+      stop(sprintf("DCA config missing %s", which_miss))
+    }
+  }
+  
+  lvl_1_props_req <- list(
+    "dcc" = list(),
+    "dca" = list(),
+    "schematic" = list()
+  )
+  lvl_1_props_ops <- list() # Placeholder for optional properties
+  lvl_1_props_conf <- names(conf)
+  name_check(names(lvl_1_props_req), lvl_1_props_conf)
+  
+  dca_props_req <- list() # Placeholder for required DCA properties
+  dca_props_ops <- list(
+    "use_compliance_dashboard" = FALSE,
+    "primary_col" = "#2a668d",
+    "secondary_col" = "#184e71",
+    "sidebar_col" = "#191919"
+  )
+  dca_props_conf <- names(conf$dca)
+  name_check(names(dca_props_req), dca_props_conf)
+  
+  if (!"use_compliance_dashboard" %in% dca_props_conf) {
+    conf$dca$use_compliance_dashboard <- FALSE
+  }
+  if (!"primary_col" %in% dca_props_conf) {
+    conf$dca$primary_col <- "#2a668d"
+  }
+  if (!"secondary_col" %in% dca_props_conf) {
+    conf$dca$secondary_col <- "#184e71"
+  }
+  if (!"primary_col" %in% dca_props_conf) {
+    conf$dca$sidebar_col <- "#191919"
+  }
+  
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  schematic_props_req <- list(
+    "manifest_generate" = list(),
+    "model_validate" = list(),
+    "model_submit" = list()
+  )
+  schematic_props_ops <- list(
+    "global" = list()
+  )
+  schematic_props_conf <- names(conf$schematic)
+  name_check(names(schematic_props_req), schematic_props_conf)
+  
+  if (!"global" %in% schematic_props_conf) {
+    conf$schematic$global <- list()
+  }
+  
+  global_ops <- list(
+    "data_model_labels" = "class_label"
+  )
+  global_conf <- names(conf$schematic$global)
+  if (!"data_model_labels" %in% global_conf) {
+    conf$schematic$global$data_model_labels <- "class_label"
+  }
+  
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  mg_props_req <- list(
+    "output_format" = "excel",
+    "use_annotations" = TRUE
+  )
+  mg_props_ops <- list()
+  mg_props_conf <- names(conf$schematic$manifest_generate)
+  name_check(names(mg_props_req), mg_props_conf)
+  
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  mv_props_req <- list(
+    "restrict_rules" = FALSE
+  )
+  mv_props_ops <- list()
+  mv_props_conf <- names(conf$schematic$model_validate)
+  name_check(names(mv_props_req), mv_props_conf)
+  
+  # required elements should not have a default. Should error if not provided.
+  # WIP, confirm required and move others to ops with defaults
+  ms_props_req <- list(
+    "table_manipulation" = "replace",
+    "manifest_record_type" = "file_only",
+    "hide_blanks" = FALSE
+  )
+  ms_props_ops <- list()
+  ms_props_conf <- names(conf$schematic$model_submit)
+  
+  conf
+  
+}

From 4996ebb78a7c376196e7fa1b23a52378bc52ab49 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 3 Jul 2024 10:11:54 -0700
Subject: [PATCH 5/7] add cross_manifest_validation to config check

---
 R/read_dca_config.R         | 8 +++++++-
 functions/read_dca_config.R | 8 +++++++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/R/read_dca_config.R b/R/read_dca_config.R
index 2bbfe4bf..8bfc1278 100644
--- a/R/read_dca_config.R
+++ b/R/read_dca_config.R
@@ -82,10 +82,16 @@ read_dca_config <- function(config) {
   mv_props_req <- list(
     "restrict_rules" = FALSE
   )
-  mv_props_ops <- list()
+  mv_props_ops <- list(
+    "cross_manifest_validation" = FALSE
+  )
   mv_props_conf <- names(conf$schematic$model_validate)
   name_check(names(mv_props_req), mv_props_conf)
   
+  if (!"cross_manifest_validation" %in% mv_props_confg) {
+    conf$schematic$model_validate$cross_manifest_validation <- FALSE
+  }
+  
   # required elements should not have a default. Should error if not provided.
   # WIP, confirm required and move others to ops with defaults
   ms_props_req <- list(
diff --git a/functions/read_dca_config.R b/functions/read_dca_config.R
index 2bbfe4bf..8bfc1278 100644
--- a/functions/read_dca_config.R
+++ b/functions/read_dca_config.R
@@ -82,10 +82,16 @@ read_dca_config <- function(config) {
   mv_props_req <- list(
     "restrict_rules" = FALSE
   )
-  mv_props_ops <- list()
+  mv_props_ops <- list(
+    "cross_manifest_validation" = FALSE
+  )
   mv_props_conf <- names(conf$schematic$model_validate)
   name_check(names(mv_props_req), mv_props_conf)
   
+  if (!"cross_manifest_validation" %in% mv_props_confg) {
+    conf$schematic$model_validate$cross_manifest_validation <- FALSE
+  }
+  
   # required elements should not have a default. Should error if not provided.
   # WIP, confirm required and move others to ops with defaults
   ms_props_req <- list(

From 95c353fefc3805bb629046b031cb005455f63e8b Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 3 Jul 2024 10:17:49 -0700
Subject: [PATCH 6/7] Update submit parameters to config check

---
 R/read_dca_config.R         | 24 +++++++++++++++++++++---
 functions/read_dca_config.R | 24 +++++++++++++++++++++---
 2 files changed, 42 insertions(+), 6 deletions(-)

diff --git a/R/read_dca_config.R b/R/read_dca_config.R
index 8bfc1278..b21aa0ea 100644
--- a/R/read_dca_config.R
+++ b/R/read_dca_config.R
@@ -88,7 +88,7 @@ read_dca_config <- function(config) {
   mv_props_conf <- names(conf$schematic$model_validate)
   name_check(names(mv_props_req), mv_props_conf)
   
-  if (!"cross_manifest_validation" %in% mv_props_confg) {
+  if (!"cross_manifest_validation" %in% mv_props_conf) {
     conf$schematic$model_validate$cross_manifest_validation <- FALSE
   }
   
@@ -96,11 +96,29 @@ read_dca_config <- function(config) {
   # WIP, confirm required and move others to ops with defaults
   ms_props_req <- list(
     "table_manipulation" = "replace",
-    "manifest_record_type" = "file_only",
+    "manifest_record_type" = "file_only"
+  )
+  ms_props_ops <- list(
+    "table_column_names" = "class_label",
+    "annotation_keys" = "class_label",
+    "file_annotations_upload" = TRUE,
     "hide_blanks" = FALSE
   )
-  ms_props_ops <- list()
   ms_props_conf <- names(conf$schematic$model_submit)
+  name_check(names(ms_props_req), ms_props_conf)
+  
+  if (!"table_column_names" %in% ms_props_conf) {
+    conf$schematic$model_submit$table_column_names <- "class_label"
+  }
+  if (!"annotation_keys" %in% ms_props_conf) {
+    conf$schematic$model_submit$annotation_keys <- "class_label"
+  }
+  if (!"file_annotations_upload" %in% ms_props_conf) {
+    conf$schematic$model_submit$file_annotations_upload <- TRUE
+  }
+  if (!"hide_blanks" %in% ms_props_conf) {
+    conf$schematic$model_submit$hide_blanks <- FALSE
+  }
   
   conf
   
diff --git a/functions/read_dca_config.R b/functions/read_dca_config.R
index 8bfc1278..b21aa0ea 100644
--- a/functions/read_dca_config.R
+++ b/functions/read_dca_config.R
@@ -88,7 +88,7 @@ read_dca_config <- function(config) {
   mv_props_conf <- names(conf$schematic$model_validate)
   name_check(names(mv_props_req), mv_props_conf)
   
-  if (!"cross_manifest_validation" %in% mv_props_confg) {
+  if (!"cross_manifest_validation" %in% mv_props_conf) {
     conf$schematic$model_validate$cross_manifest_validation <- FALSE
   }
   
@@ -96,11 +96,29 @@ read_dca_config <- function(config) {
   # WIP, confirm required and move others to ops with defaults
   ms_props_req <- list(
     "table_manipulation" = "replace",
-    "manifest_record_type" = "file_only",
+    "manifest_record_type" = "file_only"
+  )
+  ms_props_ops <- list(
+    "table_column_names" = "class_label",
+    "annotation_keys" = "class_label",
+    "file_annotations_upload" = TRUE,
     "hide_blanks" = FALSE
   )
-  ms_props_ops <- list()
   ms_props_conf <- names(conf$schematic$model_submit)
+  name_check(names(ms_props_req), ms_props_conf)
+  
+  if (!"table_column_names" %in% ms_props_conf) {
+    conf$schematic$model_submit$table_column_names <- "class_label"
+  }
+  if (!"annotation_keys" %in% ms_props_conf) {
+    conf$schematic$model_submit$annotation_keys <- "class_label"
+  }
+  if (!"file_annotations_upload" %in% ms_props_conf) {
+    conf$schematic$model_submit$file_annotations_upload <- TRUE
+  }
+  if (!"hide_blanks" %in% ms_props_conf) {
+    conf$schematic$model_submit$hide_blanks <- FALSE
+  }
   
   conf
   

From 9f6365e6ffb7c2803a5c6505baf026d621fdb565 Mon Sep 17 00:00:00 2001
From: afwillia <anthony.williams@sagebase.org>
Date: Wed, 3 Jul 2024 10:57:51 -0700
Subject: [PATCH 7/7] Add dcc options to config check

---
 R/read_dca_config.R         | 23 +++++++++++++++++++++++
 functions/read_dca_config.R | 23 +++++++++++++++++++++++
 2 files changed, 46 insertions(+)

diff --git a/R/read_dca_config.R b/R/read_dca_config.R
index b21aa0ea..747959ef 100644
--- a/R/read_dca_config.R
+++ b/R/read_dca_config.R
@@ -42,6 +42,29 @@ read_dca_config <- function(config) {
     conf$dca$sidebar_col <- "#191919"
   }
   
+  dcc_props_req <- list(
+    "name" = list(),
+    "synapse_asset_view" = list(),
+    "data_model_url" = list(),
+    "template_menu_config_file" = list()
+  )
+  dcc_props_ops <- list(
+    "data_model_info" = NA_character_,
+    "logo_location" = "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/demo/sage_logo_mark_only.png",
+    "logo_link" = "https://synapse.org",
+    "dcc_help_link" = NA_character_,
+    "portal_help_link" = NA_character_
+  )
+  dcc_props_conf <- names(conf$dcc)
+  name_check(names(dcc_props_req), dcc_props_conf)
+  
+  if (!"logo_location" %in% dcc_props_conf) {
+    conf$dcc$logo_location <- dcc_props_ops$logo_location
+  }
+  if (!"logo_link" %in% dcc_props_conf) {
+    conf$dcc$logo_link <- dcc_props_ops$logo_link
+  }
+  
   # required elements should not have a default. Should error if not provided.
   # WIP, confirm required and move others to ops with defaults
   schematic_props_req <- list(
diff --git a/functions/read_dca_config.R b/functions/read_dca_config.R
index b21aa0ea..747959ef 100644
--- a/functions/read_dca_config.R
+++ b/functions/read_dca_config.R
@@ -42,6 +42,29 @@ read_dca_config <- function(config) {
     conf$dca$sidebar_col <- "#191919"
   }
   
+  dcc_props_req <- list(
+    "name" = list(),
+    "synapse_asset_view" = list(),
+    "data_model_url" = list(),
+    "template_menu_config_file" = list()
+  )
+  dcc_props_ops <- list(
+    "data_model_info" = NA_character_,
+    "logo_location" = "https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/prod/demo/sage_logo_mark_only.png",
+    "logo_link" = "https://synapse.org",
+    "dcc_help_link" = NA_character_,
+    "portal_help_link" = NA_character_
+  )
+  dcc_props_conf <- names(conf$dcc)
+  name_check(names(dcc_props_req), dcc_props_conf)
+  
+  if (!"logo_location" %in% dcc_props_conf) {
+    conf$dcc$logo_location <- dcc_props_ops$logo_location
+  }
+  if (!"logo_link" %in% dcc_props_conf) {
+    conf$dcc$logo_link <- dcc_props_ops$logo_link
+  }
+  
   # required elements should not have a default. Should error if not provided.
   # WIP, confirm required and move others to ops with defaults
   schematic_props_req <- list(