Testing Please ignore - copy biodatacat

gen3.theanvil.io/etlMapping.yaml

@@ -1,64 +1,119 @@
 mappings:
-  - name: etl_anvil
-    doc_type: case
-    type: aggregator
-    root: case
+- name: gen3.theanvil.io_subject
+  doc_type: subject
+  type: aggregator
+  root: subject
+  props:
+  - name: submitter_id
+  - name: project_id
+  - name: sex
+  - name: age_value
+  - name: ancestry
+  - name: disease_description
+  - name: phenotype_present
+  - name: phenotype_absent
+  - name: disease_id
+  - name: solve_state
+  - name: congenital_status
+  - name: age_of_onset
+  aggregated_props:
+  - name: sample_provider
+    path: samples
+    src: sample_provider
+    fn: set
+  - name: tissue_affected_status
+    path: samples
+    src: tissue_affected_status
+    fn: set
+  - name: tissue_type
+    path: samples
+    src: tissue_type
+    fn: set
+  - name: sample_type
+    path: samples
+    src: sample_type
+    fn: set
+  - name: original_material_type
+    path: samples
+    src: original_material_type
+    fn: set
+  - name: exome_capture_platform
+    path: samples.sequencings
+    src: exome_capture_platform
+    fn: set
+  - name: library_prep_kit_method
+    path: samples.sequencings
+    src: library_prep_kit_method
+    fn: set
+  - name: capture_region_bed_file
+    path: samples.sequencings
+    src: capture_region_bed_file
+    fn: set
+  - name: reference_genome_build
+    path: samples.sequencings
+    src: reference_genome_build
+    fn: set
+  - name: sequencing_assay
+    path: samples.sequencings
+    src: sequencing_assay
+    fn: set
+  - name: alignment_method
+    path: samples.sequencings
+    src: alignment_method
+    fn: set
+  - name: data_processing_pipeline
+    path: samples.sequencings
+    src: data_processing_pipeline
+    fn: set
+  - name: _samples_count
+    path: samples
+    fn: count
+  - name: _sequencings_count
+    path: samples.sequencings
+    fn: count
+  joining_props:
+  - index: file
+    join_on: subject_id
     props:
-      - name: submitter_id
+    - name: data_format
+      src: data_format
+      fn: set
+    - name: data_type
+      src: data_type
+      fn: set
+  parent_props:
+  - path: projects[project_code:code]
+  - path: projects[project_name:name]
+  - path: projects[project_dbgap_phs:dbgap_phs]
+  - path: projects[project_dbgap_consent_text:dbgap_consent_text]
+  - path: projects[project_short_name:short_name]
+  - path: projects[project_dbgap_accession_number:dbgap_accession_number]
+- name: gen3.theanvil.io_file
+  doc_type: file
+  type: collector
+  root: None
+  category: data_file
+  props:
+  - name: project_id
+  - name: submitter_id
+  - name: object_id
+  - name: md5sum
+  - name: file_name
+  - name: file_size
+  - name: data_format
+  - name: data_type
+  - name: state
+  - name: data_category
+  - name: analyte_type
+  - name: sequencing_assay
+  injecting_props:
+    subject:
+      props:
+      - name: subject_id
+        src: id
+        fn: set
+      - name: subject_submitter_id
+        src: submitter_id
+        fn: set
       - name: project_id
-    flatten_props:
-      - path: demographics
-        props:
-          - name: sex
-          - name: race
-          - name: ethnicity
-          - name: age
-      - path: death_records
-        props:
-          - name: hardy_scale
-    aggregated_props:
-      - name: _samples_count
-        path: samples
-        fn: count
-      - name: ischemic_time
-        path: samples
-        src: ischemic_time
         fn: set
-      - name: _aliquots_count
-        path: samples.aliquots
-        fn: count
-      - name: _read_groups_count
-        path: samples.aliquots.read_groups
-        fn: count
-      - name: _submitted_aligned_reads_count
-        path: samples.aliquots.read_groups.submitted_aligned_reads_files
-        fn: count
-    joining_props:
-      - index: file
-        join_on: case_id
-        props:
-          - name: data_format
-            src: data_format
-            fn: set
-          - name: data_type
-            src: data_type
-            fn: set
-  - name: file_anvil
-    doc_type: file
-    type: collector
-    root: None
-    category: data_file
-    props:
-      - name: object_id
-      - name: md5sum
-      - name: file_name
-      - name: file_size
-      - name: data_format
-      - name: data_type
-      - name: state
-    injecting_props:
-      case:
-        props:
-          - name: case_id
-            src: id
-          - name: project_id

gen3.theanvil.io/manifest.json

@@ -7,31 +7,33 @@
     "autodeploy": "yes"
   },
   "versions": {
-    "arborist": "quay.io/cdis/arborist:2020.05",
+    "arborist": "quay.io/cdis/arborist:2020.07",
     "aws-es-proxy": "abutaha/aws-es-proxy:0.8",
-    "fence": "quay.io/cdis/fence:2020.05",
+    "fence": "quay.io/cdis/fence:2020.07",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
-    "guppy": "quay.io/cdis/guppy:2020.05",
-    "hatchery": "quay.io/cdis/hatchery:2020.05",
-    "ambassador": "quay.io/datawire/ambassador:0.60.3",
-    "indexd": "quay.io/cdis/indexd:2020.05",
-    "manifestservice": "quay.io/cdis/manifestservice:2020.05",
-    "peregrine": "quay.io/cdis/peregrine:2020.05",
-    "pidgin": "quay.io/cdis/pidgin:2020.05",
-    "portal": "quay.io/cdis/data-portal:2020.05",
-    "revproxy": "quay.io/cdis/nginx:2020.05",
-    "sheepdog": "quay.io/cdis/sheepdog:2020.05",
-    "sower": "quay.io/cdis/sower:2020.05",
-    "spark": "quay.io/cdis/gen3-spark:2020.05",
-    "tube": "quay.io/cdis/tube:2020.05",
-    "ssjdispatcher": "quay.io/cdis/ssjdispatcher:2020.05",
-    "wts": "quay.io/cdis/workspace-token-service:2020.05"
+    "guppy": "quay.io/cdis/guppy:2020.07",
+    "hatchery": "quay.io/cdis/hatchery:2020.07",
+    "ambassador": "quay.io/datawire/ambassador:1.4.2",
+    "indexd": "quay.io/cdis/indexd:2020.07",
+    "manifestservice": "quay.io/cdis/manifestservice:2020.07",
+    "peregrine": "quay.io/cdis/peregrine:2020.07",
+    "pidgin": "quay.io/cdis/pidgin:2020.07",
+    "portal": "quay.io/cdis/data-portal:2020.07",
+    "revproxy": "quay.io/cdis/nginx:2020.07",
+    "sheepdog": "quay.io/cdis/sheepdog:2020.07",
+    "sower": "quay.io/cdis/sower:2020.07",
+    "spark": "quay.io/cdis/gen3-spark:2020.07",
+    "tube": "quay.io/cdis/tube:2020.07",
+    "ssjdispatcher": "quay.io/cdis/ssjdispatcher:2020.07",
+    "wts": "quay.io/cdis/workspace-token-service:2020.07",
+    "dashboard": "quay.io/cdis/gen3-statics:2020.07",
+    "metadata": "quay.io/cdis/metadata-service:2020.07"
   },
   "global": {
     "environment": "anvilprod",
     "hostname": "gen3.theanvil.io",
     "revproxy_arn": "arn:aws:acm:us-east-1:474789003679:certificate/9fd731e3-3366-4bd0-a3ef-0453dc07289a",
-    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/1.1.6/schema.json",
+    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/2.1.10/schema.json",
     "portal_app": "gitops",
     "kube_bucket": "kube-anvilprod-gen3",
     "logs_bucket": "logs-anvilprod-gen3",
@@ -49,7 +51,7 @@
       "action": "export",
       "container": {
         "name": "job-task",
-        "image": "quay.io/cdis/pelican-export:2020.05",
+        "image": "quay.io/cdis/pelican-export:2020.07",
         "pull_policy": "Always",
         "env": [
           {
@@ -72,7 +74,7 @@
           },
           {
             "name": "ROOT_NODE",
-            "value": "case"
+            "value": "subject"
           }
         ],
         "volumeMounts": [
@@ -114,7 +116,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "quay.io/cdis/indexs3client:2020.05"
+      "indexing": "quay.io/cdis/indexs3client:2020.07"
     }
   },
   "arborist": {
@@ -123,18 +125,16 @@
   "guppy": {
     "indices": [
       {
-        "index": "etl_anvil",
-        "type": "case"
+        "index": "gen3.theanvil.io_subject",
+        "type": "subject"
       },
       {
-        "index": "file_anvil",
+        "index": "gen3.theanvil.io_file",
         "type": "file"
       }
     ],
-    "auth_filter_field": "auth_resource_path"
-  },
-  "peregrine": {
-    "sidecar": "True"
+    "auth_filter_field": "auth_resource_path",
+    "config_index": "gen3.theanvil.io_array-config"
   },
   "canary": {
     "default": 0
@@ -195,4 +195,4 @@
       "targetCpu": 40
     }
   }
-}
+}

gen3.theanvil.io/manifests/hatchery/hatchery.json

@@ -5,7 +5,7 @@
   "sidecar": {
     "cpu-limit": "1.0",
     "memory-limit": "512Mi",
-    "image": "quay.io/cdis/gen3fuse-sidecar:2020.05",
+    "image": "quay.io/cdis/gen3fuse-sidecar:2020.07",
     "env": {
       "NAMESPACE": "default",
       "HOSTNAME": "gen3.theanvil.io"
@@ -172,4 +172,4 @@
       "fs-gid": 100
     }
   ]
-}
+}