Merge branch 'master' into midrc_staging_notebooks

uc-cdis · Dec 14, 2023 · f7ee88b · f7ee88b
2 parents a4fbcda + 75b44ca
commit f7ee88b
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Showing 4 changed files with 51 additions and 50 deletions.
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -7792,7 +7792,7 @@
         "filename": "jcoin.datacommons.io/manifest.json",
         "hashed_secret": "7120244dce59930b75711144fda4b1f6d78e4865",
         "is_verified": false,
-        "line_number": 163
+        "line_number": 164
       }
     ],
     "nci-crdc-staging.datacommons.io/dashboard/Secure/reports/modules/jasmine-core/package.json": [

diff --git a/jcoin.datacommons.io/manifest.json b/jcoin.datacommons.io/manifest.json
@@ -4,28 +4,28 @@
     "That's all I have to say"
   ],
   "versions": {
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.05",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.12",
     "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1",
     "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2023.10",
-    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2023.05",
-    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.05",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.05",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.05",
+    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2023.12",
+    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.12",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.12",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.12",
     "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:3.2.1",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.05",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.05",
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.12",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.12",
     "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.13.0",
-    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:0.7.5",
-    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:0.16.1",
+    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2023.12",
+    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2023.12",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
-    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.05",
-    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.05",
-    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2023.05",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.05",
+    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.12",
+    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.12",
+    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2023.12",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.12",
     "ambassador": "quay.io/datawire/ambassador:1.4.2",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.05",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.05",
-    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.05"
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.12",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.12",
+    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.12"
   },
   "indexd": {
     "arborist": "true"
@@ -45,7 +45,8 @@
     "maintenance_mode": "off",
     "argocd": "true",
     "pdb": "on",
-    "waf_enabled": "true"
+    "waf_enabled": "true",
+    "es7": true
   },
   "canary": {
     "default": 0
@@ -121,7 +122,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.05"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.12"
     }
   },
   "sower": [
@@ -132,7 +133,7 @@
       "serviceAccountName": "jobs-jcoin-datacommons-io",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2023.05",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2023.12",
         "pull_policy": "Always",
         "env": [
           {
@@ -172,7 +173,7 @@
       "serviceAccountName": "jobs-jcoin-datacommons-io",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2023.05",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2023.12",
         "pull_policy": "Always",
         "env": [],
         "volumeMounts": [
@@ -203,7 +204,7 @@
       "serviceAccountName": "jobs-jcoin-datacommons-io",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2023.05",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2023.12",
         "pull_policy": "Always",
         "env": [
           {
@@ -244,7 +245,7 @@
       "serviceAccountName": "jobs-jcoin-datacommons-io",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cdis/manifest-merging:2023.05",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cdis/manifest-merging:2023.12",
         "pull_policy": "Always",
         "env": [
           {
@@ -285,7 +286,7 @@
       "serviceAccountName": "jobs-jcoin-datacommons-io",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2023.05",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2023.12",
         "pull_policy": "Always",
         "env": [
           {

diff --git a/staging.chordshealth.org/etlMapping.yaml b/staging.chordshealth.org/etlMapping.yaml
@@ -1,5 +1,5 @@
 mappings:
-  - name: geospatial_data_resource
+  - name: chords_geospatial_data_resource
     doc_type: geospatial_data_resource
     type: aggregator
     root: geospatial_data_resource
@@ -28,7 +28,7 @@ mappings:
       - name: exposure_media
     parent_props:
       - path: resources[resource_id, resource_name:long_name, resource_short_name:name, resource_type, resource_description:description, resource_citation:citation, payment_required, domain, keywords, license_type, license_text, verification_datetime, resource_use_agreement, resource_contact, resource_url].projects[project_code:code, project_investigator_affiliation:investigator_affiliation, project_investigator_name:investigator_name, project_date:date_collected, project_name:name, project_short_name:name, support_source, support_id, project_url].programs[program_name:name, program_short_name:name]
-  - name: geospatial_tool_resource
+  - name: chords_geospatial_tool_resource
     doc_type: geospatial_tool_resource
     type: aggregator
     root: geospatial_tool_resource
@@ -53,7 +53,7 @@ mappings:
       - name: model_methods
     parent_props:
       - path: resources[resource_id, resource_name:long_name, resource_short_name:name, resource_type, resource_description:description, resource_citation:citation, payment_required, domain, keywords, license_type, license_text, verification_datetime, resource_use_agreement, resource_contact, resource_url].projects[project_code:code, project_investigator_affiliation:investigator_affiliation, project_investigator_name:investigator_name, project_date:date_collected, project_name:name, project_short_name:name, support_source, support_id, project_url].programs[program_name:name, program_short_name:name]
-  - name: population_data_resource
+  - name: chords_population_data_resource
     doc_type: population_data_resource
     type: aggregator
     root: population_data_resource
@@ -86,4 +86,4 @@ mappings:
       - name: population_studied_other
 
     parent_props:
-      - path: resources[resource_id, resource_name:long_name, resource_short_name:name, resource_type, resource_description:description, resource_citation:citation, payment_required, domain, keywords, license_type, license_text, verification_datetime, resource_use_agreement, resource_contact, resource_url].projects[project_code:code, project_investigator_affiliation:investigator_affiliation, project_investigator_name:investigator_name, project_date:date_collected, project_name:name, project_short_name:name, support_source, support_id, project_url].programs[program_name:name, program_short_name:name]
+      - path: resources[resource_id, resource_name:long_name, resource_short_name:name, resource_type, resource_description:description, resource_citation:citation, payment_required, domain, keywords, license_type, license_text, verification_datetime, resource_use_agreement, resource_contact, resource_url].projects[project_code:code, project_investigator_affiliation:investigator_affiliation, project_investigator_name:investigator_name, project_date:date_collected, project_name:name, project_short_name:name, support_source, support_id, project_url].programs[program_name:name, program_short_name:name]
diff --git a/staging.chordshealth.org/manifest.json b/staging.chordshealth.org/manifest.json
@@ -7,25 +7,25 @@
     "autodeploy": "yes"
   },
   "versions": {
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.10",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.12",
     "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.10",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.10",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.10",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.10",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.10",
-    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2023.10",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.12",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.12",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.12",
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.12",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.12",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2023.12",
     "frontend-framework": "quay.io/cdis/frontend-framework:feat_n3c",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.10",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.12",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
-    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.10",
-    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2023.10",
-    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2023.10",
-    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.10",
+    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.12",
+    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2023.12",
+    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2023.12",
+    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.12",
     "ambassador": "quay.io/datawire/ambassador:1.4.2",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.10",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.10",
-    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.10"
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.12",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.12",
+    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.12"
   },
   "arborist": {
     "deployment_version": "2"
@@ -41,7 +41,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.10"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.12"
     }
   },
   "sower": [
@@ -50,7 +50,7 @@
       "action": "export",
       "container": {
         "name": "job-task",
-        "image": "quay.io/cdis/pelican-export:2023.10",
+        "image": "quay.io/cdis/pelican-export:2023.12",
         "pull_policy": "Always",
         "env": [
           {
@@ -126,7 +126,7 @@
       "action": "export-files",
       "container": {
         "name": "job-task",
-        "image": "quay.io/cdis/pelican-export:2023.10",
+        "image": "quay.io/cdis/pelican-export:2023.12",
         "pull_policy": "Always",
         "env": [
           {
@@ -282,19 +282,19 @@
   "guppy": {
     "indices": [
       {
-        "index": "geospatial_data_resource",
+        "index": "chords_geospatial_data_resource",
         "type": "geospatial_data_resource"
       },
       {
-        "index": "population_data_resource",
+        "index": "chords_population_data_resource",
         "type": "population_data_resource"
       },
       {
-        "index": "geospatial_tool_resource",
+        "index": "chords_geospatial_tool_resource",
         "type": "geospatial_tool_resource"
       }
     ],
-    "config_index": "chords-array-config",
+    "config_index": "chords_array-config",
     "auth_filter_field": "auth_resource_path"
   },
   "scaling": {