Merge branch 'master' into feat/GPE-1163-covid19prod

uc-cdis · Jan 18, 2024 · bff50a6 · bff50a6
2 parents 4b26163 + 8ecd03d
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diff --git a/brh.data-commons.org/dashboard/Public/notebooks/OADC_CCLE_gene_expression_data_analysis.html b/brh.data-commons.org/dashboard/Public/notebooks/OADC_CCLE_gene_expression_data_analysis.html
diff --git a/data.bloodpac.org/manifest.json b/data.bloodpac.org/manifest.json
@@ -13,7 +13,7 @@
     "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service: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",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.19.0",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
     "jupyterhub": "quay.io/occ_data/jupyterhub:2023.12",
     "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.12",

diff --git a/data.bloodpac.org/portal/gitops.json b/data.bloodpac.org/portal/gitops.json
@@ -1031,57 +1031,86 @@
         "enabled": false,
         "text": "Publication Discovery"
       },
+      "tagsColumn": {
+        "enabled": false
+      },
+      "tagsInDescription": {
+        "enabled": true
+      },
       "search": {
+        "searchBar": {
+          "enabled": true
+        },
         "tagSearchDropdown": {
           "enabled": true,
           "collapsibleButtonText": "Study Filters"
-        },
-        "searchBar": {
-          "enabled": true
         }
       },
       "authorization": {
-        "enabled": true
+        "enabled": true,
+        "supportedValues": {
+          "accessible": {
+            "enabled": true,
+            "menuText": "Available"
+          },
+          "unaccessible": {
+            "enabled": true,
+            "menuText": "Not Accessible"
+          },
+          "pending": {
+            "enabled": true,
+            "menuText": "Pending"
+          },
+          "notAvailable": {
+            "enabled": true,
+            "menuText": "Not Available"
+          }
+        }
       }
     },
     "aggregations": [{
       "name": "Publications",
       "field": "_publication_id",
       "type": "count"
-    }],
+    }
+  ],
     "tagSelector": {
       "title": "Tags by category"
     },
-    "studyColumns": [{
-      "name": "Title",
-      "field": "title",
-      "contentType": "string",
-      "width": 200,
-      "errorIfNotAvailable": false,
-      "valueIfNotAvailable": "n/a"
-    },
-    {
-      "name": "Journal",
-      "field": "journal",
-      "contentType": "string",
-      "errorIfNotAvailable": false,
-      "valueIfNotAvailable": "n/a"
-    },
-    {
-      "name": "Publication URL",
-      "field": "publication_url",
-      "contentType": "link",
-      "errorIfNotAvailable": false,
-      "valueIfNotAvailable": "n/a"
-    },
-    {
-      "name": "Condition",
-      "field": "condition",
-      "contentType": "string",
-      "errorIfNotAvailable": false,
-      "valueIfNotAvailable": "n/a"
-    }
-  ],
+    "studyColumns": [
+      {
+        "name": "Title",
+        "field": "title",
+        "contentType": "string",
+        "width": 200,
+        "errorIfNotAvailable": false,
+        "valueIfNotAvailable": "n/a"
+      },
+      {
+        "name": "Journal",
+        "field": "journal",
+        "contentType": "string",
+        "width": 200,
+        "errorIfNotAvailable": false,
+        "valueIfNotAvailable": "n/a"
+      },
+      {
+        "name": "Publication URL",
+        "field": "publication_url",
+        "contentType": "link",
+        "width": 300,
+        "errorIfNotAvailable": false,
+        "valueIfNotAvailable": "n/a"
+      },
+      {
+        "name": "Condition",
+        "field": "condition",
+        "contentType": "string",
+        "width": 200,
+        "errorIfNotAvailable": false,
+        "valueIfNotAvailable": "n/a"
+      }
+    ],
     "studyPreviewField": {
       "name": "Abstract",
       "field": "abstract",
@@ -1097,10 +1126,12 @@
       "downloadLinks": {
         "field": "data_download_links"
       },
-      "fieldsToShow": [{
+      "fieldsToShow": [
+        {
           "groupName": "Publication Identifiers",
           "includeName": false,
-          "fields": [{
+          "fields": [
+            {
               "name": "Authors",
               "field": "authors",
               "contentType": "string",
@@ -1185,19 +1216,19 @@
       "uid": "_publication_id"
     },
     "tagCategories": [
-    {
+      {
         "name": "Study Setting",
         "displayName": "Study Setting",
         "color": "#532565",
         "display": true
       },
-    {
+      {
         "name": "Study Type",
         "displayName": "Study Type",
         "color": "#981f32",
         "display": true
       },
-    {
+      {
         "name": "Study Objectives",
         "displayName": "Study Objectives",
         "color": "#532565",
@@ -1208,30 +1239,31 @@
           "displayName": "Cancer Type",
           "color": "#e07c3e",
           "display": true
-        },
+      },
       {
           "name": "Cancer Stage",
           "displayName": "Cancer Stage",
           "color": "#982568",
           "display": true
-        },
+      },
       {
           "name": "Specimen Type",
           "displayName": "Specimen Type",
           "color": "#982568",
           "display": true
       },
-    {
+      {
         "name": "Data Type",
         "displayName": "Data Type",
         "color": "#bf362e",
         "display": true
       },
-    {
+      {
         "name": "Analytical Method",
         "displayName": "Analytical Method",
         "color": "#981f32",
         "display": true
-      }]
-    }
+      }
+    ]
   }
+}
diff --git a/gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json b/gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json
@@ -12,7 +12,7 @@
     "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2023.12",
     "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2023.12",
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.12",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:9.3.3",
     "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",

diff --git a/nci-crdc.datacommons.io/manifest.json b/nci-crdc.datacommons.io/manifest.json
@@ -7,22 +7,22 @@
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-    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2023.11",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.12",
+    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2023.12",
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8",
-    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.11",
+    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.12",
     "datareplicate": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/dcf-dataservice:1.6.1",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.11",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:9.3.3",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
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-    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.11",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.11"
+    "google-sa-validation": "placeholder:2023.12",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.12",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.12",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.12",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal: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",
+    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.12",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.12"
   },
   "arborist": {
     "deployment_version": "2"
@@ -38,7 +38,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.11"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.12"
     }
   },
   "sower": [
@@ -49,7 +49,7 @@
       "serviceAccountName": "jobs-nci-crdc-datacommons-io",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2023.11",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2023.12",
         "pull_policy": "Always",
         "env": [
           {
@@ -90,7 +90,7 @@
       "serviceAccountName": "jobs-nci-crdc-datacommons-io",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2023.11",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2023.12",
         "pull_policy": "Always",
         "env": [
           {
@@ -181,4 +181,4 @@
       "targetCpu": 40
     }
   }
-}
+}
diff --git a/staging.midrc.org/manifest.json b/staging.midrc.org/manifest.json
@@ -164,7 +164,7 @@
     "kube_bucket": "kube-midrcprod-gen3",
     "dispatcher_job_num": "10",
     "logs_bucket": "logs-midrcprod-gen3",
-    "dictionary_url": "http://s3.amazonaws.com/dictionary-artifacts/midrc_dictionary/1.2.6/schema.json",
+    "dictionary_url": "http://s3.amazonaws.com/dictionary-artifacts/midrc_dictionary/1.2.7/schema.json",
     "portal_app": "gitops",
     "sync_from_dbgap": "False",
     "netpolicy": "on",

diff --git a/va-testing.data-commons.org/manifest.json b/va-testing.data-commons.org/manifest.json
@@ -8,25 +8,25 @@
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+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.12",
     "argo-wrapper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/argo-wrapper:1.7.5",
-    "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2023.11",
+    "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2023.12",
     "cohort-middleware": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cohort-middleware:0.3.5",
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-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.11",
+    "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",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
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-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.11",
+    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.12",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.12",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.12",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.12",
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     "ohdsi-webapi": "707767160287.dkr.ecr.us-east-1.amazonaws.com/ohdsi/webapi:2.13.0",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.11",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.12",
     "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:feat_login",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.11",
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-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.11",
-    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2023.11"
+    "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",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.12",
+    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2023.12"
   },
   "global": {
     "environment": "va-testing",
@@ -45,7 +45,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.11"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.12"
     }
   },
   "canary": {

diff --git a/va-testing.data-commons.org/manifests/hatchery/hatchery.json b/va-testing.data-commons.org/manifests/hatchery/hatchery.json
@@ -30,7 +30,7 @@
       "cpu-limit": "0.5",
       "memory-limit": "512Mi",
       "name": "R Studio",
-      "image": "heliumdatastage/rstudio-server:1",
+      "image": "quay.io/cdis/rstudio:4.2.1",
       "env": {
         "DISABLE_AUTH": "true"
       },
@@ -167,4 +167,4 @@
       "user-volume-location": "/home/jovyan/pd"
     }
   ]
-}
+}