Merge branch 'master' into data-library-prod

uc-cdis · Mar 3, 2025 · bad5723 · bad5723
2 parents 4f4d6a4 + 77c563e
commit bad5723
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Showing 7 changed files with 129 additions and 8 deletions.
diff --git a/bihstaging.data-commons.org/manifest.json b/bihstaging.data-commons.org/manifest.json
@@ -20,8 +20,9 @@
     "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2025.01",
     "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2025.01",
     "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2025.01",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:5.2.0",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2025.01",
     "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2025.01",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2025.01",
     "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2025.01",
     "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2025.01"
   },
@@ -31,17 +32,22 @@
   "indexd": {
     "arborist": "true"
   },
+  "ssjdispatcher": {
+    "job_images": {
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2025.01"
+    }
+  },
   "global": {
     "environment": "bihprod",
     "hostname": "bihstaging.data-commons.org",
     "revproxy_arn": "arn:aws:acm:us-east-1:533267425233:certificate/dcb6f91b-6e4c-4458-a9d7-3750ba92b754",
-    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/bih_dictionary/0.1.1/schema.json",
+    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/bih_dictionary/0.1.2/schema.json",
     "dispatcher_job_num": "10",
     "portal_app": "gitops",
     "sync_from_dbgap": "False",
     "kube_bucket": "kube_bucket.devplanetv1.gen3",
     "logs_bucket": "logs-devplanetv1-gen3",
-    "useryaml_s3path": "s3://cdis-gen3-users/midrc-bih/user.yaml",
+    "useryaml_s3path": "s3://cdis-gen3-users/midrc-bih-staging/user.yaml",
     "tier_access_level": "libre",
     "public_datasets": true,
     "netpolicy": "on",

diff --git a/gen3.biodatacatalyst.nhlbi.nih.gov/manifests/fence/fence-config-public.yaml b/gen3.biodatacatalyst.nhlbi.nih.gov/manifests/fence/fence-config-public.yaml
@@ -1402,4 +1402,49 @@ S3_BUCKETS:
   nih-nhlbi-topmed-freeze10-phs001607-v4-c6:
     cred: fence-bot
     region: us-east-1
+  nih-nhlbi-bdc-best-cli-phs003844-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biol-jhs-phs003740-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biol-jhs-phs003740-c2:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biol-jhs-phs003740-c3:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biol-jhs-phs003740-c4:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biolincc-dig-phs003872-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-escape-phs003782-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-hfn-migen-exs-bioimage-phs001058-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-petal-rose-phs003878-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-petal-violet-phs003879-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-phs001961-v3-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-react-biolincc-phs003885-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-roc-prohs-phs003826-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-shhs-phs003637-v3-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-biodata-catalyst-phs002694-v5:
+    cred: fence-bot
+    region: us-east-1
 ENABLE_VISA_UPDATE_CRON: true
diff --git a/healdata.org/manifest.json b/healdata.org/manifest.json
@@ -48,7 +48,7 @@
       "activeDeadlineSeconds": 600,
       "container": {
         "name": "job-task",
-        "image": "quay.io/cdis/batch-export:2024.12",
+        "image": "quay.io/cdis/batch-export:5.0.1",
         "pull_policy": "Always",
         "labels": {
           "internet": "yes"

diff --git a/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/fence/fence-config-public.yaml b/preprod.gen3.biodatacatalyst.nhlbi.nih.gov/manifests/fence/fence-config-public.yaml
@@ -1635,4 +1635,49 @@ S3_BUCKETS:
   nih-nhlbi-topmed-freeze10-phs001607-v4-c6:
     cred: fence-bot
     region: us-east-1
+  nih-nhlbi-bdc-best-cli-phs003844-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biol-jhs-phs003740-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biol-jhs-phs003740-c2:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biol-jhs-phs003740-c3:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biol-jhs-phs003740-c4:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-biolincc-dig-phs003872-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-escape-phs003782-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-hfn-migen-exs-bioimage-phs001058-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-petal-rose-phs003878-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-petal-violet-phs003879-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-phs001961-v3-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-react-biolincc-phs003885-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-roc-prohs-phs003826-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-bdc-shhs-phs003637-v3-c1:
+    cred: fence-bot
+    region: us-east-1
+  nih-nhlbi-biodata-catalyst-phs002694-v5:
+    cred: fence-bot
+    region: us-east-1
 ENABLE_VISA_UPDATE_CRON: true
diff --git a/preprod.healdata.org/manifest.json b/preprod.healdata.org/manifest.json
@@ -12,7 +12,7 @@
     "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.12",
     "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1",
     "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.12",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.12",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2025.01",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
     "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.12",
     "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.12",
@@ -48,7 +48,7 @@
       "activeDeadlineSeconds": 600,
       "container": {
         "name": "job-task",
-        "image": "quay.io/cdis/batch-export:2024.12",
+        "image": "quay.io/cdis/batch-export:5.0.1",
         "pull_policy": "Always",
         "labels": {
           "internet": "yes"

diff --git a/staging.midrc.org/manifest.json b/staging.midrc.org/manifest.json
@@ -17,13 +17,13 @@
     "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2025.01",
     "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2025.01",
     "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2025.01",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2025.01",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:4.0.4",
     "ohif-viewer": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohif-viewer:gen3-v3.8.0-AL2",
     "orthanc": "docker.io/osimis/orthanc:master",
     "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2025.01",
     "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2025.01",
     "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2025.01",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:5.2.0",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2025.01",
     "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2025.01",
     "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2025.01",
     "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2025.01",

diff --git a/va.data-commons.org/portal/gitops.json b/va.data-commons.org/portal/gitops.json
@@ -25,6 +25,12 @@
     },
     "navigation": {
       "items": [
+        {
+          "icon": "query",
+          "link": "/resource-browser",
+          "color": "#a2a2a2",
+          "name": "Resources"
+        },
         {
           "icon": "workspace",
           "link": "/workspace",
@@ -90,6 +96,20 @@
       }
     ]
   },
+  "resourceBrowser": {
+    "title": "Resources",
+    "description": "",
+    "public": false,
+    "resources": [
+      {
+        "title": "MVP Data Dictionary",
+        "category": "",
+        "description": "Data Dictionary for the MVP data. Includes list of all the concepts, information and basic statistics. Basic statistics includes concept values distribution.",
+        "link": "/dashboard/Secure/dd/VADataCommonsDictionary20240213.html",
+        "imageUrl": "/src/img/analysis-icons/default-app.png"
+      }
+    ]
+  },
   "featureFlags": {
     "explorer": false,
     "analysis": true,
@@ -152,6 +172,11 @@
       "resource": "/dashboard", 
       "method": "access",
       "service": "dashboard"
+    },
+    "Resources": {
+      "resource": "/dashboard",
+      "method": "access",
+      "service": "dashboard"
     }
   }
 }