Merge branch 'master' into doc/release_artifacts_1739814183

bihstaging.data-commons.org/manifest.json

@@ -12,16 +12,17 @@
     "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2025.01",
     "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",
-    "frontend-framework": "quay.io/cdis/bih-data-commons:1.1.3",
+    "frontend-framework": "quay.io/cdis/bih-data-commons:1.1.4",
     "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",
     "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2025.01",
     "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2025.01",
     "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",

brh.data-commons.org/portal/gitops.json

@@ -1,4 +1,6 @@
 {
+  "ddEnv": "brhprod",
+  "ddUrl": "ddog-gov.com",
   "gaTrackingId": "G-WM3JV9YMW3",
   "grafanaFaroConfig": {
     "grafanaFaroEnable": true,
@@ -606,12 +608,6 @@
         "imageUrl": "/dashboard/Public/notebooks/MIDRC_Clinical_Data_Demo.png",
         "link": "/dashboard/Public/notebooks/MIDRC_Clinical_Data_Demo.html"
       },
-      {
-        "title": "JCOIN Tracking Opioid Stigma",
-        "description": "In this Jupyter notebook, we used the JCOIN-MAARC (Justice Community Opioid Innovation Network - Methodology and Advanced Analytics Resource Center) Survey Core Survey Project 1/4 to track stigma related to Opioid Use Disorder (OUD) and public attitudes towards persons with OUD as well as how treatment of/for persons with OUD may impact the effect of OUD interventions.",
-        "link": "/dashboard/Public/notebooks/JCOIN_Tracking_Opioid_Stigma.html",
-        "imageUrl": "/dashboard/Public/notebooks/JCOIN_Tracking_Opioid_Stigma.png"
-      },
       {
         "title": "Identification of Potential Drug Targets of Inflammatory Bowel Disease",
         "description": "This notebook demonstrates an approach to query data in EpiGraphDB to prioritize potential alternative drug targets in the same protein-protein interaction network for Inflammatory Bowel Disease",

brhstaging.data-commons.org/portal/gitops.json

@@ -173,8 +173,8 @@
         "enableDownloadManifest": true,
         "downloadManifestButtonText": "Download",
         "documentationLinks": {
-          "gen3Client": "https://gen3.org/resources/user/gen3-client/",
-          "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/"
+          "gen3Client": "https://docs.gen3.org/gen3-resources/user-guide/access-data/#download-files-using-the-gen3-client",
+          "gen3Workspaces": "https://docs.gen3.org/gen3-resources/user-guide/analyze-data/"
         }
       },
       "pageTitle": {
@@ -495,12 +495,6 @@
         "imageUrl": "/dashboard/Public/notebooks/MIDRC_Clinical_Data_Demo.png",
         "link": "/dashboard/Public/notebooks/MIDRC_Clinical_Data_Demo.html"
       },
-      {
-        "title": "JCOIN Tracking Opioid Stigma",
-        "description": "In this Jupyter notebook, we used the JCOIN-MAARC (Justice Community Opioid Innovation Network - Methodology and Advanced Analytics Resource Center) Survey Core Survey Project 1/4 to track stigma related to Opioid Use Disorder (OUD) and public attitudes towards persons with OUD as well as how treatment of/for persons with OUD may impact the effect of OUD interventions.",
-        "link": "/dashboard/Public/notebooks/JCOIN_Tracking_Opioid_Stigma.html",
-        "imageUrl": "/dashboard/Public/notebooks/JCOIN_Tracking_Opioid_Stigma.png"
-      },
       {
         "title": "OADC Unsupervised Data Exploration on Cancer Cell Line Encyclopedia (CCLE)",
         "description": "Principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE) has become valuable tools for unsupervised data exploration. This notebook explores the application of unsupervised learning on Cancer Cell Line Encyclopedia (CCLE) gene expression profile. All results shown in this notebook are for demonstration purposes and should not be considered scientifically rigorous.",

chicagoland.pandemicresponsecommons.org/portal/gitops.json

@@ -110,7 +110,7 @@
           "name": "Cite"
         },
         {
-          "link": "https://gen3.org/resources/user/",
+          "link": "https://docs.gen3.org/gen3-resources/user-guide/",
           "name": "Documentation"
         },
         {
@@ -1344,8 +1344,8 @@
         "externalWebsiteURL": "https://pandemicresponsecommons.org",
         "fillRequestFormCheckField": "_medical_sample_id",
         "documentationLinks": {
-          "gen3Client": "https://gen3.org/resources/user/gen3-client/",
-          "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/"
+          "gen3Client": "https://docs.gen3.org/gen3-resources/user-guide/access-data/#download-files-using-the-gen3-client",
+          "gen3Workspaces": "https://docs.gen3.org/gen3-resources/user-guide/analyze-data/"
         },
         "verifyExternalLogins": true
       },
@@ -1636,4 +1636,4 @@
   "connectSrcCSPWhitelist": [
     "https://covd-map-occ-prc-prod.s3.amazonaws.com"
   ]
-}
+}

data.kidsfirstdrc.org/manifest.json

@@ -10,7 +10,7 @@
     "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2025.01",
     "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2025.01",
     "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2025.01",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2025.01",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:11.0.2",
     "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2025.01",
     "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2025.01",
     "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2025.01",
@@ -80,4 +80,4 @@
       "strategy": "auto"
     }
   }
-}
+}

data.midrc.org/manifest.json

@@ -163,7 +163,7 @@
     "kube_bucket": "kube-midrcprod-gen3",
     "dispatcher_job_num": "10",
     "logs_bucket": "logs-midrcprod-gen3",
-    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/midrc_dictionary/1.3.7/schema.json",
+    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/midrc_dictionary/1.3.8/schema.json",
     "portal_app": "gitops",
     "sync_from_dbgap": "False",
     "netpolicy": "on",

data.midrc.org/portal/gitops.json

@@ -308,7 +308,7 @@
           "name": "Resources"
         },
         {
-          "link": "https://gen3.org/resources/user/",
+          "link": "https://docs.gen3.org/gen3-resources/user-guide/",
           "name": "Gen3"
         },
         {
@@ -1852,4 +1852,4 @@
     ]
   },
   "ddUrl": "ddog-gov.com"
-}
+}

gen3.biodatacatalyst.nhlbi.nih.gov/manifest.json

@@ -7,12 +7,12 @@
     "autodeploy": "yes"
   },
   "versions": {
-    "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2025.01",
+    "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:1.6.1",
     "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2025.01",
     "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2025.01",
     "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2025.01",
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:v1.3.1",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:11.0.1",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:11.0.2",
     "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2025.01",
     "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2025.01",
     "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2025.01",

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

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"

healdata.org/manifests/hatchery/hatchery.json

@@ -63,7 +63,7 @@
       "lifecycle-post-start": [
         "/bin/sh",
         "-c",
-        "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; wget -O /data/qdr_data_download.ipynb https://raw.githubusercontent.com/uc-cdis/heal-platform-sdk/refs/heads/master/notebooks/qdr_data_download.ipynb; true"
+        "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; wget -O /data/external_data_download.ipynb https://raw.githubusercontent.com/uc-cdis/heal-platform-sdk/refs/heads/master/notebooks/external_data_download.ipynb; true"
       ],
       "user-uid": 1000,
       "fs-gid": 100,
@@ -186,4 +186,4 @@
       "gen3-volume-location": "/home/jovyan/.gen3"
     }
   ]
-}
+}

healdata.org/portal/gitops.json

@@ -528,12 +528,6 @@
         "link": "/dashboard/Public/notebooks/Opioid_Environment_Toolkit_And_OEPS_R.html",
         "imageUrl": "/dashboard/Public/notebooks/Opioid_Environment_Toolkit_And_OEPS_R.png"
       },
-      {
-        "title": "JCOIN Tracking Opioid Stigma",
-        "description": "In this Jupyter notebook, we used the JCOIN-MAARC (Justice Community Opioid Innovation Network - Methodology and Advanced Analytics Resource Center) Survey Core Survey Project 1/4 to track stigma related to Opioid Use Disorder (OUD) and public attitudes towards persons with OUD as well as how treatment of/for persons with OUD may impact the effect of OUD interventions.",
-        "link": "/dashboard/Public/notebooks/JCOIN_Tracking_Opioid_Stigma.html",
-        "imageUrl": "/dashboard/Public/notebooks/JCOIN_Tracking_Opioid_Stigma.png"
-      },
       {
         "title": "Opioid Prevalence And Overdoses",
         "description": "In this Jupyter notebook, we used the CDC WONDER, DEA ARCOS, and PDAPS datasets to demonstate how multiple datasets may be utilized within the workspace in HEAL.",

imaging-hub.data-commons.org/manifest.json

@@ -12,7 +12,7 @@
     "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2025.01",
     "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",
-    "frontend-framework": "quay.io/cdis/bih-data-commons:1.1.3",
+    "frontend-framework": "quay.io/cdis/bih-data-commons:1.1.4",
     "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",
     "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2025.01",

jcoin.datacommons.io/manifests/hatchery/hatchery.json

@@ -25,40 +25,24 @@
     ]
   },
   "containers": [
-    {
-      "target-port": 8787,
-      "cpu-limit": "1.0",
-      "memory-limit": "1024Mi",
-      "name": "RStudio 4.1.0",
-      "image": "quay.io/cdis/rstudio4.1:rstudio4.1-0.1.0",
-      "env": {
-        "DISABLE_AUTH": "true"
-      },
-      "args": [],
-      "path-rewrite": "/",
-      "use-tls": "false",
-      "ready-probe": "/",
-      "user-volume-location": "/home/rstudio/pd",
-      "fs-gid": 100
-    },
     {
       "target-port": 8888,
       "cpu-limit": "1.0",
       "memory-limit": "2Gi",
       "name": "(Generic) Jupyter Lab Notebook with R Kernel",
-      "image": "quay.io/cdis/jupyter-superslim-r:1.0.1",
+      "image": "quay.io/cdis/heal-notebooks:generic_rkernel__ff880f355bfcfbb1b1a8c6e4615e13152c71be2b",
       "env": {
         "FRAME_ANCESTORS": "https://jcoin.datacommons.io"
       },
       "args": [
-        "--NotebookApp.base_url=/lw-workspace/proxy/",
-        "--NotebookApp.default_url=/lab",
-        "--NotebookApp.password=''",
-        "--NotebookApp.token=''",
-        "--NotebookApp.ip='*'",
-        "--NotebookApp.notebook_dir='/home/jovyan'",
-        "--NotebookApp.shutdown_no_activity_timeout=5400",
-        "--NotebookApp.quit_button=False"
+        "--JupyterNotebookApp.base_url=/lw-workspace/proxy/",
+        "--JupyterNotebookApp.default_url=/lab",
+        "--JupyterNotebookApp.password=''",
+        "--JupyterNotebookApp.token=''",
+        "--JupyterNotebookApp.ip='*'",
+        "--JupyterNotebookApp.notebook_dir='/home/jovyan'",
+        "--JupyterNotebookApp.shutdown_no_activity_timeout=5400",
+        "--JupyterNotebookApp.quit_button=False"
       ],
       "command": [
         "start-notebook.sh"

jcoin.datacommons.io/portal/gitops.json

@@ -1,4 +1,6 @@
 {
+  "ddEnv": "jcoin",
+  "ddUrl": "ddog-gov.com",
   "gaTrackingId": "G-22278W6QYK",
   "grafanaFaroConfig": {
     "grafanaFaroEnable": true,

nci-crdc-staging.datacommons.io/manifest.json

@@ -5,7 +5,7 @@
     "Environment is configured for Google data access methods including service account ",
     "registration. Data is in multiple Google buckets with both public and *controlled* ",
     "data. The controlled data is actually just public data so there's no sensitive ",
-    "data in this env. "
+    "data in this env."
   ],
   "jenkins": {
     "autodeploy": "yes"
@@ -16,10 +16,10 @@
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8",
     "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2025.01",
     "datareplicate": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/dcf-dataservice:2023.09",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2025.01",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:11.0.2",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
     "google-sa-validation": "placeholder:2025.01",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2025.01",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:5.1.2",
     "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2025.01",
     "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",
@@ -186,4 +186,4 @@
       "targetCpu": 40
     }
   }
-}
+}

nci-crdc.datacommons.io/manifest.json

@@ -11,11 +11,11 @@
     "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2025.01",
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8",
     "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2025.01",
-    "datareplicate": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/dcf-dataservice:feat_change-validation",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2025.01",
+    "datareplicate": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/dcf-dataservice:2.0.0",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:11.0.2",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
     "google-sa-validation": "placeholder:2025.01",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2025.01",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:5.1.2",
     "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2025.01",
     "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",
@@ -182,4 +182,4 @@
       "targetCpu": 40
     }
   }
-}
+}