Merge branch 'master' into Nightly(12-10-2024)

uc-cdis · Dec 12, 2024 · f17f044 · f17f044
2 parents f6080ce + cd30f61
commit f17f044
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Showing 9 changed files with 85 additions and 84 deletions.
diff --git a/data.midrc.org/manifest.json b/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/1.3.6/schema.json",
+    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/midrc_dictionary/1.3.7/schema.json",
     "portal_app": "gitops",
     "sync_from_dbgap": "False",
     "netpolicy": "on",

diff --git a/externaldata.healdata.org/manifest.json b/externaldata.healdata.org/manifest.json
@@ -7,16 +7,16 @@
     "autodeploy": "yes"
   },
   "versions": {
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.10",
-    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.10",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.10",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.12",
+    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.12",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.12",
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.10",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.10",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.10",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.10",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.10",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.10"
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.12",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.12",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.12",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.12",
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.12",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.12"
   },
   "arborist": {
     "deployment_version": "2"

diff --git a/healdata.org/manifest.json b/healdata.org/manifest.json
@@ -8,24 +8,24 @@
   },
   "versions": {
     "ambassador": "quay.io/datawire/ambassador:1.4.2",
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.10",
-    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.10",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.12",
+    "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:2024.10",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.10",
+    "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",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
-    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.10",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.10",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.10",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.10",
-    "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.10",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.10",
-    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.35.0",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.10",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.10",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.10",
-    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.10",
-    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.10",
+    "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",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.12",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.12",
+    "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.12",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.12",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.12",
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.12",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.12",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.12",
+    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.12",
+    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.12",
     "frontend-framework": "quay.io/cdis/frontend-framework:0.7.5",
     "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:0.6.0"
   },
@@ -44,10 +44,11 @@
     {
       "name": "batch-export",
       "action": "batch-export",
+      "serviceAccountName": "batch-export-sa",
       "activeDeadlineSeconds": 600,
       "container": {
         "name": "job-task",
-        "image": "quay.io/cdis/batch-export:2024.10",
+        "image": "quay.io/cdis/batch-export:2024.12",
         "pull_policy": "Always",
         "labels": {
           "internet": "yes"
@@ -61,33 +62,26 @@
                 "key": "hostname"
               }
             }
-          }
-        ],
-        "volumeMounts": [
+          },
           {
-            "name": "batch-export-creds-volume",
-            "readOnly": true,
-            "mountPath": "/batch-export-creds.json",
-            "subPath": "config.json"
+            "name": "BUCKET",
+            "valueFrom": {
+              "configMapKeyRef": {
+                "name": "batch-export-g3auto",
+                "key": "bucket_name"
+              }
+            }
           }
         ],
         "cpu-limit": "1",
         "memory-limit": "1Gi"
       },
-      "volumes": [
-        {
-          "name": "batch-export-creds-volume",
-          "secret": {
-            "secretName": "batch-export-g3auto"
-          }
-        }
-      ],
       "restart_policy": "Never"
     }
   ],
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.10"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.12"
     }
   },
   "indexd": {

diff --git a/healdata.org/manifests/hatchery/hatchery.json b/healdata.org/manifests/hatchery/hatchery.json
@@ -14,7 +14,7 @@
   "sidecar": {
     "cpu-limit": "1.0",
     "memory-limit": "256Mi",
-    "image": "quay.io/cdis/ecs-ws-sidecar:2024.10",
+    "image": "quay.io/cdis/ecs-ws-sidecar:2024.12",
     "env": {
       "NAMESPACE": "default",
       "GEN3_ENDPOINT": "healdata.org",

diff --git a/preprod.healdata.org/manifest.json b/preprod.healdata.org/manifest.json
@@ -8,24 +8,24 @@
   },
   "versions": {
     "ambassador": "quay.io/datawire/ambassador:1.4.2",
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.10",
-    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.10",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.12",
+    "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:2024.10",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.10",
+    "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",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
     "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:feat_karpenter-for-cost",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.10",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.10",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.10",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.10",
-    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.35.0",
-    "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.10",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.10",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.10",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.10",
-    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.10",
-    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.10",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.12",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.12",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.12",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.12",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2024.12",
+    "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2024.12",
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.12",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.12",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.12",
+    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2024.12",
+    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.12",
     "frontend-framework": "quay.io/cdis/frontend-framework:0.7.5",
     "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:0.6.0"
   },
@@ -48,7 +48,7 @@
       "activeDeadlineSeconds": 600,
       "container": {
         "name": "job-task",
-        "image": "quay.io/cdis/batch-export:feat_GPE-1219",
+        "image": "quay.io/cdis/batch-export:2024.12",
         "pull_policy": "Always",
         "labels": {
           "internet": "yes"
@@ -81,7 +81,7 @@
   ],
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.10"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.12"
     }
   },
   "indexd": {

diff --git a/preprod.healdata.org/manifests/hatchery/hatchery.json b/preprod.healdata.org/manifests/hatchery/hatchery.json
@@ -9,7 +9,7 @@
   "sidecar": {
     "cpu-limit": "1.0",
     "memory-limit": "256Mi",
-    "image": "quay.io/cdis/ecs-ws-sidecar:2024.10",
+    "image": "quay.io/cdis/ecs-ws-sidecar:2024.12",
     "env": {
       "NAMESPACE": "healpreprod",
       "GEN3_ENDPOINT": "preprod.healdata.org"
@@ -171,4 +171,4 @@
       "gen3-volume-location": "/home/jovyan/.gen3"
     }
   ]
-}
+}
diff --git a/va-testing.data-commons.org/manifest.json b/va-testing.data-commons.org/manifest.json
@@ -8,26 +8,26 @@
   },
   "versions": {
     "ambassador": "quay.io/datawire/ambassador:1.14.4",
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.10",
-    "argo-wrapper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/argo-wrapper:2.2.6",
-    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.10",
-    "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.10",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2024.11",
+    "argo-wrapper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/argo-wrapper:2.2.7",
+    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2024.11",
+    "awshelper": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/awshelper:2024.11",
     "cohort-middleware": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cohort-middleware:0.4.7",
-    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.10",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.10",
+    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2024.11",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2024.11",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
-    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.10",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.10",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.10",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.10",
-    "ohdsi-atlas": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-atlas:feat_enable_cohort_characterization",
-    "ohdsi-webapi": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-webapi:VA-pre-2024.11.18",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.10",
-    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:feat_vadc_sprint23",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.10",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.10",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.10",
-    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.10"
+    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2024.11",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2024.11",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2024.11",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2024.11",
+    "ohdsi-atlas": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-atlas:VA-2024.12.10",
+    "ohdsi-webapi": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohdsi-webapi:VA-2024.12.10",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2024.11",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.36.0",
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2024.11",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2024.11",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2024.11",
+    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2024.11"
   },
   "global": {
     "environment": "va-testing",
@@ -47,7 +47,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.10"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2024.11"
     }
   },
   "canary": {
@@ -62,4 +62,4 @@
   "argo": {
     "argo_server_service_url": "http://argo-argo-workflows-server.argo.svc.cluster.local:2746"
   }
-}
+}
diff --git a/va-testing.data-commons.org/portal/gitops.json b/va-testing.data-commons.org/portal/gitops.json
@@ -4,7 +4,7 @@
     "grafanaFaroEnable": true,
     "grafanaFaroNamespace": "va-testing"
   },
-  "argoTemplate": "gwas-template-cholesky",
+  "argoTemplate": "gwas-template-genesisupdate",
   "graphql": {
     "boardCounts": [],
     "chartCounts": [],

diff --git a/va.data-commons.org/portal/gitops.json b/va.data-commons.org/portal/gitops.json
@@ -13,6 +13,13 @@
   },
   "components": {
     "appName": "VA Data Commons",
+    "banner": [
+      {
+        "type": "info",
+        "message": "Please note that VADC will be under maintenance (Monday 12/16) between (10 AM to 2 PM) CST. During that time users will not be able to access the portal and workflows will be paused.",
+        "resetMsgDays": 5
+      }
+    ],       
     "logoAltText": "VA logo and Seal, U.S. Department of Veterans Affairs Data Commons",
     "index": {
       "introduction": {