Merge branch 'master' into chore/apply_202212_to_nci-crdc_datacommons…

…_io_1670653954
uc-cdis · Jan 18, 2023 · 50e4450 · 50e4450
2 parents cb5b6f9 + 40b1ef0
commit 50e4450
Show file tree

Hide file tree

Showing 6 changed files with 84 additions and 285 deletions.
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -7643,19 +7643,12 @@
       }
     ],
     "preprod.healdata.org/manifest.json": [
-      {
-        "type": "Secret Keyword",
-        "filename": "preprod.healdata.org/manifest.json",
-        "hashed_secret": "7120244dce59930b75711144fda4b1f6d78e4865",
-        "is_verified": false,
-        "line_number": 82
-      },
       {
         "type": "Secret Keyword",
         "filename": "preprod.healdata.org/manifest.json",
         "hashed_secret": "ae4a2a671a528744059cd818de9af9e13005563b",
         "is_verified": false,
-        "line_number": 275
+        "line_number": 81
       }
     ],
     "preprod.healdata.org/manifests/hatchery/hatchery.json": [
@@ -9028,5 +9021,5 @@
       }
     ]
   },
-  "generated_at": "2022-12-16T16:20:14Z"
+  "generated_at": "2023-01-04T23:04:23Z"
 }
diff --git a/data.midrc.org/manifest.json b/data.midrc.org/manifest.json
@@ -5,28 +5,28 @@
   ],
   "versions": {
     "ambassador": "quay.io/datawire/ambassador:1.4.2",
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2022.12",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.01",
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:v1.3.1",
-    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2022.12",
+    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.01",
     "dicom-viewer": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohif-viewer:gen3-0.1.1",
     "dicom-server": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-orthanc:gen3-0.1.1",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2022.12",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.01",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
-    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:0.15.3",
-    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2022.12",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2022.12",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2022.12",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2022.12",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2022.12",
-    "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.12",
+    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:0.15.4",
+    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.01",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.01",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.01",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.01",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.01",
+    "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2023.01",
     "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:feat_countless_manifest_button",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.12",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.12",
-    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.12",
-    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.12",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2022.12",
-    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.12",
-    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2022.12"
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.01",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.01",
+    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.01",
+    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.01",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.01",
+    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2023.01",
+    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2023.01"
   },
   "arborist": {
     "deployment_version": "2"
@@ -42,7 +42,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2022.12"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.01"
     }
   },
   "sower": [
@@ -53,7 +53,7 @@
       "serviceAccountName": "jobs-data-midrc-org",
       "container": {
         "name": "manifest-indexing-job",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2022.12",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2023.01",
         "pull_policy": "Always",
         "env": [
           {
@@ -93,7 +93,7 @@
       "serviceAccountName": "jobs-data-midrc-org",
       "container": {
         "name": "indexd-manifest-job",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2022.12",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2023.01",
         "pull_policy": "Always",
         "env": [
           {

diff --git a/preprod.healdata.org/manifest.json b/preprod.healdata.org/manifest.json
@@ -44,200 +44,6 @@
     "GEN3_BUNDLE": "heal"
   },
   "sower": [
-    {
-      "name": "ingest-metadata-manifest",
-      "action": "ingest-metadata-manifest",
-      "activeDeadlineSeconds": 86400,
-      "serviceAccountName": "jobs-preprod-healdata-org",
-      "container": {
-        "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-manifest-ingestion:2022.11",
-        "pull_policy": "Always",
-        "env": [
-          {
-            "name": "GEN3_HOSTNAME",
-            "valueFrom": {
-              "configMapKeyRef": {
-                "name": "manifest-global",
-                "key": "hostname"
-              }
-            }
-          }
-        ],
-        "volumeMounts": [
-          {
-            "name": "creds-volume",
-            "readOnly": true,
-            "mountPath": "/creds.json",
-            "subPath": "creds.json"
-          }
-        ],
-        "cpu-limit": "1",
-        "memory-limit": "1Gi"
-      },
-      "volumes": [
-        {
-          "name": "creds-volume",
-          "secret": {
-            "secretName": "sower-jobs-g3auto"
-          }
-        }
-      ],
-      "restart_policy": "Never"
-    },
-    {
-      "name": "get-dbgap-metadata",
-      "action": "get-dbgap-metadata",
-      "serviceAccountName": "jobs-preprod-healdata-org",
-      "container": {
-        "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/get-dbgap-metadata:2022.11",
-        "pull_policy": "Always",
-        "env": [],
-        "volumeMounts": [
-          {
-            "name": "creds-volume",
-            "readOnly": true,
-            "mountPath": "/creds.json",
-            "subPath": "creds.json"
-          }
-        ],
-        "cpu-limit": "1",
-        "memory-limit": "1Gi"
-      },
-      "volumes": [
-        {
-          "name": "creds-volume",
-          "secret": {
-            "secretName": "sower-jobs-g3auto"
-          }
-        }
-      ],
-      "restart_policy": "Never"
-    },
-    {
-      "name": "manifest-indexing",
-      "action": "index-object-manifest",
-      "activeDeadlineSeconds": 86400,
-      "serviceAccountName": "jobs-preprod-healdata-org",
-      "container": {
-        "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2022.11",
-        "pull_policy": "Always",
-        "env": [
-          {
-            "name": "GEN3_HOSTNAME",
-            "valueFrom": {
-              "configMapKeyRef": {
-                "name": "manifest-global",
-                "key": "hostname"
-              }
-            }
-          }
-        ],
-        "volumeMounts": [
-          {
-            "name": "sower-jobs-creds-volume",
-            "readOnly": true,
-            "mountPath": "/creds.json",
-            "subPath": "creds.json"
-          }
-        ],
-        "cpu-limit": "1",
-        "memory-limit": "1Gi"
-      },
-      "volumes": [
-        {
-          "name": "sower-jobs-creds-volume",
-          "secret": {
-            "secretName": "sower-jobs-g3auto"
-          }
-        }
-      ],
-      "restart_policy": "Never"
-    },
-    {
-      "name": "manifest-merging",
-      "action": "merge-manifests",
-      "activeDeadlineSeconds": 86400,
-      "serviceAccountName": "jobs-preprod-healdata-org",
-      "container": {
-        "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/cdis/manifest-merging:2022.11",
-        "pull_policy": "Always",
-        "env": [
-          {
-            "name": "GEN3_HOSTNAME",
-            "valueFrom": {
-              "configMapKeyRef": {
-                "name": "manifest-global",
-                "key": "hostname"
-              }
-            }
-          }
-        ],
-        "volumeMounts": [
-          {
-            "name": "sower-jobs-creds-volume",
-            "readOnly": true,
-            "mountPath": "/creds.json",
-            "subPath": "creds.json"
-          }
-        ],
-        "cpu-limit": "1",
-        "memory-limit": "1Gi"
-      },
-      "volumes": [
-        {
-          "name": "sower-jobs-creds-volume",
-          "secret": {
-            "secretName": "sower-jobs-g3auto"
-          }
-        }
-      ],
-      "restart_policy": "Never"
-    },
-    {
-      "name": "indexd-manifest",
-      "action": "download-indexd-manifest",
-      "activeDeadlineSeconds": 86400,
-      "serviceAccountName": "jobs-preprod-healdata-org",
-      "container": {
-        "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2022.11",
-        "pull_policy": "Always",
-        "env": [
-          {
-            "name": "GEN3_HOSTNAME",
-            "valueFrom": {
-              "configMapKeyRef": {
-                "name": "manifest-global",
-                "key": "hostname"
-              }
-            }
-          }
-        ],
-        "volumeMounts": [
-          {
-            "name": "sower-jobs-creds-volume",
-            "readOnly": true,
-            "mountPath": "/creds.json",
-            "subPath": "creds.json"
-          }
-        ],
-        "cpu-limit": "1",
-        "memory-limit": "1Gi"
-      },
-      "volumes": [
-        {
-          "name": "sower-jobs-creds-volume",
-          "secret": {
-            "secretName": "sower-jobs-g3auto"
-          }
-        }
-      ],
-      "restart_policy": "Never"
-    },
     {
       "name": "batch-export",
       "action": "batch-export",

diff --git a/staging.midrc.org/manifest.json b/staging.midrc.org/manifest.json
@@ -5,28 +5,28 @@
   ],
   "versions": {
     "ambassador": "quay.io/datawire/ambassador:1.4.2",
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2022.12",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.01",
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:v1.3.1",
-    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2022.12",
+    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.01",
     "dicom-viewer": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ohif-viewer:gen3-0.1.1",
     "dicom-server": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-orthanc:gen3-0.1.1",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2022.12",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.01",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
-    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:0.15.3",
-    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2022.12",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2022.12",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2022.12",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2022.12",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2022.12",
-    "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.12",
+    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:0.15.4",
+    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.01",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.01",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.01",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.01",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.01",
+    "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2023.01",
     "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:feat_countless_manifest_button",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.12",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.12",
-    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.12",
-    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.12",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2022.12",
-    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.12",
-    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2022.12"
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.01",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.01",
+    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.01",
+    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.01",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.01",
+    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2023.01",
+    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2023.01"
   },
   "arborist": {
     "deployment_version": "2"
@@ -42,7 +42,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2022.12"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2023.01"
     }
   },
   "sower": [
@@ -53,7 +53,7 @@
       "serviceAccountName": "jobs-staging-midrc-org",
       "container": {
         "name": "manifest-indexing-job",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2022.12",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifest-indexing:2023.01",
         "pull_policy": "Always",
         "env": [
           {
@@ -93,7 +93,7 @@
       "serviceAccountName": "jobs-staging-midrc-org",
       "container": {
         "name": "indexd-manifest-job",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2022.12",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/download-indexd-manifest:2023.01",
         "pull_policy": "Always",
         "env": [
           {