Merge branch 'master' into haraprasadj-patch-3

uc-cdis · Jul 21, 2023 · fba8c5b · fba8c5b
2 parents e93f758 + 870d3d7
commit fba8c5b
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Showing 11 changed files with 289 additions and 393 deletions.
diff --git a/.secrets.baseline b/.secrets.baseline
diff --git a/qa-brh.planx-pla.net/manifest.json b/qa-brh.planx-pla.net/manifest.json
@@ -14,7 +14,7 @@
     "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.06",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
     "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.06",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.06",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:5.0.1",
     "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.1.2",
     "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.06",
     "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.06",

diff --git a/qa-brh.planx-pla.net/manifests/hatchery/hatchery.json b/qa-brh.planx-pla.net/manifests/hatchery/hatchery.json
@@ -36,7 +36,7 @@
       "cpu-limit": "2.0",
       "memory-limit": "8Gi",
       "name": "(Generic) Jupyter Lab Notebook with R Kernel",
-      "image": "quay.io/cdis/jupyter-superslim-r:1.0.4",
+      "image": "quay.io/cdis/brh-notebooks:generic_rkernel__74bc13c4cf39a164daec18234d9adfd4678a50e5",
       "env": {
         "FRAME_ANCESTORS": "https://qa-brh.planx-pla.net"
       },
@@ -133,4 +133,4 @@
       "gen3-volume-location": "/home/jovyan/.gen3"
     }
   ]
-}
+}
diff --git a/qa-brh.planx-pla.net/metadata/aggregate_config.json b/qa-brh.planx-pla.net/metadata/aggregate_config.json
@@ -193,7 +193,7 @@
 				"study_id": "path:clinical_study_designation",
 				"study_description": "",
 				"full_name": "path:clinical_study_name",
-				"short_name": "N/A",
+				"short_name": "path:clinical_study_name",
 				"commons": "CRDC Integrated Canine Data Commons",
 				"study_url": "N/A",
 				"_subjects_count" : {"path":"numberOfCases", "default" : 0 },			

diff --git a/qa-heal.planx-pla.net/manifest.json b/qa-heal.planx-pla.net/manifest.json
@@ -11,19 +11,19 @@
     "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2023.06",
     "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2023.06",
     "aws-es-proxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/aws-es-proxy:v1.3.1",
-    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:0.2.0",
+    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:feat_mds-update",
     "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2023.06",
     "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2023.06",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
     "frontend-framework": "quay.io/cdis/frontend-framework:0.4.6",
     "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2023.06",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2023.06",
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:5.0.1",
     "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.1.1",
     "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.06",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.06",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:feat_nested-fields",
     "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.06",
     "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2023.06",
-    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.7.1",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:feat_supportNestedFieldNames",
     "requestor": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/requestor:2023.06",
     "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2023.06",
     "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2023.06",

diff --git a/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json b/qa-heal.planx-pla.net/manifests/hatchery/hatchery.json
@@ -68,7 +68,7 @@
       "cpu-limit": "1.0",
       "memory-limit": "2Gi",
       "name": "(Generic, User-licensed) Stata Notebook ",
-      "image": "quay.io/cdis/stata-heal:george-portal",
+      "image": "quay.io/cdis/jupyter-pystata-user-licensed:feat_stata-license",
       "env": {
         "FRAME_ANCESTORS": "https://qa-heal.planx-pla.net"
       },
@@ -87,7 +87,7 @@
       "lifecycle-post-start": [
         "/bin/sh",
         "-c",
-        "(while true; do [ -d ~/pd ] && [ -f ~/pd/stata.lic ] && cp ~/pd/stata.lic /usr/local/stata17/; sleep 1; done) & export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true"
+        "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; rm -rf /home/$IAM/pd/lost+found; ln -s /data /home/$IAM/pd/; true"
       ],
       "user-uid": 1000,
       "fs-gid": 100,
@@ -99,7 +99,7 @@
       "cpu-limit": "1.0",
       "memory-limit": "2Gi",
       "name": "(Generic, Limited Gen3-licensed) Stata Notebook",
-      "image": "quay.io/cdis/stata-heal:jupyter_pystata_licensed__latest",
+      "image": "quay.io/cdis/jupyter-pystata-gen3-licensed:feat_stata-license",
       "env": {
         "FRAME_ANCESTORS": "https://qa-heal.planx-pla.net"
       },