Merge branch 'master' into fix/update-post-command-in-user-license

uc-cdis · Jul 12, 2023 · b491db5 · b491db5
2 parents 0334fe1 + 2eead75
commit b491db5
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Showing 19 changed files with 374 additions and 316 deletions.
diff --git a/.secrets.baseline b/.secrets.baseline
diff --git a/jenkins-blood.planx-pla.net/manifest.json b/jenkins-blood.planx-pla.net/manifest.json
@@ -17,7 +17,7 @@
     "ws-storage": "quay.io/cdis/ws-storage:master",
     "peregrine": "quay.io/cdis/peregrine:master",
     "pidgin": "quay.io/cdis/pidgin:master",
-    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
+    "revproxy": "quay.io/cdis/nginx:master",
     "sheepdog": "quay.io/cdis/sheepdog:master",
     "portal": "quay.io/cdis/data-portal:master",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
@@ -31,7 +31,9 @@
     "hatchery": "quay.io/cdis/hatchery:master",
     "metadata": "quay.io/cdis/metadata-service:master",
     "dashboard": "quay.io/cdis/gen3-statics:master",
-    "requestor": "quay.io/cdis/requestor:master"
+    "requestor": "quay.io/cdis/requestor:master",
+    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:master",
+    "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master"
   },
   "sower": [
     {

diff --git a/jenkins-blood.planx-pla.net/portal/gitops.json b/jenkins-blood.planx-pla.net/portal/gitops.json
@@ -211,7 +211,8 @@
     "analysis": true,
     "explorerPublic": true,
     "discovery": true,
-    "discoveryUseAggMDS": true
+    "discoveryUseAggMDS": true,
+    "studyRegistration": true
   },
   "discoveryConfig": {
     "features": {

diff --git a/jenkins-brain.planx-pla.net/manifest.json b/jenkins-brain.planx-pla.net/manifest.json
@@ -21,7 +21,7 @@
     "peregrine": "quay.io/cdis/peregrine:master",
     "pidgin": "quay.io/cdis/pidgin:master",
     "portal": "quay.io/cdis/data-portal:master",
-    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
+    "revproxy": "quay.io/cdis/nginx:master",
     "sheepdog": "quay.io/cdis/sheepdog:master",
     "spark": "quay.io/cdis/gen3-spark:master",
     "tube": "quay.io/cdis/tube:master",
@@ -33,7 +33,9 @@
     "hatchery": "quay.io/cdis/hatchery:master",
     "metadata": "quay.io/cdis/metadata-service:master",
     "dashboard": "quay.io/cdis/gen3-statics:master",
-    "requestor": "quay.io/cdis/requestor:master"
+    "requestor": "quay.io/cdis/requestor:master",
+    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:master",
+    "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master"
   },
   "arborist": {
     "deployment_version": "2"

diff --git a/jenkins-brain.planx-pla.net/portal/gitops.json b/jenkins-brain.planx-pla.net/portal/gitops.json
@@ -187,7 +187,8 @@
     "explorer": true,
     "noIndex": true,
     "discovery": true,
-    "discoveryUseAggMDS": true
+    "discoveryUseAggMDS": true,
+    "studyRegistration": true
   },
   "discoveryConfig": {
     "features": {

diff --git a/jenkins-dcp.planx-pla.net/manifest.json b/jenkins-dcp.planx-pla.net/manifest.json
@@ -19,7 +19,7 @@
     "peregrine": "quay.io/cdis/peregrine:master",
     "pidgin": "quay.io/cdis/pidgin:master",
     "portal": "quay.io/cdis/data-portal:master",
-    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
+    "revproxy": "quay.io/cdis/nginx:master",
     "sheepdog": "quay.io/cdis/sheepdog:master",
     "spark": "quay.io/cdis/gen3-spark:master",
     "tube": "quay.io/cdis/tube:master",
@@ -31,7 +31,9 @@
     "hatchery": "quay.io/cdis/hatchery:master",
     "metadata": "quay.io/cdis/metadata-service:master",
     "dashboard": "quay.io/cdis/gen3-statics:master",
-    "requestor": "quay.io/cdis/requestor:master"
+    "requestor": "quay.io/cdis/requestor:master",
+    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:master",
+    "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master"
   },
   "arborist": {
     "deployment_version": "2"

diff --git a/jenkins-dcp.planx-pla.net/portal/gitops.json b/jenkins-dcp.planx-pla.net/portal/gitops.json
@@ -191,7 +191,8 @@
   "featureFlags": {
     "explorer": true,
     "discovery": true,
-    "discoveryUseAggMDS": true
+    "discoveryUseAggMDS": true,
+    "studyRegistration": true
   },
   "discoveryConfig": {
     "features": {

diff --git a/jenkins-genomel.planx-pla.net/manifest.json b/jenkins-genomel.planx-pla.net/manifest.json
@@ -19,7 +19,7 @@
     "peregrine": "quay.io/cdis/peregrine:master",
     "pidgin": "quay.io/cdis/pidgin:master",
     "portal": "quay.io/cdis/data-portal:master",
-    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
+    "revproxy": "quay.io/cdis/nginx:master",
     "sheepdog": "quay.io/cdis/sheepdog:master",
     "spark": "quay.io/cdis/gen3-spark:master",
     "tube": "quay.io/cdis/tube:master",
@@ -28,10 +28,12 @@
     "wts": "quay.io/cdis/workspace-token-service:master",
     "guppy": "quay.io/cdis/guppy:master",
     "sower": "quay.io/cdis/sower:master",
-    "hatchery": "quay.io/cdis/hatchery:fix_ecs_ct_length",
+    "hatchery": "quay.io/cdis/hatchery:master",
     "metadata": "quay.io/cdis/metadata-service:master",
     "dashboard": "quay.io/cdis/gen3-statics:master",
-    "requestor": "quay.io/cdis/requestor:master"
+    "requestor": "quay.io/cdis/requestor:master",
+    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:master",
+    "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master"
   },
   "arborist": {
     "deployment_version": "2"

diff --git a/jenkins-genomel.planx-pla.net/portal/gitops.json b/jenkins-genomel.planx-pla.net/portal/gitops.json
@@ -119,7 +119,8 @@
   "featureFlags": {
     "explorer": true,
     "discovery": true,
-    "discoveryUseAggMDS": true
+    "discoveryUseAggMDS": true,
+    "studyRegistration": true
   },
   "discoveryConfig": {
     "features": {

diff --git a/jenkins-new-1.planx-pla.net/manifest.json b/jenkins-new-1.planx-pla.net/manifest.json
@@ -19,7 +19,7 @@
     "peregrine": "quay.io/cdis/peregrine:master",
     "pidgin": "quay.io/cdis/pidgin:master",
     "portal": "quay.io/cdis/data-portal:master",
-    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
+    "revproxy": "quay.io/cdis/nginx:master",
     "sheepdog": "quay.io/cdis/sheepdog:master",
     "spark": "quay.io/cdis/gen3-spark:master",
     "tube": "quay.io/cdis/tube:master",
@@ -28,10 +28,12 @@
     "wts": "quay.io/cdis/workspace-token-service:master",
     "guppy": "quay.io/cdis/guppy:master",
     "sower": "quay.io/cdis/sower:master",
-    "hatchery": "quay.io/cdis/hatchery:fix_ecs_ct_length",
+    "hatchery": "quay.io/cdis/hatchery:master",
     "metadata": "quay.io/cdis/metadata-service:master",
     "dashboard": "quay.io/cdis/gen3-statics:master",
-    "requestor": "quay.io/cdis/requestor:master"
+    "requestor": "quay.io/cdis/requestor:master",
+    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:master",
+    "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master"
   },
   "arborist": {
     "deployment_version": "2"

diff --git a/jenkins-new-1.planx-pla.net/portal/gitops.json b/jenkins-new-1.planx-pla.net/portal/gitops.json
@@ -106,7 +106,8 @@
   "featureFlags": {
     "explorer": true,
     "discovery": true,
-    "discoveryUseAggMDS": true
+    "discoveryUseAggMDS": true,
+    "studyRegistration": true
   },
   "discoveryConfig": {
     "features": {

diff --git a/jenkins-new.planx-pla.net/etlMapping.yaml b/jenkins-new.planx-pla.net/etlMapping.yaml
@@ -88,8 +88,7 @@ mappings:
             src: data_category
             fn: set
           - name: file_count
-            src: file_id
-            alternate_src: _file_id
+            src: _file_id
             fn: count
     parent_props:
       - path: projects[project_code:code]

diff --git a/jenkins-new.planx-pla.net/manifest.json b/jenkins-new.planx-pla.net/manifest.json
@@ -19,7 +19,7 @@
     "peregrine": "quay.io/cdis/peregrine:master",
     "pidgin": "quay.io/cdis/pidgin:master",
     "portal": "quay.io/cdis/data-portal:master",
-    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
+    "revproxy": "quay.io/cdis/nginx:master",
     "sheepdog": "quay.io/cdis/sheepdog:master",
     "spark": "quay.io/cdis/gen3-spark:master",
     "tube": "quay.io/cdis/tube:master",
@@ -28,10 +28,12 @@
     "wts": "quay.io/cdis/workspace-token-service:master",
     "guppy": "quay.io/cdis/guppy:master",
     "sower": "quay.io/cdis/sower:master",
-    "hatchery": "quay.io/cdis/hatchery:fix_ecs_ct_length",
+    "hatchery": "quay.io/cdis/hatchery:master",
     "metadata": "quay.io/cdis/metadata-service:master",
     "dashboard": "quay.io/cdis/gen3-statics:master",
-    "requestor": "quay.io/cdis/requestor:master"
+    "requestor": "quay.io/cdis/requestor:master",
+    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:master",
+    "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master"
   },
   "arborist": {
     "deployment_version": "2"

diff --git a/jenkins-new.planx-pla.net/portal/gitops.json b/jenkins-new.planx-pla.net/portal/gitops.json
@@ -106,7 +106,8 @@
   "featureFlags": {
     "explorer": true,
     "discovery": true,
-    "discoveryUseAggMDS": true
+    "discoveryUseAggMDS": true,
+    "studyRegistration": true
   },
   "discoveryConfig": {
     "features": {

diff --git a/jenkins-niaid.planx-pla.net/manifest.json b/jenkins-niaid.planx-pla.net/manifest.json
@@ -19,7 +19,7 @@
     "peregrine": "quay.io/cdis/peregrine:master",
     "pidgin": "quay.io/cdis/pidgin:master",
     "portal": "quay.io/cdis/data-portal:master",
-    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
+    "revproxy": "quay.io/cdis/nginx:master",
     "sheepdog": "quay.io/cdis/sheepdog:master",
     "spark": "quay.io/cdis/gen3-spark:master",
     "tube": "quay.io/cdis/tube:master",
@@ -28,9 +28,11 @@
     "wts": "quay.io/cdis/workspace-token-service:master",
     "guppy": "quay.io/cdis/guppy:master",
     "sower": "quay.io/cdis/sower:master",
-    "hatchery": "quay.io/cdis/hatchery:fix_ecs_ct_length",
+    "hatchery": "quay.io/cdis/hatchery:master",
     "metadata": "quay.io/cdis/metadata-service:master",
-    "requestor": "quay.io/cdis/requestor:master"
+    "requestor": "quay.io/cdis/requestor:master",
+    "cedar-wrapper": "quay.io/cdis/cedar-wrapper-service:master",
+    "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:master"
   },
   "portal": {
     "GEN3_BUNDLE": "nct"

diff --git a/jenkins-niaid.planx-pla.net/portal/gitops.json b/jenkins-niaid.planx-pla.net/portal/gitops.json
@@ -115,7 +115,8 @@
   "featureFlags": {
     "explorer": false,
     "discovery": true,
-    "discoveryUseAggMDS": true
+    "discoveryUseAggMDS": true,
+    "studyRegistration": true
   },
   "discoveryConfig": {
     "features": {

diff --git a/qa-brh.planx-pla.net/manifest.json b/qa-brh.planx-pla.net/manifest.json
@@ -15,7 +15,7 @@
     "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",
-    "kayako-wrapper": "quay.io/cdis/kayako-wrapper-service:0.1.1",
+    "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",
     "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2023.06",

diff --git a/qa-ibd.planx-pla.net/manifest.json b/qa-ibd.planx-pla.net/manifest.json
@@ -14,7 +14,7 @@
     "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin: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",
-    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2023.06",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:5.8.0",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.15.3-debian-cloudwatch-1.0",
     "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2023.06",
     "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2023.06",
@@ -23,7 +23,7 @@
     "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2023.06",
     "ambassador": "quay.io/datawire/ambassador:1.4.2",
     "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2023.06",
-    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2023.06",
+    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:0.16.1",
     "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2023.06",
     "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2023.06",
     "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2023.06"

diff --git a/qa-ibd.planx-pla.net/portal/gitops.json b/qa-ibd.planx-pla.net/portal/gitops.json
@@ -577,6 +577,7 @@
         "enabled": true,
         "text": "Publications"
       },
+      "guidType": "publication_discovery_metadata",
       "search": {
         "tagSearchDropdown": {
           "enabled": true,