AnVIL production service release 1654550960

staging.theanvil.io/etlMapping.yaml

@@ -40,6 +40,14 @@ mappings:
         path: samples
         src: original_material_type
         fn: set
+      - name: sample_submitter_id
+        path: samples
+        src: submitter_id
+        fn: set
+      - name: sequencing_assay_submitter_id
+        path: samples.sequencings
+        src: submitter_id
+        fn: set
       - name: exome_capture_platform
         path: samples.sequencings
         src: exome_capture_platform
@@ -104,6 +112,8 @@ mappings:
       - name: project_id
       - name: submitter_id
       - name: object_id
+      - name: drs_id
+        src: object_id
       - name: md5sum
       - name: file_name
       - name: file_size
@@ -161,3 +171,13 @@ mappings:
           - name: phenotype_group
             src: phenotype_group
             fn: set
+      sample:
+        props:
+          - name: sample_submitter_id
+            src: submitter_id
+            fn: set
+      sequencing:
+        props:
+          - name: sequencing_assay_submitter_id
+            src: submitter_id
+            fn: set

staging.theanvil.io/manifest.json

@@ -7,29 +7,29 @@
     "autodeploy": "yes"
   },
   "versions": {
-    "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2022.03",
-    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2022.03",
-    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2022.03",
+    "access-backend": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/access-backend:2022.05",
+    "arborist": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/arborist:2022.05",
+    "audit-service": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/audit-service:2022.05",
     "aws-es-proxy": "quay.io/cdis/aws-es-proxy:0.8",
-    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2022.03",
+    "fence": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/fence:2022.05",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
-    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2022.03",
-    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2022.03",
+    "guppy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/guppy:2022.05",
+    "hatchery": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/hatchery:2022.05",
     "ambassador": "quay.io/datawire/ambassador:1.4.2",
-    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2022.03",
-    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2022.03",
-    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2022.03",
-    "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.03",
-    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:3.22.1",
-    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.03",
-    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.03",
-    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.03",
-    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.03",
-    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:0.6.5",
-    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2022.03",
-    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2022.03",
-    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2022.03",
-    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2022.03"
+    "indexd": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexd:2022.05",
+    "manifestservice": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/manifestservice:2022.05",
+    "peregrine": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/peregrine:2022.05",
+    "pidgin": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pidgin:2022.05",
+    "portal": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/data-portal:2022.05",
+    "revproxy": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/nginx:2022.05",
+    "sheepdog": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sheepdog:2022.05",
+    "sower": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/sower:2022.05",
+    "spark": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-spark:2022.05",
+    "tube": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/tube:2022.05",
+    "ssjdispatcher": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/ssjdispatcher:2022.05",
+    "wts": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/workspace-token-service:2022.05",
+    "dashboard": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3-statics:2022.05",
+    "metadata": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/metadata-service:2022.05"
   },
   "indexd": {
     "arborist": "true"
@@ -38,7 +38,7 @@
     "environment": "anvilstaging",
     "hostname": "staging.theanvil.io",
     "revproxy_arn": "arn:aws:acm:us-east-1:474789003679:certificate/9fd731e3-3366-4bd0-a3ef-0453dc07289a",
-    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/2.3.2/schema.json",
+    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/anvil/2.3.6/schema.json",
     "portal_app": "gitops",
     "kube_bucket": "kube-anvilstaging-gen3",
     "logs_bucket": "logs-anvilstaging-gen3",
@@ -60,7 +60,7 @@
       "action": "export",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.03",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.05",
         "pull_policy": "Always",
         "env": [
           {
@@ -128,7 +128,7 @@
       "action": "export-files",
       "container": {
         "name": "job-task",
-        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.03",
+        "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/pelican-export:2022.05",
         "pull_policy": "Always",
         "env": [
           {
@@ -152,10 +152,6 @@
           {
             "name": "ROOT_NODE",
             "value": "file"
-          },
-          {
-            "name": "EXTRA_NODES",
-            "value": ""
           }
         ],
         "volumeMounts": [
@@ -197,7 +193,7 @@
   },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2022.03"
+      "indexing": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/indexs3client:2022.05"
     }
   },
   "arborist": {

staging.theanvil.io/manifests/hatchery/hatchery.json

@@ -5,7 +5,7 @@
   "sidecar": {
     "cpu-limit": "1.0",
     "memory-limit": "512Mi",
-    "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2022.03",
+    "image": "707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/gen3fuse-sidecar:2022.05",
     "env": {
       "NAMESPACE": "default",
       "HOSTNAME": "staging.theanvil.io"
@@ -172,4 +172,4 @@
       "fs-gid": 100
     }
   ]
-}
+}