Feat/bhcdatastaging april release (#1446)

* update services * update workspace * add sower * add export buttons * add pub page * downgrade sheepdog * remove pub page for now
uc-cdis · Apr 30, 2020 · 42b2539 · 42b2539
1 parent 7d32aed
commit 42b2539
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Showing 2 changed files with 120 additions and 18 deletions.
diff --git a/dataprep.braincommons.org/manifest.json b/dataprep.braincommons.org/manifest.json
@@ -7,24 +7,26 @@
     "autodeploy": "yes"
   },
   "versions": {
-    "arborist": "quay.io/cdis/arborist:2.3.2",
+    "arborist": "quay.io/cdis/arborist:2020.04",
+    "ambassador": "quay.io/datawire/ambassador:0.60.3",
     "aws-es-proxy": "abutaha/aws-es-proxy:0.8",
     "dashboard": "quay.io/cdis/gen3-statics:1.0.0",
-    "ambassador": "quay.io/datawire/ambassador:0.60.3",
-    "hatchery": "quay.io/cdis/hatchery:0.1.0",
-    "fence": "quay.io/cdis/fence:4.14.0",
-    "indexd": "quay.io/cdis/indexd:2.1.0",
-    "peregrine": "quay.io/cdis/peregrine:2.1.1",
-    "pidgin": "quay.io/cdis/pidgin:1.1.0",
-    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
-    "sheepdog": "quay.io/cdis/sheepdog:2.1.2",
-    "portal": "quay.io/cdis/data-portal:2.23.4",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
-    "ssjdispatcher": "quay.io/cdis/ssjdispatcher:0.0.6",
-    "spark": "quay.io/cdis/gen3-spark:1.0.0",
-    "tube": "quay.io/cdis/tube:0.3.22",
-    "guppy": "quay.io/cdis/guppy:0.3.10",
-    "wts": "quay.io/cdis/workspace-token-service:0.1.0"
+    "guppy": "quay.io/cdis/guppy:2020.04",
+    "hatchery": "quay.io/cdis/hatchery:2020.04",
+    "fence": "quay.io/cdis/fence:2020.04",
+    "indexd": "quay.io/cdis/indexd:2020.04",
+    "manifestservice": "quay.io/cdis/manifestservice:2020.04",
+    "peregrine": "quay.io/cdis/peregrine:2020.04",
+    "pidgin": "quay.io/cdis/pidgin:2020.04",
+    "portal": "quay.io/cdis/data-portal:2.25.2",
+    "revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
+    "sheepdog": "quay.io/cdis/sheepdog:3.0.0",
+    "sower": "quay.io/cdis/sower:2020.04",
+    "ssjdispatcher": "quay.io/cdis/ssjdispatcher:2020.04",
+    "spark": "quay.io/cdis/gen3-spark:2020.04",
+    "tube": "quay.io/cdis/tube:2020.04",
+    "wts": "quay.io/cdis/workspace-token-service:2020.04"
   },
   "arborist": {
     "deployment_version": "2"
@@ -69,7 +71,9 @@
         "args": [
           "--NotebookApp.base_url=/lw-workspace/proxy/",
           "--NotebookApp.password=''",
-          "--NotebookApp.token=''"
+          "--NotebookApp.token=''",
+          "--NotebookApp.notebook_dir='/home/jovyan/pd'",
+          "--NotebookApp.quit_button=False"
         ],
         "command": [
           "start-notebook.sh"
@@ -96,7 +100,9 @@
         "args": [
           "--NotebookApp.base_url=/lw-workspace/proxy/",
           "--NotebookApp.password=''",
-          "--NotebookApp.token=''"
+          "--NotebookApp.token=''",
+          "--NotebookApp.notebook_dir='/home/jovyan/pd'",
+          "--NotebookApp.quit_button=False"
         ],
         "command": [
           "start-notebook.sh"
@@ -123,7 +129,9 @@
         "args": [
           "--NotebookApp.base_url=/lw-workspace/proxy/",
           "--NotebookApp.password=''",
-          "--NotebookApp.token=''"
+          "--NotebookApp.token=''",
+          "--NotebookApp.notebook_dir='/home/jovyan/pd'",
+          "--NotebookApp.quit_button=False"
         ],
         "command": [
           "start-notebook.sh"
@@ -139,9 +147,89 @@
         "user-uid": 1000,
         "fs-gid": 100,
         "user-volume-location": "/home/jovyan/pd"
+      },
+      {
+        "target-port": 8787,
+        "cpu-limit": "1.0",
+        "memory-limit": "1024Mi",
+        "name": "R Studio",
+        "image": "quay.io/cdis/rstudio:master",
+        "env": {"DISABLE_AUTH": "true"},
+        "args": [],
+        "path-rewrite": "/",
+        "use-tls": "false",
+        "ready-probe": "/",
+        "user-volume-location": "/home/rstudio/pd",
+        "fs-gid": 100
       }
     ]
   },
+  "sower": [
+    {
+      "name": "pelican-export",
+      "action": "export",
+      "container": {
+        "name": "job-task",
+        "image": "quay.io/cdis/pelican-export:2020.04",
+        "pull_policy": "Always",
+        "env": [
+          {
+            "name": "DICTIONARY_URL",
+            "valueFrom": {
+              "configMapKeyRef": {
+                "name": "manifest-global",
+                "key": "dictionary_url"
+              }
+            }
+          },
+          {
+            "name": "GEN3_HOSTNAME",
+            "valueFrom": {
+              "configMapKeyRef": {
+                "name": "manifest-global",
+                "key": "hostname"
+              }
+            }
+          },
+          {
+            "name": "ROOT_NODE",
+            "value": "case"
+          }
+        ],
+        "volumeMounts": [
+          {
+            "name": "pelican-creds-volume",
+            "readOnly": true,
+            "mountPath": "/pelican-creds.json",
+            "subPath": "config.json"
+          },
+          {
+            "name": "peregrine-creds-volume",
+            "readOnly": true,
+            "mountPath": "/peregrine-creds.json",
+            "subPath": "creds.json"
+          }
+        ],
+        "cpu-limit": "1",
+        "memory-limit": "12Gi"
+      },
+      "volumes": [
+        {
+          "name": "pelican-creds-volume",
+          "secret": {
+            "secretName": "pelicanservice-g3auto"
+          }
+        },
+        {
+          "name": "peregrine-creds-volume",
+          "secret": {
+            "secretName": "peregrine-creds"
+          }
+        }
+      ],
+      "restart_policy": "Never"
+    }
+  ],
   "global": {
     "environment": "bhcdatastaging",
     "hostname": "dataprep.braincommons.org",

diff --git a/dataprep.braincommons.org/portal/gitops.json b/dataprep.braincommons.org/portal/gitops.json
@@ -291,6 +291,13 @@
         "leftIcon": "datafile",
         "rightIcon": "download",
         "fileName": "manifest.json"
+      },
+      {
+        "enabled": true,
+        "type": "export-to-workspace",
+        "title": "Export File Manifest to Workspace",
+        "leftIcon": "datafile",
+        "rightIcon": "download"
       }
     ]
   },
@@ -350,6 +357,13 @@
         "leftIcon": "datafile",
         "rightIcon": "download",
         "fileName": "file-manifest.json"
+      },
+      {
+        "enabled": true,
+        "type": "export-files-to-workspace",
+        "title": "Export File Manifest to Workspace",
+        "leftIcon": "datafile",
+        "rightIcon": "download"
       }
     ],
     "dropdowns": {}