uc-cdis · mfshao · Mar 15, 2021 · Mar 15, 2021 · Mar 15, 2021 · Mar 15, 2021
@@ -1,5 +1,5 @@
 mappings:
-  - name: preprod-heal_cmc
+  - name: preprod.healdata.org_clinical_trials
     doc_type: clinical_trials
     type: aggregator
     root: core_metadata_collection
@@ -30,7 +30,7 @@ mappings:
       - name: project_id
       - name: cmc_unique_id
         src: submitter_id
-  - name: preprod-heal_ct-file
+  - name: preprod.healdata.org_ctfile
     doc_type: ctfile
     type: aggregator
     root: clinical_trial_file
@@ -44,7 +44,7 @@ mappings:
       - name: project_id
     parent_props:
       - path: core_metadata_collections[cmc_unique_id:submitter_id]
-  - name: preprod-heal_oa-file
+  - name: preprod.healdata.org_oafile
     doc_type: oafile
     type: aggregator
     root: open_access_doc
@@ -58,3 +58,4 @@ mappings:
       - name: project_id
     parent_props:
       - path: core_metadata_collections[cmc_unique_id:submitter_id]
+
@@ -3,71 +3,78 @@
     "This is the dev environment manifest",
     "That's all I have to say"
   ],
-  "jenkins": {
-    "autodeploy": "yes"
-  },
   "versions": {
-    "arborist": "quay.io/cdis/arborist:2020.11",
+    "arborist": "quay.io/cdis/arborist:2021.03",
     "aws-es-proxy": "abutaha/aws-es-proxy:0.8",
-    "fence": "quay.io/cdis/fence:2020.11",
+    "fence": "quay.io/cdis/fence:2021.03",
     "fluentd": "fluent/fluentd-kubernetes-daemonset:v1.10.2-debian-cloudwatch-1.0",
-    "indexd": "quay.io/cdis/indexd:2020.11",
-    "peregrine": "quay.io/cdis/peregrine:2020.11",
-    "pidgin": "quay.io/cdis/pidgin:2020.11",
+    "indexd": "quay.io/cdis/indexd:2021.03",
+    "peregrine": "quay.io/cdis/peregrine:2021.03",
+    "pidgin": "quay.io/cdis/pidgin:2021.03",
     "portal": "quay.io/cdis/data-portal:2.45.0",
-    "revproxy": "quay.io/cdis/nginx:2020.11",
-    "sheepdog": "quay.io/cdis/sheepdog:2020.11",
-    "ssjdispatcher": "quay.io/cdis/ssjdispatcher:2020.11",
-    "metadata": "quay.io/cdis/metadata-service:2020.11",
-    "spark": "quay.io/cdis/gen3-spark:2020.11",
-    "manifestservice": "quay.io/cdis/manifestservice:2020.11",
-    "wts": "quay.io/cdis/workspace-token-service:2020.11",
-    "tube": "quay.io/cdis/tube:2020.11",
-    "guppy": "quay.io/cdis/guppy:2020.11"
+    "revproxy": "quay.io/cdis/nginx:2021.03",
+    "sheepdog": "quay.io/cdis/sheepdog:2021.03",
+    "ssjdispatcher": "quay.io/cdis/ssjdispatcher:2021.03",
+    "metadata": "quay.io/cdis/metadata-service:2021.03",
+    "spark": "quay.io/cdis/gen3-spark:2021.03",
+    "hatchery": "quay.io/cdis/hatchery:2021.03",
+    "ambassador": "quay.io/datawire/ambassador:1.4.2",
+    "manifestservice": "quay.io/cdis/manifestservice:2021.03",
+    "wts": "quay.io/cdis/workspace-token-service:2021.03",
+    "tube": "quay.io/cdis/tube:2021.03",
+    "guppy": "quay.io/cdis/guppy:2021.03"
   },
   "arborist": {
     "deployment_version": "2"
   },
+  "indexd": {
+    "arborist": "true"
+  },
   "ssjdispatcher": {
     "job_images": {
-      "indexing": "quay.io/cdis/indexs3client:2020.11"
+      "indexing": "quay.io/cdis/indexs3client:2021.03"
     }
   },
-  "indexd": {
-    "arborist": "true"
-  },
   "global": {
     "environment": "healpreprod",
     "hostname": "preprod.healdata.org",
     "revproxy_arn": "arn:aws:acm:us-east-1:205252583234:certificate/8bb3d424-be34-493c-a43b-e2c686c9dc6c",
     "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/heal_dictionary/1.1.0/schema.json",
     "portal_app": "gitops",
-    "sync_from_dbgap": "False",
     "kube_bucket": "kube-healprod-gen3",
     "logs_bucket": "logs-healprod-gen3",
+    "sync_from_dbgap": "False",
+    "useryaml_s3path": "s3://cdis-gen3-users/heal/user.yaml",
     "dispatcher_job_num": "10",
-    "netpolicy": "on",
-    "tier_access_level": "libre",
-    "useryaml_s3path": "s3://cdis-gen3-users/heal/user.yaml"
+    "netpolicy": "on"
+  },
+  "canary": {
+    "default": 0
   },
   "guppy": {
-    "indices": [{
-        "index": "preprod-heal_cmc",
-        "type": "clinical_trials"
+    "indices": [
+      {
+        "index": "preprod.healdata.org_clinical_trials",
+        "type": "clinical_trials",
+        "tier_access_level": "libre"
       },
       {
-        "index": "preprod-heal_ct-file",
-        "type": "ctfile"
+        "index": "preprod.healdata.org_clinical_trials_controlled_access",
+        "type": "clinical_trials_controlled_access",
+        "tier_access_level": "private"
       },
       {
-        "index": "preprod-heal_oa-file",
-        "type": "oafile"
+        "index": "preprod.healdata.org_ctfile",
+        "type": "ctfile",
+        "tier_access_level": "libre"
+      },
+      {
+        "index": "preprod.healdata.org_oafile",
+        "type": "oafile",
+        "tier_access_level": "libre"
       }
     ],
-    "config_index": "preprod-heal_array-config",
+    "config_index": "preprod.healdata.org_array-config",
     "auth_filter_field": "auth_resource_path"
-  },
-  "canary": {
-    "default": 0
   }
 }
@@ -0,0 +1,129 @@
+{
+  "user-namespace": "jupyter-pods-qa-heal",
+  "sub-dir": "/lw-workspace",
+  "user-volume-size": "10Gi",
+  "sidecar": {
+    "cpu-limit": "1.0",
+    "memory-limit": "256Mi",
+    "image": "quay.io/cdis/gen3fuse-sidecar:2021.03",
+    "env": {
+      "NAMESPACE": "qa-heal",
+      "HOSTNAME": "qa-heal.planx-pla.net"
+    },
+    "args": [],
+    "command": [
+      "/bin/bash",
+      "/sidecarDockerrun.sh"
+    ],
+    "lifecycle-pre-stop": [
+      "su",
+      "-c",
+      "echo test",
+      "-s",
+      "/bin/sh",
+      "root"
+    ]
+  },
+  "containers": [
+    {
+      "target-port": 8787,
+      "cpu-limit": "1.0",
+      "memory-limit": "512Mi",
+      "name": "R Studio",
+      "image": "heliumdatastage/rstudio-server:1",
+      "env": {
+        "DISABLE_AUTH": "true"
+      },
+      "args": [],
+      "path-rewrite": "/",
+      "use-tls": "false",
+      "ready-probe": "/"
+    },
+    {
+      "target-port": 8888,
+      "cpu-limit": "1.0",
+      "memory-limit": "512Mi",
+      "name": "Jupyter Notebook Bio Python",
+      "image": "quay.io/occ_data/jupyternotebook:1.9.0",
+      "env": {},
+      "args": [
+        "--NotebookApp.base_url=/lw-workspace/proxy/",
+        "--NotebookApp.password=''",
+        "--NotebookApp.token=''",
+        "--NotebookApp.notebook_dir='/home/jovyan/pd'",
+        "--NotebookApp.quit_button=False"
+      ],
+      "command": [
+        "start-notebook.sh"
+      ],
+      "path-rewrite": "/lw-workspace/proxy/",
+      "use-tls": "false",
+      "ready-probe": "/lw-workspace/proxy/",
+      "lifecycle-post-start": [
+        "/bin/sh",
+        "-c",
+        "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"
+      ],
+      "user-uid": 1000,
+      "fs-gid": 100,
+      "user-volume-location": "/home/jovyan/pd"
+    },
+    {
+      "target-port": 8888,
+      "cpu-limit": "1.0",
+      "memory-limit": "8192Mi",
+      "name": "Jupyter Notebook Power Python",
+      "image": "quay.io/occ_data/jupyternotebook:1.7.2",
+      "env": {},
+      "args": [
+        "--NotebookApp.base_url=/lw-workspace/proxy/",
+        "--NotebookApp.password=''",
+        "--NotebookApp.token=''",
+        "--NotebookApp.notebook_dir='/home/jovyan/pd'",
+        "--NotebookApp.quit_button=False"
+      ],
+      "command": [
+        "start-notebook.sh"
+      ],
+      "path-rewrite": "/lw-workspace/proxy/",
+      "use-tls": "false",
+      "ready-probe": "/lw-workspace/proxy/",
+      "lifecycle-post-start": [
+        "/bin/sh",
+        "-c",
+        "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"
+      ],
+      "user-uid": 1000,
+      "fs-gid": 100,
+      "user-volume-location": "/home/jovyan/pd"
+    },
+    {
+      "target-port": 8888,
+      "cpu-limit": "1.0",
+      "memory-limit": "8096Mi",
+      "name": "Helium Autoencoder Demo",
+      "image": "quay.io/cdis/auntoencoder-copd-demo:latest",
+      "env": {},
+      "args": [
+        "--NotebookApp.base_url=/lw-workspace/proxy/",
+        "--NotebookApp.password=''",
+        "--NotebookApp.token=''",
+        "--NotebookApp.notebook_dir='/home/jovyan/pd'",
+        "--NotebookApp.quit_button=False"
+      ],
+      "command": [
+        "start-notebook.sh"
+      ],
+      "path-rewrite": "/lw-workspace/proxy/",
+      "use-tls": "false",
+      "ready-probe": "/lw-workspace/proxy/",
+      "lifecycle-post-start": [
+        "/bin/sh",
+        "-c",
+        "export IAM=`whoami`; rm -rf /home/$IAM/pd/dockerHome; ln -s $(pwd) /home/$IAM/pd/dockerHome; mkdir -p /home/$IAM/.jupyter/custom; echo \"define(['base/js/namespace'], function(Jupyter){Jupyter._target = '_self';})\" >/home/$IAM/.jupyter/custom/custom.js; ln -s /data /home/$IAM/pd/; true"
+      ],
+      "user-uid": 1000,
+      "fs-gid": 100
+    }
+  ]
+}
@@ -1,26 +1,57 @@
 {
   "arborist": {
-    "strategy": "auto",
     "min": 1,
-    "max": 1
+    "max": 1,
+    "strategy": "auto"
+  },
+  "dashboard": {
+    "min": 1,
+    "max": 1,
+    "strategy": "auto"
+  },
+  "portal": {
+    "min": 1,
+    "max": 1,
+    "strategy": "auto"
   },
   "fence": {
-    "strategy": "auto",
     "min": 1,
-    "max": 1
+    "max": 1,
+    "strategy": "auto"
+  },
+  "presigned-url-fence": {
+    "min": 1,
+    "max": 1,
+    "strategy": "auto"
   },
   "indexd": {
-    "strategy": "auto",
     "min": 1,
-    "max": 1
+    "max": 1,
+    "strategy": "auto"
+  },
+  "metadata": {
+    "min": 1,
+    "max": 1,
+    "strategy": "auto"
+  },
+  "peregrine": {
+    "min": 1,
+    "max": 1,
+    "strategy": "auto"
   },
   "revproxy": {
-    "strategy": "auto",
     "min": 1,
-    "max": 1
+    "max": 1,
+    "strategy": "auto"
   },
   "sheepdog": {
-    "strategy": "pin",
-    "num": 2
+    "min": 1,
+    "max": 1,
+    "strategy": "auto"
+  },
+  "guppy": {
+    "min": 1,
+    "max": 1,
+    "strategy": "auto"
   }
 }