Merge branch 'main' into dependabot/npm_and_yarn/packages/vre-panel/t…

…ypescript-5.4.5

.github/workflows/make.yml

@@ -44,10 +44,8 @@ jobs:
       module_mapping_url: ${{ vars.MODULE_MAPPING_URL }}
       search_api_endpoint: ${{ vars.SEARCH_API_ENDPOINT }}
       registry_url: ${{ vars.REGISTRY_URL }}
-      argo_url: ${{ vars.ARGO_URL }}
       debug: ${{ vars.DEBUG }}
     secrets:
-      argo_api_token: ${{ secrets.ARGO_API_TOKEN }}
       cell_github_token:  ${{ secrets.CELL_GITHUB_TOKEN }}
       naavre_api_token: ${{ secrets.NAAVRE_API_TOKEN }}
       search_api_token: ${{ secrets.SEARCH_API_TOKEN }}

.github/workflows/test-build wheel.yml

@@ -9,9 +9,6 @@ on:
       api_endpoint:
         required: true
         type: string
-      argo_url:
-        required: true
-        type: string
       cell_github:
         required: true
         type: string
@@ -34,8 +31,6 @@ on:
         required: true
         type: string
     secrets:
-      argo_api_token:
-        required: true
       cell_github_token:
         required: true
       naavre_api_token:
@@ -54,8 +49,6 @@ env:
   MODULE_MAPPING_URL: ${{ inputs.module_mapping_url }}
   SEARCH_API_ENDPOINT: ${{ inputs.search_api_endpoint }}
   SEARCH_API_TOKEN: ${{ secrets.search_api_token }}
-  ARGO_URL: ${{ inputs.ARGO_URL }}
-  ARGO_API_TOKEN: ${{ secrets.ARGO_API_TOKEN }}
   ASYNC_TEST_TIMEOUT: 30
   DEBUG: ${{ inputs.debug }}
 
@@ -115,16 +108,6 @@ jobs:
             concatenated_error_message="$concatenated_error_message SEARCH_API_TOKEN not set"
             vars_not_set=1
           fi
-          if [ -z "ARGO_URL" ]; then
-            echo "ARGO_URL not set"
-            concatenated_error_message="$concatenated_error_message ARGO_URL not set"
-            vars_not_set=1
-          fi
-          if [ -z "ARGO_API_TOKEN" ]; then
-            echo "ARGO_API_TOKEN not set"
-            concatenated_error_message="$concatenated_error_message ARGO_API_TOKEN not set"
-            vars_not_set=1
-          fi
           if [ -z "$DEBUG" ]; then
             echo "DEBUG not set"
             concatenated_error_message="$concatenated_error_message DEBUG not set"

README.md

@@ -162,94 +162,3 @@ docker build -t n-a-a-vre .
 ```commandline
 docker run -it -p 8888:8888 --env-file ~/Downloads/notbooks/docker_VARS n-a-a-vre /bin/bash -c "source /venv/bin/activate && /tmp/init_script.sh && jupyter lab --debug --watch --NotebookApp.token='' --NotebookApp.ip='0.0.0.0' --NotebookApp.allow_origin='*' --collaborative"
 ```
-
-
-# Argo Workflows
-
-## Generate Token
-
-```shell
-kubectl apply -f - <<EOF
-kind: Role
-apiVersion: rbac.authorization.k8s.io/v1
-metadata:
-  name: vre-api
-  namespace: argo
-rules:
-  - verbs:
-      - get
-      - watch
-      - patch
-    apiGroups:
-      - ''
-    resources:
-      - pods
-  - verbs:
-      - get
-      - watch
-    apiGroups:
-      - ''
-    resources:
-      - pods/log
-  - verbs:
-      - create
-    apiGroups:
-      - ''
-    resources:
-      - pods/exec
-  - verbs:
-      - list
-      - watch
-      - create
-      - get
-      - update
-      - delete
-    apiGroups:
-      - argoproj.io
-    resources:
-      - workflowtasksets
-      - workflowartifactgctasks
-      - workflowtemplates
-      - workflows
-  - verbs:
-      - patch
-    apiGroups:
-      - argoproj.io
-    resources:
-      - workflowtasksets/status
-      - workflowartifactgctasks/status
-      - workflows/status
-EOF
-```
-
-```shell
-kubectl create sa vre-api -n argo
-```
-
-```shell
-kubectl create rolebinding vre-api --role=vre-api --serviceaccount=argo:vre-api -n argo
-```
-
-```shell
-kubectl apply -f - <<EOF
-apiVersion: v1
-kind: Secret
-metadata:
-  namespace: argo
-  name: vre-api.service-account-token
-  annotations:
-    kubernetes.io/service-account.name: vre-api
-type: kubernetes.io/service-account-token
-EOF
-```
-
-```shell
-ARGO_TOKEN="Bearer $(kubectl get secret vre-api.service-account-token -n argo -o=jsonpath='{.data.token}' | base64 --decode)"
-```
-
-```shell
-echo -n $ARGO_TOKEN | base64 -w 0
-```
-
-
-

docker/docker_VARS

@@ -7,11 +7,6 @@ SEARCH_API_ENDPOINT=http://HOST/api/
 SEARCH_API_TOKEN=TOKEN
 CELL_GITHUB=https://github.com/ORG/NAME
 CELL_GITHUB_TOKEN=TOKEN
+ARGO_WF_SPEC_SERVICEACCOUNT="executor"
+JUPYTERHUB_SINGLEUSER_APP="jupyter_server.serverapp.ServerApp"
 REGISTRY_URL=
-ARGO_URL=https://HOST:32443/ess-22-argowf
-ARGO_API_TOKEN="Bearer TOKEN"
-KEYCLOAK_SERVER_URL=https://HOST:32443/auth
-KEYCLOAK_CLIENT_ID=ID
-KEYCLOAK_CLIENT_SECRET_KEY=KEY
-KEYCLOAK_REALM=RELM
-SECRET_KEY=KEY

docker/export_VARS

@@ -7,11 +7,6 @@ export SEARCH_API_ENDPOINT=http://HOST/api/
 export SEARCH_API_TOKEN=TOKEN
 export CELL_GITHUB=https://github.com/ORG/NAME
 export CELL_GITHUB_TOKEN=TOKEN
+export ARGO_WF_SPEC_SERVICEACCOUNT="executor"
+export JUPYTERHUB_SINGLEUSER_APP="jupyter_server.serverapp.ServerApp"
 export REGISTRY_URL=
-export ARGO_URL=https://HOST:32443/ess-22-argowf
-export ARGO_API_TOKEN="Bearer TOKEN"
-export KEYCLOAK_SERVER_URL=https://HOST:32443/auth
-export KEYCLOAK_CLIENT_ID=ID
-export KEYCLOAK_CLIENT_SECRET_KEY=KEY
-export KEYCLOAK_REALM=RELM
-export SECRET_KEY=KEY

jupyterlab_vre/dataset_search/handlers.py

@@ -34,8 +34,10 @@ async def post(self, *args, **kwargs):
         self.check_environment_variables()
         access_token = os.environ['NAAVRE_API_TOKEN']
         api_endpoint = os.getenv('API_ENDPOINT')
+        vre_api_verify_ssl = (os.getenv('VRE_API_VERIFY_SSL', 'true').lower() == 'true')
         resp = requests.get(
             f"{api_endpoint}/api/dataprods/",
+            verify=vre_api_verify_ssl,
             headers={
                 'Authorization': f"Token {access_token}",
                 'Content-Type': 'application/json'

jupyterlab_vre/experiment_manager/handlers.py

@@ -152,13 +152,12 @@ async def post(self, *args, **kwargs):
 
         try:
             access_token = os.environ['NAAVRE_API_TOKEN']
-            vre_api_verify_ssl = os.getenv('VRE_API_VERIFY_SSL', 'true')
+            vre_api_verify_ssl = (os.getenv('VRE_API_VERIFY_SSL', 'true').lower() == 'true')
             logger.info('Workflow submission request: ' + str(json.dumps(req_body, indent=2)))
-            session = requests.Session()
-            session.verify = vre_api_verify_ssl
 
             resp = requests.post(
                 f"{api_endpoint}/api/workflows/submit/",
+                verify=vre_api_verify_ssl,
                 data=json.dumps(req_body),
                 headers={
                     'Authorization': f"Token {access_token}",
@@ -192,9 +191,11 @@ async def get(self, *args, **kwargs):
         self.check_environment_variables()
         api_endpoint = os.getenv('API_ENDPOINT')
         access_token = os.environ['NAAVRE_API_TOKEN']
+        vre_api_verify_ssl = (os.getenv('VRE_API_VERIFY_SSL', 'true').lower() == 'true')
         # This is a bug. If we don't do this, the workflow status is not updated.
         resp = requests.get(
             f"{api_endpoint}/api/workflows/",
+            verify=vre_api_verify_ssl,
             headers={
                 'Authorization': f"Token {access_token}",
                 'Content-Type': 'application/json'
@@ -210,6 +211,7 @@ async def get(self, *args, **kwargs):
         sleep(0.3)
         resp = requests.get(
             f"{api_endpoint}/api/workflows/{workflow_id}/",
+            verify=vre_api_verify_ssl,
             headers={
                 'Authorization': f"Token {access_token}",
                 'Content-Type': 'application/json'

jupyterlab_vre/templates/R_cell_template.jinja2

@@ -59,8 +59,6 @@ opt = parse_args(OptionParser(option_list=option_list))
 
 {{ cell.original_source }}
 
-
-
 {% if cell.outputs|length > 0 %}
 # capturing outputs
 {% for out in cell.outputs %}

jupyterlab_vre/tests/test_env_vars.py

@@ -17,4 +17,3 @@ def test_env_vars(self):
         self.assertIsNotNone(os.environ.get('MODULE_MAPPING_URL'))
         self.assertIsNotNone(os.environ.get('SEARCH_API_ENDPOINT'))
         self.assertIsNotNone(os.environ.get('SEARCH_API_TOKEN'))
-        self.assertIsNotNone(os.environ.get('ARGO_URL'))

jupyterlab_vre/tests/test_handlers.py

@@ -29,7 +29,6 @@
 
 cells_path = os.path.join(str(Path.home()), 'NaaVRE', 'cells')
 
-
 def delete_text(file_path, text_to_delete):
     # Read the file
     with open(file_path, 'r') as file:

packages/notebook-search/package.json

@@ -36,7 +36,7 @@
     },
     "devDependencies": {
         "@types/node": "20.2.5",
-        "@types/react-star-rating-component": "1.4.1",
+        "@types/react-star-rating-component": "1.4.4",
         "rimraf": "5.0.5",
         "typescript": "5.3.2"
     },