Merge pull request #669 from MetaCell/release/2.1.0

Release/2.1.0 back to develop

.dockerignore

@@ -5,8 +5,18 @@ docs
 /infrastructure
 /blueprint
 test
+/tools/deployment-cli-tools
 .github
 .git
 .vscode
 /deployment
-skaffold.yaml
+skaffold.yaml
+*.egg-info
+__pycache__
+.hypothesis
+.coverage
+.pytest_cache
+/application-templates
+/deployment-configuration
+/cloud-harness
+.openapi-generator

.github/workflows/trivy-analysis.yml

@@ -23,14 +23,14 @@ jobs:
       contents: read # for actions/checkout to fetch code
       security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
     name: Build
-    runs-on: "ubuntu-18.04"
+    runs-on: "ubuntu-20.04"
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Build an image from Dockerfile
         run: |
-          docker build -t cloudharness-base:${{ github.sha }} . -f ./infrastructure/base-images/cloudharness-base/Dockerfile
+          DOCKER_BUILDKIT=1 docker build -t cloudharness-base:${{ github.sha }} . -f ./infrastructure/base-images/cloudharness-base/Dockerfile
 
       - name: Run Trivy vulnerability scanner
         uses: aquasecurity/trivy-action@2a2157eb22c08c9a1fac99263430307b8d1bc7a2

.gitignore

@@ -16,4 +16,5 @@ skaffold.yaml
 .overrides
 /deployment.yaml
 .hypothesis
-__pycache__
+__pycache__
+.env

application-templates/django-app/Dockerfile

@@ -21,7 +21,8 @@ WORKDIR ${APP_DIR}
 RUN mkdir -p ${APP_DIR}/static/www
 
 COPY backend/requirements.txt ${APP_DIR}
-RUN pip3 install --no-cache-dir -r requirements.txt
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+    pip3 install --no-cache-dir -r requirements.txt --prefer-binary
 
 COPY backend/requirements.txt backend/setup.py ${APP_DIR}
 RUN python3 -m pip install -e .

application-templates/flask-server/backend/Dockerfile

@@ -8,7 +8,8 @@ ENV PORT=8080
 
 COPY requirements.txt /usr/src/app/
 
-RUN pip3 install --no-cache-dir -r requirements.txt
+RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
+    pip3 install --no-cache-dir -r requirements.txt
 
 COPY . /usr/src/app
 

applications/argo/deploy/charts/templates/controller/workflow-controller-cluster-roles.yaml

@@ -35,6 +35,8 @@ rules:
   resources:
   - persistentvolumeclaims
   verbs:
+  - get
+  - list
   - create
   - delete
 - apiGroups:

applications/common/server/requirements.txt

@@ -9,3 +9,5 @@ swagger-ui-bundle >= 0.0.2
 python_dateutil >= 2.6.0
 setuptools >= 21.0.0
 Flask == 1.1.2
+flask_sqlalchemy==2.4.4
+sqlalchemy<2.0.0

applications/common/server/setup.py

@@ -17,7 +17,8 @@
     "connexion>=2.0.2",
     "swagger-ui-bundle>=0.0.2",
     "python_dateutil>=2.6.0",
-    "psycopg2"
+    "psycopg2",
+    "flask_sqlalchemy",
 ]
 
 setup(

applications/events/deploy/resources/broker/server.properties

@@ -121,8 +121,8 @@ log.retention.hours=-1
 zookeeper.connect=zookeeper:2181
 
 # Timeout in ms for connecting to zookeeper
-#zookeeper.connection.timeout.ms=6000
-
+zookeeper.connection.timeout.ms=600000
+atlas.kafka.zookeeper.session.timeout.ms=600000
 
 ############################# Group Coordinator Settings #############################
 

applications/jupyterhub/deploy/resources/hub/jupyterhub_config.py

@@ -271,7 +271,7 @@ def camelCaseify(s):
     pvc_name_template = get_config("singleuser.storage.dynamic.pvcNameTemplate")
     c.KubeSpawner.pvc_name_template = pvc_name_template
     volume_name_template = get_config("singleuser.storage.dynamic.volumeNameTemplate")
-    c.KubeSpawner.storage_pvc_ensure = True
+    c.KubeSpawner.storage_pvc_ensure = False
     set_config_if_not_none(
         c.KubeSpawner, "storage_class", "singleuser.storage.dynamic.storageClass"
     )
@@ -524,4 +524,5 @@ def camelCaseify(s):
 
 c.apps = get_config('apps')
 c.registry = get_config('registry')
-c.domain = get_config('root.domain')
+c.domain = get_config('root.domain')
+c.namespace = get_config('root.namespace')

applications/jupyterhub/deploy/templates/hub/deployment.yaml

@@ -48,9 +48,11 @@ spec:
         - name: cloudharness-allvalues
           configMap:
             name: cloudharness-allvalues
+         {{- if .Values.apps.accounts }}            
         - name: cloudharness-kc-accounts
           secret:
             secretName: accounts
+        {{- end }}
         - name: secret
           secret:
             secretName: {{ include "jupyterhub.hub.fullname" . }}
@@ -154,9 +156,11 @@ spec:
             - name: cloudharness-allvalues
               mountPath: /opt/cloudharness/resources/allvalues.yaml
               subPath: allvalues.yaml
+            {{- if .Values.apps.accounts }}
             - name: cloudharness-kc-accounts
               mountPath: /opt/cloudharness/resources/auth
               readOnly: true
+            {{- end }}
             {{- if (include "jupyterhub.hub-existing-secret.fullname" .) }}
             - mountPath: /usr/local/etc/jupyterhub/existing-secret/
               name: existing-secret

applications/jupyterhub/src/chauthenticator/chauthenticator/auth.py

@@ -25,28 +25,26 @@ def initialize(self, force_new_server, process_user):
 
     @gen.coroutine
     def get(self):
-        raw_user = yield self.get_current_user()
-        if raw_user:
-            if self.force_new_server and user.running:
-                # Stop user's current server if it is running
-                # so we get a new one.
-                status = yield raw_user.spawner.poll_and_notify()
-                if status is None:
-                    yield self.stop_single_user(raw_user)
-        else:
-            try:
-                accessToken = self.request.cookies.get('accessToken', None)
+        self.clear_login_cookie()
+
+        try:
+
+                accessToken = self.request.cookies.get(
+                    'kc-access', None) or self.request.cookies.get('accessToken', None)
                 print("Token", accessToken)
                 if accessToken == '-1' or not accessToken:
                     self.redirect('/hub/logout')
 
                 accessToken = accessToken.value
                 user_data = AuthClient.decode_token(accessToken)
                 username = user_data['sub']
+                print("Username", username, "-",user_data['preferred_username'])
                 raw_user = self.user_from_username(username)
+                print("JH user: ", raw_user.__dict__)
                 self.set_login_cookie(raw_user)
-            except Exception as e:
+        except Exception as e:
                 logging.error("Error getting user from session", exc_info=True)
+                raise
 
         user = yield gen.maybe_future(self.process_user(raw_user, self))
         self.redirect(self.get_next_url(user))