Merge branch 'develop' into increase-n-projects-limit

LICENSE

@@ -1,3 +1,20 @@
+Copyright 2023-present SciLifeLab Data Centre (https://scilifelab.se/data)
+Copyright 2020-2023 Scaleout Systems AB
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+====================
+
 Apache License
 Version 2.0, January 2004
 http://www.apache.org/licenses/

apps/jupyter-lab/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "0.1"
 description: A Helm chart for Jupyter Lab
 name: lab
-version: 1.0.0
+version: 1.0.1
 maintainers:
   - name: Team Whale
     email: [email protected]

apps/jupyter-lab/values.yaml

@@ -68,9 +68,7 @@ flavor:
     cpu: 1
     ephemeral-storage: 800Mi
     memory: 1Gi
-    nvidia.com/gpu:
   requests:
     cpu: 500m
     ephemeral-storage: 500Mi
     memory: 500Mi
-    nvidia.com/gpu:

apps/shiny/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "0.1"
 description: A Helm chart Shiny apps
 name: shinyapp
-version: 1.0.1
+version: 1.0.2
 maintainers:
   - name: Team Whale
     email: [email protected]

apps/shiny/templates/deployment.yaml

@@ -44,5 +44,16 @@ spec:
           {{- toYaml .Values.flavor | nindent 10 }}
         ports:
           - containerPort: {{ .Values.appconfig.port }}
+        volumeMounts:
+        - name: {{ .Release.Name }}-shiny-configmap
+          mountPath: /etc/shiny-server/shiny-server.conf
+          subPath: shiny-server.conf
       terminationGracePeriodSeconds: 30
       dnsPolicy: ClusterFirst
+      volumes:
+      - name: {{ .Release.Name }}-shiny-configmap
+        configMap:
+          name: {{ .Release.Name }}-shiny-configmap
+          items:
+          - key: shiny-server.conf
+            path: shiny-server.conf

apps/shiny/templates/shiny-configmap.yaml

@@ -0,0 +1,31 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ .Release.Name }}-shiny-configmap
+  namespace: {{ .Release.Namespace }}
+data:
+  shiny-server.conf: |-
+    # Instruct Shiny Server to run applications as the user "shiny"
+    run_as shiny;
+    http_keepalive_timeout 600;
+    # Define a server that listens on user defined port
+    server {
+      listen {{ .Values.appconfig.port }} 0.0.0.0;
+      # Define a location at the base URL
+      location / {
+
+        # Host the directory of Shiny Apps stored in this directory
+        site_dir /srv/shiny-server;
+
+        # Log all Shiny output to files in this directory
+        log_dir /var/log/shiny-server;
+
+        # When a user visits the base URL rather than a particular application,
+        # an index of the applications available in this directory will be shown.
+        directory_index on;
+        app_init_timeout 600;
+        app_idle_timeout 600;
+      }
+      app_init_timeout 600;
+      app_idle_timeout 600;
+    }

apps/shinyproxy/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v2
 name: shinyproxy
 description: A Helm chart to install Shinyproxy
 type: application
-version: 1.0.0
+version: 1.1.0
 appVersion: "0.1"
 maintainers:
   - name: Team Whale

apps/shinyproxy/templates/configmap.yaml

@@ -14,8 +14,9 @@ data:
     proxy:
       authentication: none
       container-backend: kubernetes
-      heartbeat-rate: 10000
-      heartbeat-timeout: 60000
+      heartbeat-rate: {{ .Values.appconfig.proxyheartbeatrate | default 10000 }}
+      heartbeat-timeout: {{ .Values.appconfig.proxyheartbeattimeout | default 60000 }}
+      container-wait-time: {{ .Values.appconfig.proxycontainerwaittime | default 30000 }}
       kubernetes:
         internal-networking: true
         namespace: {{ .Release.Namespace }}
@@ -37,8 +38,8 @@ data:
         container-memory-request: {{ .Values.flavor.requests.memory }}
         port: {{ .Values.appconfig.port }}
         id:  {{ .Release.Name }}
-        display-name: {{ .Values.app_name }}
-        description: {{ .Values.app_description }}
+        display-name: {{ .Values.app_name | quote }}
+        description: {{ .Values.app_description | quote }}
         labels:
           sp.instance: {{ .Release.Name }}
           allow-internet-egress: "true"

serve/Chart.yaml

@@ -9,7 +9,7 @@ maintainers:
 
 dependencies:
   - name: reloader
-    version: v1.0.15
+    version: v1.0.79
     repository: https://stakater.github.io/stakater-charts
     condition: reloader.enabled
 
@@ -19,17 +19,18 @@ dependencies:
     condition: postgresql.enabled
 
   - name: redis
-    version: 17.7.4
+    version: 19.1.0
     repository: https://charts.bitnami.com/bitnami
     condition: redis.enabled
 
   - name: rabbitmq
-    version: 11.9.1
+    version: 14.0.0
     repository: https://charts.bitnami.com/bitnami
     condition: rabbitmq.enabled
 
   - name: common
     repository: https://charts.bitnami.com/bitnami
     tags:
       - bitnami-common
-    version: 2.0.4
+    version: 2.19.1
+

serve/templates/_helper.tpl

@@ -194,4 +194,4 @@ Return STACKn rabbit secret
     {{- else -}}
         [email protected]
     {{- end -}}
-    {{- end -}}
+    {{- end -}}