diff --git a/LICENSE b/LICENSE index cd482d8..db85496 100644 --- a/LICENSE +++ b/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/ diff --git a/apps/jupyter-lab/Chart.yaml b/apps/jupyter-lab/Chart.yaml index afb1ad8..accbd5b 100644 --- a/apps/jupyter-lab/Chart.yaml +++ b/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: serve@scilifelab.se diff --git a/apps/jupyter-lab/values.yaml b/apps/jupyter-lab/values.yaml index 28f1ce5..33a3527 100644 --- a/apps/jupyter-lab/values.yaml +++ b/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: diff --git a/apps/shiny/Chart.yaml b/apps/shiny/Chart.yaml index 0f0ec5d..cbfb3dc 100644 --- a/apps/shiny/Chart.yaml +++ b/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: serve@scilifelab.se diff --git a/apps/shiny/templates/deployment.yaml b/apps/shiny/templates/deployment.yaml index 95737f0..9634070 100644 --- a/apps/shiny/templates/deployment.yaml +++ b/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 diff --git a/apps/shiny/templates/shiny-configmap.yaml b/apps/shiny/templates/shiny-configmap.yaml new file mode 100644 index 0000000..d16fa39 --- /dev/null +++ b/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; + } diff --git a/apps/shinyproxy/Chart.yaml b/apps/shinyproxy/Chart.yaml index 884b1fb..81e63d7 100644 --- a/apps/shinyproxy/Chart.yaml +++ b/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 diff --git a/apps/shinyproxy/templates/configmap.yaml b/apps/shinyproxy/templates/configmap.yaml index e1c2842..d450a2a 100644 --- a/apps/shinyproxy/templates/configmap.yaml +++ b/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" diff --git a/serve/Chart.yaml b/serve/Chart.yaml index 77ac066..4a3d552 100644 --- a/serve/Chart.yaml +++ b/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 @@ -19,12 +19,12 @@ 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 @@ -32,4 +32,5 @@ dependencies: repository: https://charts.bitnami.com/bitnami tags: - bitnami-common - version: 2.0.4 + version: 2.19.1 + diff --git a/serve/templates/_helper.tpl b/serve/templates/_helper.tpl index a262242..9904f41 100644 --- a/serve/templates/_helper.tpl +++ b/serve/templates/_helper.tpl @@ -194,4 +194,4 @@ Return STACKn rabbit secret {{- else -}} event_user@test.com {{- end -}} - {{- end -}} \ No newline at end of file + {{- end -}}