diff --git a/molgenis-preview/Chart.yaml b/molgenis-preview/Chart.yaml index 8b2e040..4b35807 100644 --- a/molgenis-preview/Chart.yaml +++ b/molgenis-preview/Chart.yaml @@ -1,7 +1,7 @@ apiVersion: v1 appVersion: "1.0" -description: A Helm chart for Kubernetes -name: molgenis +description: MOLGENIS - helm stack for testing purposes +name: molgenis-preview version: 0.2.0 sources: - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git diff --git a/molgenis/Chart.yaml b/molgenis/Chart.yaml index 8b2e040..cfd1ebb 100644 --- a/molgenis/Chart.yaml +++ b/molgenis/Chart.yaml @@ -1,8 +1,8 @@ apiVersion: v1 appVersion: "1.0" -description: A Helm chart for Kubernetes +description: MOLGENIS - helm stack name: molgenis -version: 0.2.0 +version: 0.0.1 sources: - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git -icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-preview/catalogIcon-molgenis.svg \ No newline at end of file +icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg \ No newline at end of file diff --git a/molgenis/README.md b/molgenis/README.md index f2109c1..4cedc28 100644 --- a/molgenis/README.md +++ b/molgenis/README.md @@ -4,9 +4,10 @@ This chart is used for acceptance and production use cases. ## Containers This chart spins up a MOLGENIS instance with HTTPD. The created containers are: -- HTTPD - MOLGENIS ## MOLGENIS -## HTTPD + +## Firewall +Is defined \ No newline at end of file diff --git a/molgenis/questions.yml b/molgenis/questions.yml index f200b2d..107adb8 100644 --- a/molgenis/questions.yml +++ b/molgenis/questions.yml @@ -17,20 +17,64 @@ questions: - "registry.hub.docker.com" - "registry.molgenis.org" required: true - group: "MOLGENIS - Version" + group: "MOLGENIS" label: Registry - variable: molgenis.image.tag default: "stable" - description: "Select a MOLGENIS version" - type: enum - options: - - "latest" - - "stable" - - "7.1-stable" - - "7.0-stable" + description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for other tags)" + type: string required: true - group: "MOLGENIS - Version" + group: "MOLGENIS" label: Version +- variable: molgenis.services.opencpu.uriHost + default: "" + description: "Specify the OpenCPU cluster" + type: string + required: true + group: "MOLGENIS" + label: OpenCPU cluster +- variable: molgenis.services.elasticsearch.clusterName + default: "molgenis" + description: "Set the index name of MOLGENIS" + type: string + required: true + group: "MOLGENIS" + label: Elasticsearch clustername +- variable: molgenis.services.elasticsearch.transportAddress + default: "localhost:9300" + description: "Set the transport address for the elasticsearch node communication port and low-level api (which we use)" + type: string + required: true + group: "MOLGENIS" + label: Elasticsearch transport address +- variable: molgenis.services.postgres.host + default: "localhost" + description: "Set the location of the postgres cluster" + type: string + required: true + group: "MOLGENIS" + label: Postgres cluster location +- variable: molgenis.services.postgres.scheme + default: "molgenis" + description: "Set the database scheme" + type: string + required: true + group: "MOLGENIS" + label: Database scheme +- variable: molgenis.services.postgres.user + default: "molgenis" + description: "Set user of the database scheme" + type: string + required: true + group: "MOLGENIS" + label: Database username +- variable: molgenis.services.postgres.password + default: "molgenis" + description: "Set the password of the database scheme" + type: string + required: true + group: "MOLGENIS" + label: Database password - variable: molgenis.resources.limits.cpu default: 1 description: "CPU limit for this MOLGENIS instance" diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml index 1052171..c58e765 100644 --- a/molgenis/templates/deployment.yaml +++ b/molgenis/templates/deployment.yaml @@ -26,27 +26,27 @@ spec: containers: - name: molgenis {{- with .Values.molgenis }} - image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}" + image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }} imagePullPolicy: {{ .image.pullPolicy }} env: - name: molgenis.home value: /home/molgenis - name: opencpu.uri.host - value: localhost + value: {{ .services.opencpu.uriHost }} - name: elasticsearch.transport.addresses - value: localhost:9300 + value: {{ .services.elasticsearch.transportAddresses }} - name: elasticsearch.cluster.name - value: {{ $.Values.elasticsearch.clusterName }} + value: {{ .services.elasticsearch.clusterName }} - name: db_uri - value: "jdbc:postgresql://localhost/{{ $.Values.postgres.db }}" + value: jdbc:postgresql://{{ .services.postgres.host }}/{{ .services.postgres.scheme }} - name: db_user - value: {{ $.Values.postgres.user }} + value: {{ .services.postgres.user }} - name: db_password - value: {{ $.Values.postgres.password }} + value: {{ .services.postgres.password }} - name: admin.password value: {{ .adminPassword }} - name: CATALINA_OPTS - value: "{{ .javaOpts }}" + value: {{ .javaOpts }} ports: - containerPort: 8080 # livenessProbe: diff --git a/molgenis/values.yaml b/molgenis/values.yaml index c165c5c..0b6ec88 100644 --- a/molgenis/values.yaml +++ b/molgenis/values.yaml @@ -19,7 +19,7 @@ molgenis: image: repository: registry.molgenis.org name: molgenis/molgenis-app - tag: 7.0.0-SNAPSHOT + tag: stable pullPolicy: Always adminPassword: admin javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled" @@ -30,6 +30,17 @@ molgenis: requests: cpu: 200m memory: 1Gi + services: + opencpu: + uriHost: localhost + elasticsearch: + transportAddresses: localhost:9300 + clusterName: molgenis + postgres: + host: localhost + scheme: molgenis + user: molgenis + password: molgenis nodeSelector: {}