added rstudio

charts/opal/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: Opal - helm stack (in BETA)
 name: opal
-version: 0.5.4
+version: 0.0.1
 sources:
 - https://git.webhosting.rug.nl/opal/opal-ops-docker-helm.git
 icon: https://git.webhosting.rug.nl/opal/opal-ops-docker-helm/

charts/opal/questions.yml

@@ -32,106 +32,4 @@ questions:
   type: string
   required: true
   group: "Provisioning"
-- variable: molgenis.adminPassword
-  label: Administrator password
-  default: ""
-  description: "Enter an administrator password"
-  type: password
-  required: true
-  group: "Provisioning"
-- variable: service.firewall.enabled
-  label: Firewall enabled
-  default: false
-  description: "Firewall enabled (can be cluster or UMCG scoped)"
-  type: boolean
-  required: true
-  group: "Services"
-  show_subquestion_if: true
-  subquestions:
-  - variable: service.firewall.kind
-    default: "umcg"
-    description: "Firewall kind. This can be 'umcg' or 'cluster' environment"
-    type: enum
-    required: true
-    options:
-    - umcg
-    - cluster
-    label: Firewall kind
-- variable: molgenis.advanced
-  label: Advanced mode
-  default: false
-  description: "Do you want to override the default values in advanced mode"
-  type: boolean
-  required: true
-  group: "Advanced"
-  show_subquestion_if: true
-  subquestions:
-  - variable: molgenis.image.repository
-    label: Registry
-    default: "registry.hub.docker.com"
-    description: "Select a registry to pull from"
-    type: enum
-    options:
-    - "registry.hub.docker.com"
-    - "registry.molgenis.org"
-    required: true
-    group: "Provisioning"
-  - variable: molgenis.services.opencpu.host
-    label: OpenCPU cluster
-    default: "molgenis-opencpu.opencpu"
-    description: "Specify the OpenCPU cluster"
-    type: string
-    required: true
-    group: "Services"
-  - variable: molgenis.services.postgres.embedded
-    label: Postgres embedded
-    default: true
-    description: "Do you want an embedded postgres"
-    type: boolean
-    required: true
-    group: "Services"
-  - variable: molgenis.services.postgres.host
-    label: Postgres cluster location
-    default: "localhost"
-    description: "Set the location of the postgres cluster. This can be localhost when the postgres is enabled else you need to specify a cluster location if you do not want a embedded postgres instance)"
-    type: string
-    required: true
-    group: "Services"
-  - variable: molgenis.services.postgres.scheme
-    label: Database scheme
-    default: "molgenis"
-    description: "Set the database scheme"
-    type: string
-    required: true
-    group: "Services"
-  - variable: molgenis.services.postgres.user
-    label: Database username
-    default: "molgenis"
-    description: "Set user of the database scheme"
-    type: string
-    required: true
-    group: "Services"
-  - variable: molgenis.services.postgres.password
-    label: Database password
-    default: "molgenis"
-    description: "Set the password of the database scheme"
-    type: string
-    required: true
-    group: "Services"
-  - variable: persistence.retain
-    default: false
-    description: "Do you want to retain the persistent volume"
-    type: boolean
-    label: Retain volume
-    group: "Persistence"
-  - variable: persistence.molgenis.size
-    default: "default"
-    description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
-    type: enum
-    options:
-    - "default"
-    - "5Gi"
-    - "10Gi"
-    - "30Gi"
-    label: Size MOLGENIS filestore
-    group: "Persistence"
+

charts/opal/templates/deployment.yaml

@@ -42,13 +42,7 @@ spec:
             - name: admin.password
               value: "{{ .adminPassword }}"
             - name: CATALINA_OPTS
-            {{- if eq .type.kind "small" }}
-              value: "-Xmx{{ .type.small.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-            {{- else if eq .type.kind "medium"}}
-              value: "-Xmx{{ .type.medium.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-            {{- else }}
-              value: "-Xmx{{ .type.large.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-            {{- end }}
+              value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
           ports:
             - containerPort: 8080
           {{- if $.Values.persistence.enabled }}
@@ -73,13 +67,7 @@ spec:
             failureThreshold: 3
             successThreshold: 1
           resources:
-          {{- if eq .type.kind "small" }}
-{{ toYaml .type.small.resources | indent 12 }}
-          {{- else if eq .type.kind "medium" }}
-{{ toYaml .type.medium.resources | indent 12 }}
-          {{- else }}
-{{ toYaml .type.large.resources | indent 12 }}
-          {{- end }}
+{{ toYaml .resources | indent 12 }}
         {{- end }}
 
 {{- if .Values.persistence.enabled }}

charts/opal/templates/ingress.yaml

@@ -26,19 +26,15 @@ spec:
   {{- end }}
 {{- end }}
   rules:
-    {{- if eq $.Values.opal.environment "development" }}
-    - host: {{ .Release.Name }}.dev.opal.org
-    {{- else if eq $.Values.opal.environment "test" }}
-    - host: {{ .Release.Name }}.test.opal.org
-    {{- else if eq $.Values.opal.environment "acceptance" }}
-    - host: {{ .Release.Name }}.accept.opal.org
-    {{- else }}
-    - host: {{ .Release.Name }}.opal.org
-    {{- end }}
+  {{- if .Values.ingress.hosts }}
+  {{- range $host := .Values.ingress.hosts }}
+    - host: {{ $host }}
       http:
         paths:
           - path: {{ $ingressPath }}
             backend:
               serviceName: {{ $fullName }}
               servicePort: {{ $.Values.service.port }}
+  {{- end }}
+  {{- end }}
 {{- end }}

charts/opal/templates/persistence/mysql-pvc.yaml

@@ -15,11 +15,5 @@ spec:
     - ReadWriteMany
   resources:
     requests:
-    {{- if eq .Values.opal.type.kind "small" }}
-      storage: {{ .Values.mysql.type.small.persistence.size }}
-    {{- else if eq .Values.opal.type.kind "medium" }}
-      storage: {{ .Values.mysql.type.medium.persistence.size }}
-    {{- else }}
-      storage: {{ .Values.mysql.type.large.persistence.size }}
-    {{- end }}
+      storage: {{ .Values.mysql.persistence.size }}
 {{- end }}

charts/opal/templates/persistence/opal-pvc.yaml

@@ -15,11 +15,5 @@ spec:
     - ReadWriteMany
   resources:
     requests:
-    {{- if eq .Values.opal.type.kind "small" }}
-      storage: {{ .Values.opal.type.small.persistence.size }}
-    {{- else if eq .Values.opal.type.kind "medium" }}
-      storage: {{ .Values.opal.type.medium.persistence.size }}
-    {{- else }}
-      storage: {{ .Values.opal.type.large.persistence.size }}
-    {{- end }}
+      storage: {{ .Values.opal.persistence.size }}
 {{- end }}

charts/opal/values.yaml

@@ -4,68 +4,30 @@ replicaCount: 1
 
 service:
   type: LoadBalancer
-  firewall:
-    enabled: false
-    kind: "umcg"
-    umcg:
-      rules:
-      - 127.0.0.1/32
-    cluster:
-      rules:
-      - 127.0.0.1/32
   port: 8080
 
 ingress:
   enabled: true
   annotations:
     nginx.ingress.kubernetes.io/proxy-body-size: "0"
-  # This will be used again when external domains need be attached to the instance
-  # hosts:
-  # - name: test
+  hosts:
+   - name: opal.dev.molgenis.org
   path: /
   tls: []
 
 opal:
   advanced: false
-  type:
-    kind: medium
-    small:
-      javaOpts:
-        maxHeapSpace: "2g"
-      resources:
-        limits:
-          cpu: 2
-          memory: 2Gi
-        requests:
-          cpu: 200m
-          memory: 2Gi
-      persistence:
-        size: 5Gi
-    medium:
-      javaOpts:
-        maxHeapSpace: "3g"
-      resources:
-        limits:
-          cpu: 3
-          memory: 3Gi
-        requests:
-          cpu: 200m
-          memory: 3Gi
-      persistence:
-        size: 10Gi
-    large:
-      javaOpts:
-        maxHeapSpace: "4g"
-      resources:
-        limits:
-          cpu: 4
-          memory: 4Gi
-        requests:
-          cpu: 200m
-          memory: 4Gi
-      persistence:
-        size: 30Gi
-  environment: test
+  javaOpts:
+    maxHeapSpace: "4g"
+  resources:
+    limits:
+    cpu: 4
+    memory: 4Gi
+  requests:
+    cpu: 200m
+    memory: 4Gi
+  persistence:
+    size: 10Gi
   image:
     repository: registry.hub.docker.com
     name: obiba/opal
@@ -86,6 +48,10 @@ rserver:
     tag: latest
     pullPolicy: IfNotPresent
 
+mysql:
+  persistence:
+    size: 10Gi
+
 persistence:
   enabled: true
   retain: false