Merge branch 'implement-nfs-provisioning-nexus' of p281392/molgenis-ops-docker-helm into master

molgenis-nexus/templates/deployments/httpd-deployment.yaml

@@ -1,34 +0,0 @@
-apiVersion: extensions/v1beta1
-kind: Deployment
-metadata:
-  creationTimestamp: null
-  name: {{ .Values.httpd.name }}
-  labels:
-    app: {{ .Values.httpd.name }}
-    environment: {{ .Values.environment }}
-spec:
-  replicas: {{ .Values.replicaCount }}
-  strategy:
-    type: {{ .Values.httpd.strategy.type }}
-  selector:
-    matchLabels:
-      app: {{ .Values.httpd.selector }}
-  template:
-    metadata:
-      labels:
-        app: {{ .Values.httpd.name }}
-      creationTimestamp: null
-    spec:
-      restartPolicy: {{ .Values.httpd.restartPolicy }}
-      containers:
-      - name: {{ .Values.httpd.name }}
-        image: "{{ .Values.httpd.image.repository }}:{{ .Values.httpd.image.tag }}"
-        imagePullPolicy: {{ .Values.httpd.image.pullPolicy }}
-        env:
-        - name: PROXY_SERVICE
-          value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
-        - name: SERVER_NAME
-          value: {{ .Values.httpd.hostname }}
-        ports:
-        - containerPort: {{ .Values.httpd.port }}
-        resources: {}

molgenis-nexus/templates/deployments/nexus-deployment.yaml

@@ -19,18 +19,7 @@ spec:
         app: {{ .Values.nexus.name }}
       creationTimestamp: null
     spec:
-      volumes:
-      - name: {{ .Values.persistence.name }}
-        persistentVolumeClaim:
-          claimName: {{ .Values.persistence.name }}
       restartPolicy: {{ .Values.nexus.restartPolicy }}
-      initContainers:
-      - name: volume-mount-nexus
-        image: busybox
-        command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"]
-        volumeMounts:
-        - name: {{ .Values.persistence.name }}
-          mountPath: "{{ .Values.persistence.mountPath }}"
       containers:
         - name: {{ .Values.nexus.name }}
           image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
@@ -39,6 +28,31 @@ spec:
           - containerPort: {{ .Values.nexus.port.ui }}
           - containerPort: {{ .Values.nexus.port.docker }}
           volumeMounts:
-        - name: {{ .Values.persistence.name }}
+          - name: molgenis-nexus-nfs
             mountPath: "/nexus-data"
+          livenessProbe:
+            httpGet:
+              path: /
+              port: {{ .Values.nexus.port.ui }}
+            initialDelaySeconds: 90
+            periodSeconds: 20
+            failureThreshold: 5
+            successThreshold: 1
+          readinessProbe:
+            httpGet:
+              path: /
+              port: {{ .Values.nexus.port.ui }}
+            initialDelaySeconds: 90
+            periodSeconds: 5
+            failureThreshold: 5
+            successThreshold: 1
 
+      volumes:
+        - name: molgenis-nexus-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.persistence.claim }}
+
+    {{- with .Values.nodeSelector }}
+      nodeSelector:
+{{ toYaml . | indent 8 }}
+    {{- end }}

molgenis-nexus/templates/deployments/nexusProxy-deployment.yaml

@@ -0,0 +1,55 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  creationTimestamp: null
+  name: {{ .Values.nexusProxy.name }}
+  labels:
+    app: {{ .Values.nexusProxy.name }}
+    environment: {{ .Values.environment }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  strategy:
+    type: {{ .Values.nexusProxy.strategy.type }}
+  selector:
+    matchLabels:
+      app: {{ .Values.nexusProxy.selector }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.nexusProxy.name }}
+      creationTimestamp: null
+    spec:
+      restartPolicy: {{ .Values.nexusProxy.restartPolicy }}
+      containers:
+      - name: {{ .Values.nexusProxy.name }}
+        image: "{{ .Values.nexusProxy.image.repository }}:{{ .Values.nexusProxy.image.tag }}"
+        imagePullPolicy: {{ .Values.nexusProxy.image.pullPolicy }}
+        env:
+        - name: PROXY_SERVICE
+          value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
+        - name: SERVER_NAME
+          value: {{ .Values.nexusProxy.hostname }}
+        ports:
+        - containerPort: {{ .Values.nexusProxy.port }}
+        resources: {}
+        livenessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexusProxy.port }}
+          initialDelaySeconds: 90
+          periodSeconds: 5
+          failureThreshold: 5
+          successThreshold: 1
+        readinessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexusProxy.port }}
+          initialDelaySeconds: 90
+          periodSeconds: 5
+          failureThreshold: 5
+          successThreshold: 1
+
+    {{- with .Values.nodeSelector }}
+      nodeSelector:
+{{ toYaml . | indent 8 }}
+    {{- end }}

molgenis-nexus/templates/ingress.yaml

@@ -25,8 +25,8 @@ spec:
       paths:
         - path: {{ default "/" .path }}
           backend:
-            serviceName: httpd
+            serviceName: {{ $.Values.nexusProxy.name }}
-            servicePort: 80
+            servicePort: {{ $.Values.nexusProxy.port }}
 {{- if .tls }}
   tls:
   - hosts:

molgenis-nexus/templates/persistence/nexusPVC.yaml

@@ -0,0 +1,15 @@
+{{- if .Values.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.persistence.claim }}
+  annotations:
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+      storage: {{ .Values.persistence.size }}
+{{- end }}

molgenis-nexus/templates/services/httpd-service.yaml

@@ -1,13 +0,0 @@
-apiVersion: v1
-kind: Service
-metadata:
-  name: {{ .Values.httpd.name }}
-  labels:
-    app: {{ .Values.httpd.name }}
-spec:
-  type: {{ .Values.httpd.service.type }}
-  ports:
-  - name: {{ .Values.httpd.name }}
-    port: {{ .Values.httpd.port }}
-  selector:
-    app: {{ .Values.httpd.selector }}

molgenis-nexus/templates/services/nexusProxy-service.yaml

@@ -0,0 +1,13 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.nexusProxy.name }}
+  labels:
+    app: {{ .Values.nexusProxy.name }}
+spec:
+  type: {{ .Values.nexusProxy.service.type }}
+  ports:
+  - name: {{ .Values.nexusProxy.name }}
+    port: {{ .Values.nexusProxy.port }}
+  selector:
+    app: {{ .Values.nexusProxy.selector }}

molgenis-nexus/templates/volumes/nexus-pv.yaml

@@ -1,16 +0,0 @@
-apiVersion: v1
-kind: PersistentVolume
-metadata:
-  name: {{ .Values.persistence.name }}
-  labels:
-    name: nfs2
-spec:
-  storageClassName: {{ .Values.persistence.storageClass }}
-  capacity:
-    storage: {{ .Values.persistence.size }}
-  accessModes:
-    - {{ .Values.persistence.accessMode }}
-  persistentVolumeReclaimPolicy: {{ .Values.persistence.reclaimPolicy }}
-  nfs:
-    server: {{ .Values.persistence.server }}
-    path: {{ .Values.persistence.mountPath }}

molgenis-nexus/templates/volumes/nexus-pvc.yaml

@@ -1,11 +0,0 @@
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: {{ .Values.persistence.name }}
-spec:
-  storageClassName: {{ .Values.persistence.storageClass }}
-  accessModes:
-    - {{ .Values.persistence.accessMode }}
-  resources:
-    requests:
-      storage: {{ .Values.persistence.size }}

molgenis-nexus/values.yaml

@@ -24,12 +24,12 @@ nexus:
   service:
     type: ClusterIP
 
-httpd:
+nexusProxy:
-  name: httpd
+  name: nexus-proxy
   hostname: registry.molgenis.org
   strategy:
     type: Recreate
-  selector: httpd
+  selector: nexus-proxy
   restartPolicy: Always
   image:
     repository: registry.webhosting.rug.nl/molgenis/httpd
@@ -43,39 +43,22 @@ httpd:
 ingress:
   enabled: true
   annotations: {}
-    # kubernetes.io/ingress.class: nginx
-    # kubernetes.io/tls-acme: "true"
   path: /
   hosts:
   - name: registry.molgenis.org
   tls: []
-  #  - secretName: chart-example-tls
-  #    hosts:
-  #      - chart-example.local
 
 persistence:
-  name: molgenis-nexus-data
+  enabled: true
-  storageClass: nfs-class
+  claim: molgenis-nexus
-  size: 30G
+  size: 500Gi
-  reclaimPolicy: Retain
-  server: 192.168.64.12
-  accessMode: ReadWriteMany
-  mountPath: /gcc/molgenis/nexus
 
 
 resources: {}
-  # We usually recommend not to specify default resources and to leave this as a conscious
-  # choice for the user. This also increases chances charts run on environments with little
-  # resources, such as Minikube. If you do want to specify resources, uncomment the following
-  # lines, adjust them as necessary, and remove the curly braces after 'resources:'.
-  # limits:
-  #  cpu: 100m
-  #  memory: 128Mi
-  # requests:
-  #  cpu: 100m
-  #  memory: 128Mi
 
-nodeSelector: {}
+nodeSelector: {
+  deployPod: "true"
+}
 
 tolerations: []
 

molgenis-opencpu/.helmignore

@@ -0,0 +1,21 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj

molgenis-opencpu/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+appVersion: "1.0"
+description: Opencpu stack for MOLGENIS
+name: molgenis-opencpu
+version: 0.1.1
+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-opencpu/catalogIcon-molgenis-opencpu.svg

molgenis-opencpu/README.md

@@ -0,0 +1,38 @@
+# MOLGENIS - OpenCPU Helm Chart
+
+NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
+
+## Containers
+
+This chart will deploy the following containers:
+
+- OpenCPU
+- MOLGENIS-httpd (to proxy the registry and docker to one domain)
+
+## Provisioning
+You can choose for the OpenCPU image from which repository you want to pull. Experimental builds are pushed to registry.molgenis.org and the stable builds to hub.docker.com. 
+You need to fill out 2 properties to determine which repository you are going to use.
+
+- ```opencpu.image.repository```
+- ```opencpu.image.tag```
+
+You can do this in the questions in Rancher or in the ```values.yaml```.
+
+
+
+## Development
+You can test in install the chart by executing:
+
+```helm lint .```
+
+To test if your helm chart-syntax is right and:
+
+```helm install . --dry-run --debug```
+
+To test if your hem chart works and:
+
+```helm install .```
+
+To deploy it on the cluster.
+
+

molgenis-opencpu/questions.yml

@@ -0,0 +1,28 @@
+
+categories:
+- MOLGENIS
+questions:
+- variable: ingress.enabled
+  label: Enable ingress
+  default: false
+  description: "Enable ingress"
+  type: boolean
+  required: true
+  group: "Loadbalancing"
+- variable: opencpu.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: opencpu.image.tag
+  label: Version
+  default: ""
+  description: "Select a OpenCPU version (check the registry.molgenis.org or hub.docker.com for released tags)"
+  type: string
+  required: true
+  group: "Provisioning"

molgenis-opencpu/templates/_helpers.tpl

@@ -0,0 +1,32 @@
+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "opencpu.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "opencpu.fullname" -}}
+{{- if .Values.fullnameOverride -}}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- $name := default .Chart.Name .Values.nameOverride -}}
+{{- if contains $name .Release.Name -}}
+{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "opencpu.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

molgenis-opencpu/templates/deployment.yaml

@@ -0,0 +1,35 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
+  name: {{ template "opencpu.fullname" . }}
+  labels:
+    app: {{ template "opencpu.name" . }}
+    chart: {{ template "opencpu.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ template "opencpu.name" . }}
+      release: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app: {{ template "opencpu.name" . }}
+        release: {{ .Release.Name }}
+    spec:
+      containers:
+      {{- with .Values.opencpu }}
+      - name: {{ .name }}
+        image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
+        imagePullPolicy: {{ .image.pullPolicy }}
+        ports:
+        - containerPort: {{ .service.port }}
+      {{- end }}
+
+

molgenis-opencpu/templates/ingress.yaml

@@ -0,0 +1,36 @@
+{{- if .Values.ingress.enabled }}
+{{- range .Values.ingress.hosts }}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: "{{ $.Release.Name }}-ingress"
+  labels:
+    app:  {{ $.Values.opencpu.name }}
+    chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
+    release: "{{ $.Release.Name }}"
+    heritage: "{{ $.Release.Service }}"
+  annotations:
+    {{- if .tls }}
+    ingress.kubernetes.io/secure-backends: "true"
+    {{- end }}
+    {{- range $key, $value := .annotations }}
+    {{ $key }}: {{ $value | quote }}
+    {{- end }}
+spec:
+  rules:
+  - host: {{ .name }}
+    http:
+      paths:
+        - path: {{ default "/" .path }}
+          backend:
+            serviceName: {{ $.Values.opencpu.service.name }}
+            servicePort: {{ $.Values.opencpu.service.port }}
+{{- if .tls }}
+  tls:
+  - hosts:
+    - {{ .name }}
+    secretName: {{ .tlsSecret }}
+{{- end }}
+---
+{{- end }}
+{{- end }}

molgenis-opencpu/templates/service.yaml

@@ -0,0 +1,20 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.opencpu.service.name }}
+  labels:
+    app: {{ .Values.opencpu.service.name }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  type: {{ .Values.opencpu.service.type }}
+  loadBalancerSourceRanges:
+  {{- range $index, $rule := .Values.opencpu.service.firewall }}
+    - {{ $rule }}
+  {{- end }}
+  ports:
+    - name: {{ .Values.opencpu.service.name }}
+      port: {{ .Values.opencpu.service.port }}
+  selector:
+    app: {{ template "opencpu.name" . }}
+    release: {{ .Release.Name }}

molgenis-opencpu/values.yaml

@@ -0,0 +1,41 @@
+# Default values for nexus.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+environment: production
+
+opencpu:
+  name: opencpu
+  strategy:
+    type: Recreate
+  restartPolicy: Always
+  image:
+    repository: registry.hub.docker.com
+    name: molgenis/opencpu
+    tag: stable
+    pullPolicy: Always
+  service:
+    name: opencpu
+    type: LoadBalancer
+    port: 8004
+    firewall:
+    - 145.100.224.1/24
+
+ingress:
+  enabled: false
+  annotations: {
+    kubernetes.io/ingress.class: "nginx",
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
+  }
+  path: /
+  hosts:
+  - name: opencpu.molgenis.org
+  tls: []
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}