Merge branch 'add-opencpu-chart' of p281392/molgenis-ops-docker-helm into master

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/catalog-molgenis-opencpu.svg

@@ -0,0 +1 @@
+<svg id="svg" version="1.1" width="400" height="211.2" viewBox="0 0 400 211.2" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" ><g id="svgg"><path id="path0" d="M146.487 22.310 C 145.632 22.523,145.088 22.783,144.947 23.047 C 144.827 23.271,144.534 23.455,144.295 23.455 C 143.805 23.455,141.997 25.207,141.997 25.682 C 141.997 25.852,141.807 26.181,141.574 26.413 C 141.342 26.646,141.152 27.073,141.152 27.362 C 141.152 27.660,140.968 28.003,140.729 28.153 C 140.181 28.495,140.059 35.922,140.601 35.922 C 140.951 35.922,141.152 36.375,141.152 37.164 C 141.152 37.538,141.407 37.993,141.884 38.468 C 142.288 38.869,142.620 39.283,142.624 39.387 C 142.633 39.636,144.518 41.416,144.773 41.416 C 144.880 41.416,145.022 41.556,145.088 41.727 C 145.153 41.898,145.555 42.099,145.979 42.173 C 146.404 42.248,146.962 42.440,147.219 42.602 C 147.924 43.043,154.517 43.023,154.886 42.578 C 155.031 42.404,155.408 42.261,155.725 42.261 C 156.041 42.261,156.472 42.071,156.683 41.838 C 156.893 41.606,157.162 41.416,157.280 41.416 C 157.398 41.416,157.905 40.988,158.406 40.465 C 158.907 39.942,159.413 39.514,159.532 39.514 C 159.650 39.514,159.746 39.370,159.746 39.195 C 159.746 39.020,159.937 38.713,160.169 38.514 C 160.401 38.315,160.592 37.996,160.592 37.805 C 160.592 37.614,160.782 37.216,161.014 36.921 C 161.247 36.625,161.437 36.168,161.437 35.905 C 161.437 35.642,161.592 35.256,161.781 35.047 C 162.303 34.470,162.323 30.318,161.807 29.588 C 161.603 29.301,161.437 28.769,161.437 28.406 C 161.437 28.015,161.265 27.591,161.014 27.364 C 160.782 27.154,160.592 26.808,160.592 26.597 C 160.592 26.192,157.426 22.847,156.658 22.440 C 155.872 22.022,148.043 21.923,146.487 22.310 M308.399 43.013 C 307.702 43.170,306.704 43.305,306.181 43.313 C 305.658 43.321,304.848 43.500,304.382 43.712 C 303.916 43.923,303.156 44.167,302.692 44.253 C 301.885 44.403,299.535 45.069,297.517 45.720 C 296.518 46.042,295.426 46.540,293.514 47.545 C 292.882 47.877,292.216 48.203,292.035 48.269 C 290.977 48.653,285.499 52.278,284.000 53.587 C 282.400 54.984,278.352 59.082,277.941 59.722 C 277.726 60.055,277.265 60.644,276.916 61.030 C 276.567 61.416,275.831 62.414,275.280 63.249 C 274.730 64.083,274.183 64.880,274.065 65.020 C 273.947 65.161,273.851 65.341,273.851 65.421 C 273.851 65.501,273.533 66.052,273.144 66.645 C 272.397 67.784,271.699 69.225,270.880 71.315 C 270.607 72.013,270.288 72.712,270.172 72.869 C 270.056 73.026,269.814 73.594,269.634 74.132 C 269.230 75.343,268.375 75.960,266.837 76.152 C 264.656 76.424,259.843 77.698,258.659 78.316 C 258.356 78.474,257.949 78.603,257.754 78.604 C 257.559 78.605,257.270 78.735,257.111 78.894 C 256.797 79.208,254.829 80.296,254.575 80.296 C 254.438 80.296,253.118 81.167,250.363 83.075 C 246.291 85.895,241.602 91.295,239.291 95.827 C 238.699 96.989,237.986 98.368,237.707 98.891 C 237.429 99.414,237.086 100.269,236.946 100.792 C 236.805 101.315,236.448 102.606,236.152 103.660 C 235.856 104.714,235.474 106.426,235.304 107.464 C 235.134 108.501,234.898 109.778,234.781 110.301 C 234.505 111.528,234.503 116.885,234.779 118.119 C 234.896 118.642,235.172 120.116,235.392 121.395 C 235.756 123.507,235.993 124.478,236.938 127.735 C 237.107 128.317,237.554 129.363,237.932 130.059 C 238.311 130.756,238.805 131.706,239.031 132.171 C 239.257 132.636,239.531 133.159,239.640 133.333 C 239.750 133.508,239.956 133.888,240.100 134.179 C 240.372 134.729,241.113 135.897,241.306 136.080 C 241.368 136.138,241.982 136.947,242.671 137.876 C 244.784 140.729,250.013 145.672,251.757 146.467 C 252.054 146.602,252.298 146.793,252.298 146.891 C 252.298 146.988,252.405 147.068,252.536 147.068 C 252.759 147.068,254.385 147.978,255.649 148.809 C 255.956 149.011,256.350 149.239,256.524 149.316 C 257.674 149.822,259.390 150.455,260.750 150.875 C 261.622 151.145,262.522 151.492,262.752 151.647 C 262.981 151.802,263.403 151.928,263.689 151.928 C 263.975 151.928,264.929 152.142,265.808 152.404 L 267.406 152.879 319.282 152.879 L 371.157 152.879 372.669 152.404 C 373.500 152.142,374.374 151.928,374.611 151.928 C 374.848 151.928,375.095 151.841,375.161 151.735 C 375.226 151.628,375.969 151.284,376.811 150.970 C 378.861 150.205,381.135 148.982,382.465 147.930 C 383.065 147.456,383.645 147.068,383.753 147.068 C 384.001 147.068,388.801 142.220,388.801 141.970 C 388.801 141.868,388.953 141.619,389.138 141.416 C 390.675 139.731,392.990 134.936,393.449 132.488 C 393.548 131.965,393.778 131.184,393.961 130.752 C 394.514 129.450,394.446 119.908,393.872 118.276 C 393.640 117.615,393.450 116.906,393.450 116.702 C 393.450 116.498,393.256 115.832,393.019 115.221 C 392.782 114.611,392.378 113.563,392.121 112.893 C 391.864 112.223,391.378 111.247,391.040 110.724 C 388.225 106.360,386.980 104.931,383.835 102.457 C 382.673 101.543,381.622 100.712,381.499 100.612 C 381.116 100.299,375.868 97.834,375.585 97.834 C 375.509 97.834,375.147 97.696,374.781 97.527 C 373.179 96.789,369.453 96.326,365.525 96.375 C 363.449 96.401,361.699 96.371,361Line truncated

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: {}