From 8de779afa06abde4f86ebf97cd239c6b57058102 Mon Sep 17 00:00:00 2001 From: Fleur Kelpin Date: Fri, 13 Jul 2018 12:48:25 +0200 Subject: [PATCH] Add molgenis chart (WIP) --- molgenis/.helmignore | 21 +++++ molgenis/Chart.yaml | 5 ++ molgenis/templates/NOTES.txt | 19 +++++ molgenis/templates/_helpers.tpl | 32 ++++++++ molgenis/templates/deployment.yaml | 128 +++++++++++++++++++++++++++++ molgenis/templates/ingress.yaml | 38 +++++++++ molgenis/templates/service.yaml | 19 +++++ molgenis/test.yaml | 120 +++++++++++++++++++++++++++ molgenis/values.yaml | 82 ++++++++++++++++++ 9 files changed, 464 insertions(+) create mode 100644 molgenis/.helmignore create mode 100644 molgenis/Chart.yaml create mode 100644 molgenis/templates/NOTES.txt create mode 100644 molgenis/templates/_helpers.tpl create mode 100644 molgenis/templates/deployment.yaml create mode 100644 molgenis/templates/ingress.yaml create mode 100644 molgenis/templates/service.yaml create mode 100644 molgenis/test.yaml create mode 100644 molgenis/values.yaml diff --git a/molgenis/.helmignore b/molgenis/.helmignore new file mode 100644 index 0000000..f0c1319 --- /dev/null +++ b/molgenis/.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 diff --git a/molgenis/Chart.yaml b/molgenis/Chart.yaml new file mode 100644 index 0000000..071bc2d --- /dev/null +++ b/molgenis/Chart.yaml @@ -0,0 +1,5 @@ +apiVersion: v1 +appVersion: "1.0" +description: A Helm chart for Kubernetes +name: molgenis +version: 0.1.0 diff --git a/molgenis/templates/NOTES.txt b/molgenis/templates/NOTES.txt new file mode 100644 index 0000000..b5a4d24 --- /dev/null +++ b/molgenis/templates/NOTES.txt @@ -0,0 +1,19 @@ +1. Get the application URL by running these commands: +{{- if .Values.ingress.enabled }} +{{- range .Values.ingress.hosts }} + http{{ if $.Values.ingress.tls }}s{{ end }}://{{ . }}{{ $.Values.ingress.path }} +{{- end }} +{{- else if contains "NodePort" .Values.service.type }} + export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ template "molgenis.fullname" . }}) + export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}") + echo http://$NODE_IP:$NODE_PORT +{{- else if contains "LoadBalancer" .Values.service.type }} + NOTE: It may take a few minutes for the LoadBalancer IP to be available. + You can watch the status of by running 'kubectl get svc -w {{ template "molgenis.fullname" . }}' + export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "molgenis.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}') + echo http://$SERVICE_IP:{{ .Values.service.port }} +{{- else if contains "ClusterIP" .Values.service.type }} + export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app={{ template "molgenis.name" . }},release={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}") + echo "Visit http://127.0.0.1:8080 to use your application" + kubectl port-forward $POD_NAME 8080:80 +{{- end }} diff --git a/molgenis/templates/_helpers.tpl b/molgenis/templates/_helpers.tpl new file mode 100644 index 0000000..e7cf3ea --- /dev/null +++ b/molgenis/templates/_helpers.tpl @@ -0,0 +1,32 @@ +{{/* vim: set filetype=mustache: */}} +{{/* +Expand the name of the chart. +*/}} +{{- define "molgenis.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 "molgenis.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 "molgenis.chart" -}} +{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} +{{- end -}} diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml new file mode 100644 index 0000000..e71c14f --- /dev/null +++ b/molgenis/templates/deployment.yaml @@ -0,0 +1,128 @@ +apiVersion: apps/v1beta2 +kind: Deployment +metadata: + name: {{ template "molgenis.fullname" . }} + labels: + app: {{ template "molgenis.name" . }} + chart: {{ template "molgenis.chart" . }} + release: {{ .Release.Name }} + heritage: {{ .Release.Service }} +spec: + replicas: {{ .Values.replicaCount }} + selector: + matchLabels: + app: {{ template "molgenis.name" . }} + release: {{ .Release.Name }} + template: + metadata: + labels: + app: {{ template "molgenis.name" . }} + release: {{ .Release.Name }} + spec: + containers: + - name: molgenis + {{- with .Values.molgenis }} + image: "{{ .image.repository }}:{{ .image.tag }}" + imagePullPolicy: {{ .image.pullPolicy }} + env: + - name: molgenis.home + value: /home/molgenis + - name: opencpu.uri.host + value: opencpu + - name: elasticsearch.transport.addresses + value: elasticsearch:9300 + - name: elasticsearch.cluster.name + value: {{ $.Values.elasticsearch.clusterName }} + - name: db_uri + value: "jdbc:postgresql://postgres/{{ $.Values.postgres.db }}" + - name: db_user + value: {{ $.Values.postgres.user }} + - name: db_password + value: {{ $.Values.postgres.password }} + - name: admin.password + value: {{ .adminPassword }} + - name: CATALINA_OPTS + value: "{{ .javaOpts }}" + ports: + - containerPort: 8080 + command: ["sh"] + args: ["-c", "cat"] + livenessProbe: + httpGet: + path: / + port: http + readinessProbe: + httpGet: + path: /api/v2/version + port: http + resources: +{{ toYaml .resources | indent 12 }} + {{- end }} + + - name: elasticsearch + {{- with .Values.elasticsearch }} + image: "{{ .image.repository }}:{{ .image.tag }}" + imagePullPolicy: {{ .image.pullPolicy }} + env: + - name: cluster.name + value: {{ .clusterName }} + - name: bootstrap.memory_lock + value: "true" + - name: ES_JAVA_OPTS + value: "{{ .javaOpts }}" + - name: xpack.security.enabled + value: "false" + - name: discovery.type + value: single-node + ports: + - containerPort: 9200 + - containerPort: 9300 + command: ["sh"] + args: ["-c", "cat"] + resources: +{{ toYaml .resources | indent 12 }} + {{- end }} + + - name: postgres + {{- with .Values.postgres }} + image: "{{ .image.repository }}:{{ .image.tag }}" + imagePullPolicy: {{ .image.pullPolicy }} + env: + - name: POSTGRES_USER + value: {{ .user }} + - name: POSTGRES_PASSWORD + value: {{ .password }} + - name: POSTGRES_DB + value: {{ .db }} + ports: + - containerPort: 5432 + command: ["sh"] + args: ["-c", "cat"] + resources: +{{ toYaml .resources | indent 12 }} + {{- end }} + + - name: opencpu + {{- with .Values.opencpu }} + image: "{{ .image.repository }}:{{ .image.tag }}" + imagePullPolicy: {{ .image.pullPolicy }} + ports: + - containerPort: 8004 + command: ["sh"] + args: ["-c", "cat"] + resources: +{{ toYaml .resources | indent 12 }} + {{- end }} + + {{- with .Values.nodeSelector }} + nodeSelector: +{{ toYaml . | indent 8 }} + {{- end }} + {{- with .Values.affinity }} + affinity: +{{ toYaml . | indent 8 }} + {{- end }} + {{- with .Values.tolerations }} + tolerations: +{{ toYaml . | indent 8 }} + {{- end }} diff --git a/molgenis/templates/ingress.yaml b/molgenis/templates/ingress.yaml new file mode 100644 index 0000000..b62644b --- /dev/null +++ b/molgenis/templates/ingress.yaml @@ -0,0 +1,38 @@ +{{- if .Values.ingress.enabled -}} +{{- $fullName := include "molgenis.fullname" . -}} +{{- $ingressPath := .Values.ingress.path -}} +apiVersion: extensions/v1beta1 +kind: Ingress +metadata: + name: {{ $fullName }} + labels: + app: {{ template "molgenis.name" . }} + chart: {{ template "molgenis.chart" . }} + release: {{ .Release.Name }} + heritage: {{ .Release.Service }} +{{- with .Values.ingress.annotations }} + annotations: +{{ toYaml . | indent 4 }} +{{- end }} +spec: +{{- if .Values.ingress.tls }} + tls: + {{- range .Values.ingress.tls }} + - hosts: + {{- range .hosts }} + - {{ . }} + {{- end }} + secretName: {{ .secretName }} + {{- end }} +{{- end }} + rules: + {{- range .Values.ingress.hosts }} + - host: {{ . }} + http: + paths: + - path: {{ $ingressPath }} + backend: + serviceName: {{ $fullName }} + servicePort: http + {{- end }} +{{- end }} diff --git a/molgenis/templates/service.yaml b/molgenis/templates/service.yaml new file mode 100644 index 0000000..5c5b665 --- /dev/null +++ b/molgenis/templates/service.yaml @@ -0,0 +1,19 @@ +apiVersion: v1 +kind: Service +metadata: + name: {{ template "molgenis.fullname" . }} + labels: + app: {{ template "molgenis.name" . }} + chart: {{ template "molgenis.chart" . }} + release: {{ .Release.Name }} + heritage: {{ .Release.Service }} +spec: + type: {{ .Values.service.type }} + ports: + - port: {{ .Values.service.port }} + targetPort: http + protocol: TCP + name: http + selector: + app: {{ template "molgenis.name" . }} + release: {{ .Release.Name }} diff --git a/molgenis/test.yaml b/molgenis/test.yaml new file mode 100644 index 0000000..ed0e0fe --- /dev/null +++ b/molgenis/test.yaml @@ -0,0 +1,120 @@ +# Source: molgenis/templates/deployment.yaml +apiVersion: apps/v1beta2 +kind: Deployment +metadata: + name: lanky-ragdoll-molgenis + labels: + app: molgenis + chart: molgenis-0.1.0 + release: lanky-ragdoll + heritage: Tiller +spec: + replicas: 1 + selector: + matchLabels: + app: molgenis + release: lanky-ragdoll + template: + metadata: + labels: + app: molgenis + release: lanky-ragdoll + spec: + containers: + - name: molgenis + image: "registry.molgenis.org/molgenis/molgenis-app:latest" + imagePullPolicy: Always + env: + - name: molgenis.home + value: /home/molgenis + - name: opencpu.uri.host + value: opencpu + - name: elasticsearch.transport.addresses + value: elasticsearch:9300 + - name: elasticsearch.cluster.name + value: molgenis + - name: db_uri + value: "jdbc:postgresql://postgres/molgenis" + - name: db_user + value: molgenis + - name: db_password + value: molgenis + - name: admin.password + value: admin + - name: CATALINA_OPTS + value: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled" + ports: + - containerPort: 8080 + livenessProbe: + httpGet: + path: / + port: http + readinessProbe: + httpGet: + path: /api/v2/version + port: http + resources: + limits: + cpu: 1 + memory: 1250Mi + requests: + cpu: 200m + memory: 1Gi + + + - name: elasticsearch + image: "docker.elastic.co/elasticsearch/elasticsearch:5.5.3" + imagePullPolicy: IfNotPresent + env: + - name: cluster.name + value: molgenis + - name: bootstrap.memory_lock + value: true + - name: ES_JAVA_OPTS + value: "-Xms512m -Xmx512m" + - name: xpack.security.enabled + value: false + - name: discovery.type + value: single-node + ports: + - containerPort: 9200 + - containerPort: 9300 + limits: + cpu: 1 + memory: 1500Mi + requests: + cpu: 100m + memory: 1Gi + + + - name: postgres + image: "postgres:9.6-alpine" + imagePullPolicy: IfNotPresent + env: + - name: POSTGRES_USER + value: molgenis + - name: POSTGRES_PASSWORD + value: molgenis + - name: POSTGRES_DB + value: molgenis + ports: + - containerPort: 5432 + limits: + cpu: 1 + memory: 250Mi + requests: + cpu: 100m + memory: 250Mi + + + - name: opencpu + image: "molgenis/opencpu:latest" + imagePullPolicy: Always + ports: + - containerPort: 8004 + limits: + cpu: 1 + memory: 512Mi + requests: + cpu: 100m + memory: 256Mi \ No newline at end of file diff --git a/molgenis/values.yaml b/molgenis/values.yaml new file mode 100644 index 0000000..ecb09de --- /dev/null +++ b/molgenis/values.yaml @@ -0,0 +1,82 @@ +# Default values for molgenis. + +replicaCount: 1 + +service: + type: ClusterIP + port: 8080 + +ingress: + enabled: false + annotations: {} + # kubernetes.io/ingress.class: nginx + # kubernetes.io/tls-acme: "true" + path: / + hosts: + - molgenis.local + tls: [] + +molgenis: + image: + repository: registry.molgenis.org/molgenis/molgenis-app + tag: 7.0.0-SNAPSHOT + pullPolicy: Always + adminPassword: admin + javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled" + resources: + limits: + cpu: 1 + memory: 1250Mi + requests: + cpu: 200m + memory: 1Gi + +postgres: + image: + repository: postgres + tag: 9.6-alpine + pullPolicy: IfNotPresent + user: molgenis + password: molgenis + db: molgenis + resources: + limits: + cpu: 1 + memory: 250Mi + requests: + cpu: 100m + memory: 250Mi + +elasticsearch: + image: + repository: docker.elastic.co/elasticsearch/elasticsearch + tag: 5.5.3 + pullPolicy: IfNotPresent + javaOpts: "-Xms512m -Xmx512m" + clusterName: molgenis + resources: + limits: + cpu: 1 + memory: 1500Mi + requests: + cpu: 100m + memory: 1Gi + +opencpu: + image: + repository: molgenis/opencpu + tag: latest + pullPolicy: Always + resources: + limits: + cpu: 1 + memory: 512Mi + requests: + cpu: 100m + memory: 256Mi + +nodeSelector: {} + +tolerations: [] + +affinity: {}