chore (molgenis-jenkins): Retrieve pipeline secrets from vault when possible.

molgenis-jenkins/README.md

@@ -40,57 +40,62 @@ You can use [all configuration values of the jenkins subchart](https://github.co
 ### GitHub Authentication delegation
 You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
 
-### Additional configuration
+### Secrets
-There is one additional group of configuration items specific for this chart, so not prefixed with `jenkins`:
 
-* PipelineSecrets
+   When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins.
-
-   When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins and mounted in the jenkins 
-   build pods. The secrets, like the rest of the deployment, is namespaced so multiple instances can run beside
-   each other with their own secrets.
 
    You can override the values at deploy time but otherwise also configure them 
    [in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
 
-*  Vault
+#### Vault
 
-   New vault token to be used by the pods to retrieve their tokens from the vault.
+The vault secret gets mounted in the vault pod so pipeline scripts can retrieve secrets from the vault.
+
+| Parameter                 | Description                                | Default                                        |
+| ------------------------- | ------------------------------------------ | ---------------------------------------------- |
+| `secret.vault.token`      | Token to log into the hashicorp vault      | `xxxx`                                         |
+| `secret.vault.addr`       | Address of the vault                       | `https:vault-operator.vault-operator.svc:8200` |
+| `secret.vault.skipVerify` | Skip verification of the https connection  | `1`                                            |
+
+#### GitHub
+
+Token used by Jenkins to authenticate on GitHub.
+
+| Parameter             | Description              | Default            |
+| --------------------- | ------------------------ | ------------------ |
+| `secret.gitHub.user`  | username for the account | `molgenis-jenkins` |
+| `secret.gitHub.token` | token for the account    | `xxxx`             |
+
+#### Gogs
+
+Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.webhosting.rug.nl).
+
+| Parameter           | Description              | Default   |
+| ------------------- | ------------------------ | --------- |
+| `secret.gogs.user`  | username for the account | `p281392` |
+| `secret.gogs.token` | token for the account    | `xxxx`    |
+
+#### Legacy:
+
+##### Docker Hub
    
-   | Parameter                          | Description                                | Default                                        |
+Account used in pipeline builds to push docker images to `hub.docker.com`.
-   | ---------------------------------- | ------------------------------------------ | ---------------------------------------------- |
+> They should read `secret/gcc/account/dockerhub` from vault instead!
-   | `PipelineSecrets.Vault.Replace`    | Replace the molgenis-pipeline-vault secret | `true`                                         |
-   | `PipelineSecrets.Vault.Token`      | Token to log into the hashicorp vault      | `xxxx`                                         |
-   | `PipelineSecrets.Vault.Addr`       | Address of the vault                       | `https:vault-operator.vault-operator.svc:8200` |
-   | `PipelineSecrets.Vault.SkipVerify` | Skip verification of the https connection  | `1`                                            |
 
-*  Env
+| Parameter                   | Description              | Default         |
+| --------------------------- | ------------------------ | --------------- |
+| `secret.dockerHub.user`     | username for the account | `molgenisci`    |
+| `secret.dockerHub.password` | password for the account | `xxxx`          |
+
+##### Registry
    
-   Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
+Account used in pipeline builds to push docker images to `registry.molgenis.org`.
-   in the slave pods.
+> They should read `secret/ops/account/nexus` from vault instead!
 
-   | Parameter                               | Description                               | Default         |
+| Parameter                   | Description              | Default   |
-   | --------------------------------------- | ----------------------------------------- | --------------- |
+| --------------------------- | ------------------------ | --------- |
-   | `PipelineSecrets.Env.Replace`           | Replace molgenis-pipeline-env secret      | `true`          |
+| `secret.dockerHub.user`     | username for the account | `admin`   |
-   | `PipelineSecrets.Env.PGPPassphrase`     | passphrase for the pgp signing key        | `literal:xxxx`  |
+| `secret.dockerHub.password` | password for the account | `xxxx`    |
-   | `PipelineSecrets.Env.CodecovToken`      | token for codecov.io                      | `xxxx`          |
-   | `PipelineSecrets.Env.GitHubToken`       | token for GH molgenis-jenkins user        | `xxxx`          |
-   | `PipelineSecrets.Env.NexusPassword`     | token for molgenis-jenkins user in NEXUS  | `xxxx`          |
-   | `PipelineSecrets.Env.DockerHubPassword` | token for molgenis user in hub.docker.com | `xxxx`          |
-   | `PipelineSecrets.Env.SonarToken`        | token for sonarcloud.io                   | `xxxx`          |
-   | `PipelineSecrets.Env.NpmToken`          | token for npmjs.org                       | `xxxx`          | 
-   | `PipelineSecrets.Env.SauceAccessKey`    | token for saucelabs.com                   | `xxxx`          |
-
-* File
-
-  Environment variables stored in molgenis-pipeline-file secret, to be mounted as files
-  in the `/root/.m2` directory of the slave pods.
-  > The settings.xml file references the 
-
-  | Parameter                              | Description                           | Default                                                                         |
-  | -------------------------------------- | ------------------------------------- | ------------------------------------------------------------------------------- |
-  | `PipelineSecrets.File.Replace`         | Replace molgenis-pipeline-file secret | `true`                                                                          |
-  | `PipelineSecrets.File.PGPPrivateKeyAsc`| pgp signing key in ascii form         | `-----BEGIN PGP PRIVATE KEY BLOCK-----xxxxx-----END PGP PRIVATE KEY BLOCK-----` |
-  | `PipelineSecrets.File.MavenSettingsXML`| Maven settings.xml file               | `<settings>[...]</settings>` (see actual [values.yaml](values.yaml))            |
 
 ## Command line use
 Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.

molgenis-jenkins/templates/molgenis-jenkins-dockerhub-secret.yaml

@@ -8,9 +8,9 @@ metadata:
     "jenkins.io/credentials-type": "usernamePassword"
   annotations: {
 # description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "user to authenticate against Docker Hub (hub.docker.com)"
+    "jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to Docker Hub (hub.docker.com)"
   }
 type: Opaque
 data:
-  username: {{ "molgenisci" | b64enc | quote }}
+  username: {{ .Values.secret.registry.user | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.DockerHubPassword | b64enc | quote }}
+  password: {{ .Values.secret.registry.password | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-github-secret.yaml

@@ -8,9 +8,9 @@ metadata:
     "jenkins.io/credentials-type": "usernamePassword"
   annotations: {
 # description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "oauth token for the molgenis-jenkins github user"
+    "jenkins.io/credentials-description" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user"
   }
 type: Opaque
 data:
-  username: {{ "molgenis-jenkins" | b64enc | quote }}
+  username: {{ .Values.secret.gitHub.user | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
+  password: {{ .Values.secret.gitHub.token | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml

@@ -8,9 +8,9 @@ metadata:
     "jenkins.io/credentials-type": "usernamePassword"
   annotations: {
 # description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "user to authenticate against GOGS (git.webhosting.rug.nl)"
+    "jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs."
   }
 type: Opaque
 data:
-  username: {{ "p281392" | b64enc | quote }}
+  username: {{ .Values.secret.gogs.user | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.GogsToken | b64enc | quote }}
+  password: {{ .Values.secret.gogs.token | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-nexus-secret.yaml

@@ -1,16 +0,0 @@
-apiVersion: v1
-kind: Secret
-metadata:
-# this is the jenkins id.
-  name: "molgenis-jenkins-nexus-secret"
-  labels:
-# so we know what type it is.
-    "jenkins.io/credentials-type": "usernamePassword"
-  annotations: {
-# description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "user to authenticate against NEXUS"
-  }
-type: Opaque
-data:
-  username: {{ "admin" | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.NexusPassword | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-registry-secret.yaml

@@ -0,0 +1,17 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: molgenis-jenkins-registry-secret
+  labels:
+    app: {{ template "jenkins.fullname" . }}
+    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
+    release: "{{ .Release.Name }}"
+    heritage: "{{ .Release.Service }}"
+  annotations: {
+# description - can not be a label as spaces are not allowed
+    "jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to registry.molgenis.org."
+  }
+type: Opaque
+data:
+  username: {{ .Values.secret.registry.user | b64enc | quote }}
+  password: {{ .Values.secret.registry.password | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-saucelabs-secret.yaml

@@ -1,16 +0,0 @@
-apiVersion: v1
-kind: Secret
-metadata:
-# this is the jenkins id.
-  name: "molgenis-jenkins-saucelabs-secret"
-  labels:
-# so we know what type it is.
-    "jenkins.io/credentials-type": "usernamePassword"
-  annotations: {
-# description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "user to authenticate against Saucelabs (saucelabs.com)"
-  }
-type: Opaque
-data:
-  username: {{ "molgenis-jenkins" | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.SauceAccessKey | b64enc | quote }}

molgenis-jenkins/templates/molgenis-pipeline-env-secret.yaml

@@ -1,18 +0,0 @@
-{{- if .Values.PipelineSecrets.Env.Replace }}
-apiVersion: v1
-kind: Secret
-metadata:
-  name: molgenis-pipeline-env-secret
-  labels:
-    app: {{ template "jenkins.fullname" . }}
-    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
-    release: "{{ .Release.Name }}"
-    heritage: "{{ .Release.Service }}"
-type: Opaque
-data:
-  pgpPassphrase: {{ .Values.PipelineSecrets.Env.PGPPassphrase | b64enc | quote }}
-  codecovToken: {{ .Values.PipelineSecrets.Env.CodecovToken | b64enc | quote }}
-  githubToken: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
-  sonarToken: {{ .Values.PipelineSecrets.Env.SonarToken | b64enc | quote }}
-  npmToken: {{ .Values.PipelineSecrets.Env.NpmToken | b64enc | quote }}
-{{- end }}

molgenis-jenkins/templates/molgenis-pipeline-file-secret.yaml

@@ -1,15 +0,0 @@
-{{- if .Values.PipelineSecrets.File.Replace }}
-apiVersion: v1
-kind: Secret
-metadata:
-  name: molgenis-pipeline-file-secret
-  labels:
-    app: {{ template "jenkins.fullname" . }}
-    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
-    release: "{{ .Release.Name }}"
-    heritage: "{{ .Release.Service }}"
-type: Opaque
-data:
-  key.asc: {{ .Values.PipelineSecrets.File.PGPPrivateKeyAsc | b64enc | quote }}
-  settings.xml: {{ .Values.PipelineSecrets.File.MavenSettingsXML | b64enc | quote }}
-{{- end }}

molgenis-jenkins/templates/molgenis-pipeline-vault-secret.yaml

@@ -1,4 +1,3 @@
-{{- if .Values.PipelineSecrets.Vault.Replace }}
 apiVersion: v1
 kind: Secret
 metadata:
@@ -10,7 +9,6 @@ metadata:
     heritage: "{{ .Release.Service }}"
 type: Opaque
 data:
-  token: {{ .Values.PipelineSecrets.Vault.Token | b64enc | quote }}
+  token: {{ .Values.secret.vault.token | b64enc | quote }}
-  addr: {{ .Values.PipelineSecrets.Vault.Addr | b64enc | quote }}
+  addr: {{ .Values.secret.vault.addr | b64enc | quote }}
-  skipVerify: {{ .Values.PipelineSecrets.Vault.SkipVerify | b64enc | quote }}
+  skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }}
-{{- end }}

molgenis-jenkins/values.yaml

@@ -368,8 +368,8 @@ jenkins:
     install: true
   Pods:
     molgenis:
-      Label: molgenisv2
+      Label: molgenis
-      NodeUsageMode: EXCLUSIVE
+      NodeUsageMode: NORMAL
       volumes:
         - type: HostPath
           hostPath: "/var/run/docker.sock"
@@ -417,39 +417,6 @@ jenkins:
               secretName: molgenis-pipeline-vault-secret
               secretKey: addr
       NodeSelector: {}
-    molgenis-legacy:
-      InheritFrom: molgenis
-      Label: molgenis
-      NodeUsageMode: NORMAL
-      volumes:
-        - type: Secret
-          secretName: molgenis-pipeline-file-secret
-          mountPath: "/home/jenkins/.m2"
-      Containers:
-      EnvVars:
-        - type: Secret
-          key: PGP_PASSPHRASE
-          secretName: molgenis-pipeline-env-secret
-          secretKey: pgpPassphrase
-        - type: KeyValue
-          key: PGP_SECRETKEY
-          value: "keyfile:/home.jenkins/.m2/key.asc"
-        - type: KeyValue
-          key: npm_config_registry
-          value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
-        - type: Secret
-          key: SONAR_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: sonarToken
-        - type: Secret
-          key: CODECOV_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: codecovToken
-        - type: Secret
-          key: GITHUB_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: githubToken
-      NodeSelector: {}
     node:
       Label: node-carbon
       NodeUsageMode: EXCLUSIVE
@@ -461,155 +428,45 @@ jenkins:
           Command: cat
           WorkingDir: /home/jenkins
           TTY: true
-      EnvVars:
+        vault:
-        - type: KeyValue
+          Image: "vault"
-          key: npm_config_registry
+          Command: cat
-          value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
+          WorkingDir: /home/jenkins
-        - type: Secret
+          TTY: true
-          key: CODECOV_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: codecovToken
-        - type: Secret
-          key: GITHUB_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: githubToken
-        - type: Secret
-          key: NPM_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: npmToken
-      NodeSelector: {}
-    molgenis-it:
-      InheritFrom: molgenis
-      Label: molgenis-it
-      NodeUsageMode: EXCLUSIVE
-      Containers:
-        elasticsearch:
-          Image: docker.elastic.co/elasticsearch/elasticsearch
-          ImageTag: 5.5.3
-          resources:
-            requests:
-              cpu: "100m"
-              memory: "1Gi"
-            limits:
-              cpu: "1"
-              memory: "1500Mi"
           EnvVars:
-          - type: KeyValue
+            - type: Secret
-            key: ES_JAVA_OPTS
+              key: VAULT_TOKEN
-            value: "-Xms512m -Xmx512m"
+              secretName: molgenis-pipeline-vault-secret
-          - type: KeyValue
+              secretKey: token
-            key: cluster.name
+            - type: Secret
-            value: molgenis
+              key: VAULT_SKIP_VERIFY
-          - type: KeyValue
+              secretName: molgenis-pipeline-vault-secret
-            key: bootstrap.memory_lock
+              secretKey: skipVerify
-            value: "true"
+            - type: Secret
-          - type: KeyValue
+              key: VAULT_ADDR
-            key: xpack.security.enabled
+              secretName: molgenis-pipeline-vault-secret
-            value: "false"
+              secretKey: addr
-          - type: KeyValue
-            key: discovery.type
-            value: single-node
-        postgres:
-          Image: postgres
-          ImageTag: 9.6-alpine
-          resources:
-            requests:
-              cpu: "100m"
-              memory: "250Mi"
-            limits:
-              cpu: "1"
-              memory: "250Mi"
-          EnvVars:
-          - type: KeyValue
-            key: POSTGRES_USER
-            value: molgenis
-          - type: KeyValue
-            key: POSTGRES_PASSWORD
-            value: molgenis
-          - type: KeyValue
-            key: POSTGRES_DB
-            value: molgenis
-        opencpu:
-          Image: molgenis/opencpu
-          AlwaysPullImage: true
-          resources:
-            requests:
-              cpu: "100m"
-              memory: "256Mi"
-            limits:
-              cpu: "1"
-              memory: "512Mi"
       NodeSelector: {}
-PipelineSecrets:
+#secret contains configuration for the kubernetes secrets that jenkins can access
-  Vault:
+secret:
-    Replace: true
+  # vault configures the vault secret
-    Token: xxxx
+  vault:
-    Addr: "https://vault-operator.vault-operator.svc:8200"
+    token: xxxx
-    SkipVerify: 1
+    addr: "https://vault-operator.vault-operator.svc:8200"
-  Env:
+    skipVerify: "1"
-    # Set to false to keep existing secret
+  # githubToken contains access token for jenkins bot account on github.com
-    Replace: true
+  gitHub:
-    # Passphrase for the pgp private key file, prefixed with literal:
+    user: "molgenis-jenkins"
-    PGPPassphrase: literal:xxxx
+    token: xxxx
-    # Token for codecov.io service
+  # gogs contains access token for jenkins bot account on RuG GoGs
-    CodecovToken: xxxx
+  gogs:
-    # Token for github bot account
+    user: p281392
-    GitHubToken: xxxx
+    token: xxxx
-    # Token for github bot account
+  # registry contains credentials for registry.molgenis.org
-    GogsToken: xxxx
+  registry:
-    # Token for sonarcloud.io
+    user: admin
-    SonarToken: xxxx
+    password: xxxx
-    # Token for npmjs.org
+  # dockerHubPassword contains password for hub.docker.com
-    NpmToken: xxxx
+  dockerHub:
-    # Password Local NEXUS
+    user: molgenisci
-    NexusPassword: xxxx
+    password: xxxx
-    # Password hub.docker.com
-    DockerHubPassword: xxxx
-    # Access key for saucelabs.com
-    SauceAccessKey: xxxx
-  File:
-    # Set to false to keep existing secret
-    Replace: true
-    # PGP Private key in ascii format used to sign artifacts
-    PGPPrivateKeyAsc: |-
-      -----BEGIN PGP PRIVATE KEY BLOCK-----
-      xxxxx
-      -----END PGP PRIVATE KEY BLOCK-----
-    # maven.settings file
-    MavenSettingsXML: |-
-      <settings>
-        <localRepository>${user.home}/.mvnrepository</localRepository>
-        <interactiveMode>false</interactiveMode>
-        <mirrors>
-          <mirror>
-            <id>nexus</id>
-            <mirrorOf>external:*</mirrorOf>
-            <url>http://nexus.molgenis-nexus:8081/repository/maven-central/</url>
-          </mirror>
-        </mirrors>
-        <servers>
-          <!-- for snapshot builds of the master -->
-          <server>
-            <id>sonatype-nexus-staging</id>
-            <username>molgenis</username>
-            <password>xxxx</password>
-          </server>
-          <server>
-            <id>local-nexus</id>
-            <url>http://nexus.molgenis-nexus:8081/repository/maven-snapshots/</url>
-            <username>admin</username>
-            <password>xxxxx</password>
-          </server>
-          <!-- for docker images-->
-          <server>
-            <id>registry.molgenis.org</id>
-            <username>admin</username>
-            <password>xxxx</password>
-          </server>
-          <server>
-            <id>registry.hub.docker.com</id>
-            <username>molgenisci</username>
-            <password>xxxx</password>
-          </server>
-        </servers>
-      </settings>

molgenis-preview/Chart.yaml

@@ -1,7 +1,7 @@
 apiVersion: v1
 appVersion: "1.0"
-description: MOLGENIS - helm stack for testing purposes
+description: A Helm chart for Kubernetes
-name: molgenis-preview
+name: molgenis
 version: 0.2.0
 sources:
 - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git

molgenis-preview/README.md

@@ -1,5 +1,5 @@
 # MOLGENIS preview
-This chart is used for testing purposes. It can be used by data managers or developers to test MOLGENIS (e.g. integration testing).
+Is used for integration testing purposes.
 
 ## Containers
 This chart spins up a complete stack to run MOLGENIS. The created containers are:
@@ -9,8 +9,3 @@ This chart spins up a complete stack to run MOLGENIS. The created containers are
 - Elasticsearch
 - OpenCPU
 
-## Rancher
-You can spin up a test instance by navigating to https://rancher.molgenis.org:7777 and login with your LDAP-account.
-
-Go to the test-environment and click on "Launch". Search for MOLGENIS.
-

molgenis-preview/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

molgenis/Chart.yaml

@@ -1,8 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: MOLGENIS - helm stack (in BETA)
-name: molgenis-beta
-version: 0.1.0
-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/catalogIcon-molgenis.svg

molgenis/README.md

@@ -1,83 +0,0 @@
-# MOLGENIS
-This chart is used for acceptance and production use cases.
-
-## Containers
-This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
-
-- MOLGENIS
-
-## Provisioning
-You can choose from which registry you want to pull. There are 2 registries:
-- https://registry.molgenis.org
-- https://hub.docker.com
-
-The registry.molgenis.org contains the bleeding edge versions (PR's and master merges). The hub.docker.com contains the released artifacts (MOLGENIS releases and release candidates).
-
-The three properties you need to specify are:
-- ```molgenis.image.repository```
-- ```molgenis.image.name```
-- ```molgenis.image.tag```
-
-Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property. 
-- ```molgenis.adminPassword```
-
-## Services
-When you start MOLGENIS you need:
-- an elasticsearch instance (5.5.6) 
-- an postgres instance (9.6)
-
-You can attach additional services like:
-- an opencpu instance
-
-### Elasticsearch
-You can configure elasticsearch by giving in the cluster location.
-
-To configure the transport address you can address the node communication channel but also the native JAVA API. Which MOLGENIS uses to communicate with Elasticsearch.
-From Elasticsearch version 6 and further the JAVA API is not supported anymore. At this moment you can only use Elastic instance till major version 5.
-- ```molgenis.services.elasticsearch.transportAddresses: localhost:9300```
-
-To configure the index on a Elasticsearch cluster you can specify the clusterName property.
-- ```molgenis.services.elasticsearch.clusterName: molgenis```
-
-### Postgres
-You can specify the location of the postgres instance by specify the following property:
-- ```molgenis.services.postgres.host: localhost```
-
-You can specify the schema by filling out this property:
-- ```molgenis.services.postgres.scheme: molgenis```
-
-You can specify credentials for the database scheme by specifying the following properties:
-- ```molgenis.services.postgres.user: molgenis```
-- ```molgenis.services.postgres.password: molgenis```
-
-To test you can use the **PostgreSQL**-helm chart of Kubernetes and specify these answers:
-
-```bash
-# answers for postgresql chart
-postgresUser=molgenis
-postgresPassword=molgenis
-postgresDatabase=molgenis
-persistence.enabled=false
-```
-
-### OpenCPU
-You can specify the location of the OpenCPU cluster by specifying this property:
-- ```molgenis.services.opencpu.host: localhost```
-
-You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
-
-## Resources
-You can specify resources by resource type. There are 2 resource types.
-- memory of container
-- maximum heap space JVM
-
-Specify memory usage of container:
-- ```molgenis.resources.limits.memory```
-
-Specify memory usage for Java JVM:
-- ```molgenis.javaOpts.maxHeapSpace```
-
-Select the resources you need dependant on the customer you need to serve.
-
-## Firewall
-Is defined at cluster level. This chart does not facilitate firewall configuration.

molgenis/questions.yml

@@ -1,99 +0,0 @@
-
-categories:
-- MOLGENIS
-questions:
-- variable: ingress.hosts[0].name
-  label: Hostname
-  default: "test.molgenis.org"
-  description: "Hostname for your stack"
-  type: hostname
-  required: true
-  group: "Load Balancing"
-- 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.image.tag
-  label: Version
-  default: ""
-  description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for released tags)"
-  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: molgenis.services.opencpu.host
-  label: OpenCPU cluster
-  default: "localhost"
-  description: "Specify the OpenCPU cluster"
-  type: string
-  required: true
-  group: "Services"
-- variable: molgenis.services.postgres.host
-  label: Postgres cluster location
-  default: "postgresql.molgenis-postgresql.svc"
-  description: "Set the location of the postgres cluster"
-  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: molgenis.resources.limits.memory
-  label: Container memory limit
-  default: 1250Mi
-  description: "Memory limit for this MOLGENIS container"
-  type: enum
-  options:
-  - "1250Mi"
-  - "2500Mi"
-  required: true
-  group: "Resources"
-- variable: molgenis.resources.requests.memory
-  label: Container memory reservation
-  default: 1250Mi
-  description: "Memory reservation for this MOLGENIS container"
-  type: enum
-  options:
-  - "1250Mi"
-  - "2500Mi"
-  required: true
-  group: "Resources"
-- variable: molgenis.javaOpts.maxHeapSpace
-  label: Maximum heap space (JVM)
-  default: "1g"
-  description: "Maximum heap space MOLGENIS container JVM. Please not this should fit in your container memory limit"
-  type: enum
-  options:
-  - "1g"
-  - "2g"
-  group: "Resources"

molgenis/templates/NOTES.txt

@@ -1,19 +0,0 @@
-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 }}

molgenis/templates/_helpers.tpl

@@ -1,32 +0,0 @@
-{{/* 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 -}}

molgenis/templates/deployment.yaml

@@ -1,106 +0,0 @@
-apiVersion: apps/v1beta2
-kind: Deployment
-metadata:
-  {{- with .Values.ingress.annotations }}
-  annotations:
-{{ toYaml . | indent 4 }}
-  {{- end }}
-  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.name }}:{{ .image.tag }}
-          imagePullPolicy: {{ .image.pullPolicy }}
-          env:
-            - name: molgenis.home
-              value: /home/molgenis
-            - name: opencpu.uri.host
-              value: {{ .services.opencpu.host }}
-            - name: elasticsearch.transport.addresses
-              value: {{ .services.elasticsearch.transportAddresses }}
-            - name: elasticsearch.cluster.name
-              value: {{ .services.elasticsearch.clusterName }}
-            - name: db_uri
-              value: jdbc:postgresql://{{ .services.postgres.host }}/{{ .services.postgres.scheme }}
-            - name: db_user
-              value: {{ .services.postgres.user }}
-            - name: db_password
-              value: {{ .services.postgres.password }}
-            - name: admin.password
-              value: {{ .adminPassword }}
-            - name: CATALINA_OPTS
-              value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-          ports:
-            - containerPort: 8080
-          livenessProbe:
-            httpGet:
-              path: /
-              port: 8080
-            initialDelaySeconds: 60
-            periodSeconds: 5
-            failureThreshold: 25
-            successThreshold: 1
-          readinessProbe:
-            httpGet:
-              path: /api/v2/version
-              port: 8080
-            initialDelaySeconds: 120
-            periodSeconds: 30
-            failureThreshold: 3
-            successThreshold: 1
-          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
-          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 }}

molgenis/templates/ingress.yaml

@@ -1,38 +0,0 @@
-{{- 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: {{ .name }}
-      http:
-        paths:
-          - path: {{ $ingressPath }}
-            backend:
-              serviceName: {{ $fullName }}
-              servicePort: 8080
-  {{- end }}
-{{- end }}

molgenis/templates/service.yaml

@@ -1,17 +0,0 @@
-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:
-    - name: molgenis
-      port: {{ .Values.service.port }}
-  selector:
-    app: {{ template "molgenis.name" . }}
-    release: {{ .Release.Name }}

molgenis/values.yaml

@@ -1,65 +0,0 @@
-# Default values for molgenis.
-
-replicaCount: 1
-
-service:
-  type: LoadBalancer
-  port: 8080
-
-ingress:
-  enabled: true
-  annotations:
-    nginx.ingress.kubernetes.io/proxy-body-size: "0"
-  path: /
-  hosts:
-  - name: test.molgenis.org
-  tls: []
-
-molgenis:
-  image:
-    repository: registry.hub.docker.com
-    name: molgenis/molgenis-app
-    tag: stable
-    pullPolicy: Always
-  adminPassword:
-  javaOpts:
-    maxHeapSpace: "1g"
-  resources:
-   limits:
-    cpu: 1
-    memory: 1250Mi
-   requests:
-    cpu: 200m
-    memory: 1250Mi
-  services:
-    opencpu:
-      host: localhost
-    elasticsearch:
-      transportAddresses: localhost:9300
-      clusterName: molgenis
-    postgres:
-      host: localhost
-      scheme: molgenis
-      user: molgenis
-      password: molgenis
-
-elasticsearch:
-  image:
-    repository: docker.elastic.co/elasticsearch/elasticsearch
-    tag: 5.5.3
-    pullPolicy: IfNotPresent
-  javaOpts: "-Xms1g -Xmx1g"
-  clusterName: molgenis
-  resources:
-   limits:
-    cpu: 2
-    memory: 3Gi
-   requests:
-    cpu: 100m
-    memory: 1Gi
-
-nodeSelector: {}
-
-tolerations: []
-
-affinity: {}