Merge branch 'master' of P129679/molgenis-ops-docker-helm into master

README.md

@@ -77,7 +77,7 @@ When you want to see what is running on the clusters at the CIT you have to make
 You can access the cluster with kubeconfig-files. You can obtain these by downloading them from the 
 MOLGENIS kubernetes cluster.
 
-- Go to https://rancher.molgenis.org:7443 and login
+- Go to https://rancher.molgenis.org:7777 and login
 - Go to Rancher --> Cluster: *#name#* --> *Kubeconfig File*
 - Go to a **Terminal** where ```kubectl``` is available
 - Add this configuration to ~/.kube/config (or place a new file besides this one)

molgenis-jenkins/Chart.yaml

@@ -1,6 +1,6 @@
 name: molgenis-jenkins
 home: https://jenkins.io/
-version: 0.2.5
+version: 0.3.1
 appVersion: 2.107
 description: Molgenis installation for the jenkins chart.
 sources:

molgenis-jenkins/templates/config.tpl

@@ -15,12 +15,12 @@ data:
       <authorizationStrategy class="hudson.security.FullControlOnceLoggedInAuthorizationStrategy">
         <denyAnonymousReadAccess>true</denyAnonymousReadAccess>
       </authorizationStrategy>
-{{- if .Values.jenkins.Master.Security.UseGitHub }}
+{{- if .Values.Master.Security.UseGitHub }}
       <securityRealm class="org.jenkinsci.plugins.GithubSecurityRealm">
         <githubWebUri>https://github.com</githubWebUri>
         <githubApiUri>https://api.github.com</githubApiUri>
-        <clientID>{{ .Values.jenkins.Master.Security.Github.ClientID }}</clientID>
-        <clientSecret>{{ .Values.jenkins.Master.Security.Github.ClientSecret }}</clientSecret>
+        <clientID>{{ .Values.Master.Security.GitHub.ClientID }}</clientID>
+        <clientSecret>{{ .Values.Master.Security.GitHub.ClientSecret }}</clientSecret>
         <oauthScopes>read:org,user:email</oauthScopes>
       </securityRealm>
 {{- else }}
@@ -40,7 +40,7 @@ data:
           <templates>
 {{- range $podName, $pod := .Values.Pods }}
             <org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
-              <inheritFrom></inheritFrom>
+              <inheritFrom>{{ $pod.InheritFrom | default "" }}</inheritFrom>
               <name>{{ $podName }}</name>
               <instanceCap>2147483647</instanceCap>
               <idleMinutes>0</idleMinutes>
@@ -94,6 +94,15 @@ data:
 {{- else }}
                   <ttyEnabled>false</ttyEnabled>
 {{- end }}
+                  <envVars>
+{{- range $index, $envVar := .EnvVars }}
+                    <org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
+{{- range $key, $value := $envVar }}{{- if not (eq $key "type") }}
+                      <{{ $key }}>{{ $value }}</{{ $key }}>
+{{- end }}{{- end }}
+                    </org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
+{{- end }}
+                  </envVars>
 {{- if .resources }}
 {{- if .resources.requests }}
                   <resourceRequestCpu>{{ .resources.requests.cpu | default "" }}</resourceRequestCpu>

molgenis-jenkins/values.yaml

@@ -218,21 +218,6 @@ jenkins:
           Image: "spotify/alpine"
           Command: cat
           TTY: true
-# Hard to get these right memorywise!
-#        elasticsearch:
-#          Image: "elasticsearch"
-#          ImageTag: "5.5.1"
-#          Ports:
-#            - name: rest
-#              containerPort: "9200"
-#            - name: api
-#              containerPort: "9300"
-#        postgres:
-#          Image: "postgres"
-#          ImageTag: "9.6-alpine"
-#          Ports:
-#            - name: postgres
-#              containerPort: "5432"
       EnvVars:
         - type: Secret
           key: PGP_PASSPHRASE
@@ -256,8 +241,68 @@ jenkins:
           key: GITHUB_TOKEN
           secretName: molgenis-pipeline-env-secret
           secretKey: githubToken
-      # If needed
-      # ImagePullSecret: jenkins
+      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
+            key: ES_JAVA_OPTS
+            value: "-Xms512m -Xmx512m"
+          - type: KeyValue
+            key: cluster.name
+            value: molgenis
+          - type: KeyValue
+            key: bootstrap.memory_lock
+            value: "true"
+          - type: KeyValue
+            key: xpack.security.enabled
+            value: "false"
+          - 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:
   Env: