fix: Fix links to chart icons and READMEs

This reverts commit f94e6da6e3, reversing
changes made to b73fd578ea.

.gitignore

@@ -1,2 +1,3 @@
 .idea
-*.iml
+*.iml
+target

Jenkinsfile

@@ -0,0 +1,40 @@
+pipeline {
+    agent {
+        kubernetes {
+            label 'helm'
+        }
+    }
+    stages {
+        stage('Test') {
+            steps {
+                container('chart-testing') {
+                    sh "chart_test.sh --no-install --all"
+                }
+            }
+        }
+        stage('Package') {
+            steps {
+                container('chart-testing'){
+                    sh 'mkdir target'
+                    sh 'for dir in charts/*; do helm package --destination target "$dir"; done'
+                }
+            }
+        }
+        stage('Deploy') {
+            when {
+                branch 'master'
+            }
+            steps {
+                container('vault') {
+                    script {
+                        env.NEXUS_USER = sh(script: 'vault read -field=username secret/ops/account/nexus', returnStdout: true)
+                        env.NEXUS_PWD = sh(script: 'vault read -field=password secret/ops/account/nexus', returnStdout: true)
+                    }
+                }
+                container('alpine') {
+                    sh 'set +x; for chart in target/*; do curl -L -u $NEXUS_USER:$NEXUS_PWD http://registry.molgenis.org/repository/helm/ --upload-file "$chart"; done'
+                }
+            }
+        }
+    }
+}

README.md

@@ -101,12 +101,11 @@ kubectl get pods --namespace=*#namespace of application#*
 
 This repository is serves also as a catalogue for Rancher. We have serveral apps that are served through this repoistory. e.g.
 
-- [Jenkins](molgenis-jenkins/README.md)
-- [NEXUS](molgenis-nexus/README.md)
-- [HTTPD](molgenis-httpd/README.md)
-- [MOLGENIS](molgenis/README.md)
-- [MOLGENIS preview](molgenis-preview/README.md)
-- [MOLGENIS vault](molgenis-vault/README.md)
+- [Jenkins](charts/molgenis-jenkins/README.md)
+- [NEXUS](charts/molgenis-nexus/README.md)
+- [HTTPD](charts/molgenis-httpd/README.md)
+- [MOLGENIS](charts/molgenis/README.md)
+- [MOLGENIS vault](charts/molgenis-vault/README.md)
 
 ### Useful commands
 You can you need to know to easily develop and deploy helm-charts

charts/molgenis-httpd/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: HTTPD for MOLGENIS
+name: molgenis-httpd
+version: 0.1.0
+sources:
+- https://github.com/molgenis/molgenis-ops-docker-helm.git
+Icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-httpd/catalogIcon-molgenis-httpd.svg
+home: http://httpd.apache.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-httpd/values.yaml

@@ -48,4 +48,4 @@ nodeSelector: {}
 
 tolerations: []
 
-affinity: {}
+affinity: {}

charts/molgenis-jenkins/Chart.yaml

@@ -0,0 +1,11 @@
+name: molgenis-jenkins
+home: https://jenkins.io/
+version: 0.8.1
+appVersion: 2.138.1
+description: Molgenis installation for the jenkins chart.
+sources:
+- https://github.com/molgenis/molgenis-ops-docker-helm.git
+icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg
+maintainers:
+- name: fdlk
+- name: sidohaakma

charts/molgenis-jenkins/README.md

@@ -75,6 +75,10 @@ Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.w
 | `secret.gogs.user`  | username for the account | `p281392` |
 | `secret.gogs.token` | token for the account    | `xxxx`    |
 
+
+#### Slack
+The Slack integration is done mostly in the Jenkinsfile of each project. It is sufficient to only add the plugin to the Jenkins configuration in Helm.
+
 #### Legacy:
 
 ##### Docker Hub

charts/molgenis-jenkins/resources/README.md

@@ -1,3 +1,5 @@
+# Helm in Jenkins
+
 To be able to run helm inside a jenkins pod, you'll need to 
 * create a role in the namespace where tiller is installed
 * bind that role to the user that jenkins pods run as

charts/molgenis-jenkins/values.yaml

@@ -1,7 +1,5 @@
 jenkins:
   Master:
-    NodeSelector:
-      deployPod: "true"
     HostName: jenkins.molgenis.org
     ServiceType: ClusterIP
     InstallPlugins:
@@ -16,6 +14,7 @@ jenkins:
       - github-oauth:0.29
       - gogs-webhook:1.0.14
       - github-scm-trait-commit-skip:0.1.1
+      - slack:2.3
     Security:
       UseGitHub: false
       GitHub:
@@ -491,9 +490,7 @@ jenkins:
           Command: cat
           WorkingDir: /home/jenkins
           TTY: true
-      NodeSelector: {
-        deployPod: "true"
-      }
+      NodeSelector: {}
     node:
       Label: node-carbon
       NodeUsageMode: EXCLUSIVE
@@ -523,9 +520,7 @@ jenkins:
               key: VAULT_ADDR
               secretName: molgenis-pipeline-vault-secret
               secretKey: addr
-      NodeSelector: {
-        deployPod: "true"
-      }
+      NodeSelector: {}
     molgenis-it:
       InheritFrom: molgenis
       Label: molgenis-it
@@ -587,11 +582,43 @@ jenkins:
             limits:
               cpu: "1"
               memory: "512Mi"
-      NodeSelector: {
-        deployPod: "true"
-      }
+      NodeSelector: {}
+    helm:
+      Label: helm
+      NodeUsageMode: EXCLUSIVE
+      Containers:
+        chart-testing:
+          Image: "quay.io/helmpack/chart-testing"
+          ImageTag: v1.1.0
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+        alpine:
+          Image: "spotify/alpine"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+        vault:
+          Image: "vault"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+          EnvVars:
+            - type: Secret
+              key: VAULT_TOKEN
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: token
+            - type: Secret
+              key: VAULT_SKIP_VERIFY
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: skipVerify
+            - type: Secret
+              key: VAULT_ADDR
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: addr
+      NodeSelector: {}
 
-#secret contains configuration for the kubernetes secrets that jenkins can access
+# secret contains configuration for the kubernetes secrets that jenkins can access
 secret:
   # vault configures the vault secret
   vault:
@@ -613,4 +640,4 @@ secret:
   # dockerHubPassword contains password for hub.docker.com
   dockerHub:
     user: molgenisci
-    password: xxxx
+    password: xxxx

charts/molgenis-nexus/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: Nexus stack for MOLGENIS
+name: molgenis-nexus
+version: 0.4.2
+sources:
+- https://github.com/molgenis/molgenis-ops-docker-helm.git
+icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-nexus/catalogIcon-molgenis-nexus.svg
+home: https://www.sonatype.com/nexus-repository-oss
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-nexus/README.md

@@ -61,4 +61,9 @@ To test if your hem chart works and:
 
 To deploy it on the cluster.
 
+```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
+
+To push it to the registry
+
+
 

charts/molgenis-opencpu/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: Opencpu stack for MOLGENIS
+name: molgenis-opencpu
+version: 0.1.1
+sources:
+- https://github.com/molgenis/molgenis-ops-docker-helm.git
+icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-opencpu/catalog-molgenis-opencpu.svg
+home: https://www.opencpu.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-opencpu/templates/deployment.yaml

@@ -31,7 +31,5 @@ spec:
         ports:
         - containerPort: {{ .service.port }}
       {{- end }}
-      {{- with .Values.nodeSelector }}
-      nodeSelector:
-{{ toYaml . | indent 8 }}
-      {{- end }}
+
+

charts/molgenis-opencpu/values.yaml

@@ -34,9 +34,7 @@ ingress:
   - name: opencpu.molgenis.org
   tls: []
 
-nodeSelector: {
-  deployPod: "true"
-}
+nodeSelector: {}
 
 tolerations: []
 

charts/molgenis-vault/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: MOLGENIS vault
+name: molgenis-vault
+version: 0.1.1
+sources:
+- https://github.com/molgenis/molgenis-ops-docker-helm.git
+icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-vault/catalogIcon-molgenis-vault.svg
+home: https://github.com/coreos/vault-operator
+maintainers:
+- name: fdlk
+- name: sidohaakma

charts/molgenis-vault/README.md

@@ -38,7 +38,7 @@ Parameter | Description | Default
 `ui.image.repository` | Vault UI container image repository | `djenriquez/vault-ui`
 `ui.image.tag` | Vault UI container image tag | `latest`
 `ui.resources` | Vault UI pod resource requests & limits | `{}`
-`ui.nodeSelector` | node labels for Vault UI pod assignment | `{deployPod: "true"}`
+`ui.nodeSelector` | node labels for Vault UI pod assignment | `{}`
 `ui.ingress.enabled` | If true, Vault UI Ingress will be created | `true`
 `ui.ingress.annotations` | Vault UI Ingress annotations | `{}`
 `ui.ingress.host` | Vault UI Ingress hostname | `vault.molgenis.org`

charts/molgenis-vault/values.yaml

@@ -18,10 +18,6 @@ backupJob:
   # schedule gives the cron schedule for the backup job
   schedule: "0 12 * * 1"
 
-vault-operator:
-  nodeSelector:
-    deployPod: "true"
-
 ###
 # All of the config variables related to setting up the etcd-operator
 # If you want more information about the variables exposed, please visit:
@@ -48,8 +44,6 @@ etcd-operator:
   restoreOperator:
     image:
       tag: v0.9.2
-  nodeSelector:
-    deployPod: "true"
 
 ui:
   name: "vault-ui"
@@ -76,11 +70,10 @@ ui:
     # limits:
     #  cpu: 100m
     #  memory: 128Mi
-    #requests:
+    # requests:
     #  cpu: 100m
     #  memory: 128Mi
-  nodeSelector:
-    deployPod: "true"
+  nodeSelector: {}
   vault:
     auth: GITHUB
-    url: https://vault.vault-operator:8200
+    url: https://vault.vault-operator:8200

charts/molgenis/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: MOLGENIS - helm stack (in BETA)
+name: molgenis
+version: 0.4.3
+sources:
+- https://github.com/molgenis/molgenis-ops-docker-helm.git
+icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis/catalogIcon-molgenis.svg
+home: http://molgenis.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis/values.yaml

@@ -64,12 +64,12 @@ elasticsearch:
   javaOpts: "-Xms1g -Xmx1g"
   clusterName: molgenis
   resources:
-   limits:
-    cpu: 2
-    memory: 3Gi
-   requests:
-    cpu: 100m
-    memory: 1Gi
+    limits:
+      cpu: 2
+      memory: 3Gi
+    requests:
+      cpu: 100m
+      memory: 1Gi
   persistence:
     claim: elasticsearch-nfs-claim
     size: 5Gi
@@ -94,8 +94,9 @@ persistence:
   enabled: true
   retain: false
 
-nodeSelector:
+nodeSelector: {
   deployPod: "true"
+}
 
 tolerations: []
 

molgenis-httpd/Chart.yaml

@@ -1,8 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: HTTPD for MOLGENIS
-name: molgenis-httpd
-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-httpd/catalogIcon-molgenis-httpd.svg

molgenis-jenkins/Chart.yaml

@@ -1,8 +0,0 @@
-name: molgenis-jenkins
-home: https://jenkins.io/
-version: 0.7.1
-appVersion: 2.121
-description: Molgenis installation for the jenkins chart.
-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-jenkins/catalogIcon-molgenis-jenkins.svg

molgenis-nexus/Chart.yaml

@@ -1,8 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: Nexus stack for MOLGENIS
-name: molgenis-nexus
-version: 0.4.2
-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-nexus/catalogIcon-molgenis-nexus.svg

molgenis-opencpu/Chart.yaml

@@ -1,8 +0,0 @@
-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-vault/Chart.yaml

@@ -1,6 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: MOLGENIS vault
-name: molgenis-vault
-version: 0.1.1
-icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-vault/catalogIcon-molgenis-vault.svg

molgenis/Chart.yaml

@@ -1,8 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: MOLGENIS - helm stack (in BETA)
-name: molgenis
-version: 0.4.3
-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