From 2306bcb9087f57470bbc6788366915715b2dba0b Mon Sep 17 00:00:00 2001 From: Fleur Kelpin Date: Mon, 16 Jul 2018 12:57:59 +0200 Subject: [PATCH 1/4] feature (molgenis-jenkins): Add molgenis-it pod template --- molgenis-jenkins/Chart.yaml | 2 +- molgenis-jenkins/templates/config.tpl | 17 ++++-- molgenis-jenkins/values.yaml | 79 +++++++++++++++++++++------ 3 files changed, 76 insertions(+), 22 deletions(-) diff --git a/molgenis-jenkins/Chart.yaml b/molgenis-jenkins/Chart.yaml index be8727e..4bd7582 100755 --- a/molgenis-jenkins/Chart.yaml +++ b/molgenis-jenkins/Chart.yaml @@ -1,6 +1,6 @@ name: molgenis-jenkins home: https://jenkins.io/ -version: 0.2.5 +version: 0.3.0 appVersion: 2.107 description: Molgenis installation for the jenkins chart. sources: diff --git a/molgenis-jenkins/templates/config.tpl b/molgenis-jenkins/templates/config.tpl index 1626be9..7499a4b 100644 --- a/molgenis-jenkins/templates/config.tpl +++ b/molgenis-jenkins/templates/config.tpl @@ -15,12 +15,12 @@ data: true -{{- if .Values.jenkins.Master.Security.UseGitHub }} +{{- if .Values.Master.Security.UseGitHub }} https://github.com https://api.github.com - {{ .Values.jenkins.Master.Security.Github.ClientID }} - {{ .Values.jenkins.Master.Security.Github.ClientSecret }} + {{ .Values.Master.Security.Github.ClientID }} + {{ .Values.Master.Security.Github.ClientSecret }} read:org,user:email {{- else }} @@ -40,7 +40,7 @@ data: {{- range $podName, $pod := .Values.Pods }} - + {{ $pod.InheritFrom | default "" }} {{ $podName }} 2147483647 0 @@ -94,6 +94,15 @@ data: {{- else }} false {{- end }} + +{{- range $index, $envVar := .EnvVars }} + +{{- range $key, $value := $envVar }}{{- if not (eq $key "type") }} + <{{ $key }}>{{ $value }} +{{- end }}{{- end }} + +{{- end }} + {{- if .resources }} {{- if .resources.requests }} {{ .resources.requests.cpu | default "" }} diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml index bd2e473..83ba0c9 100644 --- a/molgenis-jenkins/values.yaml +++ b/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: From 90de173cc467f1c78b22322465b4a0ba100eb992 Mon Sep 17 00:00:00 2001 From: Fleur Kelpin Date: Mon, 16 Jul 2018 11:51:46 +0200 Subject: [PATCH 2/4] fix (molgenis-jenkins): Github -> GitHub --- molgenis-jenkins/templates/config.tpl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/molgenis-jenkins/templates/config.tpl b/molgenis-jenkins/templates/config.tpl index 7499a4b..76f3235 100644 --- a/molgenis-jenkins/templates/config.tpl +++ b/molgenis-jenkins/templates/config.tpl @@ -19,8 +19,8 @@ data: https://github.com https://api.github.com - {{ .Values.Master.Security.Github.ClientID }} - {{ .Values.Master.Security.Github.ClientSecret }} + {{ .Values.Master.Security.GitHub.ClientID }} + {{ .Values.Master.Security.GitHub.ClientSecret }} read:org,user:email {{- else }} From 5596956b986b5d7dc9d481034dbe541426c3d503 Mon Sep 17 00:00:00 2001 From: Fleur Kelpin Date: Mon, 16 Jul 2018 11:53:17 +0200 Subject: [PATCH 3/4] doc (molgenis-jenkins): update rancher port number 7443 -> 7777 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5ed5b96..a9f0db7 100644 --- a/README.md +++ b/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) From e72703003f4c0e8f78e01136c90f20275bb8f8b5 Mon Sep 17 00:00:00 2001 From: Fleur Kelpin Date: Mon, 16 Jul 2018 11:57:56 +0200 Subject: [PATCH 4/4] chore (molgenis-jenkins) update version 0.3.0 -> 0.3.1 --- molgenis-jenkins/Chart.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/molgenis-jenkins/Chart.yaml b/molgenis-jenkins/Chart.yaml index 4bd7582..a0f1087 100755 --- a/molgenis-jenkins/Chart.yaml +++ b/molgenis-jenkins/Chart.yaml @@ -1,6 +1,6 @@ name: molgenis-jenkins home: https://jenkins.io/ -version: 0.3.0 +version: 0.3.1 appVersion: 2.107 description: Molgenis installation for the jenkins chart. sources: