Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm into add-pvs-to-molgenis

molgenis/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: MOLGENIS - helm stack (in BETA)
 name: molgenis-beta
-version: 0.0.1
+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

@@ -6,8 +6,8 @@ This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
 
 - MOLGENIS
 
-## Versions
-You can choose from which registry you want to pull from. There are 2:
+## Provisioning
+You can choose from which registry you want to pull. There are 2 registries:
 - https://registry.molgenis.org
 - https://hub.docker.com
 
@@ -17,7 +17,10 @@ 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) 
@@ -64,19 +67,15 @@ You can specify the location of the OpenCPU cluster by specifying this property:
 You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
 
 ## Resources
-You can specify resources by resource type. There are 3 resource types.
-- cpu's
+You can specify resources by resource type. There are 2 resource types.
 - memory of container
-- memory of JVM
-
-Specify number of cpu's:
-- ```molgenis.resources.limits.cpu```
+- maximum heap space JVM
 
 Specify memory usage of container:
 - ```molgenis.resources.limits.memory```
 
 Specify memory usage for Java JVM:
-- ```molgenis.javaOpts```
+- ```molgenis.javaOpts.maxHeapSpace```
 
 Select the resources you need dependant on the customer you need to serve.
 

molgenis/questions.yml

@@ -3,13 +3,14 @@ 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"
-  label: Hostname
 - variable: molgenis.image.repository
+  label: Registry
   default: "registry.hub.docker.com"
   description: "Select a registry to pull from"
   type: enum
@@ -17,95 +18,82 @@ questions:
   - "registry.hub.docker.com"
   - "registry.molgenis.org"
   required: true
-  group: "Version"
-  label: Registry
+  group: "Provisioning"
 - variable: molgenis.image.tag
-  default: "stable"
-  description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for other tags)"
+  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: "Version"
-  label: Version
+  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"
-  label: OpenCPU cluster
 - 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"
-  label: Postgres cluster location
 - variable: molgenis.services.postgres.scheme
+  label: Database scheme
   default: "molgenis"
   description: "Set the database scheme"
   type: string
   required: true
   group: "Services"
-  label: Database scheme
 - variable: molgenis.services.postgres.user
+  label: Database username
   default: "molgenis"
   description: "Set user of the database scheme"
   type: string
   required: true
   group: "Services"
-  label: Database username
 - variable: molgenis.services.postgres.password
+  label: Database password
   default: "molgenis"
   description: "Set the password of the database scheme"
   type: string
   required: true
   group: "Services"
-  label: Database password
-- variable: molgenis.resources.limits.cpu
-  default: 1
-  description: "CPU limit for this MOLGENIS instance"
-  type: enum
-  options:
-  - "1"
-  - "2"
-  - "3"
-  - "4"
-  required: true
-  group: "Resources"
-  label: CPU limit
 - variable: molgenis.resources.limits.memory
+  label: Container memory limit
   default: 1250Mi
-  description: "Memory limit for this MOLGENIS instance"
+  description: "Memory limit for this MOLGENIS container"
   type: enum
   options:
   - "1250Mi"
-  - "1500Mi"
-  - "2000Mi"
   - "2500Mi"
   required: true
   group: "Resources"
-  label: Memory limit
-- variable: molgenis.javaOpts
-  default: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  description: "Java runtime options for the MOLGENIS instance"
+- variable: molgenis.resources.requests.memory
+  label: Container memory reservation
+  default: 1250Mi
+  description: "Memory reservation for this MOLGENIS container"
   type: enum
   options:
-  - "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  - "-Xmx2g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  group: "Resources"
-  label: Java memory options
-- variable: molgenis.persistence.enabled
-  default: false
-  description: "Do you want to use persistance"
-  type: boolean
+  - "1250Mi"
+  - "2500Mi"
   required: true
-  group: "Persistence"
-  label: Persistence
-  show_subquestion_if: true
-  subquestions:
-  - variable: molgenis.persistence.size
-    default: "30Gi"
-    description: "Size of MOLGENIS filestore (not the database size)"
-    type: string
-    label: Size filestore
-
+  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/deployment.yaml

@@ -46,7 +46,7 @@ spec:
             - name: admin.password
               value: {{ .adminPassword }}
             - name: CATALINA_OPTS
-              value: {{ .javaOpts }}
+              value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
           ports:
             - containerPort: 8080
           {{- if .persistence.enabled }}
@@ -58,14 +58,18 @@ spec:
             httpGet:
               path: /
               port: 8080
-            initialDelaySeconds: 180
+            initialDelaySeconds: 60
             periodSeconds: 5
+            failureThreshold: 25
+            successThreshold: 1
           readinessProbe:
             httpGet:
               path: /api/v2/version
               port: 8080
-            initialDelaySeconds: 180
-            periodSeconds: 5
+            initialDelaySeconds: 120
+            periodSeconds: 30
+            failureThreshold: 3
+            successThreshold: 1
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}

molgenis/values.yaml

@@ -17,19 +17,20 @@ ingress:
 
 molgenis:
   image:
-    repository: registry.molgenis.org
+    repository: registry.hub.docker.com
     name: molgenis/molgenis-app
     tag: stable
     pullPolicy: Always
-  adminPassword: admin
-  javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
+  adminPassword:
+  javaOpts:
+    maxHeapSpace: "1g"
   resources:
     limits:
       cpu: 1
       memory: 1250Mi
     requests:
       cpu: 200m
-      memory: 1Gi
+      memory: 1250Mi
   persistence:
     enabled: false
     name: molgenis-nfs-claim
@@ -51,12 +52,12 @@ elasticsearch:
     repository: docker.elastic.co/elasticsearch/elasticsearch
     tag: 5.5.3
     pullPolicy: IfNotPresent
-  javaOpts: "-Xms512m -Xmx512m"
+  javaOpts: "-Xms1g -Xmx1g"
   clusterName: molgenis
   resources:
    limits:
-    cpu: 1
-    memory: 1500Mi
+    cpu: 2
+    memory: 3Gi
    requests:
     cpu: 100m
     memory: 1Gi