added elasticsearch

molgenis/README.md

@@ -47,10 +47,22 @@ You can specify credentials for the database scheme by specifying the following
 - ```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 3 resource types.
 - cpu's
@@ -66,10 +78,7 @@ Specify memory usage of container:
 Specify memory usage for Java JVM:
 - ```molgenis.javaOpts```
 
-
-
-
-
+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

@@ -33,20 +33,6 @@ questions:
   required: true
   group: "Services"
   label: OpenCPU cluster
-- variable: molgenis.services.elasticsearch.clusterName
-  default: "molgenis"
-  description: "Set the index name of MOLGENIS"
-  type: string
-  required: true
-  group: "Services"
-  label: Elasticsearch clustername
-- variable: molgenis.services.elasticsearch.transportAddress
-  default: "localhost:9300"
-  description: "Set the transport address for the elasticsearch node communication port and low-level api (which we use)"
-  type: string
-  required: true
-  group: "Services"
-  label: Elasticsearch transport address
 - variable: molgenis.services.postgres.host
   default: "localhost"
   description: "Set the location of the postgres cluster"

molgenis/templates/deployment.yaml

@@ -61,6 +61,28 @@ spec:
 {{ 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:

molgenis/values.yaml

@@ -42,6 +42,21 @@ molgenis:
       user: molgenis
       password: molgenis
 
+elasticsearch:
+  image:
+    repository: docker.elastic.co/elasticsearch/elasticsearch
+    tag: 5.5.3
+    pullPolicy: IfNotPresent
+  javaOpts: "-Xms512m -Xmx512m"
+  clusterName: molgenis
+  resources:
+   limits:
+    cpu: 1
+    memory: 1500Mi
+   requests:
+    cpu: 100m
+    memory: 1Gi
+
 nodeSelector: {}
 
 tolerations: []