From 11b25a5df61272f6349fdb275b3d4ed78fa699ff Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 16:53:58 +0200
Subject: [PATCH 01/24] added initialDelay

---
 molgenis/templates/deployment.yaml |  4 ++++
 molgenis/values.yaml               | 23 +++++++++++++++++------
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index f809088..a718bba 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -53,10 +53,14 @@ spec:
             httpGet:
               path: /
               port: 8080
+            initialDelaySeconds: 180
+            periodSeconds: 5
           readinessProbe:
             httpGet:
               path: /api/v2/version
               port: 8080
+            initialDelaySeconds: 180
+            periodSeconds: 5
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index 873ef8b..9aa9e21 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -24,12 +24,21 @@ molgenis:
   adminPassword: admin
   javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
   resources:
-   limits:
-    cpu: 1
-    memory: 1250Mi
-   requests:
-    cpu: 200m
-    memory: 1Gi
+    limits:
+      cpu: 1
+      memory: 1250Mi
+    requests:
+     cpu: 200m
+     memory: 1Gi
+    persistence:
+      enabled: false
+      name: molgenis-nexus-data
+      storageClass: nfs-class
+      size: 30G
+      reclaimPolicy: Retain
+      server: 192.168.64.12
+      accessMode: ReadWriteMany
+      mountPath: /gcc/molgenis/nexus
   services:
     opencpu:
       host: localhost
@@ -57,6 +66,8 @@ elasticsearch:
     cpu: 100m
     memory: 1Gi
 
+
+
 nodeSelector: {}
 
 tolerations: []

From cf47b432e25e14a0adbc92d1e9addaa196bf67ec Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 16:59:14 +0200
Subject: [PATCH 02/24] added persistence to questions

---
 molgenis/questions.yml | 7 +++++++
 molgenis/values.yaml   | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index 475c8bd..bd95e94 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -94,3 +94,10 @@ questions:
   - "-Xmx2g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
   group: "Resources"
   label: Java memory options
+- variable: molgenis.resources.persistence.enabled
+  default: false
+  description: "Do you want to use persistance"
+  type: boolean
+  required: true
+  group: "Resources"
+  label: Persistence
diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index 9aa9e21..2f452fa 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -28,8 +28,8 @@ molgenis:
       cpu: 1
       memory: 1250Mi
     requests:
-     cpu: 200m
-     memory: 1Gi
+      cpu: 200m
+      memory: 1Gi
     persistence:
       enabled: false
       name: molgenis-nexus-data

From 14b27fc043237212d6d4ae892258e114d3031bf7 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 17:05:10 +0200
Subject: [PATCH 03/24] updated persistence configuration

---
 molgenis/questions.yml |  4 ++--
 molgenis/values.yaml   | 20 +++++++++-----------
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index bd95e94..cd0c528 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -94,10 +94,10 @@ questions:
   - "-Xmx2g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
   group: "Resources"
   label: Java memory options
-- variable: molgenis.resources.persistence.enabled
+- variable: molgenis.persistence.enabled
   default: false
   description: "Do you want to use persistance"
   type: boolean
   required: true
-  group: "Resources"
+  group: "Persistence"
   label: Persistence
diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index 2f452fa..bc931b4 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -30,15 +30,15 @@ molgenis:
     requests:
       cpu: 200m
       memory: 1Gi
-    persistence:
-      enabled: false
-      name: molgenis-nexus-data
-      storageClass: nfs-class
-      size: 30G
-      reclaimPolicy: Retain
-      server: 192.168.64.12
-      accessMode: ReadWriteMany
-      mountPath: /gcc/molgenis/nexus
+  persistence:
+    enabled: false
+    name: molgenis-nexus-data
+    storageClass: nfs-class
+    size: 30G
+    reclaimPolicy: Retain
+    server: 192.168.64.12
+    accessMode: ReadWriteMany
+    mountPath: /gcc/molgenis/nexus
   services:
     opencpu:
       host: localhost
@@ -66,8 +66,6 @@ elasticsearch:
     cpu: 100m
     memory: 1Gi
 
-
-
 nodeSelector: {}
 
 tolerations: []

From d9053b656c62153683af7b10739dcc645957bde2 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 17:37:50 +0200
Subject: [PATCH 04/24] updated volume claims

---
 molgenis/templates/deployment.yaml                |  8 ++++++++
 .../persistence/molgenisPersistenceClaim.yaml     | 15 +++++++++++++++
 molgenis/values.yaml                              |  4 +++-
 3 files changed, 26 insertions(+), 1 deletion(-)
 create mode 100644 molgenis/templates/persistence/molgenisPersistenceClaim.yaml

diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index a718bba..5aeeff0 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -49,6 +49,10 @@ spec:
               value: {{ .javaOpts }}
           ports:
             - containerPort: 8080
+          volumeMounts:
+          - name: molgenis-nfs
+            mountPath: "/home/molgenis"
+          restartPolicy: "Never"
           livenessProbe:
             httpGet:
               path: /
@@ -63,6 +67,10 @@ spec:
             periodSeconds: 5
           resources:
 {{ toYaml .resources | indent 12 }}
+        volumes:
+        - name: molgenis-nfs
+          persistentVolumeClaim:
+            claimName: molgenis-nfs-claim
         {{- end }}
 
         - name: elasticsearch
diff --git a/molgenis/templates/persistence/molgenisPersistenceClaim.yaml b/molgenis/templates/persistence/molgenisPersistenceClaim.yaml
new file mode 100644
index 0000000..8c02e3d
--- /dev/null
+++ b/molgenis/templates/persistence/molgenisPersistenceClaim.yaml
@@ -0,0 +1,15 @@
+{{- if .Values.molgenis.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: molgenis-nfs-claim
+  annotations:
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+storage: 1Gi
+{{- end }}
\ No newline at end of file
diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index bc931b4..6aa4016 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -66,7 +66,9 @@ elasticsearch:
     cpu: 100m
     memory: 1Gi
 
-nodeSelector: {}
+nodeSelector: {
+  deployPod: "true"
+}
 
 tolerations: []
 

From 5a98e35273dde059e12c90b15253128cd622dcdc Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 21:41:54 +0200
Subject: [PATCH 05/24] added persistence properties to values and deployment

---
 molgenis/questions.yml                            |  7 +++++++
 molgenis/templates/deployment.yaml                |  9 ++++++---
 molgenis/templates/persistence/molgenisPVC.yaml   | 15 +++++++++++++++
 .../persistence/molgenisPersistenceClaim.yaml     | 15 ---------------
 molgenis/values.yaml                              |  7 +------
 5 files changed, 29 insertions(+), 24 deletions(-)
 create mode 100644 molgenis/templates/persistence/molgenisPVC.yaml
 delete mode 100644 molgenis/templates/persistence/molgenisPersistenceClaim.yaml

diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index cd0c528..278368a 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -101,3 +101,10 @@ questions:
   required: true
   group: "Persistence"
   label: Persistence
+  show_subquestion_if: true
+  - variable: molgenis.persistence.size
+    default: "10Gi"
+    description: "Size of MOLGENIS filestore (not the database size)"
+    type: string
+    label: Size filestore
+
diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index 5aeeff0..06708a9 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -49,10 +49,11 @@ spec:
               value: {{ .javaOpts }}
           ports:
             - containerPort: 8080
+          {{- if .persistence.enabled }}
           volumeMounts:
           - name: molgenis-nfs
-            mountPath: "/home/molgenis"
-          restartPolicy: "Never"
+            mountPath: /home/molgenis
+          {{- end }}
           livenessProbe:
             httpGet:
               path: /
@@ -67,10 +68,12 @@ spec:
             periodSeconds: 5
           resources:
 {{ toYaml .resources | indent 12 }}
+        {{- if .persistence.enabled }}
         volumes:
         - name: molgenis-nfs
           persistentVolumeClaim:
-            claimName: molgenis-nfs-claim
+            claimName: {{ .Values.persistence.name }}
+        {{- end }}
         {{- end }}
 
         - name: elasticsearch
diff --git a/molgenis/templates/persistence/molgenisPVC.yaml b/molgenis/templates/persistence/molgenisPVC.yaml
new file mode 100644
index 0000000..65c07ba
--- /dev/null
+++ b/molgenis/templates/persistence/molgenisPVC.yaml
@@ -0,0 +1,15 @@
+{{- if .Values.molgenis.persistence.enabled }}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.molgenis.persistence.name }}
+  annotations:
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+  spec:
+    accessModes:
+      - ReadWriteMany
+    resources:
+      requests:
+        storage: {{ .Values.molgenis.persistence.size }}
+{{- end }}
\ No newline at end of file
diff --git a/molgenis/templates/persistence/molgenisPersistenceClaim.yaml b/molgenis/templates/persistence/molgenisPersistenceClaim.yaml
deleted file mode 100644
index 8c02e3d..0000000
--- a/molgenis/templates/persistence/molgenisPersistenceClaim.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-{{- if .Values.molgenis.persistence.enabled -}}
-apiVersion: extensions/v1beta1
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: molgenis-nfs-claim
-  annotations:
-    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
-spec:
-  accessModes:
-    - ReadWriteMany
-  resources:
-    requests:
-storage: 1Gi
-{{- end }}
\ No newline at end of file
diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index 6aa4016..a0151d7 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -32,13 +32,8 @@ molgenis:
       memory: 1Gi
   persistence:
     enabled: false
-    name: molgenis-nexus-data
-    storageClass: nfs-class
+    name: molgenis-nfs-claim
     size: 30G
-    reclaimPolicy: Retain
-    server: 192.168.64.12
-    accessMode: ReadWriteMany
-    mountPath: /gcc/molgenis/nexus
   services:
     opencpu:
       host: localhost

From 0c9548069c2e89f2517cfc62fbaa85eb604a8d71 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 21:44:34 +0200
Subject: [PATCH 06/24] add subquestion heading

---
 molgenis/questions.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index 278368a..bbccea2 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -102,6 +102,7 @@ questions:
   group: "Persistence"
   label: Persistence
   show_subquestion_if: true
+  subquestions:
   - variable: molgenis.persistence.size
     default: "10Gi"
     description: "Size of MOLGENIS filestore (not the database size)"

From a2922c4d49ae60529df5a7b5505c46fb39043f87 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 21:47:12 +0200
Subject: [PATCH 07/24] persistence keys in deploymeny

---
 molgenis/questions.yml             | 2 +-
 molgenis/templates/deployment.yaml | 2 +-
 molgenis/values.yaml               | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index bbccea2..b5f40e5 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -104,7 +104,7 @@ questions:
   show_subquestion_if: true
   subquestions:
   - variable: molgenis.persistence.size
-    default: "10Gi"
+    default: "30Gi"
     description: "Size of MOLGENIS filestore (not the database size)"
     type: string
     label: Size filestore
diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index 06708a9..7895b0d 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -72,7 +72,7 @@ spec:
         volumes:
         - name: molgenis-nfs
           persistentVolumeClaim:
-            claimName: {{ .Values.persistence.name }}
+            claimName: {{ .persistence.name }}
         {{- end }}
         {{- end }}
 
diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index a0151d7..c2c2974 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -33,7 +33,7 @@ molgenis:
   persistence:
     enabled: false
     name: molgenis-nfs-claim
-    size: 30G
+    size: 30Gi
   services:
     opencpu:
       host: localhost

From 846df81522c0e7d171d44f4b3d0aadc76bf16e35 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 21:49:12 +0200
Subject: [PATCH 08/24] udpated structure

---
 molgenis/templates/persistence/molgenisPVC.yaml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/molgenis/templates/persistence/molgenisPVC.yaml b/molgenis/templates/persistence/molgenisPVC.yaml
index 65c07ba..4de137a 100644
--- a/molgenis/templates/persistence/molgenisPVC.yaml
+++ b/molgenis/templates/persistence/molgenisPVC.yaml
@@ -4,12 +4,12 @@ kind: PersistentVolumeClaim
 apiVersion: v1
 metadata:
   name: {{ .Values.molgenis.persistence.name }}
-  annotations:
-    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
-  spec:
-    accessModes:
-      - ReadWriteMany
-    resources:
-      requests:
-        storage: {{ .Values.molgenis.persistence.size }}
+annotations:
+  volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+      storage: {{ .Values.molgenis.persistence.size }}
 {{- end }}
\ No newline at end of file

From a660aff3553443382d60f7210f403ca9b90ee888 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 21:53:29 +0200
Subject: [PATCH 09/24] udpated structure

---
 molgenis/templates/persistence/molgenisPVC.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/molgenis/templates/persistence/molgenisPVC.yaml b/molgenis/templates/persistence/molgenisPVC.yaml
index 4de137a..1ae03f0 100644
--- a/molgenis/templates/persistence/molgenisPVC.yaml
+++ b/molgenis/templates/persistence/molgenisPVC.yaml
@@ -4,8 +4,8 @@ kind: PersistentVolumeClaim
 apiVersion: v1
 metadata:
   name: {{ .Values.molgenis.persistence.name }}
-annotations:
-  volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+  annotations:
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
 spec:
   accessModes:
     - ReadWriteMany

From 59d99deab574db7f335f066385cea0287dcaaca9 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 21:57:39 +0200
Subject: [PATCH 10/24] restrcuture deployment

---
 molgenis/templates/deployment.yaml              | 8 ++++----
 molgenis/templates/persistence/molgenisPVC.yaml | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index 7895b0d..0205efb 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -68,11 +68,11 @@ spec:
             periodSeconds: 5
           resources:
 {{ toYaml .resources | indent 12 }}
-        {{- if .persistence.enabled }}
+        {{- if .persistence.enabled -}}
         volumes:
-        - name: molgenis-nfs
-          persistentVolumeClaim:
-            claimName: {{ .persistence.name }}
+          - name: molgenis-nfs
+            persistentVolumeClaim:
+              claimName: {{ .persistence.name }}
         {{- end }}
         {{- end }}
 
diff --git a/molgenis/templates/persistence/molgenisPVC.yaml b/molgenis/templates/persistence/molgenisPVC.yaml
index 1ae03f0..a10d9de 100644
--- a/molgenis/templates/persistence/molgenisPVC.yaml
+++ b/molgenis/templates/persistence/molgenisPVC.yaml
@@ -1,4 +1,4 @@
-{{- if .Values.molgenis.persistence.enabled }}
+{{- if .Values.molgenis.persistence.enabled -}}
 apiVersion: extensions/v1beta1
 kind: PersistentVolumeClaim
 apiVersion: v1

From bfb2e458776b77f1ff1a6776ba99c11bb6e85810 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 22:00:51 +0200
Subject: [PATCH 11/24] added volumes

---
 molgenis/templates/deployment.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index 0205efb..ed63b5c 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -68,13 +68,13 @@ spec:
             periodSeconds: 5
           resources:
 {{ toYaml .resources | indent 12 }}
-        {{- if .persistence.enabled -}}
-        volumes:
-          - name: molgenis-nfs
-            persistentVolumeClaim:
-              claimName: {{ .persistence.name }}
-        {{- end }}
         {{- end }}
+      {{- if .persistence.enabled }}
+      volumes:
+        - name: molgenis-nfs
+          persistentVolumeClaim:
+            claimName: {{ .persistence.name }}
+      {{- end }}
 
         - name: elasticsearch
         {{- with .Values.elasticsearch }}

From ed948c40aa38c050e2550566d79cf4e336f4529a Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 22:02:18 +0200
Subject: [PATCH 12/24] referred to right config values.yaml

---
 molgenis/templates/deployment.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index ed63b5c..a9c3008 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -69,11 +69,11 @@ spec:
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
-      {{- if .persistence.enabled }}
+      {{- if .Values.molgenis.persistence.enabled }}
       volumes:
         - name: molgenis-nfs
           persistentVolumeClaim:
-            claimName: {{ .persistence.name }}
+            claimName: {{ .Values.molgenis.persistence.name }}
       {{- end }}
 
         - name: elasticsearch

From 947e389b92eca11087f990244bf7a17b2d1c767c Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Mon, 10 Sep 2018 22:06:20 +0200
Subject: [PATCH 13/24] moved volumes down below in deployment

---
 molgenis/templates/deployment.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index a9c3008..59cd27a 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -69,12 +69,6 @@ spec:
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
-      {{- if .Values.molgenis.persistence.enabled }}
-      volumes:
-        - name: molgenis-nfs
-          persistentVolumeClaim:
-            claimName: {{ .Values.molgenis.persistence.name }}
-      {{- end }}
 
         - name: elasticsearch
         {{- with .Values.elasticsearch }}
@@ -98,6 +92,12 @@ spec:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
 
+{{- if .Values.molgenis.persistence.enabled }}
+      volumes:
+        - name: molgenis-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.molgenis.persistence.name }}
+{{- end }}
 
     {{- with .Values.nodeSelector }}
       nodeSelector:

From 04bd9cd653d0f08c3681bb5f8f1ff620fb2ab05c Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Tue, 11 Sep 2018 13:51:58 +0200
Subject: [PATCH 14/24] added persistence to questions and bumped chart

---
 molgenis/Chart.yaml    |  2 +-
 molgenis/questions.yml | 18 ++++++++++++++++--
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/molgenis/Chart.yaml b/molgenis/Chart.yaml
index e60f8cc..42ec519 100644
--- a/molgenis/Chart.yaml
+++ b/molgenis/Chart.yaml
@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: MOLGENIS - helm stack (in BETA)
 name: molgenis-beta
-version: 0.1.0
+version: 0.2.0
 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
\ No newline at end of file
diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index 27dbee5..572ac39 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -81,7 +81,7 @@ questions:
 - variable: molgenis.resources.requests.memory
   label: Container memory reservation
   default: 1250Mi
-  description: "Memory reservation for this MOLGENIS container"
+  description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
   type: enum
   options:
   - "1250Mi"
@@ -96,4 +96,18 @@ questions:
   options:
   - "1g"
   - "2g"
-  group: "Resources"
\ No newline at end of file
+  group: "Resources"
+- variable: molgenis.persistence.enabled
+  default: false
+  description: "Do you want to use persistence"
+  type: boolean
+  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
\ No newline at end of file

From e5cbcdf9333b9ace92ede47e28640371b79f1ddc Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Tue, 11 Sep 2018 15:48:56 +0200
Subject: [PATCH 15/24] added retainability for pv's

---
 molgenis/questions.yml                          |  7 ++++++-
 molgenis/templates/persistence/molgenisPVC.yaml | 12 +++++++++---
 molgenis/values.yaml                            |  1 +
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index 572ac39..cb4dc26 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -110,4 +110,9 @@ questions:
     default: "30Gi"
     description: "Size of MOLGENIS filestore (not the database size)"
     type: string
-    label: Size filestore
\ No newline at end of file
+    label: Size filestore
+  - variable: molgenis.persistence.retain
+    default: false
+    description: "Do you want to retain the persistence volume"
+    type: boolean
+    label: Retain volume
\ No newline at end of file
diff --git a/molgenis/templates/persistence/molgenisPVC.yaml b/molgenis/templates/persistence/molgenisPVC.yaml
index a10d9de..1335adb 100644
--- a/molgenis/templates/persistence/molgenisPVC.yaml
+++ b/molgenis/templates/persistence/molgenisPVC.yaml
@@ -1,15 +1,21 @@
-{{- if .Values.molgenis.persistence.enabled -}}
+{{- with .Values.molgenis.persistence }}
+{{- if .enabled -}}
 apiVersion: extensions/v1beta1
 kind: PersistentVolumeClaim
 apiVersion: v1
 metadata:
-  name: {{ .Values.molgenis.persistence.name }}
+  name: {{ .name }}
   annotations:
+    {{- if .retain }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
+    {{- else }}
     volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+    {{- end }}
 spec:
   accessModes:
     - ReadWriteMany
   resources:
     requests:
-      storage: {{ .Values.molgenis.persistence.size }}
+      storage: {{ .size }}
+{{- end }}
 {{- end }}
\ No newline at end of file
diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index 747106a..6b6d5ee 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -33,6 +33,7 @@ molgenis:
       memory: 1250Mi
   persistence:
     enabled: false
+    retain: false
     name: molgenis-nfs-claim
     size: 30Gi
   services:

From 61d550512692ef88a91e594a581992256526f727 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Tue, 11 Sep 2018 16:56:27 +0200
Subject: [PATCH 16/24] updated persistence README.md

---
 molgenis/README.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/molgenis/README.md b/molgenis/README.md
index c85b200..4c81c8e 100644
--- a/molgenis/README.md
+++ b/molgenis/README.md
@@ -79,5 +79,26 @@ Specify memory usage for Java JVM:
 
 Select the resources you need dependant on the customer you need to serve.
 
+## Persistence
+You can define your own volume by enabling persistence on your MOLGENIS instance. You can also choose to retain the volume of the NFS and specify the size of the volume.
+The following properties will setup the persistence for you.
+
+- ```molgenis.persistence.enabled```
+- ```molgenis.persistence.retain```
+- ```molgenis.persistence.size```
+
+### Resolve you persistent volume
+You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
+
+```
+kubectl get pv
+```
+
+You can now view the persistent volume claims and the attached volumes.
+
+| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
+| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
+| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner | | 33d |
+
 ## Firewall
 Is defined at cluster level. This chart does not facilitate firewall configuration.

From 5fd05f505a6aee763ece5eac09263940258940a7 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Tue, 11 Sep 2018 16:59:40 +0200
Subject: [PATCH 17/24] updated docs

---
 molgenis/README.md | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/molgenis/README.md b/molgenis/README.md
index 4c81c8e..2f56de4 100644
--- a/molgenis/README.md
+++ b/molgenis/README.md
@@ -98,7 +98,11 @@ You can now view the persistent volume claims and the attached volumes.
 
 | NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
 | ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
-| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner | | 33d |
+| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
+| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
+
+You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
+When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```. 
 
 ## Firewall
 Is defined at cluster level. This chart does not facilitate firewall configuration.

From d7ccab34c431f3609501ef761ff8a69a81a594da Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Tue, 11 Sep 2018 17:07:14 +0200
Subject: [PATCH 18/24] version bump and enumerized values for sizing volumes

---
 molgenis/Chart.yaml    | 2 +-
 molgenis/questions.yml | 9 +++++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/molgenis/Chart.yaml b/molgenis/Chart.yaml
index 42ec519..d72e338 100644
--- a/molgenis/Chart.yaml
+++ b/molgenis/Chart.yaml
@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: MOLGENIS - helm stack (in BETA)
 name: molgenis-beta
-version: 0.2.0
+version: 0.3.0
 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
\ No newline at end of file
diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index cb4dc26..f9309cf 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -107,9 +107,14 @@ questions:
   show_subquestion_if: true
   subquestions:
   - variable: molgenis.persistence.size
-    default: "30Gi"
+    default: "50Gi"
     description: "Size of MOLGENIS filestore (not the database size)"
-    type: string
+    type: enum
+    options:
+    - "50Gi"
+    - "100Gi"
+    - "200Gi"
+    - "300Gi"
     label: Size filestore
   - variable: molgenis.persistence.retain
     default: false

From 34c8f048b927f88fff701fbe1ce166bd698cd087 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Tue, 11 Sep 2018 17:08:44 +0200
Subject: [PATCH 19/24] also upgraded the default value in values.yaml

---
 molgenis/values.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index 6b6d5ee..aa0b197 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -35,7 +35,7 @@ molgenis:
     enabled: false
     retain: false
     name: molgenis-nfs-claim
-    size: 30Gi
+    size: 50Gi
   services:
     opencpu:
       host: localhost

From d17c137dd59cbe3cc0d2e5da2bdad772fbe92978 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Wed, 12 Sep 2018 08:04:59 +0200
Subject: [PATCH 20/24] added elasticsearch persistence

---
 molgenis/README.md                            | 22 +++++++++++++---
 molgenis/questions.yml                        | 26 ++++++++++++-------
 molgenis/templates/deployment.yaml            | 16 +++++++++---
 .../persistence/elasticsearchPVC.yaml         | 20 ++++++++++++++
 .../templates/persistence/molgenisPVC.yaml    |  9 +++----
 molgenis/values.yaml                          | 13 +++++++---
 6 files changed, 81 insertions(+), 25 deletions(-)
 create mode 100644 molgenis/templates/persistence/elasticsearchPVC.yaml

diff --git a/molgenis/README.md b/molgenis/README.md
index 2f56de4..03e8b2e 100644
--- a/molgenis/README.md
+++ b/molgenis/README.md
@@ -80,13 +80,27 @@ Specify memory usage for Java JVM:
 Select the resources you need dependant on the customer you need to serve.
 
 ## Persistence
-You can define your own volume by enabling persistence on your MOLGENIS instance. You can also choose to retain the volume of the NFS and specify the size of the volume.
-The following properties will setup the persistence for you.
+You can enable persistence on your MOLGENIS stack by specifying the following property.
 
-- ```molgenis.persistence.enabled```
-- ```molgenis.persistence.retain```
+- ```persistence.enabled```
+
+You can also choose to retain the volume of the NFS.
+- ```persistence.retain```
+
+The size and claim name can be specified per service. There are now two services that can be persist.
+
+- MOLGENIS
+- ElasticSearch
+
+MOLGENIS persistent properties.
+- ```molgenis.persistence.claim```
 - ```molgenis.persistence.size```
 
+ElasticSearch persistent properties.
+- ```elasticsearch.persistence.claim```
+- ```elasticsearch.persistence.size```
+
+
 ### Resolve you persistent volume
 You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
 
diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index f9309cf..1dca426 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -97,7 +97,7 @@ questions:
   - "1g"
   - "2g"
   group: "Resources"
-- variable: molgenis.persistence.enabled
+- variable: persistence.enabled
   default: false
   description: "Do you want to use persistence"
   type: boolean
@@ -106,18 +106,26 @@ questions:
   label: Persistence
   show_subquestion_if: true
   subquestions:
+  - variable: persistence.retain
+    default: false
+    description: "Do you want to retain the persistent volume"
+    type: boolean
+    label: Retain volume
   - variable: molgenis.persistence.size
+    default: "30Gi"
+    description: "Size of MOLGENIS filestore"
+    type: enum
+    options:
+    - "30Gi"
+    - "50Gi"
+    - "100Gi"
+    label: Size filestore
+  - variable: elasticsearch.persistence.size
     default: "50Gi"
-    description: "Size of MOLGENIS filestore (not the database size)"
+    description: "Size of ElasticSearch data"
     type: enum
     options:
     - "50Gi"
     - "100Gi"
     - "200Gi"
-    - "300Gi"
-    label: Size filestore
-  - variable: molgenis.persistence.retain
-    default: false
-    description: "Do you want to retain the persistence volume"
-    type: boolean
-    label: Retain volume
\ No newline at end of file
+    label: Size for ElasticSearch data
\ No newline at end of file
diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index 5ecf512..c14d714 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -49,7 +49,7 @@ spec:
               value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
           ports:
             - containerPort: 8080
-          {{- if .persistence.enabled }}
+          {{- if $.Values.persistence.enabled }}
           volumeMounts:
           - name: molgenis-nfs
             mountPath: /home/molgenis
@@ -92,15 +92,25 @@ spec:
           ports:
             - containerPort: 9200
             - containerPort: 9300
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: elastic-nfs
+            mountPath: /usr/share/elasticsearch/data
+          {{- end }}
+
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
 
-{{- if .Values.molgenis.persistence.enabled }}
+{{- if .Values.persistence.enabled }}
       volumes:
         - name: molgenis-nfs
           persistentVolumeClaim:
-            claimName: {{ .Values.molgenis.persistence.name }}
+            claimName: {{ .Values.molgenis.persistence.claim }}
+      volumes:
+        - name: elasticsearch-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.elasticsearch.persistence.claim }}
 {{- end }}
 
     {{- with .Values.nodeSelector }}
diff --git a/molgenis/templates/persistence/elasticsearchPVC.yaml b/molgenis/templates/persistence/elasticsearchPVC.yaml
new file mode 100644
index 0000000..54103b8
--- /dev/null
+++ b/molgenis/templates/persistence/elasticsearchPVC.yaml
@@ -0,0 +1,20 @@
+{{- if .Values.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.elasticsearch.persistence.claim }}
+  annotations:
+    {{- if .Values.persistence.retain }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
+    {{- else }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+    {{- end }}
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+      storage: {{ .Values.elasticsearch.persistence.size }}
+{{- end }}
+{{- end }}
\ No newline at end of file
diff --git a/molgenis/templates/persistence/molgenisPVC.yaml b/molgenis/templates/persistence/molgenisPVC.yaml
index 1335adb..9968273 100644
--- a/molgenis/templates/persistence/molgenisPVC.yaml
+++ b/molgenis/templates/persistence/molgenisPVC.yaml
@@ -1,12 +1,11 @@
-{{- with .Values.molgenis.persistence }}
-{{- if .enabled -}}
+{{- if .Values.persistence.enabled -}}
 apiVersion: extensions/v1beta1
 kind: PersistentVolumeClaim
 apiVersion: v1
 metadata:
-  name: {{ .name }}
+  name: {{ .Values.molgenis.persistence.claim }}
   annotations:
-    {{- if .retain }}
+    {{- if .Values.persistence.retain }}
     volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
     {{- else }}
     volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
@@ -16,6 +15,6 @@ spec:
     - ReadWriteMany
   resources:
     requests:
-      storage: {{ .size }}
+      storage: {{ .Values.molgenis.persistence.size }}
 {{- end }}
 {{- end }}
\ No newline at end of file
diff --git a/molgenis/values.yaml b/molgenis/values.yaml
index aa0b197..44b9f27 100644
--- a/molgenis/values.yaml
+++ b/molgenis/values.yaml
@@ -32,10 +32,8 @@ molgenis:
       cpu: 200m
       memory: 1250Mi
   persistence:
-    enabled: false
-    retain: false
-    name: molgenis-nfs-claim
-    size: 50Gi
+    claim: molgenis-nfs-claim
+    size: 30Gi
   services:
     opencpu:
       host: localhost
@@ -62,6 +60,13 @@ elasticsearch:
    requests:
     cpu: 100m
     memory: 1Gi
+  persistence:
+    claim: elasticsearch-nfs-claim
+    size: 50Gi
+
+persistence:
+  enabled: false
+  retain: false
 
 nodeSelector: {
   deployPod: "true"

From 321af8f2f2d4e9bfe19eaee2524043f086f36db0 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Wed, 12 Sep 2018 08:13:33 +0200
Subject: [PATCH 21/24] updated labels and desc

---
 molgenis/questions.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/molgenis/questions.yml b/molgenis/questions.yml
index 1dca426..69c106a 100644
--- a/molgenis/questions.yml
+++ b/molgenis/questions.yml
@@ -113,16 +113,16 @@ questions:
     label: Retain volume
   - variable: molgenis.persistence.size
     default: "30Gi"
-    description: "Size of MOLGENIS filestore"
+    description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
     type: enum
     options:
     - "30Gi"
     - "50Gi"
     - "100Gi"
-    label: Size filestore
+    label: Size MOLGENIS filestore
   - variable: elasticsearch.persistence.size
     default: "50Gi"
-    description: "Size of ElasticSearch data"
+    description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
     type: enum
     options:
     - "50Gi"

From c28f08bedd589c4c013b0c364ef8793c60745bed Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Wed, 12 Sep 2018 08:15:38 +0200
Subject: [PATCH 22/24] one end to much

---
 molgenis/templates/persistence/elasticsearchPVC.yaml | 1 -
 molgenis/templates/persistence/molgenisPVC.yaml      | 1 -
 2 files changed, 2 deletions(-)

diff --git a/molgenis/templates/persistence/elasticsearchPVC.yaml b/molgenis/templates/persistence/elasticsearchPVC.yaml
index 54103b8..6c8bef7 100644
--- a/molgenis/templates/persistence/elasticsearchPVC.yaml
+++ b/molgenis/templates/persistence/elasticsearchPVC.yaml
@@ -16,5 +16,4 @@ spec:
   resources:
     requests:
       storage: {{ .Values.elasticsearch.persistence.size }}
-{{- end }}
 {{- end }}
\ No newline at end of file
diff --git a/molgenis/templates/persistence/molgenisPVC.yaml b/molgenis/templates/persistence/molgenisPVC.yaml
index 9968273..6ec2f93 100644
--- a/molgenis/templates/persistence/molgenisPVC.yaml
+++ b/molgenis/templates/persistence/molgenisPVC.yaml
@@ -16,5 +16,4 @@ spec:
   resources:
     requests:
       storage: {{ .Values.molgenis.persistence.size }}
-{{- end }}
 {{- end }}
\ No newline at end of file

From 7305d54630cb495dd4ae2a8a9212eec6a6d46315 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Wed, 12 Sep 2018 08:17:34 +0200
Subject: [PATCH 23/24] updated volume name

---
 molgenis/templates/deployment.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index c14d714..206f670 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -94,7 +94,7 @@ spec:
             - containerPort: 9300
           {{- if $.Values.persistence.enabled }}
           volumeMounts:
-          - name: elastic-nfs
+          - name: elasticsearch-nfs
             mountPath: /usr/share/elasticsearch/data
           {{- end }}
 

From 501982ca53652559a76ff4a72f32a400127aec70 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Wed, 12 Sep 2018 08:19:48 +0200
Subject: [PATCH 24/24] removed redunant volume entry in deployment

---
 molgenis/templates/deployment.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml
index 206f670..b40a284 100644
--- a/molgenis/templates/deployment.yaml
+++ b/molgenis/templates/deployment.yaml
@@ -107,7 +107,6 @@ spec:
         - name: molgenis-nfs
           persistentVolumeClaim:
             claimName: {{ .Values.molgenis.persistence.claim }}
-      volumes:
         - name: elasticsearch-nfs
           persistentVolumeClaim:
             claimName: {{ .Values.elasticsearch.persistence.claim }}