From fd86066ceee7cdaae657c9e6583a185e100d98ed Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Thu, 27 Sep 2018 16:17:35 +0200
Subject: [PATCH] added init container and chown for nexus files

---
 molgenis-nexus/README.md                      | 29 +++++++++-
 .../deployments/nexus-deployment.yaml         | 57 +++++++++++--------
 molgenis-nexus/values.yaml                    |  6 +-
 3 files changed, 63 insertions(+), 29 deletions(-)

diff --git a/molgenis-nexus/README.md b/molgenis-nexus/README.md
index 0af9bb5..35ef133 100644
--- a/molgenis-nexus/README.md
+++ b/molgenis-nexus/README.md
@@ -6,8 +6,35 @@ NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
 
 This chart will deploy:
 
+- 1 NEXUS-nfs initialization container
+
+  We need this container to avoid permission issues on the NEXUS docker
 - 1 NEXUS container
-- 1 MOLGENIS-httpd container ()to proxy the registry and docker to one domain)
+- 1 MOLGENIS-httpd container (to proxy the registry and docker to one domain)
+
+## Backup restore
+
+Go to the commandline:
+
+```bash
+kubectl get pv
+```
+
+```bash
+| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
+| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
+| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-nexus/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 |
+```
+
+The persistent volume is the one in the molgenis-nexus namespace. 
+
+Go to the NFS-provisioner to the path of the persistent volume:
+
+```bash
+ls -t --full-time | head -7 | xargs cp ../restore-from-backup/
+```
+
 
 ## Installing the Chart
 
diff --git a/molgenis-nexus/templates/deployments/nexus-deployment.yaml b/molgenis-nexus/templates/deployments/nexus-deployment.yaml
index 72056eb..175998e 100644
--- a/molgenis-nexus/templates/deployments/nexus-deployment.yaml
+++ b/molgenis-nexus/templates/deployments/nexus-deployment.yaml
@@ -20,32 +20,39 @@ spec:
       creationTimestamp: null
     spec:
       restartPolicy: {{ .Values.nexus.restartPolicy }}
+      initContainers:
+      - name: nexus-nfs
+        image: busybox
+        command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
+        volumeMounts:
+        - name: molgenis-nexus-nfs
+          mountPath: "/nexus-data"
       containers:
-        - name: {{ .Values.nexus.name }}
-          image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
-          imagePullPolicy: {{ .Values.nexus.image.pullPolicy }}
-          ports:
-          - containerPort: {{ .Values.nexus.port.ui }}
-          - containerPort: {{ .Values.nexus.port.docker }}
-          volumeMounts:
-          - name: molgenis-nexus-nfs
-            mountPath: "/nexus-data"
-          livenessProbe:
-            httpGet:
-              path: /
-              port: {{ .Values.nexus.port.ui }}
-            initialDelaySeconds: 90
-            periodSeconds: 20
-            failureThreshold: 5
-            successThreshold: 1
-          readinessProbe:
-            httpGet:
-              path: /
-              port: {{ .Values.nexus.port.ui }}
-            initialDelaySeconds: 90
-            periodSeconds: 5
-            failureThreshold: 5
-            successThreshold: 1
+      - name: {{ .Values.nexus.name }}
+        image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
+        imagePullPolicy: {{ .Values.nexus.image.pullPolicy }}
+        ports:
+        - containerPort: {{ .Values.nexus.port.ui }}
+        - containerPort: {{ .Values.nexus.port.docker }}
+        volumeMounts:
+        - name: molgenis-nexus-nfs
+          mountPath: /nexus-data
+        livenessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexus.port.ui }}
+          initialDelaySeconds: 90
+          periodSeconds: 20
+          failureThreshold: 5
+          successThreshold: 1
+        readinessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexus.port.ui }}
+          initialDelaySeconds: 90
+          periodSeconds: 5
+          failureThreshold: 5
+          successThreshold: 1
 
       volumes:
         - name: molgenis-nexus-nfs
diff --git a/molgenis-nexus/values.yaml b/molgenis-nexus/values.yaml
index df5cdab..3203fa7 100644
--- a/molgenis-nexus/values.yaml
+++ b/molgenis-nexus/values.yaml
@@ -13,7 +13,7 @@ nexus:
   selector: nexus
   restartPolicy: Always
   image:
-    repository: sonatype/nexus3
+    repository: molgenis/nexus3
     tag: latest
     pullPolicy: Always
   port:
@@ -32,8 +32,8 @@ nexusProxy:
   selector: nexus-proxy
   restartPolicy: Always
   image:
-    repository: registry.webhosting.rug.nl/molgenis/httpd
-    tag: lts
+    repository: molgenis/httpd
+    tag: latest
     pullPolicy: Always
   port: 80
   service: