WIP: Upgrade deployments, start upgrade init-containers

.gitignore

@@ -1,2 +1,3 @@
 .idea
-.DS_Store
+.DS_Store
+*~

portal/Chart.yaml

@@ -1,4 +1,11 @@
-apiVersion: v1
+apiVersion: v2
 description: PhenoMeNal Portal
 name: portal
-version: 2.3.1
+type: application
+icon: https://pbs.twimg.com/profile_images/662304401990750208/4g1r_5gs.png
+version: 2.4.4
+
+dependencies:
+  - name: mysql
+    version: 1.6.2
+    repository: http://storage.googleapis.com/kubernetes-charts

portal/templates/NOTES.txt

@@ -3,13 +3,13 @@
   export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ template "fullname" . }})
   export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
   echo http://$NODE_IP:$NODE_PORT/login
-{{- else if contains "LoadBalancer" .Values.service.type }}
+{{- else if contains "LoadBalancer" .Values.frontend.service.type }}
      NOTE: It may take a few minutes for the LoadBalancer IP to be available.
            You can watch the status of by running 'kubectl get svc -w {{ template "fullname" . }}'
   export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
   echo http://$SERVICE_IP:{{ .Values.service.externalPort }}
-{{- else if contains "ClusterIP"  .Values.service.type }}
+{{- else if contains "ClusterIP"  .Values.frontend.service.type }}
   export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app={{ template "fullname" . }}" -o jsonpath="{.items[0].metadata.name}")
   echo "Visit http://127.0.0.1:8080 to use your application"
-  kubectl port-forward $POD_NAME 8080:{{ .Values.service.externalPort }}
+  kubectl port-forward $POD_NAME 8080:{{ .Values.frontend.service.externalPort }}
 {{- end }}

portal/templates/app-lib-deployment.yaml

@@ -1,10 +1,13 @@
-apiVersion: apps/v1beta1
+apiVersion: apps/v1
 kind: Deployment
 metadata:
   name: {{ .Release.Name }}-app-library
 spec:
   replicas: {{ .Values.app_library.replicaCount }}
-  template: 
+  selector:
+    matchLabels:
+      app:  {{ .Release.Name }}-app-library
+  template:
     metadata:
       labels:
         app: {{ .Release.Name }}-app-library
@@ -18,6 +21,6 @@ spec:
         - containerPort: {{ .Values.app_library.service.internalPort }}
         env:
            - name: "GIT_BRANCH"
-             value: {{ .Values.app_library.branch }} 
+             value: {{ .Values.app_library.branch }}
         resources:
 {{ toYaml .Values.app_library.resources | indent 12 }}

portal/templates/frontend-deployment.yaml

@@ -1,27 +1,25 @@
-apiVersion: apps/v1beta1
+apiVersion: apps/v1
 kind: Deployment
 metadata:
   name: {{ .Values.frontend.name }}
 spec:
   replicas: {{ .Values.replicaCount }}
-  template: 
+  selector:
+    matchLabels:
+      app: {{ .Values.frontend.name }}
+  template:
     metadata:
       labels:
         app: {{ .Values.frontend.name }}
       annotations:
-        pod.beta.kubernetes.io/init-containers: |-
-          [
-            {
-              "name": "metadata-listener",
-              "image": "alpine",
-              "imagePullPolicy": "IfNotPresent",
-              "command": [
-                "sh", "-c",
-                "for i in $(seq 1 200); do nc -z -w3 {{ .Release.Name }}-metadata 8888 && exit 0 || sleep 3; done; exit 1"
-              ]
-            }
-          ]
     spec:
+      initContainers:
+      - name: metadata-listener
+        image: alpine
+        command:
+          - sh
+          - -c
+          - for i in $(seq 1 200); do nc -z -w3 {{ .Release.Name }}-metadata 8888 && exit 0 || sleep 3; done; exit 1
       containers:
       - name: {{ .Chart.Name }}
         image: '{{ .Values.frontend.image.repository }}:{{ .Values.frontend.image.tag }}'
@@ -43,7 +41,7 @@ spec:
         - name: "TSI_PORTAL_URL"
           value: {{ .Values.tsi_portal_url }}
         - name: "AAP_URL"
-          value: {{ .Values.aap_url }} 
+          value: {{ .Values.aap_url }}
         - name: "PORTAL_ANNOUNCEMENT"
           value: {{ .Values.portal_announcement }}
         - name: "CLOUD_DEPLOY_GIT_REPO"

portal/templates/frontend-ingress.yaml

@@ -0,0 +1,31 @@
+{{- if semverCompare ">=1.14-0" .Capabilities.KubeVersion.GitVersion -}}
+apiVersion: networking.k8s.io/v1beta1
+{{- else -}}
+apiVersion: extensions/v1beta1
+{{- end }}
+kind: Ingress
+metadata:
+  name: {{ .Values.frontend.name }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+{{- if .Values.ingress.tls }}
+  tls:
+  {{- range .Values.ingress.tls }}
+    - hosts:
+      {{- range .hosts }}
+        - {{ . | quote }}
+      {{- end }}
+      secretName: {{ .secretName }}
+  {{- end }}
+{{- end }}
+  rules:
+  - host: {{ .Values.frontend.name }}.{{ .Values.mydomain }}
+    http:
+      paths:
+      - backend:
+          serviceName: {{ .Values.frontend.name }}
+          servicePort: 80
+        path: /

portal/templates/frontend-issuer.yaml

@@ -0,0 +1,20 @@
+apiVersion: cert-manager.io/v1alpha2
+kind: Issuer
+metadata:
+  name: portal-tls-issuer # { { .Release.Name } }-issuer
+spec:
+  acme:
+    # You must replace this email address with your own.
+    # Let's Encrypt will use this to contact you about expiring
+    # certificates, and issues related to your account.
+    email: {{ .Values.SiteAdminEmail }}
+#    server: https://acme-staging-v02.api.letsencrypt.org/directory
+    server: https://acme-v02.api.letsencrypt.org/directory
+    privateKeySecretRef:
+      # Secret resource that will be used to store the account's private key.
+      name: {{ .Release.Name }}-acme-key
+    # Add a single challenge solver, HTTP01 using nginx
+    solvers:
+    - http01:
+        ingress:
+          class: nginx

portal/templates/frontend-service.yaml

@@ -6,7 +6,6 @@ spec:
   type: {{ .Values.frontend.service.type }}
   ports:
   - name: {{ .Values.frontend.service.name }}
-    nodePort: {{ .Values.frontend.service.externalPort }}
     port: {{ .Values.frontend.service.internalPort }}
   selector:
     app: {{ .Values.frontend.name }}

portal/templates/metadata-deployment.yaml

@@ -1,27 +1,24 @@
-apiVersion: apps/v1beta1
+apiVersion: apps/v1
 kind: Deployment
 metadata:
   name: {{ .Release.Name }}-metadata
 spec:
   replicas: 1
-  template: 
+  selector:
+    matchLabels:
+      app: {{ .Release.Name }}-metadata
+  template:
     metadata:
       labels:
          app: {{ .Release.Name }}-metadata
-      annotations:
-        pod.beta.kubernetes.io/init-containers: |-
-          [
-            {
-              "name": "mysql-listener",
-              "image": "alpine",
-              "imagePullPolicy": "IfNotPresent",
-              "command": [
-                "sh", "-c",
-                "for i in $(seq 1 200); do nc -z -w3 {{ .Release.Name }}-mysql 3306 && exit 0 || sleep 3; done; exit 1"
-              ]
-            }
-          ]
     spec:
+      initContainers:
+      - name: mysql-listener
+        image: alpine
+        command:
+        - sh
+        - -c
+        - for i in $(seq 1 200); do nc -z -w3 {{ .Release.Name }}-mysql 3306 && exit 0 || sleep 3; echo -n "." ; done; exit 1
       containers:
       - name: metadata
         image: '{{ .Values.metadata.image.repository }}:{{ .Values.metadata.image.tag }}'

portal/templates/wiki-deployment.yaml

@@ -1,10 +1,13 @@
-apiVersion: apps/v1beta1
+apiVersion: apps/v1
 kind: Deployment
 metadata:
   name: {{ .Release.Name }}-wiki
 spec:
   replicas: {{ .Values.wiki.replicaCount }}
-  template: 
+  selector:
+    matchLabels:
+      app: {{ .Release.Name }}-wiki   
+  template:
     metadata:
       labels:
         app: {{ .Release.Name }}-wiki

portal/values.yaml

@@ -10,25 +10,30 @@
 #
 
 # global settings
+mydomain: "phenomenal-h2020.eu"
+
 replicaCount: 1
 tsi_portal_url: "https://api.portal.tsi.ebi.ac.uk/"
 aap_url: "https://api.aai.ebi.ac.uk/"
-cloud_deploy_git_repo: "https://github.com/phnmnl/cloud-deploy-kubenow.git"
-imagePullPolicy: "Always"
+#cloud_deploy_git_repo: "https://github.com/phnmnl/cloud-deploy-kubenow.git"
+cloud_deploy_git_repo: "https://github.com/phnmnl/cloud-deploy-kubenow-dalcotidine-20190625.git"
+#imagePullPolicy: "Always"
+imagePullPolicy: "IfNotPresent"
 galaxy_url: "https://public.phenomenal-h2020.eu"
 galaxy_api_key: ""
 enable_https: "true"
+SiteAdminEmail: "[email protected]"
 
 # frontend settings
 frontend:
-  name: phenomenal-portal
+  name: portal
   image:
     repository: container-registry.phenomenal-h2020.eu/phnmnl/phenomenal-portal
     tag: latest
   service:
     name: http
-    type: NodePort
-    externalPort: 30767
+    type: ClusterIP
+    externalPort: 80
     internalPort: 80
   resources:
     limits:
@@ -38,6 +43,17 @@ frontend:
       cpu: 100m
       memory: 128Mi
 
+ingress:
+  enabled: false
+  annotations:
+    cert-manager.io/issuer: "portal-tls-issuer"
+  hosts:
+    - host: portal.phenomenal-h2020.eu
+  tls: []
+#    - secretName: portal-cert
+#      hosts:
+#        - portal.phenomenal-h2020.eu
+
 # mysql settings
 mysql:
   mysqlRootPassword: "backend"
@@ -48,7 +64,7 @@ mysql:
 # metadata backend settings
 metadata:
   name: phenomenal-portal-metadata
-  image: 
+  image:
      repository: container-registry.phenomenal-h2020.eu/phnmnl/portal-metadata-backend
      tag: latest
   port: 8888
@@ -94,5 +110,3 @@ wiki:
     requests:
       cpu: 100m
       memory: 128Mi
-
-