Update Rstudio Helm Chart

charts/rstudio/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v2
 name: rstudio
 description: RStudio Helm Chart for Rahti platform
   Link to the repo https://github.com/CSCfi/helm-charts
-version: 1.2.1
+version: 1.2.2
 sources:
 - https://github.com/CSCfi/helm-charts
 icon: https://upload.wikimedia.org/wikipedia/commons/0/0e/Eo_circle_light-blue_white_letter-r.svg

charts/rstudio/README.md

@@ -6,40 +6,46 @@ helm upgrade --install rstudio .
 
 ## Explanations
 This Helm Chart helps you to deploy Rstudio with Shiny on CSC Rahti 2 (Openshift 4).  
-If you want to use it with different values, you can edit `values.yaml` file and then run:  
+Rstudio is accessible through NGINX. The default user is `rstudio` and the password is generated randomly. You can set you own values by editing the `values.yaml` file and then run:  
 ```sh
 helm upgrade --install rstudio . -f {custom_values.yaml}
 ```
 
 ## Parameters
 ### Common parameters
 
-| Name                                   | Description                                               | Value                                                        |
-| -------------------------------------- | --------------------------------------------------------- | ------------------------------------------------------------ |
-| `openshift.enabled`                    | If you are deploying on OKD 4                             | `true`                                                       |
-| `appName`                              | Name for the application                                  | `csc-rstudio-shiny`                                          |
-| `route.insecureEdgeTerminationPolicy`  | If `openshift.enabled`, will create a route               | `Redirect`                                                   |
-| `route.termination`                    | If `openshift.enabled`, will create a route               | `edge`                                                       |
-| `route.host`                           | If `openshift.enabled`, will create a route               | `""`                                                         |
-| `buildConfig.gitRepoUri`               | Uri of the GitHub repo where the `Dockerfile` is located  | `https://github.com/CSCfi/helm-charts.git`                   |
-| `buildConfig.gitBranch`                | Branch of the GitHub repo                                 | `main`                                                       |
-| `buildConfig.contextDir`               | Context directory for the build                           | `charts/rstudio/source`                                      |
+| Name                                   | Description                                                   | Value                                                        |
+| -------------------------------------- | ------------------------------------------------------------- | ------------------------------------------------------------ |
+| `openshift.enabled`                    | If you are deploying on OKD 4                                 | `true`                                                       |
+| `appName`                              | Name for the application                                      | `csc-rstudio-shiny`                                          |
+| `buildConfig.gitRepoUri`               | Uri of the GitHub repo where the `Dockerfile` is located      | `https://github.com/CSCfi/helm-charts.git`                   |
+| `buildConfig.gitBranch`                | Branch of the GitHub repo                                     | `main`                                                       |
+| `buildConfig.contextDir`               | Context directory for the build                               | `charts/rstudio/source`                                      |
 
 ### Rstudio parameters
 
-| Name                                   | Description                                             | Value                             |
-| -------------------------------------- | ------------------------------------------------------- | --------------------------------- |
-| `rstudio.podSecurityContext`           | Set SecurityContext for the pod                         | `{}`                              |
-| `rstudio.containerSecurityContext`     | Set SecurityContext for the container                   | `allowPrivilegeEscalation: false`<br>`runAsUser:`<br>`runAsGroup:`<br>`capabilities:`<br>&nbsp;&nbsp;`drop:`<br>&nbsp;&nbsp;`- ALL`<br>`runAsNonRoot: true`<br>`seccompProfile:`<br>&nbsp;&nbsp;`type: RuntimeDefault` |
-| `rstudio.pvc.mountName`                        | Name for the `PersistentVolumeClaim`            | `rstudio-server-home`             |
-| `rstudio.pvc.storageSize`                      | Storage size for the `PersistentVolumeClaim`    | `5Gi`                             |
+| Name                                           | Description                                                   | Value                             |
+| ---------------------------------------------- | ------------------------------------------------------------- | --------------------------------- |
+| `rstudio.podSecurityContext`                   | Set SecurityContext for the pod                               | `{}`                              |
+| `rstudio.containerSecurityContext`             | Set SecurityContext for the container                         | `allowPrivilegeEscalation: false`<br>`runAsUser:`<br>`runAsGroup:`<br>`capabilities:`<br>&nbsp;&nbsp;`drop:`<br>&nbsp;&nbsp;`- ALL`<br>`runAsNonRoot: true`<br>`seccompProfile:`<br>&nbsp;&nbsp;`type: RuntimeDefault` |
+| `rstudio.pvc.mountName`                        | Name for the `PersistentVolumeClaim`                          | `rstudio-server-home`             |
+| `rstudio.pvc.storageSize`                      | Storage size for the `PersistentVolumeClaim`                  | `5Gi`                             |
+| `rstudio.route.insecureEdgeTerminationPolicy`  | If `openshift.enabled`, will create a route                   | `Redirect`                        |
+| `rstudio.route.termination`                    | If `openshift.enabled`, will create a route                   | `edge`                            |
+| `rstudio.route.host`                           | If `openshift.enabled`, will create a route. REQUIRED VALUE   | ``                                |
+| `rstudio.random_pw_secret_key`                 | Key to store the random password                              | `nginx-password`                  |
+| `rstudio.secret.USER`                          | User to connect to Rstudio                                    | `rstudio`                         |
+| `rstudio.secret.PASSWORD`                      | Password to connect to Rstudio                                | generated randomly                |
 
 ### Shiny parameters
 
-| Name                                   | Description                                             | Value                             |
-| -------------------------------------- | ------------------------------------------------------- | --------------------------------- |
-| `shiny.pvc.mountName`                  | Name for the `PersistentVolumeClaim`                    | `shiny-server`                    |
-| `shiny.pvc.storageSize`                | Storage size for the `PersistentVolumeClaim`            | `5Gi`                             |
+| Name                                         | Description                                                   | Value                             |
+| -------------------------------------------- | ------------------------------------------------------------- | --------------------------------- |
+| `shiny.pvc.mountName`                        | Name for the `PersistentVolumeClaim`                          | `shiny-server`                    |
+| `shiny.pvc.storageSize`                      | Storage size for the `PersistentVolumeClaim`                  | `5Gi`                             |
+| `shiny.route.insecureEdgeTerminationPolicy`  | If `openshift.enabled`, will create a route                   | `Redirect`                        |
+| `shiny.route.termination`                    | If `openshift.enabled`, will create a route                   | `edge`                            |
+| `shiny.route.host`                           | If `openshift.enabled`, will create a route. REQUIRED VALUE   | ``                                |
 
 ## Cleanup
 To delete all the resources, simply uninstall the Helm Chart:

charts/rstudio/templates/NOTES.txt

@@ -12,10 +12,15 @@ Once the build is over, you can access your Rstudio by retrieving the URL:
 
 You can retrieve Rstudio URL via this command:
 
-  export RSTUDIO=$(oc get route --namespace {{ .Release.Namespace }} -o yaml | yq '.items[0].spec.host')
+  export RSTUDIO=$(oc get route rstudio --namespace {{ .Release.Namespace }} -o yaml | yq .spec.host)
   echo "Rstudio server URL: http://$RSTUDIO/"
 
+To retrieve USER and PASSWORD:
+
+  echo USER: $(oc get secret --namespace={{ .Release.Namespace }} nginx-password -o jsonpath="{.data.USER}" | base64 -d)
+  echo PASSWORD: $(oc get secret --namespace={{ .Release.Namespace }} nginx-password -o jsonpath="{.data.PASSWORD}" | base64 -d)
+
 And for the Shiny Server:
 
-  export SHINY=$(oc get route --namespace {{ .Release.Namespace }} -o yaml | yq '.items[1].spec.host')
+  export SHINY=$(oc get route shiny --namespace {{ .Release.Namespace }} -o yaml | yq .spec.host)
   echo "Shiny App URL: http://$SHINY/"

charts/rstudio/templates/_helpers.tpl

@@ -60,3 +60,38 @@ Create the name of the service account to use
 {{- default "default" .Values.serviceAccount.name }}
 {{- end }}
 {{- end }}
+
+{{/*
+Define a function that generate static password
+*/}}
+{{- define "generate_static_password" -}}
+{{- /* Create "tmp_vars" dict inside ".Release" to store various stuff. */ -}}
+{{- if not (index .Release "tmp_vars") -}}
+{{-   $_ := set .Release "tmp_vars" dict -}}
+{{- end -}}
+{{- /* Some random ID of this password, in case there will be other random values alongside this instance. */ -}}
+{{- $key := printf "%s_%s" .Release.Name "password" -}}
+{{- /* If $key does not yet exist in .Release.tmp_vars, then... */ -}}
+{{- if not (index .Release.tmp_vars $key) -}}
+{{- /* ... store random password under the $key */ -}}
+{{-   $_ := set .Release.tmp_vars $key (randAlphaNum 20) -}}
+{{- end -}}
+{{- /* Retrieve previously generated value. */ -}}
+{{- index .Release.tmp_vars $key -}}
+{{- end -}}
+
+{{/*
+Define a function that lookup the secret on upgrade. If install, it requires the name of secret to create and the key to store the password.
+*/}}
+{{- define "random_pw_reusable" -}}
+  {{- if .Release.IsUpgrade -}}
+    {{- $data := default dict (lookup "v1" "Secret" .Release.Namespace "nginx-password").data -}}
+    {{- if $data -}}
+      {{- index $data .Values.rstudio.random_pw_secret_key | b64dec -}}
+    {{- end -}}
+  {{- else -}}
+    {{- if and (required "You must pass nginx-password (the name of a secret to retrieve password from on upgrade)" "nginx-password") (required "You must pass .Values.rstudio.random_pw_secret_key (the name of the key in the secret to retrieve password from on upgrade)" .Values.rstudio.random_pw_secret_key) -}}
+      {{- (include "generate_static_password" .) -}}
+    {{- end -}}
+  {{- end -}}
+{{- end -}}

charts/rstudio/templates/buildconfig.yaml

@@ -28,3 +28,43 @@ spec:
         secretReference:
           name: webhooksecret
       type: GitHub
+
+---
+apiVersion: build.openshift.io/v1
+kind: BuildConfig
+metadata:
+  name: nginx-okd
+  annotations:
+    description: Defines how to build the application
+    template.alpha.openshift.io/wait-for-ready: "true"
+spec:
+  source:
+    dockerfile: |
+      FROM nginx:alpine
+      # support running as arbitrary user which belogs to the root group
+      RUN chmod g+rwx /var/cache/nginx /var/run /var/log/nginx && \
+          chown nginx.root /var/cache/nginx /var/run /var/log/nginx && \
+          # users are not allowed to listen on priviliged ports
+          sed -i.bak 's/listen\(.*\)80;/listen 8081;/' /etc/nginx/conf.d/default.conf && \
+          # Make /etc/nginx/html/ available to use
+          mkdir -p /etc/nginx/html/ && chmod 777 /etc/nginx/html/ && \
+          # comment user directive as master process is run as user in OpenShift anyhow
+          sed -i.bak 's/^user/#user/' /etc/nginx/nginx.conf && \
+          # Increase the number of worker connections per process
+          sed -i 's/worker_connections\s*1024/worker_connections 10240/' /etc/nginx/nginx.conf && \
+          apk add apache2-utils && \
+          mkdir /etc/nginx/secret/ && \
+          chown nginx.root /etc/nginx/secret/ && \
+          chmod g+w /etc/nginx/secret/
+      WORKDIR /usr/share/nginx/html/
+      EXPOSE 8081
+      USER nginx:root
+  strategy:
+    type: Docker
+  output:
+    to:
+      kind: ImageStreamTag
+      name: nginx-okd:latest
+  triggers:
+    - type: ImageChange
+    - type: ConfigChange

charts/rstudio/templates/configmap.yaml

@@ -0,0 +1,23 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: nginx-default
+data:
+  default.conf: |
+    server {
+      listen 8081;
+      server_name {{ tpl .Values.rstudio.route.host . }}.2.rahtiapp.fi;
+      location / {
+        root   /usr/share/nginx/html;
+        index  index.html index.htm;
+        auth_basic \"Rstudio\";
+        auth_basic_user_file /etc/nginx/secret/htpasswd;
+        proxy_pass http://{{ tpl .Values.appName . }}:8787/;
+        proxy_set_header Host $http_host;
+        client_max_body_size 2000M;
+      }
+      error_page   500 502 503 504  /50x.html;
+      location = /50x.html {
+        root   /usr/share/nginx/html;
+      }
+    }

charts/rstudio/templates/deployment.yaml

@@ -54,3 +54,74 @@ spec:
       - name: {{ .Values.shiny.pvc.mountName }}
         persistentVolumeClaim:
           claimName: {{ .Values.shiny.pvc.mountName }}
+
+---
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  labels:
+    app: nginx-okd
+  name: nginx-okd
+spec:
+  selector:
+    matchLabels:
+      app: nginx-okd
+  strategy:
+    type: RollingUpdate
+  template:
+    metadata:
+      labels:
+        app: nginx-okd
+    spec:
+      serviceAccount: build-reader
+      initContainers:
+      - name: wait-for-build
+        imagePullPolicy: IfNotPresent
+        image: quay.io/openshift/origin-cli:4.16
+        command:
+        - sh
+        - -c
+        - oc wait --for=jsonpath='{.status.phase}'=Complete build -l buildconfig=nginx-okd --timeout=900s
+      containers:
+      - name: nginx-okd
+        image: image-registry.openshift-image-registry.svc:5000/{{ .Release.Namespace }}/nginx-okd:latest
+        command:
+        - sh
+        - -xc
+        - >-
+          htpasswd -bc /etc/nginx/secret/htpasswd $USER $PASSWORD;
+          /docker-entrypoint.sh nginx -g "daemon off;"
+        env:
+        - name: USER
+          valueFrom:
+            secretKeyRef:
+              key: USER
+              name: nginx-password
+        - name: PASSWORD
+          valueFrom:
+            secretKeyRef:
+              key: PASSWORD
+              name: nginx-password
+        ports:
+        - containerPort: 8081
+          protocol: TCP
+        resources: {}
+        terminationMessagePath: /dev/termination-log
+        terminationMessagePolicy: File
+        volumeMounts:
+        - mountPath: /etc/nginx/conf.d/
+          name: nginx-default
+      dnsPolicy: ClusterFirst
+      restartPolicy: Always
+      schedulerName: default-scheduler
+      securityContext: {}
+      terminationGracePeriodSeconds: 30
+      volumes:
+      - configMap:
+          defaultMode: 420
+          name: nginx-default
+        name: nginx-default
+      - name: nginx-password
+        secret:
+          defaultMode: 420
+          secretName: nginx-password

charts/rstudio/templates/imagestream.yaml

@@ -4,6 +4,17 @@ metadata:
   annotations:
     description: Keeps track of changes in the appliation image
   name: {{ .Values.appName }}
+spec:
+  lookupPolicy:
+    local: true
+---
+
+apiVersion: image.openshift.io/v1
+kind: ImageStream
+metadata:
+  annotations:
+    description: Keeps track of changes in the appliation image
+  name: nginx-okd
 spec:
   lookupPolicy:
     local: true

charts/rstudio/templates/routes.yaml

@@ -6,15 +6,15 @@ metadata:
     app: {{ .Values.appName }}
   name: rstudio
 spec:
-  host: {{ .Values.rstudio.route.host }}
+  host: {{ required "A valid .Values.rstudio.route.host entry is required!" .Values.rstudio.route.host }}.2.rahtiapp.fi
   port:
-    targetPort: 8787
+    targetPort: 8081
   tls:
     insecureEdgeTerminationPolicy: {{ .Values.rstudio.route.insecureEdgeTerminationPolicy }}
     termination: {{ .Values.rstudio.route.termination }}
   to:
     kind: Service
-    name: {{ .Values.appName }}
+    name: nginx-okd
     weight: 100
 
 ---
@@ -25,7 +25,7 @@ metadata:
     app: {{ .Values.appName }}
   name: shiny
 spec:
-  host: {{ .Values.shiny.route.host }}
+  host: {{ required "A valid .Values.shiny.route.host entry is required!" .Values.shiny.route.host }}.2.rahtiapp.fi
   port:
     targetPort: 3838
   tls:

charts/rstudio/templates/secret.yaml

@@ -0,0 +1,11 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: nginx-password
+{{- if .Values.rstudio.secret }}
+data:
+  {{- range $key, $val := .Values.rstudio.secret }}
+    "{{ $key }}": "{{ tpl $val $ | b64enc }}"
+  {{- end }}
+{{- end }}
+type: Opaque

charts/rstudio/templates/service.yaml

@@ -12,3 +12,16 @@ spec:
   - name: shiny
     port: 3838
     targetPort: 3838
+
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: nginx-okd
+spec:
+  selector:
+    app: nginx-okd
+  ports:
+  - name: 8081-tcp
+    port: 8081
+    targetPort: 8081

charts/rstudio/values.yaml

@@ -21,7 +21,11 @@ rstudio:
   route:
     insecureEdgeTerminationPolicy: Redirect
     termination: edge
-    host: ""
+    host:  # REQUIRED
+  random_pw_secret_key: PASSWORD
+  secret:
+    USER: rstudio
+    PASSWORD: '{{- include "random_pw_reusable" . -}}'
 
 shiny:
   pvc:
@@ -30,7 +34,7 @@ shiny:
   route:
     insecureEdgeTerminationPolicy: Redirect
     termination: edge
-    host: ""
+    host:  # REQUIRED
 
 buildConfig:
   gitRepoUri: https://github.com/CSCfi/helm-charts.git