Implement deployment to staging

.gitlab-ci.yml

@@ -15,7 +15,7 @@ stages:
   - build
   - test
   - prepare_config
-  # - deploy
+  - deploy
 
 build-dev:
   image:
@@ -80,31 +80,31 @@ prepare_config_staging:
       - ${INGRESS_STAGING_FILE_PATH}
       
 
-# deploy-dev-hx:
-#   image:
-#     name: lachlanevenson/k8s-kubectl:latest
-#     entrypoint: ["/bin/sh", "-c"]
-#   only:
-#     - dev
-#   stage: deploy
-#   script:
-#     - echo $KUBE_URL_HX
-#     - echo "$KUBE_CA_PEM_HX" > "$(pwd)/kube.ca.pem"
-#     - kubectl config set-cluster ${KUBE_CLUS_NAME_HX} --server="${KUBE_URL_HX}" --certificate-authority="$(pwd)/kube.ca.pem"
-#     - kubectl config set-credentials ${KUBE_USER_HX} --token="${KUBE_TOKEN_HX}"
-#     - kubectl config set-context ${KUBE_NAMESPACE_DEV} --cluster=${KUBE_CLUS_NAME_HX} --user=${KUBE_USER_HX}
-#     - kubectl config use-context ${KUBE_NAMESPACE_DEV}
-    
-#     - kubectl create secret generic ${RUN_CONFIG_SECRET_NAME_STAGING} --from-file=RUN_CONFIG.yml=${CONFIG_STAGING_FILE_PATH} -o yaml -n ${CHEMBL_NS_STAGING} --dry-run=client | kubectl replace -f -
-#     - kubectl create secret generic ${GUNICORN_CONFIG_SECRET_NAME_STAGING} --from-file=GUNICORN_CONFIG.py=${CONFIG_GUNICORN_STAGING_FILE_PATH} -o yaml -n ${CHEMBL_NS_STAGING} --dry-run=client | kubectl replace -f -
-#     - cat ${CONFIG_STAGING_FILE_PATH}
-#     - cat ${CONFIG_GUNICORN_STAGING_FILE_PATH}
-    
-#     - echo ${KUBE_NAMESPACE_DEV} ${KUBE_URL_HH} ${KUBE_CLUS_NAME_HX} ${KUBE_USER_HX}
-#     - kubectl get pods -n ${KUBE_NAMESPACE_DEV}
-#     - sed -i "s~<VERSION>~${CI_COMMIT_SHORT_SHA}~" k8s-deployment.yml
-#     - sed -i "s~<DOCKER_IMAGE>~${DOCKER_IMAGE}~" k8s-deployment.yml
-#     - kubectl apply -n ${KUBE_NAMESPACE_DEV} -f k8s-deployment.yml
+deploy-dev-hx:
+  image:
+    name: lachlanevenson/k8s-kubectl:latest
+    entrypoint: ["/bin/sh", "-c"]
+  only:
+    - dev
+  stage: deploy
+  script:
+    - echo $KUBE_URL_HX
+    - echo "$KUBE_CA_PEM_HX" > "$(pwd)/kube.ca.pem"
+    - kubectl config set-cluster ${KUBE_CLUS_NAME_HX} --server="${KUBE_URL_HX}" --certificate-authority="$(pwd)/kube.ca.pem"
+    - kubectl config set-credentials ${KUBE_USER_HX} --token="${KUBE_TOKEN_HX}"
+    - kubectl config set-context ${KUBE_NAMESPACE_DEV} --cluster=${KUBE_CLUS_NAME_HX} --user=${KUBE_USER_HX}
+    - kubectl config use-context ${KUBE_NAMESPACE_DEV}
+    - kubectl create secret generic ${RUN_CONFIG_SECRET_NAME_STAGING} --from-file=RUN_CONFIG.yml=${CONFIG_STAGING_FILE_PATH} -o yaml -n ${CHEMBL_NS_STAGING} --dry-run=client | kubectl apply -f -
+    - cat ${CONFIG_STAGING_FILE_PATH}
+    - echo ${KUBE_NAMESPACE_DEV} ${KUBE_URL_HH} ${KUBE_CLUS_NAME_HX} ${KUBE_USER_HX}
+    - kubectl get pods -n ${KUBE_NAMESPACE_DEV}
+    - sed -i "s~<VERSION>~${CI_COMMIT_SHORT_SHA}~" k8s-deployment.yml
+    - sed -i "s~<DOCKER_IMAGE>~${DOCKER_IMAGE}~" k8s-deployment.yml
+    - sed -i "s~<HTTP_PROXY>~${HTTP_PROXY_HX}~g" k8s-deployment.yaml
+    - sed -i "s~<HTTPS_PROXY>~${HTTPS_PROXY_HX}~g" k8s-deployment.yaml
+    - sed -i "s~<NO_PROXY>~${NO_PROXY_HX_DEFAULT}~g" k8s-deployment.yaml
+    - sed -i "s~<ENV_SECRET_NAME>~${RUN_CONFIG_SECRET_NAME_STAGING}~g" k8s-deployment.yaml
+    - kubectl apply -n ${KUBE_NAMESPACE_DEV} -f k8s-deployment.yml
   
 
 # deploy-dev-hh:

Dockerfile

 FROM node:lts
+ENV ENV_FILE_PATH=${ENV_FILE_PATH:-'/etc/run_config/.env'}
 
 LABEL maintainer="heinzke@ebi.ac.uk"
 
@@ -22,4 +23,4 @@ ENV HOST 0.0.0.0
 
 EXPOSE 3000
 
-ENTRYPOINT [ "npm", "start" ]
+ENTRYPOINT ENV_FILE_PATH=${ENV_FILE_PATH} npm start

k8s-deployment.yml

 apiVersion: apps/v1 
 kind: Deployment
 metadata:
-  name: malaria-front
+  name: lina-web
   labels:
-    app: malaria-front
+    app: lina-web
 spec:
   selector:
     matchLabels:
-      app: malaria-front
+      app: lina-web
       role: master
       tier: frontend
   replicas: 2
   template:
     metadata:
       labels:
-        app: malaria-front
+        app: lina-web
         role: master
         tier: frontend
     spec:
       containers:
-      - name: malaria-front
+      - name: lina-web
         image: <DOCKER_IMAGE>:<VERSION>
         imagePullPolicy: Always
         ports:
         - containerPort: 3000
-      imagePullSecrets:
-      - name: malaria-frontend-registry
+        volumeMounts:
+          - name: run-config
+            mountPath: '/etc/run_config/'
+            readOnly: true
+        env:
+          - name: HTTP_PROXY
+            value: "<HTTP_PROXY>"
+          - name: http_proxy
+            value: "<HTTP_PROXY>"
+          - name: HTTPS_PROXY
+            value: "<HTTPS_PROXY>"
+          - name: https_proxy
+            value: "<HTTPS_PROXY>"
+          - name: NO_PROXY
+            value: "<NO_PROXY>"
+          - name: no_proxy
+            value: "<NO_PROXY>"
+      volumes:
+        - name: run-config
+          secret:
+            secretName: <ENV_SECRET_NAME>
+
 ---
 apiVersion: v1
 kind: Service