build: feat/previews-to-aks

.circleci/config.yml

@@ -6,10 +6,40 @@
 #
 version: 2.1
 
+parameters:
+  GHA_Actor:
+    type: string
+    default: ""
+  GHA_Event:
+    type: string
+    default: ""
+  GHA_Action:
+    type: string
+    default: ""
+  GHA_Meta:
+    type: string
+    default: ""
+
+orbs:
+  slack: circleci/[email protected]
+
+definitions:
+  build_config: &build_config
+    docker:
+    - image: molgenis/ci-build:1.2.3
+    working_directory: ~/repo
+    resource_class: large
+    environment:
+      JVM_OPTS: -Xmx3200m
+      GRADLE_OPTS: "-Dorg.gradle.daemon=false -Dorg.gradle.workers.max=2"
+      TERM: dumb
+
+
+
 jobs:
   build:
     docker:
-      - image: eclipse-temurin:17.0.10_7-jdk-jammy
+      - image: molgenis/ci-build:1.2.3 
 
     working_directory: ~/repo
     resource_class: large
@@ -38,30 +68,6 @@ jobs:
             pwd
             echo "$CIRCLE_WORKING_DIRECTORY"
 
-      - run:
-          name: update package manager
-          command: apt-get update
-
-      - run:
-          name: add packages for docker cli install
-          command: apt-get -y install gnupg lsb-release curl
-
-      - run:
-          name: update packages again
-          command: apt-get update
-
-      - run:
-          name: set repo keys for docker packages
-          command: curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
-
-      - run:
-          name: add repo for docker packages
-          command: echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null
-
-      - run:
-          name: update package manager again
-          command: apt-get update
-
       - run:
           name: Install Docker client
           command: apt-get -y install docker-ce docker-ce-cli containerd.io
@@ -89,7 +95,7 @@ jobs:
       - run:
           name: Build Armadillo and R CICD image
           command: |
-            ./gradlew docker
+            ./gradlew docker ci
             ./docker/bin/prepare.bash ci
 
       - store_artifacts:
@@ -134,6 +140,20 @@ jobs:
                 dockerPush
             fi
 
+      - run:
+          name: deploy preview to Azure
+          command: |
+            if [ "${CIRCLE_BRANCH}" != "master" ]; then
+              export $( cat build/ci.properties | xargs )
+              bash ci/set_kubectl_config-azure.sh
+              bash ci/create_or_update_k8s-azure.sh "preview-armadillo-pr-${CIRCLE_PULL_REQUEST##*/}" ${TAG_NAME} DELETE
+              curl -d "token=${SLACK_TOKEN}" \
+              -d "text=*<${CIRCLE_PULL_REQUEST}|Circle-CI » Armadillo » Armadillo-Service » PR-${CIRCLE_PULL_REQUEST##*/} #${CIRCLE_BUILD_NUM}>*
+              PR Preview available on https://preview-armadillo-pr-${CIRCLE_PULL_REQUEST##*/}.dev.molgenis.org" \
+              -d "channel=C0639V5KTCY" \
+              -X POST https://slack.com/api/chat.postMessage
+            fi
+
       - run:
           name: Make sure all images declared in docker-compose.yml are available and ready
           command: |
@@ -197,8 +217,41 @@ jobs:
             docker images ls
             docker compose rm
 
+  delete-helm-preview:
+    environment:
+      GHA_PREVIEW_NR: << pipeline.parameters.GHA_Meta >>
+
+    docker:
+      - image: molgenis/ci-build:1.2.3 
+
+    working_directory: ~/repo
+    resource_class: large
+
+    steps:
+    - checkout
+    - run:
+        name: delete preview on azure
+        command: |
+          export $( cat build/ci.properties | xargs )
+          bash ci/set_kubectl_config-azure.sh
+          kubectl delete namespace preview-emx2-pr-${GHA_PREVIEW_NR} || true
 
 workflows:
+  version: 2
   build-deploy:
+    unless:
+      equal: ["delete-pr-preview", << pipeline.parameters.GHA_Action >>]
+    jobs:
+    - build:
+      filters:
+        branches:
+          ignore: master
+
+  delete_preview:
+    when:
+      equal: [ "delete-pr-preview", << pipeline.parameters.GHA_Action >> ]
     jobs:
-      - build
+    - delete-helm-preview
+
+
+

.github/workflows/main.yml

@@ -0,0 +1,14 @@
+on:
+  pull_request:
+    types: [ closed ]
+jobs:
+  trigger-circleci:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Trigger CircleCI delete_preview workflow
+        id: "delete-pr-preview"
+        uses: CircleCI-Public/[email protected]
+        with:
+          GHA_Meta: ${{ github.event.number }}
+        env:
+          CCI_TOKEN: ${{ secrets.CCI_PREV_TOKEN }}

build.gradle

@@ -134,6 +134,11 @@ if (version.toString().endsWith('-SNAPSHOT')) {
     imageName = "docker.io/molgenis/molgenis-armadillo-snapshot"
     tagName = "${project.version.toString()}-${ext.hash}"
 }
+task ci(type: WriteProperties) {
+    outputFile file('build/ci.properties')
+    property 'TAG_NAME', tagName
+}
+
 docker {
     name imageName
     tags 'latest', tagName

ci/create_or_update_k8s-azure.sh

@@ -0,0 +1,39 @@
+#this scripts takes arguments
+NAME=$1
+TAG_NAME=$2
+DELETE=$3
+
+echo "Using namespace $NAME"
+echo "Using docker tag_name $TAG_NAME"
+echo "Delete=$DELETE"
+
+REPO=molgenis/molgenis-armadillo
+if [[ $TAG_NAME == *"SNAPSHOT"* ]]; then
+  REPO=molgenis/molgenis-armadillo-snapshot
+fi
+echo "Using repositorie $REPO" 
+
+# delete if exists
+# Create certs from environement
+echo ${CERTDEVMOLGENIS_KEY} | base64 --decode >> /tmp/cert_key 
+echo ${CERTDEVMOLGENIS_PEM} | base64 --decode >> /tmp/cert_pem
+
+# wait for deletion to complete
+kubectl delete namespace $NAME || true
+sleep 15s
+kubectl create namespace $NAME
+kubectl create secret tls "dev.molgenis.org" --key /tmp/cert_key --cert /tmp/cert_pem -n ${NAME}
+
+helm upgrade --install ${NAME} ./helm-chart --namespace ${NAME} \
+--set ingress.hosts[0].paths[0].path=/ \
+--set ingress.hosts[0].paths[0].pathType=ImplementationSpecific \
+--set ingress.hosts[0].host=${NAME}.dev.molgenis.org \
+--set ingress.tls[0].host=${NAME}.dev.molgenis.org \
+--set ingress.tls[0].secretName=dev.molgenis.org \
+--set adminPassword=adminArmadillo! \
+--set image.tag=${TAG_NAME} \
+--set image.pullPolicy=Always \
+
+rm /tmp/cert_key
+rm /tmp/cert_pem
+

ci/set_kubectl_config-azure.sh

@@ -0,0 +1,9 @@
+KUBE_CLUSTER=$1
+KUBE_TOKEN=$2
+
+echo " logging in to azure with service principal and get kube config"
+az login --service-principal --tenant ${AZURE_SP_TENANT} -u ${AZURE_CLIENT_ID} -p ${AZURE_CLIENT_SECRET}
+az aks get-credentials -g ${RESOURCE_GROUP} -n ${RESOURCE_GROUP}
+
+kubectl config set-cluster ${RESOURCE_GROUP}
+kubectl config use-context ${RESOURCE_GROUP}

helm-chart/.helmignore

@@ -0,0 +1,23 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*.orig
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/

helm-chart/Chart.yaml

@@ -0,0 +1,6 @@
+apiVersion: v2
+name: armadillo
+description: A Helm chart for Kubernetes
+type: application
+version: 0.1.0
+appVersion: "1.16.0"

helm-chart/templates/NOTES.txt

@@ -0,0 +1,22 @@
+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range $host := .Values.ingress.hosts }}
+  {{- range .paths }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ $host.host }}{{ .path }}
+  {{- end }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ include "armadillo.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get --namespace {{ .Release.Namespace }} svc -w {{ include "armadillo.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ include "armadillo.fullname" . }} --template "{{"{{ range (index .status.loadBalancer.ingress 0) }}{{.}}{{ end }}"}}")
+  echo http://$SERVICE_IP:{{ .Values.service.port }}
+{{- else if contains "ClusterIP" .Values.service.type }}
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app.kubernetes.io/name={{ include "armadillo.name" . }},app.kubernetes.io/instance={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  export CONTAINER_PORT=$(kubectl get pod --namespace {{ .Release.Namespace }} $POD_NAME -o jsonpath="{.spec.containers[0].ports[0].containerPort}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl --namespace {{ .Release.Namespace }} port-forward $POD_NAME 8080:$CONTAINER_PORT
+{{- end }}

helm-chart/templates/_helpers.tpl

@@ -0,0 +1,62 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "armadillo.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "armadillo.fullname" -}}
+{{- if .Values.fullnameOverride }}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- $name := default .Chart.Name .Values.nameOverride }}
+{{- if contains $name .Release.Name }}
+{{- .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
+{{- end }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "armadillo.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "armadillo.labels" -}}
+helm.sh/chart: {{ include "armadillo.chart" . }}
+{{ include "armadillo.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "armadillo.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "armadillo.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "armadillo.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "armadillo.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}