Merge pull request #7 from TheJacksonLaboratory/feature/docker

Docker, HPO-WEB integration support
TheJacksonLaboratory · Feb 7, 2024 · 41ffc91 · 41ffc91
2 parents 3321b53 + 5c6a3e4
commit 41ffc91
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diff --git a/.github/workflows/network-etl-build-deploy.yml b/.github/workflows/network-etl-build-deploy.yml
@@ -0,0 +1,78 @@
+name: Deploy Graph Container
+on:
+  workflow_dispatch:
+env:
+  GCLOUD_PROJECT_ID: ${{ secrets.GCLOUD_PROJECT_ID }}
+  GCLOUD_REGION: us-east1
+  GCLOUD_GCR: us-docker.pkg.dev
+  GCLOUD_REGISTRY_PROJECT_ID: ${{ secrets.GCLOUD_REGISTRY_PROJECT_ID }}
+  GCLOUD_REGISTRY_IMAGE_ENV: docker
+  GCLOUD_REGISTRY_IMAGE_PROJECT: ontology
+  SERVICE_NAME: ontology-annotation-network
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
+        with:
+          java-version: 17
+          distribution: temurin
+
+      - name: Authenticate to Google Cloud
+        uses: 'google-github-actions/auth@v1'
+        with:
+          credentials_json: '${{ secrets.GCLOUD_SA_KEY }}'
+
+      - name: Setup Google Cloud CLI
+        uses: 'google-github-actions/setup-gcloud@v1'
+      - name: Get project version
+        run: |
+          echo "PROJECT_VERSION=$(mvn help:evaluate -Dexpression=project.version -q -DforceStdout)" >> $GITHUB_ENV
+
+      - name: Maven Verify
+        run: mvn clean package -pl oan-etl -am
+
+      - name: Docker Login
+        run: |
+          gcloud auth configure-docker "${GCLOUD_GCR}"
+
+      - name: Start our builder database container
+        run: |
+          docker pull neo4j:community-bullseye
+          docker run -d --name=builder-neo4j  -p7474:7474 -p7687:7687 -v ./neo4j/data:/data  --env NEO4J_AUTH=neo4j/password neo4j:community-bullseye
+      - name: Fetch our data
+        run: sh oan-etl/update.sh oan-etl/data/
+
+      - name: Load our neo4j data
+        run: |
+          java -jar oan-etl/target/oan-etl-${PROJECT_VERSION}.jar -d=oan-etl/data
+          docker stop builder-neo4j
+
+      - name: Build And Push Docker Image
+        env:
+          TESTCONTAINERS_RYUK_DISABLED: true
+        run: |
+          echo "DOCKER_IMAGE=${GCLOUD_GCR}/${GCLOUD_REGISTRY_PROJECT_ID}/${GCLOUD_REGISTRY_IMAGE_ENV}/${GCLOUD_REGISTRY_IMAGE_PROJECT}/$SERVICE_NAME:PROJECT_VERSION" >> $GITHUB_ENV
+          docker build . --tag=${DOCKER_IMAGE}
+          docker push "${DOCKER_IMAGE}"
+
+      - name: Tag Artifact Registry
+        run: |
+          gcloud artifacts docker tags add "${DOCKER_IMAGE}" "${GCLOUD_GCR}/${GCLOUD_REGISTRY_PROJECT_ID}/${GCLOUD_REGISTRY_IMAGE_ENV}/${GCLOUD_REGISTRY_IMAGE_PROJECT}/$SERVICE_NAME:latest"
+
+      - name: Deploy Cloud Run
+        run: |
+          DOCKER_IMAGE_REPOSITORY=$(docker images --format "{{.Repository}}" | grep ontology-annotation-network-etl)
+          DOCKER_IMAGE=$(docker images --format "{{.Repository}}:{{.Tag}}" "${DOCKER_IMAGE_REPOSITORY}" )
+
+          gcloud run deploy $SERVICE_NAME --quiet \
+            --image "${DOCKER_IMAGE}" --project "${GCLOUD_PROJECT_ID}" \
+            --region "${GCLOUD_REGION}" --platform managed --allow-unauthenticated --format json \
+            --memory 2Gi --cpu 2 --min-instances 1 --max-instances 5 --no-cpu-throttling --ingress internal-and-cloud-load-balancing --service-account "${GCLOUD_SERVICE_ACCOUNT}"
+          
+          echo "Invoke endpoint:"
+          gcloud run services list --platform managed --format json | jq -r \
+            '.[] | select(.metadata.name == "google-cloud-run-maven-test") | .status.address.url'
diff --git a/.github/workflows/network-rest-build-deploy.yml b/.github/workflows/network-rest-build-deploy.yml
@@ -0,0 +1,66 @@
+name: Build Ontology Annotation Network Rest
+on:
+  workflow_dispatch:
+env:
+  GCLOUD_PROJECT_ID: ${{ secrets.GCLOUD_PROJECT_ID }}
+  GCLOUD_REGION: us-east1
+  GCLOUD_GCR: us-docker.pkg.dev
+  GCLOUD_REGISTRY_PROJECT_ID: ${{ secrets.GCLOUD_REGISTRY_PROJECT_ID }}
+  GCLOUD_REGISTRY_IMAGE_ENV: docker
+  GCLOUD_REGISTRY_IMAGE_PROJECT: ontology
+  SERVICE_NAME: ontology-annotation-rest
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
+        with:
+          java-version: 17
+          distribution: temurin
+
+      - name: Authenticate to Google Cloud
+        uses: 'google-github-actions/auth@v1'
+        with:
+          credentials_json: '${{ secrets.GCLOUD_SA_KEY }}'
+
+      - name: Setup Google Cloud CLI
+        uses: 'google-github-actions/setup-gcloud@v1'
+      - name: Get project version
+        run: |
+          echo "PROJECT_VERSION=$(./gradlew properties -q | awk '/^version:/ {print $2}')" >> $GITHUB_ENV
+
+      - name: Maven Verify
+        run: mvn clean package -pl oan-rest -am
+
+      - name: Docker Login
+        run: |
+          gcloud auth configure-docker "${GCLOUD_GCR}"
+      - name: Build And Push Docker Image
+        env:
+          TESTCONTAINERS_RYUK_DISABLED: true
+        run: |
+          echo "DOCKER_IMAGE=${GCLOUD_GCR}/${GCLOUD_REGISTRY_PROJECT_ID}/${GCLOUD_REGISTRY_IMAGE_ENV}/${GCLOUD_REGISTRY_IMAGE_PROJECT}/$SERVICE_NAME:PROJECT_VERSION" >> $GITHUB_ENV
+          cd oan-rest/
+          docker build . --build-arg="VERSION_ARG=${PROJECT_VERSION}" --build-arg="MICRONAUT_ENV_ARG=production" --tag=${DOCKER_IMAGE}
+          docker push "${DOCKER_IMAGE}"
+
+      - name: Tag Artifact Registry
+        run: |
+          gcloud artifacts docker tags add "${DOCKER_IMAGE}" "${GCLOUD_GCR}/${GCLOUD_REGISTRY_PROJECT_ID}/${GCLOUD_REGISTRY_IMAGE_ENV}/${GCLOUD_REGISTRY_IMAGE_PROJECT}/$SERVICE_NAME:latest"
+
+      - name: Deploy Cloud Run
+        run: |
+          DOCKER_IMAGE_REPOSITORY=$(docker images --format "{{.Repository}}" | grep ontology-annotation-network-rest)
+          DOCKER_IMAGE=$(docker images --format "{{.Repository}}:{{.Tag}}" "${DOCKER_IMAGE_REPOSITORY}" )
+
+          gcloud run deploy $SERVICE_NAME --quiet \
+            --image "${DOCKER_IMAGE}" --project "${GCLOUD_PROJECT_ID}" \
+            --region "${GCLOUD_REGION}" --platform managed --allow-unauthenticated --format json \
+            --memory 2Gi --cpu 2 --min-instances 1 --max-instances 5 --no-cpu-throttling --service-account "${GCLOUD_SERVICE_ACCOUNT}"
+          
+          echo "Invoke endpoint:"
+          gcloud run services list --platform managed --format json | jq -r \
+            '.[] | select(.metadata.name == "google-cloud-run-maven-test") | .status.address.url'
diff --git a/.gitignore b/.gitignore
@@ -15,3 +15,4 @@ out/
 .factorypath
 
 oan-etl/data/
+oan-rest/dependency-reduced-pom.xml
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,10 @@
+# Set up running image
+FROM neo4j:community-bullseye
+
+COPY ./neo4j/data/ /data
+RUN neo4j-admin dbms set-initial-password password
+EXPOSE 7474 7687
+
+CMD ["neo4j", "start", "-d neo4j"]
+
+
diff --git a/README.md b/README.md
@@ -13,20 +13,25 @@ Micronaut 4.1.2
 
 ### Modules
 
+Pre-package modules using
+```
+    ./mvnw clean package -pl <module> -am
+```
+
 #### OAN-ETL
     A ontologyModule to load our graph data which includes phenotypes, diseases, genes, assays. There
     are multiple loaders for the different ontologies that are supported
 
 Running
 
 ```
-    ./gradlew oan-etl:run
+    java -jar oan-etl/target/<jar>
 ```
 
 Testing
 
 ```
-    ./gradlew oan-etl:test
+    ./mvnw clean test -pl oan-etl -am
 ```
 
 #### OAN-REST
@@ -36,11 +41,11 @@ Testing
 Running
 
 ```
-    ./gradlew oan-rest:run
+     java -jar oan-rest/target/<jar>
 ```
 
 Testing
 
 ```
-    ./gradlew oan-rest:test
+     ./mvnw clean test -pl oan-rest -am
 ```
Original file line number	Diff line number	Diff line change
Expand Up		@@ -15,3 +15,4 @@ out/
		.factorypath

		oan-etl/data/
		oan-rest/dependency-reduced-pom.xml