Merge branch 'main' of https://github.com/reactome/release-orthoinfer…

…ence

.dockerignore

@@ -0,0 +1,9 @@
+.git
+.github
+
+.dockerignore
+.gitignore
+Dockerfile
+Jenkinsfile
+OrthoinferenceOverview.png
+README.md

.github/workflows/ci.yml

@@ -0,0 +1,92 @@
+name: release-orthoinference ci
+
+on:
+    workflow_dispatch:   
+    pull_request:
+        types:
+            - opened
+            - synchronize  
+    push:
+        branches:
+            - main
+
+permissions:
+    id-token: write
+    contents: read
+
+jobs:
+    lint:
+        if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
+        runs-on: ubuntu-latest
+        env:
+            REPO_DIR : /opt/release-orthoinference
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Run lint
+              run: |
+                docker build --build-arg REPO_DIR="$REPO_DIR" --target setup-env -t lint-image .
+                docker run --name lint-container lint-image
+            
+            - name: Display lint errors
+              if: failure()
+              run: |
+                docker cp lint-container:"$REPO_DIR"/lint.log .
+                while IFS= read -r LINT_MSG; do echo "::warning::${LINT_MSG}"; done < lint.log
+                exit 1
+
+    docker-build:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+
+            - uses: docker/setup-buildx-action@v3
+
+            - uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: Dockerfile
+                tags: tmp-tag
+                outputs: type=docker,dest=/tmp/image.tar
+
+            - uses: actions/upload-artifact@v4
+              with:
+                name: image-artifact
+                path: /tmp/image.tar
+
+    docker-push:
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        needs: docker-build
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/download-artifact@v4
+              with:
+                name: image-artifact
+                path: /tmp
+
+            - id: get-hash
+              run: |
+                FULL_SHA=${{ github.sha }}
+                echo "SHORT_SHA=${FULL_SHA:0:7}" >> $GITHUB_OUTPUT
+            
+            - env:
+                AWS_REGION : us-east-1
+              uses: aws-actions/configure-aws-credentials@v4
+              with:
+                role-to-assume: ${{ vars.AWS_ROLE }}
+                aws-region: ${{ env.AWS_REGION }}
+
+            - id: login-ecr
+              uses: aws-actions/amazon-ecr-login@v2
+              with:
+                registry-type: public
+
+            - env:
+                AWS_REGISTRY: ${{ steps.login-ecr.outputs.registry }}
+                AWS_REGISTRY_ALIAS: k2y5k6e2
+                AWS_REPO: release-orthoinference
+                IMG_TAG: ${{ steps.get-hash.outputs.SHORT_SHA }}
+              run: |
+                docker load --input /tmp/image.tar
+                docker image tag tmp-tag $AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO:$IMG_TAG
+                docker push $AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO:$IMG_TAG

Dockerfile

@@ -0,0 +1,39 @@
+ARG REPO_DIR=/opt/release-orthoinference
+
+
+# ===== stage 1 =====
+FROM maven:3.9.6-eclipse-temurin-11-focal AS setup-env
+
+ARG REPO_DIR
+
+WORKDIR ${REPO_DIR}
+
+COPY . .
+
+SHELL ["/bin/bash", "-c"]
+
+# run lint if container started
+ENTRYPOINT []
+
+CMD mvn -B -q checkstyle:check | \
+    grep -i --color=never '\.java\|failed to execute goal' > lint.log && \
+    exit 1 || \
+    exit 0
+
+
+# ===== stage 2 =====
+FROM setup-env AS build-jar
+
+RUN mvn clean compile assembly:single
+
+
+# ===== stage 3 =====
+FROM eclipse-temurin:11-jre-focal
+
+ARG REPO_DIR
+
+ARG JAR_FILE=target/orthoinference-*-jar-with-dependencies.jar
+
+WORKDIR ${REPO_DIR}
+
+COPY --from=build-jar ${REPO_DIR}/${JAR_FILE} ./target/

Jenkinsfile

@@ -121,16 +121,16 @@ pipeline{
 					utils.cloneOrUpdateLocalRepo("graph-importer")
 
 					dir("graph-importer"){
-						utils.buildJarFile()
+						utils.buildJarFileWithPackage()
 						// This generates the graph database.
 						withCredentials([usernamePassword(credentialsId: 'mySQLUsernamePassword', passwordVariable: 'pass', usernameVariable: 'user')]){
-							sh "java -jar target/GraphImporter-jar-with-dependencies.jar --name ${env.RELEASE_CURRENT_DB} --user $user --password $pass --neo4j /tmp/graph.db"
-							sh "sudo service tomcat7 stop"
+							sh "java -jar target/GraphImporter-exec.jar --name ${env.RELEASE_CURRENT_DB} --user $user --password $pass --neo4j /tmp/graph.db"
+							sh "sudo service tomcat9 stop"
 							sh "sudo service neo4j stop"
 							// This static script adjusts permissions of the graph.db folder and moves it to /var/lib/neo4j/data/databases/.
 							sh "sudo bash ${env.JENKINS_HOME_PATH}/changeGraphDatabase.sh"
 							sh "sudo service neo4j start"
-							sh "sudo service tomcat7 start"
+							sh "sudo service tomcat9 start"
 							sh "rm ${env.JENKINS_HOME_PATH}/changeGraphDatabase.sh"
 						}
 					}
@@ -143,9 +143,9 @@ pipeline{
 				script{
 					utils.cloneOrUpdateLocalRepo("graph-qa")
 					dir("graph-qa"){
-						utils.buildJarFile()
+						utils.buildJarFileWithPackage()
 						withCredentials([usernamePassword(credentialsId: 'neo4jUsernamePassword', passwordVariable: 'pass', usernameVariable: 'user')]){
-							sh "java -jar target/graph-qa-jar-with-dependencies.jar -u $user -p  $pass --verbose"
+							sh "java -jar target/graph-qa-exec.jar -u $user -p  $pass --verbose"
 						}
 					}
 				}

checkstyle.xml

@@ -0,0 +1,9 @@
+<!DOCTYPE module PUBLIC
+        "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
+        "https://checkstyle.org/dtds/configuration_1_3.dtd">
+<module name="Checker">
+    <module name="LineLength">
+        <property name="max" value="150"/>
+    </module>
+    <!-- Add more modules as needed -->
+</module>

pom.xml

@@ -65,7 +65,7 @@
 		<dependency>
 			<groupId>org.reactome.release</groupId>
 			<artifactId>release-common-lib</artifactId>
-			<version>1.2.0</version>
+			<version>2.0.0-SNAPSHOT</version>
 		</dependency>
 
 		<!-- Test dependencies -->
@@ -95,6 +95,13 @@
 		</dependency>
 	</dependencies>
 
+	<repositories>
+		<repository>
+			<id>ossrh</id>
+			<url>https://oss.sonatype.org/content/repositories/snapshots</url>
+		</repository>
+	</repositories>
+
 	<build>
 		<plugins>
 			<!-- sets the Java compiler version targeted by Maven -->
@@ -103,8 +110,8 @@
 				<artifactId>maven-compiler-plugin</artifactId>
 				<version>3.8.1</version>
 				<configuration>
-					<source>1.8</source>
-					<target>1.8</target>
+					<source>11</source>
+					<target>11</target>
 				</configuration>
 			</plugin>
 
@@ -173,6 +180,33 @@
 					</execution>
 				</executions>
 			</plugin>
+
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-checkstyle-plugin</artifactId>
+				<version>3.1.1</version>
+				<dependencies>
+					<!-- This dependency allows Checkstyle to understand Java 11 syntax -->
+					<dependency>
+						<groupId>com.puppycrawl.tools</groupId>
+						<artifactId>checkstyle</artifactId>
+						<version>8.44</version>
+					</dependency>
+				</dependencies>
+				<executions>
+					<execution>
+						<id>checkstyle-check</id>
+						<goals>
+							<goal>check</goal>
+						</goals>
+					</execution>
+				</executions>
+				<configuration>
+					<configLocation>checkstyle.xml</configLocation>
+					<!-- Optional: Set encoding -->
+					<encoding>UTF-8</encoding>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 </project>