[GEN-2332] Add workflow to build genome nexus annotator

.github/workflows/README.md

@@ -104,9 +104,22 @@ Only triggers the `lint`, `tests`, `build-container`, `determine-changes` and `i
 
 ## automate_truststore.yml
 
-This workflow will update the Genome nexus truststor file on a schedule and then run the mutation processing AND consortium release steps of the pipeline to make sure the pipeline is workfing with the new truststore.
+This workflow will update the Genome nexus truststore file on a schedule and then run the mutation processing AND consortium release steps of the pipeline to make sure the pipeline is working with the new truststore.
 
 The truststore used in our pipeline to run the genome nexus annotator on MAF data.
 
 For more background on the truststore and troubleshooting, please see:
-[Updating Genome Nexus Annotator and Dependencies](https://sagebionetworks.jira.com/wiki/spaces/APGD/pages/3016687662/Updating+Genome+Nexus+Annotator+and+Dependencies#Updating-the-trust-ssl-file)
+[Updating Genome Nexus Annotator and Dependencies](https://sagebionetworks.jira.com/wiki/spaces/APGD/pages/3016687662/Updating+Genome+Nexus+Annotator+and+Dependencies#Updating-the-trust-ssl-file)
+
+
+## build_genome_nexus_annotator.yml
+
+This workflow will update and build the Genome Nexus `annotator.jar` file from a
+user inputted param: `commit_hash`. This `commit_hash` value comes from pulling from a specific commit in the [genome-nexus-annotation-pipeline](github.com/genome-nexus/genome-nexus-annotation-pipeline).
+
+This workflow runs **on demand** [through triggering the workflow via a pull request to either modify the commit hash or updating something else](https://github.com/Sage-Bionetworks/Genie/actions/workflows/build_genome_nexus_annotator.yml).
+
+After a successful build and upload to the [Genome Nexus Testing folder on synapse](https://www.synapse.org/Synapse:syn70781006), it will run the mutation processing step of the pipeline to annotate the test data. The manual part will be checking the annotated test data after this to make sure the results are expected.
+
+For more background on the `annotator.jar`, validating the annotated results after the build and troubleshooting, please see:
+[Updating Genome Nexus Annotator and Dependencies](https://sagebionetworks.jira.com/wiki/spaces/APGD/pages/3016687662/Updating+Genome+Nexus+Annotator+and+Dependencies#Updating-the-annotator.jar)

.github/workflows/build_genome_nexus_annotator.yml

@@ -0,0 +1,145 @@
+name: Build and Upload Genome Nexus Annotator
+
+on:
+  push:
+    paths:
+      - '.github/workflows/build_genome_nexus_annotator.yml'
+
+env:
+    # versions for dependencies used in annotator.jar build
+    MAVEN_VERSION: '3.9.9'
+    COMMIT_HASH: "2e67ebd08cf7c26bf1f55f2baf4b73ac36531119"
+    JAVA_VERSION: "21"
+    JAVA_DISTRIBUTION: "corretto"
+    # synapse id of the Genome Nexus Testing folder
+    OUTPUT_FOLDER_SYNAPSE_ID: syn70781006
+    # env vars related to testing the annotator.jar
+    PROD_DOCKER: ghcr.io/sage-bionetworks/genie:main
+    SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }}
+    TEST_PROJECT_SYNID: syn7208886
+jobs:
+  build-annotator:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout workflow repo
+        uses: actions/checkout@v4
+
+      - name: Set up Java
+        uses: actions/setup-java@v4
+        with:
+          java-version: ${{ env.JAVA_VERSION }}
+          distribution: ${{ env.JAVA_DISTRIBUTION }}
+
+      - name: Install Maven
+        run: |
+          wget https://archive.apache.org/dist/maven/maven-3/${MAVEN_VERSION}/binaries/apache-maven-${MAVEN_VERSION}-bin.zip
+          unzip apache-maven-${MAVEN_VERSION}-bin.zip
+          echo "$PWD/apache-maven-${MAVEN_VERSION}/bin" >> $GITHUB_PATH
+
+      - name: Install Python & Synapse client
+        run: |
+          python3 -m pip install --upgrade pip
+          pip install synapseclient chardet
+
+      - name: Clone Genome Nexus Annotation Pipeline and check out commit hash
+        run: |
+          git clone https://github.com/genome-nexus/genome-nexus-annotation-pipeline.git
+          cd genome-nexus-annotation-pipeline
+          git checkout ${{ env.COMMIT_HASH }}
+
+      - name: Configure application.properties and log4j.properties to be GENIE-specific
+        run: |
+            cd genome-nexus-annotation-pipeline
+            CONFIG_PATH="annotationPipeline/src/main/resources"
+            mkdir -p "$CONFIG_PATH"
+
+            # Copy example configs first
+            cp "${CONFIG_PATH}/application.properties.EXAMPLE" "${CONFIG_PATH}/application.properties"
+            cp "${CONFIG_PATH}/log4j.properties.EXAMPLE" "${CONFIG_PATH}/log4j.properties"
+
+            # Modify application.properties lines in place
+            sed -i \
+            -e 's|^spring.batch.job.enabled=.*|spring.batch.job.enabled=false|' \
+            -e 's|^spring.jmx.enabled=.*|spring.jmx.enabled=false|' \
+            -e 's|^chunk=.*|chunk=100|' \
+            -e 's|^genomenexus.enrichment_fields=.*|genomenexus.enrichment_fields=annotation_summary,sift,polyphen,my_variant_info|' \
+            -e 's|^genomenexus.isoform_query_parameter=.*|genomenexus.isoform_query_parameter=isoformOverrideSource|' \
+            -e 's|^genomenexus.base=.*|genomenexus.base=https://genie.genomenexus.org/|' \
+            "${CONFIG_PATH}/application.properties"
+
+            # Modify log4j.properties line
+            sed -i \
+            -e 's|^log4j.appender.a.File.*|log4j.appender.a.File=/tmp/genomenexus-logfile.log|' \
+            "${CONFIG_PATH}/log4j.properties"
+
+            echo "[INFO] Application and log configs updated from EXAMPLE files."
+
+      - name: Build annotator.jar (skips tests)
+        run: |
+          cd genome-nexus-annotation-pipeline
+          mvn clean install -DskipTests
+          find . -name annotator.jar
+
+      - name: Upload annotator.jar, application.properties and log4j.properties to Synapse
+        run: |
+          cd genome-nexus-annotation-pipeline
+          # Locate the built JAR dynamically
+          FILE_PATH=$(ls -t annotationPipeline/target/annotationPipeline-*.jar | head -n 1)
+
+          if [ ! -f "$FILE_PATH" ]; then
+            echo "Could not find annotationPipeline JAR under annotationPipeline/target/"
+            echo "Available .jar files:"
+            find annotationPipeline/target -type f -name "*.jar" || true
+            exit 1
+          fi
+
+          echo "Found JAR: $FILE_PATH"
+
+          # Rename to annotator.jar
+          TARGET_PATH="annotationPipeline/target/annotator.jar"
+          cp "$FILE_PATH" "$TARGET_PATH"
+
+          echo "Renamed to: $TARGET_PATH"
+          ls -lh "$TARGET_PATH"
+
+          echo "Uploading to Synapse entity ${{ env.OUTPUT_FOLDER_SYNAPSE_ID }}..."
+
+          synapse login
+
+          # Upload annotator.jar file!
+          synapse store "$TARGET_PATH" --parentid ${{ env.OUTPUT_FOLDER_SYNAPSE_ID }}
+
+          # Upload application and log4j files
+          CONFIG_PATH="annotationPipeline/src/main/resources"
+          synapse store "${CONFIG_PATH}/application.properties" --parentid ${{ env.OUTPUT_FOLDER_SYNAPSE_ID }}
+          synapse store "${CONFIG_PATH}/log4j.properties" --parentid ${{ env.OUTPUT_FOLDER_SYNAPSE_ID }}
+
+  check-annotator-build:
+    needs: build-annotator
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Pull Public Docker Image from GHCR
+      run: |
+        docker pull ${{ env.PROD_DOCKER }}
+
+    - name: Start Docker Container
+      run: |
+        docker run -d --name genie-container \
+            -e SYNAPSE_AUTH_TOKEN="${{ env.SYNAPSE_AUTH_TOKEN }}" \
+            ${{ env.PROD_DOCKER }} \
+            sh -c "while true; do sleep 1; done"
+
+    - name: Run processing on mutation data in test pipeline
+      run: |
+        docker exec genie-container \
+        python3 /root/Genie/bin/input_to_database.py mutation \
+            --project_id ${{ env.TEST_PROJECT_SYNID }} \
+            --genie_annotation_pkg /root/annotation-tools \
+            --createNewMafDatabase
+
+    - name: Stop and Remove Docker Container
+      run: docker stop genie-container && docker rm genie-container