Merge origin/master

.github/workflows/deploy.yml

@@ -43,7 +43,7 @@ jobs:
           MAVEN_PASSWORD: ${{ secrets.BSC_GITLAB_MAVEN_REPO }}
 
     - name: Log into the Container registry
-      uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+      uses: docker/login-action@v3
       if: github.ref_type == 'tag'
       with:
         registry: ${{ env.REGISTRY }}
@@ -52,13 +52,13 @@ jobs:
 
     - name: Extract metadata for the Docker image
       id: meta
-      uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+      uses: docker/metadata-action@v3
       if: github.ref_type == 'tag'
       with:
         images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
     - name: Build and push the Docker image
-      uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+      uses: docker/build-push-action@v3
       if: github.ref_type == 'tag'
       with:
         context: .

README.md

@@ -0,0 +1,55 @@
+# beacon-network-backend
+
+###### Jakarta EE Platform 10
+The implementation is developed and deployed on the [WildFly 30.0.0](http://wildfly.org/) server and is based on Jakarta RESTful Web Services 3.0 API ([JAX-RS 3.0](https://jakarta.ee/specifications/restful-ws/3.0/)).
+
+###### Beacon v2 Java implementation
+The implementation uses [Beacon v2 Java beacon-frameworky](https://github.com/elixir-europe/java-beacon-v2.api) model classes.
+
+###### SQL Database
+The Beacon Network Aggregator uses [Jakarta Persistence 3.1](https://jakarta.ee/specifications/persistence/3.1/) for logging.
+The connection is defined in [persistence.xml](https://github.com/elixir-europe/beacon-network-backend/blob/master/src/main/resources/META-INF/persistence.xml).
+Although the Aggregator may be used with any SQL database, it is configured to be used with [PostgreSQL](https://www.postgresql.org/) database
+
+###### Docker Image
+This repository is configured to automatically generate docker images on release tags ('vX.Y.Z').  
+https://github.com/elixir-europe/beacon-network-backend/pkgs/container/beacon-network-backend  
+The image is based on official WildFly image that is extended with PostgreSQL driver and predeployed Beacon Network application.
+There is also a [docker-compose.yaml](https://github.com/elixir-europe/beacon-network-backend/blob/master/docker/docker-compose.yaml) receipe which provides easy deployment.
+
+###### Apache Maven build system
+The build process is based on [Apache Maven](https://maven.apache.org/).
+
+Compiling:
+```shell
+>git clone https://github.com/elixir-europe/beacon-network-backend.git
+>cd beacon-network-backend
+>mvn install
+```
+This must create `beacon-network-v2-x.x.x.war` (**W**eb application **AR**chive) application in the `/target` directory.
+
+###### BSC Maven Repository
+In addition to the provided docker images, artifacts are stored on the Barcelona Supercomputing Center's maven repository:  
+https://inb.bsc.es/maven/es/bsc/inb/ga4gh/beacon-network-v2/0.0.9/beacon-network-v2-0.0.9.war
+
+###### Configuration
+There are three configuration files in the `/BEACON-INF` directory:
+* `configuration.json` - standard beacon configuration file: [beaconConfigurationResponse.json](https://github.com/ga4gh-beacon/beacon-v2/blob/main/framework/json/responses/beaconConfigurationResponse.json)
+* `beacon-info.json` - standard beacon information file: [beaconInfoResponse.json](https://github.com/ga4gh-beacon/beacon-v2/blob/main/framework/json/responses/beaconInfoResponse.json)
+* `beacon-network.json` - Json Array of backed Beacons' endpoints  
+
+The example of the `beacon-network.json`:
+```json
+[
+  "https://beacons.bsc.es/beacon/v2.0.0",
+  "https://ega-archive.org/test-beacon-apis/cineca"
+]
+```
+Note that the **W**eb application **AR**chive (WAR) is just a usual ZIP file so one can edit these configurations manually without the need to rebuild the application.
+
+It is also possible to define external directory for the `beacon-network.json` configuration.
+```bash
+export BEACON_NETWORK_CONFIG_DIR=/wildfly/BEACON-INF
+```
+When the `BEACON_NETWORK_CONFIG_DIR` is set, the aggregator monitors the `$BEACON_NETWORK_CONFIG_DIR/beacon-network.json` to dynamically update the configuration.
+

docker/Dockerfile

@@ -1,3 +1,13 @@
+FROM maven:3.9.5-eclipse-temurin-17-alpine as builder
+
+COPY pom.xml .
+
+RUN mvn dependency:go-offline --no-transfer-progress
+
+COPY src/ /src/
+
+RUN mvn clean install -DskipTests --no-transfer-progress
+
 # Beacon Network 2.0 image
 FROM quay.io/wildfly/wildfly:30.0.0.Final-jdk17
 
@@ -14,7 +24,7 @@ stop-embedded-server" > $JBOSS_HOME/bin/wildfly-config.cli'
 RUN $JBOSS_HOME/bin/jboss-cli.sh --file="$JBOSS_HOME/bin/wildfly-config.cli"
 RUN rm -rf $JBOSS_HOME/standalone/configuration/standalone_xml_history/current/*
 
-ADD ./target/beacon-network-v2-*.war $JBOSS_HOME/standalone/deployments/beacon-network-v2.war
+COPY --from=builder /target/beacon-network-v2-*.war $JBOSS_HOME/standalone/deployments/beacon-network-v2.war
 
 # Expose AJP port
 EXPOSE 8009