Merge pull request #172 from julianu/master

- automatic docker build
- removing deprecated cached compiler

.github/workflows/maven-build.yml

@@ -52,8 +52,43 @@ jobs:
       with:
         path: |
           staging/*.zip
-          staging/*.jar
         upload-release-files: true
         release-upload-url: ${{ steps.get_current_release.outputs.upload_url }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  build_and_push_docker:
+    name: Push new Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    needs: build
+    if: ${{ github.repository == 'mpc-bioinformatics/pia' && github.event_name != 'pull_request' }}
+    env:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    steps:
+    - name: Check out the repo
+      uses: actions/checkout@v2
+
+    - name: Log in to Docker Hub
+      uses: docker/login-action@v1
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Build and push the Docker dev image
+      if: ${{ github.event_name == 'push' }}
+      run: |
+        docker build -f ./Dockerfile-dev --tag julianusz/pia:dev ./
+        docker push julianusz/pia:dev
+
+    - name: Build and push the Docker release image
+      if: ${{ github.event_name == 'release' }}
+      run: |
+        version=${{ github.ref }}
+        version=(${version//\// })
+        version=${version[2]}
+        docker build -f ./Dockerfile --tag julianusz/pia:${version} ./
+        docker tag  julianusz/pia:${version} julianusz/pia:latest
+        docker push julianusz/pia:${version}
+        docker push julianusz/pia:latest

.gitignore

@@ -52,5 +52,3 @@ log/
 logs/
 target/
 .idea/
-/docker/
-Dockerfile

Dockerfile

@@ -0,0 +1,25 @@
+FROM eclipse-temurin:8-jre-focal
+
+LABEL MAINTAINERS="Julian Uszkoreit <[email protected]>"\
+      description="Docker image for command line execution of PIA - Protein Inference Algorithms"
+
+# prepare zip and wget
+RUN apt-get update; \
+    apt-get install -y unzip wget; \
+    apt-get clean
+
+#preparing directories
+RUN mkdir -p /data/in; mkdir -p /data/out; mkdir -p /opt/pia;
+
+# download latest PIA zip and uncompress
+RUN cd /opt/pia; \
+    curl -s https://api.github.com/repos/mpc-bioinformatics/pia/releases/latest | grep -oP '"browser_download_url": "\K(.*pia.*.zip)(?=")' | wget -qi - -O pia.zip; \
+    unzip pia.zip; \
+    rm pia.zip; \
+    mv pia*.jar pia.jar;
+
+# cleanup
+RUN apt-get remove -y unzip wget;
+
+ENTRYPOINT ["java", "-jar", "/opt/pia/pia.jar"]
+CMD ["--help"]

Dockerfile-dev

@@ -0,0 +1,34 @@
+# the building container
+FROM maven:3-eclipse-temurin-8 AS builder
+
+RUN mkdir -p /tmp/pia
+COPY . /tmp/pia/
+RUN mvn -f /tmp/pia/pom.xml -Dmaven.test.skip --settings /tmp/pia/.mvn/unblock-mirrors.xml package
+
+
+# start the real container
+FROM eclipse-temurin:8-jre-focal
+
+LABEL MAINTAINERS="Julian Uszkoreit <[email protected]>"\
+      description="Docker image for command line execution of PIA - Protein Inference Algorithms"
+
+# prepare zip and wget
+RUN apt-get update; \
+    apt-get install -y unzip wget; \
+    apt-get clean
+
+#preparing directories
+RUN mkdir -p /data/in; mkdir -p /data/out; mkdir -p /opt/pia;
+
+# copy just build PIA zip and uncompress
+COPY --from=builder /tmp/pia/target/pia*.zip /opt/pia/pia.zip
+RUN cd /opt/pia; \
+    unzip pia.zip; \
+    rm pia.zip; \
+    mv pia*.jar pia.jar;
+
+# cleanup
+RUN apt-get remove -y unzip wget;
+
+ENTRYPOINT ["java", "-jar", "/opt/pia/pia.jar"]
+CMD ["--help"]

pom.xml

@@ -4,7 +4,7 @@
 
 	<groupId>de.mpc.pia</groupId>
 	<artifactId>pia</artifactId>
-	<version>1.4.0</version>
+	<version>1.4.1</version>
 	<name>PIA - Protein Inference Algorithms</name>
 	<url>https://github.com/mpc-bioinformatics/pia</url>
 
@@ -51,11 +51,10 @@
 		<xtandem-parser.version>1.13.0</xtandem-parser.version>
 		<compomics-utilities.version>5.0.24</compomics-utilities.version>
 		<biojava-ontology.version>4.2.8</biojava-ontology.version>
-		<gson.version>2.8.1</gson.version>
+		<gson.version>2.8.2</gson.version>
 		<picocli.version>4.6.1</picocli.version>
 		<sqlite4java.version>1.0.392</sqlite4java.version>
 		<sqlite-jdbc.version>3.20.1</sqlite-jdbc.version>
-		<ehcache.version>3.1.1</ehcache.version>
 		<xercesImpl.version>2.12.0</xercesImpl.version>
 
 		<!-- these are "internal" dependencies, the jar files are delivered together with the source -->
@@ -237,12 +236,6 @@
 		</dependency>
 		<!-- End SQlite support for MSF files -->
 
-		<dependency>
-			<groupId>org.ehcache</groupId>
-			<artifactId>ehcache</artifactId>
-			<version>${ehcache.version}</version>
-		</dependency>
-
 		<!--  needed by some testcases and testscenarios -->
 		<dependency>
 			<groupId>xerces</groupId>