Add biosimulators compatible docker image

Author: bilalshaikh42

.github/workflows/biosimulations_cd.yml

@@ -0,0 +1,56 @@
+name: Publish simulator to GHCR and BioSimulators
+on:
+  release:
+    types: [published, edited]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      # Checkout out
+      - uses: actions/checkout@v2
+      # Build and push Docker image
+
+      - name: Build and Push Image
+        uses: whoan/docker-build-with-cache-action@v5
+        with:
+          username: ${{ secrets.DOCKER_REGISTRY_USERNAME }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          image_name: vcell/biosimulators_vcell
+          image_tag: ${{ github.event.release.tag_name }}
+          build_extra_args: --build-arg SIMULATOR_VERSION=${{ github.event.release.tag_name }}
+          push_git_tag: false
+          registry: ghcr.io
+          context: .
+          dockerfile: Dockerfile
+
+      # Setup python dependencies
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.x" # Version range or exact version of a Python version to use, using SemVer's version range syntax
+
+      - uses: BSFishy/pip-action@v1
+        with:
+          packages: |
+            fire
+            semver
+
+      - id: tagLatest
+        run: echo ::set-output name=tagLatest::$(python tagLatest.py ${{steps.version.outputs.current}} ${{ github.event.release.tag_name }} )
+
+      - name: Tag the docker image with the latest tag
+        if: ${{steps.tagLatest.outputs.tagLatest=='True'}}
+        run: |
+          docker tag  ghcr.io/virtualcell/biosimulators_vcell::${{ github.event.release.tag_name }}  ghcr.io/virtualcell/biosimulators_vcell:latest 
+          docker push --all-tags ghcr.io/virtualcell/biosimulators_vcell
+
+      # Submit to BioSimulators registry
+      - name: Submit to BioSimulators registry
+        run: |
+          REVISION=$(git rev-parse HEAD)
+          curl \
+            -X POST \
+            -u $${{ secrets.DOCKER_REGISTRY_USERNAME }}:$${{ secrets.DOCKER_REGISTRY_TOKEN }} \
+            -H "Accept: application/vnd.github.v3+json" \
+            https://api.github.com/repos/biosimulators/Biosimulators/issues \
+            -d "{\"labels\": [\"Validate/submit simulator\"], \"title\": \"Submit VCell ${{ github.event.release.tag_name}}\", \"body\": \"---\nid: vcell\nversion: ${{ github.event.release.tag_name }}\nspecificationsUrl: https://raw.githubusercontent.com/${{ github.repository }}/${REVISION}/biosimulators.json\nspecificationsPatch:\n  version: ${{ github.event.release.tag_name }}\n  image:\n    url: ghcr.io/biosimulators/biosimulators_vcell/vcell:${{ github.event.release.tag_name }}\nvalidateImage: true\ncommitSimulator: true\n\n---\"}"

.gitignore

@@ -207,3 +207,4 @@ run_sim.sh
 
 remove_temp.sh
 
+vcell-client/UserDocumentation/originalXML/helpSearchConfig.txt

.gitmodules

@@ -0,0 +1,81 @@
+FROM maven:3.5-jdk-8-alpine as build
+COPY . /app/
+WORKDIR /app
+RUN mvn clean install -DskipTests -Dmaven.test.skip=true --quiet dependency:copy-dependencies
+
+
+# Base OS
+FROM ubuntu:latest
+
+ARG SIMULATOR_VERSION="7.4.0.10"
+
+# metadata
+LABEL \
+    org.opencontainers.image.title="VCell" \
+    org.opencontainers.image.version="${SIMULATOR_VERSION}" \
+    org.opencontainers.image.description="Open-source software package for modeling cell biological systems that is built on a central database and disseminated as a standalone application." \
+    org.opencontainers.image.url="http://vcell.org/" \
+    org.opencontainers.image.documentation="https://vcell.org/support" \
+    org.opencontainers.image.source="https://github.com/virtualcell/vcell" \
+    org.opencontainers.image.authors="BioSimulators Team <[email protected]>" \
+    org.opencontainers.image.vendor="BioSimulators Team" \
+    org.opencontainers.image.licenses="MIT" \
+    base_image="ubuntu:latest" \
+    version="${SIMULATOR_VERSION}" \
+    software="Virtual Cell" \
+    software.version="${SIMULATOR_VERSION}" \
+    about.summary="Open-source software package for modeling cell biological systems that is built on a central database and disseminated as a standalone application." \
+    about.home="http://vcell.org/" \
+    about.documentation="https://vcell.org/support" \
+    about.license_file="https://github.com/virtualcell/vcell/blob/master/license.txt" \
+    about.license="SPDX:MIT" \
+    about.tags="rule-based modeling,kinetic modeling,dynamical simulation,systems biology,BNGL,SED-ML,COMBINE,OMEX" \
+    maintainer="BioSimulators Team <[email protected]>"
+
+RUN apt-get -y update && \
+    apt-get install -y --no-install-recommends curl openjdk-8-jre dnsutils && \
+    apt-get install -y python3 && \
+    apt install -y python3-pip && \
+    mkdir -p /usr/local/app/vcell/lib && \
+    mkdir -p /usr/local/app/vcell/simulation && \
+    mkdir -p /usr/local/app/vcell/installDir && \
+    mkdir -p /usr/local/app/vcell/installDir/python/vcell_cli_utils
+
+# Add linux local solvers only
+ADD ./localsolvers /usr/local/app/vcell/installDir/localsolvers
+ADD ./nativelibs /usr/local/app/vcell/installDir/nativelibs
+COPY ./docker_run.sh /usr/local/app/vcell/installDir/
+
+
+# Declare supported environment variables
+ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES
+
+# Install required python-packages
+COPY ./vcell-cli-utils/ /usr/local/app/vcell/installDir/python/vcell_cli_utils/
+RUN pip3 install -r /usr/local/app/vcell/installDir/python/vcell_cli_utils/requirements.txt
+RUN pip3 install /usr/local/app/vcell/installDir/python/vcell_cli_utils/
+
+# Copy JAR files
+COPY --from=build /app/vcell-client/target/vcell-client-0.0.1-SNAPSHOT.jar \
+     /app/vcell-client/target/maven-jars/*.jar \
+ 	 /app/vcell-core/target/vcell-core-0.0.1-SNAPSHOT.jar \
+     /app/vcell-core/target/maven-jars/*.jar \
+ 	 /app/vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
+     /app/vcell-server/target/maven-jars/*.jar \
+ 	 /app/vcell-vmicro/target/vcell-vmicro-0.0.1-SNAPSHOT.jar \
+     /app/vcell-vmicro/target/maven-jars/*.jar \
+ 	 /app/vcell-oracle/target/vcell-oracle-0.0.1-SNAPSHOT.jar \
+     /app/vcell-oracle/target/maven-jars/*.jar \
+     /app/vcell-admin/target/vcell-admin-0.0.1-SNAPSHOT.jar \
+     /app/vcell-admin/target/maven-jars/*.jar \
+     /app/vcell-cli/target/vcell-cli-0.0.1-SNAPSHOT.jar \
+     /app/vcell-cli/target/maven-jars/*.jar \
+     /app/non-maven-java-libs/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar \
+     /app/non-maven-java-libs/com/oracle/ucp/11.2.0.4/ucp-11.2.0.4.jar \
+     /app/non-maven-java-libs/org/sbml/libcombine/libCombineLinux64/0.2.7/libCombineLinux64-0.2.7.jar \
+     /usr/local/app/vcell/lib/
+RUN  chmod -R 755 /usr/local/app/vcell && chmod +x /usr/local/app/vcell/installDir/docker_run.sh
+
+# Entrypoint
+ENTRYPOINT ["/usr/local/app/vcell/installDir/docker_run.sh"]
+CMD []