Merge pull request #521 from MD-Anderson-Bioinformatics/buildargs

This pull request merge addresses two main concerns: 1. Send git info to docker build via build arguments 2. Add action to create NG-CHM-Artifacts release - This addresses issue #514 I also refactored other action workflows for clarity.
MD-Anderson-Bioinformatics · Oct 19, 2023 · dd72fb9 · dd72fb9
2 parents a8ea8dc + 605a956
commit dd72fb9
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diff --git a/...create-tag-and-build-NG-CHM-Artifacts.yml → .../workflows/NG-CHM-Artifacts_push_main.yml b/...create-tag-and-build-NG-CHM-Artifacts.yml → .../workflows/NG-CHM-Artifacts_push_main.yml
@@ -1,7 +1,9 @@
 ##
-## GitHub Workflow of 2 sequential jobs:
+##  Create build tag, build artifacts and push to NG-CHM-Artifacts triggered by push to main
 ##
-## 1. make_build_tag
+##  This workflow has two sequential jobs:
+##
+##  1. make_build_tag
 ##
 ##     Adds a incremental build tag to the repo based on:
 ##
@@ -17,7 +19,7 @@
 ##      and the version from CompatibilityManager.js is '2.22.1', the new tag
 ##      will be: 2.22.1-build-5.
 ##
-## 2. build_artifacts
+##  2. build_artifacts
 ##
 ##     Builds all artifacts from Dockerfile and checks them into the 'NG-CHM-Artifacts'
 ##     repo with the same tag as the build tag from the first job.
@@ -33,6 +35,9 @@
 ##     - WebContent/server.app (directory)
 ##
 
+name: NG-CHM-Artifacts tag
+## concurrency group prevents race condition with NG-CHM-Artifacts_release.yml
+concurrency: artifacts
 on:
   push:
     branches:
@@ -42,12 +47,11 @@ on:
 jobs:
   make_build_tag:
     runs-on: ubuntu-22.04
-    name: Creating Build Number Tag
+    name: Tag w/ build number
     strategy:
       max-parallel: 1
     steps:
-      # https://github.com/marketplace/actions/checkout
-      - name: Checkout
+      - name: Checkout commit
         uses: actions/checkout@v3
         with:
           ref: ${{ github.sha }}
@@ -61,7 +65,7 @@ jobs:
           start_string: 'CM.version = '
       # https://github.com/marohrdanz/build-number-tag
       # Output from this step is tag name as 'build_number'.
-      - name: Create Build Number Tag
+      - name: Create build tag
         id: make_tag
         uses: marohrdanz/[email protected]
         with:
@@ -73,16 +77,20 @@ jobs:
       tag_name: ${{ steps.make_tag.outputs.tag_name }}
   build_artifacts:
     runs-on: ubuntu-latest
-    name: Build Artifacts
+    name: NG-CHM-Artifacts tag
     needs: make_build_tag
     strategy:
       max-parallel: 1
     env:
-      Artifacts_REPOSITORY: "MD-Anderson-Bioinformatics/NG-CHM-Artifacts"
+      Artifacts_REPOSITORY: "${{ github.repository_owner }}/NG-CHM-Artifacts"
       Artifacts_BRANCH: "main"
       JAVA_VERSION: 11
     steps:
-      - name: Checkout Tag Created In "Creating Build Number Tag" Job
+      - name: Make git info available for ant build
+        run: |
+          echo "GIT_COMMIT=`echo ${{ github.sha }} | cut -c1-7`" >> $GITHUB_ENV
+          echo "GIT_LATEST_TAG=${{ needs.make_build_tag.outputs.tag_name }}" >> $GITHUB_ENV
+      - name: Checkout build tag
         uses: actions/checkout@v3
         with:
           ref: ${{ needs.make_build_tag.outputs.tag_name }}
@@ -107,14 +115,14 @@ jobs:
         run: |
           cd NGCHM
           ant -f build_ngchmApp.xml
-      - name: Check out Artifacts repo
+      - name: Check out NG-CHM-Artifacts repo
         uses: actions/checkout@v3
         with:
           repository: ${{ env.Artifacts_REPOSITORY }}
           token: ${{ secrets.DQS_DEV_BCB_ACTIONS_TOKEN }}
           ref: ${{ env.Artifacts_BRANCH }}
           path: "./Artifacts"
-      - name: Copy artifacts
+      - name: Copy artifacts to NG-CHM-Artifacts
         run: |
           cd Artifacts
           cp ../NGCHM/ShaidyMapGen.jar shaidymapgen/
@@ -132,7 +140,7 @@ jobs:
           cp -r ../NGCHM/WebContent/ viewer.source/
           echo "Build tag: ${{ needs.make_build_tag.outputs.tag_name }}" > viewer.source/WebContent/build_version.txt
           echo "Git hash: ${{ github.sha }}" >> viewer.source/WebContent/build_version.txt
-      - name: Commit, tag, and push to Artifacts repo
+      - name: Commit, tag, and push to NG-CHM-Artifacts repo
         run: |
           cd Artifacts
           git config --local user.email "[email protected]"
@@ -142,4 +150,5 @@ jobs:
           git push origin ${{ env.Artifacts_BRANCH }}
           git tag ${{ needs.make_build_tag.outputs.tag_name }}
           git push origin ${{ needs.make_build_tag.outputs.tag_name }}
+          echo "::notice::Created tag ${{ needs.make_build_tag.outputs.tag_name }} in ${{ env.Artifacts_REPOSITORY }}"
 
diff --git a/.github/workflows/NG-CHM-Artifacts_release.yml b/.github/workflows/NG-CHM-Artifacts_release.yml
@@ -0,0 +1,119 @@
+##
+##  Build artifacts for NG-CHM-Artifacts triggered by release
+##
+##     Builds all artifacts from Dockerfile, checks them into the 'NG-CHM-Artifacts',
+##     and creates corresponding release.
+##
+##     Artifacts built:
+##
+##     - ShaidyMapGen.jar
+##     - GalaxyMapGen.jar
+##     - GUIBuilderMapGen.jar
+##     - ngchmWidget-min.js
+##     - ngchmEmbed-min.js
+##     - WebContent/ngChmApp.html
+##     - WebContent/server.app (directory)
+##
+
+name: NG-CHM-Artifacts release
+## concurrency group prevents race condition with NG-CHM-Artifacts_push_main.yml
+concurrency: artifacts
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build_artifacts:
+    runs-on: ubuntu-latest
+    name: NG-CHM-Artifacts release
+    strategy:
+      max-parallel: 1
+    env:
+      Artifacts_REPOSITORY: "${{ github.repository_owner }}/NG-CHM-Artifacts"
+      Artifacts_BRANCH: "main"
+      JAVA_VERSION: 11
+    steps:
+      - name: Checkout commit
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.sha }}
+      - name: Make git info available for ant build
+        run: |
+          echo "GIT_COMMIT=`echo ${{ github.sha }} | cut -c1-7`" >> $GITHUB_ENV
+          echo "GIT_LATEST_TAG=${{ github.ref_name }}" >> $GITHUB_ENV
+      # https://github.com/marohrdanz/extract-version-from-file
+      # Output from this step is version from CompatibilityManager as 'version_number'.
+      - name: Get version number
+        id: get_version_number
+        uses: marohrdanz/[email protected]
+        with:
+          file_path: 'NGCHM/WebContent/javascript/CompatibilityManager.js'
+          start_string: 'CM.version = '
+      - name: Set up JDK for java ${{ env.JAVA_VERSION }}
+        uses: actions/setup-java@v3
+        with:
+          java-version: "${{ env.JAVA_VERSION }}"
+          distribution: 'temurin'
+      - name: Build ShaidyMapGen.jar
+        run: |
+          cd NGCHM
+          ant -f build_shaidyRmapgen.xml
+      - name: Build GalaxyMapGen.jar
+        run: |
+          cd NGCHM
+          ant -f build_galaxymapgen.xml
+      - name: Build GUIBuilderMapGen.jar
+        run: |
+          cd NGCHM
+          ant -f build_guibuildermapgen.xml
+      - name: Build NG-CHM standalone files and server.app
+        run: |
+          cd NGCHM
+          ant -f build_ngchmApp.xml
+      - name: Check out NG-CHM-Artifacts repo
+        uses: actions/checkout@v3
+        with:
+          repository: ${{ env.Artifacts_REPOSITORY }}
+          token: ${{ secrets.DQS_DEV_BCB_ACTIONS_TOKEN }}
+          ref: ${{ env.Artifacts_BRANCH }}
+          path: "./Artifacts"
+      - name: Copy artifacts to NG-CHM-Artifacts
+        run: |
+          cd Artifacts
+          cp ../NGCHM/ShaidyMapGen.jar shaidymapgen/
+          cp ../NGCHM/GalaxyMapGen.jar galaxymapgen/
+          cp ../NGCHM/GUIBuilderMapGen.jar guibuildermapgen/
+          cp ../NGCHM/ngchmWidget-min.js viewer.standalone/
+          cp ../NGCHM/ngchmEmbed-min.js viewer.standalone/
+          cp ../NGCHM/WebContent/ngChmApp.html viewer.standalone/
+          echo "Build tag: ${{ github.ref_name }}" > viewer.standalone/build_version.txt
+          echo "Git hash: ${{ github.sha }}" >> viewer.standalone/build_version.txt
+          cp -r ../NGCHM/WebContent/server.app viewer.build/
+          echo "Build tag: ${{ github.ref_name }}" > viewer.build/server.app/build_version.txt
+          echo "Git hash: ${{ github.sha }}" >> viewer.build/server.app/build_version.txt
+          rm -rf ../NGCHM/WebContent/server.app
+          cp -r ../NGCHM/WebContent/ viewer.source/
+          echo "Build tag: ${{ github.ref_name }}" > viewer.source/WebContent/build_version.txt
+          echo "Git hash: ${{ github.sha }}" >> viewer.source/WebContent/build_version.txt
+      - name: Commit, tag, and push to NG-CHM-Artifacts repo
+        run: |
+          cd Artifacts
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          git add .
+          git commit -m "Build from NG-CHM tag ${{ github.ref_name }}"
+          git push origin ${{ env.Artifacts_BRANCH }}
+          git tag ${{ github.ref_name }}
+          git push origin ${{ github.ref_name }}
+      - name: Create a release in NG-CHM-Artifacts repo
+        uses: softprops/action-gh-release@v1
+        with:
+          token: ${{ secrets.DQS_DEV_BCB_ACTIONS_TOKEN }}
+          body: "Version ${{ steps.get_version_number.outputs.version_number }}"
+          repository: ${{ env.Artifacts_REPOSITORY }}
+      - name: Create notice of success 
+        run: |
+          echo "::notice::Created release ${{ steps.get_version_number.outputs.version_number }} in ${{ env.Artifacts_REPOSITORY }}"
+
+
diff --git a/...hub/workflows/build-NGCHMSupportFiles.yml → ...b/workflows/NGCHMSupportFiles_release.yml b/...hub/workflows/build-NGCHMSupportFiles.yml → ...b/workflows/NGCHMSupportFiles_release.yml
@@ -1,9 +1,16 @@
 ##
-##  GitHub Action to build artifacts for NGCHMSupportFiles,
-##  triggered by publishing a release
+##  Build artifacts for NGCHMSupportFiles triggered by release
+##
+##     Builds selected artifacts from Dockerfile, checks them into the 'NGCHMSupportFiles',
+##     and creates corresponding release.
+##
+##     Artifacts built:
+##
+##     - ShaidyMapGen.jar
+##     - ngchmWidget-min.js
 ##
 
-name: Build artifacts for NGCHMSupportFiles
+name: NGCHMSupportFiles release
 on:
   release:
     types: [published]
@@ -12,15 +19,20 @@ on:
 jobs:
   Build-ShaidyMapGen-and-ngchmWdiget-min:
     runs-on: ubuntu-22.04
+    name: NGCHMSupportFiles release
     env:
-      NGCHMSupportFiles_REPOSITORY: 'MD-Anderson-Bioinformatics/NGCHMSupportFiles'
+      NGCHMSupportFiles_REPOSITORY: '${{ github.repository_owner }}/NGCHMSupportFiles'
       NGCHMSupportFiles_BRANCH: 'main'
       JAVA_VERSION: 11
     steps:
-      - name: Check out release tag
+      - name: Checkout commit
         uses: actions/checkout@v3
         with:
-          ref: ${{ github.ref }}
+          ref: ${{ github.sha }}
+      - name: Make git info available for ant build
+        run: |
+          echo "GIT_COMMIT=`echo ${{ github.sha }} | cut -c1-7`" >> $GITHUB_ENV
+          echo "GIT_LATEST_TAG=${{ github.ref_name }}" >> $GITHUB_ENV
       # https://github.com/marohrdanz/extract-version-from-file
       # Output from this step is version from CompatibilityManager as 'version_number'.
       - name: Get version number
@@ -49,7 +61,7 @@ jobs:
           token: ${{ secrets.DQS_DEV_BCB_ACTIONS_TOKEN }}
           ref: ${{ env.NGCHMSupportFiles_BRANCH }}
           path: './NGCHMSupportFiles'
-      - name: Copy artifacts to NGCHMSupportFiles and update NGCHMSupportFiles version
+      - name: Copy artifacts and update NGCHMSupportFiles version
         run: |
           cd NGCHMSupportFiles
           cp ../NGCHM/ShaidyMapGen.jar inst/java
@@ -77,5 +89,8 @@ jobs:
           token: ${{ secrets.DQS_DEV_BCB_ACTIONS_TOKEN }}
           body: "Version ${{ steps.get_version_number.outputs.version_number }}"
           repository: ${{ env.NGCHMSupportFiles_REPOSITORY }}
+      - name: Create notice of success 
+        run: |
+          echo "::notice::Created release ${{ steps.get_version_number.outputs.version_number }} in ${{ env.NGCHMSupportFiles_REPOSITORY }}"
 
 
diff --git a/Dockerfile b/Dockerfile
@@ -22,6 +22,8 @@ RUN mkdir -p ${VIEWER} &&\
 
 # Stage 1: Create Shaidy R MapGen
 FROM ant AS shaidy
+ARG GIT_COMMIT
+ARG GIT_LATEST_TAG
 COPY NGCHM /NGCHM/
 
 ENV SMAPGEN=/artifacts/shaidymapgen
@@ -30,6 +32,8 @@ RUN mkdir -p ${SMAPGEN} &&\
 
 # Stage 2: Create Galaxy MapGen
 FROM ant AS galaxy
+ARG GIT_COMMIT
+ARG GIT_LATEST_TAG
 COPY NGCHM /NGCHM/
 
 ENV GMAPGEN=/artifacts/galaxymapgen
@@ -39,8 +43,9 @@ RUN mkdir -p ${GMAPGEN} &&\
 
 # Stage 3: Create NG-CHM Standalone
 FROM ant AS standalone
+ARG GIT_COMMIT
+ARG GIT_LATEST_TAG
 COPY NGCHM /NGCHM/
-COPY .git /.git/
 
 ENV STANDALONE=/artifacts/standalone
 ENV SERVERAPP=/artifacts/server.app
@@ -56,6 +61,8 @@ RUN mkdir -p ${STANDALONE} &&\
 
 # Stage 4: Create GUIBuilderMapGen
 FROM ant AS builder
+ARG GIT_COMMIT
+ARG GIT_LATEST_TAG
 COPY NGCHM /NGCHM/
 
 ENV BMAPGEN=/artifacts/builder

diff --git a/NGCHM/build_galaxymapgen.xml b/NGCHM/build_galaxymapgen.xml
@@ -10,6 +10,7 @@
     <property name="dir.workspace" value="${dir.buildfile}"/>
     <property name="dir.jarfile" value="."/>
     <property name="mapgen.path" value="${dir.jarfile}/GalaxyMapGen.jar"/>
+    <property environment="env"/>
 
 	<!-- Clean the NGCHM Project -->
     <target name="clean">
@@ -24,22 +25,12 @@
 
 	<!-- Execute the JAVA class to build the GalaxyMapGen JAR-->
 	<target name="create_run_jar" depends="compile">
-		<exec executable="git" outputproperty="commithash">
-			<arg value="rev-parse"/>
-			<arg value="--short"/>
-			<arg value="HEAD"/>
-		</exec>
-		<exec executable="git" outputproperty="latest_tag">
-			<arg value="describe"/>
-			<arg value="--tags"/>
-			<arg value="--abbrev=0"/>
-		</exec>
         <jar destfile="${mapgen.path}" filesetmanifest="mergewithoutmain">
             <manifest>
                 <attribute name="Main-Class" value="mda.ngchm.datagenerator.GalaxyMapGen"/>
                 <attribute name="Class-Path" value="."/>
-                <attribute name="Git-Hash" value="${commithash}"/>
-                <attribute name="Git-Tag" value="${latest_tag}"/>
+                <attribute name="Git-Hash" value="${env.GIT_COMMIT}"/>
+                <attribute name="Git-Tag" value="${env.GIT_LATEST_TAG}"/>
             </manifest>
             <fileset dir="${dir.jarfile}/build/classes">
             	<exclude name="**/WEB-INF/**"/>

diff --git a/NGCHM/build_guibuildermapgen.xml b/NGCHM/build_guibuildermapgen.xml
@@ -10,6 +10,7 @@
     <property name="dir.workspace" value="${dir.buildfile}"/>
     <property name="dir.jarfile" value="."/>
     <property name="mapgen.path" value="${dir.jarfile}/GUIBuilderMapGen.jar"/>
+    <property environment="env"/>
 
 	<!-- Clean the NGCHM Project -->
     <target name="clean">
@@ -24,22 +25,12 @@
 
 	<!-- Execute the JAVA class to build the GUIBuilderMapGen JAR-->
 	<target name="create_run_jar" depends="compile">
-		<exec executable="git" outputproperty="commithash">
-			<arg value="rev-parse"/>
-			<arg value="--short"/>
-			<arg value="HEAD"/>
-		</exec>
-		<exec executable="git" outputproperty="latest_tag">
-			<arg value="describe"/>
-			<arg value="--tags"/>
-			<arg value="--abbrev=0"/>
-		</exec>
         <jar destfile="${mapgen.path}" filesetmanifest="mergewithoutmain">
             <manifest>
                 <attribute name="Main-Class" value="mda.ngchm.datagenerator.HeatmapDataGenerator"/>
                 <attribute name="Class-Path" value="."/>
-                <attribute name="Git-Hash" value="${commithash}"/>
-                <attribute name="Git-Tag" value="${latest_tag}"/>
+                <attribute name="Git-Hash" value="${env.GIT_COMMIT}"/>
+                <attribute name="Git-Tag" value="${env.GIT_LATEST_TAG}"/>
             </manifest>
             <fileset dir="${dir.jarfile}/build/classes">
             	<exclude name="**/WEB-INF/**"/>