Merge pull request #388 from kbase/dev-gradle

Convert to GHA, fix tests, fix build

.classpath

@@ -1,7 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+		<attributes>
+			<attribute name="module" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="lib" path="/jars/lib/jars/google/guava-18.0.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/apache_commons/commons-io-2.4.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/slf4j/slf4j-api-1.7.25.jar"/>
@@ -43,13 +47,7 @@
 	<classpathentry kind="lib" path="/jars/lib/jars/jna/jna-3.4.0.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/junit/junit-4.12.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/hamcrest/hamcrest-core-1.3.jar"/>
-	<classpathentry kind="lib" path="/jars/lib/jars/equalsverifier/equalsverifier-2.2.2.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/apache_commons/commons-lang3-3.5.jar"/>
-	<classpathentry kind="lib" path="/jars/lib/jars/bytebuddy/byte-buddy-1.6.8.jar"/>
-	<classpathentry kind="lib" path="/jars/lib/jars/bytebuddy/byte-buddy-agent-1.6.8.jar"/>
-	<classpathentry kind="lib" path="/jars/lib/jars/mockito/mockito-core-2.7.10.jar"/>
-	<classpathentry kind="lib" path="/jars/lib/jars/objenesis/objenesis-2.5.1.jar"/>
-	<classpathentry kind="lib" path="/jars/lib/jars/kbase/auth2/kbase-auth2test-0.2.4.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/kbase/workspace/WorkspaceClient-0.8.0.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/kbase/auth/kbase-auth-0.4.4.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/jsemver/java-semver-0.9.0.jar"/>
@@ -59,5 +57,11 @@
 	<classpathentry kind="lib" path="/jars/lib/jars/kbase/common/kbase-common-0.0.25.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/mockserver/mockserver-netty-5.4.1-jar-with-dependencies.jar"/>
 	<classpathentry kind="lib" path="/jars/lib/jars/kafka/kafka-clients-2.1.0.jar"/>
+	<classpathentry kind="lib" path="/jars/lib/jars/kbase/auth2/kbase-auth2-test-shadow-all-0.7.0.jar"/>
+	<classpathentry kind="lib" path="/jars/lib/jars/equalsverifier/equalsverifier-3.1.10.jar"/>
+	<classpathentry kind="lib" path="/jars/lib/jars/bytebuddy/byte-buddy-1.9.10.jar"/>
+	<classpathentry kind="lib" path="/jars/lib/jars/bytebuddy/byte-buddy-agent-1.9.10.jar"/>
+	<classpathentry kind="lib" path="/jars/lib/jars/mockito/mockito-core-3.0.0.jar"/>
+	<classpathentry kind="lib" path="/jars/lib/jars/objenesis/objenesis-2.6.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

.github/codeql.yml

@@ -0,0 +1,52 @@
+name: "Code scanning - action"
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 19 * * 0'
+
+jobs:
+  CodeQL-Build:
+
+    # CodeQL runs on ubuntu-latest and windows-latest
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+      with:
+        # We must fetch at least the immediate parents so that if this is
+        # a pull request then we can checkout the head.
+        fetch-depth: 2
+
+    # If this run was triggered by a pull request event, then checkout
+    # the head of the pull request instead of the merge commit.
+    - run: git checkout HEAD^2
+      if: ${{ github.event_name == 'pull_request' }}
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      # Override language selection by uncommenting this and choosing your languages
+      # with:
+      #   languages: go, javascript, csharp, python, cpp, java
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/dependabot.yml

@@ -0,0 +1,14 @@
+version: 2
+updates:
+- package-ecosystem: docker
+  directory: "/"
+  schedule:
+    interval: weekly
+    time: '11:00'
+  open-pull-requests-limit: 10
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: daily
+    time: '11:00'
+  open-pull-requests-limit: 10

.github/workflows/manual-build.yml

@@ -0,0 +1,11 @@
+---
+name: Manual Build & Push
+on:
+ workflow_dispatch:
+jobs:
+  build-push:
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: br-${{ github.ref_name }}
+    secrets: inherit

.github/workflows/pr_build.yml

@@ -0,0 +1,43 @@
+---
+name: Pull Request Build, Tag, & Push
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+      - master
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+jobs:
+  build-develop-open:
+    if: github.base_ref == 'develop' && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build.yml@main
+    secrets: inherit
+  build-develop-merge:
+    if: github.base_ref == 'develop' && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: pr-${{ github.event.number }},latest
+    secrets: inherit
+  build-main-open:
+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }}
+    secrets: inherit
+  build-main-merge:
+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }},latest-rc
+    secrets: inherit
+  trivy-scans:
+    if: (github.base_ref == 'develop' || github.base_ref == 'main' || github.base_ref == 'master' ) && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_trivy-scans.yml@main
+    secrets: inherit

.github/workflows/release-main.yml

@@ -0,0 +1,25 @@
+---
+name: Release - Build & Push Image
+on:
+  release:
+    branches:
+      - main
+      - master
+    types: [ published ]
+jobs:
+  check-source-branch:
+    uses: kbase/.github/.github/workflows/reusable_validate-branch.yml@main
+    with:
+      build_branch: '${{ github.event.release.target_commitish }}'
+  validate-release-tag:
+    needs: check-source-branch
+    uses: kbase/.github/.github/workflows/reusable_validate-release-tag.yml@main
+    with:
+      release_tag: '${{ github.event.release.tag_name }}'
+  build-push:
+    needs: validate-release-tag
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: '${{ github.event.release.tag_name }},latest'
+    secrets: inherit

.github/workflows/test.yml

@@ -0,0 +1,87 @@
+name: KBase Groups tests
+
+on:
+  pull_request:
+    types:
+    - opened
+    - reopened
+    - synchronize
+    - ready_for_review
+  push:
+    # run workflow when merging to main or develop
+    branches:
+      - main
+      - master
+      - develop
+
+jobs:
+
+  groups_tests:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # the current production setup
+          - java: '8'
+            codecov: true
+            mongo: 'mongodb-linux-x86_64-3.6.13'
+            wired_tiger: 'false'
+            ant_test: 'test'
+          # test all code w/ java 11
+          - java: '11'
+            codecov: true
+            mongo: 'mongodb-linux-x86_64-3.6.13'
+            wired_tiger: 'false'
+            ant_test: 'test'
+          # test the latest 3X version of mongo against just the mongo storage code
+          - java: '11'
+            mongo: 'mongodb-linux-x86_64-3.6.23'
+            wired_tiger: 'true'
+            ant_test: 'test_mongo_storage'
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up java
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: ${{matrix.java}}
+
+      - name: Install dependencies and set up test config
+        shell: bash
+        run: |
+          export HOMEDIR=`pwd`
+
+          # move to parent dir of homedir to install binaries etc
+          cd ..
+          
+          # set up jars
+          git clone https://github.com/kbase/jars
+          export JARSDIR=$(pwd)/jars/lib/jars/
+
+          # set up mongo
+          wget -q http://fastdl.mongodb.org/linux/${{matrix.mongo}}.tgz
+          tar xfz ${{matrix.mongo}}.tgz
+          export MONGOD=`pwd`/${{matrix.mongo}}/bin/mongod
+
+          # set up test config
+          cd $HOMEDIR
+          cp -n test.cfg.example test.cfg
+          sed -i "s#^test.jars.dir.*#test.jars.dir=$JARSDIR#" test.cfg
+          sed -i "s#^test.temp.dir=.*#test.temp.dir=temp_test_dir#" test.cfg
+          sed -i "s#^test.mongo.exe.*#test.mongo.exe=$MONGOD#" test.cfg
+          sed -i "s#^test.mongo.useWiredTiger.*#test.mongo.useWiredTiger=${{matrix.wired_tiger}}#" test.cfg
+          cat test.cfg
+
+      - name: Run tests
+        shell: bash
+        run: |
+          ant ${{matrix.ant_test}}
+
+      - name: Upload coverage to Codecov
+        if: matrix.codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

Dockerfile

@@ -1,14 +1,20 @@
+FROM kbase/sdkbase2 as build
+
+COPY . /tmp/groups
+RUN cd /tmp \
+    && git clone https://github.com/kbase/jars \
+    && cd groups \
+    && ant buildwar
+
 FROM kbase/kb_jre:latest
 
 # These ARGs values are passed in via the docker build command
 ARG BUILD_DATE
 ARG VCS_REF
 ARG BRANCH=develop
 
-RUN apt-get -y update && apt-get -y install ant git openjdk-8-jdk
-
-COPY deployment/ /kb/deployment/
-COPY jettybase/ /kb/deployment/jettybase/
+COPY --from=build /tmp/groups/deployment/ /kb/deployment/
+COPY --from=build /tmp/groups/jettybase/ /kb/deployment/jettybase/
 
 # The BUILD_DATE value seem to bust the docker cache when the timestamp changes, move to
 # the end

LICENSE.md

@@ -1,4 +1,4 @@
-Copyright (c) 2018 The KBase Project and its Contributors
+Copyright (c) 2018-present The KBase Project and its Contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: