0.3.0 release (develop -> master)

.gitattributes

@@ -0,0 +1,9 @@
+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# Linux start script should use lf
+/gradlew        text eol=lf
+
+# These are Windows script files and should use crlf
+*.bat           text eol=crlf
+

.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 +1,70 @@
+name: KBase User Profile 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:
+
+  user_profile_tests:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - java: '8'
+            mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4'
+          - java: '11'
+            mongo: 'mongodb-linux-x86_64-3.6.23'
+    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
+        env:
+           KBASE_CI_TOKEN: ${{ secrets.KBASE_CI_TOKEN }}
+           KBASE_CI_TOKEN2: ${{ secrets.KBASE_CI_TOKEN2 }}
+        shell: bash
+        run: |
+          export HOMEDIR=`pwd`
+
+          # move to parent dir of homedir to install binaries etc
+          cd ..
+
+          # set up mongo
+          wget -q http://fastdl.mongodb.org/linux/${{matrix.mongo}}.tgz
+          tar xfz ${{matrix.mongo}}.tgz
+          export MONGOD=`pwd`/${{matrix.mongo}}/bin/mongod
+
+          # set up test config
+          cd $HOMEDIR
+          cp -n test.cfg.example test.cfg
+          sed -i "s#^test.mongo-exe-path.*#test.mongo-exe-path=$MONGOD#" test.cfg
+          sed -i "s#^test.admin-token.*#test.admin-token = $KBASE_CI_TOKEN#" test.cfg
+          sed -i "s#^test.usr1-token.*#test.usr1-token = $KBASE_CI_TOKEN2#" test.cfg
+          echo "\ntest.mongo-exe-path=$MONGOD\n" >> test.cfg
+
+      - name: Run tests
+        shell: bash
+        run: ./gradlew test
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.gitignore

@@ -4,3 +4,13 @@ classes
 dist
 /build/
 /bin/
+/.settings/
+/test.cfg
+/.pydevproject
+
+# Ignore Gradle project-specific cache directory
+.gradle
+
+# Ignore Gradle build output directory
+build
+/.classpath

.project

@@ -10,8 +10,30 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.python.pydev.pythonNature</nature>
+		<nature>org.eclipse.buildship.core.gradleprojectnature</nature>
 	</natures>
 </projectDescription>

Dockerfile

@@ -1,26 +1,35 @@
-FROM kbase/kb_jre:latest AS build
-# Multistage Build Setup
-RUN apt-get -y update && apt-get -y install ant git openjdk-8-jdk
-RUN cd /tmp && \
-    git clone https://github.com/kbase/jars
-
-COPY . /tmp/user_profile
-
-# Bypass the makefile, which has perl dependencies, and just use
-# the underlying ant compile and ant buildwar
-RUN cd /tmp/user_profile && \
-    ant compile && \
-    ant buildwar
+FROM kbase/sdkbase2:latest AS build
+
+WORKDIR /tmp/up
+
+# dependencies take a while to D/L, so D/L & cache before the build so code changes don't cause
+# a new D/L
+# can't glob *gradle because of the .gradle dir
+COPY build.gradle gradlew settings.gradle /tmp/up/
+COPY gradle/ /tmp/up/gradle/
+RUN ./gradlew dependencies
+
+# Now build the code
+# copy the deployment dir first since it's unlikely to change often
+COPY deployment/ /kb/deployment
+COPY jettybase /kb/deployment/jettybase
+COPY src /tmp/up/src/
+COPY war /tmp/up/war/
+RUN ./gradlew war
+
+# Build the deployment directory
+ENV DEPL=/kb/deployment/jettybase
+RUN mkdir -p $DEPL/webapps
+RUN cp /tmp/up/build/libs/user_profile.war $DEPL/webapps/ROOT.war
 
 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
 
-COPY deployment/ /kb/deployment/
-COPY jettybase/ /kb/deployment/jettybase/
-COPY --from=build /tmp/user_profile/dist/UserProfileService.war /kb/deployment/jettybase/webapps/ROOT.war
+COPY --from=build /kb/deployment/ /kb/deployment/
 
 # 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) 2014 The KBase Project and its Contributors
+Copyright (c) 2014-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: