Merge pull request #66 from ga4gh/release/0.3.0

Release 0.3.0 into main

.github/workflows/tests.yml

@@ -0,0 +1,140 @@
+name: Standard Tests
+on: [push, pull_request, workflow_dispatch] #workflow_dispatch works only if its active in the main branch
+jobs:
+  Unit-Test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Setting up JDK 12
+      uses: actions/setup-java@v2
+      with:
+        java-version: '12'
+        distribution: 'adopt' #using a specific distribution of jdk12 (AdoptOpenJDK)
+
+    - name: Setting up Gradle
+      uses: gradle/gradle-build-action@v2
+
+    - name: Setting up Gradle Wrapper
+      run: "gradle wrapper"
+
+    - name: Validating Wrapper
+      uses: gradle/wrapper-validation-action@v1
+
+    - name: Setting up the SQLite database and Make
+      run: | 
+        sqlite3 -version
+        make -version
+        make clean-all
+        make sqlite-db-build
+        make sqlite-db-populate-dev-dataset
+
+    - name: Running Tests
+      run: "./gradlew test --tests=org.*"
+
+    - name: After Success Submitting Code Coverage
+      run: | #jacocoTestReport is for testing code coverage, submits the last report to the link
+        ./gradlew jacocoTestReport
+        bash <(curl -s https://codecov.io/bash)
+
+  Docker-Integration-Test:
+    needs: Unit-Test
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Setting up Gradle
+      uses: gradle/gradle-build-action@v2
+
+    - name: Setting Up Docker Buildx #used for caching image layers, improves performance
+      id: buildx
+      uses: docker/setup-buildx-action@v1
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v1
+      with: 
+        username: ${{ secrets.DOCKER_HUB_USERNAME }}
+        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+    - name: Get and Set Version
+      run: |
+        source ci/set-docker-image-version.sh
+        echo "version=${DOCKER_IMG_VER}" >> $GITHUB_ENV
+
+    - name: Build and push
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        builder: ${{ steps.buildx.outputs.name }}
+        file: ./Dockerfile
+        push: true
+        tags: ga4gh/ga4gh-starter-kit-drs:test
+        build-args: VERSION=${{ env.version }}
+        cache-from: type=gha #GitHub Actions Cache Exporter
+        cache-to: type=gha,mode=max
+
+    - name: Running Tests
+      run: |
+        docker run --rm -d --name starter-kit-drs-test-default -p 4500:4500 -p 4501:4501 ga4gh/ga4gh-starter-kit-drs:test
+        docker run --rm -d --name starter-kit-drs-test-custom -p 7000:7000 -p 7001:7001 ga4gh/ga4gh-starter-kit-drs:test --config ./src/test/resources/config/test-config-01.yml
+
+    - name: Gradle Integration Test
+      run: ./gradlew test --tests=integration.*
+
+  Docker-Release:
+    needs: Docker-Integration-Test
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/main' && github.event_name == 'push' #Only runs if pushing to main
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Setting Up Docker Buildx #used for caching image layers, improves performance
+      id: buildx
+      uses: docker/setup-buildx-action@v1
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v1
+      with: 
+        username: ${{ secrets.DOCKER_HUB_USERNAME }}
+        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+    - name: Get and Set Version
+      run: |
+        source ci/set-docker-image-version.sh
+        echo "version=${DOCKER_IMG_VER}" >> $GITHUB_ENV
+    - name: Build and push
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        builder: ${{ steps.buildx.outputs.name }}
+        file: ./Dockerfile
+        push: true
+        tags: ga4gh/ga4gh-starter-kit-drs:${{ env.version }} #Using the correct version as the tag
+        build-args: VERSION=${{ env.version }}
+        cache-from: type=gha #GitHub Actions Cache Exporter
+        cache-to: type=gha,mode=max
+
+  build:
+    name: Create GitHub Release
+    needs: Docker-Integration-Test
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/main' && github.event_name == 'push' #Only runs if pushing to main
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Get and Set Version
+        run: |
+          source ci/set-docker-image-version.sh
+          echo "version=${DOCKER_IMG_VER}" >> $GITHUB_ENV
+
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: v${{ env.version }} #will be v0.2.2 for example
+          release_name: GA4GH Starter Kit - DRS v${{ env.version }}
+          draft: false
+          prerelease: true

.gitignore

@@ -38,3 +38,6 @@ bin
 *.db
 
 gradle.properties
+
+# Mac OS files
+**/.DS_Store

Dockerfile

@@ -2,15 +2,15 @@
 # BUILDER CONTAINER
 ##################################################
 
-FROM openjdk:11.0.10 as builder
+FROM openjdk:11.0.12 as builder
 
 USER root
 
 WORKDIR /usr/src/dependencies
 
 # INSTALL MAKE
-RUN apt update
-RUN apt install build-essential -y
+RUN apt update \
+    && apt install build-essential -y
 
 # INSTALL SQLITE3
 RUN wget https://www.sqlite.org/2021/sqlite-autoconf-3340100.tar.gz \
@@ -22,11 +22,26 @@ RUN wget https://www.sqlite.org/2021/sqlite-autoconf-3340100.tar.gz \
 
 # USER 'make' and 'sqlite3' to create the dev database
 COPY Makefile Makefile
-COPY settings.gradle settings.gradle
-COPY build.gradle build.gradle
 COPY database/sqlite database/sqlite
 RUN make sqlite-db-refresh
 
+##################################################
+# GRADLE CONTAINER
+##################################################
+
+FROM gradle:7.3.3-jdk11 as gradleimage
+
+WORKDIR /home/gradle/source
+
+COPY build.gradle build.gradle
+COPY gradlew gradlew
+COPY settings.gradle settings.gradle
+COPY src src
+
+RUN gradle wrapper
+
+RUN ./gradlew bootJar
+
 ##################################################
 # FINAL CONTAINER
 ##################################################
@@ -40,7 +55,7 @@ ARG VERSION
 WORKDIR /usr/src/app
 
 # copy jar, dev db, and dev resource files
-COPY build/libs/ga4gh-starter-kit-drs-${VERSION}.jar ga4gh-starter-kit-drs.jar
+COPY --from=gradleimage /home/gradle/source/build/libs/ga4gh-starter-kit-drs-${VERSION}.jar ga4gh-starter-kit-drs.jar
 COPY --from=builder /usr/src/dependencies/ga4gh-starter-kit.dev.db ga4gh-starter-kit.dev.db
 COPY src/test/resources/ src/test/resources/
 

README.md

@@ -2,9 +2,9 @@
 
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=flat-square)](https://opensource.org/licenses/Apache-2.0)
 [![Java 11+](https://img.shields.io/badge/java-11+-blue.svg?style=flat-square)](https://www.java.com)
-[![Gradle 6.1+](https://img.shields.io/badge/gradle-6.1+-blue.svg?style=flat-square)](https://gradle.org/)
-[![Travis (.org) branch](https://img.shields.io/travis/ga4gh/ga4gh-starter-kit-drs/master.svg?style=flat-square)](https://travis-ci.org/ga4gh/ga4gh-starter-kit-drs)
-![Codecov](https://img.shields.io/codecov/c/github/ga4gh/ga4gh-starter-kit-drs?style=flat-square)
+[![Gradle 7.3.2+](https://img.shields.io/badge/gradle-7.3.2+-blue.svg?style=flat-square)](https://gradle.org/)
+[![GitHub Actions](https://img.shields.io/github/workflow/status/ga4gh/ga4gh-starter-kit-drs/Standard%20Tests/main)](https://github.com/ga4gh/ga4gh-starter-kit-drs/actions)
+[![Codecov](https://img.shields.io/codecov/c/github/ga4gh/ga4gh-starter-kit-drs?style=flat-square)](https://app.codecov.io/gh/ga4gh/ga4gh-starter-kit-drs)
 
 # GA4GH Starter Kit DRS
 
@@ -35,7 +35,7 @@ docker run -p 4500:4500 ga4gh/ga4gh-starter-kit-drs:latest java -jar ga4gh-start
 
 The service can also be installed locally in cases where docker deployments are not possible, or for development of the codebase. Native installations require:
 * Java 11+
-* Gradle 6.1.1+
+* Gradle 7.3.2+
 * SQLite (for creating the dev database)
 
 First, clone the repository from Github:
@@ -186,5 +186,10 @@ Multiple datasets are currently contained in this repo for development and testi
 
 ## Changelog
 
+### v0.3.0
+* DRS object batch requests
+* Passport support - Passport mediated auth to DRS objects (using Starter Kit implementation of Passports)
+* Auth info - Discover Passport broker(s) and visa(s) for requested controlled access DRS Objects (single object and bulk request)
+
 ### v0.2.2
 * patched log4j dependencies to v2.16.0 to avoid [Log4j Vulnerability](https://www.cisa.gov/uscert/apache-log4j-vulnerability-guidance)

build.gradle

@@ -36,7 +36,7 @@ configurations.all {
 
 archivesBaseName = 'ga4gh-starter-kit-drs'
 group 'org.ga4gh'
-version '0.2.2'
+version '0.3.0'
 
 repositories {
     // Use jcenter for resolving dependencies.
@@ -46,6 +46,9 @@ repositories {
 }
 
 dependencies {
+    compileOnly 'org.projectlombok:lombok:1.18.22'
+    annotationProcessor 'org.projectlombok:lombok:1.18.22'
+
     implementation 'com.google.guava:guava:28.1-jre'
     implementation 'org.springframework.boot:spring-boot-starter-web:2.5.0'
     implementation 'commons-cli:commons-cli:1.4'
@@ -62,8 +65,12 @@ dependencies {
     implementation 'javax.xml.bind:jaxb-api:2.2.8'
     implementation 'org.springdoc:springdoc-openapi-ui:1.2.33'
     implementation 'org.xerial:sqlite-jdbc:3.8.11.2'
+    implementation 'com.auth0:java-jwt:3.19.1'
     implementation 'org.ga4gh:ga4gh-starter-kit-common:0.5.6'
 
+    testCompileOnly 'org.projectlombok:lombok:1.18.22'
+    testAnnotationProcessor 'org.projectlombok:lombok:1.18.22'
+
     testImplementation 'org.testng:testng:7.0.0'
     testImplementation 'org.springframework.boot:spring-boot-starter-test:2.5.0'
     testImplementation 'org.springframework.security:spring-security-test'

ci/set-docker-image-version.sh

@@ -0,0 +1 @@
+export DOCKER_IMG_VER=`cat build.gradle | grep "^version" | cut -f 2 -d ' ' | sed "s/'//g"`