ci: add github actions (#1)

.github/workflows/build.yml

@@ -0,0 +1,45 @@
+name: build
+on:
+  push:
+    branches:
+      - "**"
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout github repo
+        uses: actions/checkout@v4
+      - name: Set up JDK 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: 11
+      - name: Build with maven
+        run: >
+          ./mvnw clean install
+      - name: Upload the artifact
+        if: github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v2
+        with:
+          name: query-executor
+
+  sonar:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout github repo
+        uses: actions/checkout@v4
+      - name: Set up JDK 17
+        uses: actions/setup-java@v1
+        with:
+          java-version: 17
+      - name: Run sonarcloud analysis
+        run: >
+          ./mvnw verify sonar:sonar
+          -Dsonar.sources=src/main/scala
+          -Dsonar.tests=src/test/scala
+          -Dsonar.scala.coverage.reportPaths=target/scoverage.xml
+          -Dsonar.host.url=https://sonarcloud.io
+          -Dsonar.organization=aphp
+          -Dsonar.projectKey=aphp_Cohort360-QueryExecutor
+        env:
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

.github/workflows/commitlint.yml

@@ -0,0 +1,27 @@
+name: commitlint
+
+on:
+  pull_request:
+    branches:
+      - 'main'
+
+jobs:
+  commit-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Install commit-lint
+        run: |
+          npm install --force conventional-changelog-conventionalcommits @commitlint/config-conventional commitlint@latest
+      - name: Validate current commit (last commit) with commitlint
+        if: github.event_name == 'push'
+        run: npx commitlint --from HEAD~1 --to HEAD --verbose
+      - name: Validate PR commits with commitlint
+        if: github.event_name == 'pull_request'
+        run: npx commitlint --from ${{ github.event.pull_request.head.sha }}~${{ github.event.pull_request.commits }} --to ${{ github.event.pull_request.head.sha }} --verbose
+      - name: Validate PR title with commitlint
+        if: github.event_name == 'pull_request'
+        run: |
+          echo "${{github.event.pull_request.title}}" | npx commitlint

.github/workflows/publish.yml

@@ -0,0 +1,49 @@
+name: Publish Docker Image
+
+on:
+  workflow_run:
+    workflows: [ "build" ]
+    types:
+      - completed
+
+jobs:
+  build-and-publish:
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'adopt'
+          java-version: '11'
+
+      - name: Extract version from pom.xml
+        id: extract_version
+        run: |
+          VERSION=$(mvn help:evaluate -Dexpression=project.version -q -DforceStdout)
+          echo "VERSION=$VERSION" >> $GITHUB_ENV
+
+      - name: Download artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: query-executor
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          file: ./Dockerfile
+          push: true
+          tags: "${{ secrets.DOCKER_USERNAME }}/c360-query-executor:${{ env.VERSION }}"

README.md

@@ -1,5 +1,9 @@
 # COHORT REQUESTER / SPARK JOB SERVER
 
+[![Actions Status](https://github.com/aphp/Cohort360-QueryExecutor/workflows/build/badge.svg)](https://github.com/aphp/Cohort360-QueryExecutor/actions)
+[![Coverage Status](https://sonarcloud.io/api/project_badges/measure?project=aphp_Cohort360-QueryExecutor&metric=coverage)](https://sonarcloud.io/component_measures?id=aphp_Cohort360-QueryExecutor&metric=coverage)
+[![Quality Gate](https://sonarcloud.io/api/project_badges/measure?project=aphp_Cohort360-QueryExecutor&metric=alert_status)](https://sonarcloud.io/dashboard?id=aphp_Cohort360-QueryExecutor)
+
 The Cohort Requester is a spark application server for querying FHIR data with a set of criteria and return a count or list of patients that match the criteria. 
 
 ## Quick Start

pom.xml

@@ -38,7 +38,7 @@
     <snapshot.name>SNAPSHOT</snapshot.name>
     <compiler.plugin.version>3.6.2</compiler.plugin.version>
     <scoverage.plugin.version>1.4.11</scoverage.plugin.version>
-    <jacoco-maven-plugin.version>0.8.8</jacoco-maven-plugin.version>
+    <jacoco-maven-plugin.version>0.8.12</jacoco-maven-plugin.version>
 
   </properties>
 

src/main/scala/fr/aphp/id/eds/requester/query/resolver/rest/RestFhirResolver.scala

@@ -142,7 +142,7 @@ class RestFhirResolver(fhirClient: RestFhirClient) extends ResourceResolver {
         val results: Bundle =
           fhirClient.getBundle(
             resourceType,
-            addSourcePopulationConstraint(sourcePopulation, f"_id=${chunk.mkString(",")}"),
+            addSourcePopulationConstraint(sourcePopulation, f"_id=${chunk.sorted.mkString(",")}"),
             getSubsetElementsFilter(resourceQueryColumns.map(c => c.fhirPath))
           )
         getAllPagesOfResource(results, resourceQueryColumns)

src/test/scala/fr/aphp/id/eds/requester/query/resolver/rest/RestFhirResolverTest.scala

@@ -130,7 +130,7 @@ class RestFhirResolverTest extends AnyFunSuiteLike with DatasetComparer {
           restFhirClient,
           "/resolver/restfhir/testCases/withPatientJoinResource/bundle.patient.json",
           FhirResource.PATIENT,
-          "_id=1900536,1566947&_list=1,2,3,4,5,6,7,8,9,10",
+          "_id=1566947,1900536&_list=1,2,3,4,5,6,7,8,9,10",
           List("birthDate", "id")
         )
       },