From 3a37d3deced098538fe61b18d698a65af33d6b15 Mon Sep 17 00:00:00 2001
From: Ruslan Forostianov <ruslan@se4.bio>
Date: Thu, 2 May 2024 10:22:03 +0200
Subject: [PATCH] Run java integration tests with GH workflows

unit tests are already run by maven.yml now
---
 .../java-commands-integration-tests.yml       | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 .github/workflows/java-commands-integration-tests.yml

diff --git a/.github/workflows/java-commands-integration-tests.yml b/.github/workflows/java-commands-integration-tests.yml
new file mode 100644
index 00000000..d69bd26d
--- /dev/null
+++ b/.github/workflows/java-commands-integration-tests.yml
@@ -0,0 +1,46 @@
+name: Run integration tests for java loading commands
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout Code'
+        uses: actions/checkout@v4
+        with:
+          path: ./cbioportal-core
+
+      - name: 'Get the cbioportal db version from pom.xml'
+        working-directory: ./cbioportal-core
+        run: |
+          CBIO_DB_VERSION=$(python -c "import xml.etree.ElementTree as ET; tree = ET.parse('pom.xml'); root = tree.getroot(); ns = {'ns': 'http://maven.apache.org/POM/4.0.0'}; print(root.find('.//ns:cbioportal.version', ns).text)")
+          echo "$CBIO_DB_VERSION=$CBIO_DB_VERSION" | tee -a $GITHUB_ENV
+
+      - name: 'Download cgds.sql with cbioportal db schema of the given version'
+        working-directory: ./cbioportal-core
+        run: |
+          curl -o cgds.sql https://raw.githubusercontent.com/cBioPortal/cbioportal/${{ env.CBIO_DB_VERSION }}/src/main/resources/db-scripts/cgds.sql
+
+      - name: 'Prepare cbioportal db container'
+        working-directory: ./cbioportal-core
+        run: |
+          docker run -p 3306:3306 \
+            -v $(pwd)/src/test/resources/seed_mini.sql:/docker-entrypoint-initdb.d/seed.sql:ro \
+            -v $(pwd)/cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro \
+            -e MYSQL_ROOT_PASSWORD=root \
+            -e MYSQL_USER=cbio_user \
+            -e MYSQL_PASSWORD=somepassword \
+            -e MYSQL_DATABASE=cgds_test \
+            mysql:5.7
+
+      - name: 'Run database-dependent tests'
+        working-directory: ./cbioportal-core
+        run: mvn test -Dtest="**/integrationTest/**/*"
+
+      - name: Set up JDK 21
+        uses: actions/setup-java@v3
+        with:
+          java-version: '21'
+          distribution: 'temurin'
+          cache: maven