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Make sure study ids exist before using them in filter SQL (#11272) #5612

Make sure study ids exist before using them in filter SQL (#11272)

Make sure study ids exist before using them in filter SQL (#11272) #5612

Workflow file for this run

name: Core tests
on: [push, pull_request]
jobs:
build:
name: Setup and Test
runs-on: ubuntu-latest
services:
mysql:
image: mysql:5.7
env:
MYSQL_ROOT_PASSWORD: root
ports:
- 3306
options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=10
steps:
- name: 'Checkout cbioportal repo'
uses: actions/checkout@v2
with:
path: ./cbioportal
- name: 'Set up JDK 21'
uses: oracle-actions/setup-java@v1
with:
website: oracle.com
release: 21
- name: 'Cache Maven packages'
uses: actions/cache@v1
with:
path: ~/.m2
key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
restore-keys: ${{ runner.os }}-m2
- name: 'Setup mysql'
run: |
sudo systemctl start mysql && \
mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< 'SET GLOBAL local_infile=1' && \
mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< 'CREATE DATABASE cgds_test' && \
mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< "CREATE USER 'cbio_user'@'localhost' IDENTIFIED BY 'somepassword'" && \
mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< "GRANT ALL ON cgds_test.* TO 'cbio_user'@'localhost'" && \
mysql --host=127.0.0.1 --port=3306 --user=root --password=root <<< "flush privileges"
- name: 'Copy maven settings'
working-directory: ./cbioportal
run: |
mkdir -p ~/.m2 && \
cp .github/settings.xml ~/.m2
- name: 'Create application.properties'
working-directory: ./cbioportal
run: |
cp src/main/resources/application.properties.EXAMPLE src/main/resources/application.properties
- name: 'Build cBioPortal once without tests'
working-directory: ./cbioportal
run: |
mvn -q -U -Ppublic -DskipTests clean install
- name: 'Build cbioportal with tests'
working-directory: ./cbioportal
run: |
mvn -q -U -Ppublic clean install
- name: 'Run tests separately'
working-directory: ./cbioportal
run: |
mvn -U -Ppublic test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword
- name: 'Run integration tests separately'
working-directory: ./cbioportal
run: |
mvn -U -Ppublic integration-test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword