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Add clickhouse development code #341

Add clickhouse development code

Add clickhouse development code #341

name: Integration tests
on: [push, pull_request]
jobs:
build:
name: Integration tests
runs-on: ubuntu-latest
env:
PORTAL_SOURCE_DIR: /home/runner/work/cbioportal/cbioportal/cbioportal
PORTAL_COMPOSE_DIR: /home/runner/work/cbioportal/cbioportal/cbioportal-docker-compose
PORTAL_INFO_DIR: /home/runner/work/cbioportal/cbioportal/portalInfo
steps:
- name: 'Checkout cbioportal repo'
uses: actions/checkout@v2
with:
path: ./cbioportal
- name: 'Install python requirements'
working-directory: ./cbioportal
run: |
sudo apt-get install python3-setuptools && \
pip3 install -U wheel && \
pip3 install -r ./requirements.txt
- name: 'Set up JDK 11'
uses: actions/setup-java@v1
with:
java-version: 11
- name: 'Cache Maven packages'
uses: actions/cache@v1
with:
path: ~/.m2
key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
restore-keys: ${{ runner.os }}-m2
- name: 'Build cbioportal'
working-directory: ./cbioportal
run: |
mvn -DskipTests clean install
- name: 'Checkout cbioportal-docker-compose repo'
uses: actions/checkout@master
with:
repository: cbioportal/cbioportal-docker-compose
path: ./cbioportal-docker-compose
- name: 'Initialize cbioportal-docker-compose'
working-directory: ./cbioportal-docker-compose
run: |
cd ./data && ./init.sh && rm -rf ./studies/* && cd ../config && \
cat $PORTAL_SOURCE_DIR/portal/target/portal/WEB-INF/classes/portal.properties | \
sed 's/db.host=.*/db.host=cbioportal-database:3306/g' | \
sed 's|db.connection_string=.*|db.connection_string=jdbc:mysql://cbioportal-database:3306/|g' \
> portal.properties
- name: 'Start cbioportal-docker-compose'
working-directory: ./cbioportal-docker-compose
run: |
docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml up -d
- name: 'Wait for cbioportal to initialize ...'
id: startup
uses: nev7n/wait_for_response@v1
with:
url: 'http://localhost:8080/api/health'
responseCode: 200
timeout: 900000
interval: 30000
- name: 'TEST - Validate and load study_es_0'
if: steps.startup.conclusion == 'success'
working-directory: ./cbioportal-docker-compose
run: |
$PORTAL_SOURCE_DIR/test/integration/test_load_study.sh
- name: 'TEST - Add OncoKB annotations to study'
if: steps.startup.conclusion == 'success'
working-directory: ./cbioportal
run: |
export PYTHONPATH=$PORTAL_SOURCE_DIR/core/src/main/scripts && \
$PORTAL_SOURCE_DIR/test/integration/integration_test_oncokb_import.sh
- name: 'TEST - Update OncoKB annotations'
if: steps.startup.conclusion == 'success'
working-directory: ./cbioportal-docker-compose
run: |
$PORTAL_SOURCE_DIR/test/integration/test_update_oncokb.sh