Removed log_file datasets and un-hidden json params #187
Workflow file for this run
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| name: Integration Tests | |
| on: | |
| pull_request: # Run on all pull requests | |
| push: | |
| branches: # Run on any push to development or main | |
| - development | |
| - main | |
| schedule: # Run weekly on development and main | |
| - cron: 0 2 * * 1 | |
| branches: development | |
| - cron: 0 2 * * 1 | |
| branches: main | |
| jobs: | |
| build-unittests: | |
| runs-on: ubuntu-20.04 #See pre-installed software at https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md | |
| strategy: | |
| fail-fast: False #Setting so that if one of the test suites fail, the other will continue | |
| matrix: | |
| python-version: [ 3.6 ] | |
| steps: | |
| - uses: actions/checkout@v2 #Checkout the project from git | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Run Unit Tests | |
| run: make unittests | |
| build-irida-integration: | |
| runs-on: ubuntu-20.04 #See pre-installed software at https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md | |
| env: | |
| MYSQL_PORT: 3306 | |
| MYSQL_USER: test | |
| MYSQL_PASSWORD: test | |
| MYSQL_DATABASE: irida_importer_test | |
| MYSQL_HOST: 127.0.0.1 | |
| MYSQL_ROOT_PASSWORD: password | |
| NODE_OPTIONS: "--max-old-space-size=4096" | |
| CONDA_PREFIX: /usr/share/miniconda | |
| strategy: | |
| fail-fast: False #Setting so that if one of the test suites fail, the other will continue | |
| matrix: | |
| branch: ['main','development'] # IRIDA Branches to test against | |
| steps: | |
| - uses: actions/checkout@v2 #Checkout the project from git | |
| - name: Setup MySQL | |
| uses: mirromutth/[email protected] | |
| with: | |
| host port: ${{ env.MYSQL_PORT }} | |
| character set server: 'utf8' | |
| collation server: 'utf8_general_ci' | |
| mysql version: '5.7' | |
| mysql database: ${{ env.MYSQL_DATABASE }} | |
| mysql user: ${{ env.MYSQL_USER }} | |
| mysql password: ${{ env.MYSQL_PASSWORD }} | |
| mysql root password: ${{ env.MYSQL_ROOT_PASSWORD }} #The root superuser password | |
| - name: Verify MySQL connection | |
| timeout-minutes: 10 | |
| run: | | |
| while ! mysqladmin ping -h"${{ env.MYSQL_HOST }}" -P"${{ env.MYSQL_PORT }}" --silent; do | |
| sleep 1 | |
| done | |
| - name: Set up JDK 11 # Installs java 11 | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: 11 | |
| - name: MySQL Setup (SUDO) # Sets ONLY_FULL_GROUP_BY flag and gives runner privileges over database | |
| run: | | |
| sudo mysql -e "SET GLOBAL sql_mode=(SELECT REPLACE(@@sql_mode,'ONLY_FULL_GROUP_BY',''));" -h ${{ env.MYSQL_HOST }} -P ${{ env.MYSQL_PORT }} -p${{ env.MYSQL_ROOT_PASSWORD }}; | |
| sudo mysql -e "CREATE USER '${{ env.MYSQL_USER }}'@'%' IDENTIFIED BY '${{ env.MYSQL_PASSWORD }}'; GRANT ALL ON ${{ env.MYSQL_DATABASE }}.* to '${{ env.MYSQL_USER }}'@'%';" -h ${{ env.MYSQL_HOST }} -P ${{ env.MYSQL_PORT }} -p${{ env.MYSQL_ROOT_PASSWORD }}; | |
| - name: Set up PostgreSQL | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install postgresql libpq-dev | |
| sudo service postgresql start | |
| sudo -u postgres createuser --superuser "$USER" | |
| createdb runner | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: 3.6.7 | |
| activate-environment: __irida_importer_py3.6.7 | |
| - name: Conda info | |
| shell: bash -l {0} | |
| run: conda info | |
| - name: Install conda packages | |
| shell: bash -l {0} | |
| run: | | |
| conda config --add channels defaults | |
| conda config --add channels conda-forge | |
| conda config --add channels bioconda | |
| conda config --add channels iuc | |
| conda install bioblend=0.13.0 oauthlib=3.0.1 requests=2.22.0 requests-oauthlib=1.2.0 simplejson=3.8.1 | |
| - name: Setup galaxy conda env | |
| shell: bash -l {0} | |
| run: conda create --name _galaxy_ python=3.7.6 | |
| - name: Run Integration Tests ${{ matrix.branch }} | |
| timeout-minutes: 60 | |
| run: make integrationtests branch=${{ matrix.branch }} db_host=${{ env.MYSQL_HOST }} db_port=${{ env.MYSQL_PORT }} |