[redcap] new module #8214
Workflow file for this run
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| name: LORIS Test Suite | |
| on: | |
| - push | |
| - pull_request | |
| jobs: | |
| buildjs: | |
| env: | |
| EEG_VIS_ENABLED: 'true' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install EEG package dependencies | |
| # We only need to install protobuf-compiler | |
| # Other deps were added to fix an apt dependency issue introduced by a new github Ubuntu image | |
| # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md) | |
| # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images. | |
| run: | | |
| sudo apt install -y imagemagick-6-common libmagickcore-6.q16-6 libmagickwand-6.q16-6 \ | |
| libprotobuf-dev libprotobuf23 libprotoc23 protobuf-compiler | |
| cd modules/electrophysiology_browser/jsx/react-series-data-viewer/ | |
| protoc protocol-buffers/chunk.proto --js_out=import_style=commonjs,binary:./src/ | |
| - name: Install npm modules | |
| run: npm ci | |
| - name: Compile LORIS javascript | |
| run: npm run compile | |
| - name: Create LORIS JS tarball | |
| run: tar cfvz lorisjs.tar.gz htdocs/js/components/ modules/*/js/* | |
| - name: Create node_modules tarball | |
| run: tar cfvz node_modules.tar.gz node_modules | |
| - uses: actions/upload-artifact@v4 | |
| name: Upload node_modules artifact | |
| with: | |
| name: node_modules | |
| path: node_modules.tar.gz | |
| - uses: actions/upload-artifact@v4 | |
| name: Upload lorisjs.tar.gz artifact | |
| with: | |
| name: lorisjs | |
| path: lorisjs.tar.gz | |
| buildphp: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| php: ['8.3'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup PHP | |
| uses: shivammathur/setup-php@v2 | |
| with: | |
| php-version: ${{ matrix.php }} | |
| extensions: zip, php-ast | |
| - name: Validate composer.json and composer.lock | |
| run: composer validate | |
| - name: Cache Composer packages | |
| id: composer-cache | |
| run: echo "::set-output name=dir::$(composer config cache-files-dir)" | |
| - name: Composer cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ steps.composer-cache.outputs.dir }} | |
| key: ${{ runner.os }}-composer-${{ hashFiles('composer.lock') }} | |
| restore-keys: ${{ runner.os }}-composer- | |
| - name: Install composer dependencies | |
| if: steps.composer-cache.outputs.cache-hit != 'true' | |
| run: composer install --prefer-dist --no-progress --no-suggest | |
| - name: Create vendor tarball | |
| run: tar cfvz vendor-php${{matrix.php}}.tar.gz vendor | |
| - uses: actions/upload-artifact@v4 | |
| name: Upload vendor-php${{matrix.php}}.tar.gz artifact | |
| with: | |
| name: vendor-php${{matrix.php}} | |
| path: vendor-php${{matrix.php}}.tar.gz | |
| api: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - buildjs | |
| - buildphp | |
| env: | |
| DB_DATABASE: LorisTest | |
| DB_USER: SQLTestUser | |
| DB_PASSWORD: TestPassword | |
| LORIS_DB_CONFIG: project/config.xml | |
| DOCKER_WEB_SERVER: http://localhost:8000/ | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| php: ['8.3'] | |
| apiversion: ['v0.0.3', 'v0.0.4-dev'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # Cache node_modules to avoid downloading dependencies if already cached | |
| - name: Cache node_modules | |
| uses: actions/cache@v3 | |
| with: | |
| path: node_modules | |
| key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }} | |
| restore-keys: | | |
| ${{ runner.os }}-node- | |
| # Download and extract compiled LORIS JavaScript artifact (from build job) | |
| - name: Download compiled LORIS javascript artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: lorisjs | |
| path: . | |
| - uses: actions/download-artifact@v4 | |
| name: Download PHP dependencies artifact | |
| with: | |
| name: vendor-php${{matrix.php}} | |
| path: . | |
| - name: Extract compiled JS | |
| run: tar xfvz lorisjs.tar.gz | |
| - name: Extract composer vendor directory | |
| run: tar xfvz vendor-php${{matrix.php}}.tar.gz | |
| - name: Generate VERSION file | |
| run: make VERSION | |
| - name: Setup project/ directory | |
| run: | | |
| mkdir -p project/instruments | |
| cp test/config.xml project/config.xml | |
| cp test/test_instrument/NDB_BVL_Instrument_testtest.class.inc project/instruments/ | |
| cp -r raisinbread/instruments/* project/instruments/ | |
| sed -i 's/<sandbox>1<\/sandbox>/<sandbox>0<\/sandbox>/g' project/config.xml | |
| sed -i 's/<adminUser>SQLTestUser<\/adminUser>/<adminUser>root<\/adminUser>/g' project/config.xml | |
| sed -i 's/<adminPassword>TestPassword<\/adminPassword>/<adminPassword>root<\/adminPassword>/g' project/config.xml | |
| sed -i 's/<host>db<\/host>/<host>localhost<\/host>/g' project/config.xml | |
| cat project/config.xml | |
| - name: Set up MySQL | |
| run: | | |
| sudo /etc/init.d/mysql start | |
| mysql -e 'CREATE DATABASE ${{ env.DB_DATABASE }};' -uroot -proot | |
| mysql -e "CREATE USER '${{env.DB_USER}}'@'localhost' IDENTIFIED BY '${{env.DB_PASSWORD}}'" -uroot -proot | |
| mysql -e "GRANT UPDATE,INSERT,SELECT,DELETE,CREATE TEMPORARY TABLES ON ${{env.DB_DATABASE}}.* TO '${{env.DB_USER}}'@'localhost'" -uroot -proot | |
| - name: Source default schema and Raisinbread | |
| run: | | |
| mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-00-schema.sql | |
| mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-01-Modules.sql | |
| mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-02-Permission.sql | |
| mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-03-ConfigTables.sql | |
| mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-04-Help.sql | |
| mysql ${{ env.DB_DATABASE}} -uroot -proot < SQL/0000-00-05-ElectrophysiologyTables.sql | |
| find raisinbread/instruments/instrument_sql -name *.sql -not -name 9999-99-99-drop_instrument_tables.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \; | |
| find raisinbread/RB_files/ -name *.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \; | |
| - name: Source instrument schemas | |
| run: | | |
| find raisinbread/instruments/instrument_sql -name 0000-*.sql -exec sh -c "echo Sourcing {}; mysql ${{ env.DB_DATABASE}} -uroot -proot < {}" \; | |
| echo Sourcing test/test_instrument/testtest.sql | |
| mysql ${{ env.DB_DATABASE}} -uroot -proot < test/test_instrument/testtest.sql | |
| - name: Set LORIS base path | |
| run: | | |
| echo UPDATE Config SET VALUE=\'`pwd`/\' WHERE ConfigID IN \(SELECT ID FROM ConfigSettings WHERE Name=\'base\'\) | |
| echo UPDATE Config SET VALUE=\'`pwd`/\' WHERE ConfigID IN \(SELECT ID FROM ConfigSettings WHERE Name=\'base\'\) | mysql ${{env.DB_DATABASE}} -uroot -proot | |
| - name: Setup PHP | |
| uses: shivammathur/setup-php@v2 | |
| with: | |
| php-version: ${{ matrix.php }} | |
| extensions: zip, php-ast | |
| - name: Start PHP Web Server | |
| run: php -S localhost:8000 -t htdocs/ htdocs/router.php 2>error_log & | |
| - name: Test server | |
| run: | | |
| sleep 1 | |
| curl -v http://localhost:8000 | |
| - name: Run Test Suite | |
| run: | | |
| vendor/bin/phpunit --configuration test/phpunit.xml --testsuite LorisAPITests --group api-${{ matrix.apiversion }} | |
| - name: Print Error Logs | |
| if: always() | |
| run: cat error_log | |
| docker: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| testsuite: ['integration'] | |
| php: ['8.3'] | |
| ci_node_index: [0,1,2,3] | |
| include: | |
| # add a variable but do not display it in the job's name | |
| - ci_node_total: 4 | |
| - testsuite: 'static' | |
| php: '8.3' | |
| - testsuite: 'unit' | |
| php: '8.3' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup PHP | |
| uses: shivammathur/setup-php@v2 | |
| with: | |
| php-version: ${{ matrix.php }} | |
| extensions: zip, php-ast | |
| - name: Validate composer.json and composer.lock | |
| run: composer validate | |
| - name: Cache Composer packages | |
| id: composer-cache | |
| run: echo "::set-output name=dir::$(composer config cache-files-dir)" | |
| - name: Composer cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ steps.composer-cache.outputs.dir }} | |
| key: ${{ runner.os }}-composer-${{ hashFiles('composer.lock') }} | |
| restore-keys: ${{ runner.os }}-composer- | |
| - name: Change PHP Version in Dockerfile | |
| run: sed -i "s/8.0/${{ matrix.php }}/g" Dockerfile.test.php8 | |
| - name: Install package dependencies | |
| # We only need to install protobuf-compiler | |
| # Other deps were added to fix an apt dependency issue introduced by a new github Ubuntu image | |
| # (see https://github.com/actions/runner-images/blob/releases/ubuntu22/20230305/images/linux/Ubuntu2204-Readme.md) | |
| # that updated the list of installed apt packages/apt repositories. That issue may disappear in future Ubuntu images. | |
| run: | | |
| sudo apt install -y imagemagick-6-common libmagickcore-6.q16-6 libmagickwand-6.q16-6 \ | |
| libprotobuf-dev libprotobuf23 libprotoc23 protobuf-compiler | |
| cd modules/electrophysiology_browser/jsx/react-series-data-viewer/ | |
| protoc protocol-buffers/chunk.proto --js_out=import_style=commonjs,binary:./src/ | |
| - name: Install composer dependencies | |
| if: steps.composer-cache.outputs.cache-hit != 'true' | |
| run: composer install --prefer-dist --no-progress --no-suggest | |
| - name: Build LORIS | |
| run: make dev | |
| - name: Run Test Suite | |
| run: | | |
| # set sandbox to 1 before running the tests | |
| # since some tests only run in sandbox environments | |
| sed -i 's/<sandbox>0<\/sandbox>/<sandbox>1<\/sandbox>/g' test/config.xml | |
| npm run tests:${{ matrix.testsuite }} | |
| env: | |
| # Specifies how many jobs you would like to run in parallel, | |
| CI_NODE_TOTAL: ${{ matrix.ci_node_total }} | |
| # Use the index from matrix as an environment variable | |
| CI_NODE_INDEX: ${{ matrix.ci_node_index }} |