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[biobank] new module #8229

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[biobank] new module

[biobank] new module #8229

Workflow file for this run

.github/workflows/loristest.yml at 9bbffd1
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 }}