[API] Add dicom upload #8187

Workflow file for this run

.github/workflows/loristest.yml at 5656086

	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 }}

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[API] Add dicom upload #8187

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[API] Add dicom upload #8187

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