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Merge pull request #739 from OpenKnowledgeMaps/database-migration
Database migration
2 parents 585db25 + 5f6a52f commit a516b1b

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‎.gitignore‎

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server/preprocessing/other-scripts/.Rhistory
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server/preprocessing/other-scripts/renv
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/nbproject/private/
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/server/nbproject/private/
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*_local.*
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vis/images/*.pdf
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node_modules/
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dist/
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.idea/
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/config.js
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*__pycache__*
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.pytest_cache
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.cache
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.Rhistory
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.ipynb_checkpoints
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*.ipynb
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.Rprofile
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.Rproj*
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coverage/
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# local deployment files
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/lc_cache.json
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/linkedcat.sqlite
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.env
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*.env
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.Rproj.user
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backend_*.sh
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server/workers/tests/*.csv
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server/workers/tests/*.txt
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server/workers/tests/testutils/
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# PHP dev env files
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# php files
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/server/classes/headstart/vendor
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/server/classes/headstart/var/*
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/server/classes/headstart/vendor/*
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# R files
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server/preprocessing/other-scripts/.Rhistory
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server/preprocessing/other-scripts/renv
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.Rhistory
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.Rprofile
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.Rproj*
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.Rproj.user
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# python files
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*.pyc
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*.pkl
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.ipynb_checkpoints
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*.ipynb
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/nbproject/private/
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/server/nbproject/private/
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.pytest_cache
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*__pycache__*
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# python files
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*.pyc
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*.pkl
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.ipynb_checkpoints
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*.ipynb
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/nbproject/private/
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/server/nbproject/private/
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.pytest_cache
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*__pycache__*

‎docker-compose-end2endtest.yml‎

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# docker-compose-end2endtest.yml
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version: '3.7'
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services:
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end2endtest:
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build:
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context: ./server/workers/tests
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dockerfile: ./Dockerfile_tests
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container_name: end2endtest
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hostname: "end2endtest"
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environment:
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POSTGRES_USER: "testuser"
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POSTGRES_PASSWORD: "testpassword"
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POSTGRES_HOST: "test_db"
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POSTGRES_PORT: 5432
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DEFAULT_DATABASE: "testdb"
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SERVICE_VERSION: "test_version"
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ports:
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- "0.0.0.0:5000:5000"
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volumes:
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- ./server/:/app
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depends_on:
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- db
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- backend
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restart: "no"
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entrypoint: [ "pytest", '/app/workers/tests/test_end2end.py', '-s', '-rfA']
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networks:
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test:
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ipv4_address: 172.18.0.2
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backend:
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container_name: backend
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hostname: "backend"
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build:
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context: ./server/workers/tests
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dockerfile: ./Dockerfile_backend
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volumes:
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- ./server/:/var/www/html/server
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restart: "no"
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networks:
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test:
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ipv4_address: 172.18.0.3
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ports:
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- "80:80"
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db:
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container_name: test_db
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image: 'postgres:12.2-alpine'
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restart: "no"
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hostname: "db_server"
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environment:
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POSTGRES_USER: "testuser"
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POSTGRES_PASSWORD: "testpassword"
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POSTGRES_HOST: "db_server"
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POSTGRES_PORT: 5432
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DEFAULT_DATABASE: "testdb"
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command: postgres -c config_file=/etc/postgresql.conf -c hba_file=/etc/pg_hba.conf
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volumes:
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# - db_data:/var/lib/postgresql/data
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- ./server/workers/tests/test_data/pg_hba_test_local.conf:/etc/pg_hba.conf
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- ./server/workers/tests/test_data/postgresql_test_local.conf:/etc/postgresql.conf
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ports:
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- "5432:5432"
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networks:
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test:
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ipv4_address: 172.18.0.4
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volumes:
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db_data:
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networks:
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test:
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driver: bridge
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ipam:
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config:
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- subnet: 172.18.0.0/16
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gateway: 172.18.0.1

‎docker-compose-phptest.yml‎

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# docker-compose-phptest.yml
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version: '3.7'
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services:
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composer:
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image: composer:2.5.8
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environment:
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- COMPOSER_CACHE_DIR=/app/var/cache/composer
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volumes:
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- ./server/classes/headstart:/app
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restart: never
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phpcs:
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image: cytopia/phpcs:latest-php8.0
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restart: never
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volumes:
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- ./server:/data
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working_dir: /data
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phpunit80:
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image: php:8.0-cli
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restart: never
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volumes:
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- ./server/:/app
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working_dir: /app/classes/headstart
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entrypoint: vendor/bin/phpunit
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phpunit82:
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image: php:8.2-cli
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restart: never
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volumes:
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- ./server/classes/headstart:/app
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working_dir: /app
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entrypoint: vendor/bin/phpunit
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‎docker-compose.yml‎

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REDIS_DB: "${REDIS_DB}"
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BEHIND_PROXY: "${BEHIND_PROXY}"
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DEFAULT_DATABASE: "${DEFAULT_DATABASE}"
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DATABASES: "${DATABASES}"
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FLASK_ENV: "${FLASK_ENV}"
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command: ["gunicorn", "--workers", "10", "--threads", "2", "-b", "0.0.0.0:${API_PORT}", "app:app", "--timeout", "300"]
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volumes:
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SERVICE_VERSION: "${SERVICE_VERSION}"
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POSTGRES_USER: "${POSTGRES_USER}"
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POSTGRES_PASSWORD: "${POSTGRES_PASSWORD}"
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POSTGRES_HOST: "${POSTGRES_HOST}"
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POSTGRES_PORT: "${POSTGRES_PORT}"
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POSTGRES_HOSTS: "${POSTGRES_HOSTS}"
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POSTGRES_PORTS: "${POSTGRES_PORTS}"
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BEHIND_PROXY: "${BEHIND_PROXY}"
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DEFAULT_DATABASE: "${DEFAULT_DATABASE}"
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DATABASES: "${DATABASES}"
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FLASK_ENV: "${FLASK_ENV}"
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SSH_AUTH_SOCK: "/run/host-services/ssh-auth.sock"
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command: ["gunicorn", "--workers", "10", "--threads", "2", "-b", "0.0.0.0:${API_PORT}", "app:app", "--timeout", "300"]
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networks:
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- headstart

‎server/classes/headstart/README.md‎

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# How to run PHP unit tests with docker
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On root level of Headstart:
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* Install PHP unit 9 which works for PHP 8.0 and 8.2
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`docker-compose -f docker-compose-phptest.yml run composer require --dev phpunit/phpunit 9 --ignore-platform-reqs`
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* Test that PHPUnit can run for PHP versions 8.0 and 8.2
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```
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docker-compose -f docker-compose-phptest.yml run phpunit80 --version
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docker-compose -f docker-compose-phptest.yml run phpunit82 --version
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```
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Run linting
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```
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docker-compose -f docker-compose-phptest.yml run phpcs ./classes/headstart/persistence/Persistence.php \
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./classes/headstart/persistence/SQLitePersistence.php \
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./services/search.php \
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./services/getLatestRevision.php \
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./services/getLastVersion.php
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```
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Run tests
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```
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docker-compose -f docker-compose-phptest.yml run phpunit80
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docker-compose -f docker-compose-phptest.yml run phpunit82
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```
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‎server/classes/headstart/composer.json‎

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{
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"require-dev": {
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"phpunit/phpunit": "10.3.0"
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}
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}

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