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Pilot HDC 1.0
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‎.dockerignore

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# Folders
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.git
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.venv
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.env
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venv
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env
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kubernetes
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# Files
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.DS_Store
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.env.local
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.gitignore
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.gitlab-ci*
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gitlab-ci*
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Dockerfile*
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Jenkinsfile
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*.log

‎.env.example

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# Vault configuration
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# is sensitive/secret
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VAULT_TOKEN=
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# contains defaults but can be overriden
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VAULT_URL=
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VAULT_CRT=
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# Service configuration
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# contains defaults but can be overriden
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CONFIG_CENTER_ENABLED=false
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APP_NAME=bff-cli
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version=2.0.0
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port=5080
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host=0.0.0.0
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OPEN_TELEMETRY_HOST=0.0.0.0
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OPEN_TELEMETRY_PORT=6831
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OPEN_TELEMETRY_ENABLED=false
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LOG_LEVEL_DEFAULT=30
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LOG_LEVEL_FILE=30
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LOG_LEVEL_STDOUT=30
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LOG_LEVEL_STDERR=40
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# is sensitive/secret
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CLI_SECRET=
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# needs to be set (no defaults)
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CLI_PUBLIC_KEY_PATH=
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CORE_ZONE_LABEL=
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GREEN_ZONE_LABEL=
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# Redis
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# contains defaults but can be overriden
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REDIS_HOST=127.0.0.1
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REDIS_DB=0
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REDIS_PORT=6379
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# is sensitive/secret
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REDIS_PASSWORD=
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# Microservices
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# contains defaults but can be overriden
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AUTH_SERVICE=http://127.0.0.1:5061
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UPLOAD_SERVICE_GREENROOM=http://127.0.0.1:5079
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UPLOAD_SERVICE_CORE=http://127.0.0.1:5079
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DOWNLOAD_SERVICE_CORE=http://127.0.0.1:5077
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DOWNLOAD_SERVICE_GREENROOM=http://127.0.0.1:5077
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DATASET_SERVICE=http://127.0.0.1:5081
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HPC_SERVICE=http://127.0.0.1:5080
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KG_SERVICE=http://127.0.0.1:5082
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METADATA_SERVICE=http://127.0.0.1:5065
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PROJECT_SERVICE=http://127.0.0.1:5064
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# External APIs
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# contains defaults but can be overriden
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ATLAS_API=http://127.0.0.1:21000
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# needs to be set (no defaults)
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ATLAS_ADMIN=
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ATLAS_PASSWD=
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ATLAS_ENTITY_TYPE=

‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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*.__pycache__
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# C extensions
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*.so
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.idea
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# Customized
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.vscode/settings.json
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test_seeds
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build
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.DS_Store
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*.__pycache__
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*.logs
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logs
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gunicorn_error.log
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gunicorn_access.log
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.env
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test.py

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.3.0
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hooks:
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- id: check-added-large-files
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- id: check-docstring-first
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- id: check-merge-conflict
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- id: check-toml
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- id: check-yaml
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- id: double-quote-string-fixer
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- id: end-of-file-fixer
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- id: trailing-whitespace
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- repo: https://github.com/psf/black
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rev: 22.8.0
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hooks:
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- id: black
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args: [
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'--line-length=120',
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'--skip-string-normalization',
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]
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- repo: https://github.com/PyCQA/isort
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rev: 5.12.0
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hooks:
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- id: isort
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args: [
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'--line-length=120',
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'--profile=black',
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'--filter-files',
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'--force-single-line-imports',
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'--reverse-relative',
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]
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- repo: https://github.com/PyCQA/flake8
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rev: 5.0.4
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hooks:
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- id: flake8
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additional_dependencies: [
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'pycodestyle==2.9.1', # E,W
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'pyflakes==2.5.0', # F
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'mccabe==0.7.0', # C
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'flake8-bugbear==22.9.11', # B
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'flake8-builtins==1.5.3', # A
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'flake8-comprehensions==3.10.0', # C4
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'flake8-debugger==4.1.2', # T1
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'flake8-logging-format==0.7.5', # G
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'flake8-print==5.0.0', # T2
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]
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args: [
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'--select=E,W,F,C,B,A,C4,T1,G,T2',
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'--ignore=E203,W503,B008,B305,A003,G004',
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'--max-complexity=10',
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'--max-line-length=120',
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]
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- repo: https://github.com/myint/docformatter
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rev: v1.5.0
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hooks:
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- id: docformatter
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args: [
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'--wrap-summaries=120',
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'--wrap-descriptions=120',
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'--in-place',
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]
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- repo: https://github.com/Lucas-C/pre-commit-hooks
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rev: v1.4.2
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hooks:
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- id: insert-license
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files: \.py$
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args: [
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'--license-filepath=COPYRIGHT',
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'--comment-style=#',
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'--use-current-year',
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]

‎CONTRIBUTING.md

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# Contribution Guide
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## Bug Reports
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For bug reports, [submit an issue](https://github.com/PilotDataPlatform/sandbox/issues).
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## Pull Requests
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1. Fork the [main repository](https://github.com/PilotDataPlatform/sandbox).
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2. Create a feature branch to hold your changes.
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3. Work on the changes in your feature branch.
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4. Add [Unit Tests](#unit-tests).
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5. Follow the Getting Started instruction to set up the service.
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6. Create the Alembic [migration](#migrations) environment only when it's needed.
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7. Test the code and create a pull request.
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### Migrations
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To create a new migration with Alembic, run:
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```
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docker compose run --rm alembic revision -m "Migration name"
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```
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### Unit Tests
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When adding a new feature or fixing a bug, unit tests are necessary to write. Currently we use Pytest as our testing framework and all test cases are written under the `tests` directory.
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Some services may need extra dependencies to run tests. Example:
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```
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docker run redis
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```
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Run test cases with Poetry and Pytest:
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```
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poetry run pytest
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```

‎COPYRIGHT

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Copyright (C) 2022-2023 Indoc Systems
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Licensed under the GNU AFFERO GENERAL PUBLIC LICENSE, Version 3.0 (the "License") available at https://www.gnu.org/licenses/agpl-3.0.en.html.
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You may not use this file except in compliance with the License.

‎Dockerfile

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FROM python:3.9-buster
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WORKDIR /usr/src/app
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ENV TZ=America/Toronto
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RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && \
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echo $TZ > /etc/timezone && \
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apt-get update && \
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apt-get install -y vim-tiny less && \
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ln -s /usr/bin/vim.tiny /usr/bin/vim && \
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rm -rf /var/lib/apt/lists/*
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COPY . .
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RUN pip install --no-cache-dir poetry==1.2.0
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RUN poetry config virtualenvs.create false
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RUN poetry install --no-dev --no-root --no-interaction
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RUN chmod +x gunicorn_starter.sh
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CMD ["./gunicorn_starter.sh"]

‎LICENSE

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Copyright (C) 2022-2023 Indoc Systems
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GNU AFFERO GENERAL PUBLIC LICENSE
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Version 3, 19 November 2007
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You should also get your employer (if you work as a programmer) or school,
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if any, to sign a "copyright disclaimer" for the program, if necessary.
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For more information on this, and how to apply and follow the GNU AGPL, see
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<https://www.gnu.org/licenses/>.
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<https://www.gnu.org/licenses/>.

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