Resolwe

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Fixed
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- Update instructions on preparing a release to no longer build the wheel
distribution which currently fails to install Resolwe's dependency links


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Added
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- Auto-process style, type tree and category index
- Support loading JSON from a file if the string passed to the ``basic:json:``
field is a file.
- ``list:basic:integer:`` field
- Data object's checksum is automatically calculated on save
- ``get_or_create`` end point for ``Data`` objects
- ``basic:file:html:`` field for HTML files
- Helper function for comparing JSON fields in tests
- Purge directories not belonging to any data objects
- Ordering options to API endpoints
- Workflow execution engine
- ``data_by_slug`` filter for jinja expression engine
- Export ``RESOLWE_API_HOST`` environment variable in executor
- Add ``check_installed()`` test utility function
- Add support for configuring the network mode of Docker executor
- Add ``with_docker_executor`` test utility decorator
- Support for Docker image requirements
- Support version in descriptor schema YAML files
- Add ``Entity`` model that allows grouping of ``Data`` objects
- Introduce priority of Data objects
- Data objects created with processes with temporary persistence are given
high priority.
- Add ``resolwe.elastic`` application, a framework for advanced indexing of
Django models with ElasticSearch

Changed
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- Refactor linters, check PEP 8 and PEP 257
- Split expression engines into expression engines and execution engines
- Use Jinja2 instead of Django Template syntax
- Expression engine must be declared in ``requirements``
- Set Docker Compose's project name to ``resolwe`` to avoid name clashes
- Expose ``check_docker()`` test utility function
- Update versionfield to 0.5.0
- Support Django 1.10 and update filters
- Executor is no longer serialized
- Put Data objects with high priority into ``hipri`` Celery queue.

Fixed
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- Fix pylint warnings (PEP 8)
- Fix pydocstyle warnings (PEP 257)
- Take last version of process for spawned objects
- Use default values for descriptor fields that are not given
- Improve handling of validation errors
- Ignore file size in ``assertFields``
- Order data objects in ``CollectionViewSet``
- Fix tests for Django 1.10
- Add quotes to paths in a test process test-save-file


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Added
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- Sphinx extension ``autoprocess`` for automatic process documentation


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Added
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- Ability to pass certain information to the process running in the container
via environment variables (currently, user's uid and gid)
- Explicitly set working directory inside the container to the mapped directory
of the current ``Data``'s directory
- Allow overriding any ``FLOW_EXECUTOR`` setting for testing
- Support GET request on /api/<model>/<id>/permissons/ url
- Add OWNER permissions
- Validate JSON fields before saving ``Data`` object
- Add basic:dir field
- ``RESOLWE_CUSTOM_TOOLS_PATHS`` setting to support custom paths for tools
directories
- Add test coverage and track it with Codecov
- Implement data purge
- Add ``process_fields.name`` custom tamplate tag
- Return contributor information together with objects
- Added permissions filter to determine ``Storage`` permissions based on
referenced ``Data`` object

Changed
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- Move filters to separate file and systemize them
- Unify file loading in tests
- Simplify ``ProcessTestCase`` by removing the logic for handling different
uid/gid of the user running inside the Docker container
- Upgrade to django-guardian 1.4.2
- Rename ``FLOW_EXECUTOR['DATA_PATH']`` setting to
``FLOW_EXECUTOR['DATA_DIR']``
- Rename ``FLOW_EXECUTOR['UPLOAD_PATH']`` setting to
``FLOW_EXECUTOR['UPLOAD_DIR']``
- Rename ``proc.data_path`` system variable to ``proc.data_dir``
- Rename test project's data and upload directories to ``.test_data`` and
``.test_upload``
- Serve permissions in new format
- Rename ``assertFiles`` method in ``ProcessTestCase`` to ``assertFile`` and
add new ``assertFiles`` method to check ``list:basic:file`` field
- Make ``flow.tests.run_process`` function also handle file paths
- Use Travis CI to run the tests
- Include all necessary files for running the tests in source distribution
- Exclude tests from built/installed version of the package
- Put packaging tests in a separate Tox testing environment
- Put linters (pylint, pep8) into a separate Tox testing environment
- Drop django-jenkins package since we no longer use Jenkins for CI
- Move testing utilities from ``resolwe.flow.tests`` to
``resolwe.flow.utils.test`` and from ``resolwe.permissions.tests.base`` to
``resolwe.permissions.utils.test``
- Add Tox testing environment for building documentation
- Extend Reference documentation

Fixed
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- Spawn processors (add data to current collection)
- Set collection name to avoid warnings in test output
- Improve Python 3 compatibility
- Fix setting descriptor schema on create


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Added
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- Add docker-compose configuration for PostgreSQL
- Processes can be created on API
- Enable spawned processes

Changed
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- Move logic from ``Collection`` model to the ``BaseCollection`` abstract
model and make it its parent
- Remove all logic for handling ``flow_collection``
- Change default database user and port in test project's settings
- Keep track of upload files created during tests and purge them afterwards

Fixed
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- Test processes location agnostic
- Test ignore timezone support


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Changed
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- Rename ``assertFileExist`` to ``assertFileExists``
- Drop ``--process-dependency-links`` from Tox's pip configuration
- Improve documentation on preparing a new release

Added
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- Ability to use a custom executor command by specifying the
``FLOW_EXECUTOR['COMMAND']`` setting
- Make workload manager configurable in settings

Fixed
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- Make Resolwe work with Python 3 again
- Fix tests
- Render data name again after inputs are resolved
- Ensure Tox installs the package from sdist
- Pass all Resolwe's environment variables to Tox's testing environment
- Ensure tests gracefully handle unavailability of Docker


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