Resolwe

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Fixed
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- Update Features and Mappings ElasticSearch indices building to be compatible
with Resolwe 4.0


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Changed
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- **BACKWARD INCOMPATIBLE:** The ``keep_data()`` method in
``TransactionTestCase`` is no longer supported. Use the
``--keep-data`` option to the test runner instead.
- **BACKWARD INCOMPATIBLE:** Convert the manager to Django Channels
- **BACKWARD INCOMPATIBLE:** Refactor executors into standalone programs
- **BACKWARD INCOMPATIBLE:** Drop Python 2 support, require Python 3.4+
- Move common test environment preparation to ``TestCaseHelpers`` mixin

Fixed
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- Fix parents/children filter on Data objects
- Correctly handle removed processes in the changes-only mode of the
Resolwe test runner


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Added
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- Add ``resolwebio/base`` Docker image based on Ubuntu 17.04
- Add ``resolwebio/dnaseq`` Docker image
- Add ``DESeq2`` tool to ``resolwebio/rnaseq`` docker image
- Add input filename regex validator for ``upload-master-file`` process

Changed
-------
- Remove obsolete mongokey escape functionality
- Report novel splice-site junctions in HISAT2
- Use the latest stable versions of the following bioinformatics
tools in ``resolwebio/rnaseq`` docker image: Cutadapt 1.14,
FastQC 0.11.5, HTSeq 0.9.1, and SAMtools 1.5


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Added
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- Add Mus musculus to all BCM workflows' schemas
- Add ``bam-split`` process with supporting processes
``upload-bam-primary``, ``upload-bam-secondary`` and
``upload-header-sam``

Changed
-------
- Enable Chemut workflow and process tests

Fixed
-----
- Fix chemut ``intervals`` input option


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Added
-----
- **BACKWARD INCOMPATIBLE:** Add option to build only subset of
specified queryset in Elasticsearch index builder
- ``--pull`` option to the ``list_docker_images`` management command
- Test profiling and process tagging
- New test runner, which supports partial test suite execution based
on changed files
- Add ``all`` and ``any`` Jinja filters

Changed
-------
- **BACKWARD INCOMPATIBLE:** Bump Django requirement to version 1.11.x
- **BACKWARD INCOMPATIBLE:** Make ``ProcessTestCase`` non-transactional
- Pull Docker images after process registration is complete
- Generalize Jinja filters to accept lists of ``Data`` objects
- When new ``Data`` object is created, permissions are copied from
collections and entity to which it belongs

Fixed
-----
- Close schema (YAML) files after ``register`` command stops using them
- Close schema files used for validating JSON schemas after they are no
longer used
- Close stdout used to retrieve process results in executor after the
process is finished
- Remove unrelated permissions occasionally listed among group
permissions on ``permissions`` endpoint
- Fix ``ResolwePermissionsMixin`` to work correctly with multi-words
model names, i.e. ``DescriptorSchema``
- Fix incorrect handling of offset/limit in Elasticsearch viewsets


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Added
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- Add ``index-fasta-nucl`` and ``rsem`` process
- Add custom Cutadapt - STAR - RSEM workflow


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