Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0bfa1df72f8d0d140dea400ea6ad7f854714817e https://github.com/galaxyproject/galaxy/commit/0bfa1df72f8d0d140dea400ea6ad7... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-06-26 (Mon, 26 Jun 2017)

Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml

Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown

Without this fix, the Cheetah expression:

$dataset.is_of_type('unknown_ext')

in a tool command would be equivalent to:

$dataset.is_of_type('txt')

meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning.

xref. https://github.com/galaxyproject/tools-iuc/issues/1373

Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools.

Commit: 02ffcd5c8f9f30f38581d89f8b913bb587b88e6d https://github.com/galaxyproject/galaxy/commit/02ffcd5c8f9f30f38581d89f8b913... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-06-26 (Mon, 26 Jun 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/registry.py

Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/datatypes/registry.py

xref. https://github.com/galaxyproject/galaxy/issues/1715

Commit: e8c23136406fd4acd6c2b902e107dfea21a73762 https://github.com/galaxyproject/galaxy/commit/e8c23136406fd4acd6c2b902e107d... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-06-26 (Mon, 26 Jun 2017)

Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/tools/parameters/basic.py

Log Message: ----------- Small fixes

Commit: 3ec2c7831defa0486a8b3eb5a88a12458d5b5d1b https://github.com/galaxyproject/galaxy/commit/3ec2c7831defa0486a8b3eb5a88a1... Author: John Chilton jmchilton@gmail.com Date: 2017-06-26 (Mon, 26 Jun 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml

Log Message: ----------- Merge pull request #4224 from nsoranzo/fix_get_datatype_by_extension

Fix Registry.get_datatype_by_extension() to return None if ext is unknown

Compare: https://github.com/galaxyproject/galaxy/compare/73faf7c8b6e0...3ec2c7831def