Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e0b348559211a0c6b26e37ccfa9bd9413516aae https://github.com/galaxyproject/galaxy/commit/9e0b348559211a0c6b26e37ccfa9b... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: R lib/galaxy/metadata Log Message: ----------- Remove deprecated symbolic link added in 15.03. Was added for running jobs - so this may break running jobs if people upgrade from 15.03 (or earlier) to 16.04 (or later) directly. Commit: f21cde984b866ca910d8b447be24a35c796b82cb https://github.com/galaxyproject/galaxy/commit/f21cde984b866ca910d8b447be24a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Style fix - use more Pythonic name than linePieces. Commit: 2d86e00a5af20420a31e67cea5c567e41997b0e2 https://github.com/galaxyproject/galaxy/commit/2d86e00a5af20420a31e67cea5c56... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py Log Message: ----------- Cleanup some relative imports in galaxy.datatypes. Commit: 3861cffdc5c1b385d848f91fdf49213f661432b6 https://github.com/galaxyproject/galaxy/commit/3861cffdc5c1b385d848f91fdf492... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Rename galaxy.model.datatypes_registry... ... to make it clear it shouldn't be accessed outside that module. Commit: ba0d06f6ba165f2fd3d5d2742b1ada152bcd73b0 https://github.com/galaxyproject/galaxy/commit/ba0d06f6ba165f2fd3d5d2742b1ad... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Eliminate more use of relative imports in datatypes modules. Commit: 3217bc78323271db4661e4aea308497d4f58fc81 https://github.com/galaxyproject/galaxy/commit/3217bc78323271db4661e4aea3084... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M test/unit/tools/test_column_parameters.py M test/unit/tools_support.py Log Message: ----------- Don't construct a DatatypesRegistry just for tests in galaxy.model. Construct the model in the tests, this should cause galaxy.model to import much faster. Commit: 1f4b32903270926389a9993b3938c169f105371d https://github.com/galaxyproject/galaxy/commit/1f4b32903270926389a9993b3938c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/tools/exception_handling.py A lib/galaxy/util/ucsc.py M tools/filters/wiggle_to_simple.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Refactor galaxy.tools.exception_handling... ... so datatype module doesn't need to import something from galaxy.tools - which causes a bunch of more things to be imported because galaxy.tools at the top-level has so many imports. Commit: 4d9498c4c6b181779439e8211fd20c20568c40cb https://github.com/galaxyproject/galaxy/commit/4d9498c4c6b181779439e8211fd20... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Elimiante runtime sniff -> registry dependency. It only existed for testing, so only require it in tests. Commit: ae493bfde0d693ae8f1560319053230496cf932d https://github.com/galaxyproject/galaxy/commit/ae493bfde0d693ae8f15603190532... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Eliminate import of registry from galaxy.model. Commit: 5756f6059720d39a75e5786283b232787a60f14e https://github.com/galaxyproject/galaxy/commit/5756f6059720d39a75e5786283b23... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/model/__init__.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/util/none_like.py Log Message: ----------- Relocate galaxy.datatypes.metadata to galaxy.model.metadata. This eliminates the last dependency in galaxy.model on galaxy.datatypes - establishing a strict ordering of dependencies (galaxy.datatypes depends on galaxy.model and not vice versa). The galaxy.datatypes.metadata interface needs to remain in place for tool shed datatypes and is perfectly reasonable to use from within the datatypes module - it now depends on galaxy.model.metadata and exports the same interfac. In the longer run, this is a better, more explict design and should eliminate certain classes of problems with circular dependencies. Fixes #1552 Commit: df5a3a6da7749b47e50a2faffb5c8f8a8a282230 https://github.com/galaxyproject/galaxy/commit/df5a3a6da7749b47e50a2faffb5c8... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: R scripts/set_metadata.py R set_metadata.sh Log Message: ----------- Eliminate legacy set metadata entry points. Commit: 499357e508035e7c9ffb5d711e0f355e960e1e05 https://github.com/galaxyproject/galaxy/commit/499357e508035e7c9ffb5d711e0f3... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M tools/data_source/data_source.py M tools/data_source/upload.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Remove unneeded galaxy.model import in upload.py... ... and document the ability to remove from other data sources. Commit: 448aee9f004befa8ebc02de2ca726dca8e4c22c9 https://github.com/galaxyproject/galaxy/commit/448aee9f004befa8ebc02de2ca726... Author: John Chilton <jmchilton@gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- Fix for multi-byte char problem in PR #1556... ... caught by @nsoranzo of course. Commit: db1bb2f19142e8a9a0a08ffeb9d4295a4f153fcb https://github.com/galaxyproject/galaxy/commit/db1bb2f19142e8a9a0a08ffeb9d42... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/util/none_like.py A lib/galaxy/util/ucsc.py R scripts/set_metadata.py R set_metadata.sh M test/unit/tools/test_column_parameters.py M test/unit/tools_support.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge pull request #1556 from jmchilton/datatype_imports Code design and legacy cleanup of datatypes and metadata. Compare: https://github.com/galaxyproject/galaxy/compare/e6dc96def3b9...db1bb2f19142