Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 051a3173fcffb0fe682bc5c0d692b77855c37a53 https://github.com/galaxyproject/galaxy/commit/051a3173fcffb0fe682bc5c0d692b... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-11-30 (Thu, 30 Nov 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py

Log Message: ----------- Fix some datatype issues

- dmnd had a wrong class name - biom1, cool and postgresql shouldn't have `subclass="true"` - extension should be lowercase - add missing file_ext attribute to various datatype classes

Commit: 743d5a37e8d4e35313fa872f4afe6ea616cfa36c https://github.com/galaxyproject/galaxy/commit/743d5a37e8d4e35313fa872f4afe6... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-11-30 (Thu, 30 Nov 2017)

Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Fix append_to_sniff_order()

`isinstance()` was leaving out e.g. the BigWig datatype because BigBed, which was added first, is a subclass of BigWig. Instead, add a datatype only if it is not already in `sniff_order`, it has a `sniff()` method and was not defined with `subclass="true"`.

Commit: 0e0acb5200720cddaaff32bddf71c65f6cfe777e https://github.com/galaxyproject/galaxy/commit/0e0acb5200720cddaaff32bddf71c... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-11-30 (Thu, 30 Nov 2017)

Changed paths: M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/image_util.py M tools/data_source/data_source.py M tools/data_source/upload.py

Log Message: ----------- Remove is_multi_byte from upload.py

Also, when sniffing binary files, sniff images together with the other formats and respect sniff order.

Also remove `is_multi_byte` from: - `stream_to_open_named_file()` - `stream_to_file()`

Remove the now unused `get_image_ext()` and `Binary.is_sniffable_binary()` and all the calls to `Binary.register_sniffable_binary_format()`.

Commit: fea6ddeeca7ccf89f1cacf9bcf49bfa18d16ad83 https://github.com/galaxyproject/galaxy/commit/fea6ddeeca7ccf89f1cacf9bcf49b... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-11-30 (Thu, 30 Nov 2017)

Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/model/__init__.py R lib/galaxy/util/multi_byte.py

Log Message: ----------- Remove last remnants of is_multi_byte, drop wchartype dependency

Commit: f70e6f5627bc1f1e9398b9e88d398292d8e08998 https://github.com/galaxyproject/galaxy/commit/f70e6f5627bc1f1e9398b9e88d398... Author: Björn Grüning bjoern@gruenings.eu Date: 2017-11-30 (Thu, 30 Nov 2017)

Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/image_util.py R lib/galaxy/util/multi_byte.py M tools/data_source/data_source.py M tools/data_source/upload.py

Log Message: ----------- Merge pull request #5088 from nsoranzo/remove_wchartype_dep

Remove wchartype dependency and is_multi_byte [2/2]

Compare: https://github.com/galaxyproject/galaxy/compare/1b4d8e5b9a51...f70e6f5627bc