Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ef6f7f62ab679928045c816a3cb719fb3bcea507 https://github.com/galaxyproject/galaxy/commit/ef6f7f62ab679928045c816a3cb71... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/checkers.py M lib/galaxy_ext/metadata/set_metadata.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Memory usage bug fixes and code cleanup/simplification for upload tool Commit: da24d9106db1051a82c7814e847b679bac01d71c https://github.com/galaxyproject/galaxy/commit/da24d9106db1051a82c7814e847b6... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Fixes for changes to checkers.check_zip Commit: 0163a57f0ed562a7c699c6121a8bec87cd4016ea https://github.com/galaxyproject/galaxy/commit/0163a57f0ed562a7c699c6121a8be... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M tools/data_source/upload.py Log Message: ----------- Additional fixes for failing tests Commit: 2dc5cb7f47a50a0b3c79f6da1bf1b6bc08744a86 https://github.com/galaxyproject/galaxy/commit/2dc5cb7f47a50a0b3c79f6da1bf1b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix linting errors Commit: 82408eb179a482a9e24b74d0658b89df3f87f354 https://github.com/galaxyproject/galaxy/commit/82408eb179a482a9e24b74d0658b8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py Log Message: ----------- I wanted to make sure that umask was still being respected with the changes to the upload tool - it is, but there were a few places that it could be missed, so I added these. Commit: 11917108f3b4b94855453d308cbfd0649c593400 https://github.com/galaxyproject/galaxy/commit/11917108f3b4b94855453d308cbfd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Improve extension stripping Commit: ac3a0cbdc58fbefc344b16aeac6a0d238a792fa0 https://github.com/galaxyproject/galaxy/commit/ac3a0cbdc58fbefc344b16aeac6a0... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/util/checkers.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #5689 from natefoo/upload-memfix Memory and performance fixes for upload tool Compare: https://github.com/galaxyproject/galaxy/compare/dbf6f5825171...ac3a0cbdc58f