Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 794d1e03be57fdc0cde02bab79f8404c0eed7626 https://github.com/galaxyproject/galaxy/commit/794d1e03be57fdc0cde02bab79f84... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix messed up printing of shed_tool_conf.xml file This drops xml_to_string from lib/tool_shed/util/xml_util.py and uses xml_to_string form lib/galaxy/utils/__init__.py. Also reduces plain string manipulation of xml structures. Uses xml.dom.minidom to make xml pretty if necessary. Commit: 8a39f27b3c8d20c5adf933f6a3782525b3925432 https://github.com/galaxyproject/galaxy/commit/8a39f27b3c8d20c5adf933f6a3782... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix toolshed tests Commit: a4655432604a758f2725c5badc120f4836ffcbda https://github.com/galaxyproject/galaxy/commit/a4655432604a758f2725c5badc120... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Drop threading lock and global try/except The Lock wasn't actually preventing anything, and I don't think anything would need ot be protected here. mkdtemp should be thread-safe. We also remove the try/except Statement. I think it'd be better to expose any exceptions here instead of producing broken capsules and logging an exception. Commit: 57a4e50d8cfe038632bbe25ed6cbb69662491f2e https://github.com/galaxyproject/galaxy/commit/57a4e50d8cfe038632bbe25ed6cbb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix capsule export in docker testing Found this by removing the blank try/except in the previous commit. This only affects testing when python can't determine the correct locale and falls back to ASCII. Commit: 328c410fdcad8a870816dea307499fef31c812e7 https://github.com/galaxyproject/galaxy/commit/328c410fdcad8a870816dea307499... Author: John Chilton <jmchilton@gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #6904 from mvdbeek/fix_weird_xml [18.09] Fix pretty printing of shed_tool_conf.xml file Compare: https://github.com/galaxyproject/galaxy/compare/36383785697b...328c410fdcad **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.