Branch: refs/heads/dev 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: 3f172cc9880e58396e7f71b7480bea9e7163dda4 https://github.com/galaxyproject/galaxy/commit/3f172cc9880e58396e7f71b7480be... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix job stopping from DRMAA jobs broken in a1c58a708829d79859426ecb7c39b5c5f69ad735 and improve logging around it. Commit: 36383785697bed5db7e99461c3483f19836a016b https://github.com/galaxyproject/galaxy/commit/36383785697bed5db7e99461c3483... Author: John Chilton <jmchilton@gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #6912 from natefoo/fix-drmaa-job-stop [18.09] Fix stopping DRMAA jobs 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 Commit: c862d55ec8fe99e950df7984127461eaedd6f438 https://github.com/galaxyproject/galaxy/commit/c862d55ec8fe99e950df798412746... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Use with statement when handling NamedTemporaryFile Commit: 91a9dbaf5cf093ff72f39d9ea606bef59ecfc45a https://github.com/galaxyproject/galaxy/commit/91a9dbaf5cf093ff72f39d9ea606b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Revert unncessary double logging of exception Commit: 843474e5e375a2359979a8f9ae46fb0e58ac148b https://github.com/galaxyproject/galaxy/commit/843474e5e375a2359979a8f9ae46f... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #6915 from mvdbeek/6904_followup [18.09] Small followup to #6904 Commit: 51ca8dc0f5d4cb9ba4221cba5d2067f467087caa https://github.com/galaxyproject/galaxy/commit/51ca8dc0f5d4cb9ba4221cba5d206... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py 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 branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/096fe9b7b9c3...51ca8dc0f5d4 **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.