Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5ba73b0c84f6bfa297d4b75296e5614d25a07cf https://github.com/galaxyproject/galaxy/commit/d5ba73b0c84f6bfa297d4b75296e5... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Fix hang when installing data managers Commit: 82c1da4709a5ae5b52ee60b2b197f91d64c5d5d3 https://github.com/galaxyproject/galaxy/commit/82c1da4709a5ae5b52ee60b2b197f... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Add data managers to new toolbox before replacing the old toolbox, to avoid 'Tool not found or not accessible.' while installing new tools Commit: a8f794290dc1e529dd9564a95a55f4b808b2e6d9 https://github.com/galaxyproject/galaxy/commit/a8f794290dc1e529dd9564a95a55f... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Handle xml ParseError Occasionally the following Traceback can be seen in the log files: ``` Traceback (most recent call last): File "lib/galaxy/tools/toolbox/base.py", line 112, in _init_tools_from_configs self._init_tools_from_config( config_filename ) File "lib/galaxy/tools/toolbox/base.py", line 136, in _init_tools_from_config tool_conf_source = get_toolbox_parser(config_filename) File "lib/galaxy/tools/toolbox/parser.py", line 152, in get_toolbox_parser return XmlToolConfSource(config_filename) File "lib/galaxy/tools/toolbox/parser.py", line 40, in __init__ tree = parse_xml(config_filename) File "lib/galaxy/util/__init__.py", line 210, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: unclosed token: line 2636, column 0 ``` We just try parsing again, which seems to solve the issue. This may be a problem with concurrently reading/writing to the file. Commit: 89bafff06170c02e5089800a5062e3de0421ad23 https://github.com/galaxyproject/galaxy/commit/89bafff06170c02e5089800a5062e... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Whitespace fix Commit: c3886b373e8954c1f7bb193cf28357aebd8cd459 https://github.com/galaxyproject/galaxy/commit/c3886b373e8954c1f7bb193cf2835... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Specifically index new toolbox Commit: 6fd4c5a5be75a39e941ab4b4b4df95c9456ca1e9 https://github.com/galaxyproject/galaxy/commit/6fd4c5a5be75a39e941ab4b4b4df9... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Keep track of toolbox reload time Commit: 230e7df4ae293e46e4f15bf2cf811f788a9f811d https://github.com/galaxyproject/galaxy/commit/230e7df4ae293e46e4f15bf2cf811... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Use cache to get the repository containing a tool when reloading toolbox. This should prevent lots of (slow) database requests when reloading the toolbox. Commit: c5406eb192a0e2355602e5e5d7eb1e218a632d07 https://github.com/galaxyproject/galaxy/commit/c5406eb192a0e2355602e5e5d7eb1... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Improve logic handling of loading tools Commit: ab9be8c311a7943d778842522a706451e9996943 https://github.com/galaxyproject/galaxy/commit/ab9be8c311a7943d778842522a706... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fetch cached tools repository Commit: 894b77ba23fa66a8852b554aacf18cc123f5d7cd https://github.com/galaxyproject/galaxy/commit/894b77ba23fa66a8852b554aacf18... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/lineages/factory.py Log Message: ----------- Simplify lineage registration Commit: acc5b4ceb6525a9cf53bf39c3d6c00abf9069990 https://github.com/galaxyproject/galaxy/commit/acc5b4ceb6525a9cf53bf39c3d6c0... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Load all versions in a single request Commit: 971227c59dd1d32b537c04c59a16e7572aa7acbd https://github.com/galaxyproject/galaxy/commit/971227c59dd1d32b537c04c59a16e... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/util/profiling.py Log Message: ----------- Use tool version cache to boost tool panel loading Commit: 833af5e8c2121947e16bdfb99b2794b7a130d045 https://github.com/galaxyproject/galaxy/commit/833af5e8c2121947e16bdfb99b279... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/util/profiling.py Log Message: ----------- Restore peacemeal tool registration Commit: 8bed867fcfcf249838b6b24a1b5985af401b9b5a https://github.com/galaxyproject/galaxy/commit/8bed867fcfcf249838b6b24a1b598... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Reload tool_version_cache after new installs in the unit-testing code. Commit: 894ac295207430d5ec1b02a0be7ee76ce4dc2cc0 https://github.com/galaxyproject/galaxy/commit/894ac295207430d5ec1b02a0be7ee... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Reload tool_version_cache when adding new tool version relationships to the database. Commit: 09173cc6070bc914759f15854367d62ca6323c79 https://github.com/galaxyproject/galaxy/commit/09173cc6070bc914759f15854367d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/profiling.py M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Rebase and linting fixes Commit: c08db31ab22aefa23a0e6472c4f115cff537668f https://github.com/galaxyproject/galaxy/commit/c08db31ab22aefa23a0e6472c4f11... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/lineages/tool_shed.py R lib/galaxy/util/profiling.py Log Message: ----------- Document ToolVersionCache class Commit: 92d028cbae55d120326cfac61f2fd4fb5d425b35 https://github.com/galaxyproject/galaxy/commit/92d028cbae55d120326cfac61f2fd... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- Remove unnecessary self.install_model from unittest app Commit: 5c45da362ad27c788fe5f7e62fd5c779b7fa24bf https://github.com/galaxyproject/galaxy/commit/5c45da362ad27c788fe5f7e62fd5c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.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/tools/tool_version_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #2901 from mvdbeek/fix_data_manager_hangs All-around improvements to toolbox loading/reloading Compare: https://github.com/galaxyproject/galaxy/compare/0c3b5272eb53...5c45da362ad2