Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41cbe242991eb69bc821a9f2d0b8ab599b73aa9a https://github.com/galaxyproject/galaxy/commit/41cbe242991eb69bc821a9f2d0b8a... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Use floating point to log toolox reload times Commit: 4d1cae41cb7ce0d3aa10d413de8ec4000e50444a https://github.com/galaxyproject/galaxy/commit/4d1cae41cb7ce0d3aa10d413de8ec... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Add timing information for Data Manager reload Commit: c06b4c92658563fda4efe8b1dcf6045113b664fd https://github.com/galaxyproject/galaxy/commit/c06b4c92658563fda4efe8b1dcf60... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Add a short-lived (1s) ToolShedRepositoryCache This will speed up repeated ToolShedRepositories lookups, like when building the Toolbox for the first time, or when loading a shed_tool_conf.xml file with many deactivated tools. Commit: 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 https://github.com/galaxyproject/galaxy/commit/43c9c287a9a3520d77cc9235dfbfa... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Speed up tool-data table reloads by doing a os.walk and caching the result for 1s instead of repeatedly calling os.path.exists. Commit: 34ed9b48ddc2fdd0e2456b959fed5eedec9b92c1 https://github.com/galaxyproject/galaxy/commit/34ed9b48ddc2fdd0e2456b959fed5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Only index changed tools when re-indexing the toolbox This speeds up repeated toolbox reloads enourmously (from 1 second on my test-instance to 0.1 seconds). Commit: c6429bff1c38b2196fece8155449ba62723242ee https://github.com/galaxyproject/galaxy/commit/c6429bff1c38b2196fece8155449b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Always use cache to fetch tool_version objects Commit: 96cb87431402454fa52db35547fb3028c5aae807 https://github.com/galaxyproject/galaxy/commit/96cb87431402454fa52db35547fb3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Use cElementTree for light xml parsing speedup Commit: 2906f0c0857fc958f7e9049e2e7134065908852f https://github.com/galaxyproject/galaxy/commit/2906f0c0857fc958f7e9049e2e713... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Update ToolVersionCache when adding a new ToolShedLineage Commit: 6c22726db082cedee9884bde9aa913bbb93dea05 https://github.com/galaxyproject/galaxy/commit/6c22726db082cedee9884bde9aa91... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Move tool_cache.reset_status() calls to reload toolbox/data managers, so that we can use information about whether tools are new during reloads Commit: 431a4824abf91b7a10e5417d63a990ba0a5f916d https://github.com/galaxyproject/galaxy/commit/431a4824abf91b7a10e5417d63a99... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Make sure re-indexing the toolbox occurs on the new toolbox Commit: ea9ecdf57150e800115ae28f6e80d80a7bfef249 https://github.com/galaxyproject/galaxy/commit/ea9ecdf57150e800115ae28f6e80d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Remove `replace_existing` option for data managers If a data manager is defined twice for the same data manager id in the shed_tool_conf.xml the first data manager will be loaded. This is not a problem when updating a data manager through the toolshed, because the outdated data manager will be removed from the tool cache and a new toolbox is being built. Commit: db910f4f81771f91f9a5b96bfc5fb9bd6d506e2b https://github.com/galaxyproject/galaxy/commit/db910f4f81771f91f9a5b96bfc5fb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Reset the tool cache once all tools are loaded after starting up galaxy Commit: 9aa5556dedb35b748ed17b20fd26348fdcdea829 https://github.com/galaxyproject/galaxy/commit/9aa5556dedb35b748ed17b20fd263... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce logging during toolbox reloads We don't log loading of tools that have not changed when reloading the toolbox. Commit: 475b8866bad2a58b314354ae73ee1e5ccd94b8cb https://github.com/galaxyproject/galaxy/commit/475b8866bad2a58b314354ae73ee1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Fix unittests that access app.tool_cache Commit: beae93bf766fc48a3a2f2edcd275d13ae0fe8ba2 https://github.com/galaxyproject/galaxy/commit/beae93bf766fc48a3a2f2edcd275d... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Re-use ExecutionTimer abstractions for consistent log patterns. Commit: a83ef0b86c0acbfb7c0bf1b40579e5102c78ad29 https://github.com/galaxyproject/galaxy/commit/a83ef0b86c0acbfb7c0bf1b40579e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py Log Message: ----------- Log startup time Commit: 3ff2a7832a949d300d9cddab0fea05fa74b1a403 https://github.com/galaxyproject/galaxy/commit/3ff2a7832a949d300d9cddab0fea0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Fix cElementTree imports Commit: c905c4217b0397f92b2eb1019308851da043682f https://github.com/galaxyproject/galaxy/commit/c905c4217b0397f92b2eb10193088... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix import order in lib/galaxy/tools/data/__init__.py Commit: b72994fe0294326f99df880e3ba7e248f1ffe145 https://github.com/galaxyproject/galaxy/commit/b72994fe0294326f99df880e3ba7e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Add possibility explicitly rebuild ToolShedRepositoryCache Commit: 84c1559d473f7d9234173aeb802f30067fe0ffe6 https://github.com/galaxyproject/galaxy/commit/84c1559d473f7d9234173aeb802f3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix path checking for files that are not in the tool_data_path directory Commit: 0504dcd2997bc4673ded5c7fdc1e2b28a85dcb18 https://github.com/galaxyproject/galaxy/commit/0504dcd2997bc4673ded5c7fdc1e2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Use generator instead of list comprehenesion followed converting it to a set. (Thanks @nsoranzo) Commit: cbed78fbfbcb1c381af5be9442c8ce6af1a3a554 https://github.com/galaxyproject/galaxy/commit/cbed78fbfbcb1c381af5be9442c8c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Don't return toolbox (thx @nsoranzo) Commit: 4dd49c938d2c7bcfac37fe475eccb1e32653b6b4 https://github.com/galaxyproject/galaxy/commit/4dd49c938d2c7bcfac37fe475eccb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py Log Message: ----------- Use ExecutionTimer abstraction to report startup time Commit: dc1617596e47c384b8a88de395fe41a681145ffd https://github.com/galaxyproject/galaxy/commit/dc1617596e47c384b8a88de395fe4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Remove unused time import Commit: 4c44338144763819f78f99b84d5816ded18de372 https://github.com/galaxyproject/galaxy/commit/4c44338144763819f78f99b84d581... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Be more defesive when accessing app.tool_cache Commit: 5069815c0eba0a7c4c406ec0f781f138f7aee291 https://github.com/galaxyproject/galaxy/commit/5069815c0eba0a7c4c406ec0f781f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Rebuild repo cache when deciding if repository should be created. Commit: d15813cb2a489e1de8771886e9df8ebb69fc079e https://github.com/galaxyproject/galaxy/commit/d15813cb2a489e1de8771886e9df8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Avoid having tools in tool_cache marked as new when they have rapidly shifted from new to expired. Commit: 586f49486cf4c1f4597237d3df95562bb477c6f8 https://github.com/galaxyproject/galaxy/commit/586f49486cf4c1f4597237d3df955... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Don't crash if a tool has not been added to the cache properly Commit: 3d6bc1d56372b5853fdddd08362d8f57b4026adb https://github.com/galaxyproject/galaxy/commit/3d6bc1d56372b5853fdddd08362d8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Refresh tool_data_path_files if we know that a new table has been written Commit: 07da123e9d311e5ec453399024ef992859770234 https://github.com/galaxyproject/galaxy/commit/07da123e9d311e5ec453399024ef9... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Reference old_toolbox earlier, since reloading can happen in a different thread, which will lead to a hang when waiting for another toolbox reload Commit: 677d98622dfa30a65d8a8fc392c25077abdcc0e9 https://github.com/galaxyproject/galaxy/commit/677d98622dfa30a65d8a8fc392c25... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Always refresh tool_shed_repository_cache before fetching repositories by ids (since that is only called from admin_toolshed.py and installed_repository_metadata_manager.py) Commit: f940c797ff981c3f0a12b6a3abeee61e05ff2436 https://github.com/galaxyproject/galaxy/commit/f940c797ff981c3f0a12b6a3abeee... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix import order in lib/galaxy/config.py Commit: 89f57f2aa753f5de9673cd3dcf5c13ca3d3f6639 https://github.com/galaxyproject/galaxy/commit/89f57f2aa753f5de9673cd3dcf5c1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Allow looking up repositories by repository_id via ToolShedRepositoryCache Commit: 456d1b47b62d05d3fc5180d4f9da525317efc28c https://github.com/galaxyproject/galaxy/commit/456d1b47b62d05d3fc5180d4f9da5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/util/tool_dependency_util.py Log Message: ----------- Refresh TSR cache when needed Commit: 8411b0253adc947838af760e4614611ac8183464 https://github.com/galaxyproject/galaxy/commit/8411b0253adc947838af760e46146... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Restore deactivate/activate functionality Commit: 15e2c9b61aae9476b519a8c2e1c233e134e3ebbc https://github.com/galaxyproject/galaxy/commit/15e2c9b61aae9476b519a8c2e1c23... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Revert "Fix cElementTree imports" This reverts commit 6d365f03e888ef12527105119f0a7adebae23b95. Commit: 7e61f8c047ce3cb29f5d9999a93b2c7bd0ee1cde https://github.com/galaxyproject/galaxy/commit/7e61f8c047ce3cb29f5d9999a93b2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Revert "Use cElementTree for light xml parsing speedup" This reverts commit 556469f5171ef9897a5c40de9d661d2d4f4deb86. Commit: 141f15256e8ef39baf457be1e8ef1cdf5414f5aa https://github.com/galaxyproject/galaxy/commit/141f15256e8ef39baf457be1e8ef1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Use ExecutionTimer Commit: 73c7c364a25caf519dfd4cfea17b500077510a74 https://github.com/galaxyproject/galaxy/commit/73c7c364a25caf519dfd4cfea17b5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use tool_shed_repository_cache in populate_tool_shed_info Commit: 869d7bf481e77aca420cc3970844650f7ad6ff20 https://github.com/galaxyproject/galaxy/commit/869d7bf481e77aca420cc39708446... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/plugin_config.py Log Message: ----------- Replace getchildren(), which has been deprecated (https://docs.python.org/2/library/xml.etree.elementtree.html#xml.etree.Eleme...) Commit: 3079d0c239bf7c46d872e65d107eaab4b3741b46 https://github.com/galaxyproject/galaxy/commit/3079d0c239bf7c46d872e65d107ea... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Write out the datatype registry only once Commit: f88304b65b430da0a3db67e25e457044c373bf99 https://github.com/galaxyproject/galaxy/commit/f88304b65b430da0a3db67e25e457... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py Log Message: ----------- Build toolbox search in a local control task Commit: 5e7da2c910e28e13b5a79c3ad794d6f40446694a https://github.com/galaxyproject/galaxy/commit/5e7da2c910e28e13b5a79c3ad794d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M test/base/driver_util.py Log Message: ----------- Don't fail tests without internet connectivity Commit: 5a26896745c16e25ce951ee3a85bdc2cd81087e1 https://github.com/galaxyproject/galaxy/commit/5a26896745c16e25ce951ee3a85bd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/parser/xml.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Write out datatype registry when loading set_metadata tool Commit: f199d5b434da500330520f891a3188ee69eccce4 https://github.com/galaxyproject/galaxy/commit/f199d5b434da500330520f891a318... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Keep cache thread-local Commit: b4e4f3ce7a9bc6ef06b4191bf8f8f2fef493d844 https://github.com/galaxyproject/galaxy/commit/b4e4f3ce7a9bc6ef06b4191bf8f8f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Use current session Commit: ff1b66afb325ebe68a2d174503980b03100ca6d4 https://github.com/galaxyproject/galaxy/commit/ff1b66afb325ebe68a2d174503980... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Fix thread local cache use Commit: 84351de20bef488022cf82ac2610e2e5c0b369cd https://github.com/galaxyproject/galaxy/commit/84351de20bef488022cf82ac2610e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Send control task as postfork function Commit: b666649c8159316eaa22bc4c89575fda38e9838d https://github.com/galaxyproject/galaxy/commit/b666649c8159316eaa22bc4c89575... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Work around InstanceDetached errors Commit: 86684df5ef235b6390f0cfa838927cf6e5b67330 https://github.com/galaxyproject/galaxy/commit/86684df5ef235b6390f0cfa838927... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Skip time-based reloading, rely on detecting DetachedInstanceErrors to trigger cache rebuild Commit: cdad5bee9b1f9761a5b3ab56cbdc3c3eb6e63e14 https://github.com/galaxyproject/galaxy/commit/cdad5bee9b1f9761a5b3ab56cbdc3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py Log Message: ----------- Attempt to speedup proprietary datatype loading Commit: 2587ab55b8743ae626f977961e4f3c8e7cb0eb05 https://github.com/galaxyproject/galaxy/commit/2587ab55b8743ae626f977961e4f3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Remove operations from custom_datatype_manager Updating the upload file formats is handled when loading the datatype into the registry, and reloading the upload tool seems unnecessary and insufficient, since this would only affect the current web handler. In any case removed and added datatypes are immediately propagated to the upload tool. Commit: af156a8f7496dc9a9e70d3992f227c626aec7fa2 https://github.com/galaxyproject/galaxy/commit/af156a8f7496dc9a9e70d3992f227... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py Log Message: ----------- Build search index at startup, rebuild repository cache during toolbox or datamanager reload Commit: a6415b25fdb9661504505ba9c5016f7645720d30 https://github.com/galaxyproject/galaxy/commit/a6415b25fdb9661504505ba9c5016... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_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/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M test/base/driver_util.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3909 from mvdbeek/speedup_toolbox Speedup startup and toolbox operations Compare: https://github.com/galaxyproject/galaxy/compare/4b7d5e32d4a0...a6415b25fdb9