- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 9fdad3: Override walltime in dynamic rules
by GitHub 02 May '17

02 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9fdad33717d819c7370b5d2c8413170f30fba1e7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9fdad33717d819c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Override walltime in dynamic rules

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[galaxyproject/usegalaxy-playbook] e765f7: Allow overriding the walltime on a per-tool basis
by GitHub 02 May '17

02 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e765f7f020a92885a9fb74cc125bd9ddf53cdc23 https://github.com/galaxyproject/usegalaxy-playbook/commit/e765f7f020a92885… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Allow overriding the walltime on a per-tool basis

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[galaxyproject/infrastructure-playbook] 58ff4f: Change ownership of data.galaxyproject.org repo to...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 58ff4fc05465dd554f2306b7de9b8a7b2abc44c6 https://github.com/galaxyproject/infrastructure-playbook/commit/58ff4fc0546… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml Log Message: ----------- Change ownership of data.galaxyproject.org repo to g2test Commit: 7002b8f547c4015d201321c335909bc977e0f544 https://github.com/galaxyproject/infrastructure-playbook/commit/7002b8f547c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M galaxyenv/playbook.yml M galaxyenv/secret_group_vars/all.yml A galaxyenv/secret_group_vars/dockerswarmmanagers.yml Log Message: ----------- Swarm manager user setup Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/50f9fef379…

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[galaxyproject/galaxy]
by GitHub 02 May '17

02 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] f3aee7: More careful inspection of fixes for MAF tools req...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3aee70c9547c349061cbf22760d604f5f30c821 https://github.com/galaxyproject/galaxy/commit/f3aee70c9547c349061cbf22760d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- More careful inspection of fixes for MAF tools requiring Galaxy. Add two tools that required the hack, and remove one tool that doesn't seem to require it. Tracked in comment on #3934. Commit: 60e00088c8b27c04734c7f7adb3cdae6a9a9580f https://github.com/galaxyproject/galaxy/commit/60e00088c8b27c04734c7f7adb3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix edge case for workflow mapping handling when tools not available. Fixes #3960. Commit: 3fcd78564630fae9c4670cfbe198572f94f688c0 https://github.com/galaxyproject/galaxy/commit/3fcd78564630fae9c4670cfbe198… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #3962 from jmchilton/workflow_editor_mapping_test [17.01] Fix edge case for workflow mapping handling when tools not available. Commit: de46a0edba4c49bafa061a08fc49c5d7f72cbd30 https://github.com/galaxyproject/galaxy/commit/de46a0edba4c49bafa061a08fc49… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3935 from jmchilton/more_maf_fixes [17.01] More careful inspection of fixes for MAF tools requiring Galaxy. Commit: 06d0e4fce57fa29e6d7fb02c455b77f6855f783c https://github.com/galaxyproject/galaxy/commit/06d0e4fce57fa29e6d7fb02c455b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/tools/__init__.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ecf634a619e9...06d0e4fce57f

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[galaxyproject/usegalaxy-playbook] f92005: Override walltime in dynamic rules
by GitHub 02 May '17

02 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f92005350152572a09c9a7071e4aa0f9afd1c5d1 https://github.com/galaxyproject/usegalaxy-playbook/commit/f92005350152572a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Override walltime in dynamic rules

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[galaxyproject/galaxy] d224be: Implicitly set use_volumes = False if using Docker...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d224bedd3992e413363f345d64488e13d63518fe https://github.com/galaxyproject/galaxy/commit/d224bedd3992e413363f345d6448… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Implicitly set use_volumes = False if using Docker swarm Commit: ecf634a619e93ffe98b5b785e3de10125940adce https://github.com/galaxyproject/galaxy/commit/ecf634a619e93ffe98b5b785e3de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4006 from natefoo/implicit-use-volumes Implicitly set use_volumes = False if using Docker swarm Compare: https://github.com/galaxyproject/galaxy/compare/afc4fbcc3829...ecf634a619e9

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[galaxyproject/galaxy] 4b3a36: Update Jupyter image to 17.05
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b3a361a887d02e1944fd092b1c3a84b7da13f95 https://github.com/galaxyproject/galaxy/commit/4b3a361a887d02e1944fd092b1c3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Update Jupyter image to 17.05 Commit: afc4fbcc38292c90641dcac737fd08ad0c253201 https://github.com/galaxyproject/galaxy/commit/afc4fbcc38292c90641dcac737fd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Merge pull request #4007 from natefoo/jupyer-17.05 Update Jupyter image to 17.05 Compare: https://github.com/galaxyproject/galaxy/compare/0680a29a7992...afc4fbcc3829

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[galaxyproject/usegalaxy-playbook] dfe930: Update Test
by GitHub 02 May '17

02 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dfe930e2290d6cbfb91bd8cb182595b4491fd7cf https://github.com/galaxyproject/usegalaxy-playbook/commit/dfe930e2290d6cbf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version M env/test/files/interactive_environments/plugins/common/templates/ie.mako M env/test/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js M env/test/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako M env/test/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M env/test/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M env/test/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample M env/test/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M env/test/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M env/test/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version M env/test/files/interactive_environments/proxy/package.json Log Message: ----------- Update Test

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[galaxyproject/galaxy] 1c8370: Restore line accidentally removed as part of #3985...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c8370cf33a0bba05019397677c2b0a386b5136b https://github.com/galaxyproject/galaxy/commit/1c8370cf33a0bba05019397677c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Restore line accidentally removed as part of #3985. Commit: 0680a29a7992de0e606ec7047da845d5686d8029 https://github.com/galaxyproject/galaxy/commit/0680a29a7992de0e606ec7047da8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #4004 from jmchilton/filename_fixup Restore line accidentally removed as part of #3985. Compare: https://github.com/galaxyproject/galaxy/compare/1a733864842b...0680a29a7992

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[galaxyproject/galaxy] 7a6961: Undo dataset renaming
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a6961e30d013d5c3bfa53118e6fb2cc1fd1d35f https://github.com/galaxyproject/galaxy/commit/7a6961e30d013d5c3bfa53118e6f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Undo dataset renaming Commit: 1a733864842ba8c1af3591b4d1aaa85fb3152a9a https://github.com/galaxyproject/galaxy/commit/1a733864842ba8c1af3591b4d1aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #3996 from guerler/undo_url_upload_renaming Undo dataset renaming for URL uploads Compare: https://github.com/galaxyproject/galaxy/compare/a6415b25fdb9...1a733864842b

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[galaxyproject/galaxy] f3aee7: More careful inspection of fixes for MAF tools req...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f3aee70c9547c349061cbf22760d604f5f30c821 https://github.com/galaxyproject/galaxy/commit/f3aee70c9547c349061cbf22760d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- More careful inspection of fixes for MAF tools requiring Galaxy. Add two tools that required the hack, and remove one tool that doesn't seem to require it. Tracked in comment on #3934. Commit: de46a0edba4c49bafa061a08fc49c5d7f72cbd30 https://github.com/galaxyproject/galaxy/commit/de46a0edba4c49bafa061a08fc49… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3935 from jmchilton/more_maf_fixes [17.01] More careful inspection of fixes for MAF tools requiring Galaxy. Compare: https://github.com/galaxyproject/galaxy/compare/3fcd78564630...de46a0edba4c

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[galaxyproject/galaxy] 41cbe2: Use floating point to log toolox reload times
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41cbe242991eb69bc821a9f2d0b8ab599b73aa9a https://github.com/galaxyproject/galaxy/commit/41cbe242991eb69bc821a9f2d0b8… Author: mvdbeek <m.vandenbeek(a)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/4d1cae41cb7ce0d3aa10d413de8e… Author: mvdbeek <m.vandenbeek(a)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/c06b4c92658563fda4efe8b1dcf6… Author: mvdbeek <m.vandenbeek(a)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/43c9c287a9a3520d77cc9235dfbf… Author: mvdbeek <m.vandenbeek(a)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/34ed9b48ddc2fdd0e2456b959fed… Author: mvdbeek <m.vandenbeek(a)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/c6429bff1c38b2196fece8155449… Author: mvdbeek <m.vandenbeek(a)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/96cb87431402454fa52db35547fb… Author: mvdbeek <m.vandenbeek(a)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/2906f0c0857fc958f7e9049e2e71… Author: mvdbeek <m.vandenbeek(a)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/6c22726db082cedee9884bde9aa9… Author: mvdbeek <m.vandenbeek(a)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/431a4824abf91b7a10e5417d63a9… Author: mvdbeek <m.vandenbeek(a)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/ea9ecdf57150e800115ae28f6e80… Author: mvdbeek <m.vandenbeek(a)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/db910f4f81771f91f9a5b96bfc5f… Author: mvdbeek <m.vandenbeek(a)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/9aa5556dedb35b748ed17b20fd26… Author: mvdbeek <m.vandenbeek(a)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/475b8866bad2a58b314354ae73ee… Author: mvdbeek <m.vandenbeek(a)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/beae93bf766fc48a3a2f2edcd275… Author: John Chilton <jmchilton(a)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/a83ef0b86c0acbfb7c0bf1b40579… Author: mvdbeek <m.vandenbeek(a)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/3ff2a7832a949d300d9cddab0fea… Author: mvdbeek <m.vandenbeek(a)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/c905c4217b0397f92b2eb1019308… Author: mvdbeek <m.vandenbeek(a)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/b72994fe0294326f99df880e3ba7… Author: mvdbeek <m.vandenbeek(a)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/84c1559d473f7d9234173aeb802f… Author: mvdbeek <m.vandenbeek(a)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/0504dcd2997bc4673ded5c7fdc1e… Author: mvdbeek <m.vandenbeek(a)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/cbed78fbfbcb1c381af5be9442c8… Author: mvdbeek <m.vandenbeek(a)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/4dd49c938d2c7bcfac37fe475ecc… Author: mvdbeek <m.vandenbeek(a)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/dc1617596e47c384b8a88de395fe… Author: mvdbeek <m.vandenbeek(a)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/4c44338144763819f78f99b84d58… Author: mvdbeek <m.vandenbeek(a)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/5069815c0eba0a7c4c406ec0f781… Author: mvdbeek <m.vandenbeek(a)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/d15813cb2a489e1de8771886e9df… Author: mvdbeek <m.vandenbeek(a)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/586f49486cf4c1f4597237d3df95… Author: mvdbeek <m.vandenbeek(a)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/3d6bc1d56372b5853fdddd08362d… Author: mvdbeek <m.vandenbeek(a)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/07da123e9d311e5ec453399024ef… Author: mvdbeek <m.vandenbeek(a)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/677d98622dfa30a65d8a8fc392c2… Author: mvdbeek <m.vandenbeek(a)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/f940c797ff981c3f0a12b6a3abee… Author: mvdbeek <m.vandenbeek(a)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/89f57f2aa753f5de9673cd3dcf5c… Author: mvdbeek <m.vandenbeek(a)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/456d1b47b62d05d3fc5180d4f9da… Author: mvdbeek <m.vandenbeek(a)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/8411b0253adc947838af760e4614… Author: mvdbeek <m.vandenbeek(a)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/15e2c9b61aae9476b519a8c2e1c2… Author: mvdbeek <m.vandenbeek(a)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/7e61f8c047ce3cb29f5d9999a93b… Author: mvdbeek <m.vandenbeek(a)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/141f15256e8ef39baf457be1e8ef… Author: mvdbeek <m.vandenbeek(a)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/73c7c364a25caf519dfd4cfea17b… Author: mvdbeek <m.vandenbeek(a)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/869d7bf481e77aca420cc3970844… Author: mvdbeek <m.vandenbeek(a)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.Elem…) Commit: 3079d0c239bf7c46d872e65d107eaab4b3741b46 https://github.com/galaxyproject/galaxy/commit/3079d0c239bf7c46d872e65d107e… Author: mvdbeek <m.vandenbeek(a)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/f88304b65b430da0a3db67e25e45… Author: mvdbeek <m.vandenbeek(a)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/5e7da2c910e28e13b5a79c3ad794… Author: mvdbeek <m.vandenbeek(a)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/5a26896745c16e25ce951ee3a85b… Author: mvdbeek <m.vandenbeek(a)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/f199d5b434da500330520f891a31… Author: mvdbeek <m.vandenbeek(a)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/b4e4f3ce7a9bc6ef06b4191bf8f8… Author: mvdbeek <m.vandenbeek(a)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/ff1b66afb325ebe68a2d17450398… Author: mvdbeek <m.vandenbeek(a)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/84351de20bef488022cf82ac2610… Author: mvdbeek <m.vandenbeek(a)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/b666649c8159316eaa22bc4c8957… Author: mvdbeek <m.vandenbeek(a)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/86684df5ef235b6390f0cfa83892… Author: mvdbeek <m.vandenbeek(a)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/cdad5bee9b1f9761a5b3ab56cbdc… Author: mvdbeek <m.vandenbeek(a)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/2587ab55b8743ae626f977961e4f… Author: mvdbeek <m.vandenbeek(a)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/af156a8f7496dc9a9e70d3992f22… Author: mvdbeek <m.vandenbeek(a)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/a6415b25fdb9661504505ba9c501… Author: Martin Cech <marten(a)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

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[galaxyproject/galaxy] 86ebe2: Enhance filenames with collection context when dow...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 86ebe28667008d65f0c4223e22df1e74837baf11 https://github.com/galaxyproject/galaxy/commit/86ebe28667008d65f0c4223e22df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/datatypes/data.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Enhance filenames with collection context when downloading datasets from GUI. - Reduce duplication related to calculating filename. - Formalized pattern for normal dataset download using string.Tempalte - "Galaxy${hid}-[${name}].${ext}". - In the context of collections, hid and name of the datasets are pretty worthless so I used a second pattern for collections based on where it is in the current GUI frame. The new pattern is "Galaxy${hdca_hid}-[${hdca_name}__${element_identifier}].${ext}". - The patterns make this a little more tweakable - for people who want something different it should be pretty straight forward to make these patterns configurable. Fixes #2140 I think. Commit: ef92904afaa0222e66e0861dbb37fdf07e541a88 https://github.com/galaxyproject/galaxy/commit/ef92904afaa0222e66e0861dbb37… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Repack client. Commit: 4b7d5e32d4a0cd6ffa72e6551b57022a4d2dc6d2 https://github.com/galaxyproject/galaxy/commit/4b7d5e32d4a0cd6ffa72e6551b57… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/datatypes/data.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Merge pull request #3985 from jmchilton/fix_collection_download_name Enhance filenames with collection context when downloading datasets from GUI. Compare: https://github.com/galaxyproject/galaxy/compare/06e2e67872b8...4b7d5e32d4a0

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[galaxyproject/galaxy] d082f1: Purely clientside implementation of hashtag shortc...
by GitHub 01 May '17

01 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d082f1c334f3079249ed4d2404c52ac96850dc4b https://github.com/galaxyproject/galaxy/commit/d082f1c334f3079249ed4d2404c5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tag.js Log Message: ----------- Purely clientside implementation of hashtag shortcut for nametags. These are translated to 'name:nametag_value' prior to saving and are persisted in that form. Commit: f3dbf55aad06c64e26fd7dd44db9a87c73835153 https://github.com/galaxyproject/galaxy/commit/f3dbf55aad06c64e26fd7dd44db9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tag.js Log Message: ----------- Render 'name:' as hashtags. I personally like the display better and it'll nudge people towards using them I think, while still giving us the 'real' tagging hierarchy to work with. Commit: 9f36bea7f1aa25bc193ec1bcc243d303cbfff1bc https://github.com/galaxyproject/galaxy/commit/9f36bea7f1aa25bc193ec1bcc243… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tag.js Log Message: ----------- Slight refactoring, also name->hash for recommended tags. Commit: a2b8a7d26ab748d7565ef9245a678bc2740d1bdd https://github.com/galaxyproject/galaxy/commit/a2b8a7d26ab748d7565ef9245a67… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/ui/ui-select-content.js M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M test/api/test_workflows.py M test/qunit/tests/ui_tests.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into hashtags Commit: 1d9b7d592b131b69b91c40eeed3e844df65f67e4 https://github.com/galaxyproject/galaxy/commit/1d9b7d592b131b69b91c40eeed3e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into hashtags Commit: 7b50ae39b0d4ad5208e97f86c60e16bfa9fcfbff https://github.com/galaxyproject/galaxy/commit/7b50ae39b0d4ad5208e97f86c60e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M CITATION M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/tools/data_manager.py M run_tests.sh M setup.cfg M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_jobs.py M test/api/test_workflows.py M test/galaxy_selenium/navigates_galaxy.py M test/qunit/tests/form_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into hashtags Commit: 06e2e67872b8de486c189fd513ac5458c91dc2e5 https://github.com/galaxyproject/galaxy/commit/06e2e67872b8de486c189fd513ac… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tag.js Log Message: ----------- Merge pull request #3979 from dannon/hashtags Hashtags Compare: https://github.com/galaxyproject/galaxy/compare/edff1e65b9bd...06e2e67872b8

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[galaxyproject/galaxy] d638e3: Quick fix for displaying a message instead of just...
by GitHub 01 May '17

01 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d638e377054893554e31f93d009c3bb153c6ddf5 https://github.com/galaxyproject/galaxy/commit/d638e377054893554e31f93d009c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Quick fix for displaying a message instead of just redirecting on clientside routes when login is required. TODO: refactor both message display and the decoration of routes. Commit: edff1e65b9bd08b09ac864c93cbec867be23b444 https://github.com/galaxyproject/galaxy/commit/edff1e65b9bd08b09ac864c93cbe… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #4000 from dannon/error_message_for_login_required Displaying a message instead of just redirecting Compare: https://github.com/galaxyproject/galaxy/compare/37c7425eae98...edff1e65b9bd

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[galaxyproject/galaxy] 2586df: Remove pydocstyle pins - there was an update to fl...
by GitHub 01 May '17

01 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2586df45637d794c63252838573b2d1e6d692243 https://github.com/galaxyproject/galaxy/commit/2586df45637d794c63252838573b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M .ci/flake8_wrapper_docstrings.sh M setup.cfg M tox.ini Log Message: ----------- Remove pydocstyle pins - there was an update to flake8-docstrings. Commit: 37c7425eae98c8cc39b7a0d9ca6b8cf5c4e0cbcd https://github.com/galaxyproject/galaxy/commit/37c7425eae98c8cc39b7a0d9ca6b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M .ci/flake8_wrapper_docstrings.sh M setup.cfg M tox.ini Log Message: ----------- Merge pull request #3995 from jmchilton/flake8fixes Remove pydocstyle pins - there was an update to flake8-docstrings. Compare: https://github.com/galaxyproject/galaxy/compare/09404117b9d4...37c7425eae98

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[galaxyproject/galaxy] 5a6e53: Rework Jupyter IE for additional_ids handling.
by GitHub 01 May '17

01 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a6e53f728858d14064c984956c5c24666395da3 https://github.com/galaxyproject/galaxy/commit/5a6e53f728858d14064c984956c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Rework Jupyter IE for additional_ids handling. - Add a new option ``use_volumes`` to the Docker config. - If using volumes, do nothing differently. - If not using volumes, set ADDITIONAL_IDS in the environment for the IE itself to fetch (requires https://github.com/bgruening/docker-jupyter-notebook/pull/17) Commit: 9bc24aeef06b3536a6f69ddc23ac1ede4fb9b7a0 https://github.com/galaxyproject/galaxy/commit/9bc24aeef06b3536a6f69ddc23ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Update rstudio to match additional hid handling of Jupyter. Ping @erasche - does this work? I'm not sure how rstudio handles the existing DATASET_HID. Commit: 6201c61d72df9b3b0a1af454d52e4462c02fc587 https://github.com/galaxyproject/galaxy/commit/6201c61d72df9b3b0a1af454d52e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Add a note about use_volumes to Jupyter and RStudio GIEs. Commit: 09404117b9d45e73650665a612fa7001ce5006f2 https://github.com/galaxyproject/galaxy/commit/09404117b9d45e73650665a612fa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3980 from jmchilton/ie_for_mac_os_x_fixes Rework Jupyter IE for additional_ids handling. Compare: https://github.com/galaxyproject/galaxy/compare/4c1f9c8f0d8e...09404117b9d4

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[galaxyproject/galaxy] 313a00: Add entry for empty_extra_files_path validator
by GitHub 01 May '17

01 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 313a006ae3ea9d383ad102ceda17f657275ff5bf https://github.com/galaxyproject/galaxy/commit/313a006ae3ea9d383ad102ceda17… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add entry for empty_extra_files_path validator Commit: 4c1f9c8f0d8ea2a58264fdbcb53accf3f7b52dac https://github.com/galaxyproject/galaxy/commit/4c1f9c8f0d8ea2a58264fdbcb53a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3994 from gregvonkuster/xsd Add entry for empty_extra_files_path validator Compare: https://github.com/galaxyproject/galaxy/compare/7b385c2b849f...4c1f9c8f0d8e

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[galaxyproject/galaxy]
by GitHub 01 May '17

01 May '17

Branch: refs/heads/speedup_toolbox Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 41cbe2: Use floating point to log toolox reload times
by GitHub 01 May '17

01 May '17

Branch: refs/heads/speedup_toolbox Home: https://github.com/galaxyproject/galaxy Commit: 41cbe242991eb69bc821a9f2d0b8ab599b73aa9a https://github.com/galaxyproject/galaxy/commit/41cbe242991eb69bc821a9f2d0b8… Author: mvdbeek <m.vandenbeek(a)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/4d1cae41cb7ce0d3aa10d413de8e… Author: mvdbeek <m.vandenbeek(a)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/c06b4c92658563fda4efe8b1dcf6… Author: mvdbeek <m.vandenbeek(a)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/43c9c287a9a3520d77cc9235dfbf… Author: mvdbeek <m.vandenbeek(a)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/34ed9b48ddc2fdd0e2456b959fed… Author: mvdbeek <m.vandenbeek(a)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/c6429bff1c38b2196fece8155449… Author: mvdbeek <m.vandenbeek(a)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/96cb87431402454fa52db35547fb… Author: mvdbeek <m.vandenbeek(a)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/2906f0c0857fc958f7e9049e2e71… Author: mvdbeek <m.vandenbeek(a)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/6c22726db082cedee9884bde9aa9… Author: mvdbeek <m.vandenbeek(a)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/431a4824abf91b7a10e5417d63a9… Author: mvdbeek <m.vandenbeek(a)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/ea9ecdf57150e800115ae28f6e80… Author: mvdbeek <m.vandenbeek(a)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/db910f4f81771f91f9a5b96bfc5f… Author: mvdbeek <m.vandenbeek(a)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/9aa5556dedb35b748ed17b20fd26… Author: mvdbeek <m.vandenbeek(a)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/475b8866bad2a58b314354ae73ee… Author: mvdbeek <m.vandenbeek(a)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/beae93bf766fc48a3a2f2edcd275… Author: John Chilton <jmchilton(a)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/a83ef0b86c0acbfb7c0bf1b40579… Author: mvdbeek <m.vandenbeek(a)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/3ff2a7832a949d300d9cddab0fea… Author: mvdbeek <m.vandenbeek(a)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/c905c4217b0397f92b2eb1019308… Author: mvdbeek <m.vandenbeek(a)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/b72994fe0294326f99df880e3ba7… Author: mvdbeek <m.vandenbeek(a)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/84c1559d473f7d9234173aeb802f… Author: mvdbeek <m.vandenbeek(a)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/0504dcd2997bc4673ded5c7fdc1e… Author: mvdbeek <m.vandenbeek(a)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/cbed78fbfbcb1c381af5be9442c8… Author: mvdbeek <m.vandenbeek(a)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/4dd49c938d2c7bcfac37fe475ecc… Author: mvdbeek <m.vandenbeek(a)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/dc1617596e47c384b8a88de395fe… Author: mvdbeek <m.vandenbeek(a)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/4c44338144763819f78f99b84d58… Author: mvdbeek <m.vandenbeek(a)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/5069815c0eba0a7c4c406ec0f781… Author: mvdbeek <m.vandenbeek(a)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/d15813cb2a489e1de8771886e9df… Author: mvdbeek <m.vandenbeek(a)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/586f49486cf4c1f4597237d3df95… Author: mvdbeek <m.vandenbeek(a)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/3d6bc1d56372b5853fdddd08362d… Author: mvdbeek <m.vandenbeek(a)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/07da123e9d311e5ec453399024ef… Author: mvdbeek <m.vandenbeek(a)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/677d98622dfa30a65d8a8fc392c2… Author: mvdbeek <m.vandenbeek(a)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/f940c797ff981c3f0a12b6a3abee… Author: mvdbeek <m.vandenbeek(a)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/89f57f2aa753f5de9673cd3dcf5c… Author: mvdbeek <m.vandenbeek(a)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/456d1b47b62d05d3fc5180d4f9da… Author: mvdbeek <m.vandenbeek(a)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/8411b0253adc947838af760e4614… Author: mvdbeek <m.vandenbeek(a)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/15e2c9b61aae9476b519a8c2e1c2… Author: mvdbeek <m.vandenbeek(a)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/7e61f8c047ce3cb29f5d9999a93b… Author: mvdbeek <m.vandenbeek(a)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/141f15256e8ef39baf457be1e8ef… Author: mvdbeek <m.vandenbeek(a)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/73c7c364a25caf519dfd4cfea17b… Author: mvdbeek <m.vandenbeek(a)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/869d7bf481e77aca420cc3970844… Author: mvdbeek <m.vandenbeek(a)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.Elem…) Commit: 3079d0c239bf7c46d872e65d107eaab4b3741b46 https://github.com/galaxyproject/galaxy/commit/3079d0c239bf7c46d872e65d107e… Author: mvdbeek <m.vandenbeek(a)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/f88304b65b430da0a3db67e25e45… Author: mvdbeek <m.vandenbeek(a)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/5e7da2c910e28e13b5a79c3ad794… Author: mvdbeek <m.vandenbeek(a)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/5a26896745c16e25ce951ee3a85b… Author: mvdbeek <m.vandenbeek(a)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/f199d5b434da500330520f891a31… Author: mvdbeek <m.vandenbeek(a)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/b4e4f3ce7a9bc6ef06b4191bf8f8… Author: mvdbeek <m.vandenbeek(a)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/ff1b66afb325ebe68a2d17450398… Author: mvdbeek <m.vandenbeek(a)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/84351de20bef488022cf82ac2610… Author: mvdbeek <m.vandenbeek(a)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/b666649c8159316eaa22bc4c8957… Author: mvdbeek <m.vandenbeek(a)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/86684df5ef235b6390f0cfa83892… Author: mvdbeek <m.vandenbeek(a)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/cdad5bee9b1f9761a5b3ab56cbdc… Author: mvdbeek <m.vandenbeek(a)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/2587ab55b8743ae626f977961e4f… Author: mvdbeek <m.vandenbeek(a)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/af156a8f7496dc9a9e70d3992f22… Author: mvdbeek <m.vandenbeek(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/41cbe242991e^...af156a8f7496

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[galaxyproject/usegalaxy-playbook] d5480a: Update Test
by GitHub 01 May '17

01 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d5480a5d067ba3629f8ecf2a008416c4973ec508 https://github.com/galaxyproject/usegalaxy-playbook/commit/d5480a5d067ba362… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 9f449f0603c50a25c9c6bb697878f6095691bea6 https://github.com/galaxyproject/usegalaxy-playbook/commit/9f449f0603c50a25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Fix datamanager server name Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/7684bd4ff0f0...…

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[galaxyproject/galaxy] a26991: Selenium workflow run test case fix.
by GitHub 01 May '17

01 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a26991b2a8bea94a98eae38bdacc4739a818f57a https://github.com/galaxyproject/galaxy/commit/a26991b2a8bea94a98eae38bdacc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Selenium workflow run test case fix. The ``with self.main_panel():`` construct wasn't cleaning up properly - I've fixed this and eliminated the terrible workarounds in the execution test case that I guess I had added trying to figure out how to make things work. It should be more stable now. (This test case has been failing 1 out 9 times I'd say.) Commit: 7b385c2b849fc091a477b75a9194a99934454f8e https://github.com/galaxyproject/galaxy/commit/7b385c2b849fc091a477b75a9194… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #3992 from jmchilton/selenium_fixes_9 Fixes for Selenium workflow run test case. Compare: https://github.com/galaxyproject/galaxy/compare/ffed281c33be...7b385c2b849f

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[galaxyproject/usegalaxy-playbook] 3dcc06: update TTS
by GitHub 01 May '17

01 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3dcc0653c2816126d10fbdbcf518c192eb20c279 https://github.com/galaxyproject/usegalaxy-playbook/commit/3dcc0653c2816126… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-30 (Sun, 30 Apr 2017) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/galaxy] b12b95: Attempted fix for transiently failing API test_job...
by GitHub 30 Apr '17

30 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b12b951e91e6b8472f81d73f184c40aac7f9aad8 https://github.com/galaxyproject/galaxy/commit/b12b951e91e6b8472f81d73f184c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Attempted fix for transiently failing API test_jobs introduced in #3619. A couple things need to occur while the jobs are "running" and it seems that 60 seconds wasn't enough time to sleep for all that to happen on Jenkins. I checked the timing in the raw logs (they are for some reasons being filtered out in the Jenkins display of the XUnit) - and indeed the jobs are properly sleeping the correct amount of time but the client API calls need some more time it seems. My initial thought was maybe the jobs were being interrupted or something - and that does not appear to be the case. Commit: ffed281c33be5bcb1006cd3e94055fa01e5c3d18 https://github.com/galaxyproject/galaxy/commit/ffed281c33be5bcb1006cd3e9405… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-30 (Sun, 30 Apr 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Merge pull request #3988 from jmchilton/job_test_timing_improvements Attempted fix for transiently failing API test_jobs introduced in #3619. Compare: https://github.com/galaxyproject/galaxy/compare/c93afcec64d5...ffed281c33be

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