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[galaxyproject/galaxy] a904df: Only parse once
by GitHub 03 Sep '17

03 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a904df604ef6962628916635d42068ece1368d01 https://github.com/galaxyproject/galaxy/commit/a904df604ef6962628916635d420… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Only parse once Commit: cbe6970a4cf5c5a3b7bb55c97d7190fef4019388 https://github.com/galaxyproject/galaxy/commit/cbe6970a4cf5c5a3b7bb55c97d71… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- per @nsoranzo, only log error message when it is there Commit: e130b55b04c8bc7c30b85ac7e2688890b890c71c https://github.com/galaxyproject/galaxy/commit/e130b55b04c8bc7c30b85ac7e268… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- log error if does not exist Commit: 0159162c9e7b3463b2f667fec820d3ae83bfd3dc https://github.com/galaxyproject/galaxy/commit/0159162c9e7b3463b2f667fec820… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Merge branch 'parse-once' of github.com:erasche/galaxy into parse-once Commit: 8f1303217eea29e4973cbbbd13c4b3f8b47f8d5c https://github.com/galaxyproject/galaxy/commit/8f1303217eea29e4973cbbbd13c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #4495 from erasche/parse-once 41% reduction in freiburg galaxy startup time Compare: https://github.com/galaxyproject/galaxy/compare/f6fa7c39f104...8f1303217eea

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[galaxyproject/galaxy] 634f7d: Add a small howto on profiling galaxy code
by GitHub 03 Sep '17

03 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 634f7dcd3917eef17994a29c1f63f91c4b22a4b9 https://github.com/galaxyproject/galaxy/commit/634f7dcd3917eef17994a29c1f63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: A doc/source/dev/finding_and_improving_slow_code.rst Log Message: ----------- Add a small howto on profiling galaxy code Commit: 2e5bbad353ca76f25bff9588fea2958cd6d5596a https://github.com/galaxyproject/galaxy/commit/2e5bbad353ca76f25bff9588fea2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M doc/source/dev/finding_and_improving_slow_code.rst Log Message: ----------- Clarify the last section Commit: f6fa7c39f104d390f4a7df62d0b227ab1823c838 https://github.com/galaxyproject/galaxy/commit/f6fa7c39f104d390f4a7df62d0b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: A doc/source/dev/finding_and_improving_slow_code.rst Log Message: ----------- Merge pull request #4542 from mvdbeek/build_module_speedup Add a small howto on profiling galaxy code Compare: https://github.com/galaxyproject/galaxy/compare/b2ceef5b6c25...f6fa7c39f104

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[galaxyproject/galaxy] 259e12: Continue separation of FunctionalTestCase from Twi...
by GitHub 03 Sep '17

03 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 259e12d760c721badf9a6f65da90a9bb5bcb0983 https://github.com/galaxyproject/galaxy/commit/259e12d760c721badf9a6f65da90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/api.py A test/base/testcase.py M test/base/twilltestcase.py M test/functional/test_toolbox.py M test/selenium_tests/framework.py Log Message: ----------- Continue separation of FunctionalTestCase from TwillTestCase. Move non-twill stuff out into its own module including FunctionalTestCase. Commit: 6e17ff57ea62320e8764b390e50135d95aaa242d https://github.com/galaxyproject/galaxy/commit/6e17ff57ea62320e8764b390e501… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: R test/functional/test_library_templates.py Log Message: ----------- Remove test/functional/test_library_templates.py. Hasn't been run in forever and it seems like we are deprecating these features. Commit: 6d7c8b3136e24ff3e752efecb14f57574cd53174 https://github.com/galaxyproject/galaxy/commit/6d7c8b3136e24ff3e752efecb14f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/tool_shed_util.py Log Message: ----------- Cleanup sys.path hacking in test/base/tool_shed_util.py. Commit: 7343463daca00ef60836e99faecdf90f85c9fd2a https://github.com/galaxyproject/galaxy/commit/7343463daca00ef60836e99faecd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/driver_util.py R test/base/test_db_util.py R test/functional/database_contexts.py M test/shed_functional/base/test_db_util.py Log Message: ----------- Rework hack to inject database contexts into Tool Shed tests. Rather than depend on something in ``functional`` test module from ``base.driver_util``, just set these global hacks up in ``driver_util`` itself. This eliminates a dependency of ``functional`` on ``base`` - ideally ``base`` would not depend on any other test modules. Commit: aba726a89f69fe1dbd4b4147e725c7ce0a7a3a33 https://github.com/galaxyproject/galaxy/commit/aba726a89f69fe1dbd4b4147e725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: R test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Move twilltestcase from ``base`` to ``functional`` module. This way nothing in ``base`` has any dependencies on Twill anymore. Commit: 5358db58231482312850351d3d1dded25797dec8 https://github.com/galaxyproject/galaxy/commit/5358db58231482312850351d3d1d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/tool_shed_util.py Log Message: ----------- fix lint order Commit: b2ceef5b6c258b0d6bc90240549299dbcc3d6ee4 https://github.com/galaxyproject/galaxy/commit/b2ceef5b6c258b0d6bc902405492… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M test/base/api.py M test/base/driver_util.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/twilltestcase.py M test/selenium_tests/framework.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #4536 from jmchilton/test_refactoring Refactor test modules toward cleaner dependencies Compare: https://github.com/galaxyproject/galaxy/compare/ae7e1f97f0b7...b2ceef5b6c25

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[galaxyproject/galaxy] 471707: Build converters_by_datatype only once per registr...
by GitHub 03 Sep '17

03 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 471707bd7dfa048a412aad9cdcc1d0b4aea70bc7 https://github.com/galaxyproject/galaxy/commit/471707bd7dfa048a412aad9cdcc1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Build converters_by_datatype only once per registry lifetime Commit: d1a2007275f128fea051ead55fb47d2c2686abf5 https://github.com/galaxyproject/galaxy/commit/d1a2007275f128fea051ead55fb4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Cache user roles during WorkRequestContext lifetime This speeds up building the tool module by a factor of 5. Commit: 2d8b242e697a08775879fc873578b5f244d4d5cb https://github.com/galaxyproject/galaxy/commit/2d8b242e697a08775879fc873578… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix caching of `get_converters_by_datatype` result Commit: ae7e1f97f0b71f90968abd09dd2f88387d0dc2e4 https://github.com/galaxyproject/galaxy/commit/ae7e1f97f0b71f90968abd09dd2f… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/work/context.py Log Message: ----------- Merge pull request #4541 from mvdbeek/build_module_speedup Speedup toolform building Compare: https://github.com/galaxyproject/galaxy/compare/ea9f5f7eb253...ae7e1f97f0b7

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[galaxyproject/galaxy] 354ce1: Fix workflow run Selenium test and make it more ro...
by GitHub 03 Sep '17

03 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 354ce19677bae15d5cf976386ca988586a0c3eff https://github.com/galaxyproject/galaxy/commit/354ce19677bae15d5cf976386ca9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Fix workflow run Selenium test and make it more robust. This test went from transiently broken to always broken during this release cycle. This PR makes two changes to try to fix both of those conditions. It correct the frame and button Selector for the new workflow run UX for the newer error and this allows explicitly refreshing the browser when waiting for datasets to appear to deal with the transient problems. Commit: edd3b07c3dcace5263dafafef72b8564c8b7ce06 https://github.com/galaxyproject/galaxy/commit/edd3b07c3dcace5263dafafef72b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/galaxy_selenium/driver_factory.py Log Message: ----------- Fix "all" vs. "ALL" in Selenium logging configuration. The previous value broke all the tests on Jenkins. Commit: ea9f5f7eb2536765a175f7e411f8d64cb8c34cad https://github.com/galaxyproject/galaxy/commit/ea9f5f7eb2536765a175f7e411f8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #4524 from jmchilton/selenium_fixes_16 Fix workflow run Selenium test and make it more robust. Compare: https://github.com/galaxyproject/galaxy/compare/47efd8089c5b...ea9f5f7eb253

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[galaxyproject/galaxy] f5b29b: WIP - show/add/remove workflow tags
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5b29b82d29548a05da911b03d1b3e0dce5dc6e7 https://github.com/galaxyproject/galaxy/commit/f5b29b82d29548a05da911b03d1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- WIP - show/add/remove workflow tags Commit: 5e667a7d54eba623bbf6cb42865507e063bdb4a5 https://github.com/galaxyproject/galaxy/commit/5e667a7d54eba623bbf6cb428655… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Allow editing tags in workflow overview page Commit: b57b2de7dac8c2fb36e4f3a626d6d33c57da6064 https://github.com/galaxyproject/galaxy/commit/b57b2de7dac8c2fb36e4f3a626d6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Allow exporting and importing workflow tags Commit: e1b5a459dcfd183327d8ea1d3485fb5f509b6d82 https://github.com/galaxyproject/galaxy/commit/e1b5a459dcfd183327d8ea1d3485… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Allow updating workflows from partial information The workflow overview page gets workflow information from the /api/workflows, which returns a reduced amount of information, most notably the steps are not being returned. This commit skips updating the actual workflow steps if the steps are not included in the workflow payload. We can now update name, tags and whether a workflow should be shown in the tool panel. We also return owner and number of steps in the response to importing workflows. Commit: e2d1fabf58f813c2d722849ad9bf5d1d46517665 https://github.com/galaxyproject/galaxy/commit/e2d1fabf58f813c2d722849ad9bf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js Log Message: ----------- Remove unncessary boilerplate from workflow model Commit: 17be825cdf3714d2f335ba20ad2b6f51ad10c622 https://github.com/galaxyproject/galaxy/commit/17be825cdf3714d2f335ba20ad2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Allow renaming, downloading, dropping workflow files to import Commit: 5dfe36deceb6d4e38a82c0130a011956c29c06df https://github.com/galaxyproject/galaxy/commit/5dfe36deceb6d4e38a82c0130a01… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Only access tags if workflow exists Commit: 060952fa88dd84af04bc1e879e67726596cbc7ff https://github.com/galaxyproject/galaxy/commit/060952fa88dd84af04bc1e879e67… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Allow downloading .ga workflows via the UI Commit: 1a4effa70e9ad8088e19ae334753b7a898d286aa https://github.com/galaxyproject/galaxy/commit/1a4effa70e9ad8088e19ae334753… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove downloading workflows through controller Commit: 1015b510f81723b927866546390d179abef796f9 https://github.com/galaxyproject/galaxy/commit/1015b510f81723b927866546390d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Properly raise Exception if tool not found Commit: 70c889435892ebfd1fb88edaab187cb84ba1dccf https://github.com/galaxyproject/galaxy/commit/70c889435892ebfd1fb88edaab18… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Copy workflows without reloading page Commit: 1dcfe56bb9f1c81567efe68f5ebe4c2f4c6bfb7f https://github.com/galaxyproject/galaxy/commit/1dcfe56bb9f1c81567efe68f5ebe… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge WorkflowTagsEditor with TagsEditor Commit: f1f412ff298a3d859da1f4fe8b7640d722827a1f https://github.com/galaxyproject/galaxy/commit/f1f412ff298a3d859da1f4fe8b76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Make tag_editor local variable Commit: 911c969631a1dcfb7eee2f2499f81d662b617800 https://github.com/galaxyproject/galaxy/commit/911c969631a1dcfb7eee2f2499f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix logic for determining whether username should be mentioned Commit: e54b1d1c379f56f2b45ef129a9863be77c379ae7 https://github.com/galaxyproject/galaxy/commit/e54b1d1c379f56f2b45ef129a986… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix adjusting dropdown menu Commit: 0aa4e5463d410df448f484c13174b0e8d6ba87f8 https://github.com/galaxyproject/galaxy/commit/0aa4e5463d410df448f484c13174… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Use toastr for informing user about success/failure Commit: 61ac1d77a4679938c98e43f54bea9e52073ae32e https://github.com/galaxyproject/galaxy/commit/61ac1d77a4679938c98e43f54bea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less Log Message: ----------- Highlight workflow dropzone Commit: 09f66a6394303a70b279a34c8f63458b059febc5 https://github.com/galaxyproject/galaxy/commit/09f66a6394303a70b279a34c8f63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove unused $el_wf_link variable Commit: 1de485d3f70165ca1860fbc388a30f40d1a21888 https://github.com/galaxyproject/galaxy/commit/1de485d3f70165ca1860fbc388a3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- camelCase functions and variables Commit: bbaf59a05a7ff6bb048f93fe1eb192157301d6db https://github.com/galaxyproject/galaxy/commit/bbaf59a05a7ff6bb048f93fe1eb1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Display errors to user Commit: 2968e0e588e35da24caecd0cc4223f694332673b https://github.com/galaxyproject/galaxy/commit/2968e0e588e35da24caecd0cc422… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Show toast at the top-right (which is the default setting) Commit: 268a895d2b787d9c77a5b87d04ec772382615a8b https://github.com/galaxyproject/galaxy/commit/268a895d2b787d9c77a5b87d04ec… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js Log Message: ----------- Describe workflow model and collection (thx @martenson) Commit: aa49c0053a278d40dcc0affaf894b0e60b3d3949 https://github.com/galaxyproject/galaxy/commit/aa49c0053a278d40dcc0affaf894… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Move fetching out of WorkflowCollection thx for the hint @martenson. Commit: 9a331363cb51733b446aa44eca71f3439152d4ab https://github.com/galaxyproject/galaxy/commit/9a331363cb51733b446aa44eca71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Improve error reporting to user Commit: ede8c200f944a9cc21d894654fb6ec0027747333 https://github.com/galaxyproject/galaxy/commit/ede8c200f944a9cc21d894654fb6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M static/maps/mvc/tag.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tag.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Add static JS Commit: d0df3886fa7acaa3d5f63360e2af78aab2deaaaa https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- More workflow index page Selenium tests. - Fix rename test for recent change to using alert. - Test basic adding a tag. - Outline of a test for downloading workflows. - Add test for publishing display on index. - Add test for using the search box on the workflow index page. Commit: 47efd8089c5b1dfc67af7cf3887ce5b8b907e057 https://github.com/galaxyproject/galaxy/commit/47efd8089c5b1dfc67af7cf3887c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tag.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tag.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #4476 from mvdbeek/workflow_view_tags Show tags, import by drag-and-drop and avoid refreshed in workflow page Compare: https://github.com/galaxyproject/galaxy/compare/558e22a49cbd...47efd8089c5b

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[galaxyproject/galaxy] de624b: Sync non-CWL galaxy-lib changes.
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de624b48b14f491841921363e4ef7d1ba72db3f3 https://github.com/galaxyproject/galaxy/commit/de624b48b14f491841921363e4ef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/help.py M lib/galaxy/util/__init__.py Log Message: ----------- Sync non-CWL galaxy-lib changes. Covers https://github.com/galaxyproject/galaxy-lib/pull/71 and https://github.com/galaxyproject/galaxy-lib/pull/69. Commit: 558e22a49cbd9a1622a6b7db77ad6f66f17b5229 https://github.com/galaxyproject/galaxy/commit/558e22a49cbd9a1622a6b7db77ad… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/help.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #4535 from jmchilton/galaxy-lib Sync non-CWL galaxy-lib changes. Compare: https://github.com/galaxyproject/galaxy/compare/dd9c757a15e9...558e22a49cbd

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[galaxyproject/galaxy] a0bd78: Optimize loading of StoredWorkflow attributes
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0bd78034defb11adf2140f7c6dd90e63bc7da43 https://github.com/galaxyproject/galaxy/commit/a0bd78034defb11adf2140f7c6dd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Optimize loading of StoredWorkflow attributes WorkflowsManager.get_stored_workflow is used when exporting or editing workflows. In these cases we iterate over the related workflow objects steps as well as the related tags and annotation objects. Each iteration will emit a new SQL statement. Joinedloading these relations here speeds up the workflow run form and the editor. With sqlite as backend this speeds up exporting a workflow for the workflow editor by about 5X. Commit: 62204de0aeb4a833e43e5a1f81657293853ffb03 https://github.com/galaxyproject/galaxy/commit/62204de0aeb4a833e43e5a1f8165… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/model/item_attrs.py Log Message: ----------- Use pre-existing annotations object if possible This avoids additional requests to the database. Commit: db04f295d34e8ca03b151f462e7ffd1d613a1321 https://github.com/galaxyproject/galaxy/commit/db04f295d34e8ca03b151f462e7f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Do not provide a history in workflow_building_mode Commit: cb1392fd2d707587859bcbbb3e1744fb472ebf22 https://github.com/galaxyproject/galaxy/commit/cb1392fd2d707587859bcbbb3e17… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use WorkflowManager to get StoredWorkflow in workflow web controller Commit: 83bb7b108e90086ae0f421d63107c3870dea5d73 https://github.com/galaxyproject/galaxy/commit/83bb7b108e90086ae0f421d63107… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid ToolShedRepository attributes where possible Commit: d5eee194252270ebf4be008c6cf0492d5c6c3340 https://github.com/galaxyproject/galaxy/commit/d5eee194252270ebf4be008c6cf0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use workflow_building_modes.ENABLED instead of True Commit: e4f4dc91eebe7d5e4fbf8667bff52079498d88ea https://github.com/galaxyproject/galaxy/commit/e4f4dc91eebe7d5e4fbf8667bff5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Cache edam_data and edam_formats Commit: 17246225d962f4d1494b4b718440f42631fd6210 https://github.com/galaxyproject/galaxy/commit/17246225d962f4d1494b4b718440… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use joinedload for latest_workflow.steps when building workflow editor config Commit: 1a1232e11dd31b96284d2842292d13f9b67ee22e https://github.com/galaxyproject/galaxy/commit/1a1232e11dd31b96284d2842292d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Use get_item_annotation_str instead of get_item_annotation_obj Commit: 2faa56eefe7a8b029ed62b9b4402894c2a26248f https://github.com/galaxyproject/galaxy/commit/2faa56eefe7a8b029ed62b9b4402… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Rework if statement to be more explicit Commit: dd9c757a15e929be2ab6d138fb181f0ed543c156 https://github.com/galaxyproject/galaxy/commit/dd9c757a15e929be2ab6d138fb18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/item_attrs.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4500 from mvdbeek/workflow_loading_speedup Workflow loading speedup Compare: https://github.com/galaxyproject/galaxy/compare/9fb78b1010f8...dd9c757a15e9

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[galaxyproject/galaxy] a85d65: Another fix for Selenium worklow tests.
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a85d65c6a2ce3fd0a166e130f8a89dc198c3e0c7 https://github.com/galaxyproject/galaxy/commit/a85d65c6a2ce3fd0a166e130f8a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/selenium_tests/test_workflow_run.py Log Message: ----------- Another fix for Selenium worklow tests. This time for the workflow upgrade message test, mirrors the fix in #4524 - the content we are searching for in on this page is no longer in the iframe. Commit: 9fb78b1010f8e106d34bf0b44888265b980521fd https://github.com/galaxyproject/galaxy/commit/9fb78b1010f8e106d34bf0b44888… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #4531 from jmchilton/selenium_fixes_17 Another fix for Selenium worklow tests. Compare: https://github.com/galaxyproject/galaxy/compare/7db1a3fb3e6f...9fb78b1010f8

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[galaxyproject/galaxy] 326477: implement influxdb error reporter
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 326477d957bda9c32f63497b5fc911e8c2a9731d https://github.com/galaxyproject/galaxy/commit/326477d957bda9c32f63497b5fc9… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst A lib/galaxy/tools/error_reports/plugins/influxdb.py Log Message: ----------- implement influxdb error reporter Commit: f67fa22dd9bd05d72df859065a3e126af0161d62 https://github.com/galaxyproject/galaxy/commit/f67fa22dd9bd05d72df859065a3e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- also add destination id everywhere Commit: 7db1a3fb3e6f61540f1354a899fce1c55e834775 https://github.com/galaxyproject/galaxy/commit/7db1a3fb3e6f61540f1354a899fc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst A lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #4533 from erasche/influxdb-error-reporter Implement influxdb error reporter Compare: https://github.com/galaxyproject/galaxy/compare/49f243862207...7db1a3fb3e6f

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