Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab6ae42c7a7d76b3fbf024edbbdec407b7b1f490 https://github.com/galaxyproject/galaxy/commit/ab6ae42c7a7d76b3fbf024edbbdec... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.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/history/history-view.js Log Message: ----------- Cancel existing delayed updates when changing pages in the history. Commit: f155a9420a23241c6dc7e404ce487c803a911726 https://github.com/galaxyproject/galaxy/commit/f155a9420a23241c6dc7e404ce487... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.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/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- temp Commit: f53b6474828d1f8ab1170630ce5851bb913ebec7 https://github.com/galaxyproject/galaxy/commit/f53b6474828d1f8ab1170630ce585... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- WIP: Fix for conda=4.3 Commit: d37ed7e7dadcf568b22836f477ce5afd2a377af7 https://github.com/galaxyproject/galaxy/commit/d37ed7e7dadcf568b22836f477ce5... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Adjust offline fix to work for a broader range of potential target Condas. This logic could in theory be backported all the way to 16.01 I suppose now. Commit: 1e3c9ab945c4616510b5b4ff2726aab89585bef4 https://github.com/galaxyproject/galaxy/commit/1e3c9ab945c4616510b5b4ff2726a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- More revisions to fixing --offline mode to Conda. Incorporate package extraction fixes thanks to @nsoranzo, the fix for version 4.1 and 4.0 thanks to @mvdbeek, a comment for @bgruening and a new test tool that makes it a bit easier to test this. Commit: 0024aa458216589589d35b9366c6347c0c280860 https://github.com/galaxyproject/galaxy/commit/0024aa458216589589d35b9366c63... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M test/functional/tools/mulled_example_multi_incomplete.xml Log Message: ----------- Add a clarification to new test tool. Commit: f6cc1dcf077f9d98c38afdd93d47e60c42ac06e5 https://github.com/galaxyproject/galaxy/commit/f6cc1dcf077f9d98c38afdd93d47e... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3632 from jmchilton/conda_43_fix [17.01] Fix Conda --offline logic for bug in 4.0,4.1,4.3. Commit: f1f6bf6c3a765e05f8a2dc2b127ee480a485b42e https://github.com/galaxyproject/galaxy/commit/f1f6bf6c3a765e05f8a2dc2b127ee... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix annotation display for data inputs Commit: ce264f9542df6d4ba779309fb8e7822c6f351f2e https://github.com/galaxyproject/galaxy/commit/ce264f9542df6d4ba779309fb8e78... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.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/history/options-menu.js Log Message: ----------- Reimplement *old* method for unhide/delete-all-hidden using a temporary web controller endpoint. Commit: a3a7e1001cc0ffa985fd7e987c7190f2d74492ff https://github.com/galaxyproject/galaxy/commit/a3a7e1001cc0ffa985fd7e987c719... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.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/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- Strip stashed-yet-merged debug detritus from history UI fixes. Commit: bf602a8add58289900fa64cc5c1163c0721f1d10 https://github.com/galaxyproject/galaxy/commit/bf602a8add58289900fa64cc5c116... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Yet more debugging cruft. This is why we have reviews. Commit: 493cf2816134562188ba009e8bf04ffbcc18a2ac https://github.com/galaxyproject/galaxy/commit/493cf2816134562188ba009e8bf04... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.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/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3621 from dannon/fix-paginated-history-updates [17.01] History Fixes Commit: 0278753d0e2db921cd7d3f55cef483defff5cdb9 https://github.com/galaxyproject/galaxy/commit/0278753d0e2db921cd7d3f55cef48... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Increase patience of Galaxy tests throughout. This should help reduce various API and Selenium transient failures. Commit: 09c08d1f61f93ec7973cab1d2cd24532d20e3bb7 https://github.com/galaxyproject/galaxy/commit/09c08d1f61f93ec7973cab1d2cd24... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3636 from guerler/fix_annotation [17.01] Fix annotation display for data inputs Commit: caf57c6f3e21eb38e3331d1a1dd44f2cd5b68dc2 https://github.com/galaxyproject/galaxy/commit/caf57c6f3e21eb38e3331d1a1dd44... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #3637 from jmchilton/backport_3589 [17.01] Backport #3589 Commit: f7a14e1c90270f557d52fda196400653b0b9d09f https://github.com/galaxyproject/galaxy/commit/f7a14e1c90270f557d52fda196400... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Use `command -v` rather than `which` when determining Galaxy Python for external set metadata. Commit: 305f461d45ab010c10fa6061cd7d248e354a9967 https://github.com/galaxyproject/galaxy/commit/305f461d45ab010c10fa6061cd7d2... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix inability to access API key for users Commit: 62475c50a03927aa2461543c227c60909adff332 https://github.com/galaxyproject/galaxy/commit/62475c50a03927aa2461543c227c6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3640 from erasche/fix-api-access-external [17.01] Fix inability to access API key for users Commit: 29f8b54c9a8a975473ecbee96992ec400fd138b5 https://github.com/galaxyproject/galaxy/commit/29f8b54c9a8a975473ecbee96992e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #3638 from natefoo/use-version-not-which [17.01] Use `command -v` rather than `which` when determining Galaxy Python for external set metadata Commit: 24eba8c58ee9d7f8907c83f5d72ea01997d56ab4 https://github.com/galaxyproject/galaxy/commit/24eba8c58ee9d7f8907c83f5d72ea... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.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/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: client/galaxy/scripts/mvc/tool/tool-form-composite.js static/maps/mvc/tool/tool-form-composite.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-composite.js Commit: 9563a691b05f65ec3bdcd9135f75878b2ec666e3 https://github.com/galaxyproject/galaxy/commit/9563a691b05f65ec3bdcd9135f758... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.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/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3641 from nsoranzo/merge_17.01 Merge 17.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/badf49daa54a...9563a691b05f