February 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 169b45: Fix step name display for 17.01
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 169b45b138685164010043be95cefe8148c6f713 https://github.com/galaxyproject/galaxy/commit/169b45b138685164010043be95ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix step name display for 17.01 Commit: 7824cd31fd7b9351efa1cf8274b89b2b9a0d811d https://github.com/galaxyproject/galaxy/commit/7824cd31fd7b9351efa1cf8274b8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3681 from guerler/fix_name_display [17.01] Fix step name display for 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/e23facb966c9...7824cd31fd7b

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[galaxyproject/galaxy] 102fff: When using the new slow query logger, include para...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 102fffd172963c0e97a7b469c394c3d239935e9c https://github.com/galaxyproject/galaxy/commit/102fffd172963c0e97a7b469c394… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- When using the new slow query logger, include parameters. Originally left these out, but 1) logs are assumed to be secure, and 2) it's super useful Commit: f0a26f309dd330e49e8e7ad227db5e40507f60cc https://github.com/galaxyproject/galaxy/commit/f0a26f309dd330e49e8e7ad227db… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3649 from dannon/slowquery_tweak When using the new slow query logger, include parameters. Compare: https://github.com/galaxyproject/galaxy/compare/5efbab864cab...f0a26f309dd3

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[galaxyproject/galaxy] 33c528: Generate primary composite file after extra files ...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33c528ee13e6c4317ac4acc9b48ba157c5976b6c https://github.com/galaxyproject/galaxy/commit/33c528ee13e6c4317ac4acc9b48b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Generate primary composite file after extra files collection. Commit: 5efbab864cab6693d4bde2159661a6ff6c7caafd https://github.com/galaxyproject/galaxy/commit/5efbab864cab6693d4bde2159661… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #3678 from blankenberg/composite-auto-after Generate primary composite file after extra files collection. Compare: https://github.com/galaxyproject/galaxy/compare/a505fa79ac26...5efbab864cab

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[galaxyproject/galaxy] 099734: fix tool search idnex building for tools with / in...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0997348a1c0a450986d376a96af024c73d4c7f37 https://github.com/galaxyproject/galaxy/commit/0997348a1c0a450986d376a96af0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- fix tool search idnex building for tools with / in id and not from TS Commit: c11cb3dd4572e7a4f1f814a31a45477f9ecd5ae9 https://github.com/galaxyproject/galaxy/commit/c11cb3dd4572e7a4f1f814a31a45… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- fix typo spotted by :beer: :eyes: Commit: e23facb966c9962bb5bd1fdd07bf6ee28d7d5930 https://github.com/galaxyproject/galaxy/commit/e23facb966c9962bb5bd1fdd07bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #3680 from martenson/fix-id-indexing [17.01] fix tool search index building for tools with slash in id and not from TS Compare: https://github.com/galaxyproject/galaxy/compare/28875de584ac...e23facb966c9

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[galaxyproject/galaxy] cbc1fa: Set LDAP options only once.
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cbc1faf3a45d58353a9d352047fbbedb970e3215 https://github.com/galaxyproject/galaxy/commit/cbc1faf3a45d58353a9d352047fb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Set LDAP options only once. Always check option value is not empty in _get_subs() Better log message for malformed <ldap_options> Commit: a505fa79ac26e2f30a4404f9a11f3b029abb5436 https://github.com/galaxyproject/galaxy/commit/a505fa79ac26e2f30a4404f9a11f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #3663 from nsoranzo/ldap_auth Set LDAP options only once. Compare: https://github.com/galaxyproject/galaxy/compare/1bac3b3be818...a505fa79ac26

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[galaxyproject/galaxy] f64525: Only keep the last path element when naming files ...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f645259dd0633cfdac2768c7de2d1de918bc1bbe https://github.com/galaxyproject/galaxy/commit/f645259dd0633cfdac2768c7de2d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Only keep the last path element when naming files uploaded via the URL paste method Commit: 1bac3b3be81821a4cbe687165985cfafd7989b46 https://github.com/galaxyproject/galaxy/commit/1bac3b3be81821a4cbe687165985… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #3674 from natefoo/upload-drop-url-name Only keep the last path element when naming files uploaded via the URL paste method Compare: https://github.com/galaxyproject/galaxy/compare/194fb1eb07b6...1bac3b3be818

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[galaxyproject/galaxy] fb17e5: Use former version of autocomplete module for grid...
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb17e55a1daf90220e19980fd8fd56dd70b2cde2 https://github.com/galaxyproject/galaxy/commit/fb17e55a1daf90220e19980fd8fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Use former version of autocomplete module for grids Commit: 3efe748279711e89852bf7bf173612ff9cbe45de https://github.com/galaxyproject/galaxy/commit/3efe748279711e89852bf7bf1736… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako Log Message: ----------- Strip partially removed autocomplete feature for history names, removed in #1303 Commit: 194fb1eb07b627682b258d5c302aeb75b266cf89 https://github.com/galaxyproject/galaxy/commit/194fb1eb07b627682b258d5c302a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako Log Message: ----------- Merge pull request #3676 from guerler/fix_jquery_autocomplete Strip broken autocomplete feature, webbrowsers console error is an artifact Compare: https://github.com/galaxyproject/galaxy/compare/c8dd5f9b25ac...194fb1eb07b6

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[galaxyproject/galaxy] 5a5dbb: improve 17.01 get galaxy release notes
by GitHub 28 Feb '17

28 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 5a5dbb97f1e04dfe15fbf71c441eb50ae4b70b11 https://github.com/galaxyproject/galaxy/commit/5a5dbb97f1e04dfe15fbf71c441e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- improve 17.01 get galaxy release notes Commit: 28875de584ac1967a8f2c0cdc8f5fa7b37e70f21 https://github.com/galaxyproject/galaxy/commit/28875de584ac1967a8f2c0cdc8f5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3670 from martenson/fix-RN1701 [17.01] improve 17.01 get galaxy release notes Compare: https://github.com/galaxyproject/galaxy/compare/d4b677bc38b2...28875de584ac

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[galaxyproject/galaxy] 063605: Use pgcalc when possible
by GitHub 27 Feb '17

27 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0636053901545a26662ed8f42a15bb67407f2231 https://github.com/galaxyproject/galaxy/commit/0636053901545a26662ed8f42a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Use pgcalc when possible Commit: 895351cdf8e8867452d28dffb89a2067eabfadb3 https://github.com/galaxyproject/galaxy/commit/895351cdf8e8867452d28dffb89a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- initial working async recalc Commit: 45d75e3da55e43a4444c1a7982e1ea31e1aa5cb7 https://github.com/galaxyproject/galaxy/commit/45d75e3da55e43a4444c1a7982e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Encode userid in messages. Commit: c373bf27e79e48bc2e8ba983e9f08abde16db4df https://github.com/galaxyproject/galaxy/commit/c373bf27e79e48bc2e8ba983e9f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Change handling of declare in queue_async_task Commit: 00b1591f05af4743d8b16b7d1bbbbc99a3974adb https://github.com/galaxyproject/galaxy/commit/00b1591f05af4743d8b16b7d1bbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix inline doc Commit: 53c00df805e7ae7e509c08374bc941d31d20000d https://github.com/galaxyproject/galaxy/commit/53c00df805e7ae7e509c08374bc9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Rename send_local_controL_task, add at least a tiny bit of documentation. Commit: d4b677bc38b221678bc991e0fddc43622accb928 https://github.com/galaxyproject/galaxy/commit/d4b677bc38b221678bc991e0fddc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3669 from dannon/logout-recalc-improvements [17.01] Logout recalc improvements Compare: https://github.com/galaxyproject/galaxy/compare/64036a441284...d4b677bc38b2

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[galaxyproject/galaxy] d3f2df: improve wording of getgalaxy in bootstrapping scri...
by GitHub 26 Feb '17

26 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3f2df57699bf6b85fdb16f85d023d562342f778 https://github.com/galaxyproject/galaxy/commit/d3f2df57699bf6b85fdb16f85d02… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- improve wording of getgalaxy in bootstrapping script for RN Commit: c8dd5f9b25ac222ff37fe06bed5d1834f292e485 https://github.com/galaxyproject/galaxy/commit/c8dd5f9b25ac222ff37fe06bed5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-26 (Sun, 26 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3671 from martenson/improve-bootstrapping improve wording of getgalaxy in bootstrapping script for RN Compare: https://github.com/galaxyproject/galaxy/compare/a5ea10622bf2...c8dd5f9b25ac

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