Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99b... Author: MatthewRalston <mrals89@gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2f... Author: MatthewRalston <mrals89@gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babbaf... Author: Matt Ralston <mrals89@gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c971... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e7... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e30... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Commit: 449098d8b14b45269be106f6410c0b9145c51d50 https://github.com/galaxyproject/galaxy/commit/449098d8b14b45269be106f6410c0... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- upgrade mercurial wheel to latest (fixing CVE issues) Commit: dc4d4cbce7b18b33ff09f722d58a551c6f024b7a https://github.com/galaxyproject/galaxy/commit/dc4d4cbce7b18b33ff09f722d58a5... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#deprec... Commit: 7d08d1b0699a9e2adfa314af3e8324e257254ce0 https://github.com/galaxyproject/galaxy/commit/7d08d1b0699a9e2adfa314af3e832... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Specify default value when getting disable_push Commit: a560ad8999eca1137aafa466ae07683ef9f6d9d3 https://github.com/galaxyproject/galaxy/commit/a560ad8999eca1137aafa466ae076... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Update Tool Shed tests after disabling 'hg push' Commit: 28b5dd36832642b5ae519790c25fc2d15da11ca9 https://github.com/galaxyproject/galaxy/commit/28b5dd36832642b5ae519790c25fc... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0310_hg_clone.py Log Message: ----------- add TS test for disabled hg push Commit: 0bcc7e37e1d94259c6b5c29ab7e8041e4228d05d https://github.com/galaxyproject/galaxy/commit/0bcc7e37e1d94259c6b5c29ab7e80... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_clone.py Log Message: ----------- rename test to reflect insides Commit: 193eeaa60674eaa1badb65f74cb77dcb331b179b https://github.com/galaxyproject/galaxy/commit/193eeaa60674eaa1badb65f74cb77... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2056 from martenson/1601-disable-push [16.01] retroactively disable Mercurial push API in TS Commit: 90b95dc665bd736a21bd16d2852caf5c23bb83c4 https://github.com/galaxyproject/galaxy/commit/90b95dc665bd736a21bd16d2852ca... Author: John Chilton <jmchilton@gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2043 from martenson/update_mercurial_wheel [16.01] upgrade mercurial wheel to latest (fixing CVE issues) Commit: 20f61e6a2f36967e16a92cbcf8ad7f81ca76fb29 https://github.com/galaxyproject/galaxy/commit/20f61e6a2f36967e16a92cbcf8ad7... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- workaround for error message in case original toolshed had been disabled Commit: 65a7ebee23364a89d72e528bfcde6b1f6b3c5cd9 https://github.com/galaxyproject/galaxy/commit/65a7ebee23364a89d72e528bfcde6... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2072 from mvdbeek/backport_1738 [16.01] backport #1738 Commit: 2a53be67ad4ac99b6e9fe5fb803bfa44442dbd3c https://github.com/galaxyproject/galaxy/commit/2a53be67ad4ac99b6e9fe5fb803bf... Author: guerler <aysam.guerler@gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Show sections in workflow run Commit: 3002e404ef17cd7db9b817085b2f3ed5a82bd109 https://github.com/galaxyproject/galaxy/commit/3002e404ef17cd7db9b817085b2f3... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Patch in visual separation of section parameters Commit: 040410b1d3f0ea01374f183ee0b9447e0fc3cefb https://github.com/galaxyproject/galaxy/commit/040410b1d3f0ea01374f183ee0b94... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2092 from erasche/workflow-section-backport [16.01] Workflow section fix backport Commit: 9ecf99c227466a586a6299e37555655f5ff79a25 https://github.com/galaxyproject/galaxy/commit/9ecf99c227466a586a6299e375556... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- make dependencies browsable again it would be denied previously as the dependency folder is outside of the repository (symlink protection) Commit: 0882b4d8fb31752f1fa8c963c3f260f975c918f7 https://github.com/galaxyproject/galaxy/commit/0882b4d8fb31752f1fa8c963c3f26... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- use proper method for detecting admin Commit: 50268cb8ca4a5f812346a71cc640141781f22a3d https://github.com/galaxyproject/galaxy/commit/50268cb8ca4a5f812346a71cc6401... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- fix missing call; add docs and refactor a bit Commit: 455113d182236a0fec880db296b746a413a8edc4 https://github.com/galaxyproject/galaxy/commit/455113d182236a0fec880db296b74... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2101 from martenson/fix-browsing-dependencies [16.01] make dependencies browsable again Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379 https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bfd... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- mention planemo in the error message for disabled TS pushing rephrase to Norwegian Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76 https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34a... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #2114 from martenson/planemo-mention [16.01] mention planemo in the error message for disabled TS pushing Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92 https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d2... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. Fix #2135. Commit: 2ebe9405106dfc16504e3b6f775425634bb4691f https://github.com/galaxyproject/galaxy/commit/2ebe9405106dfc16504e3b6f77542... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/layout/page.js Log Message: ----------- load options from config, not from options Commit: ad952a4b8d7501d0df48e44d7c966ff22f9a63c4 https://github.com/galaxyproject/galaxy/commit/ad952a4b8d7501d0df48e44d7c966... Author: carlfeberhard <carlfeberhard@users.noreply.github.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/layout/page.js Log Message: ----------- Merge pull request #2139 from martenson/fix-inactivity [16.01] load options from config, not from options Commit: 1e3b3a15581ecd62e78999f6be9e74d9e7cfbc65 https://github.com/galaxyproject/galaxy/commit/1e3b3a15581ecd62e78999f6be9e7... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- fix the value passed to Masthead as options were options.config before Commit: 4c2bca51171efff42e2852bfa59a91d5acee3e73 https://github.com/galaxyproject/galaxy/commit/4c2bca51171efff42e2852bfa59a9... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #2141 from martenson/fix-sideeffect [16.01] fix the value passed to Masthead as options were options.config before Commit: f85aaa4a27a1067a108c05fd1f74fa6060aa4565 https://github.com/galaxyproject/galaxy/commit/f85aaa4a27a1067a108c05fd1f74f... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- port of middleware fix for TS (#2106) Commit: c0d65092fbbd1ad7380a0b17d3d9a949145d6170 https://github.com/galaxyproject/galaxy/commit/c0d65092fbbd1ad7380a0b17d3d9a... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2154 from martenson/port-middleware-fix [16.01] Port middleware fix Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35 https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c2... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.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/mvc/history/multi-panel.js Log Message: ----------- Multi-history: open rerun button in new tab Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4e... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-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/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 'release_15.10' with 'release_16.01' Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e95... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix bad merge: when HTTP_GX_SECRET is None Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3 https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-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/mvc/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2169 from carlfeberhard/release_16.01 [16.01] Merge 15.10 with 16.01 Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3 https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a49... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 [16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3 https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72ed... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: 434321915a61f53cd668170da076251a8c15889f https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da0762... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea6125... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2174 from mvdbeek/reorder_job_template [16.01] Backport #2146 #2145 Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.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/multi-panel.js Log Message: ----------- Merge #2167 manually to resolve conflicts. Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60 https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33bc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Commit: b95cca862cae9cf7e78370fd68ea5f530fb8194f https://github.com/galaxyproject/galaxy/commit/b95cca862cae9cf7e78370fd68ea5... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- always fetch new permissions as we are reusing the view Commit: e2f88296f8454e9195ad1a6f2d4c9c9ade40ee77 https://github.com/galaxyproject/galaxy/commit/e2f88296f8454e9195ad1a6f2d4c9... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- Merge pull request #2176 from martenson/fix-permissions-caching [16.01] libraries: always fetch new permissions as we are reusing the view Commit: cfb8ed32693d6aad0ef26af7af7171e0e8c3ee04 https://github.com/galaxyproject/galaxy/commit/cfb8ed32693d6aad0ef26af7af717... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-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.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- UI, citations: fix bad merge from 15.10 774487d created a difference between the imported name and the one used. Commit: 3737fc9487ad25ba09960e0d7858d4c15a3087bf https://github.com/galaxyproject/galaxy/commit/3737fc9487ad25ba09960e0d7858d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-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.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #2198 from carlfeberhard/fix.citations-again [16.01] UI, citations: fix bad merge from 15.10 Commit: ebb49d460b7cb5573a34cc386502a66594f8e3ad https://github.com/galaxyproject/galaxy/commit/ebb49d460b7cb5573a34cc386502a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client, somehow this got out of sync. Commit: 5aefe1b193d866185958645b832f2d731f933c01 https://github.com/galaxyproject/galaxy/commit/5aefe1b193d866185958645b832f2... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2207 from dannon/release_16.01 [16.01] Rebuild client, maps were out of sync. Commit: b79474083b08860923f7f28fc1e7442b53f925db https://github.com/galaxyproject/galaxy/commit/b79474083b08860923f7f28fc1e74... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M config/tool_shed.ini.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/shed_util_common.py M static/maps/layout/page.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/run.mako M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2206 from dannon/master Sanity check of master update. Compare: https://github.com/galaxyproject/galaxy/compare/7c94ac8d93b8...b79474083b08