Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fef1e548bba39c856f6086f0eb2300e6a50d8559 https://github.com/galaxyproject/galaxy/commit/fef1e548bba39c856f6086f0eb230... Author: guerler <aysam.guerler@gmail.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix job permission handling Catch unavailable history Fix test Commit: 7e6df4f46fe0eed8328b57543b069911e4988d02 https://github.com/galaxyproject/galaxy/commit/7e6df4f46fe0eed8328b57543b069... Author: John Chilton <jmchilton@gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #1043 from jmchilton/release_15.10-forward-port [15.10] Forward port 15.07 fix to 15.10. Commit: a8147327af2e8a90108d11d7fa93fe4d4893f6ab https://github.com/galaxyproject/galaxy/commit/a8147327af2e8a90108d11d7fa93f... Author: guerler <aysam.guerler@gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Derive permission from job outputs Remove history manager Use dataset manager Commit: 36797b3195c84b416710029d86cf7b7a24c1faf0 https://github.com/galaxyproject/galaxy/commit/36797b3195c84b416710029d86cf7... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Add changed static files. Commit: ad016460dc2799e95ff26fdd0a69bf605f78358b https://github.com/galaxyproject/galaxy/commit/ad016460dc2799e95ff26fdd0a69b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Fix import of history datasets into library. Commit: b88864586c760e0e644bdc32c5d2349b1613446c https://github.com/galaxyproject/galaxy/commit/b88864586c760e0e644bdc32c5d23... Author: guerler <aysam.guerler@gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix warning statement Commit: 5603a96aecb29c7065206d8797205f49f2ed32b6 https://github.com/galaxyproject/galaxy/commit/5603a96aecb29c7065206d8797205... Author: John Chilton <jmchilton@gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- Merge pull request #1054 from martenson/fix-datalib-hist-import [15.10] Fix datalib hist import Commit: b2723e7467c5fb9722a1c6cb009251b0deaf9bc4 https://github.com/galaxyproject/galaxy/commit/b2723e7467c5fb9722a1c6cb00925... Author: guerler <aysam.guerler@gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Disable invalid test case. Add validation criteria. Fix comments Fix comment Commit: 65807013957c3f845b0b8fd793b52b6d9f057505 https://github.com/galaxyproject/galaxy/commit/65807013957c3f845b0b8fd793b52... Author: guerler <aysam.guerler@gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M lib/galaxy/managers/configuration.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js Log Message: ----------- Fix parsing of message configuration Fix default value Add root to Galaxy object Commit: e4c9f06d3bd319cc1addfdf3d6fd1f6e48e9e4f3 https://github.com/galaxyproject/galaxy/commit/e4c9f06d3bd319cc1addfdf3d6fd1... Author: John Chilton <jmchilton@gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Attempt to fix timing out tests. Continuation of work started by @nsoranzo here 92a152d89c507168a6085cc34acfa13566b6eda9. In addition to increasing the max timeout it will now print the timeout in the assertion error so we can see if it is being overridden and attempt to adjust timeouts too small. Commit: c85b0d9b0b2d6853b216ebb691987632a3b6bdc6 https://github.com/galaxyproject/galaxy/commit/c85b0d9b0b2d6853b216ebb691987... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #1060 from guerler/fix_assert_000 [15.10] Fix warning statement Commit: 177f73fcdb53ab4e172f7cf7f7a9950d4c842cd3 https://github.com/galaxyproject/galaxy/commit/177f73fcdb53ab4e172f7cf7f7a99... Author: John Chilton <jmchilton@gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py Log Message: ----------- Fix lower timeout caught by @nsoranzo. Commit: 4f72178a9568e35f99a5824d66ce4c6911e50d93 https://github.com/galaxyproject/galaxy/commit/4f72178a9568e35f99a5824d66ce4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #1038 from guerler/fix_imported_rerun_000 [15.10] Fix job rerun for imported histories Commit: 6953bdf704f3e140ffc47f849fc54dc3d4c37013 https://github.com/galaxyproject/galaxy/commit/6953bdf704f3e140ffc47f849fc54... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M lib/galaxy/managers/configuration.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js Log Message: ----------- Merge pull request #1059 from guerler/fix_message_000 [15.10] Fix parsing of message configuration Commit: 559c89afde2bb8b2be28d52a9973b72aa6c03edf https://github.com/galaxyproject/galaxy/commit/559c89afde2bb8b2be28d52a9973b... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Testing: update casperjs functional tests; change expected size string; remove nice_size from expected history api keys; remove test for rerun button on uploaded dataset; attempt to fix linux+python unicode error in hda api tests Commit: 3a78d9df740cac8bdf9f0a3a0c622fc85506aba0 https://github.com/galaxyproject/galaxy/commit/3a78d9df740cac8bdf9f0a3a0c622... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M test/api/helpers.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #1062 from jmchilton/test_fixes [15.10] Test timeout fixes? Commit: a3034ab6d99d5087a7dcc1de0360fe2ebafde40f https://github.com/galaxyproject/galaxy/commit/a3034ab6d99d5087a7dcc1de0360f... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Merge pull request #1065 from jmchilton/test_fix_3 [15.10] Testing: update casperjs functional tests; change expected size strin… Commit: d824cca31fcebe97b8c7cfd1040eecbb9e5f03d3 https://github.com/galaxyproject/galaxy/commit/d824cca31fcebe97b8c7cfd1040ee... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- In interactive environments, the /import volume can now be made conditional. Also, fix a bug when using a proxy for the node proxy and cookie_path is / Commit: c4351413265796dacc15b8e3fc7382b8514f5b59 https://github.com/galaxyproject/galaxy/commit/c4351413265796dacc15b8e3fc738... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- Built image tag differs from intended. Commit: 64b084067c73cea1de455e4816d73101c3752165 https://github.com/galaxyproject/galaxy/commit/64b084067c73cea1de455e4816d73... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1076 from natefoo/ie-conditional-import-volume [15.10] Fix a bug in IEs when proxying the proxy Commit: 75e7e4c2cf7a0cb18b8096c8119e4b0cb207e2a3 https://github.com/galaxyproject/galaxy/commit/75e7e4c2cf7a0cb18b8096c8119e4... Author: Dave B <dave@bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 7150983aab78e4ceb71f8ad2592369523899d768 https://github.com/galaxyproject/galaxy/commit/7150983aab78e4ceb71f8ad259236... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1093 from martenson/release_15.10 [15.10] Fix 500 error when attempting to update installed repository. Commit: d8152f3336d68fbf9bdecd89fd866c94338c3557 https://github.com/galaxyproject/galaxy/commit/d8152f3336d68fbf9bdecd89fd866... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/managers/configuration.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/jobs.py M static/maps/galaxy-app-base.js.map M static/scripts/galaxy-app-base.js M test/api/helpers.py M test/api/test_jobs.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge branch 'release_15.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/727167b8d150...d8152f3336d6