galaxy-commits February 2016

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135 discussions

[galaxyproject/galaxy] 06e52c: Drop python2.6 (deprecated, will not be supported ...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06e52c0129581f7ed4691bc6790eb2418c20c366 https://github.com/galaxyproject/galaxy/commit/06e52c0129581f7ed4691bc6790e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Drop python2.6 (deprecated, will not be supported in 16.04) from testing. Commit: 70a96dd79e4e3479def3e9072d6d0e5076357fc8 https://github.com/galaxyproject/galaxy/commit/70a96dd79e4e3479def3e9072d6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Merge pull request #1785 from dannon/26_deprecated Drop python2.6 (deprecated, will not be supported in 16.04) from test… Compare: https://github.com/galaxyproject/galaxy/compare/874540e9120d...70a96dd79e4e

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[galaxyproject/galaxy] 87d646: Fix unused import.
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87d6467812ff1025955006db1554b3b433b544f5 https://github.com/galaxyproject/galaxy/commit/87d6467812ff1025955006db1554… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/requests_admin.py Log Message: ----------- Fix unused import. Commit: 874540e9120d33595f6a64ba34a8fcc94481fb50 https://github.com/galaxyproject/galaxy/commit/874540e9120d33595f6a64ba34a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/requests_admin.py Log Message: ----------- Merge pull request #1796 from nsoranzo/lint_fix Fix unused import. Compare: https://github.com/galaxyproject/galaxy/compare/b14e35f48ba8...874540e9120d

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 24 Feb '16

24 Feb '16

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ccabdd21cb20/ Changeset: ccabdd21cb20 Branch: release_16.01 User: natefoo Date: 2016-02-25 02:33:13+00:00 Summary: Update Tags Affected #: 1 file diff -r 0079d3c5a85d4f5316a41628a2669c442ead02c4 -r ccabdd21cb20e9d84120dbd1fb85d8c8af881158 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,18 +20,26 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -92a6a3da997408ae10e9085e6ebcd83ef0b5826c latest_2014.10.06 +a94b3a97ed7ae6672c9b1dc87922f7e9f2a70860 latest_2014.10.06 +a94b3a97ed7ae6672c9b1dc87922f7e9f2a70860 v14.10.3 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -6ee7fe93e76d91919d43a3ef2984e182601b82d7 latest_2015.01.13 +7ca8f0ecb2ae8b1ba2b53e1fd09ccae481940a49 latest_2015.01.13 +7ca8f0ecb2ae8b1ba2b53e1fd09ccae481940a49 v15.01.4 738f4ad0eb62d5e4bcf0d22a2722ee6c570382b9 v15.03 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1 bfd4635011e39aa210b2b1498dd65831dd2a365e v15.03.2 ec735da377ca3badbb6c8bf8a60b3909d2333f9b v15.03.3 -ec735da377ca3badbb6c8bf8a60b3909d2333f9b latest_15.03 +7ddb41dcb2b2e4d3a6f834d3dd11426f26fb7902 v15.03.4 +7ddb41dcb2b2e4d3a6f834d3dd11426f26fb7902 latest_15.03 c3cef260df887330c6da902caf8a5f068b9d29b4 v15.05 403973a6b841888e1a920eac266087703af53718 v15.05.1 -403973a6b841888e1a920eac266087703af53718 latest_15.05 +6c2fd7bddc6c1c4e8a64093f3fc4c4370f515b4e v15.05.2 +6c2fd7bddc6c1c4e8a64093f3fc4c4370f515b4e latest_15.05 0994712eb599fb98f63816bd9278946066784c4d v15.07 -0994712eb599fb98f63816bd9278946066784c4d latest_15.07 +034cb0fb87dfc2ae56de1072a45a68189797e979 v15.07.1 +034cb0fb87dfc2ae56de1072a45a68189797e979 latest_15.07 37d665ba001b780e08977a1faa310a651e4875db v15.10 -37d665ba001b780e08977a1faa310a651e4875db latest_15.10 +36c05261343412370f9e44f4bdd4b1e19a97aa55 v15.10.2 +36c05261343412370f9e44f4bdd4b1e19a97aa55 latest_15.10 +0079d3c5a85d4f5316a41628a2669c442ead02c4 v16.01 +0079d3c5a85d4f5316a41628a2669c442ead02c4 latest_16.01 https://bitbucket.org/galaxy/galaxy-central/commits/e9926c3b0a23/ Changeset: e9926c3b0a23 Branch: stable User: natefoo Date: 2016-02-25 02:33:32+00:00 Summary: Merge release_16.01 to stable Affected #: 1 file diff -r b3337bd87fe5c76ab37211f4daaa15a053e8e0b3 -r e9926c3b0a23b051ba96a54306da46aad263b119 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,18 +20,26 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -92a6a3da997408ae10e9085e6ebcd83ef0b5826c latest_2014.10.06 +a94b3a97ed7ae6672c9b1dc87922f7e9f2a70860 latest_2014.10.06 +a94b3a97ed7ae6672c9b1dc87922f7e9f2a70860 v14.10.3 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -6ee7fe93e76d91919d43a3ef2984e182601b82d7 latest_2015.01.13 +7ca8f0ecb2ae8b1ba2b53e1fd09ccae481940a49 latest_2015.01.13 +7ca8f0ecb2ae8b1ba2b53e1fd09ccae481940a49 v15.01.4 738f4ad0eb62d5e4bcf0d22a2722ee6c570382b9 v15.03 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1 bfd4635011e39aa210b2b1498dd65831dd2a365e v15.03.2 ec735da377ca3badbb6c8bf8a60b3909d2333f9b v15.03.3 -ec735da377ca3badbb6c8bf8a60b3909d2333f9b latest_15.03 +7ddb41dcb2b2e4d3a6f834d3dd11426f26fb7902 v15.03.4 +7ddb41dcb2b2e4d3a6f834d3dd11426f26fb7902 latest_15.03 c3cef260df887330c6da902caf8a5f068b9d29b4 v15.05 403973a6b841888e1a920eac266087703af53718 v15.05.1 -403973a6b841888e1a920eac266087703af53718 latest_15.05 +6c2fd7bddc6c1c4e8a64093f3fc4c4370f515b4e v15.05.2 +6c2fd7bddc6c1c4e8a64093f3fc4c4370f515b4e latest_15.05 0994712eb599fb98f63816bd9278946066784c4d v15.07 -0994712eb599fb98f63816bd9278946066784c4d latest_15.07 +034cb0fb87dfc2ae56de1072a45a68189797e979 v15.07.1 +034cb0fb87dfc2ae56de1072a45a68189797e979 latest_15.07 37d665ba001b780e08977a1faa310a651e4875db v15.10 -37d665ba001b780e08977a1faa310a651e4875db latest_15.10 +36c05261343412370f9e44f4bdd4b1e19a97aa55 v15.10.2 +36c05261343412370f9e44f4bdd4b1e19a97aa55 latest_15.10 +0079d3c5a85d4f5316a41628a2669c442ead02c4 v16.01 +0079d3c5a85d4f5316a41628a2669c442ead02c4 latest_16.01 https://bitbucket.org/galaxy/galaxy-central/commits/3f95c21b1a85/ Changeset: 3f95c21b1a85 User: natefoo Date: 2016-02-25 02:33:44+00:00 Summary: Merge stable to default Affected #: 1 file diff -r a601b5dfeea28d200985b5af87e3e0202be6b125 -r 3f95c21b1a85af3ae1260eb957ea041d1de8bd5b .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,18 +20,26 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -92a6a3da997408ae10e9085e6ebcd83ef0b5826c latest_2014.10.06 +a94b3a97ed7ae6672c9b1dc87922f7e9f2a70860 latest_2014.10.06 +a94b3a97ed7ae6672c9b1dc87922f7e9f2a70860 v14.10.3 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -6ee7fe93e76d91919d43a3ef2984e182601b82d7 latest_2015.01.13 +7ca8f0ecb2ae8b1ba2b53e1fd09ccae481940a49 latest_2015.01.13 +7ca8f0ecb2ae8b1ba2b53e1fd09ccae481940a49 v15.01.4 738f4ad0eb62d5e4bcf0d22a2722ee6c570382b9 v15.03 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1 bfd4635011e39aa210b2b1498dd65831dd2a365e v15.03.2 ec735da377ca3badbb6c8bf8a60b3909d2333f9b v15.03.3 -ec735da377ca3badbb6c8bf8a60b3909d2333f9b latest_15.03 +7ddb41dcb2b2e4d3a6f834d3dd11426f26fb7902 v15.03.4 +7ddb41dcb2b2e4d3a6f834d3dd11426f26fb7902 latest_15.03 c3cef260df887330c6da902caf8a5f068b9d29b4 v15.05 403973a6b841888e1a920eac266087703af53718 v15.05.1 -403973a6b841888e1a920eac266087703af53718 latest_15.05 +6c2fd7bddc6c1c4e8a64093f3fc4c4370f515b4e v15.05.2 +6c2fd7bddc6c1c4e8a64093f3fc4c4370f515b4e latest_15.05 0994712eb599fb98f63816bd9278946066784c4d v15.07 -0994712eb599fb98f63816bd9278946066784c4d latest_15.07 +034cb0fb87dfc2ae56de1072a45a68189797e979 v15.07.1 +034cb0fb87dfc2ae56de1072a45a68189797e979 latest_15.07 37d665ba001b780e08977a1faa310a651e4875db v15.10 -37d665ba001b780e08977a1faa310a651e4875db latest_15.10 +36c05261343412370f9e44f4bdd4b1e19a97aa55 v15.10.2 +36c05261343412370f9e44f4bdd4b1e19a97aa55 latest_15.10 +0079d3c5a85d4f5316a41628a2669c442ead02c4 v16.01 +0079d3c5a85d4f5316a41628a2669c442ead02c4 latest_16.01 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/galaxy] 76bcfa: Fix log comments
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 76bcfaa0ff85fe996ee2afccfb85e01f154e75b3 https://github.com/galaxyproject/galaxy/commit/76bcfaa0ff85fe996ee2afccfb85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix log comments Use emit Fix namespace Fix namespace Remove empty line Check if logger exists Fix comment Redo More Fix yet another log Fix statements More fixes Move emitter Commit: c36ff5bcc7e840289e1d6c10610ac1dd90ddee19 https://github.com/galaxyproject/galaxy/commit/c36ff5bcc7e840289e1d6c10610a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: A scripts/check_eggs.py A scripts/fetch_eggs.py Log Message: ----------- Merge pull request #1037 from natefoo/smash-eggs-bugfix1 Add stub fetch_eggs.py/check_eggs.py Commit: dc534bb258d7a9aaf262784acdb9893339ca43c0 https://github.com/galaxyproject/galaxy/commit/dc534bb258d7a9aaf262784acdb9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/web/framework/webapp.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M tools/stats/gsummary.py Log Message: ----------- Merge branch 'release_15.10' into dev Conflicts: client/galaxy/scripts/mvc/grid/grid-view.js static/maps/mvc/collection/list-of-pairs-collection-creator.js.map static/scripts/mvc/collection/list-of-pairs-collection-creator.js Commit: daccea42bdbd545e6ed9d91bd4685036b95410a8 https://github.com/galaxyproject/galaxy/commit/daccea42bdbd545e6ed9d91bd468… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #1040 from guerler/revise_logging_000 Fix log statements and link to logger Commit: 2934c2f3bd2aba6bad02d18f687b4410362738ed https://github.com/galaxyproject/galaxy/commit/2934c2f3bd2aba6bad02d18f687b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Lint fix for 15.10 to dev merge. Commit: 9c35d35c52eca6638e25459293ac9a28e40f9d63 https://github.com/galaxyproject/galaxy/commit/9c35d35c52eca6638e25459293ac… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.base.js M client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/app/app-view.js A client/galaxy/scripts/onload.js A client/galaxy/scripts/panel.js M client/galaxy/scripts/ui/autocom_tagging.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/webpack.config.js R static/maps/galaxy.base.js.map R static/maps/galaxy.panels.js.map M static/maps/mvc/app/app-view.js.map A static/maps/onload.js.map A static/maps/panel.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/galaxy.base.js R static/scripts/galaxy.panels.js M static/scripts/mvc/app/app-view.js A static/scripts/onload.js A static/scripts/panel.js M static/scripts/ui/autocom_tagging.js M static/scripts/viz/trackster/util.js Log Message: ----------- Webpack: make autocom_tagging into a module, export commatize, rename galaxy.base to onload and galaxy.panels to panels Commit: d4ca44c898d173b9a32c3bdc7c7cce313ecbfa73 https://github.com/galaxyproject/galaxy/commit/d4ca44c898d173b9a32c3bdc7c7c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add pygments back, since it's a dependency of a conditional dependency. Commit: 063390097e23e0f9c8d956ca8a4e493e41b3b38b https://github.com/galaxyproject/galaxy/commit/063390097e23e0f9c8d956ca8a4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M .ci/flake8_wrapper.sh M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-panel.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tags.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/plugins/visualizations/charts/static/build-app.js M 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static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/templates/compiled/tool_link.js M static/scripts/utils/add-logging.js M static/scripts/utils/deferred.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M templates/galaxy_client_app.mako M test/api/helpers.py M test/qunit/tests/galaxy-app-base.js M tools/filters/wig_to_bigwig.xml Log Message: ----------- Merge and resolve conflicts Commit: 649a83c1aa8026160f8d77cb423547ecb76cda28 https://github.com/galaxyproject/galaxy/commit/649a83c1aa8026160f8d77cb4235… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.frame.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/style/less/base.less M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy.frame.js.map M static/maps/galaxy.masthead.js.map M static/maps/galaxy.menu.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy.frame.js M static/scripts/galaxy.masthead.js M static/scripts/galaxy.menu.js M static/scripts/mvc/app/app-view.js M static/style/blue/base.css M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Webpack: (shoulda been 2 sep. commits) re-add minimal DOM for 1,2,3 panel layouts via server-side/js-app.mako, correct noscript tag styling; Instantiate galaxy.frame and galaxy.menu from galaxy.masthead (currently the only user), reverse dependencies in them (masthead imports them), and move GalaxyMastheadTab into galaxy.menu and GalaxyMastheadIcon into galaxy.frame - allowing a single import of galaxy.masthead Commit: a639b0c996b13d45412115009615af826ca38ed8 https://github.com/galaxyproject/galaxy/commit/a639b0c996b13d45412115009615… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.frame.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/app/app-view.js R client/galaxy/scripts/panel.js M client/webpack.config.js R static/maps/galaxy.frame.js.map R static/maps/galaxy.masthead.js.map R static/maps/galaxy.menu.js.map A static/maps/layout/masthead.js.map A static/maps/layout/menu.js.map A static/maps/layout/panel.js.map A static/maps/layout/scratchbook.js.map M static/maps/mvc/app/app-view.js.map R static/maps/panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map R static/scripts/galaxy.frame.js R static/scripts/galaxy.masthead.js R static/scripts/galaxy.menu.js A static/scripts/layout/masthead.js A static/scripts/layout/menu.js A static/scripts/layout/panel.js A static/scripts/layout/scratchbook.js M static/scripts/mvc/app/app-view.js R static/scripts/panel.js M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Webpack: move galaxy.masthead and galaxy.menu to layout/masthead and layout/menu, panel to layout/panel, and rename galaxy.frame to layout/scratchbook Commit: 54382e8c2f0e6a3e54d7968b999708dcb8bd0998 https://github.com/galaxyproject/galaxy/commit/54382e8c2f0e6a3e54d7968b9997… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M .gitignore Log Message: ----------- Added gitignore rules to ignore custom tool-data Commit: 1333f803757215a77a988bf211e315744ec00024 https://github.com/galaxyproject/galaxy/commit/1333f803757215a77a988bf211e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M .gitignore Log Message: ----------- Merge pull request #1048 from yhoogstrate/tool_data_gitignore Added gitignore rules to ignore custom tool-data Commit: b3d5f80621cc7a450158c472aa4bffa0570fbe6c https://github.com/galaxyproject/galaxy/commit/b3d5f80621cc7a450158c472aa4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/parameters/basic.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/unicode_stream.xml Log Message: ----------- Improved unicode handling stdout/stderr/command_line. Commit: c790fcb84d005025b331b2a9106e7097860a7545 https://github.com/galaxyproject/galaxy/commit/c790fcb84d005025b331b2a9106e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/model/__init__.py Log Message: ----------- Unify standard error and output trimming and unicoding. Should be more complete now (were paths for task and jobs where it wasn't be unicodified) and with less duplication. Moved logic into model layer where it probably belongs anyway. Commit: 6b521a3557bc61e37200cbd4c14dbc037cf9696d https://github.com/galaxyproject/galaxy/commit/6b521a3557bc61e37200cbd4c14d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Fix failing tests for output checker changes. Commit: 69dcf36678db48851cb6d820aec85f9fa37ccfbf https://github.com/galaxyproject/galaxy/commit/69dcf36678db48851cb6d820aec8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fixes for c790fcb84d005025b331b2a9106e7097860a7545. Thanks to @nsoranzo. Commit: df576f3d3602cad77ea6829717ea11606bce97c2 https://github.com/galaxyproject/galaxy/commit/df576f3d3602cad77ea6829717ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Remove more unneeded stuff from galaxy.jobs now. Thanks to @nsoranzo. Commit: 6dfacb6fe648097c94fb32db2df5e643cdcc45e1 https://github.com/galaxyproject/galaxy/commit/6dfacb6fe648097c94fb32db2df5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1017 from dannon/weberror_downgrade Downgrade WebError. Commit: d0751ef80c3074e9f67cde240d4b512e1bc9a445 https://github.com/galaxyproject/galaxy/commit/d0751ef80c3074e9f67cde240d4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restore lost call. Caught by @nsoranzo. Commit: 39ff0e9d767a7a4089546d76b0747d4373ea97c9 https://github.com/galaxyproject/galaxy/commit/39ff0e9d767a7a4089546d76b074… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/web/framework/webapp.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M tools/stats/gsummary.py Log Message: ----------- Merge pull request #1044 from jmchilton/release_15.10_to_dev Bring 15.10 (and 15.07) fixes into dev. Commit: a956cac4196e0e0c58b45b2efbc79256e4962e0e https://github.com/galaxyproject/galaxy/commit/a956cac4196e0e0c58b45b2efbc7… Author: Marius van den Beek <m.vandenbeek(a)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: 4f824cb920e36d2b79250bdd327e59a771b4587c https://github.com/galaxyproject/galaxy/commit/4f824cb920e36d2b79250bdd327e… Author: Marius van den Beek <m.vandenbeek(a)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: 30668fe5344192e7b17f05060062fa330c5496a0 https://github.com/galaxyproject/galaxy/commit/30668fe5344192e7b17f05060062… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/admin/reload_tool.mako Log Message: ----------- Fix for reloading tools that have non-standard tool_ids/versions. Commit: 3f898677f19d7600648802b1a428ce916dd35e11 https://github.com/galaxyproject/galaxy/commit/3f898677f19d7600648802b1a428… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- HTML escape tool name, id, version, on tool reload message. Commit: 045832bd8ecd4515d134cb5e05f64d2b7b4e933a https://github.com/galaxyproject/galaxy/commit/045832bd8ecd4515d134cb5e05f6… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-10 (Tue, 10 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Also escape tool name, id, version in message when removing tools. Commit: 75d64893489d56e1a7b80165bacdeb2a8777875c https://github.com/galaxyproject/galaxy/commit/75d64893489d56e1a7b80165bacd… Author: Martin Cech <cech.marten(a)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 #1049 from mvdbeek/library_add_from_history Fix import of history datasets into library. Commit: 8aab57a09eb322c7f10025ee4518995323fbc637 https://github.com/galaxyproject/galaxy/commit/8aab57a09eb322c7f10025ee4518… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix nit picks unrelated to PR #1052... ... as pointed out by @nsoranzo and @blankenberg. Commit: 81dc3a955bae39d90f16441dad5a67a708177844 https://github.com/galaxyproject/galaxy/commit/81dc3a955bae39d90f16441dad5a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Fix typo. Commit: 86220c7685ff831d3d5b39732706c679e77afd38 https://github.com/galaxyproject/galaxy/commit/86220c7685ff831d3d5b39732706… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Extend users API with delete action. Commit: f700e38241d302406dde9c0eef9449ae2f054c6d https://github.com/galaxyproject/galaxy/commit/f700e38241d302406dde9c0eef94… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Fix is_admin value in users API show method to show if the requested user is an admin, not the current user. Commit: d4e7c601a095c9138f5f5841b29d345c8b2d96a9 https://github.com/galaxyproject/galaxy/commit/d4e7c601a095c9138f5f5841b29d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add check for allow_user_deletion. Commit: 24a7ee6205ac4cb45f9249a6aa3f89241121c7ca https://github.com/galaxyproject/galaxy/commit/24a7ee6205ac4cb45f9249a6aa3f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/unicode_stream.xml M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Merge pull request #1052 from jmchilton/unicode_stream_3 Improved Encoding Handling for Jobs Commit: b1266b45dc4ddd63a2b2ae1cc9c28ba9d43a2bc0 https://github.com/galaxyproject/galaxy/commit/b1266b45dc4ddd63a2b2ae1cc9c2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-11 (Wed, 11 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/galaxy.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy-app-base.js A client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/onload.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/galaxy-app-base.js.map A static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/tools.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy-app-base.js A static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/tools.js M static/scripts/onload.js M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: move panel to Backbone, implement ToolPanel and HistoryPanel; simplify js-app.mako (by removing alternate layouts); clean up debugging info, make Galaxy less chatty before logging setup Commit: 43b8addcbcbe69eb1d223a3689fdb81ef1510f6d https://github.com/galaxyproject/galaxy/commit/43b8addcbcbe69eb1d223a3689fd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/managers/users.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #1063 from nsoranzo/api_delete_user Extend users API with delete action. Commit: ee721c5d360e774636d271db673d1485ddcc7a21 https://github.com/galaxyproject/galaxy/commit/ee721c5d360e774636d271db673d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M cron/build_chrom_db.py Log Message: ----------- Check len files during download from UCSC. Do not create file in case of errors, so the cron script will not overwrite a good file with a bad one. Commit: 11926b3b9c3241d0b72ee4fcea127c18c5aaf9c6 https://github.com/galaxyproject/galaxy/commit/11926b3b9c3241d0b72ee4fcea12… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- add @mr-c Commit: c1bf4caea985d53bbcdf844561a34a588f541eec https://github.com/galaxyproject/galaxy/commit/c1bf4caea985d53bbcdf844561a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #1067 from martenson/add-biocrusoe add biocrusoe to contributors Commit: c1cc3bd483fc2197b43048f467be6e80f80babea https://github.com/galaxyproject/galaxy/commit/c1cc3bd483fc2197b43048f467be… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: fix masthead in libraries; update Panel usage in base_panels.mako, galaxy.panels.mako Commit: 11b23bf8392c8ecf7c48978003f0fc3082d07234 https://github.com/galaxyproject/galaxy/commit/11b23bf8392c8ecf7c48978003f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Fix lped report output from converter Commit: 22ed188c0344a41df5cf015486be34de197b88fc https://github.com/galaxyproject/galaxy/commit/22ed188c0344a41df5cf015486be… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Merge pull request #1069 from dannon/fix_lped_report_output Fix lped report output from converter Commit: be3d9cbf70b1899f316ff7cf5aabdd0d191179ce https://github.com/galaxyproject/galaxy/commit/be3d9cbf70b1899f316ff7cf5aab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py Log Message: ----------- Fix one more hanging div. Commit: a4edf159be9996d09bb029d2098d9c0d39fb2975 https://github.com/galaxyproject/galaxy/commit/a4edf159be9996d09bb029d2098d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M .gitignore M CONTRIBUTORS.md M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/plugins/visualizations/charts/static/build-app.js M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run.sh A scripts/check_eggs.py A scripts/fetch_eggs.py M static/maps/galaxy-app-base.js.map M static/maps/libs/jquery/select2.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/libs/jquery/select2.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/api/helpers.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/unicode_stream.xml M test/unit/jobs/test_job_output_checker.py M tools/filters/wig_to_bigwig.xml M tools/stats/gsummary.py Log Message: ----------- (merge dev) Commit: dc0b960ea1242ae3ec34e7d00c5f8619e06f7b59 https://github.com/galaxyproject/galaxy/commit/dc0b960ea1242ae3ec34e7d00c5f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/onload.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/onload.js M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: lowercase DD-helper throughout project to reflect changes in 7717659 Commit: 1cf5af4c20231996e58756ace72e4a1ca96b227d https://github.com/galaxyproject/galaxy/commit/1cf5af4c20231996e58756ace72e… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py Log Message: ----------- Merge pull request #1070 from dannon/fix_lped_report_output Fix one more hanging div in lped to pbed converter. Commit: 240da5e720c069b08caf77828dc4e3e598b56089 https://github.com/galaxyproject/galaxy/commit/240da5e720c069b08caf77828dc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Update both lped pbed pbed lped converters to be in sync with their html. Thanks @nsoranzo. Commit: 67d0bcb5b3bba9c13bfa0c556a4460e1304b63a9 https://github.com/galaxyproject/galaxy/commit/67d0bcb5b3bba9c13bfa0c556a44… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/tools.js.map M static/scripts/mvc/tools.js Log Message: ----------- Trivial: Replace unnecessary duplicated var check with 'else if' Commit: 926b1a2cdd3c772f214a2ae62945427d2c36402f https://github.com/galaxyproject/galaxy/commit/926b1a2cdd3c772f214a2ae62945… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/tools.js.map M static/scripts/mvc/tools.js Log Message: ----------- Merge pull request #1073 from einon/einon Trivial: Replace unnecessary duplicated var check with 'else if' Commit: 78e6253178b51afa77346b259801f221eb9c201e https://github.com/galaxyproject/galaxy/commit/78e6253178b51afa77346b259801… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: A client/galaxy/scripts/layout/modal.js R client/galaxy/scripts/modal.js M client/galaxy/scripts/onload.js M client/webpack.config.js A static/maps/layout/modal.js.map R static/maps/modal.js.map A static/scripts/layout/modal.js R static/scripts/modal.js Log Message: ----------- Webpack: move old school modal into layout/ Commit: 215391f571f72725a87f45b556be10e8446db8a9 https://github.com/galaxyproject/galaxy/commit/215391f571f72725a87f45b556be… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy-async.js R static/maps/galaxy-async.js.map R static/scripts/galaxy-async.js Log Message: ----------- Webpack: remove galaxy-async Commit: 3a70dc395a2afb73363440edaa624d6f053467d2 https://github.com/galaxyproject/galaxy/commit/3a70dc395a2afb73363440edaa62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M templates/admin/reload_tool.mako Log Message: ----------- Merge pull request #1050 from blankenberg/reload-tool-id-fix Fix for reloading tools that have non-standard tool_ids/versions. Commit: 350a53f1ef9c686ad3617cc37f037251a79a28ef https://github.com/galaxyproject/galaxy/commit/350a53f1ef9c686ad3617cc37f03… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/base.js M client/galaxy/scripts/viz/trackster.js R static/maps/base.js.map M static/maps/viz/trackster.js.map R static/scripts/base.js M static/scripts/viz/trackster.js Log Message: ----------- Webpack: move base.Base to trackster (which uses it) Commit: f971e17f95d62662eaec47a96da88f1b45d823ce https://github.com/galaxyproject/galaxy/commit/f971e17f95d62662eaec47a96da8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/ui/scroll-panel.js R static/maps/galaxy.ui.scrollPanel.js.map A static/maps/ui/scroll-panel.js.map R static/scripts/galaxy.ui.scrollPanel.js A static/scripts/ui/scroll-panel.js Log Message: ----------- Webpack: move galaxy.ui.scrollPanel into ui/scroll-panel Commit: 2214f887a668a4eed1e3b94d880c57e2e57ef9a1 https://github.com/galaxyproject/galaxy/commit/2214f887a668a4eed1e3b94d880c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py Log Message: ----------- Merge pull request #1072 from dannon/fix_lped_report_output Update both lped pbed pbed lped converters to be in sync with their h… Commit: f2356ef819111fe2507cc96059f5e1da7fbf6b3e https://github.com/galaxyproject/galaxy/commit/f2356ef819111fe2507cc96059f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M test/base/api.py M test/base/interactor.py Log Message: ----------- extend API interactor to allow http PATCH and DELETE testing Commit: 43dc7a52e5289acdb681c30a2aeb49bb2f68e61d https://github.com/galaxyproject/galaxy/commit/43dc7a52e5289acdb681c30a2aeb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M test/api/test_libraries.py M test/base/interactor.py Log Message: ----------- add more API tests for data libraries Commit: 93629bb29e35340618aca2d1b420d948b56c695b https://github.com/galaxyproject/galaxy/commit/93629bb29e35340618aca2d1b420… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/package.json M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map Log Message: ----------- Webpack: add handlebars loader, update tools.js Commit: 2f0b64613770c8e59613bb46218e12565d260038 https://github.com/galaxyproject/galaxy/commit/2f0b64613770c8e59613bb46218e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.tools.js M client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/tools.js A client/galaxy/scripts/mvc/tools/tools.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js R static/maps/mvc/tools.js.map A static/maps/mvc/tools/tools.js.map R static/scripts/mvc/tools.js A static/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: move tools.js into mvc/tools/ Commit: 372c2e9e43854b0e5e576abcead50e22f00923d9 https://github.com/galaxyproject/galaxy/commit/372c2e9e43854b0e5e576abcead5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/mvc/data.js A client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/tools/tools.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M static/maps/galaxy.tools.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/app/app-analysis.js.map R static/maps/mvc/data.js.map A static/maps/mvc/dataset/data.js.map M static/maps/mvc/tools/tools.js.map M static/maps/onload.js.map M static/maps/ui/scroll-panel.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.tools.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/data.js A static/scripts/mvc/dataset/data.js M static/scripts/mvc/tools/tools.js M static/scripts/onload.js M static/scripts/ui/scroll-panel.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako Log Message: ----------- Webpack: move data.js into dataset/data.js; pack scripts Commit: 6d0ab669ecbd12e75cf38f8c914bbf5954caac20 https://github.com/galaxyproject/galaxy/commit/6d0ab669ecbd12e75cf38f8c914b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M client/webpack.config.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/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Webpack: correctly load jQuery-ui, require bibtex in citations, and move polyfills to first loaded Commit: c66bc7ab766e2af197a668a76e15e1dc21cfb9fa https://github.com/galaxyproject/galaxy/commit/c66bc7ab766e2af197a668a76e15… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: R client/galaxy/scripts/mvc/collection/collection-panel-edit.js R client/galaxy/scripts/mvc/collection/collection-panel.js A client/galaxy/scripts/mvc/collection/collection-view-edit.js A client/galaxy/scripts/mvc/collection/collection-view.js R client/galaxy/scripts/mvc/history/history-panel-annotated.js R client/galaxy/scripts/mvc/history/history-panel-edit-current.js R client/galaxy/scripts/mvc/history/history-panel-edit.js R client/galaxy/scripts/mvc/history/history-panel.js A client/galaxy/scripts/mvc/history/history-view-annotated.js A client/galaxy/scripts/mvc/history/history-view-edit-current.js A client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/history/history-view.js M client/webpack.config.js R static/maps/mvc/collection/collection-panel-edit.js.map R static/maps/mvc/collection/collection-panel.js.map A static/maps/mvc/collection/collection-view-edit.js.map A static/maps/mvc/collection/collection-view.js.map R static/maps/mvc/history/history-panel-annotated.js.map R static/maps/mvc/history/history-panel-edit-current.js.map R static/maps/mvc/history/history-panel-edit.js.map R static/maps/mvc/history/history-panel.js.map A static/maps/mvc/history/history-view-annotated.js.map A static/maps/mvc/history/history-view-edit-current.js.map A static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/history/history-view.js.map R static/scripts/mvc/collection/collection-panel-edit.js R static/scripts/mvc/collection/collection-panel.js A static/scripts/mvc/collection/collection-view-edit.js A static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/history/history-panel-annotated.js R static/scripts/mvc/history/history-panel-edit-current.js R static/scripts/mvc/history/history-panel-edit.js R static/scripts/mvc/history/history-panel.js A static/scripts/mvc/history/history-view-annotated.js A static/scripts/mvc/history/history-view-edit-current.js A static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/history/history-view.js Log Message: ----------- Webpack: normalize history and panel module names with other mvc modules (history-panel is not a panel - just a view) Commit: 55068dea285c82232bd9dbf024de580013c5f3d8 https://github.com/galaxyproject/galaxy/commit/55068dea285c82232bd9dbf024de… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-12 (Thu, 12 Nov 2015) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map 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/galaxy.bundled.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Webpack: normalize 'panel' names part-2: history and collection modules Commit: d6d8e5ef86bbfe460709c82590596252de2d5a71 https://github.com/galaxyproject/galaxy/commit/d6d8e5ef86bbfe460709c8259059… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M tools/data_source/upload.py Log Message: ----------- upload.py: Remove unused function parameter Commit: 625d49e2de074c240555efbff1319c6ddf9676a1 https://github.com/galaxyproject/galaxy/commit/625d49e2de074c240555efbff131… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #1078 from einon/einon upload.py: Remove unused function parameter Commit: 8efabbbcd5546441182cbff1cc66e525cf6abf48 https://github.com/galaxyproject/galaxy/commit/8efabbbcd5546441182cbff1cc66… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M templates/grid_base.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Webpack: fix load order in embedded grids by removing autocom_tagging script tag (it's in the libs.bundle), remove it from other mako templates as well; remove bibtex script from workflow/editor.mako (unused) Commit: 2dcb92aa0e83f9893595b68222fc62cf052a9220 https://github.com/galaxyproject/galaxy/commit/2dcb92aa0e83f9893595b68222fc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/webapps/tool_shed/buildapp.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh Log Message: ----------- Merge pull request #942 from davebx/docker Enable dockerized toolshed tests. Commit: 7c45bf13fad2d60fbee8be409c6879af2ebc25d1 https://github.com/galaxyproject/galaxy/commit/7c45bf13fad2d60fbee8be409c68… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 321b64d8dcc1917eb107e46124cdb945c5005511 https://github.com/galaxyproject/galaxy/commit/321b64d8dcc1917eb107e46124cd… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Ensure that invalid parameters don't break things. Commit: 6d4328766baa3f8bf35cc5824d870d8fc86e481f https://github.com/galaxyproject/galaxy/commit/6d4328766baa3f8bf35cc5824d87… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- remove whitespace at line ends Commit: 7c863eb2aeaa1418dde26ed2101b88435b3a763b https://github.com/galaxyproject/galaxy/commit/7c863eb2aeaa1418dde26ed2101b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- update the image tag Commit: ce418d33fe221b27da162717a208381aa8042ea8 https://github.com/galaxyproject/galaxy/commit/ce418d33fe221b27da162717a208… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Resolve conflicting label CSS class. Commit: f1abf1e9ab4dc4f1d3e6987c6bb68ab3b188083c https://github.com/galaxyproject/galaxy/commit/f1abf1e9ab4dc4f1d3e6987c6bb6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1086 from jgoecks/trackster-pos-label Resolve conflicting label CSS class for trackster. Commit: 87f35ea9752a37da76595db1fee481c391ee686b https://github.com/galaxyproject/galaxy/commit/87f35ea9752a37da76595db1fee4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Use preexisting library to parse query string. Commit: c3f4b54b686ba93b3bb8f65d17f3961d344b9d7c https://github.com/galaxyproject/galaxy/commit/c3f4b54b686ba93b3bb8f65d17f3… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/utils/localization.js R client/galaxy/scripts/utils/webpack-localization.js M client/package.json M client/webpack.config.js M static/maps/galaxy-app-base.js.map M static/maps/utils/localization.js.map R static/maps/utils/webpack-localization.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/utils/localization.js R static/scripts/utils/webpack-localization.js Log Message: ----------- Webpack, localization: support both requirejs and webpack i18n by including the amdi18n-loader (both now share the utils/localization file) Commit: 6f754216a4100969b18185aa705065b03a215628 https://github.com/galaxyproject/galaxy/commit/6f754216a4100969b18185aa7050… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js R client/galaxy/scripts/mvc/list/list-panel.js A client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/history/history-view.js.map R static/maps/mvc/list/list-panel.js.map A static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/history/history-view.js R static/scripts/mvc/list/list-panel.js A static/scripts/mvc/list/list-view.js Log Message: ----------- Webpack: normalize list-panel to list-view Commit: d285c01108f59d1b054955f312b16c3b978aa97a https://github.com/galaxyproject/galaxy/commit/d285c01108f59d1b054955f312b1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: A client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/annotations.js A client/galaxy/scripts/mvc/tag.js R client/galaxy/scripts/mvc/tags.js A client/galaxy/scripts/mvc/tool/tools-form-base.js A client/galaxy/scripts/mvc/tool/tools-form-workflow.js A client/galaxy/scripts/mvc/tool/tools-form.js A client/galaxy/scripts/mvc/tool/tools-jobs.js A client/galaxy/scripts/mvc/tool/tools-template.js A client/galaxy/scripts/mvc/tool/tools.js R client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/tools/tools-form-workflow.js R client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-template.js R client/galaxy/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (the names of) Commit: 894af4c5deadc75d2f1a5e11e26abc9c3f4f7256 https://github.com/galaxyproject/galaxy/commit/894af4c5deadc75d2f1a5e11e26a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: A static/maps/mvc/annotation.js.map R static/maps/mvc/annotations.js.map A static/maps/mvc/tag.js.map R static/maps/mvc/tags.js.map A static/maps/mvc/tool/tools-form-base.js.map A static/maps/mvc/tool/tools-form-workflow.js.map A static/maps/mvc/tool/tools-form.js.map A static/maps/mvc/tool/tools-jobs.js.map A static/maps/mvc/tool/tools-template.js.map A static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.js.map R static/maps/mvc/tools/tools.js.map A static/scripts/mvc/annotation.js R static/scripts/mvc/annotations.js A static/scripts/mvc/tag.js R static/scripts/mvc/tags.js A static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tool/tools-form-workflow.js A static/scripts/mvc/tool/tools-form.js A static/scripts/mvc/tool/tools-jobs.js A static/scripts/mvc/tool/tools-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js R static/scripts/mvc/tools/tools.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (2 of 3) Commit: cc6c15f3b102afd22c3a9f1c7d1a5d92daad03bc https://github.com/galaxyproject/galaxy/commit/cc6c15f3b102afd22c3a9f1c7d1a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools-form-base.js M client/galaxy/scripts/mvc/tool/tools-form-workflow.js M client/galaxy/scripts/mvc/tool/tools-form.js M client/galaxy/scripts/mvc/tool/tools-jobs.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/mvc/annotation.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tools-form-base.js.map M static/maps/mvc/tool/tools-form-workflow.js.map M static/maps/mvc/tool/tools-form.js.map M static/maps/mvc/tool/tools-jobs.js.map M static/maps/mvc/tool/tools-template.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/annotation.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tools-form-base.js M static/scripts/mvc/tool/tools-form-workflow.js M static/scripts/mvc/tool/tools-form.js M static/scripts/mvc/tool/tools-jobs.js M static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Webpack: normalize tags, annotations, and tools (change refs - 3 of 3) Commit: 2956b12e9b292e42dfd2e2309b5c7d29b5b0d48b https://github.com/galaxyproject/galaxy/commit/2956b12e9b292e42dfd2e2309b5c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-model.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-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tools-form-workflow.js M client/galaxy/scripts/mvc/tool/tools-jobs.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M static/maps/galaxy-app-base.js.map M static/maps/galaxy.library.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/citation/citation-model.js.map M 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static/maps/mvc/library/library-model.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/tool/tools-form-workflow.js.map M static/maps/mvc/tool/tools-jobs.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/maps/viz/circster.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.library.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.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-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tag.js M static/scripts/mvc/tool/tools-form-workflow.js M static/scripts/mvc/tool/tools-jobs.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: correct tool menu template loading in requirejs/galaxy.panels.mako by using require.config.map; normalize galaxy_config.root and Galaxy.options.root to Galaxy.root across the templates and js Commit: 638e36f51d2c9d1af3a0ff62a869e72c02a38f76 https://github.com/galaxyproject/galaxy/commit/638e36f51d2c9d1af3a0ff62a869… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Newer versions of WebOb set None in referer, older versions set an empty string. Handle cases where it is assumed to be a string. I checked all other trans.request attributes to find other cases where this might crop up and didn't find any. Commit: 3ba139fe1bf8a40df647282a9884eae543a656bc https://github.com/galaxyproject/galaxy/commit/3ba139fe1bf8a40df647282a9884… Author: Martin Cech <cech.marten(a)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 #1082 from davebx/hg_middleware Fix 500 error when attempting to update installed repository. Commit: 1aecca7889681ad9518e26e2a62b470809d2cdd1 https://github.com/galaxyproject/galaxy/commit/1aecca7889681ad9518e26e2a62b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: 7e67368424a718f2e156b961aaf0a1a9672df9ce https://github.com/galaxyproject/galaxy/commit/7e67368424a718f2e156b961aaf0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Don't fail if a repository is already installed If an repository is already installed `installed_tool_shed_repositories` is None and this does not work with map. Commit: f629cbdb6aa34a349e088382a51054a946e0185e https://github.com/galaxyproject/galaxy/commit/f629cbdb6aa34a349e088382a510… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Refactor tool parsing, parse id first. Small refactoring cleans up downstream diff for dynamic tool branch. Commit: 8189fb450bdb90f3ff7af220c573c128ed776085 https://github.com/galaxyproject/galaxy/commit/8189fb450bdb90f3ff7af220c573… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py Log Message: ----------- Add tool version to workflow extract. Commit: 0b070f406c650e664c413dc60897fafd6e3611a8 https://github.com/galaxyproject/galaxy/commit/0b070f406c650e664c413dc60897… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add app property to workflow contents manager. Most other managers already have this. Commit: 38f0ed5d043951cc06abeaab9bbf1f4d888e372a https://github.com/galaxyproject/galaxy/commit/38f0ed5d043951cc06abeaab9bbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Improve the API attributes on parameters page. Make clear what API ID is and add display of API value for job. Commit: bbe7fbe38c57fd89434eea850621770a1d355231 https://github.com/galaxyproject/galaxy/commit/bbe7fbe38c57fd89434eea850621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #1098 from jmchilton/show_param Improve the API attributes on parameters page. Commit: a26526b085c29d41f5662b7f80dee7e3e7a7c294 https://github.com/galaxyproject/galaxy/commit/a26526b085c29d41f5662b7f80de… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1094 from bgruening/fix_api_ts_installation Fix api TS installation Commit: cfe45d8e0c357cbe191a346a2ae05e1625bb5010 https://github.com/galaxyproject/galaxy/commit/cfe45d8e0c357cbe191a346a2ae0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Merge pull request #1095 from bgruening/ts_api_fail_if_installed Don't fail if a repository is already installed Commit: b19e71ec465c7145840acf684f8f09eeebb99b5a https://github.com/galaxyproject/galaxy/commit/b19e71ec465c7145840acf684f8f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- Update run_tests.sh help for #844. Commit: b8870bfedc008d378481bd6740f31ff516271c16 https://github.com/galaxyproject/galaxy/commit/b8870bfedc008d378481bd6740f3… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/trackster.less M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M static/maps/mvc/tool/tools.js.map A static/maps/mvc/tools.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/mvc/tool/tools.js A static/scripts/mvc/tools.js M static/scripts/viz/trackster/tracks.js M static/style/blue/trackster.css M templates/admin/reload_tool.mako M templates/show_params.mako M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/provision.yml M test/docker/base/run_test_wrapper.sh M test/docker/base/start_mysql.sh M tools/data_source/upload.py Log Message: ----------- (merge dev) Commit: 13eb47e789336f4ebfe0923ae07f0db81afd2d63 https://github.com/galaxyproject/galaxy/commit/13eb47e789336f4ebfe0923ae07f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #1020 from dannon/issue_procedure [PROCEDURES] Issue procedure linkage Commit: d2d2ff12775bc630ff6705c7989fe84fed9cbdbb https://github.com/galaxyproject/galaxy/commit/d2d2ff12775bc630ff6705c7989f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1101 from nsoranzo/run_tests_sh Update run_tests.sh help for #844. Commit: bb089dfa424cefc64e65f1dd2aab5fe8fe1dad16 https://github.com/galaxyproject/galaxy/commit/bb089dfa424cefc64e65f1dd2aab… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M static/maps/galaxy-app-base.js.map M test/qunit/test-common.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Tests, qunit: fix import of underscore from libs, fix galaxy-app-base to not require config but have it passed in Commit: 474a454958398bc3e70d16f7eaab5805aa89cf19 https://github.com/galaxyproject/galaxy/commit/474a454958398bc3e70d16f7eaab… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/history/hda-model.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Tests, qunit: galaxy_config.root->Galaxy.root, correct locations and shims of underscore and backbone in qunit tests Commit: 39fe6b44bfbab9f490524dff902ceb80bc52a2ee https://github.com/galaxyproject/galaxy/commit/39fe6b44bfbab9f490524dff902c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Rebuild styles, fixes history panel green being wrong. Commit: 65301bb9c85a1c09fdd36890b68593b320fcf3e7 https://github.com/galaxyproject/galaxy/commit/65301bb9c85a1c09fdd36890b685… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1102 from dannon/style_rebuild Rebuild styles, fixes history panel green being wrong. Commit: 0a09de5453540b55ddb43c63c430a5edfff120b1 https://github.com/galaxyproject/galaxy/commit/0a09de5453540b55ddb43c63c430… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/app/app-login.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/app/app-login.js M static/scripts/utils/utils.js Log Message: ----------- Show welcome page with required login, remove iframes Reinsert iframe for login Use iframes Commit: a610dc59a85519e3a84455ae5b2b23c3390017a5 https://github.com/galaxyproject/galaxy/commit/a610dc59a85519e3a84455ae5b2b… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Better error when tool shed repo dir missing Check for a tool shed repository directory and throw exception if it's missing. This avoids a cryptic NoneType error when searching for tool_dependencies.xml file and directory was not found. Commit: 0b788e97314a9e88b82fa3799127524b16a2adc2 https://github.com/galaxyproject/galaxy/commit/0b788e97314a9e88b82fa3799127… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/app/app-login.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/app/app-login.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #1105 from guerler/revise_require_login_003 Show welcome page with required login Commit: 51f8e21218757fa82e30986a946bbb7fc5c7a2ac https://github.com/galaxyproject/galaxy/commit/51f8e21218757fa82e30986a946b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Merge pull request #1107 from lparsons/tool_shed_repo_dir_check Better error when tool shed repo dir missing Commit: d40d384a8672b5bc58db210a6e1aca41cb50e9d6 https://github.com/galaxyproject/galaxy/commit/d40d384a8672b5bc58db210a6e1a… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- CRAM format Commit: 3df95ae9a6f081090bb554b0778f145f0ec622fa https://github.com/galaxyproject/galaxy/commit/3df95ae9a6f081090bb554b0778f… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- flake8 Commit: 727167b8d15063920d01c2f7651cc4a76c2caafc https://github.com/galaxyproject/galaxy/commit/727167b8d15063920d01c2f7651c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1083 from martenson/update-testing-docker-image Update testing docker image Commit: 71b27b0f018c6bc3997099137ff2c80ca088981d https://github.com/galaxyproject/galaxy/commit/71b27b0f018c6bc3997099137ff2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Select2 for sharing This adjusts the default 'share' template to use the select2/exposed user list implemented in 60ad9e934b3e4c50389a624a28578aa9fc326f32. As previously, if the email list is not exposed then you may still enter an email address manually. If usernames are exposed but not emails (e.g. public galaxies) we currently just hide those results even if searches match. Fixes #977 Commit: 86bb4aeaca80b9fbf98ef89f92c1ce2a5bfc6208 https://github.com/galaxyproject/galaxy/commit/86bb4aeaca80b9fbf98ef89f92c1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Patch other share implementation to handle case of undefined emails more gracefully Commit: 944df4a5647a71304bab12185b708b4bb28da049 https://github.com/galaxyproject/galaxy/commit/944df4a5647a71304bab12185b70… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Followup to #1109, #1110, add f_any to user API Commit: 312746d1698e99e13b9a60db881d0093da6cc4c0 https://github.com/galaxyproject/galaxy/commit/312746d1698e99e13b9a60db881d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_actions.py Log Message: ----------- Allow accessing collection elements in format_source. Can do it by numeric index or element name, e.g. input[0] or input["forward"]. Only works for 1-D collections. Implements #699. Run new and most relevant existing tests with the following commands: ``` nosetests test/unit/tools/test_actions.py ./run_tests.sh -framework -id output_format_collection ./run_tests.sh -framework -id output_format ``` Commit: 0030f4c5499b0121e2c7e25388ac402272728ba7 https://github.com/galaxyproject/galaxy/commit/0030f4c5499b0121e2c7e25388ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- API test fix from @nsoranzo. Commit: 7018753bc9def1ec0b461f95918bb16d569ab326 https://github.com/galaxyproject/galaxy/commit/7018753bc9def1ec0b461f95918b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Give writing job script more time to flush and sync during verification. Still having occasional failures - https://jenkins.galaxyproject.org/job/docker-api/1172/testReport/junit/api.…. Commit: d8152f3336d68fbf9bdecd89fd866c94338c3557 https://github.com/galaxyproject/galaxy/commit/d8152f3336d68fbf9bdecd89fd86… Author: Nate Coraor <nate(a)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 Commit: 2374c55f7233a9b2ff4a72ff3c2535ce9dc732e3 https://github.com/galaxyproject/galaxy/commit/2374c55f7233a9b2ff4a72ff3c25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js Log Message: ----------- Fix removal of comment missed in merge. Commit: 7b93a53a4cbe671c40bb39849ae354938fffa284 https://github.com/galaxyproject/galaxy/commit/7b93a53a4cbe671c40bb39849ae3… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/utils/localization.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/maps/polyfills.js.map M static/maps/utils/localization.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js M static/scripts/polyfills.js M static/scripts/utils/localization.js R static/style/blue/galaxy.frame.masthead.css M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M test/casperjs/api-history-permission-tests.js Log Message: ----------- Webpack: polyfill object.assign for phantomjs; remove galaxy.frame.masthead.css in favor of adding styles locally; change css load order to prevent 'ui-button' name collision between base and jquery-ui Commit: 9516b7179d541953ebaea4061300440d02f11bb7 https://github.com/galaxyproject/galaxy/commit/9516b7179d541953ebaea4061300… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Documented API call Commit: d5fe49ec6f1250da732faaf5c605549183249938 https://github.com/galaxyproject/galaxy/commit/d5fe49ec6f1250da732faaf5c605… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Incorporate @nsoranzo's suggestions Commit: e6d651be32f0afb34792a3be204df54c9e36bb53 https://github.com/galaxyproject/galaxy/commit/e6d651be32f0afb34792a3be204d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #1091 from natefoo/webob-string-to-none Fix bug with referer attribute type change in WebOb Commit: 1063c175be53962e8d55097ddb04537cdbac5da6 https://github.com/galaxyproject/galaxy/commit/1063c175be53962e8d55097ddb04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #1114 from jmchilton/sync_more Give writing job script more time to flush and sync during verification. Commit: f4db7587565c912005da35410228b293b11555cd https://github.com/galaxyproject/galaxy/commit/f4db7587565c912005da35410228… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M cron/build_chrom_db.py Log Message: ----------- Merge pull request #1066 from nsoranzo/cron_ucsc Check len files during download from UCSC. Commit: 729ed463aa87d07bc27dc669ba80d0187dd85b47 https://github.com/galaxyproject/galaxy/commit/729ed463aa87d07bc27dc669ba80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1108 from yhoogstrate/cram_datatype CRAM datatype definiton Commit: 3d933edd32dd872a1e660a061cdef4cffc587ec0 https://github.com/galaxyproject/galaxy/commit/3d933edd32dd872a1e660a061cde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M test/api/test_libraries.py M test/base/api.py M test/base/interactor.py Log Message: ----------- Merge pull request #1074 from martenson/lib-api-tests [WIP] add more data libraries API tests Commit: c252987b4c5febb7fa10db3c7359449f325fc9ca https://github.com/galaxyproject/galaxy/commit/c252987b4c5febb7fa10db3c7359… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.menu.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js Log Message: ----------- Merge branch 'master' into dev Commit: 704144c16936e6ddedee9d509ee4361f50f152f2 https://github.com/galaxyproject/galaxy/commit/704144c16936e6ddedee9d509ee4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Don't let $input hang cheetah evaluation... If $input is undefined. The Python input command was being used and causing Galaxy to hang during evaluation. Commit: 0ff8a21891f7780dd30f81047cb5f8112c924b4a https://github.com/galaxyproject/galaxy/commit/0ff8a21891f7780dd30f81047cb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add example tools demonstrating cheetah problem (unbound variable). Refine default override of input to raise an exception instead of just throwing in a dummy string. Commit: 7dedb3ff18f06b123ac9d64ac1d9b42948ba903c https://github.com/galaxyproject/galaxy/commit/7dedb3ff18f06b123ac9d64ac1d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A test/functional/tools/cheetah_problem_syntax_error.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add another cheetah syntax error example... ... ensure the test framework run the tool, detects that there is an error, and handles things appropriately. Commit: b4c77b761799b3a8752a6fec500717b1a6f3818b https://github.com/galaxyproject/galaxy/commit/b4c77b761799b3a8752a6fec5007… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py Log Message: ----------- Introduce "Format 2" workflow definitions. This is a slight tightening up of the ad-hoc, experimental workflow YAML definition used by the test framework (and by Kyle, but lets just admit Kyle is part of Galaxy's test framework). This format is still defined entirely client side by transcoding the YAML or python object description into real (or format 1) Galaxy workflows - so these cannot realisticaly be declared part of Galaxy's public interface and can remain experimental and subject to change. In addition to refactoring the code implementing these workflows for upstream modifications to explore new features, the format itself has been made slightly more stringent in two ways: - 'steps' must now be explicit (previously converted auto-convert list to dict). - Ensure the workflow declared a 'class' is defined and the class is 'GalaxyWorkflow'. This will help with discovery of workflow objects with downstream tooling (planemo for workflows?) and brings the Galaxy definition slightly more inline with the CWL definition for workflows (very slightly). Commit: b25b8c3f243e87a196a6cb0fa23328ee7c7e26f7 https://github.com/galaxyproject/galaxy/commit/b25b8c3f243e87a196a6cb0fa233… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revise and fix waiting for tool tests. - maxseconds on test tag stopped being respected at some point, fix that. - maxseconds on test tag stopped being parsed at some later point, fix that. - Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT. - Add test case to ensure there is no future regression of these behaviors. Commit: ee2b34c387d9bb6189c8befaa069887b535d413c https://github.com/galaxyproject/galaxy/commit/ee2b34c387d9bb6189c8befaa069… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #950 from fescudie/dev Add BIOM v1 in default datatypes. Commit: 7fef50f45fb6484fcb600cfd167e43d1a735a9d2 https://github.com/galaxyproject/galaxy/commit/7fef50f45fb6484fcb600cfd167e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Merge pull request #881 from scholtalbers/role-page-fix Fix the issue where too many datasets are linked to a certain role Commit: e4e44be27b7b3ddf778eb95559b4d0f11e4aecb7 https://github.com/galaxyproject/galaxy/commit/e4e44be27b7b3ddf778eb95559b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #1004 from jj-umn/uniprotxml_datatype UniProtXML datatype Commit: f770128915df3fa9d8a3a9fe2c4a210fbd9ac2c6 https://github.com/galaxyproject/galaxy/commit/f770128915df3fa9d8a3a9fe2c4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #991 from erasche/fix-932 Fixes #932 Commit: 72faca1a3a81b6104c776353ee7b4dc03d6ae9be https://github.com/galaxyproject/galaxy/commit/72faca1a3a81b6104c776353ee7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Document GIE proxy config for nginx, mention the Ansible role. Commit: 7ab070e9df6ebf0658c966942d38779fbc9d16f1 https://github.com/galaxyproject/galaxy/commit/7ab070e9df6ebf0658c966942d38… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #1123 from natefoo/ie-docfix Add nginx config for GIE proxy to documentation Commit: d1d2f8388a4bc077275f535e41841158076a56de https://github.com/galaxyproject/galaxy/commit/d1d2f8388a4bc077275f535e4184… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/utils/query-string-parsing.js M client/webpack.config.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/maps/utils/query-string-parsing.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js M static/scripts/utils/query-string-parsing.js M templates/js-app.mako Log Message: ----------- Webpack: allow extending options from template call, add /login as app entry point for login app (still allowing user/login), add root/welcome and /login to allowed paths when require_login, fix None type error for redirect when visiting user/login directly, fix rendering of masthead, add query string to object util, correct job_id loading from index Commit: 5eb9b206e798522fff1a9332e5d1a58c83528523 https://github.com/galaxyproject/galaxy/commit/5eb9b206e798522fff1a9332e5d1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A client/galaxy/scripts/apps/login.js A static/scripts/bundled/login.bundled.js A static/scripts/bundled/login.bundled.js.map Log Message: ----------- Webpack: properly add login app to the repo Commit: 17ec1b08fbc88c4960b94fbd19252c40e8a4e579 https://github.com/galaxyproject/galaxy/commit/17ec1b08fbc88c4960b94fbd1925… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Webpack: add masthead div to galaxy.panels.mako as a target for replacement and becauseiamgoingcrazyfromtheeightdifferentwayswehavetorenderwebpages Commit: bd476ce146d47e12b25e4faacc6ae7eeed09fbe2 https://github.com/galaxyproject/galaxy/commit/bd476ce146d47e12b25e4faacc6a… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Readd jquery.migrate to galaxy.panels template because it is needed for farbtastic, which is used in visualizations. Commit: d2bab13fa92a87a3c4959d782ba0bf061ecf07db https://github.com/galaxyproject/galaxy/commit/d2bab13fa92a87a3c4959d782ba0… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1119 from jmchilton/maxseconds Revise and fix waiting for tool tests. Commit: a3fee086c6dee9a688ffb7da13f71c1210cb76da https://github.com/galaxyproject/galaxy/commit/a3fee086c6dee9a688ffb7da13f7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Style: fix state-success-bg change that was not reverted during 5fd4daf Commit: 5191c2136a9131005533faff4b0c1267f1ce35c1 https://github.com/galaxyproject/galaxy/commit/5191c2136a9131005533faff4b0c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Merge pull request #1129 from carlfeberhard/fix.styles Style: fix state-success-bg change that was not reverted during 5fd4daf Commit: 40e3e7926aec154fa5f761cf5a7e84fad98b785c https://github.com/galaxyproject/galaxy/commit/40e3e7926aec154fa5f761cf5a7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Rebuild style with lessc > 2.5 (which everyone needs to update to now, or we'll have battling commits of packed css Commit: 5c285eaee751a9257e01b6ae4fcff70305e34d56 https://github.com/galaxyproject/galaxy/commit/5c285eaee751a9257e01b6ae4fcf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/GruntFile.js M client/grunt-tasks/style.js M client/package.json M static/maps/galaxy-app-base.js.map Log Message: ----------- Add grunt check task to verify npm modules are up to date Commit: d4a380b49d0c84fd1765aa5f6e6ad0f85f1b5585 https://github.com/galaxyproject/galaxy/commit/d4a380b49d0c84fd1765aa5f6e6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/package.json Log Message: ----------- Swap devDependencies for flat dependencies -- this allows npm ls (and thereby grunt-check-modules) to enforce dep versions. Commit: af36ca6d9467932036d19a448ca4c74affffae9a https://github.com/galaxyproject/galaxy/commit/af36ca6d9467932036d19a448ca4… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- add BAM iobio visualisation as Interactive Environment Commit: 5188b4179063b3cc57c5c983d48a5fb62387d2b3 https://github.com/galaxyproject/galaxy/commit/5188b4179063b3cc57c5c983d48a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- make travis happy Commit: 81f842743d0c42522f7f80b603eccbc78d697a3c https://github.com/galaxyproject/galaxy/commit/81f842743d0c42522f7f80b603ec… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1131 from bgruening/IE_iobio Add BAM iobio visualisation as Interactive Environment Commit: 96b17bd8560f938ee9d3244b6cf5b198864c44ce https://github.com/galaxyproject/galaxy/commit/96b17bd8560f938ee9d3244b6cf5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1117 from jmchilton/input_hang Don't let $input hang cheetah evaluation... Commit: f61ec1c3c01b51fe3449a583e1966cc3dff099f2 https://github.com/galaxyproject/galaxy/commit/f61ec1c3c01b51fe3449a583e196… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge and rebuild client Commit: 05ed245353331489ee443ac483b1569dab38f500 https://github.com/galaxyproject/galaxy/commit/05ed245353331489ee443ac483b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_review_grids.py Log Message: ----------- Fix the bad merge :( Commit: ed992b3b28c7f6d9d637e82e88305b665733a50b https://github.com/galaxyproject/galaxy/commit/ed992b3b28c7f6d9d637e82e8830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). Commit: 458766b00f05a2d46c834d461e59201796ff0358 https://github.com/galaxyproject/galaxy/commit/458766b00f05a2d46c834d461e59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tools.js R client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/tools/tools-form-workflow.js R client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-template.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map M static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js M static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Add run workflow tool form Move styles to css Improve handling of numeric workflow parameters Commit: 7cd5713dbb3acc82ee7c01f5110d37cb413392c8 https://github.com/galaxyproject/galaxy/commit/7cd5713dbb3acc82ee7c01f5110d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M test/casperjs/spaceghost.js Log Message: ----------- Webpack: simplify query routes in analysis, remove duplicate js in display.mako and tabular_chunked.mako, change order of requirejs import; testing, casperjs: quiet requirejs scripterrors when navigating away from pages Commit: 9c5d4cfc0e95966f8a41e8dedf83ea4b4793868e https://github.com/galaxyproject/galaxy/commit/9c5d4cfc0e95966f8a41e8dedf83… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M config/datatypes_conf.xml.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M cron/build_chrom_db.py M doc/source/admin/interactive_environments.rst M doc/source/project/organization.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M run_tests.sh M static/maps/galaxy-app-base.js.map A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/mvc/app/app-login.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/mvc/app/app-login.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js A static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M test/api/helpers.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_workflow_extraction.py M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_tool_loader.py Log Message: ----------- (merge dev) Commit: 0c22d138891604d0df98784ab7edc43e9b541c1d https://github.com/galaxyproject/galaxy/commit/0c22d138891604d0df98784ab7ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py A test/functional/tools/collection_type_source.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement type_source on output collections. Inherit collection_type from an input, the way metadata and format can be. This commit includes a test tool demonstrating this functionality. The tool test for this tool can be executed using the following command: ``` ./run_tests.sh -framework -id collection_type_source ``` Commit: 9f7dff740f0133d6ba66abe067fb2edeb7a6b705 https://github.com/galaxyproject/galaxy/commit/9f7dff740f0133d6ba66abe067fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Revise is_workflow setting Commit: b8b0e4412247bd0f7611710ce69e0b4e9a76b4d7 https://github.com/galaxyproject/galaxy/commit/b8b0e4412247bd0f7611710ce69e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js Log Message: ----------- Strip whitespace Commit: f0e28555af8129eae424c3e677b6bb22a4c68154 https://github.com/galaxyproject/galaxy/commit/f0e28555af8129eae424c3e677b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Support onclick for menu items. Commit: dba7e6640f816325c853fcc320e97c454a465bae https://github.com/galaxyproject/galaxy/commit/dba7e6640f816325c853fcc320e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/grunt-tasks/templates.js M static/maps/layout/panel.js.map M static/maps/mvc/tool/tools.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/layout/panel.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster/tracks.js M templates/base/base_panels.mako M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Webpack: correct handlebars template generation to return an AMD function - this normalizes import of templates between webpack and require, fix sweepster tools import and templates Commit: 0770d8d988b20e36c2178d906bd05c6471018edf https://github.com/galaxyproject/galaxy/commit/0770d8d988b20e36c2178d906bd0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Revise workflow mode flag handling Fix comment Commit: 7bb88b3f44a53fcd881d69f01d84d88624157ff5 https://github.com/galaxyproject/galaxy/commit/7bb88b3f44a53fcd881d69f01d84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1097 from jmchilton/cwl_refactoring Small Tool and Workflow Cleanups from CWL Work. Commit: 81f1b7f8e0ce0febe18460e67a97651aa1fd72a3 https://github.com/galaxyproject/galaxy/commit/81f1b7f8e0ce0febe18460e67a97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Remove debugging logic and shortcut. Commit: 844facd1f1ea3d669cf7e61463c8ca8966c69006 https://github.com/galaxyproject/galaxy/commit/844facd1f1ea3d669cf7e61463c8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- UI, Lists: throttle selector animation when number of list items > 20 Commit: 303af68c33699bada56ddbc95a5f8272401b2f0e https://github.com/galaxyproject/galaxy/commit/303af68c33699bada56ddbc95a5f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- Merge pull request #1149 from carlfeberhard/history.selector-anim UI, Lists: throttle selector animation when number of list items > 20 Commit: 119e26f4e5f91a2091ff1cacffb3f2f99c4c79f4 https://github.com/galaxyproject/galaxy/commit/119e26f4e5f91a2091ff1cacffb3… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.masthead.js M static/maps/galaxy.masthead.js.map M static/scripts/galaxy.masthead.js Log Message: ----------- Merge pull request #1142 from dannon/menu_onclick_addition Menu onclick addition Commit: 51e098649070435570f9b68bf17ecc005da65bc2 https://github.com/galaxyproject/galaxy/commit/51e098649070435570f9b68bf17e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A static/scripts/bundled/libs.bundled.js A static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Webpack: add in the libs bundles, Carl. They're kinda important. Commit: baeaae99059fc94ae2a0dc059cfd448d05bdcbbe https://github.com/galaxyproject/galaxy/commit/baeaae99059fc94ae2a0dc059cfd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/galaxy.bundled.js M static/scripts/bundled/galaxy.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 Log Message: ----------- Webpack: rebuild bundles using webpack 1.12.8 as defined in the package.json Commit: a664deeee76bcde33c725f37d61d8b41ea220b3d https://github.com/galaxyproject/galaxy/commit/a664deeee76bcde33c725f37d61d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/GruntFile.js M client/grunt-tasks/style.js M client/package.json M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1130 from dannon/repack_dev Enforce client build deps are up-to-date. Rebuild style with lessc > 2.5 Commit: ab0829f2e8df480d467f3b575c18a1ace38543cd https://github.com/galaxyproject/galaxy/commit/ab0829f2e8df480d467f3b575c18… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #1096 from jmchilton/format_2 Outline "Format 2" workflow definitions. Commit: 2e510bd5e12ab5e2c401e835e0f84f29376766db https://github.com/galaxyproject/galaxy/commit/2e510bd5e12ab5e2c401e835e0f8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-21 (Sat, 21 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #1113 from jmchilton/format_source_collection Allow accessing collection elements in format_source. Commit: a16cb06705676aa49e725c8ab58521c239dfea4d https://github.com/galaxyproject/galaxy/commit/a16cb06705676aa49e725c8ab585… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-22 (Sun, 22 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix for re-installing an uninstalled TS repository with a dependency where both the repository and the dependency were updated in the TS after the repository was uninstalled. Commit: 11f9fed4acb3fb912bc0e0e5c0232fb85c974f2f https://github.com/galaxyproject/galaxy/commit/11f9fed4acb3fb912bc0e0e5c023… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-22 (Sun, 22 Nov 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1154 from gregvonkuster/dev Fix for re-installing an uninstalled TS repository with a dependency Commit: b6451d0be60a3bf2ca7c65c7700cb7361cb50754 https://github.com/galaxyproject/galaxy/commit/b6451d0be60a3bf2ca7c65c7700c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/functional/tools/output_format_collection.xml M test/unit/tools/test_actions.py Log Message: ----------- Fix bugs in test and code introduced in PR #1113. Commit: 3cadcdffb51f3994ed6ca0f4a9508f31fba1c4a6 https://github.com/galaxyproject/galaxy/commit/3cadcdffb51f3994ed6ca0f4a950… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/functional/tools/output_format_collection.xml M test/unit/tools/test_actions.py Log Message: ----------- Merge pull request #1155 from nsoranzo/fix_for_1113 Fix bugs in test and code introduced in PR #1113. Commit: 368da171f5f4490029fb6e80b888e5b091051901 https://github.com/galaxyproject/galaxy/commit/368da171f5f4490029fb6e80b888… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M config/plugins/visualizations/charts/templates/charts.mako M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Call onbeforeunload before hiding iframe through display() Validated message Commit: 9cc8e08537291a85885ee3ad52daeb36b95b4f8e https://github.com/galaxyproject/galaxy/commit/9cc8e08537291a85885ee3ad52da… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M test/qunit/package.json Log Message: ----------- add local grunt-cli dependency for qunit tests Commit: 77166a7295b1fe13f366414361b1752e6c0dd953 https://github.com/galaxyproject/galaxy/commit/77166a7295b1fe13f366414361b1… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M test/qunit/package.json Log Message: ----------- Merge pull request #1159 from martenson/local-grunt-cli-dep add local grunt-cli dependency for qunit tests Commit: 6e185fa208c27564b4cd2db5e31f55bf58c6eb4e https://github.com/galaxyproject/galaxy/commit/6e185fa208c27564b4cd2db5e31f… Author: Christian-B <github(a)brenn.co.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Allowed for capitailsed packgae name such as R Commit: 32728e23921553c75fda61acadb4f5dc82a4f915 https://github.com/galaxyproject/galaxy/commit/32728e23921553c75fda61acadb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Small optimizations to running tools. Commit: 1ea68f938408b72f8f0f4ebe2545550baea85037 https://github.com/galaxyproject/galaxy/commit/1ea68f938408b72f8f0f4ebe2545… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Save a query per output during tool execution. Commit: 42d006162c095669a2c7afe1ab0f1fb67b000798 https://github.com/galaxyproject/galaxy/commit/42d006162c095669a2c7afe1ab0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Another tool dataset creation optimization... Rather than using three transactions to create an HDA, a dataset, and its roles - do this all in one transaction. Commit: 01c57908eaf8bd589ce8738fdab14d415543d072 https://github.com/galaxyproject/galaxy/commit/01c57908eaf8bd589ce8738fdab1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Another tool execution optimization... Prefetch all groups, roles, and associations when using User.all_users(). This reduces three queries down to one if the user has no groups or group roles and only belongs to the private user role, obviously the number of queries saved would increase more and more if the user belonged to multiple roles or groups. Commit: 853efcea14d1ce11961d171324dbce03e6694117 https://github.com/galaxyproject/galaxy/commit/853efcea14d1ce11961d171324db… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1163 from jmchilton/tool_opts_1 Small optimizations to running tools. Commit: f3f8fef28a55c7b4e6994b08e3125a0d66a36140 https://github.com/galaxyproject/galaxy/commit/f3f8fef28a55c7b4e6994b08e312… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/galaxy.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy-app-base.js M client/grunt-tasks/scripts.js M client/webpack.config.js M lib/galaxy/web/base/controller.py M static/maps/galaxy-app-base.js.map R static/maps/galaxy.menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map R static/scripts/bundled/galaxy.bundled.js R static/scripts/bundled/galaxy.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/galaxy-app-base.js R static/scripts/galaxy.menu.js M templates/js-app.mako Log Message: ----------- Webpack: move Galaxy object creation from mako to app js, clean up and localize page, panels, and app Commit: b15a4082939be8b533dddf9a6a63efec9be6b817 https://github.com/galaxyproject/galaxy/commit/b15a4082939be8b533dddf9a6a63… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: R client/galaxy/scripts/tools/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/tools/rgenetics/helper_functions.js R client/galaxy/scripts/tools/rgenetics/timer.js R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map R static/maps/tools/rgenetics/helper_functions.js.map R static/maps/tools/rgenetics/timer.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js R static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js Log Message: ----------- Client: remove duplicate rgenetics directory tools/rgenetics Commit: d921b4243101130d7de5517167eb38fa1aa6b1d3 https://github.com/galaxyproject/galaxy/commit/d921b4243101130d7de5517167eb… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: R client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/app/app-login.js R client/galaxy/scripts/mvc/app/app-view.js R static/maps/mvc/app/app-analysis.js.map R static/maps/mvc/app/app-login.js.map R static/maps/mvc/app/app-view.js.map R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/app/app-login.js R static/scripts/mvc/app/app-view.js Log Message: ----------- Webpack: remove mvc/app Commit: 9f91b82245fc3ba467e8bef7b57bfc58ef02e9f0 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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 R static/scripts/libs/IE/IE7.js R static/scripts/libs/IE/IE8.js R static/scripts/libs/IE/blank.gif R static/scripts/libs/IE/excanvas.js R static/scripts/libs/IE/ie7-recalc.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Client: remove IE7/8 and excanvas polyfills Commit: e3e9579a812c468fba3f8a64fae7c7455e4b5a9e https://github.com/galaxyproject/galaxy/commit/e3e9579a812c468fba3f8a64fae7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js R client/galaxy/scripts/galaxy-app-base.js A client/galaxy/scripts/galaxy.js R static/maps/galaxy-app-base.js.map A static/maps/galaxy.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 R static/scripts/galaxy-app-base.js A static/scripts/galaxy.js M templates/galaxy_client_app.mako Log Message: ----------- Webpack: pack scripts, move galaxy-app-base.js to galaxy.js Commit: 11edf3559d7092c9e3fada3f04d9291bea64f2f0 https://github.com/galaxyproject/galaxy/commit/11edf3559d7092c9e3fada3f04d9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-24 (Tue, 24 Nov 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1166 from jmchilton/tool_opts_2 Another set of tool execution optimizations Commit: 4261403fad1c5fd1346b0cfe9fd25e97459cd028 https://github.com/galaxyproject/galaxy/commit/4261403fad1c5fd1346b0cfe9fd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fixes for WorkflowContentsManager requiring app during init. Commit: 6752fcc100e0448d6fef6d27dacb8e2467de88ee https://github.com/galaxyproject/galaxy/commit/6752fcc100e0448d6fef6d27dacb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix interface and usage of WorkflowModule.get_runtime_inputs. Run workflow workflow form was broken for workflows with pause steps. Fixes #1015 (thanks @afgane). Commit: 68da0004709e88ed8a856d39e9fa4e64aa3bc653 https://github.com/galaxyproject/galaxy/commit/68da0004709e88ed8a856d39e9fa… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/rgenetics/helper_functions.js R client/galaxy/scripts/rgenetics/timer.js R static/maps/rgenetics/checkbox_and_radiobutton.js.map R static/maps/rgenetics/helper_functions.js.map R static/maps/rgenetics/timer.js.map R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js Log Message: ----------- Client, rgenetics: 'Nuke 'em all' - R.Lazarus Commit: c408b0ec6515deccd92a264edd4ab78061a06b87 https://github.com/galaxyproject/galaxy/commit/c408b0ec6515deccd92a264edd4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Do not check for tool migrations when running tests. This is an inappropriate time for the check and causes slow down when running tests. Commit: 4f6aad473d99d7327b3c2aa395f1b546a443fc02 https://github.com/galaxyproject/galaxy/commit/4f6aad473d99d7327b3c2aa395f1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M config/tool_shed.ini.sample A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/config.py M scripts/bootstrap_history.py M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge branch 'master' into dev Commit: 6fda0e0aac54c1c9e758110b4868b4a3fece16aa https://github.com/galaxyproject/galaxy/commit/6fda0e0aac54c1c9e758110b4868… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-25 (Wed, 25 Nov 2015) Log Message: ----------- Merge branch 'master' into dev Conflicts: run_tests.sh Commit: f397584538f59d03d9c37d3f9366b455022e97b2 https://github.com/galaxyproject/galaxy/commit/f397584538f59d03d9c37d3f9366… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M client/galaxy/scripts/polyfills.js M static/maps/polyfills.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/polyfills.js M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Webpack: add link rel='index' with href to Galaxy.root, rework browser testing to use the same when redirecting to error pages Commit: c11c07d9bb124d41a301c5adf8f81c42b99430cc https://github.com/galaxyproject/galaxy/commit/c11c07d9bb124d41a301c5adf8f8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .gitignore A CODE_OF_CONDUCT.md M CONTRIBUTING.md M CONTRIBUTORS.md M README.rst M client/GruntFile.js M 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test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py M test/tool_shed/functional_tests.py M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_execution.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox_filters.py M test/unit/unittest_utils/utility.py M test/unit/workflows/test_modules.py R tool-data/fastx_clipper_sequences.txt R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml M tools/data_source/data_source.py R tools/data_source/echo.py R tools/data_source/echo.xml R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wig_to_bigwig.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.xml M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into async_metadata_reset Commit: 0c75af7192b7f34260098a21ff30d98492ba738e https://github.com/galaxyproject/galaxy/commit/0c75af7192b7f34260098a21ff30… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M config/plugins/visualizations/charts/templates/charts.mako M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Merge pull request #1157 from guerler/revise_iframe_unload_001 Call onbeforeunload before hiding iframe through display() Commit: 62474100f8f075ce519d008336060dfa952da725 https://github.com/galaxyproject/galaxy/commit/62474100f8f075ce519d00833606… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- add onbeforeunload to IE Commit: 1931bd59077f97946a1af6daa93bc920fceee58e https://github.com/galaxyproject/galaxy/commit/1931bd59077f97946a1af6daa93b… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- lazy load metadata to speed up history loading Commit: 2a54ff08292d85b3ecdab79e307b4b5d0aba4cc3 https://github.com/galaxyproject/galaxy/commit/2a54ff08292d85b3ecdab79e307b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Merge pull request #1176 from jmchilton/auto_migrate Do not check for tool migrations when running tests. Commit: 7d4f0d82de328ffb763737c067fc9332b61534e9 https://github.com/galaxyproject/galaxy/commit/7d4f0d82de328ffb763737c067fc… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- fix indentation Commit: f4dab5523b687c079df68d4d2988dc830429bd93 https://github.com/galaxyproject/galaxy/commit/f4dab5523b687c079df68d4d2988… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Merge pull request #1178 from bgruening/obbeforechange_ie Prevent GIEs from being closed without user confirmation Commit: 2be9aa2569b35a86f4c593215189a07eb5dd62f0 https://github.com/galaxyproject/galaxy/commit/2be9aa2569b35a86f4c593215189… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype: support for crai indexes via pysam Commit: 2568e85e7b84a8d9c7039f4c4b44661b9930a55e https://github.com/galaxyproject/galaxy/commit/2568e85e7b84a8d9c7039f4c4b44… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: A config/reports.ini.sample R config/reports_wsgi.ini.sample Log Message: ----------- Renames reports_wsgi.ini Commit: a3668355961e3988158a8bdb1bbe0f898d475967 https://github.com/galaxyproject/galaxy/commit/a3668355961e3988158a8bdb1bbe… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M run_reports.sh Log Message: ----------- Changed reports_wsgi.ini to reports.ini Commit: 9fceddf8a2f62df2774f269755398ce7d9f203b3 https://github.com/galaxyproject/galaxy/commit/9fceddf8a2f62df2774f26975539… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M scripts/sync_reports_config.py Log Message: ----------- Changed reports_wsgi.ini to reports.ini Commit: ca3e3760ccd92e3162a5740e713a7b3daf4c4e03 https://github.com/galaxyproject/galaxy/commit/ca3e3760ccd92e3162a5740e713a… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M .gitignore Log Message: ----------- Changed reports_wsgi.ini to reports.ini Commit: d7eb84e57bbd119d788ca759e0d61a464a030c7a https://github.com/galaxyproject/galaxy/commit/d7eb84e57bbd119d788ca759e0d6… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype: support for crai index (using built-in pysam) Commit: 2e97553194a0e13dc4158c29a161c0b678bcd02e https://github.com/galaxyproject/galaxy/commit/2e97553194a0e13dc4158c29a161… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-28 (Sat, 28 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.frame.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/galaxy.frame.js.map M static/maps/galaxy.masthead.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/galaxy.frame.js M static/scripts/galaxy.masthead.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Filter download links Commit: 7b85684683b3a6ee07ec024f943bada03f51195b https://github.com/galaxyproject/galaxy/commit/7b85684683b3a6ee07ec024f943b… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-29 (Sun, 29 Nov 2015) Changed paths: M run_reports.sh Log Message: ----------- Updated run_reports.sh Updated run_reports.sh to reflect new changes. Commit: 1b06e8d674edd7f1a1f9397429b319670891a8bd https://github.com/galaxyproject/galaxy/commit/1b06e8d674edd7f1a1f9397429b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1126 from jgoecks/farbtastic-fix Readd jquery.migrate to galaxy.panels template because it is needed f… Commit: 8971badb10aa216fab3ce7318ec28389e0ea79b9 https://github.com/galaxyproject/galaxy/commit/8971badb10aa216fab3ce7318ec2… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M .gitignore Log Message: ----------- Updated gitignore Commit: 9e353028d5ad5ef6a0ba7889f5f5e8b975261811 https://github.com/galaxyproject/galaxy/commit/9e353028d5ad5ef6a0ba7889f5f5… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M run_reports.sh Log Message: ----------- Updated run_reports.sh Updated run_reports.sh to mark the latest changes. Commit: dc41856812f9064c518a8e45c4559b2f32fe9db2 https://github.com/galaxyproject/galaxy/commit/dc41856812f9064c518a8e45c455… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #1173 from jmchilton/wfcfix Fixes for WorkflowContentsManager requiring app during init. Commit: c2f93316112ce90d0f1f7fe947ce1881cae3c773 https://github.com/galaxyproject/galaxy/commit/c2f93316112ce90d0f1f7fe947ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1174 from jmchilton/workflow_runtime_fix Fix interface and usage of WorkflowModule.get_runtime_inputs. Commit: 2829cab105c202a49904d65d88a9ac37dc12d81e https://github.com/galaxyproject/galaxy/commit/2829cab105c202a49904d65d88a9… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) 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: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: f35bd9ae02aaa814d9ab62838146be2ba4791f2b https://github.com/galaxyproject/galaxy/commit/f35bd9ae02aaa814d9ab62838146… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M .gitignore A config/reports.ini.sample R config/reports_wsgi.ini.sample M run_reports.sh M scripts/sync_reports_config.py Log Message: ----------- Merge pull request #1181 from souravsingh/rename_file Renames reports_wsgi.ini Commit: 492fcdab9fa1cdc1465c191289077e103d8d8020 https://github.com/galaxyproject/galaxy/commit/492fcdab9fa1cdc1465c19128907… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) 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 #1193 from mvdbeek/gvk_ts_fixes Add enhancements to the Galaxy repository install process Commit: 9e28f2e786bcb2bc727f7dba571742f9d2773165 https://github.com/galaxyproject/galaxy/commit/9e28f2e786bcb2bc727f7dba5717… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/interval.py M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_15.10' into dev Commit: 78558beec3ebeca63a282e667948a18c2b21c508 https://github.com/galaxyproject/galaxy/commit/78558beec3ebeca63a282e667948… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype definition: flake8 correction Commit: 28715a5bca299933c69859559d5b88b381b6c998 https://github.com/galaxyproject/galaxy/commit/28715a5bca299933c69859559d5b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css Log Message: ----------- Add runtime modification switch Commit: 3524476bc6c75461fd8b793a3bf047d1ad475e2a https://github.com/galaxyproject/galaxy/commit/3524476bc6c75461fd8b793a3bf0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge branch 'master' into dev Commit: 84464288b18ca587334dba89c9fd011c7f3a0fc6 https://github.com/galaxyproject/galaxy/commit/84464288b18ca587334dba89c9fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/galaxy.frame.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/galaxy.frame.js.map M static/maps/galaxy.masthead.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/galaxy.frame.js M static/scripts/galaxy.masthead.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #1184 from guerler/fix_download_links_002 Filter download links, avoid warning dialog Commit: bb23701fa80c74a6621b1826b050d9e42c12455f https://github.com/galaxyproject/galaxy/commit/bb23701fa80c74a6621b1826b050… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- White space in BIOM1 datatype. Commit: 64506bbd43e21b299a8b42ee3cfd2ef8e40c06d2 https://github.com/galaxyproject/galaxy/commit/64506bbd43e21b299a8b42ee3cfd… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Prevent unneccessary extra read in BIOM1 sniffer. Commit: ff619df3946621b819df03909fc63ce9ee412ced https://github.com/galaxyproject/galaxy/commit/ff619df3946621b819df03909fc6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt M lib/tool_shed/util/hg_util.py Log Message: ----------- Downgrade Mercurial wheel to 3.4.2 to restore hg push of Tool Shed repositories. Fix #1183. Commit: 657afa89d3ac91e53a84ae132334f137eb07acdc https://github.com/galaxyproject/galaxy/commit/657afa89d3ac91e53a84ae132334… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/tool_shed/util/common_util.py Log Message: ----------- Small fixes. Commit: 194d871e38b3815bba120d6bb40c3eef45660738 https://github.com/galaxyproject/galaxy/commit/194d871e38b3815bba120d6bb40c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix Tool Shed export capsule for Mercurial >= 3.4 . Fix the following error: tool_shed.capsule.capsule_manager ERROR 2015-12-01 12:24:37,542 unable to find mercurial command "archive" Traceback (most recent call last): File "/opt/galaxy/lib/tool_shed/capsule/capsule_manager.py", line 88, in export_repository work_dir ) File "/opt/galaxy/lib/tool_shed/capsule/capsule_manager.py", line 148, in generate_repository_archive changeset_revision ) File "/opt/galaxy/lib/tool_shed/util/hg_util.py", line 28, in archive_repository_revision options_dict = get_mercurial_default_options_dict( 'archive' ) File "/opt/galaxy/lib/tool_shed/util/hg_util.py", line 200, in get_mercurial_default_options_dict raise Exception('unable to find mercurial command "%s"' % command) Exception: unable to find mercurial command "archive" Commit: b5c77a8e8c0255f61ca62a7ff2311d443e224bec https://github.com/galaxyproject/galaxy/commit/b5c77a8e8c0255f61ca62a7ff231… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Add metadata for BIOM1 datatype. I am not yet sure that we should store table_rows and table_columns, as these could grow quite large, but could be useful in tools. Commit: f41540f6137a2f63a6dcb27327e33bf73752f954 https://github.com/galaxyproject/galaxy/commit/f41540f6137a2f63a6dcb27327e3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Most of these should probably not be user visible. Commit: b20fb71e33c1779e42dd67bb68aa9b31b69ffca2 https://github.com/galaxyproject/galaxy/commit/b20fb71e33c1779e42dd67bb68aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Fix extraneous white space. Commit: f64d1597b84801dd48c2cdb5bc0c303355786942 https://github.com/galaxyproject/galaxy/commit/f64d1597b84801dd48c2cdb5bc0c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Extension point for environment variables. Commit: ea9f4a0467b6955ccc470da06eaf7c13e7643715 https://github.com/galaxyproject/galaxy/commit/ea9f4a0467b6955ccc470da06eaf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Initialize a ToolOutput.from_work_dir. Commit: 7ce43a0463c3d98b757d78d0600aadf5d7876eb9 https://github.com/galaxyproject/galaxy/commit/7ce43a0463c3d98b757d78d0600a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor run_request for downstream diff improvements. Commit: 77ed5681f8565b12ab1d5e5c7d0302c938e9c73d https://github.com/galaxyproject/galaxy/commit/77ed5681f8565b12ab1d5e5c7d03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Extend base api workflow _run_jobs helper... ... to allow loading content from test-data files. Commit: 42778e27539d919ff11d67a07368c0b6e4ebae75 https://github.com/galaxyproject/galaxy/commit/42778e27539d919ff11d67a07368… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Improved error handling in workflow run code. Commit: 2f31a3cbcd087f26caa9b8754920a6dddb924b30 https://github.com/galaxyproject/galaxy/commit/2f31a3cbcd087f26caa9b8754920… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Cleanup collapsible handling Commit: 3017c61f380c8caa722ff04d11e2e3d37ca56b1c https://github.com/galaxyproject/galaxy/commit/3017c61f380c8caa722ff04d11e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) 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 step order Commit: 98e738d6f0cb2faae1c304a889baaa66b10df953 https://github.com/galaxyproject/galaxy/commit/98e738d6f0cb2faae1c304a889ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) 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: ----------- Show pja info inside form portlet Improve readability Commit: 28501ab676f9df797bae316c3d24e9ae8fd58a9b https://github.com/galaxyproject/galaxy/commit/28501ab676f9df797bae316c3d24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Refactor workflow manager for extension. Commit: 4584a579a297ffd02bd77584b71a8c17d85d261a https://github.com/galaxyproject/galaxy/commit/4584a579a297ffd02bd77584b71a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix interface declaration for WorkflowModule.get_state. Implementers all take this attribute. Commit: 21213ef70f535e06bc485370686807a6d2850345 https://github.com/galaxyproject/galaxy/commit/21213ef70f535e06bc4853706868… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_render.py M test/unit/workflows/workflow_support.py Log Message: ----------- Refactor workflow testing code to quickly bootstrap workflows. Commit: 031a39aba83932fd0291f440a7e58c962deadfe8 https://github.com/galaxyproject/galaxy/commit/031a39aba83932fd0291f440a7e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Basic unit tests for workflow progress tracking. Commit: 8a01b42112ec32e5f978f3a4245127cad3219c45 https://github.com/galaxyproject/galaxy/commit/8a01b42112ec32e5f978f3a42451… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Refactor input_by_connections_name logic into model. Continue to delay calculation of this but auto-compute it if requested and module injection code hasn't been called explicitly. Moves logic internal to class where it belongs also. Commit: cf367ff0c75454837359b74046c05cc7cb456dc5 https://github.com/galaxyproject/galaxy/commit/cf367ff0c75454837359b74046c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add another workflow progress test case. This one for replacing a tool input with an input dataset. Commit: 7974c1f33486c0a66803004c5d7885a9d91b9c70 https://github.com/galaxyproject/galaxy/commit/7974c1f33486c0a66803004c5d78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add unit tests for workflow progress initialization. Commit: 07c3d10f31e48f783baf05c133b117e7f3e7ee1a https://github.com/galaxyproject/galaxy/commit/07c3d10f31e48f783baf05c133b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Extend workflow recovery progress test case to include replacement check. Commit: 48340b5829fb5ca346060d9372ba7df7e3effcef https://github.com/galaxyproject/galaxy/commit/48340b5829fb5ca346060d9372ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add TODO items to workflow progress unit tests. Commit: 67c98f54cad4f20413568417e2cbb97bee24b0e5 https://github.com/galaxyproject/galaxy/commit/67c98f54cad4f20413568417e2cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #1200 from nsoranzo/tool_shed_fixes Tool shed fixes. Commit: ffb3de9ede515d10fbdf06519140a726e0cfa7d1 https://github.com/galaxyproject/galaxy/commit/ffb3de9ede515d10fbdf06519140… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py A test/functional/tools/collection_type_source.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1153 from jmchilton/collection_type_source Implement type_source on output collections. Commit: aa90e346dd4e10850482e38c7331864bef50f007 https://github.com/galaxyproject/galaxy/commit/aa90e346dd4e10850482e38c7331… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise form base Fix style Commit: 2c6c5236323dbea196cfd2e8fe3915f0c7e4c6df https://github.com/galaxyproject/galaxy/commit/2c6c5236323dbea196cfd2e8fe39… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Only store ids for row and column in BIOM1 datatype. Commit: 3acfa9c786e1fa5567cf313b294b68ab4c508c1b https://github.com/galaxyproject/galaxy/commit/3acfa9c786e1fa5567cf313b294b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Add blank lines around internal function. Commit: 002bc6b40a4314fc5f35f6156a73cad91532484d https://github.com/galaxyproject/galaxy/commit/002bc6b40a4314fc5f35f6156a73… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M .gitignore M client/GruntFile.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/grunt-tasks/style.js M client/package.json M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/visualizations/charts/templates/charts.mako A config/reports.ini.sample R config/reports_wsgi.ini.sample M config/tool_shed.ini.sample A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01_announce.rst M lib/galaxy/datatypes/interval.py M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M run_reports.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/sync_reports_config.py M static/maps/layout/masthead.js.map M static/maps/layout/panel.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map A static/maps/mvc/list/list-panel.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tools-form-base.js.map A static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-buttons.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/masthead.js M static/scripts/layout/panel.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-buttons.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css M templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py A test/functional/tools/collection_type_source.xml A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/package.json M test/unit/tools/test_actions.py M test/unit/tools/test_parsing.py Log Message: ----------- (merge dev) Commit: cfdbf8c0e71c5cdfa0ae47f6da7cc4553efd8429 https://github.com/galaxyproject/galaxy/commit/cfdbf8c0e71c5cdfa0ae47f6da7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M test/qunit/test-app.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Testing, webpack: correct name of Galaxy module in qunit, properly call require, pass GalaxyApp data Commit: 963d8637e869a214ee0e2c352a8184feb980a40e https://github.com/galaxyproject/galaxy/commit/963d8637e869a214ee0e2c352a81… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: R client/galaxy/scripts/galaxy.tools.js R static/maps/galaxy.tools.js.map R static/maps/galaxy.workflows.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/galaxy.tools.js R static/scripts/galaxy.workflows.js Log Message: ----------- Webpack: remove cruft galaxy.tools.js and (remnants of) galaxy.workflows.js Commit: 97415de3ce2bda54fb0730a41b4e0c7d8e93778a https://github.com/galaxyproject/galaxy/commit/97415de3ce2bda54fb0730a41b4e… Author: chambm <matt.chambers42(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 Log Message: ----------- Move idpDB and MzSQlite formats from proteomics.py to binary.py, because the SQLite sniffer lives there, and more specialized formats must be registered for sniffing before the generic format Add proper idpDB sniffing logic (akin to MzSQlite) and test case Add H5 sniffing based on magic number and test case Add SQLite/IdpDB/MzSQlite/GeminiSQLite and H5 to default datatypes in registry.py Commit: dd5f3aec52d1cec8e2a98dc9cf7134cd9b381d84 https://github.com/galaxyproject/galaxy/commit/dd5f3aec52d1cec8e2a98dc9cf71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix workflow extraction test cases broken with 77ed5681f8565b12ab1d5e5c7d0302c938e9c73d Commit: dd7bddcaa682d6d7cdaba8661c2c7cc80997ade0 https://github.com/galaxyproject/galaxy/commit/dd7bddcaa682d6d7cdaba8661c2c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Optimize initial queueing of jobs. - Don't refresh job when this is the only thread fetching it. - Avoid a bunch of unnecessary flushes, just flush once essentially during process. Brings this process from taking over 1 second per job on average on sqlite for cat1 on my laptop to around 400 ms on average. Commit: 299fbe99d7e157b9c01bbf0cdfcb7057dd59791a https://github.com/galaxyproject/galaxy/commit/299fbe99d7e157b9c01bbf0cdfcb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Micro optimization, only fetch tool validation once per multi-run. Commit: 876c28f88d81a8599a3278d9deac730adbac10d9 https://github.com/galaxyproject/galaxy/commit/876c28f88d81a8599a3278d9deac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py Log Message: ----------- Add more job timers. Commit: 41d3dc62f7e967ea3b409be410310563d0737bc4 https://github.com/galaxyproject/galaxy/commit/41d3dc62f7e967ea3b409be41031… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py Log Message: ----------- Parallelize executing tool parameter combinations. Should work when mapping over collections or for big muli-run tool submissions. Because of database tension with sqlalchemy it is not strictly a linear increase, but the end user walltime experience for a 24 dataset collection being submitted using 4 threads instead 1 drops execution time from 68 seconds to 35. Rebased with fixes thanks to @nsoranzo - https://github.com/jmchilton/galaxy/commit/7f6514a21222ea787a0676764e4a4fe8…. Commit: 64b7cc9fef21caac5f9d21a8d42b60262fd28162 https://github.com/galaxyproject/galaxy/commit/64b7cc9fef21caac5f9d21a8d42b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add sample tool that creates 10 outputs. Commit: a190b69e33a41717ddcc9eaa82826a82cc3d69b1 https://github.com/galaxyproject/galaxy/commit/a190b69e33a41717ddcc9eaa8282… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Optimize tools that produce multiple outputs. Fetch HIDs for these datasets all at once and flush once for all assignments. Creating jobs from 4 threads each job producing 10 outputs - this resulted in reducing the runtime of this portion of the code by 90% and saving around 20 seconds per job. Before: galaxy.tools.actions INFO 2015-11-30 15:53:46,235 Add outputs to history (22494.829 ms) galaxy.tools.actions INFO 2015-11-30 15:53:47,295 Add outputs to history (22239.062 ms) galaxy.tools.actions INFO 2015-11-30 15:53:48,320 Add outputs to history (23781.079 ms) galaxy.tools.actions INFO 2015-11-30 15:53:51,490 Add outputs to history (21820.567 ms) galaxy.tools.actions INFO 2015-11-30 15:54:24,506 Add outputs to history (25353.837 ms) After: galaxy.tools.actions INFO 2015-11-30 16:08:47,640 Add outputs to history (2781.675 ms) galaxy.tools.actions INFO 2015-11-30 16:08:47,860 Add outputs to history (3177.738 ms) galaxy.tools.actions INFO 2015-11-30 16:08:48,776 Add outputs to history (2425.528 ms) galaxy.tools.actions INFO 2015-11-30 16:09:02,942 Add outputs to history (2579.022 ms) Commit: ab2c7c2c079b51ffd4ed7ef00724ef3f8d2636ec https://github.com/galaxyproject/galaxy/commit/ab2c7c2c079b51ffd4ed7ef00724… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool execution micro optimization... ... Don't create an extra list to reverse, just iterate over in reversed order. Commit: 3de8579633c4294abb2a3235f90463108c35d324 https://github.com/galaxyproject/galaxy/commit/3de8579633c4294abb2a3235f904… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py Log Message: ----------- Add debug statement in output checker for why job is failing. Should help tool testing and other Galaxy testing. Commit: 59944046b7f16d13886928eb6928a7d67446c1e6 https://github.com/galaxyproject/galaxy/commit/59944046b7f16d13886928eb6928… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Fix for workflow progress unit testing. Commit: bed421fbc98583fdc00db57d3bb787450766576b https://github.com/galaxyproject/galaxy/commit/bed421fbc98583fdc00db57d3bb7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Introduce model abstractions for dealing with workflow steps. Three methods to provide higher-level access and reasoning about steps than just a flat array. Commit: da6051922e51ecc43c2f5b973adf5ba2dbf7554b https://github.com/galaxyproject/galaxy/commit/da6051922e51ecc43c2f5b973adf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Unroll input connection logic. Need to extend it downstream and the one-liner is fun but not easy to extend or particularily readable. Commit: d97d8a203c7c09123f7298627ad394d6c96e5b1c https://github.com/galaxyproject/galaxy/commit/d97d8a203c7c09123f7298627ad3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Better error messages in workflow running code. Commit: 4fdea55f81756a27bff8ef66b3fe27d4bda36905 https://github.com/galaxyproject/galaxy/commit/4fdea55f81756a27bff8ef66b3fe… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Enhance the VTK datatypes to support cell data in addition to point data. Replaces https://github.com/galaxyproject/galaxy/pull/1189. Commit: 69b8d83ba2b829621183361694f341bda66a77fe https://github.com/galaxyproject/galaxy/commit/69b8d83ba2b829621183361694f3… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Make default_indicator configurable * Document classes Commit: b87c22c73b9a3f6d31507d268e945a6ae8deef60 https://github.com/galaxyproject/galaxy/commit/b87c22c73b9a3f6d31507d268e94… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: A config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Add sample dependency_resolvers_conf.xml that matches actual default Commit: a443d99fddc14b58698618860076032cb9540dca https://github.com/galaxyproject/galaxy/commit/a443d99fddc14b58698618860076… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py Log Message: ----------- Undo deprecated datatypes stuff, doesn't work with Galaxy well. Commit: 20b96d883d9ef33b51d5a32d82ce2d1251daf572 https://github.com/galaxyproject/galaxy/commit/20b96d883d9ef33b51d5a32d82ce… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #1202 from jmchilton/workflow_tool_refactoring Small Tool and Workflow Refactoring and Fixes Commit: c034dc3e33a4c4aeecefcea375ea179621be1af6 https://github.com/galaxyproject/galaxy/commit/c034dc3e33a4c4aeecefcea375ea… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py Log Message: ----------- Merge pull request #1213 from jmchilton/tool_logging_2 Add debug statement in output checker for why job is failing. Commit: 1adff983f2509e6551f9000008d614a61d9b12a6 https://github.com/galaxyproject/galaxy/commit/1adff983f2509e6551f9000008d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Wait on jobs and history in certain API test cases. This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases. Commit: 362a25e6e6b03dfada43ad1b9ab651966936c795 https://github.com/galaxyproject/galaxy/commit/362a25e6e6b03dfada43ad1b9ab6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). Commit: 6c9a82e142c5bf70ae4612f094b8d0c89e3fd2f3 https://github.com/galaxyproject/galaxy/commit/6c9a82e142c5bf70ae4612f094b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for Section upgrade messages. Commit: 2c0ad432f8485cb40719adfa8ecbbf1a342afd03 https://github.com/galaxyproject/galaxy/commit/2c0ad432f8485cb40719adfa8ecb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use test param label instead of param label in conditional upgrade missing message. Commit: a3e3bde6a2b5c2fc9433336526ec32badfc8ce9d https://github.com/galaxyproject/galaxy/commit/a3e3bde6a2b5c2fc9433336526ec… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/apps/login.js M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Webpack: restore redirect for after login when require_login; remove allowed_paths for require_login: /index, /tool_menu, /masthead, library/browse, history/list, dataset/list Commit: 56054c6d98519541b896a5145998b02688750bb6 https://github.com/galaxyproject/galaxy/commit/56054c6d98519541b896a5145998… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Fix AvailModuleChecker() invocation and propogate default default_indicator Commit: 9b085740dfddfcb67f6a2e21a51503cd2ac0741e https://github.com/galaxyproject/galaxy/commit/9b085740dfddfcb67f6a2e21a515… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 65e6a1c3b6ca26e9f0d760cb39be7ec177d6c40f https://github.com/galaxyproject/galaxy/commit/65e6a1c3b6ca26e9f0d760cb39be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 Log Message: ----------- Merge pull request #1209 from chambm/feature/idpdb_hdf5_sniffers Add idpDB and HDF5 sniffers and fix MzSQlite sniffer Commit: 4c13c92540c7ed4f8305dcb0216c2a448f33c24d https://github.com/galaxyproject/galaxy/commit/4c13c92540c7ed4f8305dcb0216c… Author: Jesse <jesse.vandam(a)wur.nl> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py Log Message: ----------- Merge pull request #2 from jmchilton/triples_2 Remove deprecated datatype stuff Commit: a57095661246fab1d9045e0cabb1845f662edb5d https://github.com/galaxyproject/galaxy/commit/a57095661246fab1d9045e0cabb1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/graph.py A lib/galaxy/datatypes/triples.py Log Message: ----------- Merge pull request #396 from jessevdam/dev Added better support for formats that store triples. Commit: 92a7b995b05f7966e2936b62f052d3a4b8ed0642 https://github.com/galaxyproject/galaxy/commit/92a7b995b05f7966e2936b62f052… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1217 from ericenns/collection-tool-input-fixes Collection tool input mapping performance fixes Commit: bd0663f65062d60de810478566604b3ee33b109d https://github.com/galaxyproject/galaxy/commit/bd0663f65062d60de81047856660… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Initialise default_indicator before using __modules Commit: b72035c9fc4136af5f3db464fd5b2a9c5e330cca https://github.com/galaxyproject/galaxy/commit/b72035c9fc4136af5f3db464fd5b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M static/maps/layout/masthead.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.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/masthead.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Webpack: fix/re-work the pub-sub connection between the quotameter and the history panel so that the meter updates properly when a new dataset is added Commit: 14ac3665ee37224aa5278ce7a3876fb204b1bf2d https://github.com/galaxyproject/galaxy/commit/14ac3665ee37224aa5278ce7a387… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako Log Message: ----------- Merge pull request #598 from davebx/async_metadata_reset Make bulk repository metadata resets asynchronous. Commit: ba3e3da946b699a03ef9cab9095ea294d6df3b69 https://github.com/galaxyproject/galaxy/commit/ba3e3da946b699a03ef9cab9095e… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Add sample config for modules resolver Commit: 9a1fc647a38007fef2a7a179648ea8f925ab5a8f https://github.com/galaxyproject/galaxy/commit/9a1fc647a38007fef2a7a179648e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1212 from jmchilton/tool_opts_6 Smaller Tool Optimization PR Commit: 6f727962945481b75dd675e70eed78e8b785cb0a https://github.com/galaxyproject/galaxy/commit/6f727962945481b75dd675e70eed… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Update sample config for modules resolver Commit: 6735c9deceadba39c0a2b34b076f37440c087fc3 https://github.com/galaxyproject/galaxy/commit/6735c9deceadba39c0a2b34b076f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst Log Message: ----------- replace the readthedocs badge, we cannot use it until https://github.com/rtfd/readthedocs.org/issues/1767 is resolved Commit: e76933b55749c619c4debf4e62cd1f4d7e3cb7e1 https://github.com/galaxyproject/galaxy/commit/e76933b55749c619c4debf4e62cd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #1229 from martenson/remove-readthecdocs-badge replace the readthedocs badge, Commit: d2ce6d4d2b03fc7ad0a40ac4b0194f8636350f52 https://github.com/galaxyproject/galaxy/commit/d2ce6d4d2b03fc7ad0a40ac4b019… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 A lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 102eeef2d7045fa5b8706497f04817cb2f75813a https://github.com/galaxyproject/galaxy/commit/102eeef2d7045fa5b8706497f048… Author: Takao Nakaguchi <takao.nakaguchi(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Replacement should be applied only to first occurrence. Commit: a8a4480d5c7e92e0f121eefd66357f5504c4cb26 https://github.com/galaxyproject/galaxy/commit/a8a4480d5c7e92e0f121eefd6635… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix dataset matching Commit: ac79cf191c0a0588cdaf45b5075a2494bf097f57 https://github.com/galaxyproject/galaxy/commit/ac79cf191c0a0588cdaf45b5075a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js M static/style/blue/base.css Log Message: ----------- Fix style naming Commit: 11c46f4f35f3c1cb579198d28402ebacd51e6ec8 https://github.com/galaxyproject/galaxy/commit/11c46f4f35f3c1cb579198d28402… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge branch 'master' into dev Commit: f969eabf268a2e07235083d37168ae9887f87876 https://github.com/galaxyproject/galaxy/commit/f969eabf268a2e07235083d37168… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Fix qunit shim to match base_panels.mako shim. QUnit tests of things with underscore require statements would not work without this change. Commit: 0c8a738a35d8c28b18dba6da92ec702096c1554a https://github.com/galaxyproject/galaxy/commit/0c8a738a35d8c28b18dba6da92ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION before installing wheels. Fix #1205. As test/docker/base/run_test_wrapper.sh does. Commit: df781dcc188193ff044a625540dc02961a8c5640 https://github.com/galaxyproject/galaxy/commit/df781dcc188193ff044a625540dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Fix missing assertion pointed out @nsoranzo. Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing. Commit: 296971c5ded17367d2a14a32a072678b727ddf05 https://github.com/galaxyproject/galaxy/commit/296971c5ded17367d2a14a32a072… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: fcabc5242ca8fc6b1e7533ade17e2a8e3d27fe82 https://github.com/galaxyproject/galaxy/commit/fcabc5242ca8fc6b1e7533ade17e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Merge pull request #1160 from Christian-B/unlinked_dependencies Allowed for capitalised package names such as R Commit: 93bfa1992cc23a411e46437547581843c0e7b952 https://github.com/galaxyproject/galaxy/commit/93bfa1992cc23a411e4643754758… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Make more workflow methods properties. As suggested by @nsoranzo. Commit: f40d4fc178cbf3a3266a56ce0108b87e21bd5be0 https://github.com/galaxyproject/galaxy/commit/f40d4fc178cbf3a3266a56ce0108… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M config/galaxy.ini.sample R templates/webapps/galaxy/root/index.mako Log Message: ----------- Webpack: re-add show_welcome_with_login config option (lost due to merge/gitignore?); remove root/index.mako Commit: 600338dac7b0dad7f514f1b9a3c7c123dd63c379 https://github.com/galaxyproject/galaxy/commit/600338dac7b0dad7f514f1b9a3c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1231 from nsoranzo/dev_tests_conditional_wheels Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION before installing wheels. Commit: bab7ae099845f4503a2e41c939abc2aca9dc7a66 https://github.com/galaxyproject/galaxy/commit/bab7ae099845f4503a2e41c939ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/base/twilltestcase.py Log Message: ----------- Improved logging related tool test timeouts. There are transient failures of maxseconds.xml's tool test on Jenkins that I can't reproduce locally, hopefully improved logging will help. https://jenkins.galaxyproject.org/job/docker-framework/1309/testReport/juni… Commit: 74f7b900368030e425f79f835e2093102dbed5ba https://github.com/galaxyproject/galaxy/commit/74f7b900368030e425f79f835e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Merge pull request #1230 from openlangrid/dev Replacement should be applied only to first occurrence. Commit: 732b5722ae7c668634185209171fa55288e19985 https://github.com/galaxyproject/galaxy/commit/732b5722ae7c668634185209171f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Do not mess with galaxy_config_file, if provided. Commit: 5c87d07e0f535ed3367bbd463fb16bc0d83d7cf9 https://github.com/galaxyproject/galaxy/commit/5c87d07e0f535ed3367bbd463fb1… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Merge pull request #1233 from jmchilton/underscore_shim Fix qunit shim to match base_panels.mako shim. Commit: 905471e32fef02b9da38d2efe0cc463cd258cbff https://github.com/galaxyproject/galaxy/commit/905471e32fef02b9da38d2efe0cc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #1226 from jmchilton/jobs_api_test_fix Wait on jobs and history in certain API test cases. Commit: 0eb87f911c4523ecb268b26ad8c74a0252ce8453 https://github.com/galaxyproject/galaxy/commit/0eb87f911c4523ecb268b26ad8c7… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Minor docstring typo Commit: 4289cf3ab2f92375e6e4d9751064325b55cceaae https://github.com/galaxyproject/galaxy/commit/4289cf3ab2f92375e6e4d9751064… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1235 from blankenberg/typo_dev Minor docstring typo Commit: 1cc57b1eb2c295dbd68837c864740b6ff079b83d https://github.com/galaxyproject/galaxy/commit/1cc57b1eb2c295dbd68837c86474… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Add icons and reorganise history menu Commit: 564f12c50ffaed386f57e1fd2d4048840e5f8288 https://github.com/galaxyproject/galaxy/commit/564f12c50ffaed386f57e1fd2d40… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Remove icons Commit: 42b6da87554b78fddd5b592a82d46deb83cada15 https://github.com/galaxyproject/galaxy/commit/42b6da87554b78fddd5b592a82d4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Comment out debugging Commit: 9bd2712c5d9aa260012ffdad267434758bf086c0 https://github.com/galaxyproject/galaxy/commit/9bd2712c5d9aa260012ffdad2674… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M static/maps/mvc/history/options-menu.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Just going to clobber everything Commit: 4d396a6945b3394cd529849076b1f6c9892962c5 https://github.com/galaxyproject/galaxy/commit/4d396a6945b3394cd529849076b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: A config/dependency_resolvers_conf.xml.sample M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #1221 from pvanheus/env-modules-resolve Add documentation and extra options to Environment Modules resolver Commit: 198cb7c9a1534e7914ca76c4648fd750234ddb9f https://github.com/galaxyproject/galaxy/commit/198cb7c9a1534e7914ca76c4648f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M static/scripts/libs/jquery/jquery.dynatree.js Log Message: ----------- Fix rebase issue Commit: 5675617178b6d103de88ff907d137974b908761e https://github.com/galaxyproject/galaxy/commit/5675617178b6d103de88ff907d13… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #985 from erasche/nicer-history-menu Add icons and reorganise history menu Commit: a0c7d87db35133c2a81d54766f0e718d7fe5f766 https://github.com/galaxyproject/galaxy/commit/a0c7d87db35133c2a81d54766f0e… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: A Makefile A client/.docker-build.sh A client/Dockerfile M doc/source/dev/faq.rst Log Message: ----------- Ease the grunt uglify process Commit: 3e8b58c5aa66da83206230d27aacba1eaa7faa00 https://github.com/galaxyproject/galaxy/commit/3e8b58c5aa66da83206230d27aac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge branch 'release_15.10' into dev Commit: 9e8068f3671cdef499ed51aca3869f91e2e5b69d https://github.com/galaxyproject/galaxy/commit/9e8068f3671cdef499ed51aca386… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M README.rst M client/galaxy/scripts/mvc/history/options-menu.js M config/datatypes_conf.xml.sample A config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 A lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/migrate/check.py M run_tests.sh M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_workflows.py A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-common.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- (merge dev) Commit: 7cf98d32d811fbf9c8b64f72334c4f4c1e502882 https://github.com/galaxyproject/galaxy/commit/7cf98d32d811fbf9c8b64f72334c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Align opinions with @jmchilton Commit: 1295f985106a9440135e139368a708ef8dcc0538 https://github.com/galaxyproject/galaxy/commit/1295f985106a9440135e139368a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M Makefile Log Message: ----------- Rename docker image Commit: 0fec39d3bd323b203d6221f087ccac8014c3fefc https://github.com/galaxyproject/galaxy/commit/0fec39d3bd323b203d6221f087cc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/Dockerfile Log Message: ----------- Less insane build recipe if it's included in the repo Commit: 0924891e31f3f215323fe7030e0d6c167f596878 https://github.com/galaxyproject/galaxy/commit/0924891e31f3f215323fe7030e0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Fix up merge issue with double underscore shim. Commit: 4a279ffb64576258f2f2755f182430e1ccbacbc2 https://github.com/galaxyproject/galaxy/commit/4a279ffb64576258f2f2755f1824… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Allow inputs section for Format 2 workflow definitions. Arguably a more natural way to define inputs, regardless it allows more CWL-like input definitions for workflows. Commit: b0b26e69019162e335ea5a331ab21009c882f0d1 https://github.com/galaxyproject/galaxy/commit/b0b26e69019162e335ea5a331ab2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py Log Message: ----------- Allow specifying Format 2 workflow by path. This will allow importing workflow relative resources in subsequent passes at this. Commit: 70a9f213932947758f9882776140727eb6c0e246 https://github.com/galaxyproject/galaxy/commit/70a9f213932947758f9882776140… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py Log Message: ----------- Update workflow format 2 code with infrastructure for nesting runnables. In downstream work this is used for subworkflows and nested tools. Not sure which of these would potentially hit main line Galaxy first so setting this all up in its own commit. Commit: 1bd0a4e9703406223f0e9bfe31df4c801998f400 https://github.com/galaxyproject/galaxy/commit/1bd0a4e9703406223f0e9bfe31df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Refactoring and more testing of format 2 workflow implementation code... ... toward more reusable design. Commit: a597e0e8349f33d4d2c642d2e0a74e3da64b156b https://github.com/galaxyproject/galaxy/commit/a597e0e8349f33d4d2c642d2e0a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Implement workflow outputs for format 2 workflow definitions. Copy CWL style of specifying a outputs specification block at the top-level of the workflow specification and within that use the "source" attribute to specify the output. Reuse the specification used by "$link"s to describe this output - namely <label_or_order_index>[#<output_name=output>]. Commit: 3d0723c812632a276102748ec6a754bbec0b9d9a https://github.com/galaxyproject/galaxy/commit/3d0723c812632a276102748ec6a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- JS Model abstractions for dealing workflow outputs. Need to modify how these are represented so I want the logic centralized in the model... also the logic should be centralized in the model. Commit: 7b3fa824b67c0c7f881a514ae5b6598ede62e14c https://github.com/galaxyproject/galaxy/commit/7b3fa824b67c0c7f881a514ae5b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/managers/workflows.py M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Update worklfow editor representation of workflow outputs. Modified this for the workflow export representation but this needed to be updated for the workflow editor because they shared some code in the manager. This was going to be needed downstream when I add labels and uuids to workflow outputs anyway. Commit: cee9d4d1b30633689d8dd5fde715aed528e578a1 https://github.com/galaxyproject/galaxy/commit/cee9d4d1b30633689d8dd5fde715… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js Log Message: ----------- Grunt the workflow JS. Commit: 40e6932a25f71c240e038e4e6dc9be6a19ff8459 https://github.com/galaxyproject/galaxy/commit/40e6932a25f71c240e038e4e6dc9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Fix workflow API tests for workflow output changes. Commit: e9e73f4828f7926a1a36654ed48325828992bed3 https://github.com/galaxyproject/galaxy/commit/e9e73f4828f7926a1a36654ed483… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js Log Message: ----------- Remove dated comment. Commit: c91a2eb33947a64ed8c03115d1de9ccf746cc195 https://github.com/galaxyproject/galaxy/commit/c91a2eb33947a64ed8c03115d1de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js M test/api/test_tools.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Multi data parameter improvements. Allow multiple collections to be fed to a multi data parameter in one reduction step. Fixes #750 and will really simplify certain classes of tools. Rebased original with fixes for rerun of such reductions. Manually tested workflow execution and everything seems fine. The workflow editor already thought this was possible, so that is another bug corrected by this enhancement. To run the associated API test, execute the following command: ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_reduce_multiple_lists_on_multi_data Conflicts: static/maps/mvc/dataset/dataset-choice.js.map static/maps/mvc/form/form-select-content.js.map static/scripts/mvc/form/form-select-content.js Commit: 62a26516cd7a3a6d1ad6441dc8d63efafa25d8d0 https://github.com/galaxyproject/galaxy/commit/62a26516cd7a3a6d1ad6441dc8d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Fix PR #805 for changes in PR #1153. Commit: 17851ba0ea9572f1c387ff1fea1012b7af737855 https://github.com/galaxyproject/galaxy/commit/17851ba0ea9572f1c387ff1fea10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/unit/tools/test_actions.py Log Message: ----------- And fix unit test for b036adcaa166153e544935c12123877c69a7450f. Commit: 9f8eb465e718d4b643120e8554d119702c264135 https://github.com/galaxyproject/galaxy/commit/9f8eb465e718d4b643120e8554d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M .gitignore A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A 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static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/style/blue/base.css R static/style/blue/galaxy.frame.masthead.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/user/logout.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1144 from carlfeberhard/webpack Webpack Commit: f7a2acdcabdfb0d2368e00c4959712bf7d5c98f2 https://github.com/galaxyproject/galaxy/commit/f7a2acdcabdfb0d2368e00c49597… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Merge pull request #1246 from jmchilton/test-commons Fix up merge issue with double underscore shim. Commit: b0c1cd7460f13075c565750298f9d4c3cb89bb80 https://github.com/galaxyproject/galaxy/commit/b0c1cd7460f13075c565750298f9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M test/base/twilltestcase.py Log Message: ----------- Merge pull request #1243 from jmchilton/maxseconds_debug Improved logging related tool test timeouts. Commit: d0a011675323ba7e8deba588ae0ae6ed9c23f0fe https://github.com/galaxyproject/galaxy/commit/d0a011675323ba7e8deba588ae0a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Enable lookup of tools from other tool sheds. Commit: c040a18b4b164e58a45d1c4f6da65f1eacf18ed5 https://github.com/galaxyproject/galaxy/commit/c040a18b4b164e58a45d1c4f6da6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Modify get_tool() directly instead of using decorator. Commit: 2d168a2c07798ab736676a1eb865ae6976b48464 https://github.com/galaxyproject/galaxy/commit/2d168a2c07798ab736676a1eb865… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove whitespaces in blank line. Commit: 1be4f85404c75be364cb20b3c460ea3f51c4dae2 https://github.com/galaxyproject/galaxy/commit/1be4f85404c75be364cb20b3c460… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Add messages inform users of changes in the tool_id. Commit: 4f1359a0a6d703c8a40b6bb015e89d991d97570e https://github.com/galaxyproject/galaxy/commit/4f1359a0a6d703c8a40b6bb015e8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M .gitignore A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A 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templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/api/helpers.py M test/api/test_jobs.py M test/base/twilltestcase.py M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into cross_toolshed_tool_fetching Commit: 77f034019b93bdd539a495a89318bcb1e51b3993 https://github.com/galaxyproject/galaxy/commit/77f034019b93bdd539a495a89318… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix failing api test Commit: 1fdde2cb4d3d685916dc82a8fc846079a8066cd5 https://github.com/galaxyproject/galaxy/commit/1fdde2cb4d3d685916dc82a8fc84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Refactor generic side workflow editor panel toward backbone. Commit: cae457d8c18ded2abf03a0a6c3fb027735e1b5ef https://github.com/galaxyproject/galaxy/commit/cae457d8c18ded2abf03a0a6c3fb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Fail maxseconds test tool if sleep is interrupted. Commit: d7f5dbe4ca1bc0943e3d3edbddd88d1c226ff5e5 https://github.com/galaxyproject/galaxy/commit/d7f5dbe4ca1bc0943e3d3edbddd8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js M test/api/test_tools.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge pull request #805 from jmchilton/multi_data_param_enhance Allow multiple collections to be supplied to a multiple data parameter. Commit: 3069e12ca741245563b9e372bf581747861fce6e https://github.com/galaxyproject/galaxy/commit/3069e12ca741245563b9e372bf58… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M .gitignore A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A 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test/unit/tools/test_data_parameters.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 6126bd0e93e17c2d9cd6512ec068f806cc9da72d https://github.com/galaxyproject/galaxy/commit/6126bd0e93e17c2d9cd6512ec068… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1214 from jmchilton/format_2_1 Small enhancements in workflow inputs and outputs Commit: 4d252119fd0057b9b9433a4d874784c86f96d42e https://github.com/galaxyproject/galaxy/commit/4d252119fd0057b9b9433a4d8747… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #1216 from jmchilton/workflow_tweaks_1 More small workflow tweaks. 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test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/base/twilltestcase.py M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml A test/functional/tools/collection_type_source.xml A test/functional/tools/create_10.xml A test/functional/tools/maxseconds.xml A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_loader.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 8e5b8016c6684e2364ba14b9061b0d5a2d218eb1 https://github.com/galaxyproject/galaxy/commit/8e5b8016c6684e2364ba14b9061b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: R client/galaxy/scripts/mvc/app/app-analysis.js R static/maps/mvc/app/app-analysis.js.map Log Message: ----------- Remove files Commit: 7e5069baff533ba61fef3f8f6fc46ecab565a9c6 https://github.com/galaxyproject/galaxy/commit/7e5069baff533ba61fef3f8f6fc4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: R client/galaxy/scripts/mvc/tool/tools-form-base.js R client/galaxy/scripts/mvc/tool/tools-form-workflow.js R client/galaxy/scripts/mvc/tool/tools-form.js R client/galaxy/scripts/mvc/tool/tools-jobs.js R client/galaxy/scripts/mvc/tool/tools-template.js R static/maps/mvc/tool/tools-form-base.js.map R static/maps/mvc/tool/tools-form-workflow.js.map R static/maps/mvc/tool/tools-form.js.map R static/maps/mvc/tool/tools-jobs.js.map R static/maps/mvc/tool/tools-template.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/scripts/mvc/tool/tools-form-base.js R static/scripts/mvc/tool/tools-form-workflow.js R static/scripts/mvc/tool/tools-form.js R static/scripts/mvc/tool/tools-jobs.js R static/scripts/mvc/tool/tools-template.js R static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Remove files Commit: 0f9cb1478f81d512d4232b42cf490b8022b3a420 https://github.com/galaxyproject/galaxy/commit/0f9cb1478f81d512d4232b42cf49… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M static/style/blue/base.css Log Message: ----------- Repack files Commit: df6470654411bfa8ce997f932e92b4c2d644c685 https://github.com/galaxyproject/galaxy/commit/df6470654411bfa8ce997f932e92… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Merge pull request #1237 from jmchilton/test_jobs_fix Fix missing assertion pointed out @nsoranzo. Commit: fef8ce2a762b82480d5f7304c345cc3168e10036 https://github.com/galaxyproject/galaxy/commit/fef8ce2a762b82480d5f7304c345… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Merge pull request #1248 from jmchilton/maxseconds_debug_2 Attempt to fix transiently failing tool test on Jenkins Commit: e12179b0160d242be870b15b8da5a46e294063bf https://github.com/galaxyproject/galaxy/commit/e12179b0160d242be870b15b8da5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Merge pull request #1211 from gregvonkuster/dev Enhance the VTK datatypes to support cell data in addition to point Commit: 91d348a73fd49453c9cde5fb6116c3b230a2f162 https://github.com/galaxyproject/galaxy/commit/91d348a73fd49453c9cde5fb6116… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #1247 from jmchilton/editor_refactor Refactor generic side workflow editor panel toward backbone. Commit: e29f7155c479365ede4a69513e729fa1bc67c369 https://github.com/galaxyproject/galaxy/commit/e29f7155c479365ede4a69513e72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: R static/maps/mvc/tools.js.map R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/tools.js Log Message: ----------- Remove files Commit: 6820b29d3b867b452205c275f274449fb55c8119 https://github.com/galaxyproject/galaxy/commit/6820b29d3b867b452205c275f274… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/datatypes/constructive_solid_geometry.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M test/api/helpers.py M test/functional/tools/maxseconds.xml Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: b11002bef32d83b058e3495f96695c8dc12cb91b https://github.com/galaxyproject/galaxy/commit/b11002bef32d83b058e3495f9669… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/workflows_format_2/converter.py Log Message: ----------- Don't iterate over unused key. Thanks to @bgruening. Commit: 2aa7f04364e10e46c655de636925883a43698694 https://github.com/galaxyproject/galaxy/commit/2aa7f04364e10e46c655de636925… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/workflows_format_2/converter.py Log Message: ----------- Replace __rip_value with dict.pop. Thanks @bgruening. Commit: 98249058e85d8133748519ac59ebed96a28a77ac https://github.com/galaxyproject/galaxy/commit/98249058e85d8133748519ac59eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Cleanup error message. Thanks @bgruening. Commit: f17a6c996a060f68bc8a250effa23f60b96b44a7 https://github.com/galaxyproject/galaxy/commit/f17a6c996a060f68bc8a250effa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/web/base/controller.py Log Message: ----------- Synchronize decoding ids across base controller and manager base. To ensure we have the same kind of exception thrown in both cases. Commit: f6d26c9ee6f148fd033d1b070c2dbe8c69b08fa8 https://github.com/galaxyproject/galaxy/commit/f6d26c9ee6f148fd033d1b070c2d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Small refactor making workflow views and modules tad more generic. - Reduce duplication between initializing generic modules and tool modules. - Switch tool_id to content_id as variable names throughout the client. - Rename get_tool_id to get_content_id on workflow modules. - Add some minimal documentation to the workflow module about get_content_id. Downstream in the subworkflow commit I switch the over-the-wire communication to use content_id instead of tool_id also and use content_ids to refer to workflow ids in subworkflow moduls. Commit: 73bfbf016347f764a0747ad7c6d138c74b6f519d https://github.com/galaxyproject/galaxy/commit/73bfbf016347f764a0747ad7c6d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Refactor some workflow API code into workflows manager. This allows for reuse outside of the API controller, such as loading subworkflows downstream. Commit: f92220a74f216d937dc5b147472261d154779512 https://github.com/galaxyproject/galaxy/commit/f92220a74f216d937dc5b1474722… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow workflow outputs on non-tool steps. Commit: d18c75ceb875632f9e68a74ebeb88389262d6fa8 https://github.com/galaxyproject/galaxy/commit/d18c75ceb875632f9e68a74ebeb8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Bring gneric and tool module styles into alignment in workflow editor. Commit: d7ac52f6bb61fe360198f91310a3e22076183d7b https://github.com/galaxyproject/galaxy/commit/d7ac52f6bb61fe360198f91310a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add icons to existing workflow steps in workflow editor. Tools have an icon there. Commit: e3161b4671e9fb19a47c7f341e3fb46617111a9e https://github.com/galaxyproject/galaxy/commit/e3161b4671e9fb19a47c7f341e3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Add support for workflow step labels in editor. - If a step has a label, display it in the step editor side panel title. - Allow clicking the title to change the label. - Display the label (if set) as the workflow node box title. - Add icon to workflow node since the title might not be related to type anymore. - Enforce unique labels accross the workflow in the editor. - Qunit test cases for some of this behavior and other recent changes. Commit: 563e363478258cb1d08802e16586c42efe511e6a https://github.com/galaxyproject/galaxy/commit/563e363478258cb1d08802e16586… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - don't set state to queued twice. Just keep the dataset in the correct NEW state until it has actually been queued. Addresses FIXME comment added by James 7 years ago in https://github.com/galaxyproject/galaxy/commit/4c3db1af95fb0520960046ae5494…. This behavior feels correct to me, but it does have ramifications in the GUI. I had previously never actually seen a dataset in the "NEW" state. Saves an extra flush per dataset, on sqlite this translates to 50ms per dataset for me. Commit: 0ac7c33522cfeb51b89ec8d14fbb2d716f956450 https://github.com/galaxyproject/galaxy/commit/0ac7c33522cfeb51b89ec8d14fbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization and comment improvement. Commit: 2b8a1423f7e9ae6bdf09571b8992493dc30e035c https://github.com/galaxyproject/galaxy/commit/2b8a1423f7e9ae6bdf09571b8992… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - remove another seemingly needless flush. Saves around a teenth of a second per job. Before: - galaxy.tools.execute DEBUG 2015-12-01 13:00:56,984 Tool [cat1] created job [24] (435.468 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:01:17,296 Tool [cat1] created job [25] (341.687 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:01:32,896 Tool [cat1] created job [26] (354.138 ms) After - - galaxy.tools.execute DEBUG 2015-12-01 12:58:51,154 Tool [cat1] created job [21] (261.932 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:11,354 Tool [cat1] created job [22] (278.699 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:43,105 Tool [cat1] created job [23] (296.438 ms) Commit: 81799bd3a72b3e704be6c12e89b85eb5bd077428 https://github.com/galaxyproject/galaxy/commit/81799bd3a72b3e704be6c12e89b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Micro-optimizations for adding many datasets to history... ... during tool execution. Build method once instead of in each function call, use imap instead of map since we don't need a list, remove some duplicated checks. Frankly this is all stuff Python is probably doing anyway - but in case it doesn't and just so the eye doesn't jump to these optimizations again. Timings before and after for a section of tool action execute that includes this additon show that this might have a small effect. Before: - galaxy.tools.actions INFO 2015-12-01 13:11:39,446 Add outputs to history (127.379 ms) - galaxy.tools.actions INFO 2015-12-01 13:12:06,598 Add outputs to history (137.029 ms) - galaxy.tools.actions INFO 2015-12-01 13:12:23,931 Add outputs to history (118.489 ms) After: - galaxy.tools.actions INFO 2015-12-01 13:13:09,999 Add outputs to history (99.456 ms) - galaxy.tools.actions INFO 2015-12-01 13:13:38,573 Add outputs to history (126.131 ms) - galaxy.tools.actions INFO 2015-12-01 13:13:54,538 Add outputs to history (137.643 ms) - galaxy.tools.actions INFO 2015-12-01 13:14:12,516 Add outputs to history (101.451 ms) Commit: bd6a34e279f8d612185fe9d8aa27084efe246e2d https://github.com/galaxyproject/galaxy/commit/bd6a34e279f8d612185fe9d8aa27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization comments for future reference. Including replacing a log statement with a comment. Commit: 59c3acfbf56e14c8f691946932be71b81774de0e https://github.com/galaxyproject/galaxy/commit/59c3acfbf56e14c8f691946932be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool execution optimization - remove another unneeded flush. Flush the job and its output datasets all at the same time in one transaction. Inuitively it makes sense that this should work and the timings seem to improve, triming another quater or third of the submission time per job. Before: - galaxy.tools.execute DEBUG 2015-12-01 12:58:51,154 Tool [cat1] created job [21] (261.932 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:11,354 Tool [cat1] created job [22] (278.699 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:43,105 Tool [cat1] created job [23] (296.438 ms) After: - galaxy.tools.execute DEBUG 2015-12-01 13:22:00,649 Tool [cat1] created job [39] (265.547 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:22:27,720 Tool [cat1] created job [40] (214.905 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:21:40,225 Tool [cat1] created job [38] (198.936 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:22:44,076 Tool [cat1] created job [41] (213.096 ms) Commit: 3bf466c8f5d554f583dfc2fe8f7b95397278b2d9 https://github.com/galaxyproject/galaxy/commit/3bf466c8f5d554f583dfc2fe8f7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Micro optimization in tool execute - eliminate repeated trans.app fetch. Commit: e72604be7c0c0a88c6267140b6433fcde88f1d01 https://github.com/galaxyproject/galaxy/commit/e72604be7c0c0a88c6267140b643… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/upload.py Log Message: ----------- Instrument upload action for timing. - Checked and cleanup datasets ~500ms - Create job ~200ms - Persisting ~20 ms Commit: 2c6819cd87520fb43f4ebea96eea5fb151787edb https://github.com/galaxyproject/galaxy/commit/2c6819cd87520fb43f4ebea96eea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - eliminate repeated role generation. For cat1 with 5 inputs - this shaves about 100 ms off of job execution time. Before: galaxy.tools.execute DEBUG 2015-12-01 15:08:56,745 Tool [cat1] created job [171] (545.776 ms) galaxy.tools.execute DEBUG 2015-12-01 15:08:31,871 Tool [cat1] created job [170] (478.813 ms) After : galaxy.tools.execute DEBUG 2015-12-01 15:07:11,401 Tool [cat1] created job [168] (371.722 ms) galaxy.tools.execute DEBUG 2015-12-01 15:07:42,060 Tool [cat1] created job [169] (333.296 ms) Commit: 836b0dfc1504357b738375b109b22243dd58efe7 https://github.com/galaxyproject/galaxy/commit/836b0dfc1504357b738375b109b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix location of timer generation for fairer comparison in next commit. Commit: c14c45be46a4a3b08b3cb0b5132cbbdf151d5100 https://github.com/galaxyproject/galaxy/commit/c14c45be46a4a3b08b3cb0b5132c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M test/unit/tools/test_execution.py Log Message: ----------- Further cache user roles across batched tool executions. Commit: 53354c7e361cc769f42c7eae42de0eca1769e9a4 https://github.com/galaxyproject/galaxy/commit/53354c7e361cc769f42c7eae42de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Fix collection output for less flushing in tool action handle_output. Commit: ab651fa89c0e24d637daa8bd5716b3932532c6a3 https://github.com/galaxyproject/galaxy/commit/ab651fa89c0e24d637daa8bd5716… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/utils/utils.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/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/utils/utils.js Log Message: ----------- Fix url, lint and packing Catch missing history, fix failing api test Commit: b55635f71b7fd3bba8393a3c267408d6dd248f99 https://github.com/galaxyproject/galaxy/commit/b55635f71b7fd3bba8393a3c2674… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M lib/galaxy/managers/configuration.py 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: ----------- Client, upload: fix passing of nginx_upload_path and ftp_upload_site to upload-view, fix default nginx_upload_path in configuration serializer Commit: 00452e1b8aecd3ed2fc4c06262f451c9efafa1c6 https://github.com/galaxyproject/galaxy/commit/00452e1b8aecd3ed2fc4c06262f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add more specific error message for workflow parameters Commit: beb4a67fb0a4b879b732fd05b35d03019481ea90 https://github.com/galaxyproject/galaxy/commit/beb4a67fb0a4b879b732fd05b35d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M lib/galaxy/managers/configuration.py 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: ----------- Merge pull request #1250 from carlfeberhard/fix.upload Client, upload: fix passing of nginx_upload_path and ftp_upload_site … Commit: a951d34c703a239ac00c780025a9657bc7101b0b https://github.com/galaxyproject/galaxy/commit/a951d34c703a239ac00c780025a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M lib/galaxy/managers/configuration.py 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: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 4fe36f8d6a151536267e3aeace2414cc148e18e8 https://github.com/galaxyproject/galaxy/commit/4fe36f8d6a151536267e3aeace24… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/execute.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #1199 from jmchilton/tool_opts_4 Yet More Tool Execution Optimizations Commit: 3a023f4cae6b9b6b25c1d389b9ba2ad7223cb24a https://github.com/galaxyproject/galaxy/commit/3a023f4cae6b9b6b25c1d389b9ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tools-form-base.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #818 from mvdbeek/cross_toolshed_tool_fetching Look up installed tools from different toolshed(s) Commit: 371125bc870a29371fba8656d3c93538a50a63ab https://github.com/galaxyproject/galaxy/commit/371125bc870a29371fba8656d3c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Merge pull request #1111 from erasche/user-search-name Add search on username/any for API calls to user, use Select2 for sharing workflows/pages/histories Commit: 8c6d530a661842a56fbb8800856237582701fc56 https://github.com/galaxyproject/galaxy/commit/8c6d530a661842a56fbb88008562… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 48064cc20352d3e38f985769ba5b2eeb66f051a8 https://github.com/galaxyproject/galaxy/commit/48064cc20352d3e38f985769ba5b… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Clarify comment in XML Commit: 01a919ce6a7cc29556e257fd0af46f5071310748 https://github.com/galaxyproject/galaxy/commit/01a919ce6a7cc29556e257fd0af4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Merge pull request #1253 from nsoranzo/dev_verify_tools Tool migration: do not mess with galaxy_config_file, if provided. Commit: bcf8ddfbd0a966fd3d6fad157f8ca87702e9c61a https://github.com/galaxyproject/galaxy/commit/bcf8ddfbd0a966fd3d6fad157f8c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Merge branch 'master' into dev Conflicts: lib/galaxy/jobs/runners/__init__.py Commit: e505a4f6123f119577955459cda1846b5f67f0b8 https://github.com/galaxyproject/galaxy/commit/e505a4f6123f119577955459cda1… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako Log Message: ----------- Add the CSG Viewer visualization plugin based on conversations here: https://github.com/galaxyproject/galaxy/issues/1191#issuecomment-162553926 Commit: ef0b6cc459a40227db2e63ee709e9dd5d8fd37c6 https://github.com/galaxyproject/galaxy/commit/ef0b6cc459a40227db2e63ee709e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- show notifications as Toasts and not like JS alerts (bleh) Commit: 4a9dad9f14b94df14b52f41466c9e66dbbfb0556 https://github.com/galaxyproject/galaxy/commit/4a9dad9f14b94df14b52f41466c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #12 from martenson/labels_toastr show notifications as Toasts and not like JS alerts (bleh) Commit: 485e8ef8f22330bce5a402c5b4bb0182ce5b180c https://github.com/galaxyproject/galaxy/commit/485e8ef8f22330bce5a402c5b4bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.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/form/form-section.js Log Message: ----------- Add fallback for missing section and repeat title Commit: 3924a5a0e3d2c7d787e81fabc4e2908f30ff0168 https://github.com/galaxyproject/galaxy/commit/3924a5a0e3d2c7d787e81fabc4e2… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Fixed indentation errors Commit: 3f8950628c3e31d9e2abe0b4f4a360c035133b8e https://github.com/galaxyproject/galaxy/commit/3f8950628c3e31d9e2abe0b4f4a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Workflow label UI refinement. - Escape workflow labels in mako. - Handle unlabelling steps properly (restore original node name to node and editor form titles). Commit: 5ff09896f7d4ee5208f2f39ca16a7846690af229 https://github.com/galaxyproject/galaxy/commit/5ff09896f7d4ee5208f2f39ca16a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) 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 require of bibtex parser Commit: 6ba86d89bc9d2b6b45dddb13d8dc79a4e2c395a0 https://github.com/galaxyproject/galaxy/commit/6ba86d89bc9d2b6b45dddb13d8dc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) 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: don't create new BibtexParser, remove debugging Commit: 0e5d42f3d67e5f75dea4abe78909539df3716f1e https://github.com/galaxyproject/galaxy/commit/0e5d42f3d67e5f75dea4abe78909… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) 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 #1261 from carlfeberhard/fix.citations UI, Citations: fix require of bibtex parser Commit: 52078baf99ed2aadae4b30f6b71ae00aecba521a https://github.com/galaxyproject/galaxy/commit/52078baf99ed2aadae4b30f6b71a… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- don't load or overwrite a value with a not-yet-loaded value (i.e. None) Commit: 7f4c3fcfc88914cb91e325fe95f08c90c034ef3e https://github.com/galaxyproject/galaxy/commit/7f4c3fcfc88914cb91e325fe95f0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Managers, users: properly return a boolean from has_requests Commit: 38a9aa6a5c3b006867e16877999545e1e0e7ddea https://github.com/galaxyproject/galaxy/commit/38a9aa6a5c3b006867e168779995… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/managers/users.py M test/unit/managers/test_UserManager.py Log Message: ----------- Managers, users: update serialized key 'requests' to 'has_requests', update test Commit: a22c09b11f5a16b4c429cf88ebd74faa433da97c https://github.com/galaxyproject/galaxy/commit/a22c09b11f5a16b4c429cf88ebd7… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M test/docker/base/Dockerfile M test/tool_shed/functional/test_1460_data_managers.py Log Message: ----------- Fix typos. Commit: f974b0f740d4ed8c44ebafde74908cdea1748a1a https://github.com/galaxyproject/galaxy/commit/f974b0f740d4ed8c44ebafde7490… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py Log Message: ----------- Extend the logging of tool dependency status changes. Also merge handle_tool_dependency_installation_error() in set_tool_dependency_attributes() and consolidate its use. Commit: fe1c9dd2931fb8efccb98fb1646c3e1063b0ab52 https://github.com/galaxyproject/galaxy/commit/fe1c9dd2931fb8efccb98fb1646c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/base.py M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/workflows_format_2/converter.py M test/qunit/tests/workflow_editor_tests.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #1251 from jmchilton/workflow_labels_2 Workflow Editor UI for Step Labels Commit: 6d16549a46a330d50eccfa73684e0090a397b3c6 https://github.com/galaxyproject/galaxy/commit/6d16549a46a330d50eccfa73684e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/managers/users.py M test/unit/managers/test_UserManager.py Log Message: ----------- Merge pull request #1262 from carlfeberhard/fix.js-app-mako Managers, users: properly return a boolean from has_requests Commit: b273e3b0c51c13f7e46ccc2977925d9247033289 https://github.com/galaxyproject/galaxy/commit/b273e3b0c51c13f7e46ccc297792… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py Log Message: ----------- Improve logging during package installation Commit: 864472870f7e1af14a5807effe1fc5685f16e92f https://github.com/galaxyproject/galaxy/commit/864472870f7e1af14a5807effe1f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py Log Message: ----------- Merge pull request #1267 from erasche/install-logging Log command executed during package installation Commit: a033d798de1c36484a1a16d135860a3b5fb5af33 https://github.com/galaxyproject/galaxy/commit/a033d798de1c36484a1a16d13586… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py R templates/webapps/galaxy/history/options.mako Log Message: ----------- Remove: history_options and options.mako (history options as a page) Commit: 2b63427e965837eb29df54e5918cf8f84004f534 https://github.com/galaxyproject/galaxy/commit/2b63427e965837eb29df54e5918c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Handle late validated dataset references Commit: 7dbbac31b3581d43445a8030e2cba990c90e1b2e https://github.com/galaxyproject/galaxy/commit/7dbbac31b3581d43445a8030e2cb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py R templates/webapps/galaxy/history/options.mako Log Message: ----------- Merge pull request #1271 from carlfeberhard/jettison.history-options Remove: history_options and options.mako (history options as a page) Commit: 37931505d4c967d70e495467fd615f9540202e4b https://github.com/galaxyproject/galaxy/commit/37931505d4c967d70e495467fd61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix tool shed tests for recent workflow changes. Thanks for bug report by @nsoranzo on https://github.com/galaxyproject/galaxy/pull/1263. Commit: 78427438adcb794af630ebb3b9b77b3628c2c5bb https://github.com/galaxyproject/galaxy/commit/78427438adcb794af630ebb3b9b7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/ui-modal.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/ui-modal.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/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/ui/ui-modal.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- UI, History: refactor the history copy dialog, use it from the options menu (instead of history/copy), pass ui-modal closing_callback a flag whether it was a cancellation or not Commit: bd1349eb9b62dfac0b1affbd1a4ea8e1fe109c2c https://github.com/galaxyproject/galaxy/commit/bd1349eb9b62dfac0b1affbd1a4e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge pull request #1274 from jmchilton/workflow_fix_3 Fix tool shed tests for recent workflow changes. Commit: c3e4ae11b06d0e10f1fd5a3c2df0433b90f527b7 https://github.com/galaxyproject/galaxy/commit/c3e4ae11b06d0e10f1fd5a3c2df0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- set client_encoding for TS dockerized test db Commit: e391fa4975800fd1d21e1e7d03183d146728f1c8 https://github.com/galaxyproject/galaxy/commit/e391fa4975800fd1d21e1e7d0318… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/copy-dialog.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/mvc/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, History: allow copy dialog to have default of copy-all-datasets passed in as option; Replace import link with copy dialog in published histories Commit: d41ea8d315be735ab506d2643cf2dcb67e030c9c https://github.com/galaxyproject/galaxy/commit/d41ea8d315be735ab506d2643cf2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #1276 from martenson/fix-ts-dbconnection-tag set client_encoding for TS dockerized test db Commit: 7187eddd2fdec95093c765b838814435c9f6b92d https://github.com/galaxyproject/galaxy/commit/7187eddd2fdec95093c765b83881… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M templates/display_base.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako Log Message: ----------- UI, published items: fix css bleeding of trackster.css into other published item displays Commit: f0fc8d6d4cc59afaacccb8a7ae036b15f5b7f681 https://github.com/galaxyproject/galaxy/commit/f0fc8d6d4cc59afaacccb8a7ae03… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- update used galaxy/testing-base to 15.10.3 Commit: c39544807565d4e345963d1d280deb28b85d281a https://github.com/galaxyproject/galaxy/commit/c39544807565d4e345963d1d280d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1277 from martenson/update-docker-image-v update used galaxy/testing-base to 15.10.3 Commit: d72dd3735c0dfd652fb45a117fe1942f10ff726d https://github.com/galaxyproject/galaxy/commit/d72dd3735c0dfd652fb45a117fe1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/polyfills.js M static/maps/mvc/base-mvc.js.map M static/maps/polyfills.js.map 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/base-mvc.js M static/scripts/polyfills.js Log Message: ----------- Client, polyfills: check for sessionStorage using a more cross-browser (apparently) way Commit: 183c3c11b60aa5a36747dbe7b0ac069dc3bac6fc https://github.com/galaxyproject/galaxy/commit/183c3c11b60aa5a36747dbe7b0ac… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/polyfills.js M static/maps/mvc/base-mvc.js.map M static/maps/polyfills.js.map 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/base-mvc.js M static/scripts/polyfills.js Log Message: ----------- Merge pull request #1279 from carlfeberhard/fix.casper Client, polyfills: check for sessionStorage using a more cross-browse… Commit: 133e5f2e24eed9650a0862ced42092d35f8a6566 https://github.com/galaxyproject/galaxy/commit/133e5f2e24eed9650a0862ced420… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py Log Message: ----------- Various small API testing fixes/improvements. Commit: 09a68adb1e2a837f4ae01ca9ec25b4d6d0fab446 https://github.com/galaxyproject/galaxy/commit/09a68adb1e2a837f4ae01ca9ec25… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Add another API test verifying validation of workflow substitions. A little different because it targets a different tool, validation, and is inside a repeat. Commit: 941109dda860325938960b93f66e50d314b67e4a https://github.com/galaxyproject/galaxy/commit/941109dda860325938960b93f66e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/copy-dialog.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 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/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M templates/grid_base.mako M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, History: use copy dialog as import dialog in published history pages, refactor copy-dialog Commit: 1959288637bf8c4f11da70df5cd5558c1bc1099a https://github.com/galaxyproject/galaxy/commit/1959288637bf8c4f11da70df5cd5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Include link to toolshed repository, and make sure upgrade message is not overwritten by tool_version changes. Commit: 928ff581efa3ace63a57e97db80e7a9c21c09841 https://github.com/galaxyproject/galaxy/commit/928ff581efa3ace63a57e97db80e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M test/base/interactor.py Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: c143748e62e976fa3a43a721ed49bdbdc78ea980 https://github.com/galaxyproject/galaxy/commit/c143748e62e976fa3a43a721ed49… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Better formatting of workflow warning message. Commit: 80bd59dd90722afb837c01a26b78eebe04dd277b https://github.com/galaxyproject/galaxy/commit/80bd59dd90722afb837c01a26b78… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.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/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/workflows_format_2/converter.py M test/docker/base/run_test_wrapper.sh M test/qunit/tests/workflow_editor_tests.js M test/unit/managers/test_UserManager.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: cd61cdc51b387d6cfb7905307c669e17111ab96d https://github.com/galaxyproject/galaxy/commit/cd61cdc51b387d6cfb7905307c66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Add back tool id to pass unit tests. Commit: ce6cd03f6c7f020a8127025c49224f1bb920bc18 https://github.com/galaxyproject/galaxy/commit/ce6cd03f6c7f020a8127025c4922… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M tox.ini Log Message: ----------- Enforce metrics related to moving toward modern client infrastructure. Having a CI enforced blacklist and then a whitelist of files failing to meet style guidelines (as well as expanding list of rules enforced) may have helped create incentive to rework Galaxy toward a more compliant and uniform Python styling. We briefly discussed the possibility of doing this with other team code base objectives on a conference call - in particular to help the transition toward replacing all of the web controllers with API controllers and eliminating the use of Python mako files for rendering web content and replacing it with client side templates. To do this I have created two rough metrics - the number of lines of web controller code in the Galaxy app and the number of mako files in the templates directory. The hope is that people feel ... compelled to lower these numbers. While these metrics are admittedly rough, they do also encourage de-duplication of mako templates and transition of API code into managers (in addition to elimination of functions) both of these secondary incentives are also good things and should be project objectives. Commit: 253ca7ec4940188d11157448d73be09e762e65f8 https://github.com/galaxyproject/galaxy/commit/253ca7ec4940188d11157448d73b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/popup-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 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/history/copy-dialog.js M static/scripts/mvc/ui/popup-menu.js M templates/webapps/galaxy/history/grid.mako Log Message: ----------- UI, History: insert/use copy dialog in the 'Saved Histories' grid Commit: 636e9900ba5e82c37a26fee84f56872c9413bd1b https://github.com/galaxyproject/galaxy/commit/636e9900ba5e82c37a26fee84f56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) 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: ----------- Improve handling of unspecified workflow editor values Commit: 09cb673a9b13f6f9faae21b48c317e485afb8eb1 https://github.com/galaxyproject/galaxy/commit/09cb673a9b13f6f9faae21b48c31… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.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/history/copy-dialog.js M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako A templates/webapps/galaxy/history/shared_grid.mako Log Message: ----------- UI, History: use copy dialog for shared history popupmenus, use custom templates for both saved and shared history lists/grids. refactor custom grid code for insertion of copy dialog Commit: 9a4c8343701c676ccf996cbbaa864f12135bac5b https://github.com/galaxyproject/galaxy/commit/9a4c8343701c676ccf996cbbaa86… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-drilldown.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/ui/ui-drilldown.js M static/style/blue/base.css Log Message: ----------- Use fa icons for drill down expansion Commit: cb23e010d7750b533be7690e72c92500ddc8e2f1 https://github.com/galaxyproject/galaxy/commit/cb23e010d7750b533be7690e72c9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M static/maps/mvc/history/copy-dialog.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/copy-dialog.js M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, History: use copy dialog in history/view for import, minor fixes Commit: 1ebc0ea9e719bf7557f0e190a7dd4883629257f5 https://github.com/galaxyproject/galaxy/commit/1ebc0ea9e719bf7557f0e190a7dd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js 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: ----------- UI, Quotameter: correctly update the quotameter for anon users Commit: bce8140bd9f9c3e069c83f765ae892d0fd1656b7 https://github.com/galaxyproject/galaxy/commit/bce8140bd9f9c3e069c83f765ae8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py Log Message: ----------- Merge pull request #1285 from jmchilton/test_improvemnts_1 Small API Test Improvements Commit: 25f420fc8f47865e2cee2da15dc283e2cf130b91 https://github.com/galaxyproject/galaxy/commit/25f420fc8f47865e2cee2da15dc2… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js 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: ----------- Merge pull request #1289 from carlfeberhard/fix.anon-user-quotameter UI, Quotameter: correctly update the quotameter for anon users Commit: d72b913c1d25bf9e2ee2c9e7320bff4f52b366e3 https://github.com/galaxyproject/galaxy/commit/d72b913c1d25bf9e2ee2c9e7320b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/utils/ajax-queue.js M static/maps/utils/ajax-queue.js.map M static/scripts/utils/ajax-queue.js M templates/webapps/galaxy/history/shared_grid.mako Log Message: ----------- UI, History: hack multiple copy by API into the 'histories shared with me' mako grid Commit: 7a3aa044fbf968c120832402091cb3b1d70afd7b https://github.com/galaxyproject/galaxy/commit/7a3aa044fbf968c120832402091c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: A Makefile A client/.docker-build.sh A client/Dockerfile M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #1238 from erasche/client-builder Ease the grunt uglify process Commit: b455157bd6f3f23ce2de81d5145b6268e4da77f3 https://github.com/galaxyproject/galaxy/commit/b455157bd6f3f23ce2de81d5145b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1198 from blankenberg/dt-biom BIOM1 Datatype enhancements Commit: f8d95abf061608e2dc544e56fc5b83ad3d54d1bd https://github.com/galaxyproject/galaxy/commit/f8d95abf061608e2dc544e56fc5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py M test/docker/base/Dockerfile M test/tool_shed/functional/test_1460_data_managers.py Log Message: ----------- Merge pull request #1263 from nsoranzo/dev_tool_shed_fixes Extend the logging of tool dependency status changes. Commit: e40fbe5374f906139f8be7a3ceb001f049a6b244 https://github.com/galaxyproject/galaxy/commit/e40fbe5374f906139f8be7a3ceb0… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst Log Message: ----------- * Add comment about base_path in sample config * Add documentation on dependency resolvers Commit: 952f3f9b7a04a6e7d3185da76d84dea0fa9bca8d https://github.com/galaxyproject/galaxy/commit/952f3f9b7a04a6e7d3185da76d84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Open select2 dropdown on click Commit: bca004eff8607e347d440ce5fc5d086d7acb45f9 https://github.com/galaxyproject/galaxy/commit/bca004eff8607e347d440ce5fc5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1298 from guerler/fix_select2_open_000 Open select2 drop down on caret click Commit: 1aafc489356d4ad62a00b82f1b0679d66f037be4 https://github.com/galaxyproject/galaxy/commit/1aafc489356d4ad62a00b82f1b06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Dead sendmail_path vars, this is unused in favor of smtp (as of a long time ago) Commit: 9e512f52465c158855c2a0750d8a7d794316940e https://github.com/galaxyproject/galaxy/commit/9e512f52465c158855c2a0750d8a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/model/__init__.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/tool/tools-form-base.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/copy-dialog.js M static/scripts/mvc/tool/tools-form-base.js M static/scripts/utils/ajax-queue.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, History: use copy dialog in the embedded histories in Pages, add autoClose option to copy dialog Commit: c0b349306f17ed924a5673fab465d105d2cfdaf2 https://github.com/galaxyproject/galaxy/commit/c0b349306f17ed924a5673fab465… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Add smtp_ssl option to toolshed mailing capabilities, update .sample to include the smtp auth/ssl. Commit: 324af9caeda230bfe35ce79cf3e6f84a3ca27ee5 https://github.com/galaxyproject/galaxy/commit/324af9caeda230bfe35ce79cf3e6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, History: remove copy and imp methods from controllers/history.py, remove history copy template Commit: 27e43e8907a5fb529cdf36175a6ffe04de762379 https://github.com/galaxyproject/galaxy/commit/27e43e8907a5fb529cdf36175a6f… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/datatypes/metadata.py Log Message: ----------- Load deferred column before pickling dataset instance Commit: 32be886f0f51103a648003997c7d06cd12ba08d9 https://github.com/galaxyproject/galaxy/commit/32be886f0f51103a648003997c7d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.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/copy-dialog.js Log Message: ----------- API, Histories: allow api/histories/create to be used as anon user; UI, Histories: minor fixes Commit: 584d886b5ee68257921dff24c4dbe0a2dbb0c00c https://github.com/galaxyproject/galaxy/commit/584d886b5ee68257921dff24c4db… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Mention modulepath attribute in dependency resolver docs * Use modulepath in both environment modules resolvers * Export MODULEPATH in generated shell command * Add logging for operation of dependency resolvers Commit: 035f1b5d663841fa61d32ba79e1b43553dab4fab https://github.com/galaxyproject/galaxy/commit/035f1b5d663841fa61d32ba79e1b… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- * Incorporate documentation fixes from nsoranzo * Replace {} and .format with %s and % to preserve Python 2.6 compatibility * Add a modulepath= paranter to the fake resolver (Bunch object) used to test the modules dependency resolver Commit: 84f3b72e1ad829e6f2f46049ff4af42f27429a5b https://github.com/galaxyproject/galaxy/commit/84f3b72e1ad829e6f2f46049ff4a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: A Makefile A client/.docker-build.sh A client/Dockerfile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M client/galaxy/style/less/ui.less M doc/source/dev/faq.rst M lib/galaxy/datatypes/text.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.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/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js M static/style/blue/base.css R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/base/interactor.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/functional/test_1460_data_managers.py M test/unit/managers/test_UserManager.py M test/unit/workflows/test_modules.py Log Message: ----------- (merge dev); Testing, histories: update tests to reflect allowing anon to create/copy histories via the API Commit: 2b90ca9b0e23715bd7a03614fa989bcf540f73e9 https://github.com/galaxyproject/galaxy/commit/2b90ca9b0e23715bd7a03614fa98… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- * Replaced incorrect %b with %s Commit: 73b6fb23db300501c9124c61c90d73d2c28dc7a4 https://github.com/galaxyproject/galaxy/commit/73b6fb23db300501c9124c61c90d… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- * Replaced all references to "version number" with "version string" Commit: 760c2b56bee664f2f874e2cc26d2129858da1bb1 https://github.com/galaxyproject/galaxy/commit/760c2b56bee664f2f874e2cc26d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Properly show and label hidden datasets on rerurn Commit: 6580d5129386ab5b8634583c5378dfc340ed2800 https://github.com/galaxyproject/galaxy/commit/6580d5129386ab5b8634583c5378… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #1296 from pvanheus/env-modules-resolve Documentation for dependency resolvers Commit: eb4b8e716d26897e58c78c08e9a2d62a770604f5 https://github.com/galaxyproject/galaxy/commit/eb4b8e716d26897e58c78c08e9a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #1299 from dannon/mail_fixes Minor mail config cleanup Commit: 66146ad5d0e17e35b6eee50699b0261422835000 https://github.com/galaxyproject/galaxy/commit/66146ad5d0e17e35b6eee50699b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1305 from guerler/fix_workflow_rerun_001 [15.10] Properly show and label hidden datasets on workflow reruns Commit: a7e60eae2c2721e7d4377112b7aaceb8424fd3da https://github.com/galaxyproject/galaxy/commit/a7e60eae2c2721e7d4377112b7aa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M tox.ini Log Message: ----------- Merge pull request #1292 from jmchilton/client_incentives Enforce metrics related to moving toward modern client infrastructure. Commit: 989f961fb6351d1f63374b4fc40429c1e897b1e2 https://github.com/galaxyproject/galaxy/commit/989f961fb6351d1f63374b4fc404… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1218 from blankenberg/rerunfix_15.10 [15.10] Fix for Section and conditional upgrade messages. Commit: 65bd907e08168daecabd984465b735f50ff0da56 https://github.com/galaxyproject/galaxy/commit/65bd907e08168daecabd984465b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-12 (Sat, 12 Dec 2015) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/special_tools.py Log Message: ----------- Refactor imp_exp toolbox toward more generic entry point. Commit: 0180c0525d5f545f67d99c79677a94382ae73ff1 https://github.com/galaxyproject/galaxy/commit/0180c0525d5f545f67d99c79677a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-12 (Sat, 12 Dec 2015) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Improve error log warning for tools with empty commands. Commit: a208961cd3145f90a04e58ac1bb23ed2d91365a4 https://github.com/galaxyproject/galaxy/commit/a208961cd3145f90a04e58ac1bb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-12 (Sat, 12 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Refactor tool actions for reuse of pieces in downstream actions. Commit: 8af5671953df12e5207a8b3e5e70c742cea9f158 https://github.com/galaxyproject/galaxy/commit/8af5671953df12e5207a8b3e5e70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-13 (Sun, 13 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_parameter_parsing.py M test/unit/workflows/test_modules.py Log Message: ----------- Allow input collections to specify mutiple collection types. Parallelling format specifier which can take multiple formats. Commit: b633c949c875788d5bba9ae0126882b3439d7f7e https://github.com/galaxyproject/galaxy/commit/b633c949c875788d5bba9ae01268… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Mention tool id as hover text on version changes. Commit: 812343d8ccc10a77bab58287178cceb64ad9cb39 https://github.com/galaxyproject/galaxy/commit/812343d8ccc10a77bab58287178c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1286 from mvdbeek/cross_toolshed_tool_fetching Include link to old and new toolshed repository, and make sure upgrade message is… Commit: f14b38124bc08c228bfce30f27d1815d7dd27c0b https://github.com/galaxyproject/galaxy/commit/f14b38124bc08c228bfce30f27d1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: prevent vice-versa pair duplication by removing paired dataset from both temp lists during auto pairing Commit: 58911edbfb5aa6e858addd9452e90d6ed389b0d2 https://github.com/galaxyproject/galaxy/commit/58911edbfb5aa6e858addd9452e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py Log Message: ----------- Remove worklfow casperjs API test. It has good and more updated coverage in the Python API testing framework. Commit: c1ce8ef0ce074271c9ba7a9a1718258482cca69f https://github.com/galaxyproject/galaxy/commit/c1ce8ef0ce074271c9ba7a9a1718… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: improve auto-pair error message to be more beginner friendly(?) Commit: dd429b640ffeb656a1fd61b49e88db890e7743cf https://github.com/galaxyproject/galaxy/commit/dd429b640ffeb656a1fd61b49e88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #1310 from carlfeberhard/fix.lop-creator UI, list of pairs creator: properly remove datasets from the filtered lists when pairing Commit: 886f6d2d707a9b4e2a80b0aaa89157e1137415ad https://github.com/galaxyproject/galaxy/commit/886f6d2d707a9b4e2a80b0aaa891… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M test/api/test_workflows.py Log Message: ----------- Improved validation of tools during workflow execution. Do a more complete validation of everything after workflow parameters have been replaced and inputs connected up. Attempt 2 at the idea in https://github.com/galaxyproject/galaxy/pull/1284. Commit: cdd9ca16f0a38ffab5fe54d559fc4bb4e4a7a37d https://github.com/galaxyproject/galaxy/commit/cdd9ca16f0a38ffab5fe54d559fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py Log Message: ----------- Don't silently swallow job creation problems when running workflows. Commit: ce787adff93dafb950341243f3951221cadfc813 https://github.com/galaxyproject/galaxy/commit/ce787adff93dafb950341243f395… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix bug related to collection reductions state. Commit: c61a5529b4c788580d2c3615c7dab2386a9b8e4e https://github.com/galaxyproject/galaxy/commit/c61a5529b4c788580d2c3615c7da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh A Makefile A client/.docker-build.sh A client/Dockerfile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/reports.ini.sample M config/tool_shed.ini.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M doc/source/dev/faq.rst M lib/galaxy/datatypes/text.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.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/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js M static/style/blue/base.css R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/base/interactor.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/functional/test_1460_data_managers.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: b8d7cf035df49f2fda9291b91eadf59fd48bfdd0 https://github.com/galaxyproject/galaxy/commit/b8d7cf035df49f2fda9291b91ead… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Add config setting, disable by default Commit: 42edfca679f204aa7e69a6c3df6dc14c8118e22c https://github.com/galaxyproject/galaxy/commit/42edfca679f204aa7e69a6c3df6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/tools/__init__.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Repack, refix section validation Commit: 148c11f403674d133bb0301ce2fc01ef108c38bd https://github.com/galaxyproject/galaxy/commit/148c11f403674d133bb0301ce2fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Adjust interface to basic.py. Commit: 10fff14ce5ba6952f21da10c81a31ceda397a666 https://github.com/galaxyproject/galaxy/commit/10fff14ce5ba6952f21da10c81a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix missing wf parameter issue in classic form Commit: 9f68003438cac76a223e84756b0584d7530df239 https://github.com/galaxyproject/galaxy/commit/9f68003438cac76a223e84756b05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise checking for workflow parameters in tooling code. - Use verbose and higher level abstractions. - Tighten up checks (use re.match instead of search when appropriate, replace startwith.("$") with more robust regex matches). Commit: 7687ed7fad52ef69002a2f985fcf682999068f00 https://github.com/galaxyproject/galaxy/commit/7687ed7fad52ef69002a2f985fcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Tighten workflow parameter check. a440813e37941d050ac503a0898dcf00c5f1b4fe always skipped validation of text/int/float values if they looked like they were workflow parameters. This restricts that check to just occurring when coming from the workflow editor tool form. Commit: fafa72dde200b05954d038902e317c8fe0d302bd https://github.com/galaxyproject/galaxy/commit/fafa72dde200b05954d038902e31… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Slightly tighten up relaxed validation of workflow paramters. Don't allow mid-parameter placement of values for integers, floats, etc... (e.g. 10${param}). This is enforced other places as well. Commit: 57bc4660cf4e21ebe8b73035095e021e4f298680 https://github.com/galaxyproject/galaxy/commit/57bc4660cf4e21ebe8b73035095e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix workflow parameter validation Commit: 9b30b134d6ab93c2a84a856352f32a6713dd49cd https://github.com/galaxyproject/galaxy/commit/9b30b134d6ab93c2a84a856352f3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Commit: 11eca70db129173ea20aac0040c9645049af189c https://github.com/galaxyproject/galaxy/commit/11eca70db129173ea20aac0040c9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Commit: 3108ba5c01ded7b0209685f57ab231c2cfe92938 https://github.com/galaxyproject/galaxy/commit/3108ba5c01ded7b0209685f57ab2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Ensure that text fields only display text Commit: 7f7010dbd96b4b9ce494ba320b853e6441162f5e https://github.com/galaxyproject/galaxy/commit/7f7010dbd96b4b9ce494ba320b85… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/history/history-panel.js R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove left over packed scripts. The source files have been deleted. Commit: 0fce226b96f98bf3393935602e0b5e9a8762bc4e https://github.com/galaxyproject/galaxy/commit/0fce226b96f98bf3393935602e0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/datatypes/metadata.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #1179 from abretaud/defer_metadata Lazy load HDA/LDDA metadata to speed up history loading Commit: a440813e37941d050ac503a0898dcf00c5f1b4fe https://github.com/galaxyproject/galaxy/commit/a440813e37941d050ac503a0898d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add workflow_mode flag to validation Commit: e838b03300964615bc2144ceeb9ba785cf5f7a7d https://github.com/galaxyproject/galaxy/commit/e838b03300964615bc2144ceeb9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js R client/galaxy/scripts/mvc/tool/tools-form-base.js R client/galaxy/scripts/mvc/tool/tools-form-workflow.js R client/galaxy/scripts/mvc/tool/tools-form.js R client/galaxy/scripts/mvc/tool/tools-jobs.js R client/galaxy/scripts/mvc/tool/tools-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/api/workflows.py A static/maps/galaxy-app-base.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tools-form-base.js.map R static/maps/mvc/tool/tools-form-workflow.js.map R static/maps/mvc/tool/tools-form.js.map R static/maps/mvc/tool/tools-jobs.js.map R static/maps/mvc/tool/tools-template.js.map M static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.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/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tools-form-base.js R static/scripts/mvc/tool/tools-form-workflow.js R static/scripts/mvc/tool/tools-form.js R static/scripts/mvc/tool/tools-jobs.js R static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1249 from guerler/run_workflow_form_004 Run workflow form Commit: 5bf926bf3ec19933c0ef82e51c919c0595bfc741 https://github.com/galaxyproject/galaxy/commit/5bf926bf3ec19933c0ef82e51c91… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #1302 from jmchilton/workflow_validation_1 Improved validation of tools during workflow execution. Commit: ce57930342c2a4f7eb672f95dc0b19c93c2322f8 https://github.com/galaxyproject/galaxy/commit/ce57930342c2a4f7eb672f95dc0b… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Show a more user-friendly error when the webserver port is blocked Commit: a42328f0002955295cfb70bc6e16fcf83e42ad82 https://github.com/galaxyproject/galaxy/commit/a42328f0002955295cfb70bc6e16… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Removing unnecessary line Commit: c14bb93a60dba72db34996cadcf20ee0e19a7f19 https://github.com/galaxyproject/galaxy/commit/c14bb93a60dba72db34996cadcf2… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Tidying code for linter Commit: 2acdbe54f76312cb748693e018d2d505cf95c3a2 https://github.com/galaxyproject/galaxy/commit/2acdbe54f76312cb748693e018d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) 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 M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- UI, Citations: fix citation-model's import of bibtex to use *either* commonjs or global Commit: 8e2db2944cbd546fa0f6f6cb46bf78d470ab31c8 https://github.com/galaxyproject/galaxy/commit/8e2db2944cbd546fa0f6f6cb46bf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix workflow output step entries Commit: 541231bb1723b2aac3fede7f45ca0455ca954894 https://github.com/galaxyproject/galaxy/commit/541231bb1723b2aac3fede7f45ca… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Config-based port checker has been removed and adding in an exception checker for paste response Commit: 4c3dfc7cd471181edc406724ca8f039e6b2a83d1 https://github.com/galaxyproject/galaxy/commit/4c3dfc7cd471181edc406724ca8f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) 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 M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #1321 from carlfeberhard/fix.citations UI, Citations: fix citation-model's import of bibtex to use *either* … Commit: 19cb62660a3779a6333696ec645f7fcee3db5bc5 https://github.com/galaxyproject/galaxy/commit/19cb62660a3779a6333696ec645f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Merge pull request #1320 from shano/dev Show a more user-friendly error when the webserver port is blocked Commit: cc67557df8483899e7058f2047607d0e5339c4eb https://github.com/galaxyproject/galaxy/commit/cc67557df8483899e7058f204760… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1322 from guerler/fix_workflow_outputs Fix workflow output step entries Commit: b2a3684f03e42d3743d02f4d4f039d429bf5e235 https://github.com/galaxyproject/galaxy/commit/b2a3684f03e42d3743d02f4d4f03… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/history/history-panel.js R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge pull request #1323 from jmchilton/fix_deleted_static Remove left over packed scripts. Commit: 946438ceba25151706ba2ca62e5c488e358c4f55 https://github.com/galaxyproject/galaxy/commit/946438ceba25151706ba2ca62e5c… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh A Makefile A client/.docker-build.sh A client/Dockerfile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js R client/galaxy/scripts/mvc/tool/tools-form-base.js R client/galaxy/scripts/mvc/tool/tools-form-workflow.js R client/galaxy/scripts/mvc/tool/tools-form.js R client/galaxy/scripts/mvc/tool/tools-jobs.js R client/galaxy/scripts/mvc/tool/tools-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M config/reports.ini.sample M config/tool_shed.ini.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M doc/source/dev/faq.rst M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/text.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py A static/maps/galaxy-app-base.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A 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static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/paired-collection-creator.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js R static/scripts/mvc/history/history-panel.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tools-form-base.js R static/scripts/mvc/tool/tools-form-workflow.js R static/scripts/mvc/tool/tools-form.js R static/scripts/mvc/tool/tools-jobs.js R static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py M test/docker/base/Dockerfile M test/tool_shed/functional/test_1460_data_managers.py M test/unit/tools/test_tool_deps.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 74be6f54cd1868f663dc89609c90a28c0db8214f https://github.com/galaxyproject/galaxy/commit/74be6f54cd1868f663dc89609c90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix for creating workflow outputs on initial workflow upload. Commit: 86632afdd3b7f2dbfed47671779818835a075496 https://github.com/galaxyproject/galaxy/commit/86632afdd3b7f2dbfed476717798… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #1316 from jmchilton/remove_casper_api_tests Remove worklfow casperjs API test. Commit: f953005f72310279fe69a0deb0b9adef973bf6da https://github.com/galaxyproject/galaxy/commit/f953005f72310279fe69a0deb0b9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Fix typo causing the option "Link files instead of copying" to be ignored. When uploading folders with the new data library interface. Commit: 54b54b1f11a30bad0b2e15802c44b30e745ca4a6 https://github.com/galaxyproject/galaxy/commit/54b54b1f11a30bad0b2e15802c44… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- UI, Users: when an first logging out, anon users may not have a history when they're serialized, return 0 usage from the user serilializer when this is the case Commit: b3e3b359aec1bce3d7ee4a23289d96318f5b0af3 https://github.com/galaxyproject/galaxy/commit/b3e3b359aec1bce3d7ee4a23289d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Update Kombu and AMQP wheels to fix problems with El Capitan's System Integrity Protection Commit: c48965ffcc5d35877f00dcf1941317cf23c3d4f4 https://github.com/galaxyproject/galaxy/commit/c48965ffcc5d35877f00dcf19413… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1326 from nsoranzo/release_15.10_link_data_only [15.10] Fix typo causing the option "Link files instead of copying" to be ignored. Commit: 31f174a4254e5cc4c85747a76c3908b0170cf358 https://github.com/galaxyproject/galaxy/commit/31f174a4254e5cc4c85747a76c39… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) 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: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: a23e644a9cd7ab64f0fa56314ae5ec2b5a768f7a https://github.com/galaxyproject/galaxy/commit/a23e644a9cd7ab64f0fa56314ae5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) 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 #1329 from martenson/release_15.10 [15.10] Add enhancements to the Galaxy repository install process Commit: bb0c1366f723b8236872d05da4c553a53d1aedc7 https://github.com/galaxyproject/galaxy/commit/bb0c1366f723b8236872d05da4c5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1327 from natefoo/kombu-el-cap-wheels Update Kombu and AMQP wheels to fix problems with El Capitan's System Integrity Protection Commit: d5cddaf7cc4fa734cb738521167e854393e5d380 https://github.com/galaxyproject/galaxy/commit/d5cddaf7cc4fa734cb738521167e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1330 from jmchilton/failing_test Fix for creating workflow outputs on initial workflow upload. Commit: 9dad7f76c41845e23d07a8583950d41e4b60b3cf https://github.com/galaxyproject/galaxy/commit/9dad7f76c41845e23d07a8583950… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix another instance of using _allow_workflow_parameters_in_context. As recommended by @nsoranzo. Commit: 7b11ebc52e30e6613e1b94c6db0db6bda70a5255 https://github.com/galaxyproject/galaxy/commit/7b11ebc52e30e6613e1b94c6db0d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1319 from jmchilton/workflow_validation_2 More tightening up of parameter validation during workflow stuff. Commit: d1fd23a2f4e5c5408f469ee5560f526833f5f682 https://github.com/galaxyproject/galaxy/commit/d1fd23a2f4e5c5408f469ee5560f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako Log Message: ----------- Merge pull request #1254 from gregvonkuster/dev Add the CSG Viewer visualization plugin Commit: cf5d209e0f01b7fb13e06f013f2a3693f194ebb4 https://github.com/galaxyproject/galaxy/commit/cf5d209e0f01b7fb13e06f013f2a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/utils/ajax-queue.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/utils/ajax-queue.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/copy-dialog.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/utils/ajax-queue.js M templates/display_base.mako M templates/grid_base.mako R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako A templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- Manual merge of #1303 to resolve build artifact conflicts. Commit: 99f9d7724c53326330a41fa6a1b1c36624fef02d https://github.com/galaxyproject/galaxy/commit/99f9d7724c53326330a41fa6a1b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Use the datetime object instead of a string for pretty interval formatting. Commit: 0c8df84685c587322f6c3b83ea45c0b20819d3ab https://github.com/galaxyproject/galaxy/commit/0c8df84685c587322f6c3b83ea45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #1328 from carlfeberhard/fix.quotameter UI, Users: when an first logging out, anon users may not have a histo… Commit: f1c36485c1ecef33667f3c35bad44899233d04f5 https://github.com/galaxyproject/galaxy/commit/f1c36485c1ecef33667f3c35bad4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Don't bother querying on unencoded IDs Commit: ea785ea598371f7aef0b37df59996e892d82f281 https://github.com/galaxyproject/galaxy/commit/ea785ea598371f7aef0b37df5999… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #1339 from dannon/library_datetime_tweak Use the datetime object instead of a string for pretty interval formatting. Commit: 41b77d0c1352e569d861ed327fd523dd12efffae https://github.com/galaxyproject/galaxy/commit/41b77d0c1352e569d861ed327fd5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M Makefile M client/README.md Log Message: ----------- Use local versions of node modules instead of system-installed, add a 'build-it-all' target for building the whole client. Fix two old typos. Commit: 8cc10c98ec4569ccfe1226d4c28a8526abbf3f44 https://github.com/galaxyproject/galaxy/commit/8cc10c98ec4569ccfe1226d4c28a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #1340 from erasche/id_decoding Don't bother querying on unencoded IDs for error form Commit: b9cba364982a9fa77fc2952fb803da75ee8d26e2 https://github.com/galaxyproject/galaxy/commit/b9cba364982a9fa77fc2952fb803… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M Makefile M client/README.md Log Message: ----------- Merge pull request #1337 from dannon/makefile_singletarget Simpler build-it-all rule in Makefile Commit: d41caa53cf24aca29bb90e32b420558558461d9c https://github.com/galaxyproject/galaxy/commit/d41caa53cf24aca29bb90e32b420… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Database migration enabling subworkflow and input parameter modules. Commit: 45962f32344a00162f5d04b94096c8a570f2adf1 https://github.com/galaxyproject/galaxy/commit/45962f32344a00162f5d04b94096… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Input parameter workflow module (experimental). - Implement a input parameter module that mirrors data and collection input modules but has a type that can currently be one of text, integer, float, color, and boolean. - Allow connections between these and tool step inputs. - Extend model to support this. - Add new input types for format 2 workflow definitions for various types that all map to this kind of step. Typed inputs such as this match well with CWL workflow inputs. Someday I imagine these will be superior to just marking a tool input "Specify at Runtime" for all the same reasons input steps are superior to leaving inputs unattached. Commit: 157939aa8f46b7599f48011d9f1e2c40c9f6cd47 https://github.com/galaxyproject/galaxy/commit/157939aa8f46b7599f48011d9f1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Implement nested workflows. Details: - Add a new workflow module describing subworkflows. - Add workflow list to editor side panel - with options to link in a subworkflow module or copy the target workflow into the workflow being editted node for node. - Update workflow, workflow step, and workflow invocation models to track subworkflow connections and execution. - Extend workflow outputs with concepts of labels (and UUIDs while I'm there) to match workflow inputs. This allow us to have something to label outputs with in the workflow editor and to reference in the format 2 workflow description language. - Extend workflow editor UI to allow labeling workflow outputs (and enforce that these are unique across a workflow). - Extend workflow invocation and progress tracking to allow invoking a subworkflow as part of another workflow invocation. - Extend workflow import and export code to allow a nested representation of workflows. - Update format 2 workflow description to allow testing nested workflows. Most relevant new and modified test cases can be run using the following commands: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_run_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_outputs nosetests test/unit/test_galaxy_mapping.py nosetests test/unit/workflows/test_workflow_progress.py ``` Commit: f88ad8d4e35b51a5f88b0d29b71755f576fc1f7a https://github.com/galaxyproject/galaxy/commit/f88ad8d4e35b51a5f88b0d29b717… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map 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/tool/tool-form-workflow.js Log Message: ----------- Fix Change type label in editor form Commit: 48eec81f48f92d7b5e7a42a9cf4be453f9f14fa5 https://github.com/galaxyproject/galaxy/commit/48eec81f48f92d7b5e7a42a9cf4b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Allow specifying workflow outputs on subworkflow nodes. Commit: 1b3ee81dbae9375443ea396280c1e418cae84876 https://github.com/galaxyproject/galaxy/commit/1b3ee81dbae9375443ea396280c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1314 from nsoranzo/release_15.10_tool_load_fixes [15.10] When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Commit: f10b968075e37b650f46811f6f83286c6aaefccd https://github.com/galaxyproject/galaxy/commit/f10b968075e37b650f46811f6f83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Build section dom in js Commit: b4bfde4089a5f1893ddd839fa4a2c34c71378ae2 https://github.com/galaxyproject/galaxy/commit/b4bfde4089a5f1893ddd839fa4a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix attribute Commit: 530ceb13befdc0850efb9db47c5389c3218338b3 https://github.com/galaxyproject/galaxy/commit/530ceb13befdc0850efb9db47c53… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix for failing qunit test. Commit: 952eb34f447772918f8af7f66779c5dfa734424a https://github.com/galaxyproject/galaxy/commit/952eb34f447772918f8af7f66779… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Upgrade Paste to 2.0.2 Commit: f54138237dcba721d61af5f692b3195e812a6939 https://github.com/galaxyproject/galaxy/commit/f54138237dcba721d61af5f692b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix optional parameters Commit: fc85857a71a270172e8390c1846daad86f547b14 https://github.com/galaxyproject/galaxy/commit/fc85857a71a270172e8390c1846d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py A lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Separate abstractions for parsing discovered datasets and discovering. This is part of a long effort to build a galaxy.tools.parser module that has no dependencies outside of say galaxy.util - so I can add it to the code shared with planemo and pulsar. This would allow planemo (and by extension Tool Shed 2.0) to reason about tools in an abstract way without the billion dependencies of galxaxy.tools.Tool. Commit: 586ab24970856f12112714759f1ead088bc48a04 https://github.com/galaxyproject/galaxy/commit/586ab24970856f12112714759f1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py R lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parser/interface.py A lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Move galaxy.tools.parameters.outputs into galaxy.tools.paraser.output_actions. This module has not external dependencies so it is prefect for the parser module. There still remains work to be done to separate it from XML. Commit: 8480f9187e8cae34fc4822ae1d2d8971f3504f5a https://github.com/galaxyproject/galaxy/commit/8480f9187e8cae34fc4822ae1d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1344 from natefoo/paste2 Upgrade Paste to 2.0.2 Commit: 191f75407ed955b3b0836b7503616f664f0d0a73 https://github.com/galaxyproject/galaxy/commit/191f75407ed955b3b0836b750361… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1343 from guerler/fix_validation_000 Fix optional parameters Commit: e38e4449cddc0a6b31ca6f19d849cae1796e22df https://github.com/galaxyproject/galaxy/commit/e38e4449cddc0a6b31ca6f19d849… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- If GALAXY_SLOTS is defined in the environment, use it for the local runner when job destinations haven't been configured. Commit: 984ceb104d91cdd23daf8a1b6c2382d1eacd1e90 https://github.com/galaxyproject/galaxy/commit/984ceb104d91cdd23daf8a1b6c23… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/util/dictifiable.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Move Dictifiable out of model package into util. Many objects that aren't model objects are Dictifiable at this point so there is no reason to have this in model. This changes eliminates Dictifiable's dependency on sqlalchemy (by using a more pythonic type check). Now that Dictifiable has no external dependencies, it is much easier to reuse it (and more important objects that extend it) in other projects such as planemo. Commit: d24bc3df1e627a0586860600a89352f6bddf49b1 https://github.com/galaxyproject/galaxy/commit/d24bc3df1e627a0586860600a893… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use both SLURM_NTASKS and SLURM_CPUS_PER_TASK to set GALAXY_SLOTS Commit: f51ee306b1e88001f76fd818e495cdbd9db2e10c https://github.com/galaxyproject/galaxy/commit/f51ee306b1e88001f76fd818e495… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- Merge pull request #1346 from dannon/local_slots If GALAXY_SLOTS is defined in the environment, use it for the local r… Commit: c8e61140e7b297356f1830d46761660a85d7b79d https://github.com/galaxyproject/galaxy/commit/c8e61140e7b297356f1830d46761… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: R lib/galaxy/util/lrucache.py Log Message: ----------- Remove unused lrucache.py file in galaxy.util. Added without context in https://github.com/galaxyproject/galaxy/commit/88164c123d3faafe04bf38193e60…. Commit: 869b1a4ef0ec647cca1420e6c0f82023c5ffbad0 https://github.com/galaxyproject/galaxy/commit/869b1a4ef0ec647cca1420e6c0f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/util/hash_util.py Log Message: ----------- Remove Python 2.4- from hash_util.py. Commit: 73dce68376df898d01cc8fcf843d363914a39adf https://github.com/galaxyproject/galaxy/commit/73dce68376df898d01cc8fcf843d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: R lib/galaxy/util/debugging.py Log Message: ----------- Remove seemingly unused debugging.py. Add in https://github.com/galaxyproject/galaxy/commit/017a3c356b8742dd09e65f1c6ce8…. Commit: 87ce6c778ffc9087d589914a5eec640da067c231 https://github.com/galaxyproject/galaxy/commit/87ce6c778ffc9087d589914a5eec… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix for loading workflows that have tool verions / step upgrade messages. Commit: 14d25e9d426ef6fb329c0a04f0c0fdf0beabe9bf https://github.com/galaxyproject/galaxy/commit/14d25e9d426ef6fb329c0a04f0c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1348 from blankenberg/workflow_fix Fix for loading workflows that have tool version / step upgrade messages. Commit: 83f57c56c183f38b6a8915d506dbf6d00c634c65 https://github.com/galaxyproject/galaxy/commit/83f57c56c183f38b6a8915d506db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py A lib/galaxy/util/multi_byte.py M tools/data_source/upload.py Log Message: ----------- Refactor is_multi_byte out of galaxy.util. It introduces a fairly esoteric dependency in galaxy.util for just a couple uses in Galaxy. Separating it out like this will allow reuse of the entire galaxy.util with only one external dependency (docutils, which planemo for instance already depends on). Commit: 61f64e828530c54bae6a090580a6e4278b32a699 https://github.com/galaxyproject/galaxy/commit/61f64e828530c54bae6a090580a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/workflow/extract.py M test/unit/tools/test_actions.py M test/unit/tools/test_evaluation.py Log Message: ----------- Refactor tool output classes out of galaxy.tools and into parser module. This makes the galaxy.tool.parser much more portable, it no longer has a dependency on anything in galaxy.tools or submodules except galaxy.tools.loader (which in turn has no dependencies on galaxy.tools or submodules). Commit: 12014cc2252d710b617953dbfcc804fc9b3f0a67 https://github.com/galaxyproject/galaxy/commit/12014cc2252d710b617953dbfcc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Show correct subworkflow name Commit: 2ff3bf0c0c66946557f21f0bafa55768b7a8cd63 https://github.com/galaxyproject/galaxy/commit/2ff3bf0c0c66946557f21f0bafa5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix label change handling Commit: c9016f9553784b3a83f448c787fa8b90e11a2599 https://github.com/galaxyproject/galaxy/commit/c9016f9553784b3a83f448c787fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #15 from guerler/fix_subworkflows_005 Fix subworkflows 005 Commit: e52cc6614769c0b332c32a1068db816917a5708c https://github.com/galaxyproject/galaxy/commit/e52cc6614769c0b332c32a1068db… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py R lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py A lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #1349 from jmchilton/planemo_refactor_0 Refactor tool parsing handling toward reuse outside Galaxy Commit: 58ce52a0bae5971670a99bf41502867b02ebb1f3 https://github.com/galaxyproject/galaxy/commit/58ce52a0bae5971670a99bf41502… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/util/dictifiable.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Merge pull request #1350 from jmchilton/dictifiable_refactor Move Dictifiable out of model package into util. Commit: 8e0b6af87658cd2a014a16cdf35349db6e61a84d https://github.com/galaxyproject/galaxy/commit/8e0b6af87658cd2a014a16cdf353… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: R lib/galaxy/util/debugging.py M lib/galaxy/util/hash_util.py R lib/galaxy/util/lrucache.py Log Message: ----------- Merge pull request #1351 from jmchilton/util_clean_0 Remove some unused stuff from galaxy.util. Commit: 1ec67c864b3af590c337d86c2f2a6b52ae96fd0e https://github.com/galaxyproject/galaxy/commit/1ec67c864b3af590c337d86c2f2a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py A lib/galaxy/util/multi_byte.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #1352 from jmchilton/multibyte_refactor Refactor is_multi_byte out of top-level galaxy.util. Commit: 66944ba7de178cc45ffa7a4aa9253ec4512cb6fd https://github.com/galaxyproject/galaxy/commit/66944ba7de178cc45ffa7a4aa925… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M tox.ini Log Message: ----------- Lint with Python 3 serveral modules. Namely the modules I'd like to be shared with planemo, pulsar, etc.... Commit: cdf9380735878d44fee863c86b69a686ab0fd76f https://github.com/galaxyproject/galaxy/commit/cdf9380735878d44fee863c86b69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- PY3 fixes for galaxy.util. Commit: 7a36b141bd72b7fc2c675254c10779dace9be6e1 https://github.com/galaxyproject/galaxy/commit/7a36b141bd72b7fc2c675254c107… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/expressions.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py Log Message: ----------- PY3 fixes for galaxy.util submodules. Commit: 41da9b0f88727759d1d2453a90b548858d10ffa7 https://github.com/galaxyproject/galaxy/commit/41da9b0f88727759d1d2453a90b5… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map 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/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/qunit/tests/workflow_editor_tests.js M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #1306 from common-workflow-language/subworkflows New Workflow Modules - Input Parameters and Subworkflows Commit: 50e531aa5971bee6f727ad0013b45c4a5d052fc9 https://github.com/galaxyproject/galaxy/commit/50e531aa5971bee6f727ad0013b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/util/checkers.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M tools/data_source/upload.py Log Message: ----------- Refactor galaxy.datatypes.checkers into galaxy.util.checkers. - Primary reason is because it is used all over the place in contexts that have nothing to do with Galaxy datatype classes or datatype registery or sniffing, most importantly by the code in the tool shed for determining if something is a tool or not. - This code has no dependencies on the datatypes module or any hard dependencies on things not in the Python standard library. Commit: b0deead9c3260598f83d1ab2ec74b3c3e8974456 https://github.com/galaxyproject/galaxy/commit/b0deead9c3260598f83d1ab2ec74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Fix change handler association Commit: 1562c74b2b93aaea78c3fed62ed1de9a76ebe3e2 https://github.com/galaxyproject/galaxy/commit/1562c74b2b93aaea78c3fed62ed1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M tox.ini Log Message: ----------- Merge pull request #1354 from jmchilton/py3_0 Lint with Python 3 several modules. Commit: b4683fbce4cf7c133fdd8af6c6fef58a5bf3c76d https://github.com/galaxyproject/galaxy/commit/b4683fbce4cf7c133fdd8af6c6fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- raise and show specific exception and warning when no files detected Commit: 6f3852188e35612800c6a5ab47b0dc800263778b https://github.com/galaxyproject/galaxy/commit/6f3852188e35612800c6a5ab47b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Update documentation in migration 131 to not be copypasta. Commit: f6557964b6b88b1752ea70e1132610596f6fa103 https://github.com/galaxyproject/galaxy/commit/f6557964b6b88b1752ea70e11326… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py Log Message: ----------- Merge pull request #1361 from dannon/oops_copypasta Update documentation in migration 131 Commit: 2d7c2019fba1b3de89a5a5183c7bd147a309f958 https://github.com/galaxyproject/galaxy/commit/2d7c2019fba1b3de89a5a5183c7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1360 from martenson/raise-specific-exception [15.10] datalibs: raise and show specific exception and warning when no files detected Commit: abd51e7f791c99a93062b9f2fee7827dea857c20 https://github.com/galaxyproject/galaxy/commit/abd51e7f791c99a93062b9f2fee7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #1358 from guerler/fix_same_upload_000 [15.10] Fix change handler association Commit: d9068a808994dee2b1c0ea873365846706e03d70 https://github.com/galaxyproject/galaxy/commit/d9068a808994dee2b1c0ea873365… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1359 from jmchilton/py3_0 PY3 fixes for galaxy.util. Commit: 872458f8b9ebda4d86863b3d0ca2a9d74e0b53ba https://github.com/galaxyproject/galaxy/commit/872458f8b9ebda4d86863b3d0ca2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/expressions.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py Log Message: ----------- Merge pull request #1362 from jmchilton/py3_1 PY3 fixes for galaxy.util submodules. Commit: e7f4ec9685f345c13309b16412fd22a6ddadf852 https://github.com/galaxyproject/galaxy/commit/e7f4ec9685f345c13309b16412fd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/special_tools.py Log Message: ----------- Merge pull request #1307 from jmchilton/collection_opts_prereq1 Refactor tool stuff for generic model actions Commit: 80a35c21841671907d326e4fb6cedb433389648d https://github.com/galaxyproject/galaxy/commit/80a35c21841671907d326e4fb6ce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/util/checkers.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #1363 from jmchilton/checkers_refactor Refactor galaxy.datatypes.checkers into galaxy.util.checkers. Commit: 455372e6bf711d64947768f8b05418f8e6b49647 https://github.com/galaxyproject/galaxy/commit/455372e6bf711d64947768f8b054… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/workflow/extract.py M test/unit/tools/test_actions.py M test/unit/tools/test_evaluation.py Log Message: ----------- Merge pull request #1353 from jmchilton/output_refactor Refactor tool output classes out of galaxy.tools and into parser module. Commit: 04f5ed4552d5b0b837eabded18704eeda5cc8c26 https://github.com/galaxyproject/galaxy/commit/04f5ed4552d5b0b837eabded1870… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-17 (Thu, 17 Dec 2015) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map 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/menu.js Log Message: ----------- Reimplement menu onclick functionality that appears to have been dropped (probably a bad merge?) in the webpack PR. Commit: b5ad20401b28e29b727c1212be5443d7dd9c2dad https://github.com/galaxyproject/galaxy/commit/b5ad20401b28e29b727c1212be54… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Refactor UI component out of AbstractToolBox. If it belongs in the base class ToolBox which is more concerned with Galaxy-spcifics like UI, AbstractToolBox is suppose to be an abstract description of a toolbox - it is about data management. Commit: 536b4e2a2038d889486bbf0836341e03d737f53c https://github.com/galaxyproject/galaxy/commit/536b4e2a2038d889486bbf083634… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/util/common_util.py Log Message: ----------- Improve some random tool shed code. Commit: 914adfcc0cd5e8b060df059da9a4f8e9b1293fde https://github.com/galaxyproject/galaxy/commit/914adfcc0cd5e8b060df059da9a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Sychronize tool shed, planemo, and toolbox code for filtering out non-tool XML files. A single abstraction will allow toolbox and planemo to deal with other kinds of tools in the future, and the stronger preconditions should eliminate some busy error logging when monitoring a tool directory. Commit: 20b47f3ca208ded3682f68591f5801b85547efc1 https://github.com/galaxyproject/galaxy/commit/20b47f3ca208ded3682f68591f58… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Update looks_like_a_tool to respect enable_beta_tool_formats. Default is off obviously, so for instance the tool shed will never think unsupported beta tools are real tools. Commit: a8ed6146e88642b17273e316c571c5a5a9f4df45 https://github.com/galaxyproject/galaxy/commit/a8ed6146e88642b17273e316c571… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/util/odict.py Log Message: ----------- Tweak YAML tools to use ordered dictionaries. Order of inputs and outputs in Galaxy is important, so preserve this order if using dictionary-style (both available) for inputs and/or outputs. Commit: 75e7276e5e9c43ec6f09f68adea2870b3a6917dc https://github.com/galaxyproject/galaxy/commit/75e7276e5e9c43ec6f09f68adea2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Eliminate sqlalchemy and tool shed dependencies from AbstractToolBox. Provide an extension point instead that allows Galaxy's ToolBox class to provide the functionality that required these dependencies. And optionally load ToolVersion class required for reasoning about tool shed logic. Commit: e06bf5a32052d6cf474cb5c3d195f632ffe8b9e4 https://github.com/galaxyproject/galaxy/commit/e06bf5a32052d6cf474cb5c3d195… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Allow installation of different repositories with the same name in a single install transaction. Commit: c6fbf987d2c4422eda793fa817f0ce83931d0119 https://github.com/galaxyproject/galaxy/commit/c6fbf987d2c4422eda793fa817f0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Whitespaces around operator. Commit: b7b8f097d5a7617b2997f254b4e0229adfaae623 https://github.com/galaxyproject/galaxy/commit/b7b8f097d5a7617b2997f254b4e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Enhance YAML/dictionary tool rep. to allow output collections. Commit: f042fe8548ec4a0f2f29b72d0c34736e2ff524f9 https://github.com/galaxyproject/galaxy/commit/f042fe8548ec4a0f2f29b72d0c34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/test_jobs.py Log Message: ----------- Attempt to fix transiently failing API tests. - Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.t… - Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem. Commit: 93c6d0542124c220e36c1e90d62e3e2aef607e9a https://github.com/galaxyproject/galaxy/commit/93c6d0542124c220e36c1e90d62e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revise and fix waiting for tool tests. - maxseconds on test tag stopped being respected at some point, fix that. - maxseconds on test tag stopped being parsed at some later point, fix that. - Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT. - Add test case to ensure there is no future regression of these behaviors. Commit: ffb973477b02c4bc1cbfa95c7a6247f1d7949fdd https://github.com/galaxyproject/galaxy/commit/ffb973477b02c4bc1cbfa95c7a62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Do not check for tool migrations when running tests. This is an inappropriate time for the check and causes slow down when running tests. Commit: 641b275aa424421591833f6a3bce3ebd8b358017 https://github.com/galaxyproject/galaxy/commit/641b275aa424421591833f6a3bce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Wait on jobs and history in certain API test cases. This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases. Commit: 57a76065a54f63a47874158c121f002308648025 https://github.com/galaxyproject/galaxy/commit/57a76065a54f63a47874158c121f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Fix missing assertion pointed out @nsoranzo. Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing. Commit: 2817eabf95a980a250e272c3917e5dcfc24743b2 https://github.com/galaxyproject/galaxy/commit/2817eabf95a980a250e272c3917e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Fail maxseconds test tool if sleep is interrupted. Commit: 2c657b98e2945f48e1339f229e7de4de9f40fe4c https://github.com/galaxyproject/galaxy/commit/2c657b98e2945f48e1339f229e7d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Break out of loop once we know the repo is already in all_repo_info_dicts. Commit: 9752fa76c54e927918560d474df4fbae6551d4ca https://github.com/galaxyproject/galaxy/commit/9752fa76c54e927918560d474df4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Typo Commit: 0203a69d88c854c1fe3a210c83ff3ee0d943f4df https://github.com/galaxyproject/galaxy/commit/0203a69d88c854c1fe3a210c83ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/grunt-tasks/install-libs.js M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/tours/__init__.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/upload/upload-button.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 A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako Log Message: ----------- Tours. Commit: 40382fb0c1d7ec38252413aa50b3cb24418d158e https://github.com/galaxyproject/galaxy/commit/40382fb0c1d7ec38252413aa50b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: A config/plugins/tours/galaxy_ui.yaml Log Message: ----------- Add slightly modified intro tour from bjoern, mostly compatible. Commit: cced5c3378937c14787884d91a613f56112ce7ff https://github.com/galaxyproject/galaxy/commit/cced5c3378937c14787884d91a61… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #1366 from mvdbeek/fix_repository_install Allow installation of different repositories with the same name in a … Commit: f107b17928bddbe4f87e757f2301d56b807253cf https://github.com/galaxyproject/galaxy/commit/f107b17928bddbe4f87e757f2301… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js M client/webpack.config.js M static/maps/mvc/tours.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/tours.js Log Message: ----------- Refactor a bit, adjust textinsert action to trigger 'change' on the element. Commit: 1e5640163a36c12e5f9e719358a1653a0fb18401 https://github.com/galaxyproject/galaxy/commit/1e5640163a36c12e5f9e719358a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.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/tours.js M static/scripts/onload.js Log Message: ----------- Tour shim in onload, check sessionStorage (or would local be more appropriate?) Commit: 43e38414e6770b447d9de19450f2fe738a07f471 https://github.com/galaxyproject/galaxy/commit/43e38414e6770b447d9de19450f2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- --pre does not exist on pip < 1.4, but on pip < 1.4, the default behavior was the same as using --pre on pip >= 1.4. Therefore, detect the version of pip and add --pre if necessary. Fixes #1134 Commit: 7110a0cc5e411062b8c6e5857e04ce10f121ffdd https://github.com/galaxyproject/galaxy/commit/7110a0cc5e411062b8c6e5857e04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Document necessary tweak. Commit: 6ed3ceafed73ace54537f79a72caec02ef798cbb https://github.com/galaxyproject/galaxy/commit/6ed3ceafed73ace54537f79a72ca… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map 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/menu.js Log Message: ----------- Merge pull request #1365 from dannon/redo_click Reimplement menu onclick functionality that appears to have been drop… Commit: 6678544caa7bc5a415984fae448826aefc1ec6ea https://github.com/galaxyproject/galaxy/commit/6678544caa7bc5a415984fae4488… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1372 from natefoo/pip-pre-fix Fix usage of --pre with pip < 1.4 Commit: 9e7eaaa7aaf9c9a6928edc08abecbc26a3a76004 https://github.com/galaxyproject/galaxy/commit/9e7eaaa7aaf9c9a6928edc08abec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.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/tours.js M static/scripts/onload.js Log Message: ----------- Finish sessionStorage and restart of tours across multiple pages. Commit: 5a3524245b41f2978b81ee01176dcf1caa382d50 https://github.com/galaxyproject/galaxy/commit/5a3524245b41f2978b81ee01176d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.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/tours.js M static/scripts/onload.js Log Message: ----------- Actually let people end a tour. Commit: ffede653023a49aabcfcc958816b20e0e183a4ba https://github.com/galaxyproject/galaxy/commit/ffede653023a49aabcfcc958816b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Debugging cruft. Commit: 8c1beb2af5633660efc8ec7caaa871416f2508ea https://github.com/galaxyproject/galaxy/commit/8c1beb2af5633660efc8ec7caaa8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- title override, working on fixing style. Commit: 4efa8e73b3479f3914b6b54d6a8bc4651aec7ef4 https://github.com/galaxyproject/galaxy/commit/4efa8e73b3479f3914b6b54d6a8b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Consolidate to standard options dict, minor refactorings. Commit: 38b3c6e97aa0d6fe595be0f6e9021109ddd17226 https://github.com/galaxyproject/galaxy/commit/38b3c6e97aa0d6fe595be0f6e902… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: 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 Log Message: ----------- Build client, bundle. Commit: 9b14d515db16d3a769532740a9b807b37a1177bd https://github.com/galaxyproject/galaxy/commit/9b14d515db16d3a769532740a9b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M static/style/blue/bootstrap-tour.css M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Stylize! Commit: e8116b8bbf22373ae8e784e83cf55426fd5b60bc https://github.com/galaxyproject/galaxy/commit/e8116b8bbf22373ae8e784e83cf5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less M static/style/blue/base.css Log Message: ----------- Flip global vars back, now that bootstrap-tours.css is included and will override. Commit: aecc5d864f8e211c6f60ea8717f726c5807a1a76 https://github.com/galaxyproject/galaxy/commit/aecc5d864f8e211c6f60ea8717f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/galaxy_ui.yaml M static/maps/mvc/tours.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/tours.js Log Message: ----------- Make tours.js safe (but possibly not functional wrt/ listing) to use on pages without Galaxy object. Commit: 2c5241dc3bba2114b43fe7f7e6e2efb17b705a28 https://github.com/galaxyproject/galaxy/commit/2c5241dc3bba2114b43fe7f7e6e2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: 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 Log Message: ----------- Full client rebuild. Commit: 048561d282d32373e4432edcccb54fe963eb6f95 https://github.com/galaxyproject/galaxy/commit/048561d282d32373e4432edcccb5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-19 (Sat, 19 Dec 2015) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M static/maps/layout/page.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/utils/uploadbox.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/ui/ui-modal.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/qunit/test-app.js A test/qunit/tests/modal_dialog_tests.html A test/qunit/tests/modal_dialog_tests.js Log Message: ----------- Avoid duplicate upload entries, revise modals, add tests Revise styles Add more tests Commit: 39e7f025ebd9386f5b07ca99f3b233cd94299c32 https://github.com/galaxyproject/galaxy/commit/39e7f025ebd9386f5b07ca99f3b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-19 (Sat, 19 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.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/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js R test/qunit/tests/modal_dialog_tests.html R test/qunit/tests/modal_dialog_tests.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js Log Message: ----------- Refine popover wrapper Revise popover, add tests Commit: 17d733b0428f125e6deb1007937dff6b9bfe80b2 https://github.com/galaxyproject/galaxy/commit/17d733b0428f125e6deb1007937d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-19 (Sat, 19 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Move closing events to show/hide function Commit: 36d9514e26037a927ad8becab9a834a4807abc50 https://github.com/galaxyproject/galaxy/commit/36d9514e26037a927ad8becab9a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-20 (Sun, 20 Dec 2015) Changed paths: M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/expressions.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/topsort.py M test/unit/test_objectstore.py Log Message: ----------- More Python 3 fixes. This fixes all unit tests for code exclusively covering the stuff I'm moving into the galaxy-lib that will be used by planemo, pulsar, and future tooling efforts. Commit: 355bb281e21e701e05d1f671f080022de9df987b https://github.com/galaxyproject/galaxy/commit/355bb281e21e701e05d1f671f080… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-20 (Sun, 20 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py Log Message: ----------- Finish swapping unencoded ids with order_index in workflows API. Running a workflow or showing a workflow can both restore the previous behavior by passing legacy=True as an API parameter. By changing these two endpoints in tandem I believe backward compatiblity for most existing code should be maintained unless: - The external application saved these workflow IDs previously and re-runs workflows without refetching the workflow definition. I could imagine Refinery for instance might do this and will have to update indexed workflows or add legacy=True to workflow requests. - The external application contacted the database directly after using this API endpoint to fetch more information about the step (seems unlikely). See conversation: - http://dev.list.galaxyproject.org/workflow-API-step-order-vs-step-id-in-bio… Rebased with changes suggested by @nsoranzo. Commit: 6eb8eae3967d62909f2b4d5fcded46f5ea411b40 https://github.com/galaxyproject/galaxy/commit/6eb8eae3967d62909f2b4d5fcded… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-20 (Sun, 20 Dec 2015) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M static/maps/layout/page.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/utils/uploadbox.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/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/qunit/test-app.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js Log Message: ----------- Merge pull request #1377 from guerler/revise_upload_000 Uploader enhancements, modal and popover cleanup, fixes and new test cases Commit: ae2b94824a322909fb29277ea2571c419d09946b https://github.com/galaxyproject/galaxy/commit/ae2b94824a322909fb29277ea257… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/expressions.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/topsort.py M test/unit/test_objectstore.py Log Message: ----------- Merge pull request #1376 from jmchilton/py3_0 More Python 3 fixes. Commit: e325eba37c159e78a20895edbd6d521657f9b650 https://github.com/galaxyproject/galaxy/commit/e325eba37c159e78a20895edbd6d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M lib/galaxy/webapps/galaxy/api/tours.py M static/maps/mvc/tours.js.map 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/tours.js Log Message: ----------- Some tweaks care of @bgruening. This adds (slightly tweaked) functionality to support a series of clicks, still needs a delay between clicks, and since it's the most common case that pre/postclick will be a single item, a list shouldn't be required here. Commit: 630ac3658f3c64bd9a9abe5757cce0ed01cad229 https://github.com/galaxyproject/galaxy/commit/630ac3658f3c64bd9a9abe5757cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Python 3 fixes and galaxy-lib updates from planemo. (Minus changes for conda which - should be merged as their own PR obviously.) Commit: f874d559b7db28c3fa7b4df6844f077da419911a https://github.com/galaxyproject/galaxy/commit/f874d559b7db28c3fa7b4df6844f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/odict.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #1368 from jmchilton/looks_like_a_tool Unify and Abstract Code for Checking if File Looks Like a Tool Commit: c3580da7b826b42de631017d4d2baf7e6ac3cfdf https://github.com/galaxyproject/galaxy/commit/c3580da7b826b42de631017d4d2b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Allow installation of different repositories with the same name in a single install transaction. Commit: 52b66d0dee8c026bfb8858671f900b862837fae5 https://github.com/galaxyproject/galaxy/commit/52b66d0dee8c026bfb8858671f90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #1385 from martenson/port-marius-ts-fix [15.10] Port marius TS fix Commit: 5d26f589cc475ff95b97ef2dcb34d5a290079e8b https://github.com/galaxyproject/galaxy/commit/5d26f589cc475ff95b97ef2dcb34… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M scripts/functional_tests.py M test/api/helpers.py M test/api/test_jobs.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1295 from jmchilton/test_fixes_backport_15_10 [15.10] Backport various testing fixes. Commit: 61cba6c9429fe790da19f843d8e2b0d415459b4c https://github.com/galaxyproject/galaxy/commit/61cba6c9429fe790da19f843d8e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/util/__init__.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge pull request #1367 from jmchilton/toolbox_refactor_0 Refactor AbstractToolbox toward reuse outside Galaxy Commit: 4eefd885eccd0c42c7a74c8415add3a948a91135 https://github.com/galaxyproject/galaxy/commit/4eefd885eccd0c42c7a74c8415ad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Improve startup options related to wheel/dependency/virtualenv management. Drop hard requirement on lzo (doubt anyone other than usegalaxy.org is using it, but it will be added as a extras option for bxlab/bx-python for anyone who is). Fixes #1150 Commit: 9934a45134283d307814058fa09e4b26d3d8452f https://github.com/galaxyproject/galaxy/commit/9934a45134283d307814058fa09e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M tox.ini Log Message: ----------- Run tox/Travis with --no-create-venv instead of --skip-venv Commit: ded904cb12580723b192fe571cf2a4f20ec16619 https://github.com/galaxyproject/galaxy/commit/ded904cb12580723b192fe571cf2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Merge pull request #1388 from jmchilton/py3_2 Python 3 fixes and galaxy-lib updates from planemo. Commit: 26d7e97ed7b4eaa845bf86fd4991b1fbf4a3ead0 https://github.com/galaxyproject/galaxy/commit/26d7e97ed7b4eaa845bf86fd4991… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M run.sh M run_tests.sh M scripts/common_startup.sh M tox.ini Log Message: ----------- Merge pull request #1389 from natefoo/wheel-startup-option-improvements Improve startup options related to wheel/dependency/virtualenv management. Commit: 6ca159136638e54a0fe9fe471202aaa788987cf1 https://github.com/galaxyproject/galaxy/commit/6ca159136638e54a0fe9fe471202… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Added hashes Fixes #1260 Commit: ddaa1189f75627f516926b5363398fe7e24fe992 https://github.com/galaxyproject/galaxy/commit/ddaa1189f75627f516926b536339… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Adding uuid support to directory_hash_id Commit: 8f34f2a6104ff595d411bfc5e77b488f2c86dfd9 https://github.com/galaxyproject/galaxy/commit/8f34f2a6104ff595d411bfc5e77b… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Fixing issues for PR unit testing and linting Commit: 4840a3d8b1caae9666eeebf95d4aeaebaee8260b https://github.com/galaxyproject/galaxy/commit/4840a3d8b1caae9666eeebf95d4a… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Fixing lint problem Commit: 2466b1cb65757b0157dab67a16c7bbfd7b48c710 https://github.com/galaxyproject/galaxy/commit/2466b1cb65757b0157dab67a16c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-24 (Thu, 24 Dec 2015) Changed paths: M lib/galaxy/util/directory_hash.py Log Message: ----------- Merge pull request #1397 from kellrott/dev Adding uuid support to directory_hash_id Commit: ed11f7ab00b0ff3f414dc23736c054a655b44663 https://github.com/galaxyproject/galaxy/commit/ed11f7ab00b0ff3f414dc23736c0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Offer galaxy_web_port in all scenarios, this can be useful in some local dev settings. Commit: 7b118990d2bee4377b364373fd596b88d0275307 https://github.com/galaxyproject/galaxy/commit/7b118990d2bee4377b364373fd59… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Catch errors in some wired cases. This will prevent the proxy to crash badly if the Docker container just disappears. Commit: 1873d2c5edbb44eb0e8138612d55510b3492782b https://github.com/galaxyproject/galaxy/commit/1873d2c5edbb44eb0e8138612d55… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- update js scripts Commit: 47a44202673839fe1ff00408c50c533ddd823a27 https://github.com/galaxyproject/galaxy/commit/47a44202673839fe1ff00408c50c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-25 (Fri, 25 Dec 2015) Changed paths: A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Add Jupyter Interactive Environment Commit: 7269f76e6e8227d26c928e76cd81941498c0acd7 https://github.com/galaxyproject/galaxy/commit/7269f76e6e8227d26c928e76cd81… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Remove transiently failing maxseconds.xml framework test. Commit: 79bbc97a189bea03392bff2ab6a819aca1fad0db https://github.com/galaxyproject/galaxy/commit/79bbc97a189bea03392bff2ab6a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Attempt to fix transiently failing capsule TS test. Guess here is that a flush is not occuring on that file because it is happening as part of garbage collection and not explictly as part of an explicit close. Commit: 6aa7691a637e86491a51d41a1672521f42a06bb5 https://github.com/galaxyproject/galaxy/commit/6aa7691a637e86491a51d41a1672… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/workflows/test_run_parameters.py Log Message: ----------- Merge pull request #1137 from jmchilton/workflow_api_order_2 Finish swapping unencoded ids with order_index in workflows API. Commit: 1148081435e6eb4075eb62783129299ebbd4d490 https://github.com/galaxyproject/galaxy/commit/1148081435e6eb4075eb62783129… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-26 (Sat, 26 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/util/checkers.py M test/unit/jobs/test_job_wrapper.py A test/unit/tools/test_conda_resolution.py Log Message: ----------- Implement a conda dependency resolver. Much more information on planemo PR that I used to build a test bed for this: https://github.com/galaxyproject/planemo/pull/392 Also syncs galaxy with planemo shared library changed. Commit: 38d40e7af11525348bb54bad3a3a8496539a2a3a https://github.com/galaxyproject/galaxy/commit/38d40e7af11525348bb54bad3a3a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- move keep_alive into jupyter.js Commit: 6ac01675f3f37a6af1d498b96cad753a03a8a776 https://github.com/galaxyproject/galaxy/commit/6ac01675f3f37a6af1d498b96cad… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample Log Message: ----------- Change default image name to a versioned tagged Docker release. Commit: 4e55f7e519a0e03805e0f3d91ab8de47c357d040 https://github.com/galaxyproject/galaxy/commit/4e55f7e519a0e03805e0f3d91ab8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1399 from bgruening/ie Interactive Environment updates Commit: 798c7e20c33860ada2bb066277a3280488e25492 https://github.com/galaxyproject/galaxy/commit/798c7e20c33860ada2bb066277a3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Merge pull request #1400 from bgruening/jupyter Add Jupyter Interactive Environment Commit: 14a618ee3ab084e43f51f72136afd6b4c482b4cf https://github.com/galaxyproject/galaxy/commit/14a618ee3ab084e43f51f72136af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-28 (Mon, 28 Dec 2015) Changed paths: M test/functional/tools/samples_tool_conf.xml M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1401 from jmchilton/transient_tests_2 Fix and potential fix for transiently failing tests. Commit: 578e201d64aa33224a586fe7928a8be5b476d332 https://github.com/galaxyproject/galaxy/commit/578e201d64aa33224a586fe7928a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-28 (Mon, 28 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map 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/tours.js M static/scripts/onload.js Log Message: ----------- Launch tour on GET arg (?tour_id=core.galaxy_ui). Commit: 4322f5e9b9e152aec75339925228b90ef759b47b https://github.com/galaxyproject/galaxy/commit/4322f5e9b9e152aec75339925228… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: A config/plugins/tours/core.galaxy_ui.yaml R config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py Log Message: ----------- Force tour_id to be locked to filename, instead of allowing these to be out of sync. Commit: 401583d730a6d5d1e57c82bb08c3216b40856d8f https://github.com/galaxyproject/galaxy/commit/401583d730a6d5d1e57c82bb08c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Move TOURS.giveTour at the top level of the namespace instead of a method of the view. Commit: d5d404c912340013aab34fe3350a2570010b0898 https://github.com/galaxyproject/galaxy/commit/d5d404c912340013aab34fe3350a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/parameters/wrapped_json.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement special config file to dump parameters as json. ``` <configfiles> <inputs name="inputs" format="json" version="1" /> </configfiles> ``` Version is specified as 1, because the Galaxy tool plumbing doesn't really distinguish between parameter is '', parameter was explicitly supplied as None, parameter was absent, etc... - everything is a just a string in some ways. This distinction may be more important with JSON and for instance the CWL will require more percision, so we may want to revise Galaxy's tool handling in a backward compatible way someday. Commit: de0c913b8bb3ca01fd0ab5c8286450dbef9b604d https://github.com/galaxyproject/galaxy/commit/de0c913b8bb3ca01fd0ab5c82864… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M test/functional/tools/inputs_as_json.xml Log Message: ----------- More work on converting tool inputs to json. - Drop version requirement per commends by @bgruening. - Add examples for conditionals, repeats, sections, colors, and booleans specified truevalue/falsevalue. - Various bug fixes unearthed by new test cases. Commit: cd32b91dc9f562d17349d8cc15ba1b60eba07f70 https://github.com/galaxyproject/galaxy/commit/cd32b91dc9f562d17349d8cc15ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M test/functional/tools/inputs_as_json.xml Log Message: ----------- Update inputs_as_json.xml to drop version attribute. Also add note about filename. Commit: 9a0ef0ed14893bf1dcaae67b466a8b1167571032 https://github.com/galaxyproject/galaxy/commit/9a0ef0ed14893bf1dcaae67b466a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- Expose hidden parameters in inputs json. Commit: 2b2f93d393a4e66c0e466e98a945222bd54e448a https://github.com/galaxyproject/galaxy/commit/2b2f93d393a4e66c0e466e98a945… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/parameters/wrapped_json.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1405 from jmchilton/json_config Implement special config file to dump parameters as json. Commit: f597b08b878f478b9beee32c59b5e4218458c4fe https://github.com/galaxyproject/galaxy/commit/f597b08b878f478b9beee32c59b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Refactor ToolBox functionality. This moves in two directions toward a better design. It moves some Galaxy tool specific logic out of the AbstractToolBox (which should just be worried about panels, etc... IMO) and it moves more galaxy-lib functionality (dependency resolution) into a galaxy-lib module (galaxy.tools.toolbox). It does this by creating a BaseGalaxyToolBox that can reason about which files look like tools and what dependency resoution should be - without dependening on Galaxy models, job running, etc... that is in galaxy.tools.__init__. Commit: 204aa96206a7fdaff69d22fde6387a9956c1a0bc https://github.com/galaxyproject/galaxy/commit/204aa96206a7fdaff69d22fde638… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/unit/test_routes.py Log Message: ----------- API-ify tool dependency resolution. Commit: b167a741a444c3988447b0d63a1ba3dc5e4e62f5 https://github.com/galaxyproject/galaxy/commit/b167a741a444c3988447b0d63a1b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Include information about whether matches are dependencies are exact. Commit: 71a876840a6c9acf11bd2ac7706ec21b32d2fb88 https://github.com/galaxyproject/galaxy/commit/71a876840a6c9acf11bd2ac7706e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Implement concept of listable dependency resolvers. DependencyResolver classes which can enumerate the requirements then can resolve "exactly" should mix in ListableDependencyResolver and implement list_dependencies. The galaxy package resolver can easily be enumerated but its subclasses like the tool shed dependency resolver couldn't, so I have separated that class into a base class that there others can inherit and an actual resolver that implements ListableDependencyResolver. Rebase into listable. Commit: 29f20cf09c18e24e898517bf685418ec1db4cd11 https://github.com/galaxyproject/galaxy/commit/29f20cf09c18e24e898517bf6854… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Implement concept of installable dependency resolvers. DependencyResolver classes which can install "simple" dependences should mix in the new InstallableDependencyResolver and implement install_dependency. Currently this is only the conda dependency resolver, one can easily imagine doing the same for the brew dependency resolver and potentially doing it for some variant of the unlinked dependency resolvers. Commit: 0aa1c5133e029196444ac9c0b32f43489cee3713 https://github.com/galaxyproject/galaxy/commit/0aa1c5133e029196444ac9c0b32f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/util/checkers.py M test/unit/jobs/test_job_wrapper.py A test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #1345 from jmchilton/conda_0 Implement a conda dependency resolver. Commit: 339ad57f3fa626fe30c1bf26f90e0647be038cc9 https://github.com/galaxyproject/galaxy/commit/339ad57f3fa626fe30c1bf26f90e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/templates/charts.mako M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/onload.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/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Cleanup Masthead and Scratchbook Cleanup Masthead and Scratchbook Commit: 4cd621dd378e3a9db0d934203a5e1cdebd817b6c https://github.com/galaxyproject/galaxy/commit/4cd621dd378e3a9db0d934203a5e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-31 (Thu, 31 Dec 2015) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js Log Message: ----------- Add test cases Commit: 868a7dfe0e03503adaf6646e10d8184d18b66a34 https://github.com/galaxyproject/galaxy/commit/868a7dfe0e03503adaf6646e10d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Modify unmodified conda behavior. - Add configuration option for overriding condarc location used by conda resolve commands. - Default location of condarc to be in tool_dependency_dir. - Delay updating the condarc to ensure channels until this would actually be needed (during package installation). - Add configuration flag to allow Galaxy to *NOT* check the PATH for conda. - Update unit test that verifies conda's installation to never use conda on PATH, since a precondition of this test is that certain packages haven't been installed previously. - Change default behavior to not check the PATH for conda, everything else here I feel pretty good about - this I'm ambivalent about - it will reduce error reports and problems with network filesystems, but doesn't seem to be good Unix best practice. Points 2 and 3 above should address this issue: https://github.com/galaxyproject/ansible-galaxy-extras/pull/33#issuecomment… This commit also addresses most of #1406. Commit: a6cbb88ad12288eca031c0469113abc831a42d37 https://github.com/galaxyproject/galaxy/commit/a6cbb88ad12288eca031c0469113… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Enable tool isolation by default and fix bugs. Commit: 1084f14dd0637bc47978a33122c74d86cb617241 https://github.com/galaxyproject/galaxy/commit/1084f14dd0637bc47978a33122c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M test/unit/jobs/test_command_factory.py Log Message: ----------- Unit test modifications for running tool commands in isolated scripts. Commit: 7f8e37d5a1aa96c2c839acea4511e071e81eb450 https://github.com/galaxyproject/galaxy/commit/7f8e37d5a1aa96c2c839acea4511… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py Log Message: ----------- Attempt to fix samtools resolution for metadata when tool command externalized. Commit: acab90d63c6c96a6e609f32080f5b610b33dd549 https://github.com/galaxyproject/galaxy/commit/acab90d63c6c96a6e609f32080f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix unicode-y problem with tool command externalization. Commit: 340aef2550d16bb987b36bc7b2df8e0ed4f6f56b https://github.com/galaxyproject/galaxy/commit/340aef2550d16bb987b36bc7b2df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-02 (Sat, 02 Jan 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix logging for tool script externalization. Commit: ef9e1876a2d4dd02718784f2b9f1045f2f9d0b59 https://github.com/galaxyproject/galaxy/commit/ef9e1876a2d4dd02718784f2b9f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Fixup dependency module and API comments. Thanks to suggestions by @bgruening. Commit: 4650d77bd988b90b6652cc108f83bf6d86cae271 https://github.com/galaxyproject/galaxy/commit/4650d77bd988b90b6652cc108f83… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix listing conda requirements if conda hasn't been installed. Fix problem discovered by @bgruening. Commit: 0da66ee8dcf5fef52b11558228c1eb95479cbce9 https://github.com/galaxyproject/galaxy/commit/0da66ee8dcf5fef52b11558228c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Small improvements to load_directory for downstream extension. Commit: a9d4783f2c3d22e7d830fc88d30b6112e2d43fc0 https://github.com/galaxyproject/galaxy/commit/a9d4783f2c3d22e7d830fc88d30b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Add CWL suppoort to tool checking and parsing. To be clear, this provides none of the infrastructure for running the tools. This is just so that planemo and future tool registry efforts can have a unified interface for accessing and reasoning about tools using the same methods Galaxy does. Commit: 2054f538be010ab6d47e0de1da646268ca6d6ff4 https://github.com/galaxyproject/galaxy/commit/2054f538be010ab6d47e0de1da64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Infrastructure for parsing CWL tools. Commit: db845fa1875bcb08aa2129830f1d405d1d894cfb https://github.com/galaxyproject/galaxy/commit/db845fa1875bcb08aa2129830f1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Refactor loader_directory to support beta formats in other ways. Commit: fcc83d4e09d4603c5fbd831e9e1933916bf00827 https://github.com/galaxyproject/galaxy/commit/fcc83d4e09d4603c5fbd831e9e19… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py Log Message: ----------- Introduce ToolBox parser. Abstract simpler ToolBox interactions to separate XML representation from handling. Doesn't cover tool shed operations since the tool shed explicitly writes XML. Commit: b68991c4caa44aefeaba752748ae62db98a446fd https://github.com/galaxyproject/galaxy/commit/b68991c4caa44aefeaba752748ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M test/unit/tools/test_toolbox.py Log Message: ----------- Allow loading tool confs written in YAML and JSON. Because lets say someone was writing a programatic way to manage elements in a tool conf, that hypothetical person probably shouldn't be writing XML. Commit: 864cc32892a1b4bf91b5d2fe70f7e64eec736393 https://github.com/galaxyproject/galaxy/commit/864cc32892a1b4bf91b5d2fe70f7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M templates/admin/reload_tool.mako Log Message: ----------- Allow toolbox reloading via app, UI, and API. Introduce an app ToolCache to help ensure this operation remains speedy. Commit: 4086dd61dafe562ec01a8b1fce687a539aedbcfe https://github.com/galaxyproject/galaxy/commit/4086dd61dafe562ec01a8b1fce68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M test/unit/tools/test_watcher.py Log Message: ----------- Implement toolbox monitoring. - Add monitor tag on toolbox root elements to force Galaxy to watch the toolbox for changes. - Refactoring and test improvements for existing tool monitoring code. - Implement toolbox shutdown process to ensure different watchers don't compete with each other. - Set the default tool conf to be monitored. Commit: 8027228639a771e4c62131ab15ba4ffbb656498a https://github.com/galaxyproject/galaxy/commit/8027228639a771e4c62131ab15ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Revise tool caching for tool shed tool loading... The tool shed appears to load the same tool in the toolbox multiple times with different settings. Get around this by not using the cache when loading tools from a few tool shed components later in this process. Commit: eddfec36fdf6d19bae398d09ee16952136d2b379 https://github.com/galaxyproject/galaxy/commit/eddfec36fdf6d19bae398d09ee16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Refactor package_tool for better separation of concerns. The tool should know how to package itself, it shouldn't be the responsiblity of the toolbox. Update the code to reflect this and use more pythonic exception handling. Commit: ce24ec6821bdb87f14f3047eef186c246de2d5ed https://github.com/galaxyproject/galaxy/commit/ce24ec6821bdb87f14f3047eef18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M templates/admin/reload_tool.mako Log Message: ----------- Remove alert from toolbox reload. Commit: 523e2b40063d2abb7662a163f0144902541bed18 https://github.com/galaxyproject/galaxy/commit/523e2b40063d2abb7662a163f014… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix shutdown of tool watcher if never activated. Caused a harmless, but distracting stacktrace to be printed on toolbox reload as pointed out by @bgruening https://github.com/galaxyproject/galaxy/pull/1398#issuecomment-168499678. Commit: 7cbf41feb3dfd6eb12c99630692776565c72c579 https://github.com/galaxyproject/galaxy/commit/7cbf41feb3dfd6eb12c996306927… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/util/__init__.py Log Message: ----------- Better exception when samtools is required but not on PATH. Commit: ce2795d87ca4e5063ca699ad75cb6e4461fba30c https://github.com/galaxyproject/galaxy/commit/ce2795d87ca4e5063ca699ad75cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/util/properties.py Log Message: ----------- Copy pastescript's NiceConfigParser into galaxy.util.properties. This is used in galaxy-lib and by utilities such as galaxy/main.py which has no reason to depend on pastescript. Commit: 308435b7391d349b0077375409d631eb96038889 https://github.com/galaxyproject/galaxy/commit/308435b7391d349b0077375409d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Fix bug in db845fa1875bcb08aa2129830f1d405d1d894cfb. Commit: 5ca71d6f292ff122d35c25d0dfd7c0e14d5366e2 https://github.com/galaxyproject/galaxy/commit/5ca71d6f292ff122d35c25d0dfd7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/unit/test_routes.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #1409 from jmchilton/dep_resolution_api Evolving from dependency resolution to dependency management. Commit: 73defd48ce70241d7cc163aaadfef6fcd6830231 https://github.com/galaxyproject/galaxy/commit/73defd48ce70241d7cc163aaadfe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/tool_util.py M templates/admin/reload_tool.mako M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge pull request #1398 from jmchilton/toolbox_overhaul ToolBox Overhaul Commit: 10677319f74f96160a4ee0b48e7d1053df242951 https://github.com/galaxyproject/galaxy/commit/10677319f74f96160a4ee0b48e7d… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #1414 from jmchilton/lib_1 Fix bug in db845fa1875bcb08aa2129830f1d405d1d894cfb. Commit: 905adbac38992ae2fc889d23f000fa2541e87939 https://github.com/galaxyproject/galaxy/commit/905adbac38992ae2fc889d23f000… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/util/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #1412 from jmchilton/isolate Isolate tool commands by default. Commit: 34bb21c411c3ebce94e67f996e70387d33e7f8cf https://github.com/galaxyproject/galaxy/commit/34bb21c411c3ebce94e67f996e70… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/templates/charts.mako M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/onload.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/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/webapps/galaxy/galaxy.masthead.mako A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #1407 from guerler/revise_masthead_000 Masthead/Scratchbook revision and test cases Commit: 61f4c82642c5f48057d36fb9c728b66242807879 https://github.com/galaxyproject/galaxy/commit/61f4c82642c5f48057d36fb9c728… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py Log Message: ----------- Add test case for importing a workflow with missing tool. Commit: bed79b5e6a90965c0c0ba73a3c14851319ab90d2 https://github.com/galaxyproject/galaxy/commit/bed79b5e6a90965c0c0ba73a3c14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix importing pre-16.01 workflows with missing tools. Fixes #1386 (thanks to @trevor for the bug report). Test with: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_import_missing_tool ``` Commit: c9870cb89d92f52d04d5dd163c340dd4f6cf499c https://github.com/galaxyproject/galaxy/commit/c9870cb89d92f52d04d5dd163c34… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Fix url formatting Commit: 607db31b0432c4bf30d84a4662aa0cc0f9cd3442 https://github.com/galaxyproject/galaxy/commit/607db31b0432c4bf30d84a4662aa… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #1415 from guerler/fix_url_001 Fix url formatting Commit: 603cb2f18dfc1f4518066e514f660f7db91eb45d https://github.com/galaxyproject/galaxy/commit/603cb2f18dfc1f4518066e514f66… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: A config/plugins/tours/core.history.yaml Log Message: ----------- Add history tour from @bgruening Commit: 28cf2822f7bb3497cedee1951c22ca21e3aca956 https://github.com/galaxyproject/galaxy/commit/28cf2822f7bb3497cedee1951c22… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/managers/workflows.py A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py Log Message: ----------- Merge pull request #1416 from jmchilton/workflow_missing_tool_import Fix importing pre-16.01 workflows with missing tools. Commit: 1c21ba82417f2a6d3e8d024ccd3a60a3416f5340 https://github.com/galaxyproject/galaxy/commit/1c21ba82417f2a6d3e8d024ccd3a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables. Commit: 9bbe4b869e000e0b86e85e19743390c0bed77d57 https://github.com/galaxyproject/galaxy/commit/9bbe4b869e000e0b86e85e197433… Author: Lance Parsons <lparsons(a)yahoo.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Merge pull request #1 from natefoo/lparsons_galaxy_slots Prefer $SLURM_CPUS_ON_NODE for $GALAXY_SLOTS to other SLURM variables. Commit: 4c0bb9902ada3ed2dea7f1eeeb047aa4f9228be0 https://github.com/galaxyproject/galaxy/commit/4c0bb9902ada3ed2dea7f1eeeb04… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Merge pull request #1347 from lparsons/galaxy_slots Use both SLURM_NTASKS and SLURM_CPUS_PER_TASK to set GALAXY_SLOTS Commit: 7b45f7b4047377dc1e5c622a3dc6449e3c68f9ad https://github.com/galaxyproject/galaxy/commit/7b45f7b4047377dc1e5c622a3dc6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #1259 from markiskander/reporter_fixes Fixed indentation errors for Reports Commit: 5a441044fbc1b773f9a59f12050a8b7dcda11694 https://github.com/galaxyproject/galaxy/commit/5a441044fbc1b773f9a59f12050a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js M test/unit/tools/test_parameter_parsing.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #1308 from jmchilton/multi_collection_types Allow input collections to specify multiple collection types. Commit: d23541092070b3dff9ef18a56620fc93837d9233 https://github.com/galaxyproject/galaxy/commit/d23541092070b3dff9ef18a56620… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Remove tour id from tour; unique and namespaced by filename and not a separate identifier. Commit: e243fe3bc1e66dfcb9de778e66ff99028c56f358 https://github.com/galaxyproject/galaxy/commit/e243fe3bc1e66dfcb9de778e66ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Slight refactoring, fix .yaml stripping bug. Commit: 0ef88e1e5397bc094a4a0f9f9683fdaffab35f48 https://github.com/galaxyproject/galaxy/commit/0ef88e1e5397bc094a4a0f9f9683… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add tour reloading API endpoint. Commit: 6cea5121b1159a1966647dafb8d7930e9c5ee53c https://github.com/galaxyproject/galaxy/commit/6cea5121b1159a1966647dafb8d7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix conda installation in debug mode Commit: b9faf84b245a39780373545f778586bcc9ace916 https://github.com/galaxyproject/galaxy/commit/b9faf84b245a39780373545f7785… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: A test/api/test_tours.py Log Message: ----------- Stub an API test for tours so I can refactor a little. Commit: 01fed4b6d4d473d81fe2e89ee8199b00d0815a00 https://github.com/galaxyproject/galaxy/commit/01fed4b6d4d473d81fe2e89ee819… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Allow .yml extensions. Though not the "official" extension for YAML files, it is actually seen much more common in the wild. Commit: b35a39bd55d088fa25d2b3999fa482b83055f38a https://github.com/galaxyproject/galaxy/commit/b35a39bd55d088fa25d2b3999fa4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tours.py Log Message: ----------- Prefer self.app to trans.app. See comments here https://github.com/galaxyproject/galaxy/pull/1392#commitcomment-15141262 for instance for argument why this is superior. Commit: da8b943f538d55c2d8290870eb19210c831cb627 https://github.com/galaxyproject/galaxy/commit/da8b943f538d55c2d8290870eb19… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/visualizations/charts/templates/charts.mako M config/tool_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/binary.py A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py A lib/galaxy/tools/parameters/wrapped_json.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/directory_hash.py M lib/galaxy/util/expressions.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/topsort.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/tool_util.py M run.sh M run_tests.sh M scripts/common_startup.sh M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/onload.js.map M static/maps/utils/uploadbox.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/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/onload.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/admin/reload_tool.mako M templates/webapps/galaxy/galaxy.masthead.mako A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-app.js A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/test_routes.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge. Commit: 7587809bb6f08a1ff4754b8d13b8ebfafaabc259 https://github.com/galaxyproject/galaxy/commit/7587809bb6f08a1ff4754b8d13b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py Log Message: ----------- Improve tour directory logic. - Refactor plugin framework logic for finding configuration directories out into util. - Rework tours to use the plugin framework logic to parse configuration directories. - Rework tour logic to allow multiple tour configuration directories. - Fix up config.ini.sample comments on interactive environments and tours to reflect these changes and include more information like the viz directory does. Commit: c97053a5e844ff19b628f65282a1392c86240b0a https://github.com/galaxyproject/galaxy/commit/c97053a5e844ff19b628f65282a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #1421 from galaxyproject/conda_install_fix Fix conda installation in debug mode Commit: c28d4d01eef483a2c8255f1ac14d636ab60351a7 https://github.com/galaxyproject/galaxy/commit/c28d4d01eef483a2c8255f1ac14d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Correctly specify default tour location. Commit: 4ef3e21c954a8bfe5b12758252ffcb5b303445f8 https://github.com/galaxyproject/galaxy/commit/4ef3e21c954a8bfe5b12758252ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Fix onclick handling broken w/ #1407 Commit: 62b80dfcc5e00ee92c2be83bbd89911158b9f9b4 https://github.com/galaxyproject/galaxy/commit/62b80dfcc5e00ee92c2be83bbd89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map 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/menu.js Log Message: ----------- Fix onclick broken in #1407 Commit: c416426522c7cf8f684f12937a42354abd4ce875 https://github.com/galaxyproject/galaxy/commit/c416426522c7cf8f684f12937a42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py Log Message: ----------- Remove dup NiceConfigParser from loadwsgi.py. We are really adopting pastescript as our own. Commit: 39f5c5d207f091f214b87d391a5aefb47402b9fc https://github.com/galaxyproject/galaxy/commit/39f5c5d207f091f214b87d391a5a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make docutils an optional dependency of galaxy-lib. Commit: 951b95e07964885e2fac88b685f498aca2f3e7fc https://github.com/galaxyproject/galaxy/commit/951b95e07964885e2fac88b685f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/multi_byte.py Log Message: ----------- Make wchartype an optional dependency of galaxy-lib. Commit: 099f1447a66631250f61f5b61920f9b11018daa2 https://github.com/galaxyproject/galaxy/commit/099f1447a66631250f61f5b61920… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map 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/menu.js Log Message: ----------- Merge pull request #1424 from dannon/fix_onclick Fix masthead/menu.js onclick functionality Commit: 5c765c08715c17c07c1916c8c7a484d8ef71a954 https://github.com/galaxyproject/galaxy/commit/5c765c08715c17c07c1916c8c7a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'dev' into interactive_tours Commit: 1d97e4271ef40969bb117e424691418ccecec7a2 https://github.com/galaxyproject/galaxy/commit/1d97e4271ef40969bb117e424691… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge dev to include menu/onclick fix. Commit: 884b1d42db8ca46dc5613e398cc22015a5384935 https://github.com/galaxyproject/galaxy/commit/884b1d42db8ca46dc5613e398cc2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map 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/ui/ui-frames.js Log Message: ----------- Change scratchbook close icon Commit: 1730c12f8d3ba9d7e32bfbd1625835ab0d7dae53 https://github.com/galaxyproject/galaxy/commit/1730c12f8d3ba9d7e32bfbd16258… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map 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/ui/ui-frames.js Log Message: ----------- Merge pull request #1425 from guerler/fix_close_icon_000 Change scratchbook close icon Commit: 1876ea6bb2565ccaf7f6475f9387e43f91e34bb5 https://github.com/galaxyproject/galaxy/commit/1876ea6bb2565ccaf7f6475f9387… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/tours.py A test/api/test_tours.py Log Message: ----------- Merge pull request #8 from jmchilton/interactive_tours Minor tweaks to interactive tours backend. Commit: 5924857c2c7e012875b9840811ab22b9d4935cfa https://github.com/galaxyproject/galaxy/commit/5924857c2c7e012875b9840811ab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Fix pre/postclick that got broken somewhere along the way w/ patches&merges. Commit: 9416e6f3f75513f8e86f741d5c2f322708abdb0b https://github.com/galaxyproject/galaxy/commit/9416e6f3f75513f8e86f741d5c2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Merge and resolve conflicts, rebuilding. Commit: 3d1b3f9806007e456ea5f409df5be96b69aabdb7 https://github.com/galaxyproject/galaxy/commit/3d1b3f9806007e456ea5f409df5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- How'd that get there? Commit: a1a549ea67b28679b079f4150cf6ce18bc87dd56 https://github.com/galaxyproject/galaxy/commit/a1a549ea67b28679b079f4150cf6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js Log Message: ----------- Re-add identifiers to masthead, new ones for scratchbook (thanks @guerler) Commit: 6bd854ebe428a69f2e5664448330b8a4b2aafe77 https://github.com/galaxyproject/galaxy/commit/6bd854ebe428a69f2e5664448330… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/bower.json M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/onload.js M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/galaxy.ini.sample A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/onload.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 A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/upload/upload-button.js M static/scripts/onload.js A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako A test/api/test_tours.py Log Message: ----------- Merge pull request #1422 from dannon/interactive_tours Interactive Tours Commit: 634a5b7fd9f289c09a963f19a9db36937fc301c9 https://github.com/galaxyproject/galaxy/commit/634a5b7fd9f289c09a963f19a9db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/properties.py Log Message: ----------- Merge pull request #1413 from jmchilton/lib_0 Copy pastescript's NiceConfigParser into galaxy.util.properties. Commit: 0bad80ebdf2a36ae23e05b1dee6152ee387b3b79 https://github.com/galaxyproject/galaxy/commit/0bad80ebdf2a36ae23e05b1dee61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1182 from yhoogstrate/bam_cram_index_via_pysam cram datatype: crai index via pysam Commit: 8bd293683bd2144a877ec7206c003d52892c5796 https://github.com/galaxyproject/galaxy/commit/8bd293683bd2144a877ec7206c00… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py Log Message: ----------- Merge pull request #1427 from jmchilton/lib-deps Revise galaxy-lib dependencies. Commit: 237ecc77898f90d8d2d5d95741ff6fbaecc9e936 https://github.com/galaxyproject/galaxy/commit/237ecc77898f90d8d2d5d95741ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-template.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/tool/tool-template.js M static/style/blue/base.css Log Message: ----------- Add form help class Commit: 1568c0db809988599f10aebe1a24457087a49a1d https://github.com/galaxyproject/galaxy/commit/1568c0db809988599f10aebe1a24… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- fix title_default to work as a default and not an override Commit: ddc2a12eb18e036e2e5cad072eb4ea99328ec7b2 https://github.com/galaxyproject/galaxy/commit/ddc2a12eb18e036e2e5cad072eb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-template.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/tool/tool-template.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1428 from guerler/add_pseudo_class_000 Add form help class Commit: 0ae86f59a1f491eaa022676cdac76fce251eb322 https://github.com/galaxyproject/galaxy/commit/0ae86f59a1f491eaa022676cdac7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Merge pull request #1429 from dannon/interactive_tours fix title_default to work as a default and not an override Commit: b4fe6e2c3d9b77593f00ef6aa4a2e3611f3125ad https://github.com/galaxyproject/galaxy/commit/b4fe6e2c3d9b77593f00ef6aa4a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #1393 from erasche/requirements-hashes-round-3 Added hashes Commit: a0610ecdc0b070a671d4439378e3e9629b8d337e https://github.com/galaxyproject/galaxy/commit/a0610ecdc0b070a671d4439378e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.01.rc1 Commit: 291d7751707d2382c1d3a24b01fafec4ae757748 https://github.com/galaxyproject/galaxy/commit/291d7751707d2382c1d3a24b01fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1430 from natefoo/version-16.01 [16.01] Update version to 16.01.rc1 Commit: 073609d005d2e5d109e7f55b839058dce005ca95 https://github.com/galaxyproject/galaxy/commit/073609d005d2e5d109e7f55b8390… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Fix casper tests. Commit: 5d32c9f8fc7ef8f287df2a1047dc1c394d9d791d https://github.com/galaxyproject/galaxy/commit/5d32c9f8fc7ef8f287df2a1047dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Merge pull request #1439 from jmchilton/backport_casper_fixes [16.01] Fix casper tests. Commit: 7a3cc410549474de18ff195c0e1dcd76fa92f64b https://github.com/galaxyproject/galaxy/commit/7a3cc410549474de18ff195c0e1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix optional watchdog handling. Broken with 4086dd61dafe562ec01a8b1fce687a539aedbcfe. Thanks for bug report from @nsoranzo. Commit: e611b8fdb80beb87196a685924abe8e71bedcbea https://github.com/galaxyproject/galaxy/commit/e611b8fdb80beb87196a685924ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Use a more typical optional default value for optional import in watcher.py. Thanks to @nsoranzo for the advice - https://github.com/galaxyproject/galaxy/pull/1448#discussion_r49210125. Commit: d05ee507253901ef69a8892f6820b953c8d05725 https://github.com/galaxyproject/galaxy/commit/d05ee507253901ef69a8892f6820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Empty cherry-pick of 93c6d05 to cleanup merge. Commit: 47361f12ecaad83d5d563be763320ae1b17edc3b https://github.com/galaxyproject/galaxy/commit/47361f12ecaad83d5d563be76332… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Conflicts: lib/galaxy/tools/toolbox/base.py Commit: e8e01bdfb19cf1cc8f8cf485762c68d3f8e2f352 https://github.com/galaxyproject/galaxy/commit/e8e01bdfb19cf1cc8f8cf485762c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Conflicts: lib/galaxy/tools/toolbox/base.py Commit: 90bed00ebe8a5b4a7e0aeb61c23c991daae03fb8 https://github.com/galaxyproject/galaxy/commit/90bed00ebe8a5b4a7e0aeb61c23c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge 15.07 into 15.10. Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Conflicts: client/galaxy/scripts/mvc/history/multi-panel.js lib/galaxy/webapps/galaxy/controllers/external_service.py lib/galaxy/webapps/galaxy/controllers/forms.py lib/galaxy/webapps/galaxy/controllers/library_admin.py lib/galaxy/webapps/galaxy/controllers/request_type.py lib/galaxy/webapps/galaxy/controllers/requests_admin.py lib/galaxy/webapps/galaxy/controllers/requests_common.py lib/galaxy/webapps/galaxy/controllers/visualization.py lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/controllers/sample_tracking.py lib/galaxy/webapps/reports/controllers/workflows.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/grids/repository_review_grids.py static/maps/mvc/history/multi-panel.js.map static/maps/mvc/ui/ui-select-default.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/collection/list-of-pairs-collection-creator.js static/scripts/mvc/dataset/dataset-li-edit.js static/scripts/mvc/dataset/dataset-li.js static/scripts/mvc/history/history-panel.js static/scripts/mvc/history/multi-panel.js static/scripts/mvc/list/list-panel.js static/scripts/mvc/ui/ui-select-default.js Commit: dff94d743fd6e438f069deae5c9e8479357190cc https://github.com/galaxyproject/galaxy/commit/dff94d743fd6e438f069deae5c9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- "Fix" collection outputs to hide the HDAs in the history. Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also. Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem. xref https://github.com/galaxyproject/tools-iuc/pull/412/files Conflicts: lib/galaxy/tools/actions/__init__.py Commit: 88a1e636b8dea04a0db7d557fa6eb1483097b69d https://github.com/galaxyproject/galaxy/commit/88a1e636b8dea04a0db7d557fa6e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #1448 from jmchilton/watcher_fix [16.01] Fix optional watchdog handling. Commit: e36d33ce74babd939b3e70f30f0bf84f3cd2e527 https://github.com/galaxyproject/galaxy/commit/e36d33ce74babd939b3e70f30f0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1451 from jmchilton/release_16.01_merge_0 [16.01] Empty cherry-pick of 93c6d05 to cleanup merge 15.10 -> 16.01 Commit: f8a7ac082036995573f849b12f64f6d4fbfb8b6b https://github.com/galaxyproject/galaxy/commit/f8a7ac082036995573f849b12f64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/extract.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-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/mvc/collection/list-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge release_15.10 into release_16.01. Conflicts: eggs.ini lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/toolbox/base.py static/maps/mvc/collection/list-collection-creator.js.map static/maps/mvc/library/library-foldertoolbar-view.js.map static/maps/utils/uploadbox.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/library/library-foldertoolbar-view.js static/scripts/utils/uploadbox.js test/base/twilltestcase.py test/functional/tools/samples_tool_conf.xml Commit: c13b1c088cfbb0c708b2ce1d9068c704aba6cc95 https://github.com/galaxyproject/galaxy/commit/c13b1c088cfbb0c708b2ce1d9068… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1458 from jmchilton/release_15.10_merge_0 [15.10] Merge 15.07 into 15.10. Commit: bb8f0f75efb971471fa65c2cc6951bfaa00b0fd0 https://github.com/galaxyproject/galaxy/commit/bb8f0f75efb971471fa65c2cc695… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1455 from jmchilton/release_16.01_merge_1 [16.01] Merge #1314 forward into 16.01. Commit: 0403a3175cbbdf45c76b8db31549ae7ec734b1ce https://github.com/galaxyproject/galaxy/commit/0403a3175cbbdf45c76b8db31549… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Fix refactoring from 7587809b Commit: 71aef50d25646325aca1eefab79f5cfff93246c3 https://github.com/galaxyproject/galaxy/commit/71aef50d25646325aca1eefab79f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #1461 from jmchilton/release_16.01 [16.01] Merge more of 15.10 forward. Commit: 252586f86cfe0467244472d75483cd182556bfef https://github.com/galaxyproject/galaxy/commit/252586f86cfe0467244472d75483… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-01-10 (Sun, 10 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- improve default tours Commit: 3dda415fb9f516630f360aba5a9cd562ee70e680 https://github.com/galaxyproject/galaxy/commit/3dda415fb9f516630f360aba5a9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M static/maps/mvc/history/history-view-edit.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-edit.js Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into release_16.01_merge_4 Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: d2702e9e4448a008b8d49744f549c160c7023ee1 https://github.com/galaxyproject/galaxy/commit/d2702e9e4448a008b8d49744f549… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix spelling mistake spotted by Nicola Commit: 54dca064fafca929ccd16625797a1eafe21da391 https://github.com/galaxyproject/galaxy/commit/54dca064fafca929ccd16625797a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.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-edit.js Log Message: ----------- UI, Multi-history: fix drop event handler to use dataTransfer of original event Commit: 107ce1986f62eaeb1fb26a49921d8e1cbc53c958 https://github.com/galaxyproject/galaxy/commit/107ce1986f62eaeb1fb26a49921d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #1464 from bgruening/tours+ Improve default tours Commit: 66c94125ee258baf6578b439e9fb4b33f2bd5499 https://github.com/galaxyproject/galaxy/commit/66c94125ee258baf6578b439e9fb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Copy workflow objects when importing them. If not anywhere workflow.stored_workflow is checked will be broken. Commit: cea1f9e617b9375e3a01b7b4bf7804d0d0117cee https://github.com/galaxyproject/galaxy/commit/cea1f9e617b9375e3a01b7b4bf78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.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-edit.js Log Message: ----------- Merge pull request #1468 from carlfeberhard/fix.multihistory-drop [16.01] UI, Multi-history: fix drop event handler to use dataTransfer of orig… Commit: 24cb97cdbf9672ea09748a58c3d6d14b97704958 https://github.com/galaxyproject/galaxy/commit/24cb97cdbf9672ea09748a58c3d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/extract.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-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/mvc/collection/list-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #1462 from jmchilton/release_16.01_merge_4 [16.01] Full merge of 15.10 into 16.01. Commit: 9dc9ddf8cdede7c62d4ba5f00283675b872891e4 https://github.com/galaxyproject/galaxy/commit/9dc9ddf8cdede7c62d4ba5f00283… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Add --replace-pip option to common_startup.sh. Needed to restore correct functionality to planemo. Commit: 8fd83df6652a40882bcc3ca8a1db917887b71c11 https://github.com/galaxyproject/galaxy/commit/8fd83df6652a40882bcc3ca8a1db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Allow override of location of virtual env Galaxy manages. Commit: 55677f2d3db723c023540b8d640563a9f3ca04c5 https://github.com/galaxyproject/galaxy/commit/55677f2d3db723c023540b8d6405… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Fix to ensure integrity of tool_script.sh also. Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected. Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable. Commit: b559cf303c1b14aa862ba394d7bc868bc517db5a https://github.com/galaxyproject/galaxy/commit/b559cf303c1b14aa862ba394d7bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M setup.cfg Log Message: ----------- Drop E731 from flake8 enforcement (though we should revisit this and see if we *do* want to follow this or not) Commit: 2f1dbeee68ddd75a561fe0f463d5b9968278ef13 https://github.com/galaxyproject/galaxy/commit/2f1dbeee68ddd75a561fe0f463d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M test/casperjs/casperjs_runner.py Log Message: ----------- Address W503 and E721 errors now enforced by pep8 1.7. Commit: 86158cbc7fb601d0f3563fa2bea67e23b464db93 https://github.com/galaxyproject/galaxy/commit/86158cbc7fb601d0f3563fa2bea6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M setup.cfg M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #1487 from dannon/release_16.01 [16.01] Cherrypick of pep8 fixes. Commit: becffe93a3f78ca74b5d093974844a3634e1ed6b https://github.com/galaxyproject/galaxy/commit/becffe93a3f78ca74b5d09397484… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M run.sh M run_tests.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #1485 from jmchilton/common_startup_fixes [16.01] Fix common_startup options for planemo. Commit: 37f8038d63f8243151e817e9d564f90c58772c1f https://github.com/galaxyproject/galaxy/commit/37f8038d63f8243151e817e9d564… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map 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/menu.js Log Message: ----------- Undo user icon in masthead Commit: 9d91be8dd3b84a5b37b6010cbb31df7070fb6170 https://github.com/galaxyproject/galaxy/commit/9d91be8dd3b84a5b37b6010cbb31… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M requirements.txt Log Message: ----------- Pin release wheel verisons. pinned-requirements.txt renamed to pinned-hashed-requirements.txt as unfortunately even Galaxy pip does not support --hash Commit: 0bcfa74ea1e0eb57927bd1850feb9331489af6bc https://github.com/galaxyproject/galaxy/commit/0bcfa74ea1e0eb57927bd1850feb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Fixes the issue of losing newlines and actual spacing (i.e. do not treat as html). Commit: cb09c35a07e3b9f8ca7e4eb5e8d37ffacdee6253 https://github.com/galaxyproject/galaxy/commit/cb09c35a07e3b9f8ca7e4eb5e8d3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix line wrapping for peek of tabular files. Commit: f78756cb79f294689227e0222c8b75f3100047b5 https://github.com/galaxyproject/galaxy/commit/f78756cb79f294689227e0222c8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix a few problems discovered through planemo. Including 'TypeError: _get_config_option() got multiple values for keyword argument 'prefix' and problem when planemo's cwltool is installed in Galaxy's virtualenv. Commit: 9d52a4a31dd9e660855bf1e12bd07d3c49b73fd9 https://github.com/galaxyproject/galaxy/commit/9d52a4a31dd9e660855bf1e12bd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map 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/menu.js Log Message: ----------- Merge pull request #1493 from guerler/undo_user_000 [16.01] Undo user icon in masthead Commit: 4b5b970d7898a33faca5557b4382ddc9d3923ae6 https://github.com/galaxyproject/galaxy/commit/4b5b970d7898a33faca5557b4382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Fix disabled css Commit: 2e62388b2f34ad83f215bb3eff4c6ae5b1efd7b7 https://github.com/galaxyproject/galaxy/commit/2e62388b2f34ad83f215bb3eff4c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #1494 from jmchilton/tool_command_integrity [16.01] Fix to ensure integrity of tool_script.sh also. Commit: 3e47aa23b8426e21f5dac573f6eb96bfeac550b6 https://github.com/galaxyproject/galaxy/commit/3e47aa23b8426e21f5dac573f6eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Switch to bash as default shell (for conda resolver). I'm making more things configurable in case someday the BSD user wants to use Galaxy - the default shell for jobs can be configured at the galaxy or job destination level now. Commit: e69638277fc4e0c56347e51ed77f93c1f9261ecf https://github.com/galaxyproject/galaxy/commit/e69638277fc4e0c56347e51ed77f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M test/functional/tools/output_action_change_format.xml Log Message: ----------- Fix tab problem in test tool. dash will convert the literal characters \t to a tab, bash doesn't seem to do this. Use portable printf as suggested by nicola. Commit: 602dc7f6649d96086b85ed0d309eef7c4ed73a13 https://github.com/galaxyproject/galaxy/commit/602dc7f6649d96086b85ed0d309e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Switch default job shell back to /bin/sh for 16.01. Commit: 0902c23f3491b4840b649a203315939d0c7caa8c https://github.com/galaxyproject/galaxy/commit/0902c23f3491b4840b649a203315… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #1501 from guerler/fix_disabled_000 [16.01] Fix disabled css Commit: eb3fc642fc1bddaeb5aaec3d4dbba8efd0ab398d https://github.com/galaxyproject/galaxy/commit/eb3fc642fc1bddaeb5aaec3d4dbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1498 from blankenberg/tab_mime [16.01] Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Commit: 7de3bcdd7e4ecfbe4202bff1ad69a0d8b6b716cc https://github.com/galaxyproject/galaxy/commit/7de3bcdd7e4ecfbe4202bff1ad69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M requirements.txt Log Message: ----------- Merge pull request #1495 from natefoo/pin-release-wheels [16.01] Pin release wheel versions Commit: 1dac5f3bb63f7b34e7a84ae79d3eb60089712d0b https://github.com/galaxyproject/galaxy/commit/1dac5f3bb63f7b34e7a84ae79d3e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #1502 from jmchilton/planemo_fix [16.01] Fix a few problems discovered through planemo. Commit: be4ddb26d4c448bee8f797b9972360c93cae33fc https://github.com/galaxyproject/galaxy/commit/be4ddb26d4c448bee8f797b99723… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M test/functional/tools/output_action_change_format.xml M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #1473 from jmchilton/job_shell [16.01] Allow override of job shell (for conda resolver). Commit: 95d00b4174efd23b0ad9c350d3463bf9d696d8cc https://github.com/galaxyproject/galaxy/commit/95d00b4174efd23b0ad9c350d346… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix MIMEText usage in galaxy.util Commit: e397ebba585ed578798645ee9352b891e3055372 https://github.com/galaxyproject/galaxy/commit/e397ebba585ed578798645ee9352… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1509 from dannon/release_16.01 Fix MIMEText usage in galaxy.util Commit: 3ee94d58e0f24d3812ac59ef91b43e24856db45b https://github.com/galaxyproject/galaxy/commit/3ee94d58e0f24d3812ac59ef91b4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- catch Exception and properly log errors Commit: c143d659d4f7b598bc89a9d06b8040dff39a1b85 https://github.com/galaxyproject/galaxy/commit/c143d659d4f7b598bc89a9d06b80… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Revise tool caching to be less broken. Just switch the default for tool caching and only cache during initial loads of tool panels - as during a toolbox refresh. This should mean that all code from tool shed will ignore the cache and should fix #1515. Additionally, reloading the tool was broken since if would call the load tool code and then just trust the cache. This should fix tool reloading as well. Commit: 12445a0524510dbafffa4c7908e243f70c55f154 https://github.com/galaxyproject/galaxy/commit/12445a0524510dbafffa4c7908e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- use log.exception instead of log.error to retain the stacktrace Commit: 3d1ad5ad8dab30aa6c6372fbe85a0c3c7d198d61 https://github.com/galaxyproject/galaxy/commit/3d1ad5ad8dab30aa6c6372fbe85a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #1511 from martenson/log-user-exceptions-properly [16.01] catch Exception and properly log errors Commit: ae2ee4a4432b55a4b0fbdd218bc34f88f7ad1b2b https://github.com/galaxyproject/galaxy/commit/ae2ee4a4432b55a4b0fbdd218bc3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1517 from jmchilton/tool_cache_fixes [16.01] Tool cache fixes Commit: 817f36626d7e720b0dbb63d0071f2889146c1c41 https://github.com/galaxyproject/galaxy/commit/817f36626d7e720b0dbb63d0071f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Merge pull request #1474 from jmchilton/workflow_copy [16.01] Copy workflow objects when importing them. Commit: fc434d62e971df92bc51b296d119030ca85af303 https://github.com/galaxyproject/galaxy/commit/fc434d62e971df92bc51b296d119… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Handle unvalidated values in depth Commit: 0e9302127f4478611170dee237d811e072100e99 https://github.com/galaxyproject/galaxy/commit/0e9302127f4478611170dee237d8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-01-16 (Sat, 16 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- sourcing Conda will write to stderr, we need to redirect it to stdout Commit: a77403cc9e6ef2d90ba78822afca601eed09e6ec https://github.com/galaxyproject/galaxy/commit/a77403cc9e6ef2d90ba78822afca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #1527 from bgruening/release_16.01 Sourcing Conda will write to stderr Commit: 16e0bc08c8333c75c05a1a47de57eed8196bf9d9 https://github.com/galaxyproject/galaxy/commit/16e0bc08c8333c75c05a1a47de57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1526 from guerler/fix_unvalidated_001 [16.01] Handle unvalidated values in depth Commit: eca2c3bcee2c9f05dee062c60607251a589a93fd https://github.com/galaxyproject/galaxy/commit/eca2c3bcee2c9f05dee062c60607… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M test/api/test_workflows.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Failing test case to exhibit #1514. Commit: f1394d250db103eda0bc88044eaa92f54f56476c https://github.com/galaxyproject/galaxy/commit/f1394d250db103eda0bc88044eaa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Fix #1514. Prior to PR #1302 workflows wouldn't validate call validate at all on inputs. 1302 was perhaps an over correction that causes validate to be called on datasets that aren't yet READY but require metadata. This rolls that back somewhat, other parameters will still validate - but validation asserting the existence of metadata won't get called in workflows. This is still not ideal but after 1302 and this - we are still in a better, more secure place than beforehand. One might argue that since we need to introduce a new validation point (right before a job is scheduled and set to QUEUED) - that we would be better off rolling back #1302 entirely. I've considered that, but I still think it is better to fail fast on the other problems, also I would rather call the validation code too many times than not enough and it would be very late in the release cycle for such a change. Commit: 3f51101527fee096761a4c22ee8841e64b98f7a6 https://github.com/galaxyproject/galaxy/commit/3f51101527fee096761a4c22ee88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Attempt to fix #1531. I was unable to reproduce #1531 in testing, but if the problem is something to do with stale state the following sledge hammer should fix it. Runt the new test case with: ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_delete_intermediate_datasets_pja_1 Commit: cd95635197eddaeee55be88f96543dc3a97e9343 https://github.com/galaxyproject/galaxy/commit/cd95635197eddaeee55be88f9654… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1538. Displaying subcollection mapping in tool forms was broken with #1308 - this fixes that I believe. Commit: bbff72e0ce9876b495971d20223780f1244d1f03 https://github.com/galaxyproject/galaxy/commit/bbff72e0ce9876b495971d202237… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix upgrade messages Commit: 035a67d0b5a1deeb54592937150a9ae82fab997e https://github.com/galaxyproject/galaxy/commit/035a67d0b5a1deeb54592937150a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Keep track of hidden datasets Commit: 1b43e8d68ffd44780f552e2472010d02dbc274b6 https://github.com/galaxyproject/galaxy/commit/1b43e8d68ffd44780f552e247201… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Logging fix. Commit: 093f1f2712eeaa3c4a23952e2488a9a7a6731b17 https://github.com/galaxyproject/galaxy/commit/093f1f2712eeaa3c4a23952e2488… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Make sciex sniffer tighter. Otherwise a bed file easily could sniff as sciex. Commit: 58d75f4bc2e4e52b9f4541d20c1253e49735a22f https://github.com/galaxyproject/galaxy/commit/58d75f4bc2e4e52b9f4541d20c12… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #1550 from guerler/fix_upgrade_000 [16.01] Fix upgrade messages Commit: a00faba4fefabd1e28f3ce58603c9f99abf9a4f8 https://github.com/galaxyproject/galaxy/commit/a00faba4fefabd1e28f3ce58603c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #1551 from guerler/fix_hidden_rerun_000 [16.01] Keep track of hidden datasets Commit: 17abd4a30d41ff070202c1818ad84c015a642733 https://github.com/galaxyproject/galaxy/commit/17abd4a30d41ff070202c1818ad8… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py M test/api/test_workflows.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1536 from jmchilton/issue_1514 [16.01] Test case and fix for issue #1514 Commit: 2fc982027cb3de555afbd1650b52dbd84897956a https://github.com/galaxyproject/galaxy/commit/2fc982027cb3de555afbd1650b52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Merge pull request #1553 from jmchilton/logging_fix [16.01] Logging fix. Commit: e48388ef6cca6505d47b3daf3c2e0c4a5041b3f4 https://github.com/galaxyproject/galaxy/commit/e48388ef6cca6505d47b3daf3c2e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1545 from jmchilton/subcollection_mapping_problem [16.01] Fix #1538. Commit: 8ceb4d8ee495d21a664e3faece1e072a88048494 https://github.com/galaxyproject/galaxy/commit/8ceb4d8ee495d21a664e3faece1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Force --skip-venv if we can detect that Python is Conda Python. Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Commit: fe96255022f4fdf72f39be959a15993d014a0d38 https://github.com/galaxyproject/galaxy/commit/fe96255022f4fdf72f39be959a15… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1554 from natefoo/conda-interop [16.01] Force --skip-venv if we can detect that Python is Conda Python. Commit: f5fbe1c5020fb432346ce6340833937d13cbf6d0 https://github.com/galaxyproject/galaxy/commit/f5fbe1c5020fb432346ce6340833… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/visualization/visualization-model.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/visualization/visualization-model.js Log Message: ----------- Client: remove older compiled backbone/backbone.js, update scatterplot and charts for same; Visualizations: fix visualization-model url; Scatterplot: fix title bug and Galaxy var Commit: c8b0057349be9a683e295c073f66163f47c257e7 https://github.com/galaxyproject/galaxy/commit/c8b0057349be9a683e295c073f66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-requirements.txt Log Message: ----------- Add a requirements file suitable for use with `conda {create,install} --file`. Commit: 1b7462644d0352d44b36e2d790d6d10d906e7be4 https://github.com/galaxyproject/galaxy/commit/1b7462644d0352d44b36e2d790d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/visualization/visualization-model.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/visualization/visualization-model.js Log Message: ----------- Merge pull request #1558 from carlfeberhard/release_16.01 [16.01] Fix redundant backbone and visualizations Commit: bc9f9b9bf1de555db3a56b50a6655862f3cb4c73 https://github.com/galaxyproject/galaxy/commit/bc9f9b9bf1de555db3a56b50a665… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Adapt release notes boot strap to new issues. Commit: 528f80e40b7f7d729ce0761a25315b2a140f758a https://github.com/galaxyproject/galaxy/commit/528f80e40b7f7d729ce0761a2531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst Log Message: ----------- Auto-generate 16.01 release notes. Commit: 4064bbf94f6d167d62e65b5fed988fb4232fd6ca https://github.com/galaxyproject/galaxy/commit/4064bbf94f6d167d62e65b5fed98… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- 16.01 release notes. Commit: f0b5f7757e4df3226db30271e64646c828306aad https://github.com/galaxyproject/galaxy/commit/f0b5f7757e4df3226db30271e646… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- add link to Main tour; add sentence to WF nesting Commit: 79dfff4d65a6e8a2e102aae5d9af129c445fe9a5 https://github.com/galaxyproject/galaxy/commit/79dfff4d65a6e8a2e102aae5d9af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Typo discovered by @nsoranzo Commit: c117d400506e605c41e3837b83d79593733c5af0 https://github.com/galaxyproject/galaxy/commit/c117d400506e605c41e3837b83d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1557 from jmchilton/sciex_sniff [16.01] Tighten up ScIdx sniffer. Commit: 281a53d97567dbc5458b47e283f891e91b680bc9 https://github.com/galaxyproject/galaxy/commit/281a53d97567dbc5458b47e283f8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Small RST fixes. Commit: 08fbd8923af0ba5012e23a774adea7e878ea2047 https://github.com/galaxyproject/galaxy/commit/08fbd8923af0ba5012e23a774ade… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Merge some entries. Add some missing PRs. Commit: dc801dc1f6097b283e01c784d09261b3c4ee21e5 https://github.com/galaxyproject/galaxy/commit/dc801dc1f6097b283e01c784d092… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst Log Message: ----------- Add admin documentation for framework dependencies (wheels) for the 16.01 release. Commit: 35f90da20ca21a8f82d1650c0cf520a064b6bd8a https://github.com/galaxyproject/galaxy/commit/35f90da20ca21a8f82d1650c0cf5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Merge pull request #1542 from jmchilton/did_fix [16.01] Attempt to fix #1531. Commit: 1486af0ef90a186b5648f737af32e84640263857 https://github.com/galaxyproject/galaxy/commit/1486af0ef90a186b5648f737af32… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-environment.txt R lib/galaxy/dependencies/conda-requirements.txt Log Message: ----------- Rename conda-requirements.txt to conda-environment.txt since it is not a requirements file, include instructions on how to install remaining dependencies from pip. Commit: 9827f32775b34a566c887963103a1f921e2b7a95 https://github.com/galaxyproject/galaxy/commit/9827f32775b34a566c887963103a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- conda-requirements.txt renamed to conda-environment.txt Commit: c2d94c43bbd5929d4773e859dc1f5d8e436b0ee8 https://github.com/galaxyproject/galaxy/commit/c2d94c43bbd5929d4773e859dc1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge pull request #1560 from natefoo/conda-interop [16.01] Add a requirements file suitable for use with `conda {create,install} --file` Commit: 168f453094d546cd1552a1a179decc4914c1d93a https://github.com/galaxyproject/galaxy/commit/168f453094d546cd1552a1a179de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Suggest installing virtualenv from brew Commit: 954aff7fa806ee77682476ac56ec95027482bb0c https://github.com/galaxyproject/galaxy/commit/954aff7fa806ee77682476ac56ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst Log Message: ----------- Merge pull request #1589 from natefoo/admin-docs [16.01] Add admin documentation for framework dependencies (wheels) Commit: b1ae5d8c67f1565084eb811a8e84632718ac5543 https://github.com/galaxyproject/galaxy/commit/b1ae5d8c67f1565084eb811a8e84… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- UI, users: allow '/user' and '/user/' to default controller and correctly return the user/index.mako template (preventing an internal error) Commit: 390c1fc275ba7128f22f533b0b512b0bc517e521 https://github.com/galaxyproject/galaxy/commit/390c1fc275ba7128f22f533b0b51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Always install a specific version of Galaxy pip in common_startup.sh. Commit: 55f67e59d654588ff0fca9e168e8f5e1411af50a https://github.com/galaxyproject/galaxy/commit/55f67e59d654588ff0fca9e168e8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Core, HDCAs: fix 'copy_item_annotation' error when copying a history with an hdca by adding UsesAnnotations mixin to HDCA model Commit: d3277072cc49d9a7e50a9619e899c0796c2a808e https://github.com/galaxyproject/galaxy/commit/d3277072cc49d9a7e50a9619e899… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #1594 from carlfeberhard/release_16.01 [16.01] UI, users: allow '/user' and '/user/' to default controller and corre… Commit: c60ddc241b9bb92ea0c67fea16b2ec5fa415bceb https://github.com/galaxyproject/galaxy/commit/c60ddc241b9bb92ea0c67fea16b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1599 from carlfeberhard/fix.hdca-copy [16.01] Core, HDCAs: fix 'copy_item_annotation' error when copying a history … Commit: f499ec0cabefb62b87d43af223d0473e2528dcc7 https://github.com/galaxyproject/galaxy/commit/f499ec0cabefb62b87d43af223d0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #1585 from jmchilton/16.01_release_notes [16.01] Release notes for 16.01 Commit: 46471d61e4349bba2d0c702de18f91a5b201bb66 https://github.com/galaxyproject/galaxy/commit/46471d61e4349bba2d0c702de18f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- pip < 1.6 cannot parse requirement specifiers to the `install` command that contain a `+` in the version. For these older versions, directly install the wheel or install from the sdist. Technically 1.4 and later can install wheels, but in testing, only 1.5+ was able to install them properly with their scripts. The new heredoc execute and redirect syntax is Bourne-compatible. pip --pre is no longer necessary since the Galaxy pip version is no longer a development version of pip. Commit: 60062b020dc2b753e5b8f034272e0b982b8c2f6f https://github.com/galaxyproject/galaxy/commit/60062b020dc2b753e5b8f034272e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- pip 1.6 -> 6.0, thanks @nsoranzo Commit: 33ba1face9e1f1bf025f37dc4e508143972845dc https://github.com/galaxyproject/galaxy/commit/33ba1face9e1f1bf025f37dc4e50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Link from the 16.01 announcement to the Admin wheels documentation, document the process of adding new wheels. Commit: 27685377f629c536e56189e795bc91bb8caf0736 https://github.com/galaxyproject/galaxy/commit/27685377f629c536e56189e795bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1612 from natefoo/admin-docs [16.01] Additional documentation regarding wheels Commit: 685fd1560e98e6d885d6cf627b691d2228807974 https://github.com/galaxyproject/galaxy/commit/685fd1560e98e6d885d6cf627b69… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1595 from natefoo/fix-pip-wheel-version [16.01] Always install a specific version of Galaxy pip in common_startup.sh. Commit: 981f904c3f8a501ffabaf7b83538151070bd8a21 https://github.com/galaxyproject/galaxy/commit/981f904c3f8a501ffabaf7b83538… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py Log Message: ----------- Attempt to fix transiently failing test due to object store makedirs call. Failing test - https://jenkins.galaxyproject.org/job/docker-api/2421/testReport/junit/api.…. If you look at the actual source code for os.makedirs - it does inconsistently handle errno.EEXIST - this is probably a better approach than raw os.makedirs for most cases. xref #1617 Commit: 81535c5778b70001bfeb3da5690eba6426ea4638 https://github.com/galaxyproject/galaxy/commit/81535c5778b70001bfeb3da5690e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1500 from blankenberg/peek-fix [16.01] Fix line wrapping for peek of tabular files. Commit: 4ae49fbfec952a2087a9cf3f9b9940f86fd05220 https://github.com/galaxyproject/galaxy/commit/4ae49fbfec952a2087a9cf3f9b99… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Fix module/step border style in workflow canvas Commit: 44336b289bd5ba7d9911bf1c1fcc0a604fda7358 https://github.com/galaxyproject/galaxy/commit/44336b289bd5ba7d9911bf1c1fcc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1620 from guerler/fix_module_border_000 [16.01] Fix module/step border style in workflow canvas Commit: 17a1683a383d7f375b77371548ff7d349a561a96 https://github.com/galaxyproject/galaxy/commit/17a1683a383d7f375b77371548ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Warn on optional select test parameter. Commit: ade18b3cd23c54c347d38585736d32da5fccc4dd https://github.com/galaxyproject/galaxy/commit/ade18b3cd23c54c347d38585736d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1623 from jmchilton/makedirs [16.01] Attempt to fix transiently failing test due to objectstore makedirs … Commit: 30ccebfb0c8ef0809bbd3f1d2d64be5ac23bb3a2 https://github.com/galaxyproject/galaxy/commit/30ccebfb0c8ef0809bbd3f1d2d64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- remove forgotten util.params that fails when POSTing a payload{} dict (because it cannot sanitize dict in dict) Commit: 61818948a163602b3c135937d053fe42c46bb4d2 https://github.com/galaxyproject/galaxy/commit/61818948a163602b3c135937d053… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.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/form/form-section.js Log Message: ----------- Fix default option for repeats Commit: ee4f58ce7d6a81477e5e4fc3e544e5da909f1198 https://github.com/galaxyproject/galaxy/commit/ee4f58ce7d6a81477e5e4fc3e544… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.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/form/form-section.js Log Message: ----------- Merge pull request #1635 from guerler/fix_repeat_default_001 [16.01] Fix default option for repeats Commit: 9170865dfbe0f8588ec47449e683236e5ba92a39 https://github.com/galaxyproject/galaxy/commit/9170865dfbe0f8588ec47449e683… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1634 from martenson/remove-utilparams [16.01] libraries: remove forgotten util.params that fails when POSTing a payload {} Commit: ccdb027d38428a38d79b4272fadb076b7f428825 https://github.com/galaxyproject/galaxy/commit/ccdb027d38428a38d79b4272fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Prevent optional test parameters in conditionals Commit: 6fa7f1e1edda25ec36f2373148af223493924803 https://github.com/galaxyproject/galaxy/commit/6fa7f1e1edda25ec36f2373148af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Bump pysam to new 0.8.4+gx1. Commit: 508ebea63f2376b5a3b452148e4a6d3c18366b3b https://github.com/galaxyproject/galaxy/commit/508ebea63f2376b5a3b452148e4a… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #8 from jmchilton/fix_optional_001 Warn on optional select test parameter. Commit: afc5f2a45399c474d86f1530a62afe280a0eb3be https://github.com/galaxyproject/galaxy/commit/afc5f2a45399c474d86f1530a62a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix: Use dependency resolvers if any config exists. This way resolvers like the Module resolver work even if tool_dependency_dir is not set. Commit: 50ea4694af82ac33eaac1ddc9ca8aee1e71e1f00 https://github.com/galaxyproject/galaxy/commit/50ea4694af82ac33eaac1ddc9ca8… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Change python print() format to be backward compatible with older versions In python versions prior to 3.1, the print("{}", .format(x)) form throws an error, use the more compatible print("{0}", .format(x)) form instead. Commit: 85eccba79151a545af1e7aa07f24cece9c5398bd https://github.com/galaxyproject/galaxy/commit/85eccba79151a545af1e7aa07f24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M templates/user/info.mako M templates/user/username.mako Log Message: ----------- Public name is mandatory not optional, update help text. Commit: ba9ad97c40bd994e0dc51888ef235cf3b434168a https://github.com/galaxyproject/galaxy/commit/ba9ad97c40bd994e0dc51888ef23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- Fix 3.bam @PG header to use : instead of = as a key:value separator. See commentary in https://github.com/galaxyproject/galaxy/pull/1638 for more details. Commit: e4e48941a6174a148cde06ef2218ef6480568716 https://github.com/galaxyproject/galaxy/commit/e4e48941a6174a148cde06ef2218… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1651 from jmchilton/backport_print_fix [16.01] Backport print fix. Commit: 916ddb575f40c445a47cf91a58aad00bf9360ae8 https://github.com/galaxyproject/galaxy/commit/916ddb575f40c445a47cf91a58aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1648 from jmchilton/dependencies_conf [16.01] Fix use_tool_dependencies for non-default dependency_resolver_conf files. Commit: 6635e91170b310beafe629bc2956607234c41cb0 https://github.com/galaxyproject/galaxy/commit/6635e91170b310beafe629bc2956… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Bump gx pip version to fix OSX platform issues. Commit: 39eb262219beca9ec6b849b49c0430d834cfd2ae https://github.com/galaxyproject/galaxy/commit/39eb262219beca9ec6b849b49c04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16 Commit: 66f20e7df91074e07cbade57b20deb68cb840a55 https://github.com/galaxyproject/galaxy/commit/66f20e7df91074e07cbade57b20d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix method signature of bam.set_meta to include a positional argument which is now required. Commit: 05e68addbe846a8f39cd1192285f936df166bf35 https://github.com/galaxyproject/galaxy/commit/05e68addbe846a8f39cd1192285f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1652 from dannon/pip_bump [16.01] Bump gx pip version to fix OSX platform issues. Commit: 39aff8457201fc383d49cc8e90798795b7923189 https://github.com/galaxyproject/galaxy/commit/39aff8457201fc383d49cc8e9079… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M templates/user/info.mako M templates/user/username.mako Log Message: ----------- Merge pull request #1655 from jmchilton/public-name-fixes [16.01] Public name is mandatory not optional, update help text. Commit: d6325c5039f28062a2cf49d00c091d83a92865c3 https://github.com/galaxyproject/galaxy/commit/d6325c5039f28062a2cf49d00c09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Update data providers pysam.AlignmentFile usage Commit: a95827751f463f35c67e76f84127f850972244c5 https://github.com/galaxyproject/galaxy/commit/a95827751f463f35c67e76f84127… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1637 from guerler/fix_optional_001 [16.01] Prevent optional test parameters in conditionals Commit: 45f523f9229f6d943e3a65042b8cad0276a0a7d7 https://github.com/galaxyproject/galaxy/commit/45f523f9229f6d943e3a65042b8c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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: ----------- fix show_welcome_with_login = True Commit: b5d1c7721ee2f8ad1095e52d4e710b998f92945d https://github.com/galaxyproject/galaxy/commit/b5d1c7721ee2f8ad1095e52d4e71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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 #1664 from bgruening/release_16.01 fix `show_welcome_with_login = True` Commit: bf989f6051303658c6bc537fc1e00c877c55c6e1 https://github.com/galaxyproject/galaxy/commit/bf989f6051303658c6bc537fc1e0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- correct typo in text datatype Commit: cd3f3b330db34e294e78374e8e8b32300c66f36e https://github.com/galaxyproject/galaxy/commit/cd3f3b330db34e294e78374e8e8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/visualization/data_providers/genome.py M test-data/3.bam Log Message: ----------- Merge pull request #1638 from dannon/pysam_84_update Pysam 84 update [16.01] Commit: 04af1ae1c609c0b73afabaf2aeb58110043847e6 https://github.com/galaxyproject/galaxy/commit/04af1ae1c609c0b73afabaf2aeb5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Always use the python hashlib for verifying the virtualenv download in common_startup.sh rather than attempting to use sha256sum. Older versions of coreutils (such as in RHEL 6) did not include the --strict argument to sha256sum. Commit: 2641f0af9ac84f91ea0cf3e849b6e8348da8909d https://github.com/galaxyproject/galaxy/commit/2641f0af9ac84f91ea0cf3e849b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1668 from natefoo/venv-checksum [16.01] Always use the python hashlib method for verifying the virtualenv download Commit: bb95a65b2201509ce950d6c3c578f8d417f83cc4 https://github.com/galaxyproject/galaxy/commit/bb95a65b2201509ce950d6c3c578… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1666 from martenson/correct-datatype-typo [16.01] correct typo in text datatype Commit: 9551fc07b475b4095b7d002315cbc05bdf0925b5 https://github.com/galaxyproject/galaxy/commit/9551fc07b475b4095b7d002315cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL. Commit: 9ead68aeca6722f62d3d6fabae6484aa00246615 https://github.com/galaxyproject/galaxy/commit/9ead68aeca6722f62d3d6fabae64… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1669 from natefoo/scientificlinux-tag-compat [16.01] Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL Commit: 4b24d95f6f95124f357b72434a29113fa9bacf73 https://github.com/galaxyproject/galaxy/commit/4b24d95f6f95124f357b72434a29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Improve documentation about binary-compatibility.cfg. Resolves #1672. Commit: ada39dea6ab68be543f53feb7a30e97167d96013 https://github.com/galaxyproject/galaxy/commit/ada39dea6ab68be543f53feb7a30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- handle correctly application/json pased in POST Commit: 530501c682be85b595bd8115bc2fc0ebc53f57a0 https://github.com/galaxyproject/galaxy/commit/530501c682be85b595bd8115bc2f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix setting library permissions to accept JSON correctly Commit: 5dd839960e1ca5170b528c4c88ad8965eebde08b https://github.com/galaxyproject/galaxy/commit/5dd839960e1ca5170b528c4c88ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- unify api for library creation; support POST with url params Commit: edd8b222acac34cd2e35e768ab1cbd888b2fc824 https://github.com/galaxyproject/galaxy/commit/edd8b222acac34cd2e35e768ab1c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- catch value errors from id decoding Commit: 0398aafb1cf0aa0863d0867d20dd79a09bc2fb85 https://github.com/galaxyproject/galaxy/commit/0398aafb1cf0aa0863d0867d20dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix updating library API to not require payload and to properly handle optional params Commit: 4b51be57d114d840112970baccb979ec1876663b https://github.com/galaxyproject/galaxy/commit/4b51be57d114d840112970baccb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- allow specifying DELETE params in JSON Commit: c288b43627d3da925c5fe4b2fd0ebd5a7bc752b2 https://github.com/galaxyproject/galaxy/commit/c288b43627d3da925c5fe4b2fd0e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow creating folders with JSON payload Commit: 7867f3e0835a2cbd99658ad25debd9be278300f2 https://github.com/galaxyproject/galaxy/commit/7867f3e0835a2cbd99658ad25deb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folders.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- accept json as input for setting permissions; fix inconsistency by leveraging role_manager Commit: a4c2098da010d79a70a9425e8ccb6c1e69807442 https://github.com/galaxyproject/galaxy/commit/a4c2098da010d79a70a9425e8ccb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow PATCHing with payload in urlparams Commit: b46636a53f579fc6ffa63fbca888196bb0ff99f6 https://github.com/galaxyproject/galaxy/commit/b46636a53f579fc6ffa63fbca888… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- remove deletion of the payload dict item it is not necessary and the key does not have to exist Commit: 170c83e6c283e97b1e399bc122ee94ddb8cb34b4 https://github.com/galaxyproject/galaxy/commit/170c83e6c283e97b1e399bc122ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix unused imports and unused vars Commit: 9c7c75b7661989b5fe6f2e4819b04ae6e7b901a1 https://github.com/galaxyproject/galaxy/commit/9c7c75b7661989b5fe6f2e4819b0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Typo Commit: c693b69b344461bd428a0ef314b3ec985e1a60d9 https://github.com/galaxyproject/galaxy/commit/c693b69b344461bd428a0ef314b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Merge pull request #1677 from natefoo/admin-docs [16.01] Improve documentation about binary-compatibility.cfg Commit: 134d792c1fcfba5d09e2937074c3263792bea991 https://github.com/galaxyproject/galaxy/commit/134d792c1fcfba5d09e2937074c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- delete the 'payload' if it is in kwd so it is not supplied twice Commit: e7b6b4b13bd93a8520942c94d0ed28d110af261b https://github.com/galaxyproject/galaxy/commit/e7b6b4b13bd93a8520942c94d0ed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Revert "delete the 'payload' if it is in kwd so it is not supplied twice" This reverts commit 134d792c1fcfba5d09e2937074c3263792bea991. Commit: 5301269fbb54753e75969ecd446b8cb74c6093b6 https://github.com/galaxyproject/galaxy/commit/5301269fbb54753e75969ecd446b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- update docs of the data libraries API Commit: 5e77af198a9b81646dbe59a02b991d496b334967 https://github.com/galaxyproject/galaxy/commit/5e77af198a9b81646dbe59a02b99… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Commit: ef6bd90f20394f6fb74b1bdedbd0f94ecb752018 https://github.com/galaxyproject/galaxy/commit/ef6bd90f20394f6fb74b1bdedbd0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- Merge pull request #1641 from martenson/libraries-load-handle-payload [16.01] libraries: handle correctly application/json pased in POST Commit: 054c04f490fe5e641c1dec8c4f8af53cf02daffd https://github.com/galaxyproject/galaxy/commit/054c04f490fe5e641c1dec8c4f8a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Merge pull request #1695 from natefoo/help-message-css [16.01] Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Commit: bf4e736c3ca8e129ff8c75f8261c08f303c76080 https://github.com/galaxyproject/galaxy/commit/bf4e736c3ca8e129ff8c75f8261c… Author: pavanvidem <videmp(a)informatik.uni-freiburg.de> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Update david identifier types David identifier types seem to be changed. Some of them are no more available on david web server. Commit: 776180ab80b352a60713fbf6576adbfc4934ed85 https://github.com/galaxyproject/galaxy/commit/776180ab80b352a60713fbf6576a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- show all available information for current library and the opened folder Commit: 65d9ec9cab2b6e46fa7a067948bba69e3255c1ff https://github.com/galaxyproject/galaxy/commit/65d9ec9cab2b6e46fa7a067948bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1705 from martenson/fix-location-info [16.01] libraries - fix location info Commit: e0ee1203c6fc176ffb56ecd717540cc6b2f0b0e7 https://github.com/galaxyproject/galaxy/commit/e0ee1203c6fc176ffb56ecd71754… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix problem with legacy workflows and duplicate output labels. Fixes #1704 - many thanks to @tzk and @mvdbeek. Commit: ff29b263630614b96c617eb9468afcec9d04d72f https://github.com/galaxyproject/galaxy/commit/ff29b263630614b96c617eb9468a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1718 from jmchilton/workflow_fixes [16.01] Fix problem with legacy workflows and duplicate output labels. Commit: 75a3797d0fa03fc80240326e6b7fdae40ee5d658 https://github.com/galaxyproject/galaxy/commit/75a3797d0fa03fc80240326e6b7f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Also fix legacy export. Commit: 00b739fc1451d7a529913ab626358bd968e75ee3 https://github.com/galaxyproject/galaxy/commit/00b739fc1451d7a529913ab62635… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1733 from mvdbeek/legacy_export [16.01] Also check for unique outputs on legacy workflow export Commit: 4a566b6db8ac69bf5f5619e9a9aa2640ce3bd9af https://github.com/galaxyproject/galaxy/commit/4a566b6db8ac69bf5f5619e9a9aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Improved debug message in workflow scheduling. Commit: 39ec09df48060e4e384d7af2669a6fe074b6d71a https://github.com/galaxyproject/galaxy/commit/39ec09df48060e4e384d7af2669a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1741 from jmchilton/workflow_schedule_fixes [16.01] Improved debug message in workflow scheduling. Commit: 37b98b773ea378bdd4a7845d60f589f7454f2291 https://github.com/galaxyproject/galaxy/commit/37b98b773ea378bdd4a7845d60f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Load whitelist regardless of whether the setting is explicit in config. This is a sensible enough default, and requiring the option to be set in galaxy.ini is cumbersome and unnecessary since it's admin-only functionality. Commit: aabc916ed20ac7f25174ce4d552b735253697081 https://github.com/galaxyproject/galaxy/commit/aabc916ed20ac7f25174ce4d552b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1749 from dannon/whitelist_loading Load whitelist regardless of whether the setting is explicit in config. Commit: 84de6b4ed31906756c3c219eda3f4462773d0a21 https://github.com/galaxyproject/galaxy/commit/84de6b4ed31906756c3c219eda3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-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/ui/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change Commit: 80a858a3afd970ca086992744b46725eb829b94e https://github.com/galaxyproject/galaxy/commit/80a858a3afd970ca086992744b46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-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/ui/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge pull request #1753 from carlfeberhard/release_16.01 [16.01] Fix target or window.location when importing histories from display.m… Commit: 4c0993cc420bc5e6a1d315677962d41803a41cd3 https://github.com/galaxyproject/galaxy/commit/4c0993cc420bc5e6a1d315677962… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix updating in-memory tools for tool shed installs into sections. Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Commit: 3f34131ff506836d400f8d55b696d8044546b162 https://github.com/galaxyproject/galaxy/commit/3f34131ff506836d400f8d55b696… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/version.py Commit: b4c823f2cd47bd0f75351c820651abfefa1a8472 https://github.com/galaxyproject/galaxy/commit/b4c823f2cd47bd0f75351c820651… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1758 from jmchilton/ts_section_fix [16.01] Fix updating in-memory tools for tool shed installs into sections. Commit: ef9362971920c6561015376d3f604bf6234f2547 https://github.com/galaxyproject/galaxy/commit/ef9362971920c6561015376d3f60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix pretty_print_time_interval for MySQL. Fix #1619. Commit: 6c83fbe24dd0dea35967021c061e975225aeb02b https://github.com/galaxyproject/galaxy/commit/6c83fbe24dd0dea35967021c061e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1761 from nsoranzo/release_15.10_fix_for_1619 [15.10] Fix pretty_print_time_interval for MySQL. Commit: b5e91d23779cc6db491b7d7b1701b25cb10da6fb https://github.com/galaxyproject/galaxy/commit/b5e91d23779cc6db491b7d7b1701… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/util/__init__.py Commit: a47a4f40b47302c43dea33f8b040f41570b0587c https://github.com/galaxyproject/galaxy/commit/a47a4f40b47302c43dea33f8b040… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove len(stderr), breaks on recent docker versions Commit: f2a27acff8fd5d199eda841fd575305c3644c439 https://github.com/galaxyproject/galaxy/commit/f2a27acff8fd5d199eda841fd575… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Drop Python 2.6 with 16.04. xref #1596 Commit: dbab6f5b979f19c33c3cd1aeb5c459dcc5612eec https://github.com/galaxyproject/galaxy/commit/dbab6f5b979f19c33c3cd1aeb5c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map 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/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Workaround for #1739 - fixing up subworkflow inut connections. Do the same relaxed thing we do for inputs of type 'input' as we do for outputs of this type. Someday we should have better tracking, but such a change is probably not wise for a release branch. Commit: 5ce771b70e44f28fde2e14bf963f97fed36bc2ae https://github.com/galaxyproject/galaxy/commit/5ce771b70e44f28fde2e14bf963f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip URL of download_file and download_by_url install actions. Commit: 5b720b4a02408a0601e7ecaf4fb2374c8c5753a7 https://github.com/galaxyproject/galaxy/commit/5b720b4a02408a0601e7ecaf4fb2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map 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/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1774 from jmchilton/wf_fixes [16.01] Workaround for #1739 - fixing up subworkflow input connections. Commit: 4c815a7d0589a00df8c8fffba730a79030ad7791 https://github.com/galaxyproject/galaxy/commit/4c815a7d0589a00df8c8fffba730… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1778 from nsoranzo/release_16.01_fix_download_file [16.01] Strip URL of download_file and download_by_url install actions. Commit: b4020934793829f3735fa696de1fa3237391d945 https://github.com/galaxyproject/galaxy/commit/b4020934793829f3735fa696de1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- format_source in workflow editor is too restrictive. Case made well by @erasche on #1746, fixes #1746. To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch. Commit: 9acbfdf3c3444ca0cb0cf87f80c57d00765673d9 https://github.com/galaxyproject/galaxy/commit/9acbfdf3c3444ca0cb0cf87f80c5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Fix chrome-only intermittent rendering error of font awesome icons that have their sizes changed by overriding 4.2 font-size inheritance rule from core.less Commit: 3621d6f2212566b8a172424177b8eafc92af7fca https://github.com/galaxyproject/galaxy/commit/3621d6f2212566b8a172424177b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1784 from carlfeberhard/fix.fa [16.01] Fix chrome-only intermittent rendering error of font awesome icons th… Commit: 805b5906b2f43947af36814fe67b5914acc35a08 https://github.com/galaxyproject/galaxy/commit/805b5906b2f43947af36814fe67b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1772 from jmchilton/python26_drop [16.01] Deprecation notice - Python 2.6. Commit: a5c30c563e878c3b0171bdc992eaea248e2371cf https://github.com/galaxyproject/galaxy/commit/a5c30c563e878c3b0171bdc992ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1771 from mvdbeek/16.01_fix_ies [16.01] Remove len(stderr), breaks on recent docker versions Commit: 6bb43aa4aff83f832997d01fc5663b9d501bc866 https://github.com/galaxyproject/galaxy/commit/6bb43aa4aff83f832997d01fc566… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/functional/tools/output_format.xml Log Message: ----------- Merge pull request #1786 from jmchilton/format_source_restrictive [16.01] format_source in workflow editor is too restrictive. Commit: ca123a4f2674351e01235bab545559b299b99ff9 https://github.com/galaxyproject/galaxy/commit/ca123a4f2674351e01235bab5455… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 3b963226a110b8de8aa11d3c4e053a220bbcba53 https://github.com/galaxyproject/galaxy/commit/3b963226a110b8de8aa11d3c4e05… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 5ab53c3fda3a43236b444a31aa408c9f5cb5c4c4 https://github.com/galaxyproject/galaxy/commit/5ab53c3fda3a43236b444a31aa40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 88277c9723c558e2b2003f1b81c7f2d16143fcc6 https://github.com/galaxyproject/galaxy/commit/88277c9723c558e2b2003f1b81c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: d650055ca824d5cf8ab1ede389e9b3060c1f4094 https://github.com/galaxyproject/galaxy/commit/d650055ca824d5cf8ab1ede389e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 32c910ac4021b0e65112d557a7f12d24e158171d https://github.com/galaxyproject/galaxy/commit/32c910ac4021b0e65112d557a7f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 37548ef8edb95d59fddd73283561e8b1a6588c10 https://github.com/galaxyproject/galaxy/commit/37548ef8edb95d59fddd73283561… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 78f441b9c7bfd68f7b3ee030f4ffe4a95b5fdc58 https://github.com/galaxyproject/galaxy/commit/78f441b9c7bfd68f7b3ee030f4ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 4f3397fa0ab187a4b5c32e1268265925fc1a8753 https://github.com/galaxyproject/galaxy/commit/4f3397fa0ab187a4b5c32e126826… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 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 M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 8468871ee481598a84888b5329139590ec75e98d https://github.com/galaxyproject/galaxy/commit/8468871ee481598a84888b532913… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: cee85bae67377d3fad42bec5b4ebb022aaf7b2c7 https://github.com/galaxyproject/galaxy/commit/cee85bae67377d3fad42bec5b4eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 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 M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 4845a39071ab4e2652e564efdf7647a942563603 https://github.com/galaxyproject/galaxy/commit/4845a39071ab4e2652e564efdf76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: ef4a9f6e2114e69f6ea3167e99a857f2ea4d28af https://github.com/galaxyproject/galaxy/commit/ef4a9f6e2114e69f6ea3167e99a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 61cd045ffa947a69abacddea459f725ba569584a https://github.com/galaxyproject/galaxy/commit/61cd045ffa947a69abacddea459f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: 2a8089749caab12c087064c840708fb05b0104cd https://github.com/galaxyproject/galaxy/commit/2a8089749caab12c087064c84070… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 6e3b74869a54558fe48d6e1633c5af7197051447 https://github.com/galaxyproject/galaxy/commit/6e3b74869a54558fe48d6e1633c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: c8963786d53efd2cf3b359b2f9a000e00688285f https://github.com/galaxyproject/galaxy/commit/c8963786d53efd2cf3b359b2f9a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: ce88f2f81caff6af7dc730ef9c1fbc2a40922dab https://github.com/galaxyproject/galaxy/commit/ce88f2f81caff6af7dc730ef9c1f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: d4b94722f992c9309aa2ec5bfa5bce2dacd9b218 https://github.com/galaxyproject/galaxy/commit/d4b94722f992c9309aa2ec5bfa5b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: fcd8f50448cd1db7b50a58321c8fa391506bf997 https://github.com/galaxyproject/galaxy/commit/fcd8f50448cd1db7b50a58321c8f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 626cade512894e54c5b3e5257543f267a1826a71 https://github.com/galaxyproject/galaxy/commit/626cade512894e54c5b3e5257543… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 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 M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 91f5fa81fe3c1c4d45b3987b27c187c4cb53f8e8 https://github.com/galaxyproject/galaxy/commit/91f5fa81fe3c1c4d45b3987b27c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 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 M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 581808aa98a6058a4bdbe13c21271ca4b0d3ef77 https://github.com/galaxyproject/galaxy/commit/581808aa98a6058a4bdbe13c2127… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: 2bda436473b116c7d98c36a8435056745bf832f2 https://github.com/galaxyproject/galaxy/commit/2bda436473b116c7d98c36a84350… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f8a1aef76c022612a8a28938e1d57412348884ab https://github.com/galaxyproject/galaxy/commit/f8a1aef76c022612a8a28938e1d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 47a8b6e86733472ad3c0dbe2d5774d69ecba44eb https://github.com/galaxyproject/galaxy/commit/47a8b6e86733472ad3c0dbe2d577… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 6190f6fa6db26ada3380c9a54b5481d12b3ac9ae https://github.com/galaxyproject/galaxy/commit/6190f6fa6db26ada3380c9a54b54… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 27d7298ec4788a2e59a5988007fde05e5fc004ce https://github.com/galaxyproject/galaxy/commit/27d7298ec4788a2e59a5988007fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: c465489ea1676905ddb4cfb88605c1e869a7019c https://github.com/galaxyproject/galaxy/commit/c465489ea1676905ddb4cfb88605… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 18b3126a15ec7fe3873253be0c1344e9f067f0ca https://github.com/galaxyproject/galaxy/commit/18b3126a15ec7fe3873253be0c13… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 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 M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: 40a90831ed28b762e90cf2b50abec7e8bef738d6 https://github.com/galaxyproject/galaxy/commit/40a90831ed28b762e90cf2b50abe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f65bcb3383ba142d514b38ab5ed03d5f9ecd5f1d https://github.com/galaxyproject/galaxy/commit/f65bcb3383ba142d514b38ab5ed0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: ab1a135dd4a422897c74ea87e5210ec5baa27ff7 https://github.com/galaxyproject/galaxy/commit/ab1a135dd4a422897c74ea87e521… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: b3e0315e1e40912366c8103412e64a645e0a93a9 https://github.com/galaxyproject/galaxy/commit/b3e0315e1e40912366c8103412e6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: 8736c7bd77bd3c5cd38225538085c0eb2a40e8f4 https://github.com/galaxyproject/galaxy/commit/8736c7bd77bd3c5cd38225538085… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 23e203c48180b6ab1e4886be81447e33afb853e5 https://github.com/galaxyproject/galaxy/commit/23e203c48180b6ab1e4886be8144… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: 64cd02ae385fb509378c78e6e4832768ff4f1e00 https://github.com/galaxyproject/galaxy/commit/64cd02ae385fb509378c78e6e483… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: 2dcbda93b29e4dd975453af8eeb4f171f7db2918 https://github.com/galaxyproject/galaxy/commit/2dcbda93b29e4dd975453af8eeb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 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 M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: b11b8e68500a3d074bf20b08958671d958d42eca https://github.com/galaxyproject/galaxy/commit/b11b8e68500a3d074bf20b089586… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: f540a16768307995ea49c5d241948537ebbfa540 https://github.com/galaxyproject/galaxy/commit/f540a16768307995ea49c5d24194… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory Commit: bf1c77d171f079f42d481ad465dbaef3bac8b4d4 https://github.com/galaxyproject/galaxy/commit/bf1c77d171f079f42d481ad465db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Security fixes for history imports Commit: 5da91bddcda3ad3a4942e752d9b4bb3e7872046c https://github.com/galaxyproject/galaxy/commit/5da91bddcda3ad3a4942e752d9b4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py Log Message: ----------- Security fixes for object store paths Commit: cd8b96553f673145ee64a86d32960ba42643baed https://github.com/galaxyproject/galaxy/commit/cd8b96553f673145ee64a86d3296… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py R templates/admin/requests/select_datasets_to_transfer.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako Log Message: ----------- Remove sample tracking manual external service transfer due to security concerns Commit: e4a1d5727805168a9fd15aca1cdd21630ada2bbc https://github.com/galaxyproject/galaxy/commit/e4a1d5727805168a9fd15aca1cdd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 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 M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Security fixes for tool shed repository browsing Commit: e845d649c672c51cc2336da0d880c9ff74ea6b5f https://github.com/galaxyproject/galaxy/commit/e845d649c672c51cc2336da0d880… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_content_util.py Log Message: ----------- Security fixes for tool shed hg push and capsule/tarball uploads Commit: 8c4542b136ef1eab3231ba0df4aab53b91f504af https://github.com/galaxyproject/galaxy/commit/8c4542b136ef1eab3231ba0df4aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Commit: 624e3837bd3d2dffdee7737f4e55d2e66316896a https://github.com/galaxyproject/galaxy/commit/624e3837bd3d2dffdee7737f4e55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Commit: c6b010af346d0fed5bba7e5610ea59210be5ceb7 https://github.com/galaxyproject/galaxy/commit/c6b010af346d0fed5bba7e5610ea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Add security announcement to v16.01 release notes. Commit: 0122040fad865487e2377cee35360af49e37d0e8 https://github.com/galaxyproject/galaxy/commit/0122040fad865487e2377cee3536… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.03.4 Commit: 3516e94e5cb0e971d8e10de018b72cf22296766e https://github.com/galaxyproject/galaxy/commit/3516e94e5cb0e971d8e10de018b7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: c8e9845c5c57714042a75053d954b1c7f0962672 https://github.com/galaxyproject/galaxy/commit/c8e9845c5c57714042a75053d954… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.05.2 Commit: 3d832aff0abe5a4ca48bfc80c84032f388bf7024 https://github.com/galaxyproject/galaxy/commit/3d832aff0abe5a4ca48bfc80c840… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 30608c177c625f4ce66f1376a66621687fe7711e https://github.com/galaxyproject/galaxy/commit/30608c177c625f4ce66f1376a666… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.07.1 Commit: 21cc5b2da540eba18445603146407c1779257bba https://github.com/galaxyproject/galaxy/commit/21cc5b2da540eba1844560314640… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Commit: b5949bcbbfbc613b0ec72ce23e4da448c9316c49 https://github.com/galaxyproject/galaxy/commit/b5949bcbbfbc613b0ec72ce23e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 15.10.2 Commit: 70329f64ab8b6dcf9e9a6b6762783543b49c36eb https://github.com/galaxyproject/galaxy/commit/70329f64ab8b6dcf9e9a6b676278… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Commit: 5677c2ee4fce70c9898ea5e6cae125b6147ae36a https://github.com/galaxyproject/galaxy/commit/5677c2ee4fce70c9898ea5e6cae1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/6a47d2d3a7f2...5677c2ee4fce

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[galaxyproject/galaxy] b14e35: Add a safe_relpath util function for ensuring a pa...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b14e35f48ba86d836ab78dad56bace573b6836f1 https://github.com/galaxyproject/galaxy/commit/b14e35f48ba86d836ab78dad56ba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory

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