- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 292642: Fix upload event binding to be input and change in...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 292642ed91de908bf4e1e3f8705147bc7fd2ca1b https://github.com/galaxyproject/galaxy/commit/292642ed91de908bf4e1e3f87051… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Fix upload event binding to be input and change instead of just relying on keyup. This fixes https://github.com/galaxyproject/galaxy/issues/762 Commit: 76a683e878246b54e14dc4f9fcf3d17916b17564 https://github.com/galaxyproject/galaxy/commit/76a683e878246b54e14dc4f9fcf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M lib/galaxy/web/base/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.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/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.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-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.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/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-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.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-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Merge branch 'dev' into upload_fix Commit: 2ee34167921a92a8c14c3f1694e43bce3efc27cf https://github.com/galaxyproject/galaxy/commit/2ee34167921a92a8c14c3f1694e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- One more location where keyup should be replaced Commit: 6a450b9c31788586ec6d781984a145c7ce570d8a https://github.com/galaxyproject/galaxy/commit/6a450b9c31788586ec6d781984a1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #778 from dannon/upload_fix Fix upload event binding to be input and change instead of just relyi… Compare: https://github.com/galaxyproject/galaxy/compare/e9ddc21661ff...6a450b9c3178

1 0

[galaxyproject/galaxy] 02e612: In log of collecting job metrics, print id, if ava...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 02e61226b5681186426809d3497fdb2f0d46e466 https://github.com/galaxyproject/galaxy/commit/02e61226b5681186426809d3497f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In log of collecting job metrics, print id, if available, in addition to the string representation of the has_metrics object. Commit: e9ddc21661ffe27ed87e04a6c852c9914a22bacc https://github.com/galaxyproject/galaxy/commit/e9ddc21661ffe27ed87e04a6c852… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #772 from blankenberg/job-metrics In log of collecting job metrics, print id of has_metrics object Compare: https://github.com/galaxyproject/galaxy/compare/8b404205c07b...e9ddc21661ff

1 0

[galaxyproject/galaxy] b1841e: Client build: do not drop console when compressing...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1841e22d924b53a3a75306bf773b0b0ad4f02a6 https://github.com/galaxyproject/galaxy/commit/b1841e22d924b53a3a75306bf773… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.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/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.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-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.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/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.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-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Client build: do not drop console when compressing, when not compressing do not mangle variable names Commit: 8b404205c07bcc7971cdc3d38cb369a0fc7d4940 https://github.com/galaxyproject/galaxy/commit/8b404205c07bcc7971cdc3d38cb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.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/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.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-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.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/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-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.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-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Resolve client merge conflict, repack. Compare: https://github.com/galaxyproject/galaxy/compare/91da5f806805...8b404205c07b

1 0

[galaxyproject/galaxy] c96f0e: Quote value to fix configparser error
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c96f0e35859beecfc76df92dee4ed11bece438bb https://github.com/galaxyproject/galaxy/commit/c96f0e35859beecfc76df92dee4e… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Quote value to fix configparser error Commit: 91da5f806805fcc3661f985d843793f1785b7e64 https://github.com/galaxyproject/galaxy/commit/91da5f806805fcc3661f985d8437… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #775 from erasche/462-followup Quote value to fix configparser error in GIEs Compare: https://github.com/galaxyproject/galaxy/compare/21f777d60815...91da5f806805

1 0

[galaxyproject/galaxy] b2433f: Add encoded IDs to job error reports and also incl...
by GitHub 22 Sep '15

22 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2433f077d0de6925792e9e2c3d04cfa13308d8d https://github.com/galaxyproject/galaxy/commit/b2433f077d0de6925792e9e2c3d0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Add encoded IDs to job error reports and also include a direct link to dataset's show_params. Commit: eac449ed1e733cb0aa01b527a2518dc712efe443 https://github.com/galaxyproject/galaxy/commit/eac449ed1e733cb0aa01b527a251… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- white space fix Commit: 21f777d6081565fc1abfcc8a6aa91d163667db9d https://github.com/galaxyproject/galaxy/commit/21f777d6081565fc1abfcc8a6aa9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #771 from blankenberg/error-report Add encoded IDs to job error reports and also include a link to show_params Compare: https://github.com/galaxyproject/galaxy/compare/419d94e8b05c...21f777d60815

1 0

[galaxyproject/galaxy] aeda77: Add "Galaxy" title to templates/webapps/galaxy/roo...
by GitHub 22 Sep '15

22 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aeda77c6005f58f4df2939098151d376bf6515a9 https://github.com/galaxyproject/galaxy/commit/aeda77c6005f58f4df2939098151… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Add "Galaxy" title to templates/webapps/galaxy/root/index.mako Commit: 419d94e8b05c3d5979415c46671126422f5d68ad https://github.com/galaxyproject/galaxy/commit/419d94e8b05c3d5979415c466711… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge pull request #769 from blankenberg/ui-fixes Add "Galaxy" title to templates/webapps/galaxy/root/index.mako Compare: https://github.com/galaxyproject/galaxy/compare/248ce3075b24...419d94e8b05c

1 0

[galaxyproject/galaxy] 87d506: Implement min/max for multiple data input paramete...
by GitHub 22 Sep '15

22 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87d5063a0dff35d6cddda3f17a8cadb6b04ff5e9 https://github.com/galaxyproject/galaxy/commit/87d5063a0dff35d6cddda3f17a8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py M test/functional/tools/multi_data_param.xml Log Message: ----------- Implement min/max for multiple data input parameters. Commit: 248ce3075b24a8da4e4142244f81c82c63a4cbff https://github.com/galaxyproject/galaxy/commit/248ce3075b24a8da4e4142244f81… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py M test/functional/tools/multi_data_param.xml Log Message: ----------- Merge pull request #765 from jmchilton/multi_min_max Implement min/max for multiple data input parameters. Compare: https://github.com/galaxyproject/galaxy/compare/fb54be77678c...248ce3075b24

1 0

[galaxyproject/galaxy] 7ca661: Fix for displaying tool form errors caused by http...
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ca661bb010e4106e4fac910612810b99f741805 https://github.com/galaxyproject/galaxy/commit/7ca661bb010e4106e4fac9106128… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Fix for displaying tool form errors caused by http exceptions and when tool form doesn't exist. Commit: aed76f3744aba7b6c83659a9ad7dd079b9be1b70 https://github.com/galaxyproject/galaxy/commit/aed76f3744aba7b6c83659a9ad7d… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Do not attempt to rerun non-rerunable tools. Commit: fb54be77678c409d12e935b28ee7068c18999263 https://github.com/galaxyproject/galaxy/commit/fb54be77678c409d12e935b28ee7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/webapps/galaxy/api/jobs.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 #766 from blankenberg/toolform-rerun Tool form error messages and rerun fixes Compare: https://github.com/galaxyproject/galaxy/compare/5e419197d1da...fb54be77678c

1 0

[galaxyproject/galaxy] 07dd69: Allow discover_datasets tag to use format attribut...
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07dd69edd5472afef305fb170f18628a0cf3402d https://github.com/galaxyproject/galaxy/commit/07dd69edd5472afef305fb170f18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/multi_output_configured.xml Log Message: ----------- Allow discover_datasets tag to use format attribute (instead of ext). https://github.com/TGAC/tgac-galaxytools/commit/93514438cb50fab48d0e211f1e1…. Commit: 5e419197d1da6122d51ded0c1782d5b1c59126ee https://github.com/galaxyproject/galaxy/commit/5e419197d1da6122d51ded0c1782… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/multi_output_configured.xml Log Message: ----------- Merge pull request #764 from jmchilton/format_discover Allow discover_datasets tag to use format attribute (instead of ext). Compare: https://github.com/galaxyproject/galaxy/compare/4525b4b911fc...5e419197d1da

1 0

[galaxyproject/galaxy] 56f10c: make except catch just Exceptions, not everything
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56f10c9a1d7fa984aa1c286abaf4fadd26f1746a https://github.com/galaxyproject/galaxy/commit/56f10c9a1d7fa984aa1c286abaf4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- make except catch just Exceptions, not everything I am not sure when these are hapenning (error initialized with encoded id & tool without id) but this should be safe fix Commit: 4525b4b911fcaaf6ce2daed04cdd25c7bea2d24e https://github.com/galaxyproject/galaxy/commit/4525b4b911fcaaf6ce2daed04cdd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #763 from martenson/fix-bare-exceptions make except catch just Exceptions, not everything Compare: https://github.com/galaxyproject/galaxy/compare/c7394bd0b31f...4525b4b911fc

1 0