September 2015 - galaxy-commits - lists.galaxyproject.org

[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

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[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

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[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

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[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

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[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

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[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

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[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

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[galaxyproject/galaxy] b89c6e: When submitting tool error reports, include 'old' ...
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b89c6e56a5559186d126afdf09ea1565a146f178 https://github.com/galaxyproject/galaxy/commit/b89c6e56a5559186d126afdf09ea… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- When submitting tool error reports, include 'old' tool id as part of subject line. Makes sifting through bug report emails easier, old id is used for brevity, but full guid is still included in text of report. Commit: c7394bd0b31f4ecab36a144897e26871eedde008 https://github.com/galaxyproject/galaxy/commit/c7394bd0b31f4ecab36a144897e2… 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: ----------- Merge pull request #761 from blankenberg/error-tool-id When submitting tool error reports, include 'old' tool id as part of subject line. Compare: https://github.com/galaxyproject/galaxy/compare/2bfc12d66694...c7394bd0b31f

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[galaxyproject/galaxy] 311100: Bugfix in test error reporting handling code.
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 311100ff9e40128b4da158fbb404a0b781765e11 https://github.com/galaxyproject/galaxy/commit/311100ff9e40128b4da158fbb404… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M test/base/interactor.py Log Message: ----------- Bugfix in test error reporting handling code. The code for showing status of histories in error would fail if there are collections in the history. This fixes that and skips over collections. Commit: 2bfc12d666946a3e057aa3801fde2df90c6ab990 https://github.com/galaxyproject/galaxy/commit/2bfc12d666946a3e057aa3801fde… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M test/base/interactor.py Log Message: ----------- Merge pull request #760 from jmchilton/test_error Bugfix in test error reporting handling code. Compare: https://github.com/galaxyproject/galaxy/compare/1f1eed0e0560...2bfc12d66694

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[galaxyproject/usegalaxy-playbook] 897be7: Fix indentation
by GitHub 21 Sep '15

21 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 897be7f26606611a641687244cc388e8940cd47e https://github.com/galaxyproject/usegalaxy-playbook/commit/897be7f26606611a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-21 (Mon, 21 Sep 2015) Changed paths: M stage/secret_vars/galaxyservers.yml Log Message: ----------- Fix indentation

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