- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4b7e86: Clean up docstrings in lib/galaxy/tools/toolbox/pa...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b7e86fa4323426e954270f2eb6d83b13d6c2752 https://github.com/galaxyproject/galaxy/commit/4b7e86fa4323426e954270f2eb6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/parser.py Log Message: ----------- Clean up docstrings in lib/galaxy/tools/toolbox/parser.py. Commit: cb5e786aa906e0bfedb3a4bd85716e46c77a4e13 https://github.com/galaxyproject/galaxy/commit/cb5e786aa906e0bfedb3a4bd8571… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Allow tool confs with a tool_path to not be interpreted as shed confs. Commit: 34e3b7f1c2e3797dcb7afac49125b9f33accad8c https://github.com/galaxyproject/galaxy/commit/34e3b7f1c2e3797dcb7afac49125… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Rename shed_conf attribute to is_shed_conf. Per discussion with @nsoranzo. Commit: 26569c3ec4b64a31f4827168cb042572ede28de0 https://github.com/galaxyproject/galaxy/commit/26569c3ec4b64a31f4827168cb04… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Merge pull request #2066 from jmchilton/static_tool_conf Allow tool confs with a tool_path to not be interpreted as shed confs. Compare: https://github.com/galaxyproject/galaxy/compare/18596a2bb47d...26569c3ec4b6

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[galaxyproject/infrastructure-playbook] b17443: Finish splitting the CVMFS tasks into a client inc...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b17443d5333b931871ac619a1ed69c4848017566 https://github.com/galaxyproject/infrastructure-playbook/commit/b17443d5333… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/main.yml M taccenv/inventory Log Message: ----------- Finish splitting the CVMFS tasks into a client include as I'd started and then forgot

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[galaxyproject/galaxy] 7d3787: Replace common_util.url_join with util.build_url.
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d378792cc697ded34a40c2ed6783cc27d534e81 https://github.com/galaxyproject/galaxy/commit/7d378792cc697ded34a40c2ed678… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Replace common_util.url_join with util.build_url. Commit: 494384171f260a924517844f4ff30db40a7dddbc https://github.com/galaxyproject/galaxy/commit/494384171f260a924517844f4ff3… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Do the same for tool_shed_get. Commit: d885367955a0aa1a6a389ae7d67a6829002f8254 https://github.com/galaxyproject/galaxy/commit/d885367955a0aa1a6a389ae7d67a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix indent broken with search/replace. Commit: 18596a2bb47d31b04e214c31b96a60b8a92fd70b https://github.com/galaxyproject/galaxy/commit/18596a2bb47d31b04e214c31b96a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge pull request #2055 from davebx/url_join Replace common_util.url_join with util.build_url. Compare: https://github.com/galaxyproject/galaxy/compare/1dc2524e0970...18596a2bb47d

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[galaxyproject/galaxy] 205850: Use a stricter regexp for microseconds.
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 205850586e87af4fb3a9d7779eb1f2852ccf45c3 https://github.com/galaxyproject/galaxy/commit/205850586e87af4fb3a9d7779eb1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/managers/base.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Use a stricter regexp for microseconds. Commit: 1dc2524e0970b9c2e8b55045c19dd8f6586892a6 https://github.com/galaxyproject/galaxy/commit/1dc2524e0970b9c2e8b55045c19d… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/managers/base.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Merge pull request #2065 from nsoranzo/stricter_microseconds_re Use a stricter regexp for microseconds. Compare: https://github.com/galaxyproject/galaxy/compare/569b87dc002f...1dc2524e0970

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[galaxyproject/galaxy] 78c839: Add a dictionary to params_dict that maps datasets...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78c839cccdd09f9eb79467e77f1ad247783efa58 https://github.com/galaxyproject/galaxy/commit/78c839cccdd09f9eb79467e77f1a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Add a dictionary to params_dict that maps datasets to identifier keys, so that element_identifiers for datasets in repeats are passed correctly to the tool wrapper. Commit: 569b87dc002f5fe09cb34496a71deda1e6678d1b https://github.com/galaxyproject/galaxy/commit/569b87dc002f5fe09cb34496a71d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #2029 from mvdbeek/element_identifier_in_repeat Better element_identifier handling in repeat sections Compare: https://github.com/galaxyproject/galaxy/compare/ff48ad9b54fc...569b87dc002f

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[galaxyproject/infrastructure-playbook] 7812fd: Install CVMFS on nodes
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 7812fd520eee03ffae2ef0bb9b1e7f4a31b0d06e https://github.com/galaxyproject/infrastructure-playbook/commit/7812fd520ee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: A .gitignore A roles/cvmfs/handlers/main.yml A roles/cvmfs/tasks/client.yml A roles/cvmfs/tasks/main.yml A roles/cvmfs/vars/main.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Install CVMFS on nodes

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[galaxyproject/galaxy] ec83fb: Change user disk usage pgcalc function up a bit to...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ec83fb64942647218f6cd56929b13405527af686 https://github.com/galaxyproject/galaxy/commit/ec83fb64942647218f6cd56929b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/model/util.py Log Message: ----------- Change user disk usage pgcalc function up a bit to make a slightly safer dry-run, since it doesn't appear that in some environments (not sure why) the rollback isn't actually happening. Commit: ff48ad9b54fca66d4abb21f83e56ee57a2eb6f1c https://github.com/galaxyproject/galaxy/commit/ff48ad9b54fca66d4abb21f83e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/model/util.py Log Message: ----------- Merge pull request #2063 from dannon/dryrun Change user disk usage pgcalc function up a bit to make a slightly sa… Compare: https://github.com/galaxyproject/galaxy/compare/1c2b2a5c71d1...ff48ad9b54fc

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[galaxyproject/galaxy] 46b4e8: Managers: remove UTC zone when parsing dates
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46b4e8d94cf989f429039a63e38cc739c14e6a76 https://github.com/galaxyproject/galaxy/commit/46b4e8d94cf989f429039a63e38c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/managers/base.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Managers: remove UTC zone when parsing dates This change creates a more complete regex for parsing dates used in filters. MySQL in particular errored when the UTC zone character 'Z' was appended to a valid iso 8601 date (because it's MySQL). The FilterParser.parse_date method now: - strips both the separator 'T' and any ending 'Z' - one space are allowed as the date/time separator - milliseconds are permitted - both time and time with milliseconds are optional - any added timezone (besides the UTC Z) will cause an error - feedback was made more clear - tests were added (and should make the above more clear) Commit: 1c2b2a5c71d105f0f2d9ac64d7a502f81b4297ec https://github.com/galaxyproject/galaxy/commit/1c2b2a5c71d105f0f2d9ac64d7a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/managers/base.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Merge pull request #2062 from carlfeberhard/fix.date_filter_parsing Managers: remove UTC zone when parsing dates Compare: https://github.com/galaxyproject/galaxy/compare/5fd5343d07f2...1c2b2a5c71d1

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[galaxyproject/usegalaxy-playbook] d11e5f: update MTS
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d11e5f83f7145c997e7355db0cbfda02b2e24bd4 https://github.com/galaxyproject/usegalaxy-playbook/commit/d11e5f83f7145c99… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/usegalaxy-playbook] 8d33c8: update TTS
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8d33c888362f023c8f48c744b8fbc11856cccd17 https://github.com/galaxyproject/usegalaxy-playbook/commit/8d33c888362f023c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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