galaxy-commits March 2016

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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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[galaxyproject/galaxy] 449098: upgrade mercurial wheel to latest (fixing CVE issu...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 449098d8b14b45269be106f6410c0b9145c51d50 https://github.com/galaxyproject/galaxy/commit/449098d8b14b45269be106f6410c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- upgrade mercurial wheel to latest (fixing CVE issues) Commit: 5fd5343d07f2713856438922697c2d7b868e18a5 https://github.com/galaxyproject/galaxy/commit/5fd5343d07f2713856438922697c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2045 from martenson/update_mercurial_wheel upgrade mercurial wheel to latest (fixing CVE issues) Compare: https://github.com/galaxyproject/galaxy/compare/cdd44e610ec0...5fd5343d07f2

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[galaxyproject/galaxy] 449098: upgrade mercurial wheel to latest (fixing CVE issu...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 449098d8b14b45269be106f6410c0b9145c51d50 https://github.com/galaxyproject/galaxy/commit/449098d8b14b45269be106f6410c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- upgrade mercurial wheel to latest (fixing CVE issues) Commit: 90b95dc665bd736a21bd16d2852caf5c23bb83c4 https://github.com/galaxyproject/galaxy/commit/90b95dc665bd736a21bd16d2852c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2043 from martenson/update_mercurial_wheel [16.01] upgrade mercurial wheel to latest (fixing CVE issues) Compare: https://github.com/galaxyproject/galaxy/compare/193eeaa60674...90b95dc665bd

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[galaxyproject/infrastructure-playbook] cf4b61: Include library
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: cf4b614b7a64776041b046149f4276979449c36f https://github.com/galaxyproject/infrastructure-playbook/commit/cf4b614b7a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M ansible.cfg Log Message: ----------- Include library

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[galaxyproject/infrastructure-playbook] 40b84d: Add decode and yum_repository modules to library
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 40b84d18b74e0f7a0d0f05e547777f8e6748e064 https://github.com/galaxyproject/infrastructure-playbook/commit/40b84d18b74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: A library/decode A library/yum_repository Log Message: ----------- Add decode and yum_repository modules to library

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[galaxyproject/galaxy] e88eda: disable 'hg push' to TS repositories deprecated in...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e88edad9a5aab16f87370de78e2ce949cdc4086a https://github.com/galaxyproject/galaxy/commit/e88edad9a5aab16f87370de78e2c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#depre… Commit: fc72b4d5c8d18614dec8683ed4c08f5c678c02d3 https://github.com/galaxyproject/galaxy/commit/fc72b4d5c8d18614dec8683ed4c0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Specify default value when getting disable_push Commit: d1f438f5fc7948917889115a98a1b1bceadf6149 https://github.com/galaxyproject/galaxy/commit/d1f438f5fc7948917889115a98a1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Update Tool Shed tests after disabling 'hg push' Commit: 20aa85b168aa0987071c44b461bbafda22660364 https://github.com/galaxyproject/galaxy/commit/20aa85b168aa0987071c44b461bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0310_hg_clone.py Log Message: ----------- add TS test for disabled hg push Commit: 18205d93757da2ef494bbc79a8bdbb271316de07 https://github.com/galaxyproject/galaxy/commit/18205d93757da2ef494bbc79a8bd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_clone.py Log Message: ----------- rename test to reflect insides Commit: cdd44e610ec0180141f7086e75d42a0e42bbc62a https://github.com/galaxyproject/galaxy/commit/cdd44e610ec0180141f7086e75d4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Log Message: ----------- Merge pull request #2044 from martenson/disable-repo-push Disable repo push for TS repositories Compare: https://github.com/galaxyproject/galaxy/compare/829c84c8cb01...cdd44e610ec0

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[galaxyproject/galaxy] dc4d4c: disable 'hg push' to TS repositories deprecated in...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc4d4cbce7b18b33ff09f722d58a551c6f024b7a https://github.com/galaxyproject/galaxy/commit/dc4d4cbce7b18b33ff09f722d58a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#depre… Commit: 7d08d1b0699a9e2adfa314af3e8324e257254ce0 https://github.com/galaxyproject/galaxy/commit/7d08d1b0699a9e2adfa314af3e83… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Specify default value when getting disable_push Commit: a560ad8999eca1137aafa466ae07683ef9f6d9d3 https://github.com/galaxyproject/galaxy/commit/a560ad8999eca1137aafa466ae07… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Update Tool Shed tests after disabling 'hg push' Commit: 28b5dd36832642b5ae519790c25fc2d15da11ca9 https://github.com/galaxyproject/galaxy/commit/28b5dd36832642b5ae519790c25f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0310_hg_clone.py Log Message: ----------- add TS test for disabled hg push Commit: 0bcc7e37e1d94259c6b5c29ab7e8041e4228d05d https://github.com/galaxyproject/galaxy/commit/0bcc7e37e1d94259c6b5c29ab7e8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_clone.py Log Message: ----------- rename test to reflect insides Commit: 193eeaa60674eaa1badb65f74cb77dcb331b179b https://github.com/galaxyproject/galaxy/commit/193eeaa60674eaa1badb65f74cb7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2056 from martenson/1601-disable-push [16.01] retroactively disable Mercurial push API in TS Commit: 829c84c8cb0125706b1f801b08bcb2e281f92d57 https://github.com/galaxyproject/galaxy/commit/829c84c8cb0125706b1f801b08bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/10db8ec8febc...829c84c8cb01

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galaxy-commits March 2016