galaxy-commits March 2016

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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/release_16.01 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 Compare: https://github.com/galaxyproject/galaxy/compare/7c94ac8d93b8...193eeaa60674

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[galaxyproject/usegalaxy-playbook] d03432: Test mutable configs
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d03432cc8dbf1f6e618b688658d0d59e2bf0cbb0 https://github.com/galaxyproject/usegalaxy-playbook/commit/d03432cc8dbf1f6e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs Commit: 4638020908509da2746151fb17a91c20395a6a6f https://github.com/galaxyproject/usegalaxy-playbook/commit/4638020908509da2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Testing Jetstream destination Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a4218f633e91...…

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[galaxyproject/infrastructure-playbook] d1d1c9: Update common_roles
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d1d1c905e3ba13327b94496c6184c18a7ec3a44d https://github.com/galaxyproject/infrastructure-playbook/commit/d1d1c905e3b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M common_roles Log Message: ----------- Update common_roles Commit: ac9ff2d689124fb857a99f6c5b7381429c9caad0 https://github.com/galaxyproject/infrastructure-playbook/commit/ac9ff2d6891… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M common_roles M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml M taccenv/group_vars/statsservers.yml M taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/infrastructure-playbook Conflicts: common_roles Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/c8c20d2ffa…

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[galaxyproject/galaxy] d730d1: Remove microseconds when parsing datetimes for MyS...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d730d1db4034b2b7152e4e847ecb1e8821450322 https://github.com/galaxyproject/galaxy/commit/d730d1db4034b2b7152e4e847ecb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/managers/base.py Log Message: ----------- Remove microseconds when parsing datetimes for MySQL Fix #2037. Commit: 2bb9fd62ab27820ba85778dbdc4605a2c4f2bf00 https://github.com/galaxyproject/galaxy/commit/2bb9fd62ab27820ba85778dbdc46… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M .gitignore Log Message: ----------- Add database/jobs_directory to .gitignore Commit: 10db8ec8febc910cb00345ceedfc8614b326237b https://github.com/galaxyproject/galaxy/commit/10db8ec8febc910cb00345ceedfc… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M .gitignore M lib/galaxy/managers/base.py Log Message: ----------- Merge pull request #2042 from nsoranzo/fix_for_2037 Remove microseconds when parsing datetimes for MySQL. Compare: https://github.com/galaxyproject/galaxy/compare/b160cd52f301...10db8ec8febc

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[galaxyproject/galaxy] f9f7ba: use dictobj as standard dependency
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9f7ba49fe5a78a6d78e63c9af13ba02573623f3 https://github.com/galaxyproject/galaxy/commit/f9f7ba49fe5a78a6d78e63c9af13… 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 M lib/galaxy/dependencies/requirements.txt M lib/galaxy/util/jstree.py Log Message: ----------- use dictobj as standard dependency Commit: 36df74be2fd1418d5ba7b403a2d70ae51ffa741b https://github.com/galaxyproject/galaxy/commit/36df74be2fd1418d5ba7b403a2d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: R lib/galaxy/util/dictobj.py Log Message: ----------- remove dictobj.py as we now import it properly Commit: 8681b5f83160a04f05284f57fc04bb29bf3c7721 https://github.com/galaxyproject/galaxy/commit/8681b5f83160a04f05284f57fc04… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- remove import from dictobj and move func to the wrapper itself Commit: b160cd52f30165b511bd44911eab88492079444b https://github.com/galaxyproject/galaxy/commit/b160cd52f30165b511bd44911eab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt R lib/galaxy/util/dictobj.py M lib/galaxy/util/jstree.py M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #2046 from martenson/jstree-dictobj use dictobj as standard dependency Compare: https://github.com/galaxyproject/galaxy/compare/9214acb96b75...b160cd52f301

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[galaxyproject/galaxy] cba0e0: Fix workflow importing (when missing tools) broken...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cba0e01b7310a4994395a79c2599bde7a06ac300 https://github.com/galaxyproject/galaxy/commit/cba0e01b7310a4994395a79c2599… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow importing (when missing tools) broken in 0dac0c207757cf160901df387214dcfc56016469 Commit: 4e5a9df7a1f1084b89275e22c0060fc440262978 https://github.com/galaxyproject/galaxy/commit/4e5a9df7a1f1084b89275e22c006… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- py3 exception 'as' syntax. Commit: 9214acb96b7592c86f08e52688e30ee49dc23a86 https://github.com/galaxyproject/galaxy/commit/9214acb96b7592c86f08e52688e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #2048 from dannon/workflow_import_fix Workflow import fix when tools are missing. Compare: https://github.com/galaxyproject/galaxy/compare/853fed9b9fff...9214acb96b75

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[galaxyproject/infrastructure-playbook] c8c20d: Properly update access list...
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c8c20d2ffad15c1c632cd1c410cdfc6223274cce https://github.com/galaxyproject/infrastructure-playbook/commit/c8c20d2ffad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Properly update access list...

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[galaxyproject/infrastructure-playbook] 4428c7: Update common_roles
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4428c72eea944e7a5eab52e4c8544779b5a1434b https://github.com/galaxyproject/infrastructure-playbook/commit/4428c72eea9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M common_roles Log Message: ----------- Update common_roles Commit: af4fb4984e66643dcd1ba8373b025b22ed2b6878 https://github.com/galaxyproject/infrastructure-playbook/commit/af4fb4984e6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M common_roles Log Message: ----------- Update common_roles Commit: 3041f30d89aed34b39e47c62aa9ca22eab3509c1 https://github.com/galaxyproject/infrastructure-playbook/commit/3041f30d89a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Update access list for orval Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/b55fdbafe0…

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[galaxyproject/galaxy]
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/revert-1537-handlebars.removal Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy]
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/revert-2033-remove-hg-direct-api Home: https://github.com/galaxyproject/galaxy

1 0

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galaxy-commits March 2016