galaxy-commits September 2015

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[galaxyproject/usegalaxy-playbook] 18417d: Update Test Galaxy and Pulsar, enable AMQP acknowl...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 18417dd20bf1ea56bf2e162b16ac64c545f21334 https://github.com/galaxyproject/usegalaxy-playbook/commit/18417dd20bf1ea56… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M stage/group_vars/all.yml M stage/group_vars/pulsarservers.yml M stage/host_vars/greenfield.psc.xsede.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Update Test Galaxy and Pulsar, enable AMQP acknowledgements

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[galaxyproject/galaxy] e95145: With Pulsar, ensure AMQP consumers receive publish...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e951455be37a787a26678e66e607004a9b8ce954 https://github.com/galaxyproject/galaxy/commit/e951455be37a787a26678e66e607… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- With Pulsar, ensure AMQP consumers receive published messages. Commit: 5bae90156fa7998b575981ac452db21f34683085 https://github.com/galaxyproject/galaxy/commit/5bae90156fa7998b575981ac452d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/util.py Log Message: ----------- Fix a couple flake8 errors including a supposed PEP-8 violation that is actually a PEP-8-suggested acceptable option of how to handle the offending situation. =P Commit: 8778da43cb641a925c421b188aabe053be56e313 https://github.com/galaxyproject/galaxy/commit/8778da43cb641a925c421b188aab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/manager.py Log Message: ----------- Disable amqp_acknowledge by default, additional fixes from Pulsar's pickier flake8 checks. Commit: ff8e821013e59527bb2bdfacffef2a2db7e562d2 https://github.com/galaxyproject/galaxy/commit/ff8e821013e59527bb2bdfacffef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Merge pull request #704 from natefoo/amqp_ack [15.07] With Pulsar, ensure AMQP consumers receive published messages Commit: 448ff738f35ad3f8d627257f46c681a6a4907778 https://github.com/galaxyproject/galaxy/commit/448ff738f35ad3f8d627257f46c6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- fix incorrect indentation preventing changing of name/description of TS categories Commit: 16fb094f1a101064d6f2981166b060b1ba30aa0e https://github.com/galaxyproject/galaxy/commit/16fb094f1a101064d6f2981166b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Merge pull request #717 from martenson/fix-ts-edit-category [15.07] fix incorrect indentation preventing changing of name/description Commit: 91799c3891fe60f94fc52501541326904cc96071 https://github.com/galaxyproject/galaxy/commit/91799c3891fe60f94fc525015413… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Merge branch 'release_15.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9ef883db64b...91799c3891fe

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[galaxyproject/galaxy] 448ff7: fix incorrect indentation preventing changing of n...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 448ff738f35ad3f8d627257f46c681a6a4907778 https://github.com/galaxyproject/galaxy/commit/448ff738f35ad3f8d627257f46c6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- fix incorrect indentation preventing changing of name/description of TS categories Commit: 16fb094f1a101064d6f2981166b060b1ba30aa0e https://github.com/galaxyproject/galaxy/commit/16fb094f1a101064d6f2981166b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Merge pull request #717 from martenson/fix-ts-edit-category [15.07] fix incorrect indentation preventing changing of name/description Compare: https://github.com/galaxyproject/galaxy/compare/ff8e821013e5...16fb094f1a10

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[galaxyproject/infrastructure-playbook] 113caf: Install git on n2
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 113caf158f19ced6abfc95152328e8bf38db5f06 https://github.com/galaxyproject/infrastructure-playbook/commit/113caf158f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- Install git on n2

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[galaxyproject/galaxy] 451196: Fix for logging in using OpenID when the OpenID is...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 451196e4d39800995d7b1ea1f69b177294c3c632 https://github.com/galaxyproject/galaxy/commit/451196e4d39800995d7b1ea1f69b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Fix for logging in using OpenID when the OpenID isn't associated with a user yet. Commit: c9ef883db64bbf9e2d4f9b8bc2dea11f8e4be60d https://github.com/galaxyproject/galaxy/commit/c9ef883db64bbf9e2d4f9b8bc2de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Merge pull request #712 from blankenberg/openid_associate_fix Fix for logging in using OpenID when the OpenID isn't associated Compare: https://github.com/galaxyproject/galaxy/compare/b79555264e6f...c9ef883db64b

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[galaxyproject/galaxy]
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/revert-704-amqp_ack Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] fab314: Revert "[15.07] With Pulsar, ensure AMQP consumers...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/revert-704-amqp_ack Home: https://github.com/galaxyproject/galaxy Commit: fab314265f7e14c0bc488b25bbff27074c0dd1be https://github.com/galaxyproject/galaxy/commit/fab314265f7e14c0bc488b25bbff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Revert "[15.07] With Pulsar, ensure AMQP consumers receive published messages"

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[galaxyproject/galaxy] e95145: With Pulsar, ensure AMQP consumers receive publish...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: e951455be37a787a26678e66e607004a9b8ce954 https://github.com/galaxyproject/galaxy/commit/e951455be37a787a26678e66e607… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- With Pulsar, ensure AMQP consumers receive published messages. Commit: 5bae90156fa7998b575981ac452db21f34683085 https://github.com/galaxyproject/galaxy/commit/5bae90156fa7998b575981ac452d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/util.py Log Message: ----------- Fix a couple flake8 errors including a supposed PEP-8 violation that is actually a PEP-8-suggested acceptable option of how to handle the offending situation. =P Commit: 8778da43cb641a925c421b188aabe053be56e313 https://github.com/galaxyproject/galaxy/commit/8778da43cb641a925c421b188aab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/manager.py Log Message: ----------- Disable amqp_acknowledge by default, additional fixes from Pulsar's pickier flake8 checks. Commit: ff8e821013e59527bb2bdfacffef2a2db7e562d2 https://github.com/galaxyproject/galaxy/commit/ff8e821013e59527bb2bdfacffef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Merge pull request #704 from natefoo/amqp_ack [15.07] With Pulsar, ensure AMQP consumers receive published messages Compare: https://github.com/galaxyproject/galaxy/compare/1203ccc49cbf...ff8e821013e5

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[galaxyproject/usegalaxy-playbook] 18e9a0: Remove Anton and myself from reserved, add Jen
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 18e9a07a40be2036b121e855a9514ebf99cadf28 https://github.com/galaxyproject/usegalaxy-playbook/commit/18e9a07a40be2036… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py Log Message: ----------- Remove Anton and myself from reserved, add Jen

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[galaxyproject/usegalaxy-playbook] 0612fa: Update test to b79555264e6f1d7b042bd5650efeed14832...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0612fabefa5e72d4bc5cdcff385591c35a7e462e https://github.com/galaxyproject/usegalaxy-playbook/commit/0612fabefa5e72d4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update test to b79555264e6f1d7b042bd5650efeed1483252095.

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galaxy-commits September 2015