- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0eb87f: Minor docstring typo
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0eb87f911c4523ecb268b26ad8c74a0252ce8453 https://github.com/galaxyproject/galaxy/commit/0eb87f911c4523ecb268b26ad8c7… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Minor docstring typo Commit: 4289cf3ab2f92375e6e4d9751064325b55cceaae https://github.com/galaxyproject/galaxy/commit/4289cf3ab2f92375e6e4d9751064… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1235 from blankenberg/typo_dev Minor docstring typo Compare: https://github.com/galaxyproject/galaxy/compare/905471e32fef...4289cf3ab2f9

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[galaxyproject/galaxy] 1adff9: Wait on jobs and history in certain API test cases...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1adff983f2509e6551f9000008d614a61d9b12a6 https://github.com/galaxyproject/galaxy/commit/1adff983f2509e6551f9000008d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Wait on jobs and history in certain API test cases. This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases. Commit: 905471e32fef02b9da38d2efe0cc463cd258cbff https://github.com/galaxyproject/galaxy/commit/905471e32fef02b9da38d2efe0cc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #1226 from jmchilton/jobs_api_test_fix Wait on jobs and history in certain API test cases. Compare: https://github.com/galaxyproject/galaxy/compare/5c87d07e0f53...905471e32fef

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[galaxyproject/galaxy] f969ea: Fix qunit shim to match base_panels.mako shim.
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f969eabf268a2e07235083d37168ae9887f87876 https://github.com/galaxyproject/galaxy/commit/f969eabf268a2e07235083d37168… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Fix qunit shim to match base_panels.mako shim. QUnit tests of things with underscore require statements would not work without this change. Commit: 5c87d07e0f535ed3367bbd463fb16bc0d83d7cf9 https://github.com/galaxyproject/galaxy/commit/5c87d07e0f535ed3367bbd463fb1… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/qunit/test-common.js Log Message: ----------- Merge pull request #1233 from jmchilton/underscore_shim Fix qunit shim to match base_panels.mako shim. Compare: https://github.com/galaxyproject/galaxy/compare/74f7b9003680...5c87d07e0f53

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[galaxyproject/usegalaxy-playbook] a30639: Increase Pulsar AMQP ack republish time to 3 minut...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a306396df1daa8474dcef64036e541d134c45021 https://github.com/galaxyproject/usegalaxy-playbook/commit/a306396df1daa847… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M production/host_vars/login5.stampede.tacc.utexas.edu.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 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase Pulsar AMQP ack republish time to 3 minutes (default is 30 seconds)

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[galaxyproject/galaxy] 102eee: Replacement should be applied only to first occurr...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 102eeef2d7045fa5b8706497f04817cb2f75813a https://github.com/galaxyproject/galaxy/commit/102eeef2d7045fa5b8706497f048… Author: Takao Nakaguchi <takao.nakaguchi(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Replacement should be applied only to first occurrence. Commit: 74f7b900368030e425f79f835e2093102dbed5ba https://github.com/galaxyproject/galaxy/commit/74f7b900368030e425f79f835e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Merge pull request #1230 from openlangrid/dev Replacement should be applied only to first occurrence. Compare: https://github.com/galaxyproject/galaxy/compare/600338dac7b0...74f7b9003680

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[galaxyproject/galaxy] 0c8a73: Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c8a738a35d8c28b18dba6da92ec702096c1554a https://github.com/galaxyproject/galaxy/commit/0c8a738a35d8c28b18dba6da92ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION before installing wheels. Fix #1205. As test/docker/base/run_test_wrapper.sh does. Commit: 600338dac7b0dad7f514f1b9a3c7c123dd63c379 https://github.com/galaxyproject/galaxy/commit/600338dac7b0dad7f514f1b9a3c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1231 from nsoranzo/dev_tests_conditional_wheels Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION before installing wheels. Compare: https://github.com/galaxyproject/galaxy/compare/fcabc5242ca8...600338dac7b0

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[galaxyproject/usegalaxy-playbook] 51b1d2: Update test to fcabc5242ca8fc6b1e7533ade17e2a8e3d2...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 51b1d23743fbcd531f3cbc677515d2f5b4cc8e42 https://github.com/galaxyproject/usegalaxy-playbook/commit/51b1d23743fbcd53… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update test to fcabc5242ca8fc6b1e7533ade17e2a8e3d27fe82

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[galaxyproject/galaxy] 6e185f: Allowed for capitailsed packgae name such as R
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e185fa208c27564b4cd2db5e31f55bf58c6eb4e https://github.com/galaxyproject/galaxy/commit/6e185fa208c27564b4cd2db5e31f… Author: Christian-B <github(a)brenn.co.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Allowed for capitailsed packgae name such as R Commit: fcabc5242ca8fc6b1e7533ade17e2a8e3d27fe82 https://github.com/galaxyproject/galaxy/commit/fcabc5242ca8fc6b1e7533ade17e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Merge pull request #1160 from Christian-B/unlinked_dependencies Allowed for capitalised package names such as R Compare: https://github.com/galaxyproject/galaxy/compare/11c46f4f35f3...fcabc5242ca8

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[galaxyproject/galaxy] 51cd41: Fix ScIdx sniff method to handle first line commen...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51cd41be94ea4e5af50201bbd0e85ade21774e69 https://github.com/galaxyproject/galaxy/commit/51cd41be94ea4e5af50201bbd0e8… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx sniff method to handle first line comment Commit: c04b3a5bb557c836e60c060f68598ea314fc9521 https://github.com/galaxyproject/galaxy/commit/c04b3a5bb557c836e60c060f6859… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Re-add egg imports Commit: 30b13bb1d6e576c4f6e32f4e98b08c9a3a5651eb https://github.com/galaxyproject/galaxy/commit/30b13bb1d6e576c4f6e32f4e98b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1203 from gregvonkuster/release_15.10 [15.10] Fix ScIdx sniff method to handle first line comment Commit: a5b7e6cb8e90387a7b9f6acb79b80a2114fa3928 https://github.com/galaxyproject/galaxy/commit/a5b7e6cb8e90387a7b9f6acb79b8… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). Commit: ee5a87af2e3d0a76da5df398826478bc4854c599 https://github.com/galaxyproject/galaxy/commit/ee5a87af2e3d0a76da5df3988264… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for updating tool parameter dicts when a new parameter has been added to a section. Fixes issues seen during rerun under mentioned condition. Commit: d83e8d358f1b04683fa20245a66f12a8d881be4e https://github.com/galaxyproject/galaxy/commit/d83e8d358f1b04683fa20245a66f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1215 from blankenberg/rerunfix_15.10 [15.10] Fix for updating tool parameter dicts when a new parameter has been added to a section Commit: c9abc2bc97dbdbe85c82946ca1138a6f6139bb33 https://github.com/galaxyproject/galaxy/commit/c9abc2bc97dbdbe85c82946ca113… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Fix for test/tool_shed/functional/test_1440_missing_env_sh_files.py . Properly order the installation of the repositories adding prior_installation_required="True". Otherwise filter_1440 is installed first and ends in INSTALLED status because of the logic of Repository.create_tool_dependency_with_initialized_env_sh_file() method contained in lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py . Commit: 2b697e3c1ae76e4c718ed558e88a3c387d6e35c9 https://github.com/galaxyproject/galaxy/commit/2b697e3c1ae76e4c718ed558e88a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository. Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py . Commit: d1684e7c9d9dc42918004dc15bf1e7d039c96088 https://github.com/galaxyproject/galaxy/commit/d1684e7c9d9dc42918004dc15bf1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1224 from jmchilton/collection_naming_performance [15.10] Backport #1217 Commit: 516b079ab97d7fc0a40255d03dcaf2cb600a2384 https://github.com/galaxyproject/galaxy/commit/516b079ab97d7fc0a40255d03dca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge pull request #1222 from nsoranzo/release_15.10_tool_shed_fixes [15.10] Tool Shed fixes. Commit: 11c46f4f35f3c1cb579198d28402ebacd51e6ec8 https://github.com/galaxyproject/galaxy/commit/11c46f4f35f3c1cb579198d28402… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e76933b55749...11c46f4f35f3

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[galaxyproject/galaxy] 51cd41: Fix ScIdx sniff method to handle first line commen...
by GitHub 04 Dec '15

04 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 51cd41be94ea4e5af50201bbd0e85ade21774e69 https://github.com/galaxyproject/galaxy/commit/51cd41be94ea4e5af50201bbd0e8… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx sniff method to handle first line comment Commit: c04b3a5bb557c836e60c060f68598ea314fc9521 https://github.com/galaxyproject/galaxy/commit/c04b3a5bb557c836e60c060f6859… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Re-add egg imports Commit: 30b13bb1d6e576c4f6e32f4e98b08c9a3a5651eb https://github.com/galaxyproject/galaxy/commit/30b13bb1d6e576c4f6e32f4e98b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1203 from gregvonkuster/release_15.10 [15.10] Fix ScIdx sniff method to handle first line comment Commit: a5b7e6cb8e90387a7b9f6acb79b80a2114fa3928 https://github.com/galaxyproject/galaxy/commit/a5b7e6cb8e90387a7b9f6acb79b8… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). Commit: ee5a87af2e3d0a76da5df398826478bc4854c599 https://github.com/galaxyproject/galaxy/commit/ee5a87af2e3d0a76da5df3988264… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for updating tool parameter dicts when a new parameter has been added to a section. Fixes issues seen during rerun under mentioned condition. Commit: d83e8d358f1b04683fa20245a66f12a8d881be4e https://github.com/galaxyproject/galaxy/commit/d83e8d358f1b04683fa20245a66f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1215 from blankenberg/rerunfix_15.10 [15.10] Fix for updating tool parameter dicts when a new parameter has been added to a section Commit: c9abc2bc97dbdbe85c82946ca1138a6f6139bb33 https://github.com/galaxyproject/galaxy/commit/c9abc2bc97dbdbe85c82946ca113… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Fix for test/tool_shed/functional/test_1440_missing_env_sh_files.py . Properly order the installation of the repositories adding prior_installation_required="True". Otherwise filter_1440 is installed first and ends in INSTALLED status because of the logic of Repository.create_tool_dependency_with_initialized_env_sh_file() method contained in lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py . Commit: 2b697e3c1ae76e4c718ed558e88a3c387d6e35c9 https://github.com/galaxyproject/galaxy/commit/2b697e3c1ae76e4c718ed558e88a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository. Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py . Commit: d1684e7c9d9dc42918004dc15bf1e7d039c96088 https://github.com/galaxyproject/galaxy/commit/d1684e7c9d9dc42918004dc15bf1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1224 from jmchilton/collection_naming_performance [15.10] Backport #1217 Commit: 516b079ab97d7fc0a40255d03dcaf2cb600a2384 https://github.com/galaxyproject/galaxy/commit/516b079ab97d7fc0a40255d03dca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge pull request #1222 from nsoranzo/release_15.10_tool_shed_fixes [15.10] Tool Shed fixes. Compare: https://github.com/galaxyproject/galaxy/compare/da2cc588e5a5...516b079ab97d

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[galaxyproject/galaxy] 6735c9: replace the readthedocs badge,
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6735c9deceadba39c0a2b34b076f37440c087fc3 https://github.com/galaxyproject/galaxy/commit/6735c9deceadba39c0a2b34b076f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst Log Message: ----------- replace the readthedocs badge, we cannot use it until https://github.com/rtfd/readthedocs.org/issues/1767 is resolved Commit: e76933b55749c619c4debf4e62cd1f4d7e3cb7e1 https://github.com/galaxyproject/galaxy/commit/e76933b55749c619c4debf4e62cd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst Log Message: ----------- Merge pull request #1229 from martenson/remove-readthecdocs-badge replace the readthedocs badge, Compare: https://github.com/galaxyproject/galaxy/compare/9a1fc647a380...e76933b55749

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[galaxyproject/galaxy]
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/revert-1222-release_15.10_tool_shed_fixes Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 1b9b05: Revert "[15.10] Tool Shed fixes."
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/revert-1222-release_15.10_tool_shed_fixes Home: https://github.com/galaxyproject/galaxy Commit: 1b9b05d40d1c50e37390740cbf6f6e50cf9db61d https://github.com/galaxyproject/galaxy/commit/1b9b05d40d1c50e37390740cbf6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Revert "[15.10] Tool Shed fixes."

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[galaxyproject/galaxy] c9abc2: Fix for test/tool_shed/functional/test_1440_missin...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: c9abc2bc97dbdbe85c82946ca1138a6f6139bb33 https://github.com/galaxyproject/galaxy/commit/c9abc2bc97dbdbe85c82946ca113… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Fix for test/tool_shed/functional/test_1440_missing_env_sh_files.py . Properly order the installation of the repositories adding prior_installation_required="True". Otherwise filter_1440 is installed first and ends in INSTALLED status because of the logic of Repository.create_tool_dependency_with_initialized_env_sh_file() method contained in lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py . Commit: 2b697e3c1ae76e4c718ed558e88a3c387d6e35c9 https://github.com/galaxyproject/galaxy/commit/2b697e3c1ae76e4c718ed558e88a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository. Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py . Commit: 516b079ab97d7fc0a40255d03dcaf2cb600a2384 https://github.com/galaxyproject/galaxy/commit/516b079ab97d7fc0a40255d03dca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge pull request #1222 from nsoranzo/release_15.10_tool_shed_fixes [15.10] Tool Shed fixes. Compare: https://github.com/galaxyproject/galaxy/compare/d1684e7c9d9d...516b079ab97d

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[galaxyproject/infrastructure-playbook] 13c670: Packages for starforge builders
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 13c6704efbd933deed082176f94d788d0abfa7a0 https://github.com/galaxyproject/infrastructure-playbook/commit/13c6704efbd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M galaxyenv/group_vars/starforgebuilders.yml Log Message: ----------- Packages for starforge builders Commit: fb562c67c2943d50d4178d2f04aa06ab5acb60c8 https://github.com/galaxyproject/infrastructure-playbook/commit/fb562c67c29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M galaxyenv/host_vars/delirium.galaxyproject.org.yml M galaxyenv/secret_group_vars/all.yml A galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Add a docs user to delirium for jenkins to update docs.galaxyproject.org Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/8597fdb06f…

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[galaxyproject/galaxy] dd7bdd: Optimize initial queueing of jobs.
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd7bddcaa682d6d7cdaba8661c2c7cc80997ade0 https://github.com/galaxyproject/galaxy/commit/dd7bddcaa682d6d7cdaba8661c2c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Optimize initial queueing of jobs. - Don't refresh job when this is the only thread fetching it. - Avoid a bunch of unnecessary flushes, just flush once essentially during process. Brings this process from taking over 1 second per job on average on sqlite for cat1 on my laptop to around 400 ms on average. Commit: 299fbe99d7e157b9c01bbf0cdfcb7057dd59791a https://github.com/galaxyproject/galaxy/commit/299fbe99d7e157b9c01bbf0cdfcb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Micro optimization, only fetch tool validation once per multi-run. Commit: 876c28f88d81a8599a3278d9deac730adbac10d9 https://github.com/galaxyproject/galaxy/commit/876c28f88d81a8599a3278d9deac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py Log Message: ----------- Add more job timers. Commit: 41d3dc62f7e967ea3b409be410310563d0737bc4 https://github.com/galaxyproject/galaxy/commit/41d3dc62f7e967ea3b409be41031… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py Log Message: ----------- Parallelize executing tool parameter combinations. Should work when mapping over collections or for big muli-run tool submissions. Because of database tension with sqlalchemy it is not strictly a linear increase, but the end user walltime experience for a 24 dataset collection being submitted using 4 threads instead 1 drops execution time from 68 seconds to 35. Rebased with fixes thanks to @nsoranzo - https://github.com/jmchilton/galaxy/commit/7f6514a21222ea787a0676764e4a4fe8…. Commit: 64b7cc9fef21caac5f9d21a8d42b60262fd28162 https://github.com/galaxyproject/galaxy/commit/64b7cc9fef21caac5f9d21a8d42b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add sample tool that creates 10 outputs. Commit: a190b69e33a41717ddcc9eaa82826a82cc3d69b1 https://github.com/galaxyproject/galaxy/commit/a190b69e33a41717ddcc9eaa8282… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Optimize tools that produce multiple outputs. Fetch HIDs for these datasets all at once and flush once for all assignments. Creating jobs from 4 threads each job producing 10 outputs - this resulted in reducing the runtime of this portion of the code by 90% and saving around 20 seconds per job. Before: galaxy.tools.actions INFO 2015-11-30 15:53:46,235 Add outputs to history (22494.829 ms) galaxy.tools.actions INFO 2015-11-30 15:53:47,295 Add outputs to history (22239.062 ms) galaxy.tools.actions INFO 2015-11-30 15:53:48,320 Add outputs to history (23781.079 ms) galaxy.tools.actions INFO 2015-11-30 15:53:51,490 Add outputs to history (21820.567 ms) galaxy.tools.actions INFO 2015-11-30 15:54:24,506 Add outputs to history (25353.837 ms) After: galaxy.tools.actions INFO 2015-11-30 16:08:47,640 Add outputs to history (2781.675 ms) galaxy.tools.actions INFO 2015-11-30 16:08:47,860 Add outputs to history (3177.738 ms) galaxy.tools.actions INFO 2015-11-30 16:08:48,776 Add outputs to history (2425.528 ms) galaxy.tools.actions INFO 2015-11-30 16:09:02,942 Add outputs to history (2579.022 ms) Commit: ab2c7c2c079b51ffd4ed7ef00724ef3f8d2636ec https://github.com/galaxyproject/galaxy/commit/ab2c7c2c079b51ffd4ed7ef00724… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool execution micro optimization... ... Don't create an extra list to reverse, just iterate over in reversed order. Commit: 9a1fc647a38007fef2a7a179648ea8f925ab5a8f https://github.com/galaxyproject/galaxy/commit/9a1fc647a38007fef2a7a179648e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1212 from jmchilton/tool_opts_6 Smaller Tool Optimization PR Compare: https://github.com/galaxyproject/galaxy/compare/14ac3665ee37...9a1fc647a380

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[galaxyproject/usegalaxy-playbook] 3f14df: $PATH is necessary. $VIRTUAL_ENV probably isn't.
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3f14dfcddc36dc40c80222fe94d8b7678c7bb8bd https://github.com/galaxyproject/usegalaxy-playbook/commit/3f14dfcddc36dc40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M templates/supervisor/galaxy.conf.j2 Log Message: ----------- $PATH is necessary. $VIRTUAL_ENV probably isn't.

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[galaxyproject/galaxy] a5b7e6: Updated tool input collection to only add items fr...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: a5b7e6cb8e90387a7b9f6acb79b80a2114fa3928 https://github.com/galaxyproject/galaxy/commit/a5b7e6cb8e90387a7b9f6acb79b8… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). Commit: d1684e7c9d9dc42918004dc15bf1e7d039c96088 https://github.com/galaxyproject/galaxy/commit/d1684e7c9d9dc42918004dc15bf1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1224 from jmchilton/collection_naming_performance [15.10] Backport #1217 Compare: https://github.com/galaxyproject/galaxy/compare/d83e8d358f1b...d1684e7c9d9d

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[galaxyproject/galaxy] 3374f9: Use asynchronous API calls for metadata reset.
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3374f948f4eba1a57a7fd863491545b082f56fa4 https://github.com/galaxyproject/galaxy/commit/3374f948f4eba1a57a7fd8634915… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako Log Message: ----------- Use asynchronous API calls for metadata reset. Commit: 2bd158dcbd9633c6fc03ca28c19d63b5d33781fd https://github.com/galaxyproject/galaxy/commit/2bd158dcbd9633c6fc03ca28c19d… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako Log Message: ----------- Minor cleanup. Commit: bc22944326944f6de80b2f70650bf6020bfe1d21 https://github.com/galaxyproject/galaxy/commit/bc22944326944f6de80b2f70650b… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako Log Message: ----------- More cleanup. Commit: c11c07d9bb124d41a301c5adf8f81c42b99430cc https://github.com/galaxyproject/galaxy/commit/c11c07d9bb124d41a301c5adf8f8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .gitignore A CODE_OF_CONDUCT.md M CONTRIBUTING.md M CONTRIBUTORS.md M README.rst M client/GruntFile.js M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M client/galaxy/scripts/libs/jquery/select2.js A client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-login.js A client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-panel.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M 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client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tags.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js A 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test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_execution.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox_filters.py M test/unit/unittest_utils/utility.py M test/unit/workflows/test_modules.py R tool-data/fastx_clipper_sequences.txt R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml M tools/data_source/data_source.py R tools/data_source/echo.py R tools/data_source/echo.xml R tools/data_source/ucsc_archaea.xml R 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tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.xml M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into async_metadata_reset Commit: 14ac3665ee37224aa5278ce7a3876fb204b1bf2d https://github.com/galaxyproject/galaxy/commit/14ac3665ee37224aa5278ce7a387… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako Log Message: ----------- Merge pull request #598 from davebx/async_metadata_reset Make bulk repository metadata resets asynchronous. Compare: https://github.com/galaxyproject/galaxy/compare/92a7b995b05f...14ac3665ee37

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[galaxyproject/galaxy] 362a25: Updated tool input collection to only add items fr...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 362a25e6e6b03dfada43ad1b9ab651966936c795 https://github.com/galaxyproject/galaxy/commit/362a25e6e6b03dfada43ad1b9ab6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). Commit: 92a7b995b05f7966e2936b62f052d3a4b8ed0642 https://github.com/galaxyproject/galaxy/commit/92a7b995b05f7966e2936b62f052… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1217 from ericenns/collection-tool-input-fixes Collection tool input mapping performance fixes Compare: https://github.com/galaxyproject/galaxy/compare/a57095661246...92a7b995b05f

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[galaxyproject/galaxy] aea04a: Added better support for formats that store triple...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aea04a98715d921eacf86d58ebf5fd754ecfcad1 https://github.com/galaxyproject/galaxy/commit/aea04a98715d921eacf86d58ebf5… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/graph.py A lib/galaxy/datatypes/triples.py Log Message: ----------- Added better support for formats that store triples, these formats include 'N-Triples', 'N3','Turtle','RDF/XML' and 'JSON-LD' Commit: e097de3570cb525687ee1800c1582375c6e22b94 https://github.com/galaxyproject/galaxy/commit/e097de3570cb525687ee1800c158… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/datatypes/triples.py Log Message: ----------- PEP-8 fixes for triples.py and to flake checks. Commit: e714759d409a3099ba04284de8167f66af32424e https://github.com/galaxyproject/galaxy/commit/e714759d409a3099ba04284de816… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py Log Message: ----------- Add restore as deprecated old path to RDF. It will be in many old datatype_conf.xml files so perhaps it should be deprecated before removing it completely. Using this new infrastructure - people will be warned if the they load it from the old location and told to update datatypes_conf.xml to reference the new location. Commit: c9e27c9425932573d7c7503dedb655ef62a92914 https://github.com/galaxyproject/galaxy/commit/c9e27c9425932573d7c7503dedb6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/triples.py Log Message: ----------- File reading infrastructure for datatypes. Use to ensure triple-related datatypes properly close file handles and restrict the amount of memory they consume when reading lines from files. Commit: 82f62bc14768e66fc1fb127058acd1c17e4ce3e1 https://github.com/galaxyproject/galaxy/commit/82f62bc14768e66fc1fb127058ac… Author: Jesse <jesse.vandam(a)wur.nl> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M .ci/pep8_sources.txt M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/triples.py Log Message: ----------- Merge pull request #1 from jmchilton/triples Various fixes for triples.py. Commit: 6c3cedcfd517ac6af3c109a6eec2c555a8313d84 https://github.com/galaxyproject/galaxy/commit/6c3cedcfd517ac6af3c109a6eec2… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- fix sniffers of the triple format Commit: e5d1b4ee26a16d6f9859de0d1f5ee5b5113430c4 https://github.com/galaxyproject/galaxy/commit/e5d1b4ee26a16d6f9859de0d1f5e… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- fix comment in triples.py (example for regexp) Commit: c03f84b1d76285f75d3b5f84c06e31fc5bf54f96 https://github.com/galaxyproject/galaxy/commit/c03f84b1d76285f75d3b5f84c06e… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/triples.py Log Message: ----------- use sizehint from python readline(s) function for sniffers in triples.py Commit: 94c00b0238d50d9703609000d25f6b1bc56a9281 https://github.com/galaxyproject/galaxy/commit/94c00b0238d50d9703609000d25f… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-06-25 (Thu, 25 Jun 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- PEP-8 fixes to triples.py Commit: ae1a56e26d1931add633970a206b97aff3f45dae https://github.com/galaxyproject/galaxy/commit/ae1a56e26d1931add633970a206b… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-06-26 (Fri, 26 Jun 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- Make the RDF sniffer in triples.py a bit more specific Commit: fb2784003d39e7ae8ce144ff7ab793f65d4771d8 https://github.com/galaxyproject/galaxy/commit/fb2784003d39e7ae8ce144ff7ab7… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R 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static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/masthead.css A static/style/blue/reports.css M static/style/blue/sprite-fugue.png M static/style/blue/sprite-history-buttons.png M static/style/blue/sprite-history-states.png M static/style/blue/trackster.css R static/welcome.rst M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/base.mako M templates/display_base.mako A templates/page_base.mako M templates/search/index.mako M templates/show_params.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/tagging_common.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako R templates/webapps/galaxy/cloud/index.mako A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako A templates/webapps/reports/run_stats.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-history-permission-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js M test/functional/test_admin_features.py M test/functional/test_data_managers.py M test/functional/test_data_security.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_toolbox.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml A test/functional/tools/environment_variables.xml A test/functional/tools/output_collection_filter.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/test_db_util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample R tool-data/fastx_clipper_sequences.txt M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample M tool_list.py M tools/data_source/data_source.py M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: .ci/pep8_sources.txt lib/galaxy/datatypes/graph.py Commit: c873d565834b8aa9f5d39901e025bbcec5fa2631 https://github.com/galaxyproject/galaxy/commit/c873d565834b8aa9f5d39901e025… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/galaxy/datatypes/graph.py Log Message: ----------- graph.RDF got defined twice after merge Commit: ba054a189ef8efe922154c34462bf49d104d1abe https://github.com/galaxyproject/galaxy/commit/ba054a189ef8efe922154c34462b… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/galaxy/datatypes/graph.py Log Message: ----------- pip8 problem Commit: 37f3bbf26772f78af132527a1aa19a8da60fb540 https://github.com/galaxyproject/galaxy/commit/37f3bbf26772f78af132527a1aa1… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- improved the specificity for the xml/rdf sniffer Commit: 1444c101aaee74d5e6512a475295970973be68df https://github.com/galaxyproject/galaxy/commit/1444c101aaee74d5e6512a475295… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- pip8 fix Commit: 4203ab5b1f032d6f0bcda11295c2856171b738ce https://github.com/galaxyproject/galaxy/commit/4203ab5b1f032d6f0bcda11295c2… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- fix Commit: 00e58e21f93b0a13caacc23081e02ea4b140bf66 https://github.com/galaxyproject/galaxy/commit/00e58e21f93b0a13caacc23081e0… Author: Jesse c j van Dam <jesse.vandam(a)wur.nl> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- changed log.warn to print because log.warn will stop a job Commit: a443d99fddc14b58698618860076032cb9540dca https://github.com/galaxyproject/galaxy/commit/a443d99fddc14b58698618860076… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py Log Message: ----------- Undo deprecated datatypes stuff, doesn't work with Galaxy well. Commit: 4c13c92540c7ed4f8305dcb0216c2a448f33c24d https://github.com/galaxyproject/galaxy/commit/4c13c92540c7ed4f8305dcb0216c… Author: Jesse <jesse.vandam(a)wur.nl> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/graph.py Log Message: ----------- Merge pull request #2 from jmchilton/triples_2 Remove deprecated datatype stuff Commit: a57095661246fab1d9045e0cabb1845f662edb5d https://github.com/galaxyproject/galaxy/commit/a57095661246fab1d9045e0cabb1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/graph.py A lib/galaxy/datatypes/triples.py Log Message: ----------- Merge pull request #396 from jessevdam/dev Added better support for formats that store triples. Compare: https://github.com/galaxyproject/galaxy/compare/65e6a1c3b6ca...a57095661246

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[galaxyproject/usegalaxy-playbook] a733df: Set $VIRTUAL_ENV for handlers.
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a733df0551b48378276c6c529b8262b8e5f18670 https://github.com/galaxyproject/usegalaxy-playbook/commit/a733df0551b48378… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M common_infrastructure.yml M galaxy_infrastructure.yml M templates/supervisor/galaxy.conf.j2 Log Message: ----------- Set $VIRTUAL_ENV for handlers.

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[galaxyproject/galaxy] 97415d: Move idpDB and MzSQlite formats from proteomics.py...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97415de3ce2bda54fb0730a41b4e0c7d8e93778a https://github.com/galaxyproject/galaxy/commit/97415de3ce2bda54fb0730a41b4e… Author: chambm <matt.chambers42(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 Log Message: ----------- Move idpDB and MzSQlite formats from proteomics.py to binary.py, because the SQLite sniffer lives there, and more specialized formats must be registered for sniffing before the generic format Add proper idpDB sniffing logic (akin to MzSQlite) and test case Add H5 sniffing based on magic number and test case Add SQLite/IdpDB/MzSQlite/GeminiSQLite and H5 to default datatypes in registry.py Commit: 65e6a1c3b6ca26e9f0d760cb39be7ec177d6c40f https://github.com/galaxyproject/galaxy/commit/65e6a1c3b6ca26e9f0d760cb39be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 Log Message: ----------- Merge pull request #1209 from chambm/feature/idpdb_hdf5_sniffers Add idpDB and HDF5 sniffers and fix MzSQlite sniffer Compare: https://github.com/galaxyproject/galaxy/compare/c034dc3e33a4...65e6a1c3b6ca

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[galaxyproject/galaxy] ee5a87: Fix for updating tool parameter dicts when a new p...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ee5a87af2e3d0a76da5df398826478bc4854c599 https://github.com/galaxyproject/galaxy/commit/ee5a87af2e3d0a76da5df3988264… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for updating tool parameter dicts when a new parameter has been added to a section. Fixes issues seen during rerun under mentioned condition. Commit: d83e8d358f1b04683fa20245a66f12a8d881be4e https://github.com/galaxyproject/galaxy/commit/d83e8d358f1b04683fa20245a66f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1215 from blankenberg/rerunfix_15.10 [15.10] Fix for updating tool parameter dicts when a new parameter has been added to a section Compare: https://github.com/galaxyproject/galaxy/compare/30b13bb1d6e5...d83e8d358f1b

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[galaxyproject/galaxy] 3de857: Add debug statement in output checker for why job ...
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3de8579633c4294abb2a3235f90463108c35d324 https://github.com/galaxyproject/galaxy/commit/3de8579633c4294abb2a3235f904… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py Log Message: ----------- Add debug statement in output checker for why job is failing. Should help tool testing and other Galaxy testing. Commit: c034dc3e33a4c4aeecefcea375ea179621be1af6 https://github.com/galaxyproject/galaxy/commit/c034dc3e33a4c4aeecefcea375ea… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py Log Message: ----------- Merge pull request #1213 from jmchilton/tool_logging_2 Add debug statement in output checker for why job is failing. Compare: https://github.com/galaxyproject/galaxy/compare/20b96d883d9e...c034dc3e33a4

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