galaxy-commits March 2016

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[galaxyproject/galaxy] 9f0ddf: Revise input wrapper, add test cases
by GitHub 30 Mar '16

30 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f0ddf57bb0b82b0225b2975982ef0579957a03f https://github.com/galaxyproject/galaxy/commit/9f0ddf57bb0b82b0225b2975982e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/style/blue/base.css A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js Log Message: ----------- Revise input wrapper, add test cases Commit: 2687002a27adf43ec526077cbd8bdaca214dc83b https://github.com/galaxyproject/galaxy/commit/2687002a27adf43ec526077cbd8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/style/blue/base.css A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js Log Message: ----------- Merge pull request #2027 from guerler/revise_input_000 Revise input wrapper, add test cases Compare: https://github.com/galaxyproject/galaxy/compare/aee2ed98a01e...2687002a27ad

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[galaxyproject/galaxy] 991e06: enable obfs datatype during upload
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 991e069ef284e7669e5dece818aef510189b2d15 https://github.com/galaxyproject/galaxy/commit/991e069ef284e7669e5dece818ae… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- enable obfs datatype during upload Commit: aee2ed98a01ef9f93623dc33b0b5730c3fbfc30b https://github.com/galaxyproject/galaxy/commit/aee2ed98a01ef9f93623dc33b0b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #2028 from bgruening/obfs_in_upload enable obfs datatype during upload Compare: https://github.com/galaxyproject/galaxy/compare/ad12042f5f17...aee2ed98a01e

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[galaxyproject/galaxy] e6d352: [16.01] Fix for running jobs when metadata tool is...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e6d3529b4c85708bb0b1fbea32e8ce36921e60e1 https://github.com/galaxyproject/galaxy/commit/e6d3529b4c85708bb0b1fbea32e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- [16.01] Fix for running jobs when metadata tool is not in toolbox. Happens when -installed or -migrated are passed into run_tests.sh because of the way the tool shed hacks up Galaxy's tool config. Commit: 68ca4b9237a5c44a88377c32cecc9014013c32cc https://github.com/galaxyproject/galaxy/commit/68ca4b9237a5c44a88377c32cecc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #2024 from jmchilton/metadata_tool_fix [16.01] Fix for running jobs when metadata tool is not in toolbox. Compare: https://github.com/galaxyproject/galaxy/compare/948a4aa55bf9...68ca4b9237a5

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[galaxyproject/galaxy] a9d51f: Don't setup a default tool_data_table_config_path ...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9d51f6dfe3748f7db5bfd1d128f03a8b6558656 https://github.com/galaxyproject/galaxy/commit/a9d51f6dfe3748f7db5bfd1d128f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Don't setup a default tool_data_table_config_path in the TS. Commit: ad12042f5f17fc2b7facc08dc5628bdafc94eca3 https://github.com/galaxyproject/galaxy/commit/ad12042f5f17fc2b7facc08dc562… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #2025 from jmchilton/ts_tool_data_table_config Don't setup a default tool_data_table_config_path in the shed. Compare: https://github.com/galaxyproject/galaxy/compare/71d8b4a6c123...ad12042f5f17

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[galaxyproject/galaxy] 1be896: data_column to json config file
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1be896fd157dffcd5c2f9b20dd0a5fc866faadbe https://github.com/galaxyproject/galaxy/commit/1be896fd157dffcd5c2f9b20dd0a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- data_column to json config file Commit: 71d8b4a6c123f05aaedffd0e38db0d921b7a0410 https://github.com/galaxyproject/galaxy/commit/71d8b4a6c123f05aaedffd0e38db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- Merge pull request #2026 from bgruening/param_configfile_data_column data_column to json config file Compare: https://github.com/galaxyproject/galaxy/compare/5a7ba04cd9f8...71d8b4a6c123

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[galaxyproject/galaxy] 962866: Remove install and test framework.
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 962866478a020b3fc794f76f89696ada60881d17 https://github.com/galaxyproject/galaxy/commit/962866478a020b3fc794f76f8969… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-25 (Fri, 25 Mar 2016) Changed paths: R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py Log Message: ----------- Remove install and test framework. Commit: 5a7ba04cd9f85661a4681b00427b3c1aa815d988 https://github.com/galaxyproject/galaxy/commit/5a7ba04cd9f85661a4681b00427b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py Log Message: ----------- Merge pull request #2018 from jmchilton/remove_iat Remove install and test code. Compare: https://github.com/galaxyproject/galaxy/compare/62fae769345e...5a7ba04cd9f8

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[galaxyproject/usegalaxy-playbook] a4218f: Replaced GCC2016 abstracts due slide: March 25 is ...
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4218f633e911fc458dcdf30516b2820b4fbdd38 https://github.com/galaxyproject/usegalaxy-playbook/commit/a4218f633e911fc4… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016OralAbstractsDueApril8.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Replaced GCC2016 abstracts due slide: March 25 is now April 8

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[galaxyproject/galaxy] 207af3: Fix multiple flag for workflow dataset inputs
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 207af3d97565885491096488621c0f7bd664b8e4 https://github.com/galaxyproject/galaxy/commit/207af3d97565885491096488621c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix multiple flag for workflow dataset inputs Commit: 62fae769345e75c3852fc89f867bbc36cdb3423e https://github.com/galaxyproject/galaxy/commit/62fae769345e75c3852fc89f867b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2021 from guerler/fix_collection_002 Fix multiple flag for workflow dataset inputs Compare: https://github.com/galaxyproject/galaxy/compare/18300c9dc66a...62fae769345e

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[galaxyproject/galaxy] ee0a65: fix duplication of select2 entries
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee0a65bf13a1fff8084aa19fdfd4831b66dd096d https://github.com/galaxyproject/galaxy/commit/ee0a65bf13a1fff8084aa19fdfd4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix duplication of select2 entries leverage caching Commit: 2c76ba7502c9fa99d2b02f44d79009b119a243f8 https://github.com/galaxyproject/galaxy/commit/2c76ba7502c9fa99d2b02f44d790… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- repack client Commit: 18300c9dc66af06fb24601a5f907be8e5ff18dcb https://github.com/galaxyproject/galaxy/commit/18300c9dc66af06fb24601a5f907… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #2022 from martenson/fix-select-dup fix duplication of select2 entries Compare: https://github.com/galaxyproject/galaxy/compare/625d9e53c3c9...18300c9dc66a

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[galaxyproject/galaxy] f70df2: Upgrade content selector, add test cases
by GitHub 29 Mar '16

29 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f70df2206097ec99683e0433c597ad2b2ac2decf https://github.com/galaxyproject/galaxy/commit/f70df2206097ec99683e0433c597… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/tests/ui_tests.js Log Message: ----------- Upgrade content selector, add test cases Commit: d0f7ce260d42daf21a26a30dd0d5ae1d4cf01ebb https://github.com/galaxyproject/galaxy/commit/d0f7ce260d42daf21a26a30dd0d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-27 (Sun, 27 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js R static/maps/mvc/form/form-select-content.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/form/form-select-content.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js M test/qunit/tests/ui_tests.js Log Message: ----------- Add workflow content selectors and test cases Commit: 625d9e53c3c91ddde6c59b6a02e5163acbc5add3 https://github.com/galaxyproject/galaxy/commit/625d9e53c3c91ddde6c59b6a02e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/style/blue/base.css M test/qunit/test-app.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #2011 from guerler/revise_content_select_000 Revise content selection, add test cases Compare: https://github.com/galaxyproject/galaxy/compare/5b16589f2901...625d9e53c3c9

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galaxy-commits March 2016