galaxy-commits August 2015

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] 6c8226: Merge nearly-identical methods in shed_util_common...
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c82266546c77361f9d2265ab749db1446142150 https://github.com/galaxyproject/galaxy/commit/6c82266546c77361f9d2265ab749… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge nearly-identical methods in shed_util_common. Commit: d74dfbefd4f24fa93a437b782d340d4fd152c079 https://github.com/galaxyproject/galaxy/commit/d74dfbefd4f24fa93a437b782d34… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add missing docstring. Commit: bb7cbc7ee556f6a0146e669792f5cc953893cf98 https://github.com/galaxyproject/galaxy/commit/bb7cbc7ee556f6a0146e669792f5… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correct parameters. Commit: 5d4d32a43221d4a0725a2d16d6bac02c9b867d4d https://github.com/galaxyproject/galaxy/commit/5d4d32a43221d4a0725a2d16d6ba… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #651 from davebx/suc_cleanup Merge nearly-identical methods in shed_util_common. Compare: https://github.com/galaxyproject/galaxy/compare/0409ad6c4a54...5d4d32a43221

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[galaxyproject/galaxy] 3261a7: remove reports style that affected the whole appli...
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3261a76828dd0e7bc834aa8a53f9e3851b59219e https://github.com/galaxyproject/galaxy/commit/3261a76828dd0e7bc834aa8a53f9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css Log Message: ----------- remove reports style that affected the whole application fixes https://github.com/galaxyproject/galaxy/pull/656/files#r38132110 Commit: 0409ad6c4a54a65b666ffbd7fbc99c3a31898b3d https://github.com/galaxyproject/galaxy/commit/0409ad6c4a54a65b666ffbd7fbc9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css Log Message: ----------- Merge pull request #661 from martenson/remove-sideeffecting-style remove reports style that affected the whole application Compare: https://github.com/galaxyproject/galaxy/compare/9711a60b82c7...0409ad6c4a54

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[galaxyproject/galaxy] d59c84: Dataset manager: allow deserializing permissions
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d59c846dc3b3bd53ab592c4db5bfec7f0a3ffec1 https://github.com/galaxyproject/galaxy/commit/d59c846dc3b3bd53ab592c4db5bf… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-24 (Fri, 24 Jul 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Dataset manager: allow deserializing permissions Commit: 9444b2eb271d03c0719b6706c830404c5567e88d https://github.com/galaxyproject/galaxy/commit/9444b2eb271d03c0719b6706c830… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/managers/datasets.py Log Message: ----------- Dataset manager: deserialize permissions Commit: 9711a60b82c74c697f550348e5d3fdd1f3333082 https://github.com/galaxyproject/galaxy/commit/9711a60b82c74c697f550348e5d3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #640 from carlfeberhard/managers Allow deserializing dataset permissions Compare: https://github.com/galaxyproject/galaxy/compare/e95804125522...9711a60b82c7

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[galaxyproject/galaxy] 1c0dac: Recursively look for package elements within tool_...
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c0daceb8fa2f9c1b4a458817aaab0c3ab3926f3 https://github.com/galaxyproject/galaxy/commit/1c0daceb8fa2f9c1b4a458817aaa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Recursively look for package elements within tool_dependencies.xml, otherwise packages needed for install, but specified within install/actions/actions groups with not be installed. Commit: 86a39cb20c79ce42fe208e5d748a536c4fa4dbbd https://github.com/galaxyproject/galaxy/commit/86a39cb20c79ce42fe208e5d748a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Cleanup in metadata_generator.py Commit: 6eb9c155857d3c85d847ce33b1e962f5fc092330 https://github.com/galaxyproject/galaxy/commit/6eb9c155857d3c85d847ce33b1e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Composition of error messages in toolshed metadata stuff. Commit: dde800b54f30fe875039507949f7ab5737b241d9 https://github.com/galaxyproject/galaxy/commit/dde800b54f30fe875039507949f7… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #2 from dannon/recurse-toolshed-changeset Collect error messages (which fixes the current travis build), some other cleanup for sanity. Commit: 30bb209e8db52455992320f3e02c62c28afb7770 https://github.com/galaxyproject/galaxy/commit/30bb209e8db52455992320f3e02c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- During installation, make invalid repository dependency definitions non-fatal errors. Commit: dc6700eec50f679f5d344eeaf8c0641f8869c6c4 https://github.com/galaxyproject/galaxy/commit/dc6700eec50f679f5d344eeaf8c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Fix yield statements at the top level of macros. Fixes #647. Commit: a3a209b8a001b8a841ea9a03ca206346bbcab439 https://github.com/galaxyproject/galaxy/commit/a3a209b8a001b8a841ea9a03ca20… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #528 from blankenberg/recurse-toolshed-changeset [15.07] Recursively look for package elements within tool_dependencies.xml when setting metadata, Commit: 71125326f842860b163b889b514cf10036915ca7 https://github.com/galaxyproject/galaxy/commit/71125326f842860b163b889b514c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-25 (Tue, 25 Aug 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge pull request #649 from jmchilton/yield_at_top_level [15.07] Fix yield statements at the top level of macros. Commit: 224c20d4b2cf0d24605f0956fe2c742bef1d6ae7 https://github.com/galaxyproject/galaxy/commit/224c20d4b2cf0d24605f0956fe2c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/util/xml_macros.py M lib/tool_shed/metadata/metadata_generator.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'release_15.07' Commit: e9580412552299d82d3e627fcf3bde45d5e95a26 https://github.com/galaxyproject/galaxy/commit/e9580412552299d82d3e627fcf3b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/util/xml_macros.py M lib/tool_shed/metadata/metadata_generator.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'master' into dev Conflicts: lib/tool_shed/metadata/metadata_generator.py Compare: https://github.com/galaxyproject/galaxy/compare/4a4ed87f11c8...e95804125522

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[galaxyproject/galaxy] b01d20: Fix for server error when installing some repos.
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: b01d20b1be9e1cf579a3c2bd42a3d524548d2240 https://github.com/galaxyproject/galaxy/commit/b01d20b1be9e1cf579a3c2bd42a3… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix for server error when installing some repos. Examples: IUC's gatk2 repository, devteam's samtools_rmdup. When attempting to install either of those, or another repository that has tool tests with an input parameter that does not have a value attribute, the repository would be stuck in state 'Cloning' and show a debug link in the log. This commit resolves that error. Commit: 19c85e070534f4318cca3e728c52c91a27163f4a https://github.com/galaxyproject/galaxy/commit/19c85e070534f4318cca3e728c52… Author: Jeremy Goecks <jgoecks(a)gwu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js Log Message: ----------- Fixes to make Sweepster work again: (a) update template syntax to match changes made in underscore v1.7 and (b) update tool rerun to account for API changes. Commit: 04a5bd78f021968ccd1b98eec2968ecdc3c93f77 https://github.com/galaxyproject/galaxy/commit/04a5bd78f021968ccd1b98eec296… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix: rdata extension type Commit: a1cc1ed94bba19bcc131f41d6cfc80fe1ca03009 https://github.com/galaxyproject/galaxy/commit/a1cc1ed94bba19bcc131f41d6cfc… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix: Typo the other way. Supposed to be "RData" Ref: https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html Commit: ac43237e49e8660b1812f8662d081d4b0d3bf3de https://github.com/galaxyproject/galaxy/commit/ac43237e49e8660b1812f8662d08… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Fix for toolshed escape method, where an error/log message contains non-ASCII characters. Commit: d2e61e8af4c933b733c640f46f831bf424bc0197 https://github.com/galaxyproject/galaxy/commit/d2e61e8af4c933b733c640f46f83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Filter deleted library datasets Commit: 8d96580fc20e2a6322fdacb1b25635fb4573c934 https://github.com/galaxyproject/galaxy/commit/8d96580fc20e2a6322fdacb1b256… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Correct examples in workflow invocations. Commit: 51991f03caf3b1ed15d4672160cf0f50e6e537db https://github.com/galaxyproject/galaxy/commit/51991f03caf3b1ed15d4672160cf… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: R templates/webapps/tool_shed/message.mako Log Message: ----------- Stop creating database/message.mako.py Commit: 64edf4e2f953f21e4e52c6647a65960c6c44945a https://github.com/galaxyproject/galaxy/commit/64edf4e2f953f21e4e52c6647a65… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M templates/webapps/reports/base_panels.mako Log Message: ----------- fix the class for reports brand so it is actually shown and not black text on dark background Commit: 4fcdf9fda1d21ec5669daa8e9a4e3e84171bb617 https://github.com/galaxyproject/galaxy/commit/4fcdf9fda1d21ec5669daa8e9a4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js M lib/galaxy/datatypes/binary.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge pull request #657 from jmchilton/dev_1507_backports [15.07] Backport various dev fixes. Compare: https://github.com/galaxyproject/galaxy/compare/71125326f842...4fcdf9fda1d2

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[galaxyproject/galaxy] 1041ca: Centered headers in firefox
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1041cad9ec4f50837158f8bbfe5d27f9e3db7d0e https://github.com/galaxyproject/galaxy/commit/1041cad9ec4f50837158f8bbfe5d… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_specified_month_in_error.mako Log Message: ----------- Centered headers in firefox Made page selection divs not wrap when window size is too small Changed name for action in Jobs in error per day this month which fixes crash Commit: 865d0153954e3be07d139f6100d21bdf5543a2f9 https://github.com/galaxyproject/galaxy/commit/865d0153954e3be07d139f6100d2… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/ui/ui-button-menu.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-popover.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/tool_data_table_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/jstree.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/render.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/common_util.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/ui/ui-button-menu.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/ui/ui-button-menu.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css 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/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py M test/tool_shed/functional_tests.py M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar M test/unit/test_galaxy_mapping.py M test/unit/tools/test_toolbox_filters.py R tool-data/fastx_clipper_sequences.txt M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: static/style/blue/base.css Commit: 4a4ed87f11c8a47dcc838bdc6a42389def73afe9 https://github.com/galaxyproject/galaxy/commit/4a4ed87f11c8a47dcc838bdc6a42… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_specified_month_in_error.mako Log Message: ----------- Merge pull request #656 from Airistotal/dev Reports - Small bug fixes Compare: https://github.com/galaxyproject/galaxy/compare/f5ca24ee2bae...4a4ed87f11c8

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[galaxyproject/galaxy] b8362b: Include link expiration time in password reset ema...
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b8362b71509013566694280cb89e967dca704a31 https://github.com/galaxyproject/galaxy/commit/b8362b71509013566694280cb89e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Include link expiration time in password reset email. Commit: 299d628531bba44d403bc191b53ae09437f050be https://github.com/galaxyproject/galaxy/commit/299d628531bba44d403bc191b53a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Validate user email input prior to attempting to reset. Commit: 29d510f7dee48bf54776773f8a2f971781b08052 https://github.com/galaxyproject/galaxy/commit/29d510f7dee48bf54776773f8a2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Force lowercase comparison for password reset. TODO: Look for more places this is potentially an issue. Commit: a98e3ff6de51d0fe43db97ade602ccd6b8eea468 https://github.com/galaxyproject/galaxy/commit/a98e3ff6de51d0fe43db97ade602… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Swap to config.pretty_datetime_format Commit: 9356ae5f3fa6155b68eba98b8eac9862bd53ba57 https://github.com/galaxyproject/galaxy/commit/9356ae5f3fa6155b68eba98b8eac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Switch password reset tokens to use UTC. This is kind of a mess, we're using both UTC and localized time in various places. Commit: c337fccbeb967c782339b5f6c812daa70014dc99 https://github.com/galaxyproject/galaxy/commit/c337fccbeb967c782339b5f6c812… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Use case-insensitive email selection only when case-sensitive comes up empty. Commit: f5ca24ee2baea35ad7a3bc62db7f5a996ccaa2a7 https://github.com/galaxyproject/galaxy/commit/f5ca24ee2baea35ad7a3bc62db7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #655 from dannon/password_reset_tweaks Password reset tweaks Compare: https://github.com/galaxyproject/galaxy/compare/949b3de56860...f5ca24ee2bae

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[galaxyproject/galaxy] 2fccd0: Finish flake8 of test/ .
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2fccd0c11f91fedabd979fc62064e4ea31a33ae2 https://github.com/galaxyproject/galaxy/commit/2fccd0c11f91fedabd979fc62064… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M test/base/asserts/__init__.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py Log Message: ----------- Finish flake8 of test/ . Commit: 6f1e1cea82aae5695b669a57d870ec173f6b8d6a https://github.com/galaxyproject/galaxy/commit/6f1e1cea82aae5695b669a57d870… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/qunit/package.json Log Message: ----------- Add mandatory "version" field to package.json . Commit: 93716ec08a1c5aedd476b137ed2b670b2e73d114 https://github.com/galaxyproject/galaxy/commit/93716ec08a1c5aedd476b137ed2b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/qunit/README.txt Log Message: ----------- Suggest to install grunt-cli globally to have grunt in PATH. Commit: 949b3de56860242c6c20c04e0b18ffc694384b76 https://github.com/galaxyproject/galaxy/commit/949b3de56860242c6c20c04e0b18… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M test/base/asserts/__init__.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/qunit/README.txt M test/qunit/package.json Log Message: ----------- Merge pull request #653 from nsoranzo/dev Finish flake8 of test/ . Compare: https://github.com/galaxyproject/galaxy/compare/c2fca17c9830...949b3de56860

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[galaxyproject/galaxy] 7f167e: Add developer documentation to docs
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f167ef3640d7bdb7e37f2b398a7d81cd15cfc83 https://github.com/galaxyproject/galaxy/commit/7f167ef3640d7bdb7e37f2b398a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: A doc/source/_api_quickstart.rst A doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/ts_api_doc.rst Log Message: ----------- Add developer documentation to docs - Extract quickstart - reorg GX/TS Doc index Commit: 1762fcde056d72414c31241c1f3965c214ad7be7 https://github.com/galaxyproject/galaxy/commit/1762fcde056d72414c31241c1f39… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: R doc/source/_api_quickstart.rst Log Message: ----------- Remove unused file Commit: b339dbf585bd6f2924de516a99823e93e4f3a6e7 https://github.com/galaxyproject/galaxy/commit/b339dbf585bd6f2924de516a9982… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- s/python/Python in FAQ Commit: 364a714aac3b422178b01d9bf0ac8e1a8bee6100 https://github.com/galaxyproject/galaxy/commit/364a714aac3b422178b01d9bf0ac… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #7 from dannon/repl s/python/Python in FAQ Commit: c2fca17c98305ca24c3ec415bd9bcbe5695a382f https://github.com/galaxyproject/galaxy/commit/c2fca17c98305ca24c3ec415bd9b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: A doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/ts_api_doc.rst Log Message: ----------- Merge pull request #654 from erasche/repl Galaxy Developer Documentation Compare: https://github.com/galaxyproject/galaxy/compare/aea250334f31...c2fca17c9830

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[galaxyproject/galaxy] 7b3fbc: Expose tool config file path to admins via the API...
by GitHub 26 Aug '15

26 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7b3fbcbd7f4e4464e7471b9d634165a20e24e834 https://github.com/galaxyproject/galaxy/commit/7b3fbcbd7f4e4464e7471b9d6341… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Expose tool config file path to admins via the API. This is useful (not to mention already kinda exposed when using wrappers) for interfacing with planemo for the smc work and I would expect other automation tasks. Commit: 5e9d1becfca27882ab9a106df2ea80e3d7d96404 https://github.com/galaxyproject/galaxy/commit/5e9d1becfca27882ab9a106df2ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Actually use the method instead of just checking it's existence Commit: dc7f7f2e3babf35dab06297245464fe16b97c8de https://github.com/galaxyproject/galaxy/commit/dc7f7f2e3babf35dab0629724546… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Fix mock_trans to provide a user_is_admin member Commit: aea250334f319788aa6281bdb2d4ddfdfcb12b84 https://github.com/galaxyproject/galaxy/commit/aea250334f319788aa6281bdb2d4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools/test_toolbox_filters.py Log Message: ----------- Merge pull request #652 from dannon/tool_path_expose Expose tool config file path to admins via the API. This is useful (… Compare: https://github.com/galaxyproject/galaxy/compare/b0f2eaec0312...aea250334f31

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