September 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4f9d5d: WIP a bunch of GIE javascript that probabaly won't...
by GitHub 27 Sep '17

27 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 4f9d5df34fb84e2547a280ab7536491a66e1da28 https://github.com/galaxyproject/galaxy/commit/4f9d5df34fb84e2547a280ab7536… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- WIP a bunch of GIE javascript that probabaly won't work Commit: 04b03b28530455ff850f41215c2cfa15b597ef19 https://github.com/galaxyproject/galaxy/commit/04b03b28530455ff850f41215c2c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js Log Message: ----------- Make the URL spinner actually work. Commit: 7edeedd7fe123ad8740f830e4c7b5e8478552137 https://github.com/galaxyproject/galaxy/commit/7edeedd7fe123ad8740f830e4c7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js Log Message: ----------- Additional GIE spinning fixes for when the error condition is not a timeout. Commit: 180bfe718485bdfd05233402d4720f67f114d88f https://github.com/galaxyproject/galaxy/commit/180bfe718485bdfd05233402d472… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js Log Message: ----------- Treat timeouts and errors the same, except that timeouts step the ajax timeout of the next request. Also fixes for toastr messages. Commit: 40900d76a96bb76542653e2c2bf886c7d88e9552 https://github.com/galaxyproject/galaxy/commit/40900d76a96bb76542653e2c2bf8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Re-enable keepalive, build client. Commit: c235382ceefb09e28c987621164f9f40450f1ed1 https://github.com/galaxyproject/galaxy/commit/c235382ceefb09e28c987621164f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- No need for this keep_alive invocation after all; removes the commented out code. Commit: 242755ee9f6a267e416a525bbf69ef513c35a2f4 https://github.com/galaxyproject/galaxy/commit/242755ee9f6a267e416a525bbf69… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge pull request #7 from dannon/gie_fixes Re-enable keepalive, build client. Commit: 8230d14fad3765585517e02a6b74126835f46fce https://github.com/galaxyproject/galaxy/commit/8230d14fad3765585517e02a6b74… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge pull request #4680 from natefoo/gie-client [17.09] Client side fixes for GIEs Compare: https://github.com/galaxyproject/galaxy/compare/1c5c046a63d6...8230d14fad37

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[galaxyproject/galaxy] 744ea8: Update versions of conda and conda-build
by GitHub 27 Sep '17

27 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 744ea8289ee29572775d2d606ab31a15e2cf4b12 https://github.com/galaxyproject/galaxy/commit/744ea8289ee29572775d2d606ab3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Update versions of conda and conda-build Creating environments for (some) Python packages now requires conda 4.3 due to the conda-forge `python`: ``` $ conda create -n __crossmap(a)0.2.2 crossmap=0.2.2 Fetching package metadata ............... ... Linking packages ... Installing conda-forge::wheel-0.30.0-py_1 requires a minimum conda version of 4.3. ``` Commit: 9075976669be95c4ee1b505fb952d246660a6f2c https://github.com/galaxyproject/galaxy/commit/9075976669be95c4ee1b505fb952… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Support conda create --offline for Conda >= 4.3.18. Commit: 1c5c046a63d6afd160d6cb7dcafd4ec273ec029a https://github.com/galaxyproject/galaxy/commit/1c5c046a63d6afd160d6cb7dcafd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #4701 from nsoranzo/release_17.09_update_conda_version [17.09] Update versions of conda and conda-build Compare: https://github.com/galaxyproject/galaxy/compare/3ae6318b02e6...1c5c046a63d6

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[galaxyproject/galaxy] b893e5: Use enumeration to provide history input index nam...
by GitHub 26 Sep '17

26 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b893e579619a29811d0a709d34e5decda2ca1bf7 https://github.com/galaxyproject/galaxy/commit/b893e579619a29811d0a709d34e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Use enumeration to provide history input index names Commit: 8f33cc627f53e4940e193a7f2d32a4cfc1efb1cf https://github.com/galaxyproject/galaxy/commit/8f33cc627f53e4940e193a7f2d32… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #4700 from guerler/history_rename_input_names Use enumeration to provide history input index names Compare: https://github.com/galaxyproject/galaxy/compare/df14b8dd02ed...8f33cc627f53

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[galaxyproject/galaxy] a373bb: Add client-side routes to connect visualization ed...
by GitHub 26 Sep '17

26 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a373bbbfe506b81fbfd260002124be4d02b8a853 https://github.com/galaxyproject/galaxy/commit/a373bbbfe506b81fbfd260002124… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client-side routes to connect visualization edit controller endpoint with front-end form builder Commit: 3e4b0a247123107a2ffe2e0e1fb8ecd6c19e9ee9 https://github.com/galaxyproject/galaxy/commit/3e4b0a247123107a2ffe2e0e1fb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add client input element definition for visualization editing form Commit: ed11e87f9b567307ad12820f55c51d0b23880241 https://github.com/galaxyproject/galaxy/commit/ed11e87f9b567307ad12820f55c5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add help text to annotation field, remove redundant visualization label from inputs Commit: 279ccd11cd830dbcd298ebc9ec45d4d872d9ab9c https://github.com/galaxyproject/galaxy/commit/279ccd11cd830dbcd298ebc9ec45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add support to save changed attributes Commit: 1547d1b91e930b438162364db4ae8b7ed6e23a69 https://github.com/galaxyproject/galaxy/commit/1547d1b91e930b438162364db4ae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/mvc/grid/grid-shared.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-shared.js Log Message: ----------- Add message handling support Commit: 78aa69d456c3bd47531651bc36760e7de98b53e8 https://github.com/galaxyproject/galaxy/commit/78aa69d456c3bd47531651bc3676… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add error handler Commit: 6dec4f79e6492cd9d33f76edd67522c6341fb572 https://github.com/galaxyproject/galaxy/commit/6dec4f79e6492cd9d33f76edd675… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add text sanitization, remove comments Commit: 1578f92e074298fd9304b79ce1dca298578f8b8b https://github.com/galaxyproject/galaxy/commit/1578f92e074298fd9304b79ce1dc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Flush visualization with new attributes to database Commit: 43bd4e6abd0a61d69ee91f5fe26b6d36b0d716bb https://github.com/galaxyproject/galaxy/commit/43bd4e6abd0a61d69ee91f5fe26b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: R templates/webapps/galaxy/visualization/create.mako Log Message: ----------- Remove visualization edit mako Commit: 88f135d0d3b283ba81f911bac410ff9ba7f149d8 https://github.com/galaxyproject/galaxy/commit/88f135d0d3b283ba81f911bac410… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Add support to change dbkey for visualizations after creation Commit: 4ee1473bab78dbb02b3c4fb7c96fdb4a40c95089 https://github.com/galaxyproject/galaxy/commit/4ee1473bab78dbb02b3c4fb7c96f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Remove trackster specific create form, visualizations are created through the visualization icon in the history Commit: 9ceb4ac2ec42296ea6af126f747fe6cd8abf5d06 https://github.com/galaxyproject/galaxy/commit/9ceb4ac2ec42296ea6af126f747f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Revise help text, make visualization dbkey optional since many do not require it Commit: daa973a5d9e47cb9cc92dd8b83823fe8be7f7f52 https://github.com/galaxyproject/galaxy/commit/daa973a5d9e47cb9cc92dd8b8382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/visualization/genomes.py Log Message: ----------- Improve resilience of backend if genome build is missing Fix Commit: b482ac162b8e04a88afdca9bf56ca6a8a05ee2f0 https://github.com/galaxyproject/galaxy/commit/b482ac162b8e04a88afdca9bf56c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CITATION M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/api/search.py R scripts/binary_compatibility.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/data_libraries/build_lucene_index.py M scripts/dump_tour.py M scripts/edam_mapping.py M scripts/fetch_eggs.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/manage_tool_dependencies.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/paster.py M scripts/rst2html.py M scripts/summarize_timings.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M templates/display_base.mako M templates/display_common.mako M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/twilltestcase.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py A test/unit/__init__.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge branch 'dev' into replace_visualization_edit_form Commit: df14b8dd02edb01b122704b89c459a928e698039 https://github.com/galaxyproject/galaxy/commit/df14b8dd02edb01b122704b89c45… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/grid/grid-shared.js M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/mvc/grid/grid-shared.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-shared.js R templates/webapps/galaxy/visualization/create.mako Log Message: ----------- Merge pull request #4682 from guerler/replace_visualization_edit_form Remove visualization edit form mako Compare: https://github.com/galaxyproject/galaxy/compare/0dd7f01008d2...df14b8dd02ed

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[galaxyproject/galaxy] 7921c8: Use client builder for history renaming form
by GitHub 26 Sep '17

26 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7921c8b8963c0b32a3d737de7f58f0d56ccf8c90 https://github.com/galaxyproject/galaxy/commit/7921c8b8963c0b32a3d737de7f58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/history-list.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-list.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/history/history-list.js Log Message: ----------- Use client builder for history renaming form Commit: 7a9d22e4dfbb167c971c165712f6f8a6c7c95367 https://github.com/galaxyproject/galaxy/commit/7a9d22e4dfbb167c971c165712f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/rename.mako Log Message: ----------- Remove history rename mako Commit: ced5b1c3b6699e4fe3c9590f20fa35273020e0c0 https://github.com/galaxyproject/galaxy/commit/ced5b1c3b6699e4fe3c9590f20fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Properly handle history lists, sanitze messages Commit: b074fbac084c206664dcc5bb2c22ffc8d80f3360 https://github.com/galaxyproject/galaxy/commit/b074fbac084c206664dcc5bb2c22… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Add a message indicating that history names have not been changed by user Commit: 4bca5670bd800b1fa0937c6740166873a718a8a9 https://github.com/galaxyproject/galaxy/commit/4bca5670bd800b1fa0937c674016… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Change message Commit: 788bf6dd5a4b2cbf4220b2b98215a8836a026335 https://github.com/galaxyproject/galaxy/commit/788bf6dd5a4b2cbf4220b2b98215… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove debug statement Commit: bb8664d29552273c5bdd1ab070666241797f3324 https://github.com/galaxyproject/galaxy/commit/bb8664d29552273c5bdd1ab07066… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Avoid redefining warning message, remove blank lines Commit: 52b100e6a27abdfea333b2ed8b3ecf883f6c52c7 https://github.com/galaxyproject/galaxy/commit/52b100e6a27abdfea333b2ed8b3e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix import order in history controller Commit: afe1ea7f20aa49ced11bb49d0d6322bfc6e00371 https://github.com/galaxyproject/galaxy/commit/afe1ea7f20aa49ced11bb49d0d63… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Fix test_saved_histories.py for #4681. Commit: 0dd7f01008d2c5982106bacdd2b84010c90f001c https://github.com/galaxyproject/galaxy/commit/0dd7f01008d2c5982106bacdd2b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/history-list.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-list.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/history/history-list.js R templates/webapps/galaxy/history/rename.mako M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4681 from guerler/replace_analysis_forms Remove history renaming mako Compare: https://github.com/galaxyproject/galaxy/compare/1a635b348040...0dd7f01008d2

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[galaxyproject/galaxy] 67e9db: Fix invalid requests imports introduced in #4604.
by GitHub 26 Sep '17

26 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 67e9dbc37aa41a873546098cad81fe4a2557281e https://github.com/galaxyproject/galaxy/commit/67e9dbc37aa41a873546098cad81… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix invalid requests imports introduced in #4604. Even when we remove the requests controller the pyc files will stick around - so probably best to keep these absolute imports for these controllers indefinitely. This broke workflow import from URL coming through the GUI and so it broke a bunch of Selenium tests. Commit: 1a635b3480403cad19c398dd4fe3a4f5562c60db https://github.com/galaxyproject/galaxy/commit/1a635b3480403cad19c398dd4fe3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #4699 from jmchilton/fix_import Fix invalid requests imports introduced in #4604. Compare: https://github.com/galaxyproject/galaxy/compare/08ef78285af9...1a635b348040

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[galaxyproject/galaxy] 8c984c: Remove unused binary_compatibility.py script
by GitHub 26 Sep '17

26 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c984c9b3e4d1c7fb323448e55a936ec5112c8c1 https://github.com/galaxyproject/galaxy/commit/8c984c9b3e4d1c7fb323448e55a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: R scripts/binary_compatibility.py Log Message: ----------- Remove unused binary_compatibility.py script Follow-up on commit 39d78c7226d8f0417577bdea94b15ac2c77c45a2 from PR https://github.com/galaxyproject/galaxy/pull/2383 Commit: 9b1832abb11b79a244e0505b4afc059ba894d944 https://github.com/galaxyproject/galaxy/commit/9b1832abb11b79a244e0505b4afc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M cron/build_chrom_db.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/visualization/plugins/plugin.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/api/search.py M scripts/dump_tour.py M scripts/edam_mapping.py M scripts/fetch_eggs.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/manage_tool_dependencies.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/paster.py M scripts/rst2html.py M scripts/summarize_timings.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/base/populators.py M test/functional/twilltestcase.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py A test/unit/__init__.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py Log Message: ----------- Fix import order for cron/, scripts/ and test/ Commit: 08ef78285af9d9ca045ba9945e5517aa2809b77c https://github.com/galaxyproject/galaxy/commit/08ef78285af9d9ca045ba9945e55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M cron/build_chrom_db.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/visualization/plugins/plugin.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/api/search.py R scripts/binary_compatibility.py M scripts/dump_tour.py M scripts/edam_mapping.py M scripts/fetch_eggs.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/manage_tool_dependencies.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/paster.py M scripts/rst2html.py M scripts/summarize_timings.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/base/populators.py M test/functional/twilltestcase.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py A test/unit/__init__.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py Log Message: ----------- Merge pull request #4697 from nsoranzo/flake8-import-order Fix import order for cron/, scripts/ and test/ Compare: https://github.com/galaxyproject/galaxy/compare/0c6dfd7a41a8...08ef78285af9

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[galaxyproject/infrastructure-playbook]
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/old-bitly Home: https://github.com/galaxyproject/infrastructure-playbook

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[galaxyproject/infrastructure-playbook] a19ba5: Updated Wiki to Hub page mapping file to reflect t...
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/blog Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a19ba56e73a9374ae3a8bef6a2661903f0d8f49b https://github.com/galaxyproject/infrastructure-playbook/commit/a19ba56e73a… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Updated Wiki to Hub page mapping file to reflect that the Communinty Log entries are now in blog.

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[galaxyproject/galaxy] 32b85e: Only permit yaml.safe_loading of data
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32b85ecb591d01acbbbb9ed1bedd1a48804a0837 https://github.com/galaxyproject/galaxy/commit/32b85ecb591d01acbbbb9ed1bedd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webhooks/__init__.py M scripts/grt/export.py M scripts/grt/upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Only permit yaml.safe_loading of data Event trusted data, belt + suspenders method. Commit: df41d4f4087f9b133750a2c350ea207753f30f54 https://github.com/galaxyproject/galaxy/commit/df41d4f4087f9b133750a2c350ea… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py Log Message: ----------- Remove some shell=True and fix commands Commit: cd6a1afaa9980d958ad324fa987a07e7608bf841 https://github.com/galaxyproject/galaxy/commit/cd6a1afaa9980d958ad324fa987a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Replace some os.system calls with subprocess Commit: 73337725bdd654904563dc54b04083a23e4a252d https://github.com/galaxyproject/galaxy/commit/73337725bdd654904563dc54b040… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Two more commands to list Commit: c85db3fd68590d3d2f61b0b3f88026773d9563a0 https://github.com/galaxyproject/galaxy/commit/c85db3fd68590d3d2f61b0b3f880… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- Some more command refactoring Commit: 670897ec5ca2284c7fad453c3d595defe3cca280 https://github.com/galaxyproject/galaxy/commit/670897ec5ca2284c7fad453c3d59… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/reports/controllers/system.py Log Message: ----------- One more os command Commit: 9b8e76f9d9df0ae0ba6238d44a8f07b97fe34d6f https://github.com/galaxyproject/galaxy/commit/9b8e76f9d9df0ae0ba6238d44a8f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/managers/citations.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py Log Message: ----------- Convert urllib to requests Which has built-in protection against urls like "file:///tmp/a" Commit: db0400298651f6d4c9d909406c3fe632d057bbf7 https://github.com/galaxyproject/galaxy/commit/db0400298651f6d4c9d909406c3f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Log Message: ----------- remove unused imports Commit: a68d6be3a1c6e6fd85c5ae94232467f193156d53 https://github.com/galaxyproject/galaxy/commit/a68d6be3a1c6e6fd85c5ae942324… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M test/functional/webhooks/phdcomics/helper/__init__.py Log Message: ----------- reorder imports Commit: 93ffc4055b145811b86191dae8b865ea45b55fcb https://github.com/galaxyproject/galaxy/commit/93ffc4055b145811b86191dae8b8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- replace check_output with python processing and shell=False Commit: d79a2459a95dfda7856b9898d40d062f00456006 https://github.com/galaxyproject/galaxy/commit/d79a2459a95dfda7856b9898d40d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/parser/factory.py M lib/galaxy/webapps/config_manage.py Log Message: ----------- These we will revert to their original yaml.load It would be nice to fix them eventually, but we'll settle for an incremental improvement. Commit: b3261309843f8cfec1a5a589b4628e44e6bf76df https://github.com/galaxyproject/galaxy/commit/b3261309843f8cfec1a5a589b462… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- import ordering Commit: 8f4491bfffce5d13e2199df5d60e06e3672a08c1 https://github.com/galaxyproject/galaxy/commit/8f4491bfffce5d13e2199df5d60e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Consume stderr Commit: 0f7dd52988269dc4567bdbbd71be0fd273741efd https://github.com/galaxyproject/galaxy/commit/0f7dd52988269dc4567bdbbd71be… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Copy changes over Commit: 75df58ae86ff1796f0bb0ea975fc1d0d518c155a https://github.com/galaxyproject/galaxy/commit/75df58ae86ff1796f0bb0ea975fc… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/parse_builds_3_sites.py Log Message: ----------- fix Commit: fd92ac3eedd145635a74530ba62bb7fea7c540f4 https://github.com/galaxyproject/galaxy/commit/fd92ac3eedd145635a74530ba62b… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- revert this change Commit: 27beb7030d99a511a428ad59211a3137a2761559 https://github.com/galaxyproject/galaxy/commit/27beb7030d99a511a428ad59211a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- revert/sync Commit: 1a57c06d6a81dc6f92eb4843c89a7333f874bc32 https://github.com/galaxyproject/galaxy/commit/1a57c06d6a81dc6f92eb4843c89a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix import ordering Thanks @nsoranzo, I appreciate all the comments here. Commit: 290971ca7a28eb579dc2d40c9653b9e160253634 https://github.com/galaxyproject/galaxy/commit/290971ca7a28eb579dc2d40c9653… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/transfer_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py Log Message: ----------- more review comments Commit: 15c73233c52b29ed94066c06ebb1e10c935ae28d https://github.com/galaxyproject/galaxy/commit/15c73233c52b29ed94066c06ebb1… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M scripts/edam_mapping.py Log Message: ----------- fix lint Commit: 19d03edc7ff8384a5360d71365076a2594fb0b8b https://github.com/galaxyproject/galaxy/commit/19d03edc7ff8384a5360d7136507… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- refactor missed call Commit: 626a3dc2995f0d797232aa666f1bdf3e6a5d22dd https://github.com/galaxyproject/galaxy/commit/626a3dc2995f0d797232aa666f1b… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build_channel.py Log Message: ----------- fix ordering Commit: 41574d022249bae4df4b89bfb50c3a599ee5585e https://github.com/galaxyproject/galaxy/commit/41574d022249bae4df4b89bfb50c… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- swap for subprocess.call per @nsoranzo suggestion Commit: 0c6dfd7a41a8df8c000b133d8833eb9963ae183e https://github.com/galaxyproject/galaxy/commit/0c6dfd7a41a8df8c000b133d8833… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/data_libraries/build_lucene_index.py M scripts/edam_mapping.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/microbes/harvest_bacteria.py M scripts/tool_shed/api/export.py M scripts/transfer.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4604 from erasche/hardening Various bits of hardening Compare: https://github.com/galaxyproject/galaxy/compare/9f2582e9fbed...0c6dfd7a41a8

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