- galaxy-commits - lists.galaxyproject.org

[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

1 0

[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

1 0

[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

1 0

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

25 Sep '17

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

1 0

[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.

1 0

[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

1 0

[galaxyproject/galaxy] caed7b: Use only latest publication
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: caed7b60aa98153049fa2e26f5855833e7cdfce0 https://github.com/galaxyproject/galaxy/commit/caed7b60aa98153049fa2e26f585… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION Log Message: ----------- Use only latest publication Commit: 9f2582e9fbed242498810aa67c508a26eb6196fa https://github.com/galaxyproject/galaxy/commit/9f2582e9fbed242498810aa67c50… Author: Dave Clements <clements(a)galaxyproject.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M CITATION Log Message: ----------- Merge pull request #4688 from nsoranzo/citation_fixes Use only latest publication Compare: https://github.com/galaxyproject/galaxy/compare/1c2c59526714...9f2582e9fbed

1 0

[galaxyproject/galaxy] 0b1dd6: Selenium - bug fix for history test options.
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b1dd637a98c9b878972a3b7b0faf783a045f2b3 https://github.com/galaxyproject/galaxy/commit/0b1dd637a98c9b878972a3b7b0fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Selenium - bug fix for history test options. Wait on something useful instead of picking an arbitrary sleep time and praying. Commit: aa825d22aa8ec934fc4ec2a30f20fc821c8e3c0b https://github.com/galaxyproject/galaxy/commit/aa825d22aa8ec934fc4ec2a30f20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Selenium - fix transient issue with saved histories test. Commit: 76fe60180a4b9059d0fb110573e93bf6274be893 https://github.com/galaxyproject/galaxy/commit/76fe60180a4b9059d0fb110573e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Selenium - fix bug where snapshots might be used in tests before it is setup. Commit: 4a4d0498d6a371dc8ddaa226d33ff5cf0a897e69 https://github.com/galaxyproject/galaxy/commit/4a4d0498d6a371dc8ddaa226d33f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Selenium - better fix for upload build click before callback registered. Should fix this transient failure. https://jenkins.galaxyproject.org/job/selenium/568/artifact/568-test-errors… Commit: 6168e243b28cd85b8b8b719acc55d3e2108af43a https://github.com/galaxyproject/galaxy/commit/6168e243b28cd85b8b8b719acc55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/test_custom_builds.py Log Message: ----------- Selenium - fix rerunning test errors for test_custom_builds. Fixed similar problem for saved histories tests with 341667437ae718258a8d543c4e09d187f7f85326. Should fix this problem https://jenkins.galaxyproject.org/job/selenium/568/artifact/568-test-errors…. Commit: c90a84e1c211daf680b7e0a8c7aca246bc3152cf https://github.com/galaxyproject/galaxy/commit/c90a84e1c211daf680b7e0a8c7ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Selenium - fix transient error in history switching test. History sometimes takes longer than that second to switch in the GUI, so start a retry cycle on that assertion after a half a second. xref https://jenkins.galaxyproject.org/job/selenium/586/artifact/586-test-errors… Commit: 97cf3b94d1571401f3d57a83dd1a644ff356e772 https://github.com/galaxyproject/galaxy/commit/97cf3b94d1571401f3d57a83dd1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_anon_history.py Log Message: ----------- Selenium - fix transiently failing test caused by not waiting on anonymous history loading. After logging out - may need to a wait a second to give the UI and backend a chance to create a new history for the now anoymous user. Pause and let that happen. xref https://jenkins.galaxyproject.org/job/selenium/585/artifact/585-test-errors… Commit: 9d3ed321be4d0179616af7478eb96bb358b29607 https://github.com/galaxyproject/galaxy/commit/9d3ed321be4d0179616af7478eb9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Selenium - fix transient history in test_saved_histories related to fetching history names. xref https://jenkins.galaxyproject.org/job/selenium/588/artifact/588-test-errors… Commit: 9f5309688eb17b92d4733a7f9752f97e5a4139db https://github.com/galaxyproject/galaxy/commit/9f5309688eb17b92d4733a7f9752… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Import order fix. Commit: 1c2c59526714b00fdf17dd854fe65719df976eba https://github.com/galaxyproject/galaxy/commit/1c2c59526714b00fdf17dd854fe6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #4687 from jmchilton/selenium_fixes_34 Ever more Selenium fixes. Compare: https://github.com/galaxyproject/galaxy/compare/c20ac3c820c3...1c2c59526714

1 0

[galaxyproject/galaxy] 4311f5: nicer logging for sentry
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4311f5574dbf82574599b4947cc2721a1132675e https://github.com/galaxyproject/galaxy/commit/4311f5574dbf82574599b4947cc2… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- nicer logging for sentry Commit: c20ac3c820c30c70dfbe4de12b645350ec15cf7c https://github.com/galaxyproject/galaxy/commit/c20ac3c820c30c70dfbe4de12b64… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #4693 from erasche/ie-logging-patch-sentry Nicer logging message for sentry Compare: https://github.com/galaxyproject/galaxy/compare/70ba94763e85...c20ac3c820c3

1 0

[galaxyproject/galaxy] 9f4c72: Un-pin flake8 deps for dev branch
by GitHub 25 Sep '17

25 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f4c72a345ff629ea4b1430026d15decddf38617 https://github.com/galaxyproject/galaxy/commit/9f4c72a345ff629ea4b1430026d1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M tox.ini Log Message: ----------- Un-pin flake8 deps for dev branch Commit: 70ba94763e8547ed761d6ba42dc14ff72f5f8320 https://github.com/galaxyproject/galaxy/commit/70ba94763e8547ed761d6ba42dc1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4689 from nsoranzo/unpin_flake8_deps Un-pin flake8 deps for dev branch Compare: https://github.com/galaxyproject/galaxy/compare/0c23d40b22b6...70ba94763e85

1 0