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

[galaxyproject/galaxy] 1bc564: Add a custom "TRACE" log level for even more verbo...
by GitHub 04 Oct '17

04 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1bc56442859fa5e5ef0d998f63169427e1bcad15 https://github.com/galaxyproject/galaxy/commit/1bc56442859fa5e5ef0d998f6316… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/__init__.py Log Message: ----------- Add a custom "TRACE" log level for even more verbosity. Import logging as usual and within the galaxy namespace you should be able to use it with log.trace(). Commit: c7ad7beda3012ceaeca1beb7b43ece79dc12fe9d https://github.com/galaxyproject/galaxy/commit/c7ad7beda3012ceaeca1beb7b43e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Move one previously overly chatty debug statement to 'TRACE' log level. Commit: d482ea89a9f6d8617d3f3f25feaa947db42b56ff https://github.com/galaxyproject/galaxy/commit/d482ea89a9f6d8617d3f3f25feaa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/__init__.py M lib/galaxy/config.py M lib/galaxy/util/log/__init__.py Log Message: ----------- Refactoring of trace logging, step 1. Custom get_logger that returns a Logger with the extra TRACE functionality. Commit: a1770a45fcd95c89ed133f66af970f06e6a1e192 https://github.com/galaxyproject/galaxy/commit/a1770a45fcd95c89ed133f66af97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/__init__.py Log Message: ----------- Removes NullHandler patching (Python 2.6 is no longer supported) Commit: 75e5aa12e487fe4015d552bfd4c8a5a35550fd5a https://github.com/galaxyproject/galaxy/commit/75e5aa12e487fe4015d552bfd4c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/__init__.py Log Message: ----------- Remove BadZipFile patch, Python 2.6 is no longer supported Commit: aca057d2ec0a2a8db6c388170a8cad5c0cce8fff https://github.com/galaxyproject/galaxy/commit/aca057d2ec0a2a8db6c388170a8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Swap the single usage of 'trace' to the new galaxy logger import. Commit: b7e24f71e1b4c661d9852ef5007e422656c0ee9b https://github.com/galaxyproject/galaxy/commit/b7e24f71e1b4c661d9852ef5007e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: R lib/galaxy/util/backports/__init__.py Log Message: ----------- Remove unused backports Commit: 58d7f557f7bb5d8be3fa5e6b621c7b2e75b0de32 https://github.com/galaxyproject/galaxy/commit/58d7f557f7bb5d8be3fa5e6b621c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/actions/post.py R lib/galaxy/util/log/__init__.py R lib/galaxy/util/log/fluent_log.py A lib/galaxy/util/logging/__init__.py A lib/galaxy/util/logging/fluent_log.py Log Message: ----------- Move galaxy.util.log to galaxy.util.logging Commit: e629c162d38d29385b7190766dba694c8def6dd4 https://github.com/galaxyproject/galaxy/commit/e629c162d38d29385b7190766dba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py Log Message: ----------- Force absolute import in much of galaxy.util Commit: ee600ff255ff1f8884dc335c14626b7a27bfe308 https://github.com/galaxyproject/galaxy/commit/ee600ff255ff1f8884dc335c1462… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- One minor tweak to fix a getLogger in rst_to_html Commit: c49adb15184c481a8165f1893d38bc37d176079a https://github.com/galaxyproject/galaxy/commit/c49adb15184c481a8165f1893d38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/__init__.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/util/__init__.py R lib/galaxy/util/backports/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py R lib/galaxy/util/log/__init__.py R lib/galaxy/util/log/fluent_log.py A lib/galaxy/util/logging/__init__.py A lib/galaxy/util/logging/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py Log Message: ----------- Merge pull request #4672 from dannon/trace_logging Add a custom "TRACE" log level for even more verbosity. Compare: https://github.com/galaxyproject/galaxy/compare/79a16da6ea70...c49adb15184c

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[galaxyproject/galaxy] 1fa4ea: Allow multiple simulatenous uploads via single POS...
by GitHub 04 Oct '17

04 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1fa4ea2a8a1e363e51f6928c7a056c0d22ebb99c https://github.com/galaxyproject/galaxy/commit/1fa4ea2a8a1e363e51f6928c7a05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Allow multiple simulatenous uploads via single POST. The upload.py tool itself already allowed this and update upload dataset grouping to handle this. Commit: 79a16da6ea70a3ef0b6b47ac3233a127dcac3b9a https://github.com/galaxyproject/galaxy/commit/79a16da6ea70a3ef0b6b47ac3233… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #4563 from jmchilton/multiple_files_per_upload Allow multiple simultaneous uploads via single POST. Compare: https://github.com/galaxyproject/galaxy/compare/6497329e1caf...79a16da6ea70

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[galaxyproject/galaxy] 096b38: update python-ldap with fix for ldaps
by GitHub 04 Oct '17

04 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 096b387f8e97a3620855793cb0d257dd3a56883f https://github.com/galaxyproject/galaxy/commit/096b387f8e97a3620855793cb0d2… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- update python-ldap with fix for ldaps Commit: d788bfb80ae1140ecb7757eea2d192de0a7e4045 https://github.com/galaxyproject/galaxy/commit/d788bfb80ae1140ecb7757eea2d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #4748 from abretaud/ldap [17.09] Fix auth with ldaps:// Compare: https://github.com/galaxyproject/galaxy/compare/7ce0d87a5973...d788bfb80ae1

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[galaxyproject/galaxy] fbf3cf: Fix joiner tool to inherit datatype, restoring pre...
by GitHub 03 Oct '17

03 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: fbf3cf30d7df5673ebbc098a2561e26a5486a18a https://github.com/galaxyproject/galaxy/commit/fbf3cf30d7df5673ebbc098a2561… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M tools/filters/joiner.xml Log Message: ----------- Fix joiner tool to inherit datatype, restoring previous behavior. Commit: 7ce0d87a597353d7915a29708a440939e73bb7a3 https://github.com/galaxyproject/galaxy/commit/7ce0d87a597353d7915a29708a44… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M tools/filters/joiner.xml Log Message: ----------- Merge pull request #4745 from dannon/joiner_fix [17.09] Fix joiner tool to inherit datatype from the input format Compare: https://github.com/galaxyproject/galaxy/compare/0827b23bd504...7ce0d87a5973

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[galaxyproject/galaxy] d57336: add PostgresqlArchive class
by GitHub 03 Oct '17

03 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5733667ec66f2a710de86c6a0f88939c96169bd https://github.com/galaxyproject/galaxy/commit/d5733667ec66f2a710de86c6a0f8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add PostgresqlArchive class Commit: 750486d96b58dca3ef9c27c064be0f321e50e657 https://github.com/galaxyproject/galaxy/commit/750486d96b58dca3ef9c27c064be… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add the postgresql datatype to the config Commit: baa6d2be46cad6c326bfd7d4ff34e8e4e1bbc800 https://github.com/galaxyproject/galaxy/commit/baa6d2be46cad6c326bfd7d4ff34… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/onload.js M client/toolshed/scripts/mvc/groups/group-model.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako 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/conda_util.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/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/genomes.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.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/buildapp.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.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/api/data_manager_example_execute.py M scripts/api/display.py M scripts/api/search.py R scripts/binary_compatibility.py 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 static/maps/galaxy.interactive_environments.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/onload.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 M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/onload.js M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/maps/mvc/groups/group-model.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js R templates/webapps/galaxy/history/rename.mako R templates/webapps/galaxy/visualization/create.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_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_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_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' of https://github.com/galaxyproject/galaxy into postgresql_datatype Commit: f4b944206cb5f1f52ecffe9462e14b673ceb92f8 https://github.com/galaxyproject/galaxy/commit/f4b944206cb5f1f52ecffe9462e1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix detection of pg database Commit: 5fd482809d66c1ba0dfadec6876eed8aa9b1b659 https://github.com/galaxyproject/galaxy/commit/5fd482809d66c1ba0dfadec6876e… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 Log Message: ----------- add example dataset Commit: 2bf3481e7de2be9159cdd6e90e25d96196dc6c39 https://github.com/galaxyproject/galaxy/commit/2bf3481e7de2be9159cdd6e90e25… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix pep8 Commit: 43b86e019e72f8e8d8958483d80e48cf87aa9afe https://github.com/galaxyproject/galaxy/commit/43b86e019e72f8e8d8958483d80e… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix test Commit: dd7366d31eb0ecc24ec9c046b27a8d1f865ad5ce https://github.com/galaxyproject/galaxy/commit/dd7366d31eb0ecc24ec9c046b27a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge branch 'postgresql_datatype' of https://github.com/bgruening/galaxy into postgresql_datatype Commit: 5a6c3e797cabf795e82408078f00ce35c628e7f5 https://github.com/galaxyproject/galaxy/commit/5a6c3e797cabf795e82408078f00… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- address Erics comments Commit: 6497329e1cafaa3803c46a97e0c28fd443edb0aa https://github.com/galaxyproject/galaxy/commit/6497329e1cafaa3803c46a97e0c2… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 Log Message: ----------- Merge pull request #4730 from bgruening/postgresql_datatype add postgresql datatype Compare: https://github.com/galaxyproject/galaxy/compare/f0972b15b0fe...6497329e1caf

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[galaxyproject/usegalaxy-playbook] 276681: Fixes for Unicycler 0.4.1 on Test
by GitHub 03 Oct '17

03 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2766812d441eeacbd159e6c246f1f8077a850113 https://github.com/galaxyproject/usegalaxy-playbook/commit/2766812d441eeacb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M CHANGELOG.md M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fixes for Unicycler 0.4.1 on Test

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[galaxyproject/galaxy] fa2d80: Fix t, a, g, s return value for tags
by GitHub 03 Oct '17

03 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa2d80d7ecddb780e29835869b94a2e3e16d12a1 https://github.com/galaxyproject/galaxy/commit/fa2d80d7ecddb780e29835869b94… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix t, a, g, s return value for tags Commit: 0827b23bd504208b51956be67f5bebf75b8fb4b0 https://github.com/galaxyproject/galaxy/commit/0827b23bd504208b51956be67f5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4742 from mvdbeek/tags_fix [17.09] Fix t, a, g, s returned in to_dict() method Commit: 251551c29b459b71e818129186fd949bc22e5a06 https://github.com/galaxyproject/galaxy/commit/251551c29b459b71e818129186fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Commit: f9967fcebdffb0e61460d67dae0c40dbbd55ec71 https://github.com/galaxyproject/galaxy/commit/f9967fcebdffb0e61460d67dae0c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merges 17.09->dev and rebuilds client. Commit: f0972b15b0fe840e1e7473eaa5a25c4556945e6c https://github.com/galaxyproject/galaxy/commit/f0972b15b0fe840e1e7473eaa5a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/model/__init__.py M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #4743 from dannon/dev Merge 17.09 to dev and rebuild client. Compare: https://github.com/galaxyproject/galaxy/compare/4a584339c78a...f0972b15b0fe

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[galaxyproject/galaxy] 3c6416: Initial work on selenium testing for libraries.
by GitHub 03 Oct '17

03 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c64167788ea40fcc95883fdd98d51022c21537f https://github.com/galaxyproject/galaxy/commit/3c64167788ea40fcc95883fdd98d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py Log Message: ----------- Initial work on selenium testing for libraries. - Test importing datasets from histories. - Test basic importing of a dataset from a path. - Test creating a folder. - Test create library, renaming a library, filtering libraries by name, and sorting of libraries. - Test various buttons (e.g. details, help). Commit: 4a584339c78a28351e855733677574f871fb964c https://github.com/galaxyproject/galaxy/commit/4a584339c78a28351e8557336775… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py Log Message: ----------- Merge pull request #4543 from jmchilton/libraries_testing Initial selenium tests for libraries. Compare: https://github.com/galaxyproject/galaxy/compare/9481b85534d8...4a584339c78a

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[galaxyproject/galaxy] fa2d80: Fix t, a, g, s return value for tags
by GitHub 03 Oct '17

03 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: fa2d80d7ecddb780e29835869b94a2e3e16d12a1 https://github.com/galaxyproject/galaxy/commit/fa2d80d7ecddb780e29835869b94… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix t, a, g, s return value for tags Commit: 0827b23bd504208b51956be67f5bebf75b8fb4b0 https://github.com/galaxyproject/galaxy/commit/0827b23bd504208b51956be67f5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4742 from mvdbeek/tags_fix [17.09] Fix t, a, g, s returned in to_dict() method Compare: https://github.com/galaxyproject/galaxy/compare/280dc48c386f...0827b23bd504

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[galaxyproject/galaxy] ac3588: Reuse existing dependency manager if possible
by GitHub 03 Oct '17

03 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac3588f8c745429e3ccf8f2dae067442321c289d https://github.com/galaxyproject/galaxy/commit/ac3588f8c745429e3ccf8f2dae06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reuse existing dependency manager if possible This does slightly speedup toolbox reloads. Commit: 9481b85534d8ccd9e31933f5888b18d4615e9ac6 https://github.com/galaxyproject/galaxy/commit/9481b85534d8ccd9e31933f5888b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4739 from mvdbeek/reuse_dependency_managers Reuse existing dependency manager if possible Compare: https://github.com/galaxyproject/galaxy/compare/d685b49ef2dc...9481b85534d8

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