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
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
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
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