Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4252724e5e5dc0088828778d36ae767f3608f23 https://github.com/galaxyproject/galaxy/commit/b4252724e5e5dc0088828778d36ae... Author: Maximilian Friedersdorff <max@friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Estimate the walltime usage over the last 30 days. Log at debug level if usage is over 20 seconds. Commit: a680d90d54c39236bedd0e8fe4fe20568aa81372 https://github.com/galaxyproject/galaxy/commit/a680d90d54c39236bedd0e8fe4fe2... Author: Maximilian Friedersdorff <max@friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/actions/admin.py M lib/galaxy/config.py M lib/galaxy/datatypes/images.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/steps.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/repository_types/unrestricted.py M lib/tool_shed/util/web_util.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/drmaa_external_runner.py M static/maps/layout/menu.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M test/api/test_datasets.py M test/api/test_history_contents_provenance.py M test/unit/test_sockets.py M tools/data_source/fetch.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 2408502c2d316869df0f84b65e50db3114f9529a https://github.com/galaxyproject/galaxy/commit/2408502c2d316869df0f84b65e50d... Author: Maximilian Friedersdorff <max@friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Add total_walltime limit type Add to sample config, config reader and unittest Commit: 8e4072179789517427727339e3e9a2e911fae6a6 https://github.com/galaxyproject/galaxy/commit/8e4072179789517427727339e3e9a... Author: Maximilian Friedersdorff <max@friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Use conf for walltime limit and window. Pause job if necessary Commit: 3d4de14840847636ad81c36bd64449fb959220b9 https://github.com/galaxyproject/galaxy/commit/3d4de14840847636ad81c36bd6444... Author: Maximilian Friedersdorff <max@friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Comply with galaxy style guide regarding whitespace. Commit: db1b51a0802e392787c3a71e7a8bd202b568bf3a https://github.com/galaxyproject/galaxy/commit/db1b51a0802e392787c3a71e7a8bd... Author: Maximilian Friedersdorff <max@friedersdorff.com> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fix errors in documentation for total_walltime limit Commit: 91e65aa42c8e2439883da1d690e770a5a9df1a79 https://github.com/galaxyproject/galaxy/commit/91e65aa42c8e2439883da1d690e77... Author: Maximilian Friedersdorff <max@friedersdorff.com> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Move datetime import to the top of the file. Commit: f467bcb70697bdaac0f94f187970b98f9b58bfe9 https://github.com/galaxyproject/galaxy/commit/f467bcb70697bdaac0f94f187970b... Author: Maximilian Friedersdorff <max@friedersdorff.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Add total_walltime to legacy job conf Commit: 982a35df087a2cd51eef97bef978144ee5bdb863 https://github.com/galaxyproject/galaxy/commit/982a35df087a2cd51eef97bef9781... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #3217 from interactomix/dev Per user total walltime limit. Compare: https://github.com/galaxyproject/galaxy/compare/2f9862f3c33c...982a35df087a