January 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 991f79: Use print() function in common_startup.sh
by GitHub 21 Jan '18

21 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 991f79e630ddad44530fa3799cfcac34422cd95a https://github.com/galaxyproject/galaxy/commit/991f79e630ddad44530fa3799cfc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-21 (Sun, 21 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Use print() function in common_startup.sh Commit: 5be96485b5a79550eb0824e46a8fac9dca99e06a https://github.com/galaxyproject/galaxy/commit/5be96485b5a79550eb0824e46a8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-21 (Sun, 21 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5357 from mvdbeek/print_statement_fix Use print() function in common_startup.sh Compare: https://github.com/galaxyproject/galaxy/compare/42b87dd5f922...5be96485b5a7

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[galaxyproject/galaxy] aa3983: fix #5129: auto create ldap role(&group) and assig...
by GitHub 20 Jan '18

20 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa3983bf9152a78bf2b577a1a4f3e51ecc387c64 https://github.com/galaxyproject/galaxy/commit/aa3983bf9152a78bf2b577a1a4f3… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/admin_util.py Log Message: ----------- fix #5129: auto create ldap role(&group) and assign to newly auto-registered user Commit: 86231f39f0b38b6d61f46c09009ad79c0b56ae11 https://github.com/galaxyproject/galaxy/commit/86231f39f0b38b6d61f46c09009a… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- #5129 - remove unused Exception variable Commit: 87da3da0c80cf4519554bd2599f22f1e2ab2f496 https://github.com/galaxyproject/galaxy/commit/87da3da0c80cf4519554bd2599f2… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- #5129 - remove unnecessary log statement Commit: b934da49b21e70b422435b87155e8bacc8003e58 https://github.com/galaxyproject/galaxy/commit/b934da49b21e70b422435b87155e… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- #5129 - add some options to only create the role, group or both. and whether or not to assign to role only to the group Commit: 79aaa3492d30dc4a612988274e0c727318c95cdd https://github.com/galaxyproject/galaxy/commit/79aaa3492d30dc4a612988274e0c… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Also catch empty string - e.g. upon create user from the admin page Commit: a6435eade58071798ba76ac8c22b01927e768ed5 https://github.com/galaxyproject/galaxy/commit/a6435eade58071798ba76ac8c22b… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/register.mako Log Message: ----------- On top of 5129, this allows to pre-populate an ldap user from the admin interface. An option is added to show/hide the pre-populate form in the admin register user form. Commit: 1128e8a4ee094d7b471730f7513b182fb135b647 https://github.com/galaxyproject/galaxy/commit/1128e8a4ee094d7b471730f7513b… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/util.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- some fixes to ensure groups and roles are created on pre-populating users Commit: aa4ab1cc0565b56c25da421fe89f5df9406f4cbd https://github.com/galaxyproject/galaxy/commit/aa4ab1cc0565b56c25da421fe89f… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-12-21 (Thu, 21 Dec 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- fix linting errors Commit: 8be4addaa995b6a4cf2c9bad1d2d4b88a4b0ce78 https://github.com/galaxyproject/galaxy/commit/8be4addaa995b6a4cf2c9bad1d2d… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/auth_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/admin_util.py M templates/user/register.mako Log Message: ----------- update ldap role creation based on comments on PR #5136 and PR #5136 Commit: dea3b73dd2ecc7117c622379ac4067f2b9a378c1 https://github.com/galaxyproject/galaxy/commit/dea3b73dd2ecc7117c622379ac40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh M .ci/jenkins/selenium/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M 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lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py R openid/yahoo.xml R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py M scripts/build_universe_config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/data_libraries/build_lucene_index.py M scripts/db_shell.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py A scripts/maintenance.sh M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh 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/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js R 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static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/bam_native_from_sam.bam M test-data/neostore.zip A test-data/new_element_sort_order.txt M test-data/sam_with_header.sam M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_1.ga M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/job_properties.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/multi_output_recurse.xml A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/dockerized_job_conf.xml A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py A test/unit/tools/test_tool_validation.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into feature/populate_ldap_user Commit: 42b87dd5f922c1d65739fd9f22ea2601220a1c65 https://github.com/galaxyproject/galaxy/commit/42b87dd5f922c1d65739fd9f22ea… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-20 (Sat, 20 Jan 2018) Changed paths: M config/auth_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/admin_util.py M templates/user/register.mako Log Message: ----------- Merge pull request #5238 from scholtalbers/feature/populate_ldap_user add an admin form to pre-populate an ldap user Compare: https://github.com/galaxyproject/galaxy/compare/718eb6cbf4db...42b87dd5f922

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[galaxyproject/galaxy] 0fdb63: remove charlimit for fetching urls
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 0fdb63e5e327ef6b82c928004b5e3301967f9eb3 https://github.com/galaxyproject/galaxy/commit/0fdb63e5e327ef6b82c928004b5e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- remove charlimit for fetching urls fixes #5349 this would only allow a number of urls that fit 1024 chars together moreover it would truncate (and break) the last one Commit: 3bf9b3ab1d718d5ecd02f7539015c5328d6c72ef https://github.com/galaxyproject/galaxy/commit/3bf9b3ab1d718d5ecd02f7539015… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #5353 from martenson/remove-charlimit-for-fetch [17.09] remove charlimit for fetching urls Compare: https://github.com/galaxyproject/galaxy/compare/8fa785427cf8...3bf9b3ab1d71

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[galaxyproject/galaxy] 7d1504: Fix bam conversion test tool
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d15049c48d030a6d7a21e039bfb91baf2094036 https://github.com/galaxyproject/galaxy/commit/7d15049c48d030a6d7a21e039bfb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Fix bam conversion test tool Starting with 16344a6 we attempt to set metadata also for files that have no content. BAM files need to contain at least a header. To avoid failing tests we only create the appropriate output based on the input. Commit: 718eb6cbf4db0719df226bb70436415e211e75d4 https://github.com/galaxyproject/galaxy/commit/718eb6cbf4db0719df226bb70436… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Merge pull request #5351 from mvdbeek/sam_to_bam_native_fix Fix bam conversion test tool Compare: https://github.com/galaxyproject/galaxy/compare/080148a16190...718eb6cbf4db

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[galaxyproject/usegalaxy-playbook] 7706bc: Collect some env variable metrics on Test jobs
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7706bce050b0902342d8d4305713a4121484a3a8 https://github.com/galaxyproject/usegalaxy-playbook/commit/7706bce050b09023… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/test/files/galaxy/config/job_metrics_conf.xml Log Message: ----------- Collect some env variable metrics on Test jobs Commit: ec2642fabe9333bdf4320503a7f4932516fff650 https://github.com/galaxyproject/usegalaxy-playbook/commit/ec2642fabe9333bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable config changes Commit: 506f8477b28018e3bbe6e4b3f3127fc86c028a6c https://github.com/galaxyproject/usegalaxy-playbook/commit/506f8477b28018e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Commit: a5ffd805369897f169d57f81428d79a036c019e4 https://github.com/galaxyproject/usegalaxy-playbook/commit/a5ffd805369897f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Main mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/aa74d76efb82...…

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[galaxyproject/galaxy] 8d8bf5: Dockerized job integration testing.
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d8bf5eaffeda0f229bf56cb45e4adbb05b12d57 https://github.com/galaxyproject/galaxy/commit/8d8bf5eaffeda0f229bf56cb45e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M lib/galaxy/config.py M test/base/driver_util.py A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml M test/functional/tools/samples_tool_conf.xml A test/integration/dockerized_job_conf.xml A test/integration/test_dockerized_jobs.py Log Message: ----------- Dockerized job integration testing. Add simple test cases for both mulled containers and explicit Docker image resolution. Commit: cd04ff30665ae6f15a6af35152af54d630458e60 https://github.com/galaxyproject/galaxy/commit/cd04ff30665ae6f15a6af35152af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Set group id in addition to user id when running docker containers by default. Noticed cwltool does this and it is a good idea. It wasn't the bug I was tracking but it is a solid improvement. Commit: 4bf47d08770c14010bf925c73ccba2262dfe78ee https://github.com/galaxyproject/galaxy/commit/4bf47d08770c14010bf925c73ccb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.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/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/base/integration_util.py A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/samples_tool_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml M test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py Log Message: ----------- Improved home and temp directory handling. Home Directory Handling ----------------------- - For profile < 18.01 tools: - If use_shared_home="false" is set on the command block - the tool will be given a clean $HOME directory. - If ``shared_home_dir`` is set in Galaxy's config or the job destination configuration, Galaxy will set $HOME in the tool's job environment to point at this directory. - For profile >= 18.01 tools, jobs will be given a clean home directory by default unless ``use_shared_home="true"`` is set. If that is set, the profile < 18.01 behavior is used. In addition to these changes for Galaxy tools, the tool framework itself has been updated to allow other potential behaviors including the CWL defaults. Integration tests for each of these cases has been added. Upgrading to 18.01 - we recommend dropping overriding ``HOME`` in any Galaxy environment configuration (e.g. env directives in job_conf.xml). If any such configuration is found, we recommend instead setting "shared_home_dir" for destinations to the that cluster destination's shared HOME directory. If all destinations share a single HOME directory, this can be set in galaxy.ini instead of job_conf.xml. Temp Directory Handling ----------------------- There were serious disagreements with how to proceed here. I felt we should aggressively isolate tool TMP directories and provide deployers options to tweak these through structured arguments. Nicola felt we should defer to the environment variables already being set job_conf.xml - but tweak their meanings by default. Nate fell somewhere in between. I think all sides have merit and could make sense depending on what you want to improve (easing cognative load, reducing out-of-box errors, easing advanced deployer configs, structured reasonsing of paths by Galaxy, etc...). I've navigated a path here that doesn't particularly reduce out of the box errors as I wanted by setting up a per-job temp directory by default but does make it possible and shouldn't break any existing configurations and doesn't make it anything more difficult to manage these things via environment variables. The new approach doesn't change any thing by default for Galaxy tools (regardless of tool profile version). The only way to achieve new behaviors is for the deployer to set a job_conf parameter called "tmp_dir". If this is set, it can be set to "True" (to default to a new, clean directory below the job directory) or to a shell expression to allow setting this dynamically at runtime to paths or paths beneath directories as needed on a per-destination basis. If a temp directory is set this way all three variables TMP, TMPDIR, and TEMP are set. Docker Environment Handling --------------------------- - Mirror the CWL behavior of mounting an external /tmp by default. - For newer tools, pass through the HOME, TMP, TMPDIR, and TEMP environment variables into the Docker container in addition to GALAXY_SLOTS. - Fix the pass through of environment variables into Docker containers. Commit: db0633eb8965306f4a7a8cca36e882cffc73ad55 https://github.com/galaxyproject/galaxy/commit/db0633eb8965306f4a7a8cca36e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M test/integration/test_dockerized_jobs.py M test/integration/test_job_environments.py M test/unit/tools/test_evaluation.py Log Message: ----------- Follow up on comments for #5193. Commit: 080148a16190988a18df6709ba1bd9f650ea10de https://github.com/galaxyproject/galaxy/commit/080148a16190988a18df6709ba1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.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/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/base/driver_util.py M test/base/integration_util.py A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml M test/functional/tools/samples_tool_conf.xml A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_evaluation.py Log Message: ----------- Merge pull request #5193 from jmchilton/structured_job_environment_1 Improved home and temp directory handling. Compare: https://github.com/galaxyproject/galaxy/compare/1cac9ad54fea...080148a16190

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[galaxyproject/galaxy] dedb1d: Fix history import by file on multi-handler setups
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dedb1d3f4ca83539baea9c4ff5654c3b44614540 https://github.com/galaxyproject/galaxy/commit/dedb1d3f4ca83539baea9c4ff565… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Fix history import by file on multi-handler setups The uploaded archive was going to be deleted before the job started running. Commit: 1cac9ad54fead782a28619ae60b46cdc73491c75 https://github.com/galaxyproject/galaxy/commit/1cac9ad54fead782a28619ae60b4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/sniff.py M scripts/functional_tests.py A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Compare: https://github.com/galaxyproject/galaxy/compare/8f65cd46b0ec...1cac9ad54fea

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[galaxyproject/galaxy] f5af95: add BamNative datatype
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5af9539b9d50e0c0e99ade18eea8af6f7beb0e4 https://github.com/galaxyproject/galaxy/commit/f5af9539b9d50e0c0e99ade18eea… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add BamNative datatype Commit: 017dad025db9a06c9c6d2430203f52fdec959f68 https://github.com/galaxyproject/galaxy/commit/017dad025db9a06c9c6d2430203f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A test-data/bam_native_from_sam.bam Log Message: ----------- add new test file Commit: eea55a9258342e8de32162c9e62563de0f6438b8 https://github.com/galaxyproject/galaxy/commit/eea55a9258342e8de32162c9e625… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A test/functional/tools/sam_to_bam_native.xml Log Message: ----------- add new test tool Commit: 2a093f25f6fdb6ebf4a8bba84050130c4929e6c3 https://github.com/galaxyproject/galaxy/commit/2a093f25f6fdb6ebf4a8bba84050… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add new bam_native datatype to the registry Commit: 4d7bc9a778afa171bd7498004733943543af5730 https://github.com/galaxyproject/galaxy/commit/4d7bc9a778afa171bd7498004733… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- bam to bigwig converter, converts also bam_native Commit: 2569851498f76d2fc416bd96ab4007c579bb0ffd https://github.com/galaxyproject/galaxy/commit/2569851498f76d2fc416bd96ab40… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M test-data/sam_with_header.sam Log Message: ----------- use unsorted sam file for tests Commit: 8b55e0a33a52fe45fc5fdaa171607c7f253021c9 https://github.com/galaxyproject/galaxy/commit/8b55e0a33a52fe45fc5fdaa17160… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- add two converters Commit: 640cfb1e7d8be8ceaba96920cfb1be72c48f4974 https://github.com/galaxyproject/galaxy/commit/640cfb1e7d8be8ceaba96920cfb1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam to BAM Commit: e519f4e7efcbb055a66a861588ceabd09e0b9b58 https://github.com/galaxyproject/galaxy/commit/e519f4e7efcbb055a66a861588ce… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- rearrange sniffer Commit: 295e5712ee2c020292754ddcb75d6d5744c4ed10 https://github.com/galaxyproject/galaxy/commit/295e5712ee2c020292754ddcb75d… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- adjust tests Commit: 2b5b6cf74fb29eb4608318477c062982d8ad955c https://github.com/galaxyproject/galaxy/commit/2b5b6cf74fb29eb4608318477c06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix test and add datatypes to test/functional/tools/sample_datatypes_conf.xml This test is still failing because `CONVERTER_sam_to_bam` will be invoked instead of CONVERTER_sam_to_bam_native. Possibly becasue Bam inherits from BamNative, so this isn't strictly speaking wrong, though not what one would expect. Commit: a8b3d23f1438f31436b86d24b48868fd3e133dad https://github.com/galaxyproject/galaxy/commit/a8b3d23f1438f31436b86d24b488… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Adjust sniffer test for unsorted bam Commit: 43dd7910f4865c9c4205ad8eaa5e8f1a71b6b6c6 https://github.com/galaxyproject/galaxy/commit/43dd7910f4865c9c4205ad8eaa5e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #37 from mvdbeek/bam_native_tests Fix test and add datatypes to test/functional/tools/sample_datatypes_… Commit: 446643159540f8db67dfd0752560b387b63fc4b8 https://github.com/galaxyproject/galaxy/commit/446643159540f8db67dfd0752560… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- resort the converters so that the accepted_formats are infront Commit: 8928b34506c1ba1f4856fad82dc42aef0f7c68f6 https://github.com/galaxyproject/galaxy/commit/8928b34506c1ba1f4856fad82dc4… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- implement priority converters Commit: b139726ed380192ecf03f10e91220a0488b573f3 https://github.com/galaxyproject/galaxy/commit/b139726ed380192ecf03f10e9122… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- fix spelling Commit: ea34bdc34d560962f3f149d9f019d0ac3a3c4f0a https://github.com/galaxyproject/galaxy/commit/ea34bdc34d560962f3f149d9f019… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #38 from bgruening/converter_resorting resort the converters so that the accepted_formats are infront Commit: 49dd02f4090b525beba735fc9ff16e32388b3fcd https://github.com/galaxyproject/galaxy/commit/49dd02f4090b525beba735fc9ff1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Keep header when converting sam to bam Otherwise the converted datasets are not valid BAM files. Commit: c32680733c8985d0db48a10d0b50fab7514dc4ff https://github.com/galaxyproject/galaxy/commit/c32680733c8985d0db48a10d0b50… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "fix spelling" This reverts commit b139726ed380192ecf03f10e91220a0488b573f3. Commit: 38c5f711983033bb01072a769e6a618528724955 https://github.com/galaxyproject/galaxy/commit/38c5f711983033bb01072a769e6a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "implement priority converters" This reverts commit 8928b34506c1ba1f4856fad82dc42aef0f7c68f6. Commit: 6b444f609d3a48d17a783e581dc077b0731673ca https://github.com/galaxyproject/galaxy/commit/6b444f609d3a48d17a783e581dc0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "resort the converters so that the accepted_formats are infront" This reverts commit 446643159540f8db67dfd0752560b387b63fc4b8. Commit: c2328e32eb18bd7a4a5c791306203b933fc73603 https://github.com/galaxyproject/galaxy/commit/c2328e32eb18bd7a4a5c79130620… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Move up sam_to_bam_native converter That should allow implicit conversion from sam to bam_native for tools that support bam_native. Commit: a36ebe35521e3e45c5c3301eef9535ebdf630f9d https://github.com/galaxyproject/galaxy/commit/a36ebe35521e3e45c5c3301eef95… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Enhance tests for sam_to_bam conversion This demonstrates that the `sam_to_bam` converter will be used for an input with `format="bam"`, and not `sam_to_bam_native`. Commit: d544adf5ee45557f2e40c2f1050f4f2a427d56e1 https://github.com/galaxyproject/galaxy/commit/d544adf5ee45557f2e40c2f1050f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/registry.py M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Merge pull request #39 from mvdbeek/bam_unsorted Fix tests and revert additional sorting of converters Commit: ae0c3524b87d1f14374ee04d452320ff0c091cf8 https://github.com/galaxyproject/galaxy/commit/ae0c3524b87d1f14374ee04d4523… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/router.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/zh/locale.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M 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config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/user_preferences_extra_conf.yml.sample M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py M doc/source/admin/production.md M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md M doc/source/api/quickstart.rst M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M 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A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako M 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templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M 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test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_parsing.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge branch 'dev' into bam_unsorted Commit: aaaf7b50a7a227e5344712f6441fce337a20d1ba https://github.com/galaxyproject/galaxy/commit/aaaf7b50a7a227e5344712f6441f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Enable conda_auto_init and conda_auto_install for framework tests Commit: 680bf685c2dfdc874277321e2c7d0673516bf62a https://github.com/galaxyproject/galaxy/commit/680bf685c2dfdc874277321e2c7d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix datatype order Commit: 8ecc86cb677bc3971baa75bf0e8c1481d8e3aef4 https://github.com/galaxyproject/galaxy/commit/8ecc86cb677bc3971baa75bf0e8c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Simplify conda framework setup Thanks @nsoranzo! Commit: 8f65cd46b0ec7c1a92a305219f43c837cd2a471a https://github.com/galaxyproject/galaxy/commit/8f65cd46b0ec7c1a92a305219f43… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/sniff.py M scripts/functional_tests.py A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5180 from bgruening/bam_unsorted Add BamNative datatype Compare: https://github.com/galaxyproject/galaxy/compare/33bd54079be7...8f65cd46b0ec

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[galaxyproject/galaxy] 5554c2: Fix import by url for history archive import tool
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 5554c2f9b98b4192e106fdce52fa067945f431e8 https://github.com/galaxyproject/galaxy/commit/5554c2f9b98b4192e106fdce52fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Fix import by url for history archive import tool Commit: b82676b8eec35313896614aa0fb5fdeeddacf541 https://github.com/galaxyproject/galaxy/commit/b82676b8eec35313896614aa0fb5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Switch to transparent readmode for history tarfiles Commit: b5d0030b3ed4bf08aa26c29b72c4f5757874669c https://github.com/galaxyproject/galaxy/commit/b5d0030b3ed4bf08aa26c29b72c4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix history import by file on multi-handler setups The uploaded archive was going to be deleted before the job started running. Commit: 662440e730791318b5ff3a9346f1ee6243c56208 https://github.com/galaxyproject/galaxy/commit/662440e730791318b5ff3a9346f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Add quotes Commit: 8fa785427cf8d41fd420092baaaf574825bb9d0b https://github.com/galaxyproject/galaxy/commit/8fa785427cf8d41fd420092baaaf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5344 from mvdbeek/history_import_fixes [17.09] History import fixes Compare: https://github.com/galaxyproject/galaxy/compare/3c85407ec801...8fa785427cf8

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[galaxyproject/usegalaxy-playbook]
by GitHub 19 Jan '18

19 Jan '18

Branch: refs/heads/test_reenable_sentry Home: https://github.com/galaxyproject/usegalaxy-playbook

1 0