Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f31290113eb1d106b8f1cf894a854c6c310a004 https://github.com/galaxyproject/galaxy/commit/4f31290113eb1d106b8f1cf894a85... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/actions/upload_common.py
Log Message: ----------- - get real user name from username and email - sudo calls with preserving PATH, LD_LIBRARY_PATH ...
Commit: b07ebdaadaf3d5d4eb089988638f193821015494 https://github.com/galaxyproject/galaxy/commit/b07ebdaadaf3d5d4eb089988638f1... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- - added path check to external chown script
Commit: 6841faac692e8b12f7634a547e69ff8a14a9506e https://github.com/galaxyproject/galaxy/commit/6841faac692e8b12f7634a547e69f... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- - removed my paths
Commit: d25e552003216d0f986148a161223b010cdcaee8 https://github.com/galaxyproject/galaxy/commit/d25e552003216d0f986148a161223... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- - removed uneccessary import - added quotes to comment
Commit: 3a16b36df8471d8c89f5ae04e82199adc3933adf https://github.com/galaxyproject/galaxy/commit/3a16b36df8471d8c89f5ae04e8219... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-05-24 (Wed, 24 May 2017)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py
Log Message: ----------- made determination of actual user configurable
Commit: 5ee0d7ec0e8d6279be5cbad44d5d41f4d66b317f https://github.com/galaxyproject/galaxy/commit/5ee0d7ec0e8d6279be5cbad44d5d4... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-05-26 (Fri, 26 May 2017)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/actions/upload_common.py
Log Message: ----------- moved sudo calls to galaxy.ini removed spaces
Commit: 01cffa6151f6086c4b944d1146a380d4b0e437da https://github.com/galaxyproject/galaxy/commit/01cffa6151f6086c4b944d1146a38... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-05-26 (Fri, 26 May 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- imroved external_chown_script now uses Popen and checks return code
Commit: 64f5e2e2fa286bc3cc4151c523d8d98bb4dcf3fe https://github.com/galaxyproject/galaxy/commit/64f5e2e2fa286bc3cc4151c523d8d... Author: rhpvorderman r.h.p.vorderman@lumc.nl Date: 2017-06-12 (Mon, 12 Jun 2017)
Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/external_chown_script.py
Log Message: ----------- Fix linting issues
Commit: e197cadd98491d8341b3894f5663ea047b2972d2 https://github.com/galaxyproject/galaxy/commit/e197cadd98491d8341b3894f5663e... Author: rhpvorderman r.h.p.vorderman@lumc.nl Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- fix typo
Commit: 71cd8ddcc73744b9e45fc1708be9601f41250dd5 https://github.com/galaxyproject/galaxy/commit/71cd8ddcc73744b9e45fc1708be96... Author: rhpvorderman r.h.p.vorderman@lumc.nl Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M lib/galaxy/model/__init__.py
Log Message: ----------- Add system_user_pwent function
Commit: 32d7a30943048e43b2700f33c399b6e0ccf2255a https://github.com/galaxyproject/galaxy/commit/32d7a30943048e43b2700f33c399b... Author: rhpvorderman r.h.p.vorderman@lumc.nl Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py
Log Message: ----------- Add system_user_pwent function to upload and jobs
Commit: 2ec805417c6a251319714178e5be088cc285ebc9 https://github.com/galaxyproject/galaxy/commit/2ec805417c6a251319714178e5be0... Author: rhpvorderman r.h.p.vorderman@lumc.nl Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- Change paramter typo
Commit: e81a2ac65454e0dd88d474210036d166c3055a5b https://github.com/galaxyproject/galaxy/commit/e81a2ac65454e0dd88d474210036d... Author: rhpvorderman r.h.p.vorderman@lumc.nl Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- Fix removed duplication in external chown script
Commit: c275d25be9873e259777506e46b6f7989213e172 https://github.com/galaxyproject/galaxy/commit/c275d25be9873e259777506e46b6f... Author: rhpvorderman r.h.p.vorderman@lumc.nl Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- Fix linting
Commit: aa200fe46351eaa6f7ab30899cdf57bdaa2b069a https://github.com/galaxyproject/galaxy/commit/aa200fe46351eaa6f7ab30899cdf5... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/external_chown_script.py
Log Message: ----------- implemented the changes requested by @mvdbeek:
- check for external_chown_script == None - switched from string split to shlex.split - changed import order for pwd - stderr + exit -> just exit
Commit: e8f44de501dec8b04864b574687d8098ea3bab1e https://github.com/galaxyproject/galaxy/commit/e8f44de501dec8b04864b574687d8... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M lib/galaxy/jobs/__init__.py
Log Message: ----------- bugfix missing colon
Commit: ae1903d396584fe51bf77127b84ea7cf7b831fb6 https://github.com/galaxyproject/galaxy/commit/ae1903d396584fe51bf77127b84ea... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M lib/galaxy/jobs/runners/drmaa.py
Log Message: ----------- shlex.split also for external kill and run scripts
Commit: 7fbd3f2bc229d60da22535b062465b1794e39335 https://github.com/galaxyproject/galaxy/commit/7fbd3f2bc229d60da22535b062465... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M scripts/external_chown_script.py
Log Message: ----------- added missing empty line
Commit: 074b90d55edc0a82115aac3adc5b189e7144c0b3 https://github.com/galaxyproject/galaxy/commit/074b90d55edc0a82115aac3adc5b1... Author: bernt@informatik.uni-leipzig.de bernt@informatik.uni-leipzig.de Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M lib/galaxy/model/__init__.py M scripts/external_chown_script.py
Log Message: ----------- bug fixes
- system_user_pwent: undefined return value when KeyError - external_chown_script: * typo * subprocess instead of os.subprocess
Commit: f83871d0707dea0256a5f409f285eec16f7bcef7 https://github.com/galaxyproject/galaxy/commit/f83871d0707dea0256a5f409f285e... Author: bernt@informatik.uni-leipzig.de bernt@informatik.uni-leipzig.de Date: 2017-06-13 (Tue, 13 Jun 2017)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/runners/drmaa.py M scripts/drmaa_external_runner.py
Log Message: ----------- moved assign_all_groups parameter to config
Commit: 351adc6574dce1e0be8f3e079a84b77f46f045f6 https://github.com/galaxyproject/galaxy/commit/351adc6574dce1e0be8f3e079a84b... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-06-14 (Wed, 14 Jun 2017)
Changed paths: M .ci/flake8_lint_include_list.txt M CONTRIBUTORS.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.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/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js A client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M 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lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/metadata/metadata_generator.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map A static/maps/mvc/page/page-list.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-slider.js.map A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.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/layout/menu.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js A static/scripts/mvc/page/page-list.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-slider.js A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/grid_base.mako M templates/sharing_base.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/workflow/configure_menu.mako M test/api/test_dataset_collections.py M test/base/populators.py A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py
Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev
Commit: 57c112442d53dfff5cc9be9c775fd81eb7cae03d https://github.com/galaxyproject/galaxy/commit/57c112442d53dfff5cc9be9c775fd... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-06-15 (Thu, 15 Jun 2017)
Changed paths: M config/galaxy.ini.sample
Log Message: ----------- fixed typos in galaxy.ini
Commit: 698075c3d7fa5745cc437d36a9c0c48e3f0c6f9f https://github.com/galaxyproject/galaxy/commit/698075c3d7fa5745cc437d36a9c0c... Author: Matthias Bernt m.bernt@ufz.de Date: 2017-06-19 (Mon, 19 Jun 2017)
Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.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/webhooks.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/webapps/galaxy/api/webhooks.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.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/layout/menu.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/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py
Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev
Commit: 153b8d4dca041f43d704cab052b1b733d74658c8 https://github.com/galaxyproject/galaxy/commit/153b8d4dca041f43d704cab052b1b... Author: Nate Coraor nate@bx.psu.edu Date: 2017-06-27 (Tue, 27 Jun 2017)
Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py
Log Message: ----------- Merge pull request #4096 from bernt-matthias/dev
get real user name from username and email (for submission as real user with drmaa)
Compare: https://github.com/galaxyproject/galaxy/compare/a57b4c171525...153b8d4dca04
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