galaxy-commits November 2017

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[galaxyproject/galaxy] c3e898: Fix integration database encoding issue with templ...
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3e89834087c6d6b0468d031356ac503525b17b0 https://github.com/galaxyproject/galaxy/commit/c3e89834087c6d6b0468d031356a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/migrate/check.py Log Message: ----------- Fix integration database encoding issue with templated database stuff. Commit: c0a3148b84b36c455a4698e5ed6b420f975fbfbd https://github.com/galaxyproject/galaxy/commit/c0a3148b84b36c455a4698e5ed6b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/migrate/check.py Log Message: ----------- Merge pull request #4914 from jmchilton/integration_test_fix Fix integration database encoding issue with templated database stuff. Compare: https://github.com/galaxyproject/galaxy/compare/7d1bdb28f105...c0a3148b84b3

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[galaxyproject/galaxy] 09c9f2: More structured app shutdown.
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09c9f27f69ae72cac34b1286dfefce125ac404a6 https://github.com/galaxyproject/galaxy/commit/09c9f27f69ae72cac34b1286dfef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py A lib/galaxy/util/monitors.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- More structured app shutdown. - Cleanup database engine when shutting down Galaxy app (this wasn't done previously and I think it can cause connection issues when testing across different databases). - Join monitor threads when shutting down (old behavior can be restored by setting wait time for monitor threads back to "0"). See note in galaxy.ini.sample. - Better error handling during shutdown, don't let a failure to cleanup one thing cause other things not to be cleaned up. - New monitor thread mixin based on jobs stuff - reuse for workflows so it properly wakes up workflow scheduling on shutdown. Commit: 7d1bdb28f105f77a0e6f6a8509a32e62765f8a45 https://github.com/galaxyproject/galaxy/commit/7d1bdb28f105f77a0e6f6a8509a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py A lib/galaxy/util/monitors.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #4910 from jmchilton/wind_down_improvement_2 More structured app shutdown. Compare: https://github.com/galaxyproject/galaxy/compare/6b68c5d10ebb...7d1bdb28f105

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[galaxyproject/galaxy] 9b9099: Improvements to database initialization.
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b909991f2fb0e19b76ce22a4362871600577165 https://github.com/galaxyproject/galaxy/commit/9b909991f2fb0e19b76ce22a4362… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/migrate/check.py M test/base/driver_util.py M test/base/integration_util.py Log Message: ----------- Improvements to database initialization. - Use sqlalchemy-utils to create postgres / mysql database if they don't exist the way it happens automatically for sqlite. - Add a new configuration parameter called database_template that allows creating postgres databases from an existing database using a TEMPLATE statement. - Use the database template parameter to give each integration test case class a clean postgres database. Commit: 6b68c5d10ebbb5ad82a70e34aae852fa00fab1b0 https://github.com/galaxyproject/galaxy/commit/6b68c5d10ebbb5ad82a70e34aae8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/migrate/check.py M test/base/driver_util.py M test/base/integration_util.py Log Message: ----------- Merge pull request #4887 from jmchilton/database_initialization Automatic-er database initialization. Compare: https://github.com/galaxyproject/galaxy/compare/605b2272b26c...6b68c5d10ebb

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[galaxyproject/galaxy] 497fe0: Remove admin tool reload mako
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 497fe0bba1ebffe5b64142106f53ab3adde07056 https://github.com/galaxyproject/galaxy/commit/497fe0bba1ebffe5b64142106f53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: R templates/admin/reload_tool.mako Log Message: ----------- Remove admin tool reload mako Commit: fab7b03d352fdfdf5be09d5bc7a9eb895b03da09 https://github.com/galaxyproject/galaxy/commit/fab7b03d352fdfdf5be09d5bc7a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove reload option from admin panel Commit: 4a5dcd067efa3329141cda76a0ec1f9bbbfc175e https://github.com/galaxyproject/galaxy/commit/4a5dcd067efa3329141cda76a0ec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove reload option from tool form Commit: ea863cd1b525a3d931d87320a7f8990e1f87b361 https://github.com/galaxyproject/galaxy/commit/ea863cd1b525a3d931d87320a7f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove associated controller endpoint from admin controller Commit: 99021c2036f009098bc1d2dbe18c36d29172abb4 https://github.com/galaxyproject/galaxy/commit/99021c2036f009098bc1d2dbe18c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-model.js A client/galaxy/scripts/mvc/library/library-util.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/tours.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/gulpfile.js M client/package.json M client/yarn.lock M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M doc/schema_template.md M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M run_tests.sh M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-model.js.map A static/maps/mvc/library/library-util.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-model.js A static/scripts/mvc/library/library-util.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/tours.js M static/style/blue/base.css R templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/monitor_repository_installation.mako R templates/admin/tool_shed_repository/repository_installation_grid.mako R templates/admin/tool_shed_repository/tool_dependencies_grid.mako M test/api/test_tools.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/functional/tools/data_source.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml M test/qunit/Gruntfile.js M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.7.js R test/qunit/test-libs/sinon-qunit-1.0.0.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/shed_functional/base/twilltestcase.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_reload_buttons Commit: dc451272be3ecbaaad5a83c032bcf9913f7b9bf9 https://github.com/galaxyproject/galaxy/commit/dc451272be3ecbaaad5a83c032bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Revise admin panel labels Commit: 760f846fdaf3284667e4b5a33c388f22255687ca https://github.com/galaxyproject/galaxy/commit/760f846fdaf3284667e4b5a33c38… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove legacy controller endpoint, partially connected to ui Commit: 497d03104b5858838a6cd60711b6be5f85aa60a0 https://github.com/galaxyproject/galaxy/commit/497d03104b5858838a6cd60711b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: R templates/admin/package_tool.mako Log Message: ----------- Remove associated mako Commit: 319b6b9bfaf1578dca445c1decca061d2cf9dd34 https://github.com/galaxyproject/galaxy/commit/319b6b9bfaf1578dca445c1decca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove link without tool id from admin panel Commit: c61d2ce774c437aeeb0a23d0aa7b33f2349bfb9e https://github.com/galaxyproject/galaxy/commit/c61d2ce774c437aeeb0a23d0aa7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Move manage views up in list Commit: 3731a9704996061545360cc339bcc8e55e7dc01a https://github.com/galaxyproject/galaxy/commit/3731a9704996061545360cc339bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M static/maps/mvc/grid/grid-template.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.map M static/scripts/mvc/grid/grid-template.js Log Message: ----------- Fix error message status in toolshed grid Commit: 8f786c36109709eca46ef8f609e219fce0e8f4af https://github.com/galaxyproject/galaxy/commit/8f786c36109709eca46ef8f609e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Revise admin labels in server section Commit: a5c365c76fe5d6fb50043c2e88000f1945bdb68b https://github.com/galaxyproject/galaxy/commit/a5c365c76fe5d6fb50043c2e8800… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Adjust labels in admin info view Commit: 62ad2da5f520b908da1664ab590d1c9494880f29 https://github.com/galaxyproject/galaxy/commit/62ad2da5f520b908da1664ab590d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: A .ci/tox_envs/flake8/Pipfile A .ci/tox_envs/flake8/requirements.txt A .ci/tox_envs/flake8_imports/Pipfile A .ci/tox_envs/flake8_imports/requirements.txt A .ci/tox_envs/update.sh M Makefile M client/galaxy/style/less/upload.less M config/local_conda_mapping.yml.sample M doc/source/releases/17.09_announce.rst M lib/galaxy/app.py M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/webapps/galaxy/config_watchers.py M scripts/bootstrap_history.py M scripts/common_startup.sh M static/style/blue/base.css M tox.ini Log Message: ----------- Merge branch 'dev' into remove_reload_buttons Commit: 48ff086efce477aa0c05fcf53ab318e92e0207e1 https://github.com/galaxyproject/galaxy/commit/48ff086efce477aa0c05fcf53ab3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/grouping.py R lib/galaxy/webapps/galaxy/api/request_types.py R lib/galaxy/webapps/galaxy/api/requests.py R lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/buildapp.py M run_tests.sh M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary Log Message: ----------- Merge branch 'dev' into remove_reload_buttons Commit: 3f14454d57631d326e79005d79898e9524d364f6 https://github.com/galaxyproject/galaxy/commit/3f14454d57631d326e79005d7989… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map Log Message: ----------- run prettier Commit: 605b2272b26c15cd8c1c5c3f6a98a593d8b00f78 https://github.com/galaxyproject/galaxy/commit/605b2272b26c15cd8c1c5c3f6a98… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/tool/tool-form-base.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.map M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/tool/tool-form-base.js R templates/admin/package_tool.mako R templates/admin/reload_tool.mako M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Merge pull request #4866 from guerler/remove_reload_buttons Remove tool reloading buttons and packaging endpoint, revise admin labels Compare: https://github.com/galaxyproject/galaxy/compare/79d91813399a...605b2272b26c

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[galaxyproject/galaxy] 5f1588: Another round of Selenium enhancements and fixes f...
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f15889ca13d5202b31b4108bcdb371a58e4317b https://github.com/galaxyproject/galaxy/commit/5f15889ca13d5202b31b4108bcdb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary Log Message: ----------- Another round of Selenium enhancements and fixes for 18.01. - Bake Selenium (chrome, chrome-wrapper, xvfb, and Selenium server) into Docker test image. (1) - Correct usage of common_startup.sh to fetch dev wheels (don't use pip directly). - Fix/enhance the test wrapper file to not set GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECATION - this prevents integration database templating (#4887) from working with the Docker image. - Update target Dockerfile. 1) The Docker compose setup for Selenium tests currently used by Jenkins is nice in that it uses official Selenium and Postgres Docker images - but it is problematic in that it takes more resources than the other single container Docker jobs, it doesn't cleanup as nicely, it doesn't have a pre-migrated database or pre-installed dependencies so it takes longer to run, and isn't easily exposed to developers via run_tests.sh. A more pragmatic Jenkins job based on this work should be runnable for every PR - the current variant simply takes too long and requires too many resources. Commit: 459a9621e2aa76aad78e5dba5ccba945532a2bba https://github.com/galaxyproject/galaxy/commit/459a9621e2aa76aad78e5dba5ccb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Fix run_test_wrapper to reflect Galaxy database isn't created with UTF8 encoding. Commit: 79d91813399a598228785325121b01409deaa4b0 https://github.com/galaxyproject/galaxy/commit/79d91813399a598228785325121b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/docker/base/selenium/LICENSE A test/docker/base/selenium/README A test/docker/base/selenium/entry_point.sh A test/docker/base/selenium/functions.sh A test/docker/base/selenium/generate_config A test/docker/base/selenium/wrap_chrome_binary Log Message: ----------- Merge pull request #4900 from jmchilton/docker_updates Another round of Docker enhancements and fixes for 18.01. Compare: https://github.com/galaxyproject/galaxy/compare/055d7773e208...79d91813399a

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[galaxyproject/galaxy] 74dc8a: otherwise it will overwrite linking source file
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74dc8a0cb55f91d9efa37936446a2d6b1304195a https://github.com/galaxyproject/galaxy/commit/74dc8a0cb55f91d9efa37936446a… Author: Ignacio Eguinoa <igegu(a)psb.ugent.be> Date: 2017-10-25 (Wed, 25 Oct 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- otherwise it will overwrite linking source file Commit: 055d7773e208b590e948079031cdae002f226b33 https://github.com/galaxyproject/galaxy/commit/055d7773e208b590e948079031cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4858 from ieguinoa/linked_files_fix Bugfix during error handling with linked files during upload Compare: https://github.com/galaxyproject/galaxy/compare/4485852b7693...055d7773e208

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[galaxyproject/galaxy] bd8c2d: Restore api functions
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd8c2d18bd366863ffff5b7128e0cf6f5fe088c0 https://github.com/galaxyproject/galaxy/commit/bd8c2d18bd366863ffff5b7128e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/samples.py Log Message: ----------- Restore api functions Commit: 7abe54e34d579f165331b7105da55309c474c76f https://github.com/galaxyproject/galaxy/commit/7abe54e34d579f165331b7105da5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/samples.py Log Message: ----------- Restore update sample state api Commit: 1a52a8da16f460eb1d6d5dfc07882553dee21073 https://github.com/galaxyproject/galaxy/commit/1a52a8da16f460eb1d6d5dfc0788… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/samples.py Log Message: ----------- Add forms mixin to samples api Commit: 031b77f1e04bfc167b0a922dca2abcefaf8562a1 https://github.com/galaxyproject/galaxy/commit/031b77f1e04bfc167b0a922dca2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/samples.py Log Message: ----------- Fix lint Commit: d64333cabfc29eb5293802e21601f87dcb12d0cb https://github.com/galaxyproject/galaxy/commit/d64333cabfc29eb5293802e21601… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-26 (Thu, 26 Oct 2017) Changed paths: R lib/galaxy/webapps/galaxy/api/request_types.py R lib/galaxy/webapps/galaxy/api/requests.py R lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove Sample requests api endpoints Commit: 746859b2d3f2c973fa63c7959bcc2aeb149d5a42 https://github.com/galaxyproject/galaxy/commit/746859b2d3f2c973fa63c7959bcc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M .travis.yml M Makefile M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-model.js A client/galaxy/scripts/mvc/library/library-util.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/tours.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml M doc/schema_template.md M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M run_tests.sh M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-model.js.map A static/maps/mvc/library/library-util.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-model.js A static/scripts/mvc/library/library-util.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/tours.js M static/style/blue/base.css R templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/monitor_repository_installation.mako R templates/admin/tool_shed_repository/repository_installation_grid.mako R templates/admin/tool_shed_repository/tool_dependencies_grid.mako M test/api/test_tools.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/functional/tools/data_source.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/test_data_source.xml M test/qunit/Gruntfile.js M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.7.js R test/qunit/test-libs/sinon-qunit-1.0.0.js M test/qunit/tests/form_tests.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/graph.js M test/qunit/tests/hda-base.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/job-dag.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/masthead_tests.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/modal_tests.js M test/qunit/tests/page_tests.js M test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/shed_functional/base/twilltestcase.py M tox.ini Log Message: ----------- Merge branch 'dev' into sample_api_removal Commit: 4485852b769326396676b8d884855765688730a8 https://github.com/galaxyproject/galaxy/commit/4485852b769326396676b8d88485… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: R lib/galaxy/webapps/galaxy/api/request_types.py R lib/galaxy/webapps/galaxy/api/requests.py R lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #4872 from guerler/sample_api_removal Remove legacy sample tracking api endpoints Compare: https://github.com/galaxyproject/galaxy/compare/2809ca47591b...4485852b7693

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[galaxyproject/galaxy] 320a6a: add nicer composite dataset names
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 320a6a0897684e1080332b22498b38792c4ca5c1 https://github.com/galaxyproject/galaxy/commit/320a6a0897684e1080332b22498b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-10-27 (Fri, 27 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- add nicer composite dataset names Commit: 2809ca47591b668132a2597c9d4d9498fdc5bb23 https://github.com/galaxyproject/galaxy/commit/2809ca47591b668132a2597c9d4d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #4886 from bgruening/proper_comp_names Add nicer composite dataset names by default Compare: https://github.com/galaxyproject/galaxy/compare/4d3382fd1c34...2809ca47591b

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[galaxyproject/galaxy] 1ccb40: Fix list collection creator dragdrop event binding...
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ccb4042223da70cb07ea64e691817514ec10a8e https://github.com/galaxyproject/galaxy/commit/1ccb4042223da70cb07ea64e6918… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Fix list collection creator dragdrop event bindings. Commit: a4b9e31c395858b327b2dc2175bde17cf94b1799 https://github.com/galaxyproject/galaxy/commit/a4b9e31c395858b327b2dc2175bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-30 (Mon, 30 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Handle same as previous commit's jquery-backbone-binding-fail with standard event binding in list of pairs collection builder. Commit: 4d3382fd1c343582c06f7df06cae8fe4e007dc6d https://github.com/galaxyproject/galaxy/commit/4d3382fd1c343582c06f7df06cae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #4901 from dannon/fix_jquery_dragdrop_collections Fix list collection creator dragdrop event bindings. Compare: https://github.com/galaxyproject/galaxy/compare/07d11c6d0b78...4d3382fd1c34

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[galaxyproject/infrastructure-playbook] 9d32f3: Include fixes for inheritance chain vars
by GitHub 01 Nov '17

01 Nov '17

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9d32f3fd87d9298bd32899ede324b1f5813cf9a7 https://github.com/galaxyproject/infrastructure-playbook/commit/9d32f3fd87d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M ansible.cfg M common_roles Log Message: ----------- Include fixes for inheritance chain vars

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