- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] fd3deb: Clean /tmp files older than 2 days on jenkins work...
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fd3deb354b80f4a855d3f29ebf35b6764168641e https://github.com/galaxyproject/infrastructure-playbook/commit/fd3deb354b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: A env/galaxy/files/jenkins/tmpfiles.d-clean-tmp.conf M env/galaxy/group_vars/jenkinsslaves/vars.yml Log Message: ----------- Clean /tmp files older than 2 days on jenkins workers **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 30aaa2: Fix sniffing of readname sorted BAM files
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 30aaa296dd50471001323cc9895560219a33ce71 https://github.com/galaxyproject/galaxy/commit/30aaa296dd50471001323cc98955… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/1.qname_sorted.bam Log Message: ----------- Fix sniffing of readname sorted BAM files This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c2a49d: Directory datatype for Galaxy.
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2a49de6cee056d6cd942e3b392ffbd15961fb42 https://github.com/galaxyproject/galaxy/commit/c2a49de6cee056d6cd942e3b392f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py Log Message: ----------- Directory datatype for Galaxy. Commit: dd6b185ab82b7e251ba7ad3b69abbda7ab4018b9 https://github.com/galaxyproject/galaxy/commit/dd6b185ab82b7e251ba7ad3b69ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M test/api/test_tools.py M test/api/test_tools_upload.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Implement composite uploads on arbitrary datatypes. Prior to this, composite uploads were only allowed for select data types. As far as I can tell, the framework itself allows arbitrary datatypes to have extra files. This allows the upload API to take in extra files for datatypes that aren't explicitly annotated has having extra files. These may be specified one at a time or in directory structures via tar files. Commit: e3bc005a8602a47e542129b5be53aa6316525e90 https://github.com/galaxyproject/galaxy/commit/e3bc005a8602a47e542129b5be53… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Implement API endpoint for indexing extra files in a dataset. Commit: f035d642ceb2a4835d774996f3b3d78588318834 https://github.com/galaxyproject/galaxy/commit/f035d642ceb2a4835d774996f3b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/tar_to_directory.xml M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #6844 from jmchilton/compressed_types_and_extra_files Infrastructure/API Support for Composite Uploads/Downloads Compare: https://github.com/galaxyproject/galaxy/compare/c312c1014d0e...f035d642ceb2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c3dfdb: Default shed tool installation to database/shed_to...
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3dfdb0dc73bbc5339e285500dcaf345e5c67d60 https://github.com/galaxyproject/galaxy/commit/c3dfdb0dc73bbc5339e285500dca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py Log Message: ----------- Default shed tool installation to database/shed_tools instead of ../shed_tools Commit: c312c1014d0e85920f630bf3d3e02e508c636b84 https://github.com/galaxyproject/galaxy/commit/c312c1014d0e85920f630bf3d3e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/migrated_tools_conf.xml.sample M config/shed_tool_conf.xml.sample M doc/source/admin/tool_panel.rst M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/common_util.py Log Message: ----------- Merge pull request #6937 from natefoo/shed-tools-relocate Default shed tool installation to database/shed_tools Compare: https://github.com/galaxyproject/galaxy/compare/3108bd3b3729...c312c1014d0e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2bf5b9: Fix style for legacy toolshed selection page
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2bf5b9b84e5f1391c8a0640255293e23f82042e1 https://github.com/galaxyproject/galaxy/commit/2bf5b9b84e5f1391c8a064025529… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M templates/webapps/galaxy/admin/tool_sheds.mako Log Message: ----------- Fix style for legacy toolshed selection page Commit: 3108bd3b37298417df5e9851d7e126c6c1b4878f https://github.com/galaxyproject/galaxy/commit/3108bd3b37298417df5e9851d7e1… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M templates/webapps/galaxy/admin/tool_sheds.mako Log Message: ----------- Merge pull request #6910 from guerler/toolshed_selection Fix style for legacy toolshed selection page Compare: https://github.com/galaxyproject/galaxy/compare/3f7425ad9308...3108bd3b3729 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 20f3c0: Use existing overflow utility instead of overwriti...
by GitHub 31 Oct '18

31 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20f3c04a421d007ad04a78e39a74c967b61b10fd https://github.com/galaxyproject/galaxy/commit/20f3c04a421d007ad04a78e39a74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M client/galaxy/style/scss/ui.scss M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Use existing overflow utility instead of overwriting card defaults Commit: 3f7425ad9308a6e1946225d155351ccc05aa4fab https://github.com/galaxyproject/galaxy/commit/3f7425ad9308a6e1946225d15535… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M client/galaxy/style/scss/ui.scss M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Merge pull request #6948 from guerler/add_overflow_auto Use recently introduced overflow utility instead of overwriting card defaults Compare: https://github.com/galaxyproject/galaxy/compare/31905f1402d9...3f7425ad9308 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] f2d9e2: Update Main
by GitHub 31 Oct '18

31 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f2d9e2cb5a9abc2b1963acb202e62121bbada045 https://github.com/galaxyproject/usegalaxy-playbook/commit/f2d9e2cb5a9abc2b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 97ec0e: Swap to webpack4
by GitHub 31 Oct '18

31 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97ec0e6ddace44a6fb16868af538c25aa4031ef7 https://github.com/galaxyproject/galaxy/commit/97ec0e6ddace44a6fb16868af538… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock Log Message: ----------- Swap to webpack4 Commit: 72657825b54f1dee5b38b68189eeac8756bf1dde https://github.com/galaxyproject/galaxy/commit/72657825b54f1dee5b38b68189ee… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M .gitignore M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/polyfills.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/webpack.config.js M static/style/blue/base.css M templates/js-app.mako Log Message: ----------- Reconfigured code-splitting in webpack, adjusted imports for backbone, underscore, jquery, removed require.js from js-app.mako Commit: 2c30c366596879c9a4ecdadfe8a62d6ecdf2076c https://github.com/galaxyproject/galaxy/commit/2c30c366596879c9a4ecdadfe8a6… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/repository/browse_repository.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/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.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/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako Log Message: ----------- Removed manual calls to javascript libraries from mako templates Commit: dd7ebb5fa0dc6a36ad10bb90a593e20d7b51722a https://github.com/galaxyproject/galaxy/commit/dd7ebb5fa0dc6a36ad10bb90a593… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/webpack.config.js M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Put requirejs session definitions back, corrected vue build reference in webpack config Commit: fd3a2639ffc9245c9dedd23ff8d6c6b4d458c8a9 https://github.com/galaxyproject/galaxy/commit/fd3a2639ffc9245c9dedd23ff8d6… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Switched to production vue library in webpack Commit: 384f4717dcc1199d8015d4088ef15103eb896234 https://github.com/galaxyproject/galaxy/commit/384f4717dcc1199d8015d4088ef1… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: A client/galaxy/scripts/apps/testEndpoint.js A client/galaxy/scripts/jquery-custom.js M client/galaxy/scripts/layout/modal.js M client/package.json M client/webpack.config.js M client/yarn.lock Log Message: ----------- Replace jquery with custom build that includes plugins Commit: 70efe90dcdc66d85cf0713b44300624ba661ef1a https://github.com/galaxyproject/galaxy/commit/70efe90dcdc66d85cf0713b44300… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M client/galaxy/scripts/jquery-custom.js Log Message: ----------- Added commentary, placeholder for more jquery plugins Commit: 1d8f219362382adc1bb77510e97176d47ccd7f33 https://github.com/galaxyproject/galaxy/commit/1d8f219362382adc1bb77510e971… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M client/yarn.lock M static/style/blue/base.css Log Message: ----------- rebuild, add hashes Commit: c6e4e17aa8a4682a0eaf94eb893efbdeae1dabbd https://github.com/galaxyproject/galaxy/commit/c6e4e17aa8a4682a0eaf94eb893e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: A client/galaxy/scripts/apps/testEndpoint.js A client/galaxy/scripts/jquery-custom.js M client/galaxy/scripts/layout/modal.js M client/package.json M client/webpack.config.js M client/yarn.lock Log Message: ----------- Merge branch 'webpack_4_minimal_flat' of github.com:dannon/galaxy into webpack_4_minimal_flat Commit: e94cf6884d61fa66e8bae23a1d8773044ea01099 https://github.com/galaxyproject/galaxy/commit/e94cf6884d61fa66e8bae23a1d87… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-02 (Tue, 02 Oct 2018) Changed paths: M client/galaxy/scripts/jquery-custom.js M client/webpack.config.js M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Added in webpack loader config for all jquery plugins, removed duplicate extended.js script calls on editor template Commit: 4615213167cb720025468fe2f5347caebdd4c41d https://github.com/galaxyproject/galaxy/commit/4615213167cb720025468fe2f534… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-02 (Tue, 02 Oct 2018) Changed paths: M client/galaxy/scripts/polyfills.js M templates/galaxy_client_app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Removed stray console debugging lines Commit: aa755b099ec09ded41be652ea971137a994ff783 https://github.com/galaxyproject/galaxy/commit/aa755b099ec09ded41be652ea971… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-02 (Tue, 02 Oct 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/jquery-custom.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/onload.js M client/package.json M client/webpack.config.js M client/yarn.lock Log Message: ----------- Simplified loading jquery, referenced npm modules when present Commit: 00d8c0a09adacab152175bfbe8f14acce391940b https://github.com/galaxyproject/galaxy/commit/00d8c0a09adacab152175bfbe8f1… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.js R client/galaxy/scripts/apps/testEndpoint.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/webpack.config.js M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Reworked exports on extended.js Commit: e009533c6b9a393144ae3f61230876a7f4532a38 https://github.com/galaxyproject/galaxy/commit/e009533c6b9a393144ae3f612308… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Removed extraneous eslint comment Commit: 8a74ee7b17e9efdde9eeded9b4e568d97a9b8234 https://github.com/galaxyproject/galaxy/commit/8a74ee7b17e9efdde9eeded9b4e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/polyfills.js M templates/js-app.mako Log Message: ----------- Logging tweaks Commit: 3c2bf7e939623b31361c4fb90c9058d1ebf82bd5 https://github.com/galaxyproject/galaxy/commit/3c2bf7e939623b31361c4fb90c90… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Rerun format Commit: 80b42e8eaef57e28f371d3835bd76a50778289d9 https://github.com/galaxyproject/galaxy/commit/80b42e8eaef57e28f371d3835bd7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade prettier. Commit: 145c89ed1217842edbd844666e6a5f68f2cdfbde https://github.com/galaxyproject/galaxy/commit/145c89ed1217842edbd844666e6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Refactoring towards a reusable vue component display fn Commit: 8f2222cd6440514c9136f3e84a86cfc3245d916e https://github.com/galaxyproject/galaxy/commit/8f2222cd6440514c9136f3e84a86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M client/galaxy/scripts/layout/router.js M client/webpack.config.js Log Message: ----------- Force babelrc for vue-loader/babel, drop redundant vue directive (which was breaking all components...), cleanup Commit: 8bd561362d134e3056855254af50d56a34c18a8f https://github.com/galaxyproject/galaxy/commit/8bd561362d134e3056855254af50… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M client/package.json M client/yarn.lock M static/style/blue/base.css Log Message: ----------- (safe) client package upgrades. Commit: e4f43af36b81296940f45974cecbcc78743105e4 https://github.com/galaxyproject/galaxy/commit/e4f43af36b81296940f45974cecb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Drop cruft from webpack.config Commit: f8af18c08391ca584ed4c98335bab9980aac68f9 https://github.com/galaxyproject/galaxy/commit/f8af18c08391ca584ed4c98335ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M client/.babelrc M client/package.json M client/webpack.config.js M client/yarn.lock Log Message: ----------- Swap to new mainline babel plugins, fix up build. Commit: 3429cc3145fd0a4a4f373adb0c09da0156d208da https://github.com/galaxyproject/galaxy/commit/3429cc3145fd0a4a4f373adb0c09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M client/webpack.config.js Log Message: ----------- babelrc is now a bool Commit: 3a1658fbbb905af8fec82b7e548d2bdfad07c806 https://github.com/galaxyproject/galaxy/commit/3a1658fbbb905af8fec82b7e548d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade (major version) file-loader, css-loader, and concurrently Commit: 13b0baf3561adc2501805f567f9a3349e628e944 https://github.com/galaxyproject/galaxy/commit/13b0baf3561adc2501805f567f9a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js Log Message: ----------- Standardize and fix duplicate import in history-view Commit: cbbc375e812f56b577f436d13ff4dc1fd2a5ad9f https://github.com/galaxyproject/galaxy/commit/cbbc375e812f56b577f436d13ff4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M templates/webapps/galaxy/visualization/display.mako M templates/webapps/reports/run_stats.mako Log Message: ----------- Untangle a lot of incorrect exports, start to standardize away from default and use explicit exports. Commit: 182b6661d65909976519eca3229ac5151cb09191 https://github.com/galaxyproject/galaxy/commit/182b6661d65909976519eca3229a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Drop chart bundle; will be accessible through extended. Commit: befa3da5b6a6bc7bf2dd061707f258a3cd602119 https://github.com/galaxyproject/galaxy/commit/befa3da5b6a6bc7bf2dd061707f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/scripts/onload.js M client/webpack.config.js M templates/base.mako M templates/base/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 Log Message: ----------- Re-add extended bundle as an application entrypoint Commit: b78ed0bcbfeddd4bee790682d7391b51714fcaf3 https://github.com/galaxyproject/galaxy/commit/b78ed0bcbfeddd4bee790682d739… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Drop test path from webpack config Commit: 63cff0d6742e11162865b61a601efe72a8874a17 https://github.com/galaxyproject/galaxy/commit/63cff0d6742e11162865b61a601e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: A client/galaxy/images/Armitagep_manhattan.png A client/galaxy/images/Armitagep_qqplot.png A client/galaxy/images/add_icon.png A client/galaxy/images/add_icon_dark.png A client/galaxy/images/aggregate_history1.png A client/galaxy/images/aggregate_history2.png A client/galaxy/images/bar_chart.png A client/galaxy/images/base_bg.png A client/galaxy/images/bed_warn.png A client/galaxy/images/button_bar_bg_light.png A client/galaxy/images/closebox.png A client/galaxy/images/dat_points_table_brows_1.png A client/galaxy/images/data_empty.png A client/galaxy/images/data_error.png A client/galaxy/images/data_ok.png A client/galaxy/images/data_queued.png A client/galaxy/images/data_running.gif A client/galaxy/images/ddarrowsplit.png A client/galaxy/images/delete_tag_icon_gray.png A client/galaxy/images/delete_tag_icon_white.png A client/galaxy/images/documents-stack-faded.png A client/galaxy/images/documents-stack.png A client/galaxy/images/done_message_icon.png A client/galaxy/images/dropdownarrow.png A client/galaxy/images/error_bg.png A client/galaxy/images/error_large.png A client/galaxy/images/error_message_icon.png A client/galaxy/images/error_small.png A client/galaxy/images/fetchTax.png A client/galaxy/images/footer_title_bg.png A client/galaxy/images/form_body_bg.png A client/galaxy/images/form_title_bg.png A client/galaxy/images/fugue.png A client/galaxy/images/galaxyIcon_noText.png A client/galaxy/images/gray_bg.png A client/galaxy/images/hatch-023858.png A client/galaxy/images/hgrad.png A client/galaxy/images/hgrad_over.png A client/galaxy/images/histogram.png A client/galaxy/images/histogram2.png A client/galaxy/images/history-buttons.png A client/galaxy/images/history-states.png A client/galaxy/images/info_large.png A client/galaxy/images/info_message_icon.png A client/galaxy/images/info_small.png A client/galaxy/images/jstree/32px.png A client/galaxy/images/jstree/40px.png A client/galaxy/images/jstree/throbber.gif A client/galaxy/images/kendall.png A client/galaxy/images/largespinner.gif A client/galaxy/images/layout_callout_top.png A client/galaxy/images/mag_glass.png A client/galaxy/images/masthead_bg.png A client/galaxy/images/menu_bg.png A client/galaxy/images/mutation_visualization_example.png A client/galaxy/images/ok_bg.png A client/galaxy/images/ok_large.png A client/galaxy/images/ok_small.png A client/galaxy/images/overview_arrows.png A client/galaxy/images/panel_header_bg.png A client/galaxy/images/pearson.png A client/galaxy/images/popupmenu_callout_top.png A client/galaxy/images/question-balloon.png A client/galaxy/images/question-octagon-frame.png A client/galaxy/images/resizable.png A client/galaxy/images/scatter.png A client/galaxy/images/scatterplot.png A client/galaxy/images/select2-spinner.gif A client/galaxy/images/select2.png A client/galaxy/images/select2x2.png A client/galaxy/images/silk/add.png A client/galaxy/images/silk/book.png A client/galaxy/images/silk/book_open.png A client/galaxy/images/silk/chart_curve.png A client/galaxy/images/silk/folder.png A client/galaxy/images/silk/folder_page.png A client/galaxy/images/silk/link.png A client/galaxy/images/silk/link_break.png A client/galaxy/images/silk/page_white.png A client/galaxy/images/silk/page_white_compressed.png A client/galaxy/images/silk/resultset_bottom.png A client/galaxy/images/silk/resultset_next.png A client/galaxy/images/silk/resultset_previous.png A client/galaxy/images/solid_qual.png A client/galaxy/images/spearman.png A client/galaxy/images/sprite-fugue.png A client/galaxy/images/sprite-history-buttons.png A client/galaxy/images/sprite-history-states.png A client/galaxy/images/thumbtack_icon.png A client/galaxy/images/thumbtack_icon_dark.png A client/galaxy/images/tiny_arrow_left.png A client/galaxy/images/tiny_arrow_right.png A client/galaxy/images/visualization/draggable_horizontal.png A client/galaxy/images/visualization/draggable_vertical.png A client/galaxy/images/visualization/strand_left.png A client/galaxy/images/visualization/strand_left_inv.png A client/galaxy/images/visualization/strand_right.png A client/galaxy/images/visualization/strand_right_inv.png A client/galaxy/images/wait_large.png A client/galaxy/images/wait_small.png A client/galaxy/images/warn_bg.png A client/galaxy/images/warn_large.png A client/galaxy/images/warn_message_icon.png A client/galaxy/images/warn_small.png A client/galaxy/images/workflow_circle_drag.png A client/galaxy/images/workflow_circle_green.png A client/galaxy/images/workflow_circle_open.png M client/galaxy/scripts/onload.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/iconic_stroke.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/select2.scss M client/galaxy/style/scss/trackster.scss M client/package.json M client/webpack.config.js M client/yarn.lock R static/images/Armitagep_manhattan.png R static/images/Armitagep_qqplot.png R static/images/add_icon.png R static/images/add_icon_dark.png R static/images/aggregate_history1.png R static/images/aggregate_history2.png R static/images/bar_chart.png R static/images/bed_warn.png R static/images/closebox.png R static/images/dat_points_table_brows_1.png R static/images/ddarrowsplit.png R static/images/delete_tag_icon_gray.png R static/images/delete_tag_icon_white.png R static/images/documents-stack-faded.png R static/images/documents-stack.png R static/images/dropdownarrow.png R static/images/fetchTax.png R static/images/galaxyIcon_noText.png R static/images/hatch-023858.png R static/images/histogram.png R static/images/histogram2.png R static/images/jstree/32px.png R static/images/jstree/40px.png R static/images/jstree/throbber.gif R static/images/kendall.png R static/images/mag_glass.png R static/images/mutation_visualization_example.png R static/images/overview_arrows.png R static/images/pearson.png R static/images/resizable.png R static/images/scatter.png R static/images/scatterplot.png R static/images/select2-spinner.gif R static/images/select2.png R static/images/select2x2.png R static/images/silk/add.png R static/images/silk/book.png R static/images/silk/book_open.png R static/images/silk/chart_curve.png R static/images/silk/folder.png R static/images/silk/folder_page.png R static/images/silk/link.png R static/images/silk/link_break.png R static/images/silk/page_white.png R static/images/silk/page_white_compressed.png R static/images/silk/resultset_bottom.png R static/images/silk/resultset_next.png R static/images/silk/resultset_previous.png R static/images/solid_qual.png R static/images/spearman.png R static/images/thumbtack_icon.png R static/images/thumbtack_icon_dark.png R static/images/visualization/draggable_horizontal.png R static/images/visualization/draggable_vertical.png R static/images/visualization/strand_left.png R static/images/visualization/strand_left_inv.png R static/images/visualization/strand_right.png R static/images/visualization/strand_right_inv.png M static/style/blue/base.css R static/style/blue/base_bg.png R static/style/blue/button_bar_bg_light.png R static/style/blue/data_empty.png R static/style/blue/data_error.png R static/style/blue/data_ok.png R static/style/blue/data_queued.png R static/style/blue/done_message_icon.png R static/style/blue/error_bg.png R static/style/blue/error_large.png R static/style/blue/error_message_icon.png R static/style/blue/error_small.png R static/style/blue/footer_title_bg.png R static/style/blue/form_body_bg.png R static/style/blue/form_title_bg.png R static/style/blue/fugue.png R static/style/blue/gray_bg.png R static/style/blue/hgrad.png R static/style/blue/hgrad_over.png R static/style/blue/history-buttons.png R static/style/blue/history-states.png R static/style/blue/info_large.png R static/style/blue/info_message_icon.png R static/style/blue/info_small.png R static/style/blue/largespinner.gif R static/style/blue/layout_callout_top.png R static/style/blue/masthead_bg.png R static/style/blue/menu_bg.png R static/style/blue/ok_bg.png R static/style/blue/ok_large.png R static/style/blue/ok_small.png R static/style/blue/panel_header_bg.png R static/style/blue/popupmenu_callout_top.png R static/style/blue/question-balloon.png R static/style/blue/question-octagon-frame.png R static/style/blue/tiny_arrow_left.png R static/style/blue/tiny_arrow_right.png M static/style/blue/trackster.css R static/style/blue/wait_large.png R static/style/blue/wait_small.png R static/style/blue/warn_bg.png R static/style/blue/warn_large.png R static/style/blue/warn_message_icon.png R static/style/blue/warn_small.png R static/style/blue/workflow_circle_drag.png R static/style/blue/workflow_circle_green.png R static/style/blue/workflow_circle_open.png R static/style/shared_images/data_running.gif R static/style/shared_images/error_large.png R static/style/shared_images/error_small.png R static/style/shared_images/info_large.png R static/style/shared_images/info_small.png R static/style/shared_images/ok_large.png R static/style/shared_images/ok_small.png R static/style/shared_images/wait_large.png R static/style/shared_images/wait_small.png R static/style/shared_images/warn_large.png R static/style/shared_images/warn_small.png Log Message: ----------- Style building and asset bundling, incremental. Commit: 02623d0005a42df3d3aa56d7ec445d31b9ebc1d5 https://github.com/galaxyproject/galaxy/commit/02623d0005a42df3d3aa56d7ec44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/gulpfile.js M client/webpack.config.js M static/style/blue/base.css M templates/js-app.mako Log Message: ----------- File loader tweaking. Commit: 6aa94a684efd90f5af775ab9f28a246c189e6fcd https://github.com/galaxyproject/galaxy/commit/6aa94a684efd90f5af775ab9f28a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: R client/galaxy/images/galaxyIcon_noText.png A static/images/galaxyIcon_noText.png Log Message: ----------- relocate default logo (again) -- need a better strategy for cleaning out dist dir Commit: 67735bf7b28b9f675b4a1e7e41ee10285d52203d https://github.com/galaxyproject/galaxy/commit/67735bf7b28b9f675b4a1e7e41ee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/webpack.config.js M templates/base.mako Log Message: ----------- Test eliminating duplicate CSS Commit: abb9be2ead59299cfba686ea3c22707f3f2f9914 https://github.com/galaxyproject/galaxy/commit/abb9be2ead59299cfba686ea3c22… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M .gitignore A client/galaxy/style/scss/sprite-fugue.scss A client/galaxy/style/scss/sprite-history-buttons.scss A client/galaxy/style/scss/sprite-history-states.scss Log Message: ----------- Keeping prebuilt sprite sheets for now Commit: 9b91a92400394d7e6354c6c4e4f35ff8aa9067c9 https://github.com/galaxyproject/galaxy/commit/9b91a92400394d7e6354c6c4e4f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/style/scss/sprite-fugue.scss Log Message: ----------- Fix sprite path resolution Commit: c221eaaef9ec5eca5240cb9f969f825e4f79b3f1 https://github.com/galaxyproject/galaxy/commit/c221eaaef9ec5eca5240cb9f969f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/karma.config.js Log Message: ----------- Karma cleanup; trying to get tests working. Commit: 66197c055f355ed54b2669537a399ff78e4480ff https://github.com/galaxyproject/galaxy/commit/66197c055f355ed54b2669537a39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/karma.config.js Log Message: ----------- Test against production bundles Commit: 860ec172285d2ee1f06bb02f117dcb5719585498 https://github.com/galaxyproject/galaxy/commit/860ec172285d2ee1f06bb02f117d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/package.json Log Message: ----------- Pipe raw through concurrently (buys us colors from managed processes) Commit: 68af39b523f4343be211f03f5a3315ecfdf64353 https://github.com/galaxyproject/galaxy/commit/68af39b523f4343be211f03f5a33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/karma.config.js Log Message: ----------- Better debug output when there are no tests Commit: 43fcf0f9a9747599f9c2a5a1f72c30945ab2df16 https://github.com/galaxyproject/galaxy/commit/43fcf0f9a9747599f9c2a5a1f72c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: R client/GruntFile.js M client/package.json M client/yarn.lock Log Message: ----------- Purge grunt. Commit: 73ea22e1ad29038c7b7a31421e41fc5e18d57e19 https://github.com/galaxyproject/galaxy/commit/73ea22e1ad29038c7b7a31421e41… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M run_tests.sh Log Message: ----------- drop watch option from run_tests (hasnt' been valid in a long time) Commit: f116cb8de824a3d9d03acbd698e545cf5ca5331f https://github.com/galaxyproject/galaxy/commit/f116cb8de824a3d9d03acbd698e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/dev/faq.rst R static/GruntFile.js Log Message: ----------- Drop more grunt cruft Commit: a8b06b0c444b4962b1129f903b33e8fc6ffb774a https://github.com/galaxyproject/galaxy/commit/a8b06b0c444b4962b1129f903b33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/jquery.rating.css R static/style/blue/jquery.rating.css M templates/base/base_panels.mako Log Message: ----------- Incremental REBASEME Commit: eeaf610ea04b59c8f554eb982fa24d17795cbc4d https://github.com/galaxyproject/galaxy/commit/eeaf610ea04b59c8f554eb982fa2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/gulpfile.js M client/package.json R static/style/blue/base.css Log Message: ----------- Drop gulp style; remove base.css from repo Commit: 5e96c2daa0ee87c1fef3883043d2f0d6a8aeac15 https://github.com/galaxyproject/galaxy/commit/5e96c2daa0ee87c1fef3883043d2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Style chunk Commit: 748ff8a7595350eed83d9eaa490246cc0f7bfe46 https://github.com/galaxyproject/galaxy/commit/748ff8a7595350eed83d9eaa4902… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock M static/style/base.css Log Message: ----------- Style chunk, now with mini-css-extract-plugin Commit: b0ddea33007f415b5710c5968c8c98ecc87e55fd https://github.com/galaxyproject/galaxy/commit/b0ddea33007f415b5710c5968c8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock M static/style/base.css Log Message: ----------- Pick a different path for style entrypoint. This reverts commit 748ff8a7595350eed83d9eaa490246cc0f7bfe46. Commit: 0118c982e7b7ca1525bb41cafcb89ad81c1d8b99 https://github.com/galaxyproject/galaxy/commit/0118c982e7b7ca1525bb41cafcb8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M client/galaxy/scripts/onload.js A client/galaxy/scripts/style.js M client/webpack.config.js M templates/js-app.mako Log Message: ----------- Add style entrypoint Commit: 8f8473c1905ad76e3196bc38f58d294c523446ea https://github.com/galaxyproject/galaxy/commit/8f8473c1905ad76e3196bc38f58d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/onload.js M client/webpack.config.js Log Message: ----------- Drop independent style chunk; we'll use onload for this. Commit: 7aa0f6afcc3ab37bc91f54ee7806de6a0f8a59d6 https://github.com/galaxyproject/galaxy/commit/7aa0f6afcc3ab37bc91f54ee7806… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/polyfills.js M client/package.json M client/yarn.lock Log Message: ----------- Added async function syntax support Commit: db67cd2f56fd831251ee3b2d713e9e883c7edde1 https://github.com/galaxyproject/galaxy/commit/db67cd2f56fd831251ee3b2d713e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/framework/run_tests.sh A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M .coveragerc M .gitignore M client/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/scratchbook.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/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.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/tool/tools.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.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/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.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-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.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/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/workflow/workflow-connector.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-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js R client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/scripts/ui/fa-icon-button.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/frame.scss R client/galaxy/style/scss/galaxy_bootstrap/overrides.scss R client/galaxy/style/scss/galaxy_bootstrap/variables.scss R client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/theme/blue.scss R client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss A client/galaxy/style/source_material/error_icon.svg M client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/info_icon.svg A client/galaxy/style/source_material/ok_icon.svg A client/galaxy/style/source_material/wait_icon.svg A client/galaxy/style/source_material/warn_icon.svg M client/gulpfile.js M client/package.json M client/yarn.lock A config/container_resolvers_conf.xml.sample M config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/oidc_backends_config.xml.sample M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/webhooks/demo/tour_generator/__init__.py M config/reports.yml.sample M config/tool_shed.yml.sample M contrib/nagios/check_galaxy.py M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/special_topics/interactive_environments.rst M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M lib/galaxy/actions/library.py M lib/galaxy/authnz/managers.py M 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lib/galaxy/managers/base.py M lib/galaxy/managers/cloud.py A lib/galaxy/managers/cloudauthzs.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/jobs.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py A lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cache.py M 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M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/managers/groups.py M lib/tool_shed/util/repository_util.py M pytest.ini M run_tests.sh M scripts/api/library_upload_dir.py M scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/pgcleanup.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/util.py A scripts/pages_identifier_conversion.py M scripts/plugin_staging.py A static/style/blue/base.css M static/style/blue/library.css M templates/display_base.mako M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api.py M test/base/populators.py A test/base/ssh_util.py M test/base/workflow_fixtures.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py M test/functional/tools/disambiguate_cond.xml A test/functional/tools/for_workflows/mapper_two.xml A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_cli_runners.py M test/integration/test_job_environments.py M test/integration/test_scripts.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_workflow_run.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py A test/unit/test_compression_util.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_utils.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into webpack_4_minimal_flat Commit: 0108a2e6932d631e030b33363ea7564207edc90d https://github.com/galaxyproject/galaxy/commit/0108a2e6932d631e030b33363ea7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: A client/galaxy/images/circle.py A client/galaxy/images/error_icon.svg A client/galaxy/images/galaxy_icons.svg A client/galaxy/images/galaxy_spinner.fla A client/galaxy/images/info_icon.svg A client/galaxy/images/ok_icon.svg A client/galaxy/images/wait_icon.svg A client/galaxy/images/warn_icon.svg M client/galaxy/style/scss/base.scss R client/galaxy/style/source_material/circle.py R client/galaxy/style/source_material/error_icon.svg R client/galaxy/style/source_material/galaxy_icons.svg R client/galaxy/style/source_material/galaxy_spinner.fla R client/galaxy/style/source_material/info_icon.svg R client/galaxy/style/source_material/ok_icon.svg R client/galaxy/style/source_material/wait_icon.svg R client/galaxy/style/source_material/warn_icon.svg Log Message: ----------- Relocate various source materials. Commit: b13caf14d5529fd44c0debd1da349f7fc8f554c8 https://github.com/galaxyproject/galaxy/commit/b13caf14d5529fd44c0debd1da34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Swap to karma-webpack@next (for 4.0 compat -- it actually works!) Commit: e09b43af0191df4574989c19ec135c51c2934ee3 https://github.com/galaxyproject/galaxy/commit/e09b43af0191df4574989c19ec13… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock M templates/js-app.mako Log Message: ----------- Added OptimizeCssAssetsPlugin fix for sourcemaps + minicss plugin Commit: 443683b80187bf202912e328621573747795316c https://github.com/galaxyproject/galaxy/commit/443683b80187bf202912e3286215… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Drop a ton of unused gulp cruft. Commit: 8ab6dee071756fb13fd841afa23f4aa4e8a643b2 https://github.com/galaxyproject/galaxy/commit/8ab6dee071756fb13fd841afa23f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Still uglify for shipped libs. Commit: c18e99505f5038b633670eca66a16565ac981232 https://github.com/galaxyproject/galaxy/commit/c18e99505f5038b633670eca66a1… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/webpack.config.js R static/style/base.css M templates/js-app.mako Log Message: ----------- exported styles to single file instead of one per entrypoint Commit: ea12d73df12a4a26a423e0c987d27c6ed96e9765 https://github.com/galaxyproject/galaxy/commit/ea12d73df12a4a26a423e0c987d2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/package.json M client/webpack.config.js M client/yarn.lock R static/style/base.css M templates/js-app.mako Log Message: ----------- Merge remote-tracking branch 'Nerdinacan/webpack_4_mapfix' into unified_webpack4 Commit: ee4908bf57efe03cb85f2ffb846cb05357adc4c5 https://github.com/galaxyproject/galaxy/commit/ee4908bf57efe03cb85f2ffb846c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: A static/style/base.css R static/style/blue/base.css Log Message: ----------- Drop style artifact, recreate link to output bundle for backwards compat. Commit: e273a549db844c3e27645c6dc568cd5f49f389af https://github.com/galaxyproject/galaxy/commit/e273a549db844c3e27645c6dc568… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Webpack -> .21 Commit: 658dce066b91ad03379f27f7311bf4e74631be87 https://github.com/galaxyproject/galaxy/commit/658dce066b91ad03379f27f7311b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/galaxy/scripts/qunit/assets/base.css Log Message: ----------- Fix link to base.css Commit: 6c77d715a82bf6b1d461ec0f67744fe76d593cbc https://github.com/galaxyproject/galaxy/commit/6c77d715a82bf6b1d461ec0f6774… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M templates/base.mako Log Message: ----------- Fix goofed bundle inclusion refactoring Commit: f98c79ea9568ae7ff4fc1c18b2b598180e5c0285 https://github.com/galaxyproject/galaxy/commit/f98c79ea9568ae7ff4fc1c18b2b5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M templates/base.mako Log Message: ----------- include base.css in base mako Commit: 1b4aa3e47e676ea5d10df74d09f954aad9a22c51 https://github.com/galaxyproject/galaxy/commit/1b4aa3e47e676ea5d10df74d09f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/js-app.mako Log Message: ----------- Fix style inclusion for js-app, after poking at merging jquery styles (todo for the future, not worth dealing with now). Commit: 21898296a676f39502fb13f2b425a49d978a4c86 https://github.com/galaxyproject/galaxy/commit/21898296a676f39502fb13f2b425… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: A client/galaxy/style/jquery.rating.css R client/galaxy/style/scss/jquery.rating.css A static/style/blue/jquery.rating.css Log Message: ----------- Fix jquery.rating.css (until it's bundled) Commit: 55bd9ede5b7b08597725f8f630867f09acca7f7d https://github.com/galaxyproject/galaxy/commit/55bd9ede5b7b08597725f8f63086… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/karma.config.js M client/webpack.config.js Log Message: ----------- Fix js unit tests to work with bundled css (TODO: Make this more robust, this is very brittle right now and will potentially break the tests (obviously) when anyone reorders plugins, for example) Commit: f1ed67cf3f8325f3f22eb0624d7b9403524a9eaf https://github.com/galaxyproject/galaxy/commit/f1ed67cf3f8325f3f22eb0624d7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/karma.config.js Log Message: ----------- Cleanup, document TODO for loader replacement Commit: 84ae932e8b7fbb0086dc12a7c44945f37f9e05ed https://github.com/galaxyproject/galaxy/commit/84ae932e8b7fbb0086dc12a7c449… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: A static/style/blue/base.css M test/base/driver_util.py Log Message: ----------- Add back extra link to base.css for selenium testing (and assumedly other deployments which have custom mappings?). We need to drop all these extra handles eventually, to consolidate the interface to single endpoints with chunked bundles. Commit: 6775befc6a67a85ff02be4eebdb12a11db2a30ed https://github.com/galaxyproject/galaxy/commit/6775befc6a67a85ff02be4eebdb1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Fix import/export in extended bundle Commit: 99bb15c1215011dc2d44170e4db2f4f75d74bcbf https://github.com/galaxyproject/galaxy/commit/99bb15c1215011dc2d44170e4db2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Continue importing base.css in base_panels.mako Commit: 03b44a84a66e07d720a34764c21241067faec199 https://github.com/galaxyproject/galaxy/commit/03b44a84a66e07d720a34764c212… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/ui/editable-text.js M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/ui.scss M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/managers/cloud.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/util/hg_util.py A static/style/blue/info_icon.svg M templates/admin/jobs.mako M templates/admin/review_tool_migration_stages.mako M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.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.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.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/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/history/share.mako M test/galaxy_selenium/navigation.yml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into unified_webpack4 Commit: 581e734dfcb9662a6c4c2f0d9288fad2a0707e54 https://github.com/galaxyproject/galaxy/commit/581e734dfcb9662a6c4c2f0d9288… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/config.yml A config/plugins/webhooks/demo/tour_generator/package.json R config/plugins/webhooks/demo/tour_generator/script.js A config/plugins/webhooks/demo/tour_generator/tour_generator.js Log Message: ----------- Incremental packaging of tour_builder Commit: 571d783517654302a5823487021848166e3a3e10 https://github.com/galaxyproject/galaxy/commit/571d783517654302a58234870218… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/package.json A config/plugins/webhooks/demo/tour_generator/script.js M config/plugins/webhooks/demo/tour_generator/tour_generator.js Log Message: ----------- Package up tool tour generator as a single artifact that doesn't reach into Galaxy code other than the Galaxy global that's required. Commit: 65bfe605d0995a5ac177a65ad64e80a597e53e3a https://github.com/galaxyproject/galaxy/commit/65bfe605d0995a5ac177a65ad64e… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M .gitignore A client/package-lock.json M client/package.json M client/webpack.config.js M client/yarn.lock M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Single css output from webpack Commit: de4030fcceebd55a77de3d33a7bc21fb09697895 https://github.com/galaxyproject/galaxy/commit/de4030fcceebd55a77de3d33a7bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Fix requirebundled being chunked together. Commit: 91d13a5a0cc87df1a01c72dca7e835f609e2dabe https://github.com/galaxyproject/galaxy/commit/91d13a5a0cc87df1a01c72dca7e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M templates/base/base_panels.mako Log Message: ----------- We also need base.chunk here. Commit: 273bf080b53e2b8cf8acfaa17ab0bcd1bbb82de0 https://github.com/galaxyproject/galaxy/commit/273bf080b53e2b8cf8acfaa17ab0… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M client/webpack.config.js Log Message: ----------- added in missing priority stats on webpack.config Commit: 09e1bfb98d4b6f88d00e665daf8a63d40224d290 https://github.com/galaxyproject/galaxy/commit/09e1bfb98d4b6f88d00e665daf8a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-19 (Fri, 19 Oct 2018) Changed paths: R client/package-lock.json M client/yarn.lock Log Message: ----------- Drop package-lock.json; regenerate yarn.lock Commit: dac9d14311ec27b40432a64b35e68cab892078d6 https://github.com/galaxyproject/galaxy/commit/dac9d14311ec27b40432a64b35e6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Minor webpack upgrade. Commit: 7244fb5153b39ba285ac3bf5a4128e2705c1279a https://github.com/galaxyproject/galaxy/commit/7244fb5153b39ba285ac3bf5a412… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Swap back to bundled jquery-ui, sort this out later (or purge it with fire) Commit: 9d94c0da95c833c49c21537336b62371420eb671 https://github.com/galaxyproject/galaxy/commit/9d94c0da95c833c49c21537336b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: A client/galaxy/images/light_gray_grid.gif M client/galaxy/style/scss/base.scss R static/images/light_gray_grid.gif M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Stage workflow editor images via webpacked styles (todo is relevant in here, it should be refactored, but I'm taking minimal steps here to get things working correctly) Commit: 1970d2d29c07aa50ef3713307eccd02861d44810 https://github.com/galaxyproject/galaxy/commit/1970d2d29c07aa50ef3713307ecc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Add jquery drop plugin to onload, seems to have been lost along the way. Commit: 129153a542ea6e4438ddbc1e7137e4c4e60759d8 https://github.com/galaxyproject/galaxy/commit/129153a542ea6e4438ddbc1e7137… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Fix problem with rxjs dep listing in yarn.lock, bump webpack (minor) Commit: 743d3b32f2426b39640d19c6dcd550727a549287 https://github.com/galaxyproject/galaxy/commit/743d3b32f2426b39640d19c6dcd5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: A client/galaxy/images/delete.gif A client/galaxy/images/star.gif R client/galaxy/style/jquery.rating.css M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/jquery.rating.scss R static/images/delete.gif R static/images/star.gif Log Message: ----------- fix rating styles -- this isn't great, but the loaders just work better this way, calling it scss and customizing it slightly. Commit: 6a2999e109d79420d261e165e366d16bcbfdf685 https://github.com/galaxyproject/galaxy/commit/6a2999e109d79420d261e165e366… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/polyfills.js M client/galaxy/style/scss/select2.scss M client/galaxy/style/scss/sprite-fugue.scss M client/galaxy/style/scss/sprite-history-buttons.scss M client/galaxy/style/scss/sprite-history-states.scss Log Message: ----------- Client format. Commit: 0c8344ee4fda3a54606bb84a23b2e1d24bfcd54e https://github.com/galaxyproject/galaxy/commit/0c8344ee4fda3a54606bb84a23b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: A client/galaxy/images/fugue/application-dock-270-bw.png A client/galaxy/images/fugue/application-dock-270.png A client/galaxy/images/fugue/arrow-000-small-bw.png A client/galaxy/images/fugue/arrow-090.png A client/galaxy/images/fugue/arrow-circle.png A client/galaxy/images/fugue/arrow-resize-090-bw.png A client/galaxy/images/fugue/arrow-resize-090.png A client/galaxy/images/fugue/arrow-split-bw.png A client/galaxy/images/fugue/arrow-split.png A client/galaxy/images/fugue/arrow-transition-270-bw.png A client/galaxy/images/fugue/arrow-transition-bw.png A client/galaxy/images/fugue/asterisk-small-outline.png A client/galaxy/images/fugue/asterisk-small-yellow.png A client/galaxy/images/fugue/asterisk-small.png A client/galaxy/images/fugue/block--plus-bw.png A client/galaxy/images/fugue/block--plus.png A client/galaxy/images/fugue/bookmarks-bw.png A client/galaxy/images/fugue/bookmarks.png A client/galaxy/images/fugue/bug.png A client/galaxy/images/fugue/chart.png A client/galaxy/images/fugue/chevron-expand-bw.png A client/galaxy/images/fugue/chevron-expand.png A client/galaxy/images/fugue/chevron.png A client/galaxy/images/fugue/control-270.png A client/galaxy/images/fugue/cross-button.png A client/galaxy/images/fugue/cross-circle-bw.png A client/galaxy/images/fugue/cross-circle.png A client/galaxy/images/fugue/cross-small-bw.png A client/galaxy/images/fugue/cross.png A client/galaxy/images/fugue/disk--arrow-bw.png A client/galaxy/images/fugue/disk--arrow.png A client/galaxy/images/fugue/disk.png A client/galaxy/images/fugue/exclamation.png A client/galaxy/images/fugue/external.png A client/galaxy/images/fugue/eye.png A client/galaxy/images/fugue/gear-bw.png A client/galaxy/images/fugue/gear.png A client/galaxy/images/fugue/globe-bw.png A client/galaxy/images/fugue/globe.png A client/galaxy/images/fugue/hammer-bw.png A client/galaxy/images/fugue/hammer.png A client/galaxy/images/fugue/information-white.png A client/galaxy/images/fugue/layer-transparent-bw.png A client/galaxy/images/fugue/layer-transparent.png A client/galaxy/images/fugue/layers-stack-bw.png A client/galaxy/images/fugue/layers-stack.png A client/galaxy/images/fugue/magnifier-left.png A client/galaxy/images/fugue/magnifier-zoom-out.png A client/galaxy/images/fugue/magnifier-zoom.png A client/galaxy/images/fugue/navigation.png A client/galaxy/images/fugue/pencil-small.png A client/galaxy/images/fugue/pencil.png A client/galaxy/images/fugue/plus-button-bw.png A client/galaxy/images/fugue/plus-button.png A client/galaxy/images/fugue/plus-circle.png A client/galaxy/images/fugue/sticky-note-text.png A client/galaxy/images/fugue/tag--plus.png A client/galaxy/images/fugue/tag-label.png A client/galaxy/images/fugue/tags.png A client/galaxy/images/fugue/toggle-bw.png A client/galaxy/images/fugue/toggle-expand-bw.png A client/galaxy/images/fugue/toggle-expand.png A client/galaxy/images/fugue/toggle.png A client/galaxy/images/fugue/toolbox-bw.png A client/galaxy/images/fugue/toolbox.png A client/galaxy/images/fugue/ui-slider-050-bw.png A client/galaxy/images/fugue/ui-slider-050.png A client/galaxy/images/tipsy.gif A client/galaxy/images/tracks/block.png A client/galaxy/images/tracks/close_btn.gif A client/galaxy/images/tracks/diag_bg.gif A client/galaxy/images/tracks/go_btn.gif A client/galaxy/images/tracks/handle-left.gif A client/galaxy/images/tracks/handle-right.gif A client/galaxy/images/tracks/pan_left.gif A client/galaxy/images/tracks/pan_right.gif A client/galaxy/images/tracks/show_history.gif A client/galaxy/images/tracks/zoom_in.gif A client/galaxy/images/tracks/zoom_in_full.gif A client/galaxy/images/tracks/zoom_out.gif A client/galaxy/images/tracks/zoom_out_full.gif M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss A static/images/fugue R static/images/fugue/application-dock-270-bw.png R static/images/fugue/application-dock-270.png R static/images/fugue/arrow-000-small-bw.png R static/images/fugue/arrow-090.png R static/images/fugue/arrow-circle.png R static/images/fugue/arrow-resize-090-bw.png R static/images/fugue/arrow-resize-090.png R static/images/fugue/arrow-split-bw.png R static/images/fugue/arrow-split.png R static/images/fugue/arrow-transition-270-bw.png R static/images/fugue/arrow-transition-bw.png R static/images/fugue/asterisk-small-outline.png R static/images/fugue/asterisk-small-yellow.png R static/images/fugue/asterisk-small.png R static/images/fugue/block--plus-bw.png R static/images/fugue/block--plus.png R static/images/fugue/bookmarks-bw.png R static/images/fugue/bookmarks.png R static/images/fugue/bug.png R static/images/fugue/chart.png R static/images/fugue/chevron-expand-bw.png R static/images/fugue/chevron-expand.png R static/images/fugue/chevron.png R static/images/fugue/control-270.png R static/images/fugue/cross-button.png R static/images/fugue/cross-circle-bw.png R static/images/fugue/cross-circle.png R static/images/fugue/cross-small-bw.png R static/images/fugue/cross.png R static/images/fugue/disk--arrow-bw.png R static/images/fugue/disk--arrow.png R static/images/fugue/disk.png R static/images/fugue/exclamation.png R static/images/fugue/external.png R static/images/fugue/eye.png R static/images/fugue/gear-bw.png R static/images/fugue/gear.png R static/images/fugue/globe-bw.png R static/images/fugue/globe.png R static/images/fugue/hammer-bw.png R static/images/fugue/hammer.png R static/images/fugue/information-white.png R static/images/fugue/layer-transparent-bw.png R static/images/fugue/layer-transparent.png R static/images/fugue/layers-stack-bw.png R static/images/fugue/layers-stack.png R static/images/fugue/magnifier-left.png R static/images/fugue/magnifier-zoom-out.png R static/images/fugue/magnifier-zoom.png R static/images/fugue/navigation.png R static/images/fugue/pencil-small.png R static/images/fugue/pencil.png R static/images/fugue/plus-button-bw.png R static/images/fugue/plus-button.png R static/images/fugue/plus-circle.png R static/images/fugue/sticky-note-text.png R static/images/fugue/tag--plus.png R static/images/fugue/tag-label.png R static/images/fugue/tags.png R static/images/fugue/toggle-bw.png R static/images/fugue/toggle-expand-bw.png R static/images/fugue/toggle-expand.png R static/images/fugue/toggle.png R static/images/fugue/toolbox-bw.png R static/images/fugue/toolbox.png R static/images/fugue/ui-slider-050-bw.png R static/images/fugue/ui-slider-050.png R static/images/tipsy.gif A static/images/tracks R static/images/tracks/block.png R static/images/tracks/close_btn.gif R static/images/tracks/diag_bg.gif R static/images/tracks/go_btn.gif R static/images/tracks/handle-left.gif R static/images/tracks/handle-right.gif R static/images/tracks/pan_left.gif R static/images/tracks/pan_right.gif R static/images/tracks/show_history.gif R static/images/tracks/zoom_in.gif R static/images/tracks/zoom_in_full.gif R static/images/tracks/zoom_out.gif R static/images/tracks/zoom_out_full.gif Log Message: ----------- Stage trackster (and potentially other fugue-consumers, which we should be getting rid of) via webpack. Commit: b27b3fe2af116301e96247576814728d525b275e https://github.com/galaxyproject/galaxy/commit/b27b3fe2af116301e96247576814… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: A lib/galaxy/datatypes/test/test.cel A lib/galaxy/datatypes/test/test.idpdb Log Message: ----------- Move test files for upstream merge (case sensitivity in git) Commit: 46f24df8e1b67dcc92d71c6849c922e57f8ffcdd https://github.com/galaxyproject/galaxy/commit/46f24df8e1b67dcc92d71c6849c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: A static/images/visualization Log Message: ----------- For simplicity, just symlink viz images for now Commit: 51273658fb5420c9e6748ed2b08e6769e33158eb https://github.com/galaxyproject/galaxy/commit/51273658fb5420c9e6748ed2b08e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M Makefile M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/collection.scss M client/galaxy/style/scss/list-item.scss M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst M lib/galaxy/authnz/managers.py M lib/galaxy/config.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py A lib/galaxy/datatypes/isa.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.afg M lib/galaxy/datatypes/test/1.bcf_uncompressed A lib/galaxy/datatypes/test/1.excel.xls M lib/galaxy/datatypes/test/1.fastq A lib/galaxy/datatypes/test/1.fastqcssanger M lib/galaxy/datatypes/test/1.fastqsanger M lib/galaxy/datatypes/test/1.fastqsolexa M lib/galaxy/datatypes/test/1.owl M lib/galaxy/datatypes/test/1.stockholm R lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/1.vcf_bgzip R lib/galaxy/datatypes/test/1.xls M lib/galaxy/datatypes/test/2.fastq R lib/galaxy/datatypes/test/2.fastqsanger M lib/galaxy/datatypes/test/2.fastqsolexa R lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam M lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.fastq M lib/galaxy/datatypes/test/3.txt M lib/galaxy/datatypes/test/454Score.pdf A lib/galaxy/datatypes/test/5e5z.pqr R lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/Acanium.snaphmm M lib/galaxy/datatypes/test/alignment.lav R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2 A lib/galaxy/datatypes/test/gff.gff3 R lib/galaxy/datatypes/test/gff_version_3.gff A lib/galaxy/datatypes/test/interv1.bed R lib/galaxy/datatypes/test/interval1.bed M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter R lib/galaxy/datatypes/test/sequence.qual M lib/galaxy/datatypes/test/sequence.qual454 M lib/galaxy/datatypes/test/sequence.qualsolid A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml R lib/galaxy/datatypes/test/test.CEL R lib/galaxy/datatypes/test/test.idpDB R lib/galaxy/datatypes/test/test_ensembl.tab A lib/galaxy/datatypes/test/test_ensembl.tabular M lib/galaxy/datatypes/test/test_tab.bed M lib/galaxy/datatypes/test/ucsc.customtrack M lib/galaxy/datatypes/test/wiggle.wig M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/managers/cloud.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/util/xml_util.py M run.sh M scripts/bootstrap_history.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/runtime_stats.py M scripts/summarize_timings.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/transfer.py M setup.cfg M static/style/blue/base.css M static/welcome.html.sample M templates/display_base.mako M templates/ind_share_base.mako M templates/message.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/common.mako A test-data/MTBLS6.zip M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/driver_util.py M test/base/populators.py M test/base/workflow_fixtures.py M test/functional/tools/output_filter.xml A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/__init__.py A test/integration/test_datatype_upload.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into unified_webpack4 Commit: 7dbc81ca825adbae503d076c88a838336790067f https://github.com/galaxyproject/galaxy/commit/7dbc81ca825adbae503d076c88a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Add images to default static-safe location Commit: dbdce6d37b075720d9d936921ae72edd66211bc1 https://github.com/galaxyproject/galaxy/commit/dbdce6d37b075720d9d936921ae7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M .gitignore A static/images/delete_tag_icon_gray.png A static/style/blue/ok_small.png Log Message: ----------- Stage two more images after inclusion in scripts. We'll inevitably find more of these, and they should all be removed, but this gives us a way to transition as things are rewritten. Commit: 4d5285b65921e8a25689d7813872619dbd6e9b23 https://github.com/galaxyproject/galaxy/commit/4d5285b65921e8a25689d7813872… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: A static/style/blue/question-octagon-frame.png Log Message: ----------- Another image link for admin_toolshed stuff. Commit: 31905f1402d9ba8af82d0ae723eaccc20d1d621c https://github.com/galaxyproject/galaxy/commit/31905f1402d9ba8af82d0ae723ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M .gitignore M client/.babelrc R client/GruntFile.js A client/galaxy/images/Armitagep_manhattan.png A client/galaxy/images/Armitagep_qqplot.png A client/galaxy/images/add_icon.png A client/galaxy/images/add_icon_dark.png A client/galaxy/images/aggregate_history1.png A client/galaxy/images/aggregate_history2.png A client/galaxy/images/bar_chart.png A client/galaxy/images/base_bg.png A client/galaxy/images/bed_warn.png A client/galaxy/images/button_bar_bg_light.png A client/galaxy/images/circle.py A client/galaxy/images/closebox.png A client/galaxy/images/dat_points_table_brows_1.png A client/galaxy/images/data_empty.png A client/galaxy/images/data_error.png A client/galaxy/images/data_ok.png A client/galaxy/images/data_queued.png A client/galaxy/images/data_running.gif A 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static/style/blue/question-octagon-frame.png R static/style/blue/tiny_arrow_left.png R static/style/blue/tiny_arrow_right.png M static/style/blue/trackster.css R static/style/blue/wait_large.png R static/style/blue/wait_small.png R static/style/blue/warn_bg.png R static/style/blue/warn_large.png R static/style/blue/warn_message_icon.png R static/style/blue/warn_small.png R static/style/blue/workflow_circle_drag.png R static/style/blue/workflow_circle_green.png R static/style/blue/workflow_circle_open.png R static/style/shared_images/data_running.gif R static/style/shared_images/error_large.png R static/style/shared_images/error_small.png R static/style/shared_images/info_large.png R static/style/shared_images/info_small.png R static/style/shared_images/ok_large.png R static/style/shared_images/ok_small.png R static/style/shared_images/wait_large.png R static/style/shared_images/wait_small.png R static/style/shared_images/warn_large.png R static/style/shared_images/warn_small.png M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/gie.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/repository/browse_repository.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/rate_repository.mako M templates/webapps/tool_shed/repository/upload.mako M templates/webapps/tool_shed/repository/view_changelog.mako M templates/webapps/tool_shed/repository/view_changeset.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/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako M templates/webapps/tool_shed/repository_review/select_previous_review.mako M test/base/driver_util.py Log Message: ----------- Merge pull request #6917 from dannon/unified_webpack4 Unified webpack4 Compare: https://github.com/galaxyproject/galaxy/compare/f40bb68141eb...31905f1402d9 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ddeef3: Fix sniffing of readname sorted BAM files
by GitHub 31 Oct '18

31 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ddeef3fbc2f884d8ad1af95adc164ca8e5bc15c3 https://github.com/galaxyproject/galaxy/commit/ddeef3fbc2f884d8ad1af95adc16… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/1.qname_sorted.bam Log Message: ----------- Fix sniffing of readname sorted BAM files This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework. Commit: c78f704c230a694d42c769bacdb23d20eb2ea810 https://github.com/galaxyproject/galaxy/commit/c78f704c230a694d42c769bacdb2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: A lib/galaxy/datatypes/test/0.txt A lib/galaxy/datatypes/test/1.json Log Message: ----------- Add two test files that exercise json and txt sniffing Commit: f40bb68141ebff020401740b8bf9b3b1fc73db60 https://github.com/galaxyproject/galaxy/commit/f40bb68141ebff020401740b8bf9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/0.txt A lib/galaxy/datatypes/test/1.json A lib/galaxy/datatypes/test/1.qname_sorted.bam Log Message: ----------- Merge pull request #6950 from mvdbeek/qname_sorted_sniffer Fix sniffing of readname sorted BAM files Compare: https://github.com/galaxyproject/galaxy/compare/b47efd4adedb...f40bb68141eb **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9c8108: Catch IOErrors when the k8s runner tries to collec...
by GitHub 31 Oct '18

31 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c81089ed1c9d5c434ecb991be8fd542bbe3c75e https://github.com/galaxyproject/galaxy/commit/9c81089ed1c9d5c434ecb991be8f… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Catch IOErrors when the k8s runner tries to collect job logs This commit should fix cases where successful job can't be marked as done by Galaxy because the logs have gone missing. Commit: ac7c2d0473d09e8a3b4b39734527a383835478ab https://github.com/galaxyproject/galaxy/commit/ac7c2d0473d09e8a3b4b39734527… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Print full job object to the DEBUG log if k8s runner finds it in an unrecognized state Commit: cd6c4d4db8bcb72ae931797c216b9829313850cf https://github.com/galaxyproject/galaxy/commit/cd6c4d4db8bcb72ae931797c216b… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Add job id to missing k8s log text Commit: c434c271598d95130439ac86c8b9060f42455e9a https://github.com/galaxyproject/galaxy/commit/c434c271598d95130439ac86c8b9… Author: Luca Pireddu <pireddu(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improve k8s runner debug log message Commit: e235343f7674a5b74a707a693e94b80633d1ca2b https://github.com/galaxyproject/galaxy/commit/e235343f7674a5b74a707a693e94… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Push k8s log IOError handling into `__produce_log_file` Handling the IOError within the function should result in other call sites within the kubernets.py module properly setting the job state even if the job directory has been removed. Commit: cf02c9812759505d61f284d6d33ee9ce2dc994e8 https://github.com/galaxyproject/galaxy/commit/cf02c9812759505d61f284d6d33e… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Prefer `with open` syntax within kubernetes.py Commit: c13da94fd75d4b0010e4e3284649366c213a205d https://github.com/galaxyproject/galaxy/commit/c13da94fd75d4b0010e4e3284649… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fix inverted log message arguments Thanks @pcm32! Commit: 4dce069209c4da228629e7dddfbeda836098aedc https://github.com/galaxyproject/galaxy/commit/4dce069209c4da228629e7dddfbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Adjust code block to try to fix release doc formatting -- I hate RST Commit: cea9521b1a0194c93c5e2bf7b7f02fa88bd2c0b9 https://github.com/galaxyproject/galaxy/commit/cea9521b1a0194c93c5e2bf7b7f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6938 from dannon/codeblock_formatting [18.09] Release announce codeblock formatting fix Commit: 1482cacee51a9fd91f65d54704c7bc36120f3a34 https://github.com/galaxyproject/galaxy/commit/1482cacee51a9fd91f65d54704c7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #6886 from ilveroluca/fix/k8s_error_handling Improve k8s job error handling Commit: 49d9409f007dfe6288de4d6a2c0e15a4b45af022 https://github.com/galaxyproject/galaxy/commit/49d9409f007dfe6288de4d6a2c0e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam index is only available for coordinate sorted bam files Commit: 4c7ba6f0fe4a99c1324f70785d27b655ac8b5538 https://github.com/galaxyproject/galaxy/commit/4c7ba6f0fe4a99c1324f70785d27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6946 from mvdbeek/bam_index_for_coordinate_sorted_only [18.09] Make Bam index only available for coordinate sorted bam files Commit: b47efd4adedb781056423bda4112a5b46a72489b https://github.com/galaxyproject/galaxy/commit/b47efd4adedb781056423bda4112… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/17efac853ad1...b47efd4adedb **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 49d940: Bam index is only available for coordinate sorted ...
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 49d9409f007dfe6288de4d6a2c0e15a4b45af022 https://github.com/galaxyproject/galaxy/commit/49d9409f007dfe6288de4d6a2c0e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam index is only available for coordinate sorted bam files Commit: 4c7ba6f0fe4a99c1324f70785d27b655ac8b5538 https://github.com/galaxyproject/galaxy/commit/4c7ba6f0fe4a99c1324f70785d27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6946 from mvdbeek/bam_index_for_coordinate_sorted_only [18.09] Make Bam index only available for coordinate sorted bam files Compare: https://github.com/galaxyproject/galaxy/compare/1482cacee51a...4c7ba6f0fe4a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a1b710: add option to strip url prefix from pair names
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1b7105b389e8a7b8f9ed9aab630c8b543825da4 https://github.com/galaxyproject/galaxy/commit/a1b7105b389e8a7b8f9ed9aab630… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- add option to strip url prefix from pair names Commit: 41d60f576122a74a87ca060a6813d0e6ca903c05 https://github.com/galaxyproject/galaxy/commit/41d60f576122a74a87ca060a6813… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- always strip url prefix Commit: 17efac853ad1b5a7f319e010b00a79d4694a09ac https://github.com/galaxyproject/galaxy/commit/17efac853ad1b5a7f319e010b00a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #6943 from shiltemann/collection-strip-urlprefix Collection builder: add option to strip url prefix from pair names Compare: https://github.com/galaxyproject/galaxy/compare/9713556b16ac...17efac853ad1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9a2433: Name datatype test files according to datatype ext...
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a24338d12001cdcea336703ce41ac4032c275b8 https://github.com/galaxyproject/galaxy/commit/9a24338d12001cdcea336703ce41… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py R lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/1.vcf_bgzip R lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/Acanium.snaphmm R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2 R lib/galaxy/datatypes/test/test.CEL A lib/galaxy/datatypes/test/test.cel R lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.idpdb R lib/galaxy/datatypes/test/test_ensembl.tab A lib/galaxy/datatypes/test/test_ensembl.tabular A test/integration/test_datatype_upload.py M test/unit/datatypes/test_vcf.py Log Message: ----------- Name datatype test files according to datatype extension Commit: b2276319d409c7d88bf3af7ff0cfa8cd4df2ab98 https://github.com/galaxyproject/galaxy/commit/b2276319d409c7d88bf3af7ff0cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Change more biom2 instances Commit: 7ce69df57c7a2bb6e7c34108a8e2e0b67487cd5d https://github.com/galaxyproject/galaxy/commit/7ce69df57c7a2bb6e7c34108a8e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/integration/test_datatype_upload.py Log Message: ----------- Add integration test for uploading datasets of known datatype We upload everything in lib/galaxy/datatypes/test and make sure that we get the correct datatype. For datatypes that have a sniffer we use `auto`, otherwise we set the correct datatype. This is fairly basic for now, but it would be trivial to extend this to also verify file integrity and metadata elements as well as testing options that affect uploads, like `auto_decompress` settings. Commit: f2d8218a5366f25601dac8342601c02a74ca6f22 https://github.com/galaxyproject/galaxy/commit/f2d8218a5366f25601dac8342601… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix uncompressed bcf This actually also fails, but at least doesn't crash the interpreter. Commit: 63eb6a145c9683651532fc7afaded7a5d930743a https://github.com/galaxyproject/galaxy/commit/63eb6a145c9683651532fc7afade… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Tighten up memepsp sniffer Values need to be floats, but float("1") also doesn't raise an exception. This prevents 454qual files to be sniffed as memepsp. Commit: f7773c39b1fb7d9ac31115b69c60f5f487e40a13 https://github.com/galaxyproject/galaxy/commit/f7773c39b1fb7d9ac31115b69c60… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/blast.py A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml Log Message: ----------- Move tblastn_four_human_vs_rhodopsin.xml to tblastn_four_human_vs_rhodopsin.blastxml Commit: 38e18c9daff58a02f1da0be23329ec9ec5d4cbe7 https://github.com/galaxyproject/galaxy/commit/38e18c9daff58a02f1da0be23329… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/gff.gff3 R lib/galaxy/datatypes/test/gff_version_3.gff Log Message: ----------- Rename gff3 test file Commit: 3529295d5512bee68e7981d036147b18a518fc6c https://github.com/galaxyproject/galaxy/commit/3529295d5512bee68e7981d03614… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: R lib/galaxy/datatypes/test/sequence.qual Log Message: ----------- Delete unused test file Commit: bc0a3c5244181a5b6af2a4d394a0d4375ceff453 https://github.com/galaxyproject/galaxy/commit/bc0a3c5244181a5b6af2a4d394a0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/interv1.bed R lib/galaxy/datatypes/test/interval1.bed Log Message: ----------- Rename interval1.bed to interv1.bed Otherwise guess_datatype would expect interval as the datatype. Commit: 81155c635a38eb0ad1201f92bb70fbdf9faf170b https://github.com/galaxyproject/galaxy/commit/81155c635a38eb0ad1201f92bb70… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: R lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam M test/unit/datatypes/test_bam.py Log Message: ----------- Rename 2.shuffled.bam to 2.shuffled.unsorted.bam Commit: a151b63a622424c1f5f21f97169121b4c7bcc5d5 https://github.com/galaxyproject/galaxy/commit/a151b63a622424c1f5f21f971691… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/test/2.fastqsanger A lib/galaxy/datatypes/test/3.fastq Log Message: ----------- Tighten up fastq sniffers significantly This requires the sequence regex to match over the entire sequence, which precludes fastqcssanger files to be sniffed as fastqsanger (fixes https://github.com/galaxyproject/galaxy/issues/6734) Further adds a sniffer for FastqCSSanger, which contains numbers in the sequence and so shouldn't interfere with the other fastq datatypes. Commit: b74f225f189688ea885ea6b52bf0f36367cd8d03 https://github.com/galaxyproject/galaxy/commit/b74f225f189688ea885ea6b52bf0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/integration/test_datatype_upload.py Log Message: ----------- Map fastqsolex to fastq datatype in integration test Commit: 720386999828150ed3b639c3600f491e75c7217b https://github.com/galaxyproject/galaxy/commit/720386999828150ed3b639c3600f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/test/1.bcf_uncompressed Log Message: ----------- Drop index file for bcf_uncompressed Even `bcftools index` complains that the file is not compressed. I think this is just not supported. Commit: 85a47ccc47b6f3504360e9f4a0486cefe3f6faa8 https://github.com/galaxyproject/galaxy/commit/85a47ccc47b6f3504360e9f4a048… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Fix totally broken memepsp sniffer The sniffer could never reach 100 sniffed lines, and the test file contains an empty line, so the comment and code that says that empty lines are not valid is wrong, but was never called. Commit: 48bdc97fce177c5f867cd31e3600ad5670a6c958 https://github.com/galaxyproject/galaxy/commit/48bdc97fce177c5f867cd31e3600… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/base/populators.py M test/integration/test_datatype_upload.py Log Message: ----------- Verify state of uploaded datasets and download datasets to verify that the file is intact after upload Commit: be939310fbd4736eaaf8e3ecb00081e7fc080463 https://github.com/galaxyproject/galaxy/commit/be939310fbd4736eaaf8e3ecb000… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: A lib/galaxy/datatypes/test/1.fastqcssanger Log Message: ----------- Add a fastqcssanger test file Commit: 7b955277566a8cb647b1a689cf1c0d18fba274f2 https://github.com/galaxyproject/galaxy/commit/7b955277566a8cb647b1a689cf1c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Missed one idpDB instance Commit: dd6a4bb2f33e39889577e9a0b60a6314355eab6b https://github.com/galaxyproject/galaxy/commit/dd6a4bb2f33e39889577e9a0b60a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.excel.xls R lib/galaxy/datatypes/test/1.xls Log Message: ----------- Move xls file to excel.xls and change xls to be excel.xls Commit: d80e4bd0a13dc5996c35cd5ecbca9c4439e5e2a1 https://github.com/galaxyproject/galaxy/commit/d80e4bd0a13dc5996c35cd5ecbca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M test/base/populators.py M test/integration/test_datatype_upload.py Log Message: ----------- Fix test logic Commit: e01e6ba2bdcf557668995f402812ff8b93474134 https://github.com/galaxyproject/galaxy/commit/e01e6ba2bdcf557668995f402812… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/test/1.afg M lib/galaxy/datatypes/test/1.fastq M lib/galaxy/datatypes/test/1.fastqsanger M lib/galaxy/datatypes/test/1.fastqsolexa M lib/galaxy/datatypes/test/1.owl M lib/galaxy/datatypes/test/1.stockholm M lib/galaxy/datatypes/test/2.fastq M lib/galaxy/datatypes/test/2.fastqsolexa M lib/galaxy/datatypes/test/2.txt M lib/galaxy/datatypes/test/3.fastq M lib/galaxy/datatypes/test/3.txt M lib/galaxy/datatypes/test/454Score.pdf M lib/galaxy/datatypes/test/alignment.lav M lib/galaxy/datatypes/test/interv1.bed M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter M lib/galaxy/datatypes/test/sequence.qual454 M lib/galaxy/datatypes/test/sequence.qualsolid M lib/galaxy/datatypes/test/test_tab.bed M lib/galaxy/datatypes/test/ucsc.customtrack M lib/galaxy/datatypes/test/wiggle.wig Log Message: ----------- Fix up various test datasets Commit: ec193d929fd81b8f0438c097ebbb3aa3fb55e224 https://github.com/galaxyproject/galaxy/commit/ec193d929fd81b8f0438c097ebbb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Fix minor typo Commit: d3cd57e29975b66ca3883b6e8dfb63839a49aaee https://github.com/galaxyproject/galaxy/commit/d3cd57e29975b66ca3883b6e8dfb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Safe JSON encoding of MetadataParameters, JSONType This fixes a couple of upload tests on python 3 (loom, Biom2). Commit: 09601ad4efdd877375dfda3e62e2657899101ae2 https://github.com/galaxyproject/galaxy/commit/09601ad4efdd877375dfda3e62e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Skip newlines/space2tab conversion for binary datatypes that fail is_binary check Commit: d168042b366dcdbacabfabe692f120e9118a2de9 https://github.com/galaxyproject/galaxy/commit/d168042b366dcdbacabfabe692f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix newline conversion on python 3 if no encoding is set Commit: 738bde01278c50a62f4d97c7afc6e4f8b919254f https://github.com/galaxyproject/galaxy/commit/738bde01278c50a62f4d97c7afc6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- Fix check_html on python 3 We can open the file in binary mode and then use unicodify on the lines, as we have to do that anyway if `chunks` is provided. Also adds the unicode flag to re.compile. Commit: 1a407429ba7ffe1476317c5ac0f5b1ad19f1e0d7 https://github.com/galaxyproject/galaxy/commit/1a407429ba7ffe1476317c5ac0f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/phylip.py Log Message: ----------- Tighten up mothur and phylip sniffers Commit: c50a0fccace2d94565ba85f0703e516139132b4b https://github.com/galaxyproject/galaxy/commit/c50a0fccace2d94565ba85f0703e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Don't sniff simple json types These should instead be text. Commit: 0fae117e672e626cc7093d0169dae241c4f54128 https://github.com/galaxyproject/galaxy/commit/0fae117e672e626cc7093d0169da… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Use raw strings in regex and allow lowercase fastq sequences Commit: ecc02bb659ce89e78b1a5aeb49dd020280864617 https://github.com/galaxyproject/galaxy/commit/ecc02bb659ce89e78b1a5aeb49dd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Fix UploadProblemException Commit: ba5d76eb934598227102ae1cb0ff4e89e0ab0b9c https://github.com/galaxyproject/galaxy/commit/ba5d76eb934598227102ae1cb0ff… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Avoid exception if no match This fixes the sniffing unit test, the datatype framework would just continue anyway. Commit: 16962ad6a16c5b5dcc5b3d06921d2c4c89c6d9d0 https://github.com/galaxyproject/galaxy/commit/16962ad6a16c5b5dcc5b3d06921d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/test/5e5z.pqr Log Message: ----------- Add newline to lib/galaxy/datatypes/test/5e5z.pqr Commit: 9713556b16acb3e4218fc9e28463cdaba654a0c5 https://github.com/galaxyproject/galaxy/commit/9713556b16acb3e4218fc9e28463… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.afg M lib/galaxy/datatypes/test/1.bcf_uncompressed A lib/galaxy/datatypes/test/1.excel.xls M lib/galaxy/datatypes/test/1.fastq A lib/galaxy/datatypes/test/1.fastqcssanger M lib/galaxy/datatypes/test/1.fastqsanger M lib/galaxy/datatypes/test/1.fastqsolexa M lib/galaxy/datatypes/test/1.owl M lib/galaxy/datatypes/test/1.stockholm R lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/1.vcf_bgzip R lib/galaxy/datatypes/test/1.xls M lib/galaxy/datatypes/test/2.fastq R lib/galaxy/datatypes/test/2.fastqsanger M lib/galaxy/datatypes/test/2.fastqsolexa R lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam M lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.fastq M lib/galaxy/datatypes/test/3.txt M lib/galaxy/datatypes/test/454Score.pdf M lib/galaxy/datatypes/test/5e5z.pqr R lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/Acanium.snaphmm M lib/galaxy/datatypes/test/alignment.lav R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2 A lib/galaxy/datatypes/test/gff.gff3 R lib/galaxy/datatypes/test/gff_version_3.gff A lib/galaxy/datatypes/test/interv1.bed R lib/galaxy/datatypes/test/interval1.bed M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter R lib/galaxy/datatypes/test/sequence.qual M lib/galaxy/datatypes/test/sequence.qual454 M lib/galaxy/datatypes/test/sequence.qualsolid A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml R lib/galaxy/datatypes/test/test.CEL A lib/galaxy/datatypes/test/test.cel R lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.idpdb R lib/galaxy/datatypes/test/test_ensembl.tab A lib/galaxy/datatypes/test/test_ensembl.tabular M lib/galaxy/datatypes/test/test_tab.bed M lib/galaxy/datatypes/test/ucsc.customtrack M lib/galaxy/datatypes/test/wiggle.wig M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/model/custom_types.py M lib/galaxy/util/checkers.py M test/base/populators.py A test/integration/test_datatype_upload.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/test_vcf.py Log Message: ----------- Merge pull request #6869 from mvdbeek/datatype_upload_integration_test Datatype upload integration test and fixes Compare: https://github.com/galaxyproject/galaxy/compare/0de9c738cf8c...9713556b16ac **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9c8108: Catch IOErrors when the k8s runner tries to collec...
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9c81089ed1c9d5c434ecb991be8fd542bbe3c75e https://github.com/galaxyproject/galaxy/commit/9c81089ed1c9d5c434ecb991be8f… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Catch IOErrors when the k8s runner tries to collect job logs This commit should fix cases where successful job can't be marked as done by Galaxy because the logs have gone missing. Commit: ac7c2d0473d09e8a3b4b39734527a383835478ab https://github.com/galaxyproject/galaxy/commit/ac7c2d0473d09e8a3b4b39734527… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Print full job object to the DEBUG log if k8s runner finds it in an unrecognized state Commit: cd6c4d4db8bcb72ae931797c216b9829313850cf https://github.com/galaxyproject/galaxy/commit/cd6c4d4db8bcb72ae931797c216b… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Add job id to missing k8s log text Commit: c434c271598d95130439ac86c8b9060f42455e9a https://github.com/galaxyproject/galaxy/commit/c434c271598d95130439ac86c8b9… Author: Luca Pireddu <pireddu(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improve k8s runner debug log message Commit: e235343f7674a5b74a707a693e94b80633d1ca2b https://github.com/galaxyproject/galaxy/commit/e235343f7674a5b74a707a693e94… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Push k8s log IOError handling into `__produce_log_file` Handling the IOError within the function should result in other call sites within the kubernets.py module properly setting the job state even if the job directory has been removed. Commit: cf02c9812759505d61f284d6d33ee9ce2dc994e8 https://github.com/galaxyproject/galaxy/commit/cf02c9812759505d61f284d6d33e… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Prefer `with open` syntax within kubernetes.py Commit: c13da94fd75d4b0010e4e3284649366c213a205d https://github.com/galaxyproject/galaxy/commit/c13da94fd75d4b0010e4e3284649… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fix inverted log message arguments Thanks @pcm32! Commit: 1482cacee51a9fd91f65d54704c7bc36120f3a34 https://github.com/galaxyproject/galaxy/commit/1482cacee51a9fd91f65d54704c7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #6886 from ilveroluca/fix/k8s_error_handling Improve k8s job error handling Compare: https://github.com/galaxyproject/galaxy/compare/cea9521b1a01...1482cacee51a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d9ce92: adjust the panel resize cursor, update docs link
by GitHub 30 Oct '18

30 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9ce92a8a2bd4323a18d69936995fc62e24458e6 https://github.com/galaxyproject/galaxy/commit/d9ce92a8a2bd4323a18d69936995… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M static/welcome.html.sample Log Message: ----------- adjust the panel resize cursor, update docs link Commit: 0de9c738cf8cb11b814d1d758268f0bcf9b71652 https://github.com/galaxyproject/galaxy/commit/0de9c738cf8cb11b814d1d758268… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M static/welcome.html.sample Log Message: ----------- Merge pull request #6833 from martenson/tinies adjust the panel resize cursor, update docs link Compare: https://github.com/galaxyproject/galaxy/compare/8e8ff78b459c...0de9c738cf8c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 4dce06: Adjust code block to try to fix release doc format...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 4dce069209c4da228629e7dddfbeda836098aedc https://github.com/galaxyproject/galaxy/commit/4dce069209c4da228629e7dddfbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Adjust code block to try to fix release doc formatting -- I hate RST Commit: cea9521b1a0194c93c5e2bf7b7f02fa88bd2c0b9 https://github.com/galaxyproject/galaxy/commit/cea9521b1a0194c93c5e2bf7b7f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6938 from dannon/codeblock_formatting [18.09] Release announce codeblock formatting fix Compare: https://github.com/galaxyproject/galaxy/compare/d0a93ff62808...cea9521b1a01 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] c59169: Fix typos in ``scripts/bootstrap_history.py``
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5916912093ffaca57281db486c263108f263e88 https://github.com/galaxyproject/galaxy/commit/c5916912093ffaca57281db486c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Fix typos in ``scripts/bootstrap_history.py`` Commit: a4abbb1d8a244e260412df8551f9f3d0f25f78c7 https://github.com/galaxyproject/galaxy/commit/a4abbb1d8a244e260412df8551f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Fix flake8 errors introduced in #6816 Commit: 8e8ff78b459c68c4b54c0c722ed5619f9d117c62 https://github.com/galaxyproject/galaxy/commit/8e8ff78b459c68c4b54c0c722ed5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/datatypes/molecules.py M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6941 from nsoranzo/bootstrap_history_typos Fix typos in ``scripts/bootstrap_history.py`` Compare: https://github.com/galaxyproject/galaxy/compare/d41837cd9ccd...8e8ff78b459c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 09e6b1: Eliminate some mutable defaults in populators.py.
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09e6b1dcde5eb30a76e7487eba9ee75475b29753 https://github.com/galaxyproject/galaxy/commit/09e6b1dcde5eb30a76e7487eba9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Eliminate some mutable defaults in populators.py. Commit: d41837cd9ccde259941c8b643ebf1c38ebed871b https://github.com/galaxyproject/galaxy/commit/d41837cd9ccde259941c8b643ebf… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/base/populators.py Log Message: ----------- Merge pull request #6933 from jmchilton/mutable_default Eliminate some mutable defaults in populators.py. Compare: https://github.com/galaxyproject/galaxy/compare/e89773a20d5c...d41837cd9ccd **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 4dce06: Adjust code block to try to fix release doc format...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 4dce069209c4da228629e7dddfbeda836098aedc https://github.com/galaxyproject/galaxy/commit/4dce069209c4da228629e7dddfbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Adjust code block to try to fix release doc formatting -- I hate RST Commit: cea9521b1a0194c93c5e2bf7b7f02fa88bd2c0b9 https://github.com/galaxyproject/galaxy/commit/cea9521b1a0194c93c5e2bf7b7f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6938 from dannon/codeblock_formatting [18.09] Release announce codeblock formatting fix Compare: https://github.com/galaxyproject/galaxy/compare/d0a93ff62808...cea9521b1a01 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] f1a3a4: galaxy test needs to count data sets and collectio...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f1a3a44b444d9914a97d26a0b0f5667efc211ac5 https://github.com/galaxyproject/galaxy/commit/f1a3a44b444d9914a97d26a0b0f5… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- galaxy test needs to count data sets and collection outputs Commit: 1ec18484df22ec0d226415a6aa9379bb176fe329 https://github.com/galaxyproject/galaxy/commit/1ec18484df22ec0d226415a6aa93… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M test/functional/tools/output_filter.xml Log Message: ----------- added test Commit: e89773a20d5c3f18fd9b4766c1c7deb6485e88da https://github.com/galaxyproject/galaxy/commit/e89773a20d5c3f18fd9b4766c1c7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge pull request #6931 from bernt-matthias/topic/test-colouts tests need to count data sets and collections Compare: https://github.com/galaxyproject/galaxy/compare/adc62f6ba7d8...e89773a20d5c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 30ac5d: Release scaffold tweaks.
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30ac5d90d937a28dc61aef5d4a6b6cb05c1a05bf https://github.com/galaxyproject/galaxy/commit/30ac5d90d937a28dc61aef5d4a6b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Release scaffold tweaks. Commit: 66b05cbfc591a5de2d5d248c1f060a67ff369c44 https://github.com/galaxyproject/galaxy/commit/66b05cbfc591a5de2d5d248c1f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Minor clarification Commit: 5d51492a538dddb5eb5c45dc117f090104f70652 https://github.com/galaxyproject/galaxy/commit/5d51492a538dddb5eb5c45dc117f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Getgalaxy links Commit: 2fb4ea1e689e03a44712fd18942d86717e773e36 https://github.com/galaxyproject/galaxy/commit/2fb4ea1e689e03a44712fd18942d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6935 from dannon/release-scaffold-tweaks Release issue scaffold tweaks. Compare: https://github.com/galaxyproject/galaxy/compare/6f6fffe9134e...2fb4ea1e689e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 79cff3: Add 18.09_announce to releases index.
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79cff3ea6b34056a9a24a130dab6b25b98ae7ee4 https://github.com/galaxyproject/galaxy/commit/79cff3ea6b34056a9a24a130dab6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Add 18.09_announce to releases index. Commit: 165123863904daa1d7e96651b16f2c6dfa0629a2 https://github.com/galaxyproject/galaxy/commit/165123863904daa1d7e96651b16f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6930 from dannon/index-update [18.09] Add 18.09_announce to releases index. Commit: cf2645f9a658c5e122fea0309bf73a1f64590c39 https://github.com/galaxyproject/galaxy/commit/cf2645f9a658c5e122fea0309bf7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix toolshed error in display_tool if tool is invalid Fixes the following exception: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/translogger.py", line 69, in __call__ return self.application(environ, replacement_start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "routes/middleware.py", line 141, in __call__ response = self.app(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 143, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 222, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/tool_shed/controllers/repository.py", line 888, in display_tool tool_state = tool_util.new_state(trans, tool, invalid=False) File "tool_shed/util/tool_util.py", line 211, in new_state log.debug('Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e) ``` (from https://sentry.galaxyproject.org/sentry/toolshed/issues/279820/) Might also fix some other issues when redering workflow svg for workflows with invalid tools. Commit: e89f746a0713df76e1e86eb9507d3336aade9419 https://github.com/galaxyproject/galaxy/commit/e89f746a0713df76e1e86eb9507d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge pull request #6932 from mvdbeek/fix_toolshed_bugs [18.09] Fix toolshed error in display_tool if tool is invalid Commit: 1fd1848a81532ecd0fb36800e7f1ae1609661141 https://github.com/galaxyproject/galaxy/commit/1fd1848a81532ecd0fb36800e7f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Additional 18.09 bugfix Commit: d0a93ff62808e7e1727c7deb4a48853639bd7ece https://github.com/galaxyproject/galaxy/commit/d0a93ff62808e7e1727c7deb4a48… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6934 from dannon/doc_update [18.09] Additional 18.09 doc update for toolshed bugfix. Commit: 6f6fffe9134e7becfd698340899a96c1cbd8a4fe https://github.com/galaxyproject/galaxy/commit/6f6fffe9134e7becfd698340899a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/index.rst M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2d7e54831944...6f6fffe9134e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] cf2645: Fix toolshed error in display_tool if tool is inva...
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: cf2645f9a658c5e122fea0309bf73a1f64590c39 https://github.com/galaxyproject/galaxy/commit/cf2645f9a658c5e122fea0309bf7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix toolshed error in display_tool if tool is invalid Fixes the following exception: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/translogger.py", line 69, in __call__ return self.application(environ, replacement_start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "routes/middleware.py", line 141, in __call__ response = self.app(environ, start_response) File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 143, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 222, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/tool_shed/controllers/repository.py", line 888, in display_tool tool_state = tool_util.new_state(trans, tool, invalid=False) File "tool_shed/util/tool_util.py", line 211, in new_state log.debug('Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e) ``` (from https://sentry.galaxyproject.org/sentry/toolshed/issues/279820/) Might also fix some other issues when redering workflow svg for workflows with invalid tools. Commit: e89f746a0713df76e1e86eb9507d3336aade9419 https://github.com/galaxyproject/galaxy/commit/e89f746a0713df76e1e86eb9507d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge pull request #6932 from mvdbeek/fix_toolshed_bugs [18.09] Fix toolshed error in display_tool if tool is invalid Commit: 1fd1848a81532ecd0fb36800e7f1ae1609661141 https://github.com/galaxyproject/galaxy/commit/1fd1848a81532ecd0fb36800e7f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Additional 18.09 bugfix Commit: d0a93ff62808e7e1727c7deb4a48853639bd7ece https://github.com/galaxyproject/galaxy/commit/d0a93ff62808e7e1727c7deb4a48… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6934 from dannon/doc_update [18.09] Additional 18.09 doc update for toolshed bugfix. Compare: https://github.com/galaxyproject/galaxy/compare/165123863904...d0a93ff62808 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy]
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/tags/v18.09 Home: https://github.com/galaxyproject/galaxy **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 1fd184: Additional 18.09 bugfix
by GitHub 29 Oct '18

29 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 1fd1848a81532ecd0fb36800e7f1ae1609661141 https://github.com/galaxyproject/galaxy/commit/1fd1848a81532ecd0fb36800e7f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Additional 18.09 bugfix Commit: d0a93ff62808e7e1727c7deb4a48853639bd7ece https://github.com/galaxyproject/galaxy/commit/d0a93ff62808e7e1727c7deb4a48… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6934 from dannon/doc_update [18.09] Additional 18.09 doc update for toolshed bugfix. Compare: https://github.com/galaxyproject/galaxy/compare/e89f746a0713...d0a93ff62808 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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