- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 786da2: Hide form instead of removing it to preserve attac...
by GitHub 05 Aug '16

05 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 786da21a3bd97da1c2f349f77515fed2b3713d6c https://github.com/galaxyproject/galaxy/commit/786da21a3bd97da1c2f349f77515… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Hide form instead of removing it to preserve attached listento events Commit: 3f8f9b7bbb0c565a07de43820dcfa5ed6e4d03e1 https://github.com/galaxyproject/galaxy/commit/3f8f9b7bbb0c565a07de43820dcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #2737 from guerler/hide_form_on_success [16.07] Hide form instead of removing it to preserve attached listenTo events Compare: https://github.com/galaxyproject/galaxy/compare/8c57ed7e5432...3f8f9b7bbb0c

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[galaxyproject/galaxy] de3c50: Python3 support and import order fixes for lib/too...
by GitHub 05 Aug '16

05 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de3c50a5ef7731961d6902a592333092a2fe85e1 https://github.com/galaxyproject/galaxy/commit/de3c50a5ef7731961d6902a59233… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.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/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/repositories.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/tool_shed/api/common.py M setup.cfg Log Message: ----------- Python3 support and import order fixes for lib/tool_shed/ Commit: 2efec4e062afbd2281271e8d30a8b1fdd627b9be https://github.com/galaxyproject/galaxy/commit/2efec4e062afbd2281271e8d30a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.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/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/repositories.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/tool_shed/api/common.py M setup.cfg Log Message: ----------- Merge pull request #2731 from nsoranzo/python3 Python3 support and import order fixes for lib/tool_shed/ Compare: https://github.com/galaxyproject/galaxy/compare/2ebef640cb63...2efec4e062af

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[galaxyproject/galaxy] 5c79aa: Allow link buttons to trigger regular click events
by GitHub 05 Aug '16

05 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 5c79aa8fbc727feec6fa2041881645acdaed75f4 https://github.com/galaxyproject/galaxy/commit/5c79aa8fbc727feec6fa20418816… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Allow link buttons to trigger regular click events Commit: fe3db95eec8fd942a9a46ad05c579c41eda9705e https://github.com/galaxyproject/galaxy/commit/fe3db95eec8fd942a9a46ad05c57… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js Log Message: ----------- Merge branch 'release_16.07' into fix_history_refresh Commit: 8c57ed7e5432e4f92b95bc41fc657b562db18430 https://github.com/galaxyproject/galaxy/commit/8c57ed7e5432e4f92b95bc41fc65… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #2743 from guerler/fix_history_refresh [16.07] Allow link buttons to trigger regular click events Compare: https://github.com/galaxyproject/galaxy/compare/258e4a7b669e...8c57ed7e5432

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[galaxyproject/galaxy] 83d4eb: Fix unused href parameter when adding scratchbook ...
by GitHub 05 Aug '16

05 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 83d4ebd0348cae7c9d0056e37b269c96768d0312 https://github.com/galaxyproject/galaxy/commit/83d4ebd0348cae7c9d0056e37b26… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js Log Message: ----------- Fix unused href parameter when adding scratchbook frames Commit: 258e4a7b669edb2aca15e295353db384bc72575a https://github.com/galaxyproject/galaxy/commit/258e4a7b669edb2aca15e295353d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/scratchbook.js Log Message: ----------- Merge pull request #2744 from guerler/fix_scratchbook_href [16.07] Fix unused href parameter when adding scratchbook frames Compare: https://github.com/galaxyproject/galaxy/compare/8b0d88b30e62...258e4a7b669e

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[galaxyproject/galaxy] 50b689: Make tool shed logging like Galaxy logging.
by GitHub 05 Aug '16

05 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50b6897fec475d62f7e8cf0e640000d088a958ac https://github.com/galaxyproject/galaxy/commit/50b6897fec475d62f7e8cf0e6400… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Make tool shed logging like Galaxy logging. - Reduces duplicated code. - Enables best practice of commenting out defaults in shed sample config. - Add auto_configure_logging option to tool shed to match Galaxy. Commit: 2116f97a2f04b78f75c4a83cc1bf3ecad0a75cd6 https://github.com/galaxyproject/galaxy/commit/2116f97a2f04b78f75c4a83cc1bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Add routes middleware to chatty loggers disabled at debug level. Also add option to skip disabling the chatty loggers. Commit: 41acdadbae8aab6d4fe38d1de354404819f7851d https://github.com/galaxyproject/galaxy/commit/41acdadbae8aab6d4fe38d1de354… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- move the configure_logging import to the app.py where it is used remove routes.middleware chatty logging as the PR is independent on this Commit: 9b86eae99569cfb6e8884afd7324e96b1b5d7028 https://github.com/galaxyproject/galaxy/commit/9b86eae99569cfb6e8884afd7324… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #49 from martenson/conf-logging move the configure_logging import to the app.py where it is used Commit: 2ebef640cb639f12012da52361891065e8d13570 https://github.com/galaxyproject/galaxy/commit/2ebef640cb639f12012da5236189… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #2735 from jmchilton/logging_dedup Slightly revise auto configuration of loggers Compare: https://github.com/galaxyproject/galaxy/compare/08d20b26784a...2ebef640cb63

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[galaxyproject/infrastructure-playbook] 1e8908: Exclude the '.cache' directory from Jenkins backup...
by GitHub 04 Aug '16

04 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1e8908cfbb6e46c3361d7222be9451d4e9cbc841 https://github.com/galaxyproject/infrastructure-playbook/commit/1e8908cfbb6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M galaxyenv/host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Exclude the '.cache' directory from Jenkins backups. Commit: 7b9d8254aa93aac7821dfd0fba84b6e3d4a1cc7e https://github.com/galaxyproject/infrastructure-playbook/commit/7b9d8254aa9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: A galaxyenv/host_vars/n4.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml A galaxyenv/secret_host_vars/n4.galaxyproject.org.yml Log Message: ----------- Set up n4 as a Jenkins build slave Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/0ee33a1ca8…

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[galaxyproject/galaxy] e13095: Changed css in base.less to allow tool search inpu...
by GitHub 04 Aug '16

04 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e13095d3d2dc802143da69b94bc87390a6ea9699 https://github.com/galaxyproject/galaxy/commit/e13095d3d2dc802143da69b94bc8… Author: galaxy <galaxy(a)galaxy.development> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M client/galaxy/style/less/base.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Changed css in base.less to allow tool search input field to remain fixed when a long list is being scroll. Issue 2375. Commit: c28f7e6b4e08624f6d690cf7899a41812ed68534 https://github.com/galaxyproject/galaxy/commit/c28f7e6b4e08624f6d690cf7899a… Author: Scott Szakonyi <sszakony(a)nd.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updating to latest from project Commit: bf54f08fc2bca68c5e158e5e88f8e70e9a84f83c https://github.com/galaxyproject/galaxy/commit/bf54f08fc2bca68c5e158e5e88f8… Author: Scott Szakonyi <sszakony(a)nd.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge branch 'Gal2375' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/style/blue/base.css Commit: ae5b844388ddd0ded9816814abc8c46398d50511 https://github.com/galaxyproject/galaxy/commit/ae5b844388ddd0ded9816814abc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M client/galaxy/style/less/base.less M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'sszakony/dev' into dev Commit: 08d20b26784aca80c54ef7be8a8422dbb9328d93 https://github.com/galaxyproject/galaxy/commit/08d20b26784aca80c54ef7be8a84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack w/ merge, not sure how the bundled libs got out of sync here. Compare: https://github.com/galaxyproject/galaxy/compare/3206a5405562...08d20b26784a

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[galaxyproject/usegalaxy-playbook] c7c0a5: Update Main
by GitHub 04 Aug '16

04 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c7c0a524a77862553496d2f53630df5ba1d53728 https://github.com/galaxyproject/usegalaxy-playbook/commit/c7c0a524a7786255… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/usegalaxy-playbook] d38689: Update Test
by GitHub 04 Aug '16

04 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d386890b73f0f18385d63c736edaa552fc7735c6 https://github.com/galaxyproject/usegalaxy-playbook/commit/d386890b73f0f183… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 62fdbd: Fix the sanitization of None values in utils. Thi...
by GitHub 04 Aug '16

04 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62fdbd526ae34357d3fbb44cedc46635c4df7cbb https://github.com/galaxyproject/galaxy/commit/62fdbd526ae34357d3fbb44cedc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix the sanitization of None values in utils. This had previously not happened because Params had only been sanitizing strings coming in as part of the request, but if you're passing off (potentially manipulated, as in adding None default params) to a secondary request for a response, this can happen. Commit: ed7c357668df5bbb3381fae94353465594c7e184 https://github.com/galaxyproject/galaxy/commit/ed7c357668df5bbb3381fae94353… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2693 from dannon/utils_fix_sanitization_of_none [16.07] Fix the sanitization of None values in utils. This had previously no… Commit: 7bf0cc72418308e54b6ec180a8913623004c8288 https://github.com/galaxyproject/galaxy/commit/7bf0cc72418308e54b6ec180a891… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- Remove the old HubAssembly class Commit: 3206199652330659aa9f1cebe75c6940787f85d4 https://github.com/galaxyproject/galaxy/commit/3206199652330659aa9f1cebe75c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- Merge pull request #2701 from remimarenco/release_16.07 [16.07] Fix: Remove the old HubAssembly class Commit: 48849b814aac6bb70a1651f063f0789da4022ce7 https://github.com/galaxyproject/galaxy/commit/48849b814aac6bb70a1651f063f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fixup metadata collection on workdir outputs for Pulsar. https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7… which gave tool's clean working directories made the function get_workdir_outputs a big sloppy. Pulsar would send it the actual remote working directory for jobs and Galaxy would send it the job directory (expecting it to append 'working'). Commit: 82430c024378e15729e5d2b52e50ad49930e5dd2 https://github.com/galaxyproject/galaxy/commit/82430c024378e15729e5d2b52e50… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #2721 from jmchilton/working_pulsar_metadata [16.07] Fix metadata collection on workdir outputs for Pulsar. Commit: 2affd08647c723014182552b09bcb4402d30d9b3 https://github.com/galaxyproject/galaxy/commit/2affd08647c723014182552b09bc… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Fix for splitting dataset collections Commit: 8b0d88b30e62997ec9b33fec402379b8e2033e5c https://github.com/galaxyproject/galaxy/commit/8b0d88b30e62997ec9b33fec4023… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Merge pull request #2723 from jmchilton/backport_2708 [16.07] Backport #2708 Commit: 3206a54055620cb524fb5265ab91c979d3a520b2 https://github.com/galaxyproject/galaxy/commit/3206a54055620cb524fb5265ab91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/datatypes/tracks.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7efa1e0e4dd0...3206a5405562

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[galaxyproject/galaxy] b16356: add a netcdf datatype for metabolomics spectre dat...
by GitHub 04 Aug '16

04 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b16356e49096849eb4f14efb21fa903945d473df https://github.com/galaxyproject/galaxy/commit/b16356e49096849eb4f14efb21fa… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add a netcdf datatype for metabolomics spectre data Commit: ad8483a7db24a9067a2f6fdac4db3d409a8410a9 https://github.com/galaxyproject/galaxy/commit/ad8483a7db24a9067a2f6fdac4db… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Update binary.py Commit: 4e64c23f463c2a8f985010a02f86c19db55ff50d https://github.com/galaxyproject/galaxy/commit/4e64c23f463c2a8f985010a02f86… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Update datatypes_conf.xml.sample Add the sniffer in the sniffers Commit: ecce2575148815f7965c5ee94864d9698a4826bb https://github.com/galaxyproject/galaxy/commit/ecce2575148815f7965c5ee94864… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Update datatypes_conf.xml.sample Change sniffer order Commit: 37a0ec597e13748f4abdf38ff8b32731ee8234de https://github.com/galaxyproject/galaxy/commit/37a0ec597e13748f4abdf38ff8b3… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Update binary.py As suggested by @bgruening Commit: 7efa1e0e4dd00759b764193104a8d37b019cc5b8 https://github.com/galaxyproject/galaxy/commit/7efa1e0e4dd00759b764193104a8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #2706 from lecorguille/add_netcdf_datatype add a netcdf datatype for metabolomics spectre data Compare: https://github.com/galaxyproject/galaxy/compare/65f0a836e0ff...7efa1e0e4dd0

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[galaxyproject/galaxy] 2affd0: Fix for splitting dataset collections
by GitHub 04 Aug '16

04 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 2affd08647c723014182552b09bcb4402d30d9b3 https://github.com/galaxyproject/galaxy/commit/2affd08647c723014182552b09bc… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Fix for splitting dataset collections Commit: 8b0d88b30e62997ec9b33fec402379b8e2033e5c https://github.com/galaxyproject/galaxy/commit/8b0d88b30e62997ec9b33fec4023… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Merge pull request #2723 from jmchilton/backport_2708 [16.07] Backport #2708 Compare: https://github.com/galaxyproject/galaxy/compare/82430c024378...8b0d88b30e62

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[galaxyproject/galaxy] d0bdd5: Fix for splitting dataset collections
by GitHub 04 Aug '16

04 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0bdd532bbd10fca2bf257bf9a8d0802ac0a0db0 https://github.com/galaxyproject/galaxy/commit/d0bdd532bbd10fca2bf257bf9a8d… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Fix for splitting dataset collections Commit: 65f0a836e0ffcccc0d0bb445e33f06a899ad47b0 https://github.com/galaxyproject/galaxy/commit/65f0a836e0ffcccc0d0bb445e33f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Merge pull request #2708 from gregvonkuster/collections_fix Fix for splitting dataset collections Compare: https://github.com/galaxyproject/galaxy/compare/24573f7ffb8e...65f0a836e0ff

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[galaxyproject/galaxy] 48849b: Fixup metadata collection on workdir outputs for P...
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 48849b814aac6bb70a1651f063f0789da4022ce7 https://github.com/galaxyproject/galaxy/commit/48849b814aac6bb70a1651f063f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fixup metadata collection on workdir outputs for Pulsar. https://github.com/galaxyproject/galaxy/pull/1688/commits/a2e31403753c407e7… which gave tool's clean working directories made the function get_workdir_outputs a big sloppy. Pulsar would send it the actual remote working directory for jobs and Galaxy would send it the job directory (expecting it to append 'working'). Commit: 82430c024378e15729e5d2b52e50ad49930e5dd2 https://github.com/galaxyproject/galaxy/commit/82430c024378e15729e5d2b52e50… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #2721 from jmchilton/working_pulsar_metadata [16.07] Fix metadata collection on workdir outputs for Pulsar. Compare: https://github.com/galaxyproject/galaxy/compare/320619965233...82430c024378

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[galaxyproject/galaxy] 9f7592: Inject data module values in connected steps on in...
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f75926e4dfc8c4d644d191ba324a5f8a40e2e7d https://github.com/galaxyproject/galaxy/commit/9f75926e4dfc8c4d644d191ba324… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Inject data module values in connected steps on initialization Commit: db4b78baad9d246d34b77f0e032cd35344f75587 https://github.com/galaxyproject/galaxy/commit/db4b78baad9d246d34b77f0e032c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Use same dom append call for tool and data steps Commit: 7b2d71e86ee9d57db0a4412b908448f03ec333a8 https://github.com/galaxyproject/galaxy/commit/7b2d71e86ee9d57db0a4412b9084… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add missing get_initial_value for collection parameters, remove unused repeat avoiding mechanism for now Commit: b34757b6b1dd71d189ea1fd2c44c6f938b9344b3 https://github.com/galaxyproject/galaxy/commit/b34757b6b1dd71d189ea1fd2c44c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py Log Message: ----------- Use hda representative agent if collections are parsed Commit: bccf3d58f5afa0b95187583c099ba67d3cc60552 https://github.com/galaxyproject/galaxy/commit/bccf3d58f5afa0b95187583c099b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Add hda agent generation to dynamic options Commit: bd194a885db94b0655c5781a25c3e0b292484cd7 https://github.com/galaxyproject/galaxy/commit/bd194a885db94b0655c5781a25c3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Use one line if to determine atomic versus listed hda agents Commit: 65328ff3b7a9b2342b3acdc822a7620eb247b23d https://github.com/galaxyproject/galaxy/commit/65328ff3b7a9b2342b3acdc822a7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/workflow/modules.py Log Message: ----------- Rename to_hda_agent to to_hda_representative Commit: 24ecf34c4f49b93d79d7d6b5f5d21aeec89733e0 https://github.com/galaxyproject/galaxy/commit/24ecf34c4f49b93d79d7d6b5f5d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Enhance collection to regular data field injection when multiple collections are parsed Commit: 4d6754f4a4e81b8dc3f90a32d72cfd9190077a2d https://github.com/galaxyproject/galaxy/commit/4d6754f4a4e81b8dc3f90a32d72c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove get initial value without repeats call from workflow run mako Commit: 15aba09847b03940167c38eb8e3a24214db4f92f https://github.com/galaxyproject/galaxy/commit/15aba09847b03940167c38eb8e3a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Align spacing style of get_column_list function Commit: c8de0edc96d37be7ee7b32c11be74f39cb616b23 https://github.com/galaxyproject/galaxy/commit/c8de0edc96d37be7ee7b32c11be7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Instantly display workflow form upgrade messages, avoid fade in Commit: 6bff8ce48b8fc19bec2d0b02aefc617f93a2d2e8 https://github.com/galaxyproject/galaxy/commit/6bff8ce48b8fc19bec2d0b02aefc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Instantly display workflow form upgrade messages, avoid fade in Commit: 52879750a7c297f6fb45c8aeec2c14712d302343 https://github.com/galaxyproject/galaxy/commit/52879750a7c297f6fb45c8aeec2c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M test/unit/tools/test_data_parameters.py Log Message: ----------- Align data tool parameter test cases for initial values Commit: efc850c32e15490df33dee5e164542791bc0b21c https://github.com/galaxyproject/galaxy/commit/efc850c32e15490df33dee5e1645… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix padding to avoid scroll bar Commit: 24573f7ffb8e5797ae1589a9353f5937d114417c https://github.com/galaxyproject/galaxy/commit/24573f7ffb8e5797ae1589a9353f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-misc.js M templates/webapps/galaxy/workflow/run.mako M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge branch 'inject_connected_inputs' into dev Compare: https://github.com/galaxyproject/galaxy/compare/66d5560da569...24573f7ffb8e

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[galaxyproject/galaxy] bf0ac1: Slight styling tweak to prevent overflow on the ri...
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf0ac1cc3e24f93f1f7948689a90c0b2424d61aa https://github.com/galaxyproject/galaxy/commit/bf0ac1cc3e24f93f1f7948689a90… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/style/less/upload.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Slight styling tweak to prevent overflow on the right edge in composite upload dialog. Commit: 66d5560da5696113bcaec612a3e5b9c375a44ce3 https://github.com/galaxyproject/galaxy/commit/66d5560da5696113bcaec612a3e5… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/style/less/upload.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge pull request #2716 from dannon/slight_upload_style_tweak Slight styling tweak to prevent overflow on the right edge in composi… Compare: https://github.com/galaxyproject/galaxy/compare/b2ab62b21f21...66d5560da569

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[galaxyproject/galaxy] 7193a5: Fix tours pasting content into text area
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7193a5c8a63d5f325851de5a3a4b4dab9d650db3 https://github.com/galaxyproject/galaxy/commit/7193a5c8a63d5f325851de5a3a4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml Log Message: ----------- Fix tours pasting content into text area Commit: b2ab62b21f2111cb50d7c1716fd2ac340cf3452a https://github.com/galaxyproject/galaxy/commit/b2ab62b21f2111cb50d7c1716fd2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/tours/core.scratchbook.yaml Log Message: ----------- Merge pull request #2715 from guerler/tour_fix Fix tours pasting content into text area Compare: https://github.com/galaxyproject/galaxy/compare/370c00124157...b2ab62b21f21

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[galaxyproject/usegalaxy-playbook] 932a05: Update Test and Main
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 932a057c48eaee7d243d2cbb96ba0b522eab6fde https://github.com/galaxyproject/usegalaxy-playbook/commit/932a057c48eaee7d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M production/galaxy_version.yml M stage/galaxy_version.yml Log Message: ----------- Update Test and Main

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[galaxyproject/galaxy] 07a94a: Revise composite row views
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07a94a6e15157cafc6fde587624d8be486f249c9 https://github.com/galaxyproject/galaxy/commit/07a94a6e15157cafc6fde587624d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/style/blue/base.css Log Message: ----------- Revise composite row views Commit: 2122ba55065e89b7b4ffbc63c1647d0e8cfcf5ea https://github.com/galaxyproject/galaxy/commit/2122ba55065e89b7b4ffbc63c164… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Revise composite main view Commit: e3003a0abf845695406ea8f4d44a4accaefdd5a7 https://github.com/galaxyproject/galaxy/commit/e3003a0abf845695406ea8f4d44a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Fix progress bar Commit: 2a14fd8ce4d5e1932eb2dc2fcf21bbf1474ddc2a https://github.com/galaxyproject/galaxy/commit/2a14fd8ce4d5e1932eb2dc2fcf21… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Revise and properly indent upload-ftp code Commit: 80c414ab98b439b06c94c35a6369b878af0112b8 https://github.com/galaxyproject/galaxy/commit/80c414ab98b439b06c94c35a6369… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/upload-model.js M static/maps/mvc/upload/upload-model.js.map Log Message: ----------- Fix indent for upload-model Commit: 9c196a822f8510934c16fe1a3a73a1c138059139 https://github.com/galaxyproject/galaxy/commit/9c196a822f8510934c16fe1a3a73… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/upload-settings.js M static/maps/mvc/upload/upload-settings.js.map Log Message: ----------- Fix indent for upload-settings Commit: ed2722996f2c3c0b33ec9212da2c722cf86a8ef8 https://github.com/galaxyproject/galaxy/commit/ed2722996f2c3c0b33ec9212da2c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Revise default-row view Commit: 966e33e3ac6a10177670c0b4616fefecb8c83958 https://github.com/galaxyproject/galaxy/commit/966e33e3ac6a10177670c0b4616f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Revise uploader default view Commit: 60a496c6dacaeaff1f58f7ad06e8d67bf7410657 https://github.com/galaxyproject/galaxy/commit/60a496c6dacaeaff1f58f7ad06e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Fix info text style and color Commit: ba10f032f1c9a1a392b4e826d01785f8c0428673 https://github.com/galaxyproject/galaxy/commit/ba10f032f1c9a1a392b4e826d017… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- Fix no transitional progress bar reset for composite uploader rows Commit: af3e0e23628a3726c803883d58e9f39db0bc2410 https://github.com/galaxyproject/galaxy/commit/af3e0e23628a3726c803883d58e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js A client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/style/less/base.less A client/galaxy/style/less/collection.less R client/galaxy/style/less/collections.less A client/galaxy/style/less/dataset.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less A client/galaxy/style/less/ui/error-modal.less M client/galaxy/style/less/ui/search-input.less M client/galaxy/style/less/upload.less M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/layout/panel.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map A static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map A static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/ui/search-input.js.map M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/panel.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js A static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js A static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/ui/search-input.js M static/scripts/utils/ajax-queue.js M static/style/blue/base.css M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M test/qunit/tests/history_contents_model_tests.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'dev' into refactor_uploader Commit: 4c6d04e3a773e25f3c8a709546c8eb65c939a1ab https://github.com/galaxyproject/galaxy/commit/4c6d04e3a773e25f3c8a709546c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/default/default-row.js M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Fix test cases Commit: e685211851c1ecfa3999df5df26c7509a1c2047a https://github.com/galaxyproject/galaxy/commit/e685211851c1ecfa3999df5df26c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix spacing, remove multi line comments Commit: ae9961eab3c98cf1fce768e55e853e10d5d456de https://github.com/galaxyproject/galaxy/commit/ae9961eab3c98cf1fce768e55e85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Use listenTo for collection events Commit: 370c00124157d5ffb01752d8c0dbb4c0283ac4c2 https://github.com/galaxyproject/galaxy/commit/370c00124157d5ffb01752d8c0db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #2711 from guerler/refactor_uploader Refactor uploader dialog, use local css classes, avoid model listeners Compare: https://github.com/galaxyproject/galaxy/compare/710174cbf98d...370c00124157

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[galaxyproject/galaxy] b2e734: Add samtools --version-only check
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2e734e6b7b42039b017c45f134850824eb14649 https://github.com/galaxyproject/galaxy/commit/b2e734e6b7b42039b017c45f1348… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add samtools --version-only check In Bam class Commit: 710174cbf98d6ff60c3793f33431cdee471844dc https://github.com/galaxyproject/galaxy/commit/710174cbf98d6ff60c3793f33431… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #2705 from remimarenco/dev Add samtools --version-only check Compare: https://github.com/galaxyproject/galaxy/compare/2d15e50d0f5c...710174cbf98d

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[galaxyproject/infrastructure-playbook] 0ee33a: Remove Jetstream @ IU instances for production pha...
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0ee33a1ca83af9e89d054f58cdee00fc8a41b00b https://github.com/galaxyproject/infrastructure-playbook/commit/0ee33a1ca83… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- Remove Jetstream @ IU instances for production phase

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[galaxyproject/galaxy] 0b8c98: Include database/jobs_directory in gitignore
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b8c984b76d696fcc36ee3bfc76ad8b91e3ea20c https://github.com/galaxyproject/galaxy/commit/0b8c984b76d696fcc36ee3bfc76a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M .gitignore Log Message: ----------- Include database/jobs_directory in gitignore Commit: c6d2c8bf50fdb4d0b0685fabe1be47693cc99fe0 https://github.com/galaxyproject/galaxy/commit/c6d2c8bf50fdb4d0b0685fabe1be… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Managers: implement a new view for history serialization to bypass state_counts, state, or state_ids; add create_time and update_time to both summaries of hdas and hdcas; serialize contents for histories using a contents serializer (avoiding hda and hdca serialization and just serializing the results of the union) Commit: 0a0edd9788357e3c9fd617f5f8ef64f589e0d9e1 https://github.com/galaxyproject/galaxy/commit/0a0edd9788357e3c9fd617f5f8ef… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- History: have controller 'current history' faux-api methods return the 'current' view from the serializer Commit: 8d1cd494ce025d5b20c6e3087e3f1f44610254a8 https://github.com/galaxyproject/galaxy/commit/8d1cd494ce025d5b20c6e3087e3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: extract history preferences to it's own module Commit: f395793704015ed2dffafe2584259ef81aa20efd https://github.com/galaxyproject/galaxy/commit/f395793704015ed2dffafe258425… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: clean up history contents Commit: 0e4118cda67dc00ebb2fbc2ee6cd1fe674555210 https://github.com/galaxyproject/galaxy/commit/0e4118cda67dc00ebb2fbc2ee6cd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- UI, history: clean up history model Commit: c030af5643ff01aa0bad0b6c6fa7bc4b3b47f6c5 https://github.com/galaxyproject/galaxy/commit/c030af5643ff01aa0bad0b6c6fa7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: 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 static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: move to History.fetch for most ajax loading Commit: 9102096f4e80580239d46a726d3aa7066806564b https://github.com/galaxyproject/galaxy/commit/9102096f4e80580239d46a726d3a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: simplify set up of sessionStorage/HistoryPrefs Commit: 40a597dfda0474675f68ae391135ae059cc93082 https://github.com/galaxyproject/galaxy/commit/40a597dfda0474675f68ae391135… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- UI, history: first pass at paginating history-contents Commit: 1465a02790bd41dba9c573d943b9c9c0cd47ada6 https://github.com/galaxyproject/galaxy/commit/1465a02790bd41dba9c573d943b9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: fix history-contents comparator Commit: 5ed4f74c8deb8a6879d329f7de0a9ab898f98839 https://github.com/galaxyproject/galaxy/commit/5ed4f74c8deb8a6879d329f7de0a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: rework fetch options building, have history-contents maintain includeHidden/Deleted Commit: 563096e302ded396766478152d71c2028a96cabe https://github.com/galaxyproject/galaxy/commit/563096e302ded396766478152d71… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js A client/galaxy/scripts/mvc/history/history-preferences.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map A static/maps/mvc/history/history-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js A static/scripts/mvc/history/history-preferences.js Log Message: ----------- UI, history: add missing history-preferences file, separate out controlled fetch collection Commit: 3102c4ca68aaacc646309517c2fd65cc14237d34 https://github.com/galaxyproject/galaxy/commit/3102c4ca68aaacc646309517c2fd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: move order into ControlledFetchCollection Commit: fc5debdd3be9a46071762c093afbd2b655ca6ef9 https://github.com/galaxyproject/galaxy/commit/fc5debdd3be9a46071762c093afb… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: fix first search loading indicator on history-view Commit: 670484cebcebb49eea8b6fab445cce42d5292002 https://github.com/galaxyproject/galaxy/commit/670484cebcebb49eea8b6fab445c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: fix current history panel loading indicator Commit: 61e4ed51eb275fa979a946d074bb71f51b1ac424 https://github.com/galaxyproject/galaxy/commit/61e4ed51eb275fa979a946d074bb… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-item.js M static/maps/mvc/list/list-item.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/list/list-item.js Log Message: ----------- UI, history, lists: fix rendered event trigger from list-items Commit: 09567db13130bdbd0d7617cd4ff136d29cab1b90 https://github.com/galaxyproject/galaxy/commit/09567db13130bdbd0d7617cd4ff1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.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/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: minor cleanup Commit: 39f1d62cefede05be1518bd44488b41ee4f10b51 https://github.com/galaxyproject/galaxy/commit/39f1d62cefede05be1518bd44488… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.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-edit.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js Log Message: ----------- UI, history: render counts from model data (instead of views), fix history-contents to filter properly Commit: ffbac21753dce1bec667539b3574dd4c3191b6d8 https://github.com/galaxyproject/galaxy/commit/ffbac21753dce1bec667539b3574… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: fix missing _attachView Commit: a0bbbaa918b51cf619303c33d2ad32e87fe3d784 https://github.com/galaxyproject/galaxy/commit/a0bbbaa918b51cf619303c33d2ad… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.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/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js A static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: add missing file (controlled-fetch-collection), fix fetchUpdated filters to bypass visible default filter for proper updating during workflows, fetch deleted and hidden via ajax when clicked, cleanup Commit: 9af60047f27f2da7f024eeb0a745d6f2bc99a7bc https://github.com/galaxyproject/galaxy/commit/9af60047f27f2da7f024eeb0a745… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.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/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, histories: progressively load search details for history contents on first search Commit: daa7625542567caf23d4081b7e7c70d6958bed26 https://github.com/galaxyproject/galaxy/commit/daa7625542567caf23d4081b7e7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.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/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: implement infinite scrolling in all histories Commit: d2d066243e02cc3c612069e6015467e462212881 https://github.com/galaxyproject/galaxy/commit/d2d066243e02cc3c612069e60154… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/list/list-view.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, history: fix history/view.mako and history/display.mako to order their collections, load contents via ajax, and paginate correctly; Routes: correct history/view to allow history/view to view current history and history/view/{id} for cleaner urls Commit: 2a6694dda56ea909a5b3a1fc856c202de46d1750 https://github.com/galaxyproject/galaxy/commit/2a6694dda56ea909a5b3a1fc856c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: 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/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, multi-history: update history collection to use PaginatedCollection, extract HistoryInnerView; Routes: re-add /history route, correct /history/view route for optional id Commit: 040f82a615489aea00040a1e232de5194c6e85d7 https://github.com/galaxyproject/galaxy/commit/040f82a615489aea00040a1e232d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/dataset/dataset-model.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/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Corrections to search and order change in history/view_multiple - Load initial histories using ajax instead of bootstrapping. - Fix rendering after order change. - Fix 'none found' message when searching datasets. - Correct fetch filters when including deleted histories. Commit: 5dab37c155650e77a04769c04258151fbd22e08e https://github.com/galaxyproject/galaxy/commit/5dab37c155650e77a04769c04258… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M .gitignore M Makefile M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_data_table_conf.xml.sample M config/tool_shed.ini.sample A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/releases/index.rst M lib/galaxy/config.py A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/model/util.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/util/__init__.py R lib/galaxy/util/dictobj.py M lib/galaxy/util/jstree.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/summarize_timings.py M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M static/style/blue/library.css A templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/preview_repository.mako M templates/base/base_panels.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/toolsheds.mako M templates/webapps/galaxy/library/common/library_info.mako A test/base/driver_util.py M test/base/twilltestcase.py R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py M test/functional/test_toolbox.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py M test/functional/tools/collection_creates_list.xml A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py M test/qunit/test-app.js A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/test_lazy_process.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- (merge conflicted bundles) Commit: ea921d2d7a529242c25acbab787a9f6c0a280fbf https://github.com/galaxyproject/galaxy/commit/ea921d2d7a529242c25acbab787a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/webapps/galaxy/api/history_contents.py M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Add view/keys ability to history_contents.create This allows the client to fetch the create_time for proper ordering of history contents directly after a copy. Commit: c4f8a30bbddffbf8e514a8112f46ec8e340f62fe https://github.com/galaxyproject/galaxy/commit/c4f8a30bbddffbf8e514a8112f46… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/layout/panel.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/panel.js M static/scripts/mvc/annotation.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js Log Message: ----------- UI, history: correct current dataset, tags, annos Correct the 'currently used dataset' indicator (the left, blue border) making sure it clears when non-dataset related content loads in the center panel. Correct the toggling of tags and annotations in the current history view forcing the subviews to show/hide based on the history view and not by toggling them individually. Commit: 747d4755742d7e2e327f549b283e680068232dd9 https://github.com/galaxyproject/galaxy/commit/747d4755742d7e2e327f549b283e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-model.js Log Message: ----------- UI, history: fix visual update of setting_metadata When a dataset moved from setting_metadata to some ready state, no change (besides the state change) would be registered by the model when the fetch returned. This would prevent an automatic re-render of the view and the dataset would appear to be stuck in setting_ metadata. Commit: 5f88d5dac5cad5836e6ee8e5f0ef18cd31fb4ba9 https://github.com/galaxyproject/galaxy/commit/5f88d5dac5cad5836e6ee8e5f0ef… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.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/style/less/history.less M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: cleanup empty and loading messages - Refactors renderEmptyMessage into base history view - Fixes contents loading indicator selector - Styles contents loading indicator (still oogly tho) Commit: 53163c3c6021e8b3d961a04ae6d7512543309587 https://github.com/galaxyproject/galaxy/commit/53163c3c6021e8b3d961a04ae6d7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.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/options-menu.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, history: revise options menu batch operations - Have both 'Unhide hidden' and 'Delete hidden' fetch hidden datasets (since we now can't rely on complete contents) - Move both from options and into history-view-edit-current - Some minor cleanup of options-menu Commit: b1d930494a8b7a4ccd181e61aa7038cdb4b49814 https://github.com/galaxyproject/galaxy/commit/b1d930494a8b7a4ccd181e61aa70… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.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/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/style/less/base.less A client/galaxy/style/less/ui/error-modal.less M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/ui-modal.js M static/style/blue/base.css Log Message: ----------- UI: extract error-modal from history Extract the error handler and display used in history-view to it's own module (mvc/ui/error-modal) and use it to remove alerts elsewhere. This may be a start at standardizing error handling in some of the mvc code. Commit: f9d61e4a4b8392554efcae89183b7fa2b75dfef9 https://github.com/galaxyproject/galaxy/commit/f9d61e4a4b8392554efcae89183b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M README.rst M client/galaxy/scripts/layout/menu.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/tool_data_table_conf.xml.sample A contrib/galaxy_supervisor.conf A 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test/unit/shed_unit/__init__.py A test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_td_common_util.py A test/unit/shed_unit/test_tool_panel_manager.py R test/unit/tool_shed_unit_tests/__init__.py R test/unit/tool_shed_unit_tests/test_fabric_util.py R test/unit/tool_shed_unit_tests/test_td_common_util.py R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py M test/unit/tools/test_conda_resolution.py A tool-data/biom_simple_display.loc.sample Log Message: ----------- (manual merge with dev) Commit: 434845fe464ba3f955b3dba349d65c35d19bdf6b https://github.com/galaxyproject/galaxy/commit/434845fe464ba3f955b3dba349d6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M test/unit/managers/test_HistoryManager.py Log Message: ----------- Tests: remove peek from history.contents serilaization Commit: 1fedef02fb634025fcf8d303cb4842b119cfbe1c https://github.com/galaxyproject/galaxy/commit/1fedef02fb634025fcf8d303cb48… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.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/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M 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https://github.com/galaxyproject/galaxy/commit/958a5e8d424a837a7e740dc95264… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/style/blue/base.css Log Message: ----------- UI, history: fix subtitle counts and cleanup - Move comma-sep into css - Correct count calc in handlers - Console stmts, templating, and method order Commit: 8a6f96f73400ef8d5749a51841cd073a273fe8b0 https://github.com/galaxyproject/galaxy/commit/8a6f96f73400ef8d5749a51841cd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: simplify createHDCA and ajaxQueue - use collection.create in createHDCA - use ajax-queue module in history-contents.ajaxQueue - Small fixes to DC.hasDetails, and item view rendering Commit: 81d36f903bc0e037cc6da67e101512aca542bad1 https://github.com/galaxyproject/galaxy/commit/81d36f903bc0e037cc6da67e1015… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: 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-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-item.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, histories: fix pagination for published - Ensure all web controller history json is using view='current' - Fix rendering of already fetched contents when 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scripts/tool_shed/api/add_repository_registry_entry.py A scripts/tool_shed/api/common.py A scripts/tool_shed/api/create_categories.py A scripts/tool_shed/api/create_users.py A scripts/tool_shed/api/export.py A scripts/tool_shed/api/get_filtered_repository_revisions.py A scripts/tool_shed/api/import_capsule.py A scripts/tool_shed/api/remove_repository_registry_entry.py A scripts/tool_shed/api/reset_metadata_on_repositories.py A scripts/tool_shed/api/tool_shed_repository_revision_update.py A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_repositories_for_functional_tests.py A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_tool_dependency_definition_repositories.py A scripts/tool_shed/clean_up_tool_dependency_directory.py A scripts/tool_shed/deprecate_repositories_without_metadata.py A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: f3b8d5b0e308c5e9ef9b0a97d311d19f3f998794 https://github.com/galaxyproject/galaxy/commit/f3b8d5b0e308c5e9ef9b0a97d311… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M Makefile M lib/galaxy/version.py M run_tool_shed.sh M scripts/bootstrap_history.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 7cb32818062b7f30647ec66608902029575a5454 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static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: remove scoping overrides Commit: 0a1d7982aa4b16b6111f92ccfc5814f49306b80a https://github.com/galaxyproject/galaxy/commit/0a1d7982aa4b16b6111f92ccfc58… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- API, history: contents_shown to contents_active Renames serialization attribute contents_shown to contents_active to better match original terminology. Adds both state_counts and active_counts to HistoryContentsManager and then has serialize_contents_states and serialize_contents_active call them from the HistorySerializer. Commit: fd3abf4104a58b7add3be22d89286356dbb4caee https://github.com/galaxyproject/galaxy/commit/fd3abf4104a58b7add3be22d8928… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- API, history: rename current view 'dev-detailed' Because current was a horrible and confusing name and dev-detailed may highlight the volitility of the view more. Commit: 0484017e6832f418cd0f20b074d27a329cd0fc22 https://github.com/galaxyproject/galaxy/commit/0484017e6832f418cd0f20b074d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/style/less/base.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view-edit-current.js M static/style/blue/base.css Log Message: ----------- UI, history: move history panel to flexbox This allows us to avoid using absolutely positioned elements and simplifies style rules a bit. Commit: 7722bf23ad4ccd60c114a3de1ceaa422924cfc7c https://github.com/galaxyproject/galaxy/commit/7722bf23ad4ccd60c114a3de1cea… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/bower.json M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/libs/underscore.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/libs/underscore.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI: update underscorejs and fix findIndex IE 11 does not have [].findIndex and the new scrolling causes an error there. Underscore 1.8 has a cross-browser version and this commit updates underscore and replaces the use of the native call. Commit: 1600d6c6e6f641c203d3f45787f19bda68d88d97 https://github.com/galaxyproject/galaxy/commit/1600d6c6e6f641c203d3f45787f1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view-edit.js Log Message: ----------- UI, history: shorten deleted/hidden load indicator Commit: 94f6f1e0049c962941b51d28ee0f0351423fbc52 https://github.com/galaxyproject/galaxy/commit/94f6f1e0049c962941b51d28ee0f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/style/less/base.less M client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit-current.js M static/style/blue/base.css Log Message: ----------- UI, history: move towards a fixed header Commit: b5580c23f63f214fb465892b430c0d62d75fc3f9 https://github.com/galaxyproject/galaxy/commit/b5580c23f63f214fb465892b430c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: R buildbot_setup.sh M config/job_conf.xml.sample_advanced R install_and_test_tool_shed_repositories.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/configuration.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M test/casperjs/casperjs_runner.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 89cb03a037d770c4c895d4e8f872de04d385ada9 https://github.com/galaxyproject/galaxy/commit/89cb03a037d770c4c895d4e8f872… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/history_contents.py Log Message: ----------- History contents manager: improve contents query Serializers in the index_v2 of history_contents were re- querying the database for mapped model attributes. - eagerload collection on hdcas - undefer _metadata on hdas - eaglerload tags and annotations for both - rework annotatable manager mixin to cycle through annotations bypassing the get_item_annotation_str call (which would bypass item.annotations even if already loaded) Anecdotally provides significant speed up. Commit: 32520078af5bf062344f9355894c3d83ebaf638d https://github.com/galaxyproject/galaxy/commit/32520078af5bf062344f9355894c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: raise pagination limits - fetch more when scroll bar is at 512, not 128 px from bottom - fetch 200 at first then 100 each fetch (from 100, 50) - fetch 500 per fetch when searching (progressivelyFetchDetails) Commit: 4c7f367680898b16c395748c501bbca0c56e02ce https://github.com/galaxyproject/galaxy/commit/4c7f367680898b16c395748c501b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/base.less M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/layout/page.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/workflow/workflow-terminals.js M static/style/blue/base.css M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/tool_shed/repository/view_changeset.mako M test/base/interactor.py M test/shed_functional/base/twilltestcase.py M tools/data_source/upload.py M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- (merge conflicts with dev) Commit: d9591127d89c61f5f172bc33d7532917facb3689 https://github.com/galaxyproject/galaxy/commit/d9591127d89c61f5f172bc33d753… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: 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/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-item.js M static/style/blue/base.css Log Message: ----------- UI, histories: move to a section based pagination Breaks history contents into 500 element sections rendering each in a accordian-style menu. Elements are sectioned according to their hids and no more than 500 are rendered at any time. Commit: 9956eecb6ab25d71153ed2c877d7d4a9b4db5f07 https://github.com/galaxyproject/galaxy/commit/9956eecb6ab25d71153ed2c877d7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, history: paginate by hid and show sections - Order by hid or hid-asc (this loses the ability use others) - Paginate by 'sections' of 500 hids showing only one expanded section at a time -- pro: this prevents large numbers of contents in the dom at once -- con: the visible contents can be very sparse (e.g. 2 of 500) - Pagination only begins if more than 500 contents - HistoryContents now has a parent reference (.history) Commit: 994300d3f65904b0532d383e5d6778520ea183ba https://github.com/galaxyproject/galaxy/commit/994300d3f65904b0532d383e5d67… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/hda-model.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/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: polish sectioning enough to show (This is an extremely rough commit meant to have a working prototype for others to test the UX abstraction of sectioning the histories) - Reworks contents so that they're nested inside sections - Fixes all a handful of the errors the previous change causes Commit: cf27a6ae28f6b2f02cee80ee4695275a0dd413c9 https://github.com/galaxyproject/galaxy/commit/cf27a6ae28f6b2f02cee80ee4695… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: 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-view-annotated.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: fetchHiddenInSection, clickSection - add fetchHiddenInSection to load hidden contents in a particular section - extract event handler from clickSection link to allow getting data-section from different part of the DOM in annotated history Commit: 3686ed55c39430d911e17a9e3821090c5de76a1f https://github.com/galaxyproject/galaxy/commit/3686ed55c39430d911e17a9e3821… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: 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/history-view-edit-current.js M client/galaxy/scripts/utils/ajax-queue.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/utils/ajax-queue.js Log Message: ----------- UI, history: use arrays when filtering contents - Moves all history filtering to returning arrays and not new HistoryContents (subset collections) - Reworks contents.ajaxQueue - Moves filterAndUpdate to contents from HistoryView Commit: a7c7af94af6564ab2bd7660b26f8bf81fc00ca4c https://github.com/galaxyproject/galaxy/commit/a7c7af94af6564ab2bd7660b26f8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: fix create HDCA and return promise Commit: 7a6794e104fc978b279c61d15812791302d6fef2 https://github.com/galaxyproject/galaxy/commit/7a6794e104fc978b279c61d15812… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.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/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: move show deleted/hidden into content - Move d/h (deleted/hidden) control into history contents - normalize names (show_deleted, showDeleted --> includeDeleted) - add History.contentsShown that checks d/h flags to return num. shown - move HistoryPreferences into HistoryContents.storage Misc. fixes: - fix collection.off to stopListening - provide interface to HistoryPreferences so that consumers don't need the model keys (easier to change them later on) - (some) cleanup Commit: 2d9ec54fe2126ab21249c0f8918a27802b7b85bb https://github.com/galaxyproject/galaxy/commit/2d9ec54fe2126ab21249c0f8918a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-06 (Fri, 06 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: auto-expand sections - track scrolling and auto expand sections when scroll 'cursor' is over them for more than a certain time - improve rendering speed by using previously existing renders Commit: f8e89ff3fc36eced72f568b8fa6cf6632b22ff06 https://github.com/galaxyproject/galaxy/commit/f8e89ff3fc36eced72f568b8fa6c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M CONTRIBUTORS.md M Makefile M client/README.md M client/bower.json M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.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/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M 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static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/display_base.mako M templates/sharing_base.mako M templates/show_params.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/api/test_tools.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py A test/functional/tools/multi_data_repeat.xml M 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test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml M test/unit/test_objectstore.py M tools/data_source/biomart.xml M tools/filters/trimmer.xml Log Message: ----------- (merge conflicts) Commit: 4423a381afa68e4ce3e47f44ed8c7973dee62a3e https://github.com/galaxyproject/galaxy/commit/4423a381afa68e4ce3e47f44ed8c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: merge sectioned history layout This merges with history-contents.pagination, adding sections of history contents by hids but reverts the auto-expansion of those sections when the scroll bar is moved 'over' them. Commit: 16830e8eb250f1ebd3db4afaee7dbddf03ebd60d https://github.com/galaxyproject/galaxy/commit/16830e8eb250f1ebd3db4afaee7d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M CONTRIBUTORS.md M Makefile M client/README.md M client/bower.json M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.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/history-view-annotated.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/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.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/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M 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test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_pulsar_embedded.py M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/form_tests.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/shed_functional/base/twilltestcase.py R test/shed_functional/functional/test_0450_skip_tool_tests.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml M test/unit/jobs/test_command_factory.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/test_objectstore.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/biomart.xml M tools/data_source/upload.py M tools/filters/trimmer.xml M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- (merge conflicts) Commit: 4db7940a5cad685b9a81bf0f2ccc9ecac7f6aa7a https://github.com/galaxyproject/galaxy/commit/4db7940a5cad685b9a81bf0f2ccc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/style/less/base.less A client/galaxy/style/less/dataset.less M client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/style/blue/base.css Log Message: ----------- History: move to a flex based layout Change right-hand side of Analysis page and the history-panel within it to use flexbox for layout. Allow scrolling withiin list-items not the entire view itself. Provides a fixed header containing the history controls. Commit: ca842c264664c6ba364e3645027858f6c1a88a8d https://github.com/galaxyproject/galaxy/commit/ca842c264664c6ba364e36450278… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.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/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less A client/galaxy/style/less/dataset.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/sharable.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/cwl.py A scripts/api/filter_failed_datasets_from_collection.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css A test-data/composite_output_expected_log M test/functional/tools/composite_output.xml M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'history.fixed-header' ...into history-contents.limiting Commit: 6e866335d207848e566926f13d255ba53b3cae3c https://github.com/galaxyproject/galaxy/commit/6e866335d207848e566926f13d25… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js M static/style/blue/base.css Log Message: ----------- UI, history: paginate w/ horizontal scrolling - Render sections side by side and allow scrolling between sections - Also: improve accesibility query by eagerloading dataset.actions and using cache for user roles Commit: c6f8a9f00cc7722c2aa28a087227c6822b6dd667 https://github.com/galaxyproject/galaxy/commit/c6f8a9f00cc7722c2aa28a087227… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js A client/galaxy/scripts/ui/scrollable-pages.js M static/maps/mvc/history/history-view.js.map A static/maps/ui/scrollable-pages.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view.js A static/scripts/ui/scrollable-pages.js Log Message: ----------- (add missing files) Commit: 9a3fb8ab37237d9b7ad5c3aa0fd3b62a0468ebc4 https://github.com/galaxyproject/galaxy/commit/9a3fb8ab37237d9b7ad5c3aa0fd3… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M client/galaxy/scripts/apps/analysis.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/history-view-annotated.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/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js R client/galaxy/scripts/ui/scrollable-pages.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map R static/maps/ui/scrollable-pages.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js R static/scripts/ui/scrollable-pages.js M static/style/blue/base.css M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, history: rollback other pagination prototypes Attempts to remove most of the sectioning/infinite scrolling prototypes but leave the cleanup/refactoring in place for another attempt. Commit: 5ff73677bbd06d6fb33e0ceb29e7af29a28adce5 https://github.com/galaxyproject/galaxy/commit/5ff73677bbd06d6fb33e0ceb29e7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M Makefile M README.rst M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/tool/tool-form-base.js R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/frame.less M 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lib/tool_shed/util/tool_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/api/data_manager_example_execute.py M scripts/api/search.py M scripts/api/upload_to_history.py M scripts/bootstrap_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/extract_dataset_part.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M 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templates/show_params.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M test/api/test_datasets.py M test/api/test_tools.py M test/api/test_workflows.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py M test/base/driver_util.py R test/base/test_data.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/composite_output_tests.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/modal_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0060_workflows.py M 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test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff2bed.xml M tools/filters/gff_to_bed_converter.py M tools/filters/gtf2bedgraph.xml M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml Log Message: ----------- (merge conflicts) Commit: 769a2e583bdbe1939d26c5e4e1e549b36b690d59 https://github.com/galaxyproject/galaxy/commit/769a2e583bdbe1939d26c5e4e1e5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: 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/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/style/less/history.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-item.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, history: re-implement pagination Hopefully in a simpler way. This version does not account for hid sections, but uses limit offset - which leaves other (non-hid) sort orders as an option. This commit also fixes: * issues with the fixed header in the published section * ajax loading for histories embedded in pages Commit: 495c352cd90e603364f6737569f83a557d878423 https://github.com/galaxyproject/galaxy/commit/495c352cd90e603364f6737569f8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: add pagination load indicator And fixes some styling issues. Commit: 2a38b11e87bf58872850c23af0185c98cab491e4 https://github.com/galaxyproject/galaxy/commit/2a38b11e87bf58872850c23af018… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M lib/galaxy/managers/base.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: fixes - re-delegates events for collection views - extends clicking for contents-container in annotated history view - loads first 10 histories *and* current history for initial set in multi-history page Commit: 8b2b289973f0ee87b14bb9688306a8dc23ac7e2f https://github.com/galaxyproject/galaxy/commit/8b2b289973f0ee87b14bb9688306… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M client/galaxy/style/less/base.less A client/galaxy/style/less/collection.less R client/galaxy/style/less/collections.less M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css Log Message: ----------- Styles: minor fixes - corrects plurality of collection.less - chmod on bootstrap-tour.css and jquery.rating.css Commit: 1297ce261a43228cb3ed11f26fccd88aebcb93df https://github.com/galaxyproject/galaxy/commit/1297ce261a43228cb3ed11f26fcc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/collection.less M client/galaxy/style/less/history.less M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: fix flex for collection view Commit: 01a25ff64f82075f0de07700a2772e3f5ff40337 https://github.com/galaxyproject/galaxy/commit/01a25ff64f82075f0de07700a277… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: rendering fixes - Tries to strike a balance between subview reuse using detach to preserve event hash and subview re-creation when fully re-rendering a history by removing views from the viewMap. - Makes actions section a full height to make empty, anon histories looking normal. - Makes dataset models wait until the change is returned from the server before triggering change on the model. Commit: d89843ead7176b90aef13b7b26cc3f73fedc4c3b https://github.com/galaxyproject/galaxy/commit/d89843ead7176b90aef13b7b26cc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/list/list-view.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: fix to delete_current most_recent Fixes delete_current's call to most_recent, filtering out the deleted and purged histories. Now, on delete_current the most recently *non- deleted* history will be switched to. Commit: 86acee5a743e7afca530f9a194f82c0ed83c4b1a https://github.com/galaxyproject/galaxy/commit/86acee5a743e7afca530f9a194f8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: 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-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, history: fix search and misc. - corrects search to work for individual history views - refactors handleItem{Deletion,Visible}Change in history view edit - reverts the experiment in the branch that recycled subviews between renders - this simplifies many things - corrects the rendering, signals, and timing of loading indicators - small fixes, refactorings, and simplifications Commit: a41ff4265b4f54b832e40c0dc71707db5eb307e6 https://github.com/galaxyproject/galaxy/commit/a41ff4265b4f54b832e40c0dc717… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.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/list/list-view.js M client/galaxy/style/less/history.less M lib/galaxy/managers/base.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: more minor fixes Commit: ae6cb1bf88ba4293c6be4c5df3a717bccaca73fd https://github.com/galaxyproject/galaxy/commit/ae6cb1bf88ba4293c6be4c5df3a7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, history: fix annotations in published history Commit: f072ee7807591902b8ae605474aa089a33ead93d https://github.com/galaxyproject/galaxy/commit/f072ee7807591902b8ae605474aa… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-14 (Tue, 14 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/dataset.less M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: change to front page when adding - Causes the contents to load the 'front' page before adding new datasets. This allows them to be added in the proper place. - Fixes annotation display on datasets. - Adds annotation loading to histories embedded in Pages. Commit: 1b2c5dea990ed91325eb6a85b16184a1647d2e20 https://github.com/galaxyproject/galaxy/commit/1b2c5dea990ed91325eb6a85b161… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, history: show search progress in subtitle Commit: 233d6d8d32e94671ce387efdb39f35bd3454eb8d https://github.com/galaxyproject/galaxy/commit/233d6d8d32e94671ce387efdb39f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view.js M static/style/blue/base.css Log Message: ----------- UI, history: minor style/pagination fixes Commit: 6eb1cefe88b50eea7beb982bbfaf5674f13e7313 https://github.com/galaxyproject/galaxy/commit/6eb1cefe88b50eea7beb982bbfaf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: get element count for all histories - Moves the ajax call for hdca element counts to a listener of the loading-done event. This allows (almost) all history views to be decorated with hdca counts. Commit: fd78f99d61bcb141475875b85d3beb2945bc3a8e https://github.com/galaxyproject/galaxy/commit/fd78f99d61bcb141475875b85d3b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M .ci/py3_sources.txt M client/bower.json R client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/library.less M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/tool_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/source/dev/faq.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py A lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/zip_collection.xml M lib/galaxy/util/__init__.py R lib/galaxy/util/directory_hash.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/external_services.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/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/hg.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/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy_utils/sequence/fastq.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py R static/maps/libs/tracekit.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/tracekit.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/repair_repository.mako M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/show_params.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/common.mako A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/interactor.py M test/base/twilltestcase.py A test/functional/tools/checksum.xml A test/functional/tools/exit_code_from_file.xml A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_1000_install_basic_repository.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/workflows/test_run_parameters.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/filters/axt_to_lav.py Log Message: ----------- (merge conflicts) Commit: 48f48e9bd29430f58363eb47d95154ff4854ebe7 https://github.com/galaxyproject/galaxy/commit/48f48e9bd29430f58363eb47d951… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js M static/style/blue/base.css M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, history: style cleanup, small tweaks - Corrects history control sizing on Safari - Corrects ul, li rendering of history in Chrome - Lengthens fadeout of loading indicator to better transition when rendering large numbers of contents - Corrects page controls in history/view Commit: 6c6bfe5614f6fed3c88b19789369ee3f5aabc86b https://github.com/galaxyproject/galaxy/commit/6c6bfe5614f6fed3c88b19789369… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako M tools/filters/sff_extract.py Log Message: ----------- (merge conflicts) Commit: cc8d421c570df3b3b8c53ba49ad1247729102ad1 https://github.com/galaxyproject/galaxy/commit/cc8d421c570df3b3b8c53ba49ad1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/style/less/ui/search-input.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/maps/ui/search-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M static/scripts/ui/search-input.js M static/style/blue/base.css Log Message: ----------- UI, history: search and ui/search-input - clarifies search progress in subtitle of edit/current histories - corrects found display in subtitle when no results are found - does not cause a search and render when entering the same terms - does not clear search on full backspace or cut of input text - does not cause clear and render if no previous terms existed - removes onchange from search input (not needed yet) Commit: b1d652e59d6ccde1e73c90ffd483bbd600d110ff https://github.com/galaxyproject/galaxy/commit/b1d652e59d6ccde1e73c90ffd483… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.xml A display_applications/igv/bigwig.xml M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M 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https://github.com/galaxyproject/galaxy/commit/dd37dedc2a1e570053b8be9b0f88… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: scroll to new items, clean up Commit: 8a159ade93040ea1cb6a0657c7089eebc5a92366 https://github.com/galaxyproject/galaxy/commit/8a159ade93040ea1cb6a0657c708… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M 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static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: clean up Commit: aee39774121ef2610387431b6024ddd12c997834 https://github.com/galaxyproject/galaxy/commit/aee39774121ef2610387431b6024… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, history: switch to front when dropping content When a history with a drop target accepts data to be copied, this has the view's current page switch to the top/front before the copy happens. Commit: e842e0b2ba5c77674e11f8a1a0eceb4765db2621 https://github.com/galaxyproject/galaxy/commit/e842e0b2ba5c77674e11f8a1a0ec… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M test/qunit/tests/history_contents_model_tests.js Log Message: ----------- Tests, history: hda delete happens after return - Change qunit test history_contents_model_tests to account for the use of the '{ wait: true }' backbone flag being used when 'save'd. This causes the attribute to be set when the ajax call returns successfully. Commit: a33203b3b5d5ad9b74ff00a693dcb85efff746e3 https://github.com/galaxyproject/galaxy/commit/a33203b3b5d5ad9b74ff00a693dc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: increase page select affordance Commit: 817c63eeea3d13604f7e9faa817d973f18ab52c6 https://github.com/galaxyproject/galaxy/commit/817c63eeea3d13604f7e9faa817d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M 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static/scripts/mvc/tool/tool-template.js M test/api/test_tools.py A test/functional/tools/identifier_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 709ae896ea40a60127d814087c6f56327f79bf3e https://github.com/galaxyproject/galaxy/commit/709ae896ea40a60127d814087c6f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- Serializer: better name & doc Commit: 87fbdc4ad6345ebe56d652358e34e9de57981535 https://github.com/galaxyproject/galaxy/commit/87fbdc4ad6345ebe56d652358e34… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: create tooltip on each render Commit: 53f34b8c9e2105972e82f22a5f802399b6656f0a https://github.com/galaxyproject/galaxy/commit/53f34b8c9e2105972e82f22a5f80… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- UI, history: rerender contents on unhiding hidden - Waits till all hidden datasets are saved as unhidden and then, if the history is not showing hidden datasets, rerenders the entire contents Commit: 97b171632d9b16e54fad4b46b0f419bf31866882 https://github.com/galaxyproject/galaxy/commit/97b171632d9b16e54fad4b46b0f4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: render on deleted/hidden toggle - Fixes lack of render when only one hidden/deleted dataset is shown by sending a `renderAll` flag then caught by the update listener Commit: 62de9bf76a6e5a6d7857ad031f8499d7453e12ea https://github.com/galaxyproject/galaxy/commit/62de9bf76a6e5a6d7857ad031f84… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .ci/py3_sources.txt M .gitignore M .travis.yml A client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.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/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.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/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.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-tabs.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/library/ui-table-form.js M 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config/plugins/visualizations/graphviz/templates/graphviz.mako M config/tool_data_table_conf.xml.sample A config/tool_destinations.yml.sample A display_applications/ucsc/trackhub.xml A doc/source/admin/grt.rst M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst M doc/source/dev/index.rst A doc/source/dev/interactive_environments.rst M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/config.py M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tracks.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M 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lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.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/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/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A lib/galaxy/webapps/reports/controllers/history.py A lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/shed_util_common.py A scripts/communication/communication_server.py A scripts/communication/template/communication.css A scripts/communication/template/communication.html A scripts/communication/template/communication.js A scripts/grt.py A scripts/grt.yml.sample M setup.cfg A static/maps/layout/generic-nav-view.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map 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templates/user/communication_settings.mako M templates/user/index.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/reports/history_and_dataset_per_user.mako A templates/webapps/reports/history_and_dataset_type.mako A templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako A templates/webapps/reports/tool_error_messages.mako A templates/webapps/reports/tool_execution_time.mako A templates/webapps/reports/tool_execution_time_per_month.mako A templates/webapps/reports/tools_and_job_state.mako A templates/webapps/reports/tools_and_job_state_per_month.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako A test-data/neostore.zip M test/api/test_users.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/twilltestcase.py A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_resolvers.py M 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test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_conda_resolution.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 21b93be1104ac2175ba128ee604425ee44ea17cf https://github.com/galaxyproject/galaxy/commit/21b93be1104ac2175ba128ee6044… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M Makefile M client/bower.json A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/version.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M run_tests.sh M scripts/bootstrap_history.py M scripts/nosetests.py A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/mvc/history/options-menu.js M static/style/blue/base.css M templates/user/change_password.mako M templates/user/register.mako M test/unit/tools/test_tool_deps.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 2d15e50d0f5c65d0dc9d896d1e47ba546d5a7e42 https://github.com/galaxyproject/galaxy/commit/2d15e50d0f5c65d0dc9d896d1e47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js A client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M 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static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map A static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/ui/search-input.js.map M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/panel.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js A static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js A static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/ui/search-input.js M static/scripts/utils/ajax-queue.js M static/style/blue/base.css M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M test/qunit/tests/history_contents_model_tests.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'history-contents.limiting' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7389b93bd613...2d15e50d0f5c

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[galaxyproject/galaxy] 7bf0cc: Remove the old HubAssembly class
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 7bf0cc72418308e54b6ec180a8913623004c8288 https://github.com/galaxyproject/galaxy/commit/7bf0cc72418308e54b6ec180a891… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- Remove the old HubAssembly class Commit: 3206199652330659aa9f1cebe75c6940787f85d4 https://github.com/galaxyproject/galaxy/commit/3206199652330659aa9f1cebe75c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- Merge pull request #2701 from remimarenco/release_16.07 [16.07] Fix: Remove the old HubAssembly class Compare: https://github.com/galaxyproject/galaxy/compare/ed7c357668df...320619965233

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[galaxyproject/galaxy] 2b7fc3: Fixing button width on Composite upload dialog
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b7fc3d3778adfae0b4ddc9967ea6183ca3c6cc9 https://github.com/galaxyproject/galaxy/commit/2b7fc3d3778adfae0b4ddc9967ea… Author: galaxy <galaxy(a)galaxy.development> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/style/less/upload.less M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Fixing button width on Composite upload dialog Commit: 7389b93bd61396f86b85cbc0b4fa818221563204 https://github.com/galaxyproject/galaxy/commit/7389b93bd61396f86b85cbc0b4fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/style/less/upload.less M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge pull request #2703 from sszakony/dev Fixing button width on Composite upload dialog #2591 Compare: https://github.com/galaxyproject/galaxy/compare/d8c22b70e897...7389b93bd613

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[galaxyproject/infrastructure-playbook] 966138: Decrease Jetstream @ TACC usage for production pha...
by GitHub 02 Aug '16

02 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 966138c57e8b91355d1235586df5b3d5d7221841 https://github.com/galaxyproject/infrastructure-playbook/commit/966138c57e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Decrease Jetstream @ TACC usage for production phase

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