[galaxy-commits] [galaxyproject/galaxy] 1b64be: API, histories: allow sorting by disk_size, move o...

1 Sep 2015


      Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 1b64bea779eab01a5a190d1f44707148b18e2d21
      https://github.com/galaxyproject/galaxy/commit/1b64bea779eab01a5a190d1f44707...
  Author: Carl Eberhard <carlfeberhard@gmail.com>
  Date:   2015-08-10 (Mon, 10 Aug 2015)

  Changed paths:
    M lib/galaxy/managers/histories.py
    M lib/galaxy/webapps/galaxy/api/histories.py

  Log Message:
  -----------
  API, histories: allow sorting by disk_size, move order parsing into manager


  Commit: ea130e2c008e100de92da78fa62ac797b635baed
      https://github.com/galaxyproject/galaxy/commit/ea130e2c008e100de92da78fa62ac...
  Author: Carl Eberhard <carlfeberhard@gmail.com>
  Date:   2015-08-21 (Fri, 21 Aug 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/history/history-model.js
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M lib/galaxy/webapps/galaxy/api/histories.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M static/maps/mvc/history/history-model.js.map
    M static/maps/mvc/history/multi-panel.js.map
    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:
  -----------
  Histories: move order parsing into managers; View multi: allow and pass ordering into bootstrapped histories, limit to 10; View multi, client: allow better collection setting and addition


  Commit: d8ee54251afbcb965c02af47d800fac1e005a004
      https://github.com/galaxyproject/galaxy/commit/d8ee54251afbcb965c02af47d800f...
  Author: Carl Eberhard <carlfeberhard@gmail.com>
  Date:   2015-08-21 (Fri, 21 Aug 2015)

  Changed paths:
    M .ci/flake8_blacklist.txt
    M CONTRIBUTING.md
    M client/galaxy/scripts/galaxy.menu.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/history/options-menu.js
    M client/galaxy/scripts/mvc/ui/ui-button-menu.js
    M client/galaxy/scripts/mvc/ui/ui-color-picker.js
    M client/galaxy/scripts/mvc/ui/ui-misc.js
    M client/galaxy/scripts/mvc/ui/ui-modal.js
    M client/galaxy/scripts/mvc/ui/ui-popover.js
    A client/galaxy/scripts/mvc/upload/composite/composite-row.js
    A client/galaxy/scripts/mvc/upload/composite/composite-view.js
    A client/galaxy/scripts/mvc/upload/default/default-row.js
    A 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
    R client/galaxy/scripts/mvc/upload/upload-row.js
    M client/galaxy/scripts/mvc/upload/upload-settings.js
    M client/galaxy/scripts/mvc/upload/upload-view.js
    M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
    M client/galaxy/scripts/reports_webapp/run_stats.js
    M client/galaxy/scripts/utils/uploadbox.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/style/less/reports.less
    M client/galaxy/style/less/ui.less
    M client/galaxy/style/less/upload.less
    M client/grunt-tasks/scripts.js
    M config/galaxy.ini.sample
    M doc/source/project/organization.rst
    M lib/galaxy/auth/providers/ldap_ad.py
    M lib/galaxy/config.py
    M lib/galaxy/datatypes/genetics.py
    M lib/galaxy/managers/base.py
    M lib/galaxy/managers/configuration.py
    M lib/galaxy/managers/histories.py
    M lib/galaxy/managers/sharable.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/tool_shed_install/__init__.py
    M lib/galaxy/quota/__init__.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/toolbox/lineages/stock.py
    M lib/galaxy/util/bunch.py
    M lib/galaxy/util/jstree.py
    M lib/galaxy/version.py
    M lib/galaxy/webapps/galaxy/api/datatypes.py
    M lib/galaxy/webapps/galaxy/api/histories.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
    R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    M lib/galaxy/webapps/galaxy/controllers/root.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M lib/galaxy/webapps/reports/controllers/jobs.py
    M lib/galaxy/webapps/reports/controllers/workflows.py
    A lib/galaxy/webapps/tool_shed/api/configuration.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/buildapp.py
    M lib/galaxy/webapps/tool_shed/config.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/workflow/render.py
    M lib/galaxy_utils/sequence/fasta.py
    M lib/galaxy_utils/sequence/fastq.py
    M lib/galaxy_utils/sequence/sequence.py
    M lib/galaxy_utils/sequence/transform.py
    M lib/galaxy_utils/sequence/vcf.py
    M lib/tool_shed/capsule/capsule_manager.py
    M lib/tool_shed/dependencies/tool/tag_attribute_handler.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/update_repository_manager.py
    M lib/tool_shed/grids/repository_grids.py
    M lib/tool_shed/metadata/metadata_generator.py
    M lib/tool_shed/metadata/repository_metadata_manager.py
    M lib/tool_shed/scripts/api/common.py
    M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
    M lib/tool_shed/tools/tool_version_manager.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 lib/tool_shed/utility_containers/__init__.py
    M lib/tool_shed/utility_containers/utility_container_manager.py
    M scripts/cleanup_datasets/cleanup_datasets.py
    R static/help.css
    R static/help.html
    R static/help.rst
    R static/images/SetAttr.png
    R static/images/SetGenome.png
    R static/images/brochure.pdf
    R static/images/galaxy.png
    R static/images/galaxyLogo_small.png
    R static/images/lock.jpg
    R static/images/qk/quickie1_small.png
    R static/images/qk/quickie2_small.png
    R static/images/qk/quickie3_small.png
    R static/images/qk/quickie4_small.png
    R static/images/qk/quickie5_small.png
    R static/images/qk/quickie6_small.png
    R static/images/qk/quickie7_small.png
    R static/images/reports_webapp/bases/home-icon-active.png
    R static/images/reports_webapp/bases/home-icon-hov.png
    R static/images/reports_webapp/bases/home-icon.png
    R static/images/reports_webapp/home-icon-active.png
    R static/images/reports_webapp/home-icon-hov.png
    R static/images/reports_webapp/home-icon.png
    R static/images/screencast.png
    R static/images/sequencer.png
    R static/images/tools.gif
    R static/images/toolsExpandingMenu.gif
    R static/images/welcomePhoto.jpg
    M static/maps/galaxy.interactive_environments.js.map
    M static/maps/galaxy.menu.js.map
    M static/maps/libs/jquery/jqtouch.js.map
    M static/maps/libs/raven.js.map
    M static/maps/libs/toastr.js.map
    M static/maps/mvc/collection/list-collection-creator.js.map
    M static/maps/mvc/data.js.map
    M static/maps/mvc/dataset/dataset-choice.js.map
    M static/maps/mvc/form/form-parameters.js.map
    M static/maps/mvc/form/form-repeat.js.map
    M static/maps/mvc/form/form-select-content.js.map
    M static/maps/mvc/form/form-view.js.map
    M static/maps/mvc/history/history-contents.js.map
    M static/maps/mvc/history/options-menu.js.map
    M static/maps/mvc/job/job-model.js.map
    M static/maps/mvc/library/library-foldertoolbar-view.js.map
    M static/maps/mvc/list/list-panel.js.map
    M static/maps/mvc/tools/tools-form-base.js.map
    M static/maps/mvc/tools/tools-form-workflow.js.map
    M static/maps/mvc/tools/tools-jobs.js.map
    M static/maps/mvc/ui/ui-button-menu.js.map
    M static/maps/mvc/ui/ui-color-picker.js.map
    M static/maps/mvc/ui/ui-frames.js.map
    M static/maps/mvc/ui/ui-misc.js.map
    M static/maps/mvc/ui/ui-modal.js.map
    M static/maps/mvc/ui/ui-popover.js.map
    M static/maps/mvc/ui/ui-select.js.map
    A static/maps/mvc/upload/composite/composite-row.js.map
    A static/maps/mvc/upload/composite/composite-view.js.map
    A static/maps/mvc/upload/default/default-row.js.map
    A 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
    R static/maps/mvc/upload/upload-row.js.map
    M static/maps/mvc/upload/upload-settings.js.map
    M static/maps/mvc/upload/upload-view.js.map
    M static/maps/mvc/workflow/workflow-terminals.js.map
    M static/maps/reports_webapp/run_stats.js.map
    M static/maps/utils/deferred.js.map
    M static/maps/utils/graph.js.map
    M static/maps/utils/metrics-logger.js.map
    M static/maps/utils/uploadbox.js.map
    M static/maps/utils/utils.js.map
    M static/maps/viz/trackster.js.map
    M static/maps/viz/trackster/filters.js.map
    M static/maps/viz/visualization.js.map
    M static/scripts/galaxy.interactive_environments.js
    M static/scripts/galaxy.menu.js
    M static/scripts/libs/jquery/jqtouch.js
    M static/scripts/libs/raven.js
    M static/scripts/libs/toastr.js
    M static/scripts/mvc/collection/list-collection-creator.js
    M static/scripts/mvc/data.js
    M static/scripts/mvc/dataset/dataset-choice.js
    M static/scripts/mvc/form/form-parameters.js
    M static/scripts/mvc/form/form-repeat.js
    M static/scripts/mvc/form/form-select-content.js
    M static/scripts/mvc/form/form-view.js
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/options-menu.js
    M static/scripts/mvc/job/job-model.js
    M static/scripts/mvc/library/library-foldertoolbar-view.js
    M static/scripts/mvc/list/list-panel.js
    M static/scripts/mvc/tools/tools-form-base.js
    M static/scripts/mvc/tools/tools-form-workflow.js
    M static/scripts/mvc/tools/tools-jobs.js
    M static/scripts/mvc/ui/ui-button-menu.js
    M static/scripts/mvc/ui/ui-color-picker.js
    M static/scripts/mvc/ui/ui-frames.js
    M static/scripts/mvc/ui/ui-misc.js
    M static/scripts/mvc/ui/ui-modal.js
    M static/scripts/mvc/ui/ui-popover.js
    M static/scripts/mvc/ui/ui-select.js
    A static/scripts/mvc/upload/composite/composite-row.js
    A static/scripts/mvc/upload/composite/composite-view.js
    A static/scripts/mvc/upload/default/default-row.js
    A static/scripts/mvc/upload/default/default-view.js
    M static/scripts/mvc/upload/upload-button.js
    M static/scripts/mvc/upload/upload-ftp.js
    M static/scripts/mvc/upload/upload-model.js
    R static/scripts/mvc/upload/upload-row.js
    M static/scripts/mvc/upload/upload-settings.js
    M static/scripts/mvc/upload/upload-view.js
    M static/scripts/mvc/workflow/workflow-terminals.js
    M static/scripts/reports_webapp/run_stats.js
    M static/scripts/utils/deferred.js
    M static/scripts/utils/graph.js
    M static/scripts/utils/metrics-logger.js
    M static/scripts/utils/uploadbox.js
    M static/scripts/utils/utils.js
    M static/scripts/viz/trackster.js
    M static/scripts/viz/trackster/filters.js
    M static/scripts/viz/visualization.js
    M static/style/blue/base.css
    M static/style/blue/reports.css
    R static/welcome.rst
    M templates/page_base.mako
    M templates/spark_base.mako
    R templates/webapps/galaxy/cloud/index.mako
    A templates/webapps/galaxy/history/as_xml.mako
    M templates/webapps/galaxy/history/view.mako
    R templates/webapps/galaxy/root/history.mako
    R templates/webapps/galaxy/root/history_as_xml.mako
    M templates/webapps/reports/base_panels.mako
    M templates/webapps/reports/index.mako
    M templates/webapps/reports/jobs_errors_per_tool.mako
    M templates/webapps/reports/jobs_per_month_all.mako
    M templates/webapps/reports/jobs_per_month_in_error.mako
    M templates/webapps/reports/jobs_per_tool.mako
    M templates/webapps/reports/jobs_per_user.mako
    M templates/webapps/reports/jobs_specified_month_in_error.mako
    M templates/webapps/reports/workflows_per_month_all.mako
    M templates/webapps/reports/workflows_per_user.mako
    M templates/webapps/reports/workflows_per_workflow.mako
    A test/qunit/test-app.js
    M test/qunit/test-common.js
    A test/qunit/test-data/bootstrapped.js
    A test/qunit/test-data/fakeserver.js
    A test/qunit/tests/upload_dialog_tests.html
    A test/qunit/tests/upload_dialog_tests.js
    M test/qunit/tests/workflow_editor_tests.js
    M test/unit/test_galaxy_mapping.py
    M tool-data/all_fasta.loc.sample
    M tool-data/faseq.loc.sample
    R tool-data/fastx_clipper_sequences.txt
    M tool-data/liftOver.loc.sample
    M tool-data/mosaik_index.loc.sample
    M tool-data/ngs_sim_fasta.loc.sample
    M tool-data/perm_base_index.loc.sample
    M tool-data/perm_color_index.loc.sample
    M tool-data/picard_index.loc.sample
    M tool-data/regions.loc.sample
    M tool-data/srma_index.loc.sample

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/dev' into history.multi


  Commit: 15fe2b7d8ff79dfbc3ac2592246401b7c6c0af52
      https://github.com/galaxyproject/galaxy/commit/15fe2b7d8ff79dfbc3ac259224640...
  Author: Carl Eberhard <carlfeberhard@gmail.com>
  Date:   2015-08-31 (Mon, 31 Aug 2015)

  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/multi-panel.js
    M lib/galaxy/managers/histories.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    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/multi-panel.js.map
    M static/maps/utils/uploadbox.js.map
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.js
    M static/scripts/mvc/history/multi-panel.js
    M static/scripts/utils/uploadbox.js
    M templates/webapps/galaxy/history/view_multiple.mako

  Log Message:
  -----------
  UI, histories: lazy-load histories in the multi-history view, handle search loading indication better, move sort/comparator code into collection


  Commit: efc1df79f195d7479cc8a7dfb4f811e8ae82329b
      https://github.com/galaxyproject/galaxy/commit/efc1df79f195d7479cc8a7dfb4f81...
  Author: Carl Eberhard <carlfeberhard@gmail.com>
  Date:   2015-08-31 (Mon, 31 Aug 2015)

  Changed paths:
    M client/galaxy/scripts/mvc/history/multi-panel.js
    M client/galaxy/style/less/history.less
    M static/maps/mvc/history/multi-panel.js.map
    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, histories: move load indicator style to less, use better name


  Commit: c47d4a715ed4acf2ed72693f9659730b402fd001
      https://github.com/galaxyproject/galaxy/commit/c47d4a715ed4acf2ed72693f96597...
  Author: Dannon Baker <dannon.baker@gmail.com>
  Date:   2015-09-01 (Tue, 01 Sep 2015)

  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/multi-panel.js
    M client/galaxy/style/less/history.less
    M lib/galaxy/managers/histories.py
    M lib/galaxy/webapps/galaxy/api/histories.py
    M lib/galaxy/webapps/galaxy/controllers/history.py
    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/multi-panel.js.map
    M static/scripts/mvc/history/history-contents.js
    M static/scripts/mvc/history/history-model.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:
  -----------
  Merge pull request #676 from carlfeberhard/history.multi

Lazy-load histories into multi-history view


Compare: https://github.com/galaxyproject/galaxy/compare/0a1617024c79...c47d4a715ed4

[galaxy-commits] [galaxyproject/galaxy] 1b64be: API, histories: allow sorting by disk_size, move o...

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