December 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0dae3e: Fix job resume functionality for non-prefixed inpu...
by GitHub 31 Dec '17

31 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0dae3e7c687a943544ce590ab8790c43ca8e7801 https://github.com/galaxyproject/galaxy/commit/0dae3e7c687a943544ce590ab879… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix job resume functionality for non-prefixed input data This should fix https://github.com/galaxyproject/galaxy/issues/5222. The problem was that HDA ids in nested parameters were not always being updated properly. In the case of bowtie2 the input dataset is provided via a conditional, but the conditional prefix is not being stored in the JobToInputDatasetAssociation, and so the `update_param` function was not able to update the dataset id in these instances. The approach now is to simply replace all occurences of the old dataset id with the new dataset id. TODO: tests, refactor the replacement functionality into a separate function and make this work for JobToInputDatasetCollectionAssociation. Commit: 39073b4b4c5cb7954310d9f7abbd2703b6e5d0ad https://github.com/galaxyproject/galaxy/commit/39073b4b4c5cb7954310d9f7abbd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Add test for resume job functionality This test runs a workflow whose first step fails, followed by a tool that uses the first step's output as an input, which is behind a nested conditional. This recapitulates the bug described in https://github.com/galaxyproject/galaxy/issues/5222. Commit: 26103416afe1843eb031586ef7bd3b896f1eb945 https://github.com/galaxyproject/galaxy/commit/26103416afe1843eb031586ef7bd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Move job remap functionality in separate function Commit: 9fdf0a62699b00e59da4cd0f0c275027b8603270 https://github.com/galaxyproject/galaxy/commit/9fdf0a62699b00e59da4cd0f0c27… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Add job resume test with HDCA input to paused dataset I am slightly surprised that this worked without change, but it appears that the remapping occurs via the HDAs that the HDCA is composed of. Commit: c0dbace7bbf33da15ba1fdb9f69777a3c881cecd https://github.com/galaxyproject/galaxy/commit/c0dbace7bbf33da15ba1fdb9f697… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/base/populators.py A test/functional/tools/fail_identifier.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Replace collection elements with re-run output This specifically addresses the problem where some jobs of a mapped-over collection have failed. Instead of filtering the failed collection and restarting the workflow at this position (involving a lot of copy-paste ...) the user can now limit the rerun to the problematic jobs and the workflow should resume from there. Should fix https://github.com/galaxyproject/galaxy/issues/2235. This is one possible implementation, it would also be feasible to not manipulate the original collection, but to copy the HDCA and then to replace collection elements and replace all references for jobs that depend on the HDCA, as we do for HDAs. This implementation seems simpler, but let me know if you see problems with this approach. Commit: 8e93c2e070af1263712d483d721d246e2f4356a1 https://github.com/galaxyproject/galaxy/commit/8e93c2e070af1263712d483d721d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/__init__.py M test/api/test_workflows.py M test/base/populators.py A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5247 from mvdbeek/job_rerun_fixes Fix and enhance job resume functionality Compare: https://github.com/galaxyproject/galaxy/compare/c78a23cb873c...8e93c2e070af

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[galaxyproject/galaxy] f017de: Tool-centric annotation of out of memory errors.
by GitHub 27 Dec '17

27 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f017de30bf7b0188f8872a9842c38750aab9a410 https://github.com/galaxyproject/galaxy/commit/f017de30bf7b0188f8872a9842c3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-22 (Fri, 22 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/exit_code_oom.xml M test/functional/tools/samples_tool_conf.xml A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_job_resubmission.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_parsing.py Log Message: ----------- Tool-centric annotation of out of memory errors. - Update explicit stdio definitions as well as detect_errors-based definitions to allow this. - Update runner code to allow resubmission in such cases. Commit: c78a23cb873cf5cbcf177cfa7052ae6dad506eea https://github.com/galaxyproject/galaxy/commit/c78a23cb873cf5cbcf177cfa7052… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-27 (Wed, 27 Dec 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/exit_code_oom.xml M test/functional/tools/samples_tool_conf.xml A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_job_resubmission.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #5196 from jmchilton/oom_detect Tool-based annotation of out of memory errors. Compare: https://github.com/galaxyproject/galaxy/compare/7eea95c4917f...c78a23cb873c

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[galaxyproject/galaxy] fde8aa: Translate tool help in french
by GitHub 22 Dec '17

22 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fde8aa970b6495ba7f20ff2932d22d98914a6fb4 https://github.com/galaxyproject/galaxy/commit/fde8aa970b6495ba7f20ff2932d2… Author: ValentinChCloud <chavaldranis(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Translate tool help in french Commit: 5c105c48986ee7c40179b8970e00743363fbd999 https://github.com/galaxyproject/galaxy/commit/5c105c48986ee7c40179b8970e00… Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- start translating Commit: 9855bd0af9f7b0e0b38c2c94bec99af639271045 https://github.com/galaxyproject/galaxy/commit/9855bd0af9f7b0e0b38c2c94bec9… Author: Valentin Chambon <chavaldranis(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #1 from yvanlebras/patch-3 start translating Commit: 58ab6a1ba1a4c3380bb63d6f08ea7633e0038e5f https://github.com/galaxyproject/galaxy/commit/58ab6a1ba1a4c3380bb63d6f08ea… Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- A first pass on the "admin" UI related section Commit: a8591e99444002123b6d14cf674ab489a568062d https://github.com/galaxyproject/galaxy/commit/a8591e99444002123b6d14cf674a… Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- fix typos Commit: c828fa4ae6d6f07c52b0fd9648e2d416eefdc0b9 https://github.com/galaxyproject/galaxy/commit/c828fa4ae6d6f07c52b0fd9648e2… Author: Valentin Chambon <chavaldranis(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #2 from yvanlebras/patch-4 A first pass on the "admin" UI related section Commit: c8dddcdbef210bbc47ee0552fb018898b754bd9e https://github.com/galaxyproject/galaxy/commit/c8dddcdbef210bbc47ee0552fb01… Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Second pass after coffee break Commit: b346a02e16ffbf68c2c0f5460aa34c6e8f9c8163 https://github.com/galaxyproject/galaxy/commit/b346a02e16ffbf68c2c0f5460aa3… Author: Valentin Chambon <chavaldranis(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #3 from yvanlebras/patch-5 Second pass after coffee break Commit: 75060db63d9b08ad6fb22b58c438761e88a26e75 https://github.com/galaxyproject/galaxy/commit/75060db63d9b08ad6fb22b58c438… Author: Valentin Chambon <chavaldranis(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Correct some translation errors Commit: bb25175d5c2e97801cdb2440d1797d7fca815d27 https://github.com/galaxyproject/galaxy/commit/bb25175d5c2e97801cdb2440d179… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-22 (Fri, 22 Dec 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Client-format. 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static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/populators.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fri18n Commit: 7eea95c4917f0ae78172a49b7aa9389738b751e6 https://github.com/galaxyproject/galaxy/commit/7eea95c4917f0ae78172a49b7aa9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-22 (Fri, 22 Dec 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/nls/fr/locale.js Log Message: ----------- Build client. Compare: https://github.com/galaxyproject/galaxy/compare/87b2540a5f46...7eea95c4917f

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[galaxyproject/galaxy] 27c22d: Removal of self, usage of fatarrow this
by GitHub 21 Dec '17

21 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27c22d8c7efe9833941d180df6a8b64242a0c873 https://github.com/galaxyproject/galaxy/commit/27c22d8c7efe9833941d180df6a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Removal of self, usage of fatarrow this Commit: 79dd0b548d46b9c28970f4fd70f793517a644749 https://github.com/galaxyproject/galaxy/commit/79dd0b548d46b9c28970f4fd70f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix workflow list showInToolPanel toggling to use a success callback for reload. Currently this is unsable in firefox, because the reload happens immediately before the request gets sent async. Commit: d7b90684968f5e1e8c98f4f0b69f2d75bba4dd80 https://github.com/galaxyproject/galaxy/commit/d7b90684968f5e1e8c98f4f0b69f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Variable scoping in workflow.js Commit: 0eeb09545faa035eaa067470f9e5f17985abcb75 https://github.com/galaxyproject/galaxy/commit/0eeb09545faa035eaa067470f9e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-21 (Thu, 21 Dec 2017) Changed paths: M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.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/data.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/nls/zh/locale.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M config/galaxy.ini.sample M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/router.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/nls/zh/locale.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/style/blue/base.css M static/style/blue/library.css M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/group/index.mako M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_tools.py M test/base/populators.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into workflow_list_fixes Commit: bda49d429feaca23ca3da05154632a26fbdd28a9 https://github.com/galaxyproject/galaxy/commit/bda49d429feaca23ca3da0515463… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-21 (Thu, 21 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Run client-format Commit: 9d4514da780e21ce4487e669248a0165b36f009a https://github.com/galaxyproject/galaxy/commit/9d4514da780e21ce4487e669248a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-21 (Thu, 21 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Build client. Commit: 87b2540a5f46f37f36714acb68e55a45e1c23b3a https://github.com/galaxyproject/galaxy/commit/87b2540a5f46f37f36714acb68e5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-22 (Fri, 22 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge pull request #5234 from dannon/workflow_list_fixes Workflow list show-in-tool-panel callback bugfix. Compare: https://github.com/galaxyproject/galaxy/compare/0bf73e4381d9...87b2540a5f46

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[galaxyproject/galaxy] 895e99: More upload configuration options testing - this t...
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 895e9971cb0e9c489a23e8197f868bc199443289 https://github.com/galaxyproject/galaxy/commit/895e9971cb0e9c489a23e8197f86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_tools.py M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- More upload configuration options testing - this time for libraries. Commit: ee297f0299d68c840028f283743c8e74732b8ba4 https://github.com/galaxyproject/galaxy/commit/ee297f0299d68c840028f283743c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/actions/library.py Log Message: ----------- Fix server dir uploads - this required method was dropped in #4908. Commit: f4442ffc807285a96fa049f9a7e961b5e945bbff https://github.com/galaxyproject/galaxy/commit/f4442ffc807285a96fa049f9a7e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Small tweaks toward more modern library API. - Use exception-aware API decorators for library contents API endpoints. - Throw exceptions to handle permission and parameter errors for library upload paths with reusable validation functions. - Re-arrange code to avoid working with empty paths and throw better configuration not allow exceptions. Commit: 0bf73e4381d959284c694b3509f2137666f3eb8b https://github.com/galaxyproject/galaxy/commit/0bf73e4381d959284c694b3509f2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/webapps/galaxy/api/library_contents.py M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_tools.py M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Merge pull request #5209 from jmchilton/library_upload_testing Library Upload Refactoring, Testing, and Fixes Compare: https://github.com/galaxyproject/galaxy/compare/63e2964c2e16...0bf73e4381d9

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[galaxyproject/galaxy] d97a74: #5187
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d97a74e9783863270697ab9a329f7dc247df1e37 https://github.com/galaxyproject/galaxy/commit/d97a74e9783863270697ab9a329f… Author: NCEichner <norbert.eichner(a)ur.de> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- #5187 In order to get rid of the conda error described in #5187 I raised the version number beginning from which conda is allowed to use the '--offline' parameter again to "4.4" Commit: 63e2964c2e161baf268a848e0abb8d2b35f3858b https://github.com/galaxyproject/galaxy/commit/63e2964c2e161baf268a848e0abb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5233 from NCEichner/#5187 #5187: altered conda version number for using '--offline' option again Compare: https://github.com/galaxyproject/galaxy/compare/b3a8f5f54b74...63e2964c2e16

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[galaxyproject/galaxy] 49f0cf: remove dead code, the object is always nonempty
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49f0cf86f05d161be9614258bdee80916444524a https://github.com/galaxyproject/galaxy/commit/49f0cf86f05d161be9614258bdee… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/layout/router.js Log Message: ----------- remove dead code, the object is always nonempty Commit: e6215dd495649e2255d0d72115eb47bcd11706a9 https://github.com/galaxyproject/galaxy/commit/e6215dd495649e2255d0d72115eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/layout/router.js Log Message: ----------- Build client. Commit: b3a8f5f54b7433bc1fcc6578f928db2e02c1c254 https://github.com/galaxyproject/galaxy/commit/b3a8f5f54b7433bc1fcc6578f928… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/layout/router.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/layout/router.js Log Message: ----------- Merge branch 'router-mods' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7eae6bf06185...b3a8f5f54b74

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[galaxyproject/galaxy] 71380d: Add chinese support
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71380da4cf9d2da114487b6567f29b6612d20c05 https://github.com/galaxyproject/galaxy/commit/71380da4cf9d2da114487b6567f2… Author: steven <ishenweiyan(a)qq.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Add chinese support Add simplified chinese support Commit: c89967f9a4a1322dd7ea85956be6264058779937 https://github.com/galaxyproject/galaxy/commit/c89967f9a4a1322dd7ea85956be6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Client-format (TODO: Set this up as a build pipeline using .po's as the canonical source, building to these bundles...) Commit: 1b301ba604723e36530d323c79d5378516e95d0c https://github.com/galaxyproject/galaxy/commit/1b301ba604723e36530d323c79d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/nls/zh/locale.js Log Message: ----------- Build client Commit: 7eae6bf06185164f1a9184bd45a48badd45882af https://github.com/galaxyproject/galaxy/commit/7eae6bf06185164f1a9184bd45a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js M static/scripts/bundled/libs.bundled.js M static/scripts/nls/zh/locale.js Log Message: ----------- Merge branch 'patch-1' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ee6512ee8a59...7eae6bf06185

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[galaxyproject/galaxy] d42eef: convert to arrow functions, eliminate self and tha...
by GitHub 20 Dec '17

20 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d42eef992df528f1591d6513a68a13f53171f954 https://github.com/galaxyproject/galaxy/commit/d42eef992df528f1591d6513a68a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- convert to arrow functions, eliminate self and that Commit: e8e12a6026289420757488bd72e726aedea87bbd https://github.com/galaxyproject/galaxy/commit/e8e12a6026289420757488bd72e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/style/less/library.less M static/style/blue/library.css Log Message: ----------- remove styles for the removed old library interface Commit: 96565e9b84cc064ab717580b143bacd8672b2e70 https://github.com/galaxyproject/galaxy/commit/96565e9b84cc064ab717580b143b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/style/blue/library.css M test/galaxy_selenium/navigation.yml Log Message: ----------- wip on importing from library to history as a collection + various es6 additions; cleanup; refactoring I tried to separate it into more commits but it kept growing too fast, sorry Commit: 88d9c669d06f5503f8337ce4d187ed83a6295ab9 https://github.com/galaxyproject/galaxy/commit/88d9c669d06f5503f8337ce4d187… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- implement support for paired and list:paired collections Commit: e344de3660a02501467fd769883cc17d359b8223 https://github.com/galaxyproject/galaxy/commit/e344de3660a02501467fd769883c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- finish the list:paired modal invocation Commit: 2f90fd87663924f39d6c264e45c66ebb80bd3bf0 https://github.com/galaxyproject/galaxy/commit/2f90fd87663924f39d6c264e45c6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- re enable and enhance the collection validator Commit: 2dfdbb645bebf4834606e8534181970a79508bb0 https://github.com/galaxyproject/galaxy/commit/2dfdbb645bebf4834606e8534181… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js Log Message: ----------- refactor modal to bind closing event at different time this allows chaining modals after each other with closing events working Commit: e4d0788a28da6f2007de700dae3f35400f7abdb0 https://github.com/galaxyproject/galaxy/commit/e4d0788a28da6f2007de700dae3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py Log Message: ----------- Improvements to library testing. - Add tests for creating a collection from a library. - Add more class names to library GUI to improve selectors for tests. - Automatically select whichever radio box makes sense in library collection builder dialog based on whether there is a selection or not. Commit: d0a9d6619d1970a6de9b2c5567f0a927d16bcded https://github.com/galaxyproject/galaxy/commit/d0a9d6619d1970a6de9b2c5567f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- hide source items by default in all library-collection creators Commit: d806cf7b3776f048b97fd7254a37c4a763894579 https://github.com/galaxyproject/galaxy/commit/d806cf7b3776f048b97fd7254a37… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #26 from jmchilton/lib-to-colllection Improvements to library testing. Commit: fb256b7aa330e43feae5a27aff72bd0b82661a21 https://github.com/galaxyproject/galaxy/commit/fb256b7aa330e43feae5a27aff72… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js Log Message: ----------- fix the modal backdrop listener to respect the config Commit: 498de3e830220556a838f71a20505b6d58794a31 https://github.com/galaxyproject/galaxy/commit/498de3e830220556a838f71a2050… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the selenium test that expects the class to be here Commit: 00e31c13f516206ff979cc0798d2dd69f044495c https://github.com/galaxyproject/galaxy/commit/00e31c13f516206ff979cc0798d2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix more selenium library tests. Commit: 9dda0ed3f117a3b29c6962713efb6543e2b30e0d https://github.com/galaxyproject/galaxy/commit/9dda0ed3f117a3b29c6962713efb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/history.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M config/galaxy.ini.sample M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/util/path/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M static/style/blue/base.css M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into lib-to-colllection Commit: 9a14f7c835bbfdb013a5860eac41e8064bc2570b https://github.com/galaxyproject/galaxy/commit/9a14f7c835bbfdb013a5860eac41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/galaxy.library.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-modal.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Rebuild client. Commit: ee6512ee8a592a4ab44c0827bff8ee04949a7b2d https://github.com/galaxyproject/galaxy/commit/ee6512ee8a592a4ab44c0827bff8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.library.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/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/style/less/library.less M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/galaxy.library.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-modal.js M static/style/blue/base.css M static/style/blue/library.css M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #5080 from martenson/lib-to-colllection Libraries to collections Compare: https://github.com/galaxyproject/galaxy/compare/77d77a935fa0...ee6512ee8a59

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[galaxyproject/galaxy] e6b650: Pages entrypoint; eliminate require.
by GitHub 19 Dec '17

19 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e6b650b6b872d50c9b2a57a9d31fed7b6b110d3d https://github.com/galaxyproject/galaxy/commit/e6b650b6b872d50c9b2a57a9d31f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.pages.js M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Pages entrypoint; eliminate require. Commit: 81bfe11fbd3ce51ae3e2d01a16620c58211c6799 https://github.com/galaxyproject/galaxy/commit/81bfe11fbd3ce51ae3e2d01a1662… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js Log Message: ----------- WYM needs this global space, this fixes the loaders in a better way (for us) than the export loaders. Compatibility fix for the ~8 year old wymeditor. We should look into newer options. Commit: 7722a2151ae6f0b1910aaf9670de6efce65c9c5e https://github.com/galaxyproject/galaxy/commit/7722a2151ae6f0b1910aaf9670de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/phyloviz.mako Log Message: ----------- Convert phyloviz loading to bundle instead of require. Commit: d8bbeae47313eb37a97f8fe301c46f182120e65e https://github.com/galaxyproject/galaxy/commit/d8bbeae47313eb37a97f8fe301c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/dataset/tabular_chunked.mako Log Message: ----------- Bundle and use createTabularDatasetChunkedView entrypoint. Commit: 00770e28090125595a0f21332be775f2672af438 https://github.com/galaxyproject/galaxy/commit/00770e28090125595a0f21332be7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- History multiview bundle/entry. Commit: 5f514d44a551d0a3521cca4345788a8da390191e https://github.com/galaxyproject/galaxy/commit/5f514d44a551d0a3521cca434578… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/view.mako Log Message: ----------- History view and view-edit bundling into extended UI. Refactored some of the bootstrapping. We really need a Galaxy singleton for logging/etc. Commit: fc37c728e9ac7eecc652fe4fe085d1090db60f03 https://github.com/galaxyproject/galaxy/commit/fc37c728e9ac7eecc652fe4fe085… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Temporary-ish fix for logging in extended bundle (add logging to whatever Galaxy object exists on the window) Commit: d795bc229bd3f76ea2b1b5737067b474e5f55b87 https://github.com/galaxyproject/galaxy/commit/d795bc229bd3f76ea2b1b5737067… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Only strap in logging when it's not already there. Commit: 32537e136e5bec6651004c5594dc67ecf51fce35 https://github.com/galaxyproject/galaxy/commit/32537e136e5bec6651004c5594dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/galaxy/dataset/display.mako Log Message: ----------- Use bundles for dataset/display; we really probably want to get rid of dataset/display_by_username_and_slug, because 1) there is no slug, and 2) username isn't used... Commit: 4c54c9dfb99e3b9f7d8f972554fbd022852d836e https://github.com/galaxyproject/galaxy/commit/4c54c9dfb99e3b9f7d8f972554fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam M lib/galaxy/visualization/data_providers/genome.py M static/scripts/bundled/extended.bundled.js A static/scripts/libs/bibtex.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into require_elimination Commit: f5dad8810fcca9fba5e8965d82555a6a4c4031e4 https://github.com/galaxyproject/galaxy/commit/f5dad8810fcca9fba5e8965d8255… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Trackster globals, argh. Needs more refactoring, but I'd like to get it working again first. Commit: f440586738284dba5ccee86ee9668368a1e45395 https://github.com/galaxyproject/galaxy/commit/f440586738284dba5ccee86ee966… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Fix circster loading error> Commit: 7f107e8e8b318db89e9fcbd94cc0c8816086cc28 https://github.com/galaxyproject/galaxy/commit/7f107e8e8b318db89e9fcbd94cc0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Swap to default d3 for circster. Commit: 4d6ab294339924b3930673e914929ddd6247442d https://github.com/galaxyproject/galaxy/commit/4d6ab294339924b3930673e91492… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Fix d3 event handling in circster. Commit: 55afdb1b25437dfb033367caf0f50604b6a63137 https://github.com/galaxyproject/galaxy/commit/55afdb1b25437dfb033367caf0f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Attach toplevel or global viz stuff to window (force_left_panel, force_right_panel, galaxy_config). Commit: 3543cd31748c3a4906e71dfcf339597d11041b4c https://github.com/galaxyproject/galaxy/commit/3543cd31748c3a4906e71dfcf339… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Embedded page entrypoints, bundling. Commit: 30f98eac21fc838ab4ba4cf0e007223fce1872c6 https://github.com/galaxyproject/galaxy/commit/30f98eac21fc838ab4ba4cf0e007… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Formatting in workflow canvas and trackster Commit: 993c0b7341ab2f1515d727b0b3c44b7fbf8e4b75 https://github.com/galaxyproject/galaxy/commit/993c0b7341ab2f1515d727b0b3c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/embed.mako Log Message: ----------- More bundling, always bundling. Commit: e69c047bd8e1df1d6cbb178b3de8488600aa076f https://github.com/galaxyproject/galaxy/commit/e69c047bd8e1df1d6cbb178b3de8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/display.mako Log Message: ----------- Trackster external display bundling. Commit: b9862425acbed31c905448c76573d266ba7cb28b https://github.com/galaxyproject/galaxy/commit/b9862425acbed31c905448c76573… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M templates/display_common.mako Log Message: ----------- Remove SampleDataset and RequestType references from display_common; this prevents any use of this mako currently. Commit: a3b25a345f02a4dab99e57e93549ea21e3c1a563 https://github.com/galaxyproject/galaxy/commit/a3b25a345f02a4dab99e57e93549… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- More request type cruft; seems to be unused and it'd blow up if tried to use Commit: f02895705d2bd171e3f51a34928e050f4563e87b https://github.com/galaxyproject/galaxy/commit/f02895705d2bd171e3f51a34928e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Bundle sweepster. Commit: d31868ad32bb237f4f72c4e2b10d75fa69b0913a https://github.com/galaxyproject/galaxy/commit/d31868ad32bb237f4f72c4e2b10d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M templates/webapps/galaxy/history/display.mako Log Message: ----------- History display mako swapped to use existing bundled javascript. Commit: 2e59e92a0b0f888c709695d130a1643d68ab3492 https://github.com/galaxyproject/galaxy/commit/2e59e92a0b0f888c709695d130a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/structure.mako Log Message: ----------- Bundle structure view (still has a bug, but that's not new) Commit: 2d2726456c1377f12faeb5ab389ae1c6bd9b0a54 https://github.com/galaxyproject/galaxy/commit/2d2726456c1377f12faeb5ab389a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Bundle history structure view. Commit: 560b2e0b963e697c51fbf90fce8446d724d7484c https://github.com/galaxyproject/galaxy/commit/560b2e0b963e697c51fbf90fce84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/galaxy_client_app.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Package GalaxyApp in extended bundle for bootstrapping outside the primary entrypoints; TODO: Refactor this to be import-based and keep a singleton Commit: ed274a7ca562ad170d86aa2f21748693c8a54e46 https://github.com/galaxyproject/galaxy/commit/ed274a7ca562ad170d86aa2f2174… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: R .ci/py3_sources.txt M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-list.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/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js M client/gulpfile.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/openid/providers.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/permutations.py M lib/galaxy/util/script.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.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/toolshed.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/async.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/admin.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/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.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/grids/util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py R openid/yahoo.xml M scripts/build_universe_config.py M scripts/data_libraries/build_lucene_index.py M scripts/galaxy-main M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js R static/scripts/libs/bibtex.js R static/scripts/libs/vue.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/user/user-preferences.js A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js M static/scripts/viz/trackster.js M static/scripts/viz/visualization.js M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/common/select_template.mako R templates/common/template_common.mako R templates/form.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into require_elimination Commit: a4899ae9b32ea081bac02dbc7e4b93c64ae6c6f6 https://github.com/galaxyproject/galaxy/commit/a4899ae9b32ea081bac02dbc7e4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M templates/base.mako M templates/base/base_panels.mako M templates/webapps/galaxy/base_panels.mako Log Message: ----------- Some bundle import reorg in old-style 'base' templates; we basically always want to load the bundle entrypoints here. Commit: e2e271d81a23d9c8a0db716f3f2d6f3d198f0bb2 https://github.com/galaxyproject/galaxy/commit/e2e271d81a23d9c8a0db716f3f2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M templates/legacy/grid_base.mako Log Message: ----------- Use bundle entrypoint for legacy grid_base Commit: 38ecceb4c5ba877658b28cce8523afa5d7bc9b29 https://github.com/galaxyproject/galaxy/commit/38ecceb4c5ba877658b28cce8523… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Expose LegacyGridView via extended application bundle. Commit: 8e650ff29bb98f347439c6e808ea919ea974b5c7 https://github.com/galaxyproject/galaxy/commit/8e650ff29bb98f347439c6e808ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Remove unused dependencies from ui-select-library Commit: 90ea47e1dae07ab7a9ddd3f0477c57d552660be5 https://github.com/galaxyproject/galaxy/commit/90ea47e1dae07ab7a9ddd3f0477c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Slight logic clarification in ui-select-library. Commit: 1b39f2d1311cc86164818bc86524a039ead85a28 https://github.com/galaxyproject/galaxy/commit/1b39f2d1311cc86164818bc86524… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/galaxy.js Log Message: ----------- Add a temporary workaround for Galaxy not being accessible at static build time Commit: 4ef30c89f43a8d266fc575fda64c8e8573aa7cbf https://github.com/galaxyproject/galaxy/commit/4ef30c89f43a8d266fc575fda64c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-15 (Fri, 15 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js Log Message: ----------- Remove unused dependencies from dataset/data.js Commit: 3f1f1727c63c682ff959e5e5ee2f32f92e52fe31 https://github.com/galaxyproject/galaxy/commit/3f1f1727c63c682ff959e5e5ee2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M templates/webapps/reports/run_stats.mako Log Message: ----------- Swap reports run_stats to extended bundle entrypoint. Commit: 9290a7e5c3cc7b20dd51a655838a3af234b7b700 https://github.com/galaxyproject/galaxy/commit/9290a7e5c3cc7b20dd51a655838a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js Log Message: ----------- Drop debug statement Commit: ddc5f90907094e5b5ebb5bfc41144c2a168b8acc https://github.com/galaxyproject/galaxy/commit/ddc5f90907094e5b5ebb5bfc4114… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/mvc/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js Log Message: ----------- Merge builds gxy/shed Commit: 759014e15e2a5a383c8f280c18eba4554b3e7a1d https://github.com/galaxyproject/galaxy/commit/759014e15e2a5a383c8f280c18eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/GruntFile.js R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js Log Message: ----------- Consolidate to the one grunt task. Commit: db1f00fa3cf8ab65d37af776b72e46b70940ee3f https://github.com/galaxyproject/galaxy/commit/db1f00fa3cf8ab65d37af776b72e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/mvc/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- Format toolshed js Commit: 426884284508f6ca949469cec06755d61631647d https://github.com/galaxyproject/galaxy/commit/426884284508f6ca949469cec067… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js R client/galaxy/scripts/toolshed/mvc/groups/group-detail-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-list-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-listrow-view.js R client/galaxy/scripts/toolshed/mvc/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Lots of incremental toolshed js/ groups refactoring, bundling. Commit: 1159c342280a82a804c2192fdd58e11095108f34 https://github.com/galaxyproject/galaxy/commit/1159c342280a82a804c2192fdd58… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/groups/group-model.js M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- More incremental es6'ing of toolshed client code. Commit: bfb2d049a1a22c474337ca5a614220f5f7d31f93 https://github.com/galaxyproject/galaxy/commit/bfb2d049a1a22c474337ca5a6142… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/toolshed.groups.js Log Message: ----------- Remove unused group-model import. Commit: 17e074068ac7c8fff25334ac555a8ff9984ffa6b https://github.com/galaxyproject/galaxy/commit/17e074068ac7c8fff25334ac555a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/groups/group-listrow-view.js M client/galaxy/scripts/toolshed/groups/group-model.js Log Message: ----------- Toolshed client refactoring, fixing, etc. Commit: d79b5fff559e029a33180ab214699def343aa86b https://github.com/galaxyproject/galaxy/commit/d79b5fff559e029a33180ab21469… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/toolshed/toolshed.groups.js M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Toolshed groups actually work now. Commit: c0eb0fadd8ebd8773d8be743d41667c16700074e https://github.com/galaxyproject/galaxy/commit/c0eb0fadd8ebd8773d8be743d416… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M client/README.md Log Message: ----------- Remove toolshed build info (part of the standard client build now) Commit: c2b709ae1c5d270f8d671b6ff8892b9aa1fc31ba https://github.com/galaxyproject/galaxy/commit/c2b709ae1c5d270f8d671b6ff889… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M templates/webapps/galaxy/history/structure.mako Log Message: ----------- Old debug cruft removal in structure.mako Commit: 648d4bd5d34ea81bd55e1239c8aea47d112ba9fe https://github.com/galaxyproject/galaxy/commit/648d4bd5d34ea81bd55e1239c8ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js Log Message: ----------- Toolshed artifacts initial commit (hopefully we don't do this much more...) Commit: 20fa0e73f2aace2bc872cd49137f4cc23fa8f5d0 https://github.com/galaxyproject/galaxy/commit/20fa0e73f2aace2bc872cd49137f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js Log Message: ----------- Build client, including toolshed. Commit: e589f1e8bd5b575aaea7992a8769322d722ffe75 https://github.com/galaxyproject/galaxy/commit/e589f1e8bd5b575aaea7992a8769… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-18 (Mon, 18 Dec 2017) Changed paths: R static/scripts/bundled/adminToolshed.bundled.js R static/scripts/bundled/library.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js Log Message: ----------- Remove old, unused bundles. Commit: 77d77a935fa0b4f4c7476e871189a5fb8ecbe54f https://github.com/galaxyproject/galaxy/commit/77d77a935fa0b4f4c7476e871189… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.pages.js M static/scripts/libs/jquery/jquery.wymeditor.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M templates/base.mako M templates/base/base_panels.mako M templates/galaxy_client_app.mako M templates/legacy/grid_base.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/group/index.mako Log Message: ----------- Merge branch 'require_elimination' into dev Compare: https://github.com/galaxyproject/galaxy/compare/62a3a5c5968c...77d77a935fa0

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