Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33a74cae2def618e9fe32d1a8b1355d00a39a525 https://github.com/galaxyproject/galaxy/commit/33a74cae2def618e9fe32d1a8b135... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix hotdata method access; this still needs a lot of love/refactoring, but this makes it work again? Commit: a64a5cdc5e1ace5981452026c4aa2857fbfd729b https://github.com/galaxyproject/galaxy/commit/a64a5cdc5e1ace5981452026c4aa2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Prefer const, none of these are reassigned. Commit: 3c9f263c69c657f8a644fceb778a7ff36c888d0a https://github.com/galaxyproject/galaxy/commit/3c9f263c69c657f8a644fceb778a7... Author: Mason <nerdinacan@gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Restored hotData to computed, but removed unnecessary side-effects Commit: 205cdd0954ffdf34efc2c364ec1b62079e4a27d8 https://github.com/galaxyproject/galaxy/commit/205cdd0954ffdf34efc2c364ec1b6... Author: Mason <nerdinacan@gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Removed slice method on non-array property Commit: 569ea9ea36e15afcbd174b50ae2de79029c4bc0a https://github.com/galaxyproject/galaxy/commit/569ea9ea36e15afcbd174b50ae2de... Author: Mason <nerdinacan@gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Removed commented code in RuleCollectionBuilder Commit: f729dab31312d1be5ef2226d533d4ad26fb25130 https://github.com/galaxyproject/galaxy/commit/f729dab31312d1be5ef2226d533d4... Author: Mason <nerdinacan@gmail.com> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: R client/.babelrc M client/galaxy/scripts/bundleEntries.js A client/galaxy/scripts/components/Tags/GalaxyTags.test.js A client/galaxy/scripts/components/Tags/GalaxyTags.vue A client/galaxy/scripts/components/Tags/StandardTags.test.js A client/galaxy/scripts/components/Tags/StandardTags.vue A client/galaxy/scripts/components/Tags/autocomplete_tagging.scss A client/galaxy/scripts/components/Tags/index.js A client/galaxy/scripts/components/Tags/inits.js A client/galaxy/scripts/components/Tags/model.js A client/galaxy/scripts/components/Tags/model.test.js A client/galaxy/scripts/components/Tags/tagService.js A client/galaxy/scripts/components/Tags/tagService.test.js A client/galaxy/scripts/components/Tags/tagStyles.scss A client/galaxy/scripts/components/Tags/testData/autocompleteResponse.txt M client/galaxy/scripts/entry/analysis/AnalysisRouter.js M client/galaxy/scripts/mvc/grid/grid-view.js R client/galaxy/scripts/sample.test.js A client/galaxy/scripts/store/gridSearchStore.js A client/galaxy/scripts/store/index.js R client/galaxy/scripts/ui/autocom_tagging.js R client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/mountVueComponent.js A client/galaxy/scripts/utils/redirect.js M client/galaxy/scripts/viz/trackster.js R client/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/mixins.scss M client/karma/karma.config.mocha.js M client/karma/karma.config.qunit.js M client/karma/webpack.config.unittest.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/reports/framework/grids.py M templates/tagging_common.mako M templates/webapps/galaxy/workflow/editor.mako M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Tagging component Commit: f138022a163475e14347e9665facbaa3222efef9 https://github.com/galaxyproject/galaxy/commit/f138022a163475e14347e9665facb... Author: Mason <nerdinacan@gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M client/karma/karma.config.mocha.js Log Message: ----------- Re-enable old mocha tests Commit: 2389b4dab241eade87fd60bd7792e3d38189c9aa https://github.com/galaxyproject/galaxy/commit/2389b4dab241eade87fd60bd7792e... Author: Mason <nerdinacan@gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M templates/tagging_common.mako Log Message: ----------- Removed unused import in tagging_common Commit: 787740561f19c90fa6b7032af6a7820eaee75187 https://github.com/galaxyproject/galaxy/commit/787740561f19c90fa6b7032af6a78... Author: Mason <nerdinacan@gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M config/galaxy.yml.sample M config/tool_shed.yml.sample M cron/add_manual_builds.py M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/config.rst M doc/source/admin/galaxy_options.rst R doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.web.framework.rst M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/datatypes/isa.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/__init__.py M lib/galaxy/util/filelock.py M lib/galaxy/util/hash_util.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/workflow/modules.py M run_tests.sh M templates/user/logout.mako M templates/webapps/galaxy/workflow/display.mako M test/api/test_histories.py M test/api/test_workflows.py M test/functional/test_toolbox.py M test/unit/test_utils.py M tools/filters/sff_extract.py M tools/maf/maf_to_bed.py M tools/phenotype_association/senatag.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into tagging_component_3 Commit: 8a6b0a1cd260d2c91b4a4f8f689de5ae8d24e940 https://github.com/galaxyproject/galaxy/commit/8a6b0a1cd260d2c91b4a4f8f689de... Author: Mason <nerdinacan@gmail.com> Date: 2019-02-02 (Sat, 02 Feb 2019) Changed paths: M client/galaxy/scripts/components/Tags/GalaxyTags.test.js M client/galaxy/scripts/components/Tags/GalaxyTags.vue M client/galaxy/scripts/components/Tags/StandardTags.test.js M client/galaxy/scripts/components/Tags/StandardTags.vue M client/galaxy/scripts/utils/mountVueComponent.js Log Message: ----------- Added localize filter and fixed optional hooks for GalaxyTags Commit: c33cd1665d3bfed2dd75086735a01b55f38d44bd https://github.com/galaxyproject/galaxy/commit/c33cd1665d3bfed2dd75086735a01... Author: Mason <nerdinacan@gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/datatypes_conf.xml.sample M config/job_conf.xml.sample_advanced M doc/Makefile M doc/source/admin/apache.md M doc/source/admin/config_logging.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md M lib/galaxy/datatypes/sniff.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/xml_util.py M scripts/check_python.py M templates/webapps/tool_shed/common/common.mako M test/api/test_workflows.py M test/galaxy_selenium/cli.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/workflows/test_modules.py M test/unit/workflows/workflow_support.py M tool-data/intermine_simple_display.loc.sample M tox.ini Log Message: ----------- Merge branch 'dev' into tagging_component_3 Commit: c89f6ef5764d26191ae4b30a2faef8c1776e65d9 https://github.com/galaxyproject/galaxy/commit/c89f6ef5764d26191ae4b30a2faef... Author: Mason <nerdinacan@gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: A client/galaxy/scripts/components/Tags/GalaxyTags.usage.txt M client/galaxy/scripts/components/Tags/GalaxyTags.vue R client/galaxy/scripts/components/Tags/autocomplete_tagging.scss M client/galaxy/scripts/components/Tags/tagStyles.scss M client/galaxy/scripts/store/index.js M client/galaxy/scripts/viz/trackster.js A client/galaxy/style/scss/autocomplete_tagging.scss Log Message: ----------- Minor refinements of main galaxy tags component Commit: 410513e4e3fba93cb5634cc8a6d1d99366f129f8 https://github.com/galaxyproject/galaxy/commit/410513e4e3fba93cb5634cc8a6d1d... Author: Mason <nerdinacan@gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M client/galaxy/scripts/components/Tags/StandardTags.vue M templates/tagging_common.mako Log Message: ----------- Disabled editing for community tags display, fixed tag loading in mako, removed redundant component styles Commit: d6836c5998d0d63156fd9043cf3a714d8718aa27 https://github.com/galaxyproject/galaxy/commit/d6836c5998d0d63156fd9043cf3a7... Author: Mason <nerdinacan@gmail.com> Date: 2019-02-18 (Mon, 18 Feb 2019) Changed paths: M client/galaxy/scripts/components/Tags/GalaxyTags.vue R client/galaxy/scripts/components/Tags/tagStyles.scss Log Message: ----------- Linked single-use styles directly into component Commit: 84d5d9dd87db423dd195818af0d82f15c46d943c https://github.com/galaxyproject/galaxy/commit/84d5d9dd87db423dd195818af0d82... 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client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload/initQueue.js M client/galaxy/scripts/ui/popupmenu.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/reports.yml.sample M config/tool_shed.yml.sample M doc/Makefile R doc/fix_schema_rst.sh M doc/parse_gx_xsd.py M doc/source/admin/apache.md M doc/source/admin/cluster.md M doc/source/admin/config.rst M 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lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py A lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/tools/tool_validator.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 scripts/common_startup.sh M templates/display_common.mako R templates/user/index.mako R templates/user/logout.mako R templates/user/register.mako M templates/webapps/tool_shed/user/login.mako A templates/webapps/tool_shed/user/logout.mako A templates/webapps/tool_shed/user/register.mako A test-data/groupby_out1.dat A test-data/groupby_out2.dat A test-data/groupby_out3.tabular A test-data/groupby_out4.tabular A test-data/matrix.cool M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_users.py M test/base/api.py M test/base/integration_util.py M test/functional/tools/output_filter.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/integration/test_containerized_jobs.py M test/integration/test_job_recovery.py A test/integration/test_kubernetes_runner.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_registration.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_toolbox_filters.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/upload.py M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge branch 'dev' into tagging_component_3 Commit: 4af2bdeaef3d493b7c55f46445aeabff720b1b1e https://github.com/galaxyproject/galaxy/commit/4af2bdeaef3d493b7c55f46445aea... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M client/galaxy/scripts/components/Tags/GalaxyTags.test.js M client/galaxy/scripts/components/Tags/GalaxyTags.vue M client/galaxy/scripts/components/Tags/StandardTags.test.js M client/galaxy/scripts/components/Tags/StandardTags.vue M client/galaxy/scripts/components/Tags/model.js M client/galaxy/scripts/components/Tags/model.test.js M client/galaxy/scripts/components/Tags/tagService.js M client/galaxy/scripts/components/Tags/tagService.test.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/store/gridSearchStore.js M client/galaxy/scripts/utils/mountVueComponent.js M client/galaxy/scripts/utils/redirect.js Log Message: ----------- Client format. Commit: 8828fec5ee2aa9506a0475f33049255c48d02883 https://github.com/galaxyproject/galaxy/commit/8828fec5ee2aa9506a0475f330492... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M client/webpack.config.js Log Message: ----------- Drop vue resolver alias, use default package entrypoint. Commit: 4e2de8facb252214902aac70f60aaefca8309e78 https://github.com/galaxyproject/galaxy/commit/4e2de8facb252214902aac70f60aa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M client/galaxy/scripts/bundleEntries.js M client/webpack.config.js Log Message: ----------- future-proof store alias used in old code Commit: 4ec49c1197e42fe2ac71a4d973955c26d3072452 https://github.com/galaxyproject/galaxy/commit/4ec49c1197e42fe2ac71a4d973955... Author: Dannon <dannon.baker@gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: R client/.babelrc M client/galaxy/scripts/bundleEntries.js A client/galaxy/scripts/components/Tags/GalaxyTags.test.js A client/galaxy/scripts/components/Tags/GalaxyTags.usage.txt A client/galaxy/scripts/components/Tags/GalaxyTags.vue A client/galaxy/scripts/components/Tags/StandardTags.test.js A client/galaxy/scripts/components/Tags/StandardTags.vue A client/galaxy/scripts/components/Tags/index.js A client/galaxy/scripts/components/Tags/inits.js A client/galaxy/scripts/components/Tags/model.js A client/galaxy/scripts/components/Tags/model.test.js A client/galaxy/scripts/components/Tags/tagService.js A client/galaxy/scripts/components/Tags/tagService.test.js A client/galaxy/scripts/components/Tags/testData/autocompleteResponse.txt M client/galaxy/scripts/entry/analysis/AnalysisRouter.js M client/galaxy/scripts/mvc/grid/grid-view.js R client/galaxy/scripts/sample.test.js A client/galaxy/scripts/store/gridSearchStore.js A client/galaxy/scripts/store/index.js R client/galaxy/scripts/ui/autocom_tagging.js R client/galaxy/scripts/unitTestBundle.js M client/galaxy/scripts/utils/mock.js A client/galaxy/scripts/utils/mountVueComponent.js A client/galaxy/scripts/utils/redirect.js M client/galaxy/style/scss/base.scss A client/galaxy/style/scss/mixins.scss M client/karma/karma.config.mocha.js M client/karma/karma.config.qunit.js M client/karma/webpack.config.unittest.js M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/reports/framework/grids.py M templates/tagging_common.mako M templates/webapps/galaxy/workflow/editor.mako M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #7270 from Nerdinacan/tagging_component_3 Tagging component Compare: https://github.com/galaxyproject/galaxy/compare/d3c51d6d29cd...4ec49c1197e4