Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9ad1ba07f8d41ac9be62726a10e9a549c39a58fb https://github.com/galaxyproject/galaxy/commit/9ad1ba07f8d41ac9be62726a10e9a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-21 (Wed, 21 Mar 2018)

Changed paths: M client/gulpfile.js

Log Message: ----------- Gulpfile standardization anticipating merges.

Commit: 2e2ad26addfae8c91395821f75e44749c1aa04b2 https://github.com/galaxyproject/galaxy/commit/2e2ad26addfae8c91395821f75e44... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-22 (Thu, 22 Mar 2018)

Changed paths: A client/deploy.js M client/gulpfile.js M client/package.json M client/yarn.lock

Log Message: ----------- Incremental work testing staging of libs. May dump this, it's awfully slow via gulp and I can do it faster with regular js.

Commit: 7fe49481d7cc37541cc9ec010a871694b5987cfb https://github.com/galaxyproject/galaxy/commit/7fe49481d7cc37541cc9ec010a871... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-22 (Thu, 22 Mar 2018)

Changed paths: M client/gulpfile.js

Log Message: ----------- Try mapping with glob syntax

Commit: 913cd1e6d2e784272ad1b4ebcaab6cb64d464d32 https://github.com/galaxyproject/galaxy/commit/913cd1e6d2e784272ad1b4ebcaab6... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-22 (Thu, 22 Mar 2018)

Changed paths: M .gitignore M client/gulpfile.js

Log Message: ----------- Fix up regex, .gitignore static/plugins

Commit: 8223c36b34dd221bf95ea591b75bb75ecef6d286 https://github.com/galaxyproject/galaxy/commit/8223c36b34dd221bf95ea591b75bb... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)

Changed paths: M client/gulpfile.js

Log Message: ----------- Stage plugin static as a part of the client build

Commit: b147abe9e58d21ee29722cedbdd12c354a6b095b https://github.com/galaxyproject/galaxy/commit/b147abe9e58d21ee29722cedbdd12... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)

Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js

Log Message: ----------- Minor es6'ing in vizview

Commit: 3fbc41af2abb744352c8ebbcf7150ed3ac49b027 https://github.com/galaxyproject/galaxy/commit/3fbc41af2abb744352c8ebbcf7150... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)

Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js

Log Message: ----------- Source viz logos out of /static

Commit: 38080f721b7c6948f80544752644bcc9a5fad362 https://github.com/galaxyproject/galaxy/commit/38080f721b7c6948f80544752644b... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)

Changed paths: M lib/galaxy/visualization/plugins/plugin.py

Log Message: ----------- Fix docstring 'visualization' typo.

Commit: 4764b46bba4f126a6bf72f3a0aee9e210426cb7c https://github.com/galaxyproject/galaxy/commit/4764b46bba4f126a6bf72f3a0aee9... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-26 (Mon, 26 Mar 2018)

Changed paths: R client/deploy.js

Log Message: ----------- Not going to pursue this deploy method, yet -- probably will want to do this later with prod/dev scripts to have more control over the build (over a big chain of package scripts)

Commit: e206af4f6de57a9d668808538892e54554611b5c https://github.com/galaxyproject/galaxy/commit/e206af4f6de57a9d668808538892e... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-26 (Mon, 26 Mar 2018)

Changed paths: M client/package.json M client/yarn.lock

Log Message: ----------- Remove gulp-ignore, unnecessary

Commit: 6875307b2ac84cdb98ebb54a14a3c1ab3a3e6adb https://github.com/galaxyproject/galaxy/commit/6875307b2ac84cdb98ebb54a14a3c... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-26 (Mon, 26 Mar 2018)

Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Drop static framework mapping for plugins; we're going to stage into the existing static paths instead since this method doesn't work in uwsgi

Commit: 4969394a3cce550ea82d7ca7fa69e95c172f56d8 https://github.com/galaxyproject/galaxy/commit/4969394a3cce550ea82d7ca7fa69e... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-26 (Mon, 26 Mar 2018)

Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js M lib/galaxy/visualization/plugins/plugin.py

Log Message: ----------- Static serving of staged logos

Commit: cf2e6dc6d2951f316e9641a05d69a3f919feb05e https://github.com/galaxyproject/galaxy/commit/cf2e6dc6d2951f316e9641a05d69a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-26 (Mon, 26 Mar 2018)

Changed paths: M config/plugins/visualizations/scatterplot/templates/scatterplot.mako

Log Message: ----------- Fix scatterplot as example of mako entrypoint -- this needs to be generalized

Commit: c12feecb76f96fd5fe058d9cf90331e7eb956c5b https://github.com/galaxyproject/galaxy/commit/c12feecb76f96fd5fe058d9cf9033... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-26 (Mon, 26 Mar 2018)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js

Log Message: ----------- Minor linting in ui-thumbnails

Commit: 70915dfc9f2b54bd88ebce92812f4edf578e18d4 https://github.com/galaxyproject/galaxy/commit/70915dfc9f2b54bd88ebce92812f4... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-27 (Tue, 27 Mar 2018)

Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/charts.less M config/galaxy.yml.sample M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M doc/source/admin/galaxy_options.rst M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/util/gff_util.py R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/galaxy-main M static/style/blue/base.css M test/api/test_tools.py M test/base/populators.py M test/docker/base/Dockerfile M test/selenium_tests/framework.py M test/selenium_tests/test_library_to_collections.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tox.ini

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into viz-staging

Commit: f21965472ca94a71466c4ca39e93bff30add229e https://github.com/galaxyproject/galaxy/commit/f21965472ca94a71466c4ca39e93b... Author: guerler aysam.guerler@gmail.com Date: 2018-03-29 (Thu, 29 Mar 2018)

Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.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/history-list.js M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/common_startup.sh M scripts/get_uwsgi_args.py M tox.ini

Log Message: ----------- Merge branch 'dev' into viz-staging-finalize

Commit: f0dde506d043b3d4070ddc0fa2b48dac23e4d645 https://github.com/galaxyproject/galaxy/commit/f0dde506d043b3d4070ddc0fa2b48... Author: guerler aysam.guerler@gmail.com Date: 2018-03-30 (Fri, 30 Mar 2018)

Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Remove unused static url, fix routes in plugins

Commit: e99c8ec65c652f51253155abe73a9b0ce77c2496 https://github.com/galaxyproject/galaxy/commit/e99c8ec65c652f51253155abe73a9... Author: guerler aysam.guerler@gmail.com Date: 2018-03-30 (Fri, 30 Mar 2018)

Changed paths: M lib/galaxy/visualization/plugins/plugin.py

Log Message: ----------- Remove static path mixin

Commit: d288b3baa83018cb9a6a96677ca8fd287d746816 https://github.com/galaxyproject/galaxy/commit/d288b3baa83018cb9a6a96677ca8f... Author: guerler aysam.guerler@gmail.com Date: 2018-03-30 (Fri, 30 Mar 2018)

Changed paths: M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py

Log Message: ----------- Adjust test cases

Commit: f2e5a69629df4dca65e35cf7a431a33874ef51c5 https://github.com/galaxyproject/galaxy/commit/f2e5a69629df4dca65e35cf7a431a... Author: guerler aysam.guerler@gmail.com Date: 2018-03-30 (Fri, 30 Mar 2018)

Changed paths: M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml

Log Message: ----------- Fix unipept and venn viewers

Commit: 075abee7666599a9b8dcf74d38ee5d337c7a85eb https://github.com/galaxyproject/galaxy/commit/075abee7666599a9b8dcf74d38ee5... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-04-06 (Fri, 06 Apr 2018)

Changed paths: M .gitignore M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/gulpfile.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/buildapp.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py

Log Message: ----------- Merge pull request #5810 from guerler/viz-staging-finalize

Plugin directory staging

Compare: https://github.com/galaxyproject/galaxy/compare/a23f0d505761...075abee76665