- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 4b2bf1: Updated snpeff_build to 4.3+T.galaxy2
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4b2bf17590afbbbaa78430fe9411d5cf405c1c0a https://github.com/galaxyproject/usegalaxy-playbook/commit/4b2bf17590afbbba… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated snpeff_build to 4.3+T.galaxy2

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[galaxyproject/galaxy] fefd68: Increase yarn's network timeout
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fefd686b298cd573b49b6fc15d4531ffd3d852d2 https://github.com/galaxyproject/galaxy/commit/fefd686b298cd573b49b6fc15d45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M Makefile Log Message: ----------- Increase yarn's network timeout Commit: ed72b94e1e3a11be8ba5c4f8bd63b93877b32cd9 https://github.com/galaxyproject/galaxy/commit/ed72b94e1e3a11be8ba5c4f8bd63… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M Makefile Log Message: ----------- Merge pull request #5870 from dannon/yarn-network-timeout Increase yarn's network timeout Compare: https://github.com/galaxyproject/galaxy/compare/d9efb4ff4c2c...ed72b94e1e3a

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[galaxyproject/usegalaxy-playbook] 0d77bf: Align images better on welcome
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0d77bf1811d55988caefb841a67bdf463c5110e9 https://github.com/galaxyproject/usegalaxy-playbook/commit/0d77bf1811d55988… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Align images better on welcome

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[galaxyproject/usegalaxy-playbook] a0735a: Warn about downtime for Main next week
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a0735ab8c51411dfdec57e765afdbdafd683c9a9 https://github.com/galaxyproject/usegalaxy-playbook/commit/a0735ab8c51411df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Warn about downtime for Main next week

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[galaxyproject/galaxy] 02e92e: Fix conditional parameter handling for textselect ...
by GitHub 09 Apr '18

09 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 02e92e21155ce19383041477d20c33ea44779f48 https://github.com/galaxyproject/galaxy/commit/02e92e21155ce19383041477d20c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M static/style/blue/base.css Log Message: ----------- Fix conditional parameter handling for textselect field Commit: 54122c15ed351808cde805362d0e47605f88e545 https://github.com/galaxyproject/galaxy/commit/54122c15ed351808cde805362d0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add wait unwait features to select field handler Commit: b184f197475e72038d3b80e4828d1298723f1f68 https://github.com/galaxyproject/galaxy/commit/b184f197475e72038d3b80e4828d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Explicitly specify options parsed to text select wrapper Commit: 4f84b9cacc31c0946d421a01f9729792850c4ae2 https://github.com/galaxyproject/galaxy/commit/4f84b9cacc31c0946d421a01f972… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Assign change handler from select model Commit: d9efb4ff4c2c15f6ebd2d133760ff08fb80a623f https://github.com/galaxyproject/galaxy/commit/d9efb4ff4c2c15f6ebd2d133760f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M static/style/blue/base.css Log Message: ----------- Merge pull request #5864 from guerler/fix_expansion Fix conditional parameter handling Compare: https://github.com/galaxyproject/galaxy/compare/075abee76665...d9efb4ff4c2c

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[galaxyproject/galaxy] 9ad1ba: Gulpfile standardization anticipating merges.
by GitHub 06 Apr '18

06 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9ad1ba07f8d41ac9be62726a10e9a549c39a58fb https://github.com/galaxyproject/galaxy/commit/9ad1ba07f8d41ac9be62726a10e9… Author: Dannon Baker <dannon.baker(a)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/2e2ad26addfae8c91395821f75e4… Author: Dannon Baker <dannon.baker(a)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/7fe49481d7cc37541cc9ec010a87… Author: Dannon Baker <dannon.baker(a)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/913cd1e6d2e784272ad1b4ebcaab… Author: Dannon Baker <dannon.baker(a)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/8223c36b34dd221bf95ea591b75b… Author: Dannon Baker <dannon.baker(a)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/b147abe9e58d21ee29722cedbdd1… Author: Dannon Baker <dannon.baker(a)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/3fbc41af2abb744352c8ebbcf715… Author: Dannon Baker <dannon.baker(a)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/38080f721b7c6948f80544752644… Author: Dannon Baker <dannon.baker(a)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/4764b46bba4f126a6bf72f3a0aee… Author: Dannon Baker <dannon.baker(a)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/e206af4f6de57a9d668808538892… Author: Dannon Baker <dannon.baker(a)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/6875307b2ac84cdb98ebb54a14a3… Author: Dannon Baker <dannon.baker(a)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/4969394a3cce550ea82d7ca7fa69… Author: Dannon Baker <dannon.baker(a)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/cf2e6dc6d2951f316e9641a05d69… Author: Dannon Baker <dannon.baker(a)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/c12feecb76f96fd5fe058d9cf903… Author: Dannon Baker <dannon.baker(a)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/70915dfc9f2b54bd88ebce92812f… Author: Dannon Baker <dannon.baker(a)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/f21965472ca94a71466c4ca39e93… Author: guerler <aysam.guerler(a)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/f0dde506d043b3d4070ddc0fa2b4… Author: guerler <aysam.guerler(a)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/e99c8ec65c652f51253155abe73a… Author: guerler <aysam.guerler(a)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/d288b3baa83018cb9a6a96677ca8… Author: guerler <aysam.guerler(a)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/f2e5a69629df4dca65e35cf7a431… Author: guerler <aysam.guerler(a)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/075abee7666599a9b8dcf74d38ee… Author: Dannon Baker <dannon.baker(a)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

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[galaxyproject/galaxy] 10ea15: Fix missing `from Import Directory` button
by GitHub 06 Apr '18

06 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10ea15079262a41a9e3c895850b111837549c97e https://github.com/galaxyproject/galaxy/commit/10ea15079262a41a9e3c895850b1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Fix missing `from Import Directory` button when `library_import_dir` is set in `config/galaxy.yml`, but `allow_path_paste` is `false`. Reported by @pvanheus. Commit: 1d0c734fcfcfaf54e676c395acdeeab72b16d517 https://github.com/galaxyproject/galaxy/commit/1d0c734fcfcfaf54e676c395acde… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client-production-maps Commit: 68b87a07635f2ca073286fd0efc7d7ad2e6bcda9 https://github.com/galaxyproject/galaxy/commit/68b87a07635f2ca073286fd0efc7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5797 from nsoranzo/release_18.01_fix_import_directory [18.01] Fix missing `from Import Directory` button Commit: a23f0d505761ba713da9484af18e7c10fc6dbed2 https://github.com/galaxyproject/galaxy/commit/a23f0d505761ba713da9484af18e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/58028e1f6dbf...a23f0d505761

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[galaxyproject/galaxy] 10ea15: Fix missing `from Import Directory` button
by GitHub 06 Apr '18

06 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 10ea15079262a41a9e3c895850b111837549c97e https://github.com/galaxyproject/galaxy/commit/10ea15079262a41a9e3c895850b1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Fix missing `from Import Directory` button when `library_import_dir` is set in `config/galaxy.yml`, but `allow_path_paste` is `false`. Reported by @pvanheus. Commit: 1d0c734fcfcfaf54e676c395acdeeab72b16d517 https://github.com/galaxyproject/galaxy/commit/1d0c734fcfcfaf54e676c395acde… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client-production-maps Commit: 68b87a07635f2ca073286fd0efc7d7ad2e6bcda9 https://github.com/galaxyproject/galaxy/commit/68b87a07635f2ca073286fd0efc7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5797 from nsoranzo/release_18.01_fix_import_directory [18.01] Fix missing `from Import Directory` button Compare: https://github.com/galaxyproject/galaxy/compare/009921387dc3...68b87a07635f

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[galaxyproject/usegalaxy-playbook] 7c10aa: Installed snpEff wrapper versions 4.3+T.galaxy1
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7c10aa4f55692b71b0cc1130ad34da1bd2b0492f https://github.com/galaxyproject/usegalaxy-playbook/commit/7c10aa4f55692b71… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed snpEff wrapper versions 4.3+T.galaxy1

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[galaxyproject/galaxy] deda75: Do not append '/' to 'js' in GIE static path, this...
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: deda753de9f6943251cf06bd02b37dae78bac59e https://github.com/galaxyproject/galaxy/commit/deda753de9f6943251cf06bd02b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Do not append '/' to 'js' in GIE static path, this breaks uWSGI static routing. Commit: 58028e1f6dbf0275f08846dc653e94d607079c86 https://github.com/galaxyproject/galaxy/commit/58028e1f6dbf0275f08846dc653e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Merge pull request #5859 from natefoo/gie-slashfix Do not append '/' to 'js' in GIE static path, this breaks uWSGI static routing Compare: https://github.com/galaxyproject/galaxy/compare/1da06ba2b34a...58028e1f6dbf

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[galaxyproject/usegalaxy-playbook] d0c7c3: add warning about bs4 to test
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d0c7c3e2bd9100546b7ba29208d6336de6a9e39d https://github.com/galaxyproject/usegalaxy-playbook/commit/d0c7c3e2bd910054… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- add warning about bs4 to test

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[galaxyproject/usegalaxy-playbook] 1ce855: update Test to run bs4 branch
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1ce855a89a24b639157a56718eb40145c3635bc4 https://github.com/galaxyproject/usegalaxy-playbook/commit/1ce855a89a24b639… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/all.yml Log Message: ----------- update Test to run bs4 branch

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[galaxyproject/usegalaxy-playbook] ccd628: Handle column ordering compatible with both bs3, b...
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ccd62883445dffa84c8a1d7f2c60f92bddd4ec1b https://github.com/galaxyproject/usegalaxy-playbook/commit/ccd62883445dffa8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Handle column ordering compatible with both bs3, bs4

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[galaxyproject/usegalaxy-playbook] 513a35: Update PSU logo, reduce size of OHSU logo.
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 513a352bfe5940cc725d0e112e14252ba43df2fa https://github.com/galaxyproject/usegalaxy-playbook/commit/513a352bfe5940cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/common/files/galaxy/static/welcome_img/ohsu_logo.png M env/common/files/galaxy/static/welcome_img/psu_logo.png Log Message: ----------- Update PSU logo, reduce size of OHSU logo.

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[galaxyproject/usegalaxy-playbook] 169ef8: Swap col-xs-N to col-sm-N for bootstrap4 changes. ...
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 169ef847fb90bf78a2c067358c1981d1db0a2a96 https://github.com/galaxyproject/usegalaxy-playbook/commit/169ef847fb90bf78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Swap col-xs-N to col-sm-N for bootstrap4 changes. Safe to deploy against bs3 as well. Commit: c56cae93d9901f2bfe79c3d86053edf96eed38b6 https://github.com/galaxyproject/usegalaxy-playbook/commit/c56cae93d9901f2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Swap hidden to d-* utilities for bs4 (this one will not work without bs4) Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/7590c6f3a09e...…

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[galaxyproject/usegalaxy-playbook] c56cae: Swap hidden to d-* utilities for bs4 (this one wil...
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/bs4_welcome_tweaks Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c56cae93d9901f2bfe79c3d86053edf96eed38b6 https://github.com/galaxyproject/usegalaxy-playbook/commit/c56cae93d9901f2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Swap hidden to d-* utilities for bs4 (this one will not work without bs4)

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[galaxyproject/usegalaxy-playbook] 169ef8: Swap col-xs-N to col-sm-N for bootstrap4 changes. ...
by GitHub 05 Apr '18

05 Apr '18

Branch: refs/heads/bs4_welcome_tweaks Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 169ef847fb90bf78a2c067358c1981d1db0a2a96 https://github.com/galaxyproject/usegalaxy-playbook/commit/169ef847fb90bf78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Swap col-xs-N to col-sm-N for bootstrap4 changes. Safe to deploy against bs3 as well.

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[galaxyproject/usegalaxy-playbook] 7590c6: Updated mothur suite to version 1.39.5
by GitHub 04 Apr '18

04 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7590c6f3a09e22dbbc8862e14aaeac1c5852f951 https://github.com/galaxyproject/usegalaxy-playbook/commit/7590c6f3a09e22db… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated mothur suite to version 1.39.5

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[galaxyproject/galaxy] 506de0: Skip new script tests in dev branch, they are brea...
by GitHub 04 Apr '18

04 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 506de02ec462d217220a531a8e40c0e02dbedcd7 https://github.com/galaxyproject/galaxy/commit/506de02ec462d217220a531a8e40… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Skip new script tests in dev branch, they are breaking integration suite. Commit: 1da06ba2b34a59ab6ea2dd4f1bd765142b423d63 https://github.com/galaxyproject/galaxy/commit/1da06ba2b34a59ab6ea2dd4f1bd7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5839 from jmchilton/integration_test_fixes Skip new script tests in dev branch, they are breaking integration suite. Compare: https://github.com/galaxyproject/galaxy/compare/fbd5541e4edd...1da06ba2b34a

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[galaxyproject/galaxy] 0043f2: Remove unused template file.
by GitHub 04 Apr '18

04 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0043f2f3a0044e359522f2fe6e485469b008f330 https://github.com/galaxyproject/galaxy/commit/0043f2f3a0044e359522f2fe6e48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: R templates/admin/view_data_tables_registry.mako Log Message: ----------- Remove unused template file. Commit: 4e4dbc88233d5309dfd5cc9b0923cc0e0d178ac7 https://github.com/galaxyproject/galaxy/commit/4e4dbc88233d5309dfd5cc9b0923… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.py M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_admin_app.py Log Message: ----------- Expand selenium test coverage. Initial admin app tests including screenshots of display applications, data tables, data types, and job management. Commit: fbd5541e4edd57870da924a2de11c2675b1d7bc4 https://github.com/galaxyproject/galaxy/commit/fbd5541e4edd57870da924a2de11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_admin_app.py Log Message: ----------- Merge pull request #5836 from jmchilton/selenium_admin_init Initial Selenium Test Coverage for Admin App Compare: https://github.com/galaxyproject/galaxy/compare/c9881fdc5ca7...fbd5541e4edd

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[galaxyproject/galaxy] 8fa866: Small improvements to scripts/grt/export.py for te...
by GitHub 03 Apr '18

03 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8fa8660b25dccf62a045597bee03441b5b68b71b https://github.com/galaxyproject/galaxy/commit/8fa8660b25dccf62a045597bee03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/hash_util.py M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Small improvements to scripts/grt/export.py for testing. - Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this). - Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell. Commit: 5f3f792f6f4ba67a2dd49e9c69b28567540c2c48 https://github.com/galaxyproject/galaxy/commit/5f3f792f6f4ba67a2dd49e9c69b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/communication/communication_server.py M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py A test/integration/test_scripts.py Log Message: ----------- Unification of Galaxy configuration parsing for scripts/* Commit: 16d821e12e53655947a6859a221b19a8d05eb2c4 https://github.com/galaxyproject/galaxy/commit/16d821e12e53655947a6859a221b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/sync_reports_config.py M scripts/transfer.py Log Message: ----------- Mark scripts/* that don't work with YAML configuraiton options as deprecated. Commit: 1911a55390eb4c6f9c7beb69b8f364ff6b76a119 https://github.com/galaxyproject/galaxy/commit/1911a55390eb4c6f9c7beb69b8f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh Log Message: ----------- Remove unused and unuseful scripts. Commit: 49fed72eeab48cda9e962f2d1a678825f40842b2 https://github.com/galaxyproject/galaxy/commit/49fed72eeab48cda9e962f2d1a67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh Log Message: ----------- Drop data library whoosh/lucene scripts. We don't set that config option in Galaxy anymore so these are broken anyway. Commit: fea7953410a4145f45afbe1656735febcf390a92 https://github.com/galaxyproject/galaxy/commit/fea7953410a4145f45afbe165673… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py Log Message: ----------- Remove two scripts - dataset purging hasn't worked this way for a very long time. Commit: b14928d97203d4d459c289c393589e4f4120e3e4 https://github.com/galaxyproject/galaxy/commit/b14928d97203d4d459c289c39358… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Cleanup script integration tests. Commit: 14e98becfe9c4d76677d9a9d0bc568c75f242bf2 https://github.com/galaxyproject/galaxy/commit/14e98becfe9c4d76677d9a9d0bc5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Cleanup incorrect FIXME - spotted by @nsoranzo. Commit: a177173672b86f4da8f83c3068dcb63f5f49cc40 https://github.com/galaxyproject/galaxy/commit/a177173672b86f4da8f83c3068dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Fix missing ENV information in config parameter args. Commit: 8fb6aa5860344cf80c18b8fef43b43b26856ec2a https://github.com/galaxyproject/galaxy/commit/8fb6aa5860344cf80c18b8fef43b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Bring in @nsoranzo's requested changes for config_file_from_args, etc. Commit: bb90ae93d810cd829ef026a3d086d51c11ac5394 https://github.com/galaxyproject/galaxy/commit/bb90ae93d810cd829ef026a3d086… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/grt/export.py M scripts/grt/upload.py M test/integration/test_scripts.py Log Message: ----------- More grt fixes - spotted by @nsoranzo. Commit: a1f0e1772ec5280a0523f2218008933f768e886e https://github.com/galaxyproject/galaxy/commit/a1f0e1772ec5280a0523f2218008… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Redact help for --config-section option for @nsoranzo. Kept the string in the file for in-code documentation but hiding it from users. Commit: 62d4582ef6913a4c681db2a08369a7757523de42 https://github.com/galaxyproject/galaxy/commit/62d4582ef6913a4c681db2a08369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py Log Message: ----------- Touch up script unification PR based on @natefoo comments. Commit: 4d742c3b1316aa808201c5bf3faec2587c345590 https://github.com/galaxyproject/galaxy/commit/4d742c3b1316aa808201c5bf3fae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M Makefile M client/README.md Log Message: ----------- Clarify make targets, update client/README Commit: b960260a3449a23dc35a0f126de41c37276d8cfd https://github.com/galaxyproject/galaxy/commit/b960260a3449a23dc35a0f126de4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention the client README specifically in CONTRIBUTING, to make it more obvious. Commit: d61268cc6d58a5fbecc0399a7fe8087be45d4861 https://github.com/galaxyproject/galaxy/commit/d61268cc6d58a5fbecc0399a7fe8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Articles are important. Commit: cbd7cb3cbcc93ef9abd651fff0760a91b5624127 https://github.com/galaxyproject/galaxy/commit/cbd7cb3cbcc93ef9abd651fff076… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Reflow text Commit: 05584244a7a5fb8790c513d6e451ac629b2f2955 https://github.com/galaxyproject/galaxy/commit/05584244a7a5fb8790c513d6e451… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Drop old bitbucket/galaxy/galaxy-dist reference. Commit: 96d9d0e5a236eb3fc7cf6f6612d82915fa5790e8 https://github.com/galaxyproject/galaxy/commit/96d9d0e5a236eb3fc7cf6f6612d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Better re-use of `tool` attribute Commit: 4f870490f2d289b2921c422ff66e92ee5decb352 https://github.com/galaxyproject/galaxy/commit/4f870490f2d289b2921c422ff66e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Simplify get_datatype_by_extension() method Commit: 334aea3adc975793d215f1622efc892718ecad75 https://github.com/galaxyproject/galaxy/commit/334aea3adc975793d215f1622efc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Erase trello from Contributing. Commit: 7d394d243b7d041ab357a0279e4920ab4a03fe7b https://github.com/galaxyproject/galaxy/commit/7d394d243b7d041ab357a0279e49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M client/README.md Log Message: ----------- Proofreading - thanks @nsoranzo Commit: d53cbe3538f186da903726ac1d00630e94cfe894 https://github.com/galaxyproject/galaxy/commit/d53cbe3538f186da903726ac1d00… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md Log Message: ----------- Merge pull request #5800 from dannon/client_readme_clarifications [18.01] Client related readme/makefile clarifications Commit: 288d13b60681a3729fd38c09b41763b520239317 https://github.com/galaxyproject/galaxy/commit/288d13b60681a3729fd38c09b417… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix metadata setting for CRAM files Should fix https://github.com/galaxyproject/galaxy/issues/5801. Commit: 7e5a90cc1fd5de729e416dd249f92621f883cce8 https://github.com/galaxyproject/galaxy/commit/7e5a90cc1fd5de729e416dd249f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Use app.datatypes_registry in ValidationContext.from_app() Commit: d5baea1dfc1998bcba5a0083b6b94769455bc247 https://github.com/galaxyproject/galaxy/commit/d5baea1dfc1998bcba5a0083b6b9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Handle an empty datatypes_registry Also transform it to an object attribute for re-use. Commit: 2c4bf95c3c5416f381cd8aea210f66ffef43498d https://github.com/galaxyproject/galaxy/commit/2c4bf95c3c5416f381cd8aea210f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5806 from nsoranzo/release_18.01_ValidationContext_fixes [18.01] Use app.datatypes_registry in ValidationContext.from_app() Commit: 241fadc98159f206b26938ba5626c1f24b1120c2 https://github.com/galaxyproject/galaxy/commit/241fadc98159f206b26938ba5626… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5805 from mvdbeek/fix_cram_metadata [18.01] Fix metadata setting for CRAM files Commit: 009921387dc3f2ea0731e82fe137c7b8d06f7e8a https://github.com/galaxyproject/galaxy/commit/009921387dc3f2ea0731e82fe137… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py Log Message: ----------- Merge pull request #5769 from jmchilton/unify_scripts [18.01] Fix scripts/ for YAML/ENV configuration processing Commit: c9881fdc5ca751e70248e199b487e98734c39e07 https://github.com/galaxyproject/galaxy/commit/c9881fdc5ca751e70248e199b487… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/62338abbd61f...c9881fdc5ca7

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[galaxyproject/galaxy] e7ecab: If psycopg2-binary is installed (as might be if sw...
by GitHub 02 Apr '18

02 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7ecab77349ee430d4d95978c7a71c0ae54b1d77 https://github.com/galaxyproject/galaxy/commit/e7ecab77349ee430d4d95978c7a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- If psycopg2-binary is installed (as might be if switching between branches), uninstalling psycopg2 will leave psycopg2-binary installed but in a broken state. If we're removing psycopg2, we need to remove psycopg2-binary at the same time, leaving psycopg2-binary to be correctly installed afterwards. Commit: 62338abbd61f7ca6b854ce0954c8cdebf2442c65 https://github.com/galaxyproject/galaxy/commit/62338abbd61f7ca6b854ce0954c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5825 from dannon/psycopg2-binary-handling-touchup psycopg2-binary handling tweak Compare: https://github.com/galaxyproject/galaxy/compare/30337f40d4bc...62338abbd61f

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[galaxyproject/galaxy] 19c652: Exclude the JS GIE proxy's node modules from linti...
by GitHub 02 Apr '18

02 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19c652cdb4ad6e444fa95be10d815fc5617e4e39 https://github.com/galaxyproject/galaxy/commit/19c652cdb4ad6e444fa95be10d81… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Exclude the JS GIE proxy's node modules from linting. Commit: 30337f40d4bc46089e0d3f79cedca2301d14123f https://github.com/galaxyproject/galaxy/commit/30337f40d4bc46089e0d3f79cedc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #5826 from natefoo/flake8-exclude-proxy Exclude the JS GIE proxy's node modules from linting Compare: https://github.com/galaxyproject/galaxy/compare/a8072a1d8bf2...30337f40d4bc

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[galaxyproject/galaxy] 03287e: Bugfix in upload_common -- ensure hda is added to ...
by GitHub 30 Mar '18

30 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03287ed195d65ce305e6414ed3659e43c9ac8444 https://github.com/galaxyproject/galaxy/commit/03287ed195d65ce305e6414ed365… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Bugfix in upload_common -- ensure hda is added to a session prior to state setting. Commit: a8072a1d8bf2bf5e232649df61fc6f954164fca3 https://github.com/galaxyproject/galaxy/commit/a8072a1d8bf2bf5e232649df61fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Merge pull request #5816 from dannon/upload_common_bugfix Bugfix in upload_common -- ensure hda is added to a session Compare: https://github.com/galaxyproject/galaxy/compare/e552bc4cbb59...a8072a1d8bf2

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[galaxyproject/galaxy] 9e71e1: Allow anonymous users to view their jobs via the A...
by GitHub 30 Mar '18

30 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e71e1d2f0e7c6586b3f5946edb033466a495258 https://github.com/galaxyproject/galaxy/commit/9e71e1d2f0e7c6586b3f5946edb0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Allow anonymous users to view their jobs via the API. Commit: 083bdcbdd84da29b1e2692058bbebd6426e8b2ae https://github.com/galaxyproject/galaxy/commit/083bdcbdd84da29b1e2692058bbe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Rule-based Collection Builder Vue-based component for defining collections by applying rules to a list of files or more general spreadsheet style information (e.g. sample sheets or tabular data from data sources containing URL or FTP file paths for files along with metadata). The widget is fairly complex but very broadly is broken into two panes - one to preview how rules are applied to build up tabular data defining collections (each row corresponding to a file with columns for metadata and such) and one that displays defined rules and allows for editing of these rules and creation of new ones. The goal behind defining rules this way instead of allowing the user to interact with the spreadsheet display directly is to enable scaling up collection creation. If a user wishes to upload hundreds of datasets - interacting with a widget directly for each input doesn't scale well and would be error prone. If a user wishes to upload hundreds of thousands of datasets - even loading this information in the GUI may not scale (though I've been impressed with the performance so far of this approach) and so we can potentially just display a preview of some of the rows and process the final set of rules on the backend. Since we can handle an arbitrary number of columns this way, we can define multiple list identifiers per file and so we can easily construct nested lists. Hence this allows creation of not just potentially larger collections but arbitrarily complex lists as well. Paired identifiers via indicator columns are also implemented. In order to operate over lists of datasets directly - the multi-select history widget now has a new option "Build Collection from Rules" along side the other collection builders. This mode uses the well established dataset collection API to build collections from HDAs. In order to operate on lists of FTP files or URLs - the upload widget has a new tab "Rule-based" tab that allows users to paste in tabular data or select a history dataset and then send this tabular data to the new builder widget. This will be extended to include FTP directories for instance over time. This mode uses the new data fetch API to build collections and handle uploads of arbitrary collections of files. The preview of the tabular data generated via rules is done via [Handsontable](https://handsontable.com/) - a JavaScript spreadsheet widget with a VueJS [wrapper component](https://github.com/handsontable/vue-handsontable-official). This turns out to be a fairly nice application for reactive components - as rules are added or modified the spreadsheet just naturally updates. In my hands the widget scales very nicely - I've uploaded files with tens of thousands of rows and rules modifying the data and changing the spreadsheet do not seem to cause siignificant delays in the web browser. Commit: ebf08c16493b8fd3e770bf3c33c1f3eea55dd374 https://github.com/galaxyproject/galaxy/commit/ebf08c16493b8fd3e770bf3c33c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Fix production build of vue-handsontable Commit: cfa1208a79dcd0bdda5c7632366c2bd2b6deea0d https://github.com/galaxyproject/galaxy/commit/cfa1208a79dcd0bdda5c7632366c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/yarn.lock Log Message: ----------- Yarn lock w/ new deps. Commit: b32e78f338fcbd586f77c64f0fa18aee6ce23d1b https://github.com/galaxyproject/galaxy/commit/b32e78f338fcbd586f77c64f0fa1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix upload view initialization. Commit: 1c04bbe9f6a95c1c8050bc5a8cd69bd8030cf350 https://github.com/galaxyproject/galaxy/commit/1c04bbe9f6a95c1c8050bc5a8cd6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/.babelrc M client/package.json M client/yarn.lock Log Message: ----------- Add babel plugin for vue template preprocessing. This allows precompilation without a vue runtime for nested local components in vue SFCs, and other situations. Commit: e552bc4cbb592eb2fcb4658e287026a742aab286 https://github.com/galaxyproject/galaxy/commit/e552bc4cbb592eb2fcb4658e2870… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/.babelrc A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/api/jobs.py A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #5365 from jmchilton/rule_based_uploader Rule-based Uploader / Builder Compare: https://github.com/galaxyproject/galaxy/compare/ac74b7ffb221...e552bc4cbb59

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