- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 571fed: Remove menu options from visualization tab, shift ...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 571fedf00654c36ee60115abff50d4d4d4031a5b https://github.com/galaxyproject/galaxy/commit/571fedf00654c36ee60115abff50… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/buildapp.py M static/style/blue/base.css Log Message: ----------- Remove menu options from visualization tab, shift tab to workflows Commit: 0bd98c320ee0ca8c998dfbfc8f84a174066969a7 https://github.com/galaxyproject/galaxy/commit/0bd98c320ee0ca8c998dfbfc8f84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: A lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Add plugins endpoint Commit: cc3e5244d603e13afcf4501aefc88868e971fe50 https://github.com/galaxyproject/galaxy/commit/cc3e5244d603e13afcf4501aefc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Remove unused imports from plugins api endpoint Commit: 1ca6499ea10c35d1647898d50dfac442055fa1cc https://github.com/galaxyproject/galaxy/commit/1ca6499ea10c35d1647898d50dfa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/PluginList.vue M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add vue list for plugins Commit: f4e52caab6027a50b631331ad3cd02fd3ca2a0a8 https://github.com/galaxyproject/galaxy/commit/f4e52caab6027a50b631331ad3cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Remove id from header value Commit: 82e58d9086e7e0da86aab270d07bf8ff442cb2e4 https://github.com/galaxyproject/galaxy/commit/82e58d9086e7e0da86aab270d07b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Redirect to list of plugins Commit: fbead2daa5ea1da1974ed60e3740a2530165996c https://github.com/galaxyproject/galaxy/commit/fbead2daa5ea1da1974ed60e3740… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Add select field to thumbnail view to allow dataset selection Commit: d5d60e95aa749c6f14dbc9ae01dcf3e515ce0c2f https://github.com/galaxyproject/galaxy/commit/d5d60e95aa749c6f14dbc9ae01dc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Remove comment and debug output Commit: 15636fa6f144f4a2203b76df0b47cd7d70d03ada https://github.com/galaxyproject/galaxy/commit/15636fa6f144f4a2203b76df0b47… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Revise resource mapping, add show action to plugins endpoint Commit: a8daf446eab87cffb5483a6d96b5f8d244d8286c https://github.com/galaxyproject/galaxy/commit/a8daf446eab87cffb5483a6d96b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Add error handlers, populate select list with applicable datasets Commit: b6ad62c0e09d3c67951849cdaeb340e9bc9f11a0 https://github.com/galaxyproject/galaxy/commit/b6ad62c0e09d3c67951849cdaeb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js Log Message: ----------- Add event handler for create button Commit: a1f9cdcf45ccb448341d60f5eed6e32303244a39 https://github.com/galaxyproject/galaxy/commit/a1f9cdcf45ccb448341d60f5eed6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Restore sub menu options for visualization tab Commit: 8763a2c25fb0237e1dc23b06845e249ca1bc687a https://github.com/galaxyproject/galaxy/commit/8763a2c25fb0237e1dc23b06845e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Add simple filter search Commit: 923286612d7e31ffaf474a60392960f36345895f https://github.com/galaxyproject/galaxy/commit/923286612d7e31ffaf474a603929… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Revise dataset selection label Commit: a077f45ba9830136f2869e39e50680e7dfc41c5b https://github.com/galaxyproject/galaxy/commit/a077f45ba9830136f2869e39e506… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Match search word with description Commit: 980f2b9708cb9e95bbacf0ae0decb42f7cd0da6c https://github.com/galaxyproject/galaxy/commit/980f2b9708cb9e95bbacf0ae0dec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js Log Message: ----------- Partial fix for internal scatterplot Commit: a6559248c9e877911ed86b08135f7aae6408fb0b https://github.com/galaxyproject/galaxy/commit/a6559248c9e877911ed86b08135f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js Log Message: ----------- Remove comments Commit: 044ca897d53c08939508935c003c5e3d665ba769 https://github.com/galaxyproject/galaxy/commit/044ca897d53c08939508935c003c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml Log Message: ----------- Add confirm option Commit: 58f0afe23b9c9590bd8cda1dd4d7c3b731fb0969 https://github.com/galaxyproject/galaxy/commit/58f0afe23b9c9590bd8cda1dd4d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Hide grid if error occurs Commit: eec8bf47036c0057f9a21578159199b6c036acbb https://github.com/galaxyproject/galaxy/commit/eec8bf47036c0057f9a215781591… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Augment button model with visibile attribute Commit: 7f342c340e7739854a1cd7fda375d947aa8addb2 https://github.com/galaxyproject/galaxy/commit/7f342c340e7739854a1cd7fda375… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Fix default inline handler, fix fullscreen switch Commit: 4f4c8967c0de717f27b5057aaeaef8e3b4d0da98 https://github.com/galaxyproject/galaxy/commit/4f4c8967c0de717f27b5057aaeae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.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 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/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml Log Message: ----------- Fix modified handler Commit: f47b88730b2dba31daeeba76f76b06aea44fdbc6 https://github.com/galaxyproject/galaxy/commit/f47b88730b2dba31daeeba76f76b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js Log Message: ----------- Remove unused variable Commit: bebc022d6f6c6a0dff627381c7c435fffbdbe3e0 https://github.com/galaxyproject/galaxy/commit/bebc022d6f6c6a0dff627381c7c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Add info notification for visualizations which require additional confirmation Commit: 5e98958c22dba2665f762052e4d017145a243395 https://github.com/galaxyproject/galaxy/commit/5e98958c22dba2665f762052e4d0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Highlight check button to confirm settings Commit: eadeb0f91717e24464279b4d694bf0725710048b https://github.com/galaxyproject/galaxy/commit/eadeb0f91717e24464279b4d694b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js Log Message: ----------- Add additional data validation Commit: e01d1a0049ebc2ca7c05b0439d461afa9a38ea70 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client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/utils/utils.js M config/datatypes_conf.xml.sample M lib/galaxy/actions/library.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/xml.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/containers.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd A lib/galaxy/util/create_history_template.py M lib/galaxy/util/inflection.py M lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/scheduling_manager.py M scripts/migrate_tools/migrate_tools.py R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako A test-data/qname_sorted.bam M test/functional/tools/multi_output_recurse.xml M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/unit/tools/test_toolbox.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: 04bfefb7dae2a0d035d76f57a6c552facee8bd19 https://github.com/galaxyproject/galaxy/commit/04bfefb7dae2a0d035d76f57a6c5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M static/style/blue/base.css M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: e57136523c5e5674c1091cfcec601a5b65fc3fd3 https://github.com/galaxyproject/galaxy/commit/e57136523c5e5674c1091cfcec60… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: 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 Log Message: ----------- Fix trackster urls Commit: 840ad914c5a3ce7ad7b8fd2f4c4f5bf051543c95 https://github.com/galaxyproject/galaxy/commit/840ad914c5a3ce7ad7b8fd2f4c4f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Move url creation to plugins Commit: f3eb82208971e151399ac2c7d7539d7d8ca1630b https://github.com/galaxyproject/galaxy/commit/f3eb82208971e151399ac2c7d753… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Revise url generator Commit: 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config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png Log Message: ----------- Add description for trackster and other visualizations Commit: dc3cd003549cd9f54e7a955af8e7ecec355c2a44 https://github.com/galaxyproject/galaxy/commit/dc3cd003549cd9f54e7a955af8e7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/unipept/config/unipept.xml Log Message: ----------- Add additional descriptions Commit: ace94178c8af8cbd8d098229d96a7a27104da798 https://github.com/galaxyproject/galaxy/commit/ace94178c8af8cbd8d098229d96a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Revise data submission tool Commit: 553474ddfd32229787630989099127e8029dd4f9 https://github.com/galaxyproject/galaxy/commit/553474ddfd322297876309890991… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/example/config/example.xml Log Message: ----------- Hide example plugin Commit: f08223bc7a7ac7e9827543601707009c2ac8a0f1 https://github.com/galaxyproject/galaxy/commit/f08223bc7a7ac7e9827543601707… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Sort plugins by display name Commit: 7d95d28d7c729ff25fe8f9f21e9bd7fcad183cbe https://github.com/galaxyproject/galaxy/commit/7d95d28d7c729ff25fe8f9f21e9b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/trackster/config/trackster.xml Log Message: ----------- Increase priority for trackster Commit: e0c25f42668f3956ee152843057fda74cdea79a4 https://github.com/galaxyproject/galaxy/commit/e0c25f42668f3956ee152843057f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/example/config/example.xml Log Message: ----------- Enable example Commit: 1aa5f8283eaaf5f03b929215ffd49982a74febc2 https://github.com/galaxyproject/galaxy/commit/1aa5f8283eaaf5f03b929215ffd4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fix lint Commit: 7afecf9d1ab0b5d6ad5c34a180ff599b318bc0a1 https://github.com/galaxyproject/galaxy/commit/7afecf9d1ab0b5d6ad5c34a180ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Fix test cases Commit: 00f282ccaab220d290a298f28fe8d9b113cf908b https://github.com/galaxyproject/galaxy/commit/00f282ccaab220d290a298f28fe8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use vue instead of backbone view Commit: cb9ecb63f533dfc648af1b016975f89cb2591bfe https://github.com/galaxyproject/galaxy/commit/cb9ecb63f533dfc648af1b016975… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: R client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Remove backbone visualization selector Commit: b325e086f20f241bc2c2a39a705b7d12bda5e06d https://github.com/galaxyproject/galaxy/commit/b325e086f20f241bc2c2a39a705b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Remove unused import Commit: 9f52c391229d07687dfa792fa525cb8c781e3b93 https://github.com/galaxyproject/galaxy/commit/9f52c391229d07687dfa792fa525… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Use parsed dataset id in visualization selector instead of showing select field Commit: 21aa7462875f064766be2e5a6e7b35f7de7dc2b0 https://github.com/galaxyproject/galaxy/commit/21aa7462875f064766be2e5a6e7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Fix button inline style Commit: c14ed8732f76cab4e72371878fd770fc01c7bfb0 https://github.com/galaxyproject/galaxy/commit/c14ed8732f76cab4e72371878fd7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Temporary use of style section in vue component Commit: 9bb1e48aba4bd5de3d0b59b113d8dce2d047612b https://github.com/galaxyproject/galaxy/commit/9bb1e48aba4bd5de3d0b59b113d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/special_tools.py M lib/galaxy/util/compression_utils.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A test-data/1.csv A test-data/example-bag.zip A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into visualization_header Commit: a706929bd6fe7f9d502e756cc592806a79480147 https://github.com/galaxyproject/galaxy/commit/a706929bd6fe7f9d502e756cc592… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M config/datatypes_conf.xml.sample A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/script.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/tool_util.py M test/functional/test_toolbox.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: ef619f5905820d635f068a5c372b4167dec121bd https://github.com/galaxyproject/galaxy/commit/ef619f5905820d635f068a5c372b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/run_request.py M scripts/common_startup.sh M test/api/test_workflows.py Log Message: ----------- Merge branch 'dev' into visualization_header Commit: c07c17e93dbd137947320b417082733a8a34345e https://github.com/galaxyproject/galaxy/commit/c07c17e93dbd137947320b417082… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M config/plugins/visualizations/msa/static/script.js Log Message: ----------- Restore missing 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client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/decorators.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/root.py M test/base/driver_util.py Log Message: ----------- Merge branch 'dev' into visualization_header Commit: df5838e6c1924e2f0303c675e0262736ece52238 https://github.com/galaxyproject/galaxy/commit/df5838e6c1924e2f0303c675e026… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed 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client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced 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 M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M 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lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M run_tests.sh A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: 8b5c0b223ef9092420b9912b153b0d257fe5a1a5 https://github.com/galaxyproject/galaxy/commit/8b5c0b223ef9092420b9912b153b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Allow target top rendering for visualizations Commit: 0cdd9b9ecd235a34ba6018542156f9780bf22f77 https://github.com/galaxyproject/galaxy/commit/0cdd9b9ecd235a34ba6018542156… 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/PluginList.vue M client/galaxy/scripts/layout/menu.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/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Client formatting Commit: 2b2fd9289857b258f7e63f64668d776c49a54ec8 https://github.com/galaxyproject/galaxy/commit/2b2fd9289857b258f7e63f64668d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use visualizations route to link to plugins Commit: 38c2a895009c03204026ca7d74af70f92dd29f4e https://github.com/galaxyproject/galaxy/commit/38c2a895009c03204026ca7d74af… 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/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'visualization_header' of github.com:guerler/galaxy into visualization_header Commit: c5beedef6b9f4498e4df0adfb39ddc519715f997 https://github.com/galaxyproject/galaxy/commit/c5beedef6b9f4498e4df0adfb39d… 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-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/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 R client/galaxy/scripts/mvc/visualization/visualization-view.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/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 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/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 lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py M static/style/blue/base.css M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge branch 'visualization_header' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bf5d472e2850...c5beedef6b9f

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[galaxyproject/usegalaxy-playbook] 6f9370: Upgraded dunovo on test and main, upgraded extract...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f9370135835b80ee1a1ec77d0133ae4aec364bf https://github.com/galaxyproject/usegalaxy-playbook/commit/6f9370135835b80e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-27 (Tue, 27 Mar 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/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Upgraded dunovo on test and main, upgraded extract genomic dna on main.

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[galaxyproject/galaxy] db47c8: Remove prepopulation of column selector
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: db47c876ee69bd034b7e131daf0a7fd5672d2221 https://github.com/galaxyproject/galaxy/commit/db47c876ee69bd034b7e131daf0a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove prepopulation of column selector Commit: fc7beca6d1d379ddfc1ea4769edfc8c22d74fb10 https://github.com/galaxyproject/galaxy/commit/fc7beca6d1d379ddfc1ea4769edf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Create input element combining text and select options Commit: 2e8c9489bfd149d12b9498ea89c5633a07509d48 https://github.com/galaxyproject/galaxy/commit/2e8c9489bfd149d12b9498ea89c5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix value handling, remove redundant value check Commit: 9fbdcd1d5ee84887c28eed727fec77d402ef95fa https://github.com/galaxyproject/galaxy/commit/9fbdcd1d5ee84887c28eed727fec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax validation conditions Commit: ff874dc4e4f4d21bb133b2730058393c7ae7a66a https://github.com/galaxyproject/galaxy/commit/ff874dc4e4f4d21bb133b2730058… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Properly switch between states, transfer current value Commit: 9fff4f1615aa7ce02561d681ae20397b22b17f02 https://github.com/galaxyproject/galaxy/commit/9fff4f1615aa7ce02561d681ae20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove redundant initial value checks, value can only be empty Commit: 1db1c0c77122edd183ab6f0bf5da24c94c83b476 https://github.com/galaxyproject/galaxy/commit/1db1c0c77122edd183ab6f0bf5da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise condition, check explicitly for none Commit: 608f3dc9d3ed59a21fba221f590240ecfdc1294a https://github.com/galaxyproject/galaxy/commit/608f3dc9d3ed59a21fba221f5902… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add check for column index values Commit: f4f275f82aa9b1e19aafe0525b4006876905ef96 https://github.com/galaxyproject/galaxy/commit/f4f275f82aa9b1e19aafe0525b40… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add dataset state check to column input Commit: a144eb1fb40eee0920e8153b3e51304c10130003 https://github.com/galaxyproject/galaxy/commit/a144eb1fb40eee0920e8153b3e51… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix integer test Commit: 29337d2b7b1d51c44ff621049483037fd9d48d1a https://github.com/galaxyproject/galaxy/commit/29337d2b7b1d51c44ff621049483… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Simplify legal value length check Commit: 05ce42d229db08c6af7425f1afe1eea625dfd1da https://github.com/galaxyproject/galaxy/commit/05ce42d229db08c6af7425f1afe1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Provide value for column index if not an integer Commit: 9febc519944dcfb5c8907b8a302fd6aff6f0f79f https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Identify implicit conversions, check reference context for datasets Commit: 1baafd07ffbaa42bd5071a659ccb82203591afa0 https://github.com/galaxyproject/galaxy/commit/1baafd07ffbaa42bd5071a659ccb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Move implicit dataset tagging to dataset state check Check attribute Commit: dae6cc7f4cb403cdee44c532f314f639d8e9f96b https://github.com/galaxyproject/galaxy/commit/dae6cc7f4cb403cdee44c532f314… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indent Commit: f305c0b0ab9182af0578078c622d024a57b9b05d https://github.com/galaxyproject/galaxy/commit/f305c0b0ab9182af0578078c622d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Reinsert legal value check handler Commit: c7e794745b1b7699a7ac34caaa684f298f562dbc https://github.com/galaxyproject/galaxy/commit/c7e794745b1b7699a7ac34caaa68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Validate value before matching dataset Commit: 81a418fe98ee2f26b35bae81060398431b9a096e https://github.com/galaxyproject/galaxy/commit/81a418fe98ee2f26b35bae810603… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove explicit integer validation Commit: 187c540cd4aac7e1059fdaa6aaf56c87913f1d09 https://github.com/galaxyproject/galaxy/commit/187c540cd4aac7e1059fdaa6aaf5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test case Commit: 04fee6070bfa94a3788c89dc0cc1414469db20e6 https://github.com/galaxyproject/galaxy/commit/04fee6070bfa94a3788c89dc0cc1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.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/dataset/dataset-model.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-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced 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 M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into select_to_text Commit: ade62bc3b15b25e76d7114c5ee9051cd5f575700 https://github.com/galaxyproject/galaxy/commit/ade62bc3b15b25e76d7114c5ee90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Revise select display matching Commit: 8290da24eaf0994c018b055ba9bbc73876540f7c https://github.com/galaxyproject/galaxy/commit/8290da24eaf0994c018b055ba9bb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indentation Commit: 241ade62cd740bf62d2348859493ed7326799597 https://github.com/galaxyproject/galaxy/commit/241ade62cd740bf62d2348859493… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Align validation order for consistency Commit: 2b3557ffce38a97080c9921846e06131aa43e2e9 https://github.com/galaxyproject/galaxy/commit/2b3557ffce38a97080c9921846e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test case verifying we check column values before tool execution. Commit: 91e97b60968d6813bd7a28d0d60e778b288ac385 https://github.com/galaxyproject/galaxy/commit/91e97b60968d6813bd7a28d0d60e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Refactor code for clarity Commit: 840e436ea1f181ebe0c8478145e2cd0e97dc1778 https://github.com/galaxyproject/galaxy/commit/840e436ea1f181ebe0c8478145e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add strict workflow building mode check to drill downs Commit: bf5d472e28505438c5f345ad29989b80fe3aae80 https://github.com/galaxyproject/galaxy/commit/bf5d472e28505438c5f345ad2998… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5702 from guerler/select_to_text Relax validation condition for dynamic parameters Compare: https://github.com/galaxyproject/galaxy/compare/61adffbd614c...bf5d472e2850

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[galaxyproject/galaxy] 527412: Use pipenv also for the default dependencies
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 52741200b24933d3c4af1f5a7fa5124d29d5daf6 https://github.com/galaxyproject/galaxy/commit/52741200b24933d3c4af1f5a7fa5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: 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/update.sh R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Use pipenv also for the default dependencies Commit: fb92257bc755ae12a5dad810c152967bfc68d8a1 https://github.com/galaxyproject/galaxy/commit/fb92257bc755ae12a5dad810c152… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Exclude 2 problematic h5py versions A warning was appearing in the stderr of upload jobs due to https://github.com/h5py/h5py/issues/995 . Commit: f8aa29e2805b932a03a577fd329f881a3d047c98 https://github.com/galaxyproject/galaxy/commit/f8aa29e2805b932a03a577fd329f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Temporarily pin WebOb to latest compatible release Commit: e625b649dc0e823d0c92f8c997254215bcf9dcab https://github.com/galaxyproject/galaxy/commit/e625b649dc0e823d0c92f8c99725… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Temporarily pin Mercurial to latest compatible release Commit: 61adffbd614cbbe409f207415073604f8e13a0ba https://github.com/galaxyproject/galaxy/commit/61adffbd614cbbe409f207415073… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: 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/update.sh R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5786 from nsoranzo/default_pipfile Use pipenv also for the default dependencies Compare: https://github.com/galaxyproject/galaxy/compare/5a86b8d706b7...61adffbd614c

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[galaxyproject/usegalaxy-playbook] d30a0a: Installed SnpEff version 4.3.1t on test and main.
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d30a0a9f96d63ec2d9c83cd05b67fdcc56177bfa https://github.com/galaxyproject/usegalaxy-playbook/commit/d30a0a9f96d63ec2… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-27 (Tue, 27 Mar 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 M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed SnpEff version 4.3.1t on test and main.

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[galaxyproject/galaxy] f63426: Fixes for testing Dockerfile recipe.
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6342616eb0b6c740b734664cc50b896ad39f4b8 https://github.com/galaxyproject/galaxy/commit/f6342616eb0b6c740b734664cc50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-25 (Sun, 25 Mar 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Fixes for testing Dockerfile recipe. The current Dockerfile build is broken because Selenium is not compatible with the latest chromedriver it seems (and the version in galaxy/testing-base:18.01.4 isn't compatible with the latest stable Chrome - version 65). I can't get older versions of Chrome to install with the current apt source but this does at least pin the version of chromedriver. Longer term it would be good to have the version of chrome we target to be pinned also, I hate that this Dockerfile isn't reproducible. Commit: 5a86b8d706b7d3b8244b2359e2f7740367df1e89 https://github.com/galaxyproject/galaxy/commit/5a86b8d706b7d3b8244b2359e2f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Merge pull request #5693 from jmchilton/docker_test_update Fixes for testing Dockerfile recipe. Compare: https://github.com/galaxyproject/galaxy/compare/f14c6ffe49b3...5a86b8d706b7

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[galaxyproject/galaxy] 412ff1: Add config rebuild left out of migration of option...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 412ff1e16ae50af06751d3aae936973ef954fc61 https://github.com/galaxyproject/galaxy/commit/412ff1e16ae50af06751d3aae936… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M doc/source/admin/galaxy_options.rst Log Message: ----------- Add config rebuild left out of migration of options from 18.01 (I think) Commit: f14c6ffe49b397b884f678812f311fc0bd451e53 https://github.com/galaxyproject/galaxy/commit/f14c6ffe49b397b884f678812f31… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M doc/source/admin/galaxy_options.rst Log Message: ----------- Merge pull request #5788 from dannon/configrebuild Config-rebuild w/ options doc Compare: https://github.com/galaxyproject/galaxy/compare/39d5ec89f885...f14c6ffe49b3

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[galaxyproject/galaxy] c99c7b: Fix type of some options in config_schema.yml
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c99c7b4d842b844677673472b9aa2b13e4123aeb https://github.com/galaxyproject/galaxy/commit/c99c7b4d842b844677673472b9aa… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix type of some options in config_schema.yml Also: - drop unused `nginx_x_archive_files_base` option, last use removed in commit fe5983aafca1fae0b60ed16838799b58f4aca11c - rebuild config samples and docs. Commit: 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8 https://github.com/galaxyproject/galaxy/commit/80ac55b3ff132cf6e1778b99cb6f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Don't quote ints in .ini to .yml config conversion Commit: ff0f0b611282fb0c4c5742c034f7cef0ec86f475 https://github.com/galaxyproject/galaxy/commit/ff0f0b611282fb0c4c5742c034f7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Fix model operations that produce datasets for 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03 Should only affect unzip I think - fixes #5780 - probably need to rebuild collections though, collections built in the meantime are going to be broken in the DB. Includes test case that fails against 18.01. Commit: 3876f12e7d3ce7ec73d14ae99f06edae01020412 https://github.com/galaxyproject/galaxy/commit/3876f12e7d3ce7ec73d14ae99f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5784 from jmchilton/1801_fix_unzip [18.01] Fix model operation tools that produce standalone datasets. Commit: fbb47f6e03d0ca9190e3f665515ba45ac64e14ce https://github.com/galaxyproject/galaxy/commit/fbb47f6e03d0ca9190e3f665515b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5745 from nsoranzo/release_18.01_fix_config [18.01] Configuration fixes Commit: 39d5ec89f885ffce8e3c9621439c76d9d0745aa6 https://github.com/galaxyproject/galaxy/commit/39d5ec89f885ffce8e3c9621439c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/45dd9889654c...39d5ec89f885

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[galaxyproject/galaxy] fb24e8: Sentry bug reports working for anonymous users
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb24e8f2e2c817ff324a57947fdf315cca969707 https://github.com/galaxyproject/galaxy/commit/fb24e8f2e2c817ff324a57947fdf… Author: E Rasche <hxr(a)hx42.org> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Sentry bug reports working for anonymous users Commit: 45dd9889654cf839740b165763f6a40019cde2e0 https://github.com/galaxyproject/galaxy/commit/45dd9889654cf839740b165763f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5721 from erasche/sentry-reporter Sentry bug reports working for anonymous users Compare: https://github.com/galaxyproject/galaxy/compare/13fff60142ed...45dd9889654c

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[galaxyproject/galaxy] c99c7b: Fix type of some options in config_schema.yml
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: c99c7b4d842b844677673472b9aa2b13e4123aeb https://github.com/galaxyproject/galaxy/commit/c99c7b4d842b844677673472b9aa… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix type of some options in config_schema.yml Also: - drop unused `nginx_x_archive_files_base` option, last use removed in commit fe5983aafca1fae0b60ed16838799b58f4aca11c - rebuild config samples and docs. Commit: 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8 https://github.com/galaxyproject/galaxy/commit/80ac55b3ff132cf6e1778b99cb6f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Don't quote ints in .ini to .yml config conversion Commit: fbb47f6e03d0ca9190e3f665515ba45ac64e14ce https://github.com/galaxyproject/galaxy/commit/fbb47f6e03d0ca9190e3f665515b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5745 from nsoranzo/release_18.01_fix_config [18.01] Configuration fixes Compare: https://github.com/galaxyproject/galaxy/compare/3876f12e7d3c...fbb47f6e03d0

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