Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 734c39d4f58cfc96c637d9121b88b14398a9c4b2
https://github.com/galaxyproject/galaxy/commit/734c39d4f58cfc96c637d9121b88…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M .gitignore
A client/galaxy/jsconfig.json
M client/galaxy/scripts/galaxy.js
A client/galaxy/scripts/galaxy.monitor.js
R client/galaxy/scripts/onload.js
A client/galaxy/scripts/onload/index.js
A client/galaxy/scripts/onload/loadConfig.js
A client/galaxy/scripts/utils/installMonitor.js
A client/galaxy/scripts/utils/mock.js
A client/galaxy/scripts/utils/serverPath.js
M client/webpack.config.js
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
added global monitor for window.Galaxy
Commit: 0cdf78956f29abf53e9e2233a6545dc1fba71f5c
https://github.com/galaxyproject/galaxy/commit/0cdf78956f29abf53e9e2233a654…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M client/galaxy/scripts/onload/loadConfig.js
M client/galaxy/scripts/utils/installMonitor.js
Log Message:
-----------
Corrected instructions, removed config function that is not used yet.
Commit: 712aa6cb8742674777c4bc0ee36df9f361bfbeab
https://github.com/galaxyproject/galaxy/commit/712aa6cb8742674777c4bc0ee36d…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M client/galaxy/scripts/utils/installMonitor.js
Log Message:
-----------
Removed debugger statements
Commit: 4c13d204c454203b17194c6174177de642c0a2ae
https://github.com/galaxyproject/galaxy/commit/4c13d204c454203b17194c617417…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M client/galaxy/scripts/utils/installMonitor.js
Log Message:
-----------
Corrected monitor value storage initialization
Commit: ef5e01da82e532a819a343457ea31bf0cb16baa7
https://github.com/galaxyproject/galaxy/commit/ef5e01da82e532a819a343457ea3…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
White space awesomeness
Commit: 3cf9dd85f4c20801807d0aef74b4628c26ca3f97
https://github.com/galaxyproject/galaxy/commit/3cf9dd85f4c20801807d0aef74b4…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-29 (Mon, 29 Oct 2018)
Changed paths:
M client/.babelrc
M client/galaxy/scripts/polyfills.js
M client/package.json
M client/yarn.lock
Log Message:
-----------
Updating babel for proxy support with karma
Commit: 04242c75034637f064173eca0c1e2f415343fe93
https://github.com/galaxyproject/galaxy/commit/04242c75034637f064173eca0c1e…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-30 (Tue, 30 Oct 2018)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Renamed selenium utility function
Commit: 66a7db94053763bfb1cc23ba5df1e537f0177219
https://github.com/galaxyproject/galaxy/commit/66a7db94053763bfb1cc23ba5df1…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-31 (Wed, 31 Oct 2018)
Changed paths:
M .gitignore
M client/.babelrc
R client/GruntFile.js
A client/galaxy/images/Armitagep_manhattan.png
A client/galaxy/images/Armitagep_qqplot.png
A client/galaxy/images/add_icon.png
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A client/galaxy/images/history-buttons.png
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A client/galaxy/images/jstree/throbber.gif
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A client/galaxy/images/mag_glass.png
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A client/galaxy/images/menu_bg.png
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A client/galaxy/images/overview_arrows.png
A client/galaxy/images/panel_header_bg.png
A client/galaxy/images/pearson.png
A client/galaxy/images/popupmenu_callout_top.png
A client/galaxy/images/question-balloon.png
A client/galaxy/images/question-octagon-frame.png
A client/galaxy/images/resizable.png
A client/galaxy/images/scatter.png
A client/galaxy/images/scatterplot.png
A client/galaxy/images/select2-spinner.gif
A client/galaxy/images/select2.png
A client/galaxy/images/select2x2.png
A client/galaxy/images/silk/add.png
A client/galaxy/images/silk/book.png
A client/galaxy/images/silk/book_open.png
A client/galaxy/images/silk/chart_curve.png
A client/galaxy/images/silk/folder.png
A client/galaxy/images/silk/folder_page.png
A client/galaxy/images/silk/link.png
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A client/galaxy/images/silk/page_white.png
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A client/galaxy/images/silk/resultset_bottom.png
A client/galaxy/images/silk/resultset_next.png
A client/galaxy/images/silk/resultset_previous.png
A client/galaxy/images/solid_qual.png
A client/galaxy/images/spearman.png
A client/galaxy/images/sprite-fugue.png
A client/galaxy/images/sprite-history-buttons.png
A client/galaxy/images/sprite-history-states.png
A client/galaxy/images/star.gif
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A client/galaxy/images/thumbtack_icon_dark.png
A client/galaxy/images/tiny_arrow_left.png
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A client/galaxy/images/tipsy.gif
A client/galaxy/images/tracks/block.png
A client/galaxy/images/tracks/close_btn.gif
A client/galaxy/images/tracks/diag_bg.gif
A client/galaxy/images/tracks/go_btn.gif
A client/galaxy/images/tracks/handle-left.gif
A client/galaxy/images/tracks/handle-right.gif
A client/galaxy/images/tracks/pan_left.gif
A client/galaxy/images/tracks/pan_right.gif
A client/galaxy/images/tracks/show_history.gif
A client/galaxy/images/tracks/zoom_in.gif
A client/galaxy/images/tracks/zoom_in_full.gif
A client/galaxy/images/tracks/zoom_out.gif
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A client/galaxy/images/visualization/draggable_horizontal.png
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A client/galaxy/images/visualization/strand_left.png
A client/galaxy/images/visualization/strand_left_inv.png
A client/galaxy/images/visualization/strand_right.png
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A client/galaxy/images/wait_icon.svg
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A client/galaxy/images/warn_bg.png
A client/galaxy/images/warn_icon.svg
A client/galaxy/images/warn_large.png
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A client/galaxy/images/workflow_circle_drag.png
A client/galaxy/images/workflow_circle_green.png
A client/galaxy/images/workflow_circle_open.png
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/chart.js
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/onload/index.js
M client/galaxy/scripts/polyfills.js
M client/galaxy/scripts/qunit/assets/base.css
M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
M client/galaxy/scripts/reports/run_stats.js
A client/galaxy/scripts/style.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/viz/phyloviz.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/scripts/viz/visualization.js
M client/galaxy/style/scss/autocomplete_tagging.scss
M client/galaxy/style/scss/base.scss
M client/galaxy/style/scss/iconic_stroke.scss
A client/galaxy/style/scss/jquery.rating.scss
M client/galaxy/style/scss/jstree.scss
M client/galaxy/style/scss/select2.scss
A client/galaxy/style/scss/sprite-fugue.scss
A client/galaxy/style/scss/sprite-history-buttons.scss
A client/galaxy/style/scss/sprite-history-states.scss
M client/galaxy/style/scss/trackster.scss
R client/galaxy/style/source_material/circle.py
R client/galaxy/style/source_material/error_icon.svg
R client/galaxy/style/source_material/galaxy_icons.svg
R client/galaxy/style/source_material/galaxy_spinner.fla
R client/galaxy/style/source_material/info_icon.svg
R client/galaxy/style/source_material/ok_icon.svg
R client/galaxy/style/source_material/wait_icon.svg
R client/galaxy/style/source_material/warn_icon.svg
M client/gulpfile.js
M client/karma.config.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
M config/datatypes_conf.xml.sample
M config/plugins/visualizations/common/templates/chart_entry_point.mako
M config/plugins/webhooks/demo/tour_generator/config.yml
A config/plugins/webhooks/demo/tour_generator/package.json
M config/plugins/webhooks/demo/tour_generator/script.js
A config/plugins/webhooks/demo/tour_generator/tour_generator.js
M doc/source/dev/faq.rst
M doc/source/releases/18.09_announce.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/phylip.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/0.txt
M lib/galaxy/datatypes/test/1.afg
M lib/galaxy/datatypes/test/1.bcf_uncompressed
A lib/galaxy/datatypes/test/1.excel.xls
M lib/galaxy/datatypes/test/1.fastq
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M lib/galaxy/datatypes/test/1.fastqsanger
M lib/galaxy/datatypes/test/1.fastqsolexa
A lib/galaxy/datatypes/test/1.json
M lib/galaxy/datatypes/test/1.owl
A lib/galaxy/datatypes/test/1.qname_sorted.bam
M lib/galaxy/datatypes/test/1.stockholm
R lib/galaxy/datatypes/test/1.vcf.gz
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M lib/galaxy/datatypes/test/2.fastq
R lib/galaxy/datatypes/test/2.fastqsanger
M lib/galaxy/datatypes/test/2.fastqsolexa
R lib/galaxy/datatypes/test/2.shuffled.bam
A lib/galaxy/datatypes/test/2.shuffled.unsorted.bam
M lib/galaxy/datatypes/test/2.txt
A lib/galaxy/datatypes/test/3.fastq
M lib/galaxy/datatypes/test/3.txt
M lib/galaxy/datatypes/test/454Score.pdf
M lib/galaxy/datatypes/test/5e5z.pqr
R lib/galaxy/datatypes/test/Acanium.hmm
A lib/galaxy/datatypes/test/Acanium.snaphmm
M lib/galaxy/datatypes/test/alignment.lav
R lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2
A lib/galaxy/datatypes/test/gff.gff3
R lib/galaxy/datatypes/test/gff_version_3.gff
A lib/galaxy/datatypes/test/interv1.bed
R lib/galaxy/datatypes/test/interval1.bed
M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
R lib/galaxy/datatypes/test/sequence.qual
M lib/galaxy/datatypes/test/sequence.qual454
M lib/galaxy/datatypes/test/sequence.qualsolid
A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml
R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
R lib/galaxy/datatypes/test/test.CEL
A lib/galaxy/datatypes/test/test.cel
R lib/galaxy/datatypes/test/test.idpDB
A lib/galaxy/datatypes/test/test.idpdb
R lib/galaxy/datatypes/test/test_ensembl.tab
A lib/galaxy/datatypes/test/test_ensembl.tabular
M lib/galaxy/datatypes/test/test_tab.bed
M lib/galaxy/datatypes/test/ucsc.customtrack
M lib/galaxy/datatypes/test/wiggle.wig
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/upload_util.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/util/checkers.py
M run_tests.sh
M scripts/bootstrap_history.py
M scripts/get_uwsgi_args.py
R static/GruntFile.js
R static/images/Armitagep_manhattan.png
R static/images/Armitagep_qqplot.png
R static/images/add_icon.png
R static/images/add_icon_dark.png
R static/images/aggregate_history1.png
R static/images/aggregate_history2.png
R static/images/bar_chart.png
R static/images/bed_warn.png
R static/images/closebox.png
R static/images/dat_points_table_brows_1.png
R static/images/ddarrowsplit.png
R static/images/delete.gif
A static/images/delete_tag_icon_gray.png
R static/images/delete_tag_icon_gray.png
R static/images/delete_tag_icon_white.png
R static/images/documents-stack-faded.png
R static/images/documents-stack.png
R static/images/dropdownarrow.png
R static/images/fetchTax.png
A static/images/fugue
R static/images/fugue/application-dock-270-bw.png
R static/images/fugue/application-dock-270.png
R static/images/fugue/arrow-000-small-bw.png
R static/images/fugue/arrow-090.png
R static/images/fugue/arrow-circle.png
R static/images/fugue/arrow-resize-090-bw.png
R static/images/fugue/arrow-resize-090.png
R static/images/fugue/arrow-split-bw.png
R static/images/fugue/arrow-split.png
R static/images/fugue/arrow-transition-270-bw.png
R static/images/fugue/arrow-transition-bw.png
R static/images/fugue/asterisk-small-outline.png
R static/images/fugue/asterisk-small-yellow.png
R static/images/fugue/asterisk-small.png
R static/images/fugue/block--plus-bw.png
R static/images/fugue/block--plus.png
R static/images/fugue/bookmarks-bw.png
R static/images/fugue/bookmarks.png
R static/images/fugue/bug.png
R static/images/fugue/chart.png
R static/images/fugue/chevron-expand-bw.png
R static/images/fugue/chevron-expand.png
R static/images/fugue/chevron.png
R static/images/fugue/control-270.png
R static/images/fugue/cross-button.png
R static/images/fugue/cross-circle-bw.png
R static/images/fugue/cross-circle.png
R static/images/fugue/cross-small-bw.png
R static/images/fugue/cross.png
R static/images/fugue/disk--arrow-bw.png
R static/images/fugue/disk--arrow.png
R static/images/fugue/disk.png
R static/images/fugue/exclamation.png
R static/images/fugue/external.png
R static/images/fugue/eye.png
R static/images/fugue/gear-bw.png
R static/images/fugue/gear.png
R static/images/fugue/globe-bw.png
R static/images/fugue/globe.png
R static/images/fugue/hammer-bw.png
R static/images/fugue/hammer.png
R static/images/fugue/information-white.png
R static/images/fugue/layer-transparent-bw.png
R static/images/fugue/layer-transparent.png
R static/images/fugue/layers-stack-bw.png
R static/images/fugue/layers-stack.png
R static/images/fugue/magnifier-left.png
R static/images/fugue/magnifier-zoom-out.png
R static/images/fugue/magnifier-zoom.png
R static/images/fugue/navigation.png
R static/images/fugue/pencil-small.png
R static/images/fugue/pencil.png
R static/images/fugue/plus-button-bw.png
R static/images/fugue/plus-button.png
R static/images/fugue/plus-circle.png
R static/images/fugue/sticky-note-text.png
R static/images/fugue/tag--plus.png
R static/images/fugue/tag-label.png
R static/images/fugue/tags.png
R static/images/fugue/toggle-bw.png
R static/images/fugue/toggle-expand-bw.png
R static/images/fugue/toggle-expand.png
R static/images/fugue/toggle.png
R static/images/fugue/toolbox-bw.png
R static/images/fugue/toolbox.png
R static/images/fugue/ui-slider-050-bw.png
R static/images/fugue/ui-slider-050.png
R static/images/hatch-023858.png
R static/images/histogram.png
R static/images/histogram2.png
R static/images/jstree/32px.png
R static/images/jstree/40px.png
R static/images/jstree/throbber.gif
R static/images/kendall.png
R static/images/light_gray_grid.gif
R static/images/mag_glass.png
R static/images/mutation_visualization_example.png
R static/images/overview_arrows.png
R static/images/pearson.png
R static/images/resizable.png
R static/images/scatter.png
R static/images/scatterplot.png
R static/images/select2-spinner.gif
R static/images/select2.png
R static/images/select2x2.png
R static/images/silk/add.png
R static/images/silk/book.png
R static/images/silk/book_open.png
R static/images/silk/chart_curve.png
R static/images/silk/folder.png
R static/images/silk/folder_page.png
R static/images/silk/link.png
R static/images/silk/link_break.png
R static/images/silk/page_white.png
R static/images/silk/page_white_compressed.png
R static/images/silk/resultset_bottom.png
R static/images/silk/resultset_next.png
R static/images/silk/resultset_previous.png
R static/images/solid_qual.png
R static/images/spearman.png
R static/images/star.gif
R static/images/thumbtack_icon.png
R static/images/thumbtack_icon_dark.png
R static/images/tipsy.gif
A static/images/tracks
R static/images/tracks/block.png
R static/images/tracks/close_btn.gif
R static/images/tracks/diag_bg.gif
R static/images/tracks/go_btn.gif
R static/images/tracks/handle-left.gif
R static/images/tracks/handle-right.gif
R static/images/tracks/pan_left.gif
R static/images/tracks/pan_right.gif
R static/images/tracks/show_history.gif
R static/images/tracks/zoom_in.gif
R static/images/tracks/zoom_in_full.gif
R static/images/tracks/zoom_out.gif
R static/images/tracks/zoom_out_full.gif
A static/images/visualization
R static/images/visualization/draggable_horizontal.png
R static/images/visualization/draggable_vertical.png
R static/images/visualization/strand_left.png
R static/images/visualization/strand_left_inv.png
R static/images/visualization/strand_right.png
R static/images/visualization/strand_right_inv.png
M static/style/base.css
A static/style/blue/base.css
R static/style/blue/base.css
R static/style/blue/base_bg.png
R static/style/blue/button_bar_bg_light.png
R static/style/blue/data_empty.png
R static/style/blue/data_error.png
R static/style/blue/data_ok.png
R static/style/blue/data_queued.png
R static/style/blue/done_message_icon.png
R static/style/blue/error_bg.png
R static/style/blue/error_large.png
R static/style/blue/error_message_icon.png
R static/style/blue/error_small.png
R static/style/blue/footer_title_bg.png
R static/style/blue/form_body_bg.png
R static/style/blue/form_title_bg.png
R static/style/blue/fugue.png
R static/style/blue/gray_bg.png
R static/style/blue/hgrad.png
R static/style/blue/hgrad_over.png
R static/style/blue/history-buttons.png
R static/style/blue/history-states.png
R static/style/blue/info_large.png
R static/style/blue/info_message_icon.png
R static/style/blue/info_small.png
R static/style/blue/largespinner.gif
R static/style/blue/layout_callout_top.png
R static/style/blue/masthead_bg.png
R static/style/blue/menu_bg.png
R static/style/blue/ok_bg.png
R static/style/blue/ok_large.png
A static/style/blue/ok_small.png
R static/style/blue/ok_small.png
R static/style/blue/panel_header_bg.png
R static/style/blue/popupmenu_callout_top.png
R static/style/blue/question-balloon.png
A static/style/blue/question-octagon-frame.png
R static/style/blue/question-octagon-frame.png
R static/style/blue/tiny_arrow_left.png
R static/style/blue/tiny_arrow_right.png
M static/style/blue/trackster.css
R static/style/blue/wait_large.png
R static/style/blue/wait_small.png
R static/style/blue/warn_bg.png
R static/style/blue/warn_large.png
R static/style/blue/warn_message_icon.png
R static/style/blue/warn_small.png
R static/style/blue/workflow_circle_drag.png
R static/style/blue/workflow_circle_green.png
R static/style/blue/workflow_circle_open.png
R static/style/shared_images/data_running.gif
R static/style/shared_images/error_large.png
R static/style/shared_images/error_small.png
R static/style/shared_images/info_large.png
R static/style/shared_images/info_small.png
R static/style/shared_images/ok_large.png
R static/style/shared_images/ok_small.png
R static/style/shared_images/wait_large.png
R static/style/shared_images/wait_small.png
R static/style/shared_images/warn_large.png
R static/style/shared_images/warn_small.png
M static/welcome.html.sample
M templates/admin/tool_shed_repository/browse_repository.mako
M templates/admin/tool_shed_repository/browse_tool_dependency.mako
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/galaxy_client_app.mako
M templates/js-app.mako
M templates/legacy/grid_base.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/gie.mako
M templates/webapps/galaxy/visualization/sweepster.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/tool_shed/repository/browse_repository.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
M templates/webapps/tool_shed/repository/rate_repository.mako
M templates/webapps/tool_shed/repository/upload.mako
M templates/webapps/tool_shed/repository/view_changelog.mako
M templates/webapps/tool_shed/repository/view_changeset.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/repository_review/browse_review.mako
M templates/webapps/tool_shed/repository_review/edit_review.mako
M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako
M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako
M templates/webapps/tool_shed/repository_review/select_previous_review.mako
M test/base/driver_util.py
M test/base/populators.py
A test/integration/test_datatype_upload.py
M test/unit/datatypes/test_bam.py
M test/unit/datatypes/test_vcf.py
Log Message:
-----------
Merged dev
Commit: 294cfbf6716dbac554da36f0c410276669c1dce9
https://github.com/galaxyproject/galaxy/commit/294cfbf6716dbac554da36f0c410…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-31 (Wed, 31 Oct 2018)
Changed paths:
M client/webpack.config.js
Log Message:
-----------
Updated provide monitored proxy for Galaxy references
Commit: d7d5e04f9276ba3c1cd9ef2c1a09ede1fc9f5ed0
https://github.com/galaxyproject/galaxy/commit/d7d5e04f9276ba3c1cd9ef2c1a09…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/utils/installMonitor.js
Log Message:
-----------
Changed toggle to installation toggle instead of logging toggle
Commit: 5ffd438ebfef26c55b9b11da2f24abd6c2772b43
https://github.com/galaxyproject/galaxy/commit/5ffd438ebfef26c55b9b11da2f24…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/utils/installMonitor.js
Log Message:
-----------
Updated install console functions and instructions
Commit: 11375a5692fe541e3df257f3ce2e36cd6f39a1f8
https://github.com/galaxyproject/galaxy/commit/11375a5692fe541e3df257f3ce2e…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M .travis.yml
M Makefile
M client/galaxy/scripts/qunit/test.js
A client/galaxy/scripts/sample.test.js
A client/galaxy/scripts/unitTestBundle.js
M client/galaxy/style/scss/ui.scss
R client/karma.config.js
A client/karma/karma.config.base.js
A client/karma/karma.config.mocha.js
A client/karma/karma.config.qunit.js
A client/karma/webpack.config.qunit.js
A client/karma/webpack.config.unittest.js
M client/package.json
M client/yarn.lock
M config/datatypes_conf.xml.sample
M config/migrated_tools_conf.xml.sample
M config/shed_tool_conf.xml.sample
M doc/source/admin/tool_panel.rst
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/tar_to_directory.xml
M lib/galaxy/datatypes/data.py
A lib/galaxy/datatypes/test/diamond.rma6
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/util/compression_utils.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/util/common_util.py
M templates/admin/tool_shed_repository/monitor_repository_installation.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
M templates/webapps/galaxy/admin/tool_sheds.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
M test/api/test_tools.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/integration/test_upload_configuration_options.py
M test/unit/workflows/test_workflow_progress.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into window_monitor
Commit: 38e9225aff0997efe3b023cf28ec869faa09d161
https://github.com/galaxyproject/galaxy/commit/38e9225aff0997efe3b023cf28ec…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/jsconfig.json
M client/galaxy/scripts/onload/index.js
M client/galaxy/scripts/sample.test.js
M client/galaxy/scripts/unitTestBundle.js
M client/galaxy/scripts/utils/installMonitor.js
M client/galaxy/scripts/utils/mock.js
Log Message:
-----------
Client format
Commit: 4405d15fea61b2610045ecfe4a6a1a0922142df8
https://github.com/galaxyproject/galaxy/commit/4405d15fea61b2610045ecfe4a6a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M .gitignore
A client/galaxy/jsconfig.json
M client/galaxy/scripts/galaxy.js
A client/galaxy/scripts/galaxy.monitor.js
R client/galaxy/scripts/onload.js
A client/galaxy/scripts/onload/index.js
A client/galaxy/scripts/onload/loadConfig.js
M client/galaxy/scripts/sample.test.js
M client/galaxy/scripts/unitTestBundle.js
A client/galaxy/scripts/utils/installMonitor.js
A client/galaxy/scripts/utils/mock.js
A client/galaxy/scripts/utils/serverPath.js
M client/webpack.config.js
M test/galaxy_selenium/navigates_galaxy.py
Log Message:
-----------
Merge branch 'window_monitor' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/e9f269393346...4405d15fea61
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 2fe7e55082bccb39d0d7042d40dd2ee0067be2cc
https://github.com/galaxyproject/usegalaxy-playbook/commit/2fe7e55082bccb39…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-26 (Fri, 26 Oct 2018)
Changed paths:
M env/test/files/galaxy/var/shed_data_manager_conf.xml
Log Message:
-----------
Test mutable config for DM upgrades
Commit: fb1d9545e605f1527537071560f0cccafcba289e
https://github.com/galaxyproject/usegalaxy-playbook/commit/fb1d9545e605f152…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-26 (Fri, 26 Oct 2018)
Changed paths:
M env/common/templates/supervisor/galaxy_handler.j2
M env/test/files/galaxy/galaxy_version.yml
M env/test/group_vars/galaxyservers/vars.yml
Log Message:
-----------
Update Test and increase its handler shutdown timeout.
Commit: 86c430efbc9db6a2577f58ca577858b8c71c7e5f
https://github.com/galaxyproject/usegalaxy-playbook/commit/86c430efbc9db6a2…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M env/main/files/galaxy/galaxy_version.yml
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
M env/testtoolshed/group_vars/toolshedservers/vars.yml
M env/toolshed/group_vars/toolshedservers/vars.yml
Log Message:
-----------
Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook
Commit: 00c9258264550ee6d460bdc2f0d5c849f5bd3118
https://github.com/galaxyproject/usegalaxy-playbook/commit/00c9258264550ee6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
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:
-----------
Test mutable configs
Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/deafd85205f9...…
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d898b672adc6924395bbb8c282999e0183891b5a
https://github.com/galaxyproject/galaxy/commit/d898b672adc6924395bbb8c28299…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/components/Alert.vue
A client/galaxy/scripts/components/admin/DataManager/DataManager.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
M client/package.json
M client/yarn.lock
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
R templates/webapps/galaxy/data_manager/index.mako
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_admin_app.py
Log Message:
-----------
Vue rewrite of admin data manager (local data): index page
* Added Alert component: Light bootstrap-vue b-alert wrapper.
- Hides automatically when given message is empty.
- Translates galaxy state keywords into bootstrap ones.
* Added vue-router integration: Display (future) Data Manager Jobs and Job
components inside router-views.
- Added router-view component DataManagerView.
* Rewrite (old mako, new json interface, new vue component)
- Index page (index.mako, data_managers_list, DataManager)
* Added Selenium test for DataManager component (index page)
Commit: 747e998d40b82117c21b80e86a347c96ff86353b
https://github.com/galaxyproject/galaxy/commit/747e998d40b82117c21b80e86a34…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManager.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
R templates/webapps/galaxy/data_manager/manage_data_manager.mako
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_admin_app.py
Log Message:
-----------
Vue rewrite of admin data manager (local data): manager page
* Rewrite (old mako, new json interface, new vue component)
- Manager page (manage_data_manager.mako, jobs_list, DataManagerJobs)
* Added Selenium test for DataManagerJobs component (manager page)
Commit: 13b8098259c9fc7a53b2db51a07b530b1d748b76
https://github.com/galaxyproject/galaxy/commit/13b8098259c9fc7a53b2db51a07b…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-09-18 (Tue, 18 Sep 2018)
Changed paths:
A client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
R templates/webapps/galaxy/data_manager/view_job.mako
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_admin_app.py
Log Message:
-----------
Vue rewrite of admin data manager (local data): view job page
* Rewrite (old mako, new json interface, new vue component)
- View job page (view_job.mako, job_info, DataManagerJob)
* Added Selenium test for DataManagerJob component (view job page)
Commit: 126c432bcf52279aea7ff952e771b0f4eefe012b
https://github.com/galaxyproject/galaxy/commit/126c432bcf52279aea7ff952e771…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M .ci/jenkins/api-py3/run_tests.sh
M .ci/jenkins/api/run_tests.sh
M .ci/jenkins/framework-py3/run_tests.sh
M .ci/jenkins/framework/run_tests.sh
M .ci/jenkins/main-tools-py3/run_tests.sh
M .ci/jenkins/main-tools/run_tests.sh
M .ci/jenkins/selenium-py3/run_tests.sh
M .ci/jenkins/selenium/run_tests.sh
M .ci/jenkins/toolshed/run_tests.sh
M .gitignore
M client/README.md
M client/galaxy/docs/bootstrap.md
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/components/admin/BaseGrid.vue
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/scratchbook.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-li-edit.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/lazy/lazy-limited.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-rules-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M 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-extension.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-settings.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/chart/views/description.js
M client/galaxy/scripts/mvc/visualization/chart/views/editor.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/settings.js
M client/galaxy/scripts/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/qunit/test.js
M client/galaxy/scripts/qunit/tests/form_tests.js
R client/galaxy/scripts/qunit/tests/popover_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js
M client/galaxy/scripts/ui/fa-icon-button.js
M client/galaxy/style/scss/base.scss
M client/galaxy/style/scss/charts.scss
M client/galaxy/style/scss/frame.scss
R client/galaxy/style/scss/galaxy_bootstrap/overrides.scss
R client/galaxy/style/scss/galaxy_bootstrap/variables.scss
R client/galaxy/style/scss/galaxy_variables.scss
M client/galaxy/style/scss/history.scss
M client/galaxy/style/scss/library.scss
M client/galaxy/style/scss/list-item.scss
A client/galaxy/style/scss/overrides.scss
M client/galaxy/style/scss/theme/blue.scss
R client/galaxy/style/scss/theme/plain.scss
M client/galaxy/style/scss/ui.scss
M client/galaxy/style/scss/upload.scss
A client/galaxy/style/source_material/error_icon.svg
M client/galaxy/style/source_material/galaxy_icons.svg
A client/galaxy/style/source_material/info_icon.svg
A client/galaxy/style/source_material/ok_icon.svg
A client/galaxy/style/source_material/wait_icon.svg
A client/galaxy/style/source_material/warn_icon.svg
M client/gulpfile.js
M client/package.json
M client/yarn.lock
M config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/webhooks/demo/tour_generator/__init__.py
M config/reports.yml.sample
M config/tool_shed.yml.sample
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/galaxy_options.rst
M doc/source/admin/jobs.md
M doc/source/admin/special_topics/interactive_environments.rst
M doc/source/dev/interactive_environments.rst
M lib/galaxy/actions/library.py
M lib/galaxy/authnz/managers.py
M lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/test/test.loom
M lib/galaxy/dependencies/conda-file.sh
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
R lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/slurm.py
A lib/galaxy/jobs/runners/util/cli/job/lsf.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/cloud.py
A lib/galaxy/managers/cloudauthzs.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
A lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/cwl/util.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/extract_dataset.xml
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/tag_collection_from_file.xml
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/examples.py.sample
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/compression_utils.py
M lib/galaxy/util/create_history_template.py
M lib/galaxy/util/rules_dsl.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/cloud.py
A lib/galaxy/webapps/galaxy/api/cloudauthz.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.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 lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/resources/example.py.sample
M lib/galaxy/workflow/run_request.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/util/repository_util.py
M scripts/bootstrap_history.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
M scripts/get_uwsgi_args.py
M scripts/plugin_staging.py
M static/style/blue/base.css
M static/style/blue/library.css
M templates/display_base.mako
M templates/galaxy_client_app.mako
M templates/ind_share_base.mako
M templates/show_params.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/share.mako
M templates/webapps/galaxy/page/editor.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/display_in_frame.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/tool_shed/common/repository_actions_menu.mako
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/role/role.mako
M templates/webapps/tool_shed/user/username.mako
A test-data/safetar_with_symlink.tar
A test-data/testdir.tar
A test-data/unsafe.tar
A test-data/unsafe.zip
A test-data/unsafe_relative_symlink.tar
M test/api/test_api_batch.py
M test/api/test_dataset_collections.py
M test/api/test_histories.py
M test/api/test_jobs.py
M test/api/test_pages.py
M test/api/test_tools.py
M test/api/test_tools_upload.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/populators.py
M test/base/workflow_fixtures.py
R test/base/workflows_format_2/README.txt
R test/base/workflows_format_2/__init__.py
R test/base/workflows_format_2/converter.py
R test/base/workflows_format_2/interface.py
R test/base/workflows_format_2/main.py
M test/functional/tools/disambiguate_cond.xml
A test/functional/tools/identifier_in_conditional.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_stock_tours.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_job_wrapper.py
A test/unit/test_compression_util.py
M test/unit/test_galaxy_mapping.py
A test/unit/test_utils.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/workflows/test_extract_summary.py
M test/unit/workflows/test_modules.py
Log Message:
-----------
Merge branch 'dev'
Commit: 2ef1aeef3c986938a3cd48e42758329e29792860
https://github.com/galaxyproject/galaxy/commit/2ef1aeef3c986938a3cd48e42758…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManager.vue
Log Message:
-----------
DataManager: delay rendering until server data is ready
Commit: 8db26fe522f9cab6d29d3b03f41975b5354bcef3
https://github.com/galaxyproject/galaxy/commit/8db26fe522f9cab6d29d3b03f419…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
Log Message:
-----------
DataManagerJobs: delay rendering until server data is ready
Commit: d3b43da3f518a8d221f8ba71883ad97a95f610f9
https://github.com/galaxyproject/galaxy/commit/d3b43da3f518a8d221f8ba71883a…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
Log Message:
-----------
DataManagerJob: delay rendering until server data is ready
Commit: 8b7d203ec8ffe685ff56479d79243536f27d0252
https://github.com/galaxyproject/galaxy/commit/8b7d203ec8ffe685ff56479d7924…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-12 (Fri, 12 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManager.vue
Log Message:
-----------
DataManager: check for empty server data
Commit: 3af83f4254a284e50e3a30ce6ed81dea82b2eabc
https://github.com/galaxyproject/galaxy/commit/3af83f4254a284e50e3a30ce6ed8…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-12 (Fri, 12 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
Log Message:
-----------
DataManagerJobs: check for empty server data
Fix jobs_list redirect in case data manager is non-existent with empty
server response containing an error message and status.
Commit: 877feae8bacd7104add9b31632843c7d3cbd2a39
https://github.com/galaxyproject/galaxy/commit/877feae8bacd7104add9b3163284…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-16 (Tue, 16 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_admin_app.py
Log Message:
-----------
DataManagerJob: check for empty server data & refactoring
* DataManagerJob
- Check for empty server data & refactoring
- Fix and numerate data-card ids
* job_info
- Fix error log in job_info.
- Fix redirect in case job is non-existent with empty server response
containing an error message and status.
* Extend DataManagerJob test
Commit: 53a505eaef3e8d91689ecfeb3b785928c54a8e42
https://github.com/galaxyproject/galaxy/commit/53a505eaef3e8d91689ecfeb3b78…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-17 (Wed, 17 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManager.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
R templates/webapps/galaxy/data_manager/manage_data_table.mako
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_admin_app.py
Log Message:
-----------
Vue rewrite of admin data manager (local data): manage data table
* Rewrite (old mako, new json interface, new vue component)
- Manage data table page (manage_data_table.mako, tool_data_table_info,
DataManagerTable)
* Added Selenium test for DataManagerTable component (Manage data table page)
Commit: 6d2a755614239149193d87e8cb695c963c17dc71
https://github.com/galaxyproject/galaxy/commit/6d2a755614239149193d87e8cb69…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-17 (Wed, 17 Oct 2018)
Changed paths:
M client/README.md
A client/galaxy/docs/README.md
M client/galaxy/docs/bootstrap.md
M client/galaxy/docs/galaxy-buttons.md
M client/galaxy/docs/galaxy-forms.md
M client/galaxy/docs/galaxy-masthead.md
M client/galaxy/docs/galaxy-menus.md
M client/galaxy/docs/galaxy-messages.md
M client/galaxy/docs/galaxy-panels.md
M client/galaxy/docs/galaxy-tables.md
M client/galaxy/docs/galaxy-tabs.md
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/ui/ui-rules-edit.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/ui/editable-text.js
M client/galaxy/style/scss/base.scss
M client/galaxy/style/scss/history.scss
M client/galaxy/style/scss/jstree.scss
M client/galaxy/style/scss/list-item.scss
M client/galaxy/style/scss/ui.scss
A config/container_resolvers_conf.xml.sample
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/dev/index.rst
A doc/source/releases/18.09.rst
A doc/source/releases/18.09_announce.rst
A doc/source/releases/19.01_announce.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/upload_util.py
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/managers/cloud.py
M lib/galaxy/model/metadata.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/monitors.py
M lib/galaxy/webapps/galaxy/api/cloudauthz.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/tool_shed/util/hg_util.py
M scripts/bootstrap_history.py
M static/style/blue/base.css
A static/style/blue/info_icon.svg
M templates/admin/jobs.mako
M templates/admin/review_tool_migration_stages.mako
M templates/admin/tool_shed_repository/browse_repository.mako
M templates/admin/tool_shed_repository/browse_tool_dependency.mako
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
M templates/admin/tool_shed_repository/monitor_repository_installation.mako
M templates/admin/tool_shed_repository/purge_repository_confirmation.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
M templates/admin/tool_shed_repository/view_workflow.mako
M templates/message.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
M test/api/test_tools.py
A test/base/ssh_util.py
A test/functional/tools/for_workflows/mapper_two.xml
M test/functional/tools/job_environment_default.xml
M test/functional/tools/job_environment_default_legacy.xml
M test/functional/tools/job_environment_explicit_shared_home.xml
M test/functional/tools/samples_tool_conf.xml
A test/integration/test_cli_runners.py
M test/integration/test_job_environments.py
M test/unit/test_remote_shell.py
Log Message:
-----------
Merge branch 'dev' into admin.data.manager.vue.steps
Commit: 31b484492260f554020ed8eed1d1a20cd98089ef
https://github.com/galaxyproject/galaxy/commit/31b484492260f554020ed8eed1d1…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-10-17 (Wed, 17 Oct 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
Log Message:
-----------
Fix linting error by removing unused import markupsafe escape
Commit: 8789713b9584c8ee58692b4dc02a282f32484502
https://github.com/galaxyproject/galaxy/commit/8789713b9584c8ee58692b4dc02a…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-11-03 (Sat, 03 Nov 2018)
Changed paths:
M .ci/jenkins/selenium-py3/run_tests.sh
M .gitignore
M Makefile
M client/.babelrc
R client/GruntFile.js
A client/galaxy/images/Armitagep_manhattan.png
A client/galaxy/images/Armitagep_qqplot.png
A client/galaxy/images/add_icon.png
A client/galaxy/images/add_icon_dark.png
A client/galaxy/images/aggregate_history1.png
A client/galaxy/images/aggregate_history2.png
A client/galaxy/images/bar_chart.png
A client/galaxy/images/base_bg.png
A client/galaxy/images/bed_warn.png
A client/galaxy/images/button_bar_bg_light.png
A client/galaxy/images/circle.py
A client/galaxy/images/closebox.png
A client/galaxy/images/dat_points_table_brows_1.png
A client/galaxy/images/data_empty.png
A client/galaxy/images/data_error.png
A client/galaxy/images/data_ok.png
A client/galaxy/images/data_queued.png
A client/galaxy/images/data_running.gif
A client/galaxy/images/ddarrowsplit.png
A client/galaxy/images/delete.gif
A client/galaxy/images/delete_tag_icon_gray.png
A client/galaxy/images/delete_tag_icon_white.png
A client/galaxy/images/documents-stack-faded.png
A client/galaxy/images/documents-stack.png
A client/galaxy/images/done_message_icon.png
A client/galaxy/images/dropdownarrow.png
A client/galaxy/images/error_bg.png
A client/galaxy/images/error_icon.svg
A client/galaxy/images/error_large.png
A client/galaxy/images/error_message_icon.png
A client/galaxy/images/error_small.png
A client/galaxy/images/fetchTax.png
A client/galaxy/images/footer_title_bg.png
A client/galaxy/images/form_body_bg.png
A client/galaxy/images/form_title_bg.png
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M client/galaxy/scripts/apps/admin.js
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M client/galaxy/scripts/layout/masthead.js
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M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/polyfills.js
M client/galaxy/scripts/qunit/assets/base.css
M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
M client/galaxy/scripts/reports/run_stats.js
A client/galaxy/scripts/style.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/viz/phyloviz.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/scripts/viz/visualization.js
M client/galaxy/style/scss/autocomplete_tagging.scss
M client/galaxy/style/scss/base.scss
M client/galaxy/style/scss/collection.scss
M client/galaxy/style/scss/iconic_stroke.scss
A client/galaxy/style/scss/jquery.rating.scss
M client/galaxy/style/scss/jstree.scss
M client/galaxy/style/scss/list-item.scss
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M client/galaxy/style/scss/trackster.scss
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R client/galaxy/style/source_material/circle.py
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M client/gulpfile.js
M client/karma.config.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/migrated_tools_conf.xml.sample
M config/plugins/visualizations/common/templates/chart_entry_point.mako
M config/plugins/visualizations/scatterplot/package.json
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/scatterplot.css
M config/plugins/visualizations/scatterplot/static/scatterplot.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
M config/plugins/webhooks/demo/tour_generator/config.yml
A config/plugins/webhooks/demo/tour_generator/package.json
M config/plugins/webhooks/demo/tour_generator/script.js
A config/plugins/webhooks/demo/tour_generator/tour_generator.js
M config/shed_tool_conf.xml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/admin/scaling.md
M doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/tool_panel.rst
M doc/source/dev/faq.rst
M doc/source/releases/18.09.rst
M doc/source/releases/18.09_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/authnz/managers.py
M lib/galaxy/config.py
M lib/galaxy/containers/docker.py
M lib/galaxy/containers/docker_model.py
M lib/galaxy/containers/docker_swarm.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
A lib/galaxy/datatypes/converters/tar_to_directory.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
A lib/galaxy/datatypes/isa.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/phylip.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
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R lib/galaxy/datatypes/test/Acanium.hmm
A lib/galaxy/datatypes/test/Acanium.snaphmm
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A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom2
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M lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
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A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.blastxml
R lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
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M lib/galaxy/datatypes/test/ucsc.customtrack
M lib/galaxy/datatypes/test/wiggle.wig
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/upload_util.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
M lib/galaxy/managers/cloud.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py
A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/cloud.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/json.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/webapps/galaxy/api/cloudauthz.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/uploads.py
M lib/galaxy/webapps/galaxy/api/users.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 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/util/xml_util.py
M run.sh
M run_tests.sh
M scripts/bootstrap_history.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/get_uwsgi_args.py
M scripts/runtime_stats.py
M scripts/summarize_timings.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/transfer.py
M setup.cfg
R static/GruntFile.js
R static/images/Armitagep_manhattan.png
R static/images/Armitagep_qqplot.png
R static/images/add_icon.png
R static/images/add_icon_dark.png
R static/images/aggregate_history1.png
R static/images/aggregate_history2.png
R static/images/bar_chart.png
R static/images/bed_warn.png
R static/images/closebox.png
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R static/images/dropdownarrow.png
R static/images/fetchTax.png
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R static/images/fugue/layers-stack.png
R static/images/fugue/magnifier-left.png
R static/images/fugue/magnifier-zoom-out.png
R static/images/fugue/magnifier-zoom.png
R static/images/fugue/navigation.png
R static/images/fugue/pencil-small.png
R static/images/fugue/pencil.png
R static/images/fugue/plus-button-bw.png
R static/images/fugue/plus-button.png
R static/images/fugue/plus-circle.png
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R static/images/fugue/tag--plus.png
R static/images/fugue/tag-label.png
R static/images/fugue/tags.png
R static/images/fugue/toggle-bw.png
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R static/images/fugue/toggle.png
R static/images/fugue/toolbox-bw.png
R static/images/fugue/toolbox.png
R static/images/fugue/ui-slider-050-bw.png
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R static/images/hatch-023858.png
R static/images/histogram.png
R static/images/histogram2.png
R static/images/jstree/32px.png
R static/images/jstree/40px.png
R static/images/jstree/throbber.gif
R static/images/kendall.png
R static/images/light_gray_grid.gif
R static/images/mag_glass.png
R static/images/mutation_visualization_example.png
R static/images/overview_arrows.png
R static/images/pearson.png
R static/images/resizable.png
R static/images/scatter.png
R static/images/scatterplot.png
R static/images/select2-spinner.gif
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R static/images/silk/add.png
R static/images/silk/book.png
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R static/images/silk/chart_curve.png
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R static/images/silk/resultset_bottom.png
R static/images/silk/resultset_next.png
R static/images/silk/resultset_previous.png
R static/images/solid_qual.png
R static/images/spearman.png
R static/images/star.gif
R static/images/thumbtack_icon.png
R static/images/thumbtack_icon_dark.png
R static/images/tipsy.gif
A static/images/tracks
R static/images/tracks/block.png
R static/images/tracks/close_btn.gif
R static/images/tracks/diag_bg.gif
R static/images/tracks/go_btn.gif
R static/images/tracks/handle-left.gif
R static/images/tracks/handle-right.gif
R static/images/tracks/pan_left.gif
R static/images/tracks/pan_right.gif
R static/images/tracks/show_history.gif
R static/images/tracks/zoom_in.gif
R static/images/tracks/zoom_in_full.gif
R static/images/tracks/zoom_out.gif
R static/images/tracks/zoom_out_full.gif
A static/images/visualization
R static/images/visualization/draggable_horizontal.png
R static/images/visualization/draggable_vertical.png
R static/images/visualization/strand_left.png
R static/images/visualization/strand_left_inv.png
R static/images/visualization/strand_right.png
R static/images/visualization/strand_right_inv.png
M static/style/base.css
A static/style/blue/base.css
R static/style/blue/base.css
R static/style/blue/base_bg.png
R static/style/blue/button_bar_bg_light.png
R static/style/blue/data_empty.png
R static/style/blue/data_error.png
R static/style/blue/data_ok.png
R static/style/blue/data_queued.png
R static/style/blue/done_message_icon.png
R static/style/blue/error_bg.png
R static/style/blue/error_large.png
R static/style/blue/error_message_icon.png
R static/style/blue/error_small.png
R static/style/blue/footer_title_bg.png
R static/style/blue/form_body_bg.png
R static/style/blue/form_title_bg.png
R static/style/blue/fugue.png
R static/style/blue/gray_bg.png
R static/style/blue/hgrad.png
R static/style/blue/hgrad_over.png
R static/style/blue/history-buttons.png
R static/style/blue/history-states.png
R static/style/blue/info_large.png
R static/style/blue/info_message_icon.png
R static/style/blue/info_small.png
R static/style/blue/largespinner.gif
R static/style/blue/layout_callout_top.png
R static/style/blue/masthead_bg.png
R static/style/blue/menu_bg.png
R static/style/blue/ok_bg.png
R static/style/blue/ok_large.png
A static/style/blue/ok_small.png
R static/style/blue/ok_small.png
R static/style/blue/panel_header_bg.png
R static/style/blue/popupmenu_callout_top.png
R static/style/blue/question-balloon.png
A static/style/blue/question-octagon-frame.png
R static/style/blue/question-octagon-frame.png
R static/style/blue/tiny_arrow_left.png
R static/style/blue/tiny_arrow_right.png
M static/style/blue/trackster.css
R static/style/blue/wait_large.png
R static/style/blue/wait_small.png
R static/style/blue/warn_bg.png
R static/style/blue/warn_large.png
R static/style/blue/warn_message_icon.png
R static/style/blue/warn_small.png
R static/style/blue/workflow_circle_drag.png
R static/style/blue/workflow_circle_green.png
R static/style/blue/workflow_circle_open.png
R static/style/shared_images/data_running.gif
R static/style/shared_images/error_large.png
R static/style/shared_images/error_small.png
R static/style/shared_images/info_large.png
R static/style/shared_images/info_small.png
R static/style/shared_images/ok_large.png
R static/style/shared_images/ok_small.png
R static/style/shared_images/wait_large.png
R static/style/shared_images/wait_small.png
R static/style/shared_images/warn_large.png
R static/style/shared_images/warn_small.png
M static/welcome.html.sample
M templates/admin/tool_shed_repository/browse_repository.mako
M templates/admin/tool_shed_repository/browse_tool_dependency.mako
M templates/admin/tool_shed_repository/manage_repository.mako
M templates/admin/tool_shed_repository/monitor_repository_installation.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/galaxy_client_app.mako
M templates/ind_share_base.mako
M templates/js-app.mako
M templates/legacy/grid_base.mako
M templates/message.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
M templates/webapps/galaxy/admin/tool_sheds.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/share.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/display_in_frame.mako
M templates/webapps/galaxy/visualization/gie.mako
M templates/webapps/galaxy/visualization/sweepster.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/galaxy/workflow/sharing.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/tool_shed/repository/browse_repository.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
M templates/webapps/tool_shed/repository/rate_repository.mako
M templates/webapps/tool_shed/repository/upload.mako
M templates/webapps/tool_shed/repository/view_changelog.mako
M templates/webapps/tool_shed/repository/view_changeset.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/repository_review/browse_review.mako
M templates/webapps/tool_shed/repository_review/edit_review.mako
M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako
M templates/webapps/tool_shed/repository_review/reviews_of_repository.mako
M templates/webapps/tool_shed/repository_review/select_previous_review.mako
A test-data/MTBLS6.zip
M test/api/test_tools.py
M test/api/test_tools_upload.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/driver_util.py
M test/base/populators.py
M test/base/workflow_fixtures.py
M test/functional/tools/output_filter.xml
A test/functional/tools/remove_value.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/webhooks/phdcomics/__init__.py
M test/galaxy_selenium/navigation.yml
A test/integration/test_datatype_upload.py
M test/integration/test_upload_configuration_options.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/base/twilltestcase.py
M test/unit/datatypes/test_bam.py
M test/unit/datatypes/test_vcf.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/web/framework/test_webapp.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/extract/extract_genomic_dna.py
M tools/filters/convert_characters.py
M tools/filters/grep.py
M tools/filters/uniq.py
M tools/stats/filtering.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge branch 'dev' into admin.data.manager.vue.steps
Commit: 91df3971be62419620c3cd08b0c9162ec6989856
https://github.com/galaxyproject/galaxy/commit/91df3971be62419620c3cd08b0c9…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-11-03 (Sat, 03 Nov 2018)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/components/admin/DataManager/DataManager.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
DataManagerRouter, DataManager, DataManagerJobs: Fix routing problem
* Forward path following the data manager url to DataManagerRouter
* encode id in DataManager and DataManagerJobs
Commit: 45d0f161c92c6fdac103ca3eecec421ac3fa3db3
https://github.com/galaxyproject/galaxy/commit/45d0f161c92c6fdac103ca3eecec…
Author: Sebastian Kapust <sebastian(a)kapust.org>
Date: 2018-11-03 (Sat, 03 Nov 2018)
Changed paths:
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1460_data_managers.py
Log Message:
-----------
Fix functional test case test_1460_data_managers
Commit: 4b3606f1acd57064c3b4a2da6842a58d5d634a9b
https://github.com/galaxyproject/galaxy/commit/4b3606f1acd57064c3b4a2da6842…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
Log Message:
-----------
Target top with rerun to avoid nested Galaxy.
Commit: e9f269393346175c2d88dd6e190d3d00547ef3c6
https://github.com/galaxyproject/galaxy/commit/e9f269393346175c2d88dd6e190d…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/components/Alert.vue
A client/galaxy/scripts/components/admin/DataManager/DataManager.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
A client/galaxy/scripts/components/admin/DataManager/DataManagerView.vue
M client/package.json
M client/yarn.lock
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
R templates/webapps/galaxy/data_manager/index.mako
R templates/webapps/galaxy/data_manager/manage_data_manager.mako
R templates/webapps/galaxy/data_manager/manage_data_table.mako
R templates/webapps/galaxy/data_manager/view_job.mako
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_admin_app.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1460_data_managers.py
Log Message:
-----------
Merge pull request #6729 from scrathat/admin.data.manager.vue.steps
Vue rewrite of admin data manager (local data) in steps
Compare: https://github.com/galaxyproject/galaxy/compare/a53de291fefd...e9f269393346
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e8a64a862212af970690fcd1969ac8f5ebaaf407
https://github.com/galaxyproject/galaxy/commit/e8a64a862212af970690fcd1969a…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-31 (Wed, 31 Oct 2018)
Changed paths:
A client/galaxy/scripts/apps/sample.test.js
A client/galaxy/scripts/unitTestBundle.js
A client/karma.config.base.js
R client/karma.config.js
A client/karma.config.mocha.js
A client/karma.config.qunit.js
M client/package.json
A client/webpack.config.test.js
M client/yarn.lock
Log Message:
-----------
Split qunit and mocha tests, clean up karma configs
Commit: 1490b6ae839bd704af45b7a415ba70d7fc013df3
https://github.com/galaxyproject/galaxy/commit/1490b6ae839bd704af45b7a415ba…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-10-31 (Wed, 31 Oct 2018)
Changed paths:
M client/galaxy/style/scss/ui.scss
M templates/admin/tool_shed_repository/monitor_repository_installation.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
Log Message:
-----------
Merge branch 'dev' into karma_chromeheadless
Commit: b52b2d8c4817295f9dad56a057fe9d5a095d3a37
https://github.com/galaxyproject/galaxy/commit/b52b2d8c4817295f9dad56a057fe…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M config/migrated_tools_conf.xml.sample
M config/shed_tool_conf.xml.sample
M doc/source/admin/tool_panel.rst
A lib/galaxy/datatypes/converters/tar_to_directory.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/util/compression_utils.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/util/common_util.py
M templates/webapps/galaxy/admin/tool_sheds.mako
M test/api/test_tools.py
M test/api/test_tools_upload.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
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into karma_chromeheadless
Commit: 2cc0417530cb33dfa43cb0c0d64f2f807d5396d5
https://github.com/galaxyproject/galaxy/commit/2cc0417530cb33dfa43cb0c0d64f…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M .travis.yml
M client/karma.config.base.js
Log Message:
-----------
Added chrome to qunit build, tried no sandbox flag on chrome
Commit: b637c7575a6cdd17960b57e803cabcaa9fe5972c
https://github.com/galaxyproject/galaxy/commit/b637c7575a6cdd17960b57e803ca…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M Makefile
M client/karma.config.base.js
M client/package.json
Log Message:
-----------
Modified test script calls
Commit: 31d3c97e757fd9e9206c815d7b0c9b9d22d0d7a8
https://github.com/galaxyproject/galaxy/commit/31d3c97e757fd9e9206c815d7b0c…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M client/karma.config.qunit.js
Log Message:
-----------
Remove one failing test just to check build
Commit: e92ce870928700917d69e9c3d939087d6d48eb56
https://github.com/galaxyproject/galaxy/commit/e92ce870928700917d69e9c3d939…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M client/galaxy/scripts/qunit/test.js
M client/karma.config.qunit.js
Log Message:
-----------
Removed bad test just to test build
Commit: b06957e90619b3b7c4cf1f7b989ae32242b55f83
https://github.com/galaxyproject/galaxy/commit/b06957e90619b3b7c4cf1f7b989a…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M client/karma.config.mocha.js
Log Message:
-----------
Added existing mocha tests back
Commit: a7a73bcfcd32de2b89a6cd4119ba64db8be045ef
https://github.com/galaxyproject/galaxy/commit/a7a73bcfcd32de2b89a6cd4119ba…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M client/karma.config.base.js
M client/karma.config.mocha.js
M client/karma.config.qunit.js
M client/package.json
A client/webpack.config.qunit.js
R client/webpack.config.test.js
A client/webpack.config.unittest.js
M client/yarn.lock
Log Message:
-----------
Documented differences bretween different webpack configs, used cleaner tool and ignore-loader for true unit-tests
Commit: c2f71c3a3ec31fd6af7479db9ae13f8b0975d584
https://github.com/galaxyproject/galaxy/commit/c2f71c3a3ec31fd6af7479db9ae1…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M client/webpack.config.qunit.js
Log Message:
-----------
Added missing settings on special qunit webpack config
Commit: 19b2fdd73ba82d0eb3ae38141134915d8a745827
https://github.com/galaxyproject/galaxy/commit/19b2fdd73ba82d0eb3ae38141134…
Author: Mason <nerdinacan(a)gmail.com>
Date: 2018-11-03 (Sat, 03 Nov 2018)
Changed paths:
R client/galaxy/scripts/apps/sample.test.js
A client/galaxy/scripts/sample.test.js
R client/karma.config.base.js
R client/karma.config.mocha.js
R client/karma.config.qunit.js
A client/karma/karma.config.base.js
A client/karma/karma.config.mocha.js
A client/karma/karma.config.qunit.js
A client/karma/webpack.config.qunit.js
A client/karma/webpack.config.unittest.js
M client/package.json
R client/webpack.config.qunit.js
R client/webpack.config.unittest.js
Log Message:
-----------
Reorganized config scripts, fleshed out comments and instructions
Commit: a53de291fefd34ca9fcdf1a03bacd9739f768edf
https://github.com/galaxyproject/galaxy/commit/a53de291fefd34ca9fcdf1a03bac…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M .travis.yml
M Makefile
M client/galaxy/scripts/qunit/test.js
A client/galaxy/scripts/sample.test.js
A client/galaxy/scripts/unitTestBundle.js
R client/karma.config.js
A client/karma/karma.config.base.js
A client/karma/karma.config.mocha.js
A client/karma/karma.config.qunit.js
A client/karma/webpack.config.qunit.js
A client/karma/webpack.config.unittest.js
M client/package.json
M client/yarn.lock
Log Message:
-----------
Merge pull request #6959 from Nerdinacan/karma_chromeheadless
Switch from PhantomJS to Chrome Headless for unit tests
Compare: https://github.com/galaxyproject/galaxy/compare/c3dc2392ce1a...a53de291fefd
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.09
Home: https://github.com/galaxyproject/galaxy
Commit: 69b447169fb96048ea492a1d99d653585571c15b
https://github.com/galaxyproject/galaxy/commit/69b447169fb96048ea492a1d99d6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-11-01 (Thu, 01 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Allow deferring 'to_ext' extension to the server, implement for collections.
Commit: 3be8d66d71bcdb3eccde2d1a37731442ed1aa63a
https://github.com/galaxyproject/galaxy/commit/3be8d66d71bcdb3eccde2d1a3773…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/neo4j.py
Log Message:
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Remove unncecessary implementations of display_data
These were not updated to use `_download_filename`,
and so this fixes the download name for collection elements
to include the element identifier.
Note that the Data class should handle composite data just
fine.
Commit: f8b160535c5f9363e85c6c1d041b69ce5c3e9cc2
https://github.com/galaxyproject/galaxy/commit/f8b160535c5f9363e85c6c1d041b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
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Some minor fixes for the blast datatype
The signature for Data.display_data wasn't quite correct,
and the description of display_data was also a little misleading.
Commit: 61bda3d11a1d608ac8e1a731faf144ff989affc9
https://github.com/galaxyproject/galaxy/commit/61bda3d11a1d608ac8e1a731faf1…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/neo4j.py
Log Message:
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Merge pull request #6960 from dannon/collection_ext_dl
[18.09] Allow deferring 'to_ext' extension to the server
Compare: https://github.com/galaxyproject/galaxy/compare/2deb302ae7be...61bda3d11a1d
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b1fe6fee9373f025341e25b248ffa003a10213b3
https://github.com/galaxyproject/galaxy/commit/b1fe6fee9373f025341e25b248ff…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-24 (Wed, 24 Oct 2018)
Changed paths:
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M test/unit/workflows/test_workflow_progress.py
Log Message:
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Refactor collection mapping workflows toward independence from tools.
Refactor get_data_inputs into get_all_inputs and use the resulting dictionaries to reason about if collection mapping should occur during invocation of tools. Using these dictionaries instead of explicit tool input objects should allow reuse within other module types since they may produce the same interface.
Commit: c1e4b0111a70e3bae63791f60a44e6b14b259a5c
https://github.com/galaxyproject/galaxy/commit/c1e4b0111a70e3bae63791f60a44…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-11-05 (Mon, 05 Nov 2018)
Changed paths:
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M test/unit/workflows/test_workflow_progress.py
Log Message:
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Merge pull request #6911 from jmchilton/workflow_mapping_refactor
Refactor collection mapping workflows toward independence from tools.
Compare: https://github.com/galaxyproject/galaxy/compare/a3f213e3c531...c1e4b0111a70
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.