December 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 706221: Some workflow formatting.
by GitHub 05 Dec '17

05 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7062219d2a0d7545ce894b7a4ac542345a2c73d3 https://github.com/galaxyproject/galaxy/commit/7062219d2a0d7545ce894b7a4ac5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Some workflow formatting. Commit: ea386b394763b69da1427e766f52cfe2e9917337 https://github.com/galaxyproject/galaxy/commit/ea386b394763b69da1427e766f52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Cleanup, fix linting in workflow-canvas.js Commit: dcadf30148e8aa13301151b06efcad1db11857bb https://github.com/galaxyproject/galaxy/commit/dcadf30148e8aa13301151b06efc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Add passthroughs for copy/paste in workflow editor event bindings. Commit: 4d3abb5eb11f36537550526b4b9c2a100ce19907 https://github.com/galaxyproject/galaxy/commit/4d3abb5eb11f36537550526b4b9c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- window.getSelection is a function. Commit: be6b52df307197d75ad15e1cea1b8d3b14ee1ca6 https://github.com/galaxyproject/galaxy/commit/be6b52df307197d75ad15e1cea1b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- On node change, we need to blur() here; otherwise the active input is still potentially a hidden input field behind the scenes. Amazing this hasn't been a bug before now? Commit: 32afe8fab56d7f609fac0994f10f40e9f5ab6644 https://github.com/galaxyproject/galaxy/commit/32afe8fab56d7f609fac0994f10f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Clear active node is a more appropriate place for this blur. Commit: 0096a5851cd3513e3674341f89f556f710758d20 https://github.com/galaxyproject/galaxy/commit/0096a5851cd3513e3674341f89f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Blur on canvas click, too. Commit: 0e346735ab6b3256a2d4d6589308bab6113b6bdb https://github.com/galaxyproject/galaxy/commit/0e346735ab6b3256a2d4d6589308… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Build client. Commit: f09944a8229bf835ad838c7579a7a2b2b425c638 https://github.com/galaxyproject/galaxy/commit/f09944a8229bf835ad838c7579a7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Merge pull request #5124 from dannon/workflow_tool_copy_cleanup Workflow tool copy tweaks Compare: https://github.com/galaxyproject/galaxy/compare/3744730a9bcd...f09944a8229b

1 0

[galaxyproject/galaxy] 1f210c: Improve resilience of filter detection
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f210c98f895b75d10010df2f702f6cc0d20fde5 https://github.com/galaxyproject/galaxy/commit/1f210c98f895b75d10010df2f702… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Improve resilience of filter detection Commit: bc24621e81baba35727f7b4593a7cc6a3a766d06 https://github.com/galaxyproject/galaxy/commit/bc24621e81baba35727f7b4593a7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Raise log level for missing filter to warning Commit: 39bf7814f8b9caf5f12983a3786643ad8046f6b2 https://github.com/galaxyproject/galaxy/commit/39bf7814f8b9caf5f12983a37866… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Check filter function before adding it on initialization Commit: 62d1f5459a3596641e823de9207e2406a9cf865f https://github.com/galaxyproject/galaxy/commit/62d1f5459a3596641e823de9207e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Fix warning message Commit: f47fde8dc0b6e4469c74fe8357fbaf6e4e060b9b https://github.com/galaxyproject/galaxy/commit/f47fde8dc0b6e4469c74fe8357fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Fix user preference identifiers for section and label filters Commit: f3f40b5a6d1baa47c44a60b714d413069422ffc9 https://github.com/galaxyproject/galaxy/commit/f3f40b5a6d1baa47c44a60b714d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/webapps/galaxy/api/users.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Highlight filter inputs with missing modules Commit: 05daad94421bf2fa8282ca7b7beec9e98a82cf7f https://github.com/galaxyproject/galaxy/commit/05daad94421bf2fa8282ca7b7bee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add criteria to existing statement Commit: 7469b6483ba8d6aa58e35a04a0640a465e5677b7 https://github.com/galaxyproject/galaxy/commit/7469b6483ba8d6aa58e35a04a064… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Avoid building prefix string if not needed Commit: 225008ccf073b1ec925060c28f9fcbba9dff82dc https://github.com/galaxyproject/galaxy/commit/225008ccf073b1ec925060c28f9f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Add module name to error log Commit: 15928b544c3542a06b727a5d12246a073a1cc3cd https://github.com/galaxyproject/galaxy/commit/15928b544c3542a06b727a5d1224… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Improve error message Commit: 3744730a9bcd015589099920b8bce434d96ae7a7 https://github.com/galaxyproject/galaxy/commit/3744730a9bcd015589099920b8bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Merge remote-tracking branch 'guerler/improve_filter_resilience' into dev Compare: https://github.com/galaxyproject/galaxy/compare/43c518a6e951...3744730a9bcd

1 0

[galaxyproject/galaxy] 4d94fb: start work on workflow tool cloning
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d94fb58d4b13562a58c2353b0778d94f1ea4f3e https://github.com/galaxyproject/galaxy/commit/4d94fb58d4b13562a58c2353b077… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/yarn.lock M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- start work on workflow tool cloning Commit: 021a5eb2e3b02c07b01887a66f1f1e4522a8a645 https://github.com/galaxyproject/galaxy/commit/021a5eb2e3b02c07b01887a66f1f… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- preserve params on copy Commit: 8fcb7578ab9dcf963ad50d8190832be9fe055d3b https://github.com/galaxyproject/galaxy/commit/8fcb7578ab9dcf963ad50d819083… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- fix a bug when a tool couldn't be copied Commit: 1173ce6cf9fc2b46da127e1177fd12a2bbc60bb0 https://github.com/galaxyproject/galaxy/commit/1173ce6cf9fc2b46da127e1177fd… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- add copy&paste feature Commit: 43c518a6e9519efbd23c0c831b9475cc9fca206d https://github.com/galaxyproject/galaxy/commit/43c518a6e9519efbd23c0c831b94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/yarn.lock M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge remote-tracking branch 'anatskiy/workflow_tools_copying' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8c87b2c401f6...43c518a6e951

1 0

[galaxyproject/galaxy] 1a0800: Remove unused import, self from ui-tabs; named exp...
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a08005847d8a722262602e44c5d1d895295f89a https://github.com/galaxyproject/galaxy/commit/1a08005847d8a722262602e44c5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Remove unused import, self from ui-tabs; named export for the View. Commit: 243855cfd4e3a3a96f93e092e4a47325ebf183b2 https://github.com/galaxyproject/galaxy/commit/243855cfd4e3a3a96f93e092e4a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- Minor cleanup; named exports for these common utils functions which we can expect external consumers of. Commit: 5e05aa114b45341cba02329ef8c20ba71e6d5994 https://github.com/galaxyproject/galaxy/commit/5e05aa114b45341cba02329ef8c2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Named exports, cleanup for ui-misc. Includes a note about eliminating the practice of re-exporting stuff, but that's another project that'll have to fix downstream consumers. Commit: 5877d0c43e5adc8fb4342062d6577adcc6a6ea6b https://github.com/galaxyproject/galaxy/commit/5877d0c43e5adc8fb4342062d657… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js Log Message: ----------- Import/Export refactoring in mvc/form and mvc/ui; adjust charts usage to fix require-based entry. Lots of cleanup, too. Commit: 1c587117b04d6f5322bcdd1d60c609e19a4c313d https://github.com/galaxyproject/galaxy/commit/1c587117b04d6f5322bcdd1d60c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/components/model.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/client/views/description.js M config/plugins/visualizations/charts/static/client/views/editor.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js M config/plugins/visualizations/charts/static/client/views/viewer.js M config/plugins/visualizations/charts/static/client/views/viewport.js M config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Charts cleanup, formatting. Commit: df1083c541f6130b2a1de9e8ad99ba03b8a4d5af https://github.com/galaxyproject/galaxy/commit/df1083c541f6130b2a1de9e8ad99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/Gruntfile.js Log Message: ----------- Drop sudo reference (local npm, non-root), elaborate comment in scatterplot gruntfile. Commit: b6509f402fe7d33fd807501a5253daa18ff22876 https://github.com/galaxyproject/galaxy/commit/b6509f402fe7d33fd807501a5253… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Scatterplot was missing require? Did not dig to see how this ever worked before, yet. Commit: c23c2324bc6c84d1f09e0dc2651c1775f1cc2ca5 https://github.com/galaxyproject/galaxy/commit/c23c2324bc6c84d1f09e0dc2651c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/package.json R config/plugins/visualizations/scatterplot/Gruntfile.js R config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js R config/plugins/visualizations/scatterplot/src/scatterplot-display.js R config/plugins/visualizations/scatterplot/src/scatterplot-model.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot-edit.js A config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js M config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Scatterplot overhaul progress. Should just need to fix bootstrap tooltip loading and it's good to go. Commit: 7ebe68d770e20abfd21d32d30566abab25e75205 https://github.com/galaxyproject/galaxy/commit/7ebe68d770e20abfd21d32d30566… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Cleanup in scatterplot. Commit: 3a532ad8e8fee5045a5d31e9f5e06d714216bb69 https://github.com/galaxyproject/galaxy/commit/3a532ad8e8fee5045a5d31e9f5e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/package.json M client/yarn.lock M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Bootstrap.js bug was preventing loading the 'correct' way; resolved with an update. Commit: 2083ce9ea0a513b3e3345c56a94fa0971d3381b1 https://github.com/galaxyproject/galaxy/commit/2083ce9ea0a513b3e3345c56a94f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/package.json M client/yarn.lock M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- jquery-ui does not like loading. jquery-ui-bundle handles this better, can easily be used as an import (we probably want to get rid of this stuff eventually, but it works for now) Commit: 6fbaced59b525466d381c1ad632626bcd8695daf https://github.com/galaxyproject/galaxy/commit/6fbaced59b525466d381c1ad6326… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Remove (now-unused) i18n loader from scatterplot's webpack config (was there for utils) Commit: 52e65537ed76b59da2bcfe2be2d53e3033860ef8 https://github.com/galaxyproject/galaxy/commit/52e65537ed76b59da2bcfe2be2d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js Log Message: ----------- Scatterplot lives! Commit: 50870d5ab6904d096312c97c6790281036a31f53 https://github.com/galaxyproject/galaxy/commit/50870d5ab6904d096312c97c6790… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/utils/utils.js Log Message: ----------- Rebuild client. Commit: 8c87b2c401f6d70cdda3c1d2c567cf13ce9a90f0 https://github.com/galaxyproject/galaxy/commit/8c87b2c401f6d70cdda3c1d2c567… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/utils/utils.js M client/package.json M client/yarn.lock M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/components/model.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/client/views/description.js M config/plugins/visualizations/charts/static/client/views/editor.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js M config/plugins/visualizations/charts/static/client/views/viewer.js M config/plugins/visualizations/charts/static/client/views/viewport.js M config/plugins/visualizations/charts/webpack.config.js R config/plugins/visualizations/scatterplot/Gruntfile.js R config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js R config/plugins/visualizations/scatterplot/src/scatterplot-display.js R config/plugins/visualizations/scatterplot/src/scatterplot-model.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot-edit.js A config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js M config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/plugins/visualizations/scatterplot/webpack.config.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #5081 from dannon/fix-charts-packing Viz plugin loading fixes Compare: https://github.com/galaxyproject/galaxy/compare/b3e207095848...8c87b2c401f6

1 0

[galaxyproject/galaxy] 6d6313: Reorg bundling into standalone apps and a 'kitchen...
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d63130fbfbd63922bdfe9080c886309a686870b https://github.com/galaxyproject/galaxy/commit/6d63130fbfbd63922bdfe9080c88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: R client/galaxy/scripts/apps/admin-toolshed.js A client/galaxy/scripts/apps/interface_ext.js R client/galaxy/scripts/apps/library.js R client/galaxy/scripts/apps/masthead.js R client/galaxy/scripts/apps/viz.js R client/galaxy/scripts/apps/workflow.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Reorg bundling into standalone apps and a 'kitchensink' type bundle as discussed for a catchall migration target as we refactor. Commit: 24e5afc5b9b7c0d5eb95dd264acd235310d18168 https://github.com/galaxyproject/galaxy/commit/24e5afc5b9b7c0d5eb95dd264acd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/interface_ext.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js Log Message: ----------- Rebuild client with new bundles. Commit: dba22f3fe868c0ab39f8e8293454494b6b586019 https://github.com/galaxyproject/galaxy/commit/dba22f3fe868c0ab39f8e8293454… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: A client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/interface_ext.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/visualization.py A static/scripts/bundled/extended.bundled.js R static/scripts/bundled/interface_ext.bundled.js M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Swap interface_ext to 'extended', and fix a masthead bug. Commit: 0a5c7aaa7a49f53f9dad52e24b63934a17557a9c https://github.com/galaxyproject/galaxy/commit/0a5c7aaa7a49f53f9dad52e24b63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Beta Admin Toolshed entrypoint fix. Commit: b3e207095848ffa584d91d849825fdf19421acf9 https://github.com/galaxyproject/galaxy/commit/b3e207095848ffa584d91d849825… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: R client/galaxy/scripts/apps/admin-toolshed.js A client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/library.js R client/galaxy/scripts/apps/masthead.js R client/galaxy/scripts/apps/viz.js R client/galaxy/scripts/apps/workflow.js M client/webpack.config.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #5093 from dannon/bundle-refactoring Bundle refactoring Compare: https://github.com/galaxyproject/galaxy/compare/358cfc14af7c...b3e207095848

1 0

[galaxyproject/galaxy] 2e288e: Fix attribute error that was missed during refacto...
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e288ef60f6a461cbd0bb4c5d82f7e6cee0f9fc8 https://github.com/galaxyproject/galaxy/commit/2e288ef60f6a461cbd0bb4c5d82f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Fix attribute error that was missed during refactor Commit: 358cfc14af7c025bcf00d614fafe68ae90ef8437 https://github.com/galaxyproject/galaxy/commit/358cfc14af7c025bcf00d614fafe… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5122 from erasche/fix-attr-error Fix attribute error that was missed during refactor of sentry Compare: https://github.com/galaxyproject/galaxy/compare/72ed629c2a33...358cfc14af7c

1 0

[galaxyproject/galaxy] 72aa96: Stricter checks for SDF sniffing
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4 https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197 https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes [17.09] Backport stricter checks for SDF sniffing #4729 Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix ICM datatype sniffer config Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108 Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2 https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5121 from mvdbeek/fix_icm_datatype_config [17.09] Fix ICM datatype sniffer config Commit: 72ed629c2a333de1adaac6892642e39aba7478c8 https://github.com/galaxyproject/galaxy/commit/72ed629c2a333de1adaac6892642… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_17.09' into dev Conflicts: config/datatypes_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/7c59b8a33be9...72ed629c2a33

1 0

[galaxyproject/galaxy] d73bb6: Fix ICM datatype sniffer config
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix ICM datatype sniffer config Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108 Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2 https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5121 from mvdbeek/fix_icm_datatype_config [17.09] Fix ICM datatype sniffer config Compare: https://github.com/galaxyproject/galaxy/compare/c41fc0a4275a...22aa02f59496

1 0

[galaxyproject/galaxy] 72aa96: Stricter checks for SDF sniffing
by GitHub 02 Dec '17

02 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4 https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197 https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes [17.09] Backport stricter checks for SDF sniffing #4729 Compare: https://github.com/galaxyproject/galaxy/compare/a82d325d1837...c41fc0a4275a

1 0

[galaxyproject/galaxy] 85bf39: change the default ot not add tags based on filena...
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85bf398fc33fb7ca230c51b09661176382923796 https://github.com/galaxyproject/galaxy/commit/85bf398fc33fb7ca230c51b09661… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/bundled/library.bundled.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- change the default ot not add tags based on filename this is fairly confusing if you do not expect it and there is no way to revert Commit: 7c59b8a33be920c72eac187ba35d0fdbba0b8e0e https://github.com/galaxyproject/galaxy/commit/7c59b8a33be920c72eac187ba35d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/bundled/library.bundled.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5115 from martenson/change-libimport-tagdefault change the default to not add tags based on filename Compare: https://github.com/galaxyproject/galaxy/compare/dad11b8ef6d7...7c59b8a33be9

1 0