[galaxy-commits] [galaxyproject/galaxy] 8e0eaf: Add biojs multiple sequence viewer

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e0eaf2427a99f093a35d686532214534c1bb043 https://github.com/galaxyproject/galaxy/commit/8e0eaf2427a99f093a35d68653221... Author: guerler aysam.guerler@gmail.com Date: 2016-08-24 (Wed, 24 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/config/charts.xml A config/plugins/visualizations/charts/static/charts/biojs/msa/config.js A config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png A config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js M config/plugins/visualizations/charts/static/charts/overview.js M config/plugins/visualizations/charts/static/charts/types.js A config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako

Log Message: ----------- Add biojs multiple sequence viewer

Commit: 97519231e536ab689d5285ce328c46e19fa2566b https://github.com/galaxyproject/galaxy/commit/97519231e536ab689d5285ce328c4... Author: guerler aysam.guerler@gmail.com Date: 2016-08-24 (Wed, 24 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.css

Log Message: ----------- Fix style

Commit: 6a450b9a06a81a58875297af7832f1d5a2cab8a5 https://github.com/galaxyproject/galaxy/commit/6a450b9a06a81a58875297af7832f... Author: guerler aysam.guerler@gmail.com Date: 2016-08-24 (Wed, 24 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js

Log Message: ----------- Add basic options to configure msa viewer

Commit: 72ea2b030242cf448829f82d02e77a10ef7ce75d https://github.com/galaxyproject/galaxy/commit/72ea2b030242cf448829f82d02e77... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js M config/plugins/visualizations/charts/static/components/jobs.js M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Avoid parsing app to chart wrappers

Commit: e02eb60296eac4339aa2265313a38d4dc36aa415 https://github.com/galaxyproject/galaxy/commit/e02eb60296eac4339aa2265313a38... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/storage.js

Log Message: ----------- Decouple storage, parse parameters explicitly

Commit: 37c1e316a74348ad1023bd071f19e4396758540a https://github.com/galaxyproject/galaxy/commit/37c1e316a74348ad1023bd071f19e... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/storage.js

Log Message: ----------- Move chart listener into storage

Commit: 48ff0790bf9b2115d891ca4c1a375f7f266b3399 https://github.com/galaxyproject/galaxy/commit/48ff0790bf9b2115d891ca4c1a375... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/storage.js

Log Message: ----------- Fix save failed message

Commit: 3048b56006cc1ee0877e24767e2535ccbe5164b7 https://github.com/galaxyproject/galaxy/commit/3048b56006cc1ee0877e24767e253... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/others/example/wrapper.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Remove unused container list

Commit: a63b07795c23a7412592d8aa7e395ff6394625ae https://github.com/galaxyproject/galaxy/commit/a63b07795c23a7412592d8aa7e395... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Fix scrolling behavior

Commit: f2c1e23409f407b773913629714c697a04fb0740 https://github.com/galaxyproject/galaxy/commit/f2c1e23409f407b773913629714c6... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/charts/overview.js M config/plugins/visualizations/charts/static/views/viewer.js

Log Message: ----------- Add description for biojs

Commit: 7107705b9c821c20a07ae3275c50eac517b44a37 https://github.com/galaxyproject/galaxy/commit/7107705b9c821c20a07ae3275c50e... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Remove unused menu div

Commit: 5f642113156435b34d3ff6de01144069d2e370c1 https://github.com/galaxyproject/galaxy/commit/5f642113156435b34d3ff6de01144... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Use shorter dom query command

Commit: ebd0dab936b4fbb82dbb21218851ca7579197bf7 https://github.com/galaxyproject/galaxy/commit/ebd0dab936b4fbb82dbb21218851c... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Change draw label to indicate that the chart will be saved too

Commit: 30bd72310e4d51f49e9fe020b119c02642ffe854 https://github.com/galaxyproject/galaxy/commit/30bd72310e4d51f49e9fe020b119c... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Fix tooltip

Commit: 9481939154269253e59a2d9ffafe506947287dc1 https://github.com/galaxyproject/galaxy/commit/9481939154269253e59a2d9ffafe5... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js M config/plugins/visualizations/charts/static/views/settings.js

Log Message: ----------- Remove separated tabular input element

Commit: 70e68c204b3f250e76032761d796f62552f63d70 https://github.com/galaxyproject/galaxy/commit/70e68c204b3f250e76032761d796f... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/settings.js

Log Message: ----------- Fix spacing

Commit: 77dddc3fa42e28eef9ad14c30d8047b2b2865c09 https://github.com/galaxyproject/galaxy/commit/77dddc3fa42e28eef9ad14c30d804... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/settings.js

Log Message: ----------- Generalize internal use panels parameter option

Commit: d6f174e487b77862c005b65843af79c53bd560c7 https://github.com/galaxyproject/galaxy/commit/d6f174e487b77862c005b65843af7... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/views/viewer.js M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-buttons.js

Log Message: ----------- Filter exportable datatypes by chart type

Commit: 6d28721158e9e385c5d734de280eb4c9d3386672 https://github.com/galaxyproject/galaxy/commit/6d28721158e9e385c5d734de280eb... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map

Log Message: ----------- Repack

Commit: 6c0df63e255c198380ca1e168ebed87a8467924f https://github.com/galaxyproject/galaxy/commit/6c0df63e255c198380ca1e168ebed... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/viewer.js

Log Message: ----------- Fix tooltip

Commit: 004fbd6e551a8fbd3bc9f9317ca34b4f55e10ea4 https://github.com/galaxyproject/galaxy/commit/004fbd6e551a8fbd3bc9f9317ca34... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/charts/others/example/config.js

Log Message: ----------- Fix developer examples config

Commit: 9e2e0dc7394814066c98b65e990e5a3750b9756e https://github.com/galaxyproject/galaxy/commit/9e2e0dc7394814066c98b65e990e5... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/charts/others/example/wrapper.js

Log Message: ----------- Fix developer example

Commit: e8eb48a9c42de08edd6e9a4ea529bcac0d698df9 https://github.com/galaxyproject/galaxy/commit/e8eb48a9c42de08edd6e9a4ea529b... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

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

Log Message: ----------- Remove unused app variable

Commit: f98ade125f0fbe5d90ca0f005a84f8f7d91fb3d5 https://github.com/galaxyproject/galaxy/commit/f98ade125f0fbe5d90ca0f005a84f... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js

Log Message: ----------- Add basic description for msa viewer

Commit: c4e9ecfe4c9dec4f9c58597fc755a4c4ab944a83 https://github.com/galaxyproject/galaxy/commit/c4e9ecfe4c9dec4f9c58597fc755a... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/others/example/config.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Allow multiple datatype matching

Commit: edfdef2853e2df3f5058d97e1578c4129fb292de https://github.com/galaxyproject/galaxy/commit/edfdef2853e2df3f5058d97e1578c... Author: guerler aysam.guerler@gmail.com Date: 2016-08-25 (Thu, 25 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-buttons.js

Log Message: ----------- Enhance ui menu button view

Commit: 72f89a4c262de328d398ebbb4c6ccfefc483b75d https://github.com/galaxyproject/galaxy/commit/72f89a4c262de328d398ebbb4c6cc... Author: guerler aysam.guerler@gmail.com Date: 2016-08-26 (Fri, 26 Aug 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js

Log Message: ----------- Fix requirements message

Commit: 59852d0e0f4897b09a964091d5792458de48deb0 https://github.com/galaxyproject/galaxy/commit/59852d0e0f4897b09a964091d5792... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/biojs/msa/config.js R config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png R config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js R config/plugins/visualizations/charts/static/charts/others/example/config.js R config/plugins/visualizations/charts/static/charts/others/example/logo.png R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/charts/overview.js R config/plugins/visualizations/charts/static/charts/types.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/components/jobs.js R config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js M config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako

Log Message: ----------- Use remote repo for chart plugins

Commit: af45adb7e6e57d4180b49581c5f48274df54117f https://github.com/galaxyproject/galaxy/commit/af45adb7e6e57d4180b49581c5f48... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako

Log Message: ----------- Add error message if charts fails to retrieve plugin resources from its repository

Commit: 3e7302fc3c6d8f0713d8698f6536662fc46f42b0 https://github.com/galaxyproject/galaxy/commit/3e7302fc3c6d8f0713d8698f65366... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Fix remote url

Commit: 42854e31ea50eae1e26ce2112696cd86ccb247be https://github.com/galaxyproject/galaxy/commit/42854e31ea50eae1e26ce2112696c... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Bundle thumbnail view

Commit: d4d403d678a9c6d5a5dbf1df5c23b8425f1a1311 https://github.com/galaxyproject/galaxy/commit/d4d403d678a9c6d5a5dbf1df5c23b... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Show list instead

Commit: 6f444e5cdbc69ba0fdca4a04c1dce7d7493420be https://github.com/galaxyproject/galaxy/commit/6f444e5cdbc69ba0fdca4a04c1dce... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Restore regular selection view

Commit: ccd265ed0705d3166f792d7d1473f229c8b5accb https://github.com/galaxyproject/galaxy/commit/ccd265ed0705d3166f792d7d1473f... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Fix tab creation behavior

Commit: d65bf1e4f773c6c6d27b83e7a850b51bfd3d3faa https://github.com/galaxyproject/galaxy/commit/d65bf1e4f773c6c6d27b83e7a850b... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Fix sorting

Commit: bee75fb77909ddc938290c134eb689a7f5729254 https://github.com/galaxyproject/galaxy/commit/bee75fb77909ddc938290c134eb68... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Fix order

Commit: 9601a0f607b71e8725dafff90288ee8486dbfcf1 https://github.com/galaxyproject/galaxy/commit/9601a0f607b71e8725dafff90288e... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Revise thumbnail view

Commit: ec038cb0904b24c6df8cb5f7b16e671997004aa7 https://github.com/galaxyproject/galaxy/commit/ec038cb0904b24c6df8cb5f7b16e6... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Use original order

Commit: 5cae6f7735436800c586065be690a43c1a1683e5 https://github.com/galaxyproject/galaxy/commit/5cae6f7735436800c586065be690a... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Fix spacing

Commit: 71fe20ab040df9393c8ac0c083a31006a65ab848 https://github.com/galaxyproject/galaxy/commit/71fe20ab040df9393c8ac0c083a31... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M client/galaxy/scripts/utils/utils.js M config/plugins/visualizations/charts/static/views/description.js M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js

Log Message: ----------- Identify links in visualizations plugins descriptions

Commit: e0617bb29b280f5f7f756ccbfdd6678ed3e185ef https://github.com/galaxyproject/galaxy/commit/e0617bb29b280f5f7f756ccbfdd66... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Add tooltip to thumbnail view?

Commit: f03a06488feb0e1c471c92d11cff14c6bf5c0cf1 https://github.com/galaxyproject/galaxy/commit/f03a06488feb0e1c471c92d11cff1... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Limit title length for thumbnails

Commit: f2b26a61cb14ff468ecc2971d6394e6cea64f889 https://github.com/galaxyproject/galaxy/commit/f2b26a61cb14ff468ecc2971d6394... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Filter suitable visualization types on initialization

Commit: 84942582b57499a753cf9e8039486c3bc9efa4f3 https://github.com/galaxyproject/galaxy/commit/84942582b57499a753cf9e8039486... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js

Log Message: ----------- Modify error message

Commit: 3e79da902163b131aff677a7b1bad9fa87e61d89 https://github.com/galaxyproject/galaxy/commit/3e79da902163b131aff677a7b1bad... Author: guerler aysam.guerler@gmail.com Date: 2016-08-30 (Tue, 30 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/templates/charts.mako

Log Message: ----------- Fix error messages

Commit: 5d780d68d1a2ec5d1928a0156637a1d522f5b743 https://github.com/galaxyproject/galaxy/commit/5d780d68d1a2ec5d1928a0156637a... Author: guerler aysam.guerler@gmail.com Date: 2016-08-31 (Wed, 31 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/screenshot.js

Log Message: ----------- Revise exporting functions, increase png quality, remove unused libraries

Commit: 78bd9e8f867eb5747218644e2a5a1f5417079b73 https://github.com/galaxyproject/galaxy/commit/78bd9e8f867eb5747218644e2a5a1... Author: guerler aysam.guerler@gmail.com Date: 2016-08-31 (Wed, 31 Aug 2016)

Changed paths: M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js R database/info.txt A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/framework/webapp.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.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/index.mako

Log Message: ----------- Merge branch 'dev' into remote_chart_plugins

Commit: a97b4bae546a5621dc37b6beaaba747d51c8ed9e https://github.com/galaxyproject/galaxy/commit/a97b4bae546a5621dc37b6beaaba7... Author: guerler aysam.guerler@gmail.com Date: 2016-08-31 (Wed, 31 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js

Log Message: ----------- Rename types to registry to avoid confusion

Commit: 494141c260514071c5187a83a8dd1700643b5423 https://github.com/galaxyproject/galaxy/commit/494141c260514071c5187a83a8dd1... Author: guerler aysam.guerler@gmail.com Date: 2016-08-31 (Wed, 31 Aug 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Use underscores for internal parameters to avoid conflicts

Commit: 61839637f098130ccd54bfe408ff9955dbffc883 https://github.com/galaxyproject/galaxy/commit/61839637f098130ccd54bfe408ff9... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/model.js R config/plugins/visualizations/charts/static/components/storage.js M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Simplify storage handling

Commit: 7d20e9055e1be434c7914fc540ceb64a8e4d1051 https://github.com/galaxyproject/galaxy/commit/7d20e9055e1be434c7914fc540ceb... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/model.js

Log Message: ----------- Remove unused options variable

Commit: 30d4e338b473797816e8b8a5da93dcd5420e24fc https://github.com/galaxyproject/galaxy/commit/30d4e338b473797816e8b8a5da93d... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/templates/charts.mako

Log Message: ----------- Revise visualization config handling

Commit: 57b41b201964b57daf9a95c06120cbe1bba14e1b https://github.com/galaxyproject/galaxy/commit/57b41b201964b57daf9a95c06120c... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/model.js

Log Message: ----------- Fix chart saving

Commit: 22e79f7aa943edb9ca6a80d1b035931ab8c9232f https://github.com/galaxyproject/galaxy/commit/22e79f7aa943edb9ca6a80d1b0359... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Improve handling for cases with missing plugins

Commit: 76c9948742d659b2dd73452cc2d3c49f44f00cd7 https://github.com/galaxyproject/galaxy/commit/76c9948742d659b2dd73452cc2d3c... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Enhance notification and handling when chart type is unavailable

Commit: 81dffca58cab841dfcf0fda42b42d5c97f54f245 https://github.com/galaxyproject/galaxy/commit/81dffca58cab841dfcf0fda42b42d... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Remove test case, replace change listeners

Commit: fa7930d20e10309aee666f280963b759571e3884 https://github.com/galaxyproject/galaxy/commit/fa7930d20e10309aee666f280963b... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Fix message persistence for missing column notification

Commit: b3451ed03d5104442b4935905e330b006e492204 https://github.com/galaxyproject/galaxy/commit/b3451ed03d5104442b4935905e330... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Fix message persistence for missing data groups

Commit: 4669d5ee26410faec0c6e49aed512352631066e3 https://github.com/galaxyproject/galaxy/commit/4669d5ee26410faec0c6e49aed512... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

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

Log Message: ----------- Remove warning notification when leaving charts, data is saved upon drawing

Commit: 00053b6d30b21ce2eed5419a3537caa0b8cd7797 https://github.com/galaxyproject/galaxy/commit/00053b6d30b21ce2eed5419a3537c... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/model.js

Log Message: ----------- Fix spacing

Commit: ffba835195737c4705e5b2717c384be05edeae91 https://github.com/galaxyproject/galaxy/commit/ffba835195737c4705e5b2717c384... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Remove spacing

Commit: 7351d67967a0750a5e351660b457d92dcb01b516 https://github.com/galaxyproject/galaxy/commit/7351d67967a0750a5e351660b457d... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/types.js

Log Message: ----------- Remove unused listener

Commit: 05fa9b9f5adcd96456348754225c72554d4e12af https://github.com/galaxyproject/galaxy/commit/05fa9b9f5adcd96456348754225c7... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako

Log Message: ----------- Rename remote to repository to avoid confusion

Commit: 3d9df6437073484d243d64fc9606dc137dc6bfb7 https://github.com/galaxyproject/galaxy/commit/3d9df6437073484d243d64fc9606d... Author: guerler aysam.guerler@gmail.com Date: 2016-09-01 (Thu, 01 Sep 2016)

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

Log Message: ----------- Rename optional config attributes name accordingly

Commit: ff301c562b87a1843d18819eb79dd580d207e9c8 https://github.com/galaxyproject/galaxy/commit/ff301c562b87a1843d18819eb79dd... Author: guerler aysam.guerler@gmail.com Date: 2016-09-02 (Fri, 02 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/templates/charts.mako

Log Message: ----------- Add debug log, fix config name, add comment for local repository

Commit: 36c1384d020bcb2d3a89da83861cccfae23e8916 https://github.com/galaxyproject/galaxy/commit/36c1384d020bcb2d3a89da83861cc... Author: guerler aysam.guerler@gmail.com Date: 2016-09-02 (Fri, 02 Sep 2016)

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

Log Message: ----------- Use rawgit for proper MIME type handling

Commit: 819cb65d2e1ecc905b22e97b9972fa8901ac09c1 https://github.com/galaxyproject/galaxy/commit/819cb65d2e1ecc905b22e97b9972f... Author: guerler aysam.guerler@gmail.com Date: 2016-09-02 (Fri, 02 Sep 2016)

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

Log Message: ----------- Add repository revision to url

Commit: d5440f7ac4170adf27f757fdfbc888a67e20cf27 https://github.com/galaxyproject/galaxy/commit/d5440f7ac4170adf27f757fdfbc88... Author: guerler aysam.guerler@gmail.com Date: 2016-09-02 (Fri, 02 Sep 2016)

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

Log Message: ----------- Upgrade repository version, allow pdb rendering type selection

Commit: 14ef3e3d448dc4190707312443b6f60e187ee962 https://github.com/galaxyproject/galaxy/commit/14ef3e3d448dc4190707312443b6f... Author: guerler aysam.guerler@gmail.com Date: 2016-09-02 (Fri, 02 Sep 2016)

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

Log Message: ----------- Upgrade repository version

Commit: d98a72d58e1cf462eb89f4a9cd3e04a5c6fea9fb https://github.com/galaxyproject/galaxy/commit/d98a72d58e1cf462eb89f4a9cd3e0... Author: guerler aysam.guerler@gmail.com Date: 2016-09-02 (Fri, 02 Sep 2016)

Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A database/info.txt M doc/source/admin/conda_faq.rst M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/deps/resolvers/conda.py R lib/galaxy/tools/toolbox/requirements.py A lib/galaxy/util/filelock.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js.map M templates/admin/tool_shed_repository/common.mako

Log Message: ----------- Merge branch 'dev' into remote_chart_plugins

Commit: 14c0365b22d238e8c48b20dc64654cc412386059 https://github.com/galaxyproject/galaxy/commit/14c0365b22d238e8c48b20dc64654... Author: guerler aysam.guerler@gmail.com Date: 2016-09-08 (Thu, 08 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako

Log Message: ----------- Upgrade repository revision

Commit: 5e8a2ced3a819a238227bbde0627d90cfd3cf728 https://github.com/galaxyproject/galaxy/commit/5e8a2ced3a819a238227bbde0627d... Author: guerler aysam.guerler@gmail.com Date: 2016-09-09 (Fri, 09 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/viewer.js

Log Message: ----------- Distinguish draw and save to avoid accumulation of saved visualizations

Commit: cf9db96a1d7076474873c5b1f6e7ed2e32a3d79e https://github.com/galaxyproject/galaxy/commit/cf9db96a1d7076474873c5b1f6e7e... Author: guerler aysam.guerler@gmail.com Date: 2016-09-09 (Fri, 09 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Change label from draw to visualize

Commit: a88942b0875f659e799d65bd00cea1d771c82570 https://github.com/galaxyproject/galaxy/commit/a88942b0875f659e799d65bd00cea... Author: guerler aysam.guerler@gmail.com Date: 2016-09-09 (Fri, 09 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/components/screenshot.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/viewer.js

Log Message: ----------- Unify labels and tooltips

Commit: 052b6e367bdeeffa5811853612a3bb1759c27039 https://github.com/galaxyproject/galaxy/commit/052b6e367bdeeffa5811853612a3b... Author: guerler aysam.guerler@gmail.com Date: 2016-09-09 (Fri, 09 Sep 2016)

Changed paths: M config/plugins/visualizations/charts/static/views/editor.js

Log Message: ----------- Fix tooltip

Commit: 8b13f63f423800bf17e51a99231fa35099b58519 https://github.com/galaxyproject/galaxy/commit/8b13f63f423800bf17e51a99231fa... Author: guerler aysam.guerler@gmail.com Date: 2016-09-14 (Wed, 14 Sep 2016)

Changed paths: M .ci/flake8_lint_include_list.txt M .gitignore M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/lazy_process.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/permutations.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/sockets.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/api/configuration.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/tools/tool_version_manager.py M setup.cfg M templates/show_params.mako M templates/webapps/galaxy/workflow/run.mako M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/unit/jobs/test_job_wrapper.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M tools/data_source/upload.xml

Log Message: ----------- Merge branch 'dev' into remote_chart_plugins

Commit: 46d05ba08017cf10467eb0334272e48733c9f684 https://github.com/galaxyproject/galaxy/commit/46d05ba08017cf10467eb0334272e... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.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-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js A client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/ui.less A doc/parse_gx_xsd.py A doc/schema_template.md M doc/source/project/issues.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/mobile.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.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/model/__init__.py M lib/galaxy/workflow/extract.py M lib/tool_shed/util/metadata_util.py M scripts/bootstrap_history.py M scripts/tool_shed/build_ts_whoosh_index.py A scripts/validate_tools.sh A static/maps/libs/bbi/bigwig.js.map A static/maps/libs/bbi/jquery-ajax-native.js.map A static/maps/libs/bbi/jszlib.js.map A static/maps/libs/bbi/spans.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/utils/utils.js.map A static/maps/viz/bbi-data-manager.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/bbi/bigwig.js A static/scripts/libs/bbi/jquery-ajax-native.js A static/scripts/libs/bbi/jszlib.js A static/scripts/libs/bbi/spans.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/utils/utils.js A static/scripts/viz/bbi-data-manager.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/common.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/base/interactor.py A test/functional/tools/metadata_column_names.xml R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/form_tests.js M test/shed_functional/functional/test_1400_review_migration_stages.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini

Log Message: ----------- Merge branch 'dev' into remote_chart_plugins

Commit: 494d50f52c33a7465e0d466a3e43fba9fd5a1dbd https://github.com/galaxyproject/galaxy/commit/494d50f52c33a7465e0d466a3e43f... Author: guerler aysam.guerler@gmail.com Date: 2016-09-29 (Thu, 29 Sep 2016)

Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js

Log Message: ----------- Repack client

Commit: fdc81bd84a76082249474782367b7b7a59706af3 https://github.com/galaxyproject/galaxy/commit/fdc81bd84a76082249474782367b7... Author: guerler aysam.guerler@gmail.com Date: 2016-10-08 (Sat, 08 Oct 2016)

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

Log Message: ----------- Upgrade repository revision

Commit: 2316075f0caf7771bafabbfa00bfe2c5ecdfacec https://github.com/galaxyproject/galaxy/commit/2316075f0caf7771bafabbfa00bfe... Author: guerler aysam.guerler@gmail.com Date: 2016-10-08 (Sat, 08 Oct 2016)

Changed paths: A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-modal.js M config/job_conf.xml.sample_advanced M doc/source/admin/conda_faq.rst M doc/source/api/guidelines.rst M lib/galaxy/datatypes/data.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py A lib/galaxy/jobs/runners/godocker.py M lib/galaxy/managers/workflows.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/genomes.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M scripts/bootstrap_history.py M setup.cfg M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-modal.js A test/api/test_workflow_batch.ga M test/api/test_workflows.py M test/base/driver_util.py A test/functional/tools/color_param.xml M test/functional/tools/samples_tool_conf.xml M test/unit/workflows/test_run_parameters.py M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini

Log Message: ----------- Merge branch 'dev' into remote_chart_plugins

Commit: b7a25fc653fa30a78d97b2aa23e9a5ad43814694 https://github.com/galaxyproject/galaxy/commit/b7a25fc653fa30a78d97b2aa23e9a... Author: guerler aysam.guerler@gmail.com Date: 2016-10-08 (Sat, 08 Oct 2016)

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

Log Message: ----------- Update repository revision to new drawrnajs logo

Commit: bf5cc30b843838f30a4b40faa9834cbc28a01991 https://github.com/galaxyproject/galaxy/commit/bf5cc30b843838f30a4b40faa9834... Author: guerler aysam.guerler@gmail.com Date: 2016-10-11 (Tue, 11 Oct 2016)

Changed paths: R config/plugins/visualizations/charts/sample.txt M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/viewport.js

Log Message: ----------- Remove tabular file from repo, fix comments

Commit: 1805ac8b5948ded11e154c887a2da99481ac70c6 https://github.com/galaxyproject/galaxy/commit/1805ac8b5948ded11e154c887a2da... Author: guerler aysam.guerler@gmail.com Date: 2016-10-11 (Tue, 11 Oct 2016)

Changed paths: R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/app.css R config/plugins/visualizations/charts/static/app.js A config/plugins/visualizations/charts/static/client/app.css A config/plugins/visualizations/charts/static/client/app.js A config/plugins/visualizations/charts/static/client/components/model.js A config/plugins/visualizations/charts/static/client/components/screenshot.js A config/plugins/visualizations/charts/static/client/views/description.js A config/plugins/visualizations/charts/static/client/views/editor.js A config/plugins/visualizations/charts/static/client/views/groups.js A config/plugins/visualizations/charts/static/client/views/settings.js A config/plugins/visualizations/charts/static/client/views/types.js A config/plugins/visualizations/charts/static/client/views/viewer.js A config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/components/model.js R config/plugins/visualizations/charts/static/components/screenshot.js A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map A 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config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/views/description.js R config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/groups.js R config/plugins/visualizations/charts/static/views/settings.js R config/plugins/visualizations/charts/static/views/types.js R config/plugins/visualizations/charts/static/views/viewer.js R config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/charts/webpack.config.js

Log Message: ----------- Add chart plugins back to plugins directory of visualization framework

Commit: f467384fdd97dba43ee0f9b7c3592498de738ee8 https://github.com/galaxyproject/galaxy/commit/f467384fdd97dba43ee0f9b7c3592... Author: guerler aysam.guerler@gmail.com Date: 2016-10-11 (Tue, 11 Oct 2016)

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

Log Message: ----------- Use fixed repository path

Commit: fe73009db5248a04844db86584064b48a86f2cb2 https://github.com/galaxyproject/galaxy/commit/fe73009db5248a04844db86584064... Author: guerler aysam.guerler@gmail.com Date: 2016-10-11 (Tue, 11 Oct 2016)

Changed paths: M config/plugins/visualizations/charts/static/client/components/model.js

Log Message: ----------- Fix default options for storing request

Commit: f053f9bb3d2820c09aab1a0bc3b29e27eed56d09 https://github.com/galaxyproject/galaxy/commit/f053f9bb3d2820c09aab1a0bc3b29... Author: guerler aysam.guerler@gmail.com Date: 2016-10-14 (Fri, 14 Oct 2016)

Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M doc/parse_gx_xsd.py M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py R lib/galaxy/datatypes/util/image_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/mulled_example_multi_1.xml A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/data_source/upload.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py

Log Message: ----------- Merge branch 'dev' into remote_chart_plugins

Commit: 1dc2d6a4ead34b9d8bdaecf85f146ca17b5e803c https://github.com/galaxyproject/galaxy/commit/1dc2d6a4ead34b9d8bdaecf85f146... Author: John Chilton jmchilton@gmail.com Date: 2016-10-17 (Mon, 17 Oct 2016)

Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/utils/utils.js R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/sample.txt R config/plugins/visualizations/charts/static/app.css R config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js R 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config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/views/description.js R config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/groups.js R config/plugins/visualizations/charts/static/views/settings.js R config/plugins/visualizations/charts/static/views/types.js R config/plugins/visualizations/charts/static/views/viewer.js R config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/charts/webpack.config.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M 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Log Message: ----------- Merge pull request #2875 from guerler/remote_chart_plugins

Link charts to external repo, adjust interface

Compare: https://github.com/galaxyproject/galaxy/compare/7eb413f4e8ee...1dc2d6a4ead3