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spreadsheet column filters, SV inspector can now show features from CSV/TSV #780

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merged 19 commits into from
Jan 23, 2020

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rbuels
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@rbuels rbuels commented Jan 8, 2020

  • adds the ability to add additional filters to the spreadsheet view, each of which adds a toolbar to the edit and remove the filter at the top, giving you a (I think) easily understandable "stack" of filters that are easy to control.
  • improves the machinery around column types, adding 4 new column types for feature locations (LocString, LocRef, LocStart, and LocEnd), and makes LocString columns be links that will open a new genome view
  • adds some basic auto-detection of column data types (Text, Number, LocString) during CSV/TSV import

So now you can make filters on each column, and the SV inspector will show features if your CSV or TSV has 2 locstrings or 2 sets of ref/start/end, and importing will do some limited type detection.

Resolves #690
Also resolves #714
Also resolves #755

@rbuels rbuels added this to To do in JBrowse team board via automation Jan 8, 2020
@rbuels rbuels moved this from To do to In progress in JBrowse team board Jan 8, 2020
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codecov bot commented Jan 8, 2020

Codecov Report

Merging #780 into master will decrease coverage by 1.38%.
The diff coverage is 34.91%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #780      +/-   ##
==========================================
- Coverage   60.33%   58.95%   -1.39%     
==========================================
  Files         303      315      +12     
  Lines       11427    12111     +684     
  Branches     2620     2756     +136     
==========================================
+ Hits         6895     7140     +245     
- Misses       4251     4646     +395     
- Partials      281      325      +44
Impacted Files Coverage Δ
packages/core/ui/App.js 89.65% <ø> (ø) ⬆️
packages/core/util/range.js 85.71% <0%> (-14.29%) ⬇️
packages/core/util/mst-reflection.js 72% <0%> (-9.82%) ⬇️
packages/core/assemblyManager.js 74.24% <0%> (-11.73%) ⬇️
...circular-view/src/CircularView/components/Ruler.js 64.7% <0%> (ø) ⬆️
.../src/SpreadsheetView/importAdapters/ImportUtils.ts 93.22% <100%> (+2.31%) ⬆️
packages/core/ui/theme.js 100% <100%> (ø)
packages/core/PluginManager.js 90.81% <100%> (+0.19%) ⬆️
...rc/SpreadsheetView/models/ColumnDataTypes/index.js 100% <100%> (ø)
...or/src/SvInspectorView/models/adhocFeatureUtils.js 13.63% <13.63%> (ø)
... and 40 more

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@rbuels rbuels force-pushed the 690_more_spreadsheet_filters branch from 504f93e to 4ea1e7e Compare January 13, 2020 17:27
@rbuels rbuels mentioned this pull request Jan 15, 2020
@rbuels rbuels force-pushed the 690_more_spreadsheet_filters branch from ce6a5fb to d6d7487 Compare January 20, 2020 23:40
@rbuels rbuels marked this pull request as ready for review January 20, 2020 23:59
@rbuels rbuels force-pushed the 690_more_spreadsheet_filters branch from c1448d4 to f858748 Compare January 21, 2020 01:16
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rbuels commented Jan 21, 2020

strategy to test some of this might be to open a CSV in the SV inspector that has some locstrings in it, check that you can filter using the locstrings, and check that the circular view properly shows the features.

"stop sorting" in favor of having checkmarks.

also changes "Filter on this" to "Create filter"
@rbuels rbuels merged commit 87b4ec3 into master Jan 23, 2020
JBrowse team board automation moved this from In progress to Done Jan 23, 2020
@rbuels rbuels deleted the 690_more_spreadsheet_filters branch January 23, 2020 03:34
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