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Add simplified URL format for loading spreadsheet and SV inspector #2981

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merged 4 commits into from
Jun 10, 2022

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cmdcolin
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Adds ability to automatically load a spreadsheet from the spec URL

http://localhost:3000/?config=test_data/volvox/config.json&session=spec-{%22views%22:[{%22type%22:%22SpreadsheetView%22,%20%22uri%22:%22test_data/volvox/volvox.filtered.vcf.gz%22,%22assembly%22:%22volvox%22}]}

prettier output for url

{
  views: [
    {
      type: "SpreadsheetView",
      uri: "test_data/volvox/volvox.filtered.vcf.gz",
      assembly: "volvox",
    },
  ],
};

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label May 26, 2022
@cmdcolin
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adapted from some earlier questions

#2528
#2424

@cmdcolin cmdcolin added enhancement New feature or request and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels May 26, 2022
@cmdcolin
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one consideration: it "waits" on the import form while its loading the file, if the file is large it could wait on the import form for awhile. if that is a concern we could make a special text on the import form saying it is loading (probably valuable for importform usage in general) or bypass the importform itself

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codecov bot commented May 31, 2022

Codecov Report

Merging #2981 (58833ca) into main (bffae77) will increase coverage by 0.27%.
The diff coverage is 65.47%.

@@            Coverage Diff             @@
##             main    #2981      +/-   ##
==========================================
+ Coverage   61.23%   61.50%   +0.27%     
==========================================
  Files         588      588              
  Lines       26762    26804      +42     
  Branches     6494     6502       +8     
==========================================
+ Hits        16387    16487     +100     
+ Misses      10065    10009      -56     
+ Partials      310      308       -2     
Impacted Files Coverage Δ
packages/core/util/types/index.ts 67.85% <ø> (ø)
plugins/sv-inspector/src/index.ts 43.47% <7.14%> (-56.53%) ⬇️
plugins/linear-genome-view/src/index.ts 75.00% <59.09%> (-2.78%) ⬇️
...ar-comparative-view/src/LaunchLinearSyntenyView.ts 72.72% <78.26%> (+66.06%) ⬆️
...omparative-view/src/LinearComparativeView/model.ts 38.46% <87.50%> (+16.64%) ⬆️
plugins/spreadsheet-view/src/index.ts 96.00% <94.11%> (-4.00%) ⬇️
.../linear-genome-view/src/LinearGenomeView/index.tsx 84.61% <0.00%> (-0.34%) ⬇️
products/jbrowse-web/src/util.ts 27.27% <0.00%> (ø)
...tenyRenderer/components/LinearSyntenyRendering.tsx 62.57% <0.00%> (+0.58%) ⬆️
products/jbrowse-web/src/SessionLoader.ts 60.77% <0.00%> (+2.15%) ⬆️
... and 6 more

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@cmdcolin
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@cmdcolin
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cmdcolin commented Jun 10, 2022

that corresponds to

{
  views: [
    {
      type: "SvInspectorView",
      uri: "test_data/volvox/volvox.dup.vcf.gz",
      assembly: "volvox",
    },
  ],
};

it does expect the url to the file to be absolute (not relative to current config)

@cmdcolin cmdcolin merged commit 1d8e7e8 into main Jun 10, 2022
@cmdcolin cmdcolin deleted the spec_spreadsheet branch June 10, 2022 21:57
@cmdcolin cmdcolin changed the title Add spreadsheet spec Add simplified URL format for loading spreadsheet and SV inspector Jun 11, 2022
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