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Use path.resolve to fix --load symlink in jbrowse CLI #2686

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merged 1 commit into from
Jan 28, 2022

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cmdcolin
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This fixes #2685

This always creates a resolved, absolute path for a symlink

This makes the change for both add-assembly and add-track

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jan 28, 2022
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cmdcolin commented Jan 28, 2022

this would always create a absolute path when using symlinks. there may be some rare cases where having relative symlinks (sort of hypothetical like moving a group of directories around or similar) but I think this is probably ok and better than the behavior currently in place with relative symlinks

@cmdcolin cmdcolin added bug Something isn't working and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels Jan 28, 2022
@cmdcolin cmdcolin changed the title Use path.resolve for symlink in add-assembly loading Use path.resolve to fix --load symlink in jbrowse CLI Jan 28, 2022
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codecov bot commented Jan 28, 2022

Codecov Report

Merging #2686 (85562f4) into main (baf56eb) will increase coverage by 0.04%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #2686      +/-   ##
==========================================
+ Coverage   60.67%   60.71%   +0.04%     
==========================================
  Files         561      561              
  Lines       26313    26313              
  Branches     6409     6409              
==========================================
+ Hits        15965    15976      +11     
+ Misses      10022    10011      -11     
  Partials      326      326              
Impacted Files Coverage Δ
products/jbrowse-cli/src/commands/add-assembly.ts 88.88% <ø> (ø)
products/jbrowse-cli/src/commands/add-track.ts 63.55% <100.00%> (ø)
products/jbrowse-web/src/util.ts 27.27% <0.00%> (ø)
.../linear-genome-view/src/LinearGenomeView/index.tsx 84.00% <0.00%> (+0.16%) ⬆️
...inearGenomeView/components/RefNameAutocomplete.tsx 80.80% <0.00%> (+3.03%) ⬆️
packages/core/TextSearch/TextSearchManager.ts 100.00% <0.00%> (+3.44%) ⬆️
...nts/src/SNPCoverageRenderer/SNPCoverageRenderer.ts 71.55% <0.00%> (+5.50%) ⬆️

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@cmdcolin cmdcolin merged commit 403788e into main Jan 28, 2022
@cmdcolin cmdcolin deleted the fix_symlink_add_assembly branch January 31, 2022 02:18
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add-assembly translates absolute path to (wrong) relative path
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