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Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink #1901

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merged 1 commit into from
Apr 12, 2021

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cmdcolin
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Fixes #1898

Also fixes issue trying to use --out on a symbolic link, use fstat instead of lstat

Currently on main using a symlink, if i am testing correctly, produces

mkdir ~/testing
ln -s testing
bin/run add-assembly --out testing volvox.fa --load copy
    Error: ELOOP: too many symbolic links encountered, open 'testing'
    Code: ELOOP

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Apr 12, 2021
@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 Apr 12, 2021
@cmdcolin cmdcolin force-pushed the addassembly_out_mkdir branch from 2051b71 to 0bffcdf Compare April 12, 2021 17:08
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codecov bot commented Apr 12, 2021

Codecov Report

Merging #1901 (0bffcdf) into main (2660153) will decrease coverage by 0.00%.
The diff coverage is 64.10%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #1901      +/-   ##
==========================================
- Coverage   58.52%   58.51%   -0.01%     
==========================================
  Files         460      460              
  Lines       21290    21311      +21     
  Branches     5059     5066       +7     
==========================================
+ Hits        12459    12470      +11     
- Misses       8526     8536      +10     
  Partials      305      305              
Impacted Files Coverage Δ
packages/core/ReExports/modules.ts 75.00% <ø> (ø)
packages/core/ui/DrawerWidget.js 93.10% <ø> (ø)
...a-management/src/AssemblyManager/AssemblyTable.tsx 82.35% <ø> (ø)
plugins/wiggle/src/index.ts 100.00% <ø> (ø)
.../core/BaseFeatureWidget/SequenceFeatureDetails.tsx 53.45% <44.00%> (-3.30%) ⬇️
products/jbrowse-cli/src/commands/add-assembly.ts 90.86% <100.00%> (+0.16%) ⬆️
...ts/jbrowse-cli/src/commands/set-default-session.ts 96.36% <100.00%> (+0.44%) ⬆️

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@cmdcolin
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I think this should be good to go, pretty small:)

@cmdcolin cmdcolin merged commit 9a4a1d1 into main Apr 12, 2021
@cmdcolin cmdcolin changed the title Make using --out for add-assembly create output directory if it does not exist Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink Apr 12, 2021
@cmdcolin cmdcolin deleted the addassembly_out_mkdir branch April 13, 2021 13:15
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Allow using --out parameter with add-assembly to create a new directory
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