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Don't throw on UCSC connection containing assemblies not matching connection->assemblyNames config #3738

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merged 3 commits into from
Jun 1, 2023

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cmdcolin
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@cmdcolin cmdcolin commented May 31, 2023

Also fixes session->connections getter in jbrowse-web to return sessionConnections and some other misc refactoring

Fixes #3737

@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 31, 2023
@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 May 31, 2023
@cmdcolin cmdcolin changed the title Don't throw on UCSC connection loading if it has assemblies not matching connection->assemblyNames config Don't throw on UCSC connection containing assemblies not matching connection->assemblyNames config May 31, 2023
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codecov bot commented May 31, 2023

Codecov Report

Merging #3738 (924e0e9) into main (b8174a5) will decrease coverage by 0.05%.
The diff coverage is 52.50%.

@@            Coverage Diff             @@
##             main    #3738      +/-   ##
==========================================
- Coverage   64.38%   64.33%   -0.05%     
==========================================
  Files         977      977              
  Lines       29892    29897       +5     
  Branches     7166     7172       +6     
==========================================
- Hits        19246    19235      -11     
- Misses      10480    10496      +16     
  Partials      166      166              
Impacted Files Coverage Δ
...get/components/dialogs/ToggleConnectionsDialog.tsx 0.00% <0.00%> (ø)
...s/linear-genome-view/src/LinearGenomeView/model.ts 84.40% <ø> (ø)
packages/product-core/src/Session/Connections.ts 32.65% <14.28%> (-7.35%) ⬇️
plugins/data-management/src/ucsc-trackhub/model.ts 75.47% <77.77%> (-1.28%) ⬇️
packages/web-core/src/BaseWebSession/index.ts 73.04% <100.00%> (+0.47%) ⬆️
...ns/legacy-jbrowse/src/JBrowse1Connection/model.tsx 75.00% <100.00%> (ø)
products/jbrowse-cli/src/base.ts 84.41% <100.00%> (ø)
...roducts/jbrowse-cli/src/commands/add-connection.ts 89.04% <100.00%> (-4.94%) ⬇️

... and 1 file with indirect coverage changes

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@cmdcolin
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cmdcolin commented Jun 1, 2023

note that technically, we could load all tracks from connection even if the 'assembly wasn't found' ...then in the rare case that the assembly is loaded later via assembly manager, it would automatically have the new tracks, but may be ok for now

@cmdcolin cmdcolin merged commit 463c4dc into main Jun 1, 2023
@cmdcolin cmdcolin deleted the model_asm branch June 1, 2023 17:58
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Connection works from UI but not from cli if some assemblies are missing
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