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Fix loading tracks from connection using assembly alias #3217

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merged 5 commits into from
Sep 26, 2022

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cmdcolin
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This fixes a bug I found with loading tracks from a connection that uses "assembly aliases" e.g. it thinks the hub is from GRCh37 but we are on an assembly named hg19

The current main branch does not display these tracks into the track list, this branch fixes that

It also does a number of refactors and typescripting

Example refactors

  • Display the raw error object for errors in some trackhubregistry code, instead of a customization of the error object with a React.ReactNode. This to me makes the code easier to read
  • Removes assumption that configuration.connections[index]===session.configurationInstances[index]

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Sep 26, 2022
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codecov bot commented Sep 26, 2022

Codecov Report

Merging #3217 (4ede1d5) into main (46d72f9) will increase coverage by 0.04%.
The diff coverage is 6.02%.

@@            Coverage Diff             @@
##             main    #3217      +/-   ##
==========================================
+ Coverage   59.40%   59.45%   +0.04%     
==========================================
  Files         673      674       +1     
  Lines       28797    28778      -19     
  Branches     6985     6982       -3     
==========================================
+ Hits        17108    17111       +3     
- Misses      11368    11372       +4     
+ Partials      321      295      -26     
Impacted Files Coverage Δ
...rarchicalTrackSelectorWidget/components/Header.tsx 42.85% <ø> (-0.63%) ⬇️
...ectorWidget/components/ManageConnectionsDialog.tsx 0.00% <0.00%> (ø)
...ectorWidget/components/ToggleConnectionsDialog.tsx 0.00% <0.00%> (ø)
...khub-registry/src/trackhub-registry/HubDetails.tsx 0.00% <0.00%> (ø)
...y/src/trackhub-registry/TrackHubRegistrySelect.tsx 0.00% <0.00%> (ø)
...s/trackhub-registry/src/trackhub-registry/util.tsx 0.00% <0.00%> (ø)
...s/trackhub-registry/src/trackhub-registry/model.ts 10.00% <10.00%> (ø)
...ement/src/HierarchicalTrackSelectorWidget/model.ts 78.26% <80.00%> (+3.68%) ⬆️
...ments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts 58.00% <0.00%> (+0.66%) ⬆️
... and 1 more

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@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 Sep 26, 2022
@cmdcolin
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I also propose in this PR, in the "Toggle connections" dialog, to make it display all connections and not just assembly-specific connections (and to display the assembly names it applies to next to the connection name)

@cmdcolin cmdcolin merged commit 9386a05 into main Sep 26, 2022
@cmdcolin cmdcolin changed the title Fix loading connections from assembly alias and add refactoring/typescripting Fix loading tracks from connection using assembly alias Sep 26, 2022
@cmdcolin cmdcolin deleted the new_typescripting branch September 26, 2022 19:16
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