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microSALT cannot update MLST profile databases due to outdated logic #199

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karlnyr opened this issue Mar 12, 2025 · 0 comments · May be fixed by #201
Open

microSALT cannot update MLST profile databases due to outdated logic #199

karlnyr opened this issue Mar 12, 2025 · 0 comments · May be fixed by #201

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@karlnyr
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karlnyr commented Mar 12, 2025 •
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Description

PubMLST has changed their schema for some of the microbes, this causes us to fetch the incorrect database for some of our validated organisms

Affected organisms:

StatusDB  PubMLST
E. coli Escherichia spp.
 Klebsiella pneumoniae  Klebsiella spp.

A fix would be to make microSALT fetch the correct database, and use the correct database, for these organisms
@karlnyr karlnyr linked a pull request Mar 12, 2025 that will close this issue
Add referencer utilities and constants for Enterobacteriaceae #201
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Add referencer utilities and constants for Enterobacteriaceae Clinical-Genomics/microSALT
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@karlnyr