Fix RKI transform #490
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Fix RKI transform #490
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Unclear if there is an upstream data issue, but the latest GenBank/open workflow failed during the `transform_rki_data` because of the lack of lineages. Default to '?' if the RKI data does not include lineages to avoid the IndexError. Resolves <#489>
Based on <#476 (comment)>, we can filter for `PANGOLIN_LATEST` to get the latest lineage assignment. If none of the lineages are marked as `PANGOLIN_LATEST`, then just use the first one in the list since this was the behavior before the change. If there are multiple `PANGOLIN_LATEST` lineages, then just use the first one and output a warning. I've removed the assertion because this should not block the whole ncov-ingest workflow. Resolves <#478>
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Will merge tomorrow before the automated workflow runs tomorrow if the trial run completes successfully. |
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Nice one! I was going to say it's great that the assertion we added proved useful, but I actually think the error was an |
Ah, yeah. If the assertion was added to the line before |
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Description of proposed changes
Fix and update the RKI transformation for pango_lineage.
PANGOLIN_LATESTto get the latest lineage assignment.Related issue(s)
Resolves #489
Resolves #478
Checklist