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Decide case-sensitivity for lineage definitions #655

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Taepper opened this issue Nov 27, 2024 · 2 comments
Open

Decide case-sensitivity for lineage definitions #655

Taepper opened this issue Nov 27, 2024 · 2 comments

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@Taepper
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Taepper commented Nov 27, 2024

Lineage definitions were created with the aim to not make any implicit assumptions about the lineage format at hand. This means that currently, the lineage_definitions file and also the queries are case-sensitive.

This now lead to issues where CovSpectrum users did not receive the expected results when querying for lower-case lineage values. This was fixed when the user does not enter a variant-query. When a variant query is entered however, parsing would be necessary to transform the lineage value to upper-case.

We can now solve this by either:

  • making lineages (both the lineage definitions file and the queries) case-insensitive (in general or by configuration)
  • creating lineage definitions with all casing-variants as aliases
@Taepper
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Taepper commented Nov 27, 2024

For now the lineage definitions will be adapted but this issue will be left as a discussion point until a final decision is made

@fengelniederhammer
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For now the lineage definitions will be adapted

in this issue: https://github.com/GenSpectrum/servers/issues/208

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