Bsweger/align with nextstrain #10
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This changeset replaces a Nextstrain API call (to get the COV-SARS-2 reference sequence and a tree) with a call to the datasets function of the Nextclade CLI. The resulting download is a .zip file that can be used as input to the Nextclade CLI's run function when assigning sequences to clades.
When testing against larger volumes of data, polars returned a schema error when reading the clade assignments file generated by nextclade run. By default, polars only looks at the first 100 rows to infer a file schema; using a larger number of rows reduces the liklihood that it will infer incorrectly. The other alternative is to provide polars with a specific schema or column type, but doing that increases the change of something breaking due to an upstream (i.e., Nextrain) change.
This patches a security alert related to Python's requests library. This project is not affected, but no harm in staying up to date.
Most of the columns in the final clade assignments file will not be used by the variant nowcast hub. There's an open issue to determine exactly what's needed (#11), but in the meantime, we'll make a reasonable guess.
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elray1
approved these changes
Aug 26, 2024
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Resolves #8
Also addresses this security alert: https://github.com/reichlab/virus-clade-utils/security/dependabot/3
The issues linked above and the Individual commit messages have more detail.