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TRON-Bioinformatics / covigator

CoVigator - Monitoring SARS-CoV-2 mutations
MIT License
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ENA API update #112

Closed johausmann closed 1 year ago

johausmann commented 1 year ago

The ENA API was updated in May 2023. We need to check if the changes affect the CoVigator accessor module.

More information here: https://docs.google.com/document/d/1RPHmK8Pvm9UxSa21Ej3MkGoGYO9baSxwxk_dOuWWyNE/edit#heading=h.jq87g3izg5xr

priesgo commented 1 year ago

Just ran the ENA accessor on Ebola virus and there is a new field tax_id returned in the payload that crashes the accessor when the database object is created as follows SampleEna(**run). As a quick fix I removed the field tax_id from the payload before creating the object, this works, but there may be better solutions. This may be connected with a potential need to support multiple viruses in the DB as tax_id would be precisely the discriminant. In the case of Ebolavirus I created a whole new set of tables using the database_prefix.

johausmann commented 1 year ago

Closed with #128