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kjolley / BIGSdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
https://pubmlst.org/software/bigsdb/
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IsolateQueryPage improvement #973

Closed mikelchtermans closed 5 months ago

mikelchtermans commented 5 months ago

if isolates are queried through url, inherit provenance fields from url just like allele designations, instead of defaulting to the first value; id

kjolley commented 5 months ago

Hi. This is the current behaviour and the patch isn't needed (unless I have misunderstood). You just need to be aware that standard provenance fields are prefixed with 'f_' in the dropdown list, e.g. https://pubmlst.org/bigsdb?db=pubmlst_neisseria_isolates&page=query&prov_field1=f_country&prov_value1=France&submit=1, whereas extended attribute fields like continent (which is linked to a country lookup table) are prefixed with 'e_', e.g. https://pubmlst.org/bigsdb?db=pubmlst_neisseria_isolates&page=query&prov_field1=e_country||continent&prov_value1=Europe&submit=1.

This is used for all the links on https://pubmlst.org/static/updates/recent_updates.shtml.

mikelchtermans commented 5 months ago

Indeed, my bad. I was using: https://pubmlst.org/bigsdb?db=pubmlst_neisseria_isolates&page=query&prov_field1=country&prov_value1=France&submit=1 , without the f , which yields a valid result, but the primary metadata field re-defaults to 'id', making it unusable if you want to continue your query through the GUI. I will use the f going forward, thank you!