Clinical-Genomics / microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.
GNU General Public License v3.0
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Accomodate pubMLST authentication change #186

Open Vince-janv opened 1 week ago

Vince-janv commented 1 week ago

Description

According to this information the pubMLST database will require users to authenticate themselves to perform any type of requests (even GETs).

In microSALT/utils/referencer.py microSALT fetches stuff from there. This is performed on the first micro-analysis run every day.

Not authenticating will result in not being able to fetch recent data

API docs: https://bigsdb.readthedocs.io/en/latest/rest.html#api-oauth

Vince-janv commented 2 days ago

Technical refinement: