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ST_profiles from pubMLST not updating #197
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@eliottBo I tried to refresh the credentials. Would you please check if this makes any difference?
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Status update:The PR should fix the authentication issue. However, we get warning messages below for the isolates databases since they don't include the
To check the expected responses, you can refer to the documentation I tested |
Describe the bug
Whenever the microsalt pipeline is started, the ST_profiles are fetched from the database PubMLST if there are new profiles. When looking at the most recent profiles for S. aureus in hasta it is ST 9541 (looked at 2025-03-10) whereas in PubMLST, the last profile at that date is 9704. As a note, ST 9541 was added 2024-12-23 suggesting that after this date the updates did not work.
This issue seems to be for all organisms.
Related update from PubMLST from 2025-01-02:
@ahdamin Did work in Microsalt in order to fix the request issue related to this PubMLST update.
Investigation with KN:
The problem seems that when we access the data on PubMLST, we are restricted to the data before 2024-12-31.
{'records': 9666, 'message': 'Please note that you are currently restricted to accessing data that was submitted on or prior to 2024-12-31. Please authenticate to access the full dataset.', 'primary_key_field': 'https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/schemes/1/fields/ST', 'profiles_csv':
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The text was updated successfully, but these errors were encountered: