mlstdb fetch 401 - Ribosomal MLST databases

[rfm-targa]

Greetings!

I am using the mlstdb fetch command to create the mlst_schemes_pubmlst.tab file used by mlst update to download the schema files. I understand that it fails if the user is not registered in the databases available in PubMLST. However, the process failed because I was not registered in the Ribosomal MLST genomes (pubmlst_rmlst_isolates) and Ribosomal MLST typing (pubmlst_rmlst_seqdef) databases. Since registration in these databases has to be manually approved, would it not be better to exclude these two databases from the default mlst fetch process?
I tried to use the --exclude parameter to stop mlstdb from fetching the information for those databases by passing rmlst or rmlst_seqdef, but it still tried to fetch the data for those databases. I managed to complete the process after my registration in the rMLST databases was approved.

Initially, I used the following command:

mlstdb fetch -v --db pubmlst

Which led to a 401 due to not being registered in the rMLST databases. I then updated the command to the following:

mlstdb fetch -v --db pubmlst --exclude "rmlst" (retried with "rmlst_seqdef")

After registration approval, I could run mlstdb fetch to completion.

Cheers,

Rafael

[himal2007]

Hi @rfm-targa,

Thanks for sharing the issue and detailed report. I agree the rMLST requirement made the default mlstdb fetch flow unnecessarily painful. The --exclude flag did not work because the filtering occurs after accessing the db.

This has been addressed in the latest update: mlstdb fetch does not get terminated after 401 issues. Also, you no longer need to run mlstdb fetch as part of the standard workflow (unless you specifically want to explore PubMLST / Pasteur data sources). The curated list used as input for mlstdb update is now built into the tool.

So to get the most up-to-date databases, you can simply run:

mlstdb connect -d pubmlst
mlstdb connect -d pasteur
mlstdb update

Thanks again, closing this issue as resolved in the latest release. If you still see mlstdb fetch not behaving as expected in a current version, please let me know.

Best,
Himal

[rfm-targa]

Greetings,

Thank for working on the updates. I used the connect+update commands to update the databases and everything went smoothly.

Cheers,

Rafael