OLC-Bioinformatics / ConFindr

Intra-species bacterial contamination detection
https://olc-bioinformatics.github.io/ConFindr/
MIT License
22 stars 8 forks source link

Can't get oauth_verifier #56

Closed chen1i6c04 closed 7 months ago

chen1i6c04 commented 7 months ago

Hi

I download rMLST scheme with confindr_database_setup , and also provide consumer key and consumer secret.

2023-11-14 09:06:32  Removing old databases... 
  2023-11-14 09:06:32  Downloading cgMLST-derived data for Escherichia, Salmonella, and Listeria... 
  2023-11-14 09:06:43  Since this is the first time you are using this database, it needs to be indexed by KMA. This might take a while 
  2023-11-14 09:06:53  Since this is the first time you are using this database, it needs to be indexed by KMA. This might take a while 
  2023-11-14 09:06:54  Since this is the first time you are using this database, it needs to be indexed by KMA. This might take a while 
Visit this URL in your browser: http://pubmlst.org/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_rmlst_seqdef&page=authorizeClient&oauth_token=
Enter oauth_verifier from browser:

When I visit the URL, it show below image

I can't get the oauth_verifier for download rMLST scheme

Do you have any idea?

pcrxn commented 7 months ago

Hi @chen1i6c04,

What is the full command that you're using with confindr_database_setup? And, does your secret file follow the format mentioned here?

i.e. Where the first line is the consumer key and the second line is the consumer secret:

efKXmqp2D0EBlMBkZaGC2lPf
F$M+fQ2AFFB2YBDfF9fpHF^qSWJdmmN%L4Fxf5Gur3
chen1i6c04 commented 7 months ago

Hi @pcrxn

I solved the issue, the reason is my system time is incorrect, so pubMLST reject the request. It can work after I adjusted system time.

pcrxn commented 7 months ago

Ok, thank you for letting us know!