adding modality for queries towards pasteur database#206
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…ty and error handling
…les for consistency
… and improve database determination logic
… improved configuration
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Testing new authentication to pasteur: [15:21] [hiseq.clinical@hasta:/home/proj/stage/bin/git/microSALT] [S_microSALT] (add-pubmlst-pasteur-auth) $ python microSALT/utils/pubmlst/get_credentials.py -s pasteur -sp klebsiella
Please log in using your user account at https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_klebsiella_seqdef&page=authorizeClient&oauth_token=token using a web browser to obtain a verification code.
Please enter verification code: verification_code
Access Token: access_token
Access Token Secret: token_secret
Tokens saved to /home/proj/stage/microbial/credentials/pasteur_credentials.env |
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…onfiguration and improve logging for session token requests
…uration and routing
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Testing with the fixed variables:
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samuell
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May 5, 2025
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I've got some various minor nitpicks, but otherwise looks good to me.
karlnyr
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May 6, 2025
karlnyr
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karlnyr
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karlnyr
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Description
##Remove elements in cursive as needed.##
The features of this PR primarily concerns end-users/bioinformaticians/internals
Summary of the changes made:
If not self-evident, mention what prompted the change.
Primary function of PR
Testing
If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.
Test routine to verify the stability of the PR:
bash /home/proj/production/servers/resources/hasta.scilifelab.se/install-microsalt-stage.sh BRANCHNAMEusconda activate S_microSALTexport MICROSALT_CONFIG=/home/proj/dropbox/microSALT.jsonmicroSALT analyse project MIC3109microSALT analyse project MIC4107microSALT analyse project MIC4109microSALT analyse project ACC5551Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, Microbial_WGS.xlsx
Test results
These are the results of the tests, and necessary conclusions, that prove the stability of the PR.
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