Conversation
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
### Fixed - Replaced custom OAuth1 header generation with rauth.OAuth1Session for handling API requests, simplifying authentication logic and improving maintainability. (microSALT/utils/pubmlst/client.py, [1] [2] - Removed the generate_oauth_header function, as it is no longer needed due to the adoption of OAuth1Session. (microSALT/utils/pubmlst/helpers.py, microSALT/utils/pubmlst/helpers.pyL143-L173) ### Added - Added a new CLI command update_organism to update specific organisms, enabling more granular database updates. (microSALT/cli.py, microSALT/cli.pyR462-R472) - Forced a fresh session token retrieval before downloading MLST profiles to ensure up-to-date access credentials. (microSALT/utils/pubmlst/client.py, microSALT/utils/pubmlst/client.pyR166-R171) ### Changed - Simplified logger initialization by removing type hints and directly assigning None. (microSALT/__init__.py, microSALT/init.pyL27-R27)
Contributor
Author
activate S_base; activate S_microSALT;
# Running:
microSALT utils resync update-organism --force-update --organism "streptococcus pneumoniae"
microSALT utils resync update-organism --force-update --organism "staphylococcus aureus"
# Checking output
tail -n 1 /home/proj/stage/microbial/references/ST_profiles/streptococcus_pneumoniae # should have at least 20253
[15:09] [hiseq.clinical@hasta:/home/proj/stage/bin/git/microSALT] [S_microSALT] (rc4.2.1) $ tail -n 1 /home/proj/stage/microbial/references/ST_profiles/streptococcus_pneumoniae # should have at least 20253
20253 12 19 2 17 15 112 9
tail -n 1 /home/proj/stage/microbial/references/ST_profiles/staphylococcus_aureus # should have at least have 9964
[15:25] [hiseq.clinical@hasta:/home/proj/stage/bin/git/microSALT] [S_microSALT] (rc4.2.1) $ tail -n 1 /home/proj/stage/microbial/references/ST_profiles/staphylococcus_aureus
10095 295 14 8 6 10 3 2Also, to ensure that pasteur is working we reran the sync of the databases from the static page: [14:18] [hiseq.clinical@hasta:/home/proj/stage/bin/git/microSALT] [S_microSALT] (rc4.2.1) $ microSALT utils resync update-from-static
2025-06 14:19:05 INFO Profile for Brachyspira pilosicoli already at the latest version.
2025-06 14:19:06 INFO Profile for Brachyspira spp. already at the latest version.
2025-06 14:19:07 INFO Profile for Citrobacter freundii already at the latest version.
2025-06 14:19:07 INFO Profile for Enterobacter cloacae already at the latest version.
2025-06 14:19:08 INFO Profile for Enterococcus faecalis already at the latest version.
2025-06 14:19:08 INFO Profile for Enterococcus faecium already at the latest version.
2025-06 14:19:09 INFO Profile for Escherichia coli already at the latest version.
2025-06 14:19:10 INFO Profile for Glaesserella parasuis already at the latest version.
2025-06 14:19:10 INFO Profile for Klebsiella aerogenes already at the latest version.
2025-06 14:19:11 INFO Profile for Klebsiella oxytoca already at the latest version.
2025-06 14:19:11 INFO pasteur reference for Klebsiella pneumoniae updated to 2025-06-02 from 2025-05-19
2025-06 14:19:12 INFO Profiles CSV downloaded to /home/proj/stage/microbial/references/ST_profiles/klebsiella_pneumoniae
2025-06 14:19:13 INFO Locus FASTA downloaded: gapA.tfa
2025-06 14:19:13 INFO Locus FASTA downloaded: infB.tfa
2025-06 14:19:14 INFO Locus FASTA downloaded: mdh.tfa
2025-06 14:19:15 INFO Locus FASTA downloaded: pgi.tfa
2025-06 14:19:16 INFO Locus FASTA downloaded: phoE.tfa
2025-06 14:19:16 INFO Locus FASTA downloaded: rpoB.tfa
2025-06 14:19:20 INFO Locus FASTA downloaded: tonB.tfa
2025-06 14:19:24 INFO Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/klebsiella_pneumoniae
2025-06 14:29:16 INFO Profile for Neisseria spp. already at the latest version.
2025-06 14:29:17 INFO Profile for Paenibacillus larvae already at the latest version.
2025-06 14:29:18 INFO Profile for Pseudomonas aeruginosa already at the latest version.
2025-06 14:29:18 INFO Profile for Pseudomonas putida already at the latest version.
2025-06 14:29:19 INFO Profile for Salmonella enterica already at the latest version.
2025-06 14:29:20 INFO Profile for Staphylococcus aureus already at the latest version.
2025-06 14:29:21 INFO Profile for Staphylococcus epidermidis already at the latest version.
2025-06 14:29:21 INFO Profile for Staphylococcus haemolyticus already at the latest version.
2025-06 14:29:22 INFO Profile for Staphylococcus pseudintermedius already at the latest version.
2025-06 14:29:23 INFO Profile for Streptococcus agalactiae already at the latest version.
2025-06 14:29:23 INFO Profile for Streptococcus pneumoniae already at the latest version.
2025-06 14:29:24 INFO Profile for Streptococcus pyogenes already at the latest version.
2025-06 14:29:24 INFO Profile for Streptococcus uberis already at the latest version.
2025-06 14:29:25 INFO Profile for Streptococcus zooepidemicus already at the latest version.
INFO - Execution finished!References are obtained without issues from pasteur. And to confirm that we have the correct versions we used the website to query the profiles and found that the latest ST is 
To confirm this we heck the profiles: [15:26] [hiseq.clinical@hasta:/home/proj/stage/bin/git/microSALT] [S_microSALT] (rc4.2.1) $ tail -n 1 /home/proj/stage/microbial/references/ST_profiles/klebsiella_pneumoniae
8503 18 22 55 1 167 13 154Which also seems good! |
samuell
approved these changes
Jun 2, 2025
Contributor
samuell
left a comment
samuell
left a comment
There was a problem hiding this comment.
LGTM with some very minor quibbles and questions that you might decide if they are worth it.
… use logging_levels
15 tasks
Contributor
Author
|
Deployed in prod: 
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Description
This hotfixes the bug we had for authenticating requests. It also adds possibilities to alter the logging levels from the CLI, and adds further debug statements to the DB_manipulator, increasing transparency when things are added into a profiles table.
Added
Changed
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.
Sign-offs