Fix-pubmlst-query-insert

[karlnyr]

Description

This PR tries to adress the issue that when we download databases and try to update existing ones we have the clonal complex and species column. Two columns that are not used in the analysis.

Code Formatting Improvements:

• microSALT/store/models.py: Simplified the formatting of error messages and file handling to improve readability. [1] [2]

Minor Logic Adjustments:

• microSALT/store/models.py: Limited the number of elements considered in the header to the first 8 elements to avoid unnecessary processing. [1] [2]

• microSALT/utils/referencer.py: Added logic to only write the first 8 columns of the profiles CSV to avoid adding unnecessary information such as "clonal_complex" and "species".

Primary function of PR

• Hotfix
• Patch
• Minor functionality improvement
• New type of analysis
• Backward-breaking functionality improvement
• This change requires internal documents to be updated
• This change requires another repository to be updated

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 BRANCHNAME
• us
• conda activate S_microSALT
• (SITUATIONAL) export MICROSALT_CONFIG=/home/proj/dropbox/microSALT.json
• Select a relevant subset of the following:
• microSALT analyse project MIC3109
• microSALT analyse project MIC4107
• microSALT analyse project MIC4109
• microSALT analyse project ACC5551

Verify 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

• Code tested by @octocat
• Approved to run at Clinical-Genomics by @karlnyr

[karlnyr]

Tested to run and generate a report for MIC4109:

New report:

Old report:

Same ST types were yielded. There is a difference in resistances, due to database updates. However, we are generating the same set of resistance groups.