Add referencer utilities and constants for Enterobacteriaceae

[karlnyr]

Description

This pull request includes several changes to the microSALT project, focusing on improving the handling of organism references and restructuring the codebase for better organization. The most important changes include updating import paths, adding utility functions for organism reference checks, and modifying methods to use these new utilities.

Codebase restructuring and improvements:

• microSALT/utils/job_creator.py: Updated the import path for Referencer and added a new import for get_reference_if_enterobacteriaceae. Modified the create_blast_search method to use the new utility function for checking Enterobacteriaceae references. [1] [2]

• microSALT/utils/referencer/constants.py: Introduced StrEnum and new enumerations for Escherichia and Klebsiella species, along with their corresponding references.

• microSALT/utils/referencer/referencer.py: Renamed the file for better organization and updated the organism2reference method to streamline the reference matching process. [1] [2]

• microSALT/utils/referencer/utils.py: Added utility functions is_escherichia, is_klebsiella, and get_reference_if_enterobacteriaceae to check organism names and return appropriate references.

• microSALT/utils/scraper.py: Updated the import path for Referencer and added a new import for get_reference_if_enterobacteriaceae. Modified the scrape_blast method to use the new utility function for checking Enterobacteriaceae references. [1] [2]

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

[samuell]

Looks good, apart from some concerns I have with the clarity of some of the code constructs. See below.

[samuell]

I think it pretty much solved it, but I suggest using a list of tuples instead of a set of tuples, as sets are not sorted (if that matters), and can be a little more confusing for people not used to them.

[samuell]

The surrounding {} also should probably preferably be changed, e.g. to [] to make it a list, since right now you actually got a "set" (consisting of tuples), since that is what you get with {} containing single items.

Well, a set might technically work here, but I think they also are not guaranteed to be in sorted order, if that matters...

[samuell]

Are these changes related to the previous discussion, or was this something else?

(No opinions here, just curious)