HOTFIX: Fetch reference version number for external references

[talnor]

Description

The features of this PR primarily concerns internals.

Summary of the changes made:

Due to changes at pubmlst.org; microSALT was unable to gather the version number for external references. This is now resolved.

Primary function of PR

• [x] 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.

Additional testing routine to verify the stability of the PR:

• _bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh fix_referencer_
• us
• _source activate S_microSALT_
• Download/copy the existing profile and loci files for Klebsiella pseudomonas
• cg workflow microsalt config-case ACC6369A43
• microSALT analyse /home/proj/stage/microbial/queries/ACC6369A43.json --input /home/proj/stage/microbial/fastq/ACC6369/ACC6369A43
• Investigate the database file, to see that Klebsiella pseudomonas recieved the correct version number ( sqlite3 microsalt.db . SELECT * FROM versions; .quit )

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

sqlite> SELECT * FROM versions; profile_klebsiella_pneumoniae|5208

Where 5208 is the latest MLST profile for K. pneumoniae. Also no error messages observed when starting the run.

Sign-offs

• [x] Code tested by @talnor
• [x] Approved to run at Clinical-Genomics by @sylvinite