Add pubmlst utils

[ahdamin]

Description

The features of this PR primarily concerns bioinformaticians/internals

Summary of the changes made:

• Add PubMLST utils to handle authenticated API calls
• Update referecer to use PubMLST utils

Primary function of PR

• 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

[diitaz93]

👍

[diitaz93]

Deployed to stage and prod

Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/js.diazboada
done.
Log deploy... done.
microSALT, version 4.0.0
[js.diazboada@hasta:~] [P_base] $