rework microbial fastq store

[diitaz93]

Description

Closes https://github.com/Clinical-Genomics/improve-order-flow/issues/111
Rework the Microbial Fastq storing service

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b [THIS-BRANCH-NAME] -a

How to test

• Do ...

Expected test outcome

• Check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
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This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[islean]

Looks super nice! But do we not need to rework the microbialordersubmitter a bit and enable some ignored tests? Also - have we tested placing an order on stage?

[ChrOertlin]

Changes here look good

[ChrOertlin]

Looks super nice! But do we not need to rework the microbialordersubmitter a bit and enable some ignored tests? Also - have we tested placing an order on stage?

I reckon all order submitters require some rework, but that seems out of scope for this PR.

[islean]

Looks super nice! But do we not need to rework the microbialordersubmitter a bit and enable some ignored tests? Also - have we tested placing an order on stage?

I reckon all order submitters require some rework, but that seems out of scope for this PR.

I guess it might be, but the submitters are almost superfluous at this point. We should stake out what is within scope but if it is to have the same scope as the minimal implementation fastq rework, then the submitter is included in scope

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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