Store balsamic

[patrikgrenfeldt]

This PR adds cg capability to store balsamic case files in housekeeper

TODO:

• call balsamic to create meta file
• parse meta file to add tags to each file
• parse meta file to collect folders
• run folders to add all files
• run folders to add all files

How to prepare for test:

• install on stage of the hasta machine: bash servers/resources/hasta.scilifelab.se/update-cg-stage.sh store-balsamic
• activate stage: us

How to test basic storing:

• run following command: cg workflow balsamic store analysis [CASEID]

Expected test outcome:

• files stored successfully in housekeeper

How to test storing using a deliverables-file:

• run following command: cg workflow balsamic store analysis --deliverables-file [CASE-METAFILE] [CASEID]

Expected test outcome:

• files stored successfully in housekeeper

How to test creating an deliverables-file:

• run following command: cg workflow balsamic store generate-deliverables-file [CASEID]

Expected test outcome:

• deliverables file generated
• Take a screenshot and attach or copy/paste the output.

Review:

• code approved by @sylvinite @adrosenbaum
• tests executed by @patrikgrenfeldt
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This is |minor| version bump because it adds functionality in a backwards compatible way

[patrikgrenfeldt]

@hassanfa could I get your opinion on the storing of balsamic files in housekeeper?

[hassanfa]

@hassanfa could I get your opinion on the storing of balsamic files in housekeeper?

Awesome! I'll try my best. Can I do that on Friday please?

[patrikgrenfeldt]

Awesome! I'll try my best. Can I do that on Friday please?

Sure!

[patrikgrenfeldt]

I also asked @sylvinite for a code review to get some reviewing back and forth. I'm still curious about your thoughts on the Balsamic specifics @hassanfa 😄

[barrystokman]

How to test:

run following command: cg workflow balsamic store analysis [CASE-METAFILE] [CASEID]

@patrikgrenfeldt @hassanfa Do you have a [CASE-METAFILE] and [CASEID] I can use to test on stage?

[hassanfa]

Scanning through this, are you sure it is following the discussions in #475

I see the dummy file in tests is still the old format

[hassanfa]

@barrystokman I don't have any test cases for this, it is not on Balsamic 4.1.0 yet. Plan is for end of next week to make a release.

[adrosenbaum]

Looks fine, but I have some comments.

[patrikgrenfeldt]

test result linked files:

👍

[patrikgrenfeldt]

Test result housekeeper:

👍

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities (and 1 Security Hotspot to review)
21 Code Smells

No Coverage information
1.9% Duplication

[patrikgrenfeldt]

deployed on hasta and clinical-db