Add tissue type when creating scout config file

[northwestwitch]

This PR should add a field tissue_type for each individual when creating a scout config file.
fix #497

How to prepare for test:

• install on hasta stage bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-cg-stage.sh pass_tissue_type
• activate stage: us

How to test:

• cg upload scout bosscod

Expected test outcome:

• The load command should create a yaml config file containing a tissue type set to 'unknown' for the case sample. (this happens because the sample is not in lims stage database, but in the lims one). Maybe there is a better case to test the command with?

Review:

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

This is a minor version update because it adds a new functionality.

[coveralls]

Coverage increased (+0.02%) to 64.902% when pulling 938fd99 on pass_tissue_type into 4d5df8e on master.

[northwestwitch]

I'm sure it's because I don't have much experience with it, but it's 2 days that I'm literally getting crazy over linting problems: the more I fix them, the more pop up at the next build.

Tried reformatting the file with black but I still get new errors every build. Any help would be very appreciated. I'm going to leave this PR for when I will have more time otherwise.

[barrystokman]

See last comment on this issue: pylint-dev/pylint#2944, the indentation message might be caused by black

line 221, col 4: Refactor: [no-self-use]: MockLims.lims_samples: Method could be a function

    def lims_samples(self):
        lims_family = json.load(open("tests/fixtures/report/lims_family.json"))
        return lims_family["samples"]

This method/function doesn't touch the class at all so maybe use @staticmethod?

[northwestwitch]

See last comment on this issue: PyCQA/pylint#2944, the indentation message might be caused by black

Very likely, the error showed immediately after I reformatted with black, I'll try to revert to a version before. Thanks!

[northwestwitch]

Thanks @hassanfa, the 4 spaces messages are gone now!

[northwestwitch]

YESSS IT PASSED!!!
Thank you so much @barrystokman and @hassanfa!
I might start crying now (happy tears), so good thing I'm working from home so I'll spare you the scene!! XD

[hassanfa]

@northwestwitch worthy of adding to resume 🤣

[northwestwitch]

@northwestwitch worthy of adding to resume 🤣

Indeed! :D

[northwestwitch]

This is ready for review, anybody?

[patrikgrenfeldt]

I have reviewed the code, looked good, seems like there is some conflicts that needs relolution:

[northwestwitch]

Thanks @patrikgrenfeldt, I'll fix them asap!

[northwestwitch]

I worked on this PR a month ago and many things have changed since then, I'll try to fix it here but it might take longer than I prevented..!

[northwestwitch]

Closing this and opening a new PR with the same code from the updated master. Otherwise it was conflict hell!