Cg-lims

preparations for new cg_lims database (89)(minor)

Added
- database colection models for load to arnold
- a EPPs to create a prep and sample document


Deleted
- the api since arnolod will serve as lims api

set reads missing (90)

* set reads missing

* set up set cli

* fixed unit tests

* count successful samples

* final clean up

* set_ -> set

* clean up exceptions and messages

* removed useless pass

* removed unused import

* implement PR feedback

* get udf

* tests

* tests

* threading?

* threading?

* all local tests pass?

* ...

* try again

* clean up

* restart server missing udf TC

* fix test

* doc string

first EPP attempt (67)

* first EPP attempt

* unit tests and improvements

* capital B

* parametrize unit tests and add mocks

* add pytest-mock to requirements-dev.txt

* add mock to requirements-dev.txt

Co-authored-by: mayabrandi <maya.brandiscilifelab.se>

Color coding the map (76) (minor)

Added
- red color code for warning samples in the pool
- different colors for different source containers to solve issue 59
- saving wanrinings on artifact if amount gets to high or to low in the pool calculations

Update sars_cov2_prep_file.py (83) (PATCH)

Changed

- file name containing container name

new script to fetch reads to sequence from the right place (80) (Minor)

Added
- new script to fetch reads to sequence from the right place