use cancer type in CIViC results

[HomoPolyethylen]

PR Checklist

• [x] This comment contains a description of changes (with reason)
• [x] Referenced issue is linked
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] Documentation in docs is updated
• [ ] CHANGELOG.rst is updated

Description of changes

• added functionality to specify cancer type to civic queries. (new CL param -d / --cancer-doid)

Technical details

• user specifies a cancer type
• querynator filters evidence items in results:
  • include evidences from same cancer type
  • include evidences from higher-level cancer type (i.e. when specifying "Cholangiocarcinoma", also include all evidences for "Bile duct adenocarcinoma")
  • include level A evidences for other cancer type as level C evidence for this cancer type (as described in AMP/ASCO/CAT guidelines)

Additional context

CGI and CIViC use different ontologies (CGI: OncoTree, CIViC: Disease-Ontology. Right now they need to be specified separately, passing the burden to map ontologies to the user. This should be attended to in the future. Let user specify one cancer type, querynator maps to OncoTree / DO, queries, ...

[famosab]

New changes look good to me.

Pytest seems to run into some kind of numpy error: ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

StackOverflow has a solution I think: https://stackoverflow.com/questions/78634235/numpy-dtype-size-changed-may-indicate-binary-incompatibility-expected-96-from

[famosab]

You'll need to fix the version of numpy to 1.26.4 for example (probably in the requirements file). https://github.com/qbic-pipelines/querynator/blob/2f24ccd990aafd280cbb04c0b6c921b0e87a5812/requirements.txt#L10