Update get_cancer_genes() to fit consensus defenition of cancer gene

[mathieulemieux]

See https://www.bcgsc.ca/jira/browse/KBDEV-1532

get_cancer_genes() will now work with both 'tumourigenesis' (for backward compatibility) and 'cancer gene' as umbrella terms for all cancer-related genes (i.e. oncogenes, tumour suppressive genes and other cancer genes)

[mathieulemieux]

@dustinbleile , do you mind we discard PR #111 ?

[elewis2]

@mathieulemieux is it possible to include this filter in the query itself, in _get_tumourigenesis_genes_list? Might reduce the number of records retrieved.

for statement in statements:
    if statement['subject'].get('biotype', '') == 'gene':

Speculating: I'm wondering if there's a way we can avoid querying gkb three times during report prep to get this same info (this step is done in get_gene_information). I think _get_tumourigenesis could probably be updated to include the matched relevance in the result, if the input relevance is a list... but I don't think the info can be processed in a way that leaves get_cancer_genes usable as-is by iprobe since it would need to change the return type to include the separate flags. Maybe something we can address in a later pr.

[elewis2]

Re subject biotype in query - Just tested, it wouldn't actually reduce the number of statements retrieved at all.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.50%. Comparing base (8777c66) to head (458f88f).
⚠️ Report is 2 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #113      +/-   ##
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+ Coverage    83.46%   83.50%   +0.03%     
===========================================
  Files           18       18              
  Lines         2546     2552       +6     
===========================================
+ Hits          2125     2131       +6     
  Misses         421      421              

Flag	Coverage Δ
unittests	83.50% <100.00%> (+0.03%)	⬆️

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[mathieulemieux]

Re subject biotype in query - Just tested, it wouldn't actually reduce the number of statements retrieved at all.

yeah, all these relevance terms are used in statement with a gene as the subject.

[mathieulemieux]

Speculating: I'm wondering if there's a way we can avoid querying gkb three times [...]

ok, let me add a new function for that, so we keep old behavior for iprobe. I'll have to refactor things a bit.