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)

A new get_cancer_gene_flags(), more polyvalent, is introduced to make sure we have one source of truth for both iprobe and ipr.

[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 83.73%. Comparing base (04a31b9) to head (27b8ed5).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #113      +/-   ##
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+ Coverage    83.56%   83.73%   +0.17%     
===========================================
  Files           18       18              
  Lines         2568     2595      +27     
===========================================
+ Hits          2146     2173      +27     
  Misses         422      422              

Flag	Coverage Δ
unittests	83.73% <100.00%> (+0.17%)	⬆️

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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.

[mathieulemieux]

@elewis2, I added the following changes based on your comments and offline discussion:

• new get_cancer_gene_flags() function as a source of truth for both iprobe and ipr
• updated get_gene_information() to use get_cancer_gene_flags()
• two new methods to GraphKBConnection to help with graph traversal

[elewis2]

->functionality