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Description of changes
Fixes #20
CGI "wildtype" biomarkers no longer raise an index error, but get parsed and logged
warning is logged, if CGI returns a wildtype biomarker for a gene in which a variant was found
expressive exception is raised, if unexpected alterations are added in the future
previous behaviour: get_all_alterations raises exception, link_biomarkers catches it and returns unlinked dataframe instead, leading to empty results but little knowledge of origin (silent error).
behaviour now: exception is not caught, terminating the program and enforcing developmental integration of new alteration
optional behaviour, one could implement: instead of raising an exception, log a warning. This seemed too silent to me, false/incomplete results could go undetected for too long
PR Checklist
docsis updatedCHANGELOG.rstis updatedDescription of changes
Fixes #20
get_all_alterationsraises exception,link_biomarkerscatches it and returns unlinked dataframe instead, leading to empty results but little knowledge of origin (silent error).Technical details
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