From 40beb8ac3ead366695836eb338774c44519b5bf5 Mon Sep 17 00:00:00 2001 From: Jake Lever Date: Fri, 3 Mar 2023 20:44:40 +0000 Subject: [PATCH] Edit tests to check variant extraction for issue #28 --- tests/test_entityrecognizer.py | 27 +++++++++++++++++++++++++-- 1 file changed, 25 insertions(+), 2 deletions(-) diff --git a/tests/test_entityrecognizer.py b/tests/test_entityrecognizer.py index 206423a..8709c62 100644 --- a/tests/test_entityrecognizer.py +++ b/tests/test_entityrecognizer.py @@ -707,8 +707,31 @@ def test_entityrecognizer_variant_2(): assert entity.entityType == 'variant' assert entity.externalID == 'substitution|V600E' - assert entity.text == 'Val600Glu' - assert entity.position == [(11,20)] + assert entity.text == 'p.Val600Glu' + assert entity.position == [(9,20)] + assert entity.sourceEntityID == 'T1' + +def test_entityrecognizer_variant_3(): + lookup = {} + + text = 'The T790M variant is well studied.' + + corpus = kindred.Corpus(text) + + parser = kindred.Parser() + parser.parse(corpus) + + ner = kindred.EntityRecognizer(lookup,detectVariants=True) + ner.annotate(corpus) + + doc = corpus.documents[0] + assert len(doc.entities) == 1 + entity = doc.entities[0] + + assert entity.entityType == 'variant' + assert entity.externalID == 'substitution|T790M' + assert entity.text == 'T790M' + assert entity.position == [(4,9)] assert entity.sourceEntityID == 'T1' def test_entityrecognizer_variant_stopwords():