def __parse_annotation(self, tree):
annotation = BioCAnnotation()
annotation.id = tree.attrib['id']
annotation.infons = self.__parse_infons(tree)
annotation.text = tree.findtext('text')
for child in tree.findall('location'):
annotation.add_location(
BioCLocation(int(child.attrib['offset']), int(child.attrib['length'])))
return annotation
def test_should_get_gene_names_normalised(self, list_dict, expected_genes):
# Arrange
sut = BiocAnnotationGenes()
bioc_doc = BioCDocument()
bioc_passage = BioCPassage()
bioc_doc.add_passage(bioc_passage)
for dict in list_dict:
annotation = BioCAnnotation()
annotation.infons = dict
bioc_passage.add_annotation(annotation)
# act
actual = sut.get_gene_names_normalised(bioc_doc)
# assert
self.assertEqual(set(expected_genes), actual)
def test_should_get_gene_names_to_normalised_dict(
self, list_gene_dict_in_passage, expected_dict):
# Arrange
sut = BiocAnnotationGenes()
bioc_doc = BioCDocument()
for list_gene_dict in list_gene_dict_in_passage:
bioc_passage = BioCPassage()
bioc_doc.add_passage(bioc_passage)
for dict in list_gene_dict:
annotation = BioCAnnotation()
annotation.text = dict["text"]
annotation.infons = dict
bioc_passage.add_annotation(annotation)
# act
actual = sut.get_gene_names_to_normalised_dict(bioc_doc)
# assert
self.assertEqual(expected_dict, actual)
