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)