def test_with_apostrophe(self): catalog_path = os.path.join(resource_dir, "disease_catalog.csv") target = DiseasesCatalog(catalog_path) target.initialize() expected_dict = { "angiosarcoma": "DOID:0001816", "ANGIOSARCOMA": "DOID:0001816", "Angiosarcoma": "DOID:0001816", "hemangiosarcoma foo": "DOID:0001816", "Hemangiosarcoma foo": "DOID:0001816", "Hemangiosarcoma Foo": "DOID:0001816", "HEMANGIOSARCOMA FOO": "DOID:0001816", "pterygium": "DOID:0002116", "PTERYGIUM": "DOID:0002116", "crohns disease": "DOID:0002116", "Crohns Disease": "DOID:0002116", "CROHNS DISEASE": "DOID:0002116", "Crohns disease": "DOID:0002116", } self.assertCountEqual(target.disease_dictionary, expected_dict) test_sentence = "Recent study showed that Hemangiosarcoma Foo and Crohn's disease both are really bad stuff" actual_found = target.find(test_sentence) expected_found = [Entity("Hemangiosarcoma Foo", "DOID0001816", DISEASE_TAG), Entity("Crohns disease", "DOID0002116", DISEASE_TAG)] self.assertCountEqual(actual_found.entities, expected_found)
# dbpedia_food_catalog = DbpediaFoodCatalog(dbpedia_food_file_path) # dbpedia_food_catalog.initialize() mixed_food_catalog = MixedFoodCatalog(mixed_food_file_path) mixed_food_catalog.initialize() all_bacteria_catalog = AllBacteriaCatalog(all_catalog_file_path) all_bacteria_catalog.initialize() gut_bacteria_catalog = GutBacteriaCatalog(gut_catalog_file_path, all_bacteria_catalog) gut_bacteria_catalog.initialize() # nutrients_catalog = NutrientsCatalogNikogosov(path=nutrients_file_path) # nutrients_catalog.initialize() diseases_catalog = DiseasesCatalog(diseases_csv_path=diseases_csv_path) diseases_catalog.initialize() prebiotics_catalog = PrebioticsCatalog(prebiotics_file_path) prebiotics_catalog.initialize() diets_catalog = DietsCatalog(diets_file_path) diets_catalog.initialize() spacy_sentence_parser = SpacySentenceParser() do_nothing_parser = DoNothingParser() do_nothing_analyzer = DoNothingSentenceAnalyzer() analyzer = SentenceAnalyzer() tags_required = [BACTERIA_TAG]