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]