def test_delete_variant(real_mongo_adapter, het_variant, case_obj): ## GIVEN a database with one variant that is observed twice db = real_mongo_adapter.db case_id = case_obj["case_id"] db.variant.insert_one({ "_id": get_variant_id(het_variant), "families": [case_id, "2"], "observations": 2, }) mongo_variant = db.variant.find_one() assert mongo_variant["observations"] == 2 ## WHEN deleting the variant for one case delete_variants( adapter=real_mongo_adapter, vcf_obj=[het_variant], case_obj=case_obj, case_id="2", ) mongo_variant = db.variant.find_one() ## THEN assert that one case has been removed from 'families' assert mongo_variant["families"] == [case_id] ## THEN assert that the observation count is decreased assert mongo_variant["observations"] == 1
def test_delete_variant(real_mongo_adapter, het_variant, case_obj): ## GIVEN a database with one variant that is observed twice db = real_mongo_adapter.db case_id = case_obj['case_id'] db.variant.insert_one({ '_id': get_variant_id(het_variant), 'families': [case_id, '2'], 'observations': 2, }) mongo_variant = db.variant.find_one() assert mongo_variant['observations'] == 2 ## WHEN deleting the variant for one case delete_variants( adapter=real_mongo_adapter, vcf_obj=[het_variant], case_obj=case_obj, case_id='2', ) mongo_variant = db.variant.find_one() ## THEN assert that one case has been removed from 'families' assert mongo_variant['families'] == [case_id] ## THEN assert that the observation count is decreased assert mongo_variant['observations'] == 1
def test_delete_non_existing_variant(mongo_adapter, het_variant, case_obj): """docstring for test_load_variants""" ## GIVEN a mongo adapter to an empty database db = mongo_adapter.db case_id = case_obj["case_id"] ## WHEN deleting the variants delete_variants(adapter=mongo_adapter, vcf_obj=[het_variant], case_obj=case_obj) # THEN assert nothing happens mongo_variant = db.variant.find_one() assert mongo_variant == None
def test_delete_variants(real_mongo_adapter, het_variant, case_obj): ## GIVEN a database with one variant db = real_mongo_adapter.db case_id = case_obj["case_id"] db.variant.insert_one({ "_id": get_variant_id(het_variant), "families": [case_id], "observations": 1, }) mongo_variant = db.variant.find_one() assert mongo_variant["families"] == [case_id] ## WHEN deleting the variant delete_variants(adapter=real_mongo_adapter, vcf_obj=[het_variant], case_obj=case_obj) mongo_variant = db.variant.find_one() ## THEN assert that the variant was not found assert mongo_variant is None
def test_delete_variants(real_mongo_adapter, het_variant, case_obj): ## GIVEN a database with one variant db = real_mongo_adapter.db case_id = case_obj['case_id'] db.variant.insert_one({ '_id': get_variant_id(het_variant), 'families': [case_id], 'observations': 1, }) mongo_variant = db.variant.find_one() assert mongo_variant['families'] == [case_id] ## WHEN deleting the variant delete_variants(adapter=real_mongo_adapter, vcf_obj=[het_variant], case_obj=case_obj) mongo_variant = db.variant.find_one() ## THEN assert that the variant was not found assert mongo_variant == None