From fd39b8ce0ad86c85636a09ca3ac15975fabf776a Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 25 Mar 2022 16:13:00 +0300 Subject: Create a fixture for pcorrs data --- tests/integration/conftest.py | 24 + tests/integration/test_data/pcorrs_data.json | 1039 ++++++++++++++++++++++++ tests/integration/test_partial_correlations.py | 5 +- 3 files changed, 1066 insertions(+), 2 deletions(-) create mode 100644 tests/integration/test_data/pcorrs_data.json diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py index 4274233..90cf985 100644 --- a/tests/integration/conftest.py +++ b/tests/integration/conftest.py @@ -78,3 +78,27 @@ def db_conn(): # # b.) Delete the test database db_cursor.execute(f"DROP DATABASE IF EXISTS {test_db_name}") + +@pytest.fixture(scope="function") +def db_conn_with_pcorrs_data(db_conn): + """Fixture with data for partial correlations tests""" + with open( + "tests/integration/test_data/pcorrs_data.json", + encoding="utf8") as data_file: + data = json.loads(data_file.read()) + with db_conn.cursor() as cursor: + for item in data: + row_keys = item["rows"][0].keys() + query = ( + f"INSERT INTO {item['dbtable']}({', '.join(row_keys)}) " + f"VALUES ({', '.join(['%s' for key in row_keys])})") + cursor.executemany( + query, + tuple( + tuple(row[key] for key in row_keys) + for row in item["rows"])) + + yield db_conn + + for item in data: + cursor.execute(f"DELETE FROM {item['dbtable']}") diff --git a/tests/integration/test_data/pcorrs_data.json b/tests/integration/test_data/pcorrs_data.json new file mode 100644 index 0000000..8f748fc --- /dev/null +++ b/tests/integration/test_data/pcorrs_data.json @@ -0,0 +1,1039 @@ +[ + { + "dbtable": "Phenotype", + "rows": [ + { + "Id": 16472, + "Pre_publication_description": "Central nervous system, be ...", + "Post_publication_description": "Central nervous system, ...", + "Original_description": "Original post publication descrip ...", + "Units": "Unknown", + "Pre_publication_abbreviation": "Learning3", + "Post_publication_abbreviation": "Touches_N", + "Lab_code": null, + "Submitter": "synomehbp", + "Owner": null, + "Authorized_Users": "synomehbp" + }, + { + "Id": 16475, + "Pre_publication_description": "Central nervous system, be ...", + "Post_publication_description": "Central nervous system, b ...", + "Original_description": "Original post publication descrip ...", + "Units": "Unknown", + "Pre_publication_abbreviation": "Learning6", + "Post_publication_abbreviation": "Final_Pretrain_Blank_Latency_S", + "Lab_code": null, + "Submitter": "synomehbp", + "Owner": null, + "Authorized_Users": "synomehbp" + }] + }, + { + "dbtable": "InbredSet", + "rows": [ + { + "Id": 1, + "InbredSetId": 1, + "InbredSetName": "BXD", + "Name": "BXD", + "SpeciesId": 1, + "FullName": "BXD Family", + "public": 2, + "MappingMethodId": 1, + "GeneticType": "riset", + "Family": "Reference Populations", + "FamilyOrder": 1, + "MenuOrderId": 0, + "InbredSetCode": "BXD" + }] + }, + { + "dbtable": "PublishXRef", + "rows": [ + { + "Id": 17937, + "InbredSetId": 1, + "PhenotypeId": 16472, + "PublicationId": 13554, + "DataId": 41005366, + "mean": 229.93754196166992, + "Locus": "16p_no_data", + "LRS": 23.7705104960664, + "additive": -46.0108582181818, + "Sequence": 1, + "comments": "a publish trait" + }, + { + "Id": 17940, + "InbredSetId": 1, + "PhenotypeId": 16475, + "PublicationId": 13557, + "DataId": 41005369, + "mean": 8.97237495581309, + "Locus": "rs30305830", + "LRS": 18.3037843139756, + "additive": -1.79666089108911, + "Sequence": 1, + "comments": "a publish trait" + }] + }, + { + "dbtable": "Publication", + "rows": [ + { + "Id": 13554, + "PubMed_ID": null, + "Abstract": "SYNOME (Partner 97). Since April 2014, when ...", + "Authors": "Horner A, Kopanitsa M, McLaren R, Human Brain Project Task 1.1.7", + "Title": "HBP MAPGENCO BXD study", + "Journal": null, + "Volume": null, + "Pages": null, + "Month": null, + "Year": 2015 + }, + { + "Id": 13557, + "PubMed_ID": null, + "Abstract": "SYNOME (Partner 97). Since April 2014, when ...", + "Authors": "Horner A, Kopanitsa M, McLaren R, Human Brain Project Task 1.1.7", + "Title": "HBP MAPGENCO BXD study", + "Journal": null, + "Volume": null, + "Pages": null, + "Month": null, + "Year": 2015 + }] + }, + { + "dbtable": "PublishFreeze", + "rows": [ + { + "Id": 1, + "Name": "BXDPublish", + "FullName": "BXD Published Phenotypes", + "ShortName": "BXDPublish", + "CreateTime": "2004-07-17", + "public": 2, + "InbredSetId": 1, + "confidentiality": 0, + "AuthorisedUsers": null + } + ] + }, + { + "dbtable": "ProbeSet", + "rows": [ + { + "Id": 162363, + "ChipId":7, + "Name": "ILM105290026", + "TargetId": "GI_38090455-S", + "Symbol": "Gm1151", + "description": "gene model 1151, (NCBI)", + "Chr": 10, + "Mb":36.833229, + "Chr_2016": 10, + "Mb_2016": 36.553035, + "alias": "", + "GeneId": 382362, + "GenbankId": null, + "SNP": null, + "BlatSeq": "GATGGTGACCGTCTTATCACAGAACCTCTGCCGGAACTACAGCTGGTGGA", + "TargetSeq": "", + "UniGeneId": null, + "Strand_Probe": "+", + 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test_part_corr_api_with_mix_of_existing_and_non_existing_control_traits( - db_conn, primary, controls, method, target): + db_conn_with_pcorrs_data, primary, controls, method, target): """ Check that calling the function with a mix of existing and missing control traits raises an warning. @@ -221,4 +221,5 @@ def test_part_corr_api_with_mix_of_existing_and_non_existing_control_traits( criteria = 10 with pytest.warns(UserWarning): partial_correlations_entry( - db_conn, primary, controls, method, criteria, target) + db_conn_with_pcorrs_data, primary, controls, method, criteria, + target) -- cgit v1.2.3