diff options
| -rw-r--r-- | gn3/db/sample_data.py | 27 | ||||
| -rw-r--r-- | tests/unit/db/test_sample_data.py | 64 |
2 files changed, 10 insertions, 81 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index 3f7e2da..f79ce97 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -1,5 +1,5 @@ """Module containing functions that work with sample data""" -from typing import Any, Tuple, Dict, Callable +from typing import Any, Tuple, Dict, Callable, Optional import re import collections @@ -425,27 +425,8 @@ def insert_sample_data( raise MySQLdb.Error(_e) from _e -def get_case_attributes(conn) -> dict: - """Get all the case attributes as a dictionary from the database. Should there - exist more than one case attribute with the same name, put the id in - brackets.""" - results = {} +def get_case_attributes(conn) -> Optional[Tuple]: + """Get all the case attributes from the database.""" with conn.cursor() as cursor: cursor.execute("SELECT Id, Name, Description FROM CaseAttribute") - _r = cursor.fetchall() - _dups = [ - item - for item, count in collections.Counter( - [name for _, name, _ in _r] - ).items() - if count > 1 - ] - for _id, _name, _desc in _r: - _name = _name.strip() - _desc = _desc if _desc else "" - if _name in _dups: - results[f"{_name} ({_id})"] = _desc - else: - results[f"{_name}"] = _desc - - return results + return cursor.fetchall() diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py index 0fc20f4..8af4d3b 100644 --- a/tests/unit/db/test_sample_data.py +++ b/tests/unit/db/test_sample_data.py @@ -239,62 +239,10 @@ def test_get_case_attributes(mocker): cursor.execute.assert_called_once_with( "SELECT Id, Name, Description FROM CaseAttribute" ) - assert results == { - "Condition (1)": "", - "Tissue": "", - "Age": "Cum sociis natoque penatibus et magnis dis", - "Condition (4)": "Description A", - "Condition (5)": "Description B", - } - - -@pytest.mark.unit_test -def test_get_trait_csv_sample_data(mocker): - """Test fetching trait sample data""" - mock_conn = mocker.MagicMock() - with mock_conn.cursor() as cursor: - cursor.fetchall.return_value = [ - ["JL00005,896.000000,x,x", "Age", "896"], - ["JL00005,896.000000,x,x", "DOB", "4/22/04"], - ["JL00005,896.000000,x,x", "Date Geno", "x"], - ["JL00005,896.000000,x,x", "Drug/Site", "4OHPBN_J"], - ["JL00005,896.000000,x,x", "MOD", "Oct"], - ["JL00005,896.000000,x,x", "Platform", "x"], - [ - "JL00005,896.000000,x,x", - "SNP", - """0 -""", - ], - ["JL00005,896.000000,x,x", "Sex", "M"], - ["JL00005,896.000000,x,x", "Site", "JL"], - ["JL00005,896.000000,x,x", "Tx", "1"], - ["JL00005,896.000000,x,x", "Year", "2004"], - ["JL00058,686.000000,x,x", "Age", "686"], - ["JL00058,686.000000,x,x", "DOB", "4/22/04"], - ["JL00058,686.000000,x,x", "Date Geno", "2017.06"], - ["JL00058,686.000000,x,x", "Drug/Site", "Cont_04_J"], - ["JL00058,686.000000,x,x", "MOD", "Mar"], - ["JL00058,686.000000,x,x", "Platform", "M"], - [ - "JL00058,686.000000,x,x", - "SNP", - """2 -""", - ], - ["JL00058,686.000000,x,x", "Sex", "M"], - ["JL00058,686.000000,x,x", "Site", "JL"], - ["JL00058,686.000000,x,x", "Tx", "0"], - ["JL00058,686.000000,x,x", "Year", "2004"], - ] - assert get_trait_csv_sample_data( - conn=mock_conn, trait_name=10007, phenotype_id=35 - ) == ( - "Strain Name,Value,SE,Count,Age,DOB," - "Date Geno,Drug/Site,MOD," - "Platform,SNP,Sex,Site,Tx,Year\n" - "JL00005,896.000000,x,x," - "896,4/22/04,x,4OHPBN_J,Oct,x,0,M,JL,1,2004\n" - "JL00058,686.000000,x,x," - "686,4/22/04,2017.06,Cont_04_J,Mar,M,2,M,JL,0,2004\n" + assert results == ( + (1, "Condition", None), + (2, "Tissue", None), + (3, "Age", "Cum sociis natoque penatibus et magnis dis"), + (4, "Condition", "Description A"), + (5, "Condition", "Description B"), ) |