diff options
| -rw-r--r-- | gn3/csvcmp.py | 14 | ||||
| -rw-r--r-- | tests/unit/test_csvcmp.py | 15 |
2 files changed, 29 insertions, 0 deletions
diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py index aa057b7..dd3f72b 100644 --- a/gn3/csvcmp.py +++ b/gn3/csvcmp.py @@ -118,3 +118,17 @@ def get_allowable_sampledata_headers(conn: Any) -> List: attributes += [attributes[0] for attributes in cursor.fetchall()] return attributes + + +def extract_invalid_csv_headers(allowed_headers: List, csv_text: str) -> List: + """Check whether a csv text's columns contains valid headers""" + csv_header = [] + for line in csv_text.split("\n"): + if line.startswith("Strain Name"): + csv_header = [_l.strip() for _l in line.split(",")] + break + invalid_headers = [] + for header in csv_header: + if header not in allowed_headers: + invalid_headers.append(header) + return invalid_headers diff --git a/tests/unit/test_csvcmp.py b/tests/unit/test_csvcmp.py index 984a61f..735979d 100644 --- a/tests/unit/test_csvcmp.py +++ b/tests/unit/test_csvcmp.py @@ -2,6 +2,7 @@ import pytest from gn3.csvcmp import csv_diff +from gn3.csvcmp import extract_invalid_csv_headers from gn3.csvcmp import fill_csv from gn3.csvcmp import get_allowable_sampledata_headers from gn3.csvcmp import remove_insignificant_edits @@ -132,3 +133,17 @@ def test_get_allowable_csv_headers(mocker): assert get_allowable_sampledata_headers(mock_conn) == expected_values cursor.execute.assert_called_once_with( "SELECT Name from CaseAttribute") + + +@pytest.mark.unit_test +def test_extract_invalid_csv_headers_with_some_wrong_headers(): + """Test that invalid column headers are extracted correctly from a csv +string""" + allowed_headers = [ + "Strain Name", "Value", "SE", "Count", + "Condition", "Tissue", "Sex", "Age", + "Ethn.", "PMI (hrs)", "pH", "Color", + ] + + csv_text = "Strain Name, Value, SE, Colour" + assert extract_invalid_csv_headers(allowed_headers, csv_text) == ["Colour"] |