diff options
| -rw-r--r-- | gn3/csvcmp.py | 12 | ||||
| -rw-r--r-- | tests/unit/test_csvcmp.py | 19 |
2 files changed, 31 insertions, 0 deletions
diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py index 43b795d..aa057b7 100644 --- a/gn3/csvcmp.py +++ b/gn3/csvcmp.py @@ -1,5 +1,7 @@ """This module contains functions for manipulating and working with csv texts""" +from typing import Any, List + import json import os import uuid @@ -106,3 +108,13 @@ def fill_csv(csv_text, width, value="x"): _n[i] = value data.append(",".join(_n + [value] * (width - len(_n)))) return "\n".join(data) + + +def get_allowable_sampledata_headers(conn: Any) -> List: + """Get a list of all the case-attributes stored in the database""" + attributes = ["Strain Name", "Value", "SE", "Count"] + with conn.cursor() as cursor: + cursor.execute("SELECT Name from CaseAttribute") + attributes += [attributes[0] for attributes in + cursor.fetchall()] + return attributes diff --git a/tests/unit/test_csvcmp.py b/tests/unit/test_csvcmp.py index c7ffe2f..984a61f 100644 --- a/tests/unit/test_csvcmp.py +++ b/tests/unit/test_csvcmp.py @@ -3,6 +3,7 @@ import pytest from gn3.csvcmp import csv_diff from gn3.csvcmp import fill_csv +from gn3.csvcmp import get_allowable_sampledata_headers from gn3.csvcmp import remove_insignificant_edits from gn3.csvcmp import extract_strain_name @@ -113,3 +114,21 @@ def test_extract_strain_name(): extract_strain_name(csv_header="Strain Name,Value,SE,Count", data="BXD1,18,x,0") == "BXD1" ) + + +@pytest.mark.unit_test +def test_get_allowable_csv_headers(mocker): + """Test that all the csv headers are fetched properly""" + mock_conn = mocker.MagicMock() + expected_values = [ + "Strain Name", "Value", "SE", "Count", + "Condition", "Tissue", "Sex", "Age", + "Ethn.", "PMI (hrs)", "pH", "Color", + ] + with mock_conn.cursor() as cursor: + cursor.fetchall.return_value = ( + ('Condition',), ('Tissue',), ('Sex',), + ('Age',), ('Ethn.',), ('PMI (hrs)',), ('pH',), ('Color',)) + assert get_allowable_sampledata_headers(mock_conn) == expected_values + cursor.execute.assert_called_once_with( + "SELECT Name from CaseAttribute") |