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"""Tests for gn3.csvcmp"""
import pytest
from gn3.csvcmp import clean_csv_text
from gn3.csvcmp import csv_diff
from gn3.csvcmp import extract_invalid_csv_headers
from gn3.csvcmp import extract_strain_name
from gn3.csvcmp import fill_csv
from gn3.csvcmp import get_allowable_sampledata_headers
from gn3.csvcmp import remove_insignificant_edits
@pytest.mark.unit_test
def test_fill_csv():
"""Test that filling a csv works properly"""
test_input = """
Strain Name,Value,SE,Count,Sex
BXD1,18,x,0,
BXD12,16,x,x,
BXD14,15,x,x,
BXD15,14,x,x
"""
expected_output = """Strain Name,Value,SE,Count,Sex
BXD1,18,x,0,x
BXD12,16,x,x,x
BXD14,15,x,x,x
BXD15,14,x,x,x"""
assert fill_csv(test_input, width=5, value="x") == expected_output
@pytest.mark.unit_test
def test_remove_insignificant_data():
"""Test that values outside ε are removed/ ignored"""
diff_data = {
"Additions": [],
"Deletions": [],
"Modifications": [
{"Current": "1.000001,3", "Original": "1,3"},
{"Current": "1,3", "Original": "1.000001,3"},
{"Current": "2.000001,3", "Original": "2,2"},
{"Current": "1.01,3", "Original": "1,2"},
],
}
expected_json = {
"Additions": [],
"Deletions": [],
"Modifications": [
{"Current": "2,3", "Original": "2,2"},
{"Current": "1.01,3", "Original": "1,2"},
],
}
assert remove_insignificant_edits(diff_data) == expected_json
@pytest.mark.unit_test
def test_csv_diff_same_columns():
"""Test csv diffing on data with the same number of columns"""
assert csv_diff(base_csv="a,b \n1,2\n", delta_csv="a,b\n1,3") == {
"Additions": [],
"Deletions": [],
"Columns": "",
"Modifications": [{"Current": "1,3", "Original": "1,2"}],
}
@pytest.mark.unit_test
def test_csv_diff_different_columns():
"""Test csv diffing on data with different columns"""
base_csv = """
Strain Name,Value,SE,Count
BXD1,18,x,0
BXD12,16,x,x
BXD14,15,x,x
BXD15,14,x,x
"""
delta_csv = """Strain Name,Value,SE,Count,Sex
BXD1,18,x,0
BXD12,16,x,x,1
BXD14,15,x,x
BXD15,14,x,x"""
assert csv_diff(base_csv=base_csv, delta_csv=delta_csv) == {
"Additions": [],
"Columns": "Strain Name,Value,SE,Count,Sex",
"Deletions": [],
"Modifications": [
{"Current": "BXD12,16,x,x,1", "Original": "BXD12,16,x,x,x"}
],
}
@pytest.mark.unit_test
def test_csv_diff_only_column_change():
"""Test csv diffing when only the column header change"""
base_csv = """
Strain Name,Value,SE,Count
BXD1,18,x,0
BXD12,16,x,x
BXD14,15,x,x
BXD15,14,x,x
"""
delta_csv = """Strain Name,Value,SE,Count,Sex
BXD1,18,x,0
BXD12,16,x,x
BXD14,15,x,x
BXD15,14,x,x
"""
assert csv_diff(base_csv=base_csv, delta_csv=delta_csv) == {
"Additions": [],
"Deletions": [],
"Modifications": [],
}
@pytest.mark.unit_test
def test_extract_strain_name():
"""Test that the strain's name is extracted given a csv header"""
assert (
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"
)
@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"]
@pytest.mark.unit_test
def test_clean_csv():
"""Test that csv text input is cleaned properly"""
csv_text = """
Strain Name,Value,SE,Count
BXD1,18,x ,0
BXD12, 16,x,x
BXD14,15 ,x,x
BXD15,14,x,
"""
expected_csv = """Strain Name,Value,SE,Count
BXD1,18,x,0
BXD12,16,x,x
BXD14,15,x,x
BXD15,14,x,"""
assert clean_csv_text(csv_text) == expected_csv
assert clean_csv_text("a,b \n1,2\n") == "a,b\n1,2"
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