Create new function for cleaning individual fields in csv text

* gn3/csvcmp.py (clean_csv_text): New function.
* tests/unit/test_csvcmp.py: Import "csv_text".
(test_clean_csv_text): Test case for the above.

2 files changed, 30 insertions, 0 deletions

diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py
index 975814a..10c5d3e 100644
--- a/gn3/csvcmp.py
+++ b/gn3/csvcmp.py
@@ -48,6 +48,15 @@ def remove_insignificant_edits(diff_data, epsilon=0.001):
     return diff_data
 
 
+def clean_csv_text(csv_text: str) -> str:
+    """Remove extra white space elements in all elements of the CSV file"""
+    _csv_text = []
+    for line in csv_text.strip().split("\n"):
+        _csv_text.append(
+            ",".join([el.strip() for el in line.split(",")]))
+    return "\n".join(_csv_text)
+
+
 def csv_diff(base_csv, delta_csv, tmp_dir="/tmp") -> dict:
     """Diff 2 csv strings"""
     base_csv_list = base_csv.strip().split("\n")
diff --git a/tests/unit/test_csvcmp.py b/tests/unit/test_csvcmp.py
index b64fe83..ec4ca71 100644
--- a/tests/unit/test_csvcmp.py
+++ b/tests/unit/test_csvcmp.py
@@ -1,6 +1,7 @@
 """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
@@ -147,3 +148,23 @@ string"""
 
     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"