Use csv.DictReader rather than csv.reader

demo/mapping_file.csv

+Annotation,Prediction
 demo_annot.bio,demo_predict.bio
 toy_test_annot.bio,toy_test_predict.bio
\ No newline at end of file

nerval/evaluate.py

+import csv
 import logging
-from csv import reader
 from pathlib import Path
 from typing import List
 
@@ -19,6 +19,10 @@ from nerval.utils import print_result_compact, print_results
 
 logger = logging.getLogger(__name__)
 
+ANNO_COLUMN = "Annotation"
+PRED_COLUMN = "Prediction"
+CSV_HEADER = [ANNO_COLUMN, PRED_COLUMN]
+
 
 def compute_matches(
     annotation: str,
@@ -346,7 +350,10 @@ def run_multiple(file_csv: Path, folder: Path, threshold: int, verbose: bool):
     """Run the program for multiple files (correlation indicated in the csv file)"""
     # Read the csv in a list
     with file_csv.open() as read_obj:
-        csv_reader = reader(read_obj)
+        csv_reader = csv.DictReader(read_obj)
+        assert (
+            csv_reader.fieldnames == CSV_HEADER
+        ), f'Columns in the CSV mapping should be: {",".join(CSV_HEADER)}'
         list_cor = list(csv_reader)
 
     if not folder.is_dir():
@@ -363,14 +370,16 @@ def run_multiple(file_csv: Path, folder: Path, threshold: int, verbose: bool):
         predict = None
 
         for file in list_bio_file:
-            if row[0] == file.name:
+            if row[ANNO_COLUMN] == file.name:
                 annot = file
         for file in list_bio_file:
-            if row[1] == file.name:
+            if row[PRED_COLUMN] == file.name:
                 predict = file
 
         if not (annot and predict):
-            raise Exception(f"No file found for files {row[0]}, {row[1]}")
+            raise Exception(
+                f"No file found for files {row[ANNO_COLUMN]}, {row[PRED_COLUMN]}"
+            )
 
         count += 1
         scores = run(annot, predict, threshold, verbose)

tests/conftest.py

@@ -45,6 +45,11 @@ def folder_bio():
     return FIXTURES
 
 
+@pytest.fixture()
+def csv_file_error():
+    return FIXTURES / "test_mapping_file_error.csv"
+
+
 @pytest.fixture()
 def csv_file():
     return FIXTURES / "test_mapping_file.csv"

tests/fixtures/test_mapping_file.csv

+Annotation,Prediction
 demo_annot.bio,demo_predict.bio
 toy_test_annot.bio,toy_test_predict.bio
\ No newline at end of file

tests/fixtures/test_mapping_file_error.csv

+Anno,Pred
+demo_annot.bio,demo_predict.bio
+toy_test_annot.bio,toy_test_predict.bio
\ No newline at end of file

tests/test_run.py

@@ -114,6 +114,13 @@ def test_run_empty_entry():
         evaluate.run(Path("invalid.bio"), Path("invalid.bio"), 0.3, False)
 
 
+def test_run_invalid_header(csv_file_error, folder_bio):
+    with pytest.raises(
+        Exception, match="Columns in the CSV mapping should be: Annotation,Prediction"
+    ):
+        evaluate.run_multiple(csv_file_error, folder_bio, 0.3, False)
+
+
 def test_run_multiple(csv_file, folder_bio):
     with pytest.raises(
         Exception, match="No file found for files demo_annot.bio, demo_predict.bio"