Improve TSV reading error handling

psm_utils/io/tsv.py

@@ -57,10 +57,10 @@
 from pydantic import ValidationError
 
 from psm_utils.io._base_classes import ReaderBase, WriterBase
+from psm_utils.io._utils import set_csv_field_size_limit
 from psm_utils.io.exceptions import PSMUtilsIOException
 from psm_utils.psm import PSM
 from psm_utils.psm_list import PSMList
-from psm_utils.io._utils import set_csv_field_size_limit
 
 set_csv_field_size_limit()
 
@@ -74,12 +74,21 @@
  """Iterate over file and return PSMs one-by-one."""
  with open(self.filename, "rt") as open_file:
  reader = csv.DictReader(open_file, delimiter="\t")
+ failed_rows = 0
  for row in reader:
  try:
  yield PSM(**self._parse_entry(row))
- except ValidationError:
+ except ValidationError as e:
+ failed_rows += 1
  logger.warning(f"Could not parse PSM from row: `{row}`")
- continue
+ if failed_rows >= 3:
+ raise PSMUtilsIOException(
+ "Could not parse PSM from three consecutive rows. Verify that the "
+ "file is formatted correctly as a psm_utils TSV file or that the "
+ "correct file type reader is used."
+ ) from e
+ else:
+ failed_rows = 0
 
  @staticmethod
  def _parse_entry(entry: dict) -> dict:

tests/test_data/test.tsv

@@ -0,0 +1,4 @@
+spectrum_id peptidoform
+peptide1 ACDEK/2
+peptide2 AC[Carbamidomethyl]DEFGR/3
+peptide3 [Acetyl]-AC[Carbamidomethyl]DEFGHIK/2

tests/test_io/test_tsv.py

@@ -1,6 +1,10 @@
 """Tests for psm_utils.io.tsv."""
 
-from psm_utils.io.tsv import TSVReader, TSVWriter # noqa: F401
+import pytest
+
+from psm_utils.io.exceptions import PSMUtilsIOException
+from psm_utils.io.tsv import TSVReader
+from psm_utils.peptidoform import Peptidoform
 
 test_cases = [
  (
@@ -30,3 +34,19 @@ class TestTSVReader:
  def test__parse_entry(self):
  for test_in, expected_out in test_cases:
  assert TSVReader._parse_entry(test_in) == expected_out
+
+ def test_iter(self):
+ reader = TSVReader("tests/test_data/test.tsv")
+ for psm in reader:
+ assert psm.peptidoform == Peptidoform("ACDEK/2")
+ assert psm.spectrum_id == "peptide1"
+ assert psm.provenance_data == {}
+ assert psm.metadata == {}
+ assert psm.rescoring_features == {}
+ break
+
+ def test_iter_raises(self):
+ with TSVReader("tests/test_data/peprec.tsv") as reader:
+ with pytest.raises(PSMUtilsIOException):
+ for psm in reader:
+ pass