Skip spectra with invalid custom fields

depthcharge/data/parsers.py

@@ -206,15 +206,15 @@ def iter_batches(self, batch_size: int | None) -> pa.RecordBatch:
                         "intensity_array": parsed.intensity,
                     }
 
+                    # Parse custom fields:
+                    entry.update(self.parse_custom_fields(spectrum))
+                    self._update_batch(entry)
+
                 except (IndexError, KeyError, ValueError) as exc:
                     last_exc = exc
                     n_skipped += 1
                     continue
 
-                # Parse custom fields:
-                entry.update(self.parse_custom_fields(spectrum))
-                self._update_batch(entry)
-
                 # Update the batch:
                 if len(self._batch["scan_id"]) == batch_size:
                     yield self._yield_batch()
@@ -225,8 +225,8 @@ def iter_batches(self, batch_size: int | None) -> pa.RecordBatch:
 
         if n_skipped:
             warnings.warn(
-                f"Skipped {n_skipped} spectra with invalid information."
-                f"Last error was: \n {str(last_exc)}"
+                f"Skipped {n_skipped} spectra with invalid information. "
+                f"Last error was:\n{str(last_exc)}"
             )
 
     def _update_batch(self, entry: dict) -> None:

tests/unit_tests/test_data/test_parsers.py

@@ -195,15 +195,36 @@ def test_custom_fields(mgf_small):
     expected = pl.Series("seq", ["LESLIEK", "EDITHR"])
     assert_series_equal(parsed["seq"], expected)
 
-    with pytest.raises(KeyError):
-        pl.from_arrow(
-            MgfParser(
-                mgf_small,
-                custom_fields=CustomField(
-                    "seq", lambda x: x["params"]["bar"], pa.string()
-                ),
-            ).iter_batches(None)
-        )
+    # Test that spectra with invalid custom fields are skipped.
+    # We don't like the amino acid "D".
+    def seq_no_d(spec):
+        if "D" in (seq := spec["params"]["seq"]):
+            raise ValueError(f"Invalid sequence: {seq}")
+        return seq
+
+    parsed = pl.from_arrow(
+        MgfParser(
+            mgf_small,
+            custom_fields=CustomField("seq", seq_no_d, pa.string()),
+        ).iter_batches(None)
+    )
+
+    assert len(parsed) == 1
+    assert_series_equal(parsed["seq"], pl.Series("seq", ["LESLIEK"]))
+
+    # Invalid custom fields will cause all spectra to get skipped.
+    parser = MgfParser(
+        mgf_small,
+        custom_fields=CustomField(
+            "seq", lambda x: x["params"]["bar"], pa.string()
+        ),
+    )
+
+    with pytest.warns(
+        UserWarning, match=r"Skipped 2 spectra with invalid information.*"
+    ):
+        spectra = list(parser.iter_batches(None))
+    assert len(spectra) == 0
 
 
 def test_invalid_file(tmp_path):