fix(results): support pyOpenMS 3.5.0 IdXMLFile.load signature

src/WorkflowTest.py

@@ -4,7 +4,6 @@
 import pandas as pd
 import plotly.express as px
 from streamlit_plotly_events import plotly_events
-from pyopenms import IdXMLFile
 from scipy.stats import ttest_ind
 import numpy as np
 import mygene
@@ -14,7 +13,7 @@
 from src.workflow.WorkflowManager import WorkflowManager
 from src.common.common import page_setup
 from src.common.results_helpers import get_abundance_data
-from src.common.results_helpers import parse_idxml, build_spectra_cache
+from src.common.results_helpers import parse_idxml, build_spectra_cache, load_idxml
 from openms_insight import Table, Heatmap, LinePlot, SequenceView
 
 # params = page_setup()
@@ -1636,9 +1635,7 @@ def results(self) -> None:
             selected_file = st.selectbox("📁 Select Identification result file", comet_files)
 
             def idxml_to_df(idxml_file):
-                proteins = []
-                peptides = []
-                IdXMLFile().load(str(idxml_file), proteins, peptides)
+                proteins, peptides = load_idxml(idxml_file)
 
                 records = []
                 for pep in peptides:

src/common/results_helpers.py

@@ -6,18 +6,37 @@
 import streamlit as st
 from pathlib import Path
 from pyopenms import IdXMLFile, MSExperiment, MzMLFile
+try:  # pyOpenMS >= 3.5.0
+    from pyopenms import PeptideIdentificationList
+except ImportError:  # pyOpenMS <= 3.4.x
+    PeptideIdentificationList = None
 from src.workflow.ParameterManager import ParameterManager
 
 def get_workflow_dir(workspace):
     """Get the workflow directory path."""
     return Path(workspace, "topp-workflow")
 
 
-def idxml_to_df(idxml_file):
-    """Parse idXML file and return DataFrame with peptide hits."""
+def load_idxml(idxml_file):
+    """Load an idXML file, returning ``(protein_ids, peptide_ids)`` as plain lists.
+
+    pyOpenMS 3.5.0 changed the third parameter of ``IdXMLFile.load()`` from a
+    ``libcpp_vector[PeptideIdentification]``, which accepted an ordinary Python
+    list, to a dedicated ``PeptideIdentificationList`` container. A list no longer
+    matches any overload there and pyOpenMS raises
+    ``Exception: can not handle type of (<path>, [], [])``. Feature-detect the
+    container so the app runs on 3.5.0 as well as earlier releases, and hand
+    callers back an ordinary list either way.
+    """
     proteins = []
-    peptides = []
+    peptides = PeptideIdentificationList() if PeptideIdentificationList else []
     IdXMLFile().load(str(idxml_file), proteins, peptides)
+    return proteins, list(peptides)
+
+
+def idxml_to_df(idxml_file):
+    """Parse idXML file and return DataFrame with peptide hits."""
+    proteins, peptides = load_idxml(idxml_file)
 
     records = []
     for pep in peptides:
@@ -99,9 +118,7 @@ def parse_idxml(idxml_path: Path) -> tuple[pl.DataFrame, list[str]]:
     Returns:
         Tuple of (id_df, spectra_data list of source filenames)
     """
-    proteins = []
-    peptides = []
-    IdXMLFile().load(str(idxml_path), proteins, peptides)
+    proteins, peptides = load_idxml(idxml_path)
 
     # Derive mzML filename from idXML filename (e.g., 02COVID_filter.idXML -> 02COVID.mzML)
     spectra_data = [extract_filename_from_idxml(idxml_path)]

tests/test_results_helpers.py

@@ -1,10 +1,13 @@
 from pathlib import Path
 
+import pyopenms as poms
+
 from src.common.results_helpers import (
     extract_filename_from_idxml,
     extract_scan_from_ref,
     extract_scan_number,
     get_workflow_dir,
+    load_idxml,
 )
 
 
@@ -25,3 +28,73 @@ def test_extract_filename_from_idxml_strips_suffixes():
     assert extract_filename_from_idxml(Path("02COVID_filter.idXML")) == "02COVID.mzML"
     assert extract_filename_from_idxml(Path("sample_comet.idXML")) == "sample.mzML"
     assert extract_filename_from_idxml(Path("run_per.idXML")) == "run.mzML"
+
+
+def _write_idxml(path):
+    """Write a small idXML with one protein and two peptide hits."""
+    prot = poms.ProteinIdentification()
+    prot.setIdentifier("SEARCH_1")
+    hit = poms.ProteinHit()
+    hit.setAccession("sp|P12345|TEST")
+    prot.setHits([hit])
+
+    peptides = []
+    for i, seq in enumerate(("PEPTIDEK", "ELVISLIVESR")):
+        pep = poms.PeptideIdentification()
+        pep.setIdentifier("SEARCH_1")
+        pep.setRT(100.0 + i)
+        pep.setMZ(500.0 + i)
+        pep.setMetaValue("spectrum_reference", f"scan={i + 1}")
+        pep_hit = poms.PeptideHit()
+        pep_hit.setSequence(poms.AASequence.fromString(seq))
+        pep_hit.setCharge(2)
+        evidence = poms.PeptideEvidence()
+        evidence.setProteinAccession("sp|P12345|TEST")
+        pep_hit.setPeptideEvidences([evidence])
+        pep.setHits([pep_hit])
+        peptides.append(pep)
+
+    # pyOpenMS >= 3.5.0 wants the dedicated container here too.
+    if hasattr(poms, "PeptideIdentificationList"):
+        container = poms.PeptideIdentificationList()
+        for pep in peptides:
+            container.push_back(pep)
+        peptides = container
+
+    poms.IdXMLFile().store(str(path), [prot], peptides)
+
+
+def test_load_idxml_reads_identifications(tmp_path):
+    """Regression test for pyOpenMS 3.5.0.
+
+    3.5.0 changed the third parameter of ``IdXMLFile.load()`` from a plain
+    ``libcpp_vector[PeptideIdentification]`` to a ``PeptideIdentificationList``,
+    so passing ``[]`` raised ``can not handle type of (<path>, [], [])``.
+    """
+    idxml = tmp_path / "sample_comet.idXML"
+    _write_idxml(idxml)
+
+    proteins, peptides = load_idxml(idxml)
+
+    # A plain list either way, so callers can index and len() it.
+    assert isinstance(peptides, list)
+    assert isinstance(proteins, list)
+    assert len(proteins) == 1
+    assert len(peptides) == 2
+
+    sequences = [
+        hit.getSequence().toString()
+        for pep in peptides
+        for hit in pep.getHits()
+    ]
+    assert sequences == ["PEPTIDEK", "ELVISLIVESR"]
+    assert peptides[0].getRT() == 100.0
+    assert peptides[0].getHits()[0].getCharge() == 2
+
+
+def test_load_idxml_accepts_str_path(tmp_path):
+    """Callers pass both Path and str; load_idxml must handle either."""
+    idxml = tmp_path / "run_per.idXML"
+    _write_idxml(idxml)
+
+    assert len(load_idxml(str(idxml))[1]) == 2