update GNPSSpectrumLoader for gnps2 (#299)

NPLinker · Jan 21, 2025 · b9524c6 · b9524c6
1 parent 1da6622
commit b9524c6
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Showing 2 changed files with 14 additions and 1 deletion.
diff --git a/src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py b/src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py
@@ -24,6 +24,10 @@ class GNPSSpectrumLoader(SpectrumLoaderBase):
         - METABOLOMICS-SNETS-V2*.mgf
     3. FEATURE-BASED-MOLECULAR-NETWORKING
         - spectra/*.mgf
+    4. GNPS2 classical_networking_workflow
+        - nf_output/clustering/specs_ms.mgf
+    5. GNPS2 feature_based_molecular_networking_workflow
+        - nf_output/clustering/specs_ms.mgf
     """
 
     def __init__(self, file: str | PathLike) -> None:

diff --git a/tests/unit/metabolomics/test_gnps_spectrum_loader.py b/tests/unit/metabolomics/test_gnps_spectrum_loader.py
@@ -7,6 +7,15 @@
     "workflow, num_spectra",
     [[GNPSFormat.FBMN, 1492], [GNPSFormat.SNETS, 25935], [GNPSFormat.SNETSV2, 7383]],
 )
-def test_gnps_spectrum_loader(workflow, num_spectra, gnps_spectra_files):
+def test_gnps_spectrum_loader_gnps1(workflow, num_spectra, gnps_spectra_files):
     loader = GNPSSpectrumLoader(gnps_spectra_files[workflow])
     assert len(loader.spectra) == num_spectra
+
+
+@pytest.mark.parametrize(
+    "workflow, num_spectra",
+    [[GNPSFormat.GNPS2CN, 1051], [GNPSFormat.GNPS2FBMN, 371]],
+)
+def test_gnps_spectrum_loader_gnps2(workflow, num_spectra, gnps2_spectra_files):
+    loader = GNPSSpectrumLoader(gnps2_spectra_files[workflow])
+    assert len(loader.spectra) == num_spectra