Merge pull request #759 from Knerten0815/fix/load-from-usi-deprecated-api

julianpollmann · web-flow · commit d46de7649a36 · 2025-03-12T17:51:56.000+01:00
Updated `load_from_usi` API call
diff --git a/matchms/importing/load_from_usi.py b/matchms/importing/load_from_usi.py
@@ -8,7 +8,7 @@
 logger = logging.getLogger("matchms")
 
 
-def load_from_usi(usi: str, server: str = "https://metabolomics-usi.ucsd.edu",
+def load_from_usi(usi: str, server: str = "https://metabolomics-usi.gnps2.org",
                   metadata_harmonization: bool = True):
     """Load spectrum from metabolomics USI.
 
@@ -39,6 +39,10 @@ def load_from_usi(usi: str, server: str = "https://metabolomics-usi.ucsd.edu",
 
     if response.status_code == 404:
         return None
+
+    if "application/json" not in response.headers.get("Content-Type"):
+        return None
+
     # Extract data and create Spectrum object
     try:
         spectral_data = response.json()
diff --git a/tests/importing/test_load_from_usi.py b/tests/importing/test_load_from_usi.py
@@ -8,8 +8,10 @@
 def test_normal(mock_get):
     mock_get.return_value = Mock(ok=True)
     mock_get.return_value.json.return_value = {"peaks": [[1., 2.], [3., 4.]]}
+    mock_get.return_value.headers.get = Mock(return_value="application/json")
+
     spec = load_from_usi("something")
-    expected_metadata = {"usi": "something", "server": "https://metabolomics-usi.ucsd.edu", "precursor_mz": None}
+    expected_metadata = {"usi": "something", "server": "https://metabolomics-usi.gnps2.org", "precursor_mz": None}
     expected = SpectrumBuilder().with_mz(np.array([1., 3.])).with_intensities(
         np.array([2., 4.])).with_metadata(expected_metadata,
                                           metadata_harmonization=True).build()
@@ -21,6 +23,8 @@ def test_404(mock_get):
     mock_get.return_value = Mock(ok=True)
     mock_get.return_value.status_code = 404
     mock_get.return_value.json.return_value = None
+    mock_get.return_value.headers.get = Mock(return_value="application/json")
+
     spec = load_from_usi("something")
     expected = None
     assert spec == expected
@@ -30,6 +34,20 @@ def test_404(mock_get):
 def test_no_peaks(mock_get):
     mock_get.return_value = Mock(ok=True)
     mock_get.return_value.json.return_value = {"peaks": []}
+    mock_get.return_value.headers.get = Mock(return_value="application/json")
+
     spec = load_from_usi("something")
     expected = None
     assert spec == expected
+
+
+def test_api_call():
+    usi = "mzspec:MASSBANK::accession:SM858102" # taken from load_from_usi docstring
+
+    spec = load_from_usi(usi)
+    
+    assert spec is not None
+    assert hasattr(spec, "peaks")
+    assert len(spec.peaks.mz) > 0
+    assert "usi" in spec.metadata
+    assert spec.metadata["usi"] == usi
