Zenodo Support v1

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "metabolomics_spectrum_resolver/mass-spec-package"]
+	path = metabolomics_spectrum_resolver/mass-spec-package
+	url = https://github.com/AkJay1722/mass-spec-package.git

metabolomics_spectrum_resolver/parsing.py

@@ -12,6 +12,9 @@
 
 from metabolomics_spectrum_resolver.error import UsiError
 
+from metabolomics_spectrum_resolver.zenodo_mzml_repo import mzml_repo
+
+
 timeout = 45  # seconds
 
 MS2LDA_SERVER = "http://ms2lda.org/basicviz/"
@@ -46,7 +49,7 @@
     # collection identifier
     # Unofficial proteomics spectral library identifier: MASSIVEKB
     # Metabolomics collection identifiers: GNPS, MASSBANK, MS2LDA, MOTIFDB, MTBLS, ST
-    r":(MASSIVEKB|GNPS|GNPS2|MASSBANK|MS2LDA|MOTIFDB|TINYMASS|MTBLS\d+|ST\d{6}|)"
+    r":(MASSIVEKB|GNPS|GNPS2|MASSBANK|MS2LDA|MOTIFDB|TINYMASS|MTBLS\d+|ST\d{6}|ZENODO-\d+|)"
     # msRun identifier
     r":(.*)"
     # index flag
@@ -136,6 +139,8 @@ def parse_usi(usi: str) -> Tuple[sus.MsmsSpectrum, str, str]:
             spectrum, source_link = _parse_metabolomics_workbench(usi)
         elif collection.startswith("tinymass"):
             spectrum, source_link = _parse_tinymass(usi)
+        elif collection.startswith("zenodo"):
+            spectrum, source_link = _parse_zenodo(usi)
         else:
             raise UsiError(f"Unknown USI collection: {match.group(1)}", 400)
         splash_key = splash_builder.splash(
@@ -473,6 +478,41 @@ def _parse_gnps2_dataset(usi: str) -> Tuple[sus.MsmsSpectrum, str]:
     except (requests.exceptions.HTTPError, json.decoder.JSONDecodeError):
         raise UsiError("Unknown GNPS2 Dataset USI", 404)
 
+# parsing from Zenodo
+def _parse_zenodo(usi: str) -> Tuple[sus.MsmsSpectrum, str]:
+    match = _match_usi(usi)
+    zenodo_id = match.group(1).split("-")[-1]
+    filename = match.group(2)
+    index_flag = match.group(3)
+    if index_flag.lower() == "scan":
+        scan = match.group(4)
+
+    zenodo_obj = mzml_repo(zenodo_id)
+    zenodo_obj.partial_indexing = False
+    scan_obj = zenodo_obj.get_scan(filename, int(scan))
+
+    # get peaks
+    intensity_list = scan_obj["intensities"]
+    mz_list = scan_obj["mz"]
+    charge = scan_obj["charge"]
+    precursor_mz = scan_obj["precursor_mz"]
+
+    try:
+        charge = int(charge)
+    except:
+        charge = 0
+
+    try:
+        precursor_mz = float(precursor_mz)
+    except:
+        precursor_mz = 0
+
+    source_link = f"https://zenodo.org/record/{zenodo_id}"
+
+    spectrum = sus.MsmsSpectrum(usi, precursor_mz, charge, mz_list, intensity_list)
+
+    return spectrum, source_link
+
 # Parse TINYMASS task spectra
 def _parse_tinymass(usi: str) -> Tuple[sus.MsmsSpectrum, str]:
     match = _match_usi(usi)

metabolomics_spectrum_resolver/templates/homepage.html

@@ -141,6 +141,12 @@ <h2>
                         </a>
                     </div>
 
+                    <div class="text-center">
+                        <a href="/spectrum/?usi=mzspec:ZENODO-10211590:D141_POS.mzML:scan:421">
+                            <button class="btn btn-primary btn-sm btn-block">Zenodo Repository Spectrum</button>
+                        </a>
+                    </div>
+
                     <br>
 
                     <div class="text-center">

metabolomics_spectrum_resolver/templates/minimal.html

@@ -50,7 +50,7 @@
     <hr>
 
     <div class="footer-copyright text-center py-3">
-        Metabolomics Spectrum Resolver - Release 2025.07.10
+        Metabolomics Spectrum Resolver - Release 2025.09.10
     </div>
 
 

test/test_unit.py

@@ -218,7 +218,6 @@ def test_parse_motifdb():
         parsing.parse_usi(usi.replace(":171163", ":this_index_does_not_exist"))
     assert exc_info.value.error_code == 404
 
-
 def test_parse_timeout():
     with unittest.mock.patch(
         "metabolomics_spectrum_resolver.parsing.requests.get",