Merge pull request #306 from Wang-Bioinformatics-Lab/udi-fix

Adding GNPS2 support for UDI for overlays

Author: mwang87

app.py

@@ -162,7 +162,7 @@
         ),
         dbc.Nav(
             [
-                dbc.NavItem(dbc.NavLink("GNPS2 LCMS Dashboard - Version 2025-10-03", href="/")),
+                dbc.NavItem(dbc.NavLink("GNPS2 LCMS Dashboard - Version 2025.10.17", href="/")),
                 dbc.NavItem(dbc.NavLink("Documentation", href="https://ccms-ucsd.github.io/GNPSDocumentation/lcms-dashboard/")),
                 dbc.NavItem(dbc.NavLink("GNPS Datasets", href="https://gnps.ucsd.edu/ProteoSAFe/datasets.jsp#%7B%22query%22%3A%7B%7D%2C%22table_sort_history%22%3A%22createdMillis_dsc%22%2C%22title_input%22%3A%22GNPS%22%7D")),
                 dbc.NavItem(id="dataset_files_nav"),

utils.py

@@ -329,11 +329,19 @@ def _spectrum_generator(filename, min_rt, max_rt):
 def _resolve_overlay(overlay_usi, overlay_mz, overlay_rt, overlay_filter_column, overlay_filter_value, overlay_size, overlay_color, overlay_hover, overlay_tabular_data=""):
     # Let's try the UDI
     try:
-        overlay_usi_splits = overlay_usi.split(":")
-        file_path = overlay_usi_splits[2].split("-")[-1]
-        task = overlay_usi_splits[2].split("-")[1]
-        url = "http://massive.ucsd.edu/ProteoSAFe/DownloadResultFile?task={}&block=main&file={}".format(task, file_path)
-        overlay_df = pd.read_csv(url, sep=None, nrows=400000)
+        if "GNPS2" in overlay_usi:
+            overlay_usi_splits = overlay_usi.split(":")
+            file_path = overlay_usi_splits[2].split("-")[-1]
+            task = overlay_usi_splits[2].split("-")[1]
+
+            url = "https://gnps2.org/resultfile?task={}&file={}".format(task, file_path)
+            overlay_df = pd.read_csv(url, sep=None, nrows=400000)
+        else:
+            overlay_usi_splits = overlay_usi.split(":")
+            file_path = overlay_usi_splits[2].split("-")[-1]
+            task = overlay_usi_splits[2].split("-")[1]
+            url = "http://massive.ucsd.edu/ProteoSAFe/DownloadResultFile?task={}&block=main&file={}".format(task, file_path)
+            overlay_df = pd.read_csv(url, sep=None, nrows=400000)
     except:
         if len(overlay_tabular_data) > 0:
             # if this fails, we can try parsing overlay_tabular_data