structure resources: use primary ID instead of names in current recor…

…d generators
saezlab · Oct 24, 2024 · d8962bd · d8962bd
1 parent abb238e
commit d8962bd
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/omnipath_metabo/schema/_main.py b/omnipath_metabo/schema/_main.py
@@ -105,7 +105,7 @@ def load(self):
         resid = self.session.execute(insert_resource).fetchall()
         self.session.commit()
 
-        _log(f'loading resource {self.resource.name}')
+        _log(f'loading resource {self.resource.name}', level = -1)
 
         raw_con = self.con.engine.raw_connection()
 
@@ -150,7 +150,7 @@ def load(self):
         raw_con.commit()
         _log('identifiers inserted.')
         #self.indexer()
-        _log(f'{self.resource.name} loaded')
+        _log(f'Finished loading {self.resource.name}.', level = -1)
 
     def update_mol_column(self):
         query = text("update structures set mol = mol_from_smiles(smiles::cstring) where mol is null")

diff --git a/omnipath_metabo/schema/_structure.py b/omnipath_metabo/schema/_structure.py
@@ -58,15 +58,15 @@ class Hmdb():
     name = 'HMDB'
     def __iter__(self):
 
-        for met in hmdb.metabolites_processed('name','smiles'):
+        for met in hmdb.metabolites_processed('accession', 'smiles'):
             yield met[0]
 
 class SwissLipids():
     scheme = Structure
     name = 'SwissLipids'
     def __iter__(self):
         for met in swisslipids.swisslipids_lipids():
-            yield met['Name'], met['SMILES (pH7.3)']
+            yield met['Lipid ID'], met['SMILES (pH7.3)']
 
 
 class LipidMaps():