From d8962bd48ee79be4ba9de67626830a02de22f4fc Mon Sep 17 00:00:00 2001
From: deeenes <turei.denes@gmail.com>
Date: Thu, 24 Oct 2024 14:49:07 +0200
Subject: [PATCH] structure resources: use primary ID instead of names in
 current record generators

---
 omnipath_metabo/schema/_main.py      | 4 ++--
 omnipath_metabo/schema/_structure.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/omnipath_metabo/schema/_main.py b/omnipath_metabo/schema/_main.py
index 7daea66..a41aed1 100644
--- 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
index 0082fc9..3ec84e0 100644
--- a/omnipath_metabo/schema/_structure.py
+++ b/omnipath_metabo/schema/_structure.py
@@ -58,7 +58,7 @@ 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():
@@ -66,7 +66,7 @@ class SwissLipids():
     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():