Added log messages for loader.load()

omnipath_metabo/schema/_main.py

@@ -2,11 +2,14 @@
 from sqlalchemy import text, select
 from sqlalchemy.dialects.postgresql import insert
 import psycopg2.extras
+from omnipath_metabo import _log
 
 from . import _structure
 from ._base import Base
 from ._connection import Connection
 
+_log("Hello from main module")
+
 def create(con):
 
     Base.metadata.create_all(con.engine)
@@ -64,58 +67,51 @@ def __init__(self, resource, con):
 
 
     def load(self):
-
+        
         insert_resource = insert(_structure.Resource).values(
             name = self.resource.name
         )
         insert_resource = insert_resource.on_conflict_do_nothing(index_elements=['name'])
         self.session.execute(insert_resource)
         ids = collections.defaultdict(set)
+        _log(f'loading resource {self.resource.name}')
+
         raw_con = self.con.engine.raw_connection()
 
         with raw_con.cursor() as cursor:
 
             query = """
                 INSERT INTO structures (name, smiles) VALUES %s ON CONFLICT (smiles) DO NOTHING
                 """
+            _log("loading insert statments for structures table")
             psycopg2.extras.execute_values(cursor, query, self.resource, page_size = 1000)
-        """
-        for i, row in enumerate(self.resource):
-
-            insert_statement = insert(self.scheme).values(
-                smiles=row[1],
-                name=row[0],
-            )
-            ids[row[1]].add(row[0])
-
-            insert_statement = insert_statement.on_conflict_do_nothing(index_elements = ['smiles'])
-            self.session.execute(insert_statement)
-
-            if i > 1000:
-                break
-        """
+
         raw_con.commit()
+        _log("structures have been inserted, creating mol column")
+
         self.update_mol_column()
 
+        _log('collecting structure ids')
         select_str_ids = text('SELECT id, smiles FROM structures')
         strids = {
             id[1]: id[0]
             for id in self.session.execute(select_str_ids)
         }
-
+        _log('structure ids collected, collecting resource ids')
         select_res_ids = text('SELECT id, name FROM resources')
         resid= {
             id[1]: id[0]
             for id in self.session.execute(select_res_ids)
         }
         resource_key = resid[self.resource.name]
+        _log('resource ids collected.')
 
         insert_ids = (
             (id, strids[smiles], resource_key)
             for smiles, _ids in ids.items()
             for id in _ids
         )
-
+        _log('inserting identifiers.')
         with raw_con.cursor() as cursor:
             query = """
                     INSERT INTO identifiers (identifier, structure_id, resource_id) VALUES %s
@@ -124,13 +120,15 @@ def load(self):
 
 
         raw_con.commit()
-
+        _log('identifiers inserted.')
         #self.indexer()
+        _log(f'{self.resource.name} loaded')
 
     def update_mol_column(self):
         query = text("update structures set mol = mol_from_smiles(smiles::cstring) where mol is null")
         self.session.execute(query)
         self.session.commit()
+        _log('Finished creating mol column.')
 
     def indexer(self):
         """