Merge pull request #111 from pagreene/fix-read-db

Fix read db

indra_db/databases.py

@@ -515,6 +515,14 @@ def delete_all(self, entry_list):
                     len(entry_list))
         return
 
+    def get_copy_cursor(self):
+        """Execute SQL queries in the context of a copy operation."""
+        # Prep the connection.
+        if self._conn is None:
+            self._conn = self.engine.raw_connection()
+            self._conn.rollback()
+        return self._conn.cursor()
+
     def make_copy_batch_id(self):
         """Generate a random batch id for copying into the database.
 

indra_db/reading/read_db.py

@@ -486,7 +486,8 @@ def dump_statements_to_db(self):
         # Dump the duplicates into a separate to all for debugging.
         self._db.copy('rejected_statements', [tpl for dlist in dups.values()
                                               for tpl in dlist],
-                      DatabaseStatementData.get_cols())
+                      DatabaseStatementData.get_cols(),
+                      commit=False)
 
         # Add the agents for the accepted statements.
         logger.info("Uploading agents to the database.")

indra_db/util/insert.py

@@ -45,14 +45,14 @@ def insert_raw_agents(db, batch_id, stmts=None, verbose=False,
     ref_tuples = []
     mod_tuples = []
     mut_tuples = []
-    cur = db._conn.cursor()
     if stmts is None:
         s_col = 'json'
         stmt_dict = None
     else:
         s_col = 'uuid'
         stmt_dict = {s.uuid: s for s in stmts}
 
+    cur = db.get_copy_cursor()
     cur.execute(f'SELECT id, {s_col} FROM raw_statements WHERE batch_id=%s',
                 (batch_id,))
     if verbose: