updated import-icd10... to use execute_values to speed up insert.

scripts/import-icd10_to_cause.py

@@ -1,6 +1,7 @@
 from drugtools.env_setup import ENV,postgres_conn
 from psycopg2 import extras
 from collections import namedtuple
+from tqdm import tqdm
 
 
 FILES=[
@@ -12,21 +13,24 @@ SEP="|"
 sql = """
 INSERT INTO "DiseaseBurden".icd10_to_cause
     (code,cause_text)
-VALUES
+VALUES %s
-    (%(code)s,%(cause)s)
 """
 
 
-#read in files
-#adjust codes?
-#load files to table
 
 with postgres_conn() as pconn, pconn.cursor(cursor_factory=extras.DictCursor) as pcurse:
+    entries = []
     for fpath in FILES:
+        print(fpath)
+
         with open(fpath,"r") as fh:
-            for line in fh.readlines():
+            for line in tqdm(fh.readlines(),desc=fpath):
                 code,cause = line.split(SEP)
                 code = code.strip()
                 cause = cause.strip()
 
-                pcurse.execute(sql,{"code":code,"cause":cause})
+                entries.append((code,cause))
+    
+    extras.execute_values(pcurse, sql , entries)
+
+