From 6421a3f57e189579643edd02209761f2d5570698 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Thu, 6 Mar 2025 11:15:06 +0000
Subject: [PATCH] (fix) removed export of sqlite_sequence. Closes #45
---
acmc/omop.py | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git a/acmc/omop.py b/acmc/omop.py
index 7bc5dce..b976191 100644
--- a/acmc/omop.py
+++ b/acmc/omop.py
@@ -312,15 +312,17 @@ def export(map_path, export_path, version, omop_metadata):
# Get the list of all tables
cur.execute("SELECT name FROM sqlite_master WHERE type='table';")
tables = cur.fetchall() # List of tables
-
+
# Export each table to a separate CSV file
for table in tables:
- table_name = table[0] # Extract table name
- df = pd.read_sql_query(f"SELECT * FROM {table_name}", conn)
- output_file = f"{table_name}.csv"
- output_path = export_path / output_file
- df.to_csv(output_path, index=False) # Save as CSV
- logger.info(f"Exported {table_name} to {table_name}.csv")
+ table_name = table[0]
+ # ignore SQLite's internal system table
+ if table_name != "sqlite_sequence":
+ df = pd.read_sql_query(f"SELECT * FROM {table_name}", conn)
+ output_file = f"{table_name}.csv"
+ output_path = export_path / output_file
+ df.to_csv(output_path, index=False) # Save as CSV
+ logger.info(f"Exported {table_name} to {table_name}.csv")
conn.close()
--
GitLab