From aa86013bf2c444b505e63d19919cd21f9153e9f0 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Fri, 21 Feb 2025 16:23:26 +0000
Subject: [PATCH] not dumped all database tables to file on export so they can
be versioned
---
acmc/omop.py | 16 +++++++++++++++-
1 file changed, 15 insertions(+), 1 deletion(-)
diff --git a/acmc/omop.py b/acmc/omop.py
index 2a0bfd1..7075994 100644
--- a/acmc/omop.py
+++ b/acmc/omop.py
@@ -186,7 +186,7 @@ def concept_set_exist(cursor, concept_set_name):
cursor.execute(query, (concept_set_name,))
# 1 if exists, 0 otherwise
- return cursor.fetchone()[0] 1
+ return cursor.fetchone()[0] == 1
def export(map_path, export_path, version, omop_metadata):
logger.debug(f"exporting with metadata {omop_metadata} at version {version}")
@@ -271,6 +271,20 @@ def export(map_path, export_path, version, omop_metadata):
df_out["concept_set_id"] = concept_set_id
df_out.to_sql("CONCEPT_SET_ITEM", conn, if_exists='append', index=False)
+ # Output all tables to CSV
+ # 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")
+
conn.close()
logger.debug(f"Created export db successfully")
--
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