.

src/bio_data_to_db/bindingdb/fix_tables.py

@@ -1,6 +1,7 @@
 import html
 
 import polars as pl
+import sqlalchemy
 
 
 def fix_assay_table(uri: str):
@@ -9,8 +10,8 @@ def fix_assay_table(uri: str):
 
     Notes:
         - original types are VARCHAR but we are converting them to TEXT. The code should work for both cases.
-        - the table is replaced
-        - this removes primary key and foreign key constraints.
+        - the table is replaced.
+        - primary key and foreign key constraints are reserved by manually adding them back just like the original table
     """
     query = """
         SELECT
@@ -36,6 +37,16 @@ def fix_assay_table(uri: str):
         if_table_exists="replace",
     )
 
+    with sqlalchemy.create_engine(uri).connect() as conn:
+        conn.execute(
+            sqlalchemy.text("""
+                ALTER TABLE assay MODIFY COLUMN `entryid` INT(11);
+                ALTER TABLE assay MODIFY COLUMN `assayid` INT(11);
+                ALTER TABLE assay ADD PRIMARY KEY (`entryid`,`assayid`);
+                ALTER TABLE assay ADD CONSTRAINT `assay_ibfk_1` FOREIGN KEY (`entryid`) REFERENCES `entry` (`entryid`);
+            """)
+        )
 
-if __name__ == "__main__":
-    fix_assay_table("mysql://user:@localhost:3306/bind")
+
+# if __name__ == "__main__":
+#     fix_assay_table("mysql://username:@localhost:3306/bind")