I am trying to pass data from a dict into a database table using sqlite3.

The first iteration runs smoothly, afterwards I receive a disk I/O error. Upon rerunning the Code I am confronted with “database is locked” errors until I restart everything or delete the database.

Here is my code for initiating the database and table (directly in main script)

import sqlite3
from utils import nested_loop_function as utils

try:
    con = sqlite3.connect(
        "<path to DB>/structures.db",
        timeout=30,
    )
    cur = con.cursor()

    cur.execute(
        """CREATE TABLE IF NOT EXISTS combinations (
            hash_ID TEXT NOT NULL PRIMARY KEY,
            path TEXT,
            u1_name TEXT,
            u2_name TEXT,
            central_H_index_1 INTEGER,
            central_H_index_2 INTEGER,
            charge_u1 INTEGER,
            charge_u2 INTEGER,
            translation FLOAT,
            rotation INTEGER,
            tilt_angle FLOAT,
            tilt_axis TEXT,
            hash_u1 INTEGER,
            hash_u2 INTEGER
        )"""
    )
    print("Sucessfully created table if not present")
    con.commit()
except Exception as e:
    print(f"An error occurred: {e}")
    con.rollback()
finally:
    con.close()

Here is my code for inserting data, which iterates in a nested ‘for’ loop. Respective function imported from utils.py.

            try:

                con = sqlite3.connect(
                    "<path to DB>/structures.db",
                    timeout=30,
                )
                cur = con.cursor()
                cur.execute(
                    """REPLACE INTO combinations (
                        hash_ID,
                        path,
                        u1_name,
                        u2_name,
                        central_H_index_1,
                        central_H_index_2,
                        charge_u1,
                        charge_u2,
                        translation,
                        rotation,
                        tilt_angle,
                        tilt_axis,
                        hash_u1,
                        hash_u2
                    ) VALUES (
                        :hash_ID,
                        :path,
                        :u1_name,
                        :u2_name,
                        :central_atom_idx_1,
                        :central_atom_idx_2,
                        :charge_u1,
                        :charge_u2,
                        :translation,
                        :rotation,
                        :tilt_angle,
                        :tilt_axis,
                        :hash_u1,
                        :hash_u2
                        )""",
                    meta,
                )
                con.commit()
            except Exception as e:
                print(f"An error occurred: {e}")
                stop = True
                con.rollback()
            finally:
                con.close()
                if stop:
                    print(f"stopped function")
                    break

I am really at my wits end here so any help is welcome!
The database and every script are saved on our shared directories but only I can access it.
Running lsof on the database file shows no active processess accessing it once the script fails.

Expected the Code to INSERT/REPLACE data from meta into my combinations table in the structures database. Which it only did for one iteration before returning above ‘disk I/O’ errors. Researching my error resulted in no useful information. Rerunning the code resulted in a ‘locked database’ error. Using context managing ‘with sqlite3.connect(”) as con:’, did not help either and presented the same disk I/O errors. The error occurs when running the code as interactive cells in VSC and when running the entire script from the terminal.