Error in reading database file

[paniash]

Hi,

Trying to read the database file seems to yield the following error:

Rolling back due to unhandled exception
Traceback (most recent call last):
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/connection.py", line 161, in atomic
    yield conn
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/connection.py", line 215, in atomic_transaction
    c = transaction(atomic_conn, sql, *args)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/connection.py", line 193, in transaction
    c.execute(sql)
sqlite3.DatabaseError: file is not a database
Traceback (most recent call last):
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/connection.py", line 161, in atomic
    yield conn
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/connection.py", line 215, in atomic_transaction
    c = transaction(atomic_conn, sql, *args)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/connection.py", line 193, in transaction
    c.execute(sql)
sqlite3.DatabaseError: file is not a database

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<string>", line 17, in __PYTHON_EL_eval
  File "/u/47/panigra1/unix/git/phd-analysis/bolometer-measurements/20260217_vtt_graphene_1917_journal.py", line 81, in <module>
    initialise_database()
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/database.py", line 232, in initialise_database
    conn = connect(get_DB_location(), get_DB_debug())
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/database.py", line 155, in connect
    db_version = get_user_version(conn)
                 ^^^^^^^^^^^^^^^^^^^^^^
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/db_upgrades/version.py", line 8, in get_user_version
    curr = atomic_transaction(conn, "PRAGMA user_version")
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/connection.py", line 214, in atomic_transaction
    with atomic(conn) as atomic_conn:
  File "/usr/lib/python3.12/contextlib.py", line 158, in __exit__
    self.gen.throw(value)
  File "/u/47/panigra1/unix/.env/lib/python3.12/site-packages/qcodes/dataset/sqlite/connection.py", line 165, in atomic
    raise RuntimeError("Rolling back due to unhandled exception") from e
RuntimeError: Rolling back due to unhandled exception

Test code for reproducing this error:

import matplotlib.pyplot as plt
import json
import gc
import numpy as np

from tqdm.auto import tqdm
import xarray as xr

import qcodes as qc
from qcodes.dataset.plotting import plot_by_id
from qcodes.dataset.sqlite.database import initialised_database_at
from qcodes.dataset import initialise_database

import sys; sys.path.insert(0, "../")

qc.config.core.db_location = "~/experiments.db"

initialise_database()
print(qc.config.core.db_location)

[astafan8]

sqlite3.DatabaseError: file is not a database

looks like the file "~/experiments.db" does exist but it's not a valid sqlite database file (perhaps it's even a folder), so take a closer look at it, perhaps remove it, and try again

[paniash]

@astafan8 Thanks for your reply. "~/experiments.db" was merely an example file. I double checked with the actual sqlite database file and indeed the file path is correct.

I must mention that when I do this with a jupyter notebook, everything works as expected but if this is done (while keeping the same jupyter notebook open) through an external editor/python process, then I get this error.

[astafan8]

that's strange, perhaps something about the drive and the system you work on. we use WAL mode for the sqlite file which allows for multiple processes to read the file without issues (only writing is single process at a time but sqlite manages that and if problems arise more specific/clear errors are printed than "file is not a db")

[jenshnielsen]

@paniash Could it be that your home folder is on a network drive (NFS or similar) SQLite is known to not always work well in such cases