SQLite Error: DatabaseError: database disk image is malformed

[michaelweinold]

peewee was recently added (#322), but it seems that an error with sqlite (added by @DerThorsten last year) is preventing us from running this small test script:

from peewee import *

# Define a database object
db = SqliteDatabase('my_database.db')

# Define a model class
class Person(Model):
    name = CharField()
    age = IntegerField()

    class Meta:
        database = db

# Create the table in the database
db.connect()
db.create_tables([Person])
person1 = Person(name='Alice', age=25)
person1.save()

This returns:

DatabaseError: database disk image is malformed

Full Error Message

---------------------------------------------------------------------------
DatabaseError                             Traceback (most recent call last)
/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in execute_sql(self, sql, params, commit)
 3235             cursor = self.cursor()
-> 3236             cursor.execute(sql, params or ())
 3237         return cursor

DatabaseError: database disk image is malformed

During handling of the above exception, another exception occurred:

DatabaseError                             Traceback (most recent call last)
/tmp/xpython_42/2390659374.py in <cell line: 2>()
    1 person1 = Person(name='Alice', age=25)
----> 2 person1.save()

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in save(self, force_insert, only)
 6745             rows = self.update(**field_dict).where(self._pk_expr()).execute()
 6746         elif pk_field is not None:
-> 6747             pk = self.insert(**field_dict).execute()
 6748             if pk is not None and (self._meta.auto_increment or
 6749                                    pk_value is None):

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in inner(self, database, *args, **kwargs)
 1960             raise InterfaceError('Query must be bound to a database in order '
 1961                                  'to call "%s".' % method.__name__)
-> 1962         return method(self, database, *args, **kwargs)
 1963     return inner
 1964 

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in execute(self, database)
 2031     @database_required
 2032     def execute(self, database):
-> 2033         return self._execute(database)
 2034 
 2035     def _execute(self, database):

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in _execute(self, database)
 2836             self._returning = (self.table._primary_key,)
 2837         try:
-> 2838             return super(Insert, self)._execute(database)
 2839         except self.DefaultValuesException:
 2840             pass

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in _execute(self, database)
 2549             cursor = self.execute_returning(database)
 2550         else:
-> 2551             cursor = database.execute(self)
 2552         return self.handle_result(database, cursor)
 2553 

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in execute(self, query, commit, **context_options)
 3242         ctx = self.get_sql_context(**context_options)
 3243         sql, params = ctx.sql(query).query()
-> 3244         return self.execute_sql(sql, params)
 3245 
 3246     def get_context_options(self):

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in execute_sql(self, sql, params, commit)
 3232             __deprecated__('"commit" has been deprecated and is a no-op.')
 3233         logger.debug((sql, params))
-> 3234         with __exception_wrapper__:
 3235             cursor = self.cursor()
 3236             cursor.execute(sql, params or ())

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in __exit__(self, exc_type, exc_value, traceback)
 3008             new_type = self.exceptions[exc_type.__name__]
 3009             exc_args = exc_value.args
-> 3010             reraise(new_type, new_type(exc_value, *exc_args), traceback)
 3011 
 3012 

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in reraise(tp, value, tb)
  190     def reraise(tp, value, tb=None):
  191         if value.__traceback__ is not tb:
--> 192             raise value.with_traceback(tb)
  193         raise value
  194 

/tmp/xeus-python-kernel/envs/xeus-python-kernel/lib/python3.10/site-packages/peewee.py in execute_sql(self, sql, params, commit)
 3234         with __exception_wrapper__:
 3235             cursor = self.cursor()
-> 3236             cursor.execute(sql, params or ())
 3237         return cursor
 3238 

DatabaseError: database disk image is malformed

To reproduce the error, access my JupyterLite Hub and open peewee_test.ipynb at https://michaelweinold.github.io/hub/

According to peewee author Charles Leifer

"the error is not coming from peewee but seems related to however you're abstracting the file-system for use by sqlite. The error is coming from sqlite and seems to indicate some problem with the file."

Could you someone have a look? I know too little about the file system underlying JupyterLite to make any meaningful contributions at this point.

[michaelweinold]

...I suppose this issue belongs to the JupyterLite repo rather than here. Moving it there