Saving a list of values for a single record fails succeeds silently once and throws IntegrityError on second save

[Zethson]

Add a description

!lamin init --storage run-tests --schema bionty

import bionty as bt

bt.Disease(name=["complexdisease"]).save()  # this silently just saves but should ideally throw already because the name field should be a single value
bt.Disease(name=["complexdisease"]).save()  # this throws with an error that users do not understand

throws

---------------------------------------------------------------------------
IntegrityError                            Traceback (most recent call last)
File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/backends/utils.py:105, in CursorWrapper._execute(self, sql, params, *ignored_wrapper_args)
    104 else:
--> 105     return self.cursor.execute(sql, params)

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/backends/sqlite3/base.py:354, in SQLiteCursorWrapper.execute(self, query, params)
    353 query = self.convert_query(query, param_names=param_names)
--> 354 return super().execute(query, params)

IntegrityError: UNIQUE constraint failed: bionty_disease.uid

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

IntegrityError                            Traceback (most recent call last)
Cell In[3], line 2
      1 bt.Disease(name=["complexdisease"]).save()
----> 2 bt.Disease(name=["complexdisease"]).save()

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/bionty/models.py:493, in BioRecord.save(self, *args, **kwargs)
    491 def save(self, *args, **kwargs) -> BioRecord:
    492     """Save the record and its parents recursively."""
--> 493     super().save(*args, **kwargs)
    494     # saving records of parents
    495     if hasattr(self, "_parents"):

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/lamindb/_record.py:759, in save(self, *args, **kwargs)
    757 check_name_change(self)
    758 check_key_change(self)
--> 759 super(BasicRecord, self).save(*args, **kwargs)
    760 # update _old_name and _old_key after saving
    761 _store_record_old_name(self)

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/models/base.py:892, in Model.save(self, force_insert, force_update, using, update_fields, *args)
    889     if loaded_fields:
    890         update_fields = frozenset(loaded_fields)
--> 892 self.save_base(
    893     using=using,
    894     force_insert=force_insert,
    895     force_update=force_update,
    896     update_fields=update_fields,
    897 )

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/models/base.py:998, in Model.save_base(self, raw, force_insert, force_update, using, update_fields)
    994         force_insert = self._validate_force_insert(force_insert)
    995         parent_inserted = self._save_parents(
    996             cls, using, update_fields, force_insert
    997         )
--> 998     updated = self._save_table(
    999         raw,
   1000         cls,
   1001         force_insert or parent_inserted,
   1002         force_update,
   1003         using,
   1004         update_fields,
   1005     )
   1006 # Store the database on which the object was saved
   1007 self._state.db = using

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/models/base.py:1161, in Model._save_table(self, raw, cls, force_insert, force_update, using, update_fields)
   1155 fields = [
   1156     f
   1157     for f in meta.local_concrete_fields
   1158     if not f.generated and (pk_set or f is not meta.auto_field)
   1159 ]
   1160 returning_fields = meta.db_returning_fields
-> 1161 results = self._do_insert(
   1162     cls._base_manager, using, fields, returning_fields, raw
   1163 )
   1164 if results:
   1165     for value, field in zip(results[0], returning_fields):

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/models/base.py:1202, in Model._do_insert(self, manager, using, fields, returning_fields, raw)
   1197 def _do_insert(self, manager, using, fields, returning_fields, raw):
   1198     """
   1199     Do an INSERT. If returning_fields is defined then this method should
   1200     return the newly created data for the model.
   1201     """
-> 1202     return manager._insert(
   1203         [self],
   1204         fields=fields,
   1205         returning_fields=returning_fields,
   1206         using=using,
   1207         raw=raw,
   1208     )

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/models/manager.py:87, in BaseManager._get_queryset_methods.<locals>.create_method.<locals>.manager_method(self, *args, **kwargs)
     85 @wraps(method)
     86 def manager_method(self, *args, **kwargs):
---> 87     return getattr(self.get_queryset(), name)(*args, **kwargs)

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/models/query.py:1847, in QuerySet._insert(self, objs, fields, returning_fields, raw, using, on_conflict, update_fields, unique_fields)
   1840 query = sql.InsertQuery(
   1841     self.model,
   1842     on_conflict=on_conflict,
   1843     update_fields=update_fields,
   1844     unique_fields=unique_fields,
   1845 )
   1846 query.insert_values(fields, objs, raw=raw)
-> 1847 return query.get_compiler(using=using).execute_sql(returning_fields)

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/models/sql/compiler.py:1836, in SQLInsertCompiler.execute_sql(self, returning_fields)
   1834 with self.connection.cursor() as cursor:
   1835     for sql, params in self.as_sql():
-> 1836         cursor.execute(sql, params)
   1837     if not self.returning_fields:
   1838         return []

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/backends/utils.py:79, in CursorWrapper.execute(self, sql, params)
     78 def execute(self, sql, params=None):
---> 79     return self._execute_with_wrappers(
     80         sql, params, many=False, executor=self._execute
     81     )

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/backends/utils.py:92, in CursorWrapper._execute_with_wrappers(self, sql, params, many, executor)
     90 for wrapper in reversed(self.db.execute_wrappers):
     91     executor = functools.partial(wrapper, executor)
---> 92 return executor(sql, params, many, context)

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/backends/utils.py:100, in CursorWrapper._execute(self, sql, params, *ignored_wrapper_args)
     98     warnings.warn(self.APPS_NOT_READY_WARNING_MSG, category=RuntimeWarning)
     99 self.db.validate_no_broken_transaction()
--> 100 with self.db.wrap_database_errors:
    101     if params is None:
    102         # params default might be backend specific.
    103         return self.cursor.execute(sql)

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/utils.py:91, in DatabaseErrorWrapper.__exit__(self, exc_type, exc_value, traceback)
     89 if dj_exc_type not in (DataError, IntegrityError):
     90     self.wrapper.errors_occurred = True
---> 91 raise dj_exc_value.with_traceback(traceback) from exc_value

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/backends/utils.py:105, in CursorWrapper._execute(self, sql, params, *ignored_wrapper_args)
    103     return self.cursor.execute(sql)
    104 else:
--> 105     return self.cursor.execute(sql, params)

File ~/miniforge3/envs/lamindb/lib/python3.12/site-packages/django/db/backends/sqlite3/base.py:354, in SQLiteCursorWrapper.execute(self, query, params)
    352 param_names = list(params) if isinstance(params, Mapping) else None
    353 query = self.convert_query(query, param_names=param_names)
--> 354 return super().execute(query, params)

IntegrityError: UNIQUE constraint failed: bionty_disease.uid

looking at the db

bt.Disease.df()

gives us

	uid	name	ontology_id	abbr	synonyms	description	space_id	source_id	run_id	created_at	created_by_id	_aux	_branch_code
id
1	4NhM08vm	['complexdisease']	None	None	None	None	1	None	None	2025-01-21 16:00:50.990000+00:00	1	None	1

[Zethson]

@sunnyosun should we solve that with Field validation? Something like:

class CharField(models.CharField):
    """Custom `CharField` with default values for `blank`, `default`, and `max_length`.

    Also prevents Python lists from being used as values.
    """

    def __init__(self, max_length: int = 255, **kwargs):
        kwargs["max_length"] = max_length
        kwargs.setdefault("blank", True)
        kwargs.setdefault("default", None)
        super().__init__(**kwargs)

    def clean(self, value, model_instance):
        if isinstance(value, list):
            raise ValidationError("This field does not accept lists as values.")
        return super().clean(value, model_instance)

Of course we can also extend that to other Collection types

[sunnyosun]

No, this will make creation very slow, it's on purpose turned off for core and bionty schema: #2177

Also clean() makes DB calls so the correct call is clean_fields() and it's already implemented: https://github.com/laminlabs/lamindb/blob/main/lamindb/_record.py#L210-L216

I think even a simple type check here is slow due to the getattr calls, need to think more how to catch such edge cases.