bionty.Source

class bionty.Source(entity: str, organism: str, name: str, version: str, currently_used: bool, description: str | None, url: str | None, md5: str | None, source_website: str | None)

Bases: Record, TracksRun, TracksUpdates

Versions of ontology sources.

Warning

Do not modify the records unless you know what you are doing!

Attributes

DoesNotExist = <class 'bionty.models.Source.DoesNotExist'>

Meta = <class 'lnschema_core.models.Record.Meta'>

MultipleObjectsReturned = <class 'bionty.models.Source.MultipleObjectsReturned'>

artifacts: Artifact

Additional files that correspond to this source.

created_by: User

Creator of record.

created_by_id

dataframe_artifact: Artifact

Dataframe artifact that corresponds to this source.

dataframe_artifact_id

objects = <django.db.models.manager.Manager object>

property pk

run: Run | None

Last run that created or updated the record.

run_id

Methods

async adelete(using=None, keep_parents=False)

async arefresh_from_db(using=None, fields=None, from_queryset=None)

async asave(*args, force_insert=False, force_update=False, using=None, update_fields=None)

clean()

Hook for doing any extra model-wide validation after clean() has been called on every field by self.clean_fields. Any ValidationError raised by this method will not be associated with a particular field; it will have a special-case association with the field defined by NON_FIELD_ERRORS.

clean_fields(exclude=None)

Clean all fields and raise a ValidationError containing a dict of all validation errors if any occur.

date_error_message(lookup_type, field_name, unique_for)

delete()

Delete.

Return type:

None

get_constraints()

get_deferred_fields()

Return a set containing names of deferred fields for this instance.

prepare_database_save(field)

refresh_from_db(using=None, fields=None, from_queryset=None)

Reload field values from the database.

By default, the reloading happens from the database this instance was loaded from, or by the read router if this instance wasn’t loaded from any database. The using parameter will override the default.

Fields can be used to specify which fields to reload. The fields should be an iterable of field attnames. If fields is None, then all non-deferred fields are reloaded.

When accessing deferred fields of an instance, the deferred loading of the field will call this method.

save(*args, **kwargs)

Save.

Always saves to the default database.

Return type:

Record

save_base(raw=False, force_insert=False, force_update=False, using=None, update_fields=None)

Handle the parts of saving which should be done only once per save, yet need to be done in raw saves, too. This includes some sanity checks and signal sending.

The ‘raw’ argument is telling save_base not to save any parent models and not to do any changes to the values before save. This is used by fixture loading.

serializable_value(field_name)

Return the value of the field name for this instance. If the field is a foreign key, return the id value instead of the object. If there’s no Field object with this name on the model, return the model attribute’s value.

Used to serialize a field’s value (in the serializer, or form output, for example). Normally, you would just access the attribute directly and not use this method.

set_as_currently_used()

Set this record as the currently used source.

Examples

>>> record = bionty.Source.get(uid="...")
>>> record.set_as_currently_used()

unique_error_message(model_class, unique_check)

validate_constraints(exclude=None)

validate_unique(exclude=None)

Check unique constraints on the model and raise ValidationError if any failed.