We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
import_from_source
bt.CellLine.import_from_source()
results in
{ "name": "TypeError", "message": "CellLine() got unexpected keyword arguments: 'DepmapModelType', 'OncotreeLineage', 'OncotreePrimaryDisease', 'OncotreeSubtype', 'OncotreeCode', 'RRID', 'PrimaryOrMetastasis', 'SampleCollectionSite', 'GrowthPattern', 'OnboardedMedia', 'FormulationID'", "stack": "--------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[3], line 1 ----> 1 bt.CellLine.import_from_source() File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/bionty/models.py:241, in BioRecord.import_from_source(cls, source, ontology_ids, organism, ignore_conflicts) 238 from .core._add_ontology import add_ontology_from_df, check_source_in_db 240 if hasattr(cls, \"ontology_id\"): --> 241 add_ontology_from_df( 242 registry=cls, 243 ontology_ids=ontology_ids, 244 organism=organism, 245 source=source, 246 ignore_conflicts=ignore_conflicts, 247 ) 248 else: 249 import lamindb as ln File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/bionty/core/_add_ontology.py:173, in add_ontology_from_df(registry, ontology_ids, organism, source, ignore_conflicts) 164 n_in_db = all_records.count() 166 check_source_in_db( 167 registry=registry, 168 source=source_record, 169 n_all=n_all, 170 n_in_db=n_in_db, 171 ) --> 173 records = create_records(registry, df_new, source_record) 174 new_records = [r for r in records if r._state.adding] 175 if ontology_ids is None: File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/bionty/core/_add_ontology.py:59, in create_records(registry, df, source_record) 56 try: 57 ln.settings.creation.search_names = False 58 records = [ ---> 59 registry(**record, source_id=source_record.id) for record in df_records 60 ] 61 finally: 62 ln.settings.creation.search_names = True File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/bionty/models.py:1083, in CellLine.__init__(self, *args, **kwargs) 1078 def __init__( 1079 self, 1080 *args, 1081 **kwargs, 1082 ): -> 1083 super().__init__(*args, **kwargs) File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/bionty/models.py:215, in BioRecord.__init__(self, *args, **kwargs) 210 raise ValueError( 211 \"not a valid parents kwarg, got to be list of ontology ids\" 212 ) 213 self._parents = parents --> 215 super().__init__(*args, **kwargs) File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/lamindb/_record.py:127, in __init__(record, *args, **kwargs) 125 init_self_from_db(record, existing_record) 126 return None --> 127 super(Record, record).__init__(**kwargs) 128 elif len(args) != len(record._meta.concrete_fields): 129 raise ValueError(\"please provide keyword arguments, not plain arguments\") File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/lnschema_core/models.py:187, in TracksRun.__init__(self, *args, **kwargs) 182 def __init__( 183 self, 184 *args, 185 **kwargs, 186 ): --> 187 super().__init__(*args, **kwargs) File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/lnschema_core/models.py:217, in TracksUpdates.__init__(self, *args, **kwargs) 212 def __init__( 213 self, 214 *args, 215 **kwargs, 216 ): --> 217 super().__init__(*args, **kwargs) File ~/miniconda3/envs/pertpy/lib/python3.12/site-packages/django/db/models/base.py:567, in Model.__init__(self, *args, **kwargs) 565 if unexpected: 566 unexpected_names = \", \".join(repr(n) for n in unexpected) --> 567 raise TypeError( 568 f\"{cls.__name__}() got unexpected keyword arguments: \" 569 f\"{unexpected_names}\" 570 ) 571 super().__init__() 572 post_init.send(sender=cls, instance=self) TypeError: CellLine() got unexpected keyword arguments: 'DepmapModelType', 'OncotreeLineage', 'OncotreePrimaryDisease', 'OncotreeSubtype', 'OncotreeCode', 'RRID', 'PrimaryOrMetastasis', 'SampleCollectionSite', 'GrowthPattern', 'OnboardedMedia', 'FormulationID'" }
The text was updated successfully, but these errors were encountered:
sunnyosun
No branches or pull requests
results in
The text was updated successfully, but these errors were encountered: