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import_from_source errors for CellLine #139

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Zethson opened this issue Oct 30, 2024 · 0 comments
Open

import_from_source errors for CellLine #139

Zethson opened this issue Oct 30, 2024 · 0 comments
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@Zethson
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Zethson commented Oct 30, 2024

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'"
}
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