KeyError: 'FieldAttr(Gene.symbol)' when trying to validate against public Gene

[Zethson]

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To reproduce:

!lamin init --storage ./run-tests --name run-tests --schema bionty

import lamindb as ln
import bionty as bt
import pandas as pd

gene_symbols = [
    'TP53', 'BRCA1', 'EGFR', 'PTEN', 'MYC', 'KRAS', 'CDKN2A', 'APC', 'SMAD4', 'RB1', 
    'VHL', 'P53', 'BRAF', 'ABL1', 'AKT1', 'PIK3CA', 'ALK', 'NRAS', 'ERBB2', 'KIT',
    'MET', 'CDK4', 'MDM2', 'FGFR1', 'FGFR3', # Real gene symbols
    'FAKE1', 'FAKE2', 'FAKE3', 'FAKE4', 'FAKE5', 'FAKE6', 'FAKE7', 'FAKE8', 'FAKE9', 'FAKE10', 
    'FAKE11', 'FAKE12', 'FAKE13', 'FAKE14', 'FAKE15', 'FAKE16', 'FAKE17', 'FAKE18', 'FAKE19', 'FAKE20',
    'FAKE21', 'FAKE22', 'FAKE23', 'FAKE24', 'FAKE25' # Non-existent gene symbols
]

df = pd.DataFrame(gene_symbols, columns=['Gene Symbol'])

bt.Gene.public().validate(df["Gene Symbol"], field=bt.Gene.symbol, organism="human")

results in:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File ~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3805, in Index.get_loc(self, key)
   [3804](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3804) try:
-> [3805](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3805)     return self._engine.get_loc(casted_key)
   [3806](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3806) except KeyError as err:

File index.pyx:167, in pandas._libs.index.IndexEngine.get_loc()

File index.pyx:196, in pandas._libs.index.IndexEngine.get_loc()

File pandas/_libs/hashtable_class_helper.pxi:7081, in pandas._libs.hashtable.PyObjectHashTable.get_item()

File pandas/_libs/hashtable_class_helper.pxi:7089, in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'FieldAttr(Gene.symbol)'

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

KeyError                                  Traceback (most recent call last)
Cell In[14], [line 1](vscode-notebook-cell:?execution_count=14&line=1)
----> [1](vscode-notebook-cell:?execution_count=14&line=1) bt.Gene.public().validate(df["Gene Symbol"], field=bt.Gene.symbol, organism="human")

File ~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:396, in PublicOntology.validate(self, values, field, mute, **kwargs)
    [393](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:393) if isinstance(values, str):
    [394](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:394)     values = [values]
--> [396](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:396) field_values = self._df[str(field)]
    [397](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:397) return validate(
    [398](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:398)     identifiers=values,
    [399](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:399)     field_values=field_values,
   (...)
    [402](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:402)     **kwargs,
    [403](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/bionty/base/_public_ontology.py:403) )

File ~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/frame.py:4102, in DataFrame.__getitem__(self, key)
   [4100](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/frame.py:4100) if self.columns.nlevels > 1:
   [4101](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/frame.py:4101)     return self._getitem_multilevel(key)
-> [4102](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/frame.py:4102) indexer = self.columns.get_loc(key)
   [4103](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/frame.py:4103) if is_integer(indexer):
   [4104](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/frame.py:4104)     indexer = [indexer]

File ~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3812, in Index.get_loc(self, key)
   [3807](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3807)     if isinstance(casted_key, slice) or (
   [3808](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3808)         isinstance(casted_key, abc.Iterable)
   [3809](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3809)         and any(isinstance(x, slice) for x in casted_key)
   [3810](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3810)     ):
   [3811](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3811)         raise InvalidIndexError(key)
-> [3812](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3812)     raise KeyError(key) from err
   [3813](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3813) except TypeError:
   [3814](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3814)     # If we have a listlike key, _check_indexing_error will raise
   [3815](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3815)     #  InvalidIndexError. Otherwise we fall through and re-raise
   [3816](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3816)     #  the TypeError.
   [3817](https://file+.vscode-resource.vscode-cdn.net/home/zeth/PycharmProjects/lamindb/~/miniconda3/envs/lamindb/lib/python3.11/site-packages/pandas/core/indexes/base.py:3817)     self._check_indexing_error(key)

KeyError: 'FieldAttr(Gene.symbol)'

but instead doing

bt.Gene.import_from_source()
bt.Gene.validate(df["Gene Symbol"], field=bt.Gene.symbol, organism="human")

works.

Version information

0.76.14