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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.
0.76.14
The text was updated successfully, but these errors were encountered:
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To reproduce:
results in:
but instead doing
works.
Version information
0.76.14
The text was updated successfully, but these errors were encountered: