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The dataset generation failed because of a cast error
Error code: DatasetGenerationCastError
Exception: DatasetGenerationCastError
Message: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 5 new columns ({'haploinsufficiency', 'inheritance_pattern', 'splicing_effects', 'pathomechanism', 'therapy_review'}) and 5 missing columns ({'question_type', 'variant', 'rubrics', 'comment', 'example_id'}).
This happened while the json dataset builder was generating data using
hf://datasets/rl-research/genetic_diseases_qa/question_types.json (at revision df6d3bfa85eb765457b4f854d6ae739d70b774d0)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1831, in _prepare_split_single
writer.write_table(table)
File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 714, in write_table
pa_table = table_cast(pa_table, self._schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2272, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2218, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
pathomechanism: struct<template: string, rubrics: list<item: struct<name: string, criterion: string>>>
child 0, template: string
child 1, rubrics: list<item: struct<name: string, criterion: string>>
child 0, item: struct<name: string, criterion: string>
child 0, name: string
child 1, criterion: string
splicing_effects: struct<template: string, rubrics: list<item: struct<name: string, criterion: string>>>
child 0, template: string
child 1, rubrics: list<item: struct<name: string, criterion: string>>
child 0, item: struct<name: string, criterion: string>
child 0, name: string
child 1, criterion: string
inheritance_pattern: struct<template: string, rubrics: list<item: struct<name: string, criterion: string>>>
child 0, template: string
child 1, rubrics: list<item: struct<name: string, criterion: string>>
child 0, item: struct<name: string, criterion: string>
child 0, name: string
child 1, criterion: string
haploinsufficiency: struct<template: string, rubrics: list<item: struct<name: string, criterion: string>>>
child 0, template: string
child 1, rubrics: list<item: struct<name: string, criterion: string>>
child 0, item: struct<name: string, criterion: string>
child 0, name: string
child 1, criterion: string
therapy_review: struct<template: string, rubrics: list<item: struct<name: string, criterion: string>>>
child 0, template: string
child 1, rubrics: list<item: struct<name: string, criterion: string>>
child 0, item: struct<name: string, criterion: string>
child 0, name: string
child 1, criterion: string
to
{'question_type': Value('string'), 'variant': Value('string'), 'rubrics': List({'criterion': Value('string'), 'name': Value('string')}), 'example_id': Value('int64'), 'comment': Value('string')}
because column names don't match
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1455, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1054, in convert_to_parquet
builder.download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 894, in download_and_prepare
self._download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 970, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1702, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1833, in _prepare_split_single
raise DatasetGenerationCastError.from_cast_error(
datasets.exceptions.DatasetGenerationCastError: An error occurred while generating the dataset
All the data files must have the same columns, but at some point there are 5 new columns ({'haploinsufficiency', 'inheritance_pattern', 'splicing_effects', 'pathomechanism', 'therapy_review'}) and 5 missing columns ({'question_type', 'variant', 'rubrics', 'comment', 'example_id'}).
This happened while the json dataset builder was generating data using
hf://datasets/rl-research/genetic_diseases_qa/question_types.json (at revision df6d3bfa85eb765457b4f854d6ae739d70b774d0)
Please either edit the data files to have matching columns, or separate them into different configurations (see docs at https://hf.co/docs/hub/datasets-manual-configuration#multiple-configurations)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
question_type
string | variant
string | rubrics
list | example_id
int64 | comment
null |
|---|---|---|---|---|
pathomechanism
|
NM_025152.3(NUBPL):c.815-27T>C
|
[
{
"criterion": "Response reports variant is loss-of-function",
"name": "correct_answer"
}
] | 0
| null |
inheritance_pattern
|
NM_025152.3(NUBPL):c.815-27T>C
|
[
{
"criterion": "Response mentions associated inheritance pattern is autosomal dominant.",
"name": "correct_answer"
}
] | 1
| null |
splicing_effects
|
NM_025152.3(NUBPL):c.815-27T>C
|
[
{
"criterion": "Response mentions that variant affects a branchpoint and leads to aberrant splicing",
"name": "correct_answer"
},
{
"criterion": "Response mentions that the branchpoint is not fully destroyed",
"name": "correct_answer"
},
{
"criterion": "Response mentions that variant is intronic",
"name": "correct_answer"
}
] | 2
| null |
therapy_review
|
NM_000350.3(ABCA4):c.769-784C>T
|
[
{
"criterion": "Identifies at least one relevant paper on an ASO for the given variant in the context of Stargardt Disease.",
"name": "correct_answer"
},
{
"criterion": "Response mentions functional evidence from patient-derived fibroblasts",
"name": "correct_answer"
}
] | 3
| null |
therapy_review
|
NM_024312.5(GNPTAB):c.3503_3504del
|
[
{
"criterion": "Response mentions a relevant study on exon skipping ASO therapy for the given variant.",
"name": "correct_answer"
},
{
"criterion": "Mentions that the therapy involves an exon skipping ASO to skip exon 19 of GNPTAB",
"name": "correct_answer"
}
] | 4
| null |
therapy_review
|
NM_020366.3(RPGRIP1):c.1468-128T>G
|
[
{
"criterion": "Response mentions evidence from patient lymphoblasts",
"name": "correct_answer"
},
{
"criterion": "Response references that an ASO exists",
"name": "correct_answer"
}
] | 6
| null |
splicing_effects
|
NM_000329.3(RPE65):c.1430A>G
|
[
{
"criterion": "Response mentions that the variant causes aberrant RNA splicing.",
"name": "correct_answer"
},
{
"criterion": "Mentions the variant is a novel acceptor site",
"name": "correct_answer"
}
] | 7
| null |
pathomechanism
|
NM_000329.3(RPE65):c.1430A>G
|
[
{
"criterion": "Response identifies the variant as dominant negative",
"name": "correct_answer"
}
] | 8
| null |
inheritance_pattern
|
NM_000329.3(RPE65):c.1430A>G
|
[
{
"criterion": "Response identifies autosomal dominant inheritance",
"name": "correct_answer"
}
] | 9
| null |
splicing_effects
|
NM_001086521.2(NDUFAF8):c.195+271C>T
|
[
{
"criterion": "Response states variant causes aberrant splicing",
"name": "correct_answer"
},
{
"criterion": "Response reference evidence from RNA in patient derived fibroblasts",
"name": "correct_answer"
}
] | 10
| null |
inheritance_pattern
|
NM_001086521.2(NDUFAF8):c.195+271C>T
|
[
{
"criterion": "Variant's inheritance pattern is autosomal recessive",
"name": "correct_answer"
}
] | 11
| null |
pathomechanism
|
NM_001086521.2(NDUFAF8):c.195+271C>T
|
[
{
"criterion": "Response identifies the variant as loss-of-function",
"name": "correct_answer"
}
] | 12
| null |
inheritance_pattern
|
NM_003907.3(EIF2B5):c.1156+13G>A
|
[
{
"criterion": "Variant is determined to have autosomal recessive inheritance pattern",
"name": "correct_answer"
}
] | 13
| null |
pathomechanism
|
NM_003907.3(EIF2B5):c.1156+13G>A
|
[
{
"criterion": "Response identifies the variant as loss-of-function",
"name": "correct_answer"
}
] | 14
| null |
splicing_effects
|
NM_003907.3(EIF2B5):c.1156+13G>A
|
[
{
"criterion": "Response determines that variant causes aberrant splicing",
"name": "correct_answer"
},
{
"criterion": "Response refers to evidence using RNA derived from patient cells",
"name": "correct_answer"
}
] | 15
| null |
therapy_review
|
NM_206933.4(USH2A):c.2692C>T
|
[
{
"criterion": "References study on existing exon skipping ASO, in exon 13 of USH2A.",
"name": "correct_answer"
}
] | 16
| null |
splicing_effects
|
NM_000391.4(TPP1):c.225A>G
|
[
{
"criterion": "Response mentions that variant causes aberrant splicing",
"name": "correct_answer"
}
] | 17
| null |
pathomechanism
|
NM_000391.4(TPP1):c.225A>G
|
[
{
"criterion": "Response identifies variant as loss-of-function",
"name": "correct_answer"
}
] | 18
| null |
inheritance_pattern
|
NM_000391.4(TPP1):c.225A>G
|
[
{
"criterion": "Response identifies variant inheritance pattern as autosomal recessive.",
"name": "correct_answer"
}
] | 19
| null |
inheritance_pattern
|
NM_024298.5(MBOAT7):c.758_778del
|
[
{
"criterion": "Response identifies inheritance pattern as autosomal recessive",
"name": "correct_answer"
}
] | 20
| null |
therapy_review
|
NM_000303.3(PMM2):c.640-15479C>T
|
[
{
"criterion": "Response identifies existing variant-specific splice correction ASO for this variant",
"name": "correct_answer"
}
] | 25
| null |
therapy_review
|
NM_000202.8(IDS):c.1122C>T
|
[
{
"criterion": "Response mentions a previously unsuccessful splice correction ASO designed for the variant",
"name": "correct_answer"
}
] | 26
| null |
pathomechanism
|
NM_000202.8(IDS):c.1122C>T
|
[
{
"criterion": "Response identifies variant as loss-of-function",
"name": "correct_answer"
}
] | 27
| null |
pathomechanism
|
NM_018075.5(ANO10):c.1025G>A
|
[
{
"criterion": "Response identifies variant as loss-of-function",
"name": "correct_answer"
}
] | 30
| null |
inheritance_pattern
|
NM_018075.5(ANO10):c.1025G>A
|
[
{
"criterion": "Response identifies an autosomal recessive inheritance pattern",
"name": "correct_answer"
}
] | 31
| null |
pathomechanism
|
NM_001127222.2(CACNA1A):c.4174G>A
|
[
{
"criterion": "Response identifies variant as gain-of-function",
"name": "correct_answer"
}
] | 33
| null |
inheritance_pattern
|
NM_001127222.2(CACNA1A):c.4174G>A
|
[
{
"criterion": "Response indicates autosomal dominant inheritance",
"name": "correct_answer"
}
] | 34
| null |
haploinsufficiency
|
NM_001127222.2(CACNA1A):c.4174G>A
|
[
{
"criterion": "Response mentions evidence supporting haploinsufficiency of the CACNA1A gene",
"name": "correct_answer"
}
] | 35
| null |
therapy_review
|
NM_024312.5(GNPTAB):c.3488del
|
[
{
"criterion": "Response reports an exon skipping ASO study relevant to the variant.",
"name": "correct_answer"
}
] | 37
| null |
splicing_effects
|
NM_133433.4(NIPBL):c.5329-15A>G
|
[
{
"criterion": "Response mentions variant results in alternate splicing.",
"name": "correct_answer"
},
{
"criterion": "Response mentions that the variant is thought to affect a branchpoint, leading to skipping of in-frame exon 28",
"name": "correct_answer"
}
] | 40
| null |
inheritance_pattern
|
NM_133433.4(NIPBL):c.5329-15A>G
|
[
{
"criterion": "Response identifies autosomal dominant inheritance",
"name": "correct_answer"
}
] | 41
| null |
inheritance_pattern
|
NM_014727.3(KMT2B):c.8079delC
|
[
{
"criterion": "Response mentions that variant is inherited in an autosomal dominant manner.",
"name": "correct_answer"
}
] | 42
| null |
pathomechanism
|
NM_014727.3(KMT2B):c.8079delC
|
[
{
"criterion": "Response indicates that gain-of-function mechanisms have been reported as a cause of disease, but addresses that the pathomechanism is uncertain (this is because the variant results in frameshift in the last exon).",
"name": "correct_answer"
}
] | 43
| null |
inheritance_pattern
|
NM_024312.5(GNPTAB):c.1123C>T
|
[
{
"criterion": "Response mentions that variant is inherited in an autosomal recessive manner.",
"name": "correct_answer"
}
] | 44
| null |
pathomechanism
|
NM_024312.5(GNPTAB):c.1123C>T
|
[
{
"criterion": "Response mentions that variant pathomechanism is loss-of-function",
"name": "correct_answer"
}
] | 45
| null |
inheritance_pattern
|
NM_005859.5(PURA):c.159dup
|
[
{
"criterion": "Response identifies that variant is inherited in an autosomal dominant manner.",
"name": "correct_answer"
}
] | 48
| null |
pathomechanism
|
NM_005859.5(PURA):c.159dup
|
[
{
"criterion": "Response identifies variant as loss-of-function",
"name": "correct_answer"
}
] | 49
| null |
therapy_review
|
NM_001167623.2(CACNA1C):c.1216G>A
|
[
{
"criterion": "Response identifies that an ASO for the variant exists",
"name": "correct_answer"
},
{
"criterion": "Response mentions the existing ASO studied involved an ASO-mediated switch from exon 8A to 8, which rescued defects in patient-derived tissue.",
"name": "correct_answer"
}
] | 50
| null |
pathomechanism
|
NM_001167623.2(CACNA1C):c.1216G>A
|
[
{
"criterion": "Response identifies variant as gain-of-function",
"name": "correct_answer"
}
] | 51
| null |
inheritance_pattern
|
NM_001167623.2(CACNA1C):c.1216G>A
|
[
{
"criterion": "Response identifies that variant is inherited in an autosomal dominant manner.",
"name": "correct_answer"
}
] | 52
| null |
therapy_review
|
NM_001244008.2(KIF1A):c.914C>T
|
[
{
"criterion": "Response reports existing allele-specific gapmer ASO has been studied for the variant.",
"name": "correct_answer"
},
{
"criterion": "Response mentions that the ASO has been tested for safety and efficacy in a human patient.",
"name": "correct_answer"
}
] | 53
| null |
inheritance_pattern
|
NM_000492.4(CFTR):c.2989-313A>T
|
[
{
"criterion": "Response mentions that variant is inherited in an autosomal recessive manner.",
"name": "correct_answer"
}
] | 54
| null |
pathomechanism
|
NM_001194.4(HCN2):c.736G>A
|
[
{
"criterion": "Response identifies variant as gain-of-function",
"name": "correct_answer"
}
] | 55
| null |
inheritance_pattern
|
NM_001194.4(HCN2):c.736G>A
|
[
{
"criterion": "Response identifies that variant is inherited in an autosomal dominant manner.",
"name": "correct_answer"
}
] | 56
| null |
haploinsufficiency
|
NM_001194.4(HCN2):c.736G>A
|
[
{
"criterion": "Response indicates haploinsufficiency is not a known cause of disease.",
"name": "correct_answer"
}
] | 57
| null |
pathomechanism
|
NM_000170.3(GLDC):c.538C>T
|
[
{
"criterion": "Response identifies variant as loss-of-function",
"name": "correct_answer"
}
] | 59
| null |
inheritance_pattern
|
NM_000170.3(GLDC):c.538C>T
|
[
{
"criterion": "Response identifies variant is inherited in an autosomal recessive manner.",
"name": "correct_answer"
}
] | 60
| null |
null | null | null | null | null |
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