Datasets:

---

casey-martin

/

GeneGPT

like 0

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 9 new columns ({'Gene alias', 'Gene location', 'Multi-species DNA aligment', 'Protein-coding genes', 'Human genome DNA aligment', 'Gene name conversion', 'Gene SNP association', 'SNP location', 'Gene disease association'}) and 3 missing columns ({'SNP gene function', 'sequence gene alias', 'Disease gene location'}).

This happened while the json dataset builder was generating data using

hf://datasets/casey-martin/GeneGPT/geneturing.json (at revision 41a993beb9793d068343f67ab3c05457bf80cf2d)

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 "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1870, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 622, in write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2292, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2240, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              Gene alias: struct<What is the official gene symbol of LMP10?: string, What is the official gene symbol of SNAT6?: string, What is the official gene symbol of IMD20?: string, What is the official gene symbol of C20orf195?: string, What is the official gene symbol of CXorf40B?: string, What is the official gene symbol of QSCN6L1?: string, What is the official gene symbol of OR11-86?: string, What is the official gene symbol of NPAP60L?: string, What is the official gene symbol of AF10?: string, What is the official gene symbol of bMRP63?: string, What is the official gene symbol of HsT1192?: string, What is the official gene symbol of ZNF482?: string, What is the official gene symbol of PTH1?: string, What is the official gene symbol of AGTIL?: string, What is the official gene symbol of LEP9?: string, What is the official gene symbol of SEP3?: string, What is the official gene symbol of FFDD3?: string, What is the official gene symbol of C6orf186?: string, What is the official gene symbol of hCAP?: string, What is the official gene symbol of CKBBP1?: string, What is the official gene symbol of TFA?: string, What is the official gene symbol of BMSC-MCP?: string, What is the official gene symbol of PCH3?: string, What is the official gene symbol of OR11-75?: string, What is the official gene symbol of RBAP1?: string, What is the official gene symbol of DCSCRIPT?: string, What is the official gene symbol of 15-LOX?: string, What is the official gene symbol of CT116?: string, Wha
              ...
              genome?: string
                child 32, Which chromosome does SNP rs1401416674 locate on human genome?: string
                child 33, Which chromosome does SNP rs76491275 locate on human genome?: string
                child 34, Which chromosome does SNP rs141272872 locate on human genome?: string
                child 35, Which chromosome does SNP rs1281763211 locate on human genome?: string
                child 36, Which chromosome does SNP rs1278117191 locate on human genome?: string
                child 37, Which chromosome does SNP rs1239675264 locate on human genome?: string
                child 38, Which chromosome does SNP rs866998836 locate on human genome?: string
                child 39, Which chromosome does SNP rs1228002921 locate on human genome?: string
                child 40, Which chromosome does SNP rs976400036 locate on human genome?: string
                child 41, Which chromosome does SNP rs397784008 locate on human genome?: string
                child 42, Which chromosome does SNP rs1170945868 locate on human genome?: string
                child 43, Which chromosome does SNP rs990783431 locate on human genome?: string
                child 44, Which chromosome does SNP rs1041819671 locate on human genome?: string
                child 45, Which chromosome does SNP rs139642661 locate on human genome?: string
                child 46, Which chromosome does SNP rs1263053296 locate on human genome?: string
                child 47, Which chromosome does SNP rs1391145256 locate on human genome?: string
                child 48, Which chromosome does SNP rs1002944049 locate on human genome?: string
                child 49, Which chromosome does SNP rs962314907 locate on human genome?: string
              to
              {'sequence gene alias': {"What are the aliases of the gene that contains this sequnece:GTAGATGGAACTGGTAGTCAGCTGGAGAGCAGCATGGAGGCGTCCTGGGGGAGCTTCAACGCTGAGCGGGGCTGGTATGTCTCTGTCCAGCAGCCTGAAGAAGCGGAGGCCGA. Let's decompose the question to sub-questions and solve them step by step.": Sequence(feature=Value(dtype='string', id=None), length=-1, id=None), "What are the aliases of the gene that contains this sequnece:ATTGTGAGAGTAACCAACGTGGGGTTACGGGGGAGAATCTGGAGAGAAGAGAAGAGGTTAACAACCCTCCCACTTCCTGGCCACCCCCCTCCACCTTTTCTGGTAAGGAGCCC. Let's decompose the question to sub-questions and solve them step by step.": Sequence(feature=Value(dtype='string', id=None), length=-1, id=None), "What are the aliases of the gene that contains this sequnece:GGAAGAGGCCCCAGCACTGACCTCCGTGGGGGTGGAGATGAGGAGGATGGAAAGGGTGTCTTCCTCCAGCATCTTCCTGAAGGTGAAGGAGGGGCACCTTGGGGTGTCTAAGA. Let's decompose the question to sub-questions and solve them step by step.": Sequence(feature=Value(dtype='string', id=None), length=-1, id=None), "What are the aliases of the gene that contains this sequnece:GCACACGTACGTTCCTCATGAAAGGGACGACGGGAGCTGCATGAAAGCCGAAGTTATGGACCGCTAGCATCTGTCACTGGCCACCGGTTTCCGGGAGTAAGCGGCAGCTACCT. Let's decompose the question to sub-questions and solve them step by step.": Sequence(feature=Value(dtype='string', id=None), length=-1, id=None), "What are the aliases of the gene that contains this sequnece:AGACGTGAAGCCTAGCAGAGGACTTTTTAGCTGCTCACTGGCCCCGCTTGTCTGGCCGACTCATCCGCCCGCGACCCCTAATCCCCTCTGCCTGCCCCAAGATGCTGAAGCCA. Le
              ...
              uestion to sub-questions and solve them step by step.": Value(dtype='string', id=None), "What is the function of the gene associated with SNP rs1199372758? Let's decompose the question to sub-questions and solve them step by step.": Value(dtype='string', id=None), "What is the function of the gene associated with SNP rs1396355441? Let's decompose the question to sub-questions and solve them step by step.": Value(dtype='string', id=None), "What is the function of the gene associated with SNP rs1432624213? Let's decompose the question to sub-questions and solve them step by step.": Value(dtype='string', id=None), "What is the function of the gene associated with SNP rs937944577? Let's decompose the question to sub-questions and solve them step by step.": Value(dtype='string', id=None), "What is the function of the gene associated with SNP rs1450106117? Let's decompose the question to sub-questions and solve them step by step.": Value(dtype='string', id=None), "What is the function of the gene associated with SNP rs34083046? Let's decompose the question to sub-questions and solve them step by step.": Value(dtype='string', id=None), "What is the function of the gene associated with SNP rs149916046? Let's decompose the question to sub-questions and solve them step by step.": Value(dtype='string', id=None), "What is the function of the gene associated with SNP rs1385096481? Let's decompose the question to sub-questions and solve them step by step.": Value(dtype='string', id=None)}}
              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 1420, 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 1052, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 924, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1000, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1741, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1872, 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 9 new columns ({'Gene alias', 'Gene location', 'Multi-species DNA aligment', 'Protein-coding genes', 'Human genome DNA aligment', 'Gene name conversion', 'Gene SNP association', 'SNP location', 'Gene disease association'}) and 3 missing columns ({'SNP gene function', 'sequence gene alias', 'Disease gene location'}).
              
              This happened while the json dataset builder was generating data using
              
              hf://datasets/casey-martin/GeneGPT/geneturing.json (at revision 41a993beb9793d068343f67ab3c05457bf80cf2d)
              
              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)