Datasets:

---

zinzinmit

/

MedNLPCombined

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 3 new columns ({'ID', 'Disease', 'Chemical'}) and 3 missing columns ({'Text', 'Type', 'Mesh'}).

This happened while the csv dataset builder was generating data using

hf://datasets/zinzinmit/MedNLPCombined/bc5cdr/data/training/bc5cdr_relation.csv (at revision 1d74d4ff3ac8a48866e88023b55a95b3949e601c), [/tmp/hf-datasets-cache/medium/datasets/18679590191154-config-parquet-and-info-zinzinmit-MedNLPCombined-4b94d53b/hub/datasets--zinzinmit--MedNLPCombined/snapshots/1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/bc5cdr_lookup_table.csv (origin=hf://datasets/zinzinmit/MedNLPCombined@1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/bc5cdr_lookup_table.csv), /tmp/hf-datasets-cache/medium/datasets/18679590191154-config-parquet-and-info-zinzinmit-MedNLPCombined-4b94d53b/hub/datasets--zinzinmit--MedNLPCombined/snapshots/1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/bc5cdr_relation.csv (origin=hf://datasets/zinzinmit/MedNLPCombined@1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/bc5cdr_relation.csv), /tmp/hf-datasets-cache/medium/datasets/18679590191154-config-parquet-and-info-zinzinmit-MedNLPCombined-4b94d53b/hub/datasets--zinzinmit--MedNLPCombined/snapshots/1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/full_bc5cdr_data.csv (origin=hf://datasets/zinzinmit/MedNLPCombined@1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/full_bc5cdr_data.csv)]

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 1887, in _prepare_split_single
                  writer.write_table(table)
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 675, 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
              Unnamed: 0: int64
              ID: int64
              Chemical: string
              Disease: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 710
              to
              {'Unnamed: 0': Value('int64'), 'Text': Value('string'), 'Type': Value('string'), 'Mesh': 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 1347, 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 980, in convert_to_parquet
                  builder.download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 884, in download_and_prepare
                  self._download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 947, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1736, 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 1889, 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 3 new columns ({'ID', 'Disease', 'Chemical'}) and 3 missing columns ({'Text', 'Type', 'Mesh'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/zinzinmit/MedNLPCombined/bc5cdr/data/training/bc5cdr_relation.csv (at revision 1d74d4ff3ac8a48866e88023b55a95b3949e601c), [/tmp/hf-datasets-cache/medium/datasets/18679590191154-config-parquet-and-info-zinzinmit-MedNLPCombined-4b94d53b/hub/datasets--zinzinmit--MedNLPCombined/snapshots/1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/bc5cdr_lookup_table.csv (origin=hf://datasets/zinzinmit/MedNLPCombined@1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/bc5cdr_lookup_table.csv), /tmp/hf-datasets-cache/medium/datasets/18679590191154-config-parquet-and-info-zinzinmit-MedNLPCombined-4b94d53b/hub/datasets--zinzinmit--MedNLPCombined/snapshots/1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/bc5cdr_relation.csv (origin=hf://datasets/zinzinmit/MedNLPCombined@1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/bc5cdr_relation.csv), /tmp/hf-datasets-cache/medium/datasets/18679590191154-config-parquet-and-info-zinzinmit-MedNLPCombined-4b94d53b/hub/datasets--zinzinmit--MedNLPCombined/snapshots/1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/full_bc5cdr_data.csv (origin=hf://datasets/zinzinmit/MedNLPCombined@1d74d4ff3ac8a48866e88023b55a95b3949e601c/bc5cdr/data/training/full_bc5cdr_data.csv)]
              
              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)