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airr_tcga

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Immunosequencing Algorithms Laboratory 4

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 31 new columns ({'study_id', 'source_tumor', 'center_id', 'tumor_stage', 'AE_type', 'sex', 'sample_id', 'time_point', 'cancer_stage', 'AE_severity', 'disease', 'cohort', 'center_name', 'tumor_type', 'AE', 'OS', 'metacohort_id', 'source_icd10', 'source_type', 'therapy', 'race', 'age', 'PFS', 'total_reads', 'therapy_info', 'response_type', 'cancer_type', 'PFS_event', 'OS_event', 'response', 'aligned_reads'}) and 7 missing columns ({'HLA-C_1', 'HLA-A_1', 'HLA-B_2', 'HLA-B_1', 'HLA-A_2', 'HLA-C_2', 'hla_source'}).

This happened while the csv dataset builder was generating data using

hf://datasets/isalgo/airr_tcga/metadata.tsv (at revision b1081f7074640defc861bb6f2e94a11151f95088), ['hf://datasets/isalgo/airr_tcga@b1081f7074640defc861bb6f2e94a11151f95088/metadata.hla.tsv', 'hf://datasets/isalgo/airr_tcga@b1081f7074640defc861bb6f2e94a11151f95088/metadata.tsv']

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/python3.14/site-packages/datasets/builder.py", line 1848, in _prepare_split_single
                  writer.write_table(table)
                  ~~~~~~~~~~~~~~~~~~^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 765, in write_table
                  self._write_table(pa_table, writer_batch_size=writer_batch_size)
                  ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/arrow_writer.py", line 773, in _write_table
                  pa_table = table_cast(pa_table, self._schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2378, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2306, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              sample_id: string
              subject_id: string
              study_id: string
              cohort: string
              cancer_type: string
              disease: string
              tumor_type: string
              source_type: string
              source_tumor: string
              source_icd10: string
              sex: string
              race: string
              age: double
              cancer_stage: string
              tumor_stage: string
              therapy: string
              therapy_info: double
              time_point: double
              response: double
              response_type: double
              OS: double
              OS_event: int64
              PFS: string
              PFS_event: double
              AE: double
              AE_type: double
              AE_severity: double
              total_reads: double
              aligned_reads: double
              center_id: string
              center_name: string
              metacohort_id: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 4045
              to
              {'subject_id': Value('string'), 'HLA-A_1': Value('string'), 'HLA-A_2': Value('string'), 'HLA-B_1': Value('string'), 'HLA-B_2': Value('string'), 'HLA-C_1': Value('string'), 'HLA-C_2': Value('string'), 'hla_source': 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 1369, in compute_config_parquet_and_info_response
                  parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
                                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~^
                      builder, max_dataset_size_bytes=max_dataset_size_bytes
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  )
                  ^
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 948, in stream_convert_to_parquet
                  builder._prepare_split(split_generator=splits_generators[split], file_format="parquet")
                  ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1694, in _prepare_split
                  for job_id, done, content in self._prepare_split_single(
                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~^
                      gen_kwargs=gen_kwargs, job_id=job_id, **_prepare_split_args
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                  ):
                  ^
                File "/usr/local/lib/python3.14/site-packages/datasets/builder.py", line 1850, in _prepare_split_single
                  raise DatasetGenerationCastError.from_cast_error(
                  ...<4 lines>...
                  )
              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 31 new columns ({'study_id', 'source_tumor', 'center_id', 'tumor_stage', 'AE_type', 'sex', 'sample_id', 'time_point', 'cancer_stage', 'AE_severity', 'disease', 'cohort', 'center_name', 'tumor_type', 'AE', 'OS', 'metacohort_id', 'source_icd10', 'source_type', 'therapy', 'race', 'age', 'PFS', 'total_reads', 'therapy_info', 'response_type', 'cancer_type', 'PFS_event', 'OS_event', 'response', 'aligned_reads'}) and 7 missing columns ({'HLA-C_1', 'HLA-A_1', 'HLA-B_2', 'HLA-B_1', 'HLA-A_2', 'HLA-C_2', 'hla_source'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/isalgo/airr_tcga/metadata.tsv (at revision b1081f7074640defc861bb6f2e94a11151f95088), ['hf://datasets/isalgo/airr_tcga@b1081f7074640defc861bb6f2e94a11151f95088/metadata.hla.tsv', 'hf://datasets/isalgo/airr_tcga@b1081f7074640defc861bb6f2e94a11151f95088/metadata.tsv']
              
              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)