Datasets:

---

fragilov

/

clinvar

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 35 new columns ({'variant_id', 'strand', 'expression', 'HGNC_ID', 'accession', 'chr', 'mapping_type', 'alt', 'disease_db', 'key', 'disease_name', 'start', 'node_id', 'rcv_accession', 'gene_symbol', 'gene_fullname', 'mapping_value', 'id', 'clinical_assertion_id', 'change', 'OMIM', 'disease_id', 'title', 'assembly', 'variant_name', 'stop', 'trait_type', 'labels', 'mapping_ref', 'type', 'source', 'variant_type', 'ref', 'gene_id', 'cytoband'}) and 3 missing columns ({'source_id', 'target_id', 'relationship_type'}).

This happened while the csv dataset builder was generating data using

hf://datasets/fragilov/clinvar/clinvar_nodes.csv (at revision 011f8837a5368370b2e990f59af3f0dc38079f9b), [/tmp/hf-datasets-cache/medium/datasets/59798216347035-config-parquet-and-info-fragilov-clinvar-d8d1e9bd/hub/datasets--fragilov--clinvar/snapshots/011f8837a5368370b2e990f59af3f0dc38079f9b/clinvar_edges.csv (origin=hf://datasets/fragilov/clinvar@011f8837a5368370b2e990f59af3f0dc38079f9b/clinvar_edges.csv), /tmp/hf-datasets-cache/medium/datasets/59798216347035-config-parquet-and-info-fragilov-clinvar-d8d1e9bd/hub/datasets--fragilov--clinvar/snapshots/011f8837a5368370b2e990f59af3f0dc38079f9b/clinvar_nodes.csv (origin=hf://datasets/fragilov/clinvar@011f8837a5368370b2e990f59af3f0dc38079f9b/clinvar_nodes.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 1890, in _prepare_split_single
                  writer.write_table(table)
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 760, 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
              node_id: int64
              labels: string
              ref: string
              variant_id: double
              stop: double
              cytoband: string
              variant_type: string
              start: double
              alt: string
              variant_name: string
              chr: string
              strand: string
              HGNC_ID: string
              gene_fullname: string
              gene_symbol: string
              OMIM: double
              gene_id: double
              expression: string
              change: string
              assembly: string
              accession: string
              type: string
              disease_id: string
              disease_db: string
              disease_name: string
              title: string
              rcv_accession: string
              key: string
              source: string
              id: string
              mapping_type: string
              mapping_ref: string
              clinical_assertion_id: double
              mapping_value: string
              trait_type: string
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 4338
              to
              {'source_id': Value('int64'), 'target_id': Value('int64'), 'relationship_type': 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 1739, 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 1892, 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 35 new columns ({'variant_id', 'strand', 'expression', 'HGNC_ID', 'accession', 'chr', 'mapping_type', 'alt', 'disease_db', 'key', 'disease_name', 'start', 'node_id', 'rcv_accession', 'gene_symbol', 'gene_fullname', 'mapping_value', 'id', 'clinical_assertion_id', 'change', 'OMIM', 'disease_id', 'title', 'assembly', 'variant_name', 'stop', 'trait_type', 'labels', 'mapping_ref', 'type', 'source', 'variant_type', 'ref', 'gene_id', 'cytoband'}) and 3 missing columns ({'source_id', 'target_id', 'relationship_type'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/fragilov/clinvar/clinvar_nodes.csv (at revision 011f8837a5368370b2e990f59af3f0dc38079f9b), [/tmp/hf-datasets-cache/medium/datasets/59798216347035-config-parquet-and-info-fragilov-clinvar-d8d1e9bd/hub/datasets--fragilov--clinvar/snapshots/011f8837a5368370b2e990f59af3f0dc38079f9b/clinvar_edges.csv (origin=hf://datasets/fragilov/clinvar@011f8837a5368370b2e990f59af3f0dc38079f9b/clinvar_edges.csv), /tmp/hf-datasets-cache/medium/datasets/59798216347035-config-parquet-and-info-fragilov-clinvar-d8d1e9bd/hub/datasets--fragilov--clinvar/snapshots/011f8837a5368370b2e990f59af3f0dc38079f9b/clinvar_nodes.csv (origin=hf://datasets/fragilov/clinvar@011f8837a5368370b2e990f59af3f0dc38079f9b/clinvar_nodes.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)