Datasets:

---

YF0808

/

GRBench_biomedical_shards

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 ({'dim', 'next_index', 'shards', 'model_tag', 'total_docs', 'dataset', 'last_flush_time', 'model', 'done'}) and 11 missing columns ({'Pharmacologic_Class_nodes', 'Side_Effect_nodes', 'Symptom_nodes', 'Pathway_nodes', 'Gene_nodes', 'Disease_nodes', 'Molecular_Function_nodes', 'Cellular_Component_nodes', 'Anatomy_nodes', 'Biological_Process_nodes', 'Compound_nodes'}).

This happened while the json dataset builder was generating data using

hf://datasets/YF0808/GRBench_biomedical_shards/manifest.json (at revision 3e3b3e0df6f70457090703ee1e029dc5ee20b233)

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 1831, in _prepare_split_single
                  writer.write_table(table)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 644, 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 2272, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2218, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              dataset: string
              model: string
              model_tag: string
              total_docs: int64
              dim: int64
              shards: list<item: string>
                child 0, item: string
              next_index: int64
              done: bool
              last_flush_time: timestamp[s]
              to
              {'Anatomy_nodes': {'features': {'bto_id': Value('string'), 'mesh_id': Value('string'), 'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Anatomy-downregulates-Gene': List(Value('string')), 'Anatomy-expresses-Gene': List(Value('string')), 'Anatomy-upregulates-Gene': List(Value('string')), 'Disease-localizes-Anatomy': List(Value('string'))}}, 'Biological_Process_nodes': {'features': {'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Gene-participates-Biological Process': List(Value('string'))}}, 'Cellular_Component_nodes': {'features': {'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Gene-participates-Cellular Component': List(Value('string'))}}, 'Compound_nodes': {'features': {'inchi': Value('string'), 'inchikey': Value('string'), 'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Compound-binds-Gene': List(Value('string')), 'Compound-causes-Side Effect': List(Value('string')), 'Compound-downregulates-Gene': List(Value('string')), 'Compound-palliates-Disease': List(Value('string')), 'Compound-resembles-Compound': List(Value('string')), 'Compound-treats-Disease': List(Value('string')), 'Compound-upregulates-Gene': List(Value('string')), 'Pharmacologic Class-includes-Compound': List(Value('string'))}}, 'Disease_nodes': {'features': {'name': Value('string'), 'node_type': Value('string'), 'url': Value('
              ...
              ssociates-Gene': List(Value('string')), 'Disease-downregulates-Gene': List(Value('string')), 'Disease-upregulates-Gene': List(Value('string')), 'Gene-covaries-Gene': List(Value('string')), 'Gene-interacts-Gene': List(Value('string')), 'Gene-participates-Biological Process': List(Value('string')), 'Gene-participates-Cellular Component': List(Value('string')), 'Gene-participates-Molecular Function': List(Value('string')), 'Gene-participates-Pathway': List(Value('string')), 'Gene-regulates-Gene': List(Value('string'))}}, 'Molecular_Function_nodes': {'features': {'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Gene-participates-Molecular Function': List(Value('string'))}}, 'Pathway_nodes': {'features': {'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Gene-participates-Pathway': List(Value('string'))}}, 'Pharmacologic_Class_nodes': {'features': {'class_type': Value('string'), 'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Pharmacologic Class-includes-Compound': List(Value('string'))}}, 'Side_Effect_nodes': {'features': {'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Compound-causes-Side Effect': List(Value('string'))}}, 'Symptom_nodes': {'features': {'name': Value('string'), 'node_type': Value('string'), 'url': Value('string')}, 'neighbors': {'Disease-presents-Symptom': List(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 1456, 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 1055, in convert_to_parquet
                  builder.download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 894, in download_and_prepare
                  self._download_and_prepare(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 970, 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 1702, 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 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 9 new columns ({'dim', 'next_index', 'shards', 'model_tag', 'total_docs', 'dataset', 'last_flush_time', 'model', 'done'}) and 11 missing columns ({'Pharmacologic_Class_nodes', 'Side_Effect_nodes', 'Symptom_nodes', 'Pathway_nodes', 'Gene_nodes', 'Disease_nodes', 'Molecular_Function_nodes', 'Cellular_Component_nodes', 'Anatomy_nodes', 'Biological_Process_nodes', 'Compound_nodes'}).
              
              This happened while the json dataset builder was generating data using
              
              hf://datasets/YF0808/GRBench_biomedical_shards/manifest.json (at revision 3e3b3e0df6f70457090703ee1e029dc5ee20b233)
              
              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)