Datasets:

---

sciexp

/

insdc-provenance

like 0

Follow

SciExp 2

Error code:   DatasetGenerationError
Exception:    CastError
Message:      Couldn't cast
accession: string
organism: string
entrez_id: int64
obs_count: int64
accession_source: string
bioproject: string
sra_study: string
biosample: string
run_count: int64
library_strategy: string
library_source: string
library_selection: string
library_layout: string
instrument_platform: string
instrument_model: string
base_count: int64
read_count: int64
first_public: string
last_updated: string
study_alias: string
broker_name: string
geo_series: string
upstream_portal: string
study_title: string
czi_collection_id: string
czi_collection_name: string
resolved_via: string
resolution_status: string
n_candidate_pubs: int64
primary_pub_doi: string
primary_pub_is_preprint: bool
pub_resolution: string
to
{'bioproject': Value('string'), 'pmid': Value('string'), 'pmcid': Value('string'), 'doi': Value('string'), 'title': Value('string'), 'pub_year': Value('string'), 'source': Value('string'), 'is_preprint': Value('bool'), 'cited_by': Value('int64'), 'is_open_access': Value('bool'), 'primary_rank': Value('int64'), 'is_disambiguated': Value('bool')}
because column names don't match
Traceback:    Traceback (most recent call last):
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1816, in _prepare_split_single
                  for key, table in generator:
                                    ^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/lance/lance.py", line 231, in _generate_tables
                  yield Key(frag_idx, batch_idx), self._cast_table(table)
                                                  ^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/lance/lance.py", line 188, in _cast_table
                  pa_table = table_cast(pa_table, self.info.features.arrow_schema)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2369, in table_cast
                  return cast_table_to_schema(table, schema)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2297, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              accession: string
              organism: string
              entrez_id: int64
              obs_count: int64
              accession_source: string
              bioproject: string
              sra_study: string
              biosample: string
              run_count: int64
              library_strategy: string
              library_source: string
              library_selection: string
              library_layout: string
              instrument_platform: string
              instrument_model: string
              base_count: int64
              read_count: int64
              first_public: string
              last_updated: string
              study_alias: string
              broker_name: string
              geo_series: string
              upstream_portal: string
              study_title: string
              czi_collection_id: string
              czi_collection_name: string
              resolved_via: string
              resolution_status: string
              n_candidate_pubs: int64
              primary_pub_doi: string
              primary_pub_is_preprint: bool
              pub_resolution: string
              to
              {'bioproject': Value('string'), 'pmid': Value('string'), 'pmcid': Value('string'), 'doi': Value('string'), 'title': Value('string'), 'pub_year': Value('string'), 'source': Value('string'), 'is_preprint': Value('bool'), 'cited_by': Value('int64'), 'is_open_access': Value('bool'), 'primary_rank': Value('int64'), 'is_disambiguated': Value('bool')}
              because column names don't match
              
              The above exception was the direct cause of the following exception:
              
              Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1348, 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 890, in download_and_prepare
                  self._download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 951, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1683, 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 1869, in _prepare_split_single
                  raise DatasetGenerationError("An error occurred while generating the dataset") from e
              datasets.exceptions.DatasetGenerationError: An error occurred while generating the dataset