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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: Couldn't cast array of type struct<pxd: string, term: string, category: string, modification: string, column: string, query: string> to string
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 2224, in cast_table_to_schema
cast_array_to_feature(
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1795, in wrapper
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2052, in cast_array_to_feature
casted_array_values = _c(array.values, feature.feature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2002, in cast_array_to_feature
_c(array.field(name) if name in array_fields else null_array, subfeature)
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2052, in cast_array_to_feature
casted_array_values = _c(array.values, feature.feature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2002, in cast_array_to_feature
_c(array.field(name) if name in array_fields else null_array, subfeature)
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2002, in cast_array_to_feature
_c(array.field(name) if name in array_fields else null_array, subfeature)
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2086, in cast_array_to_feature
return array_cast(
^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1797, in wrapper
return func(array, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 1950, in array_cast
raise TypeError(f"Couldn't cast array of type {_short_str(array.type)} to {_short_str(pa_type)}")
TypeError: Couldn't cast array of type struct<pxd: string, term: string, category: string, modification: string, column: string, query: string> to string
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 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 1919, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
messages list | tools list |
|---|---|
[
{
"role": "system",
"content": "You are an expert proteomics SDRF metadata extraction agent. Your task is to extract structured metadata from proteomics papers and format it according to SDRF (Sample and Data Relationship Format) standards.\n\nYour workflow:\n1. First call pride_lookup to get authoritative ... | [
{
"type": "function",
"function": {
"name": "pride_lookup",
"description": "Fetch authoritative metadata from the PRIDE proteomics repository for a given PXD accession. Returns instruments, organisms, modifications, and quantification methods.",
"parameters": {
"type": "object",
... |
[
{
"role": "system",
"content": "You are an expert proteomics SDRF metadata extraction agent. Your task is to extract structured metadata from proteomics papers and format it according to SDRF (Sample and Data Relationship Format) standards.\n\nYour workflow:\n1. First call pride_lookup to get authoritative ... | [
{
"type": "function",
"function": {
"name": "pride_lookup",
"description": "Fetch authoritative metadata from the PRIDE proteomics repository for a given PXD accession. Returns instruments, organisms, modifications, and quantification methods.",
"parameters": {
"type": "object",
... |
[
{
"role": "system",
"content": "You are an expert proteomics SDRF metadata extraction agent. Your task is to extract structured metadata from proteomics papers and format it according to SDRF (Sample and Data Relationship Format) standards.\n\nYour workflow:\n1. First call pride_lookup to get authoritative ... | [
{
"type": "function",
"function": {
"name": "pride_lookup",
"description": "Fetch authoritative metadata from the PRIDE proteomics repository for a given PXD accession. Returns instruments, organisms, modifications, and quantification methods.",
"parameters": {
"type": "object",
... |
[
{
"role": "system",
"content": "You are an expert proteomics SDRF metadata extraction agent. Your task is to extract structured metadata from proteomics papers and format it according to SDRF (Sample and Data Relationship Format) standards.\n\nYour workflow:\n1. First call pride_lookup to get authoritative ... | [
{
"type": "function",
"function": {
"name": "pride_lookup",
"description": "Fetch authoritative metadata from the PRIDE proteomics repository for a given PXD accession. Returns instruments, organisms, modifications, and quantification methods.",
"parameters": {
"type": "object",
... |
[
{
"role": "system",
"content": "You are an expert proteomics SDRF metadata extraction agent. Your task is to extract structured metadata from proteomics papers and format it according to SDRF (Sample and Data Relationship Format) standards.\n\nYour workflow:\n1. First call pride_lookup to get authoritative ... | [
{
"type": "function",
"function": {
"name": "pride_lookup",
"description": "Fetch authoritative metadata from the PRIDE proteomics repository for a given PXD accession. Returns instruments, organisms, modifications, and quantification methods.",
"parameters": {
"type": "object",
... |
[{"role":"system","content":"You are an expert proteomics SDRF metadata extraction agent. Your task (...TRUNCATED) | [{"type":"function","function":{"name":"pride_lookup","description":"Fetch authoritative metadata fr(...TRUNCATED) |
[{"role":"system","content":"You are an expert proteomics SDRF metadata extraction agent. Your task (...TRUNCATED) | [{"type":"function","function":{"name":"pride_lookup","description":"Fetch authoritative metadata fr(...TRUNCATED) |
[{"role":"system","content":"You are an expert proteomics SDRF metadata extraction agent. Your task (...TRUNCATED) | [{"type":"function","function":{"name":"pride_lookup","description":"Fetch authoritative metadata fr(...TRUNCATED) |
[{"role":"system","content":"You are an expert proteomics SDRF metadata extraction agent. Your task (...TRUNCATED) | [{"type":"function","function":{"name":"pride_lookup","description":"Fetch authoritative metadata fr(...TRUNCATED) |
[{"role":"system","content":"You are an expert proteomics SDRF metadata extraction agent. Your task (...TRUNCATED) | [{"type":"function","function":{"name":"pride_lookup","description":"Fetch authoritative metadata fr(...TRUNCATED) |
End of preview.
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