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The dataset generation failed
Error code: DatasetGenerationError
Exception: TypeError
Message: Couldn't cast array of type
struct<id: string, names: list<item: string>, dbLinks: struct<icd10: list<item: string>, mesh: list<item: string>>, category: string>
to
{'id': Value(dtype='string', id=None), 'names': Sequence(feature=Value(dtype='string', id=None), length=-1, id=None), 'dbLinks': {'icd10': Sequence(feature=Value(dtype='string', id=None), length=-1, id=None), 'mesh': Sequence(feature=Value(dtype='string', id=None), length=-1, id=None)}, 'category': Value(dtype='string', id=None), 'description': Value(dtype='string', id=None)}
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 2011, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 585, 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 2302, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2261, in cast_table_to_schema
arrays = [cast_array_to_feature(table[name], feature) for name, feature in features.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2261, in <listcomp>
arrays = [cast_array_to_feature(table[name], feature) for name, feature in features.items()]
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1802, in wrapper
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 1802, in <listcomp>
return pa.chunked_array([func(chunk, *args, **kwargs) for chunk in array.chunks])
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2122, in cast_array_to_feature
raise TypeError(f"Couldn't cast array of type\n{_short_str(array.type)}\nto\n{_short_str(feature)}")
TypeError: Couldn't cast array of type
struct<id: string, names: list<item: string>, dbLinks: struct<icd10: list<item: string>, mesh: list<item: string>>, category: string>
to
{'id': Value(dtype='string', id=None), 'names': Sequence(feature=Value(dtype='string', id=None), length=-1, id=None), 'dbLinks': {'icd10': Sequence(feature=Value(dtype='string', id=None), length=-1, id=None), 'mesh': Sequence(feature=Value(dtype='string', id=None), length=-1, id=None)}, 'category': Value(dtype='string', id=None), 'description': Value(dtype='string', id=None)}
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 1529, 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 1154, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1027, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1122, 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 1882, 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 2038, 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.
id string | disease dict | riskFactors list |
|---|---|---|
H00001 | {
"id": "H00001",
"names": [
"B-cell acute lymphoblastic leukemia",
"B-cell acute lymphocytic leukemia"
],
"dbLinks": {
"icd10": [
"C83.5",
"C91.0"
],
"mesh": [
"D054198"
]
},
"category": "Cancer",
"description": "Acute lymphocytic leukemia (ALL) is a clonal stem ... | [
{
"text": "obesity",
"score": 13.140652656555176,
"articlesIDs": [
"32706183"
]
},
{
"text": "underweight (or 2.11, 95% ci 1.56-2.85) and obesity",
"score": 13.092214584350586,
"articlesIDs": [
"32706183"
]
},
{
"text": "high viral burden with ebv",
"score... |
H00002 | {
"id": "H00002",
"names": [
"T-cell acute lymphoblastic leukemia",
"T-cell acute lymphocytic leukemia"
],
"dbLinks": {
"icd10": [
"C83.5",
"C91.0"
],
"mesh": [
"D054218"
]
},
"category": "Cancer",
"description": "Acute lymphocytic leukemia (ALL) is a clonal stem ... | [
{
"text": "patients with good-risk cytogenetics",
"score": 8.989250183105469,
"articlesIDs": [
"29131699"
]
},
{
"text": "patients with high-risk genetics",
"score": 6.717743873596191,
"articlesIDs": [
"29131699"
]
},
{
"text": "patients with high-risk genetic... |
H00003 | {
"id": "H00003",
"names": [
"Acute myeloid leukemia"
],
"dbLinks": {
"icd10": [
"C92.0"
],
"mesh": [
"D015470"
]
},
"category": "Cancer",
"description": "Acute myeloid leukemia (AML) is a disease that is characterized by uncontrolled proliferation of clonal neoplastic cell... | [
{
"text": "mutations in chip-related genes",
"score": 14.093645095825195,
"articlesIDs": [
"35492819"
]
},
{
"text": "active smoking",
"score": 14.088956832885742,
"articlesIDs": [
"35128571"
]
},
{
"text": "platelet count above 100 × 10/l and active smoking",... |
H00004 | {
"id": "H00004",
"names": [
"Chronic myeloid leukemia"
],
"dbLinks": {
"icd10": [
"C92.1"
],
"mesh": [
"D015464"
]
},
"category": "Cancer"
} | [
{
"text": "paternal grandfathers and grandmothers of people with achondroplasia",
"score": 14.025308609008789,
"articlesIDs": [
"15372518"
]
},
{
"text": "metabolically unhealthy obesity",
"score": 13.965067863464355,
"articlesIDs": [
"37114451"
]
},
{
"text":... |
H00005 | {
"id": "H00005",
"names": [
"Chronic lymphocytic leukemia",
"SUPERGRP Non-Hodgkin lymphoma [DS:H02418]"
],
"dbLinks": {
"icd10": [
"C91.1"
],
"mesh": [
"D015451"
]
},
"category": "Cancer"
} | [
{
"text": "relatives of mgus patients",
"score": 14.052873611450195,
"articlesIDs": [
"19182202"
]
},
{
"text": "patients with mgus",
"score": 14.029006004333496,
"articlesIDs": [
"9161471"
]
},
{
"text": "women with t2dm and with self-reported oral medication... |
H00006 | {
"id": "H00006",
"names": [
"Hairy cell leukemia",
"SUPERGRP Non-Hodgkin lymphoma [DS:H02418]"
],
"dbLinks": {
"icd10": [
"C91.4"
],
"mesh": [
"D007943"
]
},
"category": "Cancer"
} | [
{
"text": "patients with hairy cell leukemia",
"score": 13.864240646362305,
"articlesIDs": [
"17284716"
]
},
{
"text": "insecticides",
"score": 13.615367889404297,
"articlesIDs": [
"12148884",
"9667691"
]
},
{
"text": "fungicides",
"score": 13.531675... |
H00007 | {"id":"H00007","names":["Hodgkin lymphoma"],"dbLinks":{"icd10":["C81"],"mesh":["D006689"]},"category(...TRUNCATED) | [{"text":"patients with hiv infection","score":14.161015510559082,"articlesIDs":["25885746"]},{"text(...TRUNCATED) |
H00008 | {"id":"H00008","names":["Burkitt lymphoma","SUPERGRP Non-Hodgkin lymphoma [DS:H02418]","Primary cen(...TRUNCATED) | [{"text":"herbal medicine use","score":13.765249252319336,"articlesIDs":["32257153"]},{"text":"ranci(...TRUNCATED) |
H00009 | {"id":"H00009","names":["Adult T-cell leukemia"],"dbLinks":{"icd10":["C91.5"],"mesh":["D015459"]},"c(...TRUNCATED) | [{"text":"strongyloidiasis and idh","score":13.7511568069458,"articlesIDs":["23592987"]},{"text":"ch(...TRUNCATED) |
H00010 | {"id":"H00010","names":["Multiple myeloma"],"dbLinks":{"icd10":["C90.0"],"mesh":["D009101"]},"catego(...TRUNCATED) | [{"text":"patients with as","score":14.083839416503906,"articlesIDs":["27534810"]},{"text":"patients(...TRUNCATED) |
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