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The dataset generation failed because of a cast error
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 2 new columns ({'contact', 'contact is a subobject level module. It is a field in the project entity.'}) and 2 missing columns ({'This is a subobject module used in the sample entity', 'cell_line'}).
This happened while the csv dataset builder was generating data using
hf://datasets/introvoyz041/Humancellatlas/data/infrastructure_testing_files/archive/v3/v3_.contact.tsv (at revision 00a9bc3dbbcbca2a4a78f5cc45be849329dbf879)
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 1870, in _prepare_split_single
writer.write_table(table)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/arrow_writer.py", line 622, 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 2292, in table_cast
return cast_table_to_schema(table, schema)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/table.py", line 2240, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
contact: string
contact is a subobject level module. It is a field in the project entity.: string
Unnamed: 2: string
Unnamed: 3: string
Unnamed: 4: string
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 980
to
{'cell_line': Value(dtype='string', id=None), 'This is a subobject module used in the sample entity': Value(dtype='string', id=None), 'Unnamed: 2': Value(dtype='string', id=None), 'Unnamed: 3': Value(dtype='string', id=None), 'Unnamed: 4': Value(dtype='string', id=None)}
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 1438, 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 1050, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 924, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1000, 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 1741, 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 1872, 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 2 new columns ({'contact', 'contact is a subobject level module. It is a field in the project entity.'}) and 2 missing columns ({'This is a subobject module used in the sample entity', 'cell_line'}).
This happened while the csv dataset builder was generating data using
hf://datasets/introvoyz041/Humancellatlas/data/infrastructure_testing_files/archive/v3/v3_.contact.tsv (at revision 00a9bc3dbbcbca2a4a78f5cc45be849329dbf879)
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)Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
cell_line
string | This is a subobject module used in the sample entity
string | Unnamed: 2
string | Unnamed: 3
string | Unnamed: 4
string |
|---|---|---|---|---|
Information about the cell line used in the sample | null | null | null | null |
null | null | null | null | null |
Field Name | source | Priority | Type | Description |
core | ingest | required | core module | schema for cell_line |
null | null | null | null | null |
derived_from | submitter | optional | local id | Which other cell_line is this cell_line derived from, if available |
name | submitter | Required | ontology | what is the official name for the cell line? |
catalogue_number | submitter | High | ext id | the supplier catalogue number for the cell line |
catalogue_url | submitter | High | url | the supplier catalogue url for the cell line |
passage_number | submitter | High | int | how many passages the cell line as been through |
date_established | submitter | High | date | when was the cell line established |
publication | submitter | High | module | in what publication was the cell line creation cited |
cell_type | submitter | optional | ontology | what cell type was the line derived from, CLO ontology usually |
culture_protocol | submitter | High | protocol | pointer to the culture protocol |
disease | submitter | optional | ontology | text describing disease association, preferable a disease found in EFO |
karyotype | submitter | optional | text | the karyotype of the cell line |
null | null | null | null | null |
null | null | null | null | null |
null | null | Priority | Type | Description |
null | null | Required | core module | The schema definition for a contact |
null | null | Required | local id | Unique ID for this contact |
null | null | null | null | null |
null | null | Optional | text | Full mailing address except for name. Includes city, state, postal code, country. |
null | null | Optional | text | City name. See also contact.address |
null | null | Optional | text | Country (USA or UK for those countries, otherwise spelled out) |
null | null | Optional | text | State in the USA, provence, canton, or other subdivisions for other countries. |
null | null | Optional | text | Email of contact for contributingauthors |
null | null | High | text | Name of primary institute where contact works |
null | null | High | text | Name of lab (often the PI name) within institute where contact works |
null | null | Required | text | Text formatted with first name, middle, last in that order separated by commas. Usually middle is just an initial. |
null | null | null | null | null |
null | null | null | null | null |
null | null | Priority | Type | Description |
null | null | required | CV | A name for the type of object/module. By convention also the file name (without dir or extension) of json schema or entity level metadata file |
null | null | required | text | Version number in major.minor.patch format. Example 3.2.4. Major version changes likely require change to software. Patches are just documentation changes |
null | null | required | url | URL of json schema document that validates this version of this module. |
null | null | null | null | null |
null | null | null | null | null |
null | null | Priority | Type | Description |
null | null | required | core module | schema description for death module |
null | null | null | null | null |
null | null | required | ontology | Cause of death from death report for human donor, from research lab for mouse. Text is straight from death certificate. Same ontology used as donor.disease |
null | null | required | timestamp | Date and time of death on death certificate for deceased donor |
null | null | High | number | 0 - ventilator case, 1 - fast death -violent, 2 - fast-death -natural causes, 3 - intermediate death, 4 - slow death |
null | null | High | yes/no | If yes, was perfused with cold fluid to help preserve tissues before heart stopped |
null | null | High | number | Days on ventilator before dying |
null | null | null | null | null |
null | null | null | null | null |
null | null | Priority | Type | Description |
null | null | Required | core module | The schema definition for a donor |
null | null | Required? | internal id | A unique ID for this donor |
null | null | null | null | null |
null | null | Required | ontology | Scientific binomial name of donor species in text field, NCBI taxon in ontology field |
null | null | High | CV | Sex of donor. Either 'male' 'female' 'mixed' or 'unknown' |
null | null | High | number | Age in age_units. Expressed since birth. For embyos measured since fertilization. |
null | null | High | CV | Unit age is expressed, typically day, week, month, or year |
null | null | High | CV | adult "child" or "embryo" |
null | null | High | ontology | More detailed (especially for embryos) version of life_stage. Might be "E9" or "P17" for a mouse. |
null | null | High Human | array of ontology | term from https://www.ebi.ac.uk/ols/ontologies/ancestro |
null | null | High Mouse | array of ontology | Mouse inbred strain. Example C57BL/6. |
null | null | High Mouse, Low human | text | Genotype. List of genetic changes from usual. Should be strain, cross and genetic modification info in MGI format for mice. |
null | null | Required? | text | Free format string to help link back to submitter's donor database. |
null | null | null | null | null |
null | null | Optional | number | Height of donor in meters |
null | null | Optional | number | Weight of donor in kg |
null | null | Optional | number | Body mass index of donor |
null | null | null | null | null |
null | null | Required | yes/no | If yes donor is living at time of sample donation. |
null | null | Required if not living | module | Information about conditions of death (or info that donor was living at time of collection) |
null | null | High | array of ontology | Short description of disease status of individual. |
null | null | Optional | array of ontology | List of medications donor is on |
null | null | High | CV | Normal, fasting, feeding tube removed, etc |
null | null | High | text | Number of drinks consumed on a typical day |
null | null | High | text | Estimated # of cigarattes smoked per day and for how many years |
null | null | null | null | null |
null | null | high | protocol | protocol accession for how donors were recruited |
null | null | null | null | null |
null | null | null | null | null |
null | source | Priority | Type | Description |
null | submit | required | core module | schema for this object |
null | null | null | null | null |
null | submit | required | CV | How enrichment was achieved. MACS, FACS, filter, etc |
null | submit | optional | text | Text in the format of space delimited list of markers with +/-. Example: "CD4+ CD8-" |
null | submit | optional | number | Minimum size passing selection in microns |
null | submit | optional | number | Maximum size passing selection in microns |
null | submit | High | protocol | Refers to an enrichment protocol |
null | null | null | null | null |
null | null | null | null | null |
null | null | null | null | null |
null | null | Priority | Applies to | Type |
null | null | required | all | core module |
null | null | null | null | null |
null | null | High | all | text |
null | null | Optional | all | number |
null | null | Req | all | array of pos int |
null | null | High | all | array of pos int |
null | null | Req | all | array of pos int |
null | null | High | all | text |
null | null | High | all | CV |
null | null | null | null | null |
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