Datasets:

---

hlnicholls

/

GenePrioritiser-db

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 1 new columns ({'label_encoded'}) and 49 missing columns ({'SkinSunExposedLowerleg_GTExTPM', 'ColonSigmoid_GTExTPM', 'BrainFrontalCortexBA9_GTExTPM', 'BrainCortex_GTExTPM', 'BrainAnteriorcingulatecortexBA24_GTExTPM', 'Lung_GTExTPM', 'Vagina_GTExTPM', 'Uterus_GTExTPM', 'AdiposeSubcutaneous_GTExTPM', 'BrainCaudatebasalganglia_GTExTPM', 'BrainSubstantianigra_GTExTPM', 'AdiposeVisceralOmentum_GTExTPM', 'CervixEndocervix_GTExTPM', 'humancellsensitivity', 'huge_htn_bioindex', 'Ovary_GTExTPM', 'ArteryAorta_GTExTPM', 'BrainCerebellarHemisphere_GTExTPM', 'humancellspecificity', 'BreastMammaryTissue_GTExTPM', 'CervixEctocervix_GTExTPM', 'Stomach_GTExTPM', 'label', 'BrainAmygdala_GTExTPM', 'KidneyCortex_GTExTPM', 'Thyroid_GTExTPM', 'NerveTibial_GTExTPM', 'BrainCerebellum_GTExTPM', 'BrainHypothalamus_GTExTPM', 'ColonTransverse_GTExTPM', 'EsophagusGastroesophagealJunction_GTExTPM', 'gene_damage_index_score', 'MinorSalivaryGland_GTExTPM', 'BrainHippocampus_GTExTPM', 'EsophagusMuscularis_GTExTPM', 'SkinNotSunExposedSuprapubic_GTExTPM', 'panglao_ubiquitousness_index', 'mousecellsensitivity', 'BrainNucleusaccumbensbasalganglia_GTExTPM', 'SDI_essentiality', 'ArteryCoronary_GTExTPM', 'BrainPutamenbasalganglia_GTExTPM', 'SmallIntestineTerminalIleum_GTExTPM', 'mousecellspecificity', 'Prostate_GTExTPM', 'Bladder_GTExTPM', 'ArteryTibial_GTExTPM', 'HeartAtrialAppendage_GTExTPM', 'Pancreas_GTExTPM'}).

This happened while the csv dataset builder was generating data using

hf://datasets/hlnicholls/GenePrioritiser-db/example/machine_learning/eda/output/cleaned_training_data.csv (at revision 61c95b348eea7cb8b9b6dd9fca3d79694707682e)

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 "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1831, in _prepare_split_single
                  writer.write_table(table)
                File "/usr/local/lib/python3.12/site-packages/datasets/arrow_writer.py", line 714, 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 2218, in cast_table_to_schema
                  raise CastError(
              datasets.table.CastError: Couldn't cast
              Gene: string
              label_encoded: double
              BrainSpinalcordcervicalc1_GTExTPM: double
              KidneyMedulla_GTExTPM: double
              HeartLeftVentricle_GTExTPM: double
              FallopianTube_GTExTPM: double
              Liver_GTExTPM: double
              EsophagusMucosa_GTExTPM: double
              CellsEBVtransformedlymphocytes_GTExTPM: double
              CellsCulturedfibroblasts_GTExTPM: double
              MuscleSkeletal_GTExTPM: double
              Testis_GTExTPM: double
              Spleen_GTExTPM: double
              Pituitary_GTExTPM: double
              WholeBlood_GTExTPM: double
              AdrenalGland_GTExTPM: double
              GDI_Phred: double
              Effect_SBP_Median: double
              Effect_PP_Median: double
              Effect_DBP_Median: double
              HIPred_haploinsufficiency: double
              pLI_exac: double
              SDI_Drug_Probability: double
              ExomiserScore_IncreasedBP_MultiHPOTerms: double
              ExomiserScore_DecreasedBP_MultiHPOTerms: double
              RVIS_genic_intolerance: double
              -- schema metadata --
              pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 3968
              to
              {'Gene': Value('string'), 'label': Value('string'), 'HIPred_haploinsufficiency': Value('float64'), 'Effect_DBP_Median': Value('float64'), 'Effect_PP_Median': Value('float64'), 'Effect_SBP_Median': Value('float64'), 'ExomiserScore_DecreasedBP_MultiHPOTerms': Value('float64'), 'ExomiserScore_IncreasedBP_MultiHPOTerms': Value('float64'), 'SDI_essentiality': Value('float64'), 'SDI_Drug_Probability': Value('float64'), 'humancellsensitivity': Value('float64'), 'humancellspecificity': Value('float64'), 'mousecellsensitivity': Value('float64'), 'mousecellspecificity': Value('float64'), 'panglao_ubiquitousness_index': Value('float64'), 'gene_damage_index_score': Value('float64'), 'GDI_Phred': Value('float64'), 'huge_htn_bioindex': Value('float64'), 'pLI_exac': Value('float64'), 'RVIS_genic_intolerance': Value('float64'), 'AdiposeSubcutaneous_GTExTPM': Value('float64'), 'AdiposeVisceralOmentum_GTExTPM': Value('float64'), 'AdrenalGland_GTExTPM': Value('float64'), 'ArteryAorta_GTExTPM': Value('float64'), 'ArteryCoronary_GTExTPM': Value('float64'), 'ArteryTibial_GTExTPM': Value('float64'), 'Bladder_GTExTPM': Value('float64'), 'BrainAmygdala_GTExTPM': Value('float64'), 'BrainAnteriorcingulatecortexBA24_GTExTPM': Value('float64'), 'BrainCaudatebasalganglia_GTExTPM': Value('float64'), 'BrainCerebellarHemisphere_GTExTPM': Value('float64'), 'BrainCerebellum_GTExTPM': Value('float64'), 'BrainCortex_GTExTPM': Value('float64'), 'BrainFrontalCortexBA9_GTExTPM': Value('float64'), 'BrainHippocampus_
              ...
              'BreastMammaryTissue_GTExTPM': Value('float64'), 'CellsCulturedfibroblasts_GTExTPM': Value('float64'), 'CellsEBVtransformedlymphocytes_GTExTPM': Value('float64'), 'CervixEctocervix_GTExTPM': Value('float64'), 'CervixEndocervix_GTExTPM': Value('float64'), 'ColonSigmoid_GTExTPM': Value('float64'), 'ColonTransverse_GTExTPM': Value('float64'), 'EsophagusGastroesophagealJunction_GTExTPM': Value('float64'), 'EsophagusMucosa_GTExTPM': Value('float64'), 'EsophagusMuscularis_GTExTPM': Value('float64'), 'FallopianTube_GTExTPM': Value('float64'), 'HeartAtrialAppendage_GTExTPM': Value('float64'), 'HeartLeftVentricle_GTExTPM': Value('float64'), 'KidneyCortex_GTExTPM': Value('float64'), 'KidneyMedulla_GTExTPM': Value('float64'), 'Liver_GTExTPM': Value('float64'), 'Lung_GTExTPM': Value('float64'), 'MinorSalivaryGland_GTExTPM': Value('float64'), 'MuscleSkeletal_GTExTPM': Value('float64'), 'NerveTibial_GTExTPM': Value('float64'), 'Ovary_GTExTPM': Value('float64'), 'Pancreas_GTExTPM': Value('float64'), 'Pituitary_GTExTPM': Value('float64'), 'Prostate_GTExTPM': Value('float64'), 'SkinNotSunExposedSuprapubic_GTExTPM': Value('float64'), 'SkinSunExposedLowerleg_GTExTPM': Value('float64'), 'SmallIntestineTerminalIleum_GTExTPM': Value('float64'), 'Spleen_GTExTPM': Value('float64'), 'Stomach_GTExTPM': Value('float64'), 'Testis_GTExTPM': Value('float64'), 'Thyroid_GTExTPM': Value('float64'), 'Uterus_GTExTPM': Value('float64'), 'Vagina_GTExTPM': Value('float64'), 'WholeBlood_GTExTPM': Value('float64')}
              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 1455, 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 1054, in convert_to_parquet
                  builder.download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 894, in download_and_prepare
                  self._download_and_prepare(
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 970, in _download_and_prepare
                  self._prepare_split(split_generator, **prepare_split_kwargs)
                File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1702, 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 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 1 new columns ({'label_encoded'}) and 49 missing columns ({'SkinSunExposedLowerleg_GTExTPM', 'ColonSigmoid_GTExTPM', 'BrainFrontalCortexBA9_GTExTPM', 'BrainCortex_GTExTPM', 'BrainAnteriorcingulatecortexBA24_GTExTPM', 'Lung_GTExTPM', 'Vagina_GTExTPM', 'Uterus_GTExTPM', 'AdiposeSubcutaneous_GTExTPM', 'BrainCaudatebasalganglia_GTExTPM', 'BrainSubstantianigra_GTExTPM', 'AdiposeVisceralOmentum_GTExTPM', 'CervixEndocervix_GTExTPM', 'humancellsensitivity', 'huge_htn_bioindex', 'Ovary_GTExTPM', 'ArteryAorta_GTExTPM', 'BrainCerebellarHemisphere_GTExTPM', 'humancellspecificity', 'BreastMammaryTissue_GTExTPM', 'CervixEctocervix_GTExTPM', 'Stomach_GTExTPM', 'label', 'BrainAmygdala_GTExTPM', 'KidneyCortex_GTExTPM', 'Thyroid_GTExTPM', 'NerveTibial_GTExTPM', 'BrainCerebellum_GTExTPM', 'BrainHypothalamus_GTExTPM', 'ColonTransverse_GTExTPM', 'EsophagusGastroesophagealJunction_GTExTPM', 'gene_damage_index_score', 'MinorSalivaryGland_GTExTPM', 'BrainHippocampus_GTExTPM', 'EsophagusMuscularis_GTExTPM', 'SkinNotSunExposedSuprapubic_GTExTPM', 'panglao_ubiquitousness_index', 'mousecellsensitivity', 'BrainNucleusaccumbensbasalganglia_GTExTPM', 'SDI_essentiality', 'ArteryCoronary_GTExTPM', 'BrainPutamenbasalganglia_GTExTPM', 'SmallIntestineTerminalIleum_GTExTPM', 'mousecellspecificity', 'Prostate_GTExTPM', 'Bladder_GTExTPM', 'ArteryTibial_GTExTPM', 'HeartAtrialAppendage_GTExTPM', 'Pancreas_GTExTPM'}).
              
              This happened while the csv dataset builder was generating data using
              
              hf://datasets/hlnicholls/GenePrioritiser-db/example/machine_learning/eda/output/cleaned_training_data.csv (at revision 61c95b348eea7cb8b9b6dd9fca3d79694707682e)
              
              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)