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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 4 new columns ({'pval', 'setsize', 'score', 'overlap'}) and 8 missing columns ({'overlap_std', 'setsize_mean', 'score_mean', 'overlap_mean', 'score_std', 'setsize_std', 'pval_std', 'pval_mean'}).
This happened while the csv dataset builder was generating data using
hf://datasets/ligdis/msigdb_hp/fragment/C001/C001_val_log2fc/harmon.tsv (at revision 84efb8bf2fbd6097f5ecd1ad560e6024144b454c)
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
term: string
overlap: int64
setsize: int64
score: double
pval: double
-- schema metadata --
pandas: '{"index_columns": [{"kind": "range", "name": null, "start": 0, "' + 812
to
{'term': Value(dtype='string', id=None), 'overlap_mean': Value(dtype='float64', id=None), 'setsize_mean': Value(dtype='float64', id=None), 'score_mean': Value(dtype='float64', id=None), 'pval_mean': Value(dtype='float64', id=None), 'overlap_std': Value(dtype='float64', id=None), 'setsize_std': Value(dtype='float64', id=None), 'score_std': Value(dtype='float64', id=None), 'pval_std': Value(dtype='float64', 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 1433, in compute_config_parquet_and_info_response
parquet_operations, partial, estimated_dataset_info = stream_convert_to_parquet(
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 989, in stream_convert_to_parquet
builder._prepare_split(
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 4 new columns ({'pval', 'setsize', 'score', 'overlap'}) and 8 missing columns ({'overlap_std', 'setsize_mean', 'score_mean', 'overlap_mean', 'score_std', 'setsize_std', 'pval_std', 'pval_mean'}).
This happened while the csv dataset builder was generating data using
hf://datasets/ligdis/msigdb_hp/fragment/C001/C001_val_log2fc/harmon.tsv (at revision 84efb8bf2fbd6097f5ecd1ad560e6024144b454c)
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.
term
string | overlap_mean
float64 | setsize_mean
float64 | score_mean
float64 | pval_mean
float64 | overlap_std
float64 | setsize_std
float64 | score_std
float64 | pval_std
float64 |
|---|---|---|---|---|---|---|---|---|
11 pairs of ribs
| 2.701456
| 8.757282
| -0.189585
| 0.540782
| 1.699714
| 1.597729
| 0.821137
| 0.267224
|
2 3 finger syndactyly
| 1.533981
| 2
| -0.792993
| 0.389605
| 0.608444
| 0
| 1.237917
| 0.312929
|
2 3 toe cutaneous syndactyly
| 1.254854
| 2.359223
| -0.300634
| 0.57278
| 0.776225
| 0.541561
| 0.986723
| 0.323921
|
2 3 toe syndactyly
| 6.213592
| 28.966019
| 0.057491
| 0.610547
| 3.538692
| 4.239643
| 0.798758
| 0.298554
|
3 4 finger syndactyly
| 1.555825
| 2.065534
| -0.796947
| 0.39642
| 0.62651
| 0.247466
| 1.222439
| 0.314538
|
3 methylglutaconic aciduria
| 4.072816
| 10.59466
| 0.357997
| 0.437157
| 2.217437
| 1.562072
| 1.156622
| 0.333067
|
4 5 toe syndactyly
| 0.486618
| 1.065693
| 0.162144
| 0.360908
| 0.537355
| 0.247745
| 1.545466
| 0.310041
|
Abdominal aortic aneurysm
| 1.206311
| 3.271845
| 0.117309
| 0.571185
| 0.954631
| 0.861182
| 0.918099
| 0.310527
|
Abdominal distention
| 5.485437
| 22.050971
| -0.000334
| 0.418335
| 2.797759
| 3.545793
| 1.149073
| 0.286161
|
Abdominal obesity
| 2.058252
| 4.798544
| -0.196413
| 0.614933
| 1.397468
| 1.393709
| 0.748738
| 0.284359
|
Abdominal pain
| 16.963592
| 83.165049
| 0.396476
| 0.643072
| 7.055682
| 7.33769
| 0.778449
| 0.33546
|
Abdominal wall muscle weakness
| 1.502427
| 3.165049
| -0.178542
| 0.566193
| 1.050887
| 1.050632
| 0.982175
| 0.314786
|
Abducens palsy
| 1.123786
| 3.51699
| 0.766698
| 0.334899
| 0.80756
| 0.774097
| 1.133151
| 0.265455
|
Abnormal 2nd finger morphology
| 1.529126
| 5.332524
| 0.227375
| 0.524692
| 1.164452
| 1.306671
| 0.884708
| 0.289125
|
Abnormal 3rd finger morphology
| 1.145631
| 2.495146
| -0.072353
| 0.600135
| 0.811421
| 0.555184
| 0.951162
| 0.318888
|
Abnormal 4th finger morphology
| 0.414634
| 1
| 0.293677
| 0.285326
| 0.492659
| 0
| 2.337194
| 0.313334
|
Abnormal 5th finger morphology
| 22.308252
| 101.475728
| -0.239555
| 0.713044
| 9.363979
| 13.633977
| 0.591201
| 0.289767
|
Abnormal 5th finger phalanx morphology
| 0.342233
| 1.429612
| 1.082293
| 0.264627
| 0.54136
| 0.528229
| 1.787469
| 0.32153
|
Abnormal abdomen morphology
| 45.247573
| 217.067961
| 0.2638
| 0.676492
| 15.116598
| 20.132335
| 0.885374
| 0.35641
|
Abnormal acetabulum morphology
| 4.415049
| 19.133495
| 0.472611
| 0.552885
| 2.401469
| 2.890249
| 0.771053
| 0.306292
|
Abnormal activity of mitochondrial respiratory chain
| 14.847087
| 52.864078
| 0.782114
| 0.382258
| 7.203924
| 5.319954
| 1.504982
| 0.363538
|
Abnormal adipose tissue morphology
| 12.575243
| 57.072816
| 0.136134
| 0.730484
| 4.941077
| 5.644358
| 0.60914
| 0.286634
|
Abnormal aggressive impulsive or violent behavior
| 24.281553
| 100.769417
| -0.364371
| 0.669485
| 9.895736
| 11.143928
| 0.634582
| 0.302979
|
Abnormal aldolase level
| 0.951456
| 2.866505
| 0.072876
| 0.573972
| 0.780573
| 0.855675
| 0.999028
| 0.320306
|
Abnormal anatomic location of the heart
| 2.742718
| 11.225728
| 0.257241
| 0.583054
| 1.98705
| 2.123612
| 0.739862
| 0.266688
|
Abnormal anterior chamber morphology
| 1.203883
| 4.281553
| 0.294395
| 0.473586
| 1.0826
| 1.001625
| 0.97318
| 0.286665
|
Abnormal anterior eye segment morphology
| 57.866505
| 302.643204
| 0.060291
| 0.859855
| 17.401711
| 32.399679
| 0.464978
| 0.248331
|
Abnormal anterior horn cell morphology
| 1.497573
| 6.407767
| 0.004582
| 0.515444
| 1.298802
| 0.656364
| 0.935128
| 0.282986
|
Abnormal aortic arch morphology
| 2.679612
| 11.15534
| 0.234941
| 0.587959
| 2.098143
| 2.188927
| 0.764807
| 0.283557
|
Abnormal aortic morphology
| 25.796117
| 107.012136
| -0.252033
| 0.702074
| 10.503452
| 11.816039
| 0.608858
| 0.288026
|
Abnormal aortic valve cusp morphology
| 5.524272
| 24.201456
| 0.117121
| 0.738458
| 3.399299
| 2.286664
| 0.557011
| 0.261783
|
Abnormal aortic valve morphology
| 8.643204
| 40.009709
| 0.377138
| 0.601301
| 3.379173
| 4.169923
| 0.768266
| 0.321057
|
Abnormal aortic valve physiology
| 8.133495
| 38.407767
| 0.316424
| 0.583213
| 3.634936
| 4.470913
| 0.857067
| 0.329027
|
Abnormal arachnoid mater morphology
| 2.18932
| 8.786408
| 0.133216
| 0.585975
| 1.908866
| 1.449141
| 0.780477
| 0.279974
|
Abnormal arm span
| 1.253102
| 2.404467
| -0.343272
| 0.469998
| 0.961006
| 0.972413
| 1.199212
| 0.335653
|
Abnormal arterial physiology
| 6.218447
| 26.953883
| 0.679997
| 0.487142
| 2.869466
| 2.460426
| 0.863011
| 0.326428
|
Abnormal astrocyte morphology
| 3.541262
| 16.208738
| 0.473153
| 0.467513
| 2.354658
| 2.560932
| 1.084797
| 0.335645
|
Abnormal atrial arrangement
| 0.800971
| 1.524272
| -0.050932
| 0.392668
| 0.692679
| 0.61683
| 1.518788
| 0.318282
|
Abnormal atrioventricular conduction
| 3.305825
| 13.5
| 0.803491
| 0.408374
| 2.003314
| 1.76605
| 0.775383
| 0.278263
|
Abnormal atrioventricular connection
| 0.166667
| 1
| 1.685456
| 0.0357
| 0.372678
| 0
| 2.331935
| 0.065446
|
Abnormal atrioventricular valve morphology
| 8.296117
| 34.550971
| 0.355961
| 0.63883
| 3.185173
| 4.188498
| 0.695108
| 0.309289
|
Abnormal atrioventricular valve physiology
| 12.565534
| 48.907767
| 0.153994
| 0.593644
| 4.945634
| 6.038408
| 0.83744
| 0.314868
|
Abnormal auditory evoked potentials
| 2.837379
| 8.453883
| 0.811336
| 0.296638
| 1.54708
| 1.31286
| 1.172223
| 0.281399
|
Abnormal autonomic nervous system physiology
| 8.247573
| 32.320388
| 0.463848
| 0.450999
| 3.005152
| 3.650279
| 1.08996
| 0.324987
|
Abnormal b cell morphology
| 2.643204
| 9.699029
| 0.275065
| 0.513101
| 2.039983
| 1.596932
| 0.92929
| 0.299113
|
Abnormal b cell subset distribution
| 1.31068
| 2.893204
| 0.251756
| 0.581329
| 0.935068
| 0.746027
| 0.937666
| 0.313143
|
Abnormal basal ganglia mri signal intensity
| 7.813107
| 28.429612
| 0.15173
| 0.471205
| 4.645336
| 3.364203
| 1.195577
| 0.327486
|
Abnormal basophil count
| 0.328358
| 1
| 0.721651
| 0.151014
| 0.469616
| 0
| 2.159251
| 0.221835
|
Abnormal basophil morphology
| 0.423729
| 1.211864
| 0.521107
| 0.28937
| 0.543167
| 0.408629
| 1.771036
| 0.3063
|
Abnormal biliary tract morphology
| 7.427184
| 23.174757
| 1.329418
| 0.249884
| 2.892414
| 2.044064
| 1.339382
| 0.298439
|
Abnormal bleeding
| 21.043689
| 103.148058
| 0.320518
| 0.663871
| 7.482863
| 10.194703
| 0.747313
| 0.339693
|
Abnormal blistering of the skin
| 4.90534
| 20.822816
| -0.024129
| 0.614081
| 2.868183
| 2.796524
| 0.776123
| 0.289403
|
Abnormal blood carbon dioxide level
| 0.410194
| 1
| 0.289799
| 0.229693
| 0.491869
| 0
| 1.872444
| 0.253585
|
Abnormal blood chloride concentration
| 1.643204
| 2.623786
| -0.354504
| 0.560632
| 0.84266
| 0.484435
| 0.91064
| 0.301049
|
Abnormal blood folate concentration
| 0.692308
| 1
| -0.932917
| 0.191585
| 0.461538
| 0
| 1.828223
| 0.208424
|
Abnormal blood gas level
| 1.330097
| 3.050971
| 0.012012
| 0.69203
| 0.915226
| 0.219938
| 0.716628
| 0.289889
|
Abnormal blood glucose concentration
| 21.191748
| 91.735437
| -0.448994
| 0.463062
| 10.201591
| 8.705004
| 1.182057
| 0.340069
|
Abnormal blood inorganic cation concentration
| 10.002427
| 37.075243
| -0.125466
| 0.723637
| 4.564797
| 4.066399
| 0.638026
| 0.284982
|
Abnormal blood ion concentration
| 15.878641
| 68.004854
| -0.052563
| 0.768448
| 6.16125
| 6.793056
| 0.535454
| 0.264615
|
Abnormal blood monovalent inorganic cation concentration
| 4.793689
| 19.407767
| -0.063304
| 0.705176
| 2.988434
| 2.370682
| 0.61226
| 0.270576
|
Abnormal blood phosphate concentration
| 2.881068
| 8.606796
| -0.199437
| 0.634002
| 1.988543
| 1.501052
| 0.677929
| 0.267805
|
Abnormal blood potassium concentration
| 3.347087
| 12.546117
| -0.013286
| 0.644521
| 2.18188
| 1.747483
| 0.699019
| 0.274166
|
Abnormal blood sodium concentration
| 2.461165
| 9.75
| 0.155992
| 0.655603
| 2.161208
| 1.268791
| 0.649687
| 0.266357
|
Abnormal blood transition element cation concentration
| 3.34466
| 11.774272
| 0.368078
| 0.557965
| 2.097767
| 1.222769
| 0.77461
| 0.299157
|
Abnormal blood zinc concentration
| 0.822816
| 1
| -1.356658
| 0.218498
| 0.381825
| 0
| 1.560182
| 0.262549
|
Abnormal bone structure
| 37.417476
| 174.033981
| 0.505247
| 0.645109
| 11.181012
| 17.857685
| 0.878602
| 0.373142
|
Abnormal bowel sounds
| 0.827119
| 1.450847
| -0.480933
| 0.360914
| 0.622142
| 0.497578
| 1.661178
| 0.330032
|
Abnormal bowman capsule morphology
| 0.4
| 1
| 0.272802
| 0.079147
| 0.489898
| 0
| 2.665815
| 0.165357
|
Abnormal brain choline level by mrs
| 0.902913
| 2.944175
| 0.703362
| 0.335747
| 0.724261
| 0.229584
| 1.21392
| 0.279503
|
Abnormal brain lactate level by mrs
| 3.235437
| 10.376214
| 0.613311
| 0.440749
| 1.992804
| 1.682785
| 0.949118
| 0.305887
|
Abnormal brain n acetyl aspartate level by mrs
| 0.92233
| 2.978155
| 0.700849
| 0.333665
| 0.743115
| 0.290645
| 1.220314
| 0.279977
|
Abnormal brain positron emission tomography
| 1.987864
| 4.968447
| -0.203332
| 0.528105
| 1.376766
| 1.49318
| 0.895253
| 0.296948
|
Abnormal brainstem morphology
| 19.606796
| 86.769417
| 0.199264
| 0.741612
| 6.876917
| 8.90335
| 0.603552
| 0.291602
|
Abnormal brainstem mri signal intensity
| 6.252427
| 20.322816
| 0.946686
| 0.334812
| 2.907868
| 2.582646
| 1.124162
| 0.296709
|
Abnormal branching pattern of the aortic arch
| 0.918919
| 2.32973
| 0.130781
| 0.483444
| 0.831098
| 1.031626
| 1.300161
| 0.331521
|
Abnormal breath sound
| 3.803398
| 10.140777
| -0.623917
| 0.446836
| 2.030756
| 1.937015
| 0.900299
| 0.304769
|
Abnormal bronchoalveolar lavage fluid morphology
| 1.449029
| 2.01699
| -0.536176
| 0.563729
| 0.678966
| 0.129235
| 0.983615
| 0.320172
|
Abnormal bronchus morphology
| 6.429612
| 21.36165
| -0.237474
| 0.608506
| 3.422853
| 3.246026
| 0.738919
| 0.283126
|
Abnormal bronchus physiology
| 1.769417
| 4.628641
| -0.198873
| 0.568977
| 1.268642
| 1.252359
| 0.860149
| 0.299253
|
Abnormal c peptide level
| 1.546117
| 4.041262
| 0.184008
| 0.559409
| 1.21292
| 0.697253
| 0.934242
| 0.316892
|
Abnormal c reactive protein level
| 1.764563
| 4.606796
| -0.156435
| 0.470898
| 1.32943
| 1.174466
| 1.097451
| 0.317118
|
Abnormal calcification of the carpal bones
| 0.345291
| 1.116592
| 0.974028
| 0.140352
| 0.484803
| 0.320933
| 2.234827
| 0.244397
|
Abnormal calcium phosphate regulating hormone level
| 3.776699
| 10.038835
| -0.454476
| 0.584169
| 2.189702
| 1.175579
| 0.690973
| 0.300114
|
Abnormal cardiac atrium morphology
| 35.458738
| 145.18932
| -0.315503
| 0.701763
| 13.537461
| 14.563989
| 0.532757
| 0.278859
|
Abnormal cardiac exercise stress test
| 0.508251
| 1.244224
| 0.21344
| 0.226855
| 0.525675
| 0.429626
| 2.092389
| 0.286325
|
Abnormal cardiac septum morphology
| 43.723301
| 202.395631
| -0.253444
| 0.775801
| 16.247812
| 20.242853
| 0.459427
| 0.270085
|
Abnormal cardiac test
| 4.65534
| 16.961165
| -0.063488
| 0.612955
| 2.509718
| 2.328266
| 0.7707
| 0.284687
|
Abnormal cardiac ventricle morphology
| 35.660194
| 187.735437
| -0.023239
| 0.869461
| 12.218125
| 18.119222
| 0.398751
| 0.221441
|
Abnormal cardiac ventricular function
| 5.262136
| 18.648058
| 0.656148
| 0.406351
| 2.801564
| 3.037775
| 1.060802
| 0.302693
|
Abnormal cardiomyocyte morphology
| 0.912621
| 1.915049
| -0.59127
| 0.374488
| 0.613074
| 0.700254
| 1.545851
| 0.331886
|
Abnormal carotid artery morphology
| 3.40534
| 15.643204
| -0.024119
| 0.680699
| 2.479679
| 2.424867
| 0.647319
| 0.25954
|
Abnormal cartilage morphology
| 3.199029
| 12.252427
| 0.246333
| 0.491691
| 1.93817
| 1.234366
| 1.034965
| 0.295646
|
Abnormal caudate nucleus morphology
| 2.851942
| 10.133495
| 0.463001
| 0.463563
| 1.703771
| 1.77746
| 0.989157
| 0.313177
|
Abnormal cd4 cd8 ratio
| 1.745146
| 5.269417
| 0.076703
| 0.574888
| 1.336784
| 0.783778
| 0.826516
| 0.287244
|
Abnormal cell morphology
| 2.014563
| 5.148058
| -0.529952
| 0.453712
| 1.236493
| 1.405579
| 0.939479
| 0.298889
|
Abnormal cell proliferation
| 1.725728
| 3.910194
| -0.145298
| 0.5809
| 1.155409
| 0.92652
| 0.85991
| 0.306374
|
Abnormal cellular composition of bronchoalveolar fluid
| 0.754854
| 1
| -1.013823
| 0.258046
| 0.430174
| 0
| 1.666464
| 0.282543
|
Abnormal cellular phenotype
| 39.614078
| 185.546117
| 0.597451
| 0.59241
| 13.622479
| 17.109025
| 1.114269
| 0.399533
|
Abnormal central sensory function
| 1.313107
| 3.298544
| -0.095314
| 0.508666
| 0.938147
| 1.20101
| 1.090969
| 0.315675
|
Abnormal cerebellar vermis morphology
| 17.288835
| 77.65534
| -0.087513
| 0.769156
| 7.624155
| 9.70475
| 0.522505
| 0.262124
|
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