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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', 'overlap', 'setsize', 'score'}) and 8 missing columns ({'score_mean', 'overlap_std', 'pval_std', 'setsize_std', 'score_std', 'pval_mean', 'setsize_mean', 'overlap_mean'}).
This happened while the csv dataset builder was generating data using
hf://datasets/ligdis/msigdb_wp/fragment/C001/C001_val_log2fc/harmon.tsv (at revision f23f3ab074354e658742a909ce46baa9eade9793)
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, "' + 811
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 1420, 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 1052, 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 4 new columns ({'pval', 'overlap', 'setsize', 'score'}) and 8 missing columns ({'score_mean', 'overlap_std', 'pval_std', 'setsize_std', 'score_std', 'pval_mean', 'setsize_mean', 'overlap_mean'}).
This happened while the csv dataset builder was generating data using
hf://datasets/ligdis/msigdb_wp/fragment/C001/C001_val_log2fc/harmon.tsv (at revision f23f3ab074354e658742a909ce46baa9eade9793)
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 |
|---|---|---|---|---|---|---|---|---|
15q112 copy number variation syndrome
| 1.752427
| 3.958738
| 0.502893
| 0.506342
| 1.020122
| 0.676044
| 0.877538
| 0.313605
|
15q133 copy number variation syndrome
| 1.34466
| 2.88835
| -0.271879
| 0.659914
| 0.866107
| 0.474761
| 0.757497
| 0.298734
|
16p112 distal deletion syndrome
| 2.330097
| 7.475728
| -0.047762
| 0.639058
| 1.87802
| 1.292958
| 0.699561
| 0.272322
|
16p112 proximal deletion syndrome
| 9.436893
| 25.635922
| -0.56264
| 0.555359
| 5.431247
| 2.692757
| 0.83059
| 0.321851
|
1q211 copy number variation syndrome
| 1.866505
| 8.890777
| 0.755869
| 0.431774
| 1.723381
| 1.502494
| 0.794995
| 0.298169
|
22q112 copy number variation syndrome
| 8.555825
| 32.36165
| -0.420777
| 0.643781
| 4.494796
| 3.343271
| 0.60197
| 0.287675
|
3q29 copy number variation syndrome
| 2.68932
| 11.182039
| 0.004619
| 0.592515
| 2.0062
| 2.648203
| 0.812337
| 0.284252
|
4hydroxytamoxifen dexamethasone and retinoic acids regulation of p27 expression
| 3.283981
| 6.82767
| -0.021492
| 0.579973
| 1.971751
| 1.258722
| 0.833426
| 0.299862
|
7oxoc and 7betahc pathways
| 2.631068
| 9.114078
| 0.368945
| 0.379579
| 1.669197
| 1.188168
| 1.20678
| 0.291737
|
7q1123 copy number variation syndrome
| 12.961165
| 45.167476
| -0.976141
| 0.433436
| 5.606294
| 3.059858
| 0.834246
| 0.336282
|
Ace inhibitor pathway
| 0.236364
| 1.027273
| 1.118764
| 0.202364
| 0.424848
| 0.162877
| 1.78819
| 0.252271
|
Acetylcholine synthesis
| 0.410194
| 1.86165
| 0.350941
| 0.425702
| 0.578073
| 0.470267
| 1.407682
| 0.329332
|
Acquired partial lipodystrophy barraquersimons syndrome
| 1.740291
| 4.497573
| 0.906515
| 0.254867
| 1.495309
| 0.504825
| 1.235576
| 0.25741
|
Activation of nlrp3 inflammasome by sarscov2
| 0.751724
| 1
| -1.20064
| 0.161848
| 0.432013
| 0
| 1.930479
| 0.24268
|
Acute viral myocarditis
| 5.597087
| 14.682039
| -0.35381
| 0.535661
| 3.169606
| 2.586066
| 0.852072
| 0.301377
|
Adipogenesis
| 3.334951
| 14.839806
| 0.811688
| 0.43158
| 1.83002
| 1.658625
| 0.785016
| 0.300177
|
Aerobic glycolysis
| 6.915049
| 10.580097
| -1.197811
| 0.287624
| 2.342115
| 0.493543
| 1.083458
| 0.312528
|
Aflatoxin b1 metabolism
| 0.359223
| 1.898058
| 0.796851
| 0.374906
| 0.605065
| 0.302572
| 1.373636
| 0.320119
|
Agerage pathway
| 7.264563
| 16.975728
| -0.467792
| 0.551677
| 4.025454
| 3.13443
| 0.859635
| 0.324978
|
Airway smooth muscle cell contraction
| 2.036408
| 4.308252
| -0.481342
| 0.456122
| 1.248741
| 0.942332
| 0.990023
| 0.303365
|
Alanine and aspartate metabolism
| 2.400485
| 4.26699
| -1.239844
| 0.233223
| 1.276106
| 0.479257
| 0.910851
| 0.243936
|
Allograft rejection
| 3.330097
| 9.839806
| 0.795318
| 0.375973
| 1.648114
| 1.321432
| 0.931941
| 0.288328
|
Alpha 6 beta 4 signaling pathway
| 3.330097
| 9.88835
| -0.216389
| 0.588557
| 2.299803
| 2.370359
| 0.822874
| 0.302991
|
Altered glycosylation of muc1 in tumor microenvironment
| 1.003106
| 1.937888
| -0.020436
| 0.422483
| 0.903748
| 0.853851
| 1.479959
| 0.338055
|
Alternative pathway of fetal androgen synthesis
| 0.23301
| 1
| 1.270832
| 0.172726
| 0.422748
| 0
| 1.744471
| 0.237997
|
Alzheimers disease
| 18.929612
| 83.075243
| 0.8524
| 0.50899
| 9.098565
| 6.061711
| 1.080067
| 0.386521
|
Alzheimers disease and mirna effects
| 19.786408
| 84.628641
| 0.867541
| 0.501966
| 9.064119
| 6.212691
| 1.074407
| 0.386984
|
Amino acid metabolism
| 21.485437
| 54.225728
| -1.686316
| 0.275035
| 8.379198
| 2.550465
| 1.508283
| 0.346691
|
Amino acid metabolism pathway excerpt histidine catabolism extension
| 0.699507
| 1.490148
| 0.082152
| 0.426015
| 0.657169
| 0.499903
| 1.406951
| 0.329863
|
Ampactivated protein kinase ampk signaling
| 3.240291
| 15.25
| -1.101983
| 0.304068
| 1.901208
| 2.489419
| 1.123907
| 0.299995
|
Amplification and expansion of oncogenic pathways as metastatic traits
| 0.5
| 1
| 0.017932
| 0.232997
| 0.5
| 0
| 1.936954
| 0.268644
|
Amyotrophic lateral sclerosis als
| 2.730583
| 9.961165
| 0.420536
| 0.570881
| 1.655452
| 1.592899
| 0.737268
| 0.296149
|
Androgen receptor signaling pathway
| 9.521845
| 27.456311
| -0.732624
| 0.478013
| 4.534871
| 4.170578
| 0.986864
| 0.338068
|
Angiogenesis
| 1.434568
| 3.288889
| -0.111277
| 0.562101
| 1.03699
| 0.985324
| 0.984884
| 0.313644
|
Angiopoietinlike protein 8 regulatory pathway
| 7.575243
| 28.252427
| 0.055408
| 0.687639
| 4.071171
| 4.140654
| 0.724731
| 0.297564
|
Angiotensin ii receptor type 1 pathway
| 1.842233
| 3.123786
| -0.505281
| 0.463743
| 0.935732
| 0.694442
| 1.0939
| 0.31045
|
Antiviral and antiinflammatory effects of nrf2 on sarscov2 pathway
| 0.934466
| 4.468447
| 0.765126
| 0.395049
| 1.187752
| 1.695647
| 1.012808
| 0.297396
|
Apoe and mir146 in inflammation and atherosclerosis
| 0.907143
| 1.314286
| -1.075041
| 0.277465
| 0.54637
| 0.464231
| 1.670677
| 0.319511
|
Apoptosis
| 3.558252
| 12.881068
| -0.034267
| 0.658691
| 2.419381
| 3.316322
| 0.696482
| 0.273012
|
Apoptosis modulation and signaling
| 3.898058
| 15.014563
| 0.21895
| 0.605366
| 2.333649
| 3.251554
| 0.745552
| 0.277408
|
Apoptosis modulation by hsp70
| 1.116505
| 4.373786
| 0.698056
| 0.455326
| 1.256447
| 1.583008
| 0.899593
| 0.309698
|
Apoptosisrelated network due to altered notch3 in ovarian cancer
| 3.628641
| 14.682039
| -0.037348
| 0.596136
| 2.531444
| 1.639432
| 0.823852
| 0.29409
|
Arachidonate epoxygenase epoxide hydrolase
| 0.616505
| 1.623786
| 0.2675
| 0.343506
| 0.533826
| 0.484435
| 1.578932
| 0.304951
|
Arrhythmogenic right ventricular cardiomyopathy
| 4.194175
| 13.208738
| -0.179238
| 0.544781
| 2.539239
| 1.398724
| 0.945548
| 0.313406
|
Aryl hydrocarbon receptor pathway wp2586
| 3.274272
| 7.978155
| -0.021525
| 0.567143
| 2.157628
| 1.812044
| 0.865646
| 0.302148
|
Aryl hydrocarbon receptor pathway wp2873
| 1.968447
| 4.742718
| 0.312076
| 0.550968
| 1.223347
| 0.860018
| 0.838843
| 0.306455
|
Arylamine metabolism
| 0.542056
| 1
| 0.055241
| 0.262859
| 0.498228
| 0
| 1.890298
| 0.286776
|
Aspirin and mirnas
| 0.885965
| 1.897661
| -0.191048
| 0.438743
| 0.693648
| 0.83319
| 1.50581
| 0.347191
|
Atm signaling in development and disease
| 7.01699
| 23
| -0.424926
| 0.565726
| 3.658638
| 2.204365
| 0.817772
| 0.313518
|
Atm signaling pathway
| 5.725728
| 14.978155
| -0.484553
| 0.565876
| 3.048956
| 2.051996
| 0.732253
| 0.299425
|
Atr signaling
| 1.298544
| 2.589806
| -0.320125
| 0.512912
| 0.850869
| 1.085739
| 1.237006
| 0.332714
|
Autophagy
| 2.953883
| 7.742718
| -0.029976
| 0.565001
| 1.996431
| 2.479395
| 0.887831
| 0.30702
|
Autosomal recessive osteopetrosis pathways
| 1.038835
| 2.291262
| -0.134312
| 0.48557
| 0.811595
| 0.739077
| 1.155648
| 0.310711
|
B cell receptor signaling pathway
| 6.703883
| 18.873786
| -0.573491
| 0.506767
| 3.718843
| 3.761531
| 0.852917
| 0.317998
|
Base excision repair
| 6.152913
| 16.800971
| -0.287966
| 0.510825
| 3.403085
| 2.456258
| 1.029197
| 0.326654
|
Bdnftrkb signaling
| 2.580097
| 7.924757
| -0.294817
| 0.562123
| 1.753192
| 1.46535
| 0.836027
| 0.306853
|
Benzene metabolism
| 0.177184
| 1
| 1.791731
| 0.061391
| 0.381825
| 0
| 2.052033
| 0.143973
|
Benzoapyrene metabolism
| 0.373786
| 2
| 0.630846
| 0.418486
| 0.583838
| 0
| 1.248794
| 0.318995
|
Bile acids synthesis and enterohepatic circulation
| 1.225728
| 3.191748
| 0.018268
| 0.525667
| 0.955321
| 0.70341
| 1.046062
| 0.319342
|
Biogenic amine synthesis
| 0.208738
| 1
| 1.372671
| 0.140046
| 0.406407
| 0
| 1.845035
| 0.213377
|
Biomarkers for pyrimidine metabolism disorders
| 2.791262
| 6.75
| -0.218807
| 0.55666
| 1.5673
| 1.096386
| 0.853092
| 0.295743
|
Biomarkers for urea cycle disorders
| 0.949029
| 1.40534
| -0.763715
| 0.349684
| 0.62304
| 0.524424
| 1.578149
| 0.332129
|
Biotin metabolism including iems
| 5.036408
| 7.575243
| -2.050376
| 0.099784
| 1.436735
| 0.654832
| 1.48884
| 0.230528
|
Bladder cancer
| 2.686893
| 6.118932
| -0.116473
| 0.626268
| 1.738073
| 1.572806
| 0.714532
| 0.272362
|
Bmp signaling in eyelid development
| 0.808399
| 1.55643
| -0.322196
| 0.381225
| 0.669965
| 0.664109
| 1.55952
| 0.330426
|
Bmp2wnt4foxo1 pathway in primary endometrial stromal cell differentiation
| 0.546117
| 1
| -0.191977
| 0.358985
| 0.497869
| 0
| 1.505018
| 0.291496
|
Bone morphogenic protein bmp signaling and regulation
| 0.614035
| 1
| -0.739863
| 0.148397
| 0.486822
| 0
| 2.161057
| 0.206731
|
Brainderived neurotrophic factor bdnf signaling pathway
| 11.376214
| 42.063107
| -0.638729
| 0.512908
| 5.560062
| 5.412221
| 0.934941
| 0.340728
|
Breast cancer pathway
| 7.135922
| 23.48301
| -0.114566
| 0.701748
| 4.309728
| 3.389333
| 0.59029
| 0.25929
|
Burn wound healing
| 2.36165
| 8.283981
| 0.064643
| 0.637153
| 1.934055
| 1.150954
| 0.711999
| 0.271438
|
Calcium regulation in cardiac cells
| 7.305825
| 25.305825
| -0.047837
| 0.659757
| 3.982811
| 3.49461
| 0.793189
| 0.315745
|
Caloric restriction and aging
| 0.907767
| 3.856796
| 0.688463
| 0.465089
| 1.003024
| 0.66199
| 0.909339
| 0.313573
|
Camkk2 pathway
| 2.682039
| 11.245146
| 0.544534
| 0.523701
| 1.941716
| 2.139685
| 0.719216
| 0.285633
|
Cancer immunotherapy by ctla4 blockade
| 0.663317
| 1.288945
| -0.3286
| 0.342491
| 0.582156
| 0.453272
| 1.753805
| 0.332944
|
Cancer immunotherapy by pd1 blockade
| 1.223301
| 3.014563
| 0.017984
| 0.629176
| 0.902338
| 0.582747
| 0.841982
| 0.309236
|
Cannabinoid receptor signaling
| 1.86165
| 5.40534
| 0.138213
| 0.604981
| 1.46572
| 1.291597
| 0.801053
| 0.2984
|
Canonical and noncanonical notch signaling
| 0.875676
| 2.062162
| 0.147101
| 0.438297
| 0.841943
| 0.963622
| 1.472728
| 0.343442
|
Canonical and noncanonical tgfb signaling
| 0.530159
| 1.219048
| 0.280058
| 0.305746
| 0.586795
| 0.457341
| 1.680609
| 0.300424
|
Canonical nfkb pathway
| 1.071429
| 2.16369
| -0.004923
| 0.432558
| 0.942208
| 1.029327
| 1.393387
| 0.324571
|
Cardiac hypertrophic response
| 4.23301
| 11.400485
| -0.063929
| 0.606235
| 2.747298
| 3.058063
| 0.812961
| 0.298364
|
Cardiac progenitor differentiation
| 1.035176
| 2.208543
| 0.023927
| 0.502585
| 0.832004
| 0.847241
| 1.248474
| 0.332805
|
Ccl18 signaling pathway
| 3.145631
| 9.468447
| 0.71203
| 0.410282
| 1.544849
| 1.266244
| 0.905866
| 0.301564
|
Cell cycle
| 13.604369
| 49.621359
| 0.024998
| 0.75609
| 7.37493
| 5.628665
| 0.630792
| 0.283742
|
Cell differentiation expanded index
| 0.728643
| 1.203518
| -0.476312
| 0.328112
| 0.577409
| 0.402614
| 1.673992
| 0.316044
|
Cell differentiation index
| 0.612245
| 1
| -0.466124
| 0.267859
| 0.487238
| 0
| 1.820489
| 0.283858
|
Cell migration and invasion through p75ntr
| 1.791262
| 5.570388
| -0.176267
| 0.566314
| 1.314638
| 1.575725
| 0.901604
| 0.313762
|
Cells and molecules involved in local acute inflammatory response
| 0.529126
| 1
| -0.114652
| 0.301208
| 0.499151
| 0
| 1.704512
| 0.277511
|
Celltype dependent selectivity of cck2r signaling
| 0.621538
| 1.067692
| -0.377574
| 0.247893
| 0.521681
| 0.251217
| 1.907242
| 0.283668
|
Cellular proteostasis
| 2.067961
| 4.271845
| 0.526479
| 0.420605
| 1.138575
| 0.846973
| 1.017772
| 0.302767
|
Cerebral organic acidurias including diseases
| 1.961165
| 4.936893
| -0.646502
| 0.324033
| 1.319549
| 0.243155
| 1.160431
| 0.261131
|
Chemokine signaling pathway
| 7.366505
| 22.92233
| -0.344315
| 0.596727
| 4.424024
| 4.748918
| 0.760293
| 0.295087
|
Cholesterol biosynthesis pathway
| 4.01699
| 12.356796
| 0.683421
| 0.366521
| 1.821448
| 1.313255
| 1.045692
| 0.270874
|
Cholesterol biosynthesis with skeletal dysplasias
| 2.703883
| 6.024272
| 1.625054
| 0.14276
| 1.305212
| 0.710116
| 0.967576
| 0.205892
|
Cholesterol metabolism with bloch and kandutschrussell pathways
| 7.092233
| 23.070388
| 1.304588
| 0.28856
| 3.189217
| 2.132139
| 1.15158
| 0.308803
|
Chromosomal and microsatellite instability in colorectal cancer
| 5.351942
| 17.347087
| -0.147562
| 0.655062
| 3.585965
| 2.66739
| 0.720252
| 0.2826
|
Ciliary landscape
| 21.832524
| 102.298544
| 0.035396
| 0.823595
| 9.513588
| 9.411349
| 0.492381
| 0.250939
|
Ciliopathies
| 4.902913
| 17.76699
| 0.341367
| 0.572922
| 2.756333
| 3.714192
| 0.845548
| 0.315163
|
Circadian rhythm genes
| 10.157767
| 42.11165
| 0.057533
| 0.688762
| 5.01327
| 3.775516
| 0.695721
| 0.2991
|
Classical pathway of steroidogenesis with glucocorticoid and mineralocorticoid metabolism
| 0.23301
| 1
| 1.270832
| 0.172726
| 0.422748
| 0
| 1.744471
| 0.237997
|
Clear cell renal cell carcinoma pathways
| 15.385922
| 36.43932
| -1.534584
| 0.291554
| 6.02858
| 2.903581
| 1.435835
| 0.346854
|
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