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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 ({'setsize', 'score', 'pval', 'overlap'}) and 8 missing columns ({'pval_mean', 'overlap_mean', 'score_mean', 'setsize_std', 'overlap_std', 'pval_std', 'setsize_mean', 'score_std'}).
This happened while the csv dataset builder was generating data using
hf://datasets/ligdis/msigdb_reactome/fragment/C001/C001_val_log2fc/harmon.tsv (at revision b8dc22f09d7d9b6e7466a92a3b9c74d51f218254)
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 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 ({'setsize', 'score', 'pval', 'overlap'}) and 8 missing columns ({'pval_mean', 'overlap_mean', 'score_mean', 'setsize_std', 'overlap_std', 'pval_std', 'setsize_mean', 'score_std'}).
This happened while the csv dataset builder was generating data using
hf://datasets/ligdis/msigdb_reactome/fragment/C001/C001_val_log2fc/harmon.tsv (at revision b8dc22f09d7d9b6e7466a92a3b9c74d51f218254)
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 |
|---|---|---|---|---|---|---|---|---|
2 ltr circle formation
| 2.51699
| 5.317961
| -0.746004
| 0.423077
| 1.437096
| 0.564627
| 0.811052
| 0.28789
|
A tetrasaccharide linker sequence is required for gag synthesis
| 0.397306
| 1.131313
| 0.457131
| 0.215714
| 0.509565
| 0.337742
| 2.020893
| 0.274826
|
Abacavir metabolism
| 0.575309
| 1
| -0.362705
| 0.241749
| 0.494296
| 0
| 1.909709
| 0.266171
|
Abacavir transmembrane transport
| 0.224691
| 1
| 1.372308
| 0.073397
| 0.417379
| 0
| 2.217837
| 0.151569
|
Abacavir transport and metabolism
| 0.526699
| 1.966019
| 0.590576
| 0.399026
| 0.662275
| 0.181179
| 1.420406
| 0.317384
|
Abc family proteins mediated transport
| 13.317961
| 51.419903
| 0.831334
| 0.503384
| 6.603792
| 3.01789
| 1.025884
| 0.368122
|
Abc transporter disorders
| 11.927184
| 42.313107
| 0.727764
| 0.511874
| 6.253119
| 1.984533
| 1.107481
| 0.360861
|
Abc transporters in lipid homeostasis
| 0.968447
| 2.526699
| 0.678513
| 0.44754
| 0.813404
| 0.745059
| 1.070847
| 0.319369
|
Aberrant regulation of mitotic exit in cancer due to rb1 defects
| 3.584951
| 9.779126
| 0.248727
| 0.617012
| 2.234997
| 1.71154
| 0.752823
| 0.303467
|
Aberrant regulation of mitotic g1 s transition in cancer due to rb1 defects
| 1.373786
| 3.092233
| 0.286496
| 0.563371
| 1.00053
| 0.825114
| 0.933912
| 0.314301
|
Abortive elongation of hiv 1 transcript in the absence of tat
| 4.252427
| 13.682039
| -0.225969
| 0.641758
| 2.764085
| 2.32512
| 0.655513
| 0.266429
|
Acetylcholine neurotransmitter release cycle
| 0.438596
| 1.030702
| 0.177736
| 0.232861
| 0.513589
| 0.172508
| 1.961545
| 0.272911
|
Acetylcholine regulates insulin secretion
| 1
| 1.719677
| -0.819653
| 0.328716
| 0.684838
| 0.825546
| 1.553212
| 0.330267
|
Activated notch1 transmits signal to the nucleus
| 0.873786
| 2.458738
| 0.597379
| 0.461209
| 0.778093
| 0.965797
| 1.105839
| 0.324995
|
Activated ntrk2 signals through cdk5
| 1.09466
| 1.820388
| -0.24794
| 0.538866
| 0.667025
| 0.383864
| 1.170081
| 0.333429
|
Activated ntrk2 signals through frs2 and frs3
| 0.796117
| 2.012136
| 0.085718
| 0.594453
| 0.651499
| 0.371756
| 1.120614
| 0.344653
|
Activated ntrk2 signals through fyn
| 0.746154
| 1.182051
| -0.363017
| 0.398852
| 0.540345
| 0.385887
| 1.407985
| 0.31733
|
Activated ntrk2 signals through pi3k
| 0.201456
| 1
| 1.024894
| 0.24581
| 0.401088
| 0
| 1.515792
| 0.264867
|
Activated ntrk2 signals through ras
| 0.271845
| 1.126214
| 0.927853
| 0.291628
| 0.510932
| 0.404576
| 1.47807
| 0.29774
|
Activated ntrk3 signals through pi3k
| 0.5
| 1
| 0.017932
| 0.232997
| 0.5
| 0
| 1.936954
| 0.268644
|
Activated ntrk3 signals through ras
| 0.271845
| 1.126214
| 0.927853
| 0.291628
| 0.510932
| 0.404576
| 1.47807
| 0.29774
|
Activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
| 2.230583
| 3.793689
| -0.907423
| 0.372637
| 1.069315
| 0.709614
| 0.952354
| 0.30717
|
Activated tak1 mediates p38 mapk activation
| 1.752427
| 3.643204
| -0.329772
| 0.502095
| 1.256775
| 1.435127
| 1.047986
| 0.327519
|
Activation of ampk downstream of nmdars
| 3.354369
| 6.451456
| 0.556697
| 0.444048
| 1.771033
| 1.459842
| 1.088746
| 0.328317
|
Activation of anterior hox genes in hindbrain development during early embryogenesis
| 6.82767
| 16.419903
| -0.892378
| 0.411598
| 3.240657
| 2.803585
| 0.837974
| 0.305784
|
Activation of atr in response to replication stress
| 5.179612
| 19.679612
| 0.128565
| 0.65752
| 3.862538
| 3.015216
| 0.744782
| 0.294269
|
Activation of bad and translocation to mitochondria
| 3.813107
| 7.633495
| 0.250165
| 0.4669
| 2.394679
| 0.934321
| 1.09902
| 0.323145
|
Activation of bh3 only proteins
| 4.480583
| 10.592233
| -0.014279
| 0.576226
| 2.898294
| 1.228203
| 0.904246
| 0.313298
|
Activation of caspases through apoptosome mediated cleavage
| 0.825095
| 1.726236
| -0.045001
| 0.358859
| 0.713675
| 0.837089
| 1.627594
| 0.321055
|
Activation of gene expression by srebf srebp
| 4.5
| 17.614078
| -0.410479
| 0.367849
| 1.993314
| 2.321093
| 1.196656
| 0.27439
|
Activation of irf3 irf7 mediated by tbk1 ikk epsilon
| 0.992228
| 1.823834
| -0.450574
| 0.444633
| 0.65771
| 0.66757
| 1.371054
| 0.342249
|
Activation of kainate receptors upon glutamate binding
| 1.260101
| 3.166667
| 0.100119
| 0.554743
| 1.047134
| 1.389899
| 1.09078
| 0.332401
|
Activation of nima kinases nek9 nek6 nek7
| 1.961165
| 4.473301
| 0.147295
| 0.589598
| 1.299158
| 0.616729
| 0.803239
| 0.295939
|
Activation of nmda receptors and postsynaptic events
| 6.531553
| 22.640777
| 0.202718
| 0.567858
| 3.686959
| 3.400755
| 0.982551
| 0.33028
|
Activation of noxa and translocation to mitochondria
| 0.665049
| 1.063107
| -0.492129
| 0.350031
| 0.516186
| 0.243155
| 1.53607
| 0.303944
|
Activation of ppargc1a pgc 1alpha by phosphorylation
| 0.927318
| 2.358396
| 0.409156
| 0.547458
| 0.773775
| 0.846265
| 0.96728
| 0.316338
|
Activation of puma and translocation to mitochondria
| 0.73301
| 1.162621
| -0.556117
| 0.365073
| 0.522854
| 0.36902
| 1.512979
| 0.31223
|
Activation of rac1
| 2.065534
| 4.580097
| -0.143521
| 0.57488
| 1.455847
| 1.157874
| 0.807835
| 0.289189
|
Activation of rac1 downstream of nmdars
| 0.903553
| 2.147208
| 0.047996
| 0.561109
| 0.761269
| 0.782846
| 1.017095
| 0.317876
|
Activation of ras in b cells
| 0.83871
| 1
| -0.979984
| 0.294175
| 0.367799
| 0
| 1.577237
| 0.285592
|
Activation of smo
| 0.720874
| 1.927184
| 0.463582
| 0.51009
| 0.677124
| 0.806249
| 1.108555
| 0.334105
|
Activation of the ap 1 family of transcription factors
| 1.328395
| 2.590123
| -0.173831
| 0.562381
| 0.890725
| 0.636271
| 1.044993
| 0.323428
|
Activation of the mrna upon binding of the cap binding complex and eifs and subsequent binding to 43s
| 21.279126
| 50.434466
| -0.642334
| 0.450187
| 8.810973
| 1.447487
| 1.403925
| 0.370747
|
Activation of the phototransduction cascade
| 0.850575
| 1
| -1.681978
| 0.113591
| 0.356507
| 0
| 1.707207
| 0.183697
|
Activation of the pre replicative complex
| 5.68932
| 20.378641
| 0.257944
| 0.622644
| 4.264391
| 3.006034
| 0.812557
| 0.315151
|
Activation of the tfap2 ap 2 family of transcription factors
| 0.472637
| 1.064677
| 0.173233
| 0.18556
| 0.509118
| 0.245954
| 2.168219
| 0.252582
|
Acyl chain remodeling of cl
| 1.281553
| 2.512136
| -0.181679
| 0.572288
| 0.894074
| 0.499853
| 0.999598
| 0.321176
|
Acyl chain remodeling of dag and tag
| 0.5
| 1
| 0.066036
| 0.237413
| 0.5
| 0
| 1.72841
| 0.228109
|
Acyl chain remodelling of pc
| 0.744526
| 1.839416
| 0.543411
| 0.334714
| 0.754831
| 0.911406
| 1.608552
| 0.309994
|
Acyl chain remodelling of pe
| 0.572052
| 1.349345
| 0.201559
| 0.27525
| 0.59862
| 0.476763
| 1.926457
| 0.294276
|
Acyl chain remodelling of pg
| 0.819951
| 1.871046
| 0.571281
| 0.433891
| 0.636819
| 0.424796
| 1.275993
| 0.328038
|
Acyl chain remodelling of pi
| 0.163588
| 1
| 1.596679
| 0.120125
| 0.369902
| 0
| 1.770737
| 0.198568
|
Acyl chain remodelling of ps
| 0.65995
| 1.372796
| -0.190473
| 0.319014
| 0.600363
| 0.483548
| 1.778073
| 0.311433
|
Adaptive immune system
| 46.463592
| 186.400485
| 0.133943
| 0.696211
| 20.00658
| 16.487633
| 1.063353
| 0.356909
|
Adenylate cyclase activating pathway
| 0
| 1
| 2.893154
| 0.027096
| 0
| 0
| 1.052861
| 0.031497
|
Adenylate cyclase inhibitory pathway
| 1.643204
| 2.699029
| -0.217591
| 0.534562
| 0.950921
| 0.592591
| 1.037654
| 0.313043
|
Adherens junctions interactions
| 3.131068
| 6.61165
| -0.49788
| 0.462421
| 1.932679
| 0.875591
| 0.912294
| 0.303801
|
Adora2b mediated anti inflammatory cytokines production
| 3.740291
| 8.40534
| -0.169146
| 0.589948
| 2.458002
| 1.516342
| 0.852638
| 0.309866
|
Adp signalling through p2y purinoceptor 1
| 1.296296
| 2.984127
| 0.124459
| 0.520234
| 1.060117
| 1.31123
| 1.182548
| 0.34051
|
Adp signalling through p2y purinoceptor 12
| 2.128641
| 4.118932
| -0.173928
| 0.513837
| 1.377861
| 1.2338
| 1.003246
| 0.318916
|
Adrenaline noradrenaline inhibits insulin secretion
| 1.568182
| 3.244949
| -0.138577
| 0.510701
| 1.12047
| 1.083904
| 1.073964
| 0.326447
|
Advanced glycosylation endproduct receptor signaling
| 2.470874
| 7.907767
| -0.161923
| 0.566197
| 1.983335
| 0.973552
| 0.838755
| 0.29603
|
Aflatoxin activation and detoxification
| 1.262136
| 3.118932
| -0.129819
| 0.570208
| 0.875349
| 0.715929
| 0.963846
| 0.314891
|
Aggrephagy
| 5.053398
| 15.303398
| 0.017653
| 0.586042
| 3.001951
| 1.710246
| 0.938844
| 0.318926
|
Akt phosphorylates targets in the cytosol
| 1.587379
| 4.099515
| 0.375295
| 0.452059
| 1.308907
| 1.790563
| 1.197504
| 0.327627
|
Akt phosphorylates targets in the nucleus
| 0.382609
| 1.330435
| 1.235729
| 0.217929
| 0.552978
| 0.575667
| 1.606463
| 0.258835
|
Alk mutants bind tkis
| 2.538835
| 6.196602
| -0.37757
| 0.582875
| 1.70691
| 0.799082
| 0.706174
| 0.286612
|
Alpha defensins
| 0.875
| 1
| -2.308052
| 0.063486
| 0.330719
| 0
| 1.714601
| 0.165625
|
Alpha linolenic omega3 and linoleic omega6 acid metabolism
| 2.259709
| 6.533981
| 0.064335
| 0.557238
| 1.585134
| 0.890244
| 0.846462
| 0.283808
|
Alpha oxidation of phytanate
| 1.541262
| 4.174757
| 0.539716
| 0.395866
| 1.019588
| 0.67805
| 1.06551
| 0.283804
|
Alpha protein kinase 1 signaling pathway
| 0.941176
| 1.368984
| -0.750596
| 0.326247
| 0.638987
| 0.48253
| 1.591813
| 0.308766
|
Amino acid transport across the plasma membrane
| 1.601942
| 3.946602
| 0.679822
| 0.349759
| 1.2195
| 1.039073
| 1.144087
| 0.296573
|
Amino acids regulate mtorc1
| 3.975728
| 12.313107
| -0.180672
| 0.687583
| 2.642886
| 1.739468
| 0.580471
| 0.254127
|
Ampk inhibits chrebp transcriptional activation activity
| 0.238739
| 1.004505
| 0.916731
| 0.243902
| 0.426313
| 0.066964
| 1.664642
| 0.265435
|
Amyloid fiber formation
| 2.23301
| 6.373786
| -0.277494
| 0.439356
| 1.249885
| 1.346009
| 1.118928
| 0.307414
|
Anchoring of the basal body to the plasma membrane
| 10.25
| 32.033981
| 0.617759
| 0.492907
| 4.597184
| 4.443148
| 0.975258
| 0.348633
|
Androgen biosynthesis
| 0.264563
| 1
| 1.10753
| 0.175642
| 0.4411
| 0
| 1.893347
| 0.243727
|
Anti inflammatory response favouring leishmania parasite infection
| 4.533981
| 13.390777
| -0.110189
| 0.703491
| 3.385622
| 2.684948
| 0.624775
| 0.26665
|
Antigen activates b cell receptor bcr leading to generation of second messengers
| 0.990291
| 2.854369
| 0.424793
| 0.527866
| 0.870165
| 1.006366
| 0.947885
| 0.313973
|
Antigen presentation folding assembly and peptide loading of class i mhc
| 4.368932
| 15.359223
| 0.488544
| 0.552321
| 2.155329
| 1.853123
| 0.787308
| 0.308703
|
Antigen processing cross presentation
| 13.364078
| 51.038835
| 0.660634
| 0.545645
| 6.483622
| 2.525299
| 1.042253
| 0.365983
|
Antigen processing ubiquitination proteasome degradation
| 25.228155
| 89.885922
| 0.30405
| 0.534908
| 12.844718
| 7.994482
| 1.423534
| 0.383588
|
Antimicrobial peptides
| 1.131068
| 2.470874
| -0.833153
| 0.335816
| 0.742147
| 0.701335
| 1.323715
| 0.300491
|
Antiviral mechanism by ifn stimulated genes
| 15.502427
| 50.213592
| -0.394075
| 0.684298
| 6.747347
| 2.327132
| 0.543724
| 0.280244
|
Apc c cdc20 mediated degradation of cyclin b
| 4.09466
| 10.81068
| 0.44395
| 0.577212
| 2.351052
| 1.544826
| 0.760445
| 0.308945
|
Apc c cdh1 mediated degradation of cdc20 and other apc c cdh1 targeted proteins in late mitosis early g1
| 14.026699
| 48.65534
| 0.563634
| 0.564192
| 7.183906
| 2.917581
| 1.179923
| 0.375345
|
Apc c mediated degradation of cell cycle proteins
| 16.580097
| 56.259709
| 0.489499
| 0.584645
| 8.225929
| 3.549652
| 1.213496
| 0.375532
|
Apc cdc20 mediated degradation of nek2a
| 3.701456
| 11.298544
| 0.245998
| 0.637593
| 2.280287
| 1.93604
| 0.723746
| 0.299947
|
Apex1 independent resolution of ap sites via the single nucleotide replacement pathway
| 1.342233
| 2.48301
| -0.264252
| 0.541678
| 0.914746
| 0.609156
| 1.048526
| 0.32195
|
Apobec3g mediated resistance to hiv 1 infection
| 1.76699
| 2.956311
| -0.701626
| 0.453728
| 0.962439
| 0.204403
| 0.917113
| 0.293707
|
Apoptosis
| 22.723301
| 88.148058
| 0.039353
| 0.605131
| 11.015265
| 5.029517
| 1.033074
| 0.34103
|
Apoptosis induced dna fragmentation
| 4.461165
| 9.480583
| -1.239678
| 0.241394
| 1.815774
| 0.795687
| 1.19554
| 0.28131
|
Apoptotic cleavage of cell adhesion proteins
| 1.978155
| 5.764563
| -0.312456
| 0.478424
| 1.406299
| 0.884278
| 0.991486
| 0.302761
|
Apoptotic cleavage of cellular proteins
| 5.93932
| 18.621359
| -0.055732
| 0.593031
| 3.220641
| 2.312341
| 0.880138
| 0.302688
|
Apoptotic execution phase
| 8.410194
| 29.614078
| -0.64981
| 0.495653
| 4.02591
| 2.505159
| 1.027073
| 0.345875
|
Apoptotic factor mediated response
| 1.968447
| 6.368932
| 0.202077
| 0.54842
| 1.570812
| 1.781732
| 0.90841
| 0.310801
|
Aquaporin mediated transport
| 2.029126
| 5.621359
| 0.153561
| 0.608444
| 1.497288
| 1.362583
| 0.816656
| 0.311672
|
Arachidonate production from dag
| 0.934466
| 2.32767
| -0.965187
| 0.21927
| 0.475697
| 0.655012
| 1.541942
| 0.236446
|
Arachidonic acid metabolism
| 2.63835
| 7.847087
| -0.514439
| 0.307524
| 1.141786
| 1.179689
| 1.278189
| 0.247237
|
Arms mediated activation
| 0.798544
| 1.93932
| 0.238171
| 0.492695
| 0.770007
| 0.719835
| 1.210615
| 0.320663
|
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