bigscience-workshop / biomedical

Tools for curating biomedical training data for large-scale language modeling
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Closes #880 #881

Closed nachollorca closed 1 year ago

nachollorca commented 1 year ago

Closes #880 - Implementation of CARDIO:DE loader.

Checkbox

INFO:__main__:args: Namespace(dataset_name='cardiode', data_dir='C:\\Users\\admin\\Desktop\\cardiode_exp', config_name=None, bypass_splits=[], bypass_keys=[], bypass_split_key_pairs=[], test_local=True)
INFO:__main__:Running (Local) Unit Test
INFO:__main__:all_config_names: ['cardiode_source', 'cardiode_bigbio_kb']
INFO:__main__:self.DATASET_NAME: bigbio/hub/hub_repos/cardiode/cardiode.py
INFO:__main__:self.CONFIG_NAME: cardiode_source
INFO:__main__:self.DATA_DIR: C:\Users\admin\Desktop\cardiode_exp
INFO:__main__:importing module .... 
INFO:__main__:imported module <module 'datasets_modules.datasets.cardiode.d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582.cardiode' from 'C:\\Users\\admin\\.cache\\huggingface\\modules\\datasets_modules\\datasets\\cardiode\\d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582\\cardiode.py'>
INFO:__main__:Checking for _SUPPORTED_TASKS ...
INFO:__main__:Found _SUPPORTED_TASKS=['NAMED_ENTITY_RECOGNITION']
INFO:__main__:_SUPPORTED_TASKS implies _MAPPED_SCHEMAS={'KB'}
INFO:__main__:Checking load_dataset with config name cardiode_source
WARNING:datasets.builder:Using custom data configuration cardiode_source-ae223f239ced97c2
Dataset =  cardiode
DatasetModule(module_path='datasets_modules.datasets.cardiode.d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582.cardiode', hash='d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582', builder_kwargs={'hash': 'd0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582', 'base_path': 'bigbio\\hub\\hub_repos\\cardiode'})
Downloading and preparing dataset cardiode/cardiode_source to C:/Users/admin/.cache/huggingface/datasets/cardiode/cardiode_source-ae223f239ced97c2/5.0.0/d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582...

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Dataset cardiode downloaded and prepared to C:/Users/admin/.cache/huggingface/datasets/cardiode/cardiode_source-ae223f239ced97c2/5.0.0/d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582. Subsequent calls will reuse this data.

  0%|          | 0/1 [00:00<?, ?it/s]
100%|##########| 1/1 [00:00<00:00, 25.13it/s]
INFO:__main__:schema = source
.
----------------------------------------------------------------------
Ran 1 test in 622.460s

OK
INFO:__main__:self.DATASET_NAME: bigbio/hub/hub_repos/cardiode/cardiode.py
INFO:__main__:self.CONFIG_NAME: cardiode_bigbio_kb
INFO:__main__:self.DATA_DIR: C:\Users\admin\Desktop\cardiode_exp
INFO:__main__:importing module .... 
INFO:__main__:imported module <module 'datasets_modules.datasets.cardiode.d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582.cardiode' from 'C:\\Users\\admin\\.cache\\huggingface\\modules\\datasets_modules\\datasets\\cardiode\\d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582\\cardiode.py'>
INFO:__main__:Checking for _SUPPORTED_TASKS ...
INFO:__main__:Found _SUPPORTED_TASKS=['NAMED_ENTITY_RECOGNITION']
INFO:__main__:_SUPPORTED_TASKS implies _MAPPED_SCHEMAS={'KB'}
INFO:__main__:Checking load_dataset with config name cardiode_bigbio_kb
WARNING:datasets.builder:Using custom data configuration cardiode_bigbio_kb-ae223f239ced97c2
Downloading and preparing dataset cardiode/cardiode_bigbio_kb to C:/Users/admin/.cache/huggingface/datasets/cardiode/cardiode_bigbio_kb-ae223f239ced97c2/1.0.0/d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582...

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Dataset cardiode downloaded and prepared to C:/Users/admin/.cache/huggingface/datasets/cardiode/cardiode_bigbio_kb-ae223f239ced97c2/1.0.0/d0261412145ace95fa13080349f89235cc270b0cae58d94c41e78203b418d582. Subsequent calls will reuse this data.

  0%|          | 0/1 [00:00<?, ?it/s]
100%|##########| 1/1 [00:00<00:00, 31.97it/s]
INFO:__main__:schema = KB
INFO:__main__:Checking global ID uniqueness
INFO:__main__:Found 117870 unique IDs
INFO:__main__:Gathering dataset statistics
INFO:__main__:Testing schema for: train
INFO:__main__:Checking if referenced IDs are properly mapped
INFO:__main__:KB ONLY: Checking passage offsets
INFO:__main__:KB ONLY: Checking entity offsets
INFO:__main__:KB ONLY: multi-label `db_id`
INFO:__main__:KB ONLY: Checking event offsets
INFO:__main__:KB ONLY: Checking coref offsets
INFO:__main__:KB ONLY: multi-label `type` fields
.
----------------------------------------------------------------------
Ran 1 test in 980.770s

OK
train
==========
id: 400
document_id: 400
passages: 96203
entities: 21267
normalized: 0
events: 0
coreferences: 0
relations: 0