from pathlib import Path import os import numpy as np import os import time import math from huggingface_hub import login from datasets import load_dataset, concatenate_datasets from functools import reduce import pandas as pd # Load model directly from transformers import AutoTokenizer, AutoModelForCausalLM HF_TOKEN = '' DATASET_TO_LOAD = 'PlanTL-GOB-ES/pharmaconer' DATASET_TO_UPDATE = 'somosnlp/spanish_medica_llm' CSV_FILE_NAME = "enfermedades_long.csv" #Loggin to Huggin Face login(token = HF_TOKEN) dataset_CODING = load_dataset(DATASET_TO_LOAD) dataset_CODING royalListOfCode = {} issues_path = 'dataset' tokenizer = AutoTokenizer.from_pretrained("DeepESP/gpt2-spanish-medium") DATASET_SOURCE_ID = '7' #Read current path path = Path(__file__).parent.absolute() def readCsvFIle(): """ """ cantemistDstDict = { 'raw_text': '', 'topic': '', 'speciallity': '', 'raw_text_type': 'question', 'topic_type': '', 'source': DATASET_SOURCE_ID, 'country': '', 'document_id': '' } totalOfTokens = 0 corpusToLoad = [] countCopySeveralDocument = 0 counteOriginalDocument = 0 idFile = 0 path = Path(__file__).parent.absolute() both_diagnostic_tratamient = open_text = type_tratamient = type_diagnostic = both_diagnostic_tratamient = 0 df = pd.read_csv(f"{str(path)+ os.sep + CSV_FILE_NAME}",encoding='utf8') df = df.replace({np.nan: None}) print(df.columns) for i in range(len(df)): counteOriginalDocument += 1 newCorpusRow = cantemistDstDict.copy() idFile += 1 text = df.loc[i, 'Abstract'] newCorpusRow['speciallity'] = df.loc[i, 'Enfermedad'] if df.loc[i, 'Enfermedad'] != None else '' listOfTokens = tokenizer.tokenize(text) currentSizeOfTokens = len(listOfTokens) totalOfTokens += currentSizeOfTokens newCorpusRow['raw_text'] = text newCorpusRow['document_id'] = str(idFile) if df.loc[i, 'Tratamiento'] == None and df.loc[i, 'Diagnostico'] == None: open_text += 1 newCorpusRow['topic_type'] = 'open_text' newCorpusRow['raw_text_type'] = 'open_text' elif df.loc[i, 'Tratamiento'] != None and df.loc[i, 'Diagnostico'] == None: type_tratamient += 1 newCorpusRow['topic_type'] = 'medical_diagnostic' newCorpusRow['topic'] = df.loc[i, 'Tratamiento'] elif df.loc[i, 'Tratamiento'] == None and df.loc[i, 'Diagnostico'] != None: type_diagnostic += 1 newCorpusRow['topic_type'] = 'medical_topic' newCorpusRow['topic'] = df.loc[i, 'Diagnostico'] elif df.loc[i, 'Tratamiento'] != None and df.loc[i, 'Diagnostico'] != None: both_diagnostic_tratamient += 1 tratmentCorpusRow = newCorpusRow.copy() newCorpusRow['topic_type'] = 'medical_diagnostic' newCorpusRow['topic'] = df.loc[i, 'Diagnostico'] tratmentCorpusRow['topic_type'] = 'medical_topic' tratmentCorpusRow['topic'] = df.loc[i, 'Tratamiento'] corpusToLoad.append(tratmentCorpusRow) corpusToLoad.append(newCorpusRow) #print(df.loc[i, "Abstract"], df.loc[i, "Diagnostico"]) print(" Size with Open Text " + str(open_text)) print(" Size with only tratamient " + str(type_tratamient)) print(" Size with only diagnosti " + str(type_diagnostic)) print(" Size with both tratamient and diagnosti " + str(both_diagnostic_tratamient)) dfToHub = pd.DataFrame.from_records(corpusToLoad) if os.path.exists(f"{str(path)}/{issues_path}/spanish_medical_llms.jsonl"): os.remove(f"{str(path)}/{issues_path}/spanish_medical_llms.jsonl") dfToHub.to_json(f"{str(path)}/{issues_path}/spanish_medical_llms.jsonl", orient="records", lines=True) print( f"Downloaded all the issues for {DATASET_TO_LOAD}! Dataset stored at {issues_path}/spanish_medical_llms.jsonl" ) print(' On dataset there are as document ', counteOriginalDocument) print(' On dataset there are as copy document ', countCopySeveralDocument) print(' On dataset there are as size of Tokens ', totalOfTokens) file = Path(f"{str(path)}/{issues_path}/spanish_medical_llms.jsonl") # or Path('./doc.txt') size = file.stat().st_size print ('File size on Kilobytes (kB)', size >> 10) # 5242880 kilobytes (kB) print ('File size on Megabytes (MB)', size >> 20 ) # 5120 megabytes (MB) print ('File size on Gigabytes (GB)', size >> 30 ) # 5 gigabytes (GB) ##Update local dataset with cloud dataset local_spanish_dataset = load_dataset("json", data_files=f"{str(path)}/{issues_path}/spanish_medical_llms.jsonl", split="train") print ('<== Local Dataset ==> ') print(local_spanish_dataset) try: spanish_dataset = load_dataset(DATASET_TO_UPDATE, split="train") spanish_dataset = concatenate_datasets([spanish_dataset, local_spanish_dataset]) print('<--- Copy files --->') except Exception: spanish_dataset = local_spanish_dataset spanish_dataset.push_to_hub(DATASET_TO_UPDATE) print(spanish_dataset) readCsvFIle()