--- a +++ b/allennlp/elmo-ner.py @@ -0,0 +1,27 @@ +import sys, os + +sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) +print(sys.path) +from ehrkit import ehrkit +from getpass import getpass + +from allennlp.predictors.predictor import Predictor +import allennlp_models.tagging +import json + +# this should be the row ID in NOTEEVENTS +doc_id=int(input("MIMIC Document ID: ")) + +USERNAME = input('DB_username: ') +PASSWORD = getpass('DB_password: ') + +ehrdb = ehrkit.start_session(USERNAME, PASSWORD) +text = ehrdb.get_document(doc_id) + +predictor = Predictor.from_path("https://storage.googleapis.com/allennlp-public-models/ner-model-2020.02.10.tar.gz") +prediction=predictor.predict( + text +) + +with open(str(doc_id)+'.json', 'w', encoding='utf-8') as f: + json.dump(prediction, f, ensure_ascii=False, indent=4) \ No newline at end of file