# EHRKit Documentation

## Directory Structure

* EHRKit

  * ehrkit

    * ehrkit.py

    * solr_lib.py

    * classes.py

  * external

    * icd9

      * status: incorporated but doesn't seem useful

    * patient2vec

      * status: not yet incorporated

      * could be useful:

    * phrase-at-scale

      * status: incorporated, but only a crude version

      * problem: does not return the phrases but outputs it to files

  * scripts

    * helper scripts for handling data

    * see README_scripts for more descriptions

  * tests

    * see README_tests for more descriptions

## ehrkit.py functions

* helper functions:

  * *def start_session(db_user, db_pass): -> dict*:

  * *def createPatient(data):*

  * *def flatten(lst):*

  * *def numbered_print(lst):*

  * *def init_embedding_model():*

  * *def get_abbs_sent_ids(text):*

  * *def post_single_dict_to_solr(d: dict, core: str)-> None*

  * *def abbs_disambiguate(ABB):*

  * *def get_documents_solr(query):*

* *class ehr_db*

  * attributes:

    * *cnx* -- MySQL connection object

    * *cur* -- MySQL cursor

    * *patients = {}* -- Patient (from classes.py) dictionary

  * methods:

    * *def close_session(self):*

    * *def get_patients(self, n):*

    * *def count_patients(self):*

    * *def count_gender(self, gender):*

    * *def count_docs(self, query, getAll = False, inverted = False):*

    * *def get_note_events(self):*

    * *def longest_NE(self):*

    * *def get_document(self, id):*

    * *def get_all_patient_document_ids(self, patientID):*

    * *def list_all_patient_ids(self):*

    * *def list_all_document_ids(self):*

    * *def get_document_sents(self, docID):*

    * *def get_abbreviations(self, doc_id):*

    * *def get_abbreviation_sent_ids(self, doc_id):*

    * *def get_documents_d(self, date):*

    * *def get_documents_q(self, query, n = -1):*

    * *def get_documents_icd9_alt(self,query):*

    * *def get_documents_icd9(self,code):*

    * *def get_prescription(self):*

    * *def extract_key_words(self, text):*

    * *def count_all_prescriptions(self):*

    * *def get_diagnoses(self):*

    * *def get_procedures(self):*

    * *def extract_patient_words(self, patientID):*

    * *def output_note_events_file_by_patients(self, directory):*

    * *def output_note_events_discharge_summary(self, directory):*

  * yet to refactor:

    * *def extract_key_words(self, text):*

    * *def get_abbreviations(self, doc_id):*

    * *def get_abbreviation_sent_ids(self, doc_id):*

  * unfinished:

    * *def docs_with_phrase(self, phrase):*

    * *def outputAbbreviation(self, directory):*

    * *def extract_phrases(self, docID):*