--- a
+++ b/ehrkit/README.md
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+# 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):*