app.py

import streamlit as st
import pandas as pd
import numpy as np
from math import ceil
from collections import Counter
from string import punctuation
import spacy
from spacy import displacy
import en_ner_bc5cdr_md

from streamlit.components.v1 import html

def nav_page(page_name, timeout_secs=8):
    nav_script = """
        <script type="text/javascript">
            function attempt_nav_page(page_name, start_time, timeout_secs) {
                var links = window.parent.document.getElementsByTagName("a");
                for (var i = 0; i < links.length; i++) {
                    if (links[i].href.toLowerCase().endsWith("/" + page_name.toLowerCase())) {
                        links[i].click();
                        return;
                    }
                }
                var elasped = new Date() - start_time;
                if (elasped < timeout_secs * 1000) {
                    setTimeout(attempt_nav_page, 100, page_name, start_time, timeout_secs);
                } else {
                    alert("Unable to navigate to page '" + page_name + "' after " + timeout_secs + " second(s).");
                }
            }
            window.addEventListener("load", function() {
                attempt_nav_page("%s", new Date(), %d);
            });
        </script>
    """ % (page_name, timeout_secs)
    html(nav_script)
    

# Store the initial value of widgets in session state
if "visibility" not in st.session_state:
    st.session_state.visibility = "visible"
    st.session_state.disabled = False

#nlp = en_core_web_lg.load()
nlp = spacy.load("en_ner_bc5cdr_md")

st.set_page_config(page_title ='Clinical Note Summarization', 
                   #page_icon= "Notes",
                   layout='wide')
st.title('Clinical Note Summarization')
st.markdown(
    """
    <style>
    [data-testid="stSidebar"][aria-expanded="true"] > div:first-child {
        width: 400px;
    }
    [data-testid="stSidebar"][aria-expanded="false"] > div:first-child {
        width: 400px;
        margin-left: -230px;
    }
    </style>
    """,
    unsafe_allow_html=True,
)
st.sidebar.markdown('Using transformer model')

## Loading in dataset
#df = pd.read_csv('mtsamples_small.csv',index_col=0)
df = pd.read_csv('shpi_w_rouge21Nov.csv')
df['HADM_ID'] = df['HADM_ID'].astype(str).apply(lambda x: x.replace('.0',''))

#Renaming column
df.rename(columns={'SUBJECT_ID':'Patient_ID',
                  'HADM_ID':'Admission_ID',
                  'hpi_input_text':'Original_Text',
                  'hpi_reference_summary':'Reference_text'}, inplace = True)
 
 #data.rename(columns={'gdp':'log(gdp)'}, inplace=True)

#Filter selection 
st.sidebar.header("Search for Patient:")

patientid = df['Patient_ID']
patient = st.sidebar.selectbox('Select Patient ID:', patientid)
admissionid = df['Admission_ID'].loc[df['Patient_ID'] == patient]
HospitalAdmission = st.sidebar.selectbox('', admissionid) 

# List of Model available
model = st.sidebar.selectbox('Select Model', ('BertSummarizer','BertGPT2','t5seq2eq','t5','gensim','pysummarizer'))

col3,col4 = st.columns(2) 
patientid = col3.write(f"Patient ID:  {patient} ")
admissionid =col4.write(f"Admission ID:  {HospitalAdmission} ")
runtext = ''
inputNote  ='Input note here:'
# Query out relevant Clinical notes
original_text =  df.query(
    "Patient_ID  == @patient & Admission_ID == @HospitalAdmission"
)
original_text2 = original_text['Original_Text'].values
reference_text = original_text['Reference_text'].values

##========= Buttons to the 4 tabs ========
col1, col2, col3, col4 = st.columns(4)

with col1:
    if st.button("🏥 Admission"):
        #nav_page('Admission')
        inputNote = "Input Admission Note"
    
with col2:
    if st.button('📆Daily Narrative'):
        #nav_page('Daily Narrative')
        inputNote = "Input Daily Narrative Note"
with col3:
    if st.button('🗒️Discharge Plan'):
        #nav_page('Discharge Plan')  
        inputNote = "Input Discharge Plan"
with col4:
    if st.button('📝Social Notes'):
        #nav_page('Social Notes')
        inputNote = "Input Social Note"

runtext =st.text_area(inputNote, str(original_text2), height=300)

def visualize (run_text,output):
    text =''
    import spacy
    from spacy.lang.en import English # updated
    nlp=spacy.load('en_core_web_sm')
    sentences=run_text.split('.')
    summary=output.split('.')

    text = ''

    display(HTML(f'<h1>Summary - {title}</h1>'))
    for sentence in sentence_list:
        if sentence in best_sentences:
            text += ' ' + str(sentence).replace(sentence, f"<mark>{sentence}</mark>")
        else:
            text += ' ' + sentence
        display(HTML(f""" {text} """))
    best_sentences = []
    for sentence in summary:
       best_sentences.append(str(sentence))

    

def run_model(input_text):    
    if model == "BertSummarizer":
        output = original_text['BertSummarizer'].values
        st.write('Summary')
        st.success(output[0])

    elif model == "BertGPT2":
        output = original_text['BertGPT2'].values
        st.write('Summary')
        st.success(output[0])
        
      
    elif model == "t5seq2eq": 
        output = original_text['t5seq2eq'].values
        st.write('Summary')
        st.success(output)
        
    elif model == "t5":
        output = original_text['t5'].values
        st.write('Summary')
        st.success(output)
        
    elif model == "gensim": 
        output = original_text['gensim'].values
        st.write('Summary')
        st.success(output)
        
    elif model == "pysummarizer": 
        output = original_text['pysummarizer'].values
        st.write('Summary')
        st.success(output)

col1, col2 = st.columns([1,1])

with col1:
    st.button('Summarize')
    run_model(runtext)
    sentences=runtext.split('.')
    st.text_area('Reference text', str(reference_text))#,label_visibility="hidden")
with col2:
    st.button('NER')
    doc = nlp(str(original_text2))
    colors = { "DISEASE": "pink","CHEMICAL": "orange"}
    options = {"ents": [ "DISEASE", "CHEMICAL"],"colors": colors}
    ent_html = displacy.render(doc, style="ent", options=options)
    st.markdown(ent_html, unsafe_allow_html=True) 
    
    
col3, col4 = st.columns(2)
with col3: 
    st.text_area(visualize (run_text,output))
    
with col4: 
    st.text_area('testing', str(reference_text))#,label_visibility="hidden")