Update app.py

app.py

@@ -12,15 +12,21 @@ from spacy.matcher import PhraseMatcher
 from spacy.tokens import Span
 #import en_ner_bc5cdr_md
 import re
-
-
 from streamlit.components.v1 import html
 
-# 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
+if "load_state" not in st.session_state: 
+    st.session_state.load_state = False
+
+#if "button_clicked" not in st.session_state: 
+#    st.session_state.button_clicked = True  
+#    
+#if "daily_button_clicked" not in st.session_state: 
+#    st.session_state.daily_button_clicked = False
 
+if "past_button_clicked" not in st.session_state: 
+    st.session_state.past_button_clicked = False
+    
+       
 #nlp = en_core_web_lg.load()
 nlp = spacy.load("en_ner_bc5cdr_md")
 
@@ -108,9 +114,8 @@ countOfAdmission = len(pastHistoryEpDate)
 
 
 # List of Model available
-#model = st.sidebar.selectbox('Select Model', ('BertSummarizer'))
+#model = st.sidebar.selectbox('Select Model', ('BertSummarizer','BertGPT2','t5seq2eq','t5','gensim','pysummarizer'))
 st.sidebar.markdown("Model: BertSummarizer")
-model = 'BertSummarizer'
 
 # ===== to display selected patient and admission id on main page
 col3,col4 = st.columns(2) 
@@ -137,6 +142,7 @@ dailyNoteChange.rename(columns={'STORETIME':'Time of Record',
 dailyNote = df4['Full Text'].loc[(df4['Patient_ID'] == patient) & (df4['Admission_ID']==HospitalAdmission)]
 dailyNote = dailyNote.unique()
 
+    
 ##========= Buttons to the 5 tabs ======== Temp disabled Discharge Plan and Social Notes 
 ##col1, col2, col3, col4, col5 = st.columns([1,1,1,1,1]) -- to uncomment and comment below line to include discharge plan and social notes 
 col1, col2, col5 = st.columns([1,1,1])
@@ -144,14 +150,11 @@ col6, col7 =st.columns([2,2])
 with st.container():
     with col1:
         btnAdmission = st.button("🏥 Admission")
-        if btnAdmission:
-            #nav_page('Admission')
-            inputNote = "Input Admission Note"
+        inputNote = "Input Admission Note"
+ 
     with col2:
         btnDailyNarrative = st.button('📆Daily Narrative')
-        if btnDailyNarrative:
-            inputNote = "Input Daily Narrative Note"
-#    with col3:
+#    with col3:what
 #        btnDischargePlan = st.button('🗒️Discharge Plan')
 #        if btnDischargePlan:
 #            inputNote = "Input Discharge Plan"
@@ -161,62 +164,11 @@ with st.container():
 #            inputNote = "Input Social Note"
     with col5:
         btnPastHistory = st.button('📇Past History (6 Mths)')
-           
-           
-            
-##========= on Past History Tab  =========
 
-with st.container(): 
-    if btnPastHistory:
-        with col6: 
-            st.markdown('**No. of admission past 6 months:**')
-            st.markdown(countOfAdmission)
-       
-        with col7:
-            #st.date_input('Select Admission Date') # To replace with a dropdown filter instead 
-            #st.selectbox('Past Episodes',pastHistoryEp)
-            pastHistory = st.selectbox('Select Past History Admission', pastHistoryEpDate, format_func=lambda x: 'Select an option' if x == '' else x)
-            
-if btnPastHistory:
-    
-    #st.write('Past History')
-    historyAdmission =  df3.query(
-                "Patient_ID  == @patient & CHARTDATE_HADM_ID == @pastHistory"
-                )
-    runtext = historyAdmission['hospital_course_processed'].values[0]
 
-if not(btnPastHistory) and not(btnDailyNarrative):
-    runtext =st.text_area(inputNote, str(original_text2)[1:-1], height=300)
-    
-    
-
-    
-##========= END on Past History Tab  =========
-
-## ===== Commented out as no longer in use ===== 
-# Extract words associated with each entity
-#def genEntities(ann, entity):
-#              # entity colour dict
-#              #ent_col = {'DISEASE':'#B42D1B', 'CHEMICAL':'#F06292'}
-#              ent_col = {'DISEASE':'pink', 'CHEMICAL':'orange'}
-#              # separate into the different entities
-#              entities = trans_df['Class'].unique()
-#
-#              if entity in entities:
-#                             ent = list(trans_df[trans_df['Class']==entity]['Entity'].unique())
-#                             entlist = ",".join(ent)
-#                             st.markdown(f'<p style="background-color:{ent_col[entity]};color:#080808;font-size:16px;">{entlist}</p>', #unsafe_allow_html=True)
-
-##===== BERT Summary tokenizer =====
 
 ##======================== Start of NER Tagging ========================
-# ====== Old 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)
-# ====== End of Old NER ======
-                  
+                 
 #lemmatizing the notes to capture all forms of negation(e.g., deny: denies, denying)
 def lemmatize(note, nlp):
     doc = nlp(note)
@@ -284,6 +236,63 @@ def dedupe(items):
             yield item
             seen.add(item)
 
+
+
+##======================== End of NER Tagging ========================
+
+def run_model(input_text):    
+    if model == "BertSummarizer":
+        output = original_text['BertSummarizer2s'].values
+        st.write('Summary on History of Presenting illness')
+
+    
+    
+    st.success(output)
+
+##========= on Past History Tab  =========  
+  
+if btnPastHistory or st.session_state["past_button_clicked"]:
+    #st.session_state["button_clicked"] =  False
+    #st.session_state["daily_button_clicked"] =  False
+    st.session_state["past_button_clicked"] =  True
+
+    with st.container(): 
+        with col6: 
+
+            st.markdown('**No. of admission past 6 months:**')
+            st.markdown(countOfAdmission)
+       
+        with col7:
+            #st.date_input('Select Admission Date') # To replace with a dropdown filter instead 
+            #st.selectbox('Past Episodes',pastHistoryEp)
+            pastHistory = st.selectbox('Select Past History Admission', pastHistoryEpDate, format_func=lambda x: 'Select an option' if x == '' else x)        
+    
+    historyAdmission =  df3.query(
+                "Patient_ID  == @patient & CHARTDATE_HADM_ID == @pastHistory"
+                )
+    
+   
+    if historyAdmission.shape[0] == 0:
+        runtext = "No past episodes" 
+    else: 
+        #runtext = historyAdmission['hospital_course_processed'].values[0]
+        runtext = historyAdmission['hospital_course_processed'].values[0]
+        
+if btnAdmission:
+    #st.session_state["daily_button_clicked"] =  False
+    #st.session_state["past_button_clicked"] =  False
+    #st.session_state["button_clicked"] =  True
+    runtext =st.text_area(inputNote, str(original_text2)[1:-1], height=300)
+    
+#if btnDailyNarrative:
+    #st.session_state["button_clicked"] =  False
+    #st.session_state["past_button_clicked"] =  False
+    #st.session_state["daily_button_clicked"] =  True
+
+
+    
+
+
 lem_clinical_note= lemmatize(runtext, nlp)
 #creating a doc object using BC5CDR model
 doc = nlp(lem_clinical_note)
@@ -300,112 +309,104 @@ doc0 = overwrite_ent_lbl(matcher,doc)
 #visualizing identified Named Entities in clinical input text 
 ent_html = displacy.render(doc0, style='ent', options=options)
 
-##======================== End of NER Tagging ========================
-
-def run_model(input_text):    
-    if model == "BertSummarizer":
-        output = original_text['BertSummarizer2s'].values
-        st.write('Summary on History of Presenting illness')
-               
-#    elif model == "BertGPT2":
-#        output = original_text['BertGPT2'].values
-#        st.write('Summary')
-#              
-#    elif model == "t5seq2eq": 
-#        output = original_text['t5seq2eq'].values
-#        st.write('Summary')
-#         
-#    elif model == "t5":
-#        output = original_text['t5'].values
-#        st.write('Summary')
-#        
-#    elif model == "gensim": 
-#        output = original_text['gensim'].values
-#        st.write('Summary')
-#        
-#    elif model == "pysummarizer": 
-#        output = original_text['pysummarizer'].values
-#        st.write('Summary')#
-
 
     
-    st.success(output)
-
-
 col1, col2 = st.columns([1,1])
 
 #to not show summary and references text for Past History and Daily Narrative
-if not(btnPastHistory) and not(btnDailyNarrative):
-        with col1:
-            st.button('Summarize')
-            run_model(runtext)
-            #sentences=runtext.split('.')
-            st.text_area('Reference text', str(reference_text), height=150)
-        with col2:
-            st.button('NER')
-            # ===== Adding the Disease/Chemical into a list =====    
-            problem_entities = list(dedupe([t for t in doc0.ents if t.label_ == 'DISEASE']))
-            medication_entities = list(dedupe([t for t in doc0.ents if t.label_ == 'CHEMICAL']))
-            st.markdown('**CHIEF COMPLAINT:**')
-            st.write(str(AdmissionChiefCom)[1:-1])
-            st.markdown('**ADMISSION DIAGNOSIS:**')
-            st.markdown(str(diagnosis)[1:-1].capitalize())
-            st.markdown('**PROBLEM/ISSUE**')
-            #st.markdown(problem_entities)
-            st.markdown(f'<p style="background-color:PINK;color:#080808;font-size:16px;">{str(problem_entities)[1:-1]}</p>', unsafe_allow_html=True)
-            #genEntities(trans_df, 'DISEASE')
-            st.markdown('**MEDICATION**')
-            st.markdown(f'<p style="background-color:orange;color:#080808;font-size:16px;">{str(medication_entities)[1:-1]}</p>', unsafe_allow_html=True)
-            #genEntities(trans_df, 'CHEMICAL')
-            #st.table(trans_df)   
-            st.markdown('**NER**')
-            with st.expander("See NER Details"):
-                st.markdown(ent_html, unsafe_allow_html=True)
-if btnDailyNarrative: 
+if btnAdmission :
+        
+        #st.session_state["daily_button_clicked"] =  False
+        st.session_state["past_button_clicked"] =  False
+        #st.session_state["button_clicked"] =  True
+
+          
+        with st.container():
+            with col1:
+                st.button('Summarize')
+                run_model(runtext)
+                #sentences=runtext.split('.')
+                st.text_area('Reference text', str(reference_text), height=150)
+            with col2:
+                st.button('NER')
+                # ===== Adding the Disease/Chemical into a list =====    
+                problem_entities = list(dedupe([t for t in doc0.ents if t.label_ == 'DISEASE']))
+                medication_entities = list(dedupe([t for t in doc0.ents if t.label_ == 'CHEMICAL']))
+                st.markdown('**CHIEF COMPLAINT:**')
+                st.write(str(AdmissionChiefCom)[1:-1])
+                st.markdown('**ADMISSION DIAGNOSIS:**')
+                st.markdown(str(diagnosis)[1:-1].capitalize())
+                st.markdown('**PROBLEM/ISSUE**')
+                #st.markdown(problem_entities)
+                st.markdown(f'<p style="background-color:PINK;color:#080808;font-size:16px;">{str(problem_entities)[1:-1]}</p>', unsafe_allow_html=True)
+                #genEntities(trans_df, 'DISEASE')
+                st.markdown('**MEDICATION**')
+                st.markdown(f'<p style="background-color:orange;color:#080808;font-size:16px;">{str(medication_entities)[1:-1]}</p>', unsafe_allow_html=True)
+                #genEntities(trans_df, 'CHEMICAL')
+                #st.table(trans_df)   
+                st.markdown('**NER**')
+                with st.expander("See NER Details"):
+                    st.markdown(ent_html, unsafe_allow_html=True)
+
+                
+elif btnDailyNarrative :
+#    st.session_state["daily_button_clicked"] =  True
+    st.session_state["past_button_clicked"] =  False
+#    st.session_state["button_clicked"] =  False
+   
     with st.container():
         st.markdown('Daily Progress Note (24 hour event only):') 
         st.markdown(str(dailyNote)[1:-1])
  
     
     with st.container():
-#        hide_table_row_index = """
-#                    <style>
-#                    thead tr th:first-child {display:none}
-#                    tbody th {display:none}
-#                    </style>
-#                    """
-#
-#        # Inject CSS with Markdown
-#        st.markdown(hide_table_row_index, unsafe_allow_html=True)
-#        st.table(dailyNoteChange)
         styler = dailyNoteChange.style.hide_index()
         st.write(styler.to_html(), unsafe_allow_html=True)
     st.markdown(f'<p style="color:#828080;font-size:12px;">*Current prototype displays only a single section within the daily progress note, could also potentially include all sections within each progress note and allow user to select the section changes the user wants to look at</p>', unsafe_allow_html=True)
 
 #else:
-if btnPastHistory:
+elif btnPastHistory or st.session_state["past_button_clicked"]:
+    st.session_state["past_button_clicked"] =  True
+#    st.session_state["button_clicked"] =  False
+#    st.session_state["daily_button_clicked"] =  False
 # ===== Adding the Disease/Chemical into a list =====    
     problem_entities = list(dedupe([t for t in doc0.ents if t.label_ == 'DISEASE']))
     medication_entities = list(dedupe([t for t in doc0.ents if t.label_ == 'CHEMICAL']))
-    st.markdown('Admission Date: ' + historyAdmission['ADMITTIME'].values[0])
-    st.markdown('Date of Discharge: ' + historyAdmission['DISCHTIME'].values[0])
-    st.markdown('Days from current admission: ' + str(historyAdmission['days_from_index'].values[0]) +' days')
+    if historyAdmission.shape[0] == 0:
+        st.markdown('Admission Date: NA')
+        st.markdown('Date of Discharge: NA') 
+        st.markdown('Days from current admission: NA')
+    else: 
+        st.markdown('Admission Date: ' + historyAdmission['ADMITTIME'].values[0])
+        st.markdown('Date of Discharge: ' + historyAdmission['DISCHTIME'].values[0])
+        st.markdown('Days from current admission: ' + str(historyAdmission['days_from_index'].values[0]) +' days')
+
     #st.markdown('Summary: ')
     st.markdown(f'<p style="color:#080808;font-size:16px;"><b>Summary: </b></p>', unsafe_allow_html=True)
     
               
     if model == "BertSummarizer":
-        st.markdown(str(historyAdmission['BertSummarizer'].values[0]))
+        if historyAdmission.shape[0] == 0:
+            st.markdown('NA')
+        else: 
+            st.markdown(str(historyAdmission['BertSummarizer'].values[0]))
     elif model == "t5seq2eq":
-        st.markdown(str(historyAdmission['t5seq2eq'].values[0]))
+        if historyAdmission.shape[0] == 0:
+            st.markdown('NA')
+        else: 
+            st.markdown(str(historyAdmission['t5seq2eq'].values[0]))     
     st.markdown(f'<p style="color:#080808;font-size:16px;"><b>Diagnosis: </b></p>', unsafe_allow_html=True)
-    st.markdown(str(historyAdmission['Diagnosis_Description'].values[0]))
-    st.markdown('**PROBLEM/ISSUE**')
-    st.markdown(f'<p style="background-color:PINK;color:#080808;font-size:16px;">{str(problem_entities)[1:-1]}</p>', unsafe_allow_html=True)
-    st.markdown('**MEDICATION**')
-    st.markdown(f'<p style="background-color:orange;color:#080808;font-size:16px;">{str(medication_entities)[1:-1]}</p>', unsafe_allow_html=True)        
-    st.markdown('Discharge Disposition: ' + str(historyAdmission['DISCHARGE_LOCATION'].values[0]))
-    with st.expander('Full Discharge Summary'):
-            #st.write("line 1  \n  line 2  \n line 3")
-            fulldischargesummary = historyAdmission['TEXT'].values[0]
-            st.write(fulldischargesummary)
+    
+    if historyAdmission.shape[0] == 0:
+        st.markdown('NA')
+    else:
+        st.markdown(str(historyAdmission['Diagnosis_Description'].values[0]))
+        st.markdown('**PROBLEM/ISSUE**')
+        st.markdown(f'<p style="background-color:PINK;color:#080808;font-size:16px;">{str(problem_entities)[1:-1]}</p>', unsafe_allow_html=True)
+        st.markdown('**MEDICATION**')
+        st.markdown(f'<p style="background-color:orange;color:#080808;font-size:16px;">{str(medication_entities)[1:-1]}</p>', unsafe_allow_html=True)        
+        st.markdown('Discharge Disposition: ' + str(historyAdmission['DISCHARGE_LOCATION'].values[0]))
+        with st.expander('Full Discharge Summary'):
+                #st.write("line 1  \n  line 2  \n line 3")
+                fulldischargesummary = historyAdmission['TEXT'].values[0]
+                st.write(fulldischargesummary)