Update app.py

app.py

@@ -66,6 +66,7 @@ df3['HADM_ID'] = df3['HADM_ID'].astype(str).apply(lambda x: x.replace('.0',''))
 df3['INDEX_HADM_ID'] = df3['INDEX_HADM_ID'].astype(str).apply(lambda x: x.replace('.0',''))
 df3["CHARTDATE_HADM_ID"] = df3["CHARTDATE"].astype(str) +' - '+ df3["HADM_ID"]
 df3["DIAGNOSIS"] = df3["DIAGNOSIS"].str.capitalize()
+df3["DISCHARGE_LOCATION"] = df3["DISCHARGE_LOCATION"].str.capitalize()
 
 df3["TEXT"] =df3["TEXT"].replace(r'\n','  \n ', regex=True) 
 
@@ -139,6 +140,9 @@ with st.container():
         if btnPastHistory:          
             inputNote = "Input History records"
 
+            
+            
+            
 ##========= on Past History Tab  =========
 
 with st.container(): 
@@ -152,20 +156,16 @@ with st.container():
             pastHistory = st.selectbox(' ', pastHistoryEpDate,on_change=None,)
             
 if btnPastHistory:
+    
     st.write('Past History')
     historyAdmission =  df3.query(
                 "Patient_ID  == @patient & CHARTDATE_HADM_ID == @pastHistory"
                 )
-    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: ')
     if model == "BertSummarizer":
-        st.markdown(str(historyAdmission['BertSummarizer'].values[0]))
+        runtext = historyAdmission['BertSummarizer'].values[0]
     elif model == "t5seq2eq":
-        st.markdown(str(historyAdmission['t5seq2eq'].values[0]))
-    st.markdown('Diagnosis: ' + str(historyAdmission['DIAGNOSIS'].values[0]))
-    st.markdown('Discharge Disposition: ' + str(historyAdmission['DISCHARGE_LOCATION'].values[0]))
+        runtext = historyAdmission['t5seq2eq'].values[0]
+   
 else:
     runtext =st.text_area(inputNote, str(original_text2), height=300)
     
@@ -315,46 +315,51 @@ def run_model(input_text):
 
 col1, col2 = st.columns([1,1])
 
-with col1:
-    if not(btnPastHistory): #to not show summary and references text for Past History
-        st.button('Summarize')
-        run_model(runtext)
-        #sentences=runtext.split('.')
-        st.text_area('Reference text', str(reference_text), height=150)
-    else: 
-        with st.expander('Full Discharge Summary'):
-            #st.write("line 1  \n  line 2  \n line 3")
-            fulldischargesummary = historyAdmission['TEXT'].values[0]
-            st.write(fulldischargesummary)
-            
-    ##====== Storing the Diseases/Text -No longer in use 
-    # table= {"Entity":[], "Class":[]}
-    # ent_bc = {}
-    # for x in doc.ents:
-        # ent_bc[x.text] = x.label_
-    # for key in ent_bc:
-        # table["Entity"].append(key)
-        # table["Class"].append(ent_bc[key])
-    # trans_df = pd.DataFrame(table)
-    
+if not(btnPastHistory): #to not show summary and references text for Past History
+        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])
+            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)
+else: 
 # ===== 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']))
-    
-with col2:
-    st.button('NER')
-    st.markdown('**CHIEF COMPLAINT:**')
-    st.write(str(AdmissionChiefCom)[1:-1])
-    st.markdown('**ADMISSION DIAGNOSIS:**')
-    st.markdown(str(diagnosis)[1:-1])
+    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: ')
+    if model == "BertSummarizer":
+        st.markdown(str(historyAdmission['BertSummarizer'].values[0]))
+    elif model == "t5seq2eq":
+        st.markdown(str(historyAdmission['t5seq2eq'].values[0]))
+    st.markdown('Diagnosis: ' + str(historyAdmission['DIAGNOSIS'].values[0]))
     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)
+    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)