Update app.py

app.py

@@ -5,11 +5,11 @@ from math import ceil
 from collections import Counter
 from string import punctuation
 import spacy
+from negspacy.negation import Negex
 from spacy import displacy
 from spacy.lang.en import English
 from spacy.matcher import PhraseMatcher
 from spacy.tokens import Span
-from negspacy.negation import Negex
 #import en_ner_bc5cdr_md
 import re
 
@@ -63,6 +63,12 @@ del df2
 # Remove decimal point from Admission ID
 df['HADM_ID'] = df['HADM_ID'].astype(str).apply(lambda x: x.replace('.0',''))
 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["TEXT"] =df3["TEXT"].replace(r'\n','  \n ', regex=True) 
+
 
 #Renaming column
 df.rename(columns={'SUBJECT_ID':'Patient_ID',
@@ -70,7 +76,8 @@ df.rename(columns={'SUBJECT_ID':'Patient_ID',
                   'hpi_input_text':'Original_Text',
                   'hpi_reference_summary':'Reference_text'}, inplace = True)
 df3.rename(columns={'SUBJECT_ID':'Patient_ID',
-                   'HADM_ID':'Admission_ID'}, inplace = True) 
+                   'HADM_ID':'PAST_Admission_ID',
+                   'INDEX_HADM_ID':'Admission_ID'}, inplace = True) 
 
 #Filter selection 
 st.sidebar.header("Search for Patient:")
@@ -79,8 +86,8 @@ st.sidebar.header("Search for Patient:")
 patientid = df['Patient_ID']
 patient = st.sidebar.selectbox('Select Patient ID:', patientid)    #Filter Patient
 admissionid = df['Admission_ID'].loc[df['Patient_ID'] == patient]  #Filter available Admission id for patient
-HospitalAdmission = st.sidebar.selectbox(' ', admissionid)         
-pastHistoryEpid = df3['Admission_ID'].loc[df3['Patient_ID'] == patient] #Filter list of available Past History (for History tab)
+HospitalAdmission = st.sidebar.selectbox(' ', admissionid)   
+pastHistoryEpDate = df3['CHARTDATE_HADM_ID'].loc[(df3['Patient_ID'] == patient) & (df3['Admission_ID']== HospitalAdmission)] 
 
 
 # List of Model available
@@ -108,7 +115,7 @@ reference_text = original_text['Reference_text'].values
 ##========= 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])
-col6, col7, col8 =st.columns([2,2,2])
+col6, col7 =st.columns([2,2])
 with st.container():
     with col1:
         btnAdmission = st.button("🏥 Admission")
@@ -133,41 +140,53 @@ with st.container():
             inputNote = "Input History records"
 
 ##========= on Past History Tab  =========
-if btnPastHistory:
-    st.text_area('Past History','Date of discharge: xxxxxxxxx')
-    
-else:
-    runtext =st.text_area(inputNote, str(original_text2), height=300)
-    
-    
+
 with st.container(): 
     if btnPastHistory:
         with col6: 
             st.markdown('**No. of admission past 6 months: xx**')
-        with col7: 
-            st.text_area('Discharge Disposition:',' ', height=8) #to replace with dropdown list if data is available 
-        with col8:
+       
+        with col7:
             #st.date_input('Select Admission Date') # To replace with a dropdown filter instead 
             #st.selectbox('Past Episodes',pastHistoryEp)
-            pastHistory = st.selectbox(' ', pastHistoryEpid)
-
+            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]))
+    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]))
+else:
+    runtext =st.text_area(inputNote, str(original_text2), 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)
+#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)
 
 
 ##======================== Start of NER Tagging ========================
@@ -304,12 +323,11 @@ with col1:
         st.text_area('Reference text', str(reference_text), height=150)
     else: 
         with st.expander('Full Discharge Summary'):
-            historyAdmission =  df3.query(
-                "Patient_ID  == @patient & Admission_ID == @pastHistory"
-                )
-            fulldischargesummary = historyAdmission['TEXT'].values
-            st.write( str(fulldischargesummary))
-    ##====== Storing the Diseases/Text
+            #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:
@@ -319,20 +337,23 @@ with col1:
         # table["Class"].append(ent_bc[key])
     # trans_df = pd.DataFrame(table)
     
+# ===== 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))
+    st.write(str(AdmissionChiefCom)[1:-1])
     st.markdown('**ADMISSION DIAGNOSIS:**')
-    st.markdown(str(diagnosis))
+    st.markdown(str(diagnosis)[1:-1])
     st.markdown('**PROBLEM/ISSUE**')
     #st.markdown(problem_entities)
-    genEntities(trans_df, 'DISEASE')
+    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**')
-    genEntities(trans_df, 'CHEMICAL')
+    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"):