Update app.py

app.py

@@ -24,14 +24,11 @@ basedir = os.path.dirname(__file__)
 #dataOMS = pd.read_csv(basedir + "\\" + f'SnomedOMS.csv')   
 #dataICD10 = pd.read_csv(basedir + "\\" + f'ICD10Diagnosis.csv') 
 
-filepath = '/Users/konyeach/src/Biomed_NLP_AI/'
-
 dataLOINC = pd.read_csv(f'LoincTableCore.csv')
 dataPanels = pd.read_csv(f'PanelsAndForms-ACW1208Labeled.csv')     
 dataSNOMED = pd.read_csv(f'sct2_TextDefinition_Full-en_US1000124_20220901.txt',sep='\t')   
 dataOMS = pd.read_csv(f'SnomedOMS.csv')   
-dataICD10 = pd.read_csv(f'ICD10Diagnosis.csv')
-dataASMT = pd.read_csv(f'TemplateInfoMessage.csv')  
+dataICD10 = pd.read_csv(f'ICD10Diagnosis.csv')   
 
 dir_path = os.path.dirname(os.path.realpath(__file__))
 EXAMPLES = {}
@@ -79,14 +76,6 @@ def MatchICD10(name):
     swith=data.loc[data['Description'].str.contains(name, case=False, na=False)]
     return swith
 
-def MatchASMT(name):
-    #basedir = os.path.dirname(__file__)
-    pd.set_option("display.max_rows", None)
-    #data = pd.read_csv(basedir + "\\" + f'LoincTableCore.csv')    
-    data = dataLOINC
-    swith=data.loc[data['AssessmentInfo'].str.contains(name, case=False, na=False)]
-    return swith
-
 def SaveResult(text, outputfileName):
     #try:
     basedir = os.path.dirname(__file__)
@@ -112,7 +101,7 @@ def SaveResult(text, outputfileName):
 def loadFile(filename):
     try:
         basedir = os.path.dirname(__file__)
-        loadPath = basedir + "/" + filename
+        loadPath = basedir + "\\" + filename
 
         print("Loading: " + loadPath)
 
@@ -132,8 +121,7 @@ def loadFile(filename):
 
 def get_today_filename():
     from datetime import datetime
-    # date = datetime.now().strftime("%Y_%m_%d-%I.%M.%S.%p")
-    date = datetime.now().strftime("%Y_%m_%d-%I")
+    date = datetime.now().strftime("%Y_%m_%d-%I.%M.%S.%p")
     #print(f"filename_{date}")  'filename_2023_01_12-03-29-22_AM'
     return f"MedNER_{date}.csv"
 
@@ -152,7 +140,8 @@ def group_by_entity(raw):
         myEntityGroup = ent["entity_group"]
         print("Found entity group type: " + myEntityGroup)
 
-        if (myEntityGroup in ['Sign_symptom', 'Detailed_description', 'History', 'Activity', 'Medication' ]):
+#        if (myEntityGroup in ['Sign_symptom', 'Detailed_description', 'History', 'Activity', 'Medication', 'DISEASE_DISORDER' ]):
+        if (myEntityGroup not in ['Match All']):
             eterm = ent["word"].replace('#','')
             minlength = 3
             if len(eterm) > minlength:
@@ -163,7 +152,6 @@ def group_by_entity(raw):
                 g3=MatchSNOMED(eterm)
                 g4=MatchOMS(eterm)
                 g5=MatchICD10(eterm)
-                g6=MatchASMT(eterm)
                 sAll = ""
 
                 print("Saving to output file " + outputFile)
@@ -208,13 +196,6 @@ def group_by_entity(raw):
                     s5 = ("ICD10," + myEntityGroup + "," + eterm + ",descriptions of ," + g52 + "," + g51 + ", Label,Value, Label,Value, Label,Value  ")
                     if g51 != 'Series([]  )': SaveResult(s5, outputFile)
 
-                    #ASMT
-                    g61 = g6['ID'].to_string().replace(","," ").replace("\n"," ")
-                    g62 = g6['AssessmentName'].to_string().replace(","," ").replace("\n"," ")
-                    g63 = g6['AssessmentInfo'].to_string().replace(","," ").replace("\n"," ")
-                    s6 = ("ASMT," + myEntityGroup + "," + eterm + ",assessment info ," + g62 + "," + g63 + ", Label,Value, Label,Value, Label,Value  ")
-                    if g63 != 'Series([]  )': SaveResult(s6, outputFile)
-
                 except ValueError as err:
                     raise ValueError("Error in group by entity \n" + format_tb(err.__traceback__)[0] + err.args[0] + "\nEnd of error message.") from None
 
@@ -247,7 +228,6 @@ def ner(text):
     }
     
     outputFile = group_by_entity(raw)
-    # print("print" + " " + outputFile)
     label = EXAMPLES.get(text, "Unknown")
     outputDataframe = pd.read_csv(outputFile)
     return (ner_content, outputDataframe, outputFile)
@@ -286,4 +266,4 @@ with demo:
         gr.Examples(examples, inputs=input)
         input.change(fn=ner, inputs=input, outputs=output)
 #layout="vertical"
-demo.launch(debug=True)
+demo.launch(debug=True)