Update app.py

app.py

@@ -24,11 +24,14 @@ 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')   
+dataICD10 = pd.read_csv(f'ICD10Diagnosis.csv')
+dataASMT = pd.read_csv(f'TemplateInfoMessage.csv')  
 
 dir_path = os.path.dirname(os.path.realpath(__file__))
 EXAMPLES = {}
@@ -76,6 +79,14 @@ 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__)
@@ -86,12 +97,12 @@ def SaveResult(text, outputfileName):
     if file_exists:
         with open(outputfileName, "a") as f: #append
             #for line in text:
-            f.write(str(text.replace("\n"," ")))
+            f.write(str(text.replace("\n","  ")))
             f.write('\n')
     else:
         with open(outputfileName, "w") as f: #write
             #for line in text:
-            f.write(str(text.replace("\n"," ")))
+            f.write(str(text.replace("\n","  ")))
             f.write('\n')
     #except ValueError as err:
     #    raise ValueError("File Save Error in SaveResult \n" + format_tb(err.__traceback__)[0] + err.args[0] + "\nEnd of error message.") from None
@@ -121,7 +132,8 @@ 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.%M.%S.%p")
+    date = datetime.now().strftime("%Y_%m_%d-%I")
     #print(f"filename_{date}")  'filename_2023_01_12-03-29-22_AM'
     return f"MedNER_{date}.csv"
 
@@ -151,6 +163,7 @@ def group_by_entity(raw):
                 g3=MatchSNOMED(eterm)
                 g4=MatchOMS(eterm)
                 g5=MatchICD10(eterm)
+                g6=MatchASMT(eterm)
                 sAll = ""
 
                 print("Saving to output file " + outputFile)
@@ -195,6 +208,13 @@ 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
 
@@ -227,6 +247,7 @@ 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)