Script de inserción

UMLS_Extractor/insertUMLSConcepts.py

+import configparser
+import mysql.connector
+
+#Diccionario con los datos de conexion a la BBDD (se lee desde archivo de configuracion: DEFAULT --> LOCAL, TESTING --> ARES)
+configuration = configparser.ConfigParser()
+configuration.read('config.ini')
+
+config2 = {'user':configuration['ARES']['DB_USER'],
+'password':configuration['ARES']['DB_PASSWORD'],
+'port':configuration['ARES']['DB_PORT'],
+'host':configuration['ARES']['DB_HOST'],
+'db':configuration['ARES']['DB_NAME'],
+'auth_plugin':configuration['ARES']['DB_AUTH_PLUGIN']
+}
+
+text = open("./output2.txt").read()
+lines = iter(text.split("\n"))
+#Conectamos con nuestra BD
+cnx = mysql.connector.connect(**config2)
+#Creamos el cursor 
+cursor = cnx.cursor()
+
+try:
+	for line in lines:
+		item = line.split("\t")
+		query = ""
+		#print(item)
+
+		if("JKES" in item): #JKES
+			query = "insert ignore into concept_extraction.note_umls (note_id,umls_id,begin,end,concept_text,origin) values ('"+item[3]+"','"+item[1]+"','"+item[4]+"','"+item[5]+"','"+item[0]+"','JKES');"
+			query2 = "insert ignore into concept_extraction.umls (umls_id,concept) values ('"+item[1]+"','"+item[0]+"');"
+			
+		elif("UMLS" in item): #UMLS
+			jkes_concept = item[0]
+			for j in range(6,len(item)):
+				aux = item[j].split(",")
+				noteID = aux[0].replace("(","").replace("'","")
+				begin = aux[1].replace("'","").strip()
+				end = aux[2].replace(")","").replace("'","").strip()
+				print(item[4])
+				
+				query = "insert ignore into concept_extraction.note_umls (note_id,umls_id,levenshtein_distance,begin,end,concept_text,origin) values ('"+noteID+"','"+item[3]+"','"+item[4]+"','"+begin+"','"+end+"','"+item[0]+"','UMLS');"
+				query2 = "insert ignore into concept_extraction.umls (umls_id,concept) values ('"+item[3]+"','"+item[2]+"');"
+
+		print(query2)
+		print(query)
+		cursor.execute(query2)
+		cnx.commit()
+		cursor.execute(query)
+		cnx.commit()
+
+	cursor.close()
+	cnx.close()
+
+except mysql.connector.IntegrityError as err:
+  print("Error: {}".format(err))