SnomedctExpander.py

from Expander import Expander
from singletonConceptId import *

from pymedtermino import *
from pymedtermino.snomedct import *
from pymetamap import MetaMap
from Authentication import *

from flask import Flask, request, abort
import requests
import json
import diskcache as dc

import logging
from logging import config

'''
@Author: Khyathi Raghavi Chandu
@Date: October 17 2017

This code returns the sentence passed as argument with concept expansion from SNOMEDCT ontology.
'''

logging.config.fileConfig('logging.ini')
logger = logging.getLogger('bioAsqLogger')


#This is a subclass that extends the abstract class Expander.
class SnomedctExpander(Expander):

	'''
	The abstract method from the base class is implemeted here to return a string of the original sentence with
	expansion from SNOMEDCT.
	This method takes a string as input and returns the expanded string as output.
	'''
	def getExpansions(self,sentence):
		logger.info('In getExpansions function of SnomedctExpander')
		self.cache = SingletonSNOMEDCTCache.Instance().cache
		synonyms = []
		synonyms = sentence.strip().split()
		metaConcepts = self.getMetaConcepts(sentence)

		for mconcept in metaConcepts:
			try:
				for el in self.cache[mconcept]:
					synonyms.append(el)
				logger.info('Found SNOMEDCT Cached Concept: '+ str(mconcept.preferred_name))
			except:
				try:
					#a full text search is performed on the preferred names of the biomedical concepts
					termSyns = []
					prefName = mconcept.preferred_name
					conceptSyns = SNOMEDCT.search(prefName)
					for uconcept in conceptSyns:
						for el in uconcept.terms: #.terms is also possible for all synonyms
							termSyns.append(el)
							synonyms.append( el )
					self.cache[mconcept] = termSyns
					logger.info('Performed expansions using SNOMECT')
				except Exception as e:
					logger.debug('Exception in SNOMEDCT Expansion '+ str(e))
					pass
		#class method from Expander to stop the meta map instance that is running
		#self.stopMetaMap()
		listSynonyms = list(set(synonyms))
		#Returning the expanded sentence
		ExpandedSentence = ' '.join(listSynonyms)
		return ExpandedSentence

#Since the abstract method from the base class Expander is implemented, uncommenting the following lines will allow this code to run.
#Unit Testing to check the working of SnomedctExpander class
'''
instance = SnomedctExpander()
print instance.getExpansions("John has cancer")
'''