def conf_result(): ''' deprecated. returns the confidence result. Keyscore and value score. 1. get arguments from parser 2. use arguments to feed into our keydb_marginal_newkey and get_score from confidenceval 3. return the result in json format. ''' args = parser.parse_args() key = args['key'] value = args['value'] cancername = args['cancer'] if cancername.strip()=='': cancername = args.get('cancer_select') if cancername == None: cancername = request.form.get('cancer_select') marginaldbname = str(cancername)+'.data' if key == None: key = request.form.get('key') value = request.form.get('value') cancername = request.form.get('cancername') if cancername==None: cancername = request.form.get('cancer_select') marginaldbname = str(cancername)+'.data' if key==None or value == None: return ' '.join([str(item) for item in ['No info', 'key',key,'value',value,'cancername',cancername]]) else: keyresult = '' try: marginaldb = keydb_marginal_load(marginaldbname) keyresult = keydb_marginal_newkey(key,marginaldb) except Exception,err: print err print 'ERROR: key db error' stringValResult = '' try: valresult = getScore(key,value,keydb_marginal_load('Valdb.data')) stringValResult = ' '.join([str(item) for item in valresult.values()]) except Exception, err: print err print 'ERROR: val db error'
def Extract(): ''' depracted. Use jsontest instead. this is a nice web interface for testing. user only needs to input text and a univerid, Returns: json formated result from given text and universe_id ''' args = parser.parse_args() note = args['text'] cancerName = args['universe_id'] print 'args:',args print 'form:',request.form #should ahve just check form first then the args. if note == None: note = request.form.get('data') cancerName = request.form.get('cancer') if cancerName is None: cancerName = '' if note == None or note.strip()=='': return 'No info' else: result = {} try: result = checkAllcancer(note) result_confidence= result.copy() for cancer in result.keys(): if cancerName.strip() != '': marginaldbname = cancerName.lower()+'.data' else: marginaldbname=None print 'marginaldbname: ',marginaldbname if marginaldbname is not None: marginaldb = keydb_marginal_load(marginaldbname) else: marginaldb = keydb_marginal_load() ######################################## # the below code is for getting confidence score. ######################################### for k,v in result[cancer].items(): #note that v is a list contains value and original value. value = v[0] #now we can do value processing. #put your code here #now we can do key confidence processing. #it needs a library indicating which unverse it belongs to. #in here we will just try to use our pre-existing libraries. #namely, if you have breast cancer as cancer, then try: result_confidence[cancer][k].append(keydb_marginal_newkey(k,value,marginaldb,marginaldbname,True)) except Exception, err: print 'ERROR: key_confidence failed' print err try: value_score = getScore(k,value,keydb_marginal_load('Valdb.data')) result_confidence[cancer][k].append(' '.join([str(item) for item in value_score.values()])) except Exception, err: print 'ERROR: value_confidence failed' print err result['specimens']=get_section(note)
def set_key_score(self,marginaldb): self.key_score = keydb_marginal_newkey(self.key,marginaldb = marginaldb,dbName = None,add=False)