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_value_score(self,valdb):
# print "key",self.key,"value",self.value
self.value_score = getScore(self.key,self.value,valdb = valdb, add=True)