def cover_protected_data(data_list, resource, patient_id, status='full'):
'''
data_list : sometimes we don't wanna display all part of this resource, this list will tell us which to display,a list
resource : json data that wanna to display, the format is dict
patient_id : extract identifier of policy_list
'''
privacy_policy = db.select_policy(patient_id)
if (privacy_policy == -2):
#No record in the database
return resource
policy_data = jd.json2list(privacy_policy, RESERVED_WORD)
if type(data_list) is dict:
jd.json_reduce_structure(data_list)
data_list = jd.json2list(data_list, RESERVED_WORD)
if isinstance(resource['resourceType'], unicode):
s = resource['resourceType']
else:
s = unicode(resource['resourceType'], "utf-8")
jd.json_reduce_structure(resource)
resource_data = jd.json2list(resource, RESERVED_WORD)
for i in range(len(resource_data)):
resource_data[i].insert(0, s)
data = data_list
for i in range(len(data)):
data[i].insert(0, s)
#If the query is only part of data,then do the intersection
for i in range(len(data)):
if data[i][1] == 'text' or data[i][1] == 'resourceType':
continue
tmp = retrieve(data[i], resource_data)
if tmp[0] == 'Not_Found':
data[i][-1] = 'Not in the online record'
else:
data[i][-1] = tmp[1]
for i in range(len(data)):
if data[i][1] == 'text' or data[i][1] == 'resourceType':
continue
tmp = retrieve(data[i], policy_data)
# Not found or unmasked means we should not change the value
if tmp[0] == 'Mask':
# Here we need to filter the policy
data[i][-1] = 'Protected data due to privacy policy'
for i in range(len(data)):
del data[i][0]
result = jd.list2json(data, RESERVED_WORD)
return result
def cover_protected_data(data_list, resource, patient_id, status='full'):
'''
data_list : sometimes we don't wanna display all part of this resource, this list will tell us which to display,a list
resource : json data that wanna to display, the format is dict
patient_id : extract identifier of policy_list
'''
privacy_policy = db.select_policy(patient_id)
if (privacy_policy == -2):
#No record in the database
return resource
policy_data = jd.json2list(privacy_policy,RESERVED_WORD)
if type(data_list) is dict:
jd.json_reduce_structure(data_list)
data_list = jd.json2list(data_list, RESERVED_WORD)
if isinstance(resource['resourceType'], unicode):
s=resource['resourceType']
else:
s=unicode(resource['resourceType'],"utf-8")
jd.json_reduce_structure(resource)
resource_data = jd.json2list(resource,RESERVED_WORD)
for i in range(len(resource_data)):
resource_data[i].insert(0,s)
data = data_list
for i in range(len(data)):
data[i].insert(0,s)
#If the query is only part of data,then do the intersection
for i in range(len(data)):
if data[i][1] == 'text' or data[i][1] == 'resourceType':
continue
tmp = retrieve(data[i],resource_data)
if tmp[0] == 'Not_Found':
data[i][-1] = 'Not in the online record'
else:
data[i][-1] = tmp[1]
for i in range(len(data)):
if data[i][1]=='text' or data[i][1]=='resourceType':
continue
tmp = retrieve(data[i],policy_data)
# Not found or unmasked means we should not change the value
if tmp[0] == 'Mask':
# Here we need to filter the policy
data[i][-1] = 'Protected data due to privacy policy'
for i in range(len(data)):
del data[i][0]
result = jd.list2json(data,RESERVED_WORD)
return result
def get_list_and_class(json_file, reserved_word):
li = jd.json2list(json_file,reserved_word)
output = get_struct(li,reserved_word)
if output.value:
map(lambda x:x.init_type(reserved_word),output.value)
map(lambda x:x.set_level(0),output.value)
num = 0
for item in output.value:
num = item.dfs(num)
templist = []
for item in output.value:
item.set_list(templist)
class_list = []
for item in output.value:
class_list.append(item)
item.append_to_list(class_list,False)
return li,class_list
def strcture_json(json_file,reserved_word,fieldname):
li = jd.json2list(json_file,reserved_word)
output = get_struct(li,reserved_word)
if output.value:
map(lambda x:x.init_type(reserved_word),output.value)
map(lambda x:x.init_attr(),output.value)
map(lambda x:x.set_level(0),output.value)
num = 0
for item in output.value:
num = item.dfs(num)
class_list = []
for item in output.value:
class_list.append(item)
item.append_to_list(class_list)
dict_temp = []
for item in class_list:
dict_temp.append([item.get_key(),item])
class_dict = dict((key,value) for key, value in dict_temp)
class_list[len(class_list)-1].set_succ(-1)
for i in range(0,len(class_list)-1):
class_list[i].set_succ(class_list[i+1].get_level())
class_list[0].set_pred(-1)
for i in range(1,len(class_list)):
class_list[i].set_pred(class_list[i-1].get_level())
for i in range(len(class_list)):
fieldkey= fieldname+str(class_list[i].get_seq())
setattr(private_Form,fieldkey,BooleanField(fieldkey,default=False))
form = private_Form()
# for item in class_list:
# print '\t'*item.get_level()+item.get_key()
# for item in class_list:
# print str(item.get_level())+'\t'+str(item.get_pred())
return class_list,class_dict,form
def list_extension (json_data):
#Extend resource type into json_list module
data = jd.json2list(json_data,RESERVED_WORD)
if isinstance(json_data['resourceType'], unicode):
s=json_data['resourceType']
else:
s=unicode(json_data['resourceType'],"utf-8")
for i in range(len(data)):
data[i].insert(0,s)
return json.dumps(jd.list2json(json_data,RESERVED_WORD),separators=(',',':'))
def list_extension(json_data):
#Extend resource type into json_list module
data = jd.json2list(json_data, RESERVED_WORD)
if isinstance(json_data['resourceType'], unicode):
s = json_data['resourceType']
else:
s = unicode(json_data['resourceType'], "utf-8")
for i in range(len(data)):
data[i].insert(0, s)
return json.dumps(jd.list2json(json_data, RESERVED_WORD),
separators=(',', ':'))
def query_info(data_list, patient_id):
'''
data_list is a json_list(need to be extended)
Now we only support single type data
This is the query port to ask for specific sequence from remote server
And , add filter policy
'''
# Now time to ask for patient's data
resource = search_request_patient(patient_id)
if resource == 'Http_403_error':
return 'Not_Found', {}
data_list = jd.form2list(data_list, jd.formtable,
jd.json2list(resource, RESERVED_WORD))
#print json.dumps(jd.list2json(data_list,RESERVED_WORD),indent=4)
#data_list = jd.list2json(data_list, RESERVED_WORD)
#if data_list is None or data_list['resourceType'] is None:
#Catch_dataError()
#return 'Not_Found',data_list
return 'Found', cover_protected_data(data_list, resource, patient_id,
'cap')
def query_info (data_list, patient_id):
'''
data_list is a json_list(need to be extended)
Now we only support single type data
This is the query port to ask for specific sequence from remote server
And , add filter policy
'''
# Now time to ask for patient's data
resource = search_request_patient(patient_id)
if resource == 'Http_403_error' :
return 'Not_Found',{}
data_list = jd.form2list(data_list, jd.formtable, jd.json2list(resource, RESERVED_WORD))
#print json.dumps(jd.list2json(data_list,RESERVED_WORD),indent=4)
#data_list = jd.list2json(data_list, RESERVED_WORD)
#if data_list is None or data_list['resourceType'] is None:
#Catch_dataError()
#return 'Not_Found',data_list
return 'Found',cover_protected_data(
data_list,
resource,
patient_id,
'cap')
def get_observation_list(self):
self.filtered_Observation=[]
self.seq_id=[]
for x in range(0,901,50):
resource_type = 'Observation'
forward_args = request.args.to_dict(flat=False)
forward_args['_format'] = 'json'
forward_args['_offset'] = str(x)
forwarded_url = resource_type
api_url = '/%s?%s'% (forwarded_url, urlencode(forward_args, doseq=True))
print api_url
resp = api_call(api_url)
bundle =resp.json();
if ('type' in bundle and bundle['type'] != 'searchset') or ('resourceType' in bundle and bundle['resourceType']!='Bundle'):
resource = bundle
bundle = {
'resourceType': resource['resourceType'],
'entry': [{
'resource': resource,
'id': forwarded_url
}],
'is_single_resource': True,
}
elif len(bundle.get('entry', [])) > 0:
bundle['resourceType'] = bundle['entry'][0]['resource']['resourceType']
k=1;
for i in range(len(bundle['entry'])):
resource = bundle['entry'][i]['resource']
#print resource
try:
resource_subject = resource['subject']['reference'].split('/')[-1]
except:
resource_subject = "Not want to be seen"
#print resource['id'],resource_subject
#print json.dumps(resource , indent= 2)
#print resource_subject
if resource_subject == self.patient_id:
if(self.search_text=='*'):
self.filtered_Observation.append(resource)
#print self.filtered_Observation
self.add_locale_info(resource)
k+=1
else:
list_resource = json2list(resource,'FindText')
#print list_resource
flag= False;
for list in list_resource:
try:
#print list
if((list[-3]=='text' or list[-2]=='text') and (list[-1]==self.search_text or self.search_text in list[-1])):
flag= True;
break;
except:
pass
if(flag):
#print type(resource)
#print "here\n\n\n"
self.filtered_Observation.append(resource)
self.add_locale_info(resource)
k+=1
def get_observation_list(self):
self.filtered_Observation = []
self.seq_id = []
for x in range(0, 901, 50):
resource_type = 'Observation'
forward_args = request.args.to_dict(flat=False)
forward_args['_format'] = 'json'
forward_args['_offset'] = str(x)
forwarded_url = resource_type
api_url = '/%s?%s' % (forwarded_url,
urlencode(forward_args, doseq=True))
print api_url
resp = api_call(api_url)
bundle = resp.json()
if ('type' in bundle and bundle['type'] != 'searchset') or (
'resourceType' in bundle
and bundle['resourceType'] != 'Bundle'):
resource = bundle
bundle = {
'resourceType': resource['resourceType'],
'entry': [{
'resource': resource,
'id': forwarded_url
}],
'is_single_resource': True,
}
elif len(bundle.get('entry', [])) > 0:
bundle['resourceType'] = bundle['entry'][0]['resource'][
'resourceType']
k = 1
for i in range(len(bundle['entry'])):
resource = bundle['entry'][i]['resource']
#print resource
try:
resource_subject = resource['subject']['reference'].split(
'/')[-1]
except:
resource_subject = "Not want to be seen"
#print resource['id'],resource_subject
#print json.dumps(resource , indent= 2)
#print resource_subject
if resource_subject == self.patient_id:
if (self.search_text == '*'):
self.filtered_Observation.append(resource)
#print self.filtered_Observation
self.add_locale_info(resource)
k += 1
else:
list_resource = json2list(resource, 'FindText')
#print list_resource
flag = False
for list in list_resource:
try:
#print list
if ((list[-3] == 'text' or list[-2] == 'text')
and (list[-1] == self.search_text
or self.search_text in list[-1])):
flag = True
break
except:
pass
if (flag):
#print type(resource)
#print "here\n\n\n"
self.filtered_Observation.append(resource)
self.add_locale_info(resource)
k += 1
masked_part = jd.list2json(masked_list,reserved_word)
print masked_part
final_file = package(json_file,masked_part)
print json.dumps(masked_part,indent=4)
reserved_word = 'test'
if __name__ == '__main__':
e = jp.s
li = jd.json2list(e,reserved_word)
output = get_struct(li,reserved_word)
if output.value:
map(lambda x:x.init_type(reserved_word),output.value)
map(lambda x:x.dump(0),output.value)
map(lambda x:x.set_level(0),output.value)
num = 0
for item in output.value:
num = item.dfs(num)
#map(lambda x:x.dump_level(), output.value)
class_list = []