def check_subject(self, subject_1, subject_2):
try:
subject_1_response = self.s_rh.get(id=subject_1)
subject_2_response = self.s_rh.get(id=subject_2)
except:
return {'error': 'Invalid subject Selected'}
sub1 = json.loads(Subject.json_from_identity(subject_1_response))
sub2 = json.loads(Subject.json_from_identity(subject_2_response))
if sub1['id'] is None or sub2['id'] is None:
return {'error': 'Invalid subject Selected'}
return True
def put(self, request, pk, subject, *args, **kwargs):
subject_update = json.loads(request.body.decode('utf-8'))
# See if subject exists
try:
ehb_sub = self.s_rh.get(id=subject)
org = self.o_rh.get(id=subject_update['organization'])
protocol = Protocol.objects.get(pk=pk)
old_group_name = SubjectUtils.protocol_subject_record_group_name(
protocol, ehb_sub)
group = self.g_rh.get(name=old_group_name)
except:
return Response({'error': 'subject not found'}, status=404)
ehb_sub.old_subject = deepcopy(ehb_sub)
ehb_sub.first_name = subject_update['first_name']
ehb_sub.last_name = subject_update['last_name']
ehb_sub.organization_subject_id = subject_update[
'organization_subject_id']
ehb_sub.organization_id = org.id
ehb_sub.dob = datetime.strptime(subject_update['dob'], '%Y-%m-%d')
new_group_name = SubjectUtils.protocol_subject_record_group_name(
protocol, ehb_sub)
group.name = new_group_name
group.client_key = protocol._settings_prop('CLIENT_KEY', 'key', '')
group.current_client_key(group.client_key)
update = self.s_rh.update(ehb_sub)[0]
if update['errors']:
return Response(json.dumps({'error': 'Unable to update subject'}),
status=400)
# If the update is succesful, update the subject record group associated with this subject
res = self.g_rh.update(group)[0]
if not res['success']:
return Response(json.dumps({'error': 'Unable to update group'}),
status=400)
# If the update is succesful, update the cache.
sub = json.loads(Subject.json_from_identity(update['subject']))
sub['organization_name'] = org.name
cache_key = 'protocol{0}_sub_data'.format(pk)
cache_data = self.cache.get(cache_key)
if cache_data:
if 'external_ids' in list(subject_update.keys()):
sub['external_ids'] = subject_update['external_ids']
else:
sub['external_ids'] = []
sub['external_records'] = subject_update['external_records']
sub['organization_name'] = org.name
subjects = json.loads(cache_data)
for i in range(0, len(subjects)):
if subjects[i]['id'] == sub['id']:
subjects[i] = sub
self.cache.set(cache_key, json.dumps(subjects))
if hasattr(self.cache, 'persist'):
self.cache.persist(cache_key)
return Response(sub, headers={'Access-Control-Allow-Origin': '*'})
def put(self, request, pk, subject, *args, **kwargs):
subject_update = json.loads(request.body.decode('utf-8'))
# See if subject exists
try:
ehb_sub = self.s_rh.get(id=subject)
org = self.o_rh.get(id=subject_update['organization'])
protocol = Protocol.objects.get(pk=pk)
old_group_name = SubjectUtils.protocol_subject_record_group_name(protocol, ehb_sub)
group = self.g_rh.get(name=old_group_name)
except:
return Response({'error': 'subject not found'}, status=404)
ehb_sub.old_subject = deepcopy(ehb_sub)
ehb_sub.first_name = subject_update['first_name']
ehb_sub.last_name = subject_update['last_name']
ehb_sub.organization_subject_id = subject_update['organization_subject_id']
ehb_sub.organization_id = org.id
ehb_sub.dob = datetime.strptime(subject_update['dob'], '%Y-%m-%d')
new_group_name = SubjectUtils.protocol_subject_record_group_name(protocol, ehb_sub)
group.name = new_group_name
group.client_key = protocol._settings_prop(
'CLIENT_KEY', 'key', '')
group.current_client_key(group.client_key)
update = self.s_rh.update(ehb_sub)[0]
if update['errors']:
return Response(json.dumps({'error': 'Unable to update subject'}), status=400)
# If the update is succesful, update the subject record group associated with this subject
res = self.g_rh.update(group)[0]
if not res['success']:
return Response(json.dumps({'error': 'Unable to update group'}), status=400)
# If the update is succesful, update the cache.
sub = json.loads(Subject.json_from_identity(update['subject']))
sub['organization_name'] = org.name
cache_key = 'protocol{0}_sub_data'.format(pk)
cache_data = self.cache.get(cache_key)
if cache_data:
if 'external_ids' in list(subject_update.keys()):
sub['external_ids'] = subject_update['external_ids']
else:
sub['external_ids'] = []
sub['external_records'] = subject_update['external_records']
sub['organization_name'] = org.name
subjects = json.loads(cache_data)
for i in range(0, len(subjects)):
if subjects[i]['id'] == sub['id']:
subjects[i] = sub
self.cache.set(cache_key, json.dumps(subjects))
if hasattr(self.cache, 'persist'):
self.cache.persist(cache_key)
return Response(
sub,
headers={'Access-Control-Allow-Origin': '*'}
)
def test_identity_to_json():
sub = Subject(
id=2,
first_name='Jane',
last_name='Sample',
organization_id=1,
organization_subject_id='MRN123',
dob=datetime.datetime(1990, 1, 1),
modified=datetime.datetime(2015, 1, 1),
created=datetime.datetime(2015, 1, 1)
)
jsonStr = sub.json_from_identity(sub)
assert isinstance(jsonStr, str)
def get(self, request, pk, subject, *args, **kwargs):
''' get all subject data:
external records, Organization, external ids and relationships'''
# TODO: add getting relationships for subjects here
try:
p = Protocol.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'Protocol requested not found'},
status=404)
if p.isUserAuthorized(request.user):
protocoldatasources = p.getProtocolDataSources()
manageExternalIDs = False
for pds in protocoldatasources:
if pds.driver == 3:
ExIdSource = pds
manageExternalIDs = True
try:
subject = self.s_rh.get(id=subject)
organization = self.o_rh.get(id=subject.organization_id)
except:
return Response({'error': 'Subject not found'}, status=404)
sub = json.loads(Subject.json_from_identity(subject))
sub['organization_name'] = organization.name
sub['external_records'] = []
for pds in protocoldatasources:
sub['external_records'].extend(
pds.getSubjectExternalRecords(sub))
if manageExternalIDs:
# Break out external ids into a separate object for ease of use
sub['external_ids'] = []
for record in sub['external_records']:
if record['external_system'] == 3:
sub['external_ids'].append(record)
return Response(sub)
else:
return Response(
{
"detail":
"You are not authorized to view subjects in this protocol"
},
status=403)
def get(self, request, pk, subject, *args, **kwargs):
''' get subject '''
try:
p = Protocol.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'Protocol requested not found'}, status=404)
if p.isUserAuthorized(request.user):
protocoldatasources = p.getProtocolDataSources()
manageExternalIDs = False
for pds in protocoldatasources:
if pds.driver == 3:
ExIdSource = pds
manageExternalIDs = True
try:
subject = self.s_rh.get(id=subject)
organization = self.o_rh.get(id=subject.organization_id)
except:
return Response({'error': 'Subject not found'}, status=404)
sub = json.loads(Subject.json_from_identity(subject))
sub['organization_name'] = organization.name
sub['external_records'] = []
for pds in protocoldatasources:
sub['external_records'].extend(pds.getSubjectExternalRecords(sub))
if manageExternalIDs:
# Break out external ids into a separate object for ease of use
sub['external_ids'] = []
for record in sub['external_records']:
if record['external_system'] == 3:
sub['external_ids'].append(record)
return Response(sub)
else:
return Response(
{"detail": "You are not authorized to view subjects in this protocol"},
status=403
)
def post(self, request, pk, *args, **kwargs):
'''
Add a subject to the protocol
Expects a request body of the form:
{
"first_name": "John",
"last_name": "Doe",
"organization_subject_id": "123123123",
"organization": "1",
"dob": "2000-01-01"
}
'''
try:
protocol = Protocol.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'Protocol requested not found'}, status=404)
subject = json.loads(request.body.decode('utf-8'))
new_subject = Subject(
first_name=subject['first_name'],
last_name=subject['last_name'],
organization_id=int(subject['organization']),
organization_subject_id=subject['organization_subject_id'],
dob=datetime.strptime(subject['dob'], '%Y-%m-%d')
)
try:
org = self.o_rh.get(id=subject['organization'])
except:
return Response({'error': 'Invalid Organization Selected'}, status=400)
errors = []
try:
subject = self.s_rh.get(
organization_id=new_subject.organization_id,
organization_subject_id=new_subject.organization_subject_id)
success = True
# If found this indicates the subject is already in the ehb for
# this organization, but not necessarily for this protocol.
# That will be checked below in the external record search
prefix = "A subject with this " + org.subject_id_label + " exists but with "
if subject.first_name != new_subject.first_name:
success = False
errors.append(prefix + "first name: " + subject.first_name)
if subject.last_name != new_subject.last_name:
success = False
errors.append(prefix + "last name: " + subject.last_name)
if subject.dob != new_subject.dob.date():
success = False
errors.append(prefix + "birth date: " + str(subject.dob))
except PageNotFound:
# Subject is not in the system so create it
r = self.s_rh.create(new_subject)[0]
success = r.get('success')
errors = r.get('errors')
subject = r.get(Subject.identityLabel)
# Dont proceed if creation was not a success
if not success:
subject = json.loads(Subject.json_from_identity(subject))
return Response([success, subject, errors], status=422)
if not errors:
errors = []
# First check if the subject is already in the group.
if protocol.getSubjects() and subject in protocol.getSubjects():
# Subject is already in protocol
errors.append(
'This subject ' + org.subject_id_label +
' has already been added to this project.'
)
logger.error("Could not add subject. They already exist on this protocol.")
success = False
else:
# Add this subject to the protocol and create external record group
if self.subject_utils.create_protocol_subject_record_group(protocol, new_subject):
if protocol.addSubject(subject):
success = True
else:
# Could not add subject to project
errors.append(
'Failed to complete eHB transactions. Could not add subject to project. Please try again.')
success = False
else:
# For some reason we couldn't get the eHB to add the subject to the protocol group
errors.append(
'Failed to complete eHB transactions. Could not add subject to project. Please try again.')
success = False
subject = json.loads(Subject.json_from_identity(subject))
if not success:
return Response(
[success, subject, errors],
headers={'Access-Control-Allow-Origin': '*'},
status=400
)
# Add subject to cache
cache_key = 'protocol{0}_sub_data'.format(protocol.id)
cache_data = self.cache.get(cache_key)
if cache_data:
subject['external_ids'] = []
subject['external_records'] = []
subject['organization_name'] = org.name
subjects = json.loads(cache_data)
subjects.append(subject)
self.cache.set(cache_key, json.dumps(subjects))
if hasattr(self.cache, 'persist'):
self.cache.persist(cache_key)
return Response(
[success, subject, errors],
headers={'Access-Control-Allow-Origin': '*'},
status=200
)
def post(self, request, pk, *args, **kwargs):
'''
Add a subject to the protocol
Expects a request body of the form:
{
"first_name": "John",
"last_name": "Doe",
"organization_subject_id": "123123123",
"organization": "1",
"dob": "2000-01-01"
}
'''
try:
protocol = Protocol.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'Protocol requested not found'},
status=404)
subject = json.loads(request.body.decode('utf-8'))
new_subject = Subject(
first_name=subject['first_name'],
last_name=subject['last_name'],
organization_id=int(subject['organization']),
organization_subject_id=subject['organization_subject_id'],
dob=datetime.strptime(subject['dob'], '%Y-%m-%d'))
try:
org = self.o_rh.get(id=subject['organization'])
except:
return Response({'error': 'Invalid Organization Selected'},
status=400)
errors = []
try:
subject = self.s_rh.get(
organization_id=new_subject.organization_id,
organization_subject_id=new_subject.organization_subject_id)
success = True
# If found this indicates the subject is already in the ehb for
# this organization, but not necessarily for this protocol.
# That will be checked below in the external record search
prefix = "A subject with this " + org.subject_id_label + " exists but with "
if subject.first_name != new_subject.first_name:
success = False
errors.append(prefix + "first name: " + subject.first_name)
if subject.last_name != new_subject.last_name:
success = False
errors.append(prefix + "last name: " + subject.last_name)
if subject.dob != new_subject.dob.date():
success = False
errors.append(prefix + "birth date: " + str(subject.dob))
except PageNotFound:
# Subject is not in the system so create it
r = self.s_rh.create(new_subject)[0]
success = r.get('success')
errors = r.get('errors')
subject = r.get(Subject.identityLabel)
# Dont proceed if creation was not a success
if not success:
subject = json.loads(Subject.json_from_identity(subject))
return Response([success, subject, errors], status=422)
if not errors:
errors = []
# First check if the subject is already in the group.
if protocol.getSubjects() and subject in protocol.getSubjects():
# Subject is already in protocol
errors.append('This subject ' + org.subject_id_label +
' has already been added to this project.')
logger.error(
"Could not add subject. They already exist on this protocol.")
success = False
else:
# Add this subject to the protocol and create external record group
if self.subject_utils.create_protocol_subject_record_group(
protocol, new_subject):
if protocol.addSubject(subject):
success = True
else:
# Could not add subject to project
errors.append(
'Failed to complete eHB transactions. Could not add subject to project. Please try again.'
)
success = False
else:
# For some reason we couldn't get the eHB to add the subject to the protocol group
errors.append(
'Failed to complete eHB transactions. Could not add subject to project. Please try again.'
)
success = False
subject = json.loads(Subject.json_from_identity(subject))
if not success:
return Response([success, subject, errors],
headers={'Access-Control-Allow-Origin': '*'},
status=400)
# Add subject to cache
cache_key = 'protocol{0}_sub_data'.format(protocol.id)
cache_data = self.cache.get(cache_key)
if cache_data:
subject['external_ids'] = []
subject['external_records'] = []
subject['organization_name'] = org.name
subjects = json.loads(cache_data)
subjects.append(subject)
self.cache.set(cache_key, json.dumps(subjects))
if hasattr(self.cache, 'persist'):
self.cache.persist(cache_key)
return Response([success, subject, errors],
headers={'Access-Control-Allow-Origin': '*'},
status=200)
def post(self, request, pk, *args, **kwargs):
'''
Add a subject to the protocol
Expects a request body of the form:
{
"last_name": "John",
"last_name": "Doe",
"organization_subject_id": "123123123",
"organization": "1",
"dob": "2000-01-01"
}
'''
try:
protocol = Protocol.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'Protocol requested not found'},
status=404)
subject = request.data
new_subject = Subject(
first_name=subject['first_name'],
last_name=subject['last_name'],
organization_id=int(subject['organization']),
organization_subject_id=subject['organization_subject_id'],
dob=datetime.strptime(subject['dob'], '%Y-%m-%d'))
try:
org = self.o_rh.get(id=subject['organization'])
except:
return Response({'error': 'Invalid Organization Selected'},
status=400)
errors = []
try:
subject = self.s_rh.get(
organization_id=new_subject.organization_id,
organization_subject_id=new_subject.organization_subject_id)
success = True
# If found this indicates the subject is already in the ehb for
# this organization, but not necessarily for this protocol.
# That will be checked below in the external record search
prefix = "A subject with this " + org.subject_id_label + " exists but with "
if subject.first_name != new_subject.first_name:
success = False
errors.append(prefix + "first name: " + subject.first_name)
if subject.last_name != new_subject.last_name:
success = False
errors.append(prefix + "last name: " + subject.last_name)
if subject.dob != new_subject.dob.date():
success = False
errors.append(prefix + "birth date: " + str(subject.dob))
except PageNotFound:
# Subject is not in the system so create it
r = self.s_rh.create(new_subject)[0]
success = r.get('success')
errors = r.get('errors')
subject = r.get(Subject.identityLabel)
# Dont proceed if creation was not a success
if not success:
subject = json.loads(Subject.json_from_identity(subject))
return Response([success, subject, errors], status=422)
if not errors:
errors = []
# Add this subject to the protocol and create external record group
if self.subject_utils.create_protocol_subject_record_group(
protocol, new_subject):
if protocol.addSubject(subject):
success = True
# add this action to the user audit
user_audit_payload = [{
'subject':
subject.id,
'change_type':
"SubjectGroup",
'change_type_ehb_pk':
protocol._subject_group().id,
'change_action':
"Add",
'user_name':
request.user.username,
'protocol_id':
protocol.id
}]
ServiceClient.user_audit(user_audit_payload)
else:
# Could not add subject to project
errors.append(
'Failed to complete eHB transactions. Could not add subject to project. Please try again.'
)
success = False
else:
# For some reason we couldn't get the eHB to add the subject to the protocol group
subjects = protocol.getSubjects()
if subjects and subject in subjects:
# Subject is already in protocol
errors.append('This subject ' + org.subject_id_label +
' has already been added to this project.')
logger.error(
"Could not add subject. They already exist on this protocol."
)
success = False
else:
errors.append(
'Failed to complete eHB transactions. Could not add subject to project. Please try again.'
)
success = False
subject = json.loads(Subject.json_from_identity(subject))
subject['organization_name'] = org.name
if not success:
return Response([success, subject, errors],
headers={'Access-Control-Allow-Origin': '*'},
status=400)
# Add subject to cache
self.update_subject_cache(protocol.id, subject, True)
return Response([success, subject, errors],
headers={'Access-Control-Allow-Origin': '*'},
status=200)
