def post(self, request, pk, subject, record, *args, **kwargs):
'''Create a link between two subject records in the eHB
'''
try:
pds = ProtocolDataSource.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response(
{'error': 'ProtocolDatasource requested not found'},
status=404)
if pds.protocol.isUserAuthorized(request.user):
data = request.data
primary_rec = data['primaryRecord']
secondary_rec = data['secondaryRecord']
link_type = data['linkType']
# Serialize
primary_rec = ExternalRecord.identity_from_json(
json.dumps(primary_rec))
secondary_rec = ExternalRecord.identity_from_json(
json.dumps(secondary_rec))
res = self.er_rh.link(primary_rec, secondary_rec, link_type)
if res['success']:
return Response(res)
else:
return Response({
'success': False,
'error': res['error']
},
status=422)
return Response({
'success': False,
'error': 'Unknown Error'
},
status=422)
def create_new_ehb_external_record(protocol_data_source,
user,
subject,
record_id,
label=None):
"""Create a new external record for this PDS/subject in the EHB.
Creates a new external record in the ehb-service for this data source,
subject and record_id, using the credentials of the given user and the
label, if given.
Returns:
If successful, returns the new ExternalRecord object.
Raises:
RecordCreationError: If the creation request response has errors or
an Exception is raised during operation.
"""
es = protocol_data_source.data_source.getExternalSystem()
# Want to make sure we're not going to overwrite a record already in
# the system
try:
if not label:
label = 1
er = ExternalRecord(record_id=record_id,
subject_id=subject['id'],
external_system_id=es.id,
path=protocol_data_source.path,
label_id=label)
errh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD)
response = errh.create(er)[0]
if (response.get('success')):
SubjectUtils.add_record_to_subject_record_group(
protocol_data_source.protocol, subject, er)
return er
else:
errors = response.get('errors')
raise RecordCreationError('electronic Honest Broker', '',
record_id, errors)
except RecordCreationError as rce:
raise rce
except Exception as e:
raise RecordCreationError('electronic Honest Broker', '',
record_id, str(e))
def getExternalIdentifiers(pds, subject, labels):
er_rh = ServiceClient.get_rh_for(record_type=ServiceClient.EXTERNAL_RECORD)
ck = '{0}_{1}_externalrecords'.format(pds.protocol.id, subject.id)
# See if our records are in the cache.
resp = cache.get(ck)
if resp:
pds_records = []
for record in json.loads(resp):
if record['external_system'] == pds.id:
pds_records.append(
ExternalRecord(-1).identity_from_jsonObject(record))
else:
try:
pds_records = er_rh.get(external_system_url=pds.data_source.url,
path=pds.path,
subject_id=subject.id)
except PageNotFound:
pds_records = []
for ex_rec in pds_records:
for label in labels:
if ex_rec.label_id == label['id']:
if label['label'] == '':
ex_rec.label_desc = 'Record'
else:
ex_rec.label_desc = label['label']
return pds_records
def test_json_from_identity_no_label():
ExRecObject = ExternalRecord(
record_id="xyz123",
external_system_id=1,
subject_id=1,
path="testpath",
modified=datetime.datetime(2014, 1, 1),
created=datetime.datetime(2014, 1, 1),
id=1,
label_id=None,
)
json_string = ExRecObject.json_from_identity(ExRecObject)
assert isinstance(json_string, str)
ex_rec = json.loads(json_string)
assert isinstance(ex_rec, dict)
assert ex_rec["id"] == 1
def create_new_ehb_external_record(protocol_data_source, user, subject, record_id, label=None):
'''
Creates a new external record in the ehb-service for this data source,
subject, record_id and
Output
------
If successful returns the
ehb_client.external_record_request_handler.ExternalRecord object
'''
es = protocol_data_source.data_source.getExternalSystem()
# Want to make sure we're not going to overwrite a record already in the system
try:
if not label:
label = 1
er = ExternalRecord(
record_id=record_id,
subject_id=subject.id,
external_system_id=es.id,
path=protocol_data_source.path,
label_id=label
)
errh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD
)
response = errh.create(er)[0]
if(response.get('success')):
SubjectUtils.add_record_to_subject_record_group(
protocol_data_source.protocol,
subject,
er
)
return er
else:
errors = response.get('errors')
raise RecordCreationError(
'electronic Honest Broker',
'',
record_id,
errors
)
except RecordCreationError as rce:
raise rce
except Exception as e:
raise RecordCreationError(
'electronic Honest Broker',
'',
record_id,
str(e)
)
def post(self, request, pk, subject, record, *args, **kwargs):
'''Create a link between two subject records in the eHB
'''
try:
pds = ProtocolDataSource.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'ProtocolDatasource requested not found'}, status=404)
if pds.protocol.isUserAuthorized(request.user):
data = json.loads(request.body.decode('utf-8'))
primary_rec = data['primaryRecord']
secondary_rec = data['secondaryRecord']
link_type = data['linkType']
# Serialize
primary_rec = ExternalRecord.identity_from_json(json.dumps(primary_rec))
secondary_rec = ExternalRecord.identity_from_json(json.dumps(secondary_rec))
res = self.er_rh.link(primary_rec, secondary_rec, link_type)
if res['success']:
return Response(res)
else:
return Response({'success': False, 'error': res['error']}, status=422)
return Response({'success': False, 'error': 'Unknown Error'}, status=422)
def delete(self, request, pk, subject, record, *args, **kwargs):
'''Delete a link between two subject records in the eHB
'''
try:
pds = ProtocolDataSource.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'ProtocolDatasource requested not found'}, status=404)
if pds.protocol.isUserAuthorized(request.user):
data = json.loads(request.body.decode('utf-8'))
primary_rec = data['primaryRecord']
link_id = data['linkId']
# Serialize
primary_rec = ExternalRecord.identity_from_json(json.dumps(primary_rec))
res = self.er_rh.unlink(primary_rec, link_id)
if res['success']:
return Response(res)
return Response({'success': False}, status=422)
def external_records(self, external_system_id, path=None, organization_id=None, subject_id=None):
'''
Attempts to get all externalRecord information for the specified externalsystem
Inputs:
external_system_id : int value of the externalsystem record id
path (optional) If specified, this will only return records with this path
organization_id (optional) : int value of the organization. If specified, this will only return ExternalRecords
whose Subject belongs to this organization
subject_id (optional) : int value of the subject ehb id. If specified this will only return ExternalRecords
belonging to this subject
Outputs:
list of ExternalRecord objects
If no records are found PageNotFound is raised'''
ehb_service_path = self.root_path + 'id/' + str(external_system_id) + '/'
if organization_id is None:
ehb_service_path += 'records/'
else:
ehb_service_path += 'organization/' + str(organization_id) + '/records/'
response = self.processGet(ehb_service_path)
status = []
for o in json.loads(response):
er = ExternalRecord.identity_from_jsonObject(o)
if path and subject_id:
if er.subject_id == subject_id and er.path == path:
status.append(er)
elif path:
if er.path == path:
status.append(er)
elif subject_id:
if er.subject_id == subject_id:
status.append(er)
else:
status.append(er)
if len(status) == 0:
raise PageNotFound(ehb_service_path)
else:
return status
def pds_dataentry_form(request, pds_id, subject_id, form_spec, record_id):
'''renders a page with a data form as generated by the driver for protocol_data_source with pk=pds_id for
Subject with subject_id=subject_id. The specific data form is determined by the driver using the form_spec arg.
'''
def generateSubRecordForm(driver, external_record, form_spec,
attempt_count, max_attempts):
try:
key = 'subrecordform_{0}_{1}'.format(external_record.id, form_spec)
# Caching turned off for the time being on SRF
# cf = cache.get(key)
cf = None
if cf:
return cf
else:
form = driver.subRecordForm(external_record=external_record,
form_spec=form_spec,
session=request.session)
return form
except RecordDoesNotExist:
return None
pds = getProtocolDataSource(pds_id)
if not pds.protocol.isUserAuthorized(request.user):
return forbidden(request)
MANAGE_EXTERNAL_IDS = False
er_label_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
lbls = er_label_rh.query()
# Check to see if this PDS is managing external identifiers
for _pds in pds.protocol.getProtocolDataSources():
if _pds.driver == 3:
ExIdSource = _pds
MANAGE_EXTERNAL_IDS = True
subject = getPDSSubject(pds=pds, sub_id=subject_id)
# If we are managing external identifiers add them to the subject
if MANAGE_EXTERNAL_IDS:
subject.external_ids = getExternalIdentifiers(ExIdSource, subject,
lbls)
er_rh = ServiceClient.get_rh_for(record_type=ServiceClient.EXTERNAL_RECORD)
# this will be the ehb-service externalRecord for this pds, subject NOT the actual datasource record
record = None
error_msgs = []
try:
r = cache.get('externalrecord_{0}'.format(record_id))
if r:
record = ExternalRecord(1).identity_from_jsonObject(json.loads(r))
else:
record = er_rh.get(id=record_id)
except PageNotFound:
raise Http404
try:
driver = DriverUtils.getDriverFor(protocol_data_source=pds,
user=request.user)
# Need the external record for this pds, protcol, and subject
# Get all external_record objects on the ehb-service for this system,
# path, subject combination.
if request.method == 'POST':
# have the driver process this request
key = 'subrecordform_{0}_{1}'.format(record.id, form_spec)
# cache.delete(key)
errors = driver.processForm(request=request,
external_record=record,
form_spec=form_spec,
session=request.session)
if errors:
error_msgs = [e for e in errors]
else:
path = '%s/dataentry/protocoldatasource/%s/subject/%s/record/%s/start/' % (
ServiceClient.self_root_path, pds.id, subject_id,
record_id)
return HttpResponseRedirect(path)
else:
# Generate a new form
form = generateSubRecordForm(driver, record, form_spec, 0, 1)
if form:
o_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.ORGANIZATION)
org = o_rh.get(id=subject.organization_id)
form_submission_url = '%s/dataentry/protocoldatasource/%s/subject/%s/record/%s/form_spec/%s/' % (
ServiceClient.self_root_path, pds.id, subject_id,
record_id, form_spec)
# Find next form to support guided entry
try:
forms = json.loads(pds.driver_configuration)['form_order']
current_index = forms.index(form_spec)
next_form = forms[current_index + 1]
next_form_url = '%s/dataentry/protocoldatasource/%s/subject/%s/record/%s/form_spec/%s/' % (
ServiceClient.self_root_path, pds.id, subject_id,
record_id, next_form)
except:
next_form_url = ''
context = {
'subRecordForm': form,
'protocol': pds.protocol,
'organization': org,
'subject': subject,
'root_path': ServiceClient.self_root_path,
'pds': pds,
'form_submission_url': form_submission_url,
'next_form_url': next_form_url,
'rec_id': str(record_id),
'redcap_status': getRedcapStatus()
}
return render_to_response(
'pds_dataentry_srf.html',
context,
context_instance=RequestContext(request))
else:
error_msgs.append(
'No record exists in the data source with the record id supplied by the eHB.'
)
log.error('Error {0}'.format(' '.join(error_msgs)))
except PageNotFound:
error_msgs.append(
'No record could be found in the eHB for this request')
log.error('Error {0}'.format(' '.join(error_msgs)))
except ProtocolUserCredentials.DoesNotExist:
error_msgs.append(
'Your user credentials were not found for %s. Please contact system administrator.'
% pds.data_source.name)
# Some error must have occured:
log.error('Error {0}'.format(' '.join(error_msgs)))
return HttpResponse(' '.join(error_msgs))
first_name='Jane',
last_name='Sample',
organization_id=1,
organization_subject_id='MRN123',
dob=datetime.date(1990, 1, 1),
modified=datetime.datetime(2015, 1, 1),
created=datetime.datetime(2015, 1, 1))
TestOrganization = Organization(id=1,
name='Amazing Children\'s Hospital',
subject_id_label='Subject',
modified=datetime.datetime(2015, 1, 1),
created=datetime.datetime(2015, 1, 1))
TestExternalRecord = ExternalRecord(record_id='xyz123',
external_system_id=1,
subject_id=1,
path='testpath',
modified=datetime.datetime(2014, 1, 1),
created=datetime.datetime(2014, 1, 1),
id=1,
label_id=1)
TestGroup = Group(id=1,
name='TestGroup',
is_locking=False,
client_key='testck',
description='A test group')
BRPApiView.s_rh.get = MagicMock(return_value=TestSubject)
BRPApiView.s_rh.update = MagicMock(return_value=[{
'success': True,
'errors': [],
'subject': TestSubject
}])
