def create_external_system_record(self, request, driver, pds, subject, record_id=None, label=None):
def rec_id_validator(new_record_id):
return SubjectUtils.validate_new_record_id(
pds, subject, new_record_id)
grp = SubjectUtils.get_protocol_subject_record_group(pds.protocol, subject)
if grp:
rec_id_prefix = grp.ehb_key
else:
request.META['action'] = 'No subject record group found'
request.META['error'] = True
raise Exception('No subject record group found')
rec_id = None
if record_id:
if record_id.startswith(rec_id_prefix):
rec_id = driver.create(
record_id_prefix=None, record_id=record_id, record_id_validator=rec_id_validator)
else:
rec_id = driver.create(
record_id_prefix=rec_id_prefix, record_id=record_id)
else:
rec_id = driver.create(
record_id_prefix=rec_id_prefix, record_id_validator=rec_id_validator)
er = SubjectUtils.create_new_ehb_external_record(
pds, request.user, subject, rec_id, label)
return er.id
def create_external_system_record(self, request, driver, pds, subject, record_id=None, label=None):
def rec_id_validator(new_record_id):
return SubjectUtils.validate_new_record_id(
pds, subject, new_record_id)
grp = SubjectUtils.get_protocol_subject_record_group(pds.protocol, subject)
if grp:
rec_id_prefix = grp.ehb_key
else:
request.META['action'] = 'No subject record group found'
request.META['error'] = True
raise Exception('No subject record group found')
rec_id = None
if record_id:
if record_id.startswith(rec_id_prefix):
rec_id = driver.create(
record_id_prefix=None, record_id=record_id, record_id_validator=rec_id_validator)
else:
rec_id = driver.create(
record_id_prefix=rec_id_prefix, record_id=record_id)
else:
rec_id = driver.create(
record_id_prefix=rec_id_prefix, record_id_validator=rec_id_validator)
er = SubjectUtils.create_new_ehb_external_record(
pds, request.user, subject, rec_id, label)
return er.id
def delete(self, request, pk, subject, *args, **kwargs):
try:
subject = self.s_rh.get(id=subject)
protocol = Protocol.objects.get(pk=pk)
self.s_rh.delete(id=subject.id)
SubjectUtils.delete_protocol_subject_record_group(protocol, subject)
except:
return Response({'error': 'Unable to delete subject'}, status=400)
return Response({'info': 'Subject deleted'}, status=200)
def delete(self, request, pk, subject, *args, **kwargs):
try:
subject = self.s_rh.get(id=subject)
protocol = Protocol.objects.get(pk=pk)
self.s_rh.delete(id=subject.id)
SubjectUtils.delete_protocol_subject_record_group(
protocol, subject)
except:
return Response({'error': 'Unable to delete subject'}, status=400)
return Response({'info': 'Subject deleted'}, status=200)
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 update_subject_group(cls, protocol, subject_update, group):
new_group_name = SubjectUtils.protocol_subject_record_group_name(
protocol, subject_update)
group.name = new_group_name
group.client_key = protocol._settings_prop('CLIENT_KEY', 'key', '')
group.current_client_key(group.client_key)
return cls.g_rh.update(group)[0]
def delete(self, request, pk, subject, *args, **kwargs):
if request.user.is_superuser:
try:
subject = self.s_rh.get(id=subject)
protocol = Protocol.objects.get(pk=pk)
group_id = self.get_group_id(protocol.immutable_key.key)
# instead of deleting a subject - we want to just remove them from the subject group
# self.s_rh.delete(id=subject.id)
self.remove_sub_from_ehb_group(subject.id, group_id)
SubjectUtils.delete_protocol_subject_record_group(
protocol, subject)
except:
return Response({'error': 'Unable to delete subject'},
status=400)
return Response({'info': 'Subject deleted'}, status=200)
else:
return Response(
{
"detail":
"You are not authorized to view subjects in this protocol"
},
status=403)
def put(self, request, pk, subject, *args, **kwargs):
subject_update = json.loads(request.body.decode('utf-8'))
subject_api_url = "/api/subject/id/" + subject + "/"
# See if subject exists
try:
ehb_sub = ServiceClient.ehb_api(subject_api_url, "GET").json()
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)
update_subject_response = self.updateEhbSubject(
subject, subject_update, ehb_sub)
try:
success = update_subject_response['success']
except:
success = (update_subject_response.status_code == 200)
if (success is False):
return Response(json.dumps({'error': 'Unable to update subject'}),
status=400)
user_audit_payload = {
'subject': ehb_sub['id'],
'change_type': "Subject",
'change_type_ehb_pk': ehb_sub['id'],
'change_action': "Update",
'user_name': request.user.username,
'protocol_id': protocol.id
}
self.edit_subject_user_audit(subject_update, ehb_sub,
user_audit_payload)
# If the update is succesful, update the subject record group associated with this subject
update_subj_gr_resp = self.update_subject_group(
protocol, subject_update, group)
if not update_subj_gr_resp['success']:
return Response(json.dumps({'error': 'Unable to update group'}),
status=400)
# If the update is succesful, update the cache.
try:
self.update_subject_cache(pk, subject_update, False)
except:
return Response(json.dumps({'error': 'Unable to update cache'}),
status=400)
return Response(subject_update,
headers={'Access-Control-Allow-Origin': '*'})
def rec_id_validator(new_record_id, include_path):
return SubjectUtils.validate_new_record_id(context['pds'],
context['subject'],
new_record_id,
include_path)
def post(self, request, **kwargs):
context = self.get_context_data(**kwargs)
def rec_id_validator(new_record_id, include_path):
return SubjectUtils.validate_new_record_id(context['pds'],
context['subject'],
new_record_id,
include_path)
try:
grp = SubjectUtils.get_protocol_subject_record_group(
self.pds.protocol, self.subject)
grp.client_key = self.pds.protocol._settings_prop(
'CLIENT_KEY', 'key', '')
rec_id_prefix = ''
label_id = request.POST.get('label_id', 1)
if grp:
rec_id_prefix = grp.ehb_key
else:
request.META[
'action'] = 'Subject record group not found for {0}'.format(
context['subject'].id)
request.META['error'] = True
raise Exception('No subject record group found')
# Try to process the new record form
try:
rec_id = self.driver.process_new_record_form(
request=request,
record_id_prefix=rec_id_prefix,
record_id_validator=rec_id_validator)
# If we have successfully created the record. Make sure it is in the eHB.
try:
self.record_id = SubjectUtils.create_new_ehb_external_record(
self.pds, request.user, self.subject, rec_id,
label_id).id
if self.check_cache():
self.update_cache()
return HttpResponseRedirect(self.start_path)
except RecordCreationError as rce: # exception from the eHB
request.META['action'] = rce.errmsg
request.META['error'] = True
context['errors'].append(
('The record could not be created on the '
'electronic Honest Broker. Please contact a '
'system administrator. There could be a '
'connection problem.'))
except IgnoreEhbExceptions as iee:
# TODO this is a hack until BRP can create Nautilus records
rec_id = iee.record_id
ehb_rec_id = ''
try:
# this will create the ehb external_record entry
# and add that record to the subject's record group
self.record_id = SubjectUtils.create_new_ehb_external_record(
self.pds, request.user, self.subject, rec_id,
label_id).id
if self.check_cache():
self.update_cache()
self.start_path = '{0}/dataentry/protocoldatasource/{1}/subject/{2}/record/{3}/start/'.format(
self.service_client.self_root_path, self.pds.id,
self.subject.id, self.record_id)
return HttpResponseRedirect(self.start_path)
except RecordCreationError as rce: # exception from the eHB
request.META['action'] = rce.errmsg
request.META['error'] = True
record_already_exists = 6
cause = rce.raw_cause
if cause and len(
cause) == 1 and record_already_exists == cause[0]:
er_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD)
ehb_recs = er_rh.get(
external_system_url=self.pds.data_source.url,
subject_id=self.subject.id,
path=self.pds.path)
ehb_rec_id = None
for record in ehb_recs:
if record.record_id == rec_id:
ehb_rec_id = record.id
if ehb_rec_id:
self.start_path = '%s/dataentry/protocoldatasource/%s/subject/%s/record/%s/start' % (
ServiceClient.self_root_path, self.pds.id,
self.subject.id, ehb_rec_id)
else:
context['errors'].append(
'This ID has already been assigned to another subject.'
)
return render_to_response(
'pds_dataentry_rec_create.html',
context,
context_instance=RequestContext(request))
else:
request.META['action'] = 'Record could not be created'
request.META['error'] = True
context['errors'].append(
('The record could not be created on the '
'electronic Honest Broker. Please contact '
'a system administrator. There could be a'
' connection problem.'))
except:
return HttpResponse('Unknown Error')
return HttpResponseRedirect(self.start_path)
except RecordCreationError as rce:
# Handle errors in the form.
request.META['action'] = rce.errmsg
request.META['error'] = True
context['errors'].append(rce.cause)
return render_to_response('pds_dataentry_rec_create.html',
context,
context_instance=RequestContext(request))
def rec_id_validator(new_record_id):
return SubjectUtils.validate_new_record_id(pds, subject,
new_record_id)
def rec_id_validator(new_record_id, include_path):
return SubjectUtils.validate_new_record_id(
context['pds'], context['subject'], new_record_id, include_path)
def rec_id_validator(new_record_id):
return SubjectUtils.validate_new_record_id(
pds, subject, new_record_id)
def post(self, request, **kwargs):
context = self.get_context_data(**kwargs)
def rec_id_validator(new_record_id, include_path):
return SubjectUtils.validate_new_record_id(
context['pds'], context['subject'], new_record_id, include_path)
try:
grp = SubjectUtils.get_protocol_subject_record_group(
self.pds.protocol, self.subject)
grp.client_key = self.pds.protocol._settings_prop(
'CLIENT_KEY', 'key', '')
rec_id_prefix = ''
label_id = request.POST.get('label_id', 1)
if grp:
rec_id_prefix = grp.ehb_key
else:
request.META['action'] = 'Subject record group not found for {0}'.format(context['subject'].id)
request.META['error'] = True
raise Exception('No subject record group found')
# Try to process the new record form
try:
rec_id = self.driver.process_new_record_form(
request=request,
record_id_prefix=rec_id_prefix,
record_id_validator=rec_id_validator
)
# If we have successfully created the record. Make sure it is in the eHB.
try:
self.record_id = SubjectUtils.create_new_ehb_external_record(
self.pds, request.user, self.subject, rec_id, label_id).id
if self.check_cache():
self.update_cache()
return HttpResponseRedirect(self.start_path)
except RecordCreationError as rce: # exception from the eHB
request.META['action'] = rce.errmsg
request.META['error'] = True
context['errors'].append((
'The record could not be created on the '
'electronic Honest Broker. Please contact a '
'system administrator. There could be a '
'connection problem.'))
except IgnoreEhbExceptions as iee:
# TODO this is a hack until BRP can create Nautilus records
rec_id = iee.record_id
ehb_rec_id = ''
try:
# this will create the ehb external_record entry
# and add that record to the subject's record group
self.record_id = SubjectUtils.create_new_ehb_external_record(
self.pds, request.user, self.subject, rec_id, label_id).id
if self.check_cache():
self.update_cache()
self.start_path = '{0}/dataentry/protocoldatasource/{1}/subject/{2}/record/{3}/start/'.format(
self.service_client.self_root_path,
self.pds.id,
self.subject.id,
self.record_id)
return HttpResponseRedirect(self.start_path)
except RecordCreationError as rce: # exception from the eHB
request.META['action'] = rce.errmsg
request.META['error'] = True
record_already_exists = 6
cause = rce.raw_cause
if cause and len(cause) == 1 and record_already_exists == cause[0]:
er_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD)
ehb_recs = er_rh.get(
external_system_url=self.pds.data_source.url, subject_id=self.subject.id, path=self.pds.path)
ehb_rec_id = None
for record in ehb_recs:
if record.record_id == rec_id:
ehb_rec_id = record.id
if ehb_rec_id:
self.start_path = '%s/dataentry/protocoldatasource/%s/subject/%s/record/%s/start' % (
ServiceClient.self_root_path,
self.pds.id,
self.subject.id,
ehb_rec_id)
else:
context['errors'].append(
'This ID has already been assigned to another subject.')
return render_to_response(
'pds_dataentry_rec_create.html',
context,
context_instance=RequestContext(request)
)
else:
request.META['action'] = 'Record could not be created'
request.META['error'] = True
context['errors'].append((
'The record could not be created on the '
'electronic Honest Broker. Please contact '
'a system administrator. There could be a'
' connection problem.'))
except:
return HttpResponse('Unknown Error')
return HttpResponseRedirect(self.start_path)
except RecordCreationError as rce:
# Handle errors in the form.
request.META['action'] = rce.errmsg
request.META['error'] = True
context['errors'].append(rce.cause)
return render_to_response(
'pds_dataentry_rec_create.html',
context,
context_instance=RequestContext(request)
)
def handle(self, *args, **options):
if options['protocol']:
if options['continue']:
protocols = Protocol.objects.filter(
id__gte=options['protocol']).order_by('id').all()
else:
try:
protocols = Protocol.objects.filter(
id=options['protocol']).all()
except Protocol.DoesNotExist:
print('Protocol specified does not exist')
return
else:
protocols = Protocol.objects.order_by('id').all()
g_rh = ServiceClient.get_rh_for(record_type=ServiceClient.GROUP)
errors = []
msg = None
for protocol in protocols:
print('Checking {0} (ID:{1}) Group: {2}'.format(
protocol.name, protocol.id, protocol.ehb_group_name()))
try:
g_rh.get(name=protocol.ehb_group_name())
except RequestedRangeNotSatisfiable:
msg = ('Unable to find expected group: {0}'.format(
protocol.ehb_group_name()))
errors.append(msg)
print(msg)
msg = None
# Check for pds groups
subjects = protocol.getSubjects()
if subjects:
for subject in subjects:
try:
SubjectUtils.get_protocol_subject_record_group(
protocol, subject)
except RequestedRangeNotSatisfiable as e:
msg = (
'Warning: Group not found under Protocol: {0} Group name expected: {1}'
.format(protocol.name, e.errmsg))
except Organization.DoesNotExist:
msg = (
'Warning: Could not find associated Organization for protocol: {0}, eHB Org ID: {1} Likely eHB/BRP organizaiton mismatch'
.format(protocol.name, subject.organization_id))
except BadStatusLine:
msg = (
'Warning: Malformed Group Detected for Protocol: {0} Subject ID: {1} Likely Bad Organization ID'
.format(protocol.name, subject.id))
if msg:
errors.append(msg)
print(msg)
msg = None
if csv:
with open('group_report_{0}.csv'.format(
datetime.now().strftime('%Y%m%d.%H:%M.%S')),
'w',
newline='') as csvfile:
csv_writer = csv.writer(csvfile,
delimiter=' ',
quotechar='"',
quoting=csv.QUOTE_MINIMAL)
for error in errors:
csv_writer.writerow([error])
def handle(self, *args, **options):
if options['protocol']:
if options['continue']:
protocols = Protocol.objects.filter(id__gte=options['protocol']).order_by('id').all()
else:
try:
protocols = Protocol.objects.filter(id=options['protocol']).all()
except Protocol.DoesNotExist:
print('Protocol specified does not exist')
return
else:
protocols = Protocol.objects.order_by('id').all()
g_rh = ServiceClient.get_rh_for(record_type=ServiceClient.GROUP)
errors = []
msg = None
for protocol in protocols:
print('Checking {0} (ID:{1}) Group: {2}'.format(
protocol.name,
protocol.id,
protocol.ehb_group_name()))
try:
g_rh.get(name=protocol.ehb_group_name())
except RequestedRangeNotSatisfiable:
msg = ('Unable to find expected group: {0}'.format(protocol.ehb_group_name()))
errors.append(msg)
print(msg)
msg = None
# Check for pds groups
subjects = protocol.getSubjects()
if subjects:
for subject in subjects:
try:
SubjectUtils.get_protocol_subject_record_group(protocol, subject)
except RequestedRangeNotSatisfiable as e:
msg = ('Warning: Group not found under Protocol: {0} Group name expected: {1}'.format(
protocol.name,
e.errmsg
))
except Organization.DoesNotExist:
msg = ('Warning: Could not find associated Organization for protocol: {0}, eHB Org ID: {1} Likely eHB/BRP organizaiton mismatch'.format(
protocol.name,
subject.organization_id
))
except BadStatusLine:
msg = ('Warning: Malformed Group Detected for Protocol: {0} Subject ID: {1} Likely Bad Organization ID'.format(
protocol.name,
subject.id
))
if msg:
errors.append(msg)
print(msg)
msg = None
if csv:
with open('group_report_{0}.csv'.format(datetime.now().strftime('%Y%m%d.%H:%M.%S')), 'w', newline='') as csvfile:
csv_writer = csv.writer(csvfile, delimiter=' ',
quotechar='"', quoting=csv.QUOTE_MINIMAL)
for error in errors:
csv_writer.writerow([error])