def getExternalRecords(self, pds, subject, lbls):
er_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD)
try:
pds_records = er_rh.get(external_system_url=pds.data_source.url,
path=pds.path,
subject_id=subject['id'])
time.sleep(0.05)
except PageNotFound:
pds_records = []
r = []
for ex_rec in pds_records:
# Convert ehb-client object to JSON and then parse as py dict
e = json.loads(ex_rec.json_from_identity(ex_rec))
# Map label descriptions from the eHB to External Records
for label in lbls:
if e['label'] == label['id']:
if label['label'] == '':
e['label_desc'] = 'Record'
else:
e['label_desc'] = label['label']
e['pds'] = pds.id
r.append(e)
return r
def handle(self, *args, **options):
def subject_threading(self, pds, s_id, lbls, user, cache_key):
# get all records associated with subject
records = self.get_subject_records(pds, s_id, lbls)
for record in records:
r_id = record['id']
r_name = record['record_id']
self.cache_redcap_form_complete(pds, user, cache_key, s_id,
r_id, r_name)
return
def clear_cache(cache_key):
cache.delete(cache_key)
start = time.time()
er_label_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
lbls = er_label_rh.query()
protocols = self.get_protocols(options['protocol_id'])
for protocol in protocols:
protocoldatasources = self.get_protocoldatasource(
protocol) # get redcap protocol datasource
for pds in protocoldatasources:
print("\n Caching protocol datasource {} \n".format(pds))
user = self.get_protocol_user(
protocol) # get eig user in protocol
subject_id_list = self.get_protocol_subjects(
protocol, lbls) # get all subjects in protocol
try:
cache_key = 'protocoldatasource{0}'.format(
pds.id) + '_redcap_completion_codes'
cache.delete(cache_key)
except AttributeError: # protocoldatasource wasn't properly configured
print(str(pds) + ' was skipped')
continue
threads = [
] # array to hold all threads, length is # of records per subj
for s_id in subject_id_list: # for every subject
# creating threads
curr_thread = threading.Thread(target=subject_threading,
args=(
self,
pds,
s_id,
lbls,
user,
cache_key,
))
threads.append(curr_thread)
curr_thread.start()
# make sure every thread has finished
for t in threads:
t.join()
elapsed = time.time() - start
print("total caching time" + str(elapsed))
print("caching records table complete")
def handle(self, *args, **options):
erl_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
labels = erl_rh.query()
cache.set('ehb_labels', labels)
if hasattr(cache, 'persist'):
cache.persist('ehb_labels')
print("caching of ehb_labels complete")
def getExternalRecords(self, pds, subject, lbls):
"""Get external records for a subject/protocol combination.
Returns external records for a given subject from a given protocol
after labelling them with EHB labels and the protocol id.
"""
# Get the appropriate request handler for external records.
er_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD)
try:
# Retrieve the external records for the subject/protocol.
# Path argument is needed for ehb_datasources to make request.
pds_records = er_rh.get(external_system_url=pds.data_source.url,
path=pds.path,
subject_id=subject['id'])
# TODO: why is this necessary?
time.sleep(0.05)
except PageNotFound:
# Return an empty array if the subject/protocol is not found.
pds_records = []
# Result array.
r = []
for ex_rec in pds_records:
# Convert ehb-client object to JSON and then parse as py dict.
# TODO: the external record object should have this capability.
# We should examine this to refactor for simplicity. It is possible
# to remove json.loads for each json_from_identity call.
e = json.loads(ex_rec.json_from_identity(ex_rec))
# Map label descriptions from the eHB to External Records.
for label in lbls:
if e['label'] == label['id']:
if label['label'] == '':
e['label_desc'] = 'Record'
else:
e['label_desc'] = label['label']
# Add the protocol datasource id to the external record.
e['pds'] = pds.id
r.append(e)
return r
class BRPApiView(APIView):
# Cache
cache = _cache
# Honest Broker Request Handelers
s_rh = ServiceClient.get_rh_for(record_type=ServiceClient.SUBJECT)
o_rh = ServiceClient.get_rh_for(record_type=ServiceClient.ORGANIZATION)
es_rh = ServiceClient.get_rh_for(record_type=ServiceClient.EXTERNAL_SYSTEM)
er_rh = ServiceClient.get_rh_for(record_type=ServiceClient.EXTERNAL_RECORD)
erl_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD_LABEL) # noqa
err_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD_RELATION) # noqa
g_rh = ServiceClient.get_rh_for(record_type=ServiceClient.GROUP)
relationship_HB_handler = ServiceClient.get_rh_for(
record_type=ServiceClient.RELATIONSHIP)
relationship_type_HB_handler = ServiceClient.get_rh_for(
record_type=ServiceClient.RELATIONSHIP_TYPE)
# Utility Classes
subject_utils = SubjectUtils
record_utils = RecordUtils
def get_context_data(self, **kwargs):
subject_api_url = "/api/subject/id/" + kwargs['subject_id'] + "/"
context = super(DataEntryView, self).get_context_data(**kwargs)
self.pds = get_object_or_404(ProtocolDataSource, pk=kwargs['pds_id'])
if not self.subject:
self.subject = ServiceClient.ehb_api(subject_api_url, "GET").json()
if not self.record:
self.record = self.get_external_record(**kwargs)
if not self.org:
self.org = self.service_client.get_rh_for(
record_type=ServiceClient.ORGANIZATION).get(id=self.subject['organization'])
self.driver = DriverUtils.getDriverFor(
protocol_data_source=self.pds, user=self.request.user)
if not self.label_id:
self.label_id = self.request.GET.get('label_id', 1)
if not self.label:
self.label = self.get_label(context)
if self.record:
self.start_path = '{0}/dataentry/protocoldatasource/{1}/subject/{2}/record/{3}/start/'.format(
self.service_client.self_root_path,
self.pds.id,
kwargs['subject_id'],
self.record.id)
self.create_path = '{0}/dataentry/protocoldatasource/{1}/subject/{2}/create/'.format(
self.service_client.self_root_path,
self.pds.id,
kwargs['subject_id'])
context = {
'protocol': self.pds.protocol,
'organization': self.org,
'subject': self.subject,
'root_path': self.service_client.self_root_path,
'pds': self.pds,
'request': self.request,
'record': self.record,
'label_id': self.label_id,
'label': self.label,
'errors': []
}
return context
def getExternalRecords(self, pds, subject, lbls):
er_rh = ServiceClient.get_rh_for(record_type=ServiceClient.EXTERNAL_RECORD)
try:
pds_records = er_rh.get(
external_system_url=pds.data_source.url, path=pds.path, subject_id=subject['id'])
time.sleep(0.05)
except PageNotFound:
pds_records = []
r = []
for ex_rec in pds_records:
# Convert ehb-client object to JSON and then parse as py dict
e = json.loads(ex_rec.json_from_identity(ex_rec))
# Map label descriptions from the eHB to External Records
for label in lbls:
if e['label'] == label['id']:
if label['label'] == '':
e['label_desc'] = 'Record'
else:
e['label_desc'] = label['label']
e['pds'] = pds.id
r.append(e)
return r
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 cache_records(self, protocol_id):
protocol_id = protocol_id[0]
if protocol_id == 'all':
protocols = Protocol.objects.all()
else:
protocols = Protocol.objects.filter(id=int(protocol_id)).all()
er_label_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
lbls = er_label_rh.query()
print('Caching {0} protocol(s)...'.format(len(protocols)))
for protocol in protocols:
print('Caching {}'.format(protocol))
subjects = protocol.getSubjects()
organizations = protocol.organizations.all()
if subjects:
subs = [eHBSubjectSerializer(sub).data for sub in subjects]
else:
continue
ehb_orgs = []
# We can't rely on Ids being consistent across apps so we must
# append the name here for display downstream.
for o in organizations:
ehb_orgs.append(o.getEhbServiceInstance())
# Check if the protocol has external IDs configured. If so retrieve them
manageExternalIDs = False
protocoldatasources = protocol.getProtocolDataSources()
for pds in protocoldatasources:
if pds.driver == 3:
ExIdSource = pds
manageExternalIDs = True
if manageExternalIDs:
try:
config = json.loads(ExIdSource.driver_configuration)
if 'sort_on' in list(config.keys()):
# er_label_rh = ServiceClient.get_rh_for(record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
# lbl = er_label_rh.get(id=config['sort_on'])
lbl = ''
addl_id_column = lbl
except:
raise
pass
for sub in subs:
sub['external_records'] = []
sub['external_ids'] = []
sub['organization'] = sub['organization_id']
sub.pop('organization_id')
for pds in protocoldatasources:
try:
sub['external_records'].extend(
self.getExternalRecords(pds, sub, lbls))
except:
print("there was an error processing external records")
print("subject DB id:")
print(sub['id'])
print("protocol data source:")
print(pds)
pass
if manageExternalIDs:
# Break out external ids into a separate object for ease of use
for record in sub['external_records']:
if record['external_system'] == 3:
try:
sub['external_ids'].append(record)
except:
print(
"an error occured getting external records"
)
print(sub['external_ids'])
for ehb_org in ehb_orgs:
if sub['organization'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
cache_key = 'protocol{0}_sub_data'.format(protocol.id)
cache.set(cache_key, json.dumps(subs))
cache.persist(cache_key)
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 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 cache_records(self, protocol_id):
"""Cache subject records from a given protocol locally."""
# TODO: consider passing in a list if we ever need to cache a small
# number of protocols at one time. look at why only using first item in
# list.
protocol_id = protocol_id[0]
if protocol_id == 'all':
# Special "all" protocol gets all protocols.
protocols = Protocol.objects.all()
else:
protocols = Protocol.objects.filter(id=int(protocol_id)).all()
# Get external record label request handler.
er_label_rh = ServiceClient.get_rh_for(
record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
# Retrieve the actual external record labels.
lbls = er_label_rh.query()
# Tell user how many protocols are being cached.
print('Caching {0} protocol(s)...'.format(len(protocols)))
for protocol in protocols:
# Tell user which protocol is being cached.
print('Caching {}'.format(protocol))
# Get list of subjects and organizations in the protocol.
subjects = protocol.getSubjects()
organizations = protocol.organizations.all()
# Serialize retrieved subjects or continue if there are none.
if subjects:
subs = [eHBSubjectSerializer(sub).data for sub in subjects]
else:
continue
ehb_orgs = []
# We can't rely on Ids being consistent across apps so we must
# append the name here for display downstream.
for o in organizations:
ehb_orgs.append(o.getEhbServiceInstance())
# TODO: Explain this block, down to the `for sub in subs` loop.
# Check if the protocol has external IDs configured.
# If so, retrieve them.
manageExternalIDs = False
protocoldatasources = protocol.getProtocolDataSources()
for pds in protocoldatasources:
if pds.driver == 3:
ExIdSource = pds
manageExternalIDs = True
if manageExternalIDs:
try:
config = json.loads(ExIdSource.driver_configuration)
if 'sort_on' in list(config.keys()):
# er_label_rh = ServiceClient.get_rh_for(
# record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
# lbl = er_label_rh.get(id=config['sort_on'])
lbl = ''
addl_id_column = lbl # noqa
except:
raise
pass
# Transform subjects for ease of use.
for sub in subs:
# Initialize new fields.
sub['external_records'] = []
sub['external_ids'] = []
sub['organization'] = sub['organization_id']
sub.pop('organization_id')
# Add external records from all data sources.
for pds in protocoldatasources:
try:
sub['external_records'].extend(
self.getExternalRecords(pds, sub, lbls))
except:
print("there was an error processing external records")
print("subject DB id:")
print(sub['id'])
print("protocol data source:")
print(pds)
pass
# TODO: Explain this block.
if manageExternalIDs:
# Break out external ids into a separate object for ease of
# use.
for record in sub['external_records']:
if record['external_system'] == 3:
try:
sub['external_ids'].append(record)
except:
print(
"an error occured getting external records"
)
print(sub['external_ids'])
# Add organization name to subject record for display, since
# organization IDs can vary across apps. (?)
for ehb_org in ehb_orgs:
if sub['organization'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
# Cache the array of subjects.
cache_key = 'protocol{0}_sub_data'.format(protocol.id)
cache.set(cache_key, json.dumps(subs))
cache.persist(cache_key)
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 cache_records(self, protocol_id):
protocol_id = protocol_id[0]
if protocol_id == 'all':
protocols = Protocol.objects.all()
else:
protocols = Protocol.objects.filter(id=int(protocol_id)).all()
er_label_rh = ServiceClient.get_rh_for(record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
lbls = er_label_rh.query()
print('Caching {0} protocol(s)...'.format(len(protocols)))
for protocol in protocols:
print('Caching {}'.format(protocol))
subjects = protocol.getSubjects()
organizations = protocol.organizations.all()
if subjects:
subs = [eHBSubjectSerializer(sub).data for sub in subjects]
else:
continue
ehb_orgs = []
# We can't rely on Ids being consistent across apps so we must
# append the name here for display downstream.
for o in organizations:
ehb_orgs.append(o.getEhbServiceInstance())
# Check if the protocol has external IDs configured. If so retrieve them
manageExternalIDs = False
protocoldatasources = protocol.getProtocolDataSources()
for pds in protocoldatasources:
if pds.driver == 3:
ExIdSource = pds
manageExternalIDs = True
if manageExternalIDs:
try:
config = json.loads(ExIdSource.driver_configuration)
if 'sort_on' in list(config.keys()):
# er_label_rh = ServiceClient.get_rh_for(record_type=ServiceClient.EXTERNAL_RECORD_LABEL)
# lbl = er_label_rh.get(id=config['sort_on'])
lbl = ''
addl_id_column = lbl
except:
raise
pass
for sub in subs:
sub['external_records'] = []
sub['external_ids'] = []
sub['organization'] = sub['organization_id']
sub.pop('organization_id')
for pds in protocoldatasources:
sub['external_records'].extend(self.getExternalRecords(pds, sub, lbls))
if manageExternalIDs:
# Break out external ids into a separate object for ease of use
for record in sub['external_records']:
if record['external_system'] == 3:
sub['external_ids'].append(record)
for ehb_org in ehb_orgs:
if sub['organization'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
cache_key = 'protocol{0}_sub_data'.format(protocol.id)
cache.set(cache_key, json.dumps(subs))
cache.persist(cache_key)
