def subjects(self, request, *args, **kwargs):
"""
Returns a list of subjects associated with a protocol.
"""
p = self.get_object()
if p.isUserAuthorized(request.user):
subjects = p.getSubjects()
organizations = p.organizations.all()
if subjects:
subs = [eHBSubjectSerializer(sub).data for sub in subjects]
else:
return Response([])
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())
for sub in subs:
for ehb_org in ehb_orgs:
if sub['organization_id'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
else:
return Response(
{
"detail":
"You are not authorized to view subjects in this protocol"
},
status=403)
if subjects:
return Response(subs, headers={'Access-Control-Allow-Origin': '*'})
return Response([])
def subjects(self, request, *args, **kwargs):
"""
Returns a list of subjects associated with a protocol.
"""
p = self.get_object()
if p.isUserAuthorized(request.user):
subjects = p.getSubjects()
organizations = p.organizations.all()
if subjects:
subs = [eHBSubjectSerializer(sub).data for sub in subjects]
else:
return Response([])
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())
for sub in subs:
for ehb_org in ehb_orgs:
if sub['organization_id'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
else:
return Response(
{"detail": "You are not authorized to view subjects in this protocol"},
status=403
)
if subjects:
return Response(
subs,
headers={'Access-Control-Allow-Origin': '*'}
)
return Response([])
def get_protocol_subjects(self, protocol, lbls):
subjects = protocol.getSubjects()
subject_ids = []
if subjects:
subs = [eHBSubjectSerializer(sub).data for sub in subjects]
for s in subs:
subject_ids.append(s['id'])
return subject_ids
def get(self, request, pk, *args, **kwargs):
"""
Returns a list of subjects associated with the protocol datasource and
their external records
"""
try:
pds = ProtocolDataSource.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response(
{'error': 'ProtocolDatasource requested not found'},
status=404)
subjects = pds.protocol.getSubjects()
organizations = pds.protocol.organizations.all()
if pds.protocol.isUserAuthorized(request.user):
if subjects:
params = self.buildQueryParams(
subjects, pds.data_source.ehb_service_es_id, pds.path)
# TODO: Cache check
res = self.er_rh.query(*params)
subjects = [
eHBSubjectSerializer(subject).data for subject in subjects
]
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())
for sub in subjects:
sub.update({"external_records": []})
sub['organization'] = sub['organization_id']
sub.pop('organization_id')
for ehb_org in ehb_orgs:
if sub['organization'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
for ex_rec in res:
if ex_rec["success"]:
for sub in subjects:
for rec in ex_rec["external_record"]:
if rec.subject_id == sub["id"]:
sub["external_records"].append(
json.loads(
rec.json_from_identity(rec)))
return Response({"subjects": subjects, "count": len(subjects)})
else:
return Response({"subjects": [], "count": 0})
else:
return Response(
{
"detail":
"You are not authorized to view subjects from this protocol datasource"
},
status=403)
def get(self, request, pk, *args, **kwargs):
"""
Returns a list of subjects associated with the protocol datasource and
their external records
"""
try:
pds = ProtocolDataSource.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'ProtocolDatasource requested not found'}, status=404)
subjects = pds.protocol.getSubjects()
organizations = pds.protocol.organizations.all()
if pds.protocol.isUserAuthorized(request.user):
if subjects:
params = self.buildQueryParams(subjects, pds.data_source.ehb_service_es_id, pds.path)
# TODO: Cache check
res = self.er_rh.query(*params)
subjects = [eHBSubjectSerializer(subject).data for subject in subjects]
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())
for sub in subjects:
sub.update({"external_records": []})
sub['organization'] = sub['organization_id']
sub.pop('organization_id')
for ehb_org in ehb_orgs:
if sub['organization'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
for ex_rec in res:
if ex_rec["success"]:
for sub in subjects:
for rec in ex_rec["external_record"]:
if rec.subject_id == sub["id"]:
sub["external_records"].append(json.loads(rec.json_from_identity(rec)))
return Response({
"subjects": subjects,
"count": len(subjects)})
else:
return Response({
"subjects": [],
"count": 0})
else:
return Response(
{"detail": "You are not authorized to view subjects from this protocol datasource"},
status=403
)
def subjects(self, request, *args, **kwargs):
"""
Returns a list of subjects associated with the protocol datasource and their
"""
p = self.get_object()
subjects = p.protocol.getSubjects()
organizations = p.protocol.organizations.all()
if p.protocol.isUserAuthorized(request.user):
if subjects:
params = self.buildQueryParams(subjects,
p.data_source.ehb_service_es_id,
p.path)
res = ServiceClient.ext_rec_client.query(*params)
subjects = [
eHBSubjectSerializer(subject).data for subject in subjects
]
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())
for sub in subjects:
sub.update({"external_records": []})
for ehb_org in ehb_orgs:
if sub['organization_id'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
for ex_rec in res:
if ex_rec["success"]:
for sub in subjects:
for rec in ex_rec["external_record"]:
if rec.subject_id == sub["id"]:
sub["external_records"].append(
eHBExternalRecordSerializer(rec).data)
return Response({"subjects": subjects, "count": len(subjects)})
else:
return Response({"subjects": [], "count": 0})
else:
return Response(
{
"detail":
"You are not authorized to view subjects from this protocol datasource"
},
status=403)
def subjects(self, request, *args, **kwargs):
"""
Returns a list of subjects associated with the protocol datasource and their
"""
p = self.get_object()
subjects = p.protocol.getSubjects()
organizations = p.protocol.organizations.all()
if p.protocol.isUserAuthorized(request.user):
if subjects:
params = self.buildQueryParams(subjects, p.data_source.ehb_service_es_id, p.path)
res = ServiceClient.ext_rec_client.query(*params)
subjects = [eHBSubjectSerializer(subject).data for subject in subjects]
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())
for sub in subjects:
sub.update({"external_records": []})
for ehb_org in ehb_orgs:
if sub['organization_id'] == ehb_org.id:
sub['organization_name'] = ehb_org.name
for ex_rec in res:
if ex_rec["success"]:
for sub in subjects:
for rec in ex_rec["external_record"]:
if rec.subject_id == sub["id"]:
sub["external_records"].append(eHBExternalRecordSerializer(rec).data)
return Response({
"subjects": subjects,
"count": len(subjects)
})
else:
return Response({
"subjects": [],
"count": 0
})
else:
return Response(
{"detail": "You are not authorized to view subjects from this protocol datasource"},
status=403
)
def get(self, request, pk, *args, **kwargs):
"""
Returns a list of subjects associated with a protocol.
"""
try:
p = Protocol.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'Protocol requested not found'}, status=404)
# Check cache
cache_data = cache.get('protocol{0}_sub_data'.format(p.id))
if cache_data:
return Response(
json.loads(cache_data),
headers={'Access-Control-Allow-Origin': '*'}
)
if p.isUserAuthorized(request.user):
subjects = p.getSubjects()
organizations = p.organizations.all()
if subjects:
subs = [eHBSubjectSerializer(sub).data for sub in subjects]
else:
return Response([])
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 = p.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:
pass
for sub in subs:
sub['external_records'] = []
sub['external_ids'] = []
sub['organization'] = sub['organization_id']
sub['organization_id_label'] = sub['organization_id_label']
sub.pop('organization_id')
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
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
else:
return Response(
{"detail": "You are not authorized to view subjects in this protocol"},
status=403
)
if subjects:
return Response(
subs,
headers={'Access-Control-Allow-Origin': '*'}
)
return Response([])
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 get(self, request, pk, *args, **kwargs):
"""
Returns a list of subjects associated with a protocol.
"""
try:
p = Protocol.objects.get(pk=pk)
except ObjectDoesNotExist:
return Response({'error': 'Protocol requested not found'},
status=404)
# Check cache
cache_data = cache.get('protocol{0}_sub_data'.format(p.id))
if cache_data:
return Response(json.loads(cache_data),
headers={'Access-Control-Allow-Origin': '*'})
if p.isUserAuthorized(request.user):
subjects = p.getSubjects()
organizations = p.organizations.all()
if subjects:
subs = [eHBSubjectSerializer(sub).data for sub in subjects]
else:
return Response([])
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 = p.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:
pass
for sub in subs:
sub['external_records'] = []
sub['external_ids'] = []
sub['organization'] = sub['organization_id']
sub['organization_id_label'] = sub['organization_id_label']
sub.pop('organization_id')
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
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
else:
return Response(
{
"detail":
"You are not authorized to view subjects in this protocol"
},
status=403)
if subjects:
return Response(subs, headers={'Access-Control-Allow-Origin': '*'})
return Response([])
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 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)
