def from_client_json(self, resource_json, id_=None, expected_version=None, client_id=None):
parse_json_enum(resource_json, 'withdrawalStatus', WithdrawalStatus)
parse_json_enum(resource_json, 'withdrawalReason', WithdrawalReason)
parse_json_enum(resource_json, 'suspensionStatus', SuspensionStatus)
if 'withdrawalTimeStamp' in resource_json and resource_json['withdrawalTimeStamp'] is not None:
try:
resource_json['withdrawalTimeStamp'] = datetime.datetime\
.utcfromtimestamp(float(resource_json['withdrawalTimeStamp'])/1000)
except (ValueError, TypeError):
raise ValueError("Could not parse {} as TIMESTAMP"
.format(resource_json['withdrawalTimeStamp']))
# biobankId, lastModified, signUpTime are set by DAO.
return Participant(
participantId=id_,
externalId=resource_json.get('externalId'),
version=expected_version,
providerLink=json.dumps(resource_json.get('providerLink')),
clientId=client_id,
withdrawalStatus=resource_json.get('withdrawalStatus'),
withdrawalReason=resource_json.get('withdrawalReason'),
withdrawalAuthored=resource_json.get('withdrawalTimeStamp'),
withdrawalReasonJustification=resource_json.get('withdrawalReasonJustification'),
suspensionStatus=resource_json.get('suspensionStatus'),
organizationId=get_organization_id_from_external_id(resource_json, self.organization_dao),
hpoId=get_awardee_id_from_name(resource_json, self.hpo_dao),
siteId=get_site_id_from_google_group(resource_json, self.site_dao))
def validate_params(self, params):
start_date_str = params['start_date']
end_date_str = params['end_date']
enrollment_statuses = params['enrollment_statuses']
awardees = params['awardees']
stratification = params['stratification']
# Validate dates
if not start_date_str or not end_date_str:
raise BadRequest('Start date and end date should not be empty')
try:
start_date = datetime.datetime.strptime(start_date_str,
DATE_FORMAT).date()
except ValueError:
raise BadRequest('Invalid start date: %s' % start_date_str)
try:
end_date = datetime.datetime.strptime(end_date_str,
DATE_FORMAT).date()
except ValueError:
raise BadRequest('Invalid end date: %s' % end_date_str)
date_diff = abs((end_date - start_date).days)
if date_diff > DAYS_LIMIT:
raise BadRequest('Difference between start date and end date ' \
'should not be greater than %s days' % DAYS_LIMIT)
params['start_date'] = start_date
params['end_date'] = end_date
# Validate awardees, get ID list
awardee_ids = []
for awardee in awardees:
awardee_id = get_awardee_id_from_name({'awardee': awardee},
self.hpo_dao)
if awardee_id == None:
raise BadRequest('Invalid awardee name: %s' % awardee)
awardee_ids.append(awardee_ids)
params['awardee_ids'] = awardee_ids
# Validate enrollment statuses
try:
params["enrollment_statuses"] = [
EnrollmentStatus(val) for val in enrollment_statuses
]
except TypeError:
valid_enrollment_statuses = EnrollmentStatus.to_dict()
for enrollment_status in enrollment_statuses:
if enrollment_status not in valid_enrollment_statuses:
raise BadRequest('Invalid enrollment status: %s' %
enrollment_status)
# Validate stratifications
try:
params['stratification'] = Stratifications(
params['stratification'])
except TypeError:
raise BadRequest('Invalid stratification: %s' % stratification)
return params
def from_client_json(self, resource_json, id_=None, expected_version=None, client_id=None):
parse_json_enum(resource_json, 'withdrawalStatus', WithdrawalStatus)
parse_json_enum(resource_json, 'withdrawalReason', WithdrawalReason)
parse_json_enum(resource_json, 'suspensionStatus', SuspensionStatus)
# biobankId, lastModified, signUpTime are set by DAO.
return Participant(
participantId=id_,
externalId=resource_json.get('externalId'),
version=expected_version,
providerLink=json.dumps(resource_json.get('providerLink')),
clientId=client_id,
withdrawalStatus=resource_json.get('withdrawalStatus'),
withdrawalReason=resource_json.get('withdrawalReason'),
withdrawalReasonJustification=resource_json.get('withdrawalReasonJustification'),
suspensionStatus=resource_json.get('suspensionStatus'),
organizationId=get_organization_id_from_external_id(resource_json, self.organization_dao),
hpoId=get_awardee_id_from_name(resource_json, self.hpo_dao),
siteId=get_site_id_from_google_group(resource_json, self.site_dao))
def validate_params(self, start_date_str, end_date_str, stratification_str,
enrollment_statuses, awardees, history):
"""Validates URL parameters, and converts human-friendly values to canonical form
:param start_date_str: Start date string, e.g. '2018-01-01'
:param end_date_str: End date string, e.g. '2018-01-31'
:param stratification_str: How to stratify (layer) results, as in a stacked bar chart
:param enrollment_statuses: enrollment level filters
:param awardees: awardee name filters
:param history: indicate if it's for historical data
:return: Validated parameters in canonical form
"""
params = {}
# Validate stratifications
try:
params['stratification'] = Stratifications(stratification_str)
except TypeError:
raise BadRequest('Invalid stratification: %s' % stratification_str)
if params['stratification'] in [
Stratifications.FULL_STATE, Stratifications.FULL_CENSUS,
Stratifications.FULL_AWARDEE, Stratifications.LIFECYCLE
]:
# Validate dates
if not end_date_str:
raise BadRequest('end date should not be empty')
start_date = datetime.datetime.strptime('2017-01-01',
DATE_FORMAT).date()
try:
end_date = datetime.datetime.strptime(end_date_str,
DATE_FORMAT).date()
except ValueError:
raise BadRequest('Invalid end date: %s' % end_date_str)
params['start_date'] = start_date
params['end_date'] = end_date
else:
# Validate dates
if not start_date_str or not end_date_str:
raise BadRequest('Start date and end date should not be empty')
try:
start_date = datetime.datetime.strptime(
start_date_str, DATE_FORMAT).date()
except ValueError:
raise BadRequest('Invalid start date: %s' % start_date_str)
try:
end_date = datetime.datetime.strptime(end_date_str,
DATE_FORMAT).date()
except ValueError:
raise BadRequest('Invalid end date: %s' % end_date_str)
date_diff = abs((end_date - start_date).days)
if history != 'TRUE' and date_diff > DAYS_LIMIT_FOR_REALTIME_DATA:
raise BadRequest('Difference between start date and end date '
'should not be greater than %s days' %
DAYS_LIMIT_FOR_REALTIME_DATA)
if history == 'TRUE' and date_diff > DAYS_LIMIT_FOR_HISTORY_DATA:
raise BadRequest('Difference between start date and end date '
'should not be greater than %s days' %
DAYS_LIMIT_FOR_HISTORY_DATA)
params['start_date'] = start_date
params['end_date'] = end_date
# Validate awardees, get ID list
awardee_ids = []
if awardees is not None:
awardees = awardees.split(',')
for awardee in awardees:
if awardee != '':
awardee_id = get_awardee_id_from_name({'awardee': awardee},
self.hpo_dao)
if awardee_id == None:
raise BadRequest('Invalid awardee name: %s' % awardee)
awardee_ids.append(awardee_id)
params['awardee_ids'] = awardee_ids
# Validate enrollment statuses
if enrollment_statuses is not None:
enrollment_statuses = enrollment_statuses.split(',')
try:
params['enrollment_statuses'] = [
EnrollmentStatus(val) for val in enrollment_statuses
]
except TypeError:
valid_enrollment_statuses = EnrollmentStatus.to_dict()
for enrollment_status in enrollment_statuses:
if enrollment_status != '':
if enrollment_status not in valid_enrollment_statuses:
raise BadRequest('Invalid enrollment status: %s' %
enrollment_status)
return params
def validate_params(self, params):
filters = {}
# Validate stratifications
try:
filters['stratification'] = Stratifications(params['stratification'])
except TypeError:
raise BadRequest('Invalid stratification: %s' % params['stratification'])
if filters['stratification'] in [Stratifications.FULL_STATE, Stratifications.FULL_CENSUS,
Stratifications.FULL_AWARDEE, Stratifications.GEO_STATE,
Stratifications.GEO_CENSUS, Stratifications.GEO_AWARDEE,
Stratifications.LIFECYCLE]:
# Validate dates
if not params['end_date']:
raise BadRequest('end date should not be empty')
try:
end_date = datetime.datetime.strptime(params['end_date'], DATE_FORMAT).date()
start_date = end_date
except ValueError:
raise BadRequest('Invalid end date: %s' % params['end_date'])
filters['start_date'] = start_date
filters['end_date'] = end_date
else:
# Validate dates
if not params['start_date'] or not params['end_date']:
raise BadRequest('Start date and end date should not be empty')
try:
start_date = datetime.datetime.strptime(params['start_date'], DATE_FORMAT).date()
except ValueError:
raise BadRequest('Invalid start date: %s' % params['start_date'])
try:
end_date = datetime.datetime.strptime(params['end_date'], DATE_FORMAT).date()
except ValueError:
raise BadRequest('Invalid end date: %s' % params['end_date'])
date_diff = abs((end_date - start_date).days)
if params['history'] != 'TRUE' and date_diff > DAYS_LIMIT_FOR_REALTIME_DATA:
raise BadRequest('Difference between start date and end date '
'should not be greater than %s days' % DAYS_LIMIT_FOR_REALTIME_DATA)
if params['history'] == 'TRUE' and date_diff > DAYS_LIMIT_FOR_HISTORY_DATA:
raise BadRequest('Difference between start date and end date '
'should not be greater than %s days' % DAYS_LIMIT_FOR_HISTORY_DATA)
filters['start_date'] = start_date
filters['end_date'] = end_date
# Validate awardees, get ID list
awardee_ids = []
if params['awardees'] is not None:
awardees = params['awardees'].split(',')
for awardee in awardees:
if awardee != '':
awardee_id = get_awardee_id_from_name({'awardee': awardee}, self.hpo_dao)
if awardee_id is None:
raise BadRequest('Invalid awardee name: %s' % awardee)
awardee_ids.append(awardee_id)
filters['awardee_ids'] = awardee_ids
# Validate enrollment statuses
enrollment_status_strs = []
if params['enrollment_statuses'] is not None:
enrollment_statuses = params['enrollment_statuses'].split(',')
try:
enrollment_status_strs = [str(EnrollmentStatus(val)) for val in enrollment_statuses]
except TypeError:
valid_enrollment_statuses = EnrollmentStatus.to_dict()
for enrollment_status in enrollment_statuses:
if enrollment_status != '':
if enrollment_status not in valid_enrollment_statuses:
raise BadRequest('Invalid enrollment status: %s' % enrollment_status)
filters['enrollment_statuses'] = enrollment_status_strs
if params['sample_time_def'] and params['sample_time_def'] not in ['STORED', 'ORDERED']:
raise BadRequest('Invalid value for parameter filterBy: %s' % params['sample_time_def'])
else:
filters['sample_time_def'] = params['sample_time_def']
if params['history'] and params['history'] not in ['TRUE', 'FALSE']:
raise BadRequest('Invalid value for parameter history: %s' % params['history'])
else:
filters['history'] = params['history']
return filters
