def test_update_existing_site(self, time_zone, lat_long):
self._setup_data()
lat_long.return_value = 100, 110
time_zone.return_value = 'America/Los_Angeles'
request_json = {
"resourceType":
"Organization",
"id":
"a893282c-2717-4a20-b276-d5c9c2c0e51f",
'meta': {
'versionId': '2'
},
"extension": [{
"url":
"http://all-of-us.org/fhir/sites/enrollmentStatusActive",
"valueBoolean": True
}, {
"url":
"http://all-of-us.org/fhir/sites/digitalSchedulingStatusActive",
"valueBoolean": False
}, {
"url":
"http://all-of-us.org/fhir/sites/schedulingStatusActive",
"valueBoolean": True
}, {
"url": "http://all-of-us.org/fhir/sites/notes",
"valueString": "This is a note about an organization"
}, {
"url":
"http://all-of-us.org/fhir/sites/schedulingInstructions",
"valueString":
"Please schedule appointments up to a week before intended date."
}, {
"url": "http://all-of-us.org/fhir/sites/anticipatedLaunchDate",
"valueDate": "07-02-2010"
}, {
"url": "http://all-of-us.org/fhir/sites/locationName",
"valueString": "Thompson Building"
}, {
"url":
"http://all-of-us.org/fhir/sites/directions",
"valueString":
"Exit 95 N and make a left onto Fake Street"
}],
"identifier": [{
"system": "http://all-of-us.org/fhir/sites/site-id",
"value": "hpo-site-1"
}, {
"system":
"http://all-of-us.org/fhir/sites/mayo-link-identifier",
"value": "123456"
}, {
"system":
"http://all-of-us.org/fhir/sites/google-group-identifier",
"value": "Awesome Genomics Testing"
}],
"active":
True,
"type": [{
"coding": [{
"code": "SITE",
"system": "http://all-of-us.org/fhir/sites/type"
}]
}],
"name":
"Awesome Genomics Testing",
"partOf": {
"reference": "Organization/o123456"
},
"address": [{
"line": ["1855 4th Street", "AAC5/6"],
"city": "San Francisco",
"state": "CA",
"postalCode": "94158"
}],
"contact": [{
"telecom": [{
"system": "phone",
"value": "7031234567"
}]
}, {
"telecom": [{
"system": "email",
"value": "*****@*****.**"
}]
}, {
"telecom": [{
"system": "url",
"value": "http://awesome-genomic-testing.com"
}]
}]
}
self.send_put('organization/hierarchy', request_data=request_json)
existing_map = {
entity.googleGroup: entity
for entity in self.site_dao.get_all()
}
existing_entity = existing_map.get('hpo-site-1')
self.assertEqual(existing_entity.adminEmails,
'*****@*****.**')
self.assertEqual(existing_entity.siteStatus, SiteStatus('ACTIVE'))
self.assertEqual(existing_entity.isObsolete, None)
self.assertEqual(existing_entity.city, 'San Francisco')
self.assertEqual(existing_entity.googleGroup, 'hpo-site-1')
self.assertEqual(existing_entity.state, 'CA')
self.assertEqual(existing_entity.digitalSchedulingStatus,
DigitalSchedulingStatus('INACTIVE'))
self.assertEqual(existing_entity.mayolinkClientNumber, 123456)
self.assertEqual(existing_entity.address1, '1855 4th Street')
self.assertEqual(existing_entity.address2, 'AAC5/6')
self.assertEqual(existing_entity.zipCode, '94158')
self.assertEqual(existing_entity.directions,
'Exit 95 N and make a left onto Fake Street')
self.assertEqual(existing_entity.notes,
'This is a note about an organization')
self.assertEqual(existing_entity.enrollingStatus,
EnrollingStatus('ACTIVE'))
self.assertEqual(
existing_entity.scheduleInstructions,
'Please schedule appointments up to a week before intended date.')
self.assertEqual(existing_entity.physicalLocationName,
'Thompson Building')
self.assertEqual(existing_entity.link,
'http://awesome-genomic-testing.com')
self.assertEqual(existing_entity.launchDate, datetime.date(2010, 7, 2))
self.assertEqual(existing_entity.phoneNumber, '7031234567')
def _entity_from_row(self, row):
google_group = row[SITE_SITE_ID_COLUMN].lower()
organization = self.organization_dao.get_by_external_id(
row[SITE_ORGANIZATION_ID_COLUMN].upper())
if organization is None:
logging.warn('Invalid organization ID %s importing site %s',
row[SITE_ORGANIZATION_ID_COLUMN].upper(),
google_group)
self.errors.append(
'Invalid organization ID {} importing site {}'.format(
row[SITE_ORGANIZATION_ID_COLUMN].upper(), google_group))
return None
launch_date = None
launch_date_str = row.get(SITE_LAUNCH_DATE_COLUMN)
if launch_date_str:
try:
launch_date = parse(launch_date_str).date()
except ValueError:
logging.warn('Invalid launch date %s for site %s',
launch_date_str, google_group)
self.errors.append('Invalid launch date {} for site {}'.format(
launch_date_str, google_group))
return None
name = row[SITE_SITE_COLUMN]
mayolink_client_number = None
mayolink_client_number_str = row.get(
SITE_MAYOLINK_CLIENT_NUMBER_COLUMN)
if mayolink_client_number_str:
try:
mayolink_client_number = int(mayolink_client_number_str)
except ValueError:
logging.warn('Invalid Mayolink Client # %s for site %s',
mayolink_client_number_str, google_group)
self.errors.append(
'Invalid Mayolink Client # {} for site {}'.format(
mayolink_client_number_str, google_group))
return None
notes = row.get(SITE_NOTES_COLUMN)
notes_es = row.get(SITE_NOTES_COLUMN_ES)
try:
site_status = SiteStatus(row[SITE_STATUS_COLUMN +
self.environment].upper())
except TypeError:
logging.warn('Invalid site status %s for site %s',
row[SITE_STATUS_COLUMN + self.environment],
google_group)
self.errors.append('Invalid site status {} for site {}'.format(
row[SITE_STATUS_COLUMN + self.environment], google_group))
return None
try:
enrolling_status = EnrollingStatus(row[ENROLLING_STATUS_COLUMN +
self.environment].upper())
except TypeError:
logging.warn('Invalid enrollment site status %s for site %s',
row[ENROLLING_STATUS_COLUMN + self.environment],
google_group)
self.errors.append(
'Invalid enrollment site status {} for site {}'.format(
row[ENROLLING_STATUS_COLUMN + self.environment],
google_group))
directions = row.get(SITE_DIRECTIONS_COLUMN)
physical_location_name = row.get(SITE_PHYSICAL_LOCATION_NAME_COLUMN)
address_1 = row.get(SITE_ADDRESS_1_COLUMN)
address_2 = row.get(SITE_ADDRESS_2_COLUMN)
city = row.get(SITE_CITY_COLUMN)
state = row.get(SITE_STATE_COLUMN)
zip_code = row.get(SITE_ZIP_COLUMN)
phone = row.get(SITE_PHONE_COLUMN)
admin_email_addresses = row.get(SITE_ADMIN_EMAIL_ADDRESSES_COLUMN)
link = row.get(SITE_LINK_COLUMN)
digital_scheduling_status = DigitalSchedulingStatus(
row[DIGITAL_SCHEDULING_STATUS_COLUMN + self.environment].upper())
schedule_instructions = row.get(SCHEDULING_INSTRUCTIONS)
schedule_instructions_es = row.get(SCHEDULING_INSTRUCTIONS_ES)
return Site(siteName=name,
googleGroup=google_group,
mayolinkClientNumber=mayolink_client_number,
organizationId=organization.organizationId,
hpoId=organization.hpoId,
siteStatus=site_status,
enrollingStatus=enrolling_status,
digitalSchedulingStatus=digital_scheduling_status,
scheduleInstructions=schedule_instructions,
scheduleInstructions_ES=schedule_instructions_es,
launchDate=launch_date,
notes=notes,
notes_ES=notes_es,
directions=directions,
physicalLocationName=physical_location_name,
address1=address_1,
address2=address_2,
city=city,
state=state,
zipCode=zip_code,
phoneNumber=phone,
adminEmails=admin_email_addresses,
link=link)
def _update_site(self, hierarchy_org_obj):
if hierarchy_org_obj.id is None:
raise BadRequest('No id found in payload data.')
google_group = self._get_value_from_identifier(
hierarchy_org_obj, HIERARCHY_CONTENT_SYSTEM_PREFIX + 'site-id')
if google_group is None:
raise BadRequest(
'No organization-identifier info found in payload data.')
google_group = google_group.lower()
is_obsolete = ObsoleteStatus(
'OBSOLETE') if not hierarchy_org_obj.active else None
resource_id = self._get_reference(hierarchy_org_obj)
organization = self.organization_dao.get_by_resource_id(resource_id)
if organization is None:
raise BadRequest(
'Invalid partOf reference {} importing site {}'.format(
resource_id, google_group))
launch_date = None
launch_date_str = self._get_value_from_extention(
hierarchy_org_obj,
HIERARCHY_CONTENT_SYSTEM_PREFIX + 'anticipatedLaunchDate',
'valueDate')
if launch_date_str:
try:
launch_date = parse(launch_date_str).date()
except ValueError:
raise BadRequest('Invalid launch date {} for site {}'.format(
launch_date_str, google_group))
name = hierarchy_org_obj.name
mayolink_client_number = None
mayolink_client_number_str = self._get_value_from_identifier(
hierarchy_org_obj,
HIERARCHY_CONTENT_SYSTEM_PREFIX + 'mayo-link-identifier')
if mayolink_client_number_str:
try:
mayolink_client_number = int(mayolink_client_number_str)
except ValueError:
raise BadRequest(
'Invalid Mayolink Client # {} for site {}'.format(
mayolink_client_number_str, google_group))
notes = self._get_value_from_extention(
hierarchy_org_obj, HIERARCHY_CONTENT_SYSTEM_PREFIX + 'notes')
site_status_bool = self._get_value_from_extention(
hierarchy_org_obj,
HIERARCHY_CONTENT_SYSTEM_PREFIX + 'schedulingStatusActive',
'valueBoolean')
try:
site_status = SiteStatus(
'ACTIVE' if site_status_bool else 'INACTIVE')
except TypeError:
raise BadRequest('Invalid site status {} for site {}'.format(
site_status, google_group))
enrolling_status_bool = self._get_value_from_extention(
hierarchy_org_obj,
HIERARCHY_CONTENT_SYSTEM_PREFIX + 'enrollmentStatusActive',
'valueBoolean')
try:
enrolling_status = EnrollingStatus(
'ACTIVE' if enrolling_status_bool else 'INACTIVE')
except TypeError:
raise BadRequest(
'Invalid enrollment site status {} for site {}'.format(
enrolling_status_bool, google_group))
digital_scheduling_bool = self._get_value_from_extention(
hierarchy_org_obj,
HIERARCHY_CONTENT_SYSTEM_PREFIX + 'digitalSchedulingStatusActive',
'valueBoolean')
try:
digital_scheduling_status = DigitalSchedulingStatus(
'ACTIVE' if digital_scheduling_bool else 'INACTIVE')
except TypeError:
raise BadRequest(
'Invalid digital scheduling status {} for site {}'.format(
digital_scheduling_bool, google_group))
directions = self._get_value_from_extention(
hierarchy_org_obj, HIERARCHY_CONTENT_SYSTEM_PREFIX + 'directions')
physical_location_name = self._get_value_from_extention(
hierarchy_org_obj,
HIERARCHY_CONTENT_SYSTEM_PREFIX + 'locationName')
address_1, address_2, city, state, zip_code = self._get_address(
hierarchy_org_obj)
phone = self._get_contact_point(hierarchy_org_obj, 'phone')
admin_email_addresses = self._get_contact_point(
hierarchy_org_obj, 'email')
link = self._get_contact_point(hierarchy_org_obj, 'url')
schedule_instructions = self._get_value_from_extention(
hierarchy_org_obj,
HIERARCHY_CONTENT_SYSTEM_PREFIX + 'schedulingInstructions')
entity = Site(siteName=name,
googleGroup=google_group,
mayolinkClientNumber=mayolink_client_number,
organizationId=organization.organizationId,
hpoId=organization.hpoId,
siteStatus=site_status,
enrollingStatus=enrolling_status,
digitalSchedulingStatus=digital_scheduling_status,
scheduleInstructions=schedule_instructions,
scheduleInstructions_ES='',
launchDate=launch_date,
notes=notes,
notes_ES='',
directions=directions,
physicalLocationName=physical_location_name,
address1=address_1,
address2=address_2,
city=city,
state=state,
zipCode=zip_code,
phoneNumber=phone,
adminEmails=admin_email_addresses,
link=link,
isObsolete=is_obsolete,
resourceId=hierarchy_org_obj.id)
existing_map = {
entity.googleGroup: entity
for entity in self.site_dao.get_all()
}
existing_entity = existing_map.get(entity.googleGroup)
with self.site_dao.session() as session:
if existing_entity:
self._populate_lat_lng_and_time_zone(entity, existing_entity)
if entity.siteStatus == SiteStatus.ACTIVE and \
(entity.latitude is None or entity.longitude is None):
raise BadRequest(
'Active site without geocoding: {}'.format(
entity.googleGroup))
new_dict = entity.asdict()
new_dict['siteId'] = None
existing_dict = existing_entity.asdict()
existing_dict['siteId'] = None
if existing_dict == new_dict:
logging.info('Not updating {}.'.format(
new_dict['googleGroup']))
else:
for k, v in entity.asdict().iteritems():
if k != 'siteId' and k != 'googleGroup':
setattr(existing_entity, k, v)
self.site_dao.update_with_session(session, existing_entity)
else:
self._populate_lat_lng_and_time_zone(entity, None)
if entity.siteStatus == SiteStatus.ACTIVE and \
(entity.latitude is None or entity.longitude is None):
raise BadRequest(
'Active site without geocoding: {}'.format(
entity.googleGroup))
self.site_dao.insert_with_session(session, entity)
site_id = self.site_dao.get_by_google_group(google_group).siteId
bq_site_update_by_id(site_id)