def _setup_hpos(self, org_dao=None):
hpo_dao = HPODao()
hpo_dao.insert(
HPO(hpoId=UNSET_HPO_ID,
name='UNSET',
displayName='Unset',
organizationType=OrganizationType.UNSET))
hpo_dao.insert(
HPO(hpoId=PITT_HPO_ID,
name='PITT',
displayName='Pittsburgh',
organizationType=OrganizationType.HPO))
hpo_dao.insert(
HPO(hpoId=AZ_HPO_ID,
name='AZ_TUCSON',
displayName='Arizona',
organizationType=OrganizationType.HPO))
self.hpo_id = PITT_HPO_ID
org_dao = OrganizationDao()
org_dao.insert(
Organization(organizationId=AZ_ORG_ID,
externalId='AZ_TUCSON_BANNER_HEALTH',
displayName='Banner Health',
hpoId=AZ_HPO_ID))
created_org = org_dao.insert(
Organization(organizationId=PITT_ORG_ID,
externalId='PITT_BANNER_HEALTH',
displayName='PITT display Banner Health',
hpoId=PITT_HPO_ID))
self.organization_id = created_org.organizationId
site_dao = SiteDao()
created_site = site_dao.insert(
Site(siteName='Monroeville Urgent Care Center',
googleGroup='hpo-site-monroeville',
mayolinkClientNumber=7035769,
organizationId=PITT_ORG_ID,
hpoId=PITT_HPO_ID))
self.site_id = created_site.siteId
site_dao.insert(
Site(siteName='Phoenix Urgent Care Center',
googleGroup='hpo-site-bannerphoenix',
mayolinkClientNumber=7035770,
organizationId=PITT_ORG_ID,
hpoId=PITT_HPO_ID))
site_dao.insert(
Site(siteName='Phoenix clinic',
googleGroup='hpo-site-clinic-phoenix',
mayolinkClientNumber=7035770,
organizationId=AZ_ORG_ID,
hpoId=AZ_HPO_ID))
def _setup_unset_enrollment_site(self):
site_dao = SiteDao()
organization_dao = OrganizationDao()
org_2 = organization_dao.insert(
Organization(externalId='ORG_2',
displayName='Organization 2',
hpoId=PITT_HPO_ID))
site_dao.insert(
Site(siteName='not enrolling site',
googleGroup='not_enrolling_dot_com',
organizationId=org_2.organizationId,
enrollingStatus=EnrollingStatus.UNSET,
siteStatus=SiteStatus.INACTIVE))
class SiteDaoTest(SqlTestBase):
def setUp(self):
super(SiteDaoTest, self).setUp()
self.site_dao = SiteDao()
def test_get_no_sites(self):
self.assertIsNone(self.site_dao.get(9999))
self.assertIsNone(
self.site_dao.get_by_google_group('*****@*****.**'))
def test_insert(self):
site = Site(siteName='site',
googleGroup='*****@*****.**',
consortiumName='consortium',
mayolinkClientNumber=12345,
hpoId=PITT_HPO_ID)
created_site = self.site_dao.insert(site)
new_site = self.site_dao.get(created_site.siteId)
site.siteId = created_site.siteId
self.assertEquals(site.asdict(), new_site.asdict())
self.assertEquals(
site.asdict(),
self.site_dao.get_by_google_group(
'*****@*****.**').asdict())
def test_update(self):
site = Site(siteName='site',
googleGroup='*****@*****.**',
consortiumName='consortium',
mayolinkClientNumber=12345,
hpoId=PITT_HPO_ID)
created_site = self.site_dao.insert(site)
new_site = Site(siteId=created_site.siteId,
siteName='site2',
googleGroup='*****@*****.**',
consortiumName='consortium2',
mayolinkClientNumber=123456,
hpoId=UNSET_HPO_ID)
self.site_dao.update(new_site)
fetched_site = self.site_dao.get(created_site.siteId)
self.assertEquals(new_site.asdict(), fetched_site.asdict())
self.assertEquals(
new_site.asdict(),
self.site_dao.get_by_google_group(
'*****@*****.**').asdict())
self.assertIsNone(
self.site_dao.get_by_google_group('*****@*****.**'))
def _setup_data(self):
organization_dao = OrganizationDao()
site_dao = SiteDao()
org_1 = organization_dao.insert(
Organization(externalId='ORG_1',
displayName='Organization 1',
hpoId=PITT_HPO_ID,
resourceId='o123456'))
organization_dao.insert(
Organization(externalId='AARDVARK_ORG',
displayName='Aardvarks Rock',
hpoId=PITT_HPO_ID,
resourceId='o123457'))
site_dao.insert(
Site(siteName='Site 1',
googleGroup='hpo-site-1',
mayolinkClientNumber=123456,
organizationId=org_1.organizationId,
siteStatus=SiteStatus.ACTIVE,
enrollingStatus=EnrollingStatus.ACTIVE,
launchDate=datetime.datetime(2016, 1, 1),
notes='notes',
latitude=12.1,
longitude=13.1,
directions='directions',
physicalLocationName='locationName',
address1='address1',
address2='address2',
city='Austin',
state='TX',
zipCode='78751',
phoneNumber='555-555-5555',
adminEmails='[email protected], [email protected]',
link='http://www.example.com'))
site_dao.insert(
Site(siteName='Zebras Rock',
googleGroup='aaaaaaa',
organizationId=org_1.organizationId,
enrollingStatus=EnrollingStatus.INACTIVE,
siteStatus=SiteStatus.INACTIVE))
def _setup_hpos(self):
hpo_dao = HPODao()
hpo_dao.insert(HPO(hpoId=UNSET_HPO_ID, name='UNSET'))
hpo_dao.insert(
HPO(hpoId=PITT_HPO_ID,
name='PITT',
organizationType=OrganizationType.HPO))
self.hpo_id = PITT_HPO_ID
site_dao = SiteDao()
created_site = site_dao.insert(
Site(siteName='Monroeville Urgent Care Center',
googleGroup='hpo-site-monroeville',
consortiumName='Pittsburgh',
mayolinkClientNumber=7035769,
hpoId=PITT_HPO_ID))
self.site_id = created_site.siteId
site_dao.insert(
Site(siteName='Phoenix Urgent Care Center',
googleGroup='hpo-site-bannerphoenix',
consortiumName='Pittsburgh',
mayolinkClientNumber=7035770,
hpoId=PITT_HPO_ID))
class SyncConsentFilesTest(CloudStorageSqlTestBase, NdbTestBase):
"""Tests behavior of sync_consent_files
"""
def setUp(self, **kwargs):
super(SyncConsentFilesTest, self).setUp(use_mysql=True, **kwargs)
NdbTestBase.doSetUp(self)
TestBase.setup_fake(self)
self.org_dao = OrganizationDao()
self.site_dao = SiteDao()
self.participant_dao = ParticipantDao()
self.summary_dao = ParticipantSummaryDao()
def tearDown(self):
super(SyncConsentFilesTest, self).tearDown()
def _create_org(self, id_):
org = Organization(organizationId=id_,
externalId=id_,
displayName=id_,
hpoId=UNSET_HPO_ID)
self.org_dao.insert(org)
return org
def _create_site(self, id_, google_group):
site = Site(siteId=id_, siteName=id_, googleGroup=google_group)
self.site_dao.insert(site)
return site
def _create_participant(self,
id_,
org_id,
site_id,
consents=False,
ghost=None,
email=None,
null_email=False):
participant = Participant(participantId=id_,
biobankId=id_,
organizationId=org_id,
siteId=site_id,
isGhostId=ghost)
self.participant_dao.insert(participant)
summary = self.participant_summary(participant)
if consents:
summary.consentForElectronicHealthRecords = 1
summary.consentForStudyEnrollment = 1
if email:
summary.email = email
if null_email:
summary.email = None
self.summary_dao.insert(summary)
return participant
def test_iter_participants_data(self):
"""should list consenting participants
"""
org1 = self._create_org(1)
org2 = self._create_org(2)
site1 = self._create_site(1001, 'group1')
site2 = self._create_site(1002, 'group2')
self._create_participant(1,
org1.organizationId,
site1.siteId,
consents=True,
null_email=True)
self._create_participant(2, org2.organizationId, site2.siteId)
self._create_participant(3,
org1.organizationId,
None,
consents=True,
ghost=False)
self._create_participant(4,
org1.organizationId,
None,
consents=True,
ghost=True)
self._create_participant(5,
org1.organizationId,
None,
consents=True,
email='*****@*****.**')
participant_data_list = list(
sync_consent_files._iter_participants_data())
participant_ids = [d.participant_id for d in participant_data_list]
self.assertEqual(len(participant_ids), 2,
"finds correct number of results")
self.assertEqual(participant_ids, [1, 3], "finds valid participants")
self.assertEqual(participant_data_list[0].google_group, 'group1',
"Includes google group")
self.assertEqual(participant_data_list[1].google_group, None,
"allows None for google group")
@mock.patch('cloudstorage.listbucket')
@mock.patch('cloudstorage.copy2')
def test_cloudstorage_copy_objects_api_calls(self, mock_copy2,
mock_listbucket):
"""Makes the proper google cloudstorage API calls
"""
mock_listbucket.return_value = [
cloudstorage.common.GCSFileStat('/fake_bucket1/prefix1/foo', 0,
'x', 0),
cloudstorage.common.GCSFileStat('/fake_bucket1/prefix1/bar', 0,
'x', 0),
]
# with trailing slashes
sync_consent_files.cloudstorage_copy_objects('/fake_bucket1/prefix1/',
'/fake_bucket2/prefix2/')
mock_copy2.assert_has_calls([
mock.call('/fake_bucket1/prefix1/foo',
'/fake_bucket2/prefix2/foo'),
mock.call('/fake_bucket1/prefix1/bar',
'/fake_bucket2/prefix2/bar'),
])
# without trailing slashes
sync_consent_files.cloudstorage_copy_objects('/fake_bucket1/prefix1',
'/fake_bucket2/prefix2')
mock_copy2.assert_has_calls([
mock.call('/fake_bucket1/prefix1/foo',
'/fake_bucket2/prefix2/foo'),
mock.call('/fake_bucket1/prefix1/bar',
'/fake_bucket2/prefix2/bar'),
])
@staticmethod
def _write_cloud_object(cloud_filename, contents_str):
with cloudstorage.cloudstorage_api.open(cloud_filename,
mode='w') as cloud_file:
cloud_file.write(contents_str.encode('utf-8'))
def test_cloudstorage_copy_objects_actual(self):
self._write_cloud_object('/fake_bucket1/prefix/x1/foo.txt', 'foo')
self._write_cloud_object('/fake_bucket1/prefix/x1/bar.txt', 'bar')
self._write_cloud_object('/fake_bucket1/prefix/x1/y1/foo.txt', 'foo')
with cloudstorage.cloudstorage_api.open(
'/fake_bucket1/prefix/x1/foo.txt', mode='r') as f:
self.assertEqual(f.read(), 'foo', 'Wrote to cloud storage')
sync_consent_files.cloudstorage_copy_objects(
'/fake_bucket1/prefix/x1/', '/fake_bucket2/prefix/z/x1/')
self.assertEqual([
file_stat.filename
for file_stat in cloudstorage.cloudstorage_api.listbucket(
'/fake_bucket2/prefix/z/x1/')
], [
'/fake_bucket2/prefix/z/x1/bar.txt',
'/fake_bucket2/prefix/z/x1/foo.txt',
'/fake_bucket2/prefix/z/x1/y1/foo.txt',
], "copied all objects")
with cloudstorage.cloudstorage_api.open(
'/fake_bucket2/prefix/z/x1/foo.txt', mode='r') as f:
self.assertEqual(f.read(), 'foo', 'copied contents')
@mock.patch('cloudstorage.copy2')
def test_cloudstorage_copy_objects_only_new_and_changed(self, copy2):
self._write_cloud_object('/fake_bucket1/prefix/x1/foo.txt', 'foo')
self._write_cloud_object('/fake_bucket1/prefix/x1/bar.txt', 'bar')
self._write_cloud_object('/fake_bucket2/prefix/z/x1/foo.txt', 'foo')
self._write_cloud_object('/fake_bucket2/prefix/z/x1/bar.txt', 'baz')
sync_consent_files.cloudstorage_copy_objects(
'/fake_bucket1/prefix/x1/', '/fake_bucket2/prefix/z/x1/')
copy2.assert_called_once_with('/fake_bucket1/prefix/x1/bar.txt',
'/fake_bucket2/prefix/z/x1/bar.txt')
class SiteDaoTest(SqlTestBase):
def setUp(self):
super(SiteDaoTest, self).setUp()
self.site_dao = SiteDao()
self.participant_dao = ParticipantDao()
self.ps_dao = ParticipantSummaryDao()
self.ps_history = ParticipantHistoryDao()
def test_get_no_sites(self):
self.assertIsNone(self.site_dao.get(9999))
self.assertIsNone(
self.site_dao.get_by_google_group('*****@*****.**'))
def test_insert(self):
site = Site(siteName='site',
googleGroup='*****@*****.**',
mayolinkClientNumber=12345,
hpoId=PITT_HPO_ID)
created_site = self.site_dao.insert(site)
new_site = self.site_dao.get(created_site.siteId)
site.siteId = created_site.siteId
self.assertEquals(site.asdict(), new_site.asdict())
self.assertEquals(
site.asdict(),
self.site_dao.get_by_google_group(
'*****@*****.**').asdict())
def test_update(self):
site = Site(siteName='site',
googleGroup='*****@*****.**',
mayolinkClientNumber=12345,
hpoId=PITT_HPO_ID)
created_site = self.site_dao.insert(site)
new_site = Site(siteId=created_site.siteId,
siteName='site2',
googleGroup='*****@*****.**',
mayolinkClientNumber=123456,
hpoId=UNSET_HPO_ID)
self.site_dao.update(new_site)
fetched_site = self.site_dao.get(created_site.siteId)
self.assertEquals(new_site.asdict(), fetched_site.asdict())
self.assertEquals(
new_site.asdict(),
self.site_dao.get_by_google_group(
'*****@*****.**').asdict())
self.assertIsNone(
self.site_dao.get_by_google_group('*****@*****.**'))
def test_participant_pairing_updates_on_change(self):
TIME = datetime.datetime(2018, 1, 1)
TIME2 = datetime.datetime(2018, 1, 2)
provider_link = '[{"organization": {"reference": "Organization/AZ_TUCSON"}, "primary": true}]'
site = Site(siteName='site',
googleGroup='*****@*****.**',
mayolinkClientNumber=12345,
hpoId=PITT_HPO_ID,
organizationId=PITT_ORG_ID)
created_site = self.site_dao.insert(site)
with FakeClock(TIME):
p = Participant(participantId=1,
biobankId=2,
siteId=created_site.siteId)
self.participant_dao.insert(p)
fetch_p = self.participant_dao.get(p.participantId)
updated_p = self.participant_dao.get(fetch_p.participantId)
p_summary = self.ps_dao.insert(self.participant_summary(updated_p))
with FakeClock(TIME2):
update_site_parent = Site(siteId=created_site.siteId,
siteName='site2',
googleGroup='*****@*****.**',
mayolinkClientNumber=123456,
hpoId=AZ_HPO_ID,
organizationId=AZ_ORG_ID)
self.site_dao.update(update_site_parent)
updated_p = self.participant_dao.get(fetch_p.participantId)
ps = self.ps_dao.get(p_summary.participantId)
ph = self.ps_history.get([updated_p.participantId, 1])
self.assertEquals(update_site_parent.hpoId, updated_p.hpoId)
self.assertEquals(update_site_parent.organizationId,
updated_p.organizationId)
self.assertEquals(ps.organizationId, update_site_parent.organizationId)
self.assertEquals(ps.hpoId, update_site_parent.hpoId)
self.assertEquals(ps.organizationId, update_site_parent.organizationId)
self.assertEquals(ph.organizationId, update_site_parent.organizationId)
self.assertEquals(updated_p.providerLink, provider_link)
self.assertEquals(ps.lastModified, TIME2)