def test_multiple_rps_in_fhir(self):
yesterday = datetime.utcnow() - timedelta(days=1)
lastyear = datetime.utcnow() - timedelta(days=365)
org = Organization(name='Testy')
rp1 = ResearchProtocol(name='rp1')
rp2 = ResearchProtocol(name='yesterday')
rp3 = ResearchProtocol(name='last year')
with SessionScope(db):
map(db.session.add, (org, rp1, rp2, rp3))
db.session.commit()
org, rp1, rp2, rp3 = map(db.session.merge, (org, rp1, rp2, rp3))
o_rp1 = OrganizationResearchProtocol(
research_protocol=rp1, organization=org)
o_rp2 = OrganizationResearchProtocol(
research_protocol=rp2, organization=org, retired_as_of=yesterday)
o_rp3 = OrganizationResearchProtocol(
research_protocol=rp3, organization=org, retired_as_of=lastyear)
with SessionScope(db):
map(db.session.add, (o_rp1, o_rp2, o_rp3))
db.session.commit()
org, rp1, rp2, rp3 = map(db.session.merge, (org, rp1, rp2, rp3))
data = org.as_fhir()
assert org.name == data['name']
rps = [
extension for extension in data['extension']
if extension['url'] == ResearchProtocolExtension.extension_url]
assert len(rps) == 1
assert len(rps[0]['research_protocols']) == 3
# confirm the order is descending in the custom accessor method
results = [(rp, retired) for rp, retired in org.rps_w_retired()]
assert [(rp1, None), (rp2, yesterday), (rp3, lastyear)] == results
def test_rp_alteration(self):
# orgs with old rp should migrate to multiple w/ updated retired
from portal.system_uri import SHORTCUT_ALIAS, TRUENTH_CR_NAME
from portal.models.identifier import Identifier
rp1 = ResearchProtocol(name='initial')
rp2 = ResearchProtocol(name='replacement')
org = Organization(name='testy')
org.research_protocols.append(rp1)
with SessionScope(db):
db.session.add(rp2)
db.session.add(org)
db.session.commit()
mp = ModelPersistence(Organization,
lookup_field='id',
sequence_name='organizations_id_seq',
target_dir=self.tmpdir)
mp.export()
# Add second rp, mark old as retired
with open(os.path.join(self.tmpdir, 'Organization.json'),
'r') as pfile:
data = json.load(pfile)
now = datetime.utcnow().replace(microsecond=0)
updated = {
'url':
ResearchProtocolExtension.extension_url,
'research_protocols': [{
"name": 'replacement'
}, {
"name": 'initial',
"retired_as_of": FHIR_datetime.as_fhir(now)
}]
}
for i, entry in enumerate(data['entry']):
if entry['name'] != 'testy':
continue
extensions = entry['extension']
keepers = [
ext for ext in extensions
if ext['url'] != ResearchProtocolExtension.extension_url
]
keepers.append(updated)
data['entry'][i]['extension'] = keepers
with open(os.path.join(self.tmpdir, 'Organization.json'),
'w') as pfile:
pfile.write(json.dumps(data))
mp.import_(keep_unmentioned=False)
org = Organization.query.filter(Organization.name == 'testy').one()
assert len(org.research_protocols) == 2
# Make sure retired_as_of was set properly on old
rp1, rp2 = map(db.session.merge, (rp1, rp2))
expected = [(rp2, None), (rp1, now)]
results = [(rp, retired) for rp, retired in org.rps_w_retired()]
assert results == expected
def test_rp_alteration(self):
# orgs with old rp should migrate to multiple w/ updated retired
from portal.system_uri import SHORTCUT_ALIAS, TRUENTH_CR_NAME
from portal.models.identifier import Identifier
rp1 = ResearchProtocol(name='initial')
rp2 = ResearchProtocol(name='replacement')
org = Organization(name='testy')
org.research_protocols.append(rp1)
with SessionScope(db):
db.session.add(rp2)
db.session.add(org)
db.session.commit()
mp = ModelPersistence(
Organization, lookup_field='id',
sequence_name='organizations_id_seq',
target_dir=self.tmpdir)
mp.export()
# Add second rp, mark old as retired
with open(
os.path.join(self.tmpdir, 'Organization.json'), 'r') as pfile:
data = json.load(pfile)
now = datetime.utcnow().replace(microsecond=0)
updated = {
'url': ResearchProtocolExtension.extension_url,
'research_protocols': [
{"name": 'replacement'},
{"name": 'initial', "retired_as_of": FHIR_datetime.as_fhir(
now)}]}
for i, entry in enumerate(data['entry']):
if entry['name'] != 'testy':
continue
extensions = entry['extension']
keepers = [
ext for ext in extensions
if ext['url'] != ResearchProtocolExtension.extension_url]
keepers.append(updated)
data['entry'][i]['extension'] = keepers
with open(
os.path.join(self.tmpdir, 'Organization.json'), 'w') as pfile:
pfile.write(json.dumps(data))
mp.import_(keep_unmentioned=False)
org = Organization.query.filter(Organization.name == 'testy').one()
assert len(org.research_protocols) == 2
# Make sure retired_as_of was set properly on old
rp1, rp2 = map(db.session.merge, (rp1, rp2))
expected = [(rp2, None), (rp1, now)]
results = [(rp, retired) for rp, retired in org.rps_w_retired()]
assert results == expected
def test_multiple_rps_in_fhir(self):
yesterday = datetime.utcnow() - timedelta(days=1)
lastyear = datetime.utcnow() - timedelta(days=365)
org = Organization(name='Testy')
rp1 = ResearchProtocol(name='rp1')
rp2 = ResearchProtocol(name='yesterday')
rp3 = ResearchProtocol(name='last year')
with SessionScope(db):
map(db.session.add, (org, rp1, rp2, rp3))
db.session.commit()
org, rp1, rp2, rp3 = map(db.session.merge, (org, rp1, rp2, rp3))
o_rp1 = OrganizationResearchProtocol(research_protocol=rp1,
organization=org)
o_rp2 = OrganizationResearchProtocol(research_protocol=rp2,
organization=org,
retired_as_of=yesterday)
o_rp3 = OrganizationResearchProtocol(research_protocol=rp3,
organization=org,
retired_as_of=lastyear)
with SessionScope(db):
map(db.session.add, (o_rp1, o_rp2, o_rp3))
db.session.commit()
org, rp1, rp2, rp3 = map(db.session.merge, (org, rp1, rp2, rp3))
data = org.as_fhir()
assert org.name == data['name']
rps = [
extension for extension in data['extension']
if extension['url'] == ResearchProtocolExtension.extension_url
]
assert len(rps) == 1
assert len(rps[0]['research_protocols']) == 3
# confirm the order is descending in the custom accessor method
results = [(rp, retired) for rp, retired in org.rps_w_retired()]
assert [(rp1, None), (rp2, yesterday), (rp3, lastyear)] == results