def test_identifier_lookup(self):
# setup a minimal communication request
from tests.test_communication import mock_communication_request
from tests.test_assessment_status import mock_tnth_questionnairebanks
from portal.system_uri import TRUENTH_CR_NAME
from portal.models.identifier import Identifier
mock_tnth_questionnairebanks()
cr = mock_communication_request(
'symptom_tracker_recurring', '{"days": 14}')
cr.identifiers.append(
Identifier(value='2 week ST', system=TRUENTH_CR_NAME))
with SessionScope(db):
db.session.add(cr)
db.session.commit()
cr = db.session.merge(cr)
assert cr.identifiers.count() == 1
data = cr.as_fhir()
mp = ModelPersistence(
CommunicationRequest,
sequence_name='communication_requests_id_seq',
lookup_field='identifier')
new_obj = CommunicationRequest.from_fhir(data)
match, field_description = mp.lookup_existing(
new_obj=new_obj, new_data=data)
assert match.name == cr.name
def test_composite_key(self):
known_coding = Coding(
system=SNOMED, code='26294005',
display='Radical prostatectomy (nerve-sparing)').add_if_not_found(
True)
mp = ModelPersistence(
Coding, sequence_name='codings_id_seq',
lookup_field=('system', 'code'))
data = known_coding.as_fhir()
# Modify only the `display` - composite keys should still match
modified_data = data.copy()
modified_data['display'] = 'Radical prostatectomy'
modified = Coding.from_fhir(data)
match, _ = mp.lookup_existing(
new_obj=modified, new_data=modified_data)
assert data == match.as_fhir()
# Import and see the change
updated = mp.update(modified_data)
assert modified == updated
# Export and verify
serial = mp.serialize()
assert modified_data in serial
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_delete_unnamed(self):
keeper = AppText(name='keep me', custom_text='worthy')
mp = ModelPersistence(AppText,
lookup_field='name',
sequence_name='apptext_id_seq',
target_dir=self.tmpdir)
with SessionScope(db):
db.session.add(keeper)
db.session.commit()
mp.export()
# Add another app text, expecting it'll be removed
bogus = AppText(name='temp', custom_text='not worthy')
with SessionScope(db):
db.session.add(bogus)
db.session.commit()
# Import w/ keep_unmentioned and expect both
mp.import_(keep_unmentioned=True)
assert AppText.query.count() == 2
# Now import, and expect only keeper to remain
mp.import_(keep_unmentioned=False)
assert AppText.query.count() == 1
assert AppText.query.first().name == 'keep me'
def test_adjust_sequence(self):
mp = ModelPersistence(Organization,
sequence_name='organizations_id_seq')
# Insert dummy row w/ large id, confirm
# the sequence becomes greater
id = 10000
dummy = Organization(id=id, name='big id')
with SessionScope(db):
db.session.add(dummy)
db.session.commit()
mp.update_sequence()
currval = db.engine.execute("SELECT CURRVAL('{}')".format(
'organizations_id_seq')).fetchone()[0]
nextval = db.engine.execute("SELECT NEXTVAL('{}')".format(
'organizations_id_seq')).fetchone()[0]
assert currval == id
assert nextval > id
def test_adjust_sequence(self):
mp = ModelPersistence(
Organization, sequence_name='organizations_id_seq')
# Insert dummy row w/ large id, confirm
# the sequence becomes greater
id = 10000
dummy = Organization(id=id, name='big id')
with SessionScope(db):
db.session.add(dummy)
db.session.commit()
mp.update_sequence()
currval = db.engine.execute(
"SELECT CURRVAL('{}')".format(
'organizations_id_seq')).fetchone()[0]
nextval = db.engine.execute(
"SELECT NEXTVAL('{}')".format(
'organizations_id_seq')).fetchone()[0]
assert currval == id
assert nextval > id
def test_missing_scheduled_job(self):
# unmentioned scheduled job should get deleted
schedule = "45 * * * *"
sj = ScheduledJob(
name="test_sched", task="test", schedule=schedule, active=True)
sj2 = ScheduledJob(
name="test_sched2", task="test", schedule=schedule, active=True)
with SessionScope(db):
db.session.add(sj)
db.session.add(sj2)
db.session.commit()
assert ScheduledJob.query.count() == 2
mp = ModelPersistence(
ScheduledJob, lookup_field='name',
sequence_name='scheduled_jobs_id_seq',
target_dir=self.tmpdir)
mp.export()
# Reduce identifiers to one - make sure the other identifier goes away
with open(
os.path.join(self.tmpdir, 'ScheduledJob.json'), 'r') as pfile:
data = json.load(pfile)
# chop the first
data['entry'] = data['entry'][1:]
with open(
os.path.join(self.tmpdir, 'ScheduledJob.json'), 'w') as pfile:
pfile.write(json.dumps(data))
mp.import_(keep_unmentioned=False)
assert ScheduledJob.query.count() == 1
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_delete_extension(self):
org = Organization(name='testy')
org.timezone = 'Asia/Tokyo' # stored in an extension
with SessionScope(db):
db.session.add(org)
db.session.commit()
org = db.session.merge(org)
mp = ModelPersistence(
Organization, lookup_field='id',
sequence_name='organizations_id_seq',
target_dir=self.tmpdir)
mp.export()
# Strip the empty extensions, as expected in the real persistence file
with open(
os.path.join(self.tmpdir, 'Organization.json'), 'r') as pfile:
data = json.load(pfile)
# Special handling of extensions - empties only have 'url' key
for i, entry in enumerate(data['entry']):
extensions = entry['extension']
keepers = []
for e in extensions:
if len(e.keys()) > 1:
keepers.append(e)
data['entry'][i]['extension'] = keepers
empty_keys = [k for k, v in entry.items() if not v]
for k in empty_keys:
del data['entry'][i][k]
with open(
os.path.join(self.tmpdir, 'Organization.json'), 'w') as pfile:
pfile.write(json.dumps(data))
# Add an additional extension to the org, make sure
# they are deleted when importing again from
# persistence that doesn't include them
org.locales.append(LocaleConstants().AmericanEnglish)
with SessionScope(db):
db.session.commit()
org = db.session.merge(org)
assert len(org.as_fhir()['extension']) > 1
mp.import_(keep_unmentioned=False)
org = Organization.query.filter(Organization.name == 'testy').one()
assert org.locales.count() == 0
assert org.timezone == 'Asia/Tokyo'
def test_delete_identifier(self):
# orgs losing identifiers should delete the orphans
from portal.system_uri import SHORTCUT_ALIAS, TRUENTH_CR_NAME
from portal.models.identifier import Identifier
org = Organization(name='testy')
org.identifiers.append(Identifier(
value='2 week ST', system=TRUENTH_CR_NAME))
org.identifiers.append(Identifier(
value='ohsu', system=SHORTCUT_ALIAS))
with SessionScope(db):
db.session.add(org)
db.session.commit()
mp = ModelPersistence(
Organization, lookup_field='id',
sequence_name='organizations_id_seq',
target_dir=self.tmpdir)
mp.export()
# Reduce identifiers to one - make sure the other identifier goes away
with open(
os.path.join(self.tmpdir, 'Organization.json'), 'r') as pfile:
data = json.load(pfile)
for i, entry in enumerate(data['entry']):
identifiers = entry['identifier']
keepers = [
identifier for identifier in identifiers
if identifier['system'] == SHORTCUT_ALIAS]
data['entry'][i]['identifier'] = 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 org.identifiers.count() == 1
# Make sure we cleared out the orphan
with pytest.raises(NoResultFound):
Identifier.query.filter_by(
value='2 week ST', system=TRUENTH_CR_NAME).one()
def test_delete_unnamed(self):
keeper = AppText(name='keep me', custom_text='worthy')
mp = ModelPersistence(
AppText, lookup_field='name', sequence_name='apptext_id_seq',
target_dir=self.tmpdir)
with SessionScope(db):
db.session.add(keeper)
db.session.commit()
mp.export()
# Add another app text, expecting it'll be removed
bogus = AppText(name='temp', custom_text='not worthy')
with SessionScope(db):
db.session.add(bogus)
db.session.commit()
# Import w/ keep_unmentioned and expect both
mp.import_(keep_unmentioned=True)
assert AppText.query.count() == 2
# Now import, and expect only keeper to remain
mp.import_(keep_unmentioned=False)
assert AppText.query.count() == 1
assert AppText.query.first().name == 'keep me'