def test_data_with_early_test(self, dbsession, study_code):
"""
It should output earlytest ids (for backwards-compatibilty)
"""
from datetime import date
from occams import models
plan = self._create_one(dbsession)
patient = models.Patient(
pid=u'xxx-xxx',
site=models.Site(name=u'someplace', title=u'Some Place'),
enrollments=[
models.Enrollment(
consent_date=date.today(),
reference_number=u'76C000000',
study=models.Study(
name=u'some_study',
code=study_code,
consent_date=date.today(),
short_title=u'smstdy',
title=u'Some Study')
)
])
dbsession.add(patient)
query = plan.data()
data = query.one()._asdict()
assert data['early_id'] == patient.enrollments[0].reference_number
def test_by_enrollment_number(self, req, dbsession):
"""
It should be able to search by Enrollment Number
"""
from datetime import date
from occams import models
from webob.multidict import MultiDict
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
site_la = models.Site(name=u'la', title=u'LA')
patient = models.Patient(site=site_la,
pid=u'12345',
enrollments=[
models.Enrollment(
study=study,
reference_number=u'xyz',
consent_date=date.today())
])
dbsession.add_all([site_la, patient])
dbsession.flush()
req.GET = MultiDict([('query', u'xyz')])
res = self._call_fut(models.PatientFactory(req), req)
assert patient.pid == res['patients'][0]['pid']
def test_has_enrollments(self, req, dbsession, config, check_csrf_token):
"""
It should not allow deletion of a study if it has enrollments
(unless administrator)
"""
from datetime import date
from pyramid.httpexceptions import HTTPForbidden
from occams import models
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
enrollment = models.Enrollment(study=study,
consent_date=date.today(),
patient=models.Patient(site=models.Site(
name='ucsd', title=u'UCSD'),
pid=u'12345'))
dbsession.add_all([study, enrollment])
dbsession.flush()
# Should not be able to delete if not an admin
config.testing_securitypolicy(permissive=False)
with pytest.raises(HTTPForbidden):
self._call_fut(study, req)
config.testing_securitypolicy(permissive=True)
self._call_fut(study, req)
assert 0 == dbsession.query(models.Study).count()
def populate(self, app, dbsession):
import transaction
from occams import models
from datetime import date
# Any view-dependent data goes here
# Webtests will use a different scope for its transaction
with transaction.manager:
user = models.User(key=USERID)
dbsession.info['blame'] = user
dbsession.add(user)
dbsession.flush()
site = models.Site(name=u'UCSD',
title=u'UCSD',
description=u'UCSD Campus',
create_date=date.today())
patient = models.Patient(initials=u'ian',
nurse=u'*****@*****.**',
site=site,
pid=u'123')
study = models.Study(
name=u'test_study',
code=u'test_code',
consent_date=date(2014, 12, 23),
is_randomized=False,
title=u'test_title',
short_title=u'test_short',
)
dbsession.add(
models.Enrollment(patient=patient,
study=study,
consent_date=date(2014, 12, 22)))
def test_cascade_forms(self, req, dbsession, check_csrf_token):
"""
It should remove all visit-associated forms.
"""
from datetime import date
from occams import models as datastore
from occams import models
schema = datastore.Schema(
name=u'sample',
title=u'Some Sample',
publish_date=date.today())
study = models.Study(
name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
cycle = models.Cycle(
name=u'week-10',
title=u'Week 10',
week=10)
study.cycles.append(cycle)
patient = models.Patient(
site=models.Site(name=u'ucsd', title=u'UCSD'),
pid=u'12345')
enrollment = models.Enrollment(
study=study,
patient=patient,
consent_date=date.today())
visit = models.Visit(
patient=patient,
cycles=[cycle],
visit_date=date.today())
visit.entities.add(datastore.Entity(
schema=schema,
collect_date=date.today()))
dbsession.add_all([patient, enrollment, study, visit])
dbsession.flush()
visit_id = visit.id
self._call_fut(visit, req)
assert dbsession.query(models.Visit).get(visit_id) is None
assert 0 == dbsession.query(datastore.Entity).count()
def test_enrollment(self, dbsession):
"""
It should add enrollment-specific metadata to the report
"""
from datetime import date, timedelta
from occams import models as datastore
from occams import models
from occams.exports.schema import SchemaPlan
schema = datastore.Schema(name=u'termination',
title=u'Termination',
publish_date=date.today(),
attributes={
'foo':
datastore.Attribute(
name='foo',
title=u'',
type='string',
order=0,
)
})
entity = datastore.Entity(schema=schema, collect_date=date.today())
patient = models.Patient(site=models.Site(name='ucsd', title=u'UCSD'),
pid=u'12345',
entities=[entity])
study = models.Study(name=u'cooties',
short_title=u'CTY',
code=u'999',
consent_date=date.today() - timedelta(365),
title=u'Cooties')
enrollment = models.Enrollment(
patient=patient,
study=study,
consent_date=date.today() - timedelta(5),
latest_consent_date=date.today() - timedelta(3),
termination_date=date.today(),
entities=[entity])
dbsession.add_all([schema, entity, patient, study, enrollment])
plan = SchemaPlan.from_schema(dbsession, schema.name)
codebook = list(plan.codebook())
query = plan.data()
codebook_columns = [c['field'] for c in codebook]
data_columns = [c['name'] for c in query.column_descriptions]
record = query.one()
assert sorted(codebook_columns) == sorted(data_columns)
assert record.site == patient.site.name
assert record.pid == patient.pid
assert record.enrollment == enrollment.study.name
assert record.enrollment_ids == str(enrollment.id)
assert record.visit_cycles is None
assert record.collect_date == entity.collect_date
def populate(self, app, dbsession):
import transaction
from occams import models
from datetime import date
# Any view-dependent data goes here
# Webtests will use a different scope for its transaction
with transaction.manager:
user = models.User(key=USERID)
dbsession.info['blame'] = user
dbsession.add(user)
dbsession.flush()
site = models.Site(name=u'UCSD',
title=u'UCSD',
description=u'UCSD Campus',
create_date=date.today())
patient = models.Patient(initials=u'ian',
nurse=u'*****@*****.**',
site=site,
pid=u'123')
form = models.Schema(name=u'test_schema',
title=u'test_title',
publish_date=date(2015, 1, 1))
study = models.Study(name=u'test_study',
code=u'test_code',
consent_date=date(2014, 12, 23),
is_randomized=False,
title=u'test_title',
short_title=u'test_short',
schemata=set([form]))
state = (dbsession.query(
models.State).filter_by(name=u'pending-entry').one())
dbsession.add(
models.Entity(state=state,
schema=form,
collect_date=date(2015, 2, 1)))
dbsession.add(
models.Enrollment(patient=patient,
study=study,
consent_date=date(2014, 12, 22)))
def test_has_visits(self, req, dbsession, config):
"""
It should not allow deletion of a cycle if it has visit
(unless administrator)
"""
from datetime import date
from pyramid.httpexceptions import HTTPForbidden
from occams import models
cycle = models.Cycle(name='week-1', title=u'Week 1', week=1)
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today(),
cycles=[cycle])
patient = models.Patient(site=models.Site(name='ucsd', title=u'UCSD'),
pid=u'12345')
enrollment = models.Enrollment(study=study,
consent_date=date.today(),
patient=patient)
visit = models.Visit(patient=patient,
visit_date=date.today(),
cycles=[cycle])
dbsession.add_all([study, enrollment, visit])
dbsession.flush()
# Should not be able to delete if not an admin
config.testing_securitypolicy(permissive=False)
with pytest.raises(HTTPForbidden):
self._call_fut(cycle, req)
config.testing_securitypolicy(permissive=True)
self._call_fut(cycle, req)
assert 0 == study.cycles.count()
def test_rand(self, dbsession):
"""
It should add randomization-specific metadata to the report
"""
from datetime import date, timedelta
from occams import models as datastore
from occams import models
from occams.exports.schema import SchemaPlan
schema = datastore.Schema(name=u'vitals',
title=u'Vitals',
publish_date=date.today(),
attributes={
'foo':
datastore.Attribute(
name='foo',
title=u'',
type='string',
order=0,
)
})
entity = datastore.Entity(collect_date=date.today(), schema=schema)
patient = models.Patient(site=models.Site(name='ucsd', title=u'UCSD'),
pid=u'12345',
entities=[entity])
study = models.Study(name=u'study1',
short_title=u'S1',
code=u'001',
consent_date=date.today() - timedelta(365),
title=u'Study 1')
armga = models.Arm(name=u'groupa', title=u'GROUP A', study=study)
stratum = models.Stratum(study=study,
arm=armga,
block_number=12384,
randid=u'8484',
patient=patient,
entities=[entity])
enrollment = models.Enrollment(
patient=patient,
study=study,
consent_date=date.today() - timedelta(5),
latest_consent_date=date.today() - timedelta(3),
termination_date=date.today(),
entities=[entity])
dbsession.add_all([schema, entity, patient, enrollment, stratum])
dbsession.flush()
plan = SchemaPlan.from_schema(dbsession, schema.name)
codebook = list(plan.codebook())
query = plan.data()
codebook_columns = [c['field'] for c in codebook]
data_columns = [c['name'] for c in query.column_descriptions]
record = query.one()
assert sorted(codebook_columns) == sorted(data_columns)
assert record.site == patient.site.name
assert record.pid == patient.pid
assert record.enrollment == enrollment.study.name
assert record.enrollment_ids == str(enrollment.id)
assert record.collect_date == entity.collect_date
assert record.block_number == stratum.block_number
assert record.arm_name == stratum.arm.title
assert record.randid == stratum.randid
