def populate(self, app, db_session):
import transaction
from occams_studies import models as studies
from occams_datastore import models as datastore
from datetime import date
# Any view-dependent data goes here
# Webtests will use a different scope for its transaction
with transaction.manager:
user = datastore.User(key=USERID)
db_session.info['blame'] = user
db_session.add(user)
db_session.flush()
site = studies.Site(name=u'UCSD',
title=u'UCSD',
description=u'UCSD Campus',
create_date=date.today())
db_session.add(
studies.Site(name=u'UCLA',
title=u'UCLA',
description=u'UCLA Campus',
create_date=date.today()))
db_session.add(
studies.Patient(initials=u'ian',
nurse=u'*****@*****.**',
site=site,
pid=u'123'))
db_session.flush()
def populate(self, app, db_session):
import transaction
from occams_datastore import models as datastore
from occams_studies import models as studies
# Any view-dependent data goes here
# Webtests will use a different scope for its transaction
with transaction.manager:
blame = datastore.User(key=USERID)
db_session.info['blame'] = blame
db_session.add(blame)
db_session.flush()
db_session.add(studies.Site(name=u'ucsd', title=u'UCSD'))
db_session.add(studies.Site(name=u'ucla', title=u'UCSD'))
def test_by_enrollment_number(self, req, db_session):
"""
It should be able to search by Enrollment Number
"""
from datetime import date
from occams_studies 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())
])
db_session.add_all([site_la, patient])
db_session.flush()
req.GET = MultiDict([('query', u'xyz')])
res = self._call_fut(models.PatientFactory(req), req)
assert patient.pid == res['patients'][0]['pid']
def test_data_with_early_test(self, db_session, study_code):
"""
It should output earlytest ids (for backwards-compatibilty)
"""
from datetime import date
from occams_studies import models
plan = self._create_one(db_session)
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'))
])
db_session.add(patient)
query = plan.data()
data = query.one()._asdict()
assert data['early_id'] == patient.enrollments[0].reference_number
def test_by_ids(
self,
req,
db_session,
):
"""
It should allow search via direct ids (for pre-entered values)
"""
from datetime import date
from occams_studies 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())
cycle1 = models.Cycle(name='week-1', title=u'Foo Week 1', week=1)
cycle2 = models.Cycle(name='week-2', title=u'Bar Week 2', week=2)
patient = models.Patient(site=models.Site(name=u'ucsd', title=u'UCSD'),
pid=u'12345')
study.cycles.append(cycle1)
study.cycles.append(cycle2)
db_session.add_all([patient, study])
db_session.flush()
req.GET = MultiDict([('ids', cycle1.id)])
res = self._call_fut(patient['visits'], req)
assert cycle1.id == res['cycles'][0]['id']
def test_reference_valid_number(self, req, db_session, check_csrf_token):
"""
It should check reference patterns if they are supported by the type
"""
from pyramid.httpexceptions import HTTPBadRequest
from occams_studies import models
site_la = models.Site(name=u'la', title=u'LA')
reftype = models.ReferenceType(name=u'foo',
title=u'Foo',
reference_pattern=u'^[0-9]+$')
patient = models.Patient(site=site_la, pid=u'12345')
db_session.add_all([patient, reftype])
db_session.flush()
req.json_body = {
'site':
site_la.id,
'references': [{
'reference_type': reftype.id,
'reference_number': u'XYZ'
}]
}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(patient, req)
assert check_csrf_token.called
assert 'Invalid format' in \
excinfo.value.json['errors']['references-0-reference_number']
def test_data_without_refs(self, db_session):
"""
It should be able to generate reports without refs
"""
from occams_studies import models
plan = self._create_one(db_session)
patient = models.Patient(pid=u'xxx-xxx',
site=models.Site(name=u'someplace',
title=u'Some Place'))
db_session.add(patient)
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]
assert sorted(codebook_columns) == sorted(data_columns)
data = query.one()._asdict()
assert data['pid'] == patient.pid
assert data['site'] == patient.site.name
assert data['early_id'] is None
def test_data_with_refs(self, db_session):
"""
It should generate a basic listing of all the PIDs in the database
"""
from occams_studies import models
plan = self._create_one(db_session)
reference_type = models.ReferenceType(name=u'med_num',
title=u'Medical Number')
patient = models.Patient(pid=u'xxx-xxx',
references=[
models.PatientReference(
reference_type=reference_type,
reference_number=u'999')
],
site=models.Site(name=u'someplace',
title=u'Some Place'))
db_session.add(patient)
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]
assert sorted(codebook_columns) == sorted(data_columns)
data = query.one()._asdict()
assert data['med_num'] == '999'
def test_add_to_patient(self, req, db_session):
from datetime import date
from occams_datastore import models as datastore
from occams_studies import models
schema = datastore.Schema(name=u'schema',
title=u'Schema',
publish_date=date.today())
study = models.Study(name='some-study',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today(),
schemata=set([schema]))
site = models.Site(name=u'somewhere', title=u'Somewhere')
patient = models.Patient(pid=u'12345', site=site)
db_session.add_all([study, patient])
db_session.flush()
req.method = 'POST'
req.matchdict = {'patient': patient}
req.json_body = {
'schema': schema.id,
'collect_date': str(date.today()),
}
factory = models.FormFactory(req, patient)
self._call_fut(factory, req)
contexts = db_session.query(datastore.Context).all()
assert len(contexts) == 1
assert contexts[0].entity.schema == schema
def test_has_enrollments(self, req, db_session, 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_studies 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'))
db_session.add_all([study, enrollment])
db_session.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 == db_session.query(models.Study).count()
def test_generate_pid(self, req, db_session, check_csrf_token):
"""
It should generate a PID for new patients
"""
import mock
from occams_studies import models
site_la = models.Site(name=u'la', title=u'LA')
reftype = models.ReferenceType(name=u'foo', title=u'FOO')
db_session.add_all([site_la, reftype])
db_session.flush()
req.json_body = {
'site':
site_la.id,
'references': [{
'reference_type': reftype.id,
'reference_number': u'ABC'
}]
}
# Fake generate a PID, the roster should unit test this
with mock.patch('occams_studies.views.patient.generate') as generate:
generate.return_value = u'12345'
res = self._call_fut(models.PatientFactory(req), req)
assert generate.called
assert check_csrf_token.called
assert u'12345' == res['pid']
assert site_la.id == res['site']['id']
assert [(reftype.id, u'ABC')] == \
[(r['reference_type']['id'], r['reference_number'])
for r in res['references']]
def test_track_limit(self, req, db_session):
"""
It should only keep track of the last 10 recently viewed patients
"""
from collections import OrderedDict
from datetime import datetime
import mock
from occams_studies import models
site_la = models.Site(name=u'la', title=u'LA')
patient = models.Patient(site=site_la, pid=u'12345')
db_session.add(patient)
db_session.flush()
req.session['viewed'] = OrderedDict()
req.session.changed = mock.Mock()
previous = [str(i) for i in range(10)]
for pid in previous:
req.session['viewed'][pid] = \
{'pid': pid, 'view_date': datetime.now()}
self._call_fut(patient, req)
assert '12345' in req.session['viewed']
assert previous[0] not in req.session['viewed']
assert 10 == len(req.session['viewed'])
def test_reference_unique(self, req, db_session, check_csrf_token):
"""
It should enforce unique reference_types
"""
from pyramid.httpexceptions import HTTPBadRequest
from occams_studies import models
site_la = models.Site(name=u'la', title=u'LA')
reftype = models.ReferenceType(name=u'foo', title=u'Foo')
other = models.Patient(site=site_la,
pid=u'ABCDE',
references=[
models.PatientReference(
reference_type=reftype,
reference_number=u'XYZ')
])
patient = models.Patient(site=site_la, pid=u'12345')
db_session.add_all([patient, other])
db_session.flush()
req.json_body = {
'site':
site_la.id,
'references': [{
'reference_type': reftype.id,
'reference_number': u'XYZ'
}]
}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(patient, req)
assert check_csrf_token.called
assert 'Already assigned' in \
excinfo.value.json['errors']['references-0-reference_number']
def test_reference_type_invalid(self, req, db_session, check_csrf_token):
"""
It should enforce valid reference_types
"""
from pyramid.httpexceptions import HTTPBadRequest
from occams_studies import models
site_la = models.Site(name=u'la', title=u'LA')
patient = models.Patient(site=site_la, pid=u'12345')
db_session.add(patient)
db_session.flush()
req.json_body = {
'site': patient.site.id,
'references': [{
'reference_type': 123,
'reference_number': u'ABC'
}]
}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(patient, req)
assert check_csrf_token.called
assert 'not found' in \
excinfo.value.json['errors']['references-0-reference_type'].lower()
def test_update_patient(self, req, db_session, check_csrf_token):
"""
It should also mark the patient as modified
"""
from datetime import date
from occams_studies import models
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
cycle1 = models.Cycle(study=study, name='week-1', title=u'', week=1)
patient = models.Patient(site=models.Site(name=u'ucsd', title=u'UCSD'),
pid=u'12345')
db_session.add_all([patient, study])
db_session.flush()
old_modify_date = patient.modify_date
req.json_body = {
'cycles': [str(cycle1.id)],
'visit_date': str(date.today())
}
self._call_fut(patient['visits'], req)
assert old_modify_date < patient.modify_date
def test_site(self, req, db_session, check_csrf_token):
"""
It should update sites
"""
from occams_studies import models
site_la = models.Site(name=u'la', title=u'LA')
site_sd = models.Site(name=u'sd', title=u'SD')
patient = models.Patient(site=site_la, pid=u'12345')
db_session.add_all([site_la, site_sd, patient])
db_session.flush()
req.json_body = {'site': site_sd.id}
self._call_fut(patient, req)
assert check_csrf_token.called
assert patient.site.id == site_sd.id
def test_success(self, req, db_session, check_csrf_token):
"""
It should allow removal of entities from a visit.
"""
from datetime import date, timedelta
from pyramid.httpexceptions import HTTPOk
from occams_datastore import models as datastore
from occams_studies import models
cycle = models.Cycle(name='week-1', title=u'', week=1)
schema = datastore.Schema(name=u'sample',
title=u'',
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(),
cycles=[cycle],
schemata=set([schema]))
site = models.Site(name=u'ucsd', title=u'UCSD')
default_state = (db_session.query(
datastore.State).filter_by(name=u'pending-entry').one())
t_a = date.today() + timedelta(days=5)
patient_a = models.Patient(site=site, pid=u'12345')
visit_a = models.Visit(patient=patient_a,
cycles=[cycle],
visit_date=t_a)
entity_a_1 = datastore.Entity(schema=schema,
collect_date=t_a,
state=default_state)
entity_a_2 = datastore.Entity(schema=schema,
collect_date=t_a,
state=default_state)
entity_a_3 = datastore.Entity(schema=schema,
collect_date=t_a,
state=default_state)
list(map(visit_a.entities.add, [entity_a_1, entity_a_2, entity_a_3]))
db_session.add_all([visit_a, study])
db_session.flush()
req.json_body = {'forms': [entity_a_2.id, entity_a_3.id]}
res = self._call_fut(visit_a['forms'], req)
# refresh the session so we can get a correct listing
db_session.expunge_all()
visit_a = db_session.query(models.Visit).get(visit_a.id)
assert isinstance(res, HTTPOk)
assert sorted([e.id for e in [entity_a_1]]) == \
sorted([e.id for e in visit_a.entities])
def populate(self, app, db_session):
import transaction
from occams_studies import models as studies
from occams_datastore import models as datastore
from datetime import date
# Any view-dependent data goes here
# Webtests will use a different scope for its transaction
with transaction.manager:
user = datastore.User(key=USERID)
db_session.info['blame'] = user
db_session.add(user)
db_session.flush()
site = studies.Site(name=u'UCSD',
title=u'UCSD',
description=u'UCSD Campus',
create_date=date.today())
patient = studies.Patient(initials=u'ian',
nurse=u'*****@*****.**',
site=site,
pid=u'123')
form = datastore.Schema(name=u'test_schema',
title=u'test_title',
publish_date=date(2015, 1, 1))
study = studies.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]))
cycle = studies.Cycle(name=u'TestCycle',
title=u'TestCycle',
week=39,
study=study)
visit = studies.Visit(patient=patient,
cycles=[cycle],
visit_date='2015-01-01')
entity = datastore.Entity(schema=form,
collect_date=date(2015, 1, 1))
db_session.add(study)
db_session.add(patient)
db_session.add(visit)
db_session.add(entity)
patient.entities.add(entity)
def test_enrollment(self, db_session):
"""
It should add enrollment-specific metadata to the report
"""
from datetime import date, timedelta
from occams_datastore import models as datastore
from occams_studies import models
from occams_studies.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])
db_session.add_all([schema, entity, patient, study, enrollment])
plan = SchemaPlan.from_schema(db_session, 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 test_by_pid(self, req, db_session):
"""
It should search by PID
"""
from occams_studies import models
from webob.multidict import MultiDict
site_la = models.Site(name=u'la', title=u'LA')
patient = models.Patient(site=site_la, pid=u'12345')
db_session.add_all([site_la, patient])
db_session.flush()
req.GET = MultiDict([('query', u'12345')])
res = self._call_fut(models.PatientFactory(req), req)
assert patient.pid == res['patients'][0]['pid']
def populate(self, app, db_session):
import transaction
from occams_studies import models as studies
from occams_datastore import models as datastore
from datetime import date
# Any view-dependent data goes here
# Webtests will use a different scope for its transaction
with transaction.manager:
user = datastore.User(key=USERID)
db_session.info['blame'] = user
db_session.add(user)
db_session.flush()
site = studies.Site(name=u'UCSD',
title=u'UCSD',
description=u'UCSD Campus',
create_date=date.today())
patient = studies.Patient(initials=u'ian',
nurse=u'*****@*****.**',
site=site,
pid=u'123')
form = datastore.Schema(name=u'test_schema',
title=u'test_title',
publish_date=date(2015, 1, 1))
study = studies.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 = (db_session.query(
datastore.State).filter_by(name=u'pending-entry').one())
db_session.add(
datastore.Entity(state=state,
schema=form,
collect_date=date(2015, 2, 1)))
db_session.add(
studies.Enrollment(patient=patient,
study=study,
consent_date=date(2014, 12, 22)))
def test_cascade_forms(self, req, db_session, check_csrf_token):
"""
It should remove all visit-associated forms.
"""
from datetime import date
from occams_datastore import models as datastore
from occams_studies 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()))
db_session.add_all([patient, enrollment, study, visit])
db_session.flush()
visit_id = visit.id
self._call_fut(visit, req)
assert db_session.query(models.Visit).get(visit_id) is None
assert 0 == db_session.query(datastore.Entity).count()
def test_include_not_retracted_form(self, req, db_session,
check_csrf_token):
"""
It should not use retracted forms, even if there are the most recent
"""
from datetime import date, timedelta
from occams_datastore import models as datastore
from occams_studies import models
t0 = date.today()
t1 = t0 + timedelta(days=1)
t2 = t1 + timedelta(days=1)
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
cycle1 = models.Cycle(name='week-1', title=u'', week=1)
cycle1.schemata.update([
datastore.Schema(name='form1', title=u'', publish_date=t0),
datastore.Schema(name='form1',
title=u'',
publish_date=t2,
retract_date=t2)
])
study.cycles.append(cycle1)
patient = models.Patient(site=models.Site(name=u'ucsd', title=u'UCSD'),
pid=u'12345')
db_session.add_all([patient, study])
db_session.flush()
req.json_body = {
'cycles': [cycle1.id],
'visit_date': str(t2),
'include_forms': True
}
res = self._call_fut(patient['visits'], req)
assert 1 == len(res['entities'])
assert str(t0) == res['entities'][0]['schema']['publish_date']
def test_unique_cycle(self, req, db_session, check_csrf_token):
"""
It should not allow repeat cycles (unless it's interim)
"""
from datetime import date, timedelta
from pyramid.httpexceptions import HTTPBadRequest
from occams_studies import models
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='week-1', title=u'', week=1)
study.cycles.append(cycle)
patient = models.Patient(site=models.Site(name=u'ucsd', title=u'UCSD'),
pid=u'12345')
visit = models.Visit(patient=patient,
cycles=[cycle],
visit_date=date.today())
db_session.add_all([patient, study, visit])
db_session.flush()
req.json_body = {
'cycles': [cycle.id],
'visit_date': str(date.today() + timedelta(days=1))
}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(patient['visits'], req)
assert 'already in use' in \
excinfo.value.json['errors']['cycles-0'].lower()
# The exception is interims
cycle.is_interim = True
db_session.flush()
res = self._call_fut(patient['visits'], req)
assert res is not None
def test_update_patient(self, req, db_session, check_csrf_token):
"""
It should also mark the patient as modified
"""
from datetime import date
from occams_studies import models
patient = models.Patient(site=models.Site(name=u'ucsd', title=u'UCSD'),
pid=u'12345')
visit = models.Visit(patient=patient, visit_date=date.today())
db_session.add_all([patient, visit])
db_session.flush()
old_modify_date = patient.modify_date
self._call_fut(visit, req)
assert old_modify_date < patient.modify_date
def test_track_recently_viewed(self, req, db_session):
"""
It should track recently viewed patients
"""
import mock
from occams_studies import models
site_la = models.Site(name=u'la', title=u'LA')
patient = models.Patient(site=site_la, pid=u'12345')
db_session.add(patient)
db_session.flush()
req.session.changed = mock.Mock()
self._call_fut(patient, req)
assert '12345' in req.session['viewed']
assert 1 == len(req.session['viewed'])
assert req.session.changed.called
def test_site_invalid(self, req, db_session, check_csrf_token):
"""
It should enforce valid sites
"""
from pyramid.httpexceptions import HTTPBadRequest
from occams_studies import models
site_la = models.Site(name=u'la', title=u'LA')
patient = models.Patient(site=site_la, pid=u'12345')
db_session.add_all([site_la, patient])
db_session.flush()
req.json_body = {'site': site_la.id + 100}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(patient, req)
assert check_csrf_token.called
assert 'not found' in excinfo.value.json['errors']['site'].lower()
def test_unique_visit_date(self, req, db_session, check_csrf_token):
"""
It should not allow duplicate visit dates
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams_studies import models
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
cycle1 = models.Cycle(name='week-1', title=u'', week=1)
cycle2 = models.Cycle(name='week-2', title=u'', week=2)
study.cycles.append(cycle1)
study.cycles.append(cycle2)
patient = models.Patient(site=models.Site(name=u'ucsd', title=u'UCSD'),
pid=u'12345')
visit = models.Visit(patient=patient,
cycles=[cycle1],
visit_date=date.today())
db_session.add_all([patient, study, visit])
db_session.flush()
req.json_body = {
'cycles': [cycle2.id],
'visit_date': str(date.today())
}
# Update the visit, should allow to update the date
self._call_fut(visit, req)
# New visits cannot share dates
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(patient['visits'], req)
assert 'already exists' in \
excinfo.value.json['errors']['visit_date']
def test_add_drsc_entity_already_has_entity(self, db_session):
"""Should not add entity becuase it exists already."""
from datetime import date
from occams_studies import models as studies
from occams_datastore import models as datastore
patient_site = studies.Site(name=u'test_site', title=u'test_clinic')
patient = studies.Patient(pid=u'1234', site=patient_site)
default_state = (db_session.query(
datastore.State).filter_by(name='complete').one())
target_schema = datastore.Schema(name=u'Demographics',
title=u'Demographics',
publish_date=date.today(),
attributes={
'yob':
datastore.Attribute(
name=u'yob',
title=u'yob',
type=u'number',
order=0)
})
collect_date = date.today()
entity = datastore.Entity(schema=target_schema,
collect_date=collect_date,
state=default_state)
patient.entities.add(entity)
db_session.flush()
target_schema_name = u'Demographics'
self._call_fut(db_session, patient, target_schema_name, target_schema,
collect_date)
patient = (db_session.query(
studies.Patient).filter_by(pid=u'1234').one())
assert len(patient.entities) == 1
def populate(self, app, db_session):
import transaction
from occams_studies import models as studies
from occams_datastore import models as datastore
from datetime import date
# Any view-dependent data goes here
# Webtests will use a different scope for its transaction
with transaction.manager:
user = datastore.User(key=USERID)
db_session.info['blame'] = user
db_session.add(user)
db_session.flush()
site = studies.Site(name=u'UCSD',
title=u'UCSD',
description=u'UCSD Campus',
create_date=date.today())
patient = studies.Patient(initials=u'ian',
nurse=u'*****@*****.**',
site=site,
pid=u'123')
study = studies.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',
)
cycle = studies.Cycle(name=u'TestDelete',
title=u'TestDelete',
week=39,
study=study)
db_session.add(study)
db_session.add(patient)
db_session.add(cycle)
