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_edit_unique_name(self, req, db_session):
"""
It should allow the cycle to be able to change its unique name
"""
from datetime import date
from occams_studies 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])
db_session.add_all([study])
db_session.flush()
req.json_body = {
'name': 'somestudy',
'title': cycle.title,
'week': cycle.week
}
res = self._call_fut(cycle, req)
assert res is not None
def test_enable(self, req, db_session, check_csrf_token):
"""
It should successfully add a schema to a cycle
"""
from datetime import date
from occams_datastore import models as datastore
from occams_studies import models
schema = datastore.Schema(name='test',
title=u'Test',
publish_date=date.today())
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],
schemata=set([schema]))
db_session.add_all([study, schema])
db_session.flush()
req.json_body = {
'schema': schema.name,
'cycle': cycle.id,
'enabled': True
}
self._call_fut(study, req)
assert schema in cycle.schemata
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_success(self, req, db_session, check_csrf_token):
"""
It should remove the schema from the study and cascade to its cycles
"""
from datetime import date
from occams_datastore import models as datastore
from occams_studies import models
schema = datastore.Schema(name='test',
title=u'',
publish_date=date.today())
cycle = models.Cycle(name='week-1',
title=u'Week 1',
week=1,
schemata=set([schema]))
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]))
db_session.add_all([study, schema])
db_session.flush()
req.matchdict = {'schema': schema.name}
self._call_fut(study, req)
assert schema not in study.schemata
assert schema not in cycle.schemata
def test_enforce_unique_name(self, req, db_session):
"""
It should make sure the name stays unique when adding new cycles
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams_studies import models
cycle = models.Cycle(name='week-1', title=u'Week 1', week=1)
study = models.Study(name=u'some-study',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today(),
cycles=[cycle])
db_session.add_all([study])
db_session.flush()
req.json_body = {'title': u'Week 1', 'week': 2}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(study['cycles'], req)
assert 'not yield a unique' in \
excinfo.value.json['errors']['title'].lower()
def test_update_cycles(self, req, db_session, check_csrf_token):
"""
It should also update cycle versions
"""
from datetime import date, timedelta
from occams_datastore import models as datastore
from occams_studies import models
today = date.today()
tomorrow = today + timedelta(days=1)
v1 = datastore.Schema(name=u'test', title=u'', publish_date=today)
v2 = datastore.Schema(name=u'test', title=u'', publish_date=tomorrow)
cycle = models.Cycle(name=u'wk-001',
title=u'WK-001',
schemata=set([v1]))
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
cycles=[cycle],
schemata=set([v1]),
consent_date=date.today())
db_session.add_all([study, v1, v2])
db_session.flush()
req.json_body = {'schema': v1.name, 'versions': [v2.id]}
self._call_fut(study, req)
assert v2 in study.schemata
# v2 should have been passed on to the cycle using it as well
assert v2 in cycle.schemata
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 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 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_call_success(
self,
req,
db_session,
):
"""
It should be able to validate cycles via GET (for AJAX req)
"""
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([('cycles',
','.join(map(str, [cycle1.id, cycle2.id])))])
res = self._call_fut(patient['visits'], req)
assert res
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_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_cycle_in_study(self, req, db_session, check_csrf_token):
"""
It should fail if the cycle is not part of the study
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams_datastore import models as datastore
from occams_studies import models
schema = datastore.Schema(name='test',
title=u'Test',
publish_date=date.today())
other_cycle = models.Cycle(name=u'week-1', title=u'Title', week=1)
other_study = models.Study(name=u'otherstudy',
title=u'Other Study',
short_title=u'ostudy',
code=u'111',
consent_date=date.today(),
cycles=[other_cycle])
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today(),
schemata=set([schema]))
db_session.add_all([study, schema, other_study])
db_session.flush()
req.json_body = {
'schema': schema.name,
'cycle': other_cycle.id,
'enabled': True
}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(study, req)
assert 'not a valid choice' in \
excinfo.value.json['errors']['cycle'].lower()
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)
def test_not_in_study(self, req, db_session):
"""
It should fail if the form is not part of the study
"""
from datetime import date, timedelta
from pyramid.httpexceptions import HTTPBadRequest
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])
site = models.Site(name=u'ucsd', title=u'UCSD')
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)
db_session.add_all([schema, visit_a, study])
db_session.flush()
req.json_body = {
'schema': schema.id,
}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(visit_a['forms'], req)
assert 'is not part of the studies' in \
excinfo.value.json['errors']['schema']
def test_add_to_visit(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]))
cycle = models.Cycle(study=study, name=u'cycle-1', title=u'Cycle')
site = models.Site(name=u'somewhere', title=u'Somewhere')
patient = models.Patient(pid=u'12345', site=site)
visit = models.Visit(patient=patient,
visit_date=date.today(),
cycles=[cycle])
db_session.add_all([study, patient, visit])
db_session.flush()
req.matchdict = {'patient': patient, 'visit': visit}
req.json_body = {
'schema': schema.id,
'collect_date': str(date.today()),
}
factory = models.FormFactory(req, visit)
self._call_fut(factory, req)
contexts = db_session.query(datastore.Context).all()
assert len(contexts) == 2
assert sorted(['patient', 'visit']) == \
sorted([c.external for c in contexts])
def test_has_visits(self, req, db_session, 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_studies 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])
db_session.add_all([study, enrollment, visit])
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(cycle, req)
config.testing_securitypolicy(permissive=True)
self._call_fut(cycle, req)
assert 0 == study.cycles.count()
def test_no_visit(self, req, db_session):
"""
It should allow deleting of a cycle if it has no visits
"""
from datetime import date
from occams_studies 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])
db_session.add_all([study])
db_session.flush()
self._call_fut(cycle, req)
assert 0 == study.cycles.count()
def test_visit(self, db_session):
"""
It should add visit-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'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])
visit = models.Visit(
visit_date=date.today(),
patient=patient,
cycles=[
models.Cycle(name=u'study1-scr',
title=u'Study 1 Screening',
week=123,
study=models.Study(name=u'study1',
short_title=u'S1',
code=u'001',
consent_date=date.today() -
timedelta(365),
title=u'Study 1')),
models.Cycle(name=u'study2-wk1',
title=u'Study 2 Week 1',
week=5858,
study=models.Study(name=u'study21',
short_title=u'S2',
code=u'002',
consent_date=date.today() -
timedelta(365),
title=u'Study 2'))
],
entities=[entity])
db_session.add_all([schema, entity, patient, visit])
db_session.flush()
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 is None
cyclefmt = '{cycle.study.title}({cycle.week})'
assert sorted(record.visit_cycles.split(';')) == \
sorted([cyclefmt.format(cycle=c) for c in visit.cycles])
assert str(record.visit_id) == str(visit.id)
assert record.collect_date == entity.collect_date
def test_include_forms(self, req, db_session, check_csrf_token):
"""
It should allow the user to create cycle forms
"""
from datetime import date, timedelta
from occams_datastore import models as datastore
from occams_studies import models
form1 = datastore.Schema(name='form1',
title=u'',
publish_date=date.today())
form2 = datastore.Schema(name='form2',
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())
cycle1 = models.Cycle(name='week-1', title=u'', week=1)
cycle1.schemata.add(form1)
cycle2 = models.Cycle(name='week-2', title=u'', week=2)
cycle2.schemata.add(form2)
study.cycles.append(cycle1)
study.cycles.append(cycle2)
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(date.today() + timedelta(days=1)),
'include_forms': True
}
res = self._call_fut(patient['visits'], req)
assert ['form1'] == \
[e['schema']['name'] for e in res['entities']]
contexts = db_session.query(datastore.Context).all()
assert sorted(['patient', 'visit']) == \
sorted([c.external for c in contexts])
visit = db_session.query(models.Visit).get(res['id'])
# Update to demonstrate forms can still be added on edit
req.json_body = {
'cycles': [cycle1.id, cycle2.id],
'visit_date': str(date.today() + timedelta(days=1)),
'include_forms': True
}
res = self._call_fut(visit, req)
assert sorted(['form1', 'form2']) == \
sorted([e['schema']['name'] for e in res['entities']])
contexts = db_session.query(datastore.Context).all()
assert sorted([(x, e['id'])
for e in res['entities']
for x in ('patient', 'visit')]) == \
sorted([(c.external, c.entity_id) for c in contexts])
