def test_exclude_schema_used_versions(self, req, dbsession,
check_csrf_token):
"""
It should exclude general versions already used by the form (editing)
"""
from datetime import date, timedelta
from webob.multidict import MultiDict
from occams import models as datastore
from occams import models
today = date.today()
tomorrow = today + timedelta(days=1)
y0 = datastore.Schema(name='y', title=u'Y', publish_date=today)
y1 = datastore.Schema(name='y', title=u'Y', publish_date=tomorrow)
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today(),
schemata=set([y0]))
dbsession.add_all([y0, y1, study])
dbsession.flush()
req.GET = MultiDict()
res = self._call_fut(study, req)
assert 1 == len(res['schemata'])
assert str(tomorrow) == res['schemata'][0]['publish_date']
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_enforce_unique_name(self, req, dbsession, check_csrf_token):
"""
It should make sure the name stays unique when adding new studies
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams import models
study = models.Study(name='some-study',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
dbsession.add_all([study])
dbsession.flush()
req.json_body = {
'title': u'Some Study',
'short_title': u'sfstudy',
'code': u'111',
'consent_date': str(date.today())
}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(models.StudyFactory(None), req)
assert 'Does not yield a unique URL.' in \
excinfo.value.json['errors']['title']
def test_fail_if_not_same_schema(self, req, dbsession, check_csrf_token):
"""
It should fail if the schema and versions do not match
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams import models as datastore
from occams import models
schema = datastore.Schema(name='test',
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())
dbsession.add_all([study, schema])
dbsession.flush()
req.json_body = {'schema': u'otherform', 'versions': [schema.id]}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(study, req)
assert 'Incorrect versions' in \
excinfo.value.json['errors']['versions']
def test_fail_if_termination_schema(self, req, dbsession,
check_csrf_token):
"""
It should not allow termination schemata to be used as study schemata
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams import models as datastore
from occams import models
schema = datastore.Schema(name='test',
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(),
termination_schema=schema)
dbsession.add_all([study, schema])
dbsession.flush()
req.json_body = {'schema': schema.name, 'versions': [schema.id]}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(study, req)
assert 'already a termination form' in \
excinfo.value.json['errors']['schema'].lower()
def test_fail_if_not_published(self, req, dbsession, check_csrf_token):
"""
It should fail if the schema is not published
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams import models as datastore
from occams import models
schema = datastore.Schema(name='test', title=u'')
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
dbsession.add_all([study, schema])
dbsession.flush()
dbsession.execute(models.patient_schema_table.insert().values(
{'schema_id': schema.id}))
req.json_body = {'schema': schema.name, 'versions': [schema.id]}
with pytest.raises(HTTPBadRequest) as excinfo:
self._call_fut(study, req)
assert 'not published' in \
excinfo.value.json['errors']['versions-0']
def test_update_cycles(self, req, dbsession, check_csrf_token):
"""
It should also update cycle versions
"""
from datetime import date, timedelta
from occams import models as datastore
from occams 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())
dbsession.add_all([study, v1, v2])
dbsession.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_basic(self, req, dbsession, check_csrf_token):
"""
It should allow adding a schema to a study
"""
from datetime import date
from occams import models as datastore
from occams import models
schema = datastore.Schema(name='test',
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())
dbsession.add_all([study, schema])
dbsession.flush()
req.json_body = {'schema': schema.name, 'versions': [schema.id]}
self._call_fut(study, req)
assert schema in study.schemata
def test_success(self, req, dbsession, check_csrf_token):
"""
It should remove the schema from the study and cascade to its cycles
"""
from datetime import date
from occams import models as datastore
from occams 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]))
dbsession.add_all([study, schema])
dbsession.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_exclude_schema(self, req, dbsession, check_csrf_token):
"""
It should exlude general forms used by the study (editing)
"""
from datetime import date
from webob.multidict import MultiDict
from occams import models as datastore
from occams import models
x = datastore.Schema(name='x', title=u'x', publish_date=date.today())
y = datastore.Schema(name='y', title=u'Y', 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(),
schemata=set([x]))
dbsession.add_all([x, y, study])
dbsession.flush()
req.GET = MultiDict()
res = self._call_fut(study, req)
assert 1 == len(res['schemata'])
assert 'y' == res['schemata'][0]['name']
def test_update_patient(self, req, dbsession, check_csrf_token):
"""
It should also mark the patient as modified
"""
from datetime import date
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())
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')
dbsession.add_all([patient, study])
dbsession.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_by_ids(self, req, dbsession,):
"""
It should allow search via direct ids (for pre-entered values)
"""
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())
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)
dbsession.add_all([patient, study])
dbsession.flush()
req.GET = MultiDict([('ids', cycle1.id)])
res = self._call_fut(patient['visits'], req)
assert cycle1.id == res['cycles'][0]['id']
def test_call_success(self, req, dbsession,):
"""
It should be able to validate cycles via GET (for AJAX req)
"""
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())
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)
dbsession.add_all([patient, study])
dbsession.flush()
req.GET = MultiDict([
('cycles', ','.join(map(str, [cycle1.id, cycle2.id])))])
res = self._call_fut(patient['visits'], req)
assert res
def test_enforce_unique_name(self, req, dbsession):
"""
It should make sure the name stays unique when adding new cycles
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams 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])
dbsession.add_all([study])
dbsession.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_edit_unique_name(self, req, dbsession):
"""
It should allow the cycle to be able to change its unique name
"""
from datetime import date
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])
dbsession.add_all([study])
dbsession.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_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_add_to_patient(self, req, dbsession):
from datetime import date
from occams import models
schema = models.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)
dbsession.add_all([study, patient])
dbsession.flush()
req.method = 'POST'
req.matchdict = {'patient': patient}
req.json_body = {
'schema': schema.id,
'collect_date': str(date.today()),
}
factory = models.FormFactory(req)
factory.__parent__ = patient
self._call_fut(factory, req)
contexts = dbsession.query(models.Context).all()
assert len(contexts) == 1
assert contexts[0].entity.schema == schema
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_edit_unique_name(self, req, dbsession, check_csrf_token):
"""
It should allow the study to be able to change its unique name
"""
from datetime import date
from occams import models
study = models.Study(name='some-study',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
dbsession.add_all([study])
dbsession.flush()
req.json_body = {
'title': u'New Study Title',
'short_title': study.short_title,
'code': study.code,
'consent_date': str(study.consent_date)
}
res = self._call_fut(study, req)
assert res is not None
def test_enable(self, req, dbsession, check_csrf_token):
"""
It should successfully add a schema to a cycle
"""
from datetime import date
from occams import models as datastore
from occams 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]))
dbsession.add_all([study, schema])
dbsession.flush()
req.json_body = {
'schema': schema.name,
'cycle': cycle.id,
'enabled': True
}
self._call_fut(study, req)
assert schema in cycle.schemata
def test_success(self, req, dbsession, check_csrf_token):
"""
It should allow removal of entities from a visit.
"""
from datetime import date, timedelta
from pyramid.httpexceptions import HTTPOk
from occams import models as datastore
from occams 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 = (
dbsession.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]))
dbsession.add_all([visit_a, study])
dbsession.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
dbsession.expunge_all()
visit_a = dbsession.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_valid_upload(self, req, dbsession, check_csrf_token):
"""
It should be able to upload a perfectly valid CSV
"""
import tempfile
import csv
from datetime import date
from occams import models as datastore
from occams import models
schema = datastore.Schema(name='rand',
title=u'Rand',
publish_date=date.today(),
attributes={
'criteria':
datastore.Attribute(name='criteria',
title=u'Criteria',
type='string',
order=0)
})
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
is_randomized=True,
randomization_schema=schema,
consent_date=date.today())
dbsession.add_all([study])
dbsession.flush()
class DummyUpload:
pass
with tempfile.NamedTemporaryFile(prefix='nose-', suffix='.exe') as fp:
upload = DummyUpload()
upload.file = fp
upload.filename = fp.name
# forget the schema keys
writer = csv.writer(fp)
writer.writerow(
[u'ARM', u'STRATA', u'BLOCKID', u'RANDID',
u'CRITERIA']) # noqa
writer.writerow(
[u'UCSD', u'hints', u'1234567', u'987654',
u'is smart']) # noqa
fp.flush()
req.POST = {'upload': upload}
self._call_fut(study, req)
stratum = dbsession.query(models.Stratum).one()
entity = dbsession.query(datastore.Entity).one()
assert stratum.arm.name == 'UCSD'
assert entity in stratum.entities
assert entity['criteria'] == 'is smart'
def test_cycle_in_study(self, req, dbsession, 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 import models as datastore
from occams 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]))
dbsession.add_all([study, schema, other_study])
dbsession.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 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_incomplete_header(self, req, dbsession, check_csrf_token):
"""
It should include randomization schema attribute names in the header
"""
import tempfile
import csv
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
from occams import models as datastore
from occams import models
schema = datastore.Schema(name='rand',
title=u'Rand',
publish_date=date.today(),
attributes={
'criteria':
datastore.Attribute(name='criteria',
title=u'Criteria',
type='string',
order=0)
})
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
is_randomized=True,
randomization_schema=schema,
consent_date=date.today())
dbsession.add(study)
dbsession.flush()
class DummyUpload:
pass
with tempfile.NamedTemporaryFile(prefix='nose-', suffix='.exe') as fp:
upload = DummyUpload()
upload.file = fp
upload.filename = fp.name
# forget the schema keys
writer = csv.writer(fp)
writer.writerow(['ARM', 'STRATA', 'BLOCKID', 'RANDID'])
fp.flush()
with pytest.raises(HTTPBadRequest) as excinfo:
req.POST = {'upload': upload}
self._call_fut(study, req)
assert check_csrf_token.called
assert 'missing' in excinfo.value.body
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]))
cycle = models.Cycle(name=u'TestCycle',
title=u'TestCycle',
week=39,
study=study)
visit = models.Visit(patient=patient,
cycles=[cycle],
visit_date='2015-01-01')
entity = models.Entity(schema=form, collect_date=date(2015, 1, 1))
dbsession.add(study)
dbsession.add(patient)
dbsession.add(visit)
dbsession.add(entity)
patient.entities.add(entity)
def test_unique_visit_date(self, req, dbsession, check_csrf_token):
"""
It should not allow duplicate visit dates
"""
from datetime import date
from pyramid.httpexceptions import HTTPBadRequest
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())
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())
dbsession.add_all([patient, study, visit])
dbsession.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_unique_cycle(self, req, dbsession, 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 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())
dbsession.add_all([patient, study, visit])
dbsession.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
dbsession.flush()
res = self._call_fut(patient['visits'], req)
assert res is not None