def populate(self, app, db_session):
from datetime import date
import transaction
from occams_datastore import models as datastore
from occams_studies import models as studies
# Any view-dependent data goes here
with transaction.manager:
user = datastore.User(key=USERID)
drsc = studies.Study(name=u'drsc',
title=u'DRSC',
short_title=u'dr',
code=u'drs',
consent_date=date.today(),
is_randomized=False)
ucsd = studies.Study(name=u'ucsd',
title=u'UCSD',
short_title=u'ucsd',
code=u'ucsd',
consent_date=date.today(),
is_randomized=False)
db_session.add(user)
db_session.add(drsc)
db_session.add(ucsd)
db_session.flush()
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_enforce_unique_name(self, req, db_session, 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_studies import models
study = models.Study(name='some-study',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
db_session.add_all([study])
db_session.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_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_fail_if_not_same_schema(self, req, db_session, 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_datastore import models as datastore
from occams_studies 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())
db_session.add_all([study, schema])
db_session.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, db_session,
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_datastore import models as datastore
from occams_studies 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)
db_session.add_all([study, schema])
db_session.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_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_exclude_schema_used_versions(self, req, db_session,
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_datastore import models as datastore
from occams_studies 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]))
db_session.add_all([y0, y1, study])
db_session.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_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_basic(self, req, db_session, check_csrf_token):
"""
It should allow adding a schema to a study
"""
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())
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
db_session.add_all([study, schema])
db_session.flush()
req.json_body = {'schema': schema.name, 'versions': [schema.id]}
self._call_fut(study, req)
assert schema in study.schemata
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_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_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_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_fail_if_not_published(self, req, db_session, check_csrf_token):
"""
It should fail if the schema is not published
"""
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'')
study = models.Study(name=u'somestudy',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
db_session.add_all([study, schema])
db_session.flush()
db_session.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_exclude_schema(self, req, db_session, check_csrf_token):
"""
It should exlude general forms used by the study (editing)
"""
from datetime import date
from webob.multidict import MultiDict
from occams_datastore import models as datastore
from occams_studies 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]))
db_session.add_all([x, y, study])
db_session.flush()
req.GET = MultiDict()
res = self._call_fut(study, req)
assert 1 == len(res['schemata'])
assert 'y' == res['schemata'][0]['name']
def test_edit_unique_name(self, req, db_session, check_csrf_token):
"""
It should allow the study to be able to change its unique name
"""
from datetime import date
from occams_studies import models
study = models.Study(name='some-study',
title=u'Some Study',
short_title=u'sstudy',
code=u'000',
consent_date=date.today())
db_session.add_all([study])
db_session.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_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_process_import(self, db_session):
from datetime import date
from occams_datastore import models as datastore
from occams_studies import models as studies
from occams_imports.views.codebook import process_import
attr_dict = {}
schema = datastore.Schema(name=u'test_name',
title=u'test_title',
publish_date=date.today())
study = studies.Study(name=u'test_site',
title=u'test_title',
short_title=u'tt',
code=u'tt1',
consent_date=date.today(),
is_randomized=False)
process_import(schema, attr_dict, study, db_session)
imported_study = (db_session.query(
studies.Study).filter(studies.Study.title == study.title)).one()
assert imported_study.title == study.title
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 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',
)
db_session.add(study)
db_session.add(patient)
def test_get_attributes_value_value(self):
"""Should return the value to be matched."""
from datetime import date
from occams_datastore import models as datastore
from occams_studies import models as studies
from occams_imports import models
study = studies.Study(name=u'UCSD',
title=u'UCSD',
short_title=u'UCSD',
code=u'001',
consent_date=date(2015, 01, 01))
schema = datastore.Schema(name=u'PatientRegistrationAndDemographics',
title=u'PatientRegistrationAndDemographics',
publish_date=date(2013, 02, 25),
attributes={
'birthyear':
datastore.Attribute(name=u'birthyear',
title=u'birthyear',
type=u'number',
order=0)
})
record = models.SiteData(schema=schema, study=study, data=SITEDATA)
source_variable = u'birthyear'
choices_mapping = []
target_value = self._call_fut(choices_mapping, record, source_variable,
schema)
assert target_value == '35'
def populate(self, db_session):
from datetime import date
from occams_datastore import models as datastore
from occams_studies import models as studies
drsc = studies.Study(name=u'drsc',
title=u'DRSC',
short_title=u'dr',
code=u'drs',
consent_date=date.today(),
is_randomized=False)
schema1 = datastore.Schema(
name=u'demographics',
title=u'demographics',
publish_date=u'2015-01-01',
attributes={
'question':
datastore.Attribute(name=u'question',
title=u'question',
type=u'choice',
order=0,
choices={
u'0':
datastore.Choice(name=u'0',
title=u'always',
order=0),
u'1':
datastore.Choice(name=u'1',
title=u'never',
order=1)
})
})
schema2 = datastore.Schema(
name=u'ucsd_demographics',
title=u'ucsd_demographics',
publish_date=u'2015-01-01',
attributes={
'ucsd_question':
datastore.Attribute(name=u'ucsd_question',
title=u'ucsd_question',
type=u'choice',
order=0,
choices={
u'0':
datastore.Choice(name=u'0',
title=u'always',
order=0),
u'1':
datastore.Choice(name=u'1',
title=u'never',
order=1)
})
})
drsc.schemata.add(schema1)
drsc.schemata.add(schema2)
db_session.add(drsc)
db_session.flush()
def populate(self, db_session):
from datetime import date
from occams_datastore import models as datastore
from occams_studies import models as studies
drsc = studies.Study(name=u'drsc',
title=u'DRSC',
short_title=u'dr',
code=u'drs',
consent_date=date.today(),
is_randomized=False)
schema1 = datastore.Schema(name=u'demographics',
title=u'demographics',
publish_date=u'2015-01-01',
attributes={
'myfield':
datastore.Attribute(name=u'myfield',
title=u'My Field',
type=u'string',
order=0),
'question':
datastore.Attribute(name=u'question',
title=u'question',
type=u'string',
order=0)
})
drsc.schemata.add(schema1)
db_session.add(drsc)
db_session.flush()
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_valid_upload(self, req, db_session, check_csrf_token):
"""
It should be able to upload a perfectly valid CSV
"""
import tempfile
import csv
from datetime import date
from occams_datastore import models as datastore
from occams_studies 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())
db_session.add_all([study])
db_session.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 = db_session.query(models.Stratum).one()
entity = db_session.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, 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')
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
