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_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_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_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_references(self, req, db_session, check_csrf_token):
"""
It should update references
"""
from occams_studies import models
reftype1 = models.ReferenceType(name=u'foo', title=u'Foo')
reftype2 = models.ReferenceType(name=u'bar', title=u'Bar')
site_la = models.Site(name=u'la', title=u'LA')
patient = models.Patient(site=site_la, pid=u'12345')
patient.references = [
models.PatientReference(reference_type=reftype1,
reference_number=u'XYZ'),
models.PatientReference(reference_type=reftype2,
reference_number=u'ABC')
]
db_session.add_all([site_la, patient])
db_session.flush()
req.json_body = {
'site':
patient.site.id,
'references': [{
'reference_type': reftype1.id,
'reference_number': u'XYZ'
}, {
'reference_type': reftype1.id,
'reference_number': u'RST'
}]
}
self._call_fut(patient, req)
assert check_csrf_token.called
assert sorted([(reftype1.id, u'XYZ'), (reftype1.id, u'RST')]) == \
sorted([(r.reference_type.id, r.reference_number)
for r in patient.references])
def test_no_match(self, req, db_session):
from occams_studies import models
reftype = models.ReferenceType(name=u'medical_number',
title=u'Medical Number')
db_session.add(reftype)
req.GET = {'term': 'other'}
factory = models.ReferenceTypeFactory(req)
res = self._call_fut(factory, req)
assert len(res['reference_types']) == 0, \
'Reference types were found when none were expected'
def test_match(self, req, db_session):
from occams_studies import models
reftype = models.ReferenceType(name=u'medical_number',
title=u'Medical Number')
db_session.add(reftype)
req.GET = {'term': 'med'}
factory = models.ReferenceTypeFactory(req)
res = self._call_fut(factory, req)
assert len(res['reference_types']) == 1, \
'Incorrect number of results received'
def test_by_reference_number(self, req, db_session):
"""
It should be able to search by external ID
"""
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',
references=[
models.PatientReference(reference_type=models.ReferenceType(
name=u'ext', title=u'External ID'),
reference_number=u'05-01-0000-5')
])
db_session.add_all([site_la, patient])
db_session.flush()
req.GET = MultiDict([('query', u'05-01')])
res = self._call_fut(models.PatientFactory(req), req)
assert patient.pid == res['patients'][0]['pid']