class ObservationFactSQLTestCase(CRCTestCase):
opts = connection_helper(CRCTestCase.test_conf_file)
def test_insert(self):
from i2b2model.data.i2b2observationfact import ObservationFactKey
print("{} records deleted".format(
ObservationFact.delete_upload_id(self.opts.tables,
self.opts.uploadid)))
ofk = ObservationFactKey(12345, 23456, 'provider',
datetime(2017, 5, 23, 11, 17))
I2B2Core.update_date = datetime(2017, 2, 19, 12, 33)
with self.sourcesystem_cd():
I2B2CoreWithUploadId.upload_id = self.opts.uploadid
I2B2Core.sourcesystem_cd = "FHIR R4"
obsf = ObservationFact(ofk, 'fhir:concept')
n_ins, n_upd = ObservationFact.add_or_update_records(
self.opts.tables, [obsf])
self.assertEqual((0, 1), (n_upd, n_ins))
obsf.instance_num = 2
I2B2Core.sourcesystem_cd = "FHIR R4z"
obsf2 = ObservationFact(ofk, 'fhir:concept')
obsf2.instance_num = 2
obsf2.modifier_cd = "fhir:modifier"
n_ins, n_upd = ObservationFact.add_or_update_records(
self.opts.tables, [obsf, obsf2])
self.assertEqual((0, 2), (n_upd, n_ins))
self.assertEqual(
3,
ObservationFact.delete_upload_id(self.opts.tables,
self.opts.uploadid))
class SchemesTestcase(unittest.TestCase):
opts = connection_helper(CRCTestCase.test_conf_file)
rec = Schemes("TestCodeSystem", "A test coding system", "Used for unit tests - you should never see this")
def setUp(self):
self.rec.del_record(self.opts.tables)
def tearDown(self):
self.rec.del_record(self.opts.tables)
def test_create(self):
self.assertEqual("c_key\tc_name\tc_description", heading(self.rec))
self.assertEqual('TestCodeSystem\tA test coding system\tUsed for unit tests - you should never see this',
row(self.rec))
self.assertEqual(OrderedDict([
('c_key', 'TestCodeSystem'),
('c_name', 'A test coding system'),
('c_description',
'Used for unit tests - you should never see this')]), as_dict(self.rec))
self.assertEqual((1, 0), self.rec.add_or_update_record(self.opts.tables))
self.assertEqual((0, 0), self.rec.add_or_update_record(self.opts.tables))
self.rec.c_description = "Used for tests"
self.assertEqual((0, 1), self.rec.add_or_update_record(self.opts.tables))
self.assertEqual(1, self.rec.del_record(self.opts.tables))
self.assertEqual(0, self.rec.del_record(self.opts.tables))
class PatientMappingSQLTestCase(unittest.TestCase):
opts = connection_helper(CRCTestCase.test_conf_file)
def test_insert(self):
from i2b2model.data.i2b2patientmapping import PatientMapping, PatientIDEStatus
PatientMapping.delete_upload_id(self.opts.tables, self.opts.uploadid)
I2B2CoreWithUploadId.upload_id = self.opts.uploadid
pm = PatientMapping(10000001, "12345", PatientIDEStatus.active, "http://hl7.org/fhir/", "fhir")
n_ins, n_upd = PatientMapping.add_or_update_records(self.opts.tables, [pm])
self.assertEqual((0, 1), (n_upd, n_ins))
n_ins, n_upd = PatientMapping.add_or_update_records(self.opts.tables, [pm])
self.assertEqual((0, 0), (n_upd, n_ins))
pm.project_id = "TEST"
pm2 = PatientMapping(10000001, "12346", PatientIDEStatus.active, "http://hl7.org/fhir/", "fhir")
n_ins, n_upd = PatientMapping.add_or_update_records(self.opts.tables, [pm, pm2])
self.assertEqual((0, 2), (n_upd, n_ins))
self.assertEqual(3, PatientMapping.delete_upload_id(self.opts.tables, self.opts.uploadid))
class EncounterMappingSQLTest(CRCTestCase):
opts = connection_helper(CRCTestCase.test_conf_file)
def test_insert(self):
from i2b2model.data.i2b2encountermapping import EncounterIDEStatus
I2B2Core.update_date = datetime(2017, 5, 25)
with self.sourcesystem_cd():
I2B2Core.sourcesystem_cd = self._sourcesystem_cd
I2B2CoreWithUploadId.upload_id = self._upload_id
# Add a brand new encounter mapping entry
EncounterMapping.delete_sourcesystem_cd(self.opts.tables,
self._sourcesystem_cd)
em = EncounterMapping("f001x", "http://hl7.org/fhir", "FHIR",
1005000017, "patient01x",
"http://hl7.org/fhir",
EncounterIDEStatus.active)
n_ins, n_upd = EncounterMapping.add_or_update_records(
self.opts.tables, [em])
self.assertEqual((0, 1), (n_upd, n_ins))
n_ins, n_upd = EncounterMapping.add_or_update_records(
self.opts.tables, [em])
self.assertEqual((0, 0), (n_upd, n_ins))
# Modify one entry and add a second
em.encounter_ide_status = EncounterIDEStatus.inactive
em2 = EncounterMapping("f002x", "http://hl7.org/fhir", "FHIR",
1005000018, "patient01x",
"http://hl7.org/fhir",
EncounterIDEStatus.active)
n_ins, n_upd = EncounterMapping.add_or_update_records(
self.opts.tables, [em, em2])
self.assertEqual((1, 1), (n_upd, n_ins))
self.assertEqual(
2,
EncounterMapping.delete_upload_id(self.opts.tables,
self._upload_id))
class PatientDimensionSQLTestCase(CRCTestCase):
opts = connection_helper(CRCTestCase.test_conf_file)
def test_insert(self):
from i2b2model.data.i2b2patientdimension import PatientDimension, VitalStatusCd
I2B2Core.update_date = datetime(2017, 5, 25)
with self.sourcesystem_cd():
I2B2Core.sourcesystem_cd = self._sourcesystem_cd
I2B2CoreWithUploadId.upload_id = self._upload_id
# Add a brand new encounter mapping entry
PatientDimension.delete_sourcesystem_cd(self.opts.tables,
self._sourcesystem_cd)
I2B2CoreWithUploadId.upload_id = self.opts.uploadid
x = PatientDimension(12345)
# Add a new patient dimension entry
n_ins, n_upd = x.add_or_update_records(self.opts.tables, [x])
self.assertEqual((0, 1), (n_upd, n_ins))
# Make sure nothing happens when we re-enter it
n_ins, n_upd = x.add_or_update_records(self.opts.tables, [x])
self.assertEqual((0, 0), (n_upd, n_ins))
# Change some properties on one and add another
x.birth_date = datetime(2001, 12, 17)
x.vital_status_cd = VitalStatusCd(VitalStatusCd.bd_day,
VitalStatusCd.dd_living)
y = PatientDimension(
12346,
VitalStatusCd(VitalStatusCd.bd_unknown,
VitalStatusCd.dd_unknown))
n_ins, n_upd = x.add_or_update_records(self.opts.tables, [x, y])
self.assertEqual((1, 1), (n_upd, n_ins))
self.assertEqual(2,
x.delete_upload_id(self.opts.tables, x.upload_id))
class VisitDimensionSQLTestCase(unittest.TestCase):
opts = connection_helper(CRCTestCase.test_conf_file)
def test_insert(self):
from i2b2model.data.i2b2visitdimension import VisitDimension, ActiveStatusCd
VisitDimension.delete_upload_id(self.opts.tables, self.opts.uploadid)
I2B2CoreWithUploadId.upload_id = self.opts.uploadid
x = VisitDimension(5000017, 10000017, ActiveStatusCd(ActiveStatusCd.sd_day, ActiveStatusCd.ed_year),
datetime(2007, 12, 9), datetime(2008, 1, 1))
n_ins, n_upd = x.add_or_update_records(self.opts.tables, [x])
self.assertEqual((0, 1), (n_upd, n_ins))
n_ins, n_upd = x.add_or_update_records(self.opts.tables, [x])
self.assertEqual((0, 0), (n_upd, n_ins))
x.end_date = datetime(2010, 2, 1)
x.active_status_cd_.endcode = ActiveStatusCd.ed_month
y = VisitDimension(5000018, 10000017, ActiveStatusCd(ActiveStatusCd.sd_day, ActiveStatusCd.ed_year),
datetime(2007, 12, 9), datetime(2008, 1, 1))
n_ins, n_upd = x.add_or_update_records(self.opts.tables, [x, y])
self.assertEqual((1, 1), (n_upd, n_ins))
self.assertEqual(2, x.delete_upload_id(self.opts.tables, x.upload_id))