def test_what_we_want(self):
clear(I2B2Core)
I2B2Core.download_date = lambda: I2B2Core.update_date
I2B2Core.import_date = lambda: I2B2Core.update_date
I2B2Core.sourcesystem_cd = "Biggie"
self.assertEqual(
OrderedDict([('update_date', None), ('download_date', None),
('import_date', None),
('sourcesystem_cd', 'Biggie')]),
I2B2Core()._freeze())
I2B2Core.update_date = datetime(2017, 9, 27)
self.assertEqual(
OrderedDict([('update_date', datetime(2017, 9, 27, 0, 0)),
('download_date', datetime(2017, 9, 27, 0, 0)),
('import_date', datetime(2017, 9, 27, 0, 0)),
('sourcesystem_cd', 'Biggie')]),
I2B2Core()._freeze())
# Clear doesn't affect class functions
clear(I2B2Core)
self.assertEqual(
OrderedDict([('update_date', None), ('download_date', None),
('import_date', None),
('sourcesystem_cd', "Unspecified")]),
I2B2Core()._freeze())
I2B2Core.update_date = datetime(2003, 1, 4)
self.assertEqual(
OrderedDict([('update_date', datetime(2003, 1, 4)),
('download_date', None), ('import_date', None),
('sourcesystem_cd', "Unspecified")]),
I2B2Core()._freeze())
def test_extension(self):
class C1(DynProps):
""" Ordered list of properties in the i2b2 core model"""
sourcesystem_cd: Global[Optional[str]]
x: Global[str]
self.assertEqual("\t", row(C1()))
with self.assertRaises(AttributeError):
class Extension0(C1):
sourcesystem_cd = "SS2"
foo: Local[str]
_ = Extension0 # Prevent lint check
class Extension(C1):
foo: Local[str] = "Apples"
_ = Extension() # Prevent lint check
C1.sourcesystem_cd = "SS3"
self.assertEqual("SS3\t", row(C1()))
clear(C1)
self.assertEqual("\t", row(C1()))
def setUp(self):
self.assertIsNotNone(self.test_prefix,
"CRCTestCase.test_prefix must be set")
self.assertIsNotNone(
self.test_conf_file,
"CRCTestCase.test_conf_file location must be set")
clear(I2B2Core)
clear(I2B2CoreWithUploadId)
def test_settings(self):
clear(I2B2Core)
I2B2Core.sourcesystem_cd = "abcd"
I2B2Core.update_date = datetime(2014, 7, 31)
I2B2Core.download_date = datetime.now
rtn = I2B2Core()
rtnf = as_dict(rtn)
self.assertEqual(str(rtnf['update_date']), '2014-07-31 00:00:00')
self.assertAlmostNow(rtn.download_date)
self.assertEqual(rtn.update_date, rtn.import_date)
self.assertEqual(rtnf['sourcesystem_cd'], 'abcd')
self.assertEqual(
'update_date\tdownload_date\timport_date\tsourcesystem_cd',
heading(rtn))
def test_str(self):
clear(I2B2CoreUploadIdFirst)
x = I2B2Core()
y = I2B2CoreUploadIdFirst()
I2B2Core.sourcesystem_cd = "SSCODE"
I2B2Core.import_date = datetime(2017, 5, 31)
I2B2Core.download_date = datetime(2017, 5, 30, 11, 33, 20)
I2B2Core.update_date = datetime(2017, 5, 29, 8, 33, 20)
self.assertEqual(
"I2B2Core(update_date:'2017-05-29 08:33:20', download_date:'2017-05-30 "
"11:33:20', import_date:'2017-05-31 00:00:00', sourcesystem_cd:'SSCODE')",
str(x))
self.assertEqual(
"I2B2CoreUploadIdFirst(upload_id:'None', update_date:'2017-05-29 08:33:20', "
"download_date:'2017-05-30 11:33:20', import_date:'2017-05-31 00:00:00', "
"sourcesystem_cd:'SSCODE')", str(y))
def test_freeze(self):
x = I2B2Core()
y = I2B2CoreUploadIdFirst()
I2B2Core.sourcesystem_cd = "SSCODE"
I2B2Core.import_date = datetime(2017, 5, 31)
I2B2Core.download_date = datetime(2017, 5, 30, 11, 33, 20)
I2B2Core.update_date = datetime(2017, 5, 29, 8, 33, 20)
self.assertEqual(
OrderedDict([('update_date', datetime(2017, 5, 29, 8, 33, 20)),
('download_date', datetime(2017, 5, 30, 11, 33, 20)),
('import_date', datetime(2017, 5, 31, 0, 0)),
('sourcesystem_cd', 'SSCODE')]), x._freeze())
self.assertEqual(
OrderedDict([('upload_id', None),
('update_date', datetime(2017, 5, 29, 8, 33, 20)),
('download_date', datetime(2017, 5, 30, 11, 33, 20)),
('import_date', datetime(2017, 5, 31, 0, 0)),
('sourcesystem_cd', 'SSCODE')]), y._freeze())
I2B2CoreUploadIdFirst.upload_id = 12345
self.assertEqual(
OrderedDict([('update_date', datetime(2017, 5, 29, 8, 33, 20)),
('download_date', datetime(2017, 5, 30, 11, 33, 20)),
('import_date', datetime(2017, 5, 31, 0, 0)),
('sourcesystem_cd', 'SSCODE')]), x._freeze())
self.assertEqual(
OrderedDict([('upload_id', 12345),
('update_date', datetime(2017, 5, 29, 8, 33, 20)),
('download_date', datetime(2017, 5, 30, 11, 33, 20)),
('import_date', datetime(2017, 5, 31, 0, 0)),
('sourcesystem_cd', 'SSCODE')]), y._freeze())
clear(I2B2Core)
self.assertEqual(
OrderedDict([('update_date', None), ('download_date', None),
('import_date', None),
('sourcesystem_cd', ''
"Unspecified"
'')]), x._freeze())
self.assertEqual(
OrderedDict([('upload_id', 12345), ('update_date', None),
('download_date', None), ('import_date', None),
('sourcesystem_cd', ''
"Unspecified"
'')]), y._freeze())
clear(I2B2CoreUploadIdFirst)
def test_defaults(self):
rtn = I2B2Core()
rtnf = as_dict(rtn)
self.assertAlmostNow(rtn.update_date)
self.assertDatesAlmostEqual(rtn.update_date, str(rtnf['update_date']))
self.assertAlmostNow(rtn.download_date)
self.assertDatesAlmostEqual(rtn.download_date,
str(rtnf['download_date']))
self.assertAlmostNow(rtn.import_date)
self.assertDatesAlmostEqual(rtn.import_date, str(rtnf['import_date']))
self.assertEqual('Unspecified', rtn.sourcesystem_cd)
self.assertEqual(rtn.sourcesystem_cd, rtnf['sourcesystem_cd'])
self.assertEqual(
['update_date', 'download_date', 'import_date', 'sourcesystem_cd'],
list(rtnf.keys()))
rtn = I2B2Core()
I2B2Core.download_date = datetime(2009, 1, 1, 12, 0)
I2B2Core.sourcesystem_cd = "MASTER"
I2B2Core.import_date = datetime(2011, 1, 1, 12, 0)
I2B2Core.update_date = datetime.now() + timedelta(hours=2)
self.assertEqual('2009-01-01 12:00:00', str(rtn.download_date))
self.assertEqual('2011-01-01 12:00:00', str(rtn.import_date))
self.assertEqual('MASTER', rtn.sourcesystem_cd)
self.assertDatesAlmostEqual(rtn.update_date,
str(datetime.now() + timedelta(hours=2)))
clear(I2B2Core)
I2B2CoreWithUploadId.upload_id = 1777439
rtn = I2B2CoreWithUploadId()
if rtn.sourcesystem_cd != 'Unspecified':
print("Caught it")
self.assertEqual('Unspecified', rtn.sourcesystem_cd)
self.assertEqual(1777439, rtn.upload_id)
self.assertEqual(
'update_date\tdownload_date\timport_date\tsourcesystem_cd\tupload_id',
heading(rtn))
rtn = I2B2Core()
with self.assertRaises(AttributeError):
_ = rtn.upload_id
def test_repr(self):
clear(I2B2CoreUploadIdFirst)
x = I2B2Core()
y = I2B2CoreUploadIdFirst()
I2B2Core.sourcesystem_cd = "SSCODE"
I2B2Core.import_date = datetime(2017, 5, 31)
I2B2Core.download_date = datetime(2017, 5, 30, 11, 33, 20)
I2B2Core.update_date = datetime(2017, 5, 29, 8, 33, 20)
self.assertEqual(
'2017-05-29 08:33:20\t2017-05-30 11:33:20\t2017-05-31 00:00:00\tSSCODE',
row(x))
self.assertEqual(
'\t2017-05-29 08:33:20\t2017-05-30 11:33:20\t2017-05-31 00:00:00\tSSCODE',
row(y))
I2B2CoreUploadIdFirst.upload_id = 12345
self.assertEqual(
'2017-05-29 08:33:20\t2017-05-30 11:33:20\t2017-05-31 00:00:00\tSSCODE',
row(x))
self.assertEqual(
'12345\t2017-05-29 08:33:20\t2017-05-30 11:33:20\t2017-05-31 00:00:00\tSSCODE',
row(y))
I2B2Core._separator = ','
self.assertEqual(
'2017-05-29 08:33:20,2017-05-30 11:33:20,2017-05-31 00:00:00,SSCODE',
row(x))
self.assertEqual(
'12345,2017-05-29 08:33:20,2017-05-30 11:33:20,2017-05-31 00:00:00,SSCODE',
row(y))
clear(I2B2Core)
self.assertEqual(',,,Unspecified', row(x))
self.assertEqual('12345,,,,Unspecified', row(y))
clear(I2B2CoreUploadIdFirst)
I2B2Core._separator = '\t'
def test_common_elements(self):
""" Test the i2b2 core elements and demonstrate that they can't be overridden on an individual basis.
These elements are:
sourcesystem_cd = None
update_date = None
download_date = None
import_date = None
"""
from i2b2model.data.i2b2patientdimension import PatientDimension
PatientDimension._clear()
clear(I2B2CoreWithUploadId)
pd = PatientDimension(111, VitalStatusCd('U', 'D'))
I2B2Core.sourcesystem_cd = "abc"
self.assertEqual("abc", pd.sourcesystem_cd)
I2B2Core.update_date = datetime(2014, 7, 31)
self.assertEqual(datetime(2014, 7, 31), pd.update_date)
self.assertEqual(datetime(2014, 7, 31), pd.download_date)
self.assertEqual(datetime(2014, 7, 31), pd.import_date)
I2B2Core.download_date = datetime(2014, 7, 30)
I2B2Core.import_date = datetime(2014, 7, 29)
I2B2CoreWithUploadId.upload_id = 17
self.assertEqual(datetime(2014, 7, 31), pd.update_date)
self.assertEqual(datetime(2014, 7, 30), pd.download_date)
self.assertEqual(datetime(2014, 7, 29), pd.import_date)
self.assertEqual(17, pd.upload_id)
PatientDimension._clear()
self.assertEqual("abc", pd.sourcesystem_cd)
clear(I2B2Core)
self.assertEqual("Unspecified", pd.sourcesystem_cd)
def test_basics(self):
from i2b2model.metadata.i2b2conceptdimension import ConceptDimension
clear(ConceptDimension)
I2B2Core.download_date = datetime(2017, 5, 25)
I2B2Core.sourcesystem_cd = "TEST_SS"
I2B2Core.import_date = datetime(2017, 5, 25)
cd = ConceptDimension('TEST', 'root', 'Root test concept',
['L1', 'L2', 'root'], '\\TEST\\')
self.assertAlmostNow(cd.update_date)
I2B2Core.update_date = datetime(2001, 12, 1)
expected = OrderedDict([('concept_path', '\\TEST\\L1\\L2\\root\\'),
('concept_cd', 'TEST:root'),
('name_char', 'TEST Root test concept'),
('concept_blob', ''),
('update_date', datetime(2001, 12, 1, 0, 0)),
('download_date', datetime(2017, 5, 25, 0, 0)),
('import_date', datetime(2017, 5, 25, 0, 0)),
('sourcesystem_cd', 'TEST_SS'),
('upload_id', None)])
self.assertEqual(expected, as_dict(cd))
# Note - balance is actually a modifier. This is strictly an example
cd = ConceptDimension('TEST', 'root', 'Root balance test concept',
['L1', 'L2', 'balance'], '\\TEST\\')
expected = OrderedDict([
('concept_path', '\\TEST\\L1\\L2\\balance\\root\\'),
('concept_cd', 'TEST:root'),
('name_char', 'TEST Root balance test concept'),
('concept_blob', ''), ('update_date', datetime(2001, 12, 1, 0, 0)),
('download_date', datetime(2017, 5, 25, 0, 0)),
('import_date', datetime(2017, 5, 25, 0, 0)),
('sourcesystem_cd', 'TEST_SS'), ('upload_id', None)
])
self.assertEqual(expected, as_dict(cd))
def tearDown(self):
clear(I2B2Core)
def setUp(self):
clear(I2B2Core)
def tearDown(self):
# if getattr(self, "_sourcesystem_cd", None):
# remove_facts(f"--conf {self.test_conf_file} -ss {self._sourcesystem_cd}".split())
clear(I2B2Core)
clear(I2B2CoreWithUploadId)
def tearDown(self):
clear(I2B2Core)
clear(I2B2CoreWithUploadId)
def setUp(self):
clear(I2B2Core)
clear(I2B2CoreWithUploadId)
def test_attributes(self):
cwi_instance = I2B2CoreUploadIdFirst()
core_instance = I2B2Core()
# Cannot set property on the instance level
with self.assertRaises(ValueError):
core_instance.sourcesystem_cd = "test"
# Cannot access a properties' internal form on instance level
with self.assertRaises(ValueError):
core_instance._sourcesystem_cd = "test"
# Or the class level
with self.assertRaises(ValueError):
I2B2Core._sourcesystem_cd = "test"
# Properties can be set on the class level
I2B2Core.sourcesystem_cd = "test"
# Properties are visible at the instance level
self.assertEqual("test", core_instance.sourcesystem_cd)
# Properties are visible at the class level
self.assertEqual(core_instance.sourcesystem_cd,
I2B2Core.sourcesystem_cd)
# Properties are visible to subclasses
self.assertEqual(core_instance.sourcesystem_cd,
I2B2CoreUploadIdFirst.sourcesystem_cd)
self.assertEqual(core_instance.sourcesystem_cd,
cwi_instance.sourcesystem_cd)
# Global Properties CANNOT be set at the inherited class level
with self.assertRaises(ValueError):
I2B2CoreUploadIdFirst.sourcesystem_cd = "test2"
I2B2Core.sourcesystem_cd = "test3"
# And settings are visible on the instance
self.assertEqual("test3", core_instance.sourcesystem_cd)
# ... inherited instance
self.assertEqual(core_instance.sourcesystem_cd,
cwi_instance.sourcesystem_cd)
# ... class ...
self.assertEqual(core_instance.sourcesystem_cd,
I2B2CoreUploadIdFirst.sourcesystem_cd)
# ... and superclass level
self.assertEqual(core_instance.sourcesystem_cd,
I2B2Core.sourcesystem_cd)
# Subclass properties cannot be set at the instance level
with self.assertRaises(ValueError):
cwi_instance.upload_id = 117
# Only the class level
I2B2CoreUploadIdFirst.upload_id = 118
# Subclass properties are not visible to superclass instances
with self.assertRaises(AttributeError):
_ = core_instance.upload_id
# ... or the superclasses
with self.assertRaises(AttributeError):
_ = I2B2Core.upload_id
# But are visible at the subclass instance level
self.assertEqual(118, cwi_instance.upload_id)
# And class level
self.assertEqual(cwi_instance.upload_id,
I2B2CoreUploadIdFirst.upload_id)
# Clear covers base class but not inherited elements
clear(I2B2Core)
self.assertEqual("Unspecified", core_instance.sourcesystem_cd)
self.assertEqual("Unspecified", cwi_instance.sourcesystem_cd)
self.assertEqual(118, cwi_instance.upload_id)
# Clear of subclass covers superclass as well
I2B2Core.sourcesystem_cd = "test3"
clear(I2B2Core)
self.assertEqual("Unspecified", core_instance.sourcesystem_cd)
self.assertEqual("Unspecified", cwi_instance.sourcesystem_cd)
self.assertEqual(118, cwi_instance.upload_id)
clear(I2B2CoreUploadIdFirst)
self.assertIsNone(cwi_instance.upload_id)