def setup_site_labs(self):
"""Sets up the site_lab global."""
site_labs._registry = {}
site_labs.loaded = False
self.profile_aliquot_count = 3
# create aliquots and their relationship
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
# set up processes
process = Process(aliquot_type=b,
aliquot_count=self.profile_aliquot_count)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
processing_profile.add_processes(process)
# create a panel
self.panel = RequisitionPanel(name="panel",
processing_profile=processing_profile)
# lab profile
self.lab_profile = LabProfile(name="lab_profile",
requisition_model=self.requisition_model)
self.lab_profile.add_panel(self.panel)
# register with site
site_labs.register(lab_profile=self.lab_profile)
def test_assert_cannot_add_duplicate_process(self):
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
process = Process(aliquot_type=b, aliquot_count=3)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
processing_profile.add_processes(process)
self.assertRaises(ProcessingProfileAlreadyAdded,
processing_profile.add_processes, process)
def test_add_processing(self):
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
process = Process(aliquot_type=b, aliquot_count=3)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
processing_profile.add_processes(process)
panel = RequisitionPanel(name="Viral Load",
processing_profile=processing_profile)
lab_profile = LabProfile(
name="profile", requisition_model="edc_lab.subjectrequisition")
lab_profile.add_panel(panel)
def test_panel_adds_processing_profile(self):
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
process = Process(aliquot_type=b, aliquot_count=3)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
processing_profile.add_processes(process)
panel = RequisitionPanel(name="some panel",
processing_profile=processing_profile)
lab_profile = LabProfile(
name="profile", requisition_model="edc_lab.subjectrequisition")
lab_profile.add_panel(panel)
self.assertEqual(panel, lab_profile.panels.get(panel.name))
def setUp(self):
self.requisition_model = "edc_lab.subjectrequisition"
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
process = Process(aliquot_type=b, aliquot_count=3)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
processing_profile.add_processes(process)
panel = RequisitionPanel(name="Viral Load", processing_profile=processing_profile)
self.lab_profile = LabProfile(name="profile", requisition_model=self.requisition_model)
self.lab_profile.add_panel(panel)
site_labs._registry = {}
site_labs.loaded = False
site_labs.register(lab_profile=self.lab_profile)
def test_add_panel(self):
"""Assert same panel cannot be added twice."""
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
process = Process(aliquot_type=b, aliquot_count=3)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
processing_profile.add_processes(process)
panel = RequisitionPanel(name="Viral Load",
processing_profile=processing_profile)
lab_profile = LabProfile(
name="profile", requisition_model="edc_lab.subjectrequisition")
lab_profile.add_panel(panel)
self.assertRaises(PanelAlreadyRegistered, lab_profile.add_panel, panel)
def test_processing_ok(self):
"""Asserts CAN add process for aliquot B to a profile
for aliquot A since B can be derived from A.
"""
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
process = Process(aliquot_type=b, aliquot_count=3)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
try:
processing_profile.add_processes(process)
except ProcessingProfileInvalidDerivative:
self.fail(
"ProcessingProfileInvalidDerivative unexpectedly raised.")
def test_added_panel_knows_requisition_model(self):
"""Assert same panel cannot be added twice."""
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
process = Process(aliquot_type=b, aliquot_count=3)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
processing_profile.add_processes(process)
panel = RequisitionPanel(name="Viral Load",
processing_profile=processing_profile)
lab_profile = LabProfile(
name="profile", requisition_model="edc_lab.subjectrequisition")
lab_profile.add_panel(panel)
panel = lab_profile.panels.get("Viral Load")
self.assertEqual(panel.requisition_model, "edc_lab.subjectrequisition")
self.assertEqual(panel.requisition_model_cls, SubjectRequisition)
def get_panel_group():
a = AliquotType(name="aliquot_a", numeric_code="55", alpha_code="AA")
b = AliquotType(name="aliquot_b", numeric_code="66", alpha_code="BB")
a.add_derivatives(b)
process = Process(aliquot_type=b, aliquot_count=3)
processing_profile = ProcessingProfile(name="process", aliquot_type=a)
processing_profile.add_processes(process)
rft_panel = RequisitionPanel(
name="chemistry_rft",
verbose_name="Chemistry: Renal Function Tests",
abbreviation="RFT",
processing_profile=processing_profile,
utest_ids=["urea", "creatinine", "uric_acid", "egfr"],
)
lipids_panel = RequisitionPanel(
name="chemistry_lipids",
verbose_name="Chemistry: Lipids",
abbreviation="LIPIDS",
processing_profile=processing_profile,
utest_ids=["ldl", "hdl", "trig"],
)
lft_panel = RequisitionPanel(
name="chemistry_lft",
verbose_name="Chemistry: Liver Function Tests",
abbreviation="LFT",
processing_profile=processing_profile,
utest_ids=["ast", "alt", "alp", "amylase", "ggt", "albumin"],
)
return RequisitionPanelGroup(
lft_panel,
rft_panel,
lipids_panel,
name="chemistry",
verbose_name="Chemistry: LFT, RFT, Lipids",
reference_range_collection_name="default",
)