def test_iodi_location_investigator_duplicate(self):
""" Tests the IODI insertion of duplicate `LocationInvestigator` records
to ensure deduplication functions as intended.
"""
# Create a `Location` record as a fixture.
facility_id, _ = create_facility(dal=self.dal)
person_id, _ = create_person(dal=self.dal)
contact_id, _ = create_contact(dal=self.dal, person_id=person_id)
location_id, _ = create_location(
dal=self.dal,
facility_id=facility_id,
contact_primary_id=contact_id,
contact_backup_id=contact_id,
)
# Create an `Investigator` record as a fixture.
investigator_id, _ = create_investigator(
dal=self.dal,
person_id=person_id,
)
# Create additional `Investigator` record.
investigator_02_id, _ = create_investigator(
dal=self.dal,
person_id=person_id,
affiliation="NewAffiliation"
)
# IODI a new `LocationInvestigator` record.
obj_id = self.dal.iodi_location_investigator(
location_id=location_id,
investigator_id=investigator_id,
)
self.assertEqual(obj_id, 1)
# IODI an identical `Intervention` record.
obj_id = self.dal.iodi_location_investigator(
location_id=location_id,
investigator_id=investigator_id,
)
self.assertEqual(obj_id, 1)
# IODI a new `Intervention` record.
obj_id = self.dal.iodi_location_investigator(
location_id=location_id,
investigator_id=investigator_02_id,
)
self.assertEqual(obj_id, 3)
# IODI the same `Intervention` record as before.
obj_id = self.dal.iodi_location_investigator(
location_id=location_id,
investigator_id=investigator_02_id,
)
self.assertEqual(obj_id, 3)
def test_iodi_get_location_investigator(self):
""" Tests the insertion of a `LocationInvestigator` record via the
`iodi_location_investigator` method of the `DalClinicalTrials` class
and its retrieval via the `get` method.
"""
# Create a `Location` record as a fixture.
facility_id, _ = create_facility(dal=self.dal)
person_id, _ = create_person(dal=self.dal)
contact_id, _ = create_contact(dal=self.dal, person_id=person_id)
location_id, _ = create_location(
dal=self.dal,
facility_id=facility_id,
contact_primary_id=contact_id,
contact_backup_id=contact_id,
)
# Create an `Investigator` record as a fixture.
investigator_id, _ = create_investigator(
dal=self.dal,
person_id=person_id,
)
# IODI a new `LocationInvestigator` record.
obj_id = self.dal.iodi_location_investigator(
location_id=location_id,
investigator_id=investigator_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(
LocationInvestigator,
obj_id,
) # type: LocationInvestigator
# Assert that the different fields of the record match.
self.assertEqual(obj.location_investigator_id, 1)
self.assertEqual(obj.location_id, location_id)
self.assertEqual(obj.investigator_id, investigator_id)
def test_delete_location_investigator(self):
""" Tests the deletion of a `LocationInvestigator` record via the
`delete` method of the `DalClinicalTrials` class.
"""
# Create a `Location` record as a fixture.
facility_id, _ = create_facility(dal=self.dal)
person_id, _ = create_person(dal=self.dal)
contact_id, _ = create_contact(dal=self.dal, person_id=person_id)
location_id, _ = create_location(
dal=self.dal,
facility_id=facility_id,
contact_primary_id=contact_id,
contact_backup_id=contact_id,
)
# Create an `Investigator` record as a fixture.
investigator_id, _ = create_investigator(
dal=self.dal,
person_id=person_id,
)
# IODI a new `LocationInvestigator` record.
obj_id = self.dal.iodi_location_investigator(
location_id=location_id,
investigator_id=investigator_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(LocationInvestigator, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
LocationInvestigator,
obj_id,
) # type: LocationInvestigator
self.assertIsNone(obj)
def test_delete_reference(self):
""" Tests the deletion of a `Study` record via the `delete` method
of the `DalClinicalTrials` class.
"""
# Create fixtures.
person_01_id, _ = create_person(dal=self.dal, name_first="A")
person_02_id, _ = create_person(dal=self.dal, name_first="B")
contact_primary_id, _ = create_contact(
dal=self.dal,
person_id=person_01_id,
)
contact_backup_id, _ = create_contact(
dal=self.dal,
person_id=person_02_id,
)
oversight_info_id, _ = create_oversight_info(dal=self.dal)
expanded_access_info_id, _ = create_expanded_access_info(dal=self.dal)
study_design_info_id, _ = create_study_design_info(dal=self.dal)
enrollment_id, _ = create_enrollment(dal=self.dal)
eligibility_id, _ = create_eligibility(dal=self.dal)
study_dates_id, _ = create_study_dates(dal=self.dal)
responsible_party_id, _ = create_responsible_party(dal=self.dal)
patient_data_id, _ = create_patient_data(dal=self.dal)
# IODU a new `Study` record.
obj_id = self.dal.iodu_study(
org_study_id="org_study_id",
nct_id="nct_id",
brief_title="brief_title",
acronym="acronym",
official_title="official_title",
source="source",
oversight_info_id=oversight_info_id,
brief_summary="brief_summary",
detailed_description="detailed_description",
overall_status=OverallStatusType.ACTIVE_NOT,
last_known_status=OverallStatusType.APPROVED,
why_stopped="why_stopped",
start_date=datetime.date(2019, 1, 1),
completion_date=datetime.date(2019, 1, 1),
primary_completion_date=datetime.date(2019, 1, 1),
verification_date=datetime.date(2019, 1, 1),
phase=PhaseType.PHASE_1,
study_type=StudyType.EXPANDED,
expanded_access_info_id=expanded_access_info_id,
study_design_info_id=study_design_info_id,
target_duration="target_duration",
enrollment_id=enrollment_id,
biospec_retention=BiospecRetentionType.SAMPLES_W_DNA,
biospec_description="biospec_description",
eligibility_id=eligibility_id,
contact_primary_id=contact_primary_id,
contact_backup_id=contact_backup_id,
study_dates_id=study_dates_id,
responsible_party_id=responsible_party_id,
patient_data_id=patient_data_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(Study, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(Study, obj_id) # type: Study
self.assertIsNone(obj)
def test_iodu_get_study(self):
""" Tests the IODU insertion of a `Study` record via the
`iodu_study` method of the `DalClinicalTrials` class and its
retrieval via the `get` method.
"""
# Create fixtures.
person_01_id, _ = create_person(dal=self.dal, name_first="A")
person_02_id, _ = create_person(dal=self.dal, name_first="B")
contact_primary_id, _ = create_contact(
dal=self.dal,
person_id=person_01_id,
)
contact_backup_id, _ = create_contact(
dal=self.dal,
person_id=person_02_id,
)
oversight_info_id, _ = create_oversight_info(dal=self.dal)
expanded_access_info_id, _ = create_expanded_access_info(dal=self.dal)
study_design_info_id, _ = create_study_design_info(dal=self.dal)
enrollment_id, _ = create_enrollment(dal=self.dal)
eligibility_id, _ = create_eligibility(dal=self.dal)
study_dates_id, _ = create_study_dates(dal=self.dal)
responsible_party_id, _ = create_responsible_party(dal=self.dal)
patient_data_id, _ = create_patient_data(dal=self.dal)
# IODU a new `Study` record.
obj_id = self.dal.iodu_study(
org_study_id="org_study_id",
nct_id="nct_id",
brief_title="brief_title",
acronym="acronym",
official_title="official_title",
source="source",
oversight_info_id=oversight_info_id,
brief_summary="brief_summary",
detailed_description="detailed_description",
overall_status=OverallStatusType.ACTIVE_NOT,
last_known_status=OverallStatusType.APPROVED,
why_stopped="why_stopped",
start_date=datetime.date(2019, 1, 1),
completion_date=datetime.date(2019, 1, 1),
primary_completion_date=datetime.date(2019, 1, 1),
verification_date=datetime.date(2019, 1, 1),
phase=PhaseType.PHASE_1,
study_type=StudyType.EXPANDED,
expanded_access_info_id=expanded_access_info_id,
study_design_info_id=study_design_info_id,
target_duration="target_duration",
enrollment_id=enrollment_id,
biospec_retention=BiospecRetentionType.SAMPLES_W_DNA,
biospec_description="biospec_description",
eligibility_id=eligibility_id,
contact_primary_id=contact_primary_id,
contact_backup_id=contact_backup_id,
study_dates_id=study_dates_id,
responsible_party_id=responsible_party_id,
patient_data_id=patient_data_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(Study, obj_id) # type: Study
# Assert that the different fields of the record match.
self.assertEqual(obj.study_id, obj_id)
self.assertEqual(obj.org_study_id, "org_study_id")
self.assertEqual(obj.nct_id, "nct_id")
self.assertEqual(obj.brief_title, "brief_title")
self.assertEqual(obj.acronym, "acronym")
self.assertEqual(obj.official_title, "official_title")
self.assertEqual(obj.source, "source")
self.assertEqual(obj.oversight_info_id, oversight_info_id)
self.assertEqual(obj.brief_summary, "brief_summary")
self.assertEqual(obj.detailed_description, "detailed_description")
self.assertEqual(obj.overall_status, OverallStatusType.ACTIVE_NOT)
self.assertEqual(obj.last_known_status, OverallStatusType.APPROVED)
self.assertEqual(obj.why_stopped, "why_stopped")
self.assertEqual(obj.start_date, datetime.date(2019, 1, 1))
self.assertEqual(obj.completion_date, datetime.date(2019, 1, 1))
self.assertEqual(obj.primary_completion_date,
datetime.date(2019, 1, 1))
self.assertEqual(obj.verification_date, datetime.date(2019, 1, 1))
self.assertEqual(obj.phase, PhaseType.PHASE_1)
self.assertEqual(obj.study_type, StudyType.EXPANDED)
self.assertEqual(obj.expanded_access_info_id, expanded_access_info_id)
self.assertEqual(obj.study_design_info_id, study_design_info_id)
self.assertEqual(obj.target_duration, "target_duration")
self.assertEqual(obj.enrollment_id, enrollment_id)
self.assertEqual(
obj.biospec_retention,
BiospecRetentionType.SAMPLES_W_DNA,
)
self.assertEqual(obj.biospec_description, "biospec_description")
self.assertEqual(obj.eligibility_id, eligibility_id)
self.assertEqual(obj.contact_primary_id, contact_primary_id)
self.assertEqual(obj.contact_backup_id, contact_backup_id)
self.assertEqual(obj.study_dates_id, study_dates_id)
self.assertEqual(obj.responsible_party_id, responsible_party_id)
self.assertEqual(obj.patient_data_id, patient_data_id)
def test_iodu_study_duplicate(self):
""" Tests the IODU insertion of duplicate `Study` records to ensure
deduplication functions as intended.
"""
# Create fixtures.
person_01_id, _ = create_person(dal=self.dal, name_first="A")
person_02_id, _ = create_person(dal=self.dal, name_first="B")
contact_primary_id, _ = create_contact(
dal=self.dal,
person_id=person_01_id,
)
contact_backup_id, _ = create_contact(
dal=self.dal,
person_id=person_02_id,
)
oversight_info_id, _ = create_oversight_info(dal=self.dal)
expanded_access_info_id, _ = create_expanded_access_info(dal=self.dal)
study_design_info_id, _ = create_study_design_info(dal=self.dal)
enrollment_id, _ = create_enrollment(dal=self.dal)
eligibility_id, _ = create_eligibility(dal=self.dal)
study_dates_id, _ = create_study_dates(dal=self.dal)
responsible_party_id, _ = create_responsible_party(dal=self.dal)
patient_data_id, _ = create_patient_data(dal=self.dal)
# IODU a new `Study` record.
obj_id = self.dal.iodu_study(
org_study_id="org_study_id",
nct_id="nct_id",
brief_title="brief_title",
acronym="acronym",
official_title="official_title",
source="source",
oversight_info_id=oversight_info_id,
brief_summary="brief_summary",
detailed_description="detailed_description",
overall_status=OverallStatusType.ACTIVE_NOT,
last_known_status=OverallStatusType.APPROVED,
why_stopped="why_stopped",
start_date=datetime.date(2019, 1, 1),
completion_date=datetime.date(2019, 1, 1),
primary_completion_date=datetime.date(2019, 1, 1),
verification_date=datetime.date(2019, 1, 1),
phase=PhaseType.PHASE_1,
study_type=StudyType.EXPANDED,
expanded_access_info_id=expanded_access_info_id,
study_design_info_id=study_design_info_id,
target_duration="target_duration",
enrollment_id=enrollment_id,
biospec_retention=BiospecRetentionType.SAMPLES_W_DNA,
biospec_description="biospec_description",
eligibility_id=eligibility_id,
contact_primary_id=contact_primary_id,
contact_backup_id=contact_backup_id,
study_dates_id=study_dates_id,
responsible_party_id=responsible_party_id,
patient_data_id=patient_data_id,
)
self.assertEqual(obj_id, 1)
# IODU the same `Study` record.
obj_id = self.dal.iodu_study(
org_study_id="org_study_id",
nct_id="nct_id",
brief_title="brief_title",
acronym="acronym",
official_title="official_title",
source="source",
oversight_info_id=oversight_info_id,
brief_summary="brief_summary",
detailed_description="detailed_description",
overall_status=OverallStatusType.ACTIVE_NOT,
last_known_status=OverallStatusType.APPROVED,
why_stopped="why_stopped",
start_date=datetime.date(2019, 1, 1),
completion_date=datetime.date(2019, 1, 1),
primary_completion_date=datetime.date(2019, 1, 1),
verification_date=datetime.date(2019, 1, 1),
phase=PhaseType.PHASE_1,
study_type=StudyType.EXPANDED,
expanded_access_info_id=expanded_access_info_id,
study_design_info_id=study_design_info_id,
target_duration="target_duration",
enrollment_id=enrollment_id,
biospec_retention=BiospecRetentionType.SAMPLES_W_DNA,
biospec_description="biospec_description",
eligibility_id=eligibility_id,
contact_primary_id=contact_primary_id,
contact_backup_id=contact_backup_id,
study_dates_id=study_dates_id,
responsible_party_id=responsible_party_id,
patient_data_id=patient_data_id,
)
self.assertEqual(obj_id, 1)
# IODU the same `Study` record with a changed `brief_title` field
# which should trigger an update on the existing record.
obj_id = self.dal.iodu_study(
org_study_id="org_study_id",
nct_id="nct_id",
brief_title="new_brief_title",
acronym="acronym",
official_title="official_title",
source="source",
oversight_info_id=oversight_info_id,
brief_summary="brief_summary",
detailed_description="detailed_description",
overall_status=OverallStatusType.ACTIVE_NOT,
last_known_status=OverallStatusType.APPROVED,
why_stopped="why_stopped",
start_date=datetime.date(2019, 1, 1),
completion_date=datetime.date(2019, 1, 1),
primary_completion_date=datetime.date(2019, 1, 1),
verification_date=datetime.date(2019, 1, 1),
phase=PhaseType.PHASE_1,
study_type=StudyType.EXPANDED,
expanded_access_info_id=expanded_access_info_id,
study_design_info_id=study_design_info_id,
target_duration="target_duration",
enrollment_id=enrollment_id,
biospec_retention=BiospecRetentionType.SAMPLES_W_DNA,
biospec_description="biospec_description",
eligibility_id=eligibility_id,
contact_primary_id=contact_primary_id,
contact_backup_id=contact_backup_id,
study_dates_id=study_dates_id,
responsible_party_id=responsible_party_id,
patient_data_id=patient_data_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(Study, obj_id) # type: Study
self.assertEqual(obj.brief_title, "new_brief_title")
# IODU a new `Study` record.
obj_id = self.dal.iodu_study(
org_study_id="org_study_id",
nct_id="new_nct_id",
brief_title="brief_title",
acronym="acronym",
official_title="official_title",
source="source",
oversight_info_id=oversight_info_id,
brief_summary="brief_summary",
detailed_description="detailed_description",
overall_status=OverallStatusType.ACTIVE_NOT,
last_known_status=OverallStatusType.APPROVED,
why_stopped="why_stopped",
start_date=datetime.date(2019, 1, 1),
completion_date=datetime.date(2019, 1, 1),
primary_completion_date=datetime.date(2019, 1, 1),
verification_date=datetime.date(2019, 1, 1),
phase=PhaseType.PHASE_1,
study_type=StudyType.EXPANDED,
expanded_access_info_id=expanded_access_info_id,
study_design_info_id=study_design_info_id,
target_duration="target_duration",
enrollment_id=enrollment_id,
biospec_retention=BiospecRetentionType.SAMPLES_W_DNA,
biospec_description="biospec_description",
eligibility_id=eligibility_id,
contact_primary_id=contact_primary_id,
contact_backup_id=contact_backup_id,
study_dates_id=study_dates_id,
responsible_party_id=responsible_party_id,
patient_data_id=patient_data_id,
)
self.assertEqual(obj_id, 4)
# IODU the same `Descriptor` record as before.
obj_id = self.dal.iodu_study(
org_study_id="org_study_id",
nct_id="new_nct_id",
brief_title="brief_title",
acronym="acronym",
official_title="official_title",
source="source",
oversight_info_id=oversight_info_id,
brief_summary="brief_summary",
detailed_description="detailed_description",
overall_status=OverallStatusType.ACTIVE_NOT,
last_known_status=OverallStatusType.APPROVED,
why_stopped="why_stopped",
start_date=datetime.date(2019, 1, 1),
completion_date=datetime.date(2019, 1, 1),
primary_completion_date=datetime.date(2019, 1, 1),
verification_date=datetime.date(2019, 1, 1),
phase=PhaseType.PHASE_1,
study_type=StudyType.EXPANDED,
expanded_access_info_id=expanded_access_info_id,
study_design_info_id=study_design_info_id,
target_duration="target_duration",
enrollment_id=enrollment_id,
biospec_retention=BiospecRetentionType.SAMPLES_W_DNA,
biospec_description="biospec_description",
eligibility_id=eligibility_id,
contact_primary_id=contact_primary_id,
contact_backup_id=contact_backup_id,
study_dates_id=study_dates_id,
responsible_party_id=responsible_party_id,
patient_data_id=patient_data_id,
)
self.assertEqual(obj_id, 4)