def test_iodu_get_study_sponsor(self):
""" Tests the insertion of a `StudySponsor` record via the
`iodu_study_sponsor` method of the `DalClinicalTrials` class and its
retrieval via the get` method.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
sponsor_id, _ = create_sponsor(dal=self.dal)
# IODU a new `StudySponsor` record.
obj_id = self.dal.iodu_study_sponsor(
study_id=study_id,
sponsor_id=sponsor_id,
sponsor_type=SponsorType.COLLABORATOR,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(StudySponsor, obj_id) # type: StudySponsor
# Assert that the different fields of the record match.
self.assertEqual(obj.study_sponsor_id, 1)
self.assertEqual(obj.study_id, study_id)
self.assertEqual(obj.sponsor_id, sponsor_id)
self.assertEqual(obj.sponsor_type, SponsorType.COLLABORATOR)
def test_iodu_get_study_outcome(self):
""" Tests the insertion of a `StudyOutcome` record via the
`iodu_study_outcome` method of the `DalClinicalTrials` class and its
retrieval via the get` method.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
protocol_outcome_id, _ = create_protocol_outcome(dal=self.dal)
# IODU a new `StudyOutcome` record.
obj_id = self.dal.iodu_study_outcome(
study_id=study_id,
protocol_outcome_id=protocol_outcome_id,
outcome_type=OutcomeType.PRIMARY,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(StudyOutcome, obj_id) # type: StudyOutcome
# Assert that the different fields of the record match.
self.assertEqual(obj.study_outcome_id, 1)
self.assertEqual(obj.study_id, study_id)
self.assertEqual(obj.protocol_outcome_id, protocol_outcome_id)
self.assertEqual(obj.outcome_type, OutcomeType.PRIMARY)
def test_iodu_get_study_facility(self):
""" Tests the insertion of a `StudyFacility` record via the
`iodu_study_facility` method of the `DalClinicalTrials` class and its
retrieval via the get` method.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
facility_id, _ = create_facility(dal=self.dal)
# IODU a new `StudyFacility` record.
obj_id = self.dal.iodu_study_facility(
study_id=study_id,
facility_id=facility_id,
facility_canonical_id=None,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(StudyFacility, obj_id) # type: StudyFacility
# Assert that the different fields of the record match.
self.assertEqual(obj.study_facility_id, 1)
self.assertEqual(obj.study_id, study_id)
self.assertEqual(obj.facility_id, facility_id)
self.assertEqual(obj.facility_canonical_id, None)
def test_delete_study_sponsor(self):
""" Tests the deletion of a `StudySponsor` record via the `delete`
method of the `DalClinicalTrials` class.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
sponsor_id, _ = create_sponsor(dal=self.dal)
# IODU a new `StudySponsor` record.
obj_id = self.dal.iodu_study_sponsor(
study_id=study_id,
sponsor_id=sponsor_id,
sponsor_type=SponsorType.COLLABORATOR,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(StudySponsor, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(StudySponsor, obj_id) # type: StudySponsor
self.assertIsNone(obj)
def test_iodu_get_study_descriptor(self):
""" Tests the insertion of a `StudyDescriptor` record via the
`iodu_study_descriptor` method of the `DalClinicalTrials` class and
its retrieval via the get` method.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
descriptor_id, _ = create_descriptor(dal=self.dal_mesh)
# IODU a new `StudyDescriptor` record.
obj_id = self.dal.iodu_study_descriptor(
study_id=study_id,
descriptor_id=descriptor_id,
study_descriptor_type=MeshTermType.CONDITION,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(StudyDescriptor, obj_id) # type: StudyDescriptor
# Assert that the different fields of the record match.
self.assertEqual(obj.study_descriptor_id, 1)
self.assertEqual(obj.study_id, study_id)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.study_descriptor_type, MeshTermType.CONDITION)
def test_delete_study_facility(self):
""" Tests the deletion of a `StudyFacility` record via the `delete`
method of the `DalClinicalTrials` class.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
facility_id, _ = create_facility(dal=self.dal)
# IODU a new `StudyFacility` record.
obj_id = self.dal.iodu_study_facility(
study_id=study_id,
facility_id=facility_id,
facility_canonical_id=None,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(StudyFacility, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(StudyFacility, obj_id) # type: StudyFacility
self.assertIsNone(obj)
def test_delete_study_investigator(self):
""" Tests the deletion of a `StudyInvestigator` record via the `delete`
method of the `DalClinicalTrials` class.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
investigator_id, _ = create_investigator(dal=self.dal)
# IODI a new `StudyInvestigator` record.
obj_id = self.dal.iodi_study_investigator(
study_id=study_id,
investigator_id=investigator_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(StudyInvestigator, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(StudyInvestigator,
obj_id) # type: StudyInvestigator
self.assertIsNone(obj)
def test_delete_study_descriptor(self):
""" Tests the deletion of a `StudyDescriptor` record via the `delete`
method of the `DalClinicalTrials` class.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
descriptor_id, _ = create_descriptor(dal=self.dal_mesh)
# IODU a new `StudyDescriptor` record.
obj_id = self.dal.iodu_study_descriptor(
study_id=study_id,
descriptor_id=descriptor_id,
study_descriptor_type=MeshTermType.CONDITION,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(StudyDescriptor, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(StudyDescriptor, obj_id) # type: StudyDescriptor
self.assertIsNone(obj)
def test_delete_study_outcome(self):
""" Tests the deletion of a `StudyOutcome` record via the `delete`
method of the `DalClinicalTrials` class.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
protocol_outcome_id, _ = create_protocol_outcome(dal=self.dal)
# IODU a new `StudyOutcome` record.
obj_id = self.dal.iodu_study_outcome(
study_id=study_id,
protocol_outcome_id=protocol_outcome_id,
outcome_type=OutcomeType.PRIMARY,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(StudyOutcome, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(StudyOutcome, obj_id) # type: StudyOutcome
self.assertIsNone(obj)
def test_iodi_get_study_keyword(self):
""" Tests the insertion of a `StudyKeyword` record via the
`iodi_study_keyword` method of the `DalClinicalTrials` class and its
retrieval via the get` method.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
keyword_id, _ = create_keyword(dal=self.dal)
# IODI a new `StudyKeyword` record.
obj_id = self.dal.iodi_study_keyword(
study_id=study_id,
keyword_id=keyword_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(StudyKeyword, obj_id) # type: StudyKeyword
# Assert that the different fields of the record match.
self.assertEqual(obj.study_keyword_id, 1)
self.assertEqual(obj.study_id, study_id)
self.assertEqual(obj.keyword_id, keyword_id)
def test_iodu_study_descriptor_duplicate(self):
""" Tests the IODU insertion of duplicate `StudyDescriptor` records to
ensure deduplication functions as intended.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
descriptor_id, _ = create_descriptor(dal=self.dal_mesh)
descriptor_02_id, _ = create_descriptor(
dal=self.dal_mesh,
ui="new_ui",
name="new_name",
)
# IODU a new `StudyDescriptor` record.
obj_id = self.dal.iodu_study_descriptor(
study_id=study_id,
descriptor_id=descriptor_id,
study_descriptor_type=MeshTermType.CONDITION,
)
# The PK should be `1` as this is the first record.
self.assertEqual(obj_id, 1)
# IODU the same `StudyDescriptor` record as before.
obj_id = self.dal.iodu_study_descriptor(
study_id=study_id,
descriptor_id=descriptor_id,
study_descriptor_type=MeshTermType.CONDITION,
)
# The PK should still be `1` as the record was identical thus no
# insertion should've occured.
self.assertEqual(obj_id, 1)
# IODU a new `StudyDescriptor` record.
obj_id = self.dal.iodu_study_descriptor(
study_id=study_id,
descriptor_id=descriptor_02_id,
study_descriptor_type=MeshTermType.CONDITION,
)
# The PK should be `3` as the previous failed INSERT will have
# incremented the PK by 1.
self.assertEqual(obj_id, 3)
# IODU the same `StudyDescriptor` record as before.
obj_id = self.dal.iodu_study_descriptor(
study_id=study_id,
descriptor_id=descriptor_02_id,
study_descriptor_type=MeshTermType.CONDITION,
)
# The PK should still be `3` as the record is identical to the one
# before.
self.assertEqual(obj_id, 3)
def test_iodi_study_location_duplicate(self):
""" Tests the IODI insertion of duplicate `StudyLocation` records
to ensure deduplication functions as intended.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
location_id, _ = create_location(dal=self.dal)
facility_id, _ = create_facility(dal=self.dal, name="new_facility")
location_02_id, _ = create_location(
dal=self.dal,
facility_id=facility_id,
)
# IODI a new `StudyLocation` record.
obj_id = self.dal.iodi_study_location(
study_id=study_id,
location_id=location_id,
)
# The PK should be `1` as this is the first record.
self.assertEqual(obj_id, 1)
# IODI the same `StudyLocation` record as before.
obj_id = self.dal.iodi_study_location(
study_id=study_id,
location_id=location_id,
)
# The PK should still be `1` as the record was identical thus no
# insertion should've occured.
self.assertEqual(obj_id, 1)
# IODI a new `StudyLocation` record.
obj_id = self.dal.iodi_study_location(
study_id=study_id,
location_id=location_02_id,
)
# The PK should be `3` as the previous failed INSERT will have
# incremented the PK by 1.
self.assertEqual(obj_id, 3)
# IODU the same `StudyLocation` record as before.
obj_id = self.dal.iodi_study_location(
study_id=study_id,
location_id=location_02_id,
)
# The PK should still be `3` as the record is identical to the one
# before.
self.assertEqual(obj_id, 3)
def test_iodi_study_investigator_duplicate(self):
""" Tests the IODI insertion of duplicate `StudyInvestigator` records
to ensure deduplication functions as intended.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
investigator_id, _ = create_investigator(dal=self.dal)
investigator_02_id, _ = create_investigator(
dal=self.dal,
affiliation="new_affiliation",
)
# IODI a new `StudyInvestigator` record.
obj_id = self.dal.iodi_study_investigator(
study_id=study_id,
investigator_id=investigator_id,
)
# The PK should be `1` as this is the first record.
self.assertEqual(obj_id, 1)
# IODI the same `StudyInvestigator` record as before.
obj_id = self.dal.iodi_study_investigator(
study_id=study_id,
investigator_id=investigator_id,
)
# The PK should still be `1` as the record was identical thus no
# insertion should've occured.
self.assertEqual(obj_id, 1)
# IODI a new `StudyInvestigator` record.
obj_id = self.dal.iodi_study_investigator(
study_id=study_id,
investigator_id=investigator_02_id,
)
# The PK should be `3` as the previous failed INSERT will have
# incremented the PK by 1.
self.assertEqual(obj_id, 3)
# IODU the same `StudyInvestigator` record as before.
obj_id = self.dal.iodi_study_investigator(
study_id=study_id,
investigator_id=investigator_02_id,
)
# The PK should still be `3` as the record is identical to the one
# before.
self.assertEqual(obj_id, 3)
def test_iodi_study_arm_group_duplicate(self):
""" Tests the IODI insertion of duplicate `StudyArmGroup` records to
ensure deduplication functions as intended.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
arm_group_id, _ = create_arm_group(dal=self.dal)
arm_group_02_id, _ = create_arm_group(dal=self.dal, label="new_label")
# IODI a new `StudyArmGroup` record.
obj_id = self.dal.iodi_study_arm_group(
study_id=study_id,
arm_group_id=arm_group_id,
)
# The PK should be `1` as this is the first record.
self.assertEqual(obj_id, 1)
# IODI the same `StudyArmGroup` record as before.
obj_id = self.dal.iodi_study_arm_group(
study_id=study_id,
arm_group_id=arm_group_id,
)
# The PK should still be `1` as the record was identical thus no
# insertion should've occured.
self.assertEqual(obj_id, 1)
# IODI a new `StudyArmGroup` record.
obj_id = self.dal.iodi_study_arm_group(
study_id=study_id,
arm_group_id=arm_group_02_id,
)
# The PK should be `3` as the previous failed INSERT will have
# incremented the PK by 1.
self.assertEqual(obj_id, 3)
# IODU the same `StudyArmGroup` record as before.
obj_id = self.dal.iodi_study_arm_group(
study_id=study_id,
arm_group_id=arm_group_02_id,
)
# The PK should still be `3` as the record is identical to the one
# before.
self.assertEqual(obj_id, 3)
def test_insert_study_secondary_id_duplicate(self):
""" Tests the Inserts insertion of duplicate `StudySecondaryId` records
to ensure that no deduplication checks occurs.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
# Insert a new `StudySecondaryId` record.
obj_id = self.dal.insert_study_secondary_id(
study_id=study_id,
secondary_id="secondary_id",
)
self.assertEqual(obj_id, 1)
# Inserts an identical `StudySecondaryId` record.
obj_id = self.dal.insert_study_secondary_id(
study_id=study_id,
secondary_id="secondary_id",
)
self.assertEqual(obj_id, 2)
# Inserts a new `StudySecondaryId` record.
obj_id = self.dal.insert_study_secondary_id(
study_id=study_id,
secondary_id="new_secondary_id",
)
self.assertEqual(obj_id, 3)
# Inserts the same `StudySecondaryId` record as before.
obj_id = self.dal.insert_study_secondary_id(
study_id=study_id,
secondary_id="secondary_id",
)
self.assertEqual(obj_id, 4)
def test_delete_study_secondary_id(self):
""" Tests the deletion of a `StudySecondaryId` record via the `delete`
method of the `DalClinicalTrials` class.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
# Inserts a new `StudySecondaryId` record.
obj_id = self.dal.insert_study_secondary_id(
study_id=study_id,
secondary_id="secondary_id",
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(StudySecondaryId, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(StudySecondaryId, obj_id) # type: StudySecondaryId
self.assertIsNone(obj)
def test_delete_study_arm_group(self):
""" Tests the deletion of a `StudyArmGroup` record via the `delete`
method of the `DalClinicalTrials` class.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
arm_group_id, _ = create_arm_group(dal=self.dal)
# IODI a new `StudyArmGroup` record.
obj_id = self.dal.iodi_study_arm_group(
study_id=study_id,
arm_group_id=arm_group_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(StudyArmGroup, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(StudyArmGroup, obj_id) # type: StudyArmGroup
self.assertIsNone(obj)
def test_insert_get_study_secondary_id(self):
""" Tests the insertion of a `StudySecondaryId` record via the
`insert_study_secondary_id` method of the `DalClinicalTrials` class
and its retrieval via the `get` method.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
# Insert a new `StudySecondaryId` record.
obj_id = self.dal.insert_study_secondary_id(
study_id=study_id,
secondary_id="secondary_id",
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(StudySecondaryId, obj_id) # type: StudySecondaryId
# Assert that the different fields of the record match.
self.assertEqual(obj.study_secondary_id_id, 1)
self.assertEqual(obj.study_id, study_id)
self.assertEqual(obj.secondary_id, "secondary_id")
def test_iodu_study_outcome_duplicate(self):
""" Tests the IODU insertion of duplicate `StudyOutcome` records to
ensure deduplication functions as intended.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
protocol_outcome_id, _ = create_protocol_outcome(dal=self.dal)
protocol_outcome_02_id, _ = create_protocol_outcome(
dal=self.dal,
measure="new_measure",
)
# IODU a new `StudyOutcome` record.
obj_id = self.dal.iodu_study_outcome(
study_id=study_id,
protocol_outcome_id=protocol_outcome_id,
outcome_type=OutcomeType.PRIMARY,
)
# The PK should be `1` as this is the first record.
self.assertEqual(obj_id, 1)
# IODU the same `StudyOutcome` record as before.
obj_id = self.dal.iodu_study_outcome(
study_id=study_id,
protocol_outcome_id=protocol_outcome_id,
outcome_type=OutcomeType.PRIMARY,
)
# The PK should still be `1` as the record was identical thus no
# insertion should've occured.
self.assertEqual(obj_id, 1)
# IODU the same `StudyOutcome` record with a changed `outcome_type`
# field which should trigger an update on the existing record.
obj_id = self.dal.iodu_study_outcome(
study_id=study_id,
protocol_outcome_id=protocol_outcome_id,
outcome_type=OutcomeType.SECONDARY,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(StudyOutcome, obj_id) # type: StudyOutcome
self.assertEqual(obj.outcome_type, OutcomeType.SECONDARY)
# IODU a new `StudyOutcome` record.
obj_id = self.dal.iodu_study_outcome(
study_id=study_id,
protocol_outcome_id=protocol_outcome_02_id,
outcome_type=OutcomeType.POST_HOC,
)
# The PK should be `4` as the previous failed INSERT will have
# incremented the PK by 1.
self.assertEqual(obj_id, 4)
# IODU the same `StudyOutcome` record as before.
obj_id = self.dal.iodu_study_outcome(
study_id=study_id,
protocol_outcome_id=protocol_outcome_02_id,
outcome_type=OutcomeType.POST_HOC,
)
# The PK should still be `4` as the record is identical to the one
# before.
self.assertEqual(obj_id, 4)
def test_iodu_study_sponsor_duplicate(self):
""" Tests the IODU insertion of duplicate `StudySponsor` records to
ensure deduplication functions as intended.
"""
# Create fixtures.
study_id, _ = create_study(dal=self.dal)
sponsor_id, _ = create_sponsor(dal=self.dal)
sponsor_02_id, _ = create_sponsor(dal=self.dal, agency="new_agency")
# IODU a new `StudySponsor` record.
obj_id = self.dal.iodu_study_sponsor(
study_id=study_id,
sponsor_id=sponsor_id,
sponsor_type=SponsorType.COLLABORATOR,
)
# The PK should be `1` as this is the first record.
self.assertEqual(obj_id, 1)
# IODU the same `StudySponsor` record as before.
obj_id = self.dal.iodu_study_sponsor(
study_id=study_id,
sponsor_id=sponsor_id,
sponsor_type=SponsorType.COLLABORATOR,
)
# The PK should still be `1` as the record was identical thus no
# insertion should've occured.
self.assertEqual(obj_id, 1)
# IODU the same `StudySponsor` record with a changed `sponsor_type`
# field which should trigger an update on the existing record.
obj_id = self.dal.iodu_study_sponsor(
study_id=study_id,
sponsor_id=sponsor_id,
sponsor_type=SponsorType.LEAD,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(StudySponsor, obj_id) # type: StudySponsor
self.assertEqual(obj.sponsor_type, SponsorType.LEAD)
# IODU a new `StudySponsor` record.
obj_id = self.dal.iodu_study_sponsor(
study_id=study_id,
sponsor_id=sponsor_02_id,
sponsor_type=SponsorType.COLLABORATOR,
)
# The PK should be `4` as the previous failed INSERT will have
# incremented the PK by 1.
self.assertEqual(obj_id, 4)
# IODU the same `StudySponsor` record as before.
obj_id = self.dal.iodu_study_sponsor(
study_id=study_id,
sponsor_id=sponsor_02_id,
sponsor_type=SponsorType.COLLABORATOR,
)
# The PK should still be `4` as the record is identical to the one
# before.
self.assertEqual(obj_id, 4)
