def test_delete_descriptor_pharmacological_action_descriptor(self):
""" Tests the deletion of a
`DescriptorPharmacologicalActionDescriptor` record via the
`delete` method of the `DalMesh` class.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
descriptor_02_id, _ = create_descriptor(
dal=self.dal,
ui="UI2",
name="NewDescriptor"
)
# IODI a new `DescriptorPharmacologicalActionDescriptor` record.
obj_id = self.dal.iodi_descriptor_pharmacological_action_descriptor(
descriptor_id=descriptor_id,
pharmacological_action_descriptor_id=descriptor_02_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(DescriptorPharmacologicalActionDescriptor, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
DescriptorPharmacologicalActionDescriptor,
obj_id,
) # type: DescriptorPharmacologicalActionDescriptor
self.assertIsNone(obj)
def test_delete_descriptor_related_descriptor(self):
""" Tests the deletion of a `DescriptorRelatedDescriptor` record via the
`delete` method of the `DalMesh` class.
"""
# Create fixture records.
descriptor_01_id, _ = create_descriptor(
dal=self.dal,
ui="UI1",
name="Name1",
)
descriptor_02_id, _ = create_descriptor(
dal=self.dal,
ui="UI2",
name="Name2",
)
# IODI a new `DescriptorRelatedDescriptor` record.
obj_id = self.dal.iodi_descriptor_related_descriptor(
descriptor_id=descriptor_01_id,
related_descriptor_id=descriptor_02_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(DescriptorRelatedDescriptor, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
DescriptorRelatedDescriptor,
obj_id,
) # type: DescriptorRelatedDescriptor
self.assertIsNone(obj)
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_delete_descriptor_previous_indexing(self):
""" Tests the deletion of a `DescriptorPreviousIndexing` record via the
`delete` method of the `DalMesh` class.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
previous_indexing_id, _ = create_previous_indexing(dal=self.dal)
# IODI a new `DescriptorPreviousIndexing` record.
obj_id = self.dal.iodi_descriptor_previous_indexing(
descriptor_id=descriptor_id,
previous_indexing_id=previous_indexing_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(DescriptorPreviousIndexing, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
DescriptorPreviousIndexing,
obj_id,
) # type: DescriptorPreviousIndexing
self.assertIsNone(obj)
def test_iodi_get_descriptor_previous_indexing(self):
""" Tests the IODI insertion of a `DescriptorPreviousIndexing` record
via the `iodi_descriptor_previous_indexing` method of the `DalMesh`
class and its retrieval via the `get` method.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
previous_indexing_id, _ = create_previous_indexing(dal=self.dal)
# IODI a new `DescriptorPreviousIndexing` record.
obj_id = self.dal.iodi_descriptor_previous_indexing(
descriptor_id=descriptor_id,
previous_indexing_id=previous_indexing_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(
DescriptorPreviousIndexing,
obj_id,
) # type: DescriptorPreviousIndexing
# Assert that the different fields of the record match.
self.assertEqual(obj.descriptor_previous_indexing_id, 1)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.previous_indexing_id, previous_indexing_id)
def test_delete_descriptor_definition(self):
""" Tests the deletion of a `DescriptorDefinition` record via the
`delete` method of the `DalMesh` class.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
definition = "definition"
md5 = hashlib.md5(definition.encode("utf-8")).digest()
# IODI a new `DescriptorDefinition` record.
obj_id = self.dal.iodi_descriptor_definition(
descriptor_id=descriptor_id,
source=DescriptorDefinitionSourceType.AIR,
definition=definition,
md5=md5,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(DescriptorDefinition, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
DescriptorDefinition,
obj_id,
) # type: DescriptorDefinition
self.assertIsNone(obj)
def test_delete_descriptor_allowable_qualifier(self):
""" Tests the deletion of a `DescriptorAllowableQualifier` record via
the `delete` method of the `DalMesh` class.
"""
# Create a `Descriptor` record as a fixture.
descriptor_id, _ = create_descriptor(dal=self.dal)
# Create a `Qualifier` record as a fixture.
qualifier_id, _ = create_qualifier(dal=self.dal)
# IODU a new `DescriptorAllowableQualifier` record.
obj_id = self.dal.iodu_descriptor_allowable_qualifier(
descriptor_id=descriptor_id,
qualifier_id=qualifier_id,
abbreviation="abbreviation",
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(DescriptorAllowableQualifier, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
DescriptorAllowableQualifier,
obj_id,
) # type: DescriptorAllowableQualifier
self.assertIsNone(obj)
def test_iodi_get_supplemental_heading_mapped_to(self):
""" Tests the IODI insertion of a `SupplementalHeadingMappedTo` record
via the `iodi_supplemental_heading_mapped_to` method of the
`DalMesh` class and its retrieval via the `get` method.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
qualifier_id, _ = create_qualifier(dal=self.dal)
entry_combination_id, _ = create_entry_combination(
dal=self.dal,
descriptor_id=descriptor_id,
qualifier_id=qualifier_id,
)
supplemental_id, _ = create_supplemental(dal=self.dal)
# IODI a new `SupplementalHeadingMappedTo` record.
obj_id = self.dal.iodi_supplemental_heading_mapped_to(
supplemental_id=supplemental_id,
entry_combination_id=entry_combination_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(
SupplementalHeadingMappedTo,
obj_id,
) # type: SupplementalHeadingMappedTo
# Assert that the different fields of the record match.
self.assertEqual(obj.supplemental_heading_mapped_to_id, 1)
self.assertEqual(obj.supplemental_id, supplemental_id)
self.assertEqual(obj.entry_combination_id, entry_combination_id)
def test_delete_supplemental_heading_mapped_to(self):
""" Tests the deletion of a `SupplementalHeadingMappedTo` record via the
`delete` method of the `DalMesh` class.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
qualifier_id, _ = create_qualifier(dal=self.dal)
entry_combination_id, _ = create_entry_combination(
dal=self.dal,
descriptor_id=descriptor_id,
qualifier_id=qualifier_id,
)
supplemental_id, _ = create_supplemental(dal=self.dal)
# IODI a new `SupplementalHeadingMappedTo` record.
obj_id = self.dal.iodi_supplemental_heading_mapped_to(
supplemental_id=supplemental_id,
entry_combination_id=entry_combination_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(SupplementalHeadingMappedTo, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
SupplementalHeadingMappedTo,
obj_id,
) # type: SupplementalHeadingMappedTo
self.assertIsNone(obj)
def test_delete_descriptor_concept(self):
""" Tests the deletion of a `DescriptorConcept` record via the `delete`
method of the `DalMesh` class.
"""
# Create a `Descriptor` record as a fixture.
descriptor_id, _ = create_descriptor(dal=self.dal)
# Create a `Concept` record as a fixture.
concept_id, _ = create_concept(dal=self.dal)
# IODU a new `DescriptorConcept` record.
obj_id = self.dal.iodu_descriptor_concept(
descriptor_id=descriptor_id,
concept_id=concept_id,
is_preferred=True,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(DescriptorConcept, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(DescriptorConcept,
obj_id) # type: DescriptorConcept
self.assertIsNone(obj)
def test_iodi_get_descriptor_entry_combination(self):
""" Tests the IODI insertion of a `DescriptorEntryCombination` record
via the `iodi_descriptor_entry_combination` method of the `DalMesh`
class and its retrieval via the `get` method.
"""
# Create fixture records.
qualifier_id, _ = create_qualifier(dal=self.dal)
descriptor_id, _ = create_descriptor(dal=self.dal)
entry_combination_id, _ = create_entry_combination(
dal=self.dal,
descriptor_id=descriptor_id,
qualifier_id=qualifier_id,
)
# IODI a new `DescriptorEntryCombination` record.
obj_id = self.dal.iodi_descriptor_entry_combination(
descriptor_id=descriptor_id,
entry_combination_id=entry_combination_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(
DescriptorEntryCombination,
obj_id,
) # type: DescriptorEntryCombination
# Assert that the different fields of the record match.
self.assertEqual(obj.descriptor_entry_combination_id, 1)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.entry_combination_id, entry_combination_id)
def test_delete_descriptor_tree_number(self):
""" Tests the deletion of a `DescriptorTreeNumber` record via the
`delete` method of the `DalMesh` class.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
tree_number_id, _ = create_tree_number(dal=self.dal)
# IODI a new `DescriptorTreeNumber` record.
obj_id = self.dal.iodi_descriptor_tree_number(
descriptor_id=descriptor_id,
tree_number_id=tree_number_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(DescriptorTreeNumber, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
DescriptorTreeNumber,
obj_id,
) # type: DescriptorTreeNumber
self.assertIsNone(obj)
def test_iodi_get_descriptor_tree_number(self):
""" Tests the IODI insertion of a `DescriptorTreeNumber` record via the
`iodi_descriptor_tree_number` method of the `DalMesh` class and its
retrieval via the `get` method.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
tree_number_id, _ = create_tree_number(dal=self.dal)
# IODI a new `DescriptorTreeNumber` record.
obj_id = self.dal.iodi_descriptor_tree_number(
descriptor_id=descriptor_id,
tree_number_id=tree_number_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(
DescriptorTreeNumber,
obj_id,
) # type: DescriptorTreeNumber
# Assert that the different fields of the record match.
self.assertEqual(obj.descriptor_tree_number_id, 1)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.tree_number_id, tree_number_id)
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_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_iodu_get_descriptor_concept(self):
""" Tests the IODU insertion of a `DescriptorConcept` record via the
`iodu_descriptor_concept` method of the `DalMesh` class and its
retrieval via the `get` method.
"""
# Create a `Descriptor` record as a fixture.
descriptor_id, _ = create_descriptor(dal=self.dal)
# Create a `Concept` record as a fixture.
concept_id, _ = create_concept(dal=self.dal)
# IODU a new `DescriptorConcept` record.
obj_id = self.dal.iodu_descriptor_concept(
descriptor_id=descriptor_id,
concept_id=concept_id,
is_preferred=True,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(DescriptorConcept,
obj_id) # type: DescriptorConcept
# Assert that the different fields of the record match.
self.assertEqual(obj.descriptor_concept_id, obj_id)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.concept_id, concept_id)
self.assertEqual(obj.is_preferred, True)
def test_iodi_get_supplemental_pharmacological_action_descriptor(self):
""" Tests the IODI insertion of a
`SupplementalPharmacologicalActionDescriptor` record via the
`iodi_supplemental_pharmacological_action_descriptor` method of the
`DalMesh` class and its retrieval via the `get` method.
"""
# Create fixture records.
supplemental_id, _ = create_supplemental(dal=self.dal)
descriptor_id, _ = create_descriptor(dal=self.dal)
# IODI a new `SupplementalPharmacologicalActionDescriptor` record.
obj_id = self.dal.iodi_supplemental_pharmacological_action_descriptor(
supplemental_id=supplemental_id,
pharmacological_action_descriptor_id=descriptor_id,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(
SupplementalPharmacologicalActionDescriptor,
obj_id,
) # type: SupplementalPharmacologicalActionDescriptor
# Assert that the different fields of the record match.
self.assertEqual(
obj.supplemental_pharmacological_action_descriptor_id,
1,
)
self.assertEqual(obj.supplemental_id, supplemental_id)
self.assertEqual(
obj.pharmacological_action_descriptor_id,
descriptor_id,
)
def test_iodu_get_descriptor(self):
""" Tests the IODU insertion of a `Descriptor` record via the
`iodu_descriptor` method of the `DalMesh` class and its retrieval
via the `get` method.
"""
# Create a new `Descriptor` record.
obj_id, refr = create_descriptor(dal=self.dal)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(Descriptor, obj_id) # type: Descriptor
# Assert that the different fields of the record match.
self.assertEqual(obj.descriptor_id, obj_id)
self.assertEqual(obj.ui, refr["ui"])
self.assertEqual(obj.name, refr["name"])
self.assertEqual(obj.created, refr["created"])
self.assertEqual(obj.revised, refr["revised"])
self.assertEqual(obj.established, refr["established"])
self.assertEqual(obj.annotation, refr["annotation"])
self.assertEqual(obj.history_note, refr["history_note"])
self.assertEqual(
obj.nlm_classification_number,
refr["nlm_classification_number"],
)
self.assertEqual(obj.online_note, refr["online_note"])
self.assertEqual(obj.public_mesh_note, refr["public_mesh_note"])
self.assertEqual(obj.consider_also, refr["consider_also"])
def test_delete_supplemental_pharmacological_action_descriptor(self):
""" Tests the deletion of a
`SupplementalPharmacologicalActionDescriptor` record via the
`delete` method of the `DalMesh` class.
"""
# Create fixture records.
supplemental_id, _ = create_supplemental(dal=self.dal)
descriptor_id, _ = create_descriptor(dal=self.dal)
# IODI a new `SupplementalPharmacologicalActionDescriptor` record.
obj_id = self.dal.iodi_supplemental_pharmacological_action_descriptor(
supplemental_id=supplemental_id,
pharmacological_action_descriptor_id=descriptor_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(SupplementalPharmacologicalActionDescriptor, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
SupplementalPharmacologicalActionDescriptor,
obj_id,
) # type: SupplementalPharmacologicalActionDescriptor
self.assertIsNone(obj)
def test_iodi_get_descriptor_definition(self):
""" Tests the IODI insertion of a `DescriptorDefinition` record via the
`iodi_descriptor_definition` method of the `DalMesh` class and its
retrieval via the `get` method.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
definition = "definition"
md5 = hashlib.md5(definition.encode("utf-8")).digest()
# IODI a new `DescriptorDefinition` record.
obj_id = self.dal.iodi_descriptor_definition(
descriptor_id=descriptor_id,
source=DescriptorDefinitionSourceType.AIR,
definition=definition,
md5=md5,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(
DescriptorDefinition,
obj_id,
) # type: DescriptorDefinition
# Assert that the different fields of the record match.
self.assertEqual(obj.descriptor_definition_id, 1)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.source, DescriptorDefinitionSourceType.AIR)
self.assertEqual(obj.definition, definition)
self.assertEqual(obj.md5, md5)
def test_delete_descriptor_entry_combination(self):
""" Tests the deletion of a `DescriptorEntryCombination` record via the
`delete` method of the `DalMesh` class.
"""
# Create fixture records.
qualifier_id, _ = create_qualifier(dal=self.dal)
descriptor_id, _ = create_descriptor(dal=self.dal)
entry_combination_id, _ = create_entry_combination(
dal=self.dal,
descriptor_id=descriptor_id,
qualifier_id=qualifier_id,
)
# IODI a new `DescriptorEntryCombination` record.
obj_id = self.dal.iodi_descriptor_entry_combination(
descriptor_id=descriptor_id,
entry_combination_id=entry_combination_id,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(DescriptorEntryCombination, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(
DescriptorEntryCombination,
obj_id,
) # type: DescriptorEntryCombination
self.assertIsNone(obj)
def test_iodu_get_descriptor_allowable_qualifier(self):
""" Tests the IODU insertion of a `DescriptorAllowableQualifier` record
via the `iodu_descriptor_allowable_qualifier` method of the
`DalMesh` class and its retrieval via the `get` method.
"""
# Create a `Descriptor` record as a fixture.
descriptor_id, _ = create_descriptor(dal=self.dal)
# Create a `Qualifier` record as a fixture.
qualifier_id, _ = create_qualifier(dal=self.dal)
# IODU a new `DescriptorAllowableQualifier` record.
obj_id = self.dal.iodu_descriptor_allowable_qualifier(
descriptor_id=descriptor_id,
qualifier_id=qualifier_id,
abbreviation="abbreviation",
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(
DescriptorAllowableQualifier,
obj_id,
) # type: DescriptorAllowableQualifier
# Assert that the different fields of the record match.
self.assertEqual(obj.descriptor_allowable_qualifier_id, obj_id)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.qualifier_id, qualifier_id)
self.assertEqual(obj.abbreviation, "abbreviation")
def test_biodi_get_descriptor_synonyms(self):
""" Tests the BIODI insertion of multiple `DescriptorSynonym` records
via the `biodi_descriptor_synonyms` method of the `DalMesh` class
and its retrieval via the `get` method.
"""
# Create a new `Descriptor` record.
descriptor_id, _ = create_descriptor(dal=self.dal)
synonyms = ["synonym01", "synonym02", "synonym03", "synonym04"]
# Create a new `DescriptorSynonym` record.
self.dal.biodi_descriptor_synonyms(
descriptor_id=descriptor_id,
synonyms=synonyms,
md5s=self._get_md5s(values=synonyms),
)
# Retrieve all `DescriptorSynonym` records for the new `Descriptor`.
objs = self.dal.bget_by_attr(
orm_class=DescriptorSynonym,
attr_name="descriptor_id",
attr_values=[descriptor_id],
do_sort=True,
) # type: List[DescriptorSynonym]
self.assertEqual(len(objs), len(synonyms))
synonyms_eval = [obj.synonym for obj in objs]
self.assertListEqual(synonyms_eval, synonyms)
def test_biodi_get_descriptor_synonym(self):
""" Tests the BIODI insertion of a single `DescriptorSynonym` record via
the `biodi_descriptor_synonyms` method of the `DalMesh` class and
its retrieval via the `get` method.
"""
# Create a new `Descriptor` record.
descriptor_id, _ = create_descriptor(dal=self.dal)
synonyms = ["synonym"]
# Create a new `DescriptorSynonym` record.
self.dal.biodi_descriptor_synonyms(
descriptor_id=descriptor_id,
synonyms=synonyms,
md5s=self._get_md5s(values=synonyms),
)
# Retrieve all `DescriptorSynonym` records for the new `Descriptor`.
objs = self.dal.bget_by_attr(
orm_class=DescriptorSynonym,
attr_name="descriptor_id",
attr_values=[descriptor_id],
do_sort=True,
) # type: List[DescriptorSynonym]
self.assertEqual(len(objs), 1)
obj = objs[0]
# Assert that the different fields of the record match.
self.assertEqual(obj.descriptor_synonym_id, 1)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.synonym, synonyms[0])
self.assertEqual(obj.md5, self._get_md5s(values=synonyms)[0])
def test_get_joined_mutliple_relationship(self):
""" Tests the `get_joined` method with multiple relationships."""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
tree_number_id, _ = create_tree_number(dal=self.dal)
concept_id, _ = create_concept(dal=self.dal)
# IODI a new `DescriptorTreeNumber` record.
self.dal.iodi_descriptor_tree_number(
descriptor_id=descriptor_id,
tree_number_id=tree_number_id,
)
# IODU a new `DescriptorConcept` record.
self.dal.iodu_descriptor_concept(
descriptor_id=descriptor_id,
concept_id=concept_id,
is_preferred=True,
)
# Retrieve the `Descriptor` join-loaded with its `TreeNumber` and
# `Concept` record.
obj = self.dal.get_joined(
orm_class=Descriptor,
pk=descriptor_id,
joined_relationships=["tree_numbers",
"concepts"]) # type: Descriptor
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertIsNotNone(obj.tree_numbers)
self.assertIsNotNone(obj.concepts)
def test_iodu_get_entry_combination(self):
""" Tests the IODU insertion of a `EntryCombination` record via the
`iodu_entry_combination` method of the `DalMesh` class and its
retrieval via the `get` method.
"""
# Create a `Qualifier` record as a fixture.
qualifier_id, _ = create_qualifier(dal=self.dal)
# Create a `Descriptor` record as a fixture.
descriptor_id, _ = create_descriptor(dal=self.dal)
# IODU a new `EntryCombination` record.
obj_id = self.dal.iodu_entry_combination(
descriptor_id=descriptor_id,
qualifier_id=qualifier_id,
combination_type=EntryCombinationType.ECIN,
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(EntryCombination, obj_id) # type: EntryCombination
# Assert that the different fields of the record match.
self.assertEqual(obj.entry_combination_id, obj_id)
self.assertEqual(obj.descriptor_id, descriptor_id)
self.assertEqual(obj.qualifier_id, qualifier_id)
self.assertEqual(obj.combination_type, EntryCombinationType.ECIN)
def test_delete_entry_combination(self):
""" Tests the deletion of a `EntryCombination` record via the `delete`
method of the `DalMesh` class.
"""
# Create a `Qualifier` record as a fixture.
qualifier_id, _ = create_qualifier(dal=self.dal)
# Create a `Descriptor` record as a fixture.
descriptor_id, _ = create_descriptor(dal=self.dal)
# IODU a new `EntryCombination` record.
obj_id = self.dal.iodu_entry_combination(
descriptor_id=descriptor_id,
qualifier_id=qualifier_id,
combination_type=EntryCombinationType.ECIN,
)
self.assertEqual(obj_id, 1)
# Delete the new record.
self.dal.delete(EntryCombination, obj_id)
# (Attempt to) retrieve the deleted record.
obj = self.dal.get(EntryCombination, obj_id) # type: EntryCombination
self.assertIsNone(obj)
def test_iodu_descriptor_duplicate(self):
""" Tests the IODU insertion of duplicate `Descriptor` records to ensure
deduplication functions as intended.
"""
# Create a new `Descriptor` record.
obj_id, refr = create_descriptor(dal=self.dal)
self.assertEqual(obj_id, 1)
# IODU the same `Descriptor` record.
obj_id, refr = create_descriptor(dal=self.dal)
self.assertEqual(obj_id, 1)
# IODU the same `Descriptor` record with a changed `history_note` field
# which should trigger an update on the existing record.
obj_id, refr = create_descriptor(
dal=self.dal,
history_note="different history note"
)
self.assertEqual(obj_id, 1)
# Retrieve the new record.
obj = self.dal.get(Descriptor, obj_id) # type: Descriptor
self.assertEqual(obj.history_note, "different history note")
# IODU a new `Descriptor` record.
obj_id, refr = create_descriptor(
dal=self.dal,
ui="D000057",
name="NewDescriptor"
)
self.assertEqual(obj_id, 4)
# IODU the same `Descriptor` record as before.
obj_id, refr = create_descriptor(
dal=self.dal,
ui="D000057",
name="NewDescriptor"
)
self.assertEqual(obj_id, 4)
def test_iodi_descriptor_related_descriptor_duplicate(self):
""" Tests the IODI insertion of duplicate `DescriptorRelatedDescriptor`
records to ensure deduplication functions as intended.
"""
# Create fixture records.
descriptor_01_id, _ = create_descriptor(
dal=self.dal,
ui="UI1",
name="Name1",
)
descriptor_02_id, _ = create_descriptor(
dal=self.dal,
ui="UI2",
name="Name2",
)
descriptor_03_id, _ = create_descriptor(
dal=self.dal,
ui="UI3",
name="Name3",
)
# IODI a new `DescriptorRelatedDescriptor` record.
obj_id = self.dal.iodi_descriptor_related_descriptor(
descriptor_id=descriptor_01_id,
related_descriptor_id=descriptor_02_id,
)
self.assertEqual(obj_id, 1)
# IODI an identical `DescriptorRelatedDescriptor` record.
obj_id = self.dal.iodi_descriptor_related_descriptor(
descriptor_id=descriptor_01_id,
related_descriptor_id=descriptor_02_id,
)
self.assertEqual(obj_id, 1)
# IODI a new `DescriptorRelatedDescriptor` record.
obj_id = self.dal.iodi_descriptor_related_descriptor(
descriptor_id=descriptor_01_id,
related_descriptor_id=descriptor_03_id,
)
self.assertEqual(obj_id, 3)
def test_iodi_descriptor_pharmacological_action_descriptor_duplicate(
self
):
""" Tests the IODI insertion of duplicate
`DescriptorPharmacologicalActionDescriptor` records to ensure
deduplication functions as intended.
"""
# Create fixture records.
descriptor_id, _ = create_descriptor(dal=self.dal)
descriptor_02_id, _ = create_descriptor(
dal=self.dal,
ui="UI2",
name="NewDescriptor"
)
descriptor_03_id, _ = create_descriptor(
dal=self.dal,
ui="UI3",
name="NewerDescriptor"
)
# IODI a new `DescriptorPharmacologicalActionDescriptor` record.
obj_id = self.dal.iodi_descriptor_pharmacological_action_descriptor(
descriptor_id=descriptor_id,
pharmacological_action_descriptor_id=descriptor_id,
)
self.assertEqual(obj_id, 1)
# IODI an identical `DescriptorPharmacologicalActionDescriptor`
# record.
obj_id = self.dal.iodi_descriptor_pharmacological_action_descriptor(
descriptor_id=descriptor_id,
pharmacological_action_descriptor_id=descriptor_id,
)
self.assertEqual(obj_id, 1)
# IODI a new `DescriptorPharmacologicalActionDescriptor` record.
obj_id = self.dal.iodi_descriptor_pharmacological_action_descriptor(
descriptor_id=descriptor_id,
pharmacological_action_descriptor_id=descriptor_02_id,
)
self.assertEqual(obj_id, 3)
