diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index 2a62923aa..cae165f13 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -407,7 +407,6 @@ class Node(Entity): class NodeHierarchy(ConfiguredBaseModel): super_classes: List[Entity] = Field(default_factory=list) - equivalent_classes: List[Entity] = Field(default_factory=list) sub_classes: List[Entity] = Field(default_factory=list) diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml index 236e0d0db..0ebf43c9a 100644 --- a/backend/src/monarch_py/datamodels/model.yaml +++ b/backend/src/monarch_py/datamodels/model.yaml @@ -210,7 +210,6 @@ classes: NodeHierarchy: slots: - super_classes - - equivalent_classes - sub_classes Results: abstract: true @@ -261,12 +260,6 @@ slots: the object or in the object closure, the direction is backwards. range: AssociationDirectionEnum required: true - equivalent_classes: - range: Entity - multivalued: true - inlined: true - inlined_as_list: true - required: true evidence_count: description: count of supporting documents, evidence codes, and sources supplying evidence range: integer @@ -371,8 +364,6 @@ slots: multivalued: true qualifiers: multivalued: true - relation: - range: string score: range: float sex_qualifier: diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py index 4ffa0617a..83d64d74d 100644 --- a/backend/src/monarch_py/implementations/solr/solr_implementation.py +++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py @@ -96,13 +96,13 @@ def get_entity(self, id: str, extra: bool) -> Union[Node, Entity]: def _get_associated_entity(self, association: Association, this_entity: Entity) -> Entity: """Returns the id, name, and category of the other Entity in an Association given this_entity""" - if this_entity.id in association.subject_closure: + if this_entity.id == association.subject: entity = Entity( id=association.object, name=association.object_label, category=association.object_category, ) - elif this_entity.id in association.object_closure: + elif this_entity.id == association.object: entity = Entity( id=association.subject, name=association.subject_label, @@ -156,13 +156,15 @@ def _get_node_hierarchy(self, entity: Entity) -> NodeHierarchy: NodeHierarchy: A NodeHierarchy object """ - super_classes = self._get_associated_entities(entity, subject=entity.id, predicate="biolink:subclass_of") - equivalent_classes = self._get_associated_entities(entity, entity=entity.id, predicate="biolink:same_as") - sub_classes = self._get_associated_entities(entity, object=entity.id, predicate="biolink:subclass_of") + super_classes = self._get_associated_entities( + this_entity=entity, subject=entity.id, predicate="biolink:subclass_of" + ) + sub_classes = self._get_associated_entities( + this_entity=entity, object=entity.id, predicate="biolink:subclass_of" + ) return NodeHierarchy( super_classes=super_classes, - equivalent_classes=equivalent_classes, sub_classes=sub_classes, ) diff --git a/backend/src/monarch_py/implementations/sql/sql_implementation.py b/backend/src/monarch_py/implementations/sql/sql_implementation.py index cf8b7b90d..0aa6f98df 100644 --- a/backend/src/monarch_py/implementations/sql/sql_implementation.py +++ b/backend/src/monarch_py/implementations/sql/sql_implementation.py @@ -139,13 +139,15 @@ def _get_node_hierarchy(self, entity: Entity) -> NodeHierarchy: NodeHierarchy: A NodeHierarchy object """ - super_classes = self._get_associated_entities(entity, subject=entity.id, predicate="biolink:subclass_of") - equivalent_classes = self._get_associated_entities(entity, entity=entity.id, predicate="biolink:same_as") - sub_classes = self._get_associated_entities(entity, object=entity.id, predicate="biolink:subclass_of") + super_classes = self._get_associated_entities( + this_entity=entity, subject=entity.id, predicate="biolink:subclass_of" + ) + sub_classes = self._get_associated_entities( + this_entity=entity, object=entity.id, predicate="biolink:subclass_of" + ) return NodeHierarchy( super_classes=super_classes, - equivalent_classes=equivalent_classes, sub_classes=sub_classes, ) @@ -242,13 +244,12 @@ def get_associations( "original_object": row["original_object"], "category": row["category"], "aggregator_knowledge_source": row["aggregator_knowledge_source"].split("|"), - "primary_knowledge_source": row["primary_knowledge_source"].split("|"), + "primary_knowledge_source": row["primary_knowledge_source"], "publications": row["publications"].split("|"), "qualifiers": row["qualifiers"].split("|"), "provided_by": row["provided_by"], - "has_evidence": row["has_evidence"], + "has_evidence": row["has_evidence"].split("|"), "stage_qualifier": row["stage_qualifier"], - "relation": row["relation"], "negated": False if not row["negated"] else True, "frequency_qualifier": row["frequency_qualifier"], "onset_qualifier": row["onset_qualifier"], diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py index 9de0c622c..79467b039 100644 --- a/backend/tests/fixtures/association_counts.py +++ b/backend/tests/fixtures/association_counts.py @@ -5,8 +5,20 @@ def association_counts(): return { "items": [ - {"label": "Phenotypes", "count": 4011, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, - {"label": "Causal Genes", "count": 121, "category": "biolink:CausalGeneToDiseaseAssociation"}, - {"label": "Correlated Genes", "count": 147, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, + { + "label": "Phenotypes", + "count": 4011, + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + }, + { + "label": "Causal Genes", + "count": 121, + "category": "biolink:CausalGeneToDiseaseAssociation", + }, + { + "label": "Correlated Genes", + "count": 147, + "category": "biolink:CorrelatedGeneToDiseaseAssociation", + }, ] } diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index 620176411..d784dc83f 100644 --- a/backend/tests/fixtures/association_counts_response.py +++ b/backend/tests/fixtures/association_counts_response.py @@ -96,7 +96,12 @@ def association_counts_response(): "subject_label": "muscular dystrophy, Barnes type", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -169,7 +174,12 @@ def association_counts_response(): "subject_label": "facioscapulohumeral muscular dystrophy 1", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -260,7 +270,12 @@ def association_counts_response(): "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -325,7 +340,12 @@ def association_counts_response(): "subject_label": "myopathy, distal, infantile-onset", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -398,7 +418,12 @@ def association_counts_response(): "subject_label": "MYH7-related skeletal myopathy", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -495,7 +520,12 @@ def association_counts_response(): "subject_label": "myotonic dystrophy type 1", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -574,7 +604,12 @@ def association_counts_response(): "subject_label": "oculopharyngeal muscular dystrophy", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -649,7 +684,12 @@ def association_counts_response(): "subject_label": "Ullrich congenital muscular dystrophy 1", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -712,7 +752,12 @@ def association_counts_response(): "subject_label": "muscular dystrophy, Hemizygous lethal type", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -795,7 +840,12 @@ def association_counts_response(): "subject_label": "tibial muscular dystrophy", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -888,7 +938,12 @@ def association_counts_response(): "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -971,7 +1026,12 @@ def association_counts_response(): "subject_label": "myotonic dystrophy type 2", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1058,7 +1118,12 @@ def association_counts_response(): "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1129,7 +1194,12 @@ def association_counts_response(): "subject_label": "distal myopathy, Welander type", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1202,7 +1272,12 @@ def association_counts_response(): "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1289,7 +1364,12 @@ def association_counts_response(): "subject_label": "myofibrillar myopathy 2", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1362,7 +1442,12 @@ def association_counts_response(): "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1451,7 +1536,12 @@ def association_counts_response(): "subject_label": "myofibrillar myopathy 3", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1542,7 +1632,12 @@ def association_counts_response(): "subject_label": "fibrosis of extraocular muscles, congenital, 3c", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1627,7 +1722,12 @@ def association_counts_response(): "subject_label": "myofibrillar myopathy 4", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py index 7567e4e68..6a8c4839e 100644 --- a/backend/tests/fixtures/association_response.py +++ b/backend/tests/fixtures/association_response.py @@ -74,7 +74,12 @@ def association_response(): "subject_label": "muscular dystrophy, Barnes type", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -147,7 +152,12 @@ def association_response(): "subject_label": "facioscapulohumeral muscular dystrophy 1", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -238,7 +248,12 @@ def association_response(): "subject_label": "muscular dystrophy, pseudohypertrophic, with Internalized capillaries", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -303,7 +318,12 @@ def association_response(): "subject_label": "myopathy, distal, infantile-onset", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -376,7 +396,12 @@ def association_response(): "subject_label": "MYH7-related skeletal myopathy", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -473,7 +498,12 @@ def association_response(): "subject_label": "myotonic dystrophy type 1", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -552,7 +582,12 @@ def association_response(): "subject_label": "oculopharyngeal muscular dystrophy", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -627,7 +662,12 @@ def association_response(): "subject_label": "Ullrich congenital muscular dystrophy 1", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -690,7 +730,12 @@ def association_response(): "subject_label": "muscular dystrophy, Hemizygous lethal type", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -773,7 +818,12 @@ def association_response(): "subject_label": "tibial muscular dystrophy", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -866,7 +916,12 @@ def association_response(): "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -949,7 +1004,12 @@ def association_response(): "subject_label": "myotonic dystrophy type 2", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1036,7 +1096,12 @@ def association_response(): "subject_label": "myopathy, myofibrillar, 9, with early respiratory failure", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1107,7 +1172,12 @@ def association_response(): "subject_label": "distal myopathy, Welander type", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1180,7 +1250,12 @@ def association_response(): "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1F", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1267,7 +1342,12 @@ def association_response(): "subject_label": "myofibrillar myopathy 2", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1340,7 +1420,12 @@ def association_response(): "subject_label": "autosomal dominant limb-girdle muscular dystrophy type 1G", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1429,7 +1514,12 @@ def association_response(): "subject_label": "myofibrillar myopathy 3", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1520,7 +1610,12 @@ def association_response(): "subject_label": "fibrosis of extraocular muscles, congenital, 3c", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", @@ -1605,7 +1700,12 @@ def association_response(): "subject_label": "myofibrillar myopathy 4", "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_closure_label": [ "All (HPO)", "Mode of inheritance (HPO)", diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py index f3273e2c8..62681df60 100644 --- a/backend/tests/fixtures/association_table.py +++ b/backend/tests/fixtures/association_table.py @@ -160,8 +160,16 @@ def association_table(): "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040282", + "HP:0040279", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Frequent (HPO)", + ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -378,8 +386,16 @@ def association_table(): "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040282", + "HP:0040279", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Frequent (HPO)", + ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -660,8 +676,16 @@ def association_table(): "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040279", + "HP:0040280", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Obligate (HPO)", + ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -831,8 +855,16 @@ def association_table(): "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040279", + "HP:0040280", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Obligate (HPO)", + ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -998,8 +1030,16 @@ def association_table(): "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040279", + "HP:0040280", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Obligate (HPO)", + ], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py index 6789cb465..ff41176c8 100644 --- a/backend/tests/fixtures/association_table_response.py +++ b/backend/tests/fixtures/association_table_response.py @@ -163,8 +163,16 @@ def association_table_response(): "object_label": "Distal muscle weakness (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040282", + "HP:0040279", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Frequent (HPO)", + ], "frequency_qualifier_label": "Frequent (HPO)", "evidence_count": 6, }, @@ -353,8 +361,16 @@ def association_table_response(): "object_label": "Dysphagia (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040282", + "HP:0040279", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Frequent (HPO)", + ], "frequency_qualifier_label": "Frequent (HPO)", "evidence_count": 6, }, @@ -607,8 +623,16 @@ def association_table_response(): "object_label": "Elevated circulating creatine kinase concentration (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040279", + "HP:0040280", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Obligate (HPO)", + ], "frequency_qualifier_label": "Obligate (HPO)", "evidence_count": 5, }, @@ -750,8 +774,16 @@ def association_table_response(): "object_label": "Distal joint laxity (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040279", + "HP:0040280", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Obligate (HPO)", + ], "frequency_qualifier_label": "Obligate (HPO)", "evidence_count": 5, }, @@ -889,8 +921,16 @@ def association_table_response(): "object_label": "Proximal muscle weakness (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], - "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], + "frequency_qualifier_closure": [ + "HP:0000001", + "HP:0040279", + "HP:0040280", + ], + "frequency_qualifier_closure_label": [ + "All (HPO)", + "Frequency (HPO)", + "Obligate (HPO)", + ], "frequency_qualifier_label": "Obligate (HPO)", "evidence_count": 5, }, diff --git a/backend/tests/fixtures/associations.py b/backend/tests/fixtures/associations.py index 45488b44e..f09d669fb 100644 --- a/backend/tests/fixtures/associations.py +++ b/backend/tests/fixtures/associations.py @@ -58,7 +58,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -167,7 +172,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -294,7 +304,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -395,7 +410,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -504,7 +524,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -637,7 +662,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -752,7 +782,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -863,7 +898,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -962,7 +1002,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -1081,7 +1126,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -1210,7 +1260,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -1329,7 +1384,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -1452,7 +1512,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -1559,7 +1624,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -1668,7 +1738,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -1791,7 +1866,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -1900,7 +1980,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -2025,7 +2110,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -2152,7 +2242,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", @@ -2273,7 +2368,12 @@ def associations(): "original_object": None, "object_namespace": "HP", "object_category": "biolink:GeneticInheritance", - "object_closure": ["HP:0000001", "HP:0000006", "HP:0000005", "HP:0034345"], + "object_closure": [ + "HP:0000001", + "HP:0000006", + "HP:0000005", + "HP:0034345", + ], "object_label": "Autosomal dominant inheritance (HPO)", "object_closure_label": [ "All (HPO)", diff --git a/backend/tests/fixtures/autocomplete.py b/backend/tests/fixtures/autocomplete.py index 4d10cfd1a..c1d5201a5 100644 --- a/backend/tests/fixtures/autocomplete.py +++ b/backend/tests/fixtures/autocomplete.py @@ -40,7 +40,14 @@ def autocomplete(): "name": "Fanconi renotubular syndrome", "full_name": None, "description": "A genetic or acquired disorder characterized by impairment of the function of the proximal tubules of the kidney. It results in decreased reabsorption of electrolytes, glucose, amino acids, and other nutrients.", - "xref": ["DOID:1062", "GARD:0009120", "MESH:D005198", "NCIT:C3034", "SCTID:40488004", "UMLS:C0015624"], + "xref": [ + "DOID:1062", + "GARD:0009120", + "MESH:D005198", + "NCIT:C3034", + "SCTID:40488004", + "UMLS:C0015624", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -96,7 +103,13 @@ def autocomplete(): "name": "Fanconi-like syndrome", "full_name": None, "description": "A syndrome characterized by pancytopenia, immune deficiency and cutaneous malignancies.", - "xref": ["DOID:0090066", "MESH:C536855", "OMIM:227850", "SCTID:236469003", "UMLS:C0151638"], + "xref": [ + "DOID:0090066", + "MESH:C536855", + "OMIM:227850", + "SCTID:236469003", + "UMLS:C0151638", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -231,7 +244,12 @@ def autocomplete(): "name": "Fanconi anemia complementation group C", "full_name": None, "description": "Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.", - "xref": ["DOID:0111087", "NCIT:C125704", "OMIM:227645", "UMLS:C3468041"], + "xref": [ + "DOID:0111087", + "NCIT:C125704", + "OMIM:227645", + "UMLS:C3468041", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -246,7 +264,12 @@ def autocomplete(): "name": "Fanconi anemia complementation group D2", "full_name": None, "description": "Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.", - "xref": ["DOID:0111083", "NCIT:C125706", "OMIM:227646", "UMLS:C3160738"], + "xref": [ + "DOID:0111083", + "NCIT:C125706", + "OMIM:227646", + "UMLS:C3160738", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -283,7 +306,13 @@ def autocomplete(): "name": "Fanconi anemia complementation group B", "full_name": None, "description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.", - "xref": ["DOID:0111098", "MESH:C564497", "NCIT:C125703", "OMIM:300514", "UMLS:C1845292"], + "xref": [ + "DOID:0111098", + "MESH:C564497", + "NCIT:C125703", + "OMIM:300514", + "UMLS:C1845292", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -298,7 +327,12 @@ def autocomplete(): "name": "Fanconi anemia complementation group E", "full_name": None, "description": "Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.", - "xref": ["DOID:0111084", "NCIT:C125709", "OMIM:600901", "UMLS:C3160739"], + "xref": [ + "DOID:0111084", + "NCIT:C125709", + "OMIM:600901", + "UMLS:C3160739", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py index bcccca1de..257103133 100644 --- a/backend/tests/fixtures/autocomplete_response.py +++ b/backend/tests/fixtures/autocomplete_response.py @@ -87,7 +87,13 @@ def autocomplete_response(): "id": "MONDO:0009217", "category": "biolink:Disease", "name": "Fanconi-like syndrome", - "xref": ["DOID:0090066", "MESH:C536855", "OMIM:227850", "SCTID:236469003", "UMLS:C0151638"], + "xref": [ + "DOID:0090066", + "MESH:C536855", + "OMIM:227850", + "SCTID:236469003", + "UMLS:C0151638", + ], "provided_by": "phenio_nodes", "description": "A syndrome characterized by pancytopenia, immune deficiency and cutaneous malignancies.", }, @@ -155,7 +161,12 @@ def autocomplete_response(): "id": "MONDO:0009213", "category": "biolink:Disease", "name": "Fanconi anemia complementation group C", - "xref": ["DOID:0111087", "NCIT:C125704", "OMIM:227645", "UMLS:C3468041"], + "xref": [ + "DOID:0111087", + "NCIT:C125704", + "OMIM:227645", + "UMLS:C3468041", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.", }, @@ -163,7 +174,12 @@ def autocomplete_response(): "id": "MONDO:0009214", "category": "biolink:Disease", "name": "Fanconi anemia complementation group D2", - "xref": ["DOID:0111083", "NCIT:C125706", "OMIM:227646", "UMLS:C3160738"], + "xref": [ + "DOID:0111083", + "NCIT:C125706", + "OMIM:227646", + "UMLS:C3160738", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.", }, @@ -186,7 +202,13 @@ def autocomplete_response(): "id": "MONDO:0010351", "category": "biolink:Disease", "name": "Fanconi anemia complementation group B", - "xref": ["DOID:0111098", "MESH:C564497", "NCIT:C125703", "OMIM:300514", "UMLS:C1845292"], + "xref": [ + "DOID:0111098", + "MESH:C564497", + "NCIT:C125703", + "OMIM:300514", + "UMLS:C1845292", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.", }, @@ -194,7 +216,12 @@ def autocomplete_response(): "id": "MONDO:0010953", "category": "biolink:Disease", "name": "Fanconi anemia complementation group E", - "xref": ["DOID:0111084", "NCIT:C125709", "OMIM:600901", "UMLS:C3160739"], + "xref": [ + "DOID:0111084", + "NCIT:C125709", + "OMIM:600901", + "UMLS:C3160739", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.", }, @@ -202,7 +229,12 @@ def autocomplete_response(): "id": "MONDO:0011325", "category": "biolink:Disease", "name": "Fanconi anemia complementation group F", - "xref": ["DOID:0111088", "EFO:0009045", "NCIT:C125707", "OMIM:603467"], + "xref": [ + "DOID:0111088", + "EFO:0009045", + "NCIT:C125707", + "OMIM:603467", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.", }, diff --git a/backend/tests/fixtures/compare.py b/backend/tests/fixtures/compare.py deleted file mode 100644 index 424dddc30..000000000 --- a/backend/tests/fixtures/compare.py +++ /dev/null @@ -1,100 +0,0 @@ -import pytest - - -@pytest.fixture -def compare(): - return { - "subject_termset": { - "MP:0010771": {"id": "MP:0010771", "label": None}, - "MP:0002169": {"id": "MP:0002169", "label": None}, - }, - "object_termset": {"HP:0004325": {"id": "HP:0004325", "label": None}}, - "subject_best_matches": { - "MP:0002169": { - "match_source": "MP:0002169", - "match_source_label": None, - "match_target": "HP:0004325", - "match_target_label": None, - "score": 1.5616002210519475, - "match_subsumer": None, - "match_subsumer_label": None, - "similarity": { - "subject_id": "MP:0002169", - "subject_label": None, - "subject_source": None, - "object_id": "HP:0004325", - "object_label": None, - "object_source": None, - "ancestor_id": "UPHENO:0001003", - "ancestor_label": None, - "ancestor_source": None, - "object_information_content": None, - "subject_information_content": None, - "ancestor_information_content": 1.5616002210519475, - "jaccard_similarity": 0.16216216216216217, - "cosine_similarity": None, - "dice_similarity": None, - "phenodigm_score": 0.5032220864376823, - }, - }, - "MP:0010771": { - "match_source": "MP:0010771", - "match_source_label": None, - "match_target": "HP:0004325", - "match_target_label": None, - "score": 2.2728188647181566, - "match_subsumer": None, - "match_subsumer_label": None, - "similarity": { - "subject_id": "MP:0010771", - "subject_label": None, - "subject_source": None, - "object_id": "HP:0004325", - "object_label": None, - "object_source": None, - "ancestor_id": "UBERON:0000468", - "ancestor_label": None, - "ancestor_source": None, - "object_information_content": None, - "subject_information_content": None, - "ancestor_information_content": 2.2728188647181566, - "jaccard_similarity": 0.325, - "cosine_similarity": None, - "dice_similarity": None, - "phenodigm_score": 0.8594568814276845, - }, - }, - }, - "object_best_matches": { - "HP:0004325": { - "match_source": "HP:0004325", - "match_source_label": None, - "match_target": "MP:0010771", - "match_target_label": None, - "score": 2.2728188647181566, - "match_subsumer": None, - "match_subsumer_label": None, - "similarity": { - "subject_id": "MP:0010771", - "subject_label": None, - "subject_source": None, - "object_id": "HP:0004325", - "object_label": None, - "object_source": None, - "ancestor_id": "UBERON:0000468", - "ancestor_label": None, - "ancestor_source": None, - "object_information_content": None, - "subject_information_content": None, - "ancestor_information_content": 2.2728188647181566, - "jaccard_similarity": 0.325, - "cosine_similarity": None, - "dice_similarity": None, - "phenodigm_score": 0.8594568814276845, - }, - } - }, - "average_score": 2.0357459834960867, - "best_score": 2.2728188647181566, - "metric": None, - } diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index 78c0fdcd1..cdf285790 100644 --- a/backend/tests/fixtures/histopheno_response.py +++ b/backend/tests/fixtures/histopheno_response.py @@ -5,7 +5,7 @@ def histopheno_response(): return { "responseHeader": { - "QTime": 1, + "QTime": 0, "params": { "facet.query": [ 'object_closure:"HP:0000924"', diff --git a/backend/tests/fixtures/metadata.py b/backend/tests/fixtures/metadata.py deleted file mode 100644 index 55287fd43..000000000 --- a/backend/tests/fixtures/metadata.py +++ /dev/null @@ -1,14 +0,0 @@ -import pytest - - -@pytest.fixture -def metadata(): - return [ - {"label": "biolink:Gene", "count": 514018}, - {"label": "biolink:PhenotypicQuality", "count": 89431}, - {"label": "biolink:Disease", "count": 26469}, - {"label": "biolink:GeneToPhenotypicFeatureAssociation", "count": 735039}, - {"label": "biolink:DiseaseToPhenotypicFeatureAssociation", "count": 241110}, - {"label": "biolink:CorrelatedGeneToDiseaseAssociation", "count": 8519}, - {"label": "biolink:CausalGeneToDiseaseAssociation", "count": 6491}, - ] diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index d3ba511bc..46a964b4a 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -32,21 +32,39 @@ def node(): {"id": "GARD:0007922", "url": None}, {"id": "ICD10CM:G71.0", "url": None}, {"id": "ICD9:359.1", "url": None}, - {"id": "MESH:D009136", "url": "http://purl.obolibrary.org/obo/MESH_D009136"}, + { + "id": "MESH:D009136", + "url": "http://purl.obolibrary.org/obo/MESH_D009136", + }, {"id": "MedDRA:10028356", "url": None}, {"id": "NCIT:C84910", "url": "http://purl.obolibrary.org/obo/NCIT_C84910"}, {"id": "Orphanet:98473", "url": "http://www.orpha.net/ORDO/Orphanet_98473"}, {"id": "SCTID:73297009", "url": None}, - {"id": "UMLS:C0026850", "url": "http://linkedlifedata.com/resource/umls/id/C0026850"}, + { + "id": "UMLS:C0026850", + "url": "http://linkedlifedata.com/resource/umls/id/C0026850", + }, ], "provided_by_link": { "id": "phenio", "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", }, "association_counts": [ - {"label": "Phenotypes", "count": 4011, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, - {"label": "Causal Genes", "count": 121, "category": "biolink:CausalGeneToDiseaseAssociation"}, - {"label": "Correlated Genes", "count": 147, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, + { + "label": "Phenotypes", + "count": 4011, + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + }, + { + "label": "Causal Genes", + "count": 121, + "category": "biolink:CausalGeneToDiseaseAssociation", + }, + { + "label": "Correlated Genes", + "count": 147, + "category": "biolink:CorrelatedGeneToDiseaseAssociation", + }, ], "node_hierarchy": { "super_classes": [ @@ -90,12 +108,11 @@ def node(): "synonym": [], }, ], - "equivalent_classes": [], "sub_classes": [ { - "id": "MONDO:0020121", + "id": "MONDO:0008028", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, Barnes type", "full_name": None, "description": None, "xref": [], @@ -106,9 +123,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0010675", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, cardiac type", "full_name": None, "description": None, "xref": [], @@ -119,9 +136,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0010676", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, Hemizygous lethal type", "full_name": None, "description": None, "xref": [], @@ -132,9 +149,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0010677", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, Mabry type", "full_name": None, "description": None, "xref": [], @@ -145,9 +162,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0010678", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, progressive Pectorodorsal", "full_name": None, "description": None, "xref": [], @@ -158,9 +175,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0016106", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "progressive muscular dystrophy", "full_name": None, "description": None, "xref": [], @@ -171,9 +188,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0018949", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "distal myopathy", "full_name": None, "description": None, "xref": [], @@ -184,9 +201,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0019950", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "congenital muscular dystrophy", "full_name": None, "description": None, "xref": [], @@ -197,9 +214,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0023204", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "Fukuda-Miyanomae-Nakata syndrome", "full_name": None, "description": None, "xref": [], @@ -210,9 +227,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0020121", + "id": "MONDO:0100228", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "LAMA2-related muscular dystrophy", "full_name": None, "description": None, "xref": [], diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py index 03383e406..9f04ded8f 100644 --- a/backend/tests/fixtures/phenotype_explorer_compare.py +++ b/backend/tests/fixtures/phenotype_explorer_compare.py @@ -5,8 +5,11 @@ def phenotype_explorer_compare(): return { "subject_termset": { + "MP:0002169": { + "id": "MP:0002169", + "label": "no abnormal phenotype detected (MPO)", + }, "MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"}, - "MP:0002169": {"id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)"}, }, "object_termset": {"HP:0004325": {"id": "HP:0004325", "label": "Decreased body weight (HPO)"}}, "subject_best_matches": { diff --git a/backend/tests/fixtures/search.py b/backend/tests/fixtures/search.py index c40558ae7..4c585d6e5 100644 --- a/backend/tests/fixtures/search.py +++ b/backend/tests/fixtures/search.py @@ -40,7 +40,14 @@ def search(): "name": "Fanconi renotubular syndrome", "full_name": None, "description": "A genetic or acquired disorder characterized by impairment of the function of the proximal tubules of the kidney. It results in decreased reabsorption of electrolytes, glucose, amino acids, and other nutrients.", - "xref": ["DOID:1062", "GARD:0009120", "MESH:D005198", "NCIT:C3034", "SCTID:40488004", "UMLS:C0015624"], + "xref": [ + "DOID:1062", + "GARD:0009120", + "MESH:D005198", + "NCIT:C3034", + "SCTID:40488004", + "UMLS:C0015624", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -70,7 +77,13 @@ def search(): "name": "Fanconi-like syndrome", "full_name": None, "description": "A syndrome characterized by pancytopenia, immune deficiency and cutaneous malignancies.", - "xref": ["DOID:0090066", "MESH:C536855", "OMIM:227850", "SCTID:236469003", "UMLS:C0151638"], + "xref": [ + "DOID:0090066", + "MESH:C536855", + "OMIM:227850", + "SCTID:236469003", + "UMLS:C0151638", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -205,7 +218,12 @@ def search(): "name": "Fanconi anemia complementation group C", "full_name": None, "description": "Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.", - "xref": ["DOID:0111087", "NCIT:C125704", "OMIM:227645", "UMLS:C3468041"], + "xref": [ + "DOID:0111087", + "NCIT:C125704", + "OMIM:227645", + "UMLS:C3468041", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -220,7 +238,12 @@ def search(): "name": "Fanconi anemia complementation group D2", "full_name": None, "description": "Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.", - "xref": ["DOID:0111083", "NCIT:C125706", "OMIM:227646", "UMLS:C3160738"], + "xref": [ + "DOID:0111083", + "NCIT:C125706", + "OMIM:227646", + "UMLS:C3160738", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -257,7 +280,13 @@ def search(): "name": "Fanconi anemia complementation group B", "full_name": None, "description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.", - "xref": ["DOID:0111098", "MESH:C564497", "NCIT:C125703", "OMIM:300514", "UMLS:C1845292"], + "xref": [ + "DOID:0111098", + "MESH:C564497", + "NCIT:C125703", + "OMIM:300514", + "UMLS:C1845292", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -272,7 +301,12 @@ def search(): "name": "Fanconi anemia complementation group E", "full_name": None, "description": "Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.", - "xref": ["DOID:0111084", "NCIT:C125709", "OMIM:600901", "UMLS:C3160739"], + "xref": [ + "DOID:0111084", + "NCIT:C125709", + "OMIM:600901", + "UMLS:C3160739", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, @@ -325,7 +359,13 @@ def search(): "name": "Fanconi anemia complementation group I", "full_name": None, "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", - "xref": ["DOID:0111091", "MESH:C563802", "NCIT:C129026", "OMIM:609053", "UMLS:C1836861"], + "xref": [ + "DOID:0111091", + "MESH:C563802", + "NCIT:C129026", + "OMIM:609053", + "UMLS:C1836861", + ], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index d89711872..eb6e12db2 100644 --- a/backend/tests/fixtures/search_response.py +++ b/backend/tests/fixtures/search_response.py @@ -69,7 +69,13 @@ def search_response(): "id": "MONDO:0009217", "category": "biolink:Disease", "name": "Fanconi-like syndrome", - "xref": ["DOID:0090066", "MESH:C536855", "OMIM:227850", "SCTID:236469003", "UMLS:C0151638"], + "xref": [ + "DOID:0090066", + "MESH:C536855", + "OMIM:227850", + "SCTID:236469003", + "UMLS:C0151638", + ], "provided_by": "phenio_nodes", "description": "A syndrome characterized by pancytopenia, immune deficiency and cutaneous malignancies.", }, @@ -137,7 +143,12 @@ def search_response(): "id": "MONDO:0009213", "category": "biolink:Disease", "name": "Fanconi anemia complementation group C", - "xref": ["DOID:0111087", "NCIT:C125704", "OMIM:227645", "UMLS:C3468041"], + "xref": [ + "DOID:0111087", + "NCIT:C125704", + "OMIM:227645", + "UMLS:C3468041", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.", }, @@ -145,7 +156,12 @@ def search_response(): "id": "MONDO:0009214", "category": "biolink:Disease", "name": "Fanconi anemia complementation group D2", - "xref": ["DOID:0111083", "NCIT:C125706", "OMIM:227646", "UMLS:C3160738"], + "xref": [ + "DOID:0111083", + "NCIT:C125706", + "OMIM:227646", + "UMLS:C3160738", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.", }, @@ -168,7 +184,13 @@ def search_response(): "id": "MONDO:0010351", "category": "biolink:Disease", "name": "Fanconi anemia complementation group B", - "xref": ["DOID:0111098", "MESH:C564497", "NCIT:C125703", "OMIM:300514", "UMLS:C1845292"], + "xref": [ + "DOID:0111098", + "MESH:C564497", + "NCIT:C125703", + "OMIM:300514", + "UMLS:C1845292", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.", }, @@ -176,7 +198,12 @@ def search_response(): "id": "MONDO:0010953", "category": "biolink:Disease", "name": "Fanconi anemia complementation group E", - "xref": ["DOID:0111084", "NCIT:C125709", "OMIM:600901", "UMLS:C3160739"], + "xref": [ + "DOID:0111084", + "NCIT:C125709", + "OMIM:600901", + "UMLS:C3160739", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.", }, @@ -184,7 +211,12 @@ def search_response(): "id": "MONDO:0011325", "category": "biolink:Disease", "name": "Fanconi anemia complementation group F", - "xref": ["DOID:0111088", "EFO:0009045", "NCIT:C125707", "OMIM:603467"], + "xref": [ + "DOID:0111088", + "EFO:0009045", + "NCIT:C125707", + "OMIM:603467", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.", }, @@ -208,7 +240,13 @@ def search_response(): "id": "MONDO:0012186", "category": "biolink:Disease", "name": "Fanconi anemia complementation group I", - "xref": ["DOID:0111091", "MESH:C563802", "NCIT:C129026", "OMIM:609053", "UMLS:C1836861"], + "xref": [ + "DOID:0111091", + "MESH:C563802", + "NCIT:C129026", + "OMIM:609053", + "UMLS:C1836861", + ], "provided_by": "phenio_nodes", "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", }, diff --git a/backend/tests/unit/test_fixtures.py b/backend/tests/unit/test_fixtures.py index 1cdbc9986..4abeaf439 100644 --- a/backend/tests/unit/test_fixtures.py +++ b/backend/tests/unit/test_fixtures.py @@ -13,8 +13,8 @@ def test_autocomplete(autocomplete): assert autocomplete.total != 0 -def test_compare(compare): - tsps = TermSetPairwiseSimilarity(**compare) +def test_compare(phenotype_explorer_compare): + tsps = TermSetPairwiseSimilarity(**phenotype_explorer_compare) assert len(tsps.subject_best_matches) != 0 diff --git a/backend/tests/unit/test_solr_entity_utils.py b/backend/tests/unit/test_solr_entity_utils.py index 180986c6e..aae04ad59 100644 --- a/backend/tests/unit/test_solr_entity_utils.py +++ b/backend/tests/unit/test_solr_entity_utils.py @@ -18,8 +18,8 @@ object_label="Test Case 2", predicate="biolink:subclass_of", ), - Entity(id="ENT:0000001", name="Test Case 1", category="biolink:testCase"), Entity(id="ENT:0000002", name="Test Case 2", category="biolink:testCase"), + Entity(id="ENT:0000003", name="Test Case 3", category="biolink:testCase"), ), ( Association( @@ -27,10 +27,10 @@ object="ENT:0000004", object_category="biolink:testCase", object_label="Test Case 4", - object_closure=["ENT:0000003"], - subject="ENT:0000004", + object_closure=["ENT:0000001"], + subject="ENT:0000003", subject_category="biolink:testCase", - subject_label="Test Case 4", + subject_label="Test Case 3", predicate="biolink:subclass_of", ), Entity(id="ENT:0000003", name="Test Case 3", category="biolink:testCase"), diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index 8324c4e37..664a372ea 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -127,12 +127,11 @@ "synonym": [] } ], - "equivalent_classes": [], "sub_classes": [ { - "id": "MONDO:0020121", + "id": "MONDO:0008028", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, Barnes type", "full_name": null, "description": null, "xref": [], @@ -143,9 +142,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0010675", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, cardiac type", "full_name": null, "description": null, "xref": [], @@ -156,9 +155,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0010676", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, Hemizygous lethal type", "full_name": null, "description": null, "xref": [], @@ -169,9 +168,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0010677", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, Mabry type", "full_name": null, "description": null, "xref": [], @@ -182,9 +181,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0010678", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "muscular dystrophy, progressive Pectorodorsal", "full_name": null, "description": null, "xref": [], @@ -195,9 +194,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0016106", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "progressive muscular dystrophy", "full_name": null, "description": null, "xref": [], @@ -208,9 +207,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0018949", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "distal myopathy", "full_name": null, "description": null, "xref": [], @@ -221,9 +220,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0019950", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "congenital muscular dystrophy", "full_name": null, "description": null, "xref": [], @@ -234,9 +233,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0023204", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "Fukuda-Miyanomae-Nakata syndrome", "full_name": null, "description": null, "xref": [], @@ -247,9 +246,9 @@ "synonym": [] }, { - "id": "MONDO:0020121", + "id": "MONDO:0100228", "category": "biolink:Disease", - "name": "muscular dystrophy", + "name": "LAMA2-related muscular dystrophy", "full_name": null, "description": null, "xref": [], diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index fdee933ea..9eee78b95 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -1,12 +1,12 @@ { "subject_termset": { - "MP:0010771": { - "id": "MP:0010771", - "label": "integument phenotype (MPO)" - }, "MP:0002169": { "id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)" + }, + "MP:0010771": { + "id": "MP:0010771", + "label": "integument phenotype (MPO)" } }, "object_termset": { diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts index 0c73b918d..310c48aa5 100644 --- a/frontend/src/api/model.ts +++ b/frontend/src/api/model.ts @@ -344,7 +344,6 @@ export interface Node extends Entity { export interface NodeHierarchy { super_classes: Entity[], - equivalent_classes: Entity[], sub_classes: Entity[], }; diff --git a/frontend/src/pages/metadata.json b/frontend/src/pages/metadata.json index 39e43a425..e961fb426 100644 --- a/frontend/src/pages/metadata.json +++ b/frontend/src/pages/metadata.json @@ -28,12 +28,12 @@ "count": 15010 }, { - "label": "Gene to Pheno.", + "label": "Gene to Phenotype", "icon": "association-gene-to-phenotype", "count": 735039 }, { - "label": "Disease to Pheno.", + "label": "Disease to Phenotype", "icon": "association-disease-to-phenotype", "count": 241110 }, diff --git a/frontend/src/pages/node/SectionHierarchy.vue b/frontend/src/pages/node/SectionHierarchy.vue index 3db67e23f..e172c38cf 100644 --- a/frontend/src/pages/node/SectionHierarchy.vue +++ b/frontend/src/pages/node/SectionHierarchy.vue @@ -31,27 +31,6 @@ - - - - - - -