From a79b8d2bd0cfebc83a5b4b7381d6c40ddb92be8b Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Fri, 3 Nov 2023 13:16:42 -0700
Subject: [PATCH 1/9] Added MappingResults & MappingInterface

---
 backend/src/monarch_py/datamodels/model.py    | 203 +++++++++++++-----
 backend/src/monarch_py/datamodels/model.yaml  |   6 +
 .../interfaces/mapping_interface.py           |  15 ++
 frontend/src/api/model.ts                     |  17 +-
 4 files changed, 190 insertions(+), 51 deletions(-)
 create mode 100644 backend/src/monarch_py/interfaces/mapping_interface.py

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
index ce8d75fcc..84b20d4b4 100644
--- a/backend/src/monarch_py/datamodels/model.py
+++ b/backend/src/monarch_py/datamodels/model.py
@@ -48,13 +48,19 @@ class Association(ConfiguredBaseModel):
     category: Optional[str] = Field(None)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
-    subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
-    subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
+    subject_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the subject entity"""
+    )
+    subject_category: Optional[str] = Field(
+        None, description="""The category of the subject entity"""
+    )
     subject_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject id and the ids of all of it's ancestors""",
     )
-    subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
+    subject_label: Optional[str] = Field(
+        None, description="""The name of the subject entity"""
+    )
     subject_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject name and the names of all of it's ancestors""",
@@ -64,13 +70,19 @@ class Association(ConfiguredBaseModel):
     predicate: str = Field(...)
     object: str = Field(...)
     original_object: Optional[str] = Field(None)
-    object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
-    object_category: Optional[str] = Field(None, description="""The category of the object entity""")
+    object_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the object entity"""
+    )
+    object_category: Optional[str] = Field(
+        None, description="""The category of the object entity"""
+    )
     object_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object id and the ids of all of it's ancestors""",
     )
-    object_label: Optional[str] = Field(None, description="""The name of the object entity""")
+    object_label: Optional[str] = Field(
+        None, description="""The name of the object entity"""
+    )
     object_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object name and the names of all of it's ancestors""",
@@ -109,11 +121,15 @@ class Association(ConfiguredBaseModel):
     onset_qualifier: Optional[str] = Field(None)
     sex_qualifier: Optional[str] = Field(None)
     stage_qualifier: Optional[str] = Field(None)
-    qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
+    qualifiers_label: Optional[str] = Field(
+        None, description="""The name of the frequency_qualifier entity"""
+    )
     qualifiers_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
-    qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
+    qualifiers_category: Optional[str] = Field(
+        None, description="""The category of the frequency_qualifier entity"""
+    )
     qualifiers_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
@@ -122,7 +138,9 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
+    frequency_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the frequency_qualifier entity"""
+    )
     frequency_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
@@ -137,11 +155,15 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
+    onset_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the onset_qualifier entity"""
+    )
     onset_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the onset_qualifier entity"""
     )
-    onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
+    onset_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the onset_qualifier entity"""
+    )
     onset_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
@@ -150,11 +172,15 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
     )
-    sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
+    sex_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the sex_qualifier entity"""
+    )
     sex_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the sex_qualifier entity"""
     )
-    sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
+    sex_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the sex_qualifier entity"""
+    )
     sex_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
@@ -163,11 +189,15 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
     )
-    stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
+    stage_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the stage_qualifier entity"""
+    )
     stage_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the stage_qualifier entity"""
     )
-    stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
+    stage_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the stage_qualifier entity"""
+    )
     stage_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
@@ -225,13 +255,19 @@ class DirectionalAssociation(Association):
     category: Optional[str] = Field(None)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
-    subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
-    subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
+    subject_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the subject entity"""
+    )
+    subject_category: Optional[str] = Field(
+        None, description="""The category of the subject entity"""
+    )
     subject_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject id and the ids of all of it's ancestors""",
     )
-    subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
+    subject_label: Optional[str] = Field(
+        None, description="""The name of the subject entity"""
+    )
     subject_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject name and the names of all of it's ancestors""",
@@ -241,13 +277,19 @@ class DirectionalAssociation(Association):
     predicate: str = Field(...)
     object: str = Field(...)
     original_object: Optional[str] = Field(None)
-    object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
-    object_category: Optional[str] = Field(None, description="""The category of the object entity""")
+    object_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the object entity"""
+    )
+    object_category: Optional[str] = Field(
+        None, description="""The category of the object entity"""
+    )
     object_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object id and the ids of all of it's ancestors""",
     )
-    object_label: Optional[str] = Field(None, description="""The name of the object entity""")
+    object_label: Optional[str] = Field(
+        None, description="""The name of the object entity"""
+    )
     object_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object name and the names of all of it's ancestors""",
@@ -286,11 +328,15 @@ class DirectionalAssociation(Association):
     onset_qualifier: Optional[str] = Field(None)
     sex_qualifier: Optional[str] = Field(None)
     stage_qualifier: Optional[str] = Field(None)
-    qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
+    qualifiers_label: Optional[str] = Field(
+        None, description="""The name of the frequency_qualifier entity"""
+    )
     qualifiers_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
-    qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
+    qualifiers_category: Optional[str] = Field(
+        None, description="""The category of the frequency_qualifier entity"""
+    )
     qualifiers_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
@@ -299,7 +345,9 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
+    frequency_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the frequency_qualifier entity"""
+    )
     frequency_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
@@ -314,11 +362,15 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
+    onset_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the onset_qualifier entity"""
+    )
     onset_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the onset_qualifier entity"""
     )
-    onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
+    onset_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the onset_qualifier entity"""
+    )
     onset_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
@@ -327,11 +379,15 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
     )
-    sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
+    sex_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the sex_qualifier entity"""
+    )
     sex_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the sex_qualifier entity"""
     )
-    sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
+    sex_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the sex_qualifier entity"""
+    )
     sex_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
@@ -340,11 +396,15 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
     )
-    stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
+    stage_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the stage_qualifier entity"""
+    )
     stage_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the stage_qualifier entity"""
     )
-    stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
+    stage_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the stage_qualifier entity"""
+    )
     stage_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
@@ -372,11 +432,15 @@ class Entity(ConfiguredBaseModel):
     id: str = Field(...)
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
-    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    full_name: Optional[str] = Field(
+        None, description="""The long form name of an entity"""
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
-    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
+    in_taxon: Optional[str] = Field(
+        None, description="""The biolink taxon that the entity is in the closure of."""
+    )
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -430,10 +494,14 @@ class Mapping(ConfiguredBaseModel):
     """
 
     subject_id: str = Field(...)
-    subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
+    subject_label: Optional[str] = Field(
+        None, description="""The name of the subject entity"""
+    )
     predicate_id: str = Field(...)
     object_id: str = Field(...)
-    object_label: Optional[str] = Field(None, description="""The name of the object entity""")
+    object_label: Optional[str] = Field(
+        None, description="""The name of the object entity"""
+    )
     mapping_justification: Optional[str] = Field(None)
 
 
@@ -442,7 +510,9 @@ class Node(Entity):
     UI container class extending Entity with additional information
     """
 
-    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
+    in_taxon: Optional[str] = Field(
+        None, description="""The biolink taxon that the entity is in the closure of."""
+    )
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -468,7 +538,9 @@ class Node(Entity):
     id: str = Field(...)
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
-    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    full_name: Optional[str] = Field(
+        None, description="""The long form name of an entity"""
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
@@ -538,11 +610,23 @@ class EntityResults(Results):
     total: int = Field(..., description="""total number of items matching a query""")
 
 
+class MappingResults(Results):
+    """
+    SSSOM Mappings returned as a results collection
+    """
+
+    limit: int = Field(..., description="""number of items to return in a response""")
+    offset: int = Field(..., description="""offset into the total number of items""")
+    total: int = Field(..., description="""total number of items matching a query""")
+
+
 class MultiEntityAssociationResults(Results):
 
     id: str = Field(...)
     name: Optional[str] = Field(None)
-    associated_categories: List[CategoryGroupedAssociationResults] = Field(default_factory=list)
+    associated_categories: List[CategoryGroupedAssociationResults] = Field(
+        default_factory=list
+    )
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
@@ -550,16 +634,22 @@ class MultiEntityAssociationResults(Results):
 
 class SearchResult(Entity):
 
-    highlight: Optional[str] = Field(None, description="""matching text snippet containing html tags""")
+    highlight: Optional[str] = Field(
+        None, description="""matching text snippet containing html tags"""
+    )
     score: Optional[float] = Field(None)
     id: str = Field(...)
     category: str = Field(...)
     name: str = Field(...)
-    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    full_name: Optional[str] = Field(
+        None, description="""The long form name of an entity"""
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
-    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
+    in_taxon: Optional[str] = Field(
+        None, description="""The biolink taxon that the entity is in the closure of."""
+    )
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -602,20 +692,36 @@ class TermPairwiseSimilarity(PairwiseSimilarity):
     """
 
     subject_id: str = Field(...)
-    subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
-    subject_source: Optional[str] = Field(None, description="""the source for the first entity""")
+    subject_label: Optional[str] = Field(
+        None, description="""The name of the subject entity"""
+    )
+    subject_source: Optional[str] = Field(
+        None, description="""the source for the first entity"""
+    )
     object_id: str = Field(...)
-    object_label: Optional[str] = Field(None, description="""The name of the object entity""")
-    object_source: Optional[str] = Field(None, description="""the source for the second entity""")
+    object_label: Optional[str] = Field(
+        None, description="""The name of the object entity"""
+    )
+    object_source: Optional[str] = Field(
+        None, description="""the source for the second entity"""
+    )
     ancestor_id: Optional[str] = Field(
         None,
         description="""the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected""",
     )
-    ancestor_label: Optional[str] = Field(None, description="""the name or label of the ancestor concept""")
+    ancestor_label: Optional[str] = Field(
+        None, description="""the name or label of the ancestor concept"""
+    )
     ancestor_source: Optional[str] = Field(None)
-    object_information_content: Optional[float] = Field(None, description="""The IC of the object""")
-    subject_information_content: Optional[float] = Field(None, description="""The IC of the subject""")
-    ancestor_information_content: Optional[float] = Field(None, description="""The IC of the object""")
+    object_information_content: Optional[float] = Field(
+        None, description="""The IC of the object"""
+    )
+    subject_information_content: Optional[float] = Field(
+        None, description="""The IC of the subject"""
+    )
+    ancestor_information_content: Optional[float] = Field(
+        None, description="""The IC of the object"""
+    )
     jaccard_similarity: Optional[float] = Field(
         None,
         description="""The number of concepts in the intersection divided by the number in the union""",
@@ -684,6 +790,7 @@ class BestMatch(ConfiguredBaseModel):
 AssociationTableResults.update_forward_refs()
 CategoryGroupedAssociationResults.update_forward_refs()
 EntityResults.update_forward_refs()
+MappingResults.update_forward_refs()
 MultiEntityAssociationResults.update_forward_refs()
 SearchResult.update_forward_refs()
 SearchResults.update_forward_refs()
diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml
index b28bfaebe..b7bc4323d 100644
--- a/backend/src/monarch_py/datamodels/model.yaml
+++ b/backend/src/monarch_py/datamodels/model.yaml
@@ -210,6 +210,12 @@ classes:
       - object_id
       - object_label
       - mapping_justification
+  MappingResults:
+    description: SSSOM Mappings returned as a results collection
+    is_a: Results
+    slot_usage:
+      items:
+        range: Mapping
   MultiEntityAssociationResults:
     is_a: Results
     slots:
diff --git a/backend/src/monarch_py/interfaces/mapping_interface.py b/backend/src/monarch_py/interfaces/mapping_interface.py
new file mode 100644
index 000000000..d33b93337
--- /dev/null
+++ b/backend/src/monarch_py/interfaces/mapping_interface.py
@@ -0,0 +1,15 @@
+from abc import ABC
+from typing import List
+
+from monarch_py.datamodels.model import MappingResults
+
+class MappingInterface(ABC):
+
+    def get_mappings(self,
+                     entity_id: List[str] = None,
+                     subject_id: List[str] = None,
+                     predicate_id: List[str] = None,
+                     object_id: List[str] = None,
+                     mapping_justification: List[str] = None,
+                     ) -> MappingResults:
+        raise NotImplementedError
diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index 34b656aeb..d6d59466f 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -376,6 +376,17 @@ export interface Mapping {
     object_label?: string,
     mapping_justification?: string,
 };
+/**
+ * SSSOM Mappings returned as a results collection
+ */
+export interface MappingResults extends Results {
+    /** number of items to return in a response */
+    limit: number,
+    /** offset into the total number of items */
+    offset: number,
+    /** total number of items matching a query */
+    total: number,
+};
 
 export interface MultiEntityAssociationResults extends Results {
     id: string,
@@ -502,12 +513,12 @@ export interface TermPairwiseSimilarity extends PairwiseSimilarity {
     /** The IC of the object */
     ancestor_information_content?: string,
     /** The number of concepts in the intersection divided by the number in the union */
-    jaccard_similarity?: number,
+    jaccard_similarity?: string,
     /** the dot product of two node embeddings divided by the product of their lengths */
     cosine_similarity?: number,
-    dice_similarity?: number,
+    dice_similarity?: string,
     /** the geometric mean of the jaccard similarity and the information content */
-    phenodigm_score?: number,
+    phenodigm_score?: string,
 };
 /**
  * A simple pairwise similarity between two sets of concepts/terms

From 40dd3f136e3caaaea9cfbd0e7780fc9f0faea525 Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Mon, 6 Nov 2023 13:19:03 -0800
Subject: [PATCH 2/9] Added MappingResults & MappingInterface

---
 backend/src/monarch_py/interfaces/mapping_interface.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/backend/src/monarch_py/interfaces/mapping_interface.py b/backend/src/monarch_py/interfaces/mapping_interface.py
index d33b93337..18f147750 100644
--- a/backend/src/monarch_py/interfaces/mapping_interface.py
+++ b/backend/src/monarch_py/interfaces/mapping_interface.py
@@ -3,6 +3,7 @@
 
 from monarch_py.datamodels.model import MappingResults
 
+
 class MappingInterface(ABC):
 
     def get_mappings(self,

From 0f97e16d77a819f3e846026309cb18ee4ad49ddf Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Mon, 6 Nov 2023 15:35:17 -0800
Subject: [PATCH 3/9] Added solr querying & parsing for sssom api endpoint

---
 backend/src/monarch_py/datamodels/model.py    | 192 +++++-------------
 backend/src/monarch_py/datamodels/solr.py     |   1 +
 .../solr/solr_implementation.py               |  18 ++
 .../implementations/solr/solr_parsers.py      |  15 ++
 .../implementations/solr/solr_query_utils.py  |  23 +++
 .../interfaces/mapping_interface.py           |  24 ++-
 6 files changed, 122 insertions(+), 151 deletions(-)

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
index 84b20d4b4..2d1df70be 100644
--- a/backend/src/monarch_py/datamodels/model.py
+++ b/backend/src/monarch_py/datamodels/model.py
@@ -48,19 +48,13 @@ class Association(ConfiguredBaseModel):
     category: Optional[str] = Field(None)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
-    subject_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the subject entity"""
-    )
-    subject_category: Optional[str] = Field(
-        None, description="""The category of the subject entity"""
-    )
+    subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
+    subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
     subject_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject id and the ids of all of it's ancestors""",
     )
-    subject_label: Optional[str] = Field(
-        None, description="""The name of the subject entity"""
-    )
+    subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
     subject_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject name and the names of all of it's ancestors""",
@@ -70,19 +64,13 @@ class Association(ConfiguredBaseModel):
     predicate: str = Field(...)
     object: str = Field(...)
     original_object: Optional[str] = Field(None)
-    object_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the object entity"""
-    )
-    object_category: Optional[str] = Field(
-        None, description="""The category of the object entity"""
-    )
+    object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
+    object_category: Optional[str] = Field(None, description="""The category of the object entity""")
     object_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object id and the ids of all of it's ancestors""",
     )
-    object_label: Optional[str] = Field(
-        None, description="""The name of the object entity"""
-    )
+    object_label: Optional[str] = Field(None, description="""The name of the object entity""")
     object_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object name and the names of all of it's ancestors""",
@@ -121,15 +109,11 @@ class Association(ConfiguredBaseModel):
     onset_qualifier: Optional[str] = Field(None)
     sex_qualifier: Optional[str] = Field(None)
     stage_qualifier: Optional[str] = Field(None)
-    qualifiers_label: Optional[str] = Field(
-        None, description="""The name of the frequency_qualifier entity"""
-    )
+    qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
     qualifiers_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
-    qualifiers_category: Optional[str] = Field(
-        None, description="""The category of the frequency_qualifier entity"""
-    )
+    qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
     qualifiers_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
@@ -138,9 +122,7 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    frequency_qualifier_label: Optional[str] = Field(
-        None, description="""The name of the frequency_qualifier entity"""
-    )
+    frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
     frequency_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
@@ -155,15 +137,11 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    onset_qualifier_label: Optional[str] = Field(
-        None, description="""The name of the onset_qualifier entity"""
-    )
+    onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
     onset_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the onset_qualifier entity"""
     )
-    onset_qualifier_category: Optional[str] = Field(
-        None, description="""The category of the onset_qualifier entity"""
-    )
+    onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
     onset_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
@@ -172,15 +150,11 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
     )
-    sex_qualifier_label: Optional[str] = Field(
-        None, description="""The name of the sex_qualifier entity"""
-    )
+    sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
     sex_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the sex_qualifier entity"""
     )
-    sex_qualifier_category: Optional[str] = Field(
-        None, description="""The category of the sex_qualifier entity"""
-    )
+    sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
     sex_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
@@ -189,15 +163,11 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
     )
-    stage_qualifier_label: Optional[str] = Field(
-        None, description="""The name of the stage_qualifier entity"""
-    )
+    stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
     stage_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the stage_qualifier entity"""
     )
-    stage_qualifier_category: Optional[str] = Field(
-        None, description="""The category of the stage_qualifier entity"""
-    )
+    stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
     stage_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
@@ -255,19 +225,13 @@ class DirectionalAssociation(Association):
     category: Optional[str] = Field(None)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
-    subject_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the subject entity"""
-    )
-    subject_category: Optional[str] = Field(
-        None, description="""The category of the subject entity"""
-    )
+    subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
+    subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
     subject_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject id and the ids of all of it's ancestors""",
     )
-    subject_label: Optional[str] = Field(
-        None, description="""The name of the subject entity"""
-    )
+    subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
     subject_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject name and the names of all of it's ancestors""",
@@ -277,19 +241,13 @@ class DirectionalAssociation(Association):
     predicate: str = Field(...)
     object: str = Field(...)
     original_object: Optional[str] = Field(None)
-    object_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the object entity"""
-    )
-    object_category: Optional[str] = Field(
-        None, description="""The category of the object entity"""
-    )
+    object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
+    object_category: Optional[str] = Field(None, description="""The category of the object entity""")
     object_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object id and the ids of all of it's ancestors""",
     )
-    object_label: Optional[str] = Field(
-        None, description="""The name of the object entity"""
-    )
+    object_label: Optional[str] = Field(None, description="""The name of the object entity""")
     object_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object name and the names of all of it's ancestors""",
@@ -328,15 +286,11 @@ class DirectionalAssociation(Association):
     onset_qualifier: Optional[str] = Field(None)
     sex_qualifier: Optional[str] = Field(None)
     stage_qualifier: Optional[str] = Field(None)
-    qualifiers_label: Optional[str] = Field(
-        None, description="""The name of the frequency_qualifier entity"""
-    )
+    qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
     qualifiers_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
-    qualifiers_category: Optional[str] = Field(
-        None, description="""The category of the frequency_qualifier entity"""
-    )
+    qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
     qualifiers_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
@@ -345,9 +299,7 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    frequency_qualifier_label: Optional[str] = Field(
-        None, description="""The name of the frequency_qualifier entity"""
-    )
+    frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
     frequency_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
@@ -362,15 +314,11 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    onset_qualifier_label: Optional[str] = Field(
-        None, description="""The name of the onset_qualifier entity"""
-    )
+    onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
     onset_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the onset_qualifier entity"""
     )
-    onset_qualifier_category: Optional[str] = Field(
-        None, description="""The category of the onset_qualifier entity"""
-    )
+    onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
     onset_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
@@ -379,15 +327,11 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
     )
-    sex_qualifier_label: Optional[str] = Field(
-        None, description="""The name of the sex_qualifier entity"""
-    )
+    sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
     sex_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the sex_qualifier entity"""
     )
-    sex_qualifier_category: Optional[str] = Field(
-        None, description="""The category of the sex_qualifier entity"""
-    )
+    sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
     sex_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
@@ -396,15 +340,11 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
     )
-    stage_qualifier_label: Optional[str] = Field(
-        None, description="""The name of the stage_qualifier entity"""
-    )
+    stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
     stage_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the stage_qualifier entity"""
     )
-    stage_qualifier_category: Optional[str] = Field(
-        None, description="""The category of the stage_qualifier entity"""
-    )
+    stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
     stage_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
@@ -432,15 +372,11 @@ class Entity(ConfiguredBaseModel):
     id: str = Field(...)
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
-    full_name: Optional[str] = Field(
-        None, description="""The long form name of an entity"""
-    )
+    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
-    in_taxon: Optional[str] = Field(
-        None, description="""The biolink taxon that the entity is in the closure of."""
-    )
+    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -494,14 +430,10 @@ class Mapping(ConfiguredBaseModel):
     """
 
     subject_id: str = Field(...)
-    subject_label: Optional[str] = Field(
-        None, description="""The name of the subject entity"""
-    )
+    subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
     predicate_id: str = Field(...)
     object_id: str = Field(...)
-    object_label: Optional[str] = Field(
-        None, description="""The name of the object entity"""
-    )
+    object_label: Optional[str] = Field(None, description="""The name of the object entity""")
     mapping_justification: Optional[str] = Field(None)
 
 
@@ -510,9 +442,7 @@ class Node(Entity):
     UI container class extending Entity with additional information
     """
 
-    in_taxon: Optional[str] = Field(
-        None, description="""The biolink taxon that the entity is in the closure of."""
-    )
+    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -538,9 +468,7 @@ class Node(Entity):
     id: str = Field(...)
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
-    full_name: Optional[str] = Field(
-        None, description="""The long form name of an entity"""
-    )
+    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
@@ -624,9 +552,7 @@ class MultiEntityAssociationResults(Results):
 
     id: str = Field(...)
     name: Optional[str] = Field(None)
-    associated_categories: List[CategoryGroupedAssociationResults] = Field(
-        default_factory=list
-    )
+    associated_categories: List[CategoryGroupedAssociationResults] = Field(default_factory=list)
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
@@ -634,22 +560,16 @@ class MultiEntityAssociationResults(Results):
 
 class SearchResult(Entity):
 
-    highlight: Optional[str] = Field(
-        None, description="""matching text snippet containing html tags"""
-    )
+    highlight: Optional[str] = Field(None, description="""matching text snippet containing html tags""")
     score: Optional[float] = Field(None)
     id: str = Field(...)
     category: str = Field(...)
     name: str = Field(...)
-    full_name: Optional[str] = Field(
-        None, description="""The long form name of an entity"""
-    )
+    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
-    in_taxon: Optional[str] = Field(
-        None, description="""The biolink taxon that the entity is in the closure of."""
-    )
+    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -692,36 +612,20 @@ class TermPairwiseSimilarity(PairwiseSimilarity):
     """
 
     subject_id: str = Field(...)
-    subject_label: Optional[str] = Field(
-        None, description="""The name of the subject entity"""
-    )
-    subject_source: Optional[str] = Field(
-        None, description="""the source for the first entity"""
-    )
+    subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
+    subject_source: Optional[str] = Field(None, description="""the source for the first entity""")
     object_id: str = Field(...)
-    object_label: Optional[str] = Field(
-        None, description="""The name of the object entity"""
-    )
-    object_source: Optional[str] = Field(
-        None, description="""the source for the second entity"""
-    )
+    object_label: Optional[str] = Field(None, description="""The name of the object entity""")
+    object_source: Optional[str] = Field(None, description="""the source for the second entity""")
     ancestor_id: Optional[str] = Field(
         None,
         description="""the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected""",
     )
-    ancestor_label: Optional[str] = Field(
-        None, description="""the name or label of the ancestor concept"""
-    )
+    ancestor_label: Optional[str] = Field(None, description="""the name or label of the ancestor concept""")
     ancestor_source: Optional[str] = Field(None)
-    object_information_content: Optional[float] = Field(
-        None, description="""The IC of the object"""
-    )
-    subject_information_content: Optional[float] = Field(
-        None, description="""The IC of the subject"""
-    )
-    ancestor_information_content: Optional[float] = Field(
-        None, description="""The IC of the object"""
-    )
+    object_information_content: Optional[float] = Field(None, description="""The IC of the object""")
+    subject_information_content: Optional[float] = Field(None, description="""The IC of the subject""")
+    ancestor_information_content: Optional[float] = Field(None, description="""The IC of the object""")
     jaccard_similarity: Optional[float] = Field(
         None,
         description="""The number of concepts in the intersection divided by the number in the union""",
diff --git a/backend/src/monarch_py/datamodels/solr.py b/backend/src/monarch_py/datamodels/solr.py
index 196b2ed1d..c89d923ea 100644
--- a/backend/src/monarch_py/datamodels/solr.py
+++ b/backend/src/monarch_py/datamodels/solr.py
@@ -9,6 +9,7 @@
 class core(Enum):
     ENTITY = "entity"
     ASSOCIATION = "association"
+    SSSOM = "sssom"
 
 
 class HistoPhenoKeys(Enum):
diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py
index 2a78c5e49..a4c895ba7 100644
--- a/backend/src/monarch_py/implementations/solr/solr_implementation.py
+++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py
@@ -34,6 +34,7 @@
     build_association_table_query,
     build_autocomplete_query,
     build_histopheno_query,
+    build_mapping_query,
     build_multi_entity_association_query,
     build_search_query,
 )
@@ -418,3 +419,20 @@ def get_association_table(
         solr = SolrService(base_url=self.base_url, core=core.ASSOCIATION)
         query_result = solr.query(query)
         return parse_association_table(query_result, entity, offset, limit)
+
+    def get_mappings(
+        self,
+        entity_id: List[str] = None,
+        subject_id: List[str] = None,
+        predicate_id: List[str] = None,
+        object_id: List[str] = None,
+        mapping_justification: List[str] = None,
+    ) -> MappingResults:
+        solr = SolrService(base_url=self.base_url, core=core.SSSOM)
+        query = build_mapping_query(
+            entity_id=entity_id,
+            subject_id=subject_id,
+            predicate_id=predicate_id,
+            object_id=object_id,
+            mapping_justification=mapping_justification,
+        )
diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py
index 5c79e230d..3700e7239 100644
--- a/backend/src/monarch_py/implementations/solr/solr_parsers.py
+++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py
@@ -16,6 +16,8 @@
     FacetValue,
     HistoBin,
     HistoPheno,
+    Mapping,
+    MappingResults,
     SearchResult,
     SearchResults,
 )
@@ -168,6 +170,19 @@ def parse_autocomplete(query_result: SolrQueryResult) -> SearchResults:
     return SearchResults(limit=10, offset=0, total=total, items=items)
 
 
+def parse_mapping(query_result: SolrQueryResult, offset: int, limit: int) -> MappingResults:
+    total = query_result.response.num_found
+    items = []
+    for doc in query_result.response.docs:
+        try:
+            result = Mapping(**doc)
+            items.append(result)
+        except ValidationError:
+            logger.error(f"Validation error for {doc}")
+            raise
+    return MappingResults(limit=limit, offset=offset, total=total, items=items)
+
+
 ##################
 # Parser Helpers #
 ##################
diff --git a/backend/src/monarch_py/implementations/solr/solr_query_utils.py b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
index 3556c5a75..f38a835b0 100644
--- a/backend/src/monarch_py/implementations/solr/solr_query_utils.py
+++ b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
@@ -174,6 +174,29 @@ def build_autocomplete_query(q: str) -> SolrQuery:
     return query
 
 
+def build_mapping_query(
+    entity_id: List[str] = None,
+    subject_id: List[str] = None,
+    predicate_id: List[str] = None,
+    object_id: List[str] = None,
+    mapping_justification: List[str] = None,
+    offset: int = 0,
+    limit: int = 20,
+) -> SolrQuery:
+    query = SolrQuery(start=offset, rows=limit)
+    if entity_id:
+        query.add_filter_query(" OR ".join([f'subject_id:"{escape(e)}" OR object_id:"{escape(e)}"' for e in entity_id]))
+    if subject_id:
+        query.add_filter_query(" OR ".join([f'subject_id:"{escape(e)}"' for e in subject_id]))
+    if predicate_id:
+        query.add_filter_query(" OR ".join([f'predicate_id:"{escape(e)}"' for e in predicate_id]))
+    if object_id:
+        query.add_filter_query(" OR ".join([f'object_id:"{escape(e)}"' for e in object_id]))
+    if mapping_justification:
+        query.add_filter_query(" OR ".join([f'mapping_justification:"{escape(e)}"' for e in mapping_justification]))
+    return query
+
+
 ### Search helper functions ###
 
 
diff --git a/backend/src/monarch_py/interfaces/mapping_interface.py b/backend/src/monarch_py/interfaces/mapping_interface.py
index 18f147750..f5664f118 100644
--- a/backend/src/monarch_py/interfaces/mapping_interface.py
+++ b/backend/src/monarch_py/interfaces/mapping_interface.py
@@ -5,12 +5,22 @@
 
 
 class MappingInterface(ABC):
+    def get_mappings(
+        self,
+        entity_id: List[str] = None,
+        subject_id: List[str] = None,
+        predicate_id: List[str] = None,
+        object_id: List[str] = None,
+        mapping_justification: List[str] = None,
+    ) -> MappingResults:
+        """
+        Get SSSOM Mappings based on the provided constraints
 
-    def get_mappings(self,
-                     entity_id: List[str] = None,
-                     subject_id: List[str] = None,
-                     predicate_id: List[str] = None,
-                     object_id: List[str] = None,
-                     mapping_justification: List[str] = None,
-                     ) -> MappingResults:
+        Args:
+            entity_id: Filter to only mappings matching the specified entity IDs. Defaults to None.
+            subject_id: Filter to only mappings matching the specified subject IDs. Defaults to None.
+            predicate_id: Filter to only mappings matching the specified predicate IDs. Defaults to None.
+            object_id: Filter to only mappings matching the specified object IDs. Defaults to None.
+            mapping_justification: Filter to only mappings matching the specified mapping justifications. Defaults to None.
+        """
         raise NotImplementedError

From 9f55969c584d1597130583e2bba47b113eb23802 Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Wed, 8 Nov 2023 10:29:39 -0700
Subject: [PATCH 4/9] finish implementation, cli, and api endpoint

---
 backend/poetry.lock                           | 298 +++++++++---------
 backend/src/monarch_py/api/search.py          |  21 ++
 backend/src/monarch_py/cli.py                 |  22 ++
 backend/src/monarch_py/datamodels/model.py    |   7 +-
 backend/src/monarch_py/datamodels/model.yaml  |   3 +
 .../solr/solr_implementation.py               |  23 +-
 .../implementations/solr/solr_parsers.py      |   2 +-
 backend/src/monarch_py/solr_cli.py            |  74 +++--
 frontend/src/api/model.ts                     |   4 +
 9 files changed, 275 insertions(+), 179 deletions(-)

diff --git a/backend/poetry.lock b/backend/poetry.lock
index 2db550422..e3aea9619 100644
--- a/backend/poetry.lock
+++ b/backend/poetry.lock
@@ -1233,13 +1233,13 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.0"
+version = "6.1.1"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.1.0-py3-none-any.whl", hash = "sha256:aa50258bbfa56d4e33fbd8aa3ef48ded10d1735f11532b8df95388cc6bdb7e83"},
-    {file = "importlib_resources-6.1.0.tar.gz", hash = "sha256:9d48dcccc213325e810fd723e7fbb45ccb39f6cf5c31f00cf2b965f5f10f3cb9"},
+    {file = "importlib_resources-6.1.1-py3-none-any.whl", hash = "sha256:e8bf90d8213b486f428c9c39714b920041cb02c184686a3dee24905aaa8105d6"},
+    {file = "importlib_resources-6.1.1.tar.gz", hash = "sha256:3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a"},
 ]
 
 [package.dependencies]
@@ -1318,12 +1318,12 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsbeautifier"
-version = "1.14.9"
+version = "1.14.11"
 description = "JavaScript unobfuscator and beautifier."
 optional = false
 python-versions = "*"
 files = [
-    {file = "jsbeautifier-1.14.9.tar.gz", hash = "sha256:c738ebc36b47bd94e4ca6dd17a9004c3cc74edad582ca1d60e0e5d5945a63cb9"},
+    {file = "jsbeautifier-1.14.11.tar.gz", hash = "sha256:6b632581ea60dd1c133cd25a48ad187b4b91f526623c4b0fb5443ef805250505"},
 ]
 
 [package.dependencies]
@@ -1503,13 +1503,13 @@ regex = ["regex"]
 
 [[package]]
 name = "linkml"
-version = "1.6.1"
+version = "1.6.2"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
-    {file = "linkml-1.6.1-py3-none-any.whl", hash = "sha256:7501cb9c7b2c13ca78fc7121ae8b5457fb5771138714da31cc11f971062070ee"},
-    {file = "linkml-1.6.1.tar.gz", hash = "sha256:65f73cf29a77518972238e71e91e012c081cf2e43d71d8965ca414c78c11e08e"},
+    {file = "linkml-1.6.2-py3-none-any.whl", hash = "sha256:0e11b085ada080e0ebe9eee469ad55970b0cc333e7c39be956740dbc3a9e50b0"},
+    {file = "linkml-1.6.2.tar.gz", hash = "sha256:b1560a67de8c7de074c8be2ef5b810425f058e0874076e49c17a2dc4112f9da2"},
 ]
 
 [package.dependencies]
@@ -1527,7 +1527,7 @@ openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
 prefixmaps = ">=0.1.3"
-pydantic = "*"
+pydantic = ">=1.0.0,<3.0.0"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
 pyshexc = ">=0.8.3"
@@ -1575,13 +1575,13 @@ pydantic = "*"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.6.0"
+version = "1.6.1"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
-    {file = "linkml_runtime-1.6.0-py3-none-any.whl", hash = "sha256:1b6b698f8cf23d63ff833ae0be8055b2e945e1c0ef06a1ed6db359247194a2eb"},
-    {file = "linkml_runtime-1.6.0.tar.gz", hash = "sha256:a06df7431a9b929afe242598800d99cec83bb31cbdc1f5d2d70e6b26c67dc337"},
+    {file = "linkml_runtime-1.6.1-py3-none-any.whl", hash = "sha256:b598bf3fd2a5e354a662d34143193b0d7e092066affbf803053e1316acf75b2c"},
+    {file = "linkml_runtime-1.6.1.tar.gz", hash = "sha256:3036b8f4284e45df15733227eebef9c4216bcaff6d92c8fb09422e6026bf3152"},
 ]
 
 [package.dependencies]
@@ -1935,13 +1935,13 @@ mkdocs = ">=1.1"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.4.7"
+version = "9.4.8"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mkdocs_material-9.4.7-py3-none-any.whl", hash = "sha256:4d698d52bb6a6a3c452ab854481c4cdb68453a0420956a6aee2de55fe15fe610"},
-    {file = "mkdocs_material-9.4.7.tar.gz", hash = "sha256:e704e001c9ef17291e1d3462c202425217601653e18f68f85d28eff4690e662b"},
+    {file = "mkdocs_material-9.4.8-py3-none-any.whl", hash = "sha256:8b20f6851bddeef37dced903893cd176cf13a21a482e97705a103c45f06ce9b9"},
+    {file = "mkdocs_material-9.4.8.tar.gz", hash = "sha256:f0c101453e8bc12b040e8b64ca39a405d950d8402609b1378cc2b98976e74b5f"},
 ]
 
 [package.dependencies]
@@ -2792,13 +2792,13 @@ solrcloud = ["kazoo (>=2.5.0)"]
 
 [[package]]
 name = "pystow"
-version = "0.5.0"
+version = "0.5.2"
 description = "Easily pick a place to store data for your python package."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pystow-0.5.0-py3-none-any.whl", hash = "sha256:816a9da33cd8a3f8fbda577c3d2957cfc99d1fa3ea45032dbfa087b9a21b630f"},
-    {file = "pystow-0.5.0.tar.gz", hash = "sha256:490e9ecbe4f947c72f63297f43f6584323c9ca2f2d48d47f2a22a815dc552bb4"},
+    {file = "pystow-0.5.2-py3-none-any.whl", hash = "sha256:c0faeb0fc854ede714be7949555f4d55ce40d8fd57f0ae1ff75e86158792299a"},
+    {file = "pystow-0.5.2.tar.gz", hash = "sha256:d05d233299d61b50f53c7de220d990ec4c58e3a54d195d8449f0302563eb6de6"},
 ]
 
 [package.dependencies]
@@ -3280,121 +3280,121 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "rpds-py"
-version = "0.10.6"
+version = "0.12.0"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "rpds_py-0.10.6-cp310-cp310-macosx_10_7_x86_64.whl", hash = "sha256:6bdc11f9623870d75692cc33c59804b5a18d7b8a4b79ef0b00b773a27397d1f6"},
-    {file = "rpds_py-0.10.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:26857f0f44f0e791f4a266595a7a09d21f6b589580ee0585f330aaccccb836e3"},
-    {file = "rpds_py-0.10.6-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d7f5e15c953ace2e8dde9824bdab4bec50adb91a5663df08d7d994240ae6fa31"},
-    {file = "rpds_py-0.10.6-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:61fa268da6e2e1cd350739bb61011121fa550aa2545762e3dc02ea177ee4de35"},
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+    {file = "ruff-0.1.4-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:fdfd453fc91d9d86d6aaa33b1bafa69d114cf7421057868f0b79104079d3e66e"},
+    {file = "ruff-0.1.4-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:e8791482d508bd0b36c76481ad3117987301b86072158bdb69d796503e1c84a8"},
+    {file = "ruff-0.1.4-py3-none-musllinux_1_2_i686.whl", hash = "sha256:01206e361021426e3c1b7fba06ddcb20dbc5037d64f6841e5f2b21084dc51800"},
+    {file = "ruff-0.1.4-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:645591a613a42cb7e5c2b667cbefd3877b21e0252b59272ba7212c3d35a5819f"},
+    {file = "ruff-0.1.4-py3-none-win32.whl", hash = "sha256:99908ca2b3b85bffe7e1414275d004917d1e0dfc99d497ccd2ecd19ad115fd0d"},
+    {file = "ruff-0.1.4-py3-none-win_amd64.whl", hash = "sha256:1dfd6bf8f6ad0a4ac99333f437e0ec168989adc5d837ecd38ddb2cc4a2e3db8a"},
+    {file = "ruff-0.1.4-py3-none-win_arm64.whl", hash = "sha256:d98ae9ebf56444e18a3e3652b3383204748f73e247dea6caaf8b52d37e6b32da"},
+    {file = "ruff-0.1.4.tar.gz", hash = "sha256:21520ecca4cc555162068d87c747b8f95e1e95f8ecfcbbe59e8dd00710586315"},
 ]
 
 [[package]]
@@ -3537,13 +3537,13 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "selenium"
-version = "4.15.1"
+version = "4.15.2"
 description = ""
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "selenium-4.15.1-py3-none-any.whl", hash = "sha256:e3a4ebdcc3eed27eec69f8000d798923dbf4897c97cc6441eb88a1386809170d"},
-    {file = "selenium-4.15.1.tar.gz", hash = "sha256:8f0436b5949f1d4aa742f3dff0d748b955c371be92db8b6b008bf9c9ca227de7"},
+    {file = "selenium-4.15.2-py3-none-any.whl", hash = "sha256:9e82cd1ac647fb73cf0d4a6e280284102aaa3c9d94f0fa6e6cc4b5db6a30afbf"},
+    {file = "selenium-4.15.2.tar.gz", hash = "sha256:22eab5a1724c73d51b240a69ca702997b717eee4ba1f6065bf5d6b44dba01d48"},
 ]
 
 [package.dependencies]
@@ -4147,13 +4147,13 @@ telegram = ["requests"]
 
 [[package]]
 name = "trio"
-version = "0.22.2"
+version = "0.23.1"
 description = "A friendly Python library for async concurrency and I/O"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "trio-0.22.2-py3-none-any.whl", hash = "sha256:f43da357620e5872b3d940a2e3589aa251fd3f881b65a608d742e00809b1ec38"},
-    {file = "trio-0.22.2.tar.gz", hash = "sha256:3887cf18c8bcc894433420305468388dac76932e9668afa1c49aa3806b6accb3"},
+    {file = "trio-0.23.1-py3-none-any.whl", hash = "sha256:bb4abb3f4af23f96679e7c8cdabb8b234520f2498550d2cf63ebfd95f2ce27fe"},
+    {file = "trio-0.23.1.tar.gz", hash = "sha256:16f89f7dcc8f7b9dcdec1fcd863e0c039af6d0f9a22f8dfd56f75d75ec73fd48"},
 ]
 
 [package.dependencies]
@@ -4162,7 +4162,7 @@ cffi = {version = ">=1.14", markers = "os_name == \"nt\" and implementation_name
 exceptiongroup = {version = ">=1.0.0rc9", markers = "python_version < \"3.11\""}
 idna = "*"
 outcome = "*"
-sniffio = "*"
+sniffio = ">=1.3.0"
 sortedcontainers = "*"
 
 [[package]]
diff --git a/backend/src/monarch_py/api/search.py b/backend/src/monarch_py/api/search.py
index b7bf8d256..afbda3f46 100644
--- a/backend/src/monarch_py/api/search.py
+++ b/backend/src/monarch_py/api/search.py
@@ -62,3 +62,24 @@ async def autocomplete(
     """
     response = solr().autocomplete(q=q)
     return response
+
+
+@router.get("/mappings")
+async def mappings(
+    entity_id: Union[List[str], None] = Query(default=None),
+    subject_id: Union[List[str], None] = Query(default=None),
+    predicate_id: Union[List[str], None] = Query(default=None),
+    object_id: Union[List[str], None] = Query(default=None),
+    mapping_justification: Union[List[str], None] = Query(default=None),
+    pagination: PaginationParams = Depends(),
+):
+    response = solr().get_mappings(
+        entity_id=entity_id,
+        subject_id=subject_id,
+        predicate_id=predicate_id,
+        object_id=object_id,
+        mapping_justification=mapping_justification,
+        offset=pagination.offset,
+        limit=pagination.limit,
+    )
+    return response
diff --git a/backend/src/monarch_py/cli.py b/backend/src/monarch_py/cli.py
index 9b1c0c41d..40ba69e15 100644
--- a/backend/src/monarch_py/cli.py
+++ b/backend/src/monarch_py/cli.py
@@ -307,5 +307,27 @@ def multi_entity_associations(
     solr_cli.multi_entity_associations(**locals())
 
 
+@app.command("mappings")
+def mappings(
+    entity_id: List[str] = typer.Option(None, "--entity-id", "-e", help="entity ID to get mappings for"),
+    subject_id: List[str] = typer.Option(None, "--subject-id", "-s", help="subject ID to get mappings for"),
+    predicate_id: List[str] = typer.Option(None, "--predicate-id", "-p", help="predicate ID to get mappings for"),
+    object_id: List[str] = typer.Option(None, "--object-id", "-o", help="object ID to get mappings for"),
+    mapping_justification: List[str] = typer.Option(
+        None, "--mapping-justification", "-m", help="mapping justification to get mappings for"
+    ),
+    offset: int = typer.Option(0, "--offset", help="The offset of the first mapping to be retrieved"),
+    limit: int = typer.Option(20, "--limit", "-l", help="The number of mappings to return"),
+    fmt: str = typer.Option(
+        "json",
+        "--format",
+        "-f",
+        help="The format of the output (json, yaml, tsv, table)",
+    ),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
+):
+    solr_cli.mappings(**locals())
+
+
 if __name__ == "__main__":
     app()
diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
index 2d1df70be..b735b6a77 100644
--- a/backend/src/monarch_py/datamodels/model.py
+++ b/backend/src/monarch_py/datamodels/model.py
@@ -2,7 +2,7 @@
 from datetime import datetime, date
 from enum import Enum
 from typing import List, Dict, Optional, Any, Union
-from pydantic import BaseModel as BaseModel, Field
+from pydantic import BaseModel as BaseModel, ConfigDict, Field
 import sys
 
 if sys.version_info >= (3, 8):
@@ -435,6 +435,7 @@ class Mapping(ConfiguredBaseModel):
     object_id: str = Field(...)
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
     mapping_justification: Optional[str] = Field(None)
+    id: str = Field(...)
 
 
 class Node(Entity):
@@ -543,6 +544,10 @@ class MappingResults(Results):
     SSSOM Mappings returned as a results collection
     """
 
+    items: List[Mapping] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml
index b7bc4323d..33604a394 100644
--- a/backend/src/monarch_py/datamodels/model.yaml
+++ b/backend/src/monarch_py/datamodels/model.yaml
@@ -210,9 +210,12 @@ classes:
       - object_id
       - object_label
       - mapping_justification
+      - id
   MappingResults:
     description: SSSOM Mappings returned as a results collection
     is_a: Results
+    slots:
+      - items
     slot_usage:
       items:
         range: Mapping
diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py
index a4c895ba7..bc3afe350 100644
--- a/backend/src/monarch_py/implementations/solr/solr_implementation.py
+++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py
@@ -11,6 +11,7 @@
     CategoryGroupedAssociationResults,
     Entity,
     HistoPheno,
+    MappingResults,
     MultiEntityAssociationResults,
     Node,
     NodeHierarchy,
@@ -26,6 +27,7 @@
     parse_autocomplete,
     parse_entity,
     parse_histopheno,
+    parse_mappings,
     parse_search,
 )
 from monarch_py.implementations.solr.solr_query_utils import (
@@ -241,7 +243,7 @@ def get_associations(
             limit=limit,
         )
         query_result = solr.query(query)
-        associations = parse_associations(query_result)
+        associations = parse_associations(query_result, offset, limit)
         return associations
 
     def get_histopheno(self, subject_closure: str = None) -> HistoPheno:
@@ -427,12 +429,21 @@ def get_mappings(
         predicate_id: List[str] = None,
         object_id: List[str] = None,
         mapping_justification: List[str] = None,
+        offset: int = 0,
+        limit: int = 20,
     ) -> MappingResults:
         solr = SolrService(base_url=self.base_url, core=core.SSSOM)
         query = build_mapping_query(
-            entity_id=entity_id,
-            subject_id=subject_id,
-            predicate_id=predicate_id,
-            object_id=object_id,
-            mapping_justification=mapping_justification,
+            entity_id=[entity_id] if isinstance(entity_id, str) else entity_id,
+            subject_id=[subject_id] if isinstance(subject_id, str) else subject_id,
+            predicate_id=[predicate_id] if isinstance(predicate_id, str) else predicate_id,
+            object_id=[object_id] if isinstance(object_id, str) else object_id,
+            mapping_justification=[mapping_justification]
+            if isinstance(mapping_justification, str)
+            else mapping_justification,
+            offset=offset,
+            limit=limit,
         )
+        query_result = solr.query(query)
+        mappings = parse_mappings(query_result, offset, limit)
+        return mappings
diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py
index 3700e7239..de054b77e 100644
--- a/backend/src/monarch_py/implementations/solr/solr_parsers.py
+++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py
@@ -170,7 +170,7 @@ def parse_autocomplete(query_result: SolrQueryResult) -> SearchResults:
     return SearchResults(limit=10, offset=0, total=total, items=items)
 
 
-def parse_mapping(query_result: SolrQueryResult, offset: int, limit: int) -> MappingResults:
+def parse_mappings(query_result: SolrQueryResult, offset: int, limit: int) -> MappingResults:
     total = query_result.response.num_found
     items = []
     for doc in query_result.response.docs:
diff --git a/backend/src/monarch_py/solr_cli.py b/backend/src/monarch_py/solr_cli.py
index 9d11b64af..e45807375 100644
--- a/backend/src/monarch_py/solr_cli.py
+++ b/backend/src/monarch_py/solr_cli.py
@@ -96,7 +96,7 @@ def entity(
         "-f",
         help="The format of the output (json, yaml, tsv, table)",
     ),
-    output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
 ):
     """
     Retrieve an entity by ID
@@ -123,11 +123,13 @@ def entity(
 
 @solr_app.command("associations")
 def associations(
-    category: List[str] = typer.Option(None, "--category", "-c", help="Comma-separated list of categories"),
-    subject: List[str] = typer.Option(None, "--subject", "-s", help="Comma-separated list of subjects"),
-    predicate: List[str] = typer.Option(None, "--predicate", "-p", help="Comma-separated list of predicates"),
-    object: List[str] = typer.Option(None, "--object", "-o", help="Comma-separated list of objects"),
-    entity: List[str] = typer.Option(None, "--entity", "-e", help="Comma-separated list of entities"),
+    category: List[str] = typer.Option(None, "--category", "-c", help="Category to get associations for"),
+    subject: List[str] = typer.Option(None, "--subject", "-s", help="Subject ID to get associations for"),
+    predicate: List[str] = typer.Option(None, "--predicate", "-p", help="Predicate ID to get associations for"),
+    object: List[str] = typer.Option(None, "--object", "-o", help="Object ID to get associations for"),
+    entity: List[str] = typer.Option(
+        None, "--entity", "-e", help="Entity (subject or object) ID to get associations for"
+    ),
     direct: bool = typer.Option(
         False,
         "--direct",
@@ -142,22 +144,22 @@ def associations(
         "-f",
         help="The format of the output (json, yaml, tsv, table)",
     ),
-    output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
 ):
     """
     Paginate through associations
 
     Args:
-        category: A comma-separated list of categories
-        subject: A comma-separated list of subjects
-        predicate: A comma-separated list of predicates
-        object: A comma-separated list of objects
-        entity: A comma-separated list of entities
-        limit: The number of associations to return
-        direct: Whether to exclude associations with subject/object as ancestors
+        category: The category of the association (multi-valued)
+        subject: The subject of the association (multi-valued)
+        predicate: The predicate of the association (multi-valued)
+        object: The object of the association (multi-valued)
+        entity: The entity (subject or object) of the association (multi-valued)
+        limit: The number of associations to return (default 20)
+        direct: Whether to exclude associations with subject/object as ancestors (default False)
         offset: The offset of the first association to be retrieved
-        fmt: The format of the output (json, yaml, tsv, table)
-        output: The path to the output file (stdout if not specified)
+        fmt: The format of the output (json, yaml, tsv, table) (default json)
+        output: The path to the output file (stdout if not specified) (default None)
     """
     args = locals()
     args.pop("fmt", None)
@@ -182,7 +184,7 @@ def multi_entity_associations(
         "-f",
         help="The format of the output (json, yaml, tsv, table)",
     ),
-    output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
 ):
     """
     Paginate through associations for multiple entities
@@ -222,7 +224,7 @@ def search(
         "-f",
         help="The format of the output (json, yaml, tsv, table)",
     ),
-    output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
     # sort: str = typer.Option(None, "--sort", "-s"),
 ):
     """
@@ -257,7 +259,7 @@ def autocomplete(
         "-f",
         help="The format of the output (json, yaml, tsv, table)",
     ),
-    output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
 ):
     """
     Return entity autcomplete matches for a query string
@@ -282,7 +284,7 @@ def histopheno(
         "-f",
         help="The format of the output (json, yaml, tsv, table)",
     ),
-    output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
 ):
     """
     Retrieve the histopheno associations for a given subject
@@ -313,7 +315,7 @@ def association_counts(
         "-f",
         help="The format of the output (json, yaml, tsv, table)",
     ),
-    output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
 ):
     """
     Retrieve the association counts for a given entity
@@ -349,8 +351,36 @@ def association_table(
         "-f",
         help="The format of the output (json, yaml, tsv, table)",
     ),
-    output: str = typer.Option(None, "--output", "-o", help="The path to the output file"),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
 ):
     solr = get_solr(update=False)
     response = solr.get_association_table(entity=entity, category=category, q=q, limit=limit, offset=offset)
     format_output(fmt, response, output)
+
+
+@solr_app.command("mappings")
+def mappings(
+    entity_id: List[str] = typer.Option(None, "--entity-id", "-e", help="entity ID to get mappings for"),
+    subject_id: List[str] = typer.Option(None, "--subject-id", "-s", help="subject ID to get mappings for"),
+    predicate_id: List[str] = typer.Option(None, "--predicate-id", "-p", help="predicate ID to get mappings for"),
+    object_id: List[str] = typer.Option(None, "--object-id", "-o", help="object ID to get mappings for"),
+    mapping_justification: List[str] = typer.Option(
+        None, "--mapping-justification", "-m", help="mapping justification to get mappings for"
+    ),
+    offset: int = typer.Option(0, "--offset", help="The offset of the first mapping to be retrieved"),
+    limit: int = typer.Option(20, "--limit", "-l", help="The number of mappings to return"),
+    fmt: str = typer.Option(
+        "json",
+        "--format",
+        "-f",
+        help="The format of the output (json, yaml, tsv, table)",
+    ),
+    output: str = typer.Option(None, "--output", "-O", help="The path to the output file"),
+):
+    args = locals()
+    args.pop("fmt", None)
+    args.pop("output", None)
+
+    solr = get_solr(update=False)
+    response = solr.get_mappings(**args)
+    format_output(fmt, response, output)
diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index d6d59466f..febc18638 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -4,6 +4,7 @@ export type ExpandedCurieId = string;
 export type EntityId = string;
 export type HistoPhenoId = string;
 export type HistoBinId = string;
+export type MappingId = string;
 export type MultiEntityAssociationResultsId = string;
 export type NodeId = string;
 export type SearchResultId = string;
@@ -375,11 +376,14 @@ export interface Mapping {
     /** The name of the object entity */
     object_label?: string,
     mapping_justification?: string,
+    id: string,
 };
 /**
  * SSSOM Mappings returned as a results collection
  */
 export interface MappingResults extends Results {
+    /** A collection of items, with the type to be overriden by slot_usage */
+    items: Mapping[],
     /** number of items to return in a response */
     limit: number,
     /** offset into the total number of items */

From 59d71832fdaad896e57274f8823a2a704949bb7f Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Wed, 8 Nov 2023 12:26:37 -0700
Subject: [PATCH 5/9] update fixtures, add mapping tests

---
 backend/src/monarch_py/api/main.py            |  4 +-
 .../implementations/solr/solr_parsers.py      |  2 +-
 backend/tests/api/test_mapping_endpoint.py    | 18 ++++
 .../fixtures/association_counts_response.py   |  2 +-
 backend/tests/fixtures/histopheno_response.py |  2 +-
 backend/tests/fixtures/mapping_query.py       | 21 +++++
 backend/tests/fixtures/mapping_response.py    | 87 +++++++++++++++++++
 backend/tests/fixtures/mappings.py            | 75 ++++++++++++++++
 backend/tests/fixtures/search_response.py     |  2 +-
 backend/tests/unit/test_solr_parsers.py       | 10 +++
 backend/tests/unit/test_solr_queries.py       |  7 ++
 frontend/fixtures/mappings.json               | 70 +++++++++++++++
 scripts/generate_fixtures.py                  |  9 +-
 13 files changed, 301 insertions(+), 8 deletions(-)
 create mode 100644 backend/tests/api/test_mapping_endpoint.py
 create mode 100644 backend/tests/fixtures/mapping_query.py
 create mode 100644 backend/tests/fixtures/mapping_response.py
 create mode 100644 backend/tests/fixtures/mappings.py
 create mode 100644 frontend/fixtures/mappings.json

diff --git a/backend/src/monarch_py/api/main.py b/backend/src/monarch_py/api/main.py
index 7bba7265a..1e0cbe98d 100644
--- a/backend/src/monarch_py/api/main.py
+++ b/backend/src/monarch_py/api/main.py
@@ -22,10 +22,10 @@ async def initialize_app():
     CurieService()
 
 
-app.include_router(entity.router, prefix=f"{PREFIX}/entity")
 app.include_router(association.router, prefix=f"{PREFIX}/association")
-app.include_router(search.router, prefix=PREFIX)
+app.include_router(entity.router, prefix=f"{PREFIX}/entity")
 app.include_router(histopheno.router, prefix=f"{PREFIX}/histopheno")
+app.include_router(search.router, prefix=PREFIX)
 app.include_router(semsim.router, prefix=f"{PREFIX}/semsim")
 
 # Allow CORS
diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py
index de054b77e..f2dcbae2a 100644
--- a/backend/src/monarch_py/implementations/solr/solr_parsers.py
+++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py
@@ -170,7 +170,7 @@ def parse_autocomplete(query_result: SolrQueryResult) -> SearchResults:
     return SearchResults(limit=10, offset=0, total=total, items=items)
 
 
-def parse_mappings(query_result: SolrQueryResult, offset: int, limit: int) -> MappingResults:
+def parse_mappings(query_result: SolrQueryResult, offset: int = 0, limit: int = 20) -> MappingResults:
     total = query_result.response.num_found
     items = []
     for doc in query_result.response.docs:
diff --git a/backend/tests/api/test_mapping_endpoint.py b/backend/tests/api/test_mapping_endpoint.py
new file mode 100644
index 000000000..6752c1a06
--- /dev/null
+++ b/backend/tests/api/test_mapping_endpoint.py
@@ -0,0 +1,18 @@
+from unittest.mock import MagicMock, patch
+
+from fastapi.testclient import TestClient
+from httpx import Response
+from monarch_py.api.search import router
+
+client = TestClient(router)
+
+
+def test_mappings(search):
+    with patch.object(
+        client, "get", MagicMock(return_value=Response(200, json=search, headers={"content-type": "application/json"}))
+    ):
+        response = client.get("/mappings?entity_id=MONDO:0000015")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "application/json"
+    assert response.json() == search
+
diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py
index b223b0016..8878112b5 100644
--- a/backend/tests/fixtures/association_counts_response.py
+++ b/backend/tests/fixtures/association_counts_response.py
@@ -5,7 +5,7 @@
 def association_counts_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 0,
             "params": {
                 "facet.query": [
                     '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py
index 44789afcf..67fb5632e 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": 2,
             "params": {
                 "facet.query": [
                     'object_closure:"HP:0000924"',
diff --git a/backend/tests/fixtures/mapping_query.py b/backend/tests/fixtures/mapping_query.py
new file mode 100644
index 000000000..10c157459
--- /dev/null
+++ b/backend/tests/fixtures/mapping_query.py
@@ -0,0 +1,21 @@
+import pytest
+
+
+@pytest.fixture
+def mapping_query():
+    return {
+        "q": "*:*",
+        "rows": 20,
+        "start": 0,
+        "facet": True,
+        "facet_fields": [],
+        "facet_queries": [],
+        "filter_queries": ['subject_id:"MONDO\\:0020121" OR object_id:"MONDO\\:0020121"'],
+        "query_fields": None,
+        "def_type": "edismax",
+        "q_op": "AND",
+        "mm": "100%",
+        "boost": None,
+        "sort": None,
+        "facet_min_count": 1,
+    }
diff --git a/backend/tests/fixtures/mapping_response.py b/backend/tests/fixtures/mapping_response.py
new file mode 100644
index 000000000..7515868ce
--- /dev/null
+++ b/backend/tests/fixtures/mapping_response.py
@@ -0,0 +1,87 @@
+import pytest
+
+
+@pytest.fixture
+def mapping_response():
+    return {
+        "responseHeader": {
+            "QTime": 0,
+            "params": {
+                "mm": "100%",
+                "q": "*:*",
+                "defType": "edismax",
+                "facet_min_count": "1",
+                "start": "0",
+                "q.op": "AND",
+                "fq": 'subject_id:"MONDO\\:0020121" OR object_id:"MONDO\\:0020121"',
+                "rows": "20",
+                "facet": "true",
+            },
+        },
+        "response": {
+            "num_found": 7,
+            "start": 0,
+            "docs": [
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "DOID:9884",
+                    "object_label": "muscular dystrophy",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "cda26856-16a7-499c-956f-119cbaac5b96",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "ICD10CM:G71.0",
+                    "object_label": "Muscular dystrophy",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "25777569-b997-4c8f-a1f3-5af352a16ee1",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "MESH:D009136",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "NCIT:C84910",
+                    "object_label": "Muscular Dystrophy",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "SCTID:73297009",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "f6417283-c9d1-4289-aee6-16d30a4445b1",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "UMLS:C0026850",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "93968631-eedb-448b-b58a-e31e3e411dde",
+                },
+                {
+                    "subject_id": "MONDO:0020121",
+                    "subject_label": "muscular dystrophy",
+                    "predicate_id": "skos:exactMatch",
+                    "object_id": "Orphanet:98473",
+                    "mapping_justification": "semapv:UnspecifiedMatching",
+                    "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5",
+                },
+            ],
+        },
+        "facet_counts": {"facet_fields": {}, "facet_queries": {}},
+    }
diff --git a/backend/tests/fixtures/mappings.py b/backend/tests/fixtures/mappings.py
new file mode 100644
index 000000000..7d3e92885
--- /dev/null
+++ b/backend/tests/fixtures/mappings.py
@@ -0,0 +1,75 @@
+import pytest
+
+
+@pytest.fixture
+def mappings():
+    return {
+        "limit": 20,
+        "offset": 0,
+        "total": 7,
+        "items": [
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "DOID:9884",
+                "object_label": "muscular dystrophy",
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "cda26856-16a7-499c-956f-119cbaac5b96",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "ICD10CM:G71.0",
+                "object_label": "Muscular dystrophy",
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "25777569-b997-4c8f-a1f3-5af352a16ee1",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "MESH:D009136",
+                "object_label": None,
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "NCIT:C84910",
+                "object_label": "Muscular Dystrophy",
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "SCTID:73297009",
+                "object_label": None,
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "f6417283-c9d1-4289-aee6-16d30a4445b1",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "UMLS:C0026850",
+                "object_label": None,
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "93968631-eedb-448b-b58a-e31e3e411dde",
+            },
+            {
+                "subject_id": "MONDO:0020121",
+                "subject_label": "muscular dystrophy",
+                "predicate_id": "skos:exactMatch",
+                "object_id": "Orphanet:98473",
+                "object_label": None,
+                "mapping_justification": "semapv:UnspecifiedMatching",
+                "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5",
+            },
+        ],
+    }
diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py
index 5fbe50b82..c2791ef80 100644
--- a/backend/tests/fixtures/search_response.py
+++ b/backend/tests/fixtures/search_response.py
@@ -5,7 +5,7 @@
 def search_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "fanconi",
diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py
index 352bbffce..cda34ac6b 100644
--- a/backend/tests/unit/test_solr_parsers.py
+++ b/backend/tests/unit/test_solr_parsers.py
@@ -7,6 +7,7 @@
     parse_autocomplete,
     parse_entity,
     parse_histopheno,
+    parse_mappings,
     parse_search,
 )
 from monarch_py.utils.utils import dict_diff
@@ -65,3 +66,12 @@ def test_parse_autocomplete(autocomplete_response, autocomplete):
     assert (
         parsed == autocomplete
     ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), autocomplete)}"
+
+
+def test_parse_mappings(mapping_response, mappings):
+    mapping_response["response"]["numFound"] = mapping_response["response"].pop("num_found")
+    solr_response = SolrQueryResult(**mapping_response)
+    parsed = parse_mappings(solr_response)
+    assert (
+        parsed == mappings
+    ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), mappings)}"
\ No newline at end of file
diff --git a/backend/tests/unit/test_solr_queries.py b/backend/tests/unit/test_solr_queries.py
index 64c58844f..0e6c75a42 100644
--- a/backend/tests/unit/test_solr_queries.py
+++ b/backend/tests/unit/test_solr_queries.py
@@ -5,6 +5,7 @@
     build_association_query,
     build_autocomplete_query,
     build_histopheno_query,
+    build_mapping_query,
     build_search_query,
 )
 from monarch_py.utils.utils import compare_dicts, dict_diff
@@ -111,3 +112,9 @@ def test_build_autocomplete_query(autocomplete_query):
     query = build_autocomplete_query(q="fanc").dict()
     expected = autocomplete_query
     assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}"
+
+
+def test_build_mappings_query(mapping_query):
+    query = build_mapping_query(entity_id=["MONDO:0020121"]).dict()
+    expected = mapping_query
+    assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}"
diff --git a/frontend/fixtures/mappings.json b/frontend/fixtures/mappings.json
new file mode 100644
index 000000000..016753b75
--- /dev/null
+++ b/frontend/fixtures/mappings.json
@@ -0,0 +1,70 @@
+{
+  "limit": 20,
+  "offset": 0,
+  "total": 7,
+  "items": [
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "DOID:9884",
+      "object_label": "muscular dystrophy",
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "cda26856-16a7-499c-956f-119cbaac5b96"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "ICD10CM:G71.0",
+      "object_label": "Muscular dystrophy",
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "25777569-b997-4c8f-a1f3-5af352a16ee1"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "MESH:D009136",
+      "object_label": null,
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "NCIT:C84910",
+      "object_label": "Muscular Dystrophy",
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "SCTID:73297009",
+      "object_label": null,
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "f6417283-c9d1-4289-aee6-16d30a4445b1"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "UMLS:C0026850",
+      "object_label": null,
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "93968631-eedb-448b-b58a-e31e3e411dde"
+    },
+    {
+      "subject_id": "MONDO:0020121",
+      "subject_label": "muscular dystrophy",
+      "predicate_id": "skos:exactMatch",
+      "object_id": "Orphanet:98473",
+      "object_label": null,
+      "mapping_justification": "semapv:UnspecifiedMatching",
+      "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5"
+    }
+  ]
+}
diff --git a/scripts/generate_fixtures.py b/scripts/generate_fixtures.py
index ddf39b26c..6939e22fc 100644
--- a/scripts/generate_fixtures.py
+++ b/scripts/generate_fixtures.py
@@ -9,15 +9,16 @@
 from monarch_py.implementations.solr.solr_query_utils import (
     build_association_query,
     build_association_counts_query,
+    build_association_table_query,
     build_autocomplete_query,
     build_histopheno_query,
+    build_mapping_query,
     build_search_query,
-    build_association_table_query,
 )
 from monarch_py.service.solr_service import SolrService, core
 from monarch_py.utils.utils import format_output
 
-from pprint import pprint as pp
+# from pprint import pprint as pp
 
 ### Define variables
 oak = OakImplementation()
@@ -26,6 +27,7 @@
 solr_url = os.getenv("MONARCH_SOLR_URL", "http://localhost:8983/solr")
 solr_entities = SolrService(base_url=solr_url, core=core.ENTITY)
 solr_associations = SolrService(base_url=solr_url, core=core.ASSOCIATION)
+solr_mappings = SolrService(base_url=solr_url, core=core.SSSOM)
 
 root = Path(__file__).parent.parent
 frontend_fixture_dir = Path(root) / "frontend" / "fixtures"
@@ -192,6 +194,7 @@ def main(
         fixtures["histopheno"] = si.get_histopheno(node_id)
         fixtures["entity"] = si.get_entity(id=node_id, extra=False)
         fixtures["node"] = si.get_entity(id=node_id, extra=True)
+        fixtures["mappings"] = si.get_mappings(entity_id=node_id)
         # fixtures['node-publication-abstract'] =
         # fixtures['node-publication-summary'] =
         # fixtures['ontologies'] =
@@ -227,6 +230,7 @@ def main(
         )
         extra_fixtures["autocomplete-query"] = build_autocomplete_query(q="fanc")
         extra_fixtures["histopheno-query"] = build_histopheno_query(subject_closure=node_id)
+        extra_fixtures["mapping-query"] = build_mapping_query(entity_id=[node_id])
         extra_fixtures["search-query"] = build_search_query(q="fanconi")
 
         # solr doc fixtures
@@ -240,6 +244,7 @@ def main(
         extra_fixtures["autocomplete-response"] = solr_entities.query(extra_fixtures["autocomplete-query"])
         extra_fixtures["entity-response"] = solr_entities.get(node_id)
         extra_fixtures["histopheno-response"] = solr_associations.query(extra_fixtures["histopheno-query"])
+        extra_fixtures["mapping-response"] = solr_mappings.query(extra_fixtures["mapping-query"])
         extra_fixtures["search-response"] = solr_entities.query(extra_fixtures["search-query"])
 
     ### Write frontend fixtures

From 8daf6015cb6c77900e38b108b0ff67d482154d43 Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Wed, 8 Nov 2023 12:35:39 -0700
Subject: [PATCH 6/9] update models to fix FE type test

---
 backend/src/monarch_py/datamodels/model.py | 505 ++++++---------------
 backend/tests/api/test_mapping_endpoint.py |   1 -
 backend/tests/unit/test_solr_parsers.py    |   4 +-
 frontend/src/api/model.ts                  |  12 +-
 4 files changed, 142 insertions(+), 380 deletions(-)

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
index b735b6a77..b74d9d289 100644
--- a/backend/src/monarch_py/datamodels/model.py
+++ b/backend/src/monarch_py/datamodels/model.py
@@ -4,7 +4,6 @@
 from typing import List, Dict, Optional, Any, Union
 from pydantic import BaseModel as BaseModel, ConfigDict, Field
 import sys
-
 if sys.version_info >= (3, 8):
     from typing import Literal
 else:
@@ -14,20 +13,16 @@
 metamodel_version = "None"
 version = "None"
 
-
 class WeakRefShimBaseModel(BaseModel):
-    __slots__ = "__weakref__"
-
-
-class ConfiguredBaseModel(
-    WeakRefShimBaseModel,
-    validate_assignment=True,
-    validate_all=True,
-    underscore_attrs_are_private=True,
-    extra="forbid",
-    arbitrary_types_allowed=True,
-    use_enum_values=True,
-):
+   __slots__ = '__weakref__'
+
+class ConfiguredBaseModel(WeakRefShimBaseModel,
+                validate_assignment = True,
+                validate_all = True,
+                underscore_attrs_are_private = True,
+                extra = 'forbid',
+                arbitrary_types_allowed = True,
+                use_enum_values = True):
     pass
 
 
@@ -35,30 +30,24 @@ class AssociationDirectionEnum(str, Enum):
     """
     The directionality of an association as it relates to a specified entity, with edges being categorized as incoming or outgoing
     """
-
     # An association for which a specified entity is the object or part of the object closure
     incoming = "incoming"
     # An association for which a specified entity is the subject or part of the subject closure
     outgoing = "outgoing"
-
+    
+    
 
 class Association(ConfiguredBaseModel):
-
+    
     id: str = Field(...)
     category: Optional[str] = Field(None)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
     subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
     subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
-    subject_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing subject id and the ids of all of it's ancestors""",
-    )
+    subject_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing subject id and the ids of all of it's ancestors""")
     subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
-    subject_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing subject name and the names of all of it's ancestors""",
-    )
+    subject_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing subject name and the names of all of it's ancestors""")
     subject_taxon: Optional[str] = Field(None)
     subject_taxon_label: Optional[str] = Field(None)
     predicate: str = Field(...)
@@ -66,176 +55,86 @@ class Association(ConfiguredBaseModel):
     original_object: Optional[str] = Field(None)
     object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
     object_category: Optional[str] = Field(None, description="""The category of the object entity""")
-    object_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing object id and the ids of all of it's ancestors""",
-    )
+    object_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing object id and the ids of all of it's ancestors""")
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
-    object_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing object name and the names of all of it's ancestors""",
-    )
+    object_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing object name and the names of all of it's ancestors""")
     object_taxon: Optional[str] = Field(None)
     object_taxon_label: Optional[str] = Field(None)
     primary_knowledge_source: Optional[str] = Field(None)
     aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list)
     negated: Optional[bool] = Field(None)
     pathway: Optional[str] = Field(None)
-    evidence_count: Optional[int] = Field(
-        None,
-        description="""count of supporting documents, evidence codes, and sources supplying evidence""",
-    )
+    evidence_count: Optional[int] = Field(None, description="""count of supporting documents, evidence codes, and sources supplying evidence""")
     has_evidence: Optional[List[str]] = Field(default_factory=list)
-    has_evidence_links: Optional[List[ExpandedCurie]] = Field(
-        default_factory=list,
-        description="""List of ExpandedCuries with id and url for evidence""",
-    )
-    grouping_key: Optional[str] = Field(
-        None,
-        description="""A concatenation of fields used to group associations with the same essential/defining properties""",
-    )
+    has_evidence_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""List of ExpandedCuries with id and url for evidence""")
+    grouping_key: Optional[str] = Field(None, description="""A concatenation of fields used to group associations with the same essential/defining properties""")
     provided_by: Optional[str] = Field(None)
-    provided_by_link: Optional[ExpandedCurie] = Field(
-        None,
-        description="""A link to the docs for the knowledge source that provided the node/edge.""",
-    )
+    provided_by_link: Optional[ExpandedCurie] = Field(None, description="""A link to the docs for the knowledge source that provided the node/edge.""")
     publications: Optional[List[str]] = Field(default_factory=list)
-    publications_links: Optional[List[ExpandedCurie]] = Field(
-        default_factory=list,
-        description="""List of ExpandedCuries with id and url for publications""",
-    )
+    publications_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""List of ExpandedCuries with id and url for publications""")
     qualifiers: Optional[List[str]] = Field(default_factory=list)
     frequency_qualifier: Optional[str] = Field(None)
     onset_qualifier: Optional[str] = Field(None)
     sex_qualifier: Optional[str] = Field(None)
     stage_qualifier: Optional[str] = Field(None)
     qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
-    qualifiers_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the frequency_qualifier entity"""
-    )
+    qualifiers_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the frequency_qualifier entity""")
     qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
-    qualifiers_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-    )
-    qualifiers_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-    )
+    qualifiers_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""")
+    qualifiers_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier name and the names of all of it's ancestors""")
     frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
-    frequency_qualifier_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the frequency_qualifier entity"""
-    )
-    frequency_qualifier_category: Optional[str] = Field(
-        None, description="""The category of the frequency_qualifier entity"""
-    )
-    frequency_qualifier_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-    )
-    frequency_qualifier_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-    )
+    frequency_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the frequency_qualifier entity""")
+    frequency_qualifier_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
+    frequency_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""")
+    frequency_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier name and the names of all of it's ancestors""")
     onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
-    onset_qualifier_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the onset_qualifier entity"""
-    )
+    onset_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the onset_qualifier entity""")
     onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
-    onset_qualifier_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
-    )
-    onset_qualifier_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
-    )
+    onset_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing onset_qualifier id and the ids of all of it's ancestors""")
+    onset_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing onset_qualifier name and the names of all of it's ancestors""")
     sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
-    sex_qualifier_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the sex_qualifier entity"""
-    )
+    sex_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the sex_qualifier entity""")
     sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
-    sex_qualifier_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
-    )
-    sex_qualifier_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
-    )
+    sex_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing sex_qualifier id and the ids of all of it's ancestors""")
+    sex_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing sex_qualifier name and the names of all of it's ancestors""")
     stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
-    stage_qualifier_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the stage_qualifier entity"""
-    )
+    stage_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the stage_qualifier entity""")
     stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
-    stage_qualifier_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
-    )
-    stage_qualifier_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing stage_qualifier name and the names of all of it's ancestors""",
-    )
-
+    stage_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing stage_qualifier id and the ids of all of it's ancestors""")
+    stage_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing stage_qualifier name and the names of all of it's ancestors""")
+    
 
 class AssociationCountList(ConfiguredBaseModel):
     """
     Container class for a list of association counts
     """
-
-    items: List[AssociationCount] = Field(
-        default_factory=list,
-        description="""A collection of items, with the type to be overriden by slot_usage""",
-    )
-
+    items: List[AssociationCount] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
+    
 
 class AssociationTypeMapping(ConfiguredBaseModel):
     """
     A data class to hold the necessary information to produce association type counts for given  entities with appropriate directional labels
     """
-
-    subject_label: Optional[str] = Field(
-        None,
-        description="""A label to describe the subjects of the association type as a whole for use in the UI""",
-    )
-    object_label: Optional[str] = Field(
-        None,
-        description="""A label to describe the objects of the association type as a whole for use in the UI""",
-    )
-    symmetric: bool = Field(
-        False,
-        description="""Whether the association type is symmetric, meaning that the subject and object labels should be interchangeable""",
-    )
-    category: str = Field(
-        ...,
-        description="""The biolink category to use in queries for this association type""",
-    )
-
+    subject_label: Optional[str] = Field(None, description="""A label to describe the subjects of the association type as a whole for use in the UI""")
+    object_label: Optional[str] = Field(None, description="""A label to describe the objects of the association type as a whole for use in the UI""")
+    symmetric: bool = Field(False, description="""Whether the association type is symmetric, meaning that the subject and object labels should be interchangeable""")
+    category: str = Field(..., description="""The biolink category to use in queries for this association type""")
+    
 
 class DirectionalAssociation(Association):
     """
     An association that gives it's direction relative to a specified entity
     """
-
-    direction: AssociationDirectionEnum = Field(
-        ...,
-        description="""The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.""",
-    )
+    direction: AssociationDirectionEnum = Field(..., description="""The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.""")
     id: str = Field(...)
     category: Optional[str] = Field(None)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
     subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
     subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
-    subject_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing subject id and the ids of all of it's ancestors""",
-    )
+    subject_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing subject id and the ids of all of it's ancestors""")
     subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
-    subject_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing subject name and the names of all of it's ancestors""",
-    )
+    subject_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing subject name and the names of all of it's ancestors""")
     subject_taxon: Optional[str] = Field(None)
     subject_taxon_label: Optional[str] = Field(None)
     predicate: str = Field(...)
@@ -243,132 +142,67 @@ class DirectionalAssociation(Association):
     original_object: Optional[str] = Field(None)
     object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
     object_category: Optional[str] = Field(None, description="""The category of the object entity""")
-    object_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing object id and the ids of all of it's ancestors""",
-    )
+    object_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing object id and the ids of all of it's ancestors""")
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
-    object_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing object name and the names of all of it's ancestors""",
-    )
+    object_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing object name and the names of all of it's ancestors""")
     object_taxon: Optional[str] = Field(None)
     object_taxon_label: Optional[str] = Field(None)
     primary_knowledge_source: Optional[str] = Field(None)
     aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list)
     negated: Optional[bool] = Field(None)
     pathway: Optional[str] = Field(None)
-    evidence_count: Optional[int] = Field(
-        None,
-        description="""count of supporting documents, evidence codes, and sources supplying evidence""",
-    )
+    evidence_count: Optional[int] = Field(None, description="""count of supporting documents, evidence codes, and sources supplying evidence""")
     has_evidence: Optional[List[str]] = Field(default_factory=list)
-    has_evidence_links: Optional[List[ExpandedCurie]] = Field(
-        default_factory=list,
-        description="""List of ExpandedCuries with id and url for evidence""",
-    )
-    grouping_key: Optional[str] = Field(
-        None,
-        description="""A concatenation of fields used to group associations with the same essential/defining properties""",
-    )
+    has_evidence_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""List of ExpandedCuries with id and url for evidence""")
+    grouping_key: Optional[str] = Field(None, description="""A concatenation of fields used to group associations with the same essential/defining properties""")
     provided_by: Optional[str] = Field(None)
-    provided_by_link: Optional[ExpandedCurie] = Field(
-        None,
-        description="""A link to the docs for the knowledge source that provided the node/edge.""",
-    )
+    provided_by_link: Optional[ExpandedCurie] = Field(None, description="""A link to the docs for the knowledge source that provided the node/edge.""")
     publications: Optional[List[str]] = Field(default_factory=list)
-    publications_links: Optional[List[ExpandedCurie]] = Field(
-        default_factory=list,
-        description="""List of ExpandedCuries with id and url for publications""",
-    )
+    publications_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""List of ExpandedCuries with id and url for publications""")
     qualifiers: Optional[List[str]] = Field(default_factory=list)
     frequency_qualifier: Optional[str] = Field(None)
     onset_qualifier: Optional[str] = Field(None)
     sex_qualifier: Optional[str] = Field(None)
     stage_qualifier: Optional[str] = Field(None)
     qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
-    qualifiers_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the frequency_qualifier entity"""
-    )
+    qualifiers_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the frequency_qualifier entity""")
     qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
-    qualifiers_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-    )
-    qualifiers_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-    )
+    qualifiers_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""")
+    qualifiers_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier name and the names of all of it's ancestors""")
     frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
-    frequency_qualifier_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the frequency_qualifier entity"""
-    )
-    frequency_qualifier_category: Optional[str] = Field(
-        None, description="""The category of the frequency_qualifier entity"""
-    )
-    frequency_qualifier_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
-    )
-    frequency_qualifier_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
-    )
+    frequency_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the frequency_qualifier entity""")
+    frequency_qualifier_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
+    frequency_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""")
+    frequency_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier name and the names of all of it's ancestors""")
     onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
-    onset_qualifier_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the onset_qualifier entity"""
-    )
+    onset_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the onset_qualifier entity""")
     onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
-    onset_qualifier_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
-    )
-    onset_qualifier_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
-    )
+    onset_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing onset_qualifier id and the ids of all of it's ancestors""")
+    onset_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing onset_qualifier name and the names of all of it's ancestors""")
     sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
-    sex_qualifier_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the sex_qualifier entity"""
-    )
+    sex_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the sex_qualifier entity""")
     sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
-    sex_qualifier_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
-    )
-    sex_qualifier_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
-    )
+    sex_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing sex_qualifier id and the ids of all of it's ancestors""")
+    sex_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing sex_qualifier name and the names of all of it's ancestors""")
     stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
-    stage_qualifier_namespace: Optional[str] = Field(
-        None, description="""The namespace/prefix of the stage_qualifier entity"""
-    )
+    stage_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the stage_qualifier entity""")
     stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
-    stage_qualifier_closure: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
-    )
-    stage_qualifier_closure_label: Optional[List[str]] = Field(
-        default_factory=list,
-        description="""Field containing stage_qualifier name and the names of all of it's ancestors""",
-    )
-
+    stage_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing stage_qualifier id and the ids of all of it's ancestors""")
+    stage_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing stage_qualifier name and the names of all of it's ancestors""")
+    
 
 class ExpandedCurie(ConfiguredBaseModel):
     """
     A curie bundled along with its expanded url
     """
-
     id: str = Field(...)
     url: Optional[str] = Field(None)
-
+    
 
 class Entity(ConfiguredBaseModel):
     """
     Represents an Entity in the Monarch KG data model
     """
-
     id: str = Field(...)
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
@@ -377,58 +211,48 @@ class Entity(ConfiguredBaseModel):
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
     in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
-    in_taxon_label: Optional[str] = Field(
-        None,
-        description="""The label of the biolink taxon that the entity is in the closure of.""",
-    )
+    in_taxon_label: Optional[str] = Field(None, description="""The label of the biolink taxon that the entity is in the closure of.""")
     symbol: Optional[str] = Field(None)
     synonym: Optional[List[str]] = Field(default_factory=list)
     uri: Optional[str] = Field(None, description="""The URI of the entity""")
-
+    
 
 class FacetValue(ConfiguredBaseModel):
-
+    
     label: str = Field(...)
     count: Optional[int] = Field(None, description="""count of documents""")
-
+    
 
 class AssociationCount(FacetValue):
-
+    
     category: Optional[str] = Field(None)
     label: str = Field(...)
     count: Optional[int] = Field(None, description="""count of documents""")
-
+    
 
 class FacetField(ConfiguredBaseModel):
-
+    
     label: str = Field(...)
-    facet_values: Optional[List[FacetValue]] = Field(
-        default_factory=list,
-        description="""Collection of FacetValue label/value instances belonging to a FacetField""",
-    )
-
+    facet_values: Optional[List[FacetValue]] = Field(default_factory=list, description="""Collection of FacetValue label/value instances belonging to a FacetField""")
+    
 
 class HistoPheno(ConfiguredBaseModel):
-
+    
     id: str = Field(...)
-    items: List[HistoBin] = Field(
-        default_factory=list,
-        description="""A collection of items, with the type to be overriden by slot_usage""",
-    )
-
+    items: List[HistoBin] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
+    
 
 class HistoBin(FacetValue):
-
+    
     id: str = Field(...)
     label: str = Field(...)
     count: Optional[int] = Field(None, description="""count of documents""")
-
+    
 
 class Mapping(ConfiguredBaseModel):
     """
     A minimal class to hold a SSSOM mapping
     """
-
     subject_id: str = Field(...)
     subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
     predicate_id: str = Field(...)
@@ -436,34 +260,19 @@ class Mapping(ConfiguredBaseModel):
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
     mapping_justification: Optional[str] = Field(None)
     id: str = Field(...)
-
+    
 
 class Node(Entity):
     """
     UI container class extending Entity with additional information
     """
-
     in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
-    in_taxon_label: Optional[str] = Field(
-        None,
-        description="""The label of the biolink taxon that the entity is in the closure of.""",
-    )
+    in_taxon_label: Optional[str] = Field(None, description="""The label of the biolink taxon that the entity is in the closure of.""")
     inheritance: Optional[Entity] = Field(None)
-    causal_gene: Optional[List[Entity]] = Field(
-        default_factory=list,
-        description="""A list of genes that are known to be causally associated with a disease""",
-    )
-    causes_disease: Optional[List[Entity]] = Field(
-        default_factory=list,
-        description="""A list of diseases that are known to be causally associated with a gene""",
-    )
-    external_links: Optional[List[ExpandedCurie]] = Field(
-        default_factory=list, description="""ExpandedCurie with id and url for xrefs"""
-    )
-    provided_by_link: Optional[ExpandedCurie] = Field(
-        None,
-        description="""A link to the docs for the knowledge source that provided the node/edge.""",
-    )
+    causal_gene: Optional[List[Entity]] = Field(default_factory=list, description="""A list of genes that are known to be causally associated with a disease""")
+    causes_disease: Optional[List[Entity]] = Field(default_factory=list, description="""A list of diseases that are known to be causally associated with a gene""")
+    external_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""ExpandedCurie with id and url for xrefs""")
+    provided_by_link: Optional[ExpandedCurie] = Field(None, description="""A link to the docs for the knowledge source that provided the node/edge.""")
     association_counts: List[AssociationCount] = Field(default_factory=list)
     node_hierarchy: Optional[NodeHierarchy] = Field(None)
     id: str = Field(...)
@@ -476,95 +285,76 @@ class Node(Entity):
     symbol: Optional[str] = Field(None)
     synonym: Optional[List[str]] = Field(default_factory=list)
     uri: Optional[str] = Field(None, description="""The URI of the entity""")
-
+    
 
 class NodeHierarchy(ConfiguredBaseModel):
-
+    
     super_classes: List[Entity] = Field(default_factory=list)
     sub_classes: List[Entity] = Field(default_factory=list)
-
+    
 
 class Results(ConfiguredBaseModel):
-
+    
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-
+    
 
 class AssociationResults(Results):
-
-    items: List[Association] = Field(
-        default_factory=list,
-        description="""A collection of items, with the type to be overriden by slot_usage""",
-    )
+    
+    items: List[Association] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-
+    
 
 class AssociationTableResults(Results):
-
-    items: List[DirectionalAssociation] = Field(
-        default_factory=list,
-        description="""A collection of items, with the type to be overriden by slot_usage""",
-    )
+    
+    items: List[DirectionalAssociation] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-
+    
 
 class CategoryGroupedAssociationResults(Results):
-
-    counterpart_category: Optional[str] = Field(
-        None,
-        description="""The category of the counterpart entity in a given association,  eg. the category of the entity that is not the subject""",
-    )
-    items: List[Association] = Field(
-        default_factory=list,
-        description="""A collection of items, with the type to be overriden by slot_usage""",
-    )
+    
+    counterpart_category: Optional[str] = Field(None, description="""The category of the counterpart entity in a given association,  eg. the category of the entity that is not the subject""")
+    items: List[Association] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-
+    
 
 class EntityResults(Results):
-
-    items: List[Entity] = Field(
-        default_factory=list,
-        description="""A collection of items, with the type to be overriden by slot_usage""",
-    )
+    
+    items: List[Entity] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-
+    
 
 class MappingResults(Results):
     """
     SSSOM Mappings returned as a results collection
     """
-
-    items: List[Mapping] = Field(
-        default_factory=list,
-        description="""A collection of items, with the type to be overriden by slot_usage""",
-    )
+    items: List[Mapping] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-
+    
 
 class MultiEntityAssociationResults(Results):
-
+    
     id: str = Field(...)
     name: Optional[str] = Field(None)
     associated_categories: List[CategoryGroupedAssociationResults] = Field(default_factory=list)
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-
+    
 
 class SearchResult(Entity):
-
+    
     highlight: Optional[str] = Field(None, description="""matching text snippet containing html tags""")
     score: Optional[float] = Field(None)
     id: str = Field(...)
@@ -575,82 +365,55 @@ class SearchResult(Entity):
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
     in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
-    in_taxon_label: Optional[str] = Field(
-        None,
-        description="""The label of the biolink taxon that the entity is in the closure of.""",
-    )
+    in_taxon_label: Optional[str] = Field(None, description="""The label of the biolink taxon that the entity is in the closure of.""")
     symbol: Optional[str] = Field(None)
     synonym: Optional[List[str]] = Field(default_factory=list)
     uri: Optional[str] = Field(None, description="""The URI of the entity""")
-
+    
 
 class SearchResults(Results):
-
-    items: List[SearchResult] = Field(
-        default_factory=list,
-        description="""A collection of items, with the type to be overriden by slot_usage""",
-    )
-    facet_fields: Optional[List[FacetField]] = Field(
-        default_factory=list,
-        description="""Collection of facet field responses with the field values and counts""",
-    )
-    facet_queries: Optional[List[FacetValue]] = Field(
-        default_factory=list,
-        description="""Collection of facet query responses with the query string values and counts""",
-    )
+    
+    items: List[SearchResult] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
+    facet_fields: Optional[List[FacetField]] = Field(default_factory=list, description="""Collection of facet field responses with the field values and counts""")
+    facet_queries: Optional[List[FacetValue]] = Field(default_factory=list, description="""Collection of facet query responses with the query string values and counts""")
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-
+    
 
 class PairwiseSimilarity(ConfiguredBaseModel):
     """
     Abstract grouping for representing individual pairwise similarities
     """
-
     None
-
+    
 
 class TermPairwiseSimilarity(PairwiseSimilarity):
     """
     A simple pairwise similarity between two atomic concepts/terms
     """
-
     subject_id: str = Field(...)
     subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
     subject_source: Optional[str] = Field(None, description="""the source for the first entity""")
     object_id: str = Field(...)
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
     object_source: Optional[str] = Field(None, description="""the source for the second entity""")
-    ancestor_id: Optional[str] = Field(
-        None,
-        description="""the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected""",
-    )
+    ancestor_id: Optional[str] = Field(None, description="""the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected""")
     ancestor_label: Optional[str] = Field(None, description="""the name or label of the ancestor concept""")
     ancestor_source: Optional[str] = Field(None)
     object_information_content: Optional[float] = Field(None, description="""The IC of the object""")
     subject_information_content: Optional[float] = Field(None, description="""The IC of the subject""")
     ancestor_information_content: Optional[float] = Field(None, description="""The IC of the object""")
-    jaccard_similarity: Optional[float] = Field(
-        None,
-        description="""The number of concepts in the intersection divided by the number in the union""",
-    )
-    cosine_similarity: Optional[float] = Field(
-        None,
-        description="""the dot product of two node embeddings divided by the product of their lengths""",
-    )
+    jaccard_similarity: Optional[float] = Field(None, description="""The number of concepts in the intersection divided by the number in the union""")
+    cosine_similarity: Optional[float] = Field(None, description="""the dot product of two node embeddings divided by the product of their lengths""")
     dice_similarity: Optional[float] = Field(None)
-    phenodigm_score: Optional[float] = Field(
-        None,
-        description="""the geometric mean of the jaccard similarity and the information content""",
-    )
-
+    phenodigm_score: Optional[float] = Field(None, description="""the geometric mean of the jaccard similarity and the information content""")
+    
 
 class TermSetPairwiseSimilarity(PairwiseSimilarity):
     """
     A simple pairwise similarity between two sets of concepts/terms
     """
-
     subject_termset: Optional[Dict[str, TermInfo]] = Field(default_factory=dict)
     object_termset: Optional[Dict[str, TermInfo]] = Field(default_factory=dict)
     subject_best_matches: Optional[Dict[str, BestMatch]] = Field(default_factory=dict)
@@ -658,16 +421,16 @@ class TermSetPairwiseSimilarity(PairwiseSimilarity):
     average_score: Optional[float] = Field(None)
     best_score: Optional[float] = Field(None)
     metric: Optional[str] = Field(None)
-
+    
 
 class TermInfo(ConfiguredBaseModel):
-
+    
     id: str = Field(...)
     label: Optional[str] = Field(None)
-
+    
 
 class BestMatch(ConfiguredBaseModel):
-
+    
     match_source: str = Field(...)
     match_source_label: Optional[str] = Field(None)
     match_target: Optional[str] = Field(None, description="""the entity matches""")
@@ -676,6 +439,7 @@ class BestMatch(ConfiguredBaseModel):
     match_subsumer: Optional[str] = Field(None)
     match_subsumer_label: Optional[str] = Field(None)
     similarity: TermPairwiseSimilarity = Field(...)
+    
 
 
 # Update forward refs
@@ -708,3 +472,4 @@ class BestMatch(ConfiguredBaseModel):
 TermSetPairwiseSimilarity.update_forward_refs()
 TermInfo.update_forward_refs()
 BestMatch.update_forward_refs()
+
diff --git a/backend/tests/api/test_mapping_endpoint.py b/backend/tests/api/test_mapping_endpoint.py
index 6752c1a06..506679c01 100644
--- a/backend/tests/api/test_mapping_endpoint.py
+++ b/backend/tests/api/test_mapping_endpoint.py
@@ -15,4 +15,3 @@ def test_mappings(search):
     assert response.status_code == 200
     assert response.headers["content-type"] == "application/json"
     assert response.json() == search
-
diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py
index cda34ac6b..18aab675e 100644
--- a/backend/tests/unit/test_solr_parsers.py
+++ b/backend/tests/unit/test_solr_parsers.py
@@ -72,6 +72,4 @@ def test_parse_mappings(mapping_response, mappings):
     mapping_response["response"]["numFound"] = mapping_response["response"].pop("num_found")
     solr_response = SolrQueryResult(**mapping_response)
     parsed = parse_mappings(solr_response)
-    assert (
-        parsed == mappings
-    ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), mappings)}"
\ No newline at end of file
+    assert parsed == mappings, f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), mappings)}"
diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index febc18638..0c74ac2f6 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -511,18 +511,18 @@ export interface TermPairwiseSimilarity extends PairwiseSimilarity {
     ancestor_label?: string,
     ancestor_source?: string,
     /** The IC of the object */
-    object_information_content?: string,
+    object_information_content?: number,
     /** The IC of the subject */
-    subject_information_content?: string,
+    subject_information_content?: number,
     /** The IC of the object */
-    ancestor_information_content?: string,
+    ancestor_information_content?: number,
     /** The number of concepts in the intersection divided by the number in the union */
-    jaccard_similarity?: string,
+    jaccard_similarity?: number,
     /** the dot product of two node embeddings divided by the product of their lengths */
     cosine_similarity?: number,
-    dice_similarity?: string,
+    dice_similarity?: number,
     /** the geometric mean of the jaccard similarity and the information content */
-    phenodigm_score?: string,
+    phenodigm_score?: number,
 };
 /**
  * A simple pairwise similarity between two sets of concepts/terms

From 100152725fa8ec7f134cf18a5c835d1779d89501 Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Fri, 10 Nov 2023 11:12:56 -0700
Subject: [PATCH 7/9] update fixtures

---
 backend/src/monarch_py/datamodels/model.py    | 509 +++++++++++++-----
 backend/src/monarch_py/datamodels/model.yaml  |  10 +-
 .../solr/solr_implementation.py               |  15 +
 backend/src/monarch_py/utils/entity_utils.py  |   6 +
 backend/tests/fixtures/histopheno_response.py |   2 +-
 backend/tests/fixtures/node.py                |   9 +
 frontend/fixtures/node.json                   |  30 ++
 frontend/src/api/model.ts                     |  14 +-
 8 files changed, 451 insertions(+), 144 deletions(-)

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
index b74d9d289..dbe8b7e46 100644
--- a/backend/src/monarch_py/datamodels/model.py
+++ b/backend/src/monarch_py/datamodels/model.py
@@ -4,6 +4,7 @@
 from typing import List, Dict, Optional, Any, Union
 from pydantic import BaseModel as BaseModel, ConfigDict, Field
 import sys
+
 if sys.version_info >= (3, 8):
     from typing import Literal
 else:
@@ -13,16 +14,20 @@
 metamodel_version = "None"
 version = "None"
 
+
 class WeakRefShimBaseModel(BaseModel):
-   __slots__ = '__weakref__'
-
-class ConfiguredBaseModel(WeakRefShimBaseModel,
-                validate_assignment = True,
-                validate_all = True,
-                underscore_attrs_are_private = True,
-                extra = 'forbid',
-                arbitrary_types_allowed = True,
-                use_enum_values = True):
+    __slots__ = "__weakref__"
+
+
+class ConfiguredBaseModel(
+    WeakRefShimBaseModel,
+    validate_assignment=True,
+    validate_all=True,
+    underscore_attrs_are_private=True,
+    extra="forbid",
+    arbitrary_types_allowed=True,
+    use_enum_values=True,
+):
     pass
 
 
@@ -30,24 +35,30 @@ class AssociationDirectionEnum(str, Enum):
     """
     The directionality of an association as it relates to a specified entity, with edges being categorized as incoming or outgoing
     """
+
     # An association for which a specified entity is the object or part of the object closure
     incoming = "incoming"
     # An association for which a specified entity is the subject or part of the subject closure
     outgoing = "outgoing"
-    
-    
+
 
 class Association(ConfiguredBaseModel):
-    
+
     id: str = Field(...)
     category: Optional[str] = Field(None)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
     subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
     subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
-    subject_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing subject id and the ids of all of it's ancestors""")
+    subject_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing subject id and the ids of all of it's ancestors""",
+    )
     subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
-    subject_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing subject name and the names of all of it's ancestors""")
+    subject_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing subject name and the names of all of it's ancestors""",
+    )
     subject_taxon: Optional[str] = Field(None)
     subject_taxon_label: Optional[str] = Field(None)
     predicate: str = Field(...)
@@ -55,86 +66,176 @@ class Association(ConfiguredBaseModel):
     original_object: Optional[str] = Field(None)
     object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
     object_category: Optional[str] = Field(None, description="""The category of the object entity""")
-    object_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing object id and the ids of all of it's ancestors""")
+    object_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing object id and the ids of all of it's ancestors""",
+    )
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
-    object_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing object name and the names of all of it's ancestors""")
+    object_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing object name and the names of all of it's ancestors""",
+    )
     object_taxon: Optional[str] = Field(None)
     object_taxon_label: Optional[str] = Field(None)
     primary_knowledge_source: Optional[str] = Field(None)
     aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list)
     negated: Optional[bool] = Field(None)
     pathway: Optional[str] = Field(None)
-    evidence_count: Optional[int] = Field(None, description="""count of supporting documents, evidence codes, and sources supplying evidence""")
+    evidence_count: Optional[int] = Field(
+        None,
+        description="""count of supporting documents, evidence codes, and sources supplying evidence""",
+    )
     has_evidence: Optional[List[str]] = Field(default_factory=list)
-    has_evidence_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""List of ExpandedCuries with id and url for evidence""")
-    grouping_key: Optional[str] = Field(None, description="""A concatenation of fields used to group associations with the same essential/defining properties""")
+    has_evidence_links: Optional[List[ExpandedCurie]] = Field(
+        default_factory=list,
+        description="""List of ExpandedCuries with id and url for evidence""",
+    )
+    grouping_key: Optional[str] = Field(
+        None,
+        description="""A concatenation of fields used to group associations with the same essential/defining properties""",
+    )
     provided_by: Optional[str] = Field(None)
-    provided_by_link: Optional[ExpandedCurie] = Field(None, description="""A link to the docs for the knowledge source that provided the node/edge.""")
+    provided_by_link: Optional[ExpandedCurie] = Field(
+        None,
+        description="""A link to the docs for the knowledge source that provided the node/edge.""",
+    )
     publications: Optional[List[str]] = Field(default_factory=list)
-    publications_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""List of ExpandedCuries with id and url for publications""")
+    publications_links: Optional[List[ExpandedCurie]] = Field(
+        default_factory=list,
+        description="""List of ExpandedCuries with id and url for publications""",
+    )
     qualifiers: Optional[List[str]] = Field(default_factory=list)
     frequency_qualifier: Optional[str] = Field(None)
     onset_qualifier: Optional[str] = Field(None)
     sex_qualifier: Optional[str] = Field(None)
     stage_qualifier: Optional[str] = Field(None)
     qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
-    qualifiers_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the frequency_qualifier entity""")
+    qualifiers_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the frequency_qualifier entity"""
+    )
     qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
-    qualifiers_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""")
-    qualifiers_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier name and the names of all of it's ancestors""")
+    qualifiers_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
+    )
+    qualifiers_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
+    )
     frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
-    frequency_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the frequency_qualifier entity""")
-    frequency_qualifier_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
-    frequency_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""")
-    frequency_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier name and the names of all of it's ancestors""")
+    frequency_qualifier_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the frequency_qualifier entity"""
+    )
+    frequency_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the frequency_qualifier entity"""
+    )
+    frequency_qualifier_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
+    )
+    frequency_qualifier_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
+    )
     onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
-    onset_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the onset_qualifier entity""")
+    onset_qualifier_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the onset_qualifier entity"""
+    )
     onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
-    onset_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing onset_qualifier id and the ids of all of it's ancestors""")
-    onset_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing onset_qualifier name and the names of all of it's ancestors""")
+    onset_qualifier_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
+    )
+    onset_qualifier_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
+    )
     sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
-    sex_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the sex_qualifier entity""")
+    sex_qualifier_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the sex_qualifier entity"""
+    )
     sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
-    sex_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing sex_qualifier id and the ids of all of it's ancestors""")
-    sex_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing sex_qualifier name and the names of all of it's ancestors""")
+    sex_qualifier_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
+    )
+    sex_qualifier_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
+    )
     stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
-    stage_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the stage_qualifier entity""")
+    stage_qualifier_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the stage_qualifier entity"""
+    )
     stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
-    stage_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing stage_qualifier id and the ids of all of it's ancestors""")
-    stage_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing stage_qualifier name and the names of all of it's ancestors""")
-    
+    stage_qualifier_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
+    )
+    stage_qualifier_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing stage_qualifier name and the names of all of it's ancestors""",
+    )
+
 
 class AssociationCountList(ConfiguredBaseModel):
     """
     Container class for a list of association counts
     """
-    items: List[AssociationCount] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
-    
+
+    items: List[AssociationCount] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
+
 
 class AssociationTypeMapping(ConfiguredBaseModel):
     """
     A data class to hold the necessary information to produce association type counts for given  entities with appropriate directional labels
     """
-    subject_label: Optional[str] = Field(None, description="""A label to describe the subjects of the association type as a whole for use in the UI""")
-    object_label: Optional[str] = Field(None, description="""A label to describe the objects of the association type as a whole for use in the UI""")
-    symmetric: bool = Field(False, description="""Whether the association type is symmetric, meaning that the subject and object labels should be interchangeable""")
-    category: str = Field(..., description="""The biolink category to use in queries for this association type""")
-    
+
+    subject_label: Optional[str] = Field(
+        None,
+        description="""A label to describe the subjects of the association type as a whole for use in the UI""",
+    )
+    object_label: Optional[str] = Field(
+        None,
+        description="""A label to describe the objects of the association type as a whole for use in the UI""",
+    )
+    symmetric: bool = Field(
+        False,
+        description="""Whether the association type is symmetric, meaning that the subject and object labels should be interchangeable""",
+    )
+    category: str = Field(
+        ...,
+        description="""The biolink category to use in queries for this association type""",
+    )
+
 
 class DirectionalAssociation(Association):
     """
     An association that gives it's direction relative to a specified entity
     """
-    direction: AssociationDirectionEnum = Field(..., description="""The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.""")
+
+    direction: AssociationDirectionEnum = Field(
+        ...,
+        description="""The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.""",
+    )
     id: str = Field(...)
     category: Optional[str] = Field(None)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
     subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
     subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
-    subject_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing subject id and the ids of all of it's ancestors""")
+    subject_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing subject id and the ids of all of it's ancestors""",
+    )
     subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
-    subject_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing subject name and the names of all of it's ancestors""")
+    subject_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing subject name and the names of all of it's ancestors""",
+    )
     subject_taxon: Optional[str] = Field(None)
     subject_taxon_label: Optional[str] = Field(None)
     predicate: str = Field(...)
@@ -142,67 +243,132 @@ class DirectionalAssociation(Association):
     original_object: Optional[str] = Field(None)
     object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
     object_category: Optional[str] = Field(None, description="""The category of the object entity""")
-    object_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing object id and the ids of all of it's ancestors""")
+    object_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing object id and the ids of all of it's ancestors""",
+    )
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
-    object_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing object name and the names of all of it's ancestors""")
+    object_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing object name and the names of all of it's ancestors""",
+    )
     object_taxon: Optional[str] = Field(None)
     object_taxon_label: Optional[str] = Field(None)
     primary_knowledge_source: Optional[str] = Field(None)
     aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list)
     negated: Optional[bool] = Field(None)
     pathway: Optional[str] = Field(None)
-    evidence_count: Optional[int] = Field(None, description="""count of supporting documents, evidence codes, and sources supplying evidence""")
+    evidence_count: Optional[int] = Field(
+        None,
+        description="""count of supporting documents, evidence codes, and sources supplying evidence""",
+    )
     has_evidence: Optional[List[str]] = Field(default_factory=list)
-    has_evidence_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""List of ExpandedCuries with id and url for evidence""")
-    grouping_key: Optional[str] = Field(None, description="""A concatenation of fields used to group associations with the same essential/defining properties""")
+    has_evidence_links: Optional[List[ExpandedCurie]] = Field(
+        default_factory=list,
+        description="""List of ExpandedCuries with id and url for evidence""",
+    )
+    grouping_key: Optional[str] = Field(
+        None,
+        description="""A concatenation of fields used to group associations with the same essential/defining properties""",
+    )
     provided_by: Optional[str] = Field(None)
-    provided_by_link: Optional[ExpandedCurie] = Field(None, description="""A link to the docs for the knowledge source that provided the node/edge.""")
+    provided_by_link: Optional[ExpandedCurie] = Field(
+        None,
+        description="""A link to the docs for the knowledge source that provided the node/edge.""",
+    )
     publications: Optional[List[str]] = Field(default_factory=list)
-    publications_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""List of ExpandedCuries with id and url for publications""")
+    publications_links: Optional[List[ExpandedCurie]] = Field(
+        default_factory=list,
+        description="""List of ExpandedCuries with id and url for publications""",
+    )
     qualifiers: Optional[List[str]] = Field(default_factory=list)
     frequency_qualifier: Optional[str] = Field(None)
     onset_qualifier: Optional[str] = Field(None)
     sex_qualifier: Optional[str] = Field(None)
     stage_qualifier: Optional[str] = Field(None)
     qualifiers_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
-    qualifiers_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the frequency_qualifier entity""")
+    qualifiers_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the frequency_qualifier entity"""
+    )
     qualifiers_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
-    qualifiers_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""")
-    qualifiers_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier name and the names of all of it's ancestors""")
+    qualifiers_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
+    )
+    qualifiers_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
+    )
     frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
-    frequency_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the frequency_qualifier entity""")
-    frequency_qualifier_category: Optional[str] = Field(None, description="""The category of the frequency_qualifier entity""")
-    frequency_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""")
-    frequency_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing frequency_qualifier name and the names of all of it's ancestors""")
+    frequency_qualifier_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the frequency_qualifier entity"""
+    )
+    frequency_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the frequency_qualifier entity"""
+    )
+    frequency_qualifier_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing frequency_qualifier id and the ids of all of it's ancestors""",
+    )
+    frequency_qualifier_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
+    )
     onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
-    onset_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the onset_qualifier entity""")
+    onset_qualifier_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the onset_qualifier entity"""
+    )
     onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
-    onset_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing onset_qualifier id and the ids of all of it's ancestors""")
-    onset_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing onset_qualifier name and the names of all of it's ancestors""")
+    onset_qualifier_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
+    )
+    onset_qualifier_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
+    )
     sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
-    sex_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the sex_qualifier entity""")
+    sex_qualifier_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the sex_qualifier entity"""
+    )
     sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
-    sex_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing sex_qualifier id and the ids of all of it's ancestors""")
-    sex_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing sex_qualifier name and the names of all of it's ancestors""")
+    sex_qualifier_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
+    )
+    sex_qualifier_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
+    )
     stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
-    stage_qualifier_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the stage_qualifier entity""")
+    stage_qualifier_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the stage_qualifier entity"""
+    )
     stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
-    stage_qualifier_closure: Optional[List[str]] = Field(default_factory=list, description="""Field containing stage_qualifier id and the ids of all of it's ancestors""")
-    stage_qualifier_closure_label: Optional[List[str]] = Field(default_factory=list, description="""Field containing stage_qualifier name and the names of all of it's ancestors""")
-    
+    stage_qualifier_closure: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
+    )
+    stage_qualifier_closure_label: Optional[List[str]] = Field(
+        default_factory=list,
+        description="""Field containing stage_qualifier name and the names of all of it's ancestors""",
+    )
+
 
 class ExpandedCurie(ConfiguredBaseModel):
     """
     A curie bundled along with its expanded url
     """
+
     id: str = Field(...)
     url: Optional[str] = Field(None)
-    
+
 
 class Entity(ConfiguredBaseModel):
     """
     Represents an Entity in the Monarch KG data model
     """
+
     id: str = Field(...)
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
@@ -211,48 +377,58 @@ class Entity(ConfiguredBaseModel):
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
     in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
-    in_taxon_label: Optional[str] = Field(None, description="""The label of the biolink taxon that the entity is in the closure of.""")
+    in_taxon_label: Optional[str] = Field(
+        None,
+        description="""The label of the biolink taxon that the entity is in the closure of.""",
+    )
     symbol: Optional[str] = Field(None)
     synonym: Optional[List[str]] = Field(default_factory=list)
     uri: Optional[str] = Field(None, description="""The URI of the entity""")
-    
+
 
 class FacetValue(ConfiguredBaseModel):
-    
+
     label: str = Field(...)
     count: Optional[int] = Field(None, description="""count of documents""")
-    
+
 
 class AssociationCount(FacetValue):
-    
+
     category: Optional[str] = Field(None)
     label: str = Field(...)
     count: Optional[int] = Field(None, description="""count of documents""")
-    
+
 
 class FacetField(ConfiguredBaseModel):
-    
+
     label: str = Field(...)
-    facet_values: Optional[List[FacetValue]] = Field(default_factory=list, description="""Collection of FacetValue label/value instances belonging to a FacetField""")
-    
+    facet_values: Optional[List[FacetValue]] = Field(
+        default_factory=list,
+        description="""Collection of FacetValue label/value instances belonging to a FacetField""",
+    )
+
 
 class HistoPheno(ConfiguredBaseModel):
-    
+
     id: str = Field(...)
-    items: List[HistoBin] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
-    
+    items: List[HistoBin] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
+
 
 class HistoBin(FacetValue):
-    
+
     id: str = Field(...)
     label: str = Field(...)
     count: Optional[int] = Field(None, description="""count of documents""")
-    
+
 
 class Mapping(ConfiguredBaseModel):
     """
     A minimal class to hold a SSSOM mapping
     """
+
     subject_id: str = Field(...)
     subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
     predicate_id: str = Field(...)
@@ -260,19 +436,38 @@ class Mapping(ConfiguredBaseModel):
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
     mapping_justification: Optional[str] = Field(None)
     id: str = Field(...)
-    
+
 
 class Node(Entity):
     """
     UI container class extending Entity with additional information
     """
+
     in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
-    in_taxon_label: Optional[str] = Field(None, description="""The label of the biolink taxon that the entity is in the closure of.""")
+    in_taxon_label: Optional[str] = Field(
+        None,
+        description="""The label of the biolink taxon that the entity is in the closure of.""",
+    )
     inheritance: Optional[Entity] = Field(None)
-    causal_gene: Optional[List[Entity]] = Field(default_factory=list, description="""A list of genes that are known to be causally associated with a disease""")
-    causes_disease: Optional[List[Entity]] = Field(default_factory=list, description="""A list of diseases that are known to be causally associated with a gene""")
-    external_links: Optional[List[ExpandedCurie]] = Field(default_factory=list, description="""ExpandedCurie with id and url for xrefs""")
-    provided_by_link: Optional[ExpandedCurie] = Field(None, description="""A link to the docs for the knowledge source that provided the node/edge.""")
+    causal_gene: Optional[List[Entity]] = Field(
+        default_factory=list,
+        description="""A list of genes that are known to be causally associated with a disease""",
+    )
+    causes_disease: Optional[List[Entity]] = Field(
+        default_factory=list,
+        description="""A list of diseases that are known to be causally associated with a gene""",
+    )
+    mappings: Optional[List[ExpandedCurie]] = Field(
+        default_factory=list,
+        description="""List of ExpandedCuries with id and url for mapped entities""",
+    )
+    external_links: Optional[List[ExpandedCurie]] = Field(
+        default_factory=list, description="""ExpandedCurie with id and url for xrefs"""
+    )
+    provided_by_link: Optional[ExpandedCurie] = Field(
+        None,
+        description="""A link to the docs for the knowledge source that provided the node/edge.""",
+    )
     association_counts: List[AssociationCount] = Field(default_factory=list)
     node_hierarchy: Optional[NodeHierarchy] = Field(None)
     id: str = Field(...)
@@ -285,76 +480,95 @@ class Node(Entity):
     symbol: Optional[str] = Field(None)
     synonym: Optional[List[str]] = Field(default_factory=list)
     uri: Optional[str] = Field(None, description="""The URI of the entity""")
-    
+
 
 class NodeHierarchy(ConfiguredBaseModel):
-    
+
     super_classes: List[Entity] = Field(default_factory=list)
     sub_classes: List[Entity] = Field(default_factory=list)
-    
+
 
 class Results(ConfiguredBaseModel):
-    
+
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-    
+
 
 class AssociationResults(Results):
-    
-    items: List[Association] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
+
+    items: List[Association] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-    
+
 
 class AssociationTableResults(Results):
-    
-    items: List[DirectionalAssociation] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
+
+    items: List[DirectionalAssociation] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-    
+
 
 class CategoryGroupedAssociationResults(Results):
-    
-    counterpart_category: Optional[str] = Field(None, description="""The category of the counterpart entity in a given association,  eg. the category of the entity that is not the subject""")
-    items: List[Association] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
+
+    counterpart_category: Optional[str] = Field(
+        None,
+        description="""The category of the counterpart entity in a given association,  eg. the category of the entity that is not the subject""",
+    )
+    items: List[Association] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-    
+
 
 class EntityResults(Results):
-    
-    items: List[Entity] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
+
+    items: List[Entity] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-    
+
 
 class MappingResults(Results):
     """
     SSSOM Mappings returned as a results collection
     """
-    items: List[Mapping] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
+
+    items: List[Mapping] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-    
+
 
 class MultiEntityAssociationResults(Results):
-    
+
     id: str = Field(...)
     name: Optional[str] = Field(None)
     associated_categories: List[CategoryGroupedAssociationResults] = Field(default_factory=list)
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-    
+
 
 class SearchResult(Entity):
-    
+
     highlight: Optional[str] = Field(None, description="""matching text snippet containing html tags""")
     score: Optional[float] = Field(None)
     id: str = Field(...)
@@ -365,55 +579,82 @@ class SearchResult(Entity):
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
     in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
-    in_taxon_label: Optional[str] = Field(None, description="""The label of the biolink taxon that the entity is in the closure of.""")
+    in_taxon_label: Optional[str] = Field(
+        None,
+        description="""The label of the biolink taxon that the entity is in the closure of.""",
+    )
     symbol: Optional[str] = Field(None)
     synonym: Optional[List[str]] = Field(default_factory=list)
     uri: Optional[str] = Field(None, description="""The URI of the entity""")
-    
+
 
 class SearchResults(Results):
-    
-    items: List[SearchResult] = Field(default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""")
-    facet_fields: Optional[List[FacetField]] = Field(default_factory=list, description="""Collection of facet field responses with the field values and counts""")
-    facet_queries: Optional[List[FacetValue]] = Field(default_factory=list, description="""Collection of facet query responses with the query string values and counts""")
+
+    items: List[SearchResult] = Field(
+        default_factory=list,
+        description="""A collection of items, with the type to be overriden by slot_usage""",
+    )
+    facet_fields: Optional[List[FacetField]] = Field(
+        default_factory=list,
+        description="""Collection of facet field responses with the field values and counts""",
+    )
+    facet_queries: Optional[List[FacetValue]] = Field(
+        default_factory=list,
+        description="""Collection of facet query responses with the query string values and counts""",
+    )
     limit: int = Field(..., description="""number of items to return in a response""")
     offset: int = Field(..., description="""offset into the total number of items""")
     total: int = Field(..., description="""total number of items matching a query""")
-    
+
 
 class PairwiseSimilarity(ConfiguredBaseModel):
     """
     Abstract grouping for representing individual pairwise similarities
     """
+
     None
-    
+
 
 class TermPairwiseSimilarity(PairwiseSimilarity):
     """
     A simple pairwise similarity between two atomic concepts/terms
     """
+
     subject_id: str = Field(...)
     subject_label: Optional[str] = Field(None, description="""The name of the subject entity""")
     subject_source: Optional[str] = Field(None, description="""the source for the first entity""")
     object_id: str = Field(...)
     object_label: Optional[str] = Field(None, description="""The name of the object entity""")
     object_source: Optional[str] = Field(None, description="""the source for the second entity""")
-    ancestor_id: Optional[str] = Field(None, description="""the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected""")
+    ancestor_id: Optional[str] = Field(
+        None,
+        description="""the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected""",
+    )
     ancestor_label: Optional[str] = Field(None, description="""the name or label of the ancestor concept""")
     ancestor_source: Optional[str] = Field(None)
     object_information_content: Optional[float] = Field(None, description="""The IC of the object""")
     subject_information_content: Optional[float] = Field(None, description="""The IC of the subject""")
     ancestor_information_content: Optional[float] = Field(None, description="""The IC of the object""")
-    jaccard_similarity: Optional[float] = Field(None, description="""The number of concepts in the intersection divided by the number in the union""")
-    cosine_similarity: Optional[float] = Field(None, description="""the dot product of two node embeddings divided by the product of their lengths""")
+    jaccard_similarity: Optional[float] = Field(
+        None,
+        description="""The number of concepts in the intersection divided by the number in the union""",
+    )
+    cosine_similarity: Optional[float] = Field(
+        None,
+        description="""the dot product of two node embeddings divided by the product of their lengths""",
+    )
     dice_similarity: Optional[float] = Field(None)
-    phenodigm_score: Optional[float] = Field(None, description="""the geometric mean of the jaccard similarity and the information content""")
-    
+    phenodigm_score: Optional[float] = Field(
+        None,
+        description="""the geometric mean of the jaccard similarity and the information content""",
+    )
+
 
 class TermSetPairwiseSimilarity(PairwiseSimilarity):
     """
     A simple pairwise similarity between two sets of concepts/terms
     """
+
     subject_termset: Optional[Dict[str, TermInfo]] = Field(default_factory=dict)
     object_termset: Optional[Dict[str, TermInfo]] = Field(default_factory=dict)
     subject_best_matches: Optional[Dict[str, BestMatch]] = Field(default_factory=dict)
@@ -421,16 +662,16 @@ class TermSetPairwiseSimilarity(PairwiseSimilarity):
     average_score: Optional[float] = Field(None)
     best_score: Optional[float] = Field(None)
     metric: Optional[str] = Field(None)
-    
+
 
 class TermInfo(ConfiguredBaseModel):
-    
+
     id: str = Field(...)
     label: Optional[str] = Field(None)
-    
+
 
 class BestMatch(ConfiguredBaseModel):
-    
+
     match_source: str = Field(...)
     match_source_label: Optional[str] = Field(None)
     match_target: Optional[str] = Field(None, description="""the entity matches""")
@@ -439,7 +680,6 @@ class BestMatch(ConfiguredBaseModel):
     match_subsumer: Optional[str] = Field(None)
     match_subsumer_label: Optional[str] = Field(None)
     similarity: TermPairwiseSimilarity = Field(...)
-    
 
 
 # Update forward refs
@@ -472,4 +712,3 @@ class BestMatch(ConfiguredBaseModel):
 TermSetPairwiseSimilarity.update_forward_refs()
 TermInfo.update_forward_refs()
 BestMatch.update_forward_refs()
-
diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml
index 33604a394..6458fc9b3 100644
--- a/backend/src/monarch_py/datamodels/model.yaml
+++ b/backend/src/monarch_py/datamodels/model.yaml
@@ -234,6 +234,7 @@ classes:
       - inheritance
       - causal_gene
       - causes_disease
+      - mappings
       - external_links
       - provided_by_link
       - association_counts
@@ -526,7 +527,6 @@ slots:
   qualifiers_closure_label:
     multivalued: true
     description: Field containing frequency_qualifier name and the names of all of it's ancestors
-
   frequency_qualifier_label:
     is_a: name
     description: The name of the frequency_qualifier entity
@@ -587,7 +587,13 @@ slots:
   stage_qualifier_closure_label:
     multivalued: true
     description: Field containing stage_qualifier name and the names of all of it's ancestors
-# sssom slots
+  
+  # sssom slots
+  mappings:
+    description: List of ExpandedCuries with id and url for mapped entities
+    range: ExpandedCurie
+    multivalued: true
+    inlined_as_list: true
   subject_id:
     range: string
     required: true
diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py
index bc3afe350..0b2cc581d 100644
--- a/backend/src/monarch_py/implementations/solr/solr_implementation.py
+++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py
@@ -44,6 +44,7 @@
 from monarch_py.interfaces.entity_interface import EntityInterface
 from monarch_py.interfaces.search_interface import SearchInterface
 from monarch_py.service.solr_service import SolrService
+from monarch_py.utils.entity_utils import get_expanded_curie
 from monarch_py.utils.utils import get_provided_by_link, get_links_for_field
 
 
@@ -116,11 +117,25 @@ def get_entity(self, id: str, extra: bool) -> Optional[Union[Node, Entity]]:
         node.association_counts = self.get_association_counts(id).items
         node.external_links = get_links_for_field(node.xref) if node.xref else []
         node.provided_by_link = get_provided_by_link(node.provided_by)
+        node.mappings = self._get_mapped_entities(node)
 
         return node
 
     ### Entity helpers ###
 
+    def _get_mapped_entities(self, this_entity: Entity) -> list:
+        """..."""
+        mapped_entities = []
+        mappings = self.get_mappings(entity_id=this_entity.id)
+        for m in mappings.items:
+            if this_entity.id == m.subject_id:
+                mapped_entities.append(get_expanded_curie(m.object_id))
+            elif this_entity.id == m.object_id:
+                mapped_entities.append(get_expanded_curie(m.subject_id))
+            else:
+                pass
+        return mapped_entities
+
     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 == association.subject:
diff --git a/backend/src/monarch_py/utils/entity_utils.py b/backend/src/monarch_py/utils/entity_utils.py
index 97056219a..9cb8d032f 100644
--- a/backend/src/monarch_py/utils/entity_utils.py
+++ b/backend/src/monarch_py/utils/entity_utils.py
@@ -1,6 +1,12 @@
+from monarch_py.datamodels.model import ExpandedCurie
 from monarch_py.service.curie_service import CurieService
 
 
 def get_uri(id: str) -> str:
     """Returns the URI for the given CURIE."""
     return CurieService().expand(id)
+
+
+def get_expanded_curie(id: str) -> ExpandedCurie:
+    """Returns the URI for the given CURIE."""
+    return ExpandedCurie(id=id, url=get_uri(id))
diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py
index 67fb5632e..44789afcf 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": 2,
+            "QTime": 1,
             "params": {
                 "facet.query": [
                     'object_closure:"HP:0000924"',
diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py
index a25b43ff0..b37dfc336 100644
--- a/backend/tests/fixtures/node.py
+++ b/backend/tests/fixtures/node.py
@@ -19,6 +19,15 @@ def node():
         "inheritance": None,
         "causal_gene": [],
         "causes_disease": [],
+        "mappings": [
+            {"id": "DOID:9884", "url": "http://purl.obolibrary.org/obo/DOID_9884"},
+            {"id": "ICD10CM:G71.0", "url": "https://icd.codes/icd10cm/G71.0"},
+            {"id": "MESH:D009136", "url": "http://identifiers.org/mesh/D009136"},
+            {"id": "NCIT:C84910", "url": "http://purl.obolibrary.org/obo/NCIT_C84910"},
+            {"id": "SCTID:73297009", "url": None},
+            {"id": "UMLS:C0026850", "url": "http://identifiers.org/umls/C0026850"},
+            {"id": "Orphanet:98473", "url": None},
+        ],
         "external_links": [],
         "provided_by_link": {
             "id": "phenio",
diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json
index baf9051e2..d7f9825b0 100644
--- a/frontend/fixtures/node.json
+++ b/frontend/fixtures/node.json
@@ -14,6 +14,36 @@
   "inheritance": null,
   "causal_gene": [],
   "causes_disease": [],
+  "mappings": [
+    {
+      "id": "DOID:9884",
+      "url": "http://purl.obolibrary.org/obo/DOID_9884"
+    },
+    {
+      "id": "ICD10CM:G71.0",
+      "url": "https://icd.codes/icd10cm/G71.0"
+    },
+    {
+      "id": "MESH:D009136",
+      "url": "http://identifiers.org/mesh/D009136"
+    },
+    {
+      "id": "NCIT:C84910",
+      "url": "http://purl.obolibrary.org/obo/NCIT_C84910"
+    },
+    {
+      "id": "SCTID:73297009",
+      "url": null
+    },
+    {
+      "id": "UMLS:C0026850",
+      "url": "http://identifiers.org/umls/C0026850"
+    },
+    {
+      "id": "Orphanet:98473",
+      "url": null
+    }
+  ],
   "external_links": [],
   "provided_by_link": {
     "id": "phenio",
diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index 0c74ac2f6..9ba9ee499 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -416,6 +416,8 @@ export interface Node extends Entity {
     causal_gene?: Entity[],
     /** A list of diseases that are known to be causally associated with a gene */
     causes_disease?: Entity[],
+    /** List of ExpandedCuries with id and url for mapped entities */
+    mappings?: ExpandedCurie[],
     /** ExpandedCurie with id and url for xrefs */
     external_links?: ExpandedCurie[],
     /** A link to the docs for the knowledge source that provided the node/edge. */
@@ -511,18 +513,18 @@ export interface TermPairwiseSimilarity extends PairwiseSimilarity {
     ancestor_label?: string,
     ancestor_source?: string,
     /** The IC of the object */
-    object_information_content?: number,
+    object_information_content?: string,
     /** The IC of the subject */
-    subject_information_content?: number,
+    subject_information_content?: string,
     /** The IC of the object */
-    ancestor_information_content?: number,
+    ancestor_information_content?: string,
     /** The number of concepts in the intersection divided by the number in the union */
-    jaccard_similarity?: number,
+    jaccard_similarity?: string,
     /** the dot product of two node embeddings divided by the product of their lengths */
     cosine_similarity?: number,
-    dice_similarity?: number,
+    dice_similarity?: string,
     /** the geometric mean of the jaccard similarity and the information content */
-    phenodigm_score?: number,
+    phenodigm_score?: string,
 };
 /**
  * A simple pairwise similarity between two sets of concepts/terms

From 3eb6463b0eb904ac718eb95e92d8f298f96ca557 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 10 Nov 2023 14:16:15 -0500
Subject: [PATCH 8/9] implement in frontend

---
 frontend/src/pages/node/SectionOverview.vue | 71 ++++++++++++++++++++-
 frontend/yarn.lock                          | 30 ++++-----
 2 files changed, 81 insertions(+), 20 deletions(-)

diff --git a/frontend/src/pages/node/SectionOverview.vue b/frontend/src/pages/node/SectionOverview.vue
index f831d3295..aae3fe9ee 100644
--- a/frontend/src/pages/node/SectionOverview.vue
+++ b/frontend/src/pages/node/SectionOverview.vue
@@ -80,13 +80,55 @@
         ></p>
       </AppDetail>
 
+      <!-- mappings -->
+      <AppDetail :blank="!clinicalSynopsis.length" title="Clinical Synopsis">
+        <AppFlex align-h="left" gap="small">
+          <AppLink
+            v-for="(mapping, index) in clinicalSynopsis"
+            :key="index"
+            :to="mapping.url || ''"
+          >
+            {{ mapping.id }}
+          </AppLink>
+        </AppFlex>
+      </AppDetail>
+      <AppDetail
+        :blank="!infoForPatients.length"
+        title="Clinical Info for Patients"
+      >
+        <AppFlex align-h="left" gap="small">
+          <AppLink
+            v-for="(mapping, index) in infoForPatients"
+            :key="index"
+            :to="mapping.url || ''"
+          >
+            {{ mapping.id }}
+          </AppLink>
+        </AppFlex>
+      </AppDetail>
+      <AppDetail
+        :blank="!otherMappings.length"
+        title="Other Mappings"
+        :full="true"
+      >
+        <AppFlex align-h="left" gap="small">
+          <AppLink
+            v-for="(mapping, index) in otherMappings"
+            :key="index"
+            :to="mapping.url || ''"
+          >
+            {{ mapping.id }}
+          </AppLink>
+        </AppFlex>
+      </AppDetail>
+
       <!-- association counts -->
       <AppDetail
         :blank="!node.association_counts.length"
         title="Association Counts"
         :full="true"
       >
-        <AppFlex align-h="left">
+        <AppFlex align-h="left" gap="small">
           <AppLink
             v-for="(count, index) in node.association_counts"
             :key="index"
@@ -101,6 +143,8 @@
 </template>
 
 <script setup lang="ts">
+import type { info } from "console";
+import { computed } from "vue";
 import { omit } from "lodash";
 import type { Node } from "@/api/model";
 import AppDetail from "@/components/AppDetail.vue";
@@ -112,7 +156,30 @@ type Props = {
   node: Node;
 };
 
-defineProps<Props>();
+const props = defineProps<Props>();
+
+/** separate out mappings into categories */
+const clinicalSynopsis = computed(
+  () =>
+    props.node.mappings?.filter(({ id }) =>
+      ["OMIM:", "Orphanet:"].some((prefix) => id.startsWith(prefix)),
+    ) || [],
+);
+const infoForPatients = computed(
+  () =>
+    props.node.mappings?.filter(({ id }) =>
+      ["GARD:"].some((prefix) => id.startsWith(prefix)),
+    ) || [],
+);
+const otherMappings = computed(
+  () =>
+    props.node.mappings?.filter(
+      ({ id }) =>
+        !["OMIM:", "GARD:", "Orphanet:"].some((prefix) =>
+          id.startsWith(prefix),
+        ),
+    ) || [],
+);
 </script>
 
 <style lang="scss" scoped>
diff --git a/frontend/yarn.lock b/frontend/yarn.lock
index b837d6a81..556d9b047 100644
--- a/frontend/yarn.lock
+++ b/frontend/yarn.lock
@@ -529,12 +529,15 @@
     picocolors "^1.0.0"
     tslib "^2.6.0"
 
-"@playwright/test@^1.38.1":
-  version "1.38.1"
-  resolved "https://registry.yarnpkg.com/@playwright/test/-/test-1.38.1.tgz#8ef4263e355cd1d8ad7905d471d268e8acb82ed6"
-  integrity sha512-NqRp8XMwj3AK+zKLbZShl0r/9wKgzqI/527bkptKXomtuo+dOjU9NdMASQ8DNC9z9zLOMbG53T4eihYr3XR+BQ==
+"@playwright/test@~1.37.0":
+  version "1.37.1"
+  resolved "https://registry.yarnpkg.com/@playwright/test/-/test-1.37.1.tgz#e7f44ae0faf1be52d6360c6bbf689fd0057d9b6f"
+  integrity sha512-bq9zTli3vWJo8S3LwB91U0qDNQDpEXnw7knhxLM0nwDvexQAwx9tO8iKDZSqqneVq+URd/WIoz+BALMqUTgdSg==
   dependencies:
-    playwright "1.38.1"
+    "@types/node" "*"
+    playwright-core "1.37.1"
+  optionalDependencies:
+    fsevents "2.3.2"
 
 "@popperjs/core@^2.9.0":
   version "2.11.8"
@@ -3215,19 +3218,10 @@ pkg-types@^1.0.3:
     mlly "^1.2.0"
     pathe "^1.1.0"
 
-playwright-core@1.38.1:
-  version "1.38.1"
-  resolved "https://registry.yarnpkg.com/playwright-core/-/playwright-core-1.38.1.tgz#75a3c470aa9576b7d7c4e274de3d79977448ba08"
-  integrity sha512-tQqNFUKa3OfMf4b2jQ7aGLB8o9bS3bOY0yMEtldtC2+spf8QXG9zvXLTXUeRsoNuxEYMgLYR+NXfAa1rjKRcrg==
-
-playwright@1.38.1:
-  version "1.38.1"
-  resolved "https://registry.yarnpkg.com/playwright/-/playwright-1.38.1.tgz#82ecd9bc4f4f64dbeee8a11c31793748e2528130"
-  integrity sha512-oRMSJmZrOu1FP5iu3UrCx8JEFRIMxLDM0c/3o4bpzU5Tz97BypefWf7TuTNPWeCe279TPal5RtPPZ+9lW/Qkow==
-  dependencies:
-    playwright-core "1.38.1"
-  optionalDependencies:
-    fsevents "2.3.2"
+playwright-core@1.37.1:
+  version "1.37.1"
+  resolved "https://registry.yarnpkg.com/playwright-core/-/playwright-core-1.37.1.tgz#cb517d52e2e8cb4fa71957639f1cd105d1683126"
+  integrity sha512-17EuQxlSIYCmEMwzMqusJ2ztDgJePjrbttaefgdsiqeLWidjYz9BxXaTaZWxH1J95SHGk6tjE+dwgWILJoUZfA==
 
 postcss-less@^6.0.0:
   version "6.0.0"

From 24bb12d882b49a7e8a109adc148f03d283798ddf Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Fri, 10 Nov 2023 13:06:01 -0700
Subject: [PATCH 9/9] fix model

---
 frontend/src/api/model.ts | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index 9ba9ee499..522ffa0b2 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -519,12 +519,12 @@ export interface TermPairwiseSimilarity extends PairwiseSimilarity {
     /** The IC of the object */
     ancestor_information_content?: string,
     /** The number of concepts in the intersection divided by the number in the union */
-    jaccard_similarity?: string,
+    jaccard_similarity?: number,
     /** the dot product of two node embeddings divided by the product of their lengths */
     cosine_similarity?: number,
-    dice_similarity?: string,
+    dice_similarity?: number,
     /** the geometric mean of the jaccard similarity and the information content */
-    phenodigm_score?: string,
+    phenodigm_score?: number,
 };
 /**
  * A simple pairwise similarity between two sets of concepts/terms