Add deprecated slot, down rank deprecated search results (#474)

Adds deprecated so that we can handle obsolete ontology terms properly

backend/pyproject.toml

@@ -19,7 +19,7 @@ packages = [
 python = "^3.9"
 pydantic = "^1.10.2"
 curies = "<1"
-linkml = "^1.6.1"
+linkml = "^1.6.2"
 prefixmaps = "^0.1.7"
 
 requests = "^2.28.1"

backend/src/monarch_py/datamodels/model.py

@@ -373,6 +373,10 @@ class Entity(ConfiguredBaseModel):
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
     full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    deprecated: Optional[bool] = Field(
+        None,
+        description="""A boolean flag indicating that an entity is no longer considered current or valid.""",
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
@@ -474,6 +478,10 @@ class Node(Entity):
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
     full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    deprecated: Optional[bool] = Field(
+        None,
+        description="""A boolean flag indicating that an entity is no longer considered current or valid.""",
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
@@ -575,6 +583,10 @@ class SearchResult(Entity):
     category: str = Field(...)
     name: str = Field(...)
     full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    deprecated: Optional[bool] = Field(
+        None,
+        description="""A boolean flag indicating that an entity is no longer considered current or valid.""",
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)

backend/src/monarch_py/datamodels/model.yaml

@@ -166,6 +166,7 @@ classes:
       - category
       - name
       - full_name
+      - deprecated
       - description
       - xref
       - provided_by
@@ -304,6 +305,13 @@ slots:
       The category of the counterpart entity in a given association, 
       eg. the category of the entity that is not the subject
     range: string
+  deprecated:
+    description: >-
+      A boolean flag indicating that an entity is no longer considered current or valid.
+    range: boolean
+    exact_mappings:
+      - oboInOwl:ObsoleteClass
+
   description:
     range: string
   direction:

backend/src/monarch_py/implementations/solr/solr_parsers.py

@@ -88,6 +88,7 @@ def parse_association_counts(query_result: SolrQueryResult, entity: str) -> Asso
 def parse_entity(solr_document: Dict) -> Entity:
     try:
         entity = Entity(**solr_document)
+
         entity.uri = get_uri(entity.id)
     except ValidationError:
         logger.error(f"Validation error for {solr_document}")

backend/src/monarch_py/implementations/solr/solr_query_utils.py

@@ -204,7 +204,8 @@ def entity_boost():
     """Shared boost function between search and autocomplete"""
     disease_boost = 'if(termfreq(category,"biolink:Disease"),10.0,1)'
     human_gene_boost = 'if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1)'
-    return f"product({disease_boost},{human_gene_boost})"
+    obsolete_unboost = 'if(termfreq(deprecated,"true"),0.1,1)'
+    return f"product({disease_boost},{human_gene_boost},{obsolete_unboost})"
 
 
 def entity_query_fields():

backend/src/monarch_py/service/solr_service.py

@@ -18,7 +18,7 @@ def get(self, id):
         response.raise_for_status()
         entity = response.json()["doc"]
         try:
-            self._strip_json(entity, "_version_")
+            self._strip_json(entity, "_version_", "iri")
         except TypeError:  # if entity is None
             return None
         return entity
@@ -33,7 +33,7 @@ def query(self, q: SolrQuery) -> SolrQueryResult:
         response.raise_for_status()
         solr_query_result = SolrQueryResult.parse_obj(data)
         for doc in solr_query_result.response.docs:
-            self._strip_json(doc, "_version_")
+            self._strip_json(doc, "_version_", "iri")
 
         return solr_query_result