merge main

.github/workflows/build-and-deploy-images.yaml

@@ -104,8 +104,18 @@ jobs:
         with:
           version: ">= 447.0.0"
 
+      - name: "Cache SSH Key"
+        uses: actions/cache@v3
+        with:
+          path: ~/.ssh/google_compute_engine
+          key: ${{ runner.os }}-ssh-key
+
       - name: "Update API Service"
-        run: gcloud compute ssh --zone us-central1-a monarch-v3-dev-manager -- sudo docker service update monarch-v3_api --with-registry-auth  --update-order=start-first --force --image us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-api:${{ github.sha }}
+        run: | 
+          gcloud compute ssh --ssh-key-expiration 60m --zone us-central1-a monarch-v3-dev-manager -- sudo docker system prune -f
+          gcloud compute ssh --ssh-key-expiration 60m --zone us-central1-a monarch-v3-dev-manager -- sudo docker service update monarch-v3_api --with-registry-auth  --update-order=start-first --force --image us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-api:${{ github.sha }}
           
       - name: "Update UI Service"
-        run: gcloud compute ssh --zone us-central1-a monarch-v3-dev-manager -- sudo docker service update monarch-v3_nginx --with-registry-auth  --update-order=start-first --force --image us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-ui:${{ github.sha }}
+        run: |
+          gcloud compute ssh --ssh-key-expiration 60m --zone us-central1-a monarch-v3-dev-manager -- sudo docker system prune -f
+          gcloud compute ssh --ssh-key-expiration 60m --zone us-central1-a monarch-v3-dev-manager -- sudo docker service update monarch-v3_nginx --with-registry-auth  --update-order=start-first --force --image us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-ui:${{ github.sha }}

Makefile

@@ -77,7 +77,7 @@ install-frontend:
 model: install-backend	
 	$(RUN) gen-pydantic $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py
 	$(RUN) gen-typescript $(SCHEMADIR)/model.yaml > frontend/src/api/model.ts
-	$(RUN) black $(SCHEMADIR)/model.py
+	make format
 
 
 ### Documentation ###
@@ -111,11 +111,20 @@ test-frontend:
 
 .PHONY: fixtures
 fixtures: 
-	@echo "Generating fixtures..."
+	@echo "Generating fixtures and data..."
 	$(RUN) python scripts/generate_fixtures.py --all-fixtures
-	$(RUN) black -l 120 backend/tests/fixtures/
-	cd frontend && \
-		yarn lint 
+	make format
+
+
+.PHONY: data
+data:
+	@echo "Generating frontpage metadata..."
+	$(RUN) python scripts/generate_fixtures.py --metadata
+	@echo "Generating publications data..."
+	$(RUN) python scripts/get_publications.py
+	@echo "Generating resources data..."
+	wget https://raw.githubusercontent.com/monarch-initiative/monarch-documentation/main/src/docs/resources/monarch-app-resources.json -O frontend/src/pages/resources/resources.json
+	make format-frontend
 
 ### Development ###
 

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/curie_service.py

@@ -1,7 +1,7 @@
 ### make a singleton class that uses prefixmap and curies to expand curies
 
 from curies import Converter
-from prefixmaps.io.parser import load_multi_context
+from prefixmaps import load_converter
 
 
 class CurieService:
@@ -17,9 +17,7 @@ def __new__(cls):
     def initialize(self):
         # this is a magic keyword that represents the "merged" context from Chris M's algorithm
         # (https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/merged.csv)
-        context = load_multi_context(["merged"])
-        extended_prefix_map = context.as_extended_prefix_map()
-        self.converter = Converter.from_extended_prefix_map(extended_prefix_map)
+        self.converter = load_converter(["merged"])
 
     def expand(self, curie: str) -> str:
         return self.converter.expand(curie)

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