Minimal tests working

prez/app.py

@@ -35,6 +35,13 @@
     populate_api_info,
     add_prefixes_to_prefix_graph,
 )
+from prez.services.app_service import (
+    healthcheck_sparql_endpoints,
+    count_objects,
+    create_endpoints_graph,
+    populate_api_info,
+    add_prefixes_to_prefix_graph,
+)
 from prez.services.exception_catchers import (
     catch_400,
     catch_404,

prez/renderers/renderer.py

@@ -12,7 +12,7 @@
 from prez.models.profiles_and_mediatypes import ProfilesMediatypesInfo
 from prez.models.profiles_item import ProfileItem
 from prez.reference_data.prez_ns import PREZ
-from prez.sparql.methods import send_queries
+from prez.sparql.methods import send_queries, rdf_queries_to_graph
 from prez.services.curie_functions import get_curie_id_for_uri
 from prez.sparql.objects_listings import (
     generate_item_construct,
@@ -81,7 +81,7 @@ async def get_annotations_graph(profile, graph, cache):
     if queries_for_uncached is None:
         anots_from_triplestore = Graph()
     else:
-        anots_from_triplestore = await queries_to_graph([queries_for_uncached])
+        anots_from_triplestore = await rdf_queries_to_graph(queries_for_uncached)
 
     if len(anots_from_triplestore) > 1:
         annotations_graph += anots_from_triplestore

prez/routers/vocprez.py

@@ -15,7 +15,7 @@
     return_from_graph,
 )
 from prez.services.curie_functions import get_curie_id_for_uri
-from prez.sparql.methods import queries_to_graph
+from prez.sparql.methods import rdf_queries_to_graph
 from prez.sparql.objects_listings import (
     generate_listing_construct,
     generate_listing_count_construct,
@@ -41,8 +41,16 @@ async def vocprez_home():
     return PlainTextResponse("VocPrez Home")
 
 
-@router.get("/v/collection", summary="List Collections", name="https://prez.dev/endpoint/vocprez/collection-listing")
-@router.get("/v/vocab", summary="List Vocabularies", name="https://prez.dev/endpoint/vocprez/vocabs-listing")
+@router.get(
+    "/v/collection",
+    summary="List Collections",
+    name="https://prez.dev/endpoint/vocprez/collection-listing",
+)
+@router.get(
+    "/v/vocab",
+    summary="List Vocabularies",
+    name="https://prez.dev/endpoint/vocprez/vocabs-listing",
+)
 async def schemes_endpoint(
     request: Request,
     page: int = 1,
@@ -75,9 +83,9 @@ async def schemes_endpoint(
 
 
 @router.get(
-    "/v/vocab/{scheme_curie}/all", 
+    "/v/vocab/{scheme_curie}/all",
     summary="Get Concept Scheme and all its concepts",
-    name="https://prez.dev/endpoint/vocprez/vocab"
+    name="https://prez.dev/endpoint/vocprez/vocab",
 )
 async def vocprez_scheme(request: Request, scheme_curie: str):
     """Get a SKOS Concept Scheme and all of its concepts.
@@ -149,7 +157,7 @@ async def concept_scheme_top_concepts_route(
         iri, page, per_page
     )
 
-    graph = await queries_to_graph([concept_scheme_top_concepts_query])
+    graph = await rdf_queries_to_graph(concept_scheme_top_concepts_query)
     for concept in graph.objects(iri, SKOS.hasTopConcept):
         if isinstance(concept, URIRef):
             concept_curie = get_curie_id_for_uri(concept)
@@ -204,7 +212,7 @@ async def concept_narrowers_route(
     iri = get_iri_route(concept_curie)
     concept_narrowers_query = get_concept_narrowers_query(iri, page, per_page)
 
-    graph = await queries_to_graph([concept_narrowers_query])
+    graph = await rdf_queries_to_graph(concept_narrowers_query)
     for concept in graph.objects(iri, SKOS.narrower):
         if isinstance(concept, URIRef):
             concept_curie = get_curie_id_for_uri(concept)
@@ -279,9 +287,11 @@ async def vocprez_collection(request: Request, collection_curie: str):
     return await item_endpoint(request)
 
 
-@router.get("/v/collection/{collection_curie}/{concept_curie}",
-            summary="Get Concept",
-            name="https://prez.dev/endpoint/vocprez/collection-concept")
+@router.get(
+    "/v/collection/{collection_curie}/{concept_curie}",
+    summary="Get Concept",
+    name="https://prez.dev/endpoint/vocprez/collection-concept",
+)
 async def vocprez_collection_concept(
     request: Request, collection_curie: str, concept_curie: str
 ):
@@ -295,7 +305,7 @@ async def item_endpoint(request: Request, vp_item: Optional[VocabItem] = None):
             **request.path_params,
             **request.query_params,
             url_path=str(request.url.path),
-            endpoint_uri=request.scope["route"].name
+            endpoint_uri=request.scope["route"].name,
         )
     prof_and_mt_info = ProfilesMediatypesInfo(request=request, classes=vp_item.classes)
     vp_item.selected_class = prof_and_mt_info.selected_class

prez/services/app_service.py

@@ -14,8 +14,7 @@
 )
 from prez.config import settings
 from prez.reference_data.prez_ns import PREZ, ALTREXT
-from prez.sparql.methods import rdf_queries_to_graph
-from prez.sparql.methods import query_to_graph, sparql_query_non_async
+from prez.sparql.methods import rdf_queries_to_graph, sparql_query_non_async
 from prez.sparql.objects_listings import startup_count_objects
 from prez.services.curie_functions import get_curie_id_for_uri
 
@@ -109,7 +108,7 @@ async def add_prefixes_to_prefix_graph():
             SELECT DISTINCT ?iri
             WHERE {
               ?iri ?p ?o .
-              FILTER(isIRI(?iri)) 
+              FILTER(isIRI(?iri))
             }
         """
 

prez/sparql/methods.py

@@ -102,7 +102,7 @@ async def send_query(query: str, mediatype="text/turtle"):
     return await async_client.send(query_rq, stream=True)
 
 
-async def rdf_queries_to_graph(query: str):
+async def rdf_queries_to_graph(query: str) -> Graph:
     """
     Sends a SPARQL query asynchronously and parses the response into an RDFLib Graph.
     Args: query: str: A SPARQL query to be sent asynchronously.

prez/sparql/objects_listings.py

@@ -117,8 +117,8 @@ def generate_listing_construct(
             {{
                 SELECT ?top_level_item ?child_item
                 WHERE {{
-                    {f'{uri_or_tl_item} a <{focus_item.general_class}> .{chr(10)}' if focus_item.top_level_listing else generate_outbound_predicates(uri_or_tl_item, outbound_children, outbound_parents)}\
-                    
+                    {f'{uri_or_tl_item} a <{focus_item.base_class}> .{chr(10)}' if focus_item.top_level_listing else generate_focus_to_x_predicates(uri_or_tl_item, focus_to_child, focus_to_parent)}\
+
                     OPTIONAL {{
                         {f'{uri_or_tl_item} <{profile_item.label}> ?label .' if focus_item.top_level_listing else ""}\
                     }}
@@ -142,7 +142,7 @@ def generate_listing_construct(
         "top_level_gen_class": focus_item.base_class
         if focus_item.top_level_listing
         else None,
-        # if this is a top level class, include it's general class here so we can create
+        # if this is a top level class, include it's base class here so we can create
         # links to instances of the top level class,
     }
     return query, predicates_for_link_addition
@@ -520,7 +520,7 @@ def generate_listing_count_construct(
     """
     Generates a SPARQL construct query to count either:
     1. the members of a collection, if a URI is given, or;
-    2. the number of instances of a general class, given a general class.
+    2. the number of instances of a base class, given a base class.
     """
     if not item.top_level_listing:
         query = dedent(
@@ -772,7 +772,7 @@ def select_profile_mediatype(
     defaults, and the availability of these in profiles.
 
     NB: Most specific class refers to the rdfs:Class of an object which has the most specific rdfs:subClassOf links to
-    the general class delivered by that API endpoint. The general classes delivered by each API endpoint are:
+    the base class delivered by that API endpoint. The base classes delivered by each API endpoint are:
 
     SpacePrez:
     /s/datasets -> prez:DatasetList

prez/sparql/resource.py

@@ -1,8 +1,8 @@
 from rdflib import Graph
 
-from prez.sparql.methods import query_to_graph
+from prez.sparql.methods import rdf_queries_to_graph
 
 
 async def get_resource(iri: str) -> Graph:
     query = f"""DESCRIBE <{iri}>"""
-    return await query_to_graph(query)
+    return await rdf_queries_to_graph(query)