black repo

function_app.py

@@ -9,7 +9,9 @@
 
 
 if assemble_app is None:
-    raise RuntimeError("Cannot import prez in the Azure function app. Check requirements.py and pyproject.toml.")
+    raise RuntimeError(
+        "Cannot import prez in the Azure function app. Check requirements.py and pyproject.toml."
+    )
 
 
 # This is the base URL path that Prez routes will stem from
@@ -32,7 +34,8 @@
 if __name__ == "__main__":
     from azure.functions import HttpRequest, Context
     import asyncio
-    req = HttpRequest("GET", "/v", headers={}, body=b'')
+
+    req = HttpRequest("GET", "/v", headers={}, body=b"")
     context = dict()
     loop = asyncio.get_event_loop()
 

prez/app.py

@@ -16,12 +16,15 @@
     load_local_data_to_oxigraph,
     get_oxrdflib_store,
     get_system_store,
-    load_system_data_to_oxigraph, load_annotations_data_to_oxigraph, get_annotations_store,
+    load_system_data_to_oxigraph,
+    load_annotations_data_to_oxigraph,
+    get_annotations_store,
 )
 from prez.exceptions.model_exceptions import (
     ClassNotFoundException,
     URINotFoundException,
-    NoProfilesException, InvalidSPARQLQueryException,
+    NoProfilesException,
+    InvalidSPARQLQueryException,
 )
 from prez.repositories import RemoteSparqlRepo, PyoxigraphRepo, OxrdflibRepo
 from prez.routers.identifier import router as identifier_router
@@ -161,7 +164,7 @@ def assemble_app(
             ClassNotFoundException: catch_class_not_found_exception,
             URINotFoundException: catch_uri_not_found_exception,
             NoProfilesException: catch_no_profiles_exception,
-            InvalidSPARQLQueryException: catch_invalid_sparql_query
+            InvalidSPARQLQueryException: catch_invalid_sparql_query,
         },
         **kwargs
     )

prez/config.py

@@ -52,10 +52,7 @@ class Settings(BaseSettings):
         SDO.description,
     ]
     provenance_predicates: Optional[List[URIRef]] = [DCTERMS.provenance]
-    other_predicates: Optional[List[URIRef]] = [
-        SDO.color,
-        REG.status
-    ]
+    other_predicates: Optional[List[URIRef]] = [SDO.color, REG.status]
     sparql_repo_type: str = "remote"
     sparql_timeout: int = 30
     log_level: str = "INFO"

prez/exceptions/model_exceptions.py

@@ -44,4 +44,4 @@ class InvalidSPARQLQueryException(Exception):
 
     def __init__(self, error: str):
         self.message = f"Invalid SPARQL query: {error}"
-        super().__init__(self.message)
+        super().__init__(self.message)

prez/routers/api_extras_examples.py

@@ -5,10 +5,7 @@
 responses = json.loads(responses_json.read_text())
 cql_json_examples_dir = Path(__file__).parent.parent / "examples/cql"
 cql_examples = {
-    file.stem: {
-        "summary": file.stem,
-        "value": json.loads(file.read_text())
-    }
+    file.stem: {"summary": file.stem, "value": json.loads(file.read_text())}
     for file in cql_json_examples_dir.glob("*.json")
 }
 

prez/routers/identifier.py

@@ -4,8 +4,8 @@
 from rdflib.term import _is_valid_uri
 
 from prez.dependencies import get_data_repo
-from prez.services.query_generation.identifier import get_foaf_homepage_query
 from prez.services.curie_functions import get_uri_for_curie_id, get_curie_id_for_uri
+from prez.services.query_generation.identifier import get_foaf_homepage_query
 
 router = APIRouter(tags=["Identifier Resolution"])
 

prez/routers/ogc_router.py

@@ -10,7 +10,8 @@
     get_negotiated_pmts,
     get_profile_nodeshape,
     get_endpoint_structure,
-    generate_concept_hierarchy_query, cql_post_parser_dependency,
+    generate_concept_hierarchy_query,
+    cql_post_parser_dependency,
 )
 from prez.models.query_params import QueryParams
 from prez.reference_data.prez_ns import EP, ONT, OGCE
@@ -26,71 +27,63 @@
 router = APIRouter(tags=["ogcprez"])
 
 
-@router.get(
-    path="/search",
-    summary="Search",
-    name=OGCE["search"],
-    responses=responses
-)
+@router.get(path="/search", summary="Search", name=OGCE["search"], responses=responses)
 @router.get(
     "/profiles",
     summary="List Profiles",
     name=EP["system/profile-listing"],
-    responses=responses
+    responses=responses,
 )
 @router.get(
-    path="/cql",
-    summary="CQL GET endpoint",
-    name=OGCE["cql-get"],
-    responses=responses
+    path="/cql", summary="CQL GET endpoint", name=OGCE["cql-get"], responses=responses
 )
 @router.get(
     "/catalogs",
     summary="Catalog Listing",
     name=OGCE["catalog-listing"],
-    responses=responses
+    responses=responses,
 )
 @router.get(
     "/catalogs/{catalogId}/collections",
     summary="Collection Listing",
     name=OGCE["collection-listing"],
     openapi_extra=openapi_extras.get("collection-listing"),
-    responses=responses
+    responses=responses,
 )
 @router.get(
     "/catalogs/{catalogId}/collections/{collectionId}/items",
     summary="Item Listing",
     name=OGCE["item-listing"],
     openapi_extra=openapi_extras.get("item-listing"),
-    responses=responses
+    responses=responses,
 )
 @router.get(
     "/concept-hierarchy/{parent_curie}/top-concepts",
     summary="Top Concepts",
     name=OGCE["top-concepts"],
     openapi_extra=openapi_extras.get("top-concepts"),
-    responses=responses
+    responses=responses,
 )
 @router.get(
     "/concept-hierarchy/{parent_curie}/narrowers",
     summary="Narrowers",
     name=OGCE["narrowers"],
     openapi_extra=openapi_extras.get("narrowers"),
-    responses=responses
+    responses=responses,
 )
 async def listings(
-        query_params: QueryParams = Depends(),
-        endpoint_nodeshape: NodeShape = Depends(get_endpoint_nodeshapes),
-        pmts: NegotiatedPMTs = Depends(get_negotiated_pmts),
-        endpoint_structure: tuple[str, ...] = Depends(get_endpoint_structure),
-        profile_nodeshape: NodeShape = Depends(get_profile_nodeshape),
-        cql_parser: CQLParser = Depends(cql_get_parser_dependency),
-        search_query: ConstructQuery = Depends(generate_search_query),
-        concept_hierarchy_query: ConceptHierarchyQuery = Depends(
-            generate_concept_hierarchy_query
-        ),
-        data_repo: Repo = Depends(get_data_repo),
-        system_repo: Repo = Depends(get_system_repo),
+    query_params: QueryParams = Depends(),
+    endpoint_nodeshape: NodeShape = Depends(get_endpoint_nodeshapes),
+    pmts: NegotiatedPMTs = Depends(get_negotiated_pmts),
+    endpoint_structure: tuple[str, ...] = Depends(get_endpoint_structure),
+    profile_nodeshape: NodeShape = Depends(get_profile_nodeshape),
+    cql_parser: CQLParser = Depends(cql_get_parser_dependency),
+    search_query: ConstructQuery = Depends(generate_search_query),
+    concept_hierarchy_query: ConceptHierarchyQuery = Depends(
+        generate_concept_hierarchy_query
+    ),
+    data_repo: Repo = Depends(get_data_repo),
+    system_repo: Repo = Depends(get_system_repo),
 ):
     return await listing_function(
         data_repo=data_repo,
@@ -112,26 +105,20 @@ async def listings(
     summary="CQL POST endpoint",
     name=OGCE["cql-post"],
     openapi_extra={
-        "requestBody": {
-            "content": {
-                "application/json": {
-                    "examples": cql_examples
-                }
-            }
-        }
+        "requestBody": {"content": {"application/json": {"examples": cql_examples}}}
     },
-    responses=responses
+    responses=responses,
 )
 async def cql_post_listings(
-        query_params: QueryParams = Depends(),
-        endpoint_nodeshape: NodeShape = Depends(get_endpoint_nodeshapes),
-        pmts: NegotiatedPMTs = Depends(get_negotiated_pmts),
-        endpoint_structure: tuple[str, ...] = Depends(get_endpoint_structure),
-        profile_nodeshape: NodeShape = Depends(get_profile_nodeshape),
-        cql_parser: CQLParser = Depends(cql_post_parser_dependency),
-        search_query: ConstructQuery = Depends(generate_search_query),
-        data_repo: Repo = Depends(get_data_repo),
-        system_repo: Repo = Depends(get_system_repo),
+    query_params: QueryParams = Depends(),
+    endpoint_nodeshape: NodeShape = Depends(get_endpoint_nodeshapes),
+    pmts: NegotiatedPMTs = Depends(get_negotiated_pmts),
+    endpoint_structure: tuple[str, ...] = Depends(get_endpoint_structure),
+    profile_nodeshape: NodeShape = Depends(get_profile_nodeshape),
+    cql_parser: CQLParser = Depends(cql_post_parser_dependency),
+    search_query: ConstructQuery = Depends(generate_search_query),
+    data_repo: Repo = Depends(get_data_repo),
+    system_repo: Repo = Depends(get_system_repo),
 ):
     return await listing_function(
         data_repo=data_repo,
@@ -160,45 +147,42 @@ async def cql_post_listings(
 
 
 @router.get(
-    path="/object",
-    summary="Object",
-    name=EP["system/object"],
-    responses=responses
+    path="/object", summary="Object", name=EP["system/object"], responses=responses
 )
 @router.get(
     path="/profiles/{profile_curie}",
     summary="Profile",
     name=EP["system/profile-object"],
     openapi_extra=openapi_extras.get("profile-object"),
-    responses=responses
+    responses=responses,
 )
 @router.get(
     path="/catalogs/{catalogId}",
     summary="Catalog Object",
     name=OGCE["catalog-object"],
     openapi_extra=openapi_extras.get("catalog-object"),
-    responses=responses
+    responses=responses,
 )
 @router.get(
     path="/catalogs/{catalogId}/collections/{collectionId}",
     summary="Collection Object",
     name=OGCE["collection-object"],
     openapi_extra=openapi_extras.get("collection-object"),
-    responses=responses
+    responses=responses,
 )
 @router.get(
     path="/catalogs/{catalogId}/collections/{collectionId}/items/{itemId}",
     summary="Item Object",
     name=OGCE["item-object"],
     openapi_extra=openapi_extras.get("item-object"),
-    responses=responses
+    responses=responses,
 )
 async def objects(
-        pmts: NegotiatedPMTs = Depends(get_negotiated_pmts),
-        endpoint_structure: tuple[str, ...] = Depends(get_endpoint_structure),
-        profile_nodeshape: NodeShape = Depends(get_profile_nodeshape),
-        data_repo: Repo = Depends(get_data_repo),
-        system_repo: Repo = Depends(get_system_repo),
+    pmts: NegotiatedPMTs = Depends(get_negotiated_pmts),
+    endpoint_structure: tuple[str, ...] = Depends(get_endpoint_structure),
+    profile_nodeshape: NodeShape = Depends(get_profile_nodeshape),
+    data_repo: Repo = Depends(get_data_repo),
+    system_repo: Repo = Depends(get_system_repo),
 ):
     return await object_function(
         data_repo=data_repo,

prez/routers/sparql.py

@@ -9,7 +9,7 @@
 from starlette.requests import Request
 from starlette.responses import StreamingResponse
 
-from prez.dependencies import get_data_repo, get_system_repo, get_negotiated_pmts
+from prez.dependencies import get_data_repo, get_system_repo
 from prez.renderers.renderer import return_annotated_rdf
 from prez.repositories import Repo
 from prez.services.connegp_service import NegotiatedPMTs
@@ -21,29 +21,35 @@
 
 @router.post("/sparql")
 async def sparql_post_passthrough(
-        # To maintain compatibility with the other SPARQL endpoints,
-        # /sparql POST endpoint is not a JSON API, it uses
-        # values encoded with x-www-form-urlencoded
-        query: Annotated[str, Form()],
-        # Pydantic validation prevents update queries (the Form would need to be "update")
-        request: Request,
-        repo: Repo = Depends(get_data_repo),
-        system_repo: Repo = Depends(get_system_repo),
+    # To maintain compatibility with the other SPARQL endpoints,
+    # /sparql POST endpoint is not a JSON API, it uses
+    # values encoded with x-www-form-urlencoded
+    query: Annotated[str, Form()],
+    # Pydantic validation prevents update queries (the Form would need to be "update")
+    request: Request,
+    repo: Repo = Depends(get_data_repo),
+    system_repo: Repo = Depends(get_system_repo),
 ):
-    return await sparql_endpoint_handler(query, request, repo, system_repo, method="POST")
+    return await sparql_endpoint_handler(
+        query, request, repo, system_repo, method="POST"
+    )
 
 
 @router.get("/sparql")
 async def sparql_get_passthrough(
-        query: str,
-        request: Request,
-        repo: Repo = Depends(get_data_repo),
-        system_repo: Repo = Depends(get_system_repo),
+    query: str,
+    request: Request,
+    repo: Repo = Depends(get_data_repo),
+    system_repo: Repo = Depends(get_system_repo),
 ):
-    return await sparql_endpoint_handler(query, request, repo, system_repo, method="GET")
+    return await sparql_endpoint_handler(
+        query, request, repo, system_repo, method="GET"
+    )
 
 
-async def sparql_endpoint_handler(query: str, request: Request, repo: Repo, system_repo, method="GET"):
+async def sparql_endpoint_handler(
+    query: str, request: Request, repo: Repo, system_repo, method="GET"
+):
     pmts = NegotiatedPMTs(
         **{
             "headers": request.headers,
@@ -72,13 +78,14 @@ async def sparql_endpoint_handler(query: str, request: Request, repo: Repo, syst
             media_type=non_anot_mediatype,
             headers=pmts.generate_response_headers(),
         )
-    query_result: 'httpx.Response' = await repo.sparql(query, request.headers.raw, method=method)
+    query_result: "httpx.Response" = await repo.sparql(
+        query, request.headers.raw, method=method
+    )
     if isinstance(query_result, dict):
         return JSONResponse(content=query_result)
     elif isinstance(query_result, Graph):
         return Response(
-            content=query_result.serialize(format="text/turtle"),
-            status_code=200
+            content=query_result.serialize(format="text/turtle"), status_code=200
         )
 
     dispositions = query_result.headers.get_list("Content-Disposition")
@@ -92,7 +99,11 @@ async def sparql_endpoint_handler(query: str, request: Request, repo: Repo, syst
         # remove transfer-encoding chunked, disposition=attachment, and content-length
         headers = dict()
         for k, v in query_result.headers.items():
-            if k.lower() not in ("transfer-encoding", "content-disposition", "content-length"):
+            if k.lower() not in (
+                "transfer-encoding",
+                "content-disposition",
+                "content-length",
+            ):
                 headers[k] = v
         content = await query_result.aread()
         await query_result.aclose()

prez/services/curie_functions.py

@@ -42,7 +42,7 @@ def generate_new_prefix(uri):
     else:
         ns = f'{parsed_url.scheme}://{parsed_url.netloc}{parsed_url.path.rsplit("/", 1)[0]}/'
 
-    split_prefix_path = ns[:-1].rsplit('/', 1)
+    split_prefix_path = ns[:-1].rsplit("/", 1)
     if len(split_prefix_path) > 1:
         to_generate_prefix_from = split_prefix_path[-1].lower()
         # attempt to just use the last part of the path prior to the fragment or "identifier"