Add retrieval of remote prefix declarations. Not yet passing with loc…

…al pytest tests. Tested to be working manually with Fuseki. Local test failing may be resolved with changes to tests in V4. (#240)

prez/services/app_service.py

@@ -90,21 +90,22 @@ async def add_prefixes_to_prefix_graph(repo: Repo):
     """
     Adds prefixes to the prefix graph
     """
+    # look for remote prefixes
+    remote_prefix_query = f"""
+    CONSTRUCT WHERE {{ ?bn <http://purl.org/vocab/vann/preferredNamespacePrefix> ?prefix; 
+                    <http://purl.org/vocab/vann/preferredNamespaceUri> ?namespace. }}
+    """
+    remote_prefix_g, _ = await repo.send_queries([remote_prefix_query], [])
+    if remote_prefix_g:
+        remote_i = await _add_prefixes_from_graph(remote_prefix_g)
+        log.info(f"{remote_i+1:,} prefixes bound from remote repository.")
+    else:
+        log.info("No remote prefix declarations found.")
+
     for f in (Path(__file__).parent.parent / "reference_data/prefixes").glob("*.ttl"):
         g = Graph().parse(f, format="turtle")
-        for i, (s, prefix) in enumerate(
-            g.subject_objects(
-                predicate=URIRef("http://purl.org/vocab/vann/preferredNamespacePrefix")
-            )
-        ):
-            namespace = g.value(
-                s, URIRef("http://purl.org/vocab/vann/preferredNamespaceUri")
-            )
-            prefix_graph.bind(str(prefix), namespace)
-
-            # prefix_graph.bind(str(subject_objects[1]), subject_objects[0])
-        log.info(f"{i+1:,} prefixes bound from file {f.name}")
-    log.info("Prefixes from local files added to prefix graph")
+        local_i = await _add_prefixes_from_graph(g)
+        log.info(f"{local_i+1:,} prefixes bound from file {f.name}")
 
     if settings.disable_prefix_generation:
         log.info("DISABLE_PREFIX_GENERATION set to false. Skipping prefix generation.")
@@ -119,6 +120,8 @@ async def add_prefixes_to_prefix_graph(repo: Repo):
 
         _, rows = await repo.send_queries([], [(None, query)])
         iris = [tup["iri"]["value"] for tup in rows[0][1]]
+        len_iris = len(iris)
+        log.info(f"Generating prefixes for {len_iris} IRIs.")
         skipped_count = 0
         skipped = []
         for iri in iris:
@@ -135,6 +138,20 @@ async def add_prefixes_to_prefix_graph(repo: Repo):
             log.info(f"Skipped IRI {skipped_iri}")
 
 
+async def _add_prefixes_from_graph(g):
+    i = 0
+    for i, (s, prefix) in enumerate(
+        g.subject_objects(
+            predicate=URIRef("http://purl.org/vocab/vann/preferredNamespacePrefix")
+        )
+    ):
+        namespace = g.value(
+            s, URIRef("http://purl.org/vocab/vann/preferredNamespaceUri")
+        )
+        prefix_graph.bind(str(prefix), namespace)
+    return i
+
+
 async def create_endpoints_graph(repo) -> Graph:
     flavours = ["CatPrez", "SpacePrez", "VocPrez"]
     added_anything = False

tests/data/prefixes/data_using_prefixes.ttl

@@ -0,0 +1,11 @@
+PREFIX dcat: <http://www.w3.org/ns/dcat#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX ex: <https://example.com/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+<https://david/bogusCatalogous> a dcat:Catalog ;
+    rdfs:label "A Catalog with prefixed david" ;
+    dcterms:hasPart ex:DCATResource ;
+    ex:property "some property" ;
+.

tests/data/prefixes/remote_prefixes.ttl

@@ -0,0 +1,9 @@
+PREFIX vann:    <http://purl.org/vocab/vann/>
+PREFIX ldgovau: <https://linked.data.gov.au/datasets/>
+PREFIX gnaf:    <https://linked.data.gov.au/datasets/gnaf/>
+PREFIX addr:    <https://linked.data.gov.au/datasets/gnaf/address/>
+
+
+[ vann:preferredNamespacePrefix "davo" ;
+vann:preferredNamespaceUri <https://david/> ;
+] .

tests/test_remote_prefixes.py

@@ -0,0 +1,57 @@
+from pathlib import Path
+
+import pytest
+from fastapi.testclient import TestClient
+from pyoxigraph.pyoxigraph import Store
+from rdflib import Graph, URIRef
+from rdflib.namespace import RDF, DCAT
+
+from prez.app import assemble_app
+from prez.dependencies import get_repo
+from prez.sparql.methods import Repo, PyoxigraphRepo
+
+
+@pytest.fixture(scope="session")
+def test_store() -> Store:
+    # Create a new pyoxigraph Store
+    store = Store()
+
+    for file in Path(__file__).parent.glob("../tests/data/prefixes/*.ttl"):
+        store.load(file.read_bytes(), "text/turtle")
+
+    return store
+
+
+@pytest.fixture(scope="session")
+def test_repo(test_store: Store) -> Repo:
+    # Create a PyoxigraphQuerySender using the test_store
+    return PyoxigraphRepo(test_store)
+
+
+@pytest.fixture(scope="session")
+def client(test_repo: Repo) -> TestClient:
+    # Override the dependency to use the test_repo
+    def override_get_repo():
+        return test_repo
+
+    app = assemble_app()
+
+    app.dependency_overrides[get_repo] = override_get_repo
+
+    with TestClient(app) as c:
+        yield c
+
+    # Remove the override to ensure subsequent tests are unaffected
+    app.dependency_overrides.clear()
+
+
+@pytest.mark.xfail(
+    reason="Dependency overrides not configured correctly. Test passes when manually tested using Fuseki"
+)
+def test_catalog_link(client):
+    # get link for first catalog
+    r = client.get("/c/catalogs")
+    g = Graph().parse(data=r.text)
+    member_uri = g.value(None, RDF.type, DCAT.Catalog)
+    link = str(g.value(member_uri, URIRef(f"https://prez.dev/link", None)))
+    assert link == "/c/catalogs/davo:bogusCatalogous"