Added broader concept to vocprez test data

.gitignore

@@ -6,3 +6,7 @@ __pycache__/
 .pytest_cache/
 .env*
 !.env-template
+http/
+/.python-version
+http/
+rdf/

Dockerfile

@@ -31,7 +31,7 @@ RUN curl -sSL https://install.python-poetry.org | python && \
     chmod a+x /opt/poetry/bin/poetry
 
 WORKDIR /app
-COPY poetry.lock pyproject.toml connegp-0.1.5-py3-none-any.whl ./
+COPY poetry.lock pyproject.toml ./
 RUN poetry install --only main --no-root --no-ansi
 
 FROM python:3.11-slim-buster
@@ -44,6 +44,8 @@ ENV PYTHONDONTWRITEBYTECODE=1 \
     PATH="/app/.venv/bin:$PATH"
 WORKDIR /app
 COPY ./prez /app/prez
+COPY ./temp /app/temp
+COPY ./test_data /app/test_data
 # copy the pyproject.toml as the application reads the version from here
 COPY pyproject.toml .
 

demo/prez-v4-backend/config.ttl

@@ -0,0 +1,54 @@
+## Licensed under the terms of http://www.apache.org/licenses/LICENSE-2.0
+
+PREFIX :        <#>
+PREFIX fuseki:  <http://jena.apache.org/fuseki#>
+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX ja:      <http://jena.hpl.hp.com/2005/11/Assembler#>
+PREFIX geosparql: <http://jena.apache.org/geosparql#>
+
+[] rdf:type fuseki:Server ;
+   fuseki:services (
+     :service
+   ) .
+
+:service rdf:type fuseki:Service ;
+    fuseki:name "dataset" ;
+
+    fuseki:endpoint [ fuseki:operation fuseki:query ; ] ;
+    fuseki:endpoint [
+        fuseki:operation fuseki:query ;
+        fuseki:name "sparql"
+    ];
+    fuseki:endpoint [
+        fuseki:operation fuseki:query ;
+        fuseki:name "query"
+    ] ;
+    fuseki:endpoint [
+        fuseki:operation fuseki:gsp-r ;
+        fuseki:name "get"
+    ] ;
+    fuseki:dataset <#geo_ds>  ;
+    .
+
+<#geo_ds> rdf:type geosparql:GeosparqlDataset ;
+    geosparql:dataset :dataset ;
+    geosparql:inference            true ;
+    geosparql:queryRewrite         true ;
+    geosparql:indexEnabled         true ;
+    geosparql:applyDefaultGeometry true ;
+.
+
+# Transactional in-memory dataset.
+:dataset rdf:type ja:MemoryDataset ;
+    ## Optional load with data on start-up
+    ja:data "/rdf/catprez.ttl";
+    ja:data "/rdf/vocprez.ttl";
+    ja:data "/rdf/catprez.ttl";
+    ja:data "/rdf/sandgate.ttl";
+    ja:data "/rdf/object_catalog_bblocks_catalog.ttl";
+    ja:data "/rdf/object_vocab_api_bblocks.ttl";
+    ja:data "/rdf/object_vocab_datatype_bblocks.ttl";
+    ja:data "/rdf/object_vocab_parameter_bblocks.ttl";
+    ja:data "/rdf/object_vocab_schema_bblocks.ttl";
+    .

demo/prez-v4-backend/docker-compose.yml

@@ -0,0 +1,33 @@
+version: "3"
+services:
+
+  fuseki:
+    image: "ghcr.io/zazuko/fuseki-geosparql:v3.3.0"
+    ports:
+      - "3030:3030"
+    volumes:
+      - type: bind
+        source: config.ttl
+        target: /fuseki/config.ttl
+      - type: bind
+        source: ../../test_data
+        target: /rdf
+    environment:
+      ADMIN_PASSWORD: pw
+    healthcheck:
+      test: ["CMD-SHELL", "wget -qO- http://localhost:3030 || exit 1"]
+      interval: 5s
+      timeout: 10s
+      retries: 3
+
+  prez:
+    build:
+      context: ../../
+      dockerfile: ./Dockerfile
+    ports:
+      - "8000:8000"
+    environment:
+      SPARQL_ENDPOINT: 'http://fuseki:3030/dataset'
+    depends_on:
+      fuseki:
+        condition: service_healthy

demo/prez-v4-backend/readme.md

@@ -0,0 +1,3 @@
+This directory contains a docker compose file which will run the Prez backend and Fuseki GeoSPARQL together with some sample data.
+
+NB any data added to the test_data folder must also be specified in the fuseki config.ttl file.

prez/app.py

@@ -1,10 +1,9 @@
 import logging
-import os
+import time
 from textwrap import dedent
 
 import uvicorn
 from fastapi import FastAPI
-from fastapi.openapi.utils import get_openapi
 from rdflib import Graph
 from starlette.middleware.cors import CORSMiddleware
 
@@ -15,30 +14,28 @@
     load_local_data_to_oxigraph,
     get_oxrdflib_store,
     get_system_store,
-    load_profile_data_to_oxigraph,
+    load_system_data_to_oxigraph,
+    get_annotations_store,
+    load_annotations_data_to_oxigraph,
 )
 from prez.models.model_exceptions import (
     ClassNotFoundException,
     URINotFoundException,
     NoProfilesException,
 )
-from prez.routers.catprez import router as catprez_router
+from prez.repositories import RemoteSparqlRepo, PyoxigraphRepo, OxrdflibRepo
 from prez.routers.cql import router as cql_router
 from prez.routers.identifier import router as identifier_router
 from prez.routers.management import router as management_router
-from prez.routers.object import router as object_router
-from prez.routers.profiles import router as profiles_router
+from prez.routers.ogc_router import router as ogc_records_router
 from prez.routers.search import router as search_router
-from prez.routers.spaceprez import router as spaceprez_router
 from prez.routers.sparql import router as sparql_router
-from prez.routers.vocprez import router as vocprez_router
 from prez.services.app_service import (
     healthcheck_sparql_endpoints,
     count_objects,
     create_endpoints_graph,
     populate_api_info,
     add_prefixes_to_prefix_graph,
-    add_common_context_ontologies_to_tbox_cache,
 )
 from prez.services.exception_catchers import (
     catch_400,
@@ -50,8 +47,6 @@
 )
 from prez.services.generate_profiles import create_profiles_graph
 from prez.services.prez_logging import setup_logger
-from prez.services.search_methods import get_all_search_methods
-from prez.sparql.methods import RemoteSparqlRepo, PyoxigraphRepo, OxrdflibRepo
 
 app = FastAPI(
     exception_handlers={
@@ -64,19 +59,11 @@
     }
 )
 
-
 app.include_router(cql_router)
 app.include_router(management_router)
-app.include_router(object_router)
 app.include_router(sparql_router)
 app.include_router(search_router)
-app.include_router(profiles_router)
-if "CatPrez" in settings.prez_flavours:
-    app.include_router(catprez_router)
-if "VocPrez" in settings.prez_flavours:
-    app.include_router(vocprez_router)
-if "SpacePrez" in settings.prez_flavours:
-    app.include_router(spaceprez_router)
+app.include_router(ogc_records_router)
 app.include_router(identifier_router)
 
 
@@ -100,25 +87,14 @@ async def add_cors_headers(request, call_next):
 )
 
 
-def prez_open_api_metadata():
-    return get_openapi(
-        title=settings.prez_title,
-        version=settings.prez_version,
-        description=settings.prez_desc,
-        routes=app.routes,
-    )
-
-
-app.openapi = prez_open_api_metadata
-
-
 @app.on_event("startup")
 async def app_startup():
     """
     This function runs at startup and will continually poll the separate backends until their SPARQL endpoints
     are available. Initial caching can be triggered within the try block. NB this function does not check that data is
     appropriately configured at the SPARQL endpoint(s), only that the SPARQL endpoint(s) are reachable.
     """
+    a = time.time()
     setup_logger(settings)
     log = logging.getLogger("prez")
     log.info("Starting up")
@@ -140,15 +116,18 @@ async def app_startup():
         )
 
     await add_prefixes_to_prefix_graph(app.state.repo)
-    await get_all_search_methods(app.state.repo)
     await create_profiles_graph(app.state.repo)
     await create_endpoints_graph(app.state.repo)
     await count_objects(app.state.repo)
     await populate_api_info()
-    await add_common_context_ontologies_to_tbox_cache()
 
     app.state.pyoxi_system_store = get_system_store()
-    await load_profile_data_to_oxigraph(app.state.pyoxi_system_store)
+    await load_system_data_to_oxigraph(app.state.pyoxi_system_store)
+
+    app.state.pyoxi_annotations_store = get_annotations_store()
+    await load_annotations_data_to_oxigraph(app.state.pyoxi_annotations_store)
+
+    log.info(f"Startup took {time.time() - a} seconds")
 
 
 @app.on_event("shutdown")

prez/cache.py

@@ -1,9 +1,10 @@
+from aiocache import caches
 from pyoxigraph.pyoxigraph import Store
 from rdflib import Graph, ConjunctiveGraph, Dataset
 
-tbox_cache = Graph()
+from prez.repositories import PyoxigraphRepo
 
-profiles_graph_cache = ConjunctiveGraph()
+profiles_graph_cache = Dataset()
 profiles_graph_cache.bind("prez", "https://prez.dev/")
 
 endpoints_graph_cache = ConjunctiveGraph()
@@ -26,4 +27,20 @@
 
 system_store = Store()
 
+annotations_store = Store()
+annotations_repo = PyoxigraphRepo(annotations_store)
+
 oxrdflib_store = Graph(store="Oxigraph")
+
+caches.set_config(
+    {
+        "default": {
+            "cache": "aiocache.SimpleMemoryCache",
+            "serializer": {"class": "aiocache.serializers.PickleSerializer"},
+        },
+        "curies": {
+            "cache": "aiocache.SimpleMemoryCache",
+            "serializer": {"class": "aiocache.serializers.PickleSerializer"},
+        },
+    }
+)