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"""Tests federated SPARQL queries with a locally deployed triple store."""
import itertools as itt
import time
import unittest
from multiprocessing import Process
from typing import ClassVar
import uvicorn
from curies import Converter
from curies.mapping_service import get_fastapi_mapping_app
from curies.mapping_service.utils import (
get_sparql_record_so_tuples,
get_sparql_records,
require_service,
sparql_service_available,
)
from tests.test_mapping_service import PREFIX_MAP
BLAZEGRAPH_ENDPOINT = "http://localhost:9999/blazegraph/namespace/kb/sparql"
BLAZEGRAPH_JAR_URL = (
"https://github.com/blazegraph/database/releases/download/BLAZEGRAPH_2_1_6_RC/blazegraph.jar"
)
SPARQL_VALUES_FMT = """\
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?s ?o WHERE {{
SERVICE <{mapping_service}> {{
VALUES ?s {{ <http://purl.obolibrary.org/obo/CHEBI_24867> }}
?s owl:sameAs ?o
}}
}}
""".rstrip()
SPARQL_VALUES_FMT_2 = """\
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?s ?o WHERE {{
VALUES ?s {{ <http://purl.obolibrary.org/obo/CHEBI_24867> }}
SERVICE <{mapping_service}> {{
?s owl:sameAs ?o
}}
}}
""".rstrip()
SPARQL_VALUES_FMT_3 = """\
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?s ?o WHERE {{
SERVICE <{mapping_service}> {{
?s owl:sameAs ?o
}}
VALUES ?s {{ <http://purl.obolibrary.org/obo/CHEBI_24867> }}
}}
""".rstrip()
SPARQL_SIMPLE_FMT = """\
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?s ?o WHERE {{
SERVICE <{mapping_service}> {{
<http://purl.obolibrary.org/obo/CHEBI_24867> owl:sameAs ?o .
?s owl:sameAs ?o .
}}
}}
""".rstrip()
SPARQL_SIMPLE_FMT_2 = """\
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?s ?o WHERE {{
SERVICE <{mapping_service}> {{
?s owl:sameAs ?o .
<http://purl.obolibrary.org/obo/CHEBI_24867> owl:sameAs ?o .
}}
}}
""".rstrip()
# TODO test
SPARQL_SIMPLE_FMT_3 = """\
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?s ?o WHERE {{
<http://purl.obolibrary.org/obo/CHEBI_24867> owl:sameAs ?o .
SERVICE <{mapping_service}> {{
?s owl:sameAs ?o .
}}
}}
""".rstrip()
# TODO test
SPARQL_SIMPLE_FMT_4 = """\
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?s ?o WHERE {{
SERVICE <{mapping_service}> {{
?s owl:sameAs ?o .
}}
<http://purl.obolibrary.org/obo/CHEBI_24867> owl:sameAs ?o .
}}
""".rstrip()
class FederationMixin(unittest.TestCase):
"""A shared mixin for testing."""
def assert_service_works(self, endpoint: str):
"""Assert that a service is able to accept a simple SPARQL query."""
self.assertTrue(sparql_service_available(endpoint))
def _get_app():
converter = Converter.from_priority_prefix_map(PREFIX_MAP)
app = get_fastapi_mapping_app(converter)
return app
@require_service(BLAZEGRAPH_ENDPOINT, "Blazegraph")
class TestFederatedSparql(FederationMixin):
"""Test the identifier mapping service."""
endpoint: ClassVar[str] = BLAZEGRAPH_ENDPOINT
mimetypes: ClassVar[list[str]] = [
"application/sparql-results+json",
"application/sparql-results+xml",
"text/csv", # for some reason, Blazegraph wants this instead of application/sparql-results+csv
]
query_formats: ClassVar[list[str]] = [
SPARQL_VALUES_FMT,
SPARQL_VALUES_FMT_2,
SPARQL_VALUES_FMT_3,
SPARQL_SIMPLE_FMT,
SPARQL_SIMPLE_FMT_2,
]
host: ClassVar[str] = "localhost"
port: ClassVar[int] = 8000
mapping_service_process: Process
def setUp(self):
"""Set up the test case."""
# Start the curies mapping service SPARQL endpoint
self.mapping_service_process = Process(
target=uvicorn.run,
# uvicorn.run accepts a zero-argument callable that returns an app
args=(_get_app,),
kwargs={"host": self.host, "port": self.port, "log_level": "info"},
daemon=True,
)
self.mapping_service_process.start()
time.sleep(5)
self.mapping_service = f"http://{self.host}:{self.port}/sparql"
self.queries = [
query_format.format(mapping_service=self.mapping_service)
for query_format in self.query_formats
]
self.assert_service_works(self.mapping_service)
def tearDown(self):
"""Tear down the testing case."""
self.mapping_service_process.kill()
def test_federated_local(self):
"""Test sending a federated query to a local mapping service from a local service."""
for mimetype, sparql in itt.product(self.mimetypes, self.queries):
with self.subTest(mimetype=mimetype, sparql=sparql):
records = get_sparql_records(self.endpoint, sparql, accept=mimetype)
self.assertIn(
(
"http://purl.obolibrary.org/obo/CHEBI_24867",
"http://identifiers.org/chebi/24867",
),
get_sparql_record_so_tuples(records),
)
|
