Ontology from upload deadlock test

Author: namedgraph

http-tests/admin/model/ontology-import-upload-no-deadlock.sh

@@ -0,0 +1,154 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Test that ontology imports of uploaded files do not cause deadlock
+# This verifies the fix for circular dependency when:
+# 1. Request arrives for /uploads/xyz
+# 2. OntologyFilter intercepts it and loads ontology
+# 3. Ontology has owl:imports for /uploads/xyz
+# 4. Jena FileManager makes HTTP request to /uploads/xyz
+# 5. Would cause infinite loop/deadlock without the fix
+
+initialize_dataset "$END_USER_BASE_URL" "$TMP_END_USER_DATASET" "$END_USER_ENDPOINT_URL"
+initialize_dataset "$ADMIN_BASE_URL" "$TMP_ADMIN_DATASET" "$ADMIN_ENDPOINT_URL"
+purge_cache "$END_USER_VARNISH_SERVICE"
+purge_cache "$ADMIN_VARNISH_SERVICE"
+purge_cache "$FRONTEND_VARNISH_SERVICE"
+
+pwd=$(realpath "$PWD")
+
+# add agent to the writers group so they can upload files
+
+add-agent-to-group.sh \
+  -f "$OWNER_CERT_FILE" \
+  -p "$OWNER_CERT_PWD" \
+  --agent "$AGENT_URI" \
+  "${ADMIN_BASE_URL}acl/groups/writers/"
+
+# Step 1: Upload an RDF file
+
+file_content_type="text/turtle"
+
+file_doc=$(create-file.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  -b "$END_USER_BASE_URL" \
+  --title "Test ontology for upload import" \
+  --file "$pwd/test-ontology-import.ttl" \
+  --file-content-type "${file_content_type}")
+
+# Step 2: Extract the uploaded file URI (content-addressed)
+
+file_doc_ntriples=$(get.sh \
+  -f "$AGENT_CERT_FILE" \
+  -p "$AGENT_CERT_PWD" \
+  --accept 'application/n-triples' \
+  "$file_doc")
+
+upload_uri=$(echo "$file_doc_ntriples" | sed -rn "s/<${file_doc//\//\\/}> <http:\/\/xmlns.com\/foaf\/0.1\/primaryTopic> <(.*)> \./\1/p")
+
+echo "Uploaded file URI: $upload_uri"
+
+# Verify the uploaded file is accessible before we add it as an import
+curl -k -f -s \
+  -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" \
+  -H "Accept: ${file_content_type}" \
+  "$upload_uri" > /dev/null
+
+echo "Upload file is accessible"
+
+# Step 3: Add the uploaded file as an owl:import to the namespace ontology
+
+namespace_doc="${END_USER_BASE_URL}ns"
+namespace="${namespace_doc}#"
+ontology_doc="${ADMIN_BASE_URL}ontologies/namespace/"
+
+add-ontology-import.sh \
+  -f "$OWNER_CERT_FILE" \
+  -p "$OWNER_CERT_PWD" \
+  --import "$upload_uri" \
+  "$ontology_doc"
+
+echo "Added owl:import of uploaded file to namespace ontology"
+
+# Step 4: Clear the namespace ontology from memory to force reload on next request
+
+clear-ontology.sh \
+  -f "$OWNER_CERT_FILE" \
+  -p "$OWNER_CERT_PWD" \
+  -b "$ADMIN_BASE_URL" \
+  --ontology "$namespace"
+
+echo "Cleared ontology cache to force reload"
+
+# Step 5: Make a request that triggers ontology loading
+# This would cause a deadlock without the OntologyFilter fix
+# Use portable timeout implementation (works on both macOS and Linux)
+
+echo "Making request to trigger ontology loading (testing for deadlock)..."
+
+# Portable timeout function - works on both macOS and Linux
+request_pid=""
+(
+  curl -k -f -s \
+    -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
+    -H "Accept: application/n-triples" \
+    "$namespace_doc" > /dev/null
+) &
+request_pid=$!
+
+# Wait up to 30 seconds for the request to complete
+timeout_seconds=30
+elapsed=0
+while kill -0 "$request_pid" 2>/dev/null; do
+  if [ $elapsed -ge $timeout_seconds ]; then
+    kill -9 "$request_pid" 2>/dev/null || true
+    echo "ERROR: Request timed out after ${timeout_seconds} seconds - deadlock detected!"
+    exit 1
+  fi
+  sleep 1
+  ((elapsed++))
+done
+
+# Check if curl succeeded
+wait "$request_pid"
+curl_exit_code=$?
+if [ $curl_exit_code -ne 0 ]; then
+  echo "ERROR: Request failed with exit code $curl_exit_code"
+  exit 1
+fi
+
+echo "Request completed successfully in ${elapsed}s (no deadlock)"
+
+# Step 6: Verify the import is present in the loaded ontology
+
+curl -k -f -s \
+  -H "Accept: application/n-triples" \
+  "$namespace_doc" \
+| grep "<${namespace}> <http://www.w3.org/2002/07/owl#imports> <${upload_uri}>" > /dev/null
+
+echo "Verified owl:import is present in namespace ontology"
+
+# Step 7: Verify the uploaded file is still accessible after ontology loading
+
+curl -k -f -s \
+  -E "$AGENT_CERT_FILE":"$AGENT_CERT_PWD" \
+  -H "Accept: ${file_content_type}" \
+  "$upload_uri" > /dev/null
+
+echo "Uploaded file is still accessible after ontology import"
+
+# Step 8: Verify that the imported ontology content is accessible via the namespace document
+# This confirms the import was actually loaded (not just skipped)
+
+curl -k -f -s \
+  -G \
+  -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
+  -H 'Accept: application/sparql-results+xml' \
+  --data-urlencode "query=SELECT * { <https://example.org/test#TestClass> ?p ?o }" \
+  "$namespace_doc" \
+| grep '<literal>Test Class</literal>' > /dev/null
+
+echo "Verified imported ontology content is accessible via SPARQL"
+
+echo "✓ All tests passed - no deadlock detected when importing uploaded files in ontology"

http-tests/admin/model/test-ontology-import.ttl

@@ -0,0 +1,17 @@
+@prefix : <https://example.org/test#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+: a owl:Ontology ;
+    rdfs:label "Test ontology for upload import" ;
+    rdfs:comment "This ontology is uploaded to test that ontology imports of uploaded files do not cause deadlock" .
+
+:TestClass a owl:Class ;
+    rdfs:label "Test Class" ;
+    rdfs:comment "A test class to verify ontology was loaded" .
+
+:testProperty a owl:DatatypeProperty ;
+    rdfs:label "Test Property" ;
+    rdfs:domain :TestClass ;
+    rdfs:range xsd:string .