Fix test 20251223 (#5637)

Author: hmottestad

.github/workflows/develop-status.yml

@@ -29,7 +29,7 @@ jobs:
     - name: Build
       run: mvn -B -U clean install -Pquick,\!formatting
     - name: Verify
-      run: mvn -B install -P-skipSlowTests -Dmaven.javadoc.skip=true
+      run: ./scripts/ci/run-with-thread-dump.sh mvn -B install -P-skipSlowTests -Dmaven.javadoc.skip=true
     - name: Publish Test Report
       if: failure()
       uses: scacap/action-surefire-report@v1

.github/workflows/main-status.yml

@@ -29,7 +29,7 @@ jobs:
     - name: Build
       run: mvn -B -U -T 2C clean install -DskipTests
     - name: Run all tests
-      run: mvn -B install -P-skipSlowTests -Dmaven.javadoc.skip=true
+      run: ./scripts/ci/run-with-thread-dump.sh mvn -B install -P-skipSlowTests -Dmaven.javadoc.skip=true
     - name: Publish Test Report
       if: failure()
       uses: scacap/action-surefire-report@v1

.github/workflows/pr-verify.yml

@@ -62,7 +62,7 @@ jobs:
       - name: Build
         run: mvn --quiet clean && mvn -B --quiet -T 2C install -Pquick
       - name: Test
-        run: mvn -B test -DskipITs -P-formatting -Dmaven.javadoc.skip -Djapicmp.skip -Denforcer.skip -Danimal.sniffer.skip
+        run: ./scripts/ci/run-with-thread-dump.sh mvn -B test -DskipITs -P-formatting -Dmaven.javadoc.skip -Djapicmp.skip -Denforcer.skip -Danimal.sniffer.skip
       - name: Publish Test Report
         if: failure()
         uses: scacap/action-surefire-report@v1.9.0
@@ -84,7 +84,7 @@ jobs:
       - name: Build
         run: mvn --quiet clean && mvn -B --quiet -T 2C install -Pquick
       - name: Verify
-        run: mvn -B verify -PskipUnitTests,-formatting -Dmaven.javadoc.skip -Denforcer.skip -Danimal.sniffer.skip
+        run: ./scripts/ci/run-with-thread-dump.sh mvn -B verify -PskipUnitTests,-formatting -Dmaven.javadoc.skip -Denforcer.skip -Danimal.sniffer.skip
       - name: Publish Test Report
         if: failure()
         uses: scacap/action-surefire-report@v1.9.0
@@ -105,7 +105,7 @@ jobs:
       - name: Build
         run: mvn --quiet clean && mvn -B --quiet -T 2C install -Pquick
       - name: Verify
-        run: mvn -B verify -PslowTestsOnly,-skipSlowTests,-formatting -Dmaven.javadoc.skip -Djapicmp.skip -Denforcer.skip -Danimal.sniffer.skip
+        run: ./scripts/ci/run-with-thread-dump.sh mvn -B verify -PslowTestsOnly,-skipSlowTests,-formatting -Dmaven.javadoc.skip -Djapicmp.skip -Denforcer.skip -Danimal.sniffer.skip
       - name: Publish Test Report
         if: failure()
         uses: scacap/action-surefire-report@v1.9.0
@@ -148,12 +148,11 @@ jobs:
           node-version: 18
       - name: Run end-to-end tests of RDF4J Server and Workbench
         working-directory: ./e2e
-        run: ./run.sh
+        run: ../scripts/ci/run-with-thread-dump.sh ./run.sh
 
   copyright-check:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: check copyright header present
         run: scripts/checkCopyrightPresent.sh
-

AGENTS.md

@@ -126,48 +126,6 @@ When writing complex features or significant refactors, use an ExecPlan (as desc
 
 When writing complex features or significant refactors, use an ExecPlan (as described in PLANS.md) from design to implementation.
 
-## PIOSEE Decision Model (Adopted)
-
-Use this as a compact, repeatable loop for anything from a one‑line bug fix to a multi‑quarter program.
-
-### P — **Problem**
-
-**Goal:** State the core problem and what “good” looks like.
-**Ask:** Who’s affected? What outcome is required? What happens if we do nothing?
-**Tip:** Include measurable target(s): error rate ↓, latency p95 ↓, revenue ↑, risk ↓.
-
-### I — **Information**
-
-**Goal:** Gather only the facts needed to move.
-**Ask:** What do logs/metrics/user feedback say? What constraints (security, compliance, budget, SLA/SLO)? What assumptions must we test?
-
-### O — **Options**
-
-**Goal:** Generate viable ways forward, including “do nothing.”
-**Ask:** What are 2–4 distinct approaches (patch, redesign, buy vs. build, defer)? What risks, costs, and second‑order effects?
-**Tip:** Check guardrails: reliability, security/privacy, accessibility, performance, operability, unit economics.
-
-### S — **Select**
-
-**Goal:** Decide deliberately and document why.
-**Ask:** Which option best meets the success criteria under constraints? Who is the decision owner? What’s the fallback/abort condition?
-**Tip:** Use lightweight scoring (e.g., Impact×Confidence÷Effort) to avoid bike‑shedding.
-
-### E — **Execute**
-
-**Goal:** Ship safely and visibly.
-**Ask:** What is the smallest safe slice? How do we de‑risk (feature flag, canary, dark launch, rollback)? Who owns what?
-**Checklist:** Traces/logs/alerts; security & privacy checks; docs & changelog; incident plan if relevant.
-
-### E — **Evaluate**
-
-**Goal:** Verify outcomes and learn.
-**Ask:** Did metrics hit targets? Any regressions or side effects? What will we keep/change next loop?
-**Output:** Post‑release review (or retro), decision log entry, follow‑ups (tickets), debt captured.
-**Tip:** If outcomes miss, either **iterate** (new Options) or **reframe** (back to Problem).
-
----
-
 ### Benchmarking workflow (repository-wide)
 
 The `scripts/run-single-benchmark.sh` helper is the supported path for spot-checking performance optimisations. It builds the chosen module with the `benchmarks` profile, constrains the benchmark selection to a single `@Benchmark` method, and when `--enable-jfr` is supplied it enforces repeatable profiling defaults (no warmup, ten 10-second measurements, one fork) while clearly reporting the destination of the generated JFR recording. Lean on this script whenever you need a reproducible measurement harness.
@@ -466,7 +424,6 @@ When writing complex features or significant refactors, use an ExecPlan (as desc
 
 ## Working Loop
 
-* **PIOSEE first:** restate Problem, gather Information, list Options; then Select, Execute, Evaluate.
 * **Plan:** small, verifiable steps; keep one `in_progress`, or follow PLANS.md (ExecPlans)
 * **Change:** minimal, surgical edits; keep style/structure consistent.
 * **Format:** `mvn -o -Dmaven.repo.local=.m2_repo -q -T 2C formatter:format impsort:sort xml-format:xml-format`
@@ -657,7 +614,6 @@ Immediately after creating any new Java source file, add the signature comment (
 * **Files touched:** list file paths.
 * **Commands run:** key build/test commands.
 * **Verification:** which tests passed, where you checked reports.
-* **PIOSEE trace (concise):** P/I/O summary, selected option/routine, key evaluate outcomes.
 * **Evidence:**
   *Routine A:* failing output (pre‑fix) and passing output (post‑fix).
   *Routine B:* pre‑ and post‑green snippets from the **same selection** + **Hit Proof**.

core/sail/shacl/src/main/java/org/eclipse/rdf4j/sail/shacl/ast/planNodes/FilterByPredicateObject.java

@@ -73,7 +73,10 @@ public FilterByPredicateObject(SailConnection connection, Resource[] dataGraph,
 		if (connection instanceof MemoryStoreConnection) {
 			cache = null;
 		} else {
-			cache = CacheBuilder.newBuilder().maximumSize(10000).build();
+			cache = CacheBuilder.newBuilder()
+					.concurrencyLevel(Runtime.getRuntime().availableProcessors() * 2)
+					.maximumSize(10000)
+					.build();
 		}
 
 		this.connectionsGroup = connectionsGroup;

core/sail/shacl/src/test/java/org/eclipse/rdf4j/sail/shacl/ShutdownDuringValidationIT.java

@@ -115,6 +115,7 @@ void tearDown() {
 	@ParameterizedTest
 	@MethodSource("sleepTimes")
 	public void shutdownDuringValidation(int sleepMillis) {
+		System.err.println(Thread.currentThread() + " shutdownDuringValidation with sleepMillis=" + sleepMillis);
 		try {
 // clear interrupted flag
 			Thread.interrupted();
@@ -156,15 +157,15 @@ public void shutdownDuringValidation(int sleepMillis) {
 			}
 		} catch (Exception e) {
 			if (e instanceof RepositoryException && causedByInterruptedException(e)) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e instanceof RepositoryException && e.getCause() instanceof InterruptedSailException) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e.toString().contains("closed")) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			throw e;
@@ -174,6 +175,8 @@ public void shutdownDuringValidation(int sleepMillis) {
 	@ParameterizedTest
 	@MethodSource("sleepTimes")
 	public void shutdownDuringValidationTransactional(int sleepMillis) {
+		System.err.println(
+				Thread.currentThread() + " shutdownDuringValidationTransactional with sleepMillis=" + sleepMillis);
 		try {
 // clear interrupted flag
 			Thread.interrupted();
@@ -221,15 +224,15 @@ public void shutdownDuringValidationTransactional(int sleepMillis) {
 			}
 		} catch (Exception e) {
 			if (e instanceof RepositoryException && causedByInterruptedException(e)) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e instanceof RepositoryException && e.getCause() instanceof InterruptedSailException) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e.toString().contains("closed")) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			throw e;
@@ -239,6 +242,7 @@ public void shutdownDuringValidationTransactional(int sleepMillis) {
 	@ParameterizedTest
 	@MethodSource("sleepTimes")
 	public void shutdownDuringValidationFailure(int sleepMillis) {
+		System.err.println(Thread.currentThread() + " shutdownDuringValidationFailure with sleepMillis=" + sleepMillis);
 		try {
 
 // clear interrupted flag
@@ -280,15 +284,15 @@ public void shutdownDuringValidationFailure(int sleepMillis) {
 			}
 		} catch (Exception e) {
 			if (e instanceof RepositoryException && causedByInterruptedException(e)) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e instanceof RepositoryException && e.getCause() instanceof InterruptedSailException) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e.toString().contains("closed")) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			throw e;
@@ -298,6 +302,8 @@ public void shutdownDuringValidationFailure(int sleepMillis) {
 	@ParameterizedTest
 	@MethodSource("sleepTimes")
 	public void shutdownDuringValidationFailureNonParallel(int sleepMillis) {
+		System.err.println(
+				Thread.currentThread() + " shutdownDuringValidationFailureNonParallel with sleepMillis=" + sleepMillis);
 		try {
 // clear interrupted flag
 			Thread.interrupted();
@@ -339,15 +345,15 @@ public void shutdownDuringValidationFailureNonParallel(int sleepMillis) {
 			}
 		} catch (Exception e) {
 			if (e instanceof RepositoryException && causedByInterruptedException(e)) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e instanceof RepositoryException && e.getCause() instanceof InterruptedSailException) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e.toString().contains("closed")) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 
@@ -358,6 +364,8 @@ public void shutdownDuringValidationFailureNonParallel(int sleepMillis) {
 	@ParameterizedTest
 	@MethodSource("sleepTimes")
 	public void shutdownDuringValidationTransactionalNonParallel(int sleepMillis) {
+		System.err.println(Thread.currentThread()
+				+ " shutdownDuringValidationTransactionalNonParallel with sleepMillis=" + sleepMillis);
 		try {
 			// clear interrupted flag
 			boolean interrupted = Thread.interrupted();
@@ -378,7 +386,7 @@ public void shutdownDuringValidationTransactionalNonParallel(int sleepMillis) {
 
 				commitAndExpect(connection, EXPECTED_REPOSITORY_SIZE + 1, 1);
 			} catch (RepositoryException | SailException e) {
-				System.out.println(e);
+				System.err.println(e);
 				if (e instanceof InterruptedSailException) {
 					// ignore this exception
 					return;
@@ -413,15 +421,15 @@ public void shutdownDuringValidationTransactionalNonParallel(int sleepMillis) {
 			}
 		} catch (Exception e) {
 			if (e instanceof RepositoryException && causedByInterruptedException(e)) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e instanceof RepositoryException && e.getCause() instanceof InterruptedSailException) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			if (e.toString().contains("closed")) {
-				System.out.println(e);
+				System.err.println(e);
 				return;
 			}
 			throw e;
@@ -430,6 +438,7 @@ public void shutdownDuringValidationTransactionalNonParallel(int sleepMillis) {
 
 	@Test
 	void nestedInterruptedExceptionShouldBeDetected() {
+		System.err.println(Thread.currentThread() + " nestedInterruptedExceptionShouldBeDetected");
 		InterruptedException interruptedException = new InterruptedException("nested");
 		SailException sailException = new SailException("wrapper", new SailException("inner", interruptedException));
 		RepositoryException repositoryException = new RepositoryException("top", sailException);
@@ -473,7 +482,7 @@ private static void commitAndExpect(SailRepositoryConnection connection, long ex
 				throw e;
 			}
 		} catch (RepositoryException ignored) {
-			System.out.println(ignored.getMessage());
+			System.err.println(ignored.getMessage());
 			try {
 				connection.rollback();
 			} catch (Exception e) {

scripts/ci/run-with-thread-dump.sh

@@ -0,0 +1,56 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+dump_threads() {
+  echo "== Cancellation received: capturing JVM thread dumps =="
+  local pids
+  pids=$(pgrep -f '[j]ava' || true)
+  if [[ -z "${pids}" ]]; then
+    echo "No Java processes found."
+    return 0
+  fi
+
+  if command -v jcmd >/dev/null 2>&1; then
+    for pid in ${pids}; do
+      echo "-- jcmd Thread.print for PID ${pid} --"
+      jcmd "${pid}" Thread.print || true
+    done
+    return 0
+  fi
+
+  if command -v jstack >/dev/null 2>&1; then
+    for pid in ${pids}; do
+      echo "-- jstack for PID ${pid} --"
+      jstack "${pid}" || true
+    done
+    return 0
+  fi
+
+  for pid in ${pids}; do
+    echo "-- kill -QUIT ${pid} (no jcmd/jstack available) --"
+    kill -QUIT "${pid}" || true
+  done
+}
+
+on_term() {
+  dump_threads
+  if [[ -n "${child_pid:-}" ]]; then
+    kill -TERM "${child_pid}" 2>/dev/null || true
+  fi
+}
+
+if [[ $# -eq 0 ]]; then
+  echo "Usage: $0 <command> [args...]" >&2
+  exit 2
+fi
+
+trap on_term INT TERM
+
+"$@" &
+child_pid=$!
+
+wait "${child_pid}"
+status=$?
+
+trap - INT TERM
+exit "${status}"