wip (+34 squashed commits)

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[89b4fca74e] NO-ISSUE: add run bootstrap for server-boot

Author: hmottestad

.gitignore

@@ -5,8 +5,6 @@
 **/.classpath
 .settings
 **/.settings
-bin
-**/bin
 **/.factorypath
 
 # Eclipse Plug-In Settings

AGENTS.md

@@ -300,6 +300,8 @@ Why this is mandatory
     * `mvn -o -Dmaven.repo.local=.m2_repo -Pquick install | tail -200`
 3. **Format (Java, imports, XML)**
     * `mvn -o -Dmaven.repo.local=.m2_repo -q -T 2C formatter:format impsort:sort xml-format:xml-format`
+    * Ensure every touched Java file has the correct agent signature comment (`// Some portions generated by Codex` for Codex, `// Some portions generated by Co-Pilot` for GitHub Co-Pilot) inserted immediately below the header before formatting.
+    * Before invoking the formatter, `cd scripts && ./checkCopyrightPresent.sh` (or use `pushd/popd`) to ensure every new or edited source file still carries the required header; fix any findings before formatting.
 4. **Targeted tests (tight loops)**
     * Module: `mvn -o -Dmaven.repo.local=.m2_repo -pl <module> verify  | tail -500`
     * Class: `mvn -o -Dmaven.repo.local=.m2_repo -pl <module> -Dtest=ClassName verify  | tail -500`
@@ -509,6 +511,10 @@ Hint: get the current year with `date +%Y`.
 
 Do **not** modify existing headers’ years.
 
+Right below the header block, insert an agent signature comment: Codex agents must add `// Some portions generated by Codex`, and GitHub Co-Pilot agents must add `// Some portions generated by Co-Pilot`. Align the wording with whatever agent name you are currently operating under.
+
+Immediately after creating any new Java source file, add the signature comment (per rule above) and run `cd scripts && ./checkCopyrightPresent.sh` (or an equivalent pushd/popd invocation) so you catch missing copyright/SPDX lines before moving on.
+
 ---
 
 ## Pre‑Commit Checklist

core/common/iterator/src/main/java/org/eclipse/rdf4j/common/iteration/DualUnionIteration.java

@@ -220,6 +220,8 @@ public final void close() {
 		if (!closed) {
 			closed = true;
 			nextElement = null;
+			var iteration1 = this.iteration1;
+			var iteration2 = this.iteration2;
 			try {
 				if (iteration1 != null) {
 					iteration1.close();

core/common/transaction/src/main/java/org/eclipse/rdf4j/common/transaction/IsolationLevelFactory.java

@@ -0,0 +1,36 @@
+/*******************************************************************************
+ * Copyright (c) 2025 Eclipse RDF4J contributors.
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Distribution License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/org/documents/edl-v10.php.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ *******************************************************************************/
+package org.eclipse.rdf4j.common.transaction;
+
+import java.util.Optional;
+
+/**
+ * {@link TransactionSettingFactory} for {@link IsolationLevel}s exposed by the RDF4J API.
+ */
+public class IsolationLevelFactory implements TransactionSettingFactory {
+
+	@Override
+	public String getName() {
+		return IsolationLevel.NAME;
+	}
+
+	@Override
+	public Optional<TransactionSetting> getTransactionSetting(String value) {
+		if (value == null || value.isBlank()) {
+			return Optional.empty();
+		}
+		try {
+			return Optional.of(IsolationLevels.valueOf(value.trim()));
+		} catch (IllegalArgumentException e) {
+			return Optional.empty();
+		}
+	}
+}

core/common/transaction/src/main/resources/META-INF/services/org.eclipse.rdf4j.common.transaction.TransactionSettingFactory

@@ -0,0 +1 @@
+org.eclipse.rdf4j.common.transaction.IsolationLevelFactory

docker/build.sh

@@ -21,9 +21,8 @@ if [ -z ${SKIP_BUILD+x} ]; then
 
   #Clean, format and package
   echo "Building with Maven"
-  mvn clean
   mvn -T 2C formatter:format impsort:sort && mvn xml-format:xml-format
-  mvn install -DskipTests
+  mvn install -Pquick
   mvn -Passembly package -DskipTests -Dmaven.javadoc.skip=true -Dformatter.skip=true -Dimpsort.skip=true -Dxml-format.skip=true  -Djapicmp.skip -Denforcer.skip=true -Dbuildnumber.plugin.phase=none -Danimal.sniffer.skip=true
 
   # find .zip file

e2e/.gitignore

@@ -2,3 +2,4 @@ node_modules/
 /test-results/
 /playwright-report/
 /playwright/.cache/
+/.npm-cache/

e2e/README.md

@@ -1,20 +1,17 @@
 # End-to-end tests
 
-This directory contains end-to-end tests for the project. These tests use docker to run the RDF4J server and workbench.
+This directory contains end-to-end tests for the project. The suite now boots the RDF4J Server and Workbench using a Spring Boot wrapper with an embedded Tomcat instance, so Docker is no longer required.
 
-The tests are written using Microsoft Playwright and interact with the server and workbench using the browser.
+The tests are written using Microsoft Playwright and interact with the server and workbench in a real browser.
 
 ## Running the tests
 
 Requirements:
- - docker
  - java
  - maven
  - npm
  - npx
 
-The tests can be run using the `run.sh` script. This script will build the project, start the server and workbench and run the tests.
+The tests can be run using the `run.sh` script. The script builds the Spring Boot runner, launches it in the background, waits until the HTTP endpoints are reachable, and then executes the Playwright test suite.
 
 To run the tests interactively use `npx playwright test --ui`
-
-The RDF4J server and workbench can be started independently using the `run.sh` script in the `docker` directory.

e2e/run.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 #
-# Copyright (c) 2023 Eclipse RDF4J contributors.
+# Copyright (c) 2025 Eclipse RDF4J contributors.
 #
 # All rights reserved. This program and the accompanying materials
 # are made available under the terms of the Eclipse Distribution License v1.0
@@ -12,45 +12,87 @@
 
 set -e
 
+SERVER_PID=""
+
+cleanup() {
+  if [ -z "${SERVER_PID:-}" ]; then
+    return
+  fi
+
+  # If the process is already gone, nothing to do
+  if ! kill -0 "$SERVER_PID" 2>/dev/null; then
+    return
+  fi
+
+  echo "Sending SIGINT to server-boot module (pid=$SERVER_PID)"
+  kill -s INT "$SERVER_PID" 2>/dev/null || true
+
+  # Wait for graceful shutdown after SIGINT
+  for i in 1 2 3 4 5 6 7 8 9 10; do
+    if ! kill -0 "$SERVER_PID" 2>/dev/null; then
+      echo "server-boot module stopped gracefully after SIGINT"
+      wait "$SERVER_PID" 2>/dev/null || true
+      return
+    fi
+    kill -s INT "$SERVER_PID" 2>/dev/null || true
+    sleep 0.5
+  done
+
+  # Still alive: send a more aggressive TERM
+  echo "Sending SIGTERM to server-boot module (pid=$SERVER_PID)"
+  kill "$SERVER_PID" 2>/dev/null || true
+
+  # Wait for graceful shutdown after SIGTERM
+  for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20; do
+    if ! kill -0 "$SERVER_PID" 2>/dev/null; then
+      echo "server-boot module stopped after SIGTERM"
+      wait "$SERVER_PID" 2>/dev/null || true
+      return
+    fi
+    sleep 0.5
+  done
+
+  # Still alive after: kill definitively
+  echo "Sending SIGKILL to server-boot module (pid=$SERVER_PID)"
+  kill -9 "$SERVER_PID" 2>/dev/null || true
+  wait "$SERVER_PID" 2>/dev/null || true
+}
+
+trap cleanup EXIT
+
 npm install
 
-for APP_SERVER in tomcat jetty; do
-  export APP_SERVER
+cd ..
 
-  cd ..
-  cd docker
-  ./run.sh
-  ./waitForDocker.sh
-  cd ..
-  cd e2e
+mvn -q install -Pquick
 
-  sleep 10
+mvn -pl tools/server-boot spring-boot:run &
+SERVER_PID=$!
+# server-boot module will be stopped automatically on script exit (see cleanup trap above).
 
-  if [ ! -d  'node_modules' ]; then
-    echo "npm ci"
-    npm ci
-  fi
+cd e2e
 
-  docker ps
+sleep 10
 
-  npx playwright install --with-deps # install browsers
-  npx playwright test
+if [ ! -d 'node_modules' ]; then
+  echo "npm ci"
+  npm ci
+fi
 
-  status_npx=$?
+npx playwright install --with-deps # install browsers
+npx playwright test
 
-  cd ..
-  cd docker
-  ./shutdown.sh
+status_npx=$?
 
-  # test for error code
-  if [ $status_npx -ne 0 ] ; then
-    echo "Error in E2E test for $APP_SERVER"
-    exit $status_npx
-  fi
+cd ..
 
-  echo "E2E test for $APP_SERVER OK"
+# test for error code
+if [ $status_npx -ne 0 ]; then
+  echo "Error in E2E test"
+  exit $status_npx
+fi
 
-  # don't redo the whole build process just for making another docker image
-  export SKIP_BUILD="skip"
-done
+echo "E2E test OK"
 
+# don't redo the whole build process just for making another docker image
+export SKIP_BUILD="skip"

e2e/tests/workbench.spec.js

@@ -83,3 +83,33 @@ test('SPARQL update', async ({page}) => {
 
 });
 
+
+test('Add Turtle data to repository', async ({page}) => {
+    await page.goto('http://localhost:8080/rdf4j-workbench/');
+    page.on('dialog', dialog => {
+        console.log(dialog.message());
+        dialog.dismiss();
+    });
+
+    await createRepo(page);
+
+    await page.getByText('Add').click();
+    await page.waitForSelector('#text');
+
+    await page.locator('#source-text').check();
+    await page.locator('#baseURI').fill('http://example.org/ns#');
+    await page.locator('#Content-Type').selectOption('text/turtle');
+
+    const turtleData = '@prefix ex: <http://example.org/ns#> .\n\n' +
+        'ex:alice a ex:Person ;\n' +
+        '        ex:name "Alice" .';
+
+    await page.locator('#text').fill(turtleData);
+
+    await page.getByRole('button', { name: 'Upload' }).click();
+
+    await page.getByText('Types').click();
+
+    let type = await page.getByText('ex:Person');
+    await expect(type).toHaveText('ex:Person');
+});