[bot] Merge 26.7 to 26.8

api/src/org/labkey/api/ApiModule.java

@@ -23,6 +23,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.json.JSONObject;
 import org.labkey.api.action.ApiXmlWriter;
+import org.labkey.api.action.ConcurrencyLimiter;
 import org.labkey.api.action.SpringActionController;
 import org.labkey.api.admin.SubfolderWriter;
 import org.labkey.api.assay.AssayResultsFileWriter;
@@ -182,6 +183,7 @@
 import org.labkey.api.util.SystemMaintenanceStartupListener;
 import org.labkey.api.util.URIUtil;
 import org.labkey.api.util.URLHelper;
+import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.util.emailTemplate.EmailTemplate;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.FileServlet;
@@ -414,6 +416,7 @@ public void registerServlets(ServletContext servletCtx)
             ChecksumUtil.TestCase.class,
             CollectionUtils.TestCase.class,
             Compress.TestCase.class,
+            ConcurrencyLimiter.TestCase.class,
             Constants.TestCase.class,
             ConvertHelper.TestCase.class,
             CspCommentScanner.TestCase.class,
@@ -485,7 +488,8 @@ public void registerServlets(ServletContext servletCtx)
             TabLoader.HeaderMatchTest.class,
             Table.IsSelectTestCase.class,
             URIUtil.TestCase.class,
-            ValidEmail.TestCase.class
+            ValidEmail.TestCase.class,
+            XmlBeansUtil.TestCase.class
         );
     }
 

api/src/org/labkey/api/action/ConcurrencyLimit.java

@@ -0,0 +1,54 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.api.action;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.Target;
+
+/**
+ * Caps the number of requests executing an action at the same time, server-wide, for actions expensive enough that a
+ * few simultaneous callers can exhaust heap or the request thread pool.
+ * <p>
+ * {@link ConcurrencyLimiter} enforces the limit from {@link SpringActionController#handleRequest}, after the permission
+ * check and around the whole action including rendering. A request that can't get a permit within
+ * {@link #timeoutSeconds()} is rejected with a 429 and never executes the action.
+ * <p>
+ * Not inherited: a subclass of an annotated action is unlimited unless it declares its own {@code @ConcurrencyLimit}.
+ */
+@Retention(java.lang.annotation.RetentionPolicy.RUNTIME)
+@Target(ElementType.TYPE)
+public @interface ConcurrencyLimit
+{
+    int DEFAULT_TIMEOUT_SECONDS = 2;
+    int DEFAULT_RETRY_AFTER_SECONDS = 30;
+    String DEFAULT_MESSAGE = "";
+
+    /** Maximum number of requests allowed to execute this action concurrently, across the whole server. Must be positive. */
+    int value();
+
+    /**
+     * How long an incoming request waits for a permit before it's rejected with a 429. Keep it short - a parked thread
+     * still consumes a connector thread, so a long wait just moves the exhaustion problem.
+     */
+    long timeoutSeconds() default DEFAULT_TIMEOUT_SECONDS;
+
+    /** Value sent in the {@code Retry-After} response header when a request is rejected. */
+    int retryAfterSeconds() default DEFAULT_RETRY_AFTER_SECONDS;
+
+    /** Message sent to the client when a request is rejected. Defaults to a generic message when not specified. */
+    String message() default DEFAULT_MESSAGE;
+}

api/src/org/labkey/api/action/ConcurrencyLimiter.java

@@ -0,0 +1,244 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.api.action;
+
+import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+import org.junit.Assert;
+import org.junit.Test;
+import org.labkey.api.util.logging.LogHelper;
+import org.labkey.api.view.TooManyRequestsException;
+import org.labkey.api.view.ViewContext;
+
+import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.Semaphore;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicBoolean;
+
+/**
+ * Enforces {@link ConcurrencyLimit} on behalf of {@link SpringActionController}. Holds one {@link Semaphore} per
+ * action class that declares the annotation.
+ */
+public class ConcurrencyLimiter
+{
+    private static final Logger LOG = LogHelper.getLogger(ConcurrencyLimiter.class, "Rejects requests to actions that limit their concurrency when too many are already in flight");
+
+    static final String GENERIC_MESSAGE = "The server is already handling as many simultaneous requests for this operation as it allows. Please retry in a few moments.";
+
+    /**
+     * One limiter (and therefore one set of permits) per action class. {@link ConcurrentHashMap} won't store a null
+     * value, so unannotated actions map to {@link #UNLIMITED}.
+     */
+    private static final Map<Class<?>, ConcurrencyLimiter> LIMITERS = new ConcurrentHashMap<>();
+
+    /**
+     * Limiter for an action that declares no limit.
+     */
+    private static final ConcurrencyLimiter UNLIMITED = new ConcurrencyLimiter();
+
+    /**
+     * Handed out by {@link #UNLIMITED}; holds no permit, so closing it must do nothing.
+     */
+    private static final Permit NOOP_PERMIT = () -> {};
+
+    /**
+     * Returned by {@link #acquire}; release the permit by closing it, ideally via try-with-resources
+     */
+    public interface Permit extends AutoCloseable
+    {
+        @Override
+        void close();
+    }
+
+    /**
+     * Reserve one of the action's permits, if it declares a {@link ConcurrencyLimit}.
+     *
+     * @return a {@link Permit} that the caller must close once the action has finished executing
+     * @throws TooManyRequestsException if no permit becomes available within the action's configured timeout
+     */
+    public static Permit acquire(@NotNull Class<?> actionClass, @Nullable ViewContext context)
+    {
+        // This runs on every request, and computeIfAbsent() locks the bin even on a hit unless the key happens to be
+        // its first node, so take the lock-free get() whenever the limiter is already resolved.
+        ConcurrencyLimiter limiter = LIMITERS.get(actionClass);
+
+        if (null == limiter)
+            limiter = LIMITERS.computeIfAbsent(actionClass, ConcurrencyLimiter::resolve);
+
+        return limiter.acquirePermit(context);
+    }
+
+    private static ConcurrencyLimiter resolve(Class<?> actionClass)
+    {
+        ConcurrencyLimit limit = actionClass.getDeclaredAnnotation(ConcurrencyLimit.class);
+
+        return null == limit ? UNLIMITED : new ConcurrencyLimiter(actionClass, limit);
+    }
+
+    /**
+     * All three are null for the {@link #UNLIMITED} sentinel and non-null for every other instance.
+     */
+    private final Class<?> _actionClass;
+    private final ConcurrencyLimit _limit;
+    private final Semaphore _semaphore;
+
+    private ConcurrencyLimiter()
+    {
+        _actionClass = null;
+        _limit = null;
+        _semaphore = null;
+    }
+
+    private ConcurrencyLimiter(@NotNull Class<?> actionClass, @NotNull ConcurrencyLimit limit)
+    {
+        if (limit.value() < 1)
+            throw new IllegalStateException("@ConcurrencyLimit on " + actionClass.getName() + " must allow at least one concurrent request, but was " + limit.value());
+
+        _actionClass = actionClass;
+        _limit = limit;
+        // Fair, so a steady stream of new requests can't starve one that's already waiting
+        _semaphore = new Semaphore(limit.value(), true);
+    }
+
+    private Permit acquirePermit(@Nullable ViewContext context)
+    {
+        if (this == UNLIMITED)
+            return NOOP_PERMIT;
+
+        try
+        {
+            if (!_semaphore.tryAcquire(_limit.timeoutSeconds(), TimeUnit.SECONDS))
+                throw reject(context);
+        }
+        catch (InterruptedException e)
+        {
+            Thread.currentThread().interrupt();
+            throw reject(context);
+        }
+
+        // Releasing twice would permanently inflate the pool and quietly defeat the limit, so make close() idempotent
+        AtomicBoolean released = new AtomicBoolean();
+        return () -> {
+            if (released.compareAndSet(false, true))
+                _semaphore.release();
+        };
+    }
+
+    private TooManyRequestsException reject(@Nullable ViewContext context)
+    {
+        LOG.info("Rejecting request to {} for user {} in {}: {} requests already in progress", _actionClass.getName(),
+                null == context ? "<unknown>" : context.getUser(),
+                null == context || null == context.getContainer() ? "<unknown>" : context.getContainer().getPath(),
+                _limit.value());
+
+        String message = _limit.message().isEmpty() ? GENERIC_MESSAGE : _limit.message();
+        return new TooManyRequestsException(message, _limit.retryAfterSeconds());
+    }
+
+    public static class TestCase extends Assert
+    {
+        @ConcurrencyLimit(value = 2, timeoutSeconds = 0, retryAfterSeconds = 7, message = "Slow down")
+        private static class LimitedAction
+        {
+        }
+
+        /**
+         * Deliberately carries no annotation of its own - the limit is not inherited.
+         */
+        private static class SubclassAction extends LimitedAction
+        {
+        }
+
+        @ConcurrencyLimit(1)
+        private static class SingleRequestAction
+        {
+        }
+
+        private static class UnlimitedAction
+        {
+        }
+
+        @ConcurrencyLimit(0)
+        private static class BadLimitAction
+        {
+        }
+
+        @Test
+        public void testUnlimitedActionIsNotThrottled()
+        {
+            // Many more than any limit would allow, all held at once
+            for (int i = 0; i < 100; i++)
+                //noinspection resource
+                ConcurrencyLimiter.acquire(UnlimitedAction.class, null);
+        }
+
+        @Test
+        public void testRejectsBeyondLimit()
+        {
+            try (Permit p1 = acquire(LimitedAction.class, null); Permit p2 = acquire(LimitedAction.class, null))
+            {
+                assertNotNull(p1);
+                assertNotNull(p2);
+
+                @SuppressWarnings("resource") TooManyRequestsException e = assertThrows(TooManyRequestsException.class, () -> acquire(LimitedAction.class, null));
+                assertEquals(TooManyRequestsException.SC_TOO_MANY_REQUESTS, e.getStatus());
+                assertEquals("Slow down", e.getMessage());
+                assertEquals(7, e.getRetryAfterSeconds());
+            }
+
+            // Permits are back after the try-with-resources released them
+            acquire(LimitedAction.class, null).close();
+        }
+
+        @Test
+        public void testLimitIsNotInherited()
+        {
+            // More than the superclass's limit of two
+            try (Permit p1 = acquire(SubclassAction.class, null); Permit p2 = acquire(SubclassAction.class, null); Permit p3 = acquire(SubclassAction.class, null))
+            {
+                assertNotNull(p1);
+                assertNotNull(p2);
+                assertNotNull(p3);
+
+                // The superclass still has both of its own permits available
+                try (Permit p4 = acquire(LimitedAction.class, null); Permit p5 = acquire(LimitedAction.class, null))
+                {
+                    assertNotNull(p4);
+                    assertNotNull(p5);
+                }
+            }
+        }
+
+        @Test
+        public void testGenericMessage()
+        {
+            try (Permit ignored = acquire(SingleRequestAction.class, null))
+            {
+                //noinspection resource
+                assertEquals(GENERIC_MESSAGE, assertThrows(TooManyRequestsException.class, () -> acquire(SingleRequestAction.class, null)).getMessage());
+            }
+        }
+
+        @Test
+        public void testNonPositiveLimitIsRejected()
+        {
+            //noinspection resource
+            assertThrows(IllegalStateException.class, () -> acquire(BadLimitAction.class, null));
+        }
+    }
+}

api/src/org/labkey/api/action/SpringActionController.java

@@ -532,11 +532,16 @@ public ModelAndView handleRequest(HttpServletRequest request, @NotNull HttpServl
                 QueryService.get().setEnvironment(QueryService.Environment.ACTION, actionAnnotation.value());
             }
 
-            beforeAction(controller);
-            ModelAndView mv = controller.handleRequest(request, response);
-            if (mv != null)
+            // After the permission check so unauthorized requests can't consume @ConcurrencyLimit permits, and held
+            // through rendering because the action's memory is live for that whole time.
+            try (ConcurrencyLimiter.Permit ignored = ConcurrencyLimiter.acquire(actionClass, context))
             {
-                renderInTemplate(context, controller, pageConfig, mv);
+                beforeAction(controller);
+                ModelAndView mv = controller.handleRequest(request, response);
+                if (mv != null)
+                {
+                    renderInTemplate(context, controller, pageConfig, mv);
+                }
             }
         }
         catch (HttpRequestMethodNotSupportedException x)

api/src/org/labkey/api/assay/transform/DataTransformService.java

@@ -157,6 +157,11 @@ public TransformResult transformAndValidate(
 
                         bindings.put(ExternalScriptEngine.WORKING_DIRECTORY, scriptDir.toNioPathForWrite().toString());
                         bindings.put(ExternalScriptEngine.SCRIPT_PATH, scriptFile.toNioPathForRead().toFile().getAbsolutePath());
+                        bindings.put(ExternalScriptEngine.INVOCATION_LABEL, "transform protocol=" + context.getProtocol().getRowId()
+                                + " name='" + context.getProtocol().getName() + "'"
+                                + " operation=" + operation.name()
+                                + " script='" + scriptFile.getName() + "'"
+                                + " container=" + context.getContainer().getPath());
 
                         Map<String, String> paramMap = new HashMap<>();