[bot] Merge 25.8 to develop

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

@@ -39,6 +39,7 @@
 import org.labkey.api.util.MimeMap;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.ResponseHelper;
+import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.view.BadRequestException;
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.UnauthorizedException;
@@ -52,6 +53,7 @@
 import jakarta.servlet.http.HttpServletRequest;
 import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
+import java.io.InputStreamReader;
 import java.io.Reader;
 import java.net.SocketTimeoutException;
 import java.time.Duration;
@@ -511,12 +513,23 @@ protected long getMaximumJsonInputLength()
 
     private @Nullable JSONObject getJsonObject() throws IOException
     {
+        HttpServletRequest request = getViewContext().getRequest();
+        if (request == null)
+            return null;
+
+        String characterEncoding = request.getCharacterEncoding();
+        if (characterEncoding == null)
+            characterEncoding = StringUtilsLabKey.DEFAULT_CHARSET.name();
+
         long maxLength = getMaximumJsonInputLength();
-        try (Reader r = getViewContext().getRequest().getReader();
-            Reader jsonReader = maxLength > 0 ? new StrictBoundedReader(r, maxLength) : r)
+
+        // Issue 53699: Use request.getInputStream() instead of request.getReader() to
+        // avoid BufferUnderflowException when processing multibyte character JSON payloads.
+        try (Reader streamReader = new InputStreamReader(request.getInputStream(), characterEncoding);
+             Reader jsonReader = maxLength > 0 ? new StrictBoundedReader(streamReader, maxLength) : streamReader)
         {
-            JSONTokener tokener = new JSONTokener(r);
-            return tokener.more() ? new JSONObject(new JSONTokener(jsonReader)) : null;
+            JSONTokener tokener = new JSONTokener(jsonReader);
+            return tokener.more() ? new JSONObject(tokener) : null;
         }
     }
 

api/src/org/labkey/api/data/validator/LengthValidator.java

@@ -35,8 +35,9 @@ public String _validate(int rowNum, Object value)
     {
         if (value instanceof String s)
         {
-            if (s.length() > scale)
-                return "Value is too long for column '" + _columnName + "', a maximum length of " + scale + " is allowed. The supplied value, '" + StringUtils.abbreviateMiddle(s, "...", 50) + "', was " + s.length() + " characters long.";
+            int charLength = Character.codePointCount(s, 0, s.length());
+            if (charLength > scale)
+                return "Value is too long for column '" + _columnName + "', a maximum length of " + scale + " is allowed. The supplied value, '" + StringUtils.abbreviateMiddle(s, "...", 50) + "', was " + charLength + " characters long.";
         }
 
         return null;

api/src/org/labkey/api/dataiterator/ExistingRecordDataIterator.java

@@ -172,6 +172,9 @@ public Object getConstantValue(int i)
     @Override
     public boolean next() throws BatchValidationException
     {
+        if (_context.getErrors().hasErrors())
+            return false;
+
         // NOTE: we have to call mark() before we call next() if we want the 'next' row to be cached
         if (useMark)
             _unwrapped.mark();  // unwrapped _delegate

assay/src/org/labkey/assay/plate/PlateImpl.java

@@ -23,7 +23,11 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
+import org.junit.Assert;
+import org.junit.Before;
 import org.junit.Test;
+import org.junit.experimental.runners.Enclosed;
+import org.junit.runner.RunWith;
 import org.labkey.api.assay.plate.Plate;
 import org.labkey.api.assay.plate.PlateCustomField;
 import org.labkey.api.assay.plate.PlateService;
@@ -42,6 +46,8 @@
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
 import org.labkey.api.util.GUID;
+import org.labkey.api.util.JunitUtil;
+import org.labkey.api.util.TestContext;
 import org.labkey.api.util.UnexpectedException;
 import org.labkey.api.view.ActionURL;
 import org.labkey.assay.PlateController;
@@ -58,9 +64,7 @@
 import java.util.List;
 import java.util.Map;
 
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
+@RunWith(Enclosed.class)
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public class PlateImpl extends PropertySetImpl implements Plate, Cloneable
 {
@@ -160,9 +164,9 @@ public static PlateImpl from(PlateBean bean)
         Container container = ContainerManager.getForId(bean.getContainerId());
         plate.setContainer(container);
         plate.setCreated(bean.getCreated());
-        plate.setCreatedBy(UserManager.getUser(bean.getCreatedBy()));
+        plate.setCreatedBy(bean.getCreatedBy());
         plate.setModified(bean.getModified());
-        plate.setModifiedBy(UserManager.getUser(bean.getModifiedBy()));
+        plate.setModifiedBy(bean.getModifiedBy());
 
         // plate type and plate set objects
         PlateType plateType = PlateManager.get().getPlateType(bean.getPlateType());
@@ -436,9 +440,9 @@ public JSONObject getCreatedBy()
         return user != null ? user.getUserProps() : null;
     }
 
-    public void setCreatedBy(User createdBy)
+    public void setCreatedBy(int createdBy)
     {
-        _createdBy = createdBy.getUserId();
+        _createdBy = createdBy;
     }
 
     public Date getModified()
@@ -458,9 +462,9 @@ public JSONObject getModifiedBy()
         return user != null ? user.getUserProps() : null;
     }
 
-    public void setModifiedBy(User modifiedBy)
+    public void setModifiedBy(int modifiedBy)
     {
-        _modifiedBy = modifiedBy.getUserId();
+        _modifiedBy = modifiedBy;
     }
 
     public String getDataFileId()
@@ -758,8 +762,17 @@ public boolean isNew()
         return _rowId == null || _rowId <= 0;
     }
 
-    public static final class TestCase
+    public static class TestCase extends Assert
     {
+        private PlateSetImpl _plateSet;
+
+        @Before
+        public void setup() throws Exception
+        {
+            PlateSetImpl plateSet = new PlateSetImpl();
+            _plateSet = PlateManager.get().createPlateSet(JunitUtil.getTestContainer(), TestContext.get().getUser(), plateSet, null, null);
+        }
+
         @Test
         public void testIdentifierMatch()
         {
@@ -781,5 +794,54 @@ public void testIdentifierMatch()
             assertFalse("Expected plate to not match invalid name", plate.isIdentifierMatch(""));
             assertFalse("Expected plate to not match invalid name", plate.isIdentifierMatch(null));
         }
+
+        @Test
+        public void testFromInitializer()
+        {
+            String testContainerId = JunitUtil.getTestContainer().getId();
+            int testUserId = TestContext.get().getUser().getUserId();
+            Long plateTypeId = PlateManager.get().getPlateTypes().stream().findFirst().orElseThrow().getRowId();
+            Long plateSetId = _plateSet.getRowId();
+
+            PlateBean bean = new PlateBean();
+            Long expectedRowId = 1L;
+            String expectedName = "Test Name";
+            Boolean archived = null;
+            bean.setPlateType(plateTypeId);
+            bean.setPlateSet(plateSetId);
+            bean.setContainerId(testContainerId);
+            bean.setCreatedBy(testUserId);
+            bean.setModifiedBy(testUserId);
+            bean.setRowId(expectedRowId);
+            bean.setPlateId("test-id");
+            bean.setName(expectedName);
+            bean.setArchived(archived);
+
+            PlateImpl plate = PlateImpl.from(bean);
+            assertNotNull(plate.getCreatedBy());
+            assertEquals(testUserId, plate.getCreatedBy().getInt("id"));
+            assertNotNull(plate.getModifiedBy());
+            assertEquals(testUserId, plate.getModifiedBy().getInt("id"));
+            assertEquals(expectedName, plate.getName());
+            assertEquals(expectedRowId, plate.getRowId());
+            assertFalse(plate.isArchived());
+            assertFalse(plate.isNew());
+
+            // Issue 53633: Verify an invalid user does not cause an error initializing from bean
+            {
+                bean = new PlateBean();
+                bean.setPlateType(plateTypeId);
+                bean.setPlateSet(plateSetId);
+                bean.setContainerId(testContainerId);
+                bean.setCreatedBy(-1);
+                bean.setModifiedBy(-1);
+
+                plate = PlateImpl.from(bean);
+                assertNull(plate.getCreatedBy());
+                assertNull(plate.getModifiedBy());
+                assertFalse(plate.isArchived());
+                assertTrue(plate.isNew());
+            }
+        }
     }
 }

study/test/src/org/labkey/test/tests/study/AutoLinkToStudyTest.java

@@ -13,15 +13,11 @@
 import org.labkey.test.categories.Daily;
 import org.labkey.test.components.CustomizeView;
 import org.labkey.test.components.assay.AssayConstants;
-import org.labkey.test.components.ext4.Window;
 import org.labkey.test.pages.query.ExecuteQueryPage;
 import org.labkey.test.util.ApiPermissionsHelper;
 import org.labkey.test.util.DataRegionTable;
-import org.labkey.test.util.Ext4Helper;
 import org.labkey.test.util.PermissionsHelper;
 import org.labkey.test.util.StudyHelper;
-import org.openqa.selenium.Keys;
-import org.openqa.selenium.WebElement;
 
 import java.io.File;
 import java.util.List;
@@ -300,20 +296,8 @@ private void importAssayRun(File runFile, String assayName, String runName)
     private void createDatasetCategory(String projectName, String name)
     {
         goToProjectHome(projectName);
-        goToManageViews();
-        Locator.linkWithText("Manage Categories").findElement(getDriver()).click();
-        _extHelper.waitForExtDialog("Manage Categories");
-        Window<?> categoryWindow = new Window.WindowFinder(getDriver()).withTitle("Manage Categories").waitFor();
-        categoryWindow.clickButton("New Category", 0);
-        WebElement newCategoryField = Locator.input("label").withAttributeContaining("id", "textfield").notHidden().waitForElement(getDriver(), WAIT_FOR_JAVASCRIPT);
-        actionClear(newCategoryField);
-        sleep(500);
-        newCategoryField.sendKeys(name);
-        sleep(500);
-        newCategoryField.sendKeys(Keys.ENTER);
-        waitForElement(Ext4Helper.Locators.window("Manage Categories").append("//div").withText(name));
-        clickButton("Done", 0);
-        _extHelper.waitForExtDialogToDisappear("Manage Categories");
+        goToManageViews()
+                .createCategory(name);
     }
 
     private String getCategory(String projectName, String datasetName)