[bot] Fast-forward for 26.7.0

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

@@ -189,6 +189,7 @@
 import org.labkey.api.view.ViewServlet;
 import org.labkey.api.view.WebPartFactory;
 import org.labkey.api.webdav.WebdavResolverImpl;
+import org.labkey.api.wiki.WikiRendererType;
 import org.labkey.api.writer.ContainerUser;
 import org.labkey.filters.ContentSecurityPolicyFilter;
 
@@ -562,6 +563,7 @@ public void registerServlets(ServletContext servletCtx)
             UserManager.TestCase.class,
             ViewCategoryManager.TestCase.class,
             WebdavResolverImpl.TestCase.class,
+            WikiRendererType.TestCase.class,
             WorkbookContainerType.TestCase.class,
             WriteableLookAndFeelProperties.TestCase.class
         );

api/src/org/labkey/api/admin/AdminBean.java

@@ -24,7 +24,6 @@
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.CoreSchema;
 import org.labkey.api.data.DbScope;
-import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.security.UserManager;
 import org.labkey.api.settings.AppProps;
@@ -43,7 +42,6 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.List;
 import java.util.Map;
 import java.util.TreeMap;
@@ -82,7 +80,6 @@ public static class RecentUser
     public static final String sessionTimeout = Formats.commaf0.format(ModuleLoader.getServletContext().getSessionTimeout());
     public static final String buildTime = ModuleLoader.getInstance().getCoreModule().getBuildTime();
     public static final String serverStartupTime = DateUtil.formatDateTime(ContainerManager.getRoot());
-    public static final List<Module> modules;
 
     public static String asserts = "disabled";
 
@@ -116,9 +113,6 @@ public static class RecentUser
 
         //noinspection ConstantConditions,AssertWithSideEffects
         assert null != (asserts = "enabled");
-
-        modules = new ArrayList<>(ModuleLoader.getInstance().getModules());
-        modules.sort(Comparator.comparing(Module::getName, String.CASE_INSENSITIVE_ORDER));
     }
 
     private static @Nullable String getValue(Field field)

api/src/org/labkey/api/data/DataColumn.java

@@ -191,6 +191,12 @@ protected ColumnInfo getDisplayField(@NotNull ColumnInfo col, boolean withLookup
         return null==display ? col : display;
     }
 
+    @Override
+    public void setWithLookup(boolean withLookup)
+    {
+        _displayColumn = withLookup ? getDisplayField(_boundColumn, true) : _boundColumn;
+    }
+
     @Override
     public String toString()
     {

api/src/org/labkey/api/data/DisplayColumn.java

@@ -1232,6 +1232,11 @@ public void setRequiresHtmlFiltering(boolean requiresHtmlFiltering)
         _requiresHtmlFiltering = requiresHtmlFiltering;
     }
 
+    public void setWithLookup(boolean withLookup)
+    {
+        // subclasses override as needed
+    }
+
     public void setLinkTarget(String linkTarget)
     {
         _linkTarget = linkTarget;

api/src/org/labkey/api/data/dialect/BasePostgreSqlDialect.java

@@ -924,6 +924,19 @@ public boolean supportsNativeGreatestAndLeast()
         return true;
     }
 
+    @Override
+    public boolean supportsIsNumeric()
+    {
+        return true;
+    }
+
+    @Override
+    public SQLFragment isNumericExpr(SQLFragment expression)
+    {
+        return new SQLFragment("(CASE WHEN CAST((").append(expression)
+                .append(") AS TEXT) ~ '^[+-]?([0-9]+([.][0-9]*)?|[.][0-9]+)$' THEN 1 ELSE 0 END)");
+    }
+
     private class PostgreSqlColumnMetaDataReader extends ColumnMetaDataReader
     {
         private final TableInfo _table;

api/src/org/labkey/api/data/dialect/SqlDialect.java

@@ -59,6 +59,7 @@
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.util.ExceptionUtil;
+import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.MemTracker;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.SystemMaintenance;
@@ -80,6 +81,8 @@
 import java.sql.SQLException;
 import java.sql.Statement;
 import java.sql.Types;
+import java.time.Duration;
+import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Calendar;
@@ -95,6 +98,7 @@
 import java.util.regex.Pattern;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertThrows;
 import static org.junit.Assert.assertTrue;
 
@@ -168,7 +172,7 @@ public String getOtherDatabaseThreads()
     {
         StringBuilder sb = new StringBuilder();
 
-        // Per 18789, also include threads without db connections.
+        // Per Issue 18789, also include threads without db connections.
         List<Thread> dbThreads = new ArrayList<>();
 
         for (Map.Entry<Thread, StackTraceElement[]> entry : Thread.getAllStackTraces().entrySet())
@@ -868,6 +872,16 @@ public SQLFragment getGreatestAndLeastSQL(String method, SQLFragment... argument
         throw new UnsupportedOperationException(getClass().getSimpleName() + " does not implement");
     }
 
+    public boolean supportsIsNumeric()
+    {
+        return false;
+    }
+
+    public SQLFragment isNumericExpr(SQLFragment expression)
+    {
+        throw new UnsupportedOperationException(getClass().getSimpleName() + " does not implement");
+    }
+
     public void handleCreateDatabaseException(SQLException e) throws ServletException
     {
         throw(new ServletException("Can't create database", e));
@@ -1980,12 +1994,61 @@ public final Collection<String> getExecutionPlan(DbScope scope, SQLFragment sql,
     // Add any database configuration warnings (e.g., missing aggregate function or deprecated database server version)
     // to display in the page header for administrators. This will be called:
     // - Only on the LabKey DataSource's dialect instance (not external data sources)
-    // - After the core module has been upgraded and the dialect has been prepared for the last time, meaning the dialect
+    // - After the core module has been upgraded, and the dialect has been prepared for the last time, meaning the dialect
     //   should reflect the final database configuration
     public void addAdminWarningMessages(Warnings warnings, boolean showAllWarnings)
     {
     }
 
+    public static final long TIME_DIFFERENCE_WARNING_SECONDS = 10;
+
+    public static ServerDatabaseTimeDifference getServerDatabaseTimeDifference(DbScope scope)
+    {
+        // Compare LocalDateTime to capture any difference in server and database times (skew or timezone).
+        LocalDateTime serverTime = LocalDateTime.now();
+        LocalDateTime databaseTime = new SqlSelector(scope, "SELECT CURRENT_TIMESTAMP").getObject(LocalDateTime.class);
+
+        return new ServerDatabaseTimeDifference(serverTime, databaseTime);
+    }
+
+    public record ServerDatabaseTimeDifference(LocalDateTime serverTime, LocalDateTime databaseTime)
+    {
+        public long getSeconds()
+        {
+            return Math.abs(Duration.between(serverTime, databaseTime).toSeconds());
+        }
+
+        public boolean exceedsWarningThreshold()
+        {
+            return getSeconds() > TIME_DIFFERENCE_WARNING_SECONDS;
+        }
+    }
+
+    // GH Issue #1223: Add a site configuration warning for administrators if the server and database clocks differ.
+    protected void addTimeDifferenceWarning(Warnings warnings, boolean showAllWarnings)
+    {
+        try
+        {
+            ServerDatabaseTimeDifference difference = getServerDatabaseTimeDifference(DbScope.getLabKeyScope());
+
+            if (difference.exceedsWarningThreshold())
+                warnings.add(getTimeDifferenceWarning(difference.getSeconds()));
+            else if (showAllWarnings)
+                warnings.add(getTimeDifferenceWarning(TIME_DIFFERENCE_WARNING_SECONDS + 1));
+        }
+        catch (Exception e)
+        {
+            LOG.warn("Unable to compare web server and database server times", e);
+        }
+    }
+
+    private HtmlString getTimeDifferenceWarning(long seconds)
+    {
+        return HtmlString.of("The web server and database server times differ by " + seconds + " seconds. " +
+            "LabKey Server often relies on comparing timestamps stored in the database with timestamps generated by " +
+            "the web server, so this difference can lead to data integrity issues. Synchronize the clocks on these servers.");
+    }
+
     public abstract List<SQLFragment> getChangeStatements(TableChange change);
 
     public abstract void purgeTempSchema(Map<String, TempTableTracker> createdTableNames);
@@ -2007,7 +2070,7 @@ protected void trackTempTables(Map<String, TempTableTracker> createdTableNames)
     // Defragment an index, if necessary
     public void defragmentIndex(DbSchema schema, String tableSelectName, String indexName)
     {
-        // By default do nothing
+        // By default, do nothing
     }
 
     public boolean isTableExists(DbScope scope, String schema, String name)
@@ -2035,7 +2098,7 @@ public boolean hasTriggers(DbSchema scope, String schema, String tableName)
 
     /**
      *
-     * @return true If the dialect is one supported for the backend LabKey database. ie, Postgres or SQL Server
+     * @return true If the dialect is one supported for the backend LabKey database. i.e., Postgres or SQL Server
      */
     public boolean isLabKeyDbDialect()
     {
@@ -2409,5 +2472,37 @@ public void testProcedureIdentifierQuoting()
             // A dotted name is rejected: schema and procedure are separate parameters, so a '.' in a single component is an ambiguous schema-qualified reference
             assertThrows(IllegalArgumentException.class, () -> dialect.buildProcedureCall(core.getName(), "a.b", 0, false, false, scope));
         }
+
+        // GH Issue #1223: Verify the server/database clock-skew arithmetic and warning threshold
+        @Test
+        public void testServerDatabaseTimeDifference()
+        {
+            LocalDateTime base = LocalDateTime.of(2026, 7, 6, 12, 0, 0);
+
+            // Identical times: zero difference, no warning
+            ServerDatabaseTimeDifference equal = new ServerDatabaseTimeDifference(base, base);
+            assertEquals(0, equal.getSeconds());
+            assertFalse(equal.exceedsWarningThreshold());
+
+            // Comfortably below the threshold: no warning
+            ServerDatabaseTimeDifference below = new ServerDatabaseTimeDifference(base, base.plusSeconds(5));
+            assertEquals(5, below.getSeconds());
+            assertFalse(below.exceedsWarningThreshold());
+
+            // Exactly at the threshold: no warning (comparison is strictly greater-than)
+            ServerDatabaseTimeDifference atThreshold = new ServerDatabaseTimeDifference(base, base.plusSeconds(TIME_DIFFERENCE_WARNING_SECONDS));
+            assertEquals(TIME_DIFFERENCE_WARNING_SECONDS, atThreshold.getSeconds());
+            assertFalse(atThreshold.exceedsWarningThreshold());
+
+            // Just past the threshold: warning
+            ServerDatabaseTimeDifference over = new ServerDatabaseTimeDifference(base, base.plusSeconds(TIME_DIFFERENCE_WARNING_SECONDS + 1));
+            assertEquals(TIME_DIFFERENCE_WARNING_SECONDS + 1, over.getSeconds());
+            assertTrue(over.exceedsWarningThreshold());
+
+            // Difference is absolute: database clock behind the web server is treated the same as ahead
+            ServerDatabaseTimeDifference behind = new ServerDatabaseTimeDifference(base, base.minusSeconds(TIME_DIFFERENCE_WARNING_SECONDS + 1));
+            assertEquals(TIME_DIFFERENCE_WARNING_SECONDS + 1, behind.getSeconds());
+            assertTrue(behind.exceedsWarningThreshold());
+        }
     }
 }

api/src/org/labkey/api/mcp/AbstractAgentAction.java

@@ -85,9 +85,18 @@ protected String handleEscape(String prompt)
     @Override
     public void validateForm(F form, Errors errors)
     {
+        if (!McpService.get().isAIFeaturesEnabled())
+        {
+            errors.reject(ERROR_GENERIC, "Agent actions are not available.");
+            return;
+        }
+
         String prompt = form.getPrompt();
         if (prompt != null && prompt.length() > MAX_PROMPT_CHAR_LENGTH)
+        {
             errors.rejectValue("prompt", ERROR_GENERIC, "Prompt cannot exceed " + MAX_PROMPT_CHAR_LENGTH + " characters.");
+            return;
+        }
 
         // Only honor a client-supplied conversationId if this agent previously issued this session that
         // id. Otherwise, generate a fresh one. This prevents a same-session caller from splicing into

api/src/org/labkey/api/mcp/McpService.java

@@ -25,6 +25,8 @@
 import org.labkey.api.settings.OptionalFeatureService;
 import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.logging.LogHelper;
+import org.labkey.api.view.HtmlView;
+import org.labkey.api.view.HttpView;
 import org.labkey.api.writer.ContainerUser;
 import org.springframework.ai.chat.client.ChatClient;
 import org.springframework.ai.chat.model.ToolContext;
@@ -36,6 +38,7 @@
 
 import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 import java.util.function.Supplier;
 
 ///
@@ -94,8 +97,11 @@
 ///
 public interface McpService extends ToolCallbackProvider
 {
+    String VECTOR_SCHEMA = "vector_indexes"; // for pgvector extension, see core-26.005-26.006.sql
+
     Logger LOG = LogHelper.getLogger(McpService.class, "MCP registration exceptions");
     String ENABLE_MCP_SERVER_FLAG = "enableMcpServer";
+    String ENABLE_AI_FEATURES = "enableAIFeatures";
 
     // Interface for MCP classes that we will "ingest" using Spring annotations. Provides a few helper methods.
     interface McpImpl
@@ -117,9 +123,6 @@ default User getUser(ToolContext toolContext)
         // Every MCP resource should call this on every invocation
         default void incrementResourceRequestCount(String resource)
         {
-            if (!get().isEnabled())
-                throw new RuntimeException("The MCP server is not enabled for external requests. Consider toggling the optional feature flag.");
-
             get().incrementResourceRequestCount(resource);
         }
     }
@@ -142,8 +145,19 @@ default boolean isEnabled()
         return OptionalFeatureService.get().isFeatureEnabled(ENABLE_MCP_SERVER_FLAG);
     }
 
+    default boolean isAIFeaturesEnabled()
+    {
+        return OptionalFeatureService.get().isFeatureEnabled(ENABLE_AI_FEATURES);
+    }
+
     boolean isReady();
 
+    // Convenience for in-product AI features: the AI feature flag is on AND the service has started.
+    default boolean isAIFeaturesReady()
+    {
+        return isAIFeaturesEnabled() && isReady();
+    }
+
     // Register MCPs in Module.startup()
     default void register(McpImpl mcp)
     {
@@ -187,6 +201,8 @@ default ChatClient getChat(HttpSession session, String conversationName, Supplie
 
     record MessageResponse(String contentType, String text, HtmlString html) {}
 
+    record VectorDocument(String id, String text, Map<String, Object> metadata) {}
+
     /** get a consolidated response (good for many text-oriented agents/use-cases) */
     MessageResponse sendMessage(ChatClient chat, String message);
 
@@ -201,4 +217,26 @@ default List<MessageResponse> sendMessageEx(ChatClient chat, String message)
      * CONSIDER: Is it possible to implement VectorStoreRetriever wrapper for SearchService???
      */
     VectorStore getVectorStore();
+
+    /** Returns true if the vector store exists and contains at least one document. */
+    boolean isVectorStorePopulated(@NotNull VectorStore vs);
+
+    /**
+     * Adds documents to the vector store, automatically splitting any document whose token
+     * count exceeds the embedding model's input limit. Prefer this over
+     * {@code getVectorStore().add(...)} for indexing — it prevents the
+     * {@code IllegalArgumentException} that {@code TokenCountBatchingStrategy} throws on
+     * oversized inputs.
+     */
+    void addDocuments(List<VectorDocument> documents);
+
+    void saveVectorStore();
+
+    /** Drop and recreate the vector store table. Use when the embedding model has changed and dimensions no longer match. */
+    void resetVectorStore();
+
+    default HttpView<Object> getAssistantStatusView()
+    {
+        return new HtmlView(HtmlString.of("AI Assistant features are not available."));
+    }
 }