DocumentationMCP

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;
 
@@ -552,6 +553,7 @@ 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/mcp/McpService.java

@@ -36,6 +36,7 @@
 
 import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 import java.util.function.Supplier;
 
 ///
@@ -94,6 +95,8 @@
 ///
 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";
 
@@ -187,6 +190,8 @@ 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 +206,21 @@ 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();
 }

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

@@ -101,4 +101,25 @@ public VectorStore getVectorStore()
     {
         return null;
     }
+
+    @Override
+    public boolean isVectorStorePopulated(@NotNull VectorStore vs)
+    {
+        return false;
+    }
+
+    @Override
+    public void addDocuments(List<VectorDocument> documents)
+    {
+    }
+
+    @Override
+    public void saveVectorStore()
+    {
+    }
+
+    @Override
+    public void resetVectorStore()
+    {
+    }
 }

api/src/org/labkey/api/wiki/WikiService.java

@@ -50,6 +50,15 @@ record RenderedWiki (String name, String title, HtmlString html, String entityId
 
     RenderedWiki getRenderedWiki(Container c, String name);
 
+    record WikiMarkdown(String name, String title, String markdown, String entityId) {}
+
+    /**
+     * Returns a best-effort Markdown rendering of the wiki's raw source, intended for indexing
+     * (search, embedding, vector stores) — NOT for user display. Conversion is lossy and may
+     * drop or mangle markup details that don't have a direct Markdown equivalent.
+     */
+    WikiMarkdown getWikiMarkdown(Container c, String name);
+
     default HtmlString getHtml(Container c, String name)
     {
         var wiki = getRenderedWiki(c, name);
@@ -105,4 +114,18 @@ default HtmlString getHtml(Container c, String name)
     String updateAttachments(Container c, User user, String wikiName, @Nullable List<AttachmentFile> attachmentFiles, @Nullable List<String> deleteAttachmentNames);
 
     AttachmentParentType getAttachmentType();
+
+    /**
+     * Loads all wikis from the given container into the MCP vector store.
+     *
+     * <p>Each {@link org.labkey.api.mcp.McpService.VectorDocument} is assigned an ID of the form
+     * {@code "<containerEntityId>/<wikiEntityId>"}, where both components are GUIDs
+     * (as returned by {@link Container#getId()} and the wiki's own entity ID).
+     * Tools that consume vector store results (e.g. {@code listDocuments},
+     * {@code retrieveDocument}) must use this same format when constructing or
+     * interpreting document IDs.</p>
+     *
+     * @return the number of documents added
+     */
+    int populateVectorStore(Container container);
 }

core/module.properties

@@ -1,13 +1,13 @@
-Name: Core
-ModuleClass: org.labkey.core.CoreModule
-SchemaVersion: 26.005
-Label: Administration and Essential Services
-Description: The Core module provides central services such as login, \
-    security, administration, folder management, user management, \
-    module upgrade, file attachments, analytics, and portal page management.
-Organization: LabKey
-OrganizationURL: https://www.labkey.com/
-License: Apache 2.0
-LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
-SupportedDatabases: mssql, pgsql
-ManageVersion: true
+Name: Core
+ModuleClass: org.labkey.core.CoreModule
+SchemaVersion: 26.006
+Label: Administration and Essential Services
+Description: The Core module provides central services such as login, \
+    security, administration, folder management, user management, \
+    module upgrade, file attachments, analytics, and portal page management.
+Organization: LabKey
+OrganizationURL: https://www.labkey.com/
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+SupportedDatabases: mssql, pgsql
+ManageVersion: true

core/resources/schemas/dbscripts/postgresql/core-26.005-26.006.sql

@@ -0,0 +1 @@
+CREATE SCHEMA IF NOT EXISTS "vector_indexes";

core/src/org/labkey/core/CoreMcp.java

@@ -19,11 +19,13 @@
 import io.modelcontextprotocol.spec.McpSchema.ReadResourceResult;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.collections.LabKeyCollectors;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.mcp.McpService;
+import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.security.RequiresNoPermission;
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.User;
@@ -145,11 +147,32 @@ String setContainer(ToolContext context, @ToolParam(description = "Container pat
         return message;
     }
 
+
+    // TODO replace/augment with available feature list
+    @Tool(description = "List the modules installed on this server, this may be useful in inferring the available funcitonality.  For instance, " +
+            "the presence of the `premium` module implies the availability of premium featues.")
+    @RequiresNoPermission
+    public String listModules(ToolContext context)
+    {
+        JSONArray modules = new JSONArray();
+        ModuleLoader.getInstance().getModules().stream()
+                .map(module -> {
+                    JSONObject obj = new JSONObject();
+                    obj.put("name", module.getName());
+                    if (StringUtils.isNotEmpty(module.getLabel()))
+                        obj.put("label", module.getLabel());
+                    return obj;
+                })
+                .forEach(modules::put);
+        return new JSONObject(Map.of("modules",modules)).toString();
+    }
+
+
     @McpResource(
         uri = "resource://org/labkey/core/FileBasedModules.md",
         mimeType = "application/markdown",
         name = "File-Based Module Development Guide",
-        description = "Provide documentation for developing LabKey file-based modules")
+        description = "Required reading before building file-based modules. Covers module.properties, directory structure, web parts, SQL queries, reports, and deployment.")
     public ReadResourceResult getFileBasedModuleDevelopmentGuide() throws IOException
     {
         incrementResourceRequestCount("File-Based Modules");
@@ -167,7 +190,7 @@ public ReadResourceResult getFileBasedModuleDevelopmentGuide() throws IOExceptio
             uri = "resource://org/labkey/core/DataAnalysis_Python.md",
             mimeType = "application/markdown",
             name = "Python Data Analysis Development Guide",
-            description = "Provide documentation for developers using Python to analyze LabKey data")
+            description = "Required reading before writing Python scripts. Covers APIWrapper setup, .netrc auth, select_rows, execute_sql, QueryFilter, and pandas workflows.")
     public ReadResourceResult getPythonDataAnalysisGuide() throws IOException
     {
         incrementResourceRequestCount("Python Data Analysis");
@@ -185,7 +208,7 @@ public ReadResourceResult getPythonDataAnalysisGuide() throws IOException
             uri = "resource://org/labkey/core/DataAnalysis_R.md",
             mimeType = "application/markdown",
             name = "R Data Analysis Development Guide",
-            description = "Provide documentation for developers using R to analyze LabKey data")
+            description = "Required reading before writing R scripts. Covers Rlabkey setup, .netrc auth, labkey.selectRows, labkey.executeSql, makeFilter, and data frame workflows.")
     public ReadResourceResult getRDataAnalysisGuide() throws IOException
     {
         incrementResourceRequestCount("R Data Analysis");

core/src/org/labkey/core/CoreModule.java

@@ -368,6 +368,7 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
+import static org.labkey.api.mcp.McpService.VECTOR_SCHEMA;
 import static org.labkey.api.settings.StashedStartupProperties.homeProjectFolderType;
 import static org.labkey.api.settings.StashedStartupProperties.homeProjectResetPermissions;
 import static org.labkey.api.settings.StashedStartupProperties.homeProjectWebparts;
@@ -1552,7 +1553,8 @@ public Collection<String> getSchemaNames()
             CoreSchema.getInstance().getSchemaName(),       // core
             PropertySchema.getInstance().getSchemaName(),   // prop
             TestSchema.getInstance().getSchemaName(),       // test
-            DbSchema.TEMP_SCHEMA_NAME                       // temp
+            DbSchema.TEMP_SCHEMA_NAME,                      // temp
+            VECTOR_SCHEMA                                   // used by pgvector - see core-26.005-26.006.sql
         );
     }
 

devtools/src/org/labkey/devtools/TestController.java

@@ -18,12 +18,10 @@
 
 import jakarta.servlet.http.HttpServletResponse;
 import org.apache.logging.log4j.Logger;
-import org.jetbrains.annotations.NotNull;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
-import org.labkey.api.action.ConfirmAction;
 import org.labkey.api.action.FormArrayList;
 import org.labkey.api.action.FormViewAction;
 import org.labkey.api.action.JsonInputLimit;
@@ -35,7 +33,6 @@
 import org.labkey.api.action.SimpleResponse;
 import org.labkey.api.action.SimpleViewAction;
 import org.labkey.api.action.SpringActionController;
-import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.mcp.AbstractAgentAction;
 import org.labkey.api.mcp.McpService;
@@ -57,9 +54,7 @@
 import org.labkey.api.util.ConfigurationException;
 import org.labkey.api.util.DOM;
 import org.labkey.api.util.ExceptionUtil;
-import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.HtmlString;
-import org.labkey.api.util.HtmlStringBuilder;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.TestContext;
 import org.labkey.api.util.URLHelper;
@@ -74,15 +69,10 @@
 import org.labkey.api.view.ViewServlet;
 import org.labkey.api.view.template.ClientDependency;
 import org.labkey.api.view.template.PageConfig;
-import org.labkey.api.wiki.WikiService;
-import org.springframework.ai.document.Document;
-import org.springframework.ai.vectorstore.SimpleVectorStore;
-import org.springframework.ai.vectorstore.VectorStore;
 import org.springframework.dao.PessimisticLockingFailureException;
 import org.springframework.mock.web.MockHttpServletResponse;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
-import org.springframework.validation.ObjectError;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.Controller;
 
@@ -92,9 +82,6 @@
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
-import java.util.Objects;
-import java.util.concurrent.atomic.AtomicInteger;
-import java.util.stream.Gatherers;
 
 import static org.labkey.api.util.DOM.Attribute.name;
 import static org.labkey.api.util.DOM.Attribute.src;
@@ -1322,88 +1309,6 @@ protected String getServicePrompt()
         }
     }
 
-
-    @RequiresLogin
-    public static class PopulateVectorStoreAction extends ConfirmAction<Object>
-    {
-        AtomicInteger count = new AtomicInteger();
-
-        @Override
-        public ModelAndView getConfirmView(Object o, BindException errors)
-        {
-            var db = FileUtil.getTempDirectoryFileLike().resolveChild("VectorStore.database");
-            HtmlStringBuilder message = HtmlStringBuilder.of();
-            message.append("This will add the contents of /Documention wikis to the vector store.").append(HtmlString.BR);
-            message.append("This may take a few minutes.");
-            if (db.exists())
-                message.unsafeAppend("<p/><p/>").append("I see a vector store file already exists. Just FYI.");
-            return new HtmlView(message);
-        }
-
-        @Override
-        public void validateCommand(Object o, Errors errors)
-        {
-        }
-
-        @Override
-        public @NotNull URLHelper getSuccessURL(Object o)
-        {
-            return null;
-        }
-
-
-        // not usually used but some actions return views that close the current window etc...
-        @Override
-        public ModelAndView getSuccessView(Object form)
-        {
-            return HtmlView.of(count.get() + " documents added to vector store");
-        }
-
-        @Override
-        public boolean handlePost(Object o, BindException errors)
-        {
-            Container documentsContainer = ContainerManager.getForPath("/Documentation");
-            if (null == documentsContainer)
-                throw new NotFoundException();
-            VectorStore vs = McpService.get().getVectorStore();
-            if (null == vs)
-                throw new NotFoundException("/Documentation project was not found");
-
-            ActionURL wikiBase = new ActionURL("wiki","page",documentsContainer);
-
-            WikiService service = Objects.requireNonNull(WikiService.get());
-            List<String> all = service.getNames(documentsContainer);
-            all.stream()
-                    .map(name -> service.getRenderedWiki(documentsContainer, name))
-                    .filter(Objects::nonNull)
-                    .map(wiki ->
-                    {
-                        count.incrementAndGet();
-                        var metadata = Map.of(
-                                "Content-Type", "text/html",
-                                "filename", wiki.name() + ".html",
-                                "title", (Object)wiki.title(),
-                                "source", wikiBase.clone().addParameter("name",wiki.name()).getURIString()
-                        );
-                        return new Document(wiki.entityId(), wiki.html().toString(), metadata);
-                    })
-                    .gather(Gatherers.windowFixed(50))
-                    .forEach(vs);
-
-            var db = FileUtil.getTempDirectoryFileLike().resolveChild("VectorStore.database");
-            try
-            {
-                ((SimpleVectorStore)vs).save(db.toNioPathForRead().toFile());
-                return true;
-            }
-            catch (Exception x)
-            {
-                errors.addError(new ObjectError("form", "error saving vectordb: " + x.getMessage()));
-                return false;
-            }
-        }
-    }
-
     @AdminConsoleAction(AdminOperationsPermission.class)
     @JsonInputLimit(50)
     public static class TestJsonObjectInputLimitAction extends MutatingApiAction<SimpleApiJsonForm>

query/src/org/labkey/query/controllers/QueryMcp.java

@@ -67,7 +67,7 @@ public class QueryMcp implements McpService.McpImpl
         uri = "resource://org/labkey/query/controllers/prompts/LabKeySql.md",
         mimeType = "application/markdown",
         name = "LabKey SQL",
-        description = "Provide documentation for LabKey SQL specific syntax")
+        description = "Required reading before writing or debugging LabKey SQL. Covers lookup traversal, PIVOT, parameterized queries, cross-folder queries, and all available functions.")
     public ReadResourceResult getLabKeySQLDocumentation() throws IOException
     {
         incrementResourceRequestCount("LabKey SQL");