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For testing/prototyping labkey documentation RAG #7634

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43bae3e
For testing/prototyping labkey documentation RAG
labkey-matthewb Apr 29, 2026
8aefc05
Merge remote-tracking branch 'origin/release26.3-SNAPSHOT' into 26.3_…
labkey-matthewb May 1, 2026
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2 changes: 2 additions & 0 deletions devtools/src/org/labkey/devtools/DevtoolsModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@

import org.jetbrains.annotations.NotNull;
import org.labkey.api.exp.property.Domain;
import org.labkey.api.mcp.McpService;
import org.labkey.api.module.CodeOnlyModule;
import org.labkey.api.module.ModuleContext;
import org.labkey.api.security.AuthenticationManager;
Expand Down Expand Up @@ -71,6 +72,7 @@ protected void init()
@Override
public void doStartup(ModuleContext moduleContext)
{
McpService.get().register(new TestController.DocumentationMCP());
}

@Override
Expand Down
123 changes: 121 additions & 2 deletions devtools/src/org/labkey/devtools/TestController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@
import jakarta.servlet.http.HttpServletResponse;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.NotNull;
import org.json.JSONArray;
import org.json.JSONObject;
import org.labkey.api.action.ApiResponse;
import org.labkey.api.action.ApiSimpleResponse;
import org.labkey.api.action.ConfirmAction;
Expand All @@ -28,8 +30,13 @@
import org.labkey.api.action.SimpleResponse;
import org.labkey.api.action.SimpleViewAction;
import org.labkey.api.action.SpringActionController;
import org.labkey.api.announcements.CommSchema;
import org.labkey.api.collections.LabKeyCollectors;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.TableSelector;
import org.labkey.api.mcp.AbstractAgentAction;
import org.labkey.api.mcp.McpService;
import org.labkey.api.security.CSRF;
Expand All @@ -52,6 +59,7 @@
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.HtmlStringBuilder;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Path;
import org.labkey.api.util.URLHelper;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HtmlView;
Expand All @@ -64,7 +72,11 @@
import org.labkey.api.view.template.ClientDependency;
import org.labkey.api.view.template.PageConfig;
import org.labkey.api.wiki.WikiService;
import org.springframework.ai.chat.model.ToolContext;
import org.springframework.ai.document.Document;
import org.springframework.ai.tool.annotation.Tool;
import org.springframework.ai.tool.annotation.ToolParam;
import org.springframework.ai.vectorstore.SearchRequest;
import org.springframework.ai.vectorstore.SimpleVectorStore;
import org.springframework.ai.vectorstore.VectorStore;
import org.springframework.dao.PessimisticLockingFailureException;
Expand All @@ -76,14 +88,17 @@

import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Gatherers;

import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.labkey.api.util.DOM.Attribute.name;
import static org.labkey.api.util.DOM.Attribute.src;
import static org.labkey.api.util.DOM.Attribute.style;
Expand Down Expand Up @@ -1382,11 +1397,11 @@ public boolean handlePost(Object o, BindException errors)
count.incrementAndGet();
var metadata = Map.of(
"Content-Type", "text/html",
"filename", wiki.name() + ".html",
"filename", wiki.name() + ".html", // CONSIDER add path information
"title", (Object)wiki.title(),
"source", wikiBase.clone().addParameter("name",wiki.name()).getURIString()
);
return new Document(wiki.entityId(), wiki.html().toString(), metadata);
return new Document("documentation/"+wiki.name(), wiki.html().toString(), metadata);
})
.gather(Gatherers.windowFixed(50))
.forEach(vs);
Expand All @@ -1404,4 +1419,108 @@ public boolean handlePost(Object o, BindException errors)
}
}
}

public static class DocumentationMCP implements McpService.McpImpl
{
@Tool(description = "List of available documents from the LabKey user and administration manuals.")
@RequiresNoPermission
JSONObject listDocuments(ToolContext toolContext)
{
Container documentsContainer = ContainerManager.getForPath("/Documentation");
if (null == documentsContainer)
return new JSONObject(Map.of("error","There is no /Documentation project on this server"));

// CONSIDER include hierarchy or paths
// TODO WikiService doesn't expose this, just do a query for now (even though this info is cached)
TableInfo currentWikiVersions = CommSchema.getInstance().getSchema().getTable("CurrentWikiVersions");
SimpleFilter filter = SimpleFilter.createContainerFilter(documentsContainer);
Collection<Map<String, Object>> rows = new TableSelector(currentWikiVersions, Set.of("Name","Title","RowId","Parent"), filter, null).getMapCollection();

JSONArray array = new JSONArray();
for (var row : rows)
{
array.put(new JSONObject(row));
}
var ret = new JSONObject();
ret.put("Version", "26.3");
ret.put("Documents", array);
return ret;
}

@Tool(description = "Return the entire document from the LabKey documentation using the `id` as returned by `searchDocumentation`.")
@RequiresNoPermission
JSONObject retrieveDocument(
ToolContext context,
@ToolParam(description = "Id of the document to return") String id)
{
WikiService service = Objects.requireNonNull(WikiService.get());
Container documentsContainer = ContainerManager.getForPath("/Documentation");
if (null == documentsContainer)
return new JSONObject(Map.of("error","There is not /Documentation project on this server"));

ActionURL wikiBase = new ActionURL("wiki","page",documentsContainer);
var path = Path.parse(id);
var name = path.getName();
var wiki = service.getRenderedWiki(documentsContainer, name);
if (null == wiki)
throw new NotFoundException();

var ret = new JSONObject();
ret.put("Content-Type", "text/html");
ret.put("filename", wiki.name() + ".html");
ret.put("id", "documentation/" + wiki.name());
ret.put("title", wiki.title());
ret.put("source", wikiBase.clone().addParameter("name",wiki.name()).getURIString());
ret.put("contents", wiki.html().toString());
return ret;
}

@Tool(description = "Search the LabKey documentation for documents semantically similar to a natural language query. " +
"Returns matching documents with their content, metadata (title, source URL, content type), and similarity scores.")
@RequiresNoPermission
JSONObject searchDocumentation(
ToolContext context,
@ToolParam(description = "Natural language search query describing what you're looking for") String query,
@ToolParam(required = false, description = "Maximum number of results to return, defaults to 5") String topK)
{
VectorStore vs = McpService.get().getVectorStore();
if (vs == null)
throw new IllegalStateException("Vector store is not available. An embedding model may not be configured.");

int k = 5;
if (isNotBlank(topK))
{
try { k = Math.clamp(Integer.parseInt(topK), 1, 20); }
catch (NumberFormatException ignored) {}
}

SearchRequest request = SearchRequest.builder()
.query(query)
.topK(k)
.build();

List<Document> results = vs.similaritySearch(request);

var docs = results.stream()
.map(doc -> {
var obj = new JSONObject();
obj.put("id", doc.getId());
String text = doc.getText();
if (text != null && text.length() > 2000)
text = text.substring(0, 2000) + "...";
obj.put("content", text);
obj.put("metadata", new JSONObject(doc.getMetadata()));
if (doc.getScore() != null)
obj.put("score", doc.getScore());
return obj;
})
.collect(LabKeyCollectors.toJSONArray());

return new JSONObject(Map.of(
"query", query,
"resultCount", results.size(),
"results", docs
));
}
}
}
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