Update MCP Tools Handling and Fix Data Loss Bugs

org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/SynapseLanguageService.java

@@ -802,9 +802,13 @@ public CompletableFuture<List<List<Object>>> getInputOutputMappings(MappingsGenR
     @Override
     public CompletableFuture<MCPToolResponse> getMCPTools(MCPToolRequest param) {
 
+        log.log(Level.INFO, "Fetching MCP tools for connection: {}", param.connectionName);
         Connections connections = ConnectionFinder.findConnections(projectUri, Constant.LOWERCASE_AI, connectorHolder, isLegacyProject).getLeft();
         AIConnectorHandler aiConnectorHandler = new AIConnectorHandler(mediatorHandler, projectUri);
-        return CompletableFuture.supplyAsync(() -> aiConnectorHandler.fetchMcpTools(connections.getConnections(), param.connectionName));
+        log.log(Level.INFO, "Initialized AI connector handler for MCP tools fetch");
+        return CompletableFuture.supplyAsync(
+                () -> aiConnectorHandler.fetchMcpTools(param.documentUri, param.range, connections.getConnections(),
+                        param.connectionName));
     }
 
     public String getProjectUri() {

org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/customservice/synapse/mediatorService/pojo/MCPToolRequest.java

@@ -14,9 +14,11 @@
 
 package org.eclipse.lemminx.customservice.synapse.mediatorService.pojo;
 
-import java.util.Map;
+import org.eclipse.lsp4j.Range;
 
 public class MCPToolRequest {
 
+    public String documentUri;
+    public Range range;
     public String connectionName;
 }

org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/customservice/synapse/mediatorService/pojo/MCPToolResponse.java

@@ -14,12 +14,13 @@
 
 package org.eclipse.lemminx.customservice.synapse.mediatorService.pojo;
 
-import org.eclipse.lsp4j.Range;
-
 import java.util.Map;
+import java.util.List;
 
 public class MCPToolResponse {
 
     public Map<String, String> tools;
     public String error;
+    // Names of tools already present in the document for the requested connection
+    public List<String> selectedTools;
 }

org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/customservice/synapse/syntaxTree/factory/mediators/ai/AIAgentConnectorFactory.java

@@ -20,6 +20,7 @@
 import org.eclipse.lemminx.customservice.synapse.syntaxTree.pojo.connector.ai.AIConnector;
 import org.eclipse.lemminx.customservice.synapse.syntaxTree.pojo.connector.ai.AgentTool;
 import org.eclipse.lemminx.customservice.synapse.syntaxTree.pojo.connector.ai.AgentTools;
+import org.eclipse.lemminx.customservice.synapse.syntaxTree.pojo.connector.ai.MCPConnections;
 import org.eclipse.lemminx.customservice.synapse.syntaxTree.pojo.mediator.Mediator;
 import org.eclipse.lemminx.customservice.synapse.syntaxTree.pojo.template.Template;
 import org.eclipse.lemminx.customservice.synapse.utils.ConfigFinder;
@@ -52,10 +53,49 @@ protected Mediator createSpecificMediator(DOMElement element) {
             ((AIAgent) aiAgent).setAgentID(Utils.getInlineString(agentIDNode.getFirstChild()));
         }
 
+        populateMCPConnections((AIAgent) aiAgent, element);
         populateTools((AIAgent) aiAgent, element);
         return aiAgent;
     }
 
+    /**
+     * Extracts MCP connection configuration details from the given DOM element
+     * and populates the provided {@link AIAgent} instance.
+     *
+     * <p>This method searches for a child element named {@code <mcpConnections>}
+     * inside the provided element. If found, it iterates through its
+     * child nodes and collects the values of all {@code <mcpConfigKey>} elements.
+     * Non-null and non-blank values are added to a list of MCP connection keys.</p>
+     *
+     * <p>The collected connection keys are then set into a {@link MCPConnections}
+     * object, which is attached to the given {@link AIAgent}.</p>
+     *
+     * @param aiAgent the {@link AIAgent} instance to populate with MCP connection data
+     * @param element the DOM element that potentially contains the
+     *                {@code <mcpConnections>} configuration
+     */
+    private void populateMCPConnections(AIAgent aiAgent, DOMElement element) {
+
+        DOMNode mcpConnectionsElement = Utils.getChildNodeByName(element, Constant.MCP_CONNECTIONS);
+        if (mcpConnectionsElement != null) {
+            LOGGER.log(Level.INFO, "Processing MCP connections for AI agent");
+            MCPConnections mcpConnectionsObj = new MCPConnections();
+            List<DOMNode> mcpChildren = mcpConnectionsElement.getChildren();
+            List<String> mcpConnectionList = new java.util.ArrayList<>();
+            for (DOMNode child : mcpChildren) {
+                if (child instanceof DOMElement && Constant.MCP_CONFIG_KEY.equals(child.getNodeName())) {
+                    String value = Utils.getInlineString(child.getFirstChild());
+                    if (value != null && !value.isBlank()) {
+                        mcpConnectionList.add(value);
+                    }
+                }
+            }
+            mcpConnectionsObj.setMcpConnections(mcpConnectionList);
+            aiAgent.setMcpConnections(mcpConnectionsObj);
+            LOGGER.log(Level.INFO, "MCP connections configured for AI agent with {} connections", mcpConnectionList.size());
+        }
+    }
+
     private void populateTools(AIAgent aiAgent, DOMElement element) {
 
         DOMNode toolsElement = Utils.getChildNodeByName(element, Constant.TOOLS);

org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/customservice/synapse/syntaxTree/pojo/connector/ai/AIAgent.java

@@ -17,6 +17,7 @@
 public class AIAgent extends AIConnector {
 
     private String agentID;
+    private MCPConnections mcpConnections;
     private AgentTools tools;
 
     public String getAgentID() {
@@ -38,4 +39,14 @@ public void setTools(AgentTools tools) {
 
         this.tools = tools;
     }
+
+    public MCPConnections getMcpConnections() {
+
+        return mcpConnections;
+    }
+
+    public void setMcpConnections(MCPConnections mcpConnections) {
+
+        this.mcpConnections = mcpConnections;
+    }
 }

org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/customservice/synapse/syntaxTree/pojo/connector/ai/MCPConnections.java

@@ -0,0 +1,45 @@
+/*
+ * Copyright (c) 2026, WSO2 LLC. (http://www.wso2.com).
+ *
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v2.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v20.html
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ *
+ * Contributors:
+ *     WSO2 LLC - support for WSO2 Micro Integrator Configuration
+ */
+
+package org.eclipse.lemminx.customservice.synapse.syntaxTree.pojo.connector.ai;
+
+import org.eclipse.lemminx.customservice.synapse.syntaxTree.pojo.STNode;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class MCPConnections extends STNode {
+
+    private List<String> mcpConnections;
+
+    public MCPConnections() {
+
+        this.mcpConnections = new ArrayList<>();
+    }
+
+    public List<String> getMcpConnections() {
+
+        return mcpConnections;
+    }
+
+    public void setMcpConnections(List<String> mcpConnections) {
+
+        this.mcpConnections = mcpConnections;
+    }
+
+    public void addMcpConnection(String mcpConnection) {
+
+        this.mcpConnections.add(mcpConnection);
+    }
+}

org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/customservice/synapse/utils/Constant.java

@@ -604,6 +604,8 @@ public class Constant {
     public static final String TOOLS = "tools";
     public static final String TOOL = "tool";
     public static final String MCP_TOOLS = "mcpTools";
+    public static final String MCP_CONFIG_KEY = "mcpConfigKey";
+    public static final String MCP_CONNECTIONS = "mcpConnections";
     public static final String AI_AGENT_TAG = "ai.agent";
     public static final String ATTRIBUTE_GROUP = "attributeGroup";
     public static final String CURRENT_VALUE = "currentValue";

org.eclipse.lemminx/src/main/java/org/eclipse/lemminx/customservice/synapse/utils/Utils.java

@@ -31,6 +31,7 @@
 import org.apache.maven.shared.invoker.Invoker;
 import org.apache.maven.shared.invoker.InvocationResult;
 import org.apache.maven.shared.invoker.InvocationRequest;
+import org.eclipse.lemminx.commons.BadLocationException;
 import org.eclipse.lemminx.commons.TextDocument;
 import org.eclipse.lemminx.customservice.synapse.connectors.ConnectorHolder;
 import org.eclipse.lemminx.customservice.synapse.connectors.entity.Connector;
@@ -47,6 +48,7 @@
 import org.eclipse.lemminx.dom.DOMParser;
 import org.eclipse.lemminx.uriresolver.URIResolverExtensionManager;
 import org.eclipse.lsp4j.InitializeParams;
+import org.eclipse.lsp4j.Position;
 import org.w3c.dom.Node;
 
 import java.io.BufferedInputStream;
@@ -221,6 +223,33 @@ public static DOMDocument getDOMDocument(File file) throws IOException {
         return domDocument;
     }
 
+    /**
+     * Returns the {@link DOMNode} located at the given LSP {@link Position} in the document identified
+     * by {@code documentUri}.
+     *
+     * @param documentUri the document URI as a string
+     * @param position the position inside the document
+     * @return the {@link DOMNode} at the given position, or {@code null} if not found
+     * @throws IOException if an I/O error occurs while reading or parsing the document
+     * @throws BadLocationException if the provided {@code position} is invalid for the document
+     */
+    public static DOMNode getDOMNode(String documentUri, Position position)
+            throws IOException, BadLocationException {
+
+        if (StringUtils.isEmpty(documentUri) || position == null) {
+            logger.log(Level.INFO, "Invalid input: documentUri is empty or position is null");
+            return null;
+        }
+        logger.log(Level.INFO,
+                String.format("Retrieving DOM node at position [%d:%d] in document: %s", position.getLine(),
+                        position.getCharacter(), documentUri));
+        DOMDocument document = Utils.getDOMDocumentFromPath(getAbsolutePath(documentUri));
+        int offset = document.offsetAt(position);
+        DOMNode node = document.findNodeAt(offset);
+        logger.log(Level.INFO, "Found DOM node of type '%s'", node != null ? node.getNodeName() : "null");
+        return node;
+    }
+
     /**
      * Get the DOM document from the given xml content
      *
@@ -778,6 +807,8 @@ public static String getAbsolutePath(String path) {
             try {
                 return Paths.get(new URI(path)).toAbsolutePath().toString();
             } catch (URISyntaxException e) {
+                logger.log(Level.SEVERE,
+                        String.format("Failed to convert URI to absolute path: %s", path), e);
             }
         }
         return path;

org.eclipse.lemminx/src/main/resources/org/eclipse/lemminx/mediators/440/templates/AIConnector.mustache

@@ -5,13 +5,16 @@
         {{/connections}}
     </connections>
     {{#supportTools}}<mcpConnections>
+        {{#mcpConnections}}
+        <mcpConfigKey>{{.}}</mcpConfigKey>
+        {{/mcpConnections}}
     </mcpConnections>{{/supportTools}}
     {{#parameters}}
     <{{{name}}} {{#value}}{{#namespaces}} xmlns:{{{prefix}}}="{{{uri}}}"{{/namespaces}}>{{#isCDATA}}<![CDATA[{{{value}}}]]>{{/isCDATA}}{{^isCDATA}}{{value}}{{/isCDATA}}{{/value}}</{{{name}}}>
     {{/parameters}}
     {{#supportTools}}<tools>
         {{#tools}}
-        <tool name="{{name}}" template="{{template}}" resultExpression="{{resultExpression}}" description="{{description}}"/>
+        <tool name="{{name}}" {{#isMCP}}type="mcp" mcpConnection="{{mcpConnection}}"{{/isMCP}}{{^isMCP}}template="{{template}}" resultExpression="{{resultExpression}}"{{/isMCP}} description="{{description}}"/>
         {{/tools}}
     </tools>{{/supportTools}}
 </{{tag}}>

org.eclipse.lemminx/src/main/resources/org/eclipse/lemminx/schemas/440/mediators/ai/aiAgent.xsd

@@ -38,7 +38,7 @@
                 <xs:element name="mcpConnections">
                     <xs:complexType>
                         <xs:sequence>
-                            <xs:element name="mcpConfigKey" type="xs:string" maxOccurs="unbounded"/>
+                            <xs:element name="mcpConfigKey" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
                         </xs:sequence>
                     </xs:complexType>
                 </xs:element>