Adding tests for scm.GitDiff and update notebook so git diff now works

Signed-off-by: John Matthews <jwmatthews@gmail.com>

notebooks/jms_to_smallrye_reactive/03_few_shot_with_analysis_jms-to-reactive-quarkus-00010.ipynb

@@ -165,9 +165,11 @@
     "    ## Solved Example Filename\n",
     "    Filename: \"{solved_example_file_name}\"\n",
     "\n",
-    "    ## Solved Example source code that has been migrated from Java EE to Quarkus\n",
-    "    ```java\n",
-    "    {solved_file_contents}\n",
+    "    ## Solved Example Git Diff \n",
+    "    This diff of the solved example shows what changes we made in past to address a similar problem.\n",
+    "    Please consider this heavily in your response.\n",
+    "    ```diff\n",
+    "    {solved_example_diff}\n",
     "    ```\n",
     "\n",
     "    ## Input file name\n",
@@ -242,15 +244,17 @@
     "cmt_src_path = \"../../samples/sample_repos/cmt\"\n",
     "cmt_diff = GitDiff(cmt_src_path)\n",
     "\n",
+    "# Ensure we checked out the 'quarkus' branch of the CMT repo\n",
+    "cmt_diff.checkout_branch(\"quarkus\")\n",
+    "\n",
     "helloworld_src_path = \"../../samples/sample_repos/helloworld-mdb-quarkus\"\n",
     "helloworld_diff = GitDiff(helloworld_src_path)\n",
     "\n",
     "# We want to be sure the the 'quarkus' branch of both repos has been checked out\n",
     "# so it's available to consult\n",
     "cmt_diff.checkout_branch(\"quarkus\")\n",
     "helloworld_diff.checkout_branch(\"quarkus\")\n",
-    "# Resetting to 'main' as what is currently checked out\n",
-    "cmt_diff.checkout_branch(\"main\")\n",
+    "# Resetting to 'main' for HelloWorld as that represents th initial state of the repo\n",
     "helloworld_diff.checkout_branch(\"main\")\n",
     "\n",
     "# Now we can extract the info we need\n",
@@ -266,12 +270,14 @@
     "\n",
     "cmt_entry = cmt_rule_data[\"incidents\"][0]\n",
     "solved_example_file_name = cmt_report.get_cleaned_file_path(cmt_entry[\"uri\"])\n",
-    "solved_file_contents = cmt_diff.get_file_contents(solved_example_file_name, \"quarkus\")\n",
-    "##\n",
-    "## Todo:  Update so we pass in a diff of what changed\n",
-    "## We do not have the ability to extract a diff working at present\n",
-    "# solved_example_diff = cmt_diff.get_patch_for_file('main', 'quarkus', solved_example_file_name)\n",
-    "##"
+    "# solved_file_contents = cmt_diff.get_file_contents(solved_example_file_name, \"quarkus\")\n",
+    "\n",
+    "start_commit_id = cmt_diff.get_commit_from_branch(\"main\").hexsha\n",
+    "end_commit_id = cmt_diff.get_commit_from_branch(\"quarkus\").hexsha\n",
+    "\n",
+    "solved_example_diff = cmt_diff.get_patch_for_file(\n",
+    "    start_commit_id, end_commit_id, solved_example_file_name\n",
+    ")"
    ]
   },
   {
@@ -290,11 +296,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved template to output/gpt-3.5-turbo-16k/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/template.txt\n",
-      "Saved result to output/gpt-3.5-turbo-16k/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/result.txt\n",
-      "Saved updated java file to output/gpt-3.5-turbo-16k/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/updated_file.java\n",
-      "Saved original java file to output/gpt-3.5-turbo-16k/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/original_file.java\n",
-      "Saved Quarkus version from Git to output/gpt-3.5-turbo-16k/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/quarkus_version_from_git.java\n"
+      "Saved template to output/gpt-4-1106-preview/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/template.txt\n",
+      "Saved result to output/gpt-4-1106-preview/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/result.txt\n",
+      "Saved updated java file to output/gpt-4-1106-preview/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/updated_file.java\n",
+      "Saved original java file to output/gpt-4-1106-preview/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/original_file.java\n",
+      "Saved Quarkus version from Git to output/gpt-4-1106-preview/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/quarkus_version_from_git.java\n"
      ]
     }
    ],
@@ -306,13 +312,13 @@
     "    \"analysis_message\": analysis_message,\n",
     "    \"analysis_lineNumber\": analysis_lineNumber,\n",
     "    \"solved_example_file_name\": solved_example_file_name,\n",
-    "    # \"solved_example_diff\": solved_example_diff\n",
-    "    \"solved_file_contents\": solved_file_contents,\n",
+    "    \"solved_example_diff\": solved_example_diff,\n",
+    "    # \"solved_file_contents\": solved_file_contents,\n",
     "}\n",
     "formatted_prompt = template_with_solved_example_and_analysis.format(**template_args)\n",
     "\n",
-    "model_name = \"gpt-4-1106-preview\"\n",
-    "# model_name=\"gpt-3.5-turbo-16k\"\n",
+    "# model_name = \"gpt-4-1106-preview\"\n",
+    "model_name = \"gpt-3.5-turbo-16k\"\n",
     "\n",
     "llm = ChatOpenAI(temperature=0.1, model_name=model_name)\n",
     "prompt = PromptTemplate.from_template(template_with_solved_example_and_analysis)\n",

notebooks/jms_to_smallrye_reactive/output/gpt-3.5-turbo-16k/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/result.txt

@@ -1,9 +1,8 @@
 ## Reasoning
 1. The issue found from static code analysis is that the `@MessageDriven` annotation is not supported in Quarkus and needs to be replaced with a CDI scope annotation like `@ApplicationScoped`.
-2. In the solved example, the `@MessageDriven` annotation was replaced with `@ApplicationScoped` to make the class a CDI bean.
-3. The `@Incoming` annotation from the `org.eclipse.microprofile.reactive.messaging` package is used to specify the incoming channel for the message-driven bean.
-4. The `Log` class from the `io.quarkus.logging` package is used to log the received message.
-5. The `HelloWorldMDB` class is annotated with `@ApplicationScoped` to make it a CDI bean.
+2. Looking at the solved example, we can see that the `@MessageDriven` annotation was replaced with `@ApplicationScoped`.
+3. We need to update the import statements to use the correct annotations for Quarkus. The import statements for `@MessageDriven`, `@ActivationConfigProperty`, `@Message`, `@MessageListener`, and `@TextMessage` should be removed. Instead, we need to import `org.eclipse.microprofile.reactive.messaging.Incoming` for the `@Incoming` annotation and `io.quarkus.logging.Log` for the logging statement.
+4. The `onMessage` method should be updated to accept a `String` parameter instead of a `Message` parameter. The logging statement should also be updated to use `Log.info` instead of `LOGGER.info`.
 
 ## Updated File
 ```java
@@ -25,16 +24,9 @@
  */
 package org.jboss.as.quickstarts.mdb;
 
-import java.util.logging.Logger;
-import javax.ejb.ActivationConfigProperty;
-import javax.ejb.MessageDriven;
-import javax.jms.JMSException;
-import javax.jms.Message;
-import javax.jms.MessageListener;
-import javax.jms.TextMessage;
-import org.eclipse.microprofile.reactive.messaging.Incoming;
 import io.quarkus.logging.Log;
 import jakarta.enterprise.context.ApplicationScoped;
+import org.eclipse.microprofile.reactive.messaging.Incoming;
 
 /**
  * <p>
@@ -44,26 +36,11 @@ import jakarta.enterprise.context.ApplicationScoped;
  * @author Serge Pagop (spagop@redhat.com)
  */
 @ApplicationScoped
-public class HelloWorldQueueMDB implements MessageListener {
-
-    private static final Logger LOGGER = Logger.getLogger(HelloWorldQueueMDB.class.toString());
+public class HelloWorldQueueMDB {
 
-    /**
-     * @see MessageListener#onMessage(Message)
-     */
     @Incoming("HELLOWORLDMDBQueue")
-    public void onMessage(Message rcvMessage) {
-        TextMessage msg = null;
-        try {
-            if (rcvMessage instanceof TextMessage) {
-                msg = (TextMessage) rcvMessage;
-                Log.info("Received Message from queue: " + msg.getText());
-            } else {
-                LOGGER.warning("Message of wrong type: " + rcvMessage.getClass().getName());
-            }
-        } catch (JMSException e) {
-            throw new RuntimeException(e);
-        }
+    public void onMessage(String msg) {
+        Log.info("Received Message from queue: " + msg);
     }
 }
 ```

notebooks/jms_to_smallrye_reactive/output/gpt-3.5-turbo-16k/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/template.txt

@@ -30,47 +30,62 @@
     ## Solved Example Filename
     Filename: "src/main/java/org/jboss/as/quickstarts/cmt/mdb/HelloWorldMDB.java"
 
-    ## Solved Example source code that has been migrated from Java EE to Quarkus
-    ```java
-    /*
- * JBoss, Home of Professional Open Source
- * Copyright 2015, Red Hat, Inc. and/or its affiliates, and individual
- * contributors by the @authors tag. See the copyright.txt in the
- * distribution for a full listing of individual contributors.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.jboss.as.quickstarts.cmt.mdb;
-
-import org.eclipse.microprofile.reactive.messaging.Incoming;
-
-import io.quarkus.logging.Log;
-import jakarta.enterprise.context.ApplicationScoped;
-
-/**
- * <p>
- * A simple Message Driven Bean that asynchronously receives and processes the messages that are sent to the queue.
- * </p>
- *
- * @author Serge Pagop (spagop@redhat.com)
- *
- */
-@ApplicationScoped
-public class HelloWorldMDB {
-
-    @Incoming("CMTQueue")
-    public void onMessage(String msg) {
-        Log.info("Received Message: " + msg);
-    }
-}
+    ## Solved Example Git Diff 
+    This diff of the solved example shows what changes we made in past to address a similar problem.
+    Please consider this heavily in your response.
+    ```diff
+    @@ -16,14 +16,10 @@
+  */
+ package org.jboss.as.quickstarts.cmt.mdb;
+
+-import java.util.logging.Logger;
++import org.eclipse.microprofile.reactive.messaging.Incoming;
+
+-import javax.ejb.ActivationConfigProperty;
+-import javax.ejb.MessageDriven;
+-import javax.jms.JMSException;
+-import javax.jms.Message;
+-import javax.jms.MessageListener;
+-import javax.jms.TextMessage;
++import io.quarkus.logging.Log;
++import jakarta.enterprise.context.ApplicationScoped;
+
+ /**
+  * <p>
+@@ -33,28 +29,11 @@ import javax.jms.TextMessage;
+  * @author Serge Pagop (spagop@redhat.com)
+  *
+  */
+-@MessageDriven(name = "HelloWorldMDB", activationConfig = {
+-    @ActivationConfigProperty(propertyName = "destinationType", propertyValue = "javax.jms.Queue"),
+-    @ActivationConfigProperty(propertyName = "destination", propertyValue = "queue/CMTQueue"),
+-    @ActivationConfigProperty(propertyName = "acknowledgeMode", propertyValue = "Auto-acknowledge") })
+-public class HelloWorldMDB implements MessageListener {
++@ApplicationScoped
++public class HelloWorldMDB {
+
+-    private static final Logger LOGGER = Logger.getLogger(HelloWorldMDB.class.toString());
+-
+-    /**
+-     * @see MessageListener#onMessage(Message)
+-     */
+-    public void onMessage(Message rcvMessage) {
+-        TextMessage msg = null;
+-        try {
+-            if (rcvMessage instanceof TextMessage) {
+-                msg = (TextMessage) rcvMessage;
+-                LOGGER.info("Received Message: " + msg.getText());
+-            } else {
+-                LOGGER.warning("Message of wrong type: " + rcvMessage.getClass().getName());
+-            }
+-        } catch (JMSException e) {
+-            throw new RuntimeException(e);
+-        }
++    @Incoming("CMTQueue")
++    public void onMessage(String msg) {
++        Log.info("Received Message: " + msg);
+     }
+ }
 
     ```
 

notebooks/jms_to_smallrye_reactive/output/gpt-3.5-turbo-16k/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/updated_file.java

@@ -17,16 +17,9 @@
  */
 package org.jboss.as.quickstarts.mdb;
 
-import java.util.logging.Logger;
-import javax.ejb.ActivationConfigProperty;
-import javax.ejb.MessageDriven;
-import javax.jms.JMSException;
-import javax.jms.Message;
-import javax.jms.MessageListener;
-import javax.jms.TextMessage;
-import org.eclipse.microprofile.reactive.messaging.Incoming;
 import io.quarkus.logging.Log;
 import jakarta.enterprise.context.ApplicationScoped;
+import org.eclipse.microprofile.reactive.messaging.Incoming;
 
 /**
  * <p>
@@ -36,25 +29,10 @@
  * @author Serge Pagop (spagop@redhat.com)
  */
 @ApplicationScoped
-public class HelloWorldQueueMDB implements MessageListener {
-
-    private static final Logger LOGGER = Logger.getLogger(HelloWorldQueueMDB.class.toString());
+public class HelloWorldQueueMDB {
 
-    /**
-     * @see MessageListener#onMessage(Message)
-     */
     @Incoming("HELLOWORLDMDBQueue")
-    public void onMessage(Message rcvMessage) {
-        TextMessage msg = null;
-        try {
-            if (rcvMessage instanceof TextMessage) {
-                msg = (TextMessage) rcvMessage;
-                Log.info("Received Message from queue: " + msg.getText());
-            } else {
-                LOGGER.warning("Message of wrong type: " + rcvMessage.getClass().getName());
-            }
-        } catch (JMSException e) {
-            throw new RuntimeException(e);
-        }
+    public void onMessage(String msg) {
+        Log.info("Received Message from queue: " + msg);
     }
 }

notebooks/jms_to_smallrye_reactive/output/gpt-4-1106-preview/helloworldmdb/custom-ruleset/jms-to-reactive-quarkus-00010/few_shot/result.txt

@@ -1,17 +1,21 @@
 ## Reasoning
 
-To migrate the Java EE Message Driven Bean (MDB) to Quarkus, we need to address the issue identified by the static code analysis. The `@MessageDriven` annotation is not supported in Quarkus, and we need to use Contexts and Dependency Injection (CDI) instead. Here are the steps we will take:
+To migrate the Java EE Message Driven Bean (MDB) to Quarkus, we need to address the issue identified by the static code analysis, which is the use of `@MessageDriven` annotation. Quarkus does not support EJBs, and therefore we need to use CDI (Contexts and Dependency Injection) beans instead.
+
+Here are the steps we will follow:
 
 1. Replace the `@MessageDriven` annotation with `@ApplicationScoped` to define the bean as a CDI managed bean with application scope.
-2. Use MicroProfile Reactive Messaging to handle the JMS messages. This is done by using the `@Incoming` annotation to mark the method that will receive the messages.
-3. Replace the Java Util Logging with Quarkus logging (`io.quarkus.logging.Log`) for consistency with Quarkus standards.
-4. Remove the `MessageListener` interface and its `onMessage` method signature, as it is specific to Java EE MDBs and not required in Quarkus.
-5. The `ActivationConfigProperty` annotations are no longer needed because the configuration will be handled differently in Quarkus, typically through the `application.properties` file.
-6. Update the `pom.xml` file to include the Quarkus Reactive Messaging dependency if it's not already present.
+2. Remove the `MessageListener` interface and its `onMessage` method signature, as Quarkus uses the MicroProfile Reactive Messaging API for handling messages.
+3. Use the `@Incoming` annotation to mark the method that will be invoked for each message received on the specified channel.
+4. Replace the `Logger` from `java.util.logging` with `io.quarkus.logging.Log` which is the preferred logging framework in Quarkus.
+5. Remove the `ActivationConfigProperty` annotations as they are specific to EJBs and not needed in Quarkus.
+6. Update the `pom.xml` to include the Quarkus Reactive Messaging dependency if not already present.
+7. Ensure that the application properties or configuration files are updated to define the connection to the message broker and the channel configuration.
 
-The solved example shows how the MDB is converted to a CDI bean and uses MicroProfile Reactive Messaging to consume messages. We will follow a similar pattern for the input file.
+Now, let's proceed with the migration.
 
 ## Updated File
+
 ```java
 package org.jboss.as.quickstarts.mdb;
 
@@ -21,7 +25,7 @@ import org.eclipse.microprofile.reactive.messaging.Incoming;
 
 /**
  * <p>
- * A simple bean that asynchronously receives and processes the messages that are sent to the queue.
+ * A simple bean that asynchronously receives and processes the messages that are sent to the queue using Quarkus.
  * </p>
  *
  * @author Serge Pagop (spagop@redhat.com)
@@ -30,20 +34,29 @@ import org.eclipse.microprofile.reactive.messaging.Incoming;
 public class HelloWorldQueueMDB {
 
     @Incoming("HELLOWORLDMDBQueue")
-    public void receiveMessage(String messageText) {
-        Log.info("Received Message from queue: " + messageText);
+    public void onMessage(String msg) {
+        Log.info("Received Message from queue: " + msg);
     }
 }
 ```
 
-### Notes on pom.xml and Configuration
-- Ensure that the `quarkus-smallrye-reactive-messaging` dependency is included in the `pom.xml` file.
-- The `application.properties` file should contain the configuration for the message queue, similar to the `ActivationConfigProperty` values from the original Java EE code. For example:
-  ```
-  mp.messaging.incoming.HELLOWORLDMDBQueue.connector=smallrye-jms
-  mp.messaging.incoming.HELLOWORLDMDBQueue.destination=queue/HELLOWORLDMDBQueue
-  ```
-- The `connector` property would depend on the specific JMS connector being used in the Quarkus application.
-- The `destination` property should match the JNDI name of the JMS queue.
-
-By following these steps and making the necessary updates, the Java EE MDB should be successfully migrated to a Quarkus application.
+### Additional Notes:
+
+- The `@Incoming` annotation's value should match the name of the channel configured in the `application.properties` file for the incoming messages from the queue.
+- The `pom.xml` file should include the `quarkus-smallrye-reactive-messaging` dependency to enable MicroProfile Reactive Messaging:
+
+```xml
+<dependency>
+    <groupId>io.quarkus</groupId>
+    <artifactId>quarkus-smallrye-reactive-messaging</artifactId>
+</dependency>
+```
+
+- The `application.properties` file should be updated to include the configuration for the message broker and the channel, for example:
+
+```properties
+mp.messaging.incoming.HELLOWORLDMDBQueue.connector=smallrye-jms
+mp.messaging.incoming.HELLOWORLDMDBQueue.destination=queue/HELLOWORLDMDBQueue
+```
+
+- Ensure that the message broker is properly configured and accessible from the Quarkus application.