Submission

README.md

@@ -99,6 +99,12 @@ setx SONARQUBE_TOKEN "paste-your-token"
 # Restart the terminal afterwards
 ```
 
+### Run SonarQube
+```bash
+python remediate_repos.py
+        --token SONARQUBE_TOKEN # If you haven't added a token in the environment
+```
+
 ### Run the Remediator
 ```bash
 python AntiPattern_Remediator/main.py
@@ -122,4 +128,4 @@ Verify JDK 11 and Maven are on `PATH`.
 - **IBM** - For providing technical expertise and computational resources, and mentorship from Dr Amrin Maria Khan and Prof. John McNamara
 - **University College London (UCL)** - For research guidance and academic support, under the supervision of Dr Jens Krinke
 - **LangChain Community** - For the foundational LLM orchestration framework
-- **Ollama Project** - For making LLM deployment accessible and efficient
+- **Ollama Project** - For making LLM deployment accessible and efficient

sonarqube_tool/sonarqube_api.py

@@ -174,9 +174,8 @@ def save_all_issues(self, project_key: str, file_path: str) -> None:
 if __name__ == "__main__":
     api = SonarQubeAPI()
     project_key = "commons-lang"
-    file_path = "src\main\java\org\apache\commons\lang3\BooleanUtils.java"
-    test_file_path = "src/main/java/org/apache/commons/lang3/BooleanUtils.java"
-    issues_file_path = "D:\FILES\IBM-Project-Analysis-Results\common-lang3.9-original\issues.json"
+    file_path = "path/to/java/file" # Testing if SonarQube is working
+    issues_file_path = "path/to/issues.json (post-transformation analysis requirement)"
     rule_key_1 = "java:S2160"
     rule_key_2 = "java:S1117"
     rule_key_3 = "java:S5993"