From 42898080d785fbeb58e9f3b9af0f9259d1dabdcb Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Sun, 3 Aug 2025 23:23:55 +0800
Subject: [PATCH 01/55] Add IssueRequest model to handle issue data in API

---
 prometheus/app/api/issue.py                | 79 +---------------------
 prometheus/app/models/__init__.py          |  0
 prometheus/app/models/requests/__init__.py |  0
 prometheus/app/models/requests/issue.py    | 77 +++++++++++++++++++++
 prometheus/app/models/response/__init__.py |  0
 5 files changed, 78 insertions(+), 78 deletions(-)
 create mode 100644 prometheus/app/models/__init__.py
 create mode 100644 prometheus/app/models/requests/__init__.py
 create mode 100644 prometheus/app/models/requests/issue.py
 create mode 100644 prometheus/app/models/response/__init__.py

diff --git a/prometheus/app/api/issue.py b/prometheus/app/api/issue.py
index 19963fb9..00fd8b05 100644
--- a/prometheus/app/api/issue.py
+++ b/prometheus/app/api/issue.py
@@ -1,87 +1,10 @@
-from typing import Mapping, Optional, Sequence
-
 from fastapi import APIRouter, HTTPException, Request
-from litellm import Field
-from pydantic import BaseModel
 
-from prometheus.lang_graph.graphs.issue_state import IssueType
+from prometheus.app.models.requests.issue import IssueRequest
 
 router = APIRouter()
 
 
-class IssueRequest(BaseModel):
-    issue_number: int = Field(description="The number of the issue", examples=[42])
-    issue_title: str = Field(
-        description="The title of the issue", examples=["There is a memory leak"]
-    )
-    issue_body: str = Field(
-        description="The description of the issue", examples=["foo/bar.c is causing a memory leak"]
-    )
-    issue_comments: Optional[Sequence[Mapping[str, str]]] = Field(
-        default=None,
-        description="Comments on the issue",
-        examples=[
-            [
-                {"username": "user1", "comment": "I've experienced this issue as well."},
-                {
-                    "username": "user2",
-                    "comment": "A potential fix is to adjust the memory settings.",
-                },
-            ]
-        ],
-    )
-    issue_type: IssueType = Field(
-        default=IssueType.AUTO,
-        description="The type of the issue, set to auto if you do not know",
-        examples=[IssueType.AUTO],
-    )
-    run_build: Optional[bool] = Field(
-        default=False,
-        description="When editing the code, whenver we should run the build to verify the fix",
-        examples=[False],
-    )
-    run_existing_test: Optional[bool] = Field(
-        default=False,
-        description="When editing the code, whenver we should run the existing test to verify the fix",
-        examples=[False],
-    )
-    number_of_candidate_patch: Optional[int] = Field(
-        default=4,
-        description="When the patch is not verfied (through build or test), number of candidate patches we generate to select the best one",
-        examples=[4],
-    )
-    dockerfile_content: Optional[str] = Field(
-        default=None,
-        description="Specify the containerized environment with dockerfile content",
-        examples=["FROM python:3.11\nWORKDIR /app\nCOPY . /app"],
-    )
-    image_name: Optional[str] = Field(
-        default=None,
-        description="Specify the containerized environment with image name that should be pulled from dockerhub",
-        examples=["python:3.11-slim"],
-    )
-    workdir: Optional[str] = Field(
-        default=None,
-        description="If you specified the container environment, you must also specify the workdir",
-        examples=["/app"],
-    )
-    build_commands: Optional[Sequence[str]] = Field(
-        default=None,
-        description="If you specified dockerfile_content and run_build is True, you must also specify the build commands.",
-        examples=[["pip install -r requirements.txt", "python -m build"]],
-    )
-    test_commands: Optional[Sequence[str]] = Field(
-        default=None,
-        description="If you specified dockerfile_content and run_test is True, you must also specify the test commands.",
-        examples=[["pytest ."]],
-    )
-    push_to_remote: Optional[bool] = Field(
-        default=False,
-        description="When editing the code, whenver we should push the changes to a remote branch",
-        examples=[True],
-    )
-
-
 @router.post(
     "/answer/",
     summary="Process and generate a response for an issue",
diff --git a/prometheus/app/models/__init__.py b/prometheus/app/models/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/prometheus/app/models/requests/__init__.py b/prometheus/app/models/requests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/prometheus/app/models/requests/issue.py b/prometheus/app/models/requests/issue.py
new file mode 100644
index 00000000..52842775
--- /dev/null
+++ b/prometheus/app/models/requests/issue.py
@@ -0,0 +1,77 @@
+from pydantic import BaseModel, Field
+from typing import Mapping, Optional, Sequence
+
+from prometheus.lang_graph.graphs.issue_state import IssueType
+
+
+class IssueRequest(BaseModel):
+    issue_number: int = Field(description="The number of the issue", examples=[42])
+    issue_title: str = Field(
+        description="The title of the issue", examples=["There is a memory leak"]
+    )
+    issue_body: str = Field(
+        description="The description of the issue", examples=["foo/bar.c is causing a memory leak"]
+    )
+    issue_comments: Optional[Sequence[Mapping[str, str]]] = Field(
+        default=None,
+        description="Comments on the issue",
+        examples=[
+            [
+                {"username": "user1", "comment": "I've experienced this issue as well."},
+                {
+                    "username": "user2",
+                    "comment": "A potential fix is to adjust the memory settings.",
+                },
+            ]
+        ],
+    )
+    issue_type: IssueType = Field(
+        default=IssueType.AUTO,
+        description="The type of the issue, set to auto if you do not know",
+        examples=[IssueType.AUTO],
+    )
+    run_build: Optional[bool] = Field(
+        default=False,
+        description="When editing the code, whenver we should run the build to verify the fix",
+        examples=[False],
+    )
+    run_existing_test: Optional[bool] = Field(
+        default=False,
+        description="When editing the code, whenver we should run the existing test to verify the fix",
+        examples=[False],
+    )
+    number_of_candidate_patch: Optional[int] = Field(
+        default=4,
+        description="When the patch is not verfied (through build or test), number of candidate patches we generate to select the best one",
+        examples=[4],
+    )
+    dockerfile_content: Optional[str] = Field(
+        default=None,
+        description="Specify the containerized environment with dockerfile content",
+        examples=["FROM python:3.11\nWORKDIR /app\nCOPY . /app"],
+    )
+    image_name: Optional[str] = Field(
+        default=None,
+        description="Specify the containerized environment with image name that should be pulled from dockerhub",
+        examples=["python:3.11-slim"],
+    )
+    workdir: Optional[str] = Field(
+        default=None,
+        description="If you specified the container environment, you must also specify the workdir",
+        examples=["/app"],
+    )
+    build_commands: Optional[Sequence[str]] = Field(
+        default=None,
+        description="If you specified dockerfile_content and run_build is True, you must also specify the build commands.",
+        examples=[["pip install -r requirements.txt", "python -m build"]],
+    )
+    test_commands: Optional[Sequence[str]] = Field(
+        default=None,
+        description="If you specified dockerfile_content and run_test is True, you must also specify the test commands.",
+        examples=[["pytest ."]],
+    )
+    push_to_remote: Optional[bool] = Field(
+        default=False,
+        description="When editing the code, whenver we should push the changes to a remote branch",
+        examples=[True],
+    )
\ No newline at end of file
diff --git a/prometheus/app/models/response/__init__.py b/prometheus/app/models/response/__init__.py
new file mode 100644
index 00000000..e69de29b

From c83f10f1e8ea2e77488da87646fb439d39d2f37b Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Sun, 3 Aug 2025 23:24:21 +0800
Subject: [PATCH 02/55] Fix formatting in issue.py by adding missing newline at
 end of file

---
 prometheus/app/models/requests/issue.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/prometheus/app/models/requests/issue.py b/prometheus/app/models/requests/issue.py
index 52842775..f0d1f2b7 100644
--- a/prometheus/app/models/requests/issue.py
+++ b/prometheus/app/models/requests/issue.py
@@ -1,6 +1,7 @@
-from pydantic import BaseModel, Field
 from typing import Mapping, Optional, Sequence
 
+from pydantic import BaseModel, Field
+
 from prometheus.lang_graph.graphs.issue_state import IssueType
 
 
@@ -74,4 +75,4 @@ class IssueRequest(BaseModel):
         default=False,
         description="When editing the code, whenver we should push the changes to a remote branch",
         examples=[True],
-    )
\ No newline at end of file
+    )

From 1c5a2745fa920b82e039cb97ee9abd09de9b6fb8 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Sun, 3 Aug 2025 23:27:00 +0800
Subject: [PATCH 03/55] Remove upload_local_repository endpoint from
 repository.py

---
 prometheus/app/api/repository.py | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/prometheus/app/api/repository.py b/prometheus/app/api/repository.py
index 65655cf4..9f4af412 100644
--- a/prometheus/app/api/repository.py
+++ b/prometheus/app/api/repository.py
@@ -1,35 +1,9 @@
-from pathlib import Path
-
 import git
 from fastapi import APIRouter, HTTPException, Request
 
 router = APIRouter()
 
 
-@router.get(
-    "/local/",
-    description="""
-    Upload a local codebase to Prometheus.
-    """,
-    responses={
-        404: {"description": "Local repository not found"},
-        200: {"description": "Repository uploaded successfully"},
-    },
-)
-def upload_local_repository(local_repository: str, request: Request):
-    local_path = Path(local_repository)
-
-    if not local_path.exists():
-        raise HTTPException(
-            status_code=404,
-            detail=f"Local repository not found at path: {local_repository}",
-        )
-
-    request.app.state.service_coordinator.upload_local_repository(local_path)
-
-    return {"message": "Repository uploaded successfully"}
-
-
 @router.get(
     "/github/",
     description="""

From 1256c33fb9201a70e442b5bdae50685cb8509d2d Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 00:43:14 +0800
Subject: [PATCH 04/55] Add Settings class for configuration management using
 Pydantic

---
 prometheus/configuration/config.py | 53 ++++++++++++++++++++++++++++--
 1 file changed, 51 insertions(+), 2 deletions(-)

diff --git a/prometheus/configuration/config.py b/prometheus/configuration/config.py
index ea0b2860..ef3cce2e 100644
--- a/prometheus/configuration/config.py
+++ b/prometheus/configuration/config.py
@@ -1,3 +1,52 @@
-from dynaconf import Dynaconf
+from typing import Literal, List
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
-settings = Dynaconf(envvar_prefix="PROMETHEUS", load_dotenv=True)
+
+class Settings(BaseSettings):
+    model_config = SettingsConfigDict(env_file='.env',
+                                      env_file_encoding='utf-8',
+                                      env_prefix='PROMETHEUS_'
+                                      )
+    # General settings
+    version: str = "1.1"
+    BASE_URL: str = f"/api/v{version}"
+    ENVIRONMENT: Literal["local", "production"]
+    BACKEND_CORS_ORIGINS: List[str]
+    PROJECT_NAME: str = "Prometheus"
+
+    # Logging
+    LOGGING_LEVEL: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
+
+    # Neo4j
+    NEO4J_URI: str
+    NEO4J_USERNAME: str
+    NEO4J_PASSWORD: str
+    NEO4J_BATCH_SIZE: int
+
+    # Knowledge Graph
+    WORKING_DIRECTORY: str
+    KNOWLEDGE_GRAPH_MAX_AST_DEPTH: int
+    KNOWLEDGE_GRAPH_CHUNK_SIZE: int
+    KNOWLEDGE_GRAPH_CHUNK_OVERLAP: int
+    MAX_TOKEN_PER_NEO4J_RESULT: int
+
+    # LLM models
+    ADVANCED_MODEL: str
+    BASE_MODEL: str
+
+    # API Keys
+    ANTHROPIC_API_KEY: str
+    GEMINI_API_KEY: str
+    OPENAI_FORMAT_BASE_URL: str
+    OPENAI_API_KEY: str
+
+    # Model parameters
+    MAX_INPUT_TOKENS: int
+    TEMPERATURE: float
+    MAX_OUTPUT_TOKENS: int
+
+    # Database
+    DATABASE_URL: str
+
+
+settings = Settings()

From 202c28c0cd6ecd69788243b6fae932050f83119b Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 00:43:38 +0800
Subject: [PATCH 05/55] Refactor config.py for improved formatting and
 readability

---
 prometheus/configuration/config.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/prometheus/configuration/config.py b/prometheus/configuration/config.py
index ef3cce2e..11b7432c 100644
--- a/prometheus/configuration/config.py
+++ b/prometheus/configuration/config.py
@@ -1,12 +1,12 @@
-from typing import Literal, List
+from typing import List, Literal
+
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
 class Settings(BaseSettings):
-    model_config = SettingsConfigDict(env_file='.env',
-                                      env_file_encoding='utf-8',
-                                      env_prefix='PROMETHEUS_'
-                                      )
+    model_config = SettingsConfigDict(
+        env_file=".env", env_file_encoding="utf-8", env_prefix="PROMETHEUS_"
+    )
     # General settings
     version: str = "1.1"
     BASE_URL: str = f"/api/v{version}"

From 01b6530851beba1ce576ed34465bec2fb469eb73 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 00:59:12 +0800
Subject: [PATCH 06/55] Implement BaseService class and refactor service
 classes to inherit from it

---
 prometheus/app/services/base_service.py       |  11 ++
 prometheus/app/services/issue_service.py      | 140 +++++++++++-------
 .../app/services/knowledge_graph_service.py   |   7 +-
 prometheus/app/services/llm_service.py        |   3 +-
 prometheus/app/services/neo4j_service.py      |   4 +-
 prometheus/app/services/repository_service.py |   7 +-
 6 files changed, 116 insertions(+), 56 deletions(-)
 create mode 100644 prometheus/app/services/base_service.py

diff --git a/prometheus/app/services/base_service.py b/prometheus/app/services/base_service.py
new file mode 100644
index 00000000..9b55a597
--- /dev/null
+++ b/prometheus/app/services/base_service.py
@@ -0,0 +1,11 @@
+class BaseService:
+    """
+    Base class for all services in the Prometheus application.
+    """
+
+    def close(self):
+        """
+        Close the service and release any resources.
+        This method should be overridden by subclasses to implement specific cleanup logic.
+        """
+        pass
diff --git a/prometheus/app/services/issue_service.py b/prometheus/app/services/issue_service.py
index cebf7a87..924f223c 100644
--- a/prometheus/app/services/issue_service.py
+++ b/prometheus/app/services/issue_service.py
@@ -1,5 +1,10 @@
+import logging
+import traceback
+from datetime import datetime
+from pathlib import Path
 from typing import Mapping, Optional, Sequence
 
+from prometheus.app.services.base_service import BaseService
 from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
 from prometheus.app.services.llm_service import LLMService
 from prometheus.app.services.neo4j_service import Neo4jService
@@ -10,7 +15,7 @@
 from prometheus.lang_graph.graphs.issue_state import IssueType
 
 
-class IssueService:
+class IssueService(BaseService):
     def __init__(
         self,
         kg_service: KnowledgeGraphService,
@@ -18,15 +23,20 @@ def __init__(
         neo4j_service: Neo4jService,
         llm_service: LLMService,
         max_token_per_neo4j_result: int,
+        working_directory: Path,
     ):
         self.kg_service = kg_service
         self.repository_service = repository_service
         self.neo4j_service = neo4j_service
         self.llm_service = llm_service
         self.max_token_per_neo4j_result = max_token_per_neo4j_result
+        self.working_directory = working_directory
+        self.answer_issue_log_dir = self.working_directory / "answer_issue_logs"
+        self.answer_issue_log_dir.mkdir(parents=True, exist_ok=True)
 
     def answer_issue(
         self,
+        issue_number: int,
         issue_title: str,
         issue_body: str,
         issue_comments: Sequence[Mapping[str, str]],
@@ -39,11 +49,13 @@ def answer_issue(
         workdir: Optional[str] = None,
         build_commands: Optional[Sequence[str]] = None,
         test_commands: Optional[Sequence[str]] = None,
+        push_to_remote: Optional[bool] = None,
     ):
         """
         Processes an issue, generates patches if needed, runs optional builds and tests, and returning the results.
 
         Args:
+            issue_number (int): The number of the issue.
             issue_title (str): The title of the issue.
             issue_body (str): The body of the issue.
             issue_comments (Sequence[Mapping[str, str]]): Comments on the issue.
@@ -56,6 +68,7 @@ def answer_issue(
             workdir (Optional[str]): Working directory for the container.
             build_commands (Optional[Sequence[str]]): Commands to build the project.
             test_commands (Optional[Sequence[str]]): Commands to test the project.
+            push_to_remote (Optional[bool]): Whether to push changes to a remote branch.
         Returns:
             Tuple containing:
                 - edit_patch (str): The generated patch for the issue.
@@ -64,58 +77,81 @@ def answer_issue(
                 - passed_existing_test (bool): Whether the existing tests passed.
                 - issue_response (str): Response generated for the issue.
         """
-        # Construct the working directory
-        if dockerfile_content or image_name:
-            container = UserDefinedContainer(
-                self.kg_service.kg.get_local_path(),
-                workdir,
-                build_commands,
-                test_commands,
-                dockerfile_content,
-                image_name,
-            )
-        else:
-            container = GeneralContainer(self.kg_service.kg.get_local_path())
-        # Initialize the issue graph with the necessary services and parameters
-        issue_graph = IssueGraph(
-            advanced_model=self.llm_service.advanced_model,
-            base_model=self.llm_service.base_model,
-            kg=self.kg_service.kg,
-            git_repo=self.repository_service.git_repo,
-            neo4j_driver=self.neo4j_service.neo4j_driver,
-            max_token_per_neo4j_result=self.max_token_per_neo4j_result,
-            container=container,
-            build_commands=build_commands,
-            test_commands=test_commands,
-        )
-        # Invoke the issue graph with the provided parameters
-        output_state = issue_graph.invoke(
-            issue_title,
-            issue_body,
-            issue_comments,
-            issue_type,
-            run_build,
-            run_existing_test,
-            number_of_candidate_patch,
-        )
+        logger = logging.getLogger("prometheus")
+        formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+        timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
+        log_file = self.answer_issue_log_dir / f"{timestamp}.log"
+        file_handler = logging.FileHandler(log_file)
+        file_handler.setFormatter(formatter)
+        logger.addHandler(file_handler)
 
-        if output_state["issue_type"] == IssueType.BUG:
-            return (
-                output_state["edit_patch"],
-                output_state["passed_reproducing_test"],
-                output_state["passed_build"],
-                output_state["passed_existing_test"],
-                output_state["issue_response"],
+        try:
+            # Construct the working directory
+            if dockerfile_content or image_name:
+                container = UserDefinedContainer(
+                    self.kg_service.kg.get_local_path(),
+                    workdir,
+                    build_commands,
+                    test_commands,
+                    dockerfile_content,
+                    image_name,
+                )
+            else:
+                container = GeneralContainer(self.kg_service.kg.get_local_path())
+            # Initialize the issue graph with the necessary services and parameters
+            issue_graph = IssueGraph(
+                advanced_model=self.llm_service.advanced_model,
+                base_model=self.llm_service.base_model,
+                kg=self.kg_service.kg,
+                git_repo=self.repository_service.git_repo,
+                neo4j_driver=self.neo4j_service.neo4j_driver,
+                max_token_per_neo4j_result=self.max_token_per_neo4j_result,
+                container=container,
+                build_commands=build_commands,
+                test_commands=test_commands,
             )
-        elif output_state["issue_type"] == IssueType.QUESTION:
-            return (
-                None,
-                False,
-                False,
-                False,
-                output_state["issue_response"],
+            # Invoke the issue graph with the provided parameters
+            output_state = issue_graph.invoke(
+                issue_title,
+                issue_body,
+                issue_comments,
+                issue_type,
+                run_build,
+                run_existing_test,
+                number_of_candidate_patch,
             )
 
-        raise ValueError(
-            f"Unknown issue type: {output_state['issue_type']}. Expected BUG or QUESTION."
-        )
+            if output_state["issue_type"] == IssueType.BUG:
+                # push to remote if requested
+                remote_branch_name = None
+                if output_state["edit_patch"] and push_to_remote:
+                    remote_branch_name = self.repository_service.push_change_to_remote(
+                        f"Fixes #{issue_number}", output_state["edit_patch"]
+                    )
+
+                return (
+                    remote_branch_name,
+                    output_state["edit_patch"],
+                    output_state["passed_reproducing_test"],
+                    output_state["passed_build"],
+                    output_state["passed_existing_test"],
+                    output_state["issue_response"],
+                )
+            elif output_state["issue_type"] == IssueType.QUESTION:
+                return (
+                    None,
+                    False,
+                    False,
+                    False,
+                    output_state["issue_response"],
+                )
+
+            raise ValueError(
+                f"Unknown issue type: {output_state['issue_type']}. Expected BUG or QUESTION."
+            )
+        except Exception as e:
+            logger.error(f"Error in answer_issue: {str(e)}\n{traceback.format_exc()}")
+            return None, None, False, False, False, None
+        finally:
+            logger.removeHandler(file_handler)
+            file_handler.close()
diff --git a/prometheus/app/services/knowledge_graph_service.py b/prometheus/app/services/knowledge_graph_service.py
index 5ccaee41..f85751ec 100644
--- a/prometheus/app/services/knowledge_graph_service.py
+++ b/prometheus/app/services/knowledge_graph_service.py
@@ -3,12 +3,13 @@
 from pathlib import Path
 from typing import Optional
 
+from prometheus.app.services.base_service import BaseService
 from prometheus.app.services.neo4j_service import Neo4jService
 from prometheus.graph.knowledge_graph import KnowledgeGraph
 from prometheus.neo4j import knowledge_graph_handler
 
 
-class KnowledgeGraphService:
+class KnowledgeGraphService(BaseService):
     """Manages the lifecycle and operations of Knowledge Graphs.
 
     This service handles the creation, persistence, and management of Knowledge Graphs
@@ -84,3 +85,7 @@ def exists(self) -> bool:
     def clear(self):
         self.kg_handler.clear_knowledge_graph()
         self.kg = None
+
+    def close(self):
+        """Clear the knowledge graph before closing the service."""
+        self.clear()
diff --git a/prometheus/app/services/llm_service.py b/prometheus/app/services/llm_service.py
index 33567807..143a5669 100644
--- a/prometheus/app/services/llm_service.py
+++ b/prometheus/app/services/llm_service.py
@@ -4,10 +4,11 @@
 from langchain_core.language_models.chat_models import BaseChatModel
 from langchain_google_genai import ChatGoogleGenerativeAI
 
+from prometheus.app.services.base_service import BaseService
 from prometheus.chat_models.custom_chat_openai import CustomChatOpenAI
 
 
-class LLMService:
+class LLMService(BaseService):
     def __init__(
         self,
         advanced_model_name: str,
diff --git a/prometheus/app/services/neo4j_service.py b/prometheus/app/services/neo4j_service.py
index 2ee7f08e..bdb1cfd7 100644
--- a/prometheus/app/services/neo4j_service.py
+++ b/prometheus/app/services/neo4j_service.py
@@ -2,8 +2,10 @@
 
 from neo4j import GraphDatabase
 
+from prometheus.app.services.base_service import BaseService
 
-class Neo4jService:
+
+class Neo4jService(BaseService):
     def __init__(self, neo4j_uri: str, neo4j_username: str, neo4j_password: str):
         self.neo4j_driver = GraphDatabase.driver(
             neo4j_uri,
diff --git a/prometheus/app/services/repository_service.py b/prometheus/app/services/repository_service.py
index 8a02717d..5e6d88d6 100644
--- a/prometheus/app/services/repository_service.py
+++ b/prometheus/app/services/repository_service.py
@@ -5,11 +5,12 @@
 from pathlib import Path
 from typing import Optional
 
+from prometheus.app.services.base_service import BaseService
 from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
 from prometheus.git.git_repository import GitRepository
 
 
-class RepositoryService:
+class RepositoryService(BaseService):
     """Manages repository operations.
 
     This service provides functionality for Git repository operations including
@@ -93,3 +94,7 @@ def clean(self):
         self.git_repo = None
         shutil.rmtree(self.target_directory)
         self.target_directory.mkdir(parents=True)
+
+    def close(self):
+        """Cleans up the repository service before shutdown."""
+        self.clean()

From e17a25c12546bdbc84c49d95821f174561e45da7 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 00:59:32 +0800
Subject: [PATCH 07/55] Refactor service initialization to return a dictionary
 of services instead of a ServiceCoordinator

---
 prometheus/app/dependencies.py | 25 +++++++++----------------
 prometheus/app/main.py         |  7 ++++---
 2 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/prometheus/app/dependencies.py b/prometheus/app/dependencies.py
index 5b3986d1..684dfe04 100644
--- a/prometheus/app/dependencies.py
+++ b/prometheus/app/dependencies.py
@@ -1,17 +1,15 @@
 """Initializes and configures all prometheus services."""
 
-from pathlib import Path
-
+from prometheus.app.services.base_service import BaseService
 from prometheus.app.services.issue_service import IssueService
 from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
 from prometheus.app.services.llm_service import LLMService
 from prometheus.app.services.neo4j_service import Neo4jService
 from prometheus.app.services.repository_service import RepositoryService
-from prometheus.app.services.service_coordinator import ServiceCoordinator
 from prometheus.configuration.config import settings
 
 
-def initialize_services() -> ServiceCoordinator:
+def initialize_services() -> dict[str, BaseService]:
     """Initializes and configures the complete prometheus service stack.
 
     This function creates and configures all required services for prometheus
@@ -60,15 +58,10 @@ def initialize_services() -> ServiceCoordinator:
         settings.MAX_TOKEN_PER_NEO4J_RESULT,
     )
 
-    service_coordinator = ServiceCoordinator(
-        issue_service,
-        knowledge_graph_service,
-        llm_service,
-        neo4j_service,
-        repository_service,
-        settings.MAX_TOKEN_PER_NEO4J_RESULT,
-        settings.GITHUB_ACCESS_TOKEN,
-        Path(settings.WORKING_DIRECTORY).absolute(),
-    )
-
-    return service_coordinator
+    return {
+        "neo4j_service": neo4j_service,
+        "llm_service": llm_service,
+        "knowledge_graph_service": knowledge_graph_service,
+        "repository_service": repository_service,
+        "issue_service": issue_service,
+    }
diff --git a/prometheus/app/main.py b/prometheus/app/main.py
index 2eeca317..8947c7b9 100644
--- a/prometheus/app/main.py
+++ b/prometheus/app/main.py
@@ -35,12 +35,13 @@
 @asynccontextmanager
 async def lifespan(app: FastAPI):
     # Initialization on startup
-    app.state.service_coordinator = dependencies.initialize_services()
+    app.state.service = dependencies.initialize_services()
     # Initialization Completed
     yield
     # Cleanup on shutdown
-    app.state.service_coordinator.clear()
-    app.state.service_coordinator.close()
+    logger.info("Shutting down services...")
+    for service in app.state.service.values():
+        service.close()
 
 
 app = FastAPI(lifespan=lifespan)

From 5ecf4a13f3afc9482d54007690ca00d93b3d7686 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 01:07:45 +0800
Subject: [PATCH 08/55] Add GITHUB_ACCESS_TOKEN to configuration settings

---
 prometheus/configuration/config.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/prometheus/configuration/config.py b/prometheus/configuration/config.py
index 11b7432c..ede7c576 100644
--- a/prometheus/configuration/config.py
+++ b/prometheus/configuration/config.py
@@ -45,6 +45,9 @@ class Settings(BaseSettings):
     TEMPERATURE: float
     MAX_OUTPUT_TOKENS: int
 
+    # GitHub Token
+    GITHUB_ACCESS_TOKEN: str
+
     # Database
     DATABASE_URL: str
 

From 385a9bbe96bd32325132f10504d098afa30a506a Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 01:21:57 +0800
Subject: [PATCH 09/55] Refactor GitHub repository upload functions to use
 service dictionary and improve knowledge graph handling

---
 prometheus/app/api/issue.py                   |   2 +-
 prometheus/app/api/repository.py              |  43 +++-
 .../app/services/service_coordinator.py       | 213 ------------------
 3 files changed, 38 insertions(+), 220 deletions(-)
 delete mode 100644 prometheus/app/services/service_coordinator.py

diff --git a/prometheus/app/api/issue.py b/prometheus/app/api/issue.py
index 00fd8b05..9a183dab 100644
--- a/prometheus/app/api/issue.py
+++ b/prometheus/app/api/issue.py
@@ -12,7 +12,7 @@
     response_description="Returns the patch, test results, and issue response",
 )
 def answer_issue(issue: IssueRequest, request: Request):
-    if not request.app.state.service_coordinator.exists_knowledge_graph():
+    if not request.app.state.service["knowledge_graph_service"].exists():
         raise HTTPException(
             status_code=404,
             detail="A repository is not uploaded, use /repository/ endpoint to upload one",
diff --git a/prometheus/app/api/repository.py b/prometheus/app/api/repository.py
index 9f4af412..3c70fae0 100644
--- a/prometheus/app/api/repository.py
+++ b/prometheus/app/api/repository.py
@@ -10,9 +10,24 @@
     Upload a GitHub repository to Prometheus, default to the latest commit in the main branch.
     """,
 )
-def upload_github_repository(https_url: str, request: Request):
+def upload_github_repository(github_token: str, https_url: str, request: Request):
     try:
-        request.app.state.service_coordinator.upload_github_repository(https_url)
+        # Get the repository and knowledge graph services
+        repository_service = request.app.state.service["repository_service"]
+        knowledge_graph_service = request.app.state.service["knowledge_graph_service"]
+
+        # Clean the services to ensure no previous data is present
+        repository_service.clean()
+        knowledge_graph_service.clean()
+
+        # Clone the repository
+        saved_path = repository_service.clone_github_repo(
+            github_token, https_url
+        )
+        # Build and save the knowledge graph from the cloned repository
+        knowledge_graph_service.build_and_save_knowledge_graph(
+            saved_path, https_url
+        )
     except git.exc.GitCommandError:
         raise HTTPException(status_code=400, detail=f"Unable to clone {https_url}")
 
@@ -23,9 +38,25 @@ def upload_github_repository(https_url: str, request: Request):
     Upload a GitHub repository at a specific commit to Prometheus.
     """,
 )
-def upload_github_repository_at_commit(https_url: str, commit_id: str, request: Request):
+def upload_github_repository_at_commit(github_token, https_url: str, commit_id: str, request: Request):
     try:
-        request.app.state.service_coordinator.upload_github_repository(https_url, commit_id)
+        # Get the repository and knowledge graph services
+        repository_service = request.app.state.service["repository_service"]
+        knowledge_graph_service = request.app.state.service["knowledge_graph_service"]
+
+        # Clean the services to ensure no previous data is present
+        repository_service.clean()
+        knowledge_graph_service.clean()
+
+        # Clone the repository
+        saved_path = repository_service.clone_github_repo(
+            github_token, https_url, commit_id
+        )
+
+        # Build and save the knowledge graph from the cloned repository
+        knowledge_graph_service.build_and_save_knowledge_graph(
+            saved_path, https_url, commit_id
+        )
     except git.exc.GitCommandError:
         raise HTTPException(
             status_code=400, detail=f"Unable to clone {https_url} with commit {commit_id}"
@@ -39,7 +70,7 @@ def upload_github_repository_at_commit(https_url: str, commit_id: str, request:
     """,
 )
 def delete(request: Request):
-    if not request.app.state.service_coordinator.exists_knowledge_graph():
+    if not request.app.state.service["knowledge_graph_service"].exists():
         return {"message": "No knowledge graph to delete"}
 
     request.app.state.service_coordinator.clear()
@@ -54,4 +85,4 @@ def delete(request: Request):
     response_model=bool,
 )
 def knowledge_graph_exists(request: Request) -> bool:
-    return request.app.state.service_coordinator.exists_knowledge_graph()
+    return request.app.state.service["knowledge_graph_service"].exists()
diff --git a/prometheus/app/services/service_coordinator.py b/prometheus/app/services/service_coordinator.py
deleted file mode 100644
index 05955eb2..00000000
--- a/prometheus/app/services/service_coordinator.py
+++ /dev/null
@@ -1,213 +0,0 @@
-"""Central coordinator for managing interactions between various prometheus services.
-
-This coordinator orchestrates the interactions between multiple specialized services
-including knowledge graph management, LLM operations, database connections, and
-repository management. It provides a unified interface for codebase analysis,
-issue handling, and conversation management.
-"""
-
-import logging
-import traceback
-from datetime import datetime
-from pathlib import Path
-from typing import Mapping, Optional, Sequence
-
-from prometheus.app.services.issue_service import IssueService
-from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
-from prometheus.app.services.llm_service import LLMService
-from prometheus.app.services.neo4j_service import Neo4jService
-from prometheus.app.services.repository_service import RepositoryService
-from prometheus.lang_graph.graphs.issue_state import IssueType
-
-
-class ServiceCoordinator:
-    """Coordinates operations between various prometheus services.
-
-    This class serves as the central orchestrator for all service interactions,
-    managing the lifecycle of various operations including codebase analysis,
-    issue handling, and conversation management. It ensures proper initialization,
-    coordination, and cleanup of all dependent services.
-    """
-
-    def __init__(
-        self,
-        issue_service: IssueService,
-        knowledge_graph_service: KnowledgeGraphService,
-        llm_service: LLMService,
-        neo4j_service: Neo4jService,
-        repository_service: RepositoryService,
-        max_token_per_neo4j_result: int,
-        github_token: str,
-        working_directory: Path,
-    ):
-        """Initializes the service coordinator with required services.
-
-        Args:
-          issue_service: Service for issue handling.
-          knowledge_graph_service: Service for knowledge graph operations.
-          llm_service: Service for language model operations.
-          neo4j_service: Service for Neo4j database operations.
-          repository_service: Service for repository management.
-          max_token_per_neo4j_result: Maximum number of tokens per Neo4j result.
-          github_token: GitHub access token for repository operations.
-          working_directory: Working directory for all Prometheus related files.
-        """
-        self.issue_service = issue_service
-        self.knowledge_graph_service = knowledge_graph_service
-        self.llm_service = llm_service
-        self.neo4j_service = neo4j_service
-        self.repository_service = repository_service
-        self.max_token_per_neo4j_result = max_token_per_neo4j_result
-        self.github_token = github_token
-        self.working_directory = working_directory
-        self.answer_issue_log_dir = self.working_directory / "answer_issue_logs"
-        self.answer_issue_log_dir.mkdir(parents=True, exist_ok=True)
-        self._logger = logging.getLogger("prometheus.app.services.service_coordinator")
-
-        if (
-            self.knowledge_graph_service.get_local_path()
-            != self.repository_service.get_working_dir()
-        ):
-            self._logger.critical(
-                f"Knowledge graph and repository working directories do not match: {self.knowledge_graph_service.get_local_path()} vs {self.repository_service.get_working_dir()}. Resetting all services."
-            )
-            self.clear()
-
-    def answer_issue(
-        self,
-        issue_number: int,
-        issue_title: str,
-        issue_body: str,
-        issue_comments: Sequence[Mapping[str, str]],
-        issue_type: IssueType,
-        run_build: bool,
-        run_existing_test: bool,
-        number_of_candidate_patch: int,
-        dockerfile_content: Optional[str] = None,
-        image_name: Optional[str] = None,
-        workdir: Optional[str] = None,
-        build_commands: Optional[Sequence[str]] = None,
-        test_commands: Optional[Sequence[str]] = None,
-        push_to_remote: Optional[bool] = None,
-    ):
-        """
-        Processes an issue, generates patches if needed, runs optional builds and tests,
-        and can push changes to a remote branch.
-
-        Args:
-            issue_number: The issue number to process.
-            issue_title: Title of the issue.
-            issue_body: Body of the issue.
-            issue_comments: Comments on the issue.
-            issue_type: Type of the issue (e.g., bug, feature).
-            run_build: Whether to run a build after applying the patch.
-            run_existing_test: Whether to run existing tests after applying the patch.
-            number_of_candidate_patch: Number of candidate patches to generate.
-            dockerfile_content: Optional Dockerfile content for user-defined environment.
-            image_name: Optional name for the Docker image.
-            workdir: Working directory for the container.
-            build_commands: Commands to build the project.
-            test_commands: Commands to test the project.
-            push_to_remote: Whether to push changes to a remote branch.
-        Returns:
-            A tuple containing:
-                - remote_branch_name: Name of the remote branch if changes were pushed.
-                - patch: The generated patch for the issue.
-                - passed_reproducing_test: Whether the reproducing test passed.
-                - passed_build: Whether the build passed.
-                - passed_existing_test: Whether existing tests passed.
-                - issue_response: Response from the issue service after processing.
-        """
-        logger = logging.getLogger("prometheus")
-        formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
-        timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
-        log_file = self.answer_issue_log_dir / f"{timestamp}.log"
-        file_handler = logging.FileHandler(log_file)
-        file_handler.setFormatter(formatter)
-        logger.addHandler(file_handler)
-
-        try:
-            # fix issue
-            patch, passed_reproducing_test, passed_build, passed_existing_test, issue_response = (
-                self.issue_service.answer_issue(
-                    issue_title=issue_title,
-                    issue_body=issue_body,
-                    issue_comments=issue_comments,
-                    issue_type=issue_type,
-                    run_build=run_build,
-                    run_existing_test=run_existing_test,
-                    number_of_candidate_patch=number_of_candidate_patch,
-                    dockerfile_content=dockerfile_content,
-                    image_name=image_name,
-                    workdir=workdir,
-                    build_commands=build_commands,
-                    test_commands=test_commands,
-                )
-            )
-            # push to remote if requested
-            remote_branch_name = None
-            if patch and push_to_remote:
-                remote_branch_name = self.repository_service.push_change_to_remote(
-                    f"Fixes #{issue_number}", patch
-                )
-            return (
-                remote_branch_name,
-                patch,
-                passed_reproducing_test,
-                passed_build,
-                passed_existing_test,
-                issue_response,
-            )
-        except Exception as e:
-            logger.error(f"Error in answer_issue: {str(e)}\n{traceback.format_exc()}")
-            return None, None, False, False, False, None
-        finally:
-            logger.removeHandler(file_handler)
-            file_handler.close()
-
-    def exists_knowledge_graph(self) -> bool:
-        return self.knowledge_graph_service.exists()
-
-    def upload_local_repository(self, path: Path):
-        """Uploads a local repository.
-
-        Args:
-          path: Path to the local repository directory.
-        """
-        self.clear()
-        self.knowledge_graph_service.build_and_save_knowledge_graph(path)
-
-    def upload_github_repository(self, https_url: str, commit_id: Optional[str] = None):
-        """Uploads a GitHub repository.
-
-        Args:
-            https_url: HTTPS URL of the GitHub repository.
-            commit_id: Optional specific commit to analyze.
-        """
-        # CLean the existing knowledge graph and repository state
-        self.clear()
-        # Clone the repository
-        saved_path = self.repository_service.clone_github_repo(
-            self.github_token, https_url, commit_id
-        )
-        # Build and save the knowledge graph from the cloned repository
-        self.knowledge_graph_service.build_and_save_knowledge_graph(
-            saved_path, https_url, commit_id
-        )
-
-    def clear(self):
-        """Clears all service state and working directories.
-
-        Resets the knowledge graph, cleans repository working directory,
-        and reinitializes subgraph services.
-        """
-        self.knowledge_graph_service.clear()
-        self.repository_service.clean()
-
-    def close(self):
-        """Closes all database connections and releases resources.
-
-        This method should be called when the coordinator is no longer needed
-        to ensure proper cleanup of database connections and resources.
-        """
-        self.neo4j_service.close()

From eba7732ec8bc2a76d47b0c451d0fc8137f6878fd Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 01:34:46 +0800
Subject: [PATCH 10/55] Update working_directory type to string and ensure
 proper Path handling for answer_issue_log_dir

---
 prometheus/app/dependencies.py           | 1 +
 prometheus/app/services/issue_service.py | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/prometheus/app/dependencies.py b/prometheus/app/dependencies.py
index 684dfe04..cacb6112 100644
--- a/prometheus/app/dependencies.py
+++ b/prometheus/app/dependencies.py
@@ -56,6 +56,7 @@ def initialize_services() -> dict[str, BaseService]:
         neo4j_service,
         llm_service,
         settings.MAX_TOKEN_PER_NEO4J_RESULT,
+        settings.WORKING_DIRECTORY,
     )
 
     return {
diff --git a/prometheus/app/services/issue_service.py b/prometheus/app/services/issue_service.py
index 924f223c..0d7800be 100644
--- a/prometheus/app/services/issue_service.py
+++ b/prometheus/app/services/issue_service.py
@@ -23,7 +23,7 @@ def __init__(
         neo4j_service: Neo4jService,
         llm_service: LLMService,
         max_token_per_neo4j_result: int,
-        working_directory: Path,
+        working_directory: str,
     ):
         self.kg_service = kg_service
         self.repository_service = repository_service
@@ -31,7 +31,7 @@ def __init__(
         self.llm_service = llm_service
         self.max_token_per_neo4j_result = max_token_per_neo4j_result
         self.working_directory = working_directory
-        self.answer_issue_log_dir = self.working_directory / "answer_issue_logs"
+        self.answer_issue_log_dir = Path(self.working_directory) / "answer_issue_logs"
         self.answer_issue_log_dir.mkdir(parents=True, exist_ok=True)
 
     def answer_issue(

From f51660c585ca6f8fa520306ef193bf8958d49ac7 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 01:35:32 +0800
Subject: [PATCH 11/55] Rename OPENAI_API_KEY to OPENAI_FORMAT_API_KEY and
 update example.env to include new general settings

---
 example.env                        | 7 ++++---
 prometheus/configuration/config.py | 5 +----
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/example.env b/example.env
index d2b2c063..6dd48b14 100644
--- a/example.env
+++ b/example.env
@@ -1,6 +1,10 @@
 # Logging
 PROMETHEUS_LOGGING_LEVEL=DEBUG
 
+# General settings
+PROMETHEUS_ENVIRONMENT=local
+PROMETHEUS_BACKEND_CORS_ORIGINS=["http://localhost:9002"]
+
 # Neo4j settings
 PROMETHEUS_NEO4J_URI=bolt://neo4j:7687
 PROMETHEUS_NEO4J_USERNAME=neo4j
@@ -29,8 +33,5 @@ PROMETHEUS_MAX_INPUT_TOKENS=64000
 PROMETHEUS_TEMPERATURE=0.3
 PROMETHEUS_MAX_OUTPUT_TOKENS=15000
 
-# GitHub settings
-PROMETHEUS_GITHUB_ACCESS_TOKEN=github_access_token
-
 # Database settings
 PROMETHEUS_DATABASE_URL=postgresql://postgres:password@localhost:5432/postgres?sslmode=disable
diff --git a/prometheus/configuration/config.py b/prometheus/configuration/config.py
index ede7c576..e43b8484 100644
--- a/prometheus/configuration/config.py
+++ b/prometheus/configuration/config.py
@@ -38,16 +38,13 @@ class Settings(BaseSettings):
     ANTHROPIC_API_KEY: str
     GEMINI_API_KEY: str
     OPENAI_FORMAT_BASE_URL: str
-    OPENAI_API_KEY: str
+    OPENAI_FORMAT_API_KEY: str
 
     # Model parameters
     MAX_INPUT_TOKENS: int
     TEMPERATURE: float
     MAX_OUTPUT_TOKENS: int
 
-    # GitHub Token
-    GITHUB_ACCESS_TOKEN: str
-
     # Database
     DATABASE_URL: str
 

From a1ae76638e25ecc2479bc28a00fc8f2158352446 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 01:35:37 +0800
Subject: [PATCH 12/55] Refactor repository cloning functions for improved
 readability and consistency

---
 prometheus/app/api/repository.py | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

diff --git a/prometheus/app/api/repository.py b/prometheus/app/api/repository.py
index 3c70fae0..052aa3b5 100644
--- a/prometheus/app/api/repository.py
+++ b/prometheus/app/api/repository.py
@@ -21,13 +21,9 @@ def upload_github_repository(github_token: str, https_url: str, request: Request
         knowledge_graph_service.clean()
 
         # Clone the repository
-        saved_path = repository_service.clone_github_repo(
-            github_token, https_url
-        )
+        saved_path = repository_service.clone_github_repo(github_token, https_url)
         # Build and save the knowledge graph from the cloned repository
-        knowledge_graph_service.build_and_save_knowledge_graph(
-            saved_path, https_url
-        )
+        knowledge_graph_service.build_and_save_knowledge_graph(saved_path, https_url)
     except git.exc.GitCommandError:
         raise HTTPException(status_code=400, detail=f"Unable to clone {https_url}")
 
@@ -38,7 +34,9 @@ def upload_github_repository(github_token: str, https_url: str, request: Request
     Upload a GitHub repository at a specific commit to Prometheus.
     """,
 )
-def upload_github_repository_at_commit(github_token, https_url: str, commit_id: str, request: Request):
+def upload_github_repository_at_commit(
+    github_token, https_url: str, commit_id: str, request: Request
+):
     try:
         # Get the repository and knowledge graph services
         repository_service = request.app.state.service["repository_service"]
@@ -49,14 +47,10 @@ def upload_github_repository_at_commit(github_token, https_url: str, commit_id:
         knowledge_graph_service.clean()
 
         # Clone the repository
-        saved_path = repository_service.clone_github_repo(
-            github_token, https_url, commit_id
-        )
+        saved_path = repository_service.clone_github_repo(github_token, https_url, commit_id)
 
         # Build and save the knowledge graph from the cloned repository
-        knowledge_graph_service.build_and_save_knowledge_graph(
-            saved_path, https_url, commit_id
-        )
+        knowledge_graph_service.build_and_save_knowledge_graph(saved_path, https_url, commit_id)
     except git.exc.GitCommandError:
         raise HTTPException(
             status_code=400, detail=f"Unable to clone {https_url} with commit {commit_id}"

From ea618a614a4945bf417ec6b387e2b457a87c3717 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 01:52:43 +0800
Subject: [PATCH 13/55] Add general settings to Docker Compose files and remove
 GitHub access token

---
 docker-compose.win_mac.yml | 7 ++++---
 docker-compose.yml         | 7 ++++---
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/docker-compose.win_mac.yml b/docker-compose.win_mac.yml
index 8eeec133..bdeb6cd2 100644
--- a/docker-compose.win_mac.yml
+++ b/docker-compose.win_mac.yml
@@ -36,6 +36,10 @@ services:
       # Logging
       - PROMETHEUS_LOGGING_LEVEL=${PROMETHEUS_LOGGING_LEVEL}
 
+      # General settings
+      - PROMETHEUS_ENVIRONMENT=${PROMETHEUS_ENVIRONMENT}
+      - PROMETHEUS_BACKEND_CORS_ORIGINS=${PROMETHEUS_BACKEND_CORS_ORIGINS}
+
       # Neo4j settings
       - PROMETHEUS_NEO4J_URI=${PROMETHEUS_NEO4J_URI}
       - PROMETHEUS_NEO4J_USERNAME=${PROMETHEUS_NEO4J_USERNAME}
@@ -64,9 +68,6 @@ services:
       - PROMETHEUS_MAX_OUTPUT_TOKENS=${PROMETHEUS_MAX_OUTPUT_TOKENS}
       - PROMETHEUS_TEMPERATURE=${PROMETHEUS_TEMPERATURE}
 
-      # GitHub settings
-      - PROMETHEUS_GITHUB_ACCESS_TOKEN=${PROMETHEUS_GITHUB_ACCESS_TOKEN}
-
       # Database settings
       - PROMETHEUS_DATABASE_URL=${PROMETHEUS_DATABASE_URL}
     networks:
diff --git a/docker-compose.yml b/docker-compose.yml
index 03fb66f3..72f3a56b 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -57,6 +57,10 @@ services:
       # Logging
       - PROMETHEUS_LOGGING_LEVEL=${PROMETHEUS_LOGGING_LEVEL}
 
+      # General settings
+      - PROMETHEUS_ENVIRONMENT=${PROMETHEUS_ENVIRONMENT}
+      - PROMETHEUS_BACKEND_CORS_ORIGINS=${PROMETHEUS_BACKEND_CORS_ORIGINS}
+
       # Neo4j settings
       - PROMETHEUS_NEO4J_URI=${PROMETHEUS_NEO4J_URI}
       - PROMETHEUS_NEO4J_USERNAME=${PROMETHEUS_NEO4J_USERNAME}
@@ -85,9 +89,6 @@ services:
       - PROMETHEUS_MAX_OUTPUT_TOKENS=${PROMETHEUS_MAX_OUTPUT_TOKENS}
       - PROMETHEUS_TEMPERATURE=${PROMETHEUS_TEMPERATURE}
 
-      # GitHub settings
-      - PROMETHEUS_GITHUB_ACCESS_TOKEN=${PROMETHEUS_GITHUB_ACCESS_TOKEN}
-
       # Database settings
       - PROMETHEUS_DATABASE_URL=${PROMETHEUS_DATABASE_URL}
     volumes:

From 41ef1d9ad91584c29b463a73f34eb9fcd72690d2 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 01:56:42 +0800
Subject: [PATCH 14/55] Refactor GitHub repository upload functions to use type
 hints and improve service cleanup

---
 prometheus/app/api/repository.py | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/prometheus/app/api/repository.py b/prometheus/app/api/repository.py
index 052aa3b5..f78e5fa3 100644
--- a/prometheus/app/api/repository.py
+++ b/prometheus/app/api/repository.py
@@ -1,6 +1,9 @@
 import git
 from fastapi import APIRouter, HTTPException, Request
 
+from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
+from prometheus.app.services.repository_service import RepositoryService
+
 router = APIRouter()
 
 
@@ -13,12 +16,14 @@
 def upload_github_repository(github_token: str, https_url: str, request: Request):
     try:
         # Get the repository and knowledge graph services
-        repository_service = request.app.state.service["repository_service"]
-        knowledge_graph_service = request.app.state.service["knowledge_graph_service"]
+        repository_service: RepositoryService = request.app.state.service["repository_service"]
+        knowledge_graph_service: KnowledgeGraphService = request.app.state.service[
+            "knowledge_graph_service"
+        ]
 
         # Clean the services to ensure no previous data is present
         repository_service.clean()
-        knowledge_graph_service.clean()
+        knowledge_graph_service.clear()
 
         # Clone the repository
         saved_path = repository_service.clone_github_repo(github_token, https_url)
@@ -39,12 +44,14 @@ def upload_github_repository_at_commit(
 ):
     try:
         # Get the repository and knowledge graph services
-        repository_service = request.app.state.service["repository_service"]
-        knowledge_graph_service = request.app.state.service["knowledge_graph_service"]
+        repository_service: RepositoryService = request.app.state.service["repository_service"]
+        knowledge_graph_service: KnowledgeGraphService = request.app.state.service[
+            "knowledge_graph_service"
+        ]
 
         # Clean the services to ensure no previous data is present
         repository_service.clean()
-        knowledge_graph_service.clean()
+        knowledge_graph_service.clear()
 
         # Clone the repository
         saved_path = repository_service.clone_github_repo(github_token, https_url, commit_id)

From a8376ea0180f25bccf1582c3e8ba6a8e463faf41 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 02:08:23 +0800
Subject: [PATCH 15/55] Refactor issue handling and repository deletion logic
 for improved clarity and service access

---
 prometheus/app/api/issue.py              |  2 +-
 prometheus/app/api/repository.py         | 11 +++++++++--
 prometheus/app/services/issue_service.py |  1 +
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/prometheus/app/api/issue.py b/prometheus/app/api/issue.py
index 9a183dab..10bd5753 100644
--- a/prometheus/app/api/issue.py
+++ b/prometheus/app/api/issue.py
@@ -32,7 +32,7 @@ def answer_issue(issue: IssueRequest, request: Request):
         passed_build,
         passed_existing_test,
         issue_response,
-    ) = request.app.state.service_coordinator.answer_issue(
+    ) = request.app.state.service["issue_service"].answer_issue(
         issue_number=issue.issue_number,
         issue_title=issue.issue_title,
         issue_body=issue.issue_body,
diff --git a/prometheus/app/api/repository.py b/prometheus/app/api/repository.py
index f78e5fa3..cb177555 100644
--- a/prometheus/app/api/repository.py
+++ b/prometheus/app/api/repository.py
@@ -71,10 +71,17 @@ def upload_github_repository_at_commit(
     """,
 )
 def delete(request: Request):
-    if not request.app.state.service["knowledge_graph_service"].exists():
+    knowledge_graph_service: KnowledgeGraphService = request.app.state.service[
+        "knowledge_graph_service"
+    ]
+    if not knowledge_graph_service.exists():
         return {"message": "No knowledge graph to delete"}
+    # Get the repository service to clean up the repository data
+    repository_service: RepositoryService = request.app.state.service["repository_service"]
 
-    request.app.state.service_coordinator.clear()
+    # Clear the knowledge graph and repository data
+    knowledge_graph_service.clear()
+    repository_service.clean()
     return {"message": "Successfully deleted knowledge graph"}
 
 
diff --git a/prometheus/app/services/issue_service.py b/prometheus/app/services/issue_service.py
index 0d7800be..a66898bc 100644
--- a/prometheus/app/services/issue_service.py
+++ b/prometheus/app/services/issue_service.py
@@ -139,6 +139,7 @@ def answer_issue(
                 )
             elif output_state["issue_type"] == IssueType.QUESTION:
                 return (
+                    None,
                     None,
                     False,
                     False,

From 870d1f86ce2b80f76ccf08c6a74efeb02be3620c Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 02:10:47 +0800
Subject: [PATCH 16/55] Add logging for environment and CORS origins in main.py

---
 prometheus/app/main.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/prometheus/app/main.py b/prometheus/app/main.py
index 8947c7b9..59f0e5f2 100644
--- a/prometheus/app/main.py
+++ b/prometheus/app/main.py
@@ -19,6 +19,8 @@
 
 # Log the configuration settings
 logger.info(f"LOGGING_LEVEL={settings.LOGGING_LEVEL}")
+logger.info(f"ENVIRONMENT={settings.ENVIRONMENT}")
+logger.info(f"BACKEND_CORS_ORIGINS={settings.BACKEND_CORS_ORIGINS}")
 logger.info(f"ADVANCED_MODEL={settings.ADVANCED_MODEL}")
 logger.info(f"BASE_MODEL={settings.BASE_MODEL}")
 logger.info(f"NEO4J_BATCH_SIZE={settings.NEO4J_BATCH_SIZE}")

From c21d744f808046652e59cc534d4fa9cc6342d22e Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 02:20:26 +0800
Subject: [PATCH 17/55] Add custom unique ID generation for API routes in
 FastAPI application

---
 prometheus/app/main.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/prometheus/app/main.py b/prometheus/app/main.py
index 59f0e5f2..13e72e37 100644
--- a/prometheus/app/main.py
+++ b/prometheus/app/main.py
@@ -3,6 +3,7 @@
 from datetime import datetime, timezone
 
 from fastapi import FastAPI
+from fastapi.routing import APIRoute
 
 from prometheus.app import dependencies
 from prometheus.app.api import issue, repository
@@ -46,7 +47,21 @@ async def lifespan(app: FastAPI):
         service.close()
 
 
-app = FastAPI(lifespan=lifespan)
+def custom_generate_unique_id(route: APIRoute) -> str:
+    """
+    Custom function to generate unique IDs for API routes based on their tags and names.
+    """
+    return f"{route.tags[0]}-{route.name}"
+
+
+app = FastAPI(
+    lifespan=lifespan,
+    title=settings.PROJECT_NAME,  # Title on generated documentation
+    openapi_url=f"{settings.BASE_URL}/openapi.json",  # Path to generated OpenAPI documentation
+    generate_unique_id_function=custom_generate_unique_id,  # Custom function for generating unique route IDs
+    version=settings.version,  # Version of the API
+    debug=True if settings.ENVIRONMENT == "local" else False,
+)
 
 app.include_router(repository.router, prefix="/repository", tags=["repository"])
 app.include_router(issue.router, prefix="/issue", tags=["issue"])

From 0fef3b899a7b25a34a532a510b98fe100affa001 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 02:28:07 +0800
Subject: [PATCH 18/55] Update API documentation to correct endpoint URL for
 issue answering

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 0044bed3..f2ccaba8 100644
--- a/README.md
+++ b/README.md
@@ -124,7 +124,7 @@ governed by a state machine to ensure code quality through automated reviews, bu
    You can ask Prometheus to analyze and answer a specific issue in your codebase using the `/issue/answer/` API endpoint.
    
    - **Endpoint:** `POST /issue/answer/`
-     - **Request Body:** JSON object matching the `IssueRequest` schema (see [API Documents](http://localhost:9002/docs#/issue/answer_issue_issue_answer__post))
+     - **Request Body:** JSON object matching the `IssueRequest` schema (see [API Documents](http://127.0.0.1:9002/docs#/issue/issue-answer_issue))
      - **Response:** Returns the generated patch, test/build results, and a summary response.
 
 ---

From 6df68b96527eb2060d9ee2efb2b88d159b3764ae Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:05:07 +0800
Subject: [PATCH 19/55] Add DatabaseService for database management and
 integrate into dependencies

---
 prometheus/app/db.py                        | 57 ---------------------
 prometheus/app/dependencies.py              |  3 ++
 prometheus/app/services/database_service.py | 22 ++++++++
 3 files changed, 25 insertions(+), 57 deletions(-)
 delete mode 100644 prometheus/app/db.py
 create mode 100644 prometheus/app/services/database_service.py

diff --git a/prometheus/app/db.py b/prometheus/app/db.py
deleted file mode 100644
index a95fa8f1..00000000
--- a/prometheus/app/db.py
+++ /dev/null
@@ -1,57 +0,0 @@
-import logging
-from typing import Optional
-
-from passlib.hash import bcrypt
-from sqlmodel import Session, SQLModel, create_engine
-
-from prometheus.app.entity.user import User
-from prometheus.configuration.config import settings
-
-engine = create_engine(settings.DATABASE_URL, echo=True)
-_logger = logging.getLogger("prometheus.app.db")
-
-
-# Create the database and tables
-def create_db_and_tables():
-    SQLModel.metadata.create_all(engine)
-
-
-# Create a superuser and commit it to the database
-def create_superuser(
-    username: str,
-    email: str,
-    password: str,
-    github_token: Optional[str] = None,
-) -> None:
-    """
-    Create a new superuser and commit it to the database.
-
-    Args:
-        username (str): Desired username.
-        email (str): Email address.
-        password (str): Plaintext password (will be hashed).
-        github_token (Optional[str]): Optional GitHub token.
-
-    Returns:
-        User: The created superuser instance.
-    """
-    with Session(engine) as session:
-        if session.query(User).filter(User.username == username).first():
-            raise ValueError(f"Username '{username}' already exists")
-        if session.query(User).filter(User.email == email).first():
-            raise ValueError(f"Email '{email}' already exists")
-
-        hashed_password = bcrypt.hash(password)
-
-        user = User(
-            username=username,
-            email=email,
-            password_hash=hashed_password,
-            github_token=github_token,
-            issue_credit=999999,
-            is_superuser=True,
-        )
-        session.add(user)
-        session.commit()
-        session.refresh(user)
-    _logger.info(f"Superuser '{username}' created successfully.")
diff --git a/prometheus/app/dependencies.py b/prometheus/app/dependencies.py
index cacb6112..6b5a02bb 100644
--- a/prometheus/app/dependencies.py
+++ b/prometheus/app/dependencies.py
@@ -1,6 +1,7 @@
 """Initializes and configures all prometheus services."""
 
 from prometheus.app.services.base_service import BaseService
+from prometheus.app.services.database_service import DatabaseService
 from prometheus.app.services.issue_service import IssueService
 from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
 from prometheus.app.services.llm_service import LLMService
@@ -58,6 +59,7 @@ def initialize_services() -> dict[str, BaseService]:
         settings.MAX_TOKEN_PER_NEO4J_RESULT,
         settings.WORKING_DIRECTORY,
     )
+    database_service = DatabaseService(settings.DATABASE_URL)
 
     return {
         "neo4j_service": neo4j_service,
@@ -65,4 +67,5 @@ def initialize_services() -> dict[str, BaseService]:
         "knowledge_graph_service": knowledge_graph_service,
         "repository_service": repository_service,
         "issue_service": issue_service,
+        "database_service": database_service,
     }
diff --git a/prometheus/app/services/database_service.py b/prometheus/app/services/database_service.py
new file mode 100644
index 00000000..42b684d6
--- /dev/null
+++ b/prometheus/app/services/database_service.py
@@ -0,0 +1,22 @@
+import logging
+
+from sqlmodel import SQLModel, create_engine
+
+from prometheus.app.services.base_service import BaseService
+
+
+class DatabaseService(BaseService):
+    def __init__(self, DATABASE_URL: str):
+        self.engine = create_engine(DATABASE_URL, echo=True)
+        self._logger = logging.getLogger("prometheus.app.services.database_service")
+
+    # Create the database and tables
+    def create_db_and_tables(self):
+        SQLModel.metadata.create_all(self.engine)
+
+    def close(self):
+        """
+        Close the database connection and release any resources.
+        """
+        self.engine.dispose()
+        self._logger.info("Database connection closed.")

From e512457069c4147985b09f049640beea3e9e3ff8 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:05:20 +0800
Subject: [PATCH 20/55] Add logging for Neo4j driver connection closure in
 Neo4jService

---
 prometheus/app/services/neo4j_service.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/prometheus/app/services/neo4j_service.py b/prometheus/app/services/neo4j_service.py
index bdb1cfd7..da27fea3 100644
--- a/prometheus/app/services/neo4j_service.py
+++ b/prometheus/app/services/neo4j_service.py
@@ -1,5 +1,7 @@
 """Service for managing Neo4j database driver."""
 
+import logging
+
 from neo4j import GraphDatabase
 
 from prometheus.app.services.base_service import BaseService
@@ -7,6 +9,7 @@
 
 class Neo4jService(BaseService):
     def __init__(self, neo4j_uri: str, neo4j_username: str, neo4j_password: str):
+        self._logger = logging.getLogger("prometheus.app.services.neo4j_service")
         self.neo4j_driver = GraphDatabase.driver(
             neo4j_uri,
             auth=(neo4j_username, neo4j_password),
@@ -17,3 +20,4 @@ def __init__(self, neo4j_uri: str, neo4j_username: str, neo4j_password: str):
 
     def close(self):
         self.neo4j_driver.close()
+        self._logger.info("Neo4j driver connection closed.")

From b1f42a673baf4b10262cb09fec1c25c5a424781a Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:05:28 +0800
Subject: [PATCH 21/55] Update user model field constraints for username,
 email, and github_token

---
 prometheus/app/entity/user.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/prometheus/app/entity/user.py b/prometheus/app/entity/user.py
index 6ed3776c..e6bdf13f 100644
--- a/prometheus/app/entity/user.py
+++ b/prometheus/app/entity/user.py
@@ -5,15 +5,18 @@ class User(SQLModel, table=True):
     id: int = Field(primary_key=True, description="User ID")
 
     username: str = Field(
-        index=True, unique=True, max_length=50, description="Username of the user"
+        index=True, unique=True, max_length=20, description="Username of the user"
     )
     email: str = Field(
-        index=True, unique=True, max_length=100, description="Email address of the user"
+        index=True, unique=True, max_length=30, description="Email address of the user"
     )
     password_hash: str = Field(max_length=128, description="Hashed password of the user")
 
     github_token: str = Field(
-        default=None, nullable=True, description="Optional GitHub token for integrations"
+        default=None,
+        nullable=True,
+        description="Optional GitHub token for integrations",
+        max_length=100,
     )
 
     issue_credit: int = Field(default=0, ge=0, description="Number of issue credits the user has")

From f18839ea3ef9ac51d57f3624270c4a6e3c9dbef4 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:15:17 +0800
Subject: [PATCH 22/55] Add UserService and user model for user management

---
 prometheus/app/dependencies.py          |  3 +
 prometheus/app/models/requests/user.py  | 27 +++++++++
 prometheus/app/services/user_service.py | 78 +++++++++++++++++++++++++
 3 files changed, 108 insertions(+)
 create mode 100644 prometheus/app/models/requests/user.py
 create mode 100644 prometheus/app/services/user_service.py

diff --git a/prometheus/app/dependencies.py b/prometheus/app/dependencies.py
index 6b5a02bb..c66b7470 100644
--- a/prometheus/app/dependencies.py
+++ b/prometheus/app/dependencies.py
@@ -7,6 +7,7 @@
 from prometheus.app.services.llm_service import LLMService
 from prometheus.app.services.neo4j_service import Neo4jService
 from prometheus.app.services.repository_service import RepositoryService
+from prometheus.app.services.user_service import UserService
 from prometheus.configuration.config import settings
 
 
@@ -60,6 +61,7 @@ def initialize_services() -> dict[str, BaseService]:
         settings.WORKING_DIRECTORY,
     )
     database_service = DatabaseService(settings.DATABASE_URL)
+    user_service = UserService(database_service)
 
     return {
         "neo4j_service": neo4j_service,
@@ -68,4 +70,5 @@ def initialize_services() -> dict[str, BaseService]:
         "repository_service": repository_service,
         "issue_service": issue_service,
         "database_service": database_service,
+        "user_service": user_service,
     }
diff --git a/prometheus/app/models/requests/user.py b/prometheus/app/models/requests/user.py
new file mode 100644
index 00000000..c3f4dbfd
--- /dev/null
+++ b/prometheus/app/models/requests/user.py
@@ -0,0 +1,27 @@
+import re
+
+from pydantic import BaseModel, Field, field_validator
+
+
+class CreateUserRequest(BaseModel):
+    username: str = Field(description="username of the user", max_length=20)
+    email: str = Field(
+        description="email of the user",
+        examples=["your_email@gmail.com"],
+        max_length=30,
+    )
+    password: str = Field(
+        description="password of the user",
+        examples=["P@ssw0rd!"],
+        min_length=12,
+        max_length=30,
+    )
+    github_token: str = Field(description="github token of the user", max_length=100)
+
+    @field_validator("email", mode="after")
+    @classmethod
+    def validate_email_format(cls, v: str) -> str:
+        pattern = r"^[^@\s]+@[^@\s]+\.[^@\s]+$"
+        if not re.match(pattern, v):
+            raise ValueError("Invalid email format")
+        return v
diff --git a/prometheus/app/services/user_service.py b/prometheus/app/services/user_service.py
new file mode 100644
index 00000000..a4669a74
--- /dev/null
+++ b/prometheus/app/services/user_service.py
@@ -0,0 +1,78 @@
+import logging
+from typing import Optional
+
+from passlib.hash import bcrypt
+from sqlmodel import Session
+
+from prometheus.app.entity.user import User
+from prometheus.app.services.base_service import BaseService
+from prometheus.app.services.database_service import DatabaseService
+
+
+class UserService(BaseService):
+    def __init__(self, database_service: DatabaseService):
+        self.database_service = database_service
+        self.engine = database_service.engine
+        self._logger = logging.getLogger("prometheus.app.services.user_service")
+
+    def create_user(
+        self,
+        username: str,
+        email: str,
+        password: str,
+        github_token: Optional[str] = None,
+        issue_credit: int = 0,
+        is_superuser: bool = False,
+    ) -> None:
+        """
+        Create a new user in the database.
+
+        This method is a placeholder and should be implemented with actual user creation logic.
+        """
+        """
+                Create a new superuser and commit it to the database.
+
+                Args:
+                    username (str): Desired username.
+                    email (str): Email address.
+                    password (str): Plaintext password (will be hashed).
+                    github_token (Optional[str]): Optional GitHub token.
+
+                Returns:
+                    User: The created superuser instance.
+                """
+        with Session(self.engine) as session:
+            if session.query(User).filter(User.username == username).first():
+                raise ValueError(f"Username '{username}' already exists")
+            if session.query(User).filter(User.email == email).first():
+                raise ValueError(f"Email '{email}' already exists")
+
+            hashed_password = bcrypt.hash(password)
+
+            user = User(
+                username=username,
+                email=email,
+                password_hash=hashed_password,
+                github_token=github_token,
+                issue_credit=issue_credit,
+                is_superuser=is_superuser,
+            )
+            session.add(user)
+            session.commit()
+            session.refresh(user)
+
+    # Create a superuser and commit it to the database
+    def create_superuser(
+        self,
+        username: str,
+        email: str,
+        password: str,
+        github_token: Optional[str] = None,
+    ) -> None:
+        """
+        Create a new superuser in the database.
+
+        This method creates a superuser with the provided credentials and commits it to the database.
+        """
+        self.create_user(username, email, password, github_token, is_superuser=True)
+        self._logger.info(f"Superuser '{username}' created successfully.")

From 971008f73f0d794e4068cedb1bfd36c8dae30e16 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:19:13 +0800
Subject: [PATCH 23/55] Add start method to BaseService and DatabaseService for
 service initialization

---
 prometheus/app/main.py                      | 3 +++
 prometheus/app/services/base_service.py     | 7 +++++++
 prometheus/app/services/database_service.py | 8 ++++++++
 3 files changed, 18 insertions(+)

diff --git a/prometheus/app/main.py b/prometheus/app/main.py
index 13e72e37..037bbda0 100644
--- a/prometheus/app/main.py
+++ b/prometheus/app/main.py
@@ -39,6 +39,9 @@
 async def lifespan(app: FastAPI):
     # Initialization on startup
     app.state.service = dependencies.initialize_services()
+    logger.info("Starting services...")
+    for service in app.state.service.values():
+        service.start()
     # Initialization Completed
     yield
     # Cleanup on shutdown
diff --git a/prometheus/app/services/base_service.py b/prometheus/app/services/base_service.py
index 9b55a597..4bb9ff0d 100644
--- a/prometheus/app/services/base_service.py
+++ b/prometheus/app/services/base_service.py
@@ -3,6 +3,13 @@ class BaseService:
     Base class for all services in the Prometheus application.
     """
 
+    def start(self):
+        """
+        Start the service.
+        This method should be overridden by subclasses to implement specific startup logic.
+        """
+        pass
+
     def close(self):
         """
         Close the service and release any resources.
diff --git a/prometheus/app/services/database_service.py b/prometheus/app/services/database_service.py
index 42b684d6..ae4cfc7b 100644
--- a/prometheus/app/services/database_service.py
+++ b/prometheus/app/services/database_service.py
@@ -14,6 +14,14 @@ def __init__(self, DATABASE_URL: str):
     def create_db_and_tables(self):
         SQLModel.metadata.create_all(self.engine)
 
+    def start(self):
+        """
+        Start the database service by creating the database and tables.
+        This method is called when the service is initialized.
+        """
+        self.create_db_and_tables()
+        self._logger.info("Database and tables created successfully.")
+
     def close(self):
         """
         Close the database connection and release any resources.

From 0f4117251215f86c7a471ad4aa5da525338beadf Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:22:34 +0800
Subject: [PATCH 24/55] delete create_db_and_tables.py

---
 prometheus/script/create_db_and_tables.py | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 prometheus/script/create_db_and_tables.py

diff --git a/prometheus/script/create_db_and_tables.py b/prometheus/script/create_db_and_tables.py
deleted file mode 100644
index 3147c90e..00000000
--- a/prometheus/script/create_db_and_tables.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from prometheus.app.db import create_db_and_tables
-
-if __name__ == "__main__":
-    create_db_and_tables()

From b6a66a4a936a001d16e7648e40c4542c4021ad01 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:38:26 +0800
Subject: [PATCH 25/55] Add superuser creation functionality with email
 validation

---
 prometheus/app/services/user_service.py |  4 +++-
 prometheus/script/create_superuser.py   | 14 ++++++++++++--
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/prometheus/app/services/user_service.py b/prometheus/app/services/user_service.py
index a4669a74..3328e821 100644
--- a/prometheus/app/services/user_service.py
+++ b/prometheus/app/services/user_service.py
@@ -74,5 +74,7 @@ def create_superuser(
 
         This method creates a superuser with the provided credentials and commits it to the database.
         """
-        self.create_user(username, email, password, github_token, is_superuser=True)
+        self.create_user(
+            username, email, password, github_token, is_superuser=True, issue_credit=999999
+        )
         self._logger.info(f"Superuser '{username}' created successfully.")
diff --git a/prometheus/script/create_superuser.py b/prometheus/script/create_superuser.py
index bf6bf5f9..20829308 100644
--- a/prometheus/script/create_superuser.py
+++ b/prometheus/script/create_superuser.py
@@ -1,6 +1,12 @@
 import argparse
+import re
 
-from prometheus.app.db import create_superuser
+from prometheus.app.services.database_service import DatabaseService
+from prometheus.app.services.user_service import UserService
+from prometheus.configuration.config import settings
+
+database_service: DatabaseService = DatabaseService(settings.DATABASE_URL)
+user_service: UserService = UserService(database_service)
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Create a superuser account.")
@@ -11,7 +17,11 @@
 
     args = parser.parse_args()
 
-    create_superuser(
+    pattern = r"^[^@\s]+@[^@\s]+\.[^@\s]+$"
+    if not re.match(pattern, args.email):
+        raise ValueError("Invalid email format")
+
+    user_service.create_superuser(
         username=args.username,
         email=args.email,
         password=args.password,

From 23403939d6b682302fa682d223580a352583dd4f Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:41:11 +0800
Subject: [PATCH 26/55] Refactor user creation method documentation to include
 issue_credit parameter and clarify superuser creation

---
 prometheus/app/services/user_service.py | 24 ++++++++++--------------
 1 file changed, 10 insertions(+), 14 deletions(-)

diff --git a/prometheus/app/services/user_service.py b/prometheus/app/services/user_service.py
index 3328e821..3412d0c1 100644
--- a/prometheus/app/services/user_service.py
+++ b/prometheus/app/services/user_service.py
@@ -25,22 +25,18 @@ def create_user(
         is_superuser: bool = False,
     ) -> None:
         """
-        Create a new user in the database.
+        Create a new superuser and commit it to the database.
 
-        This method is a placeholder and should be implemented with actual user creation logic.
+        Args:
+            username (str): Desired username.
+            email (str): Email address.
+            password (str): Plaintext password (will be hashed).
+            github_token (Optional[str]): Optional GitHub token.
+            issue_credit (int): Optional issue credit.
+            is_superuser (bool): Whether the user is a superuser.
+        Returns:
+            User: The created superuser instance.
         """
-        """
-                Create a new superuser and commit it to the database.
-
-                Args:
-                    username (str): Desired username.
-                    email (str): Email address.
-                    password (str): Plaintext password (will be hashed).
-                    github_token (Optional[str]): Optional GitHub token.
-
-                Returns:
-                    User: The created superuser instance.
-                """
         with Session(self.engine) as session:
             if session.query(User).filter(User.username == username).first():
                 raise ValueError(f"Username '{username}' already exists")

From 0e662b9a26cb7d25c8d62b2a563cb5de95a0a6a5 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:52:51 +0800
Subject: [PATCH 27/55] Replace bcrypt with argon2 for password hashing in user
 creation

---
 prometheus/app/services/user_service.py | 5 +++--
 pyproject.toml                          | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/prometheus/app/services/user_service.py b/prometheus/app/services/user_service.py
index 3412d0c1..29d1d1d4 100644
--- a/prometheus/app/services/user_service.py
+++ b/prometheus/app/services/user_service.py
@@ -1,7 +1,7 @@
 import logging
 from typing import Optional
 
-from passlib.hash import bcrypt
+from argon2 import PasswordHasher
 from sqlmodel import Session
 
 from prometheus.app.entity.user import User
@@ -14,6 +14,7 @@ def __init__(self, database_service: DatabaseService):
         self.database_service = database_service
         self.engine = database_service.engine
         self._logger = logging.getLogger("prometheus.app.services.user_service")
+        self.ph = PasswordHasher()
 
     def create_user(
         self,
@@ -43,7 +44,7 @@ def create_user(
             if session.query(User).filter(User.email == email).first():
                 raise ValueError(f"Email '{email}' already exists")
 
-            hashed_password = bcrypt.hash(password)
+            hashed_password = self.ph.hash(password)
 
             user = User(
                 username=username,
diff --git a/pyproject.toml b/pyproject.toml
index 43acfb9b..9d02d232 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,7 @@ dependencies = [
   "dynaconf>=3.2.6",
   "docker>=7.1.0",
   "unidiff>=0.7.5",
-  "passlib[bcrypt]>=1.7.4",
+  "argon2-cffi>=23.1.0",
   "sqlmodel==0.0.24",
   "psycopg2-binary"
 ]

From 4e1a11785f6c48f4809db48faba64fe7a7da162e Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 15:59:40 +0800
Subject: [PATCH 28/55] Fix import path for FileOperationException and rename
 exception file

---
 ...file_operation_exceptions.py => file_operation_exception.py} | 0
 prometheus/lang_graph/nodes/context_extraction_node.py          | 2 +-
 prometheus/utils/file_utils.py                                  | 2 +-
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename prometheus/exceptions/{file_operation_exceptions.py => file_operation_exception.py} (100%)

diff --git a/prometheus/exceptions/file_operation_exceptions.py b/prometheus/exceptions/file_operation_exception.py
similarity index 100%
rename from prometheus/exceptions/file_operation_exceptions.py
rename to prometheus/exceptions/file_operation_exception.py
diff --git a/prometheus/lang_graph/nodes/context_extraction_node.py b/prometheus/lang_graph/nodes/context_extraction_node.py
index e1f8db73..cf331b34 100644
--- a/prometheus/lang_graph/nodes/context_extraction_node.py
+++ b/prometheus/lang_graph/nodes/context_extraction_node.py
@@ -5,7 +5,7 @@
 from langchain_core.messages import SystemMessage
 from pydantic import BaseModel, Field
 
-from prometheus.exceptions.file_operation_exceptions import FileOperationException
+from prometheus.exceptions.file_operation_exception import FileOperationException
 from prometheus.lang_graph.subgraphs.context_retrieval_state import ContextRetrievalState
 from prometheus.models.context import Context
 from prometheus.utils.file_utils import read_file_with_line_numbers
diff --git a/prometheus/utils/file_utils.py b/prometheus/utils/file_utils.py
index fb3252af..c63f79dd 100644
--- a/prometheus/utils/file_utils.py
+++ b/prometheus/utils/file_utils.py
@@ -1,7 +1,7 @@
 import os
 from pathlib import Path
 
-from prometheus.exceptions.file_operation_exceptions import FileOperationException
+from prometheus.exceptions.file_operation_exception import FileOperationException
 
 
 def read_file_with_line_numbers(

From 03b2f4f7bd9834fc131a743b9098f1e213b71cf6 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:02:20 +0800
Subject: [PATCH 29/55] Add JWT configuration settings to config and
 example.env

---
 example.env                        | 3 +++
 prometheus/configuration/config.py | 4 ++++
 2 files changed, 7 insertions(+)

diff --git a/example.env b/example.env
index 6dd48b14..3283dffb 100644
--- a/example.env
+++ b/example.env
@@ -35,3 +35,6 @@ PROMETHEUS_MAX_OUTPUT_TOKENS=15000
 
 # Database settings
 PROMETHEUS_DATABASE_URL=postgresql://postgres:password@localhost:5432/postgres?sslmode=disable
+
+# JWT settings
+PROMETHEUS_JWT_SECRET_KEY=your_jwt_secret_key
diff --git a/prometheus/configuration/config.py b/prometheus/configuration/config.py
index e43b8484..f9320acb 100644
--- a/prometheus/configuration/config.py
+++ b/prometheus/configuration/config.py
@@ -48,5 +48,9 @@ class Settings(BaseSettings):
     # Database
     DATABASE_URL: str
 
+    # JWT Configuration
+    JWT_SECRET_KEY: str
+    ACCESS_TOKEN_EXPIRE_TIME: int = 7  # days
+
 
 settings = Settings()

From e14e7e520390ce003fadd45c0aa2c421a806c036 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:02:54 +0800
Subject: [PATCH 30/55] Add JWTException and ServerException classes for error
 handling

---
 prometheus/exceptions/jwt_exception.py    | 12 ++++++++++++
 prometheus/exceptions/server_exception.py | 10 ++++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 prometheus/exceptions/jwt_exception.py
 create mode 100644 prometheus/exceptions/server_exception.py

diff --git a/prometheus/exceptions/jwt_exception.py b/prometheus/exceptions/jwt_exception.py
new file mode 100644
index 00000000..d5589110
--- /dev/null
+++ b/prometheus/exceptions/jwt_exception.py
@@ -0,0 +1,12 @@
+from prometheus.exceptions.server_exception import ServerException
+
+
+class JWTException(ServerException):
+    """
+    class for JWT exceptions.
+    This exception is raised when there is an issue with JWT operations,
+    such as token generation or validation.
+    """
+
+    def __init__(self, code: int = 401, message: str = "An error occurred with the JWT operation."):
+        super().__init__(code, message)
diff --git a/prometheus/exceptions/server_exception.py b/prometheus/exceptions/server_exception.py
new file mode 100644
index 00000000..5bf81cc7
--- /dev/null
+++ b/prometheus/exceptions/server_exception.py
@@ -0,0 +1,10 @@
+class ServerException(Exception):
+    """
+    Base class for server exceptions.
+    This exception is raised when there is an issue with server operations.
+    """
+
+    def __init__(self, code: int, message: str):
+        super().__init__(message)
+        self.code = code
+        self.message = message

From c5d5a588c398d0c08619f6f60bb535bd447dced3 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:06:35 +0800
Subject: [PATCH 31/55] Add JWT utility class for token generation and
 validation

---
 prometheus/utils/jwt_utils.py | 32 ++++++++++++++++++++++++++++++++
 pyproject.toml                |  3 ++-
 2 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 prometheus/utils/jwt_utils.py

diff --git a/prometheus/utils/jwt_utils.py b/prometheus/utils/jwt_utils.py
new file mode 100644
index 00000000..db3971e8
--- /dev/null
+++ b/prometheus/utils/jwt_utils.py
@@ -0,0 +1,32 @@
+import datetime
+import jwt
+from prometheus.configuration.config import settings
+
+from prometheus.exceptions.jwt_exception import JWTException
+
+
+class JWTUtils:
+    """JWT Utility for token generation and validation"""
+
+    def __init__(self, algorithm='HS256'):
+        """Initialize JWT utils with configuration"""
+        self.secret_key = settings.JWT_SECRET_KEY
+        self.algorithm = algorithm
+        self.expire_time = int(settings.ACCESS_TOKEN_EXPIRE_TIME)
+
+    def generate_token(self, payload):
+        """Generate JWT token"""
+        payload_copy = payload.copy()
+        payload_copy['exp'] = datetime.datetime.now() + datetime.timedelta(days=self.expire_time)
+        token = jwt.encode(payload_copy, self.secret_key, algorithm=self.algorithm)
+        return token
+
+    def decode_token(self, token):
+        """Decode and parse JWT token"""
+        try:
+            decoded = jwt.decode(token, self.secret_key, algorithms=[self.algorithm])
+            return decoded
+        except jwt.ExpiredSignatureError:
+            raise JWTException(message="Token expired")
+        except jwt.InvalidTokenError:
+            raise JWTException(message="Invalid token")
diff --git a/pyproject.toml b/pyproject.toml
index 9d02d232..1d163fcb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,7 +26,8 @@ dependencies = [
   "unidiff>=0.7.5",
   "argon2-cffi>=23.1.0",
   "sqlmodel==0.0.24",
-  "psycopg2-binary"
+  "psycopg2-binary",
+  "pyjwt==2.6.0",
 ]
 requires-python = ">= 3.11"
 

From 0ceb27d55a063b04a9a031864570572d48265702 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:13:12 +0800
Subject: [PATCH 32/55] Add script to generate secure JWT secret token and
 update README

---
 README.md                               | 10 ++++++++++
 prometheus/script/generate_jwt_token.py | 15 +++++++++++++++
 2 files changed, 25 insertions(+)
 create mode 100644 prometheus/script/generate_jwt_token.py

diff --git a/README.md b/README.md
index f2ccaba8..780984ac 100644
--- a/README.md
+++ b/README.md
@@ -73,10 +73,20 @@ governed by a state machine to ensure code quality through automated reviews, bu
    ```
 
 2. #### Copy the `example.env` file to `.env` and update it with your API keys and other required configurations:
+
    ```bash
    mv example.env .env
    ```
 
+   > You need to provide a secure `JWT_SECRET_KEY` in the `.env` file.
+   > You can generate a strong key by running the following command:
+
+   ```bash
+   python -m prometheus.script.generate_jwt_token
+   ```
+
+   This will print a secure token you can copy and paste into your `.env` file
+
 3. #### Create the working directory to store logs and cloned repositories:
 
    ```bash
diff --git a/prometheus/script/generate_jwt_token.py b/prometheus/script/generate_jwt_token.py
new file mode 100644
index 00000000..5e500c8f
--- /dev/null
+++ b/prometheus/script/generate_jwt_token.py
@@ -0,0 +1,15 @@
+import base64
+import secrets
+
+
+def generate_jwt_secret_token(length: int = 64) -> str:
+    """
+    Generate a secure JWT secret token.
+    """
+    token_bytes = secrets.token_bytes(length)
+    return base64.urlsafe_b64encode(token_bytes).decode("utf-8")
+
+
+if __name__ == "__main__":
+    secret = generate_jwt_secret_token()
+    print(f"JWT_SECRET_TOKEN={secret}")

From b8214ae17e85fa19b6ada832e7fcd285a4445e9e Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:13:27 +0800
Subject: [PATCH 33/55] Refactor JWTUtils to use double quotes for string
 literals and improve code formatting

---
 prometheus/utils/jwt_utils.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/prometheus/utils/jwt_utils.py b/prometheus/utils/jwt_utils.py
index db3971e8..684652f5 100644
--- a/prometheus/utils/jwt_utils.py
+++ b/prometheus/utils/jwt_utils.py
@@ -1,14 +1,15 @@
 import datetime
+
 import jwt
-from prometheus.configuration.config import settings
 
+from prometheus.configuration.config import settings
 from prometheus.exceptions.jwt_exception import JWTException
 
 
 class JWTUtils:
     """JWT Utility for token generation and validation"""
 
-    def __init__(self, algorithm='HS256'):
+    def __init__(self, algorithm="HS256"):
         """Initialize JWT utils with configuration"""
         self.secret_key = settings.JWT_SECRET_KEY
         self.algorithm = algorithm
@@ -17,7 +18,7 @@ def __init__(self, algorithm='HS256'):
     def generate_token(self, payload):
         """Generate JWT token"""
         payload_copy = payload.copy()
-        payload_copy['exp'] = datetime.datetime.now() + datetime.timedelta(days=self.expire_time)
+        payload_copy["exp"] = datetime.datetime.now() + datetime.timedelta(days=self.expire_time)
         token = jwt.encode(payload_copy, self.secret_key, algorithm=self.algorithm)
         return token
 

From 77f3418f0595d514e8e019273cc844d5eb5e955c Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:28:08 +0800
Subject: [PATCH 34/55] Add authentication module with login request and
 response models

---
 prometheus/app/api/auth.py              | 29 +++++++++++++++++++++++
 prometheus/app/models/requests/auth.py  | 31 +++++++++++++++++++++++++
 prometheus/app/models/requests/user.py  |  3 +--
 prometheus/app/models/response/auth.py  |  9 +++++++
 prometheus/app/services/user_service.py | 28 ++++++++++++++++++++++
 5 files changed, 98 insertions(+), 2 deletions(-)
 create mode 100644 prometheus/app/api/auth.py
 create mode 100644 prometheus/app/models/requests/auth.py
 create mode 100644 prometheus/app/models/response/auth.py

diff --git a/prometheus/app/api/auth.py b/prometheus/app/api/auth.py
new file mode 100644
index 00000000..6feb6e17
--- /dev/null
+++ b/prometheus/app/api/auth.py
@@ -0,0 +1,29 @@
+from fastapi import APIRouter, Request
+
+from prometheus.app.models.requests.auth import LoginRequest
+from prometheus.app.models.response.auth import LoginResponse
+from prometheus.app.services.user_service import UserService
+
+router = APIRouter()
+
+
+@router.post(
+    "/login/",
+    summary="Login to the system",
+    description="Login to the system using username, email, and password. Returns an access token.",
+    response_description="Returns an access token for authenticated requests",
+    response_model=LoginResponse,
+)
+def login(login_request: LoginRequest, request: Request) -> LoginResponse:
+    """
+    Login to the system using username, email, and password.
+    Returns an access token for authenticated requests.
+    """
+
+    user_service: UserService = request.app.state.service["user_service"]
+    access_token = user_service.login(
+        username=login_request.username,
+        email=login_request.email,
+        password=login_request.password,
+    )
+    return LoginResponse(access_token=access_token)
diff --git a/prometheus/app/models/requests/auth.py b/prometheus/app/models/requests/auth.py
new file mode 100644
index 00000000..96ef3fea
--- /dev/null
+++ b/prometheus/app/models/requests/auth.py
@@ -0,0 +1,31 @@
+import re
+
+from pydantic import BaseModel, Field, field_validator, model_validator
+
+
+class LoginRequest(BaseModel):
+    username: str = Field(description="username of the user", max_length=20)
+    email: str = Field(
+        description="email of the user",
+        examples=["your_email@gmail.com"],
+        max_length=30,
+    )
+    password: str = Field(
+        description="password of the user",
+        examples=["P@ssw0rd!"],
+        min_length=12,
+        max_length=30,
+    )
+
+    @field_validator("email", mode="after")
+    def validate_email_format(self, v: str) -> str:
+        pattern = r"^[^@\s]+@[^@\s]+\.[^@\s]+$"
+        if not re.match(pattern, v):
+            raise ValueError("Invalid email format")
+        return v
+
+    @model_validator(mode="after")
+    def check_username_or_email(self) -> "LoginRequest":
+        if not self.username and not self.email:
+            raise ValueError("At least one of 'username' or 'email' must be provided.")
+        return self
diff --git a/prometheus/app/models/requests/user.py b/prometheus/app/models/requests/user.py
index c3f4dbfd..6a0e3144 100644
--- a/prometheus/app/models/requests/user.py
+++ b/prometheus/app/models/requests/user.py
@@ -19,8 +19,7 @@ class CreateUserRequest(BaseModel):
     github_token: str = Field(description="github token of the user", max_length=100)
 
     @field_validator("email", mode="after")
-    @classmethod
-    def validate_email_format(cls, v: str) -> str:
+    def validate_email_format(self, v: str) -> str:
         pattern = r"^[^@\s]+@[^@\s]+\.[^@\s]+$"
         if not re.match(pattern, v):
             raise ValueError("Invalid email format")
diff --git a/prometheus/app/models/response/auth.py b/prometheus/app/models/response/auth.py
new file mode 100644
index 00000000..56efc9f6
--- /dev/null
+++ b/prometheus/app/models/response/auth.py
@@ -0,0 +1,9 @@
+from pydantic import BaseModel
+
+
+class LoginResponse(BaseModel):
+    """
+    Response model for user login.
+    """
+
+    access_token: str
diff --git a/prometheus/app/services/user_service.py b/prometheus/app/services/user_service.py
index 29d1d1d4..e865c943 100644
--- a/prometheus/app/services/user_service.py
+++ b/prometheus/app/services/user_service.py
@@ -7,6 +7,7 @@
 from prometheus.app.entity.user import User
 from prometheus.app.services.base_service import BaseService
 from prometheus.app.services.database_service import DatabaseService
+from prometheus.utils.jwt_utils import JWTUtils
 
 
 class UserService(BaseService):
@@ -15,6 +16,7 @@ def __init__(self, database_service: DatabaseService):
         self.engine = database_service.engine
         self._logger = logging.getLogger("prometheus.app.services.user_service")
         self.ph = PasswordHasher()
+        self.jwt_utils = JWTUtils()
 
     def create_user(
         self,
@@ -58,6 +60,32 @@ def create_user(
             session.commit()
             session.refresh(user)
 
+    def login(self, username: str, email: str, password: str) -> str:
+        """
+        Log in a user by verifying their credentials and return an access token.
+
+        Args:
+            username (str): Username of the user.
+            email (str): Email address of the user.
+            password (str): Plaintext password.
+        """
+        with Session(self.engine) as session:
+            user = (
+                session.query(User)
+                .filter((User.username == username) | (User.email == email))
+                .first()
+            )
+
+            if not user:
+                raise ValueError("Invalid username or email")
+
+            if not self.ph.verify(user.password_hash, password):
+                raise ValueError("Invalid password")
+
+            # Generate and return a JWT token for the user
+            token = self.jwt_utils.generate_token({"user_id": user.id})
+            return token
+
     # Create a superuser and commit it to the database
     def create_superuser(
         self,

From cbd70829844f3c26d41bd9a7d3300b777cf24f19 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:38:17 +0800
Subject: [PATCH 35/55] Add IssueResponse model and update answer_issue
 function to return structured response

---
 prometheus/app/api/issue.py             | 20 +++++++++++---------
 prometheus/app/models/response/issue.py | 10 ++++++++++
 2 files changed, 21 insertions(+), 9 deletions(-)
 create mode 100644 prometheus/app/models/response/issue.py

diff --git a/prometheus/app/api/issue.py b/prometheus/app/api/issue.py
index 10bd5753..e155b564 100644
--- a/prometheus/app/api/issue.py
+++ b/prometheus/app/api/issue.py
@@ -1,6 +1,7 @@
 from fastapi import APIRouter, HTTPException, Request
 
 from prometheus.app.models.requests.issue import IssueRequest
+from prometheus.app.models.response.issue import IssueResponse
 
 router = APIRouter()
 
@@ -10,8 +11,9 @@
     summary="Process and generate a response for an issue",
     description="Analyzes an issue, generates patches if needed, runs optional builds and tests, and can push changes to a remote branch.",
     response_description="Returns the patch, test results, and issue response",
+    response_model=IssueResponse,
 )
-def answer_issue(issue: IssueRequest, request: Request):
+def answer_issue(issue: IssueRequest, request: Request) -> IssueResponse:
     if not request.app.state.service["knowledge_graph_service"].exists():
         raise HTTPException(
             status_code=404,
@@ -48,11 +50,11 @@ def answer_issue(issue: IssueRequest, request: Request):
         test_commands=issue.test_commands,
         push_to_remote=issue.push_to_remote,
     )
-    return {
-        "patch": patch,
-        "passed_reproducing_test": passed_reproducing_test,
-        "passed_build": passed_build,
-        "passed_existing_test": passed_existing_test,
-        "issue_response": issue_response,
-        "remote_branch_name": remote_branch_name,
-    }
+    return IssueResponse(
+        patch=patch,
+        passed_reproducing_test=passed_reproducing_test,
+        passed_build=passed_build,
+        passed_existing_test=passed_existing_test,
+        issue_response=issue_response,
+        remote_branch_name=remote_branch_name,
+    )
diff --git a/prometheus/app/models/response/issue.py b/prometheus/app/models/response/issue.py
new file mode 100644
index 00000000..d06f46a7
--- /dev/null
+++ b/prometheus/app/models/response/issue.py
@@ -0,0 +1,10 @@
+from pydantic import BaseModel
+
+
+class IssueResponse(BaseModel):
+    patch: str
+    passed_reproducing_test: bool
+    passed_build: bool
+    passed_existing_test: bool
+    issue_response: str
+    remote_branch_name: str | None = None

From b36286ce3f03189a5fa1471a2ff321544c9fa13a Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:48:46 +0800
Subject: [PATCH 36/55] Refactor upload_github_repository functions to raise
 ServerException on clone errors

---
 prometheus/app/api/repository.py | 55 +++++++++++++++-----------------
 1 file changed, 26 insertions(+), 29 deletions(-)

diff --git a/prometheus/app/api/repository.py b/prometheus/app/api/repository.py
index cb177555..78a717f7 100644
--- a/prometheus/app/api/repository.py
+++ b/prometheus/app/api/repository.py
@@ -1,8 +1,9 @@
 import git
-from fastapi import APIRouter, HTTPException, Request
+from fastapi import APIRouter, Request
 
 from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
 from prometheus.app.services.repository_service import RepositoryService
+from prometheus.exceptions.server_exception import ServerException
 
 router = APIRouter()
 
@@ -14,23 +15,22 @@
     """,
 )
 def upload_github_repository(github_token: str, https_url: str, request: Request):
-    try:
-        # Get the repository and knowledge graph services
-        repository_service: RepositoryService = request.app.state.service["repository_service"]
-        knowledge_graph_service: KnowledgeGraphService = request.app.state.service[
-            "knowledge_graph_service"
-        ]
-
-        # Clean the services to ensure no previous data is present
-        repository_service.clean()
-        knowledge_graph_service.clear()
+    # Get the repository and knowledge graph services
+    repository_service: RepositoryService = request.app.state.service["repository_service"]
+    knowledge_graph_service: KnowledgeGraphService = request.app.state.service[
+        "knowledge_graph_service"
+    ]
 
+    # Clean the services to ensure no previous data is present
+    repository_service.clean()
+    knowledge_graph_service.clear()
+    try:
         # Clone the repository
         saved_path = repository_service.clone_github_repo(github_token, https_url)
-        # Build and save the knowledge graph from the cloned repository
-        knowledge_graph_service.build_and_save_knowledge_graph(saved_path, https_url)
     except git.exc.GitCommandError:
-        raise HTTPException(status_code=400, detail=f"Unable to clone {https_url}")
+        raise ServerException(code=400, message=f"Unable to clone {https_url}")
+    # Build and save the knowledge graph from the cloned repository
+    knowledge_graph_service.build_and_save_knowledge_graph(saved_path, https_url)
 
 
 @router.get(
@@ -42,26 +42,23 @@ def upload_github_repository(github_token: str, https_url: str, request: Request
 def upload_github_repository_at_commit(
     github_token, https_url: str, commit_id: str, request: Request
 ):
-    try:
-        # Get the repository and knowledge graph services
-        repository_service: RepositoryService = request.app.state.service["repository_service"]
-        knowledge_graph_service: KnowledgeGraphService = request.app.state.service[
-            "knowledge_graph_service"
-        ]
+    # Get the repository and knowledge graph services
+    repository_service: RepositoryService = request.app.state.service["repository_service"]
+    knowledge_graph_service: KnowledgeGraphService = request.app.state.service[
+        "knowledge_graph_service"
+    ]
 
-        # Clean the services to ensure no previous data is present
-        repository_service.clean()
-        knowledge_graph_service.clear()
+    # Clean the services to ensure no previous data is present
+    repository_service.clean()
+    knowledge_graph_service.clear()
 
+    try:
         # Clone the repository
         saved_path = repository_service.clone_github_repo(github_token, https_url, commit_id)
-
-        # Build and save the knowledge graph from the cloned repository
-        knowledge_graph_service.build_and_save_knowledge_graph(saved_path, https_url, commit_id)
     except git.exc.GitCommandError:
-        raise HTTPException(
-            status_code=400, detail=f"Unable to clone {https_url} with commit {commit_id}"
-        )
+        raise ServerException(code=400, message=f"Unable to clone {https_url}")
+    # Build and save the knowledge graph from the cloned repository
+    knowledge_graph_service.build_and_save_knowledge_graph(saved_path, https_url, commit_id)
 
 
 @router.get(

From 8f87edaeb0ae8ebecf2b995f81d6e06623bf0078 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 16:50:13 +0800
Subject: [PATCH 37/55] Add global exception handlers for FastAPI application

---
 prometheus/app/exception_handler.py | 26 ++++++++++++++++++++++++++
 prometheus/app/main.py              |  4 ++++
 2 files changed, 30 insertions(+)
 create mode 100644 prometheus/app/exception_handler.py

diff --git a/prometheus/app/exception_handler.py b/prometheus/app/exception_handler.py
new file mode 100644
index 00000000..2a9a56f0
--- /dev/null
+++ b/prometheus/app/exception_handler.py
@@ -0,0 +1,26 @@
+from fastapi import FastAPI, Request
+from fastapi.responses import JSONResponse
+
+from prometheus.exceptions.server_exception import ServerException
+
+
+def register_exception_handlers(app: FastAPI):
+    """Global exception handlers for the FastAPI application."""
+
+    @app.exception_handler(ServerException)
+    async def custom_exception_handler(_request: Request, exc: ServerException):
+        """
+        Custom exception handler for ServerException.
+        """
+        return JSONResponse(
+            status_code=exc.code, content={"code": exc.code, "message": exc.message, "data": None}
+        )
+
+    @app.exception_handler(Exception)
+    async def global_exception_handler(_request: Request, _exc: Exception):
+        """
+        Global exception handler for all uncaught exceptions.
+        """
+        return JSONResponse(
+            status_code=500, content={"code": 500, "message": "Internal Server Error", "data": None}
+        )
diff --git a/prometheus/app/main.py b/prometheus/app/main.py
index 037bbda0..fe7bc600 100644
--- a/prometheus/app/main.py
+++ b/prometheus/app/main.py
@@ -7,6 +7,7 @@
 
 from prometheus.app import dependencies
 from prometheus.app.api import issue, repository
+from prometheus.app.exception_handler import register_exception_handlers
 from prometheus.configuration.config import settings
 
 # Create a logger for the application's namespace
@@ -66,6 +67,9 @@ def custom_generate_unique_id(route: APIRoute) -> str:
     debug=True if settings.ENVIRONMENT == "local" else False,
 )
 
+# Register the exception handlers
+register_exception_handlers(app)
+
 app.include_router(repository.router, prefix="/repository", tags=["repository"])
 app.include_router(issue.router, prefix="/issue", tags=["issue"])
 

From 2151208ff2355990825176672cf99415dbab02e0 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 17:00:20 +0800
Subject: [PATCH 38/55] add unified return json format

---
 prometheus/app/main.py                        |  4 +++
 prometheus/app/middlewares/__init__.py        |  0
 .../response_wrapper_middleware.py            | 25 +++++++++++++++++++
 3 files changed, 29 insertions(+)
 create mode 100644 prometheus/app/middlewares/__init__.py
 create mode 100644 prometheus/app/middlewares/response_wrapper_middleware.py

diff --git a/prometheus/app/main.py b/prometheus/app/main.py
index fe7bc600..b04db85b 100644
--- a/prometheus/app/main.py
+++ b/prometheus/app/main.py
@@ -8,6 +8,7 @@
 from prometheus.app import dependencies
 from prometheus.app.api import issue, repository
 from prometheus.app.exception_handler import register_exception_handlers
+from prometheus.app.middlewares.response_wrapper_middleware import ResponseWrapperMiddleware
 from prometheus.configuration.config import settings
 
 # Create a logger for the application's namespace
@@ -67,6 +68,9 @@ def custom_generate_unique_id(route: APIRoute) -> str:
     debug=True if settings.ENVIRONMENT == "local" else False,
 )
 
+# Register middlewares
+app.add_middleware(ResponseWrapperMiddleware)
+
 # Register the exception handlers
 register_exception_handlers(app)
 
diff --git a/prometheus/app/middlewares/__init__.py b/prometheus/app/middlewares/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/prometheus/app/middlewares/response_wrapper_middleware.py b/prometheus/app/middlewares/response_wrapper_middleware.py
new file mode 100644
index 00000000..fea9b792
--- /dev/null
+++ b/prometheus/app/middlewares/response_wrapper_middleware.py
@@ -0,0 +1,25 @@
+from fastapi.responses import JSONResponse
+from starlette.middleware.base import BaseHTTPMiddleware
+from fastapi import Request
+import json
+
+
+class ResponseWrapperMiddleware(BaseHTTPMiddleware):
+    async def dispatch(self, request: Request, call_next):
+        response = await call_next(request)
+        # Check if the response is a JSON response
+        if response.headers.get("content-type") == "application/json":
+            # Decode the JSON response body
+            original_data = json.loads(response.body.decode("utf-8"))
+
+            # Check if the original data is already in the expected format
+            if isinstance(original_data, dict) and set(original_data.keys()) == {"code", "message", "data"}:
+                new_data = original_data
+            else:
+                new_data = {
+                    "code": response.status_code,
+                    "message": "Success",
+                    "data": original_data,
+                }
+            return JSONResponse(content=new_data, status_code=response.status_code)
+        return response

From 60e5787f5f80f8e707580377826ecee954b0fbee Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 17:14:38 +0800
Subject: [PATCH 39/55] Refactor authentication and repository endpoints to use
 a unified response model

---
 prometheus/app/api/auth.py                    |  7 +++---
 prometheus/app/api/repository.py              | 16 ++++++++----
 prometheus/app/main.py                        |  4 ---
 .../response_wrapper_middleware.py            | 25 -------------------
 prometheus/app/models/response/response.py    | 14 +++++++++++
 5 files changed, 29 insertions(+), 37 deletions(-)
 delete mode 100644 prometheus/app/middlewares/response_wrapper_middleware.py
 create mode 100644 prometheus/app/models/response/response.py

diff --git a/prometheus/app/api/auth.py b/prometheus/app/api/auth.py
index 6feb6e17..cb55a352 100644
--- a/prometheus/app/api/auth.py
+++ b/prometheus/app/api/auth.py
@@ -2,6 +2,7 @@
 
 from prometheus.app.models.requests.auth import LoginRequest
 from prometheus.app.models.response.auth import LoginResponse
+from prometheus.app.models.response.response import Response
 from prometheus.app.services.user_service import UserService
 
 router = APIRouter()
@@ -12,9 +13,9 @@
     summary="Login to the system",
     description="Login to the system using username, email, and password. Returns an access token.",
     response_description="Returns an access token for authenticated requests",
-    response_model=LoginResponse,
+    response_model=Response[LoginResponse],
 )
-def login(login_request: LoginRequest, request: Request) -> LoginResponse:
+def login(login_request: LoginRequest, request: Request) -> Response[LoginResponse]:
     """
     Login to the system using username, email, and password.
     Returns an access token for authenticated requests.
@@ -26,4 +27,4 @@ def login(login_request: LoginRequest, request: Request) -> LoginResponse:
         email=login_request.email,
         password=login_request.password,
     )
-    return LoginResponse(access_token=access_token)
+    return Response(data=LoginResponse(access_token=access_token))
diff --git a/prometheus/app/api/repository.py b/prometheus/app/api/repository.py
index 78a717f7..49784a32 100644
--- a/prometheus/app/api/repository.py
+++ b/prometheus/app/api/repository.py
@@ -1,6 +1,7 @@
 import git
 from fastapi import APIRouter, Request
 
+from prometheus.app.models.response.response import Response
 from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
 from prometheus.app.services.repository_service import RepositoryService
 from prometheus.exceptions.server_exception import ServerException
@@ -13,6 +14,7 @@
     description="""
     Upload a GitHub repository to Prometheus, default to the latest commit in the main branch.
     """,
+    response_model=Response,
 )
 def upload_github_repository(github_token: str, https_url: str, request: Request):
     # Get the repository and knowledge graph services
@@ -31,6 +33,7 @@ def upload_github_repository(github_token: str, https_url: str, request: Request
         raise ServerException(code=400, message=f"Unable to clone {https_url}")
     # Build and save the knowledge graph from the cloned repository
     knowledge_graph_service.build_and_save_knowledge_graph(saved_path, https_url)
+    return Response()
 
 
 @router.get(
@@ -38,6 +41,7 @@ def upload_github_repository(github_token: str, https_url: str, request: Request
     description="""
     Upload a GitHub repository at a specific commit to Prometheus.
     """,
+    response_model=Response,
 )
 def upload_github_repository_at_commit(
     github_token, https_url: str, commit_id: str, request: Request
@@ -59,6 +63,7 @@ def upload_github_repository_at_commit(
         raise ServerException(code=400, message=f"Unable to clone {https_url}")
     # Build and save the knowledge graph from the cloned repository
     knowledge_graph_service.build_and_save_knowledge_graph(saved_path, https_url, commit_id)
+    return Response()
 
 
 @router.get(
@@ -66,20 +71,21 @@ def upload_github_repository_at_commit(
     description="""
     Delete the repository uploaded to Prometheus, along with other information.
     """,
+    response_model=Response,
 )
 def delete(request: Request):
     knowledge_graph_service: KnowledgeGraphService = request.app.state.service[
         "knowledge_graph_service"
     ]
     if not knowledge_graph_service.exists():
-        return {"message": "No knowledge graph to delete"}
+        return Response(message="No knowledge graph to delete")
     # Get the repository service to clean up the repository data
     repository_service: RepositoryService = request.app.state.service["repository_service"]
 
     # Clear the knowledge graph and repository data
     knowledge_graph_service.clear()
     repository_service.clean()
-    return {"message": "Successfully deleted knowledge graph"}
+    return Response()
 
 
 @router.get(
@@ -87,7 +93,7 @@ def delete(request: Request):
     description="""
     If there is a codebase uploaded to Promtheus.
     """,
-    response_model=bool,
+    response_model=Response[bool],
 )
-def knowledge_graph_exists(request: Request) -> bool:
-    return request.app.state.service["knowledge_graph_service"].exists()
+def knowledge_graph_exists(request: Request) -> Response[bool]:
+    return Response(data=request.app.state.service["knowledge_graph_service"].exists())
diff --git a/prometheus/app/main.py b/prometheus/app/main.py
index b04db85b..fe7bc600 100644
--- a/prometheus/app/main.py
+++ b/prometheus/app/main.py
@@ -8,7 +8,6 @@
 from prometheus.app import dependencies
 from prometheus.app.api import issue, repository
 from prometheus.app.exception_handler import register_exception_handlers
-from prometheus.app.middlewares.response_wrapper_middleware import ResponseWrapperMiddleware
 from prometheus.configuration.config import settings
 
 # Create a logger for the application's namespace
@@ -68,9 +67,6 @@ def custom_generate_unique_id(route: APIRoute) -> str:
     debug=True if settings.ENVIRONMENT == "local" else False,
 )
 
-# Register middlewares
-app.add_middleware(ResponseWrapperMiddleware)
-
 # Register the exception handlers
 register_exception_handlers(app)
 
diff --git a/prometheus/app/middlewares/response_wrapper_middleware.py b/prometheus/app/middlewares/response_wrapper_middleware.py
deleted file mode 100644
index fea9b792..00000000
--- a/prometheus/app/middlewares/response_wrapper_middleware.py
+++ /dev/null
@@ -1,25 +0,0 @@
-from fastapi.responses import JSONResponse
-from starlette.middleware.base import BaseHTTPMiddleware
-from fastapi import Request
-import json
-
-
-class ResponseWrapperMiddleware(BaseHTTPMiddleware):
-    async def dispatch(self, request: Request, call_next):
-        response = await call_next(request)
-        # Check if the response is a JSON response
-        if response.headers.get("content-type") == "application/json":
-            # Decode the JSON response body
-            original_data = json.loads(response.body.decode("utf-8"))
-
-            # Check if the original data is already in the expected format
-            if isinstance(original_data, dict) and set(original_data.keys()) == {"code", "message", "data"}:
-                new_data = original_data
-            else:
-                new_data = {
-                    "code": response.status_code,
-                    "message": "Success",
-                    "data": original_data,
-                }
-            return JSONResponse(content=new_data, status_code=response.status_code)
-        return response
diff --git a/prometheus/app/models/response/response.py b/prometheus/app/models/response/response.py
new file mode 100644
index 00000000..11a53180
--- /dev/null
+++ b/prometheus/app/models/response/response.py
@@ -0,0 +1,14 @@
+from typing import TypeVar, Generic
+
+from pydantic import BaseModel
+
+T = TypeVar('T')
+
+
+class Response(BaseModel, Generic[T]):
+    """
+    Generic response model for API responses.
+    """
+    code: int = 200
+    message: str = "Success"
+    data: T | None = None

From c4b8c38bfea7cb0a997c7a9d4c11809e787eff9a Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 17:20:50 +0800
Subject: [PATCH 40/55] Refactor answer_issue function to use a generic
 Response model and raise ServerException for error handling

---
 prometheus/app/api/issue.py                | 39 ++++++++++++----------
 prometheus/app/models/response/response.py |  5 +--
 2 files changed, 25 insertions(+), 19 deletions(-)

diff --git a/prometheus/app/api/issue.py b/prometheus/app/api/issue.py
index e155b564..803ebb90 100644
--- a/prometheus/app/api/issue.py
+++ b/prometheus/app/api/issue.py
@@ -1,7 +1,9 @@
-from fastapi import APIRouter, HTTPException, Request
+from fastapi import APIRouter, Request
 
 from prometheus.app.models.requests.issue import IssueRequest
 from prometheus.app.models.response.issue import IssueResponse
+from prometheus.app.models.response.response import Response
+from prometheus.exceptions.server_exception import ServerException
 
 router = APIRouter()
 
@@ -9,22 +11,23 @@
 @router.post(
     "/answer/",
     summary="Process and generate a response for an issue",
-    description="Analyzes an issue, generates patches if needed, runs optional builds and tests, and can push changes to a remote branch.",
+    description="Analyzes an issue, generates patches if needed, runs optional builds and tests, and can push changes "
+    "to a remote branch.",
     response_description="Returns the patch, test results, and issue response",
-    response_model=IssueResponse,
+    response_model=Response[IssueResponse],
 )
-def answer_issue(issue: IssueRequest, request: Request) -> IssueResponse:
+def answer_issue(issue: IssueRequest, request: Request) -> Response[IssueResponse]:
     if not request.app.state.service["knowledge_graph_service"].exists():
-        raise HTTPException(
-            status_code=404,
-            detail="A repository is not uploaded, use /repository/ endpoint to upload one",
+        raise ServerException(
+            code=404,
+            message="A repository is not uploaded, use /repository/ endpoint to upload one",
         )
 
     if issue.dockerfile_content or issue.image_name:
         if issue.workdir is None:
-            raise HTTPException(
-                status_code=400,
-                detail="workdir must be provided for user defined environment",
+            raise ServerException(
+                code=400,
+                message="workdir must be provided for user defined environment",
             )
 
     (
@@ -50,11 +53,13 @@ def answer_issue(issue: IssueRequest, request: Request) -> IssueResponse:
         test_commands=issue.test_commands,
         push_to_remote=issue.push_to_remote,
     )
-    return IssueResponse(
-        patch=patch,
-        passed_reproducing_test=passed_reproducing_test,
-        passed_build=passed_build,
-        passed_existing_test=passed_existing_test,
-        issue_response=issue_response,
-        remote_branch_name=remote_branch_name,
+    return Response(
+        data=IssueResponse(
+            patch=patch,
+            passed_reproducing_test=passed_reproducing_test,
+            passed_build=passed_build,
+            passed_existing_test=passed_existing_test,
+            issue_response=issue_response,
+            remote_branch_name=remote_branch_name,
+        )
     )
diff --git a/prometheus/app/models/response/response.py b/prometheus/app/models/response/response.py
index 11a53180..a483c2a2 100644
--- a/prometheus/app/models/response/response.py
+++ b/prometheus/app/models/response/response.py
@@ -1,14 +1,15 @@
-from typing import TypeVar, Generic
+from typing import Generic, TypeVar
 
 from pydantic import BaseModel
 
-T = TypeVar('T')
+T = TypeVar("T")
 
 
 class Response(BaseModel, Generic[T]):
     """
     Generic response model for API responses.
     """
+
     code: int = 200
     message: str = "Success"
     data: T | None = None

From 0b09e9d1bfffdae9dac9044d1967c83d1115de71 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 20:54:43 +0800
Subject: [PATCH 41/55] Update test fixtures to use a consistent working
 directory path

---
 tests/app/services/test_issue_service.py      | 1 +
 tests/app/services/test_repository_service.py | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/app/services/test_issue_service.py b/tests/app/services/test_issue_service.py
index 861b608f..003bb978 100644
--- a/tests/app/services/test_issue_service.py
+++ b/tests/app/services/test_issue_service.py
@@ -49,6 +49,7 @@ def issue_service(mock_kg_service, mock_repository_service, mock_neo4j_service,
         mock_neo4j_service,
         mock_llm_service,
         max_token_per_neo4j_result=1000,
+        working_directory="/test/working/dir",
     )
 
 
diff --git a/tests/app/services/test_repository_service.py b/tests/app/services/test_repository_service.py
index 99d1af27..6ce2ac65 100644
--- a/tests/app/services/test_repository_service.py
+++ b/tests/app/services/test_repository_service.py
@@ -32,7 +32,7 @@ def mock_knowledge_graph():
 
 @pytest.fixture
 def service(mock_kg_service):
-    working_dir = Path("/test/working/dir")
+    working_dir = "/test/working/dir"
     # Don't mock GitRepository in the fixture anymore
     with patch("pathlib.Path.mkdir"):
         return RepositoryService(

From 6179b2793380291847f1740122748dfaf5a78c75 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 20:55:38 +0800
Subject: [PATCH 42/55] Remove unused test functions for local repository
 uploads

---
 tests/app/api/test_repository.py | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/tests/app/api/test_repository.py b/tests/app/api/test_repository.py
index 3f983899..f4facc09 100644
--- a/tests/app/api/test_repository.py
+++ b/tests/app/api/test_repository.py
@@ -5,7 +5,6 @@
 from fastapi.testclient import TestClient
 
 from prometheus.app.api import repository
-from tests.test_utils import test_project_paths
 
 app = FastAPI()
 app.include_router(repository.router, prefix="/repository", tags=["repository"])
@@ -19,23 +18,6 @@ def mock_service_coordinator():
     yield service_coordinator
 
 
-def test_upload_local_repository(mock_service_coordinator):
-    mock_service_coordinator.upload_local_repository.return_value = None
-    response = client.get(
-        "/repository/local",
-        params={"local_repository": test_project_paths.TEST_PROJECT_PATH.absolute().as_posix()},
-    )
-    assert response.status_code == 200
-
-
-def test_upload_fake_local_repository():
-    response = client.get(
-        "/repository/local/",
-        params={"local_repository": "/foo/bar/"},
-    )
-    assert response.status_code == 404
-
-
 def test_delete(mock_service_coordinator):
     mock_service_coordinator.exists_knowledge_graph.return_value = True
     mock_service_coordinator.clear.return_value = None

From 0d79e8c52b42ad406719e3378feec52bfcd0cb98 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 21:49:28 +0800
Subject: [PATCH 43/55] Normalize success message to lowercase in response
 model

---
 prometheus/app/models/response/response.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/prometheus/app/models/response/response.py b/prometheus/app/models/response/response.py
index a483c2a2..09c7e595 100644
--- a/prometheus/app/models/response/response.py
+++ b/prometheus/app/models/response/response.py
@@ -11,5 +11,5 @@ class Response(BaseModel, Generic[T]):
     """
 
     code: int = 200
-    message: str = "Success"
+    message: str = "success"
     data: T | None = None

From 9351c635dcb79f3e600662bff687ccfc674a8e89 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 22:00:21 +0800
Subject: [PATCH 44/55] Refactor test files to use a unified mock service
 structure and register exception handlers

---
 tests/app/api/test_issue.py                   |  48 ++++----
 tests/app/api/test_repository.py              |  16 +--
 tests/app/services/test_db_engine.py          |  12 --
 .../app/services/test_service_coordinator.py  | 115 ------------------
 tests/app/test_db.py                          |  49 --------
 tests/app/test_main.py                        |  12 +-
 6 files changed, 42 insertions(+), 210 deletions(-)
 delete mode 100644 tests/app/services/test_db_engine.py
 delete mode 100644 tests/app/services/test_service_coordinator.py
 delete mode 100644 tests/app/test_db.py

diff --git a/tests/app/api/test_issue.py b/tests/app/api/test_issue.py
index ae5e7c1a..475b4607 100644
--- a/tests/app/api/test_issue.py
+++ b/tests/app/api/test_issue.py
@@ -5,23 +5,25 @@
 from fastapi.testclient import TestClient
 
 from prometheus.app.api import issue
+from prometheus.app.exception_handler import register_exception_handlers
 from prometheus.lang_graph.graphs.issue_state import IssueType
 
 app = FastAPI()
+register_exception_handlers(app)
 app.include_router(issue.router, prefix="/issue", tags=["issue"])
 client = TestClient(app)
 
 
 @pytest.fixture
-def mock_service_coordinator():
-    service_coordinator = mock.MagicMock()
-    app.state.service_coordinator = service_coordinator
-    yield service_coordinator
+def mock_service():
+    service = mock.MagicMock()
+    app.state.service = service
+    yield service
 
 
-def test_answer_issue(mock_service_coordinator):
-    mock_service_coordinator.exists_knowledge_graph.return_value = True
-    mock_service_coordinator.answer_issue.return_value = (
+def test_answer_issue(mock_service):
+    mock_service["knowledge_graph_service"].exists_knowledge_graph.return_value = True
+    mock_service["issue_service"].answer_issue.return_value = (
         "feature/fix-42",  # remote_branch_name
         "test patch",  # patch
         True,  # passed_reproducing_test
@@ -41,17 +43,21 @@ def test_answer_issue(mock_service_coordinator):
 
     assert response.status_code == 200
     assert response.json() == {
-        "remote_branch_name": "feature/fix-42",
-        "patch": "test patch",
-        "passed_reproducing_test": True,
-        "passed_build": True,
-        "passed_existing_test": True,
-        "issue_response": "Issue fixed",
+        "code": 200,
+        "message": "success",
+        "data": {
+            "remote_branch_name": "feature/fix-42",
+            "patch": "test patch",
+            "passed_reproducing_test": True,
+            "passed_build": True,
+            "passed_existing_test": True,
+            "issue_response": "Issue fixed",
+        }
     }
 
 
-def test_answer_issue_no_repository(mock_service_coordinator):
-    mock_service_coordinator.exists_knowledge_graph.return_value = False
+def test_answer_issue_no_repository(mock_service):
+    mock_service["knowledge_graph_service"].exists.return_value = False
 
     response = client.post(
         "/issue/answer",
@@ -61,8 +67,8 @@ def test_answer_issue_no_repository(mock_service_coordinator):
     assert response.status_code == 404
 
 
-def test_answer_issue_invalid_container_config(mock_service_coordinator):
-    mock_service_coordinator.exists_knowledge_graph.return_value = True
+def test_answer_issue_invalid_container_config(mock_service):
+    mock_service["knowledge_graph_service"].exists.return_value = True
 
     response = client.post(
         "/issue/answer",
@@ -78,9 +84,9 @@ def test_answer_issue_invalid_container_config(mock_service_coordinator):
     assert response.status_code == 400
 
 
-def test_answer_issue_with_container(mock_service_coordinator):
-    mock_service_coordinator.exists_knowledge_graph.return_value = True
-    mock_service_coordinator.answer_issue.return_value = (
+def test_answer_issue_with_container(mock_service):
+    mock_service["knowledge_graph_service"].exists.return_value = True
+    mock_service["issue_service"].answer_issue.return_value = (
         "feature/fix-42",
         "test patch",
         True,
@@ -102,7 +108,7 @@ def test_answer_issue_with_container(mock_service_coordinator):
     response = client.post("/issue/answer", json=test_payload)
 
     assert response.status_code == 200
-    mock_service_coordinator.answer_issue.assert_called_once_with(
+    mock_service["issue_service"].answer_issue.assert_called_once_with(
         issue_number=42,
         issue_title="Test Issue",
         issue_body="Test description",
diff --git a/tests/app/api/test_repository.py b/tests/app/api/test_repository.py
index f4facc09..73f5bcf4 100644
--- a/tests/app/api/test_repository.py
+++ b/tests/app/api/test_repository.py
@@ -5,21 +5,23 @@
 from fastapi.testclient import TestClient
 
 from prometheus.app.api import repository
+from prometheus.app.exception_handler import register_exception_handlers
 
 app = FastAPI()
+register_exception_handlers(app)
 app.include_router(repository.router, prefix="/repository", tags=["repository"])
 client = TestClient(app)
 
 
 @pytest.fixture
-def mock_service_coordinator():
-    service_coordinator = mock.MagicMock()
-    app.state.service_coordinator = service_coordinator
-    yield service_coordinator
+def mock_service():
+    service = mock.MagicMock()
+    app.state.service = service
+    yield service
 
 
-def test_delete(mock_service_coordinator):
-    mock_service_coordinator.exists_knowledge_graph.return_value = True
-    mock_service_coordinator.clear.return_value = None
+def test_delete(mock_service):
+    mock_service["knowledge_graph_service"].exists.return_value = True
+    mock_service["knowledge_graph_service"].clear.return_value = None
     response = client.get("repository/delete")
     assert response.status_code == 200
diff --git a/tests/app/services/test_db_engine.py b/tests/app/services/test_db_engine.py
deleted file mode 100644
index 86f3c949..00000000
--- a/tests/app/services/test_db_engine.py
+++ /dev/null
@@ -1,12 +0,0 @@
-import pytest
-from sqlmodel import create_engine
-
-from prometheus.app.db import create_db_and_tables
-
-
-@pytest.fixture(scope="session")
-def test_engine(postgres_container_fixture):
-    url = postgres_container_fixture.get_connection_url()
-    engine = create_engine(url, echo=True)
-    create_db_and_tables()
-    yield engine
diff --git a/tests/app/services/test_service_coordinator.py b/tests/app/services/test_service_coordinator.py
deleted file mode 100644
index 71652628..00000000
--- a/tests/app/services/test_service_coordinator.py
+++ /dev/null
@@ -1,115 +0,0 @@
-import tempfile
-from pathlib import Path
-from unittest.mock import Mock
-
-import pytest
-
-from prometheus.app.services.issue_service import IssueService
-from prometheus.app.services.knowledge_graph_service import KnowledgeGraphService
-from prometheus.app.services.llm_service import LLMService
-from prometheus.app.services.neo4j_service import Neo4jService
-from prometheus.app.services.repository_service import RepositoryService
-from prometheus.app.services.service_coordinator import ServiceCoordinator
-
-
-@pytest.fixture
-def mock_services():
-    llm_service = Mock(spec=LLMService)
-    llm_service.model = Mock()
-
-    issue_service = Mock(sepc=IssueService)
-    knowledge_graph_service = Mock(spec=KnowledgeGraphService)
-    knowledge_graph_service.kg = None
-    knowledge_graph_service.get_local_path.return_value = None
-    neo4j_service = Mock(spec=Neo4jService)
-    repository_service = Mock(spec=RepositoryService)
-    repository_service.get_working_dir.return_value = None
-
-    yield {
-        "issue_service": issue_service,
-        "knowledge_graph_service": knowledge_graph_service,
-        "llm_service": llm_service,
-        "neo4j_service": neo4j_service,
-        "max_token_per_neo4j_result": 1000,
-        "repository_service": repository_service,
-        "github_token": "test_token",
-        "working_directory": Path(tempfile.TemporaryDirectory().name),
-    }
-
-
-@pytest.fixture
-def service_coordinator(mock_services):
-    coordinator = ServiceCoordinator(
-        mock_services["issue_service"],
-        mock_services["knowledge_graph_service"],
-        mock_services["llm_service"],
-        mock_services["neo4j_service"],
-        mock_services["repository_service"],
-        mock_services["max_token_per_neo4j_result"],
-        mock_services["github_token"],
-        mock_services["working_directory"],
-    )
-    return coordinator
-
-
-def test_initialization(service_coordinator, mock_services):
-    """Test that services are properly initialized"""
-    assert service_coordinator.knowledge_graph_service == mock_services["knowledge_graph_service"]
-    assert service_coordinator.llm_service == mock_services["llm_service"]
-    assert service_coordinator.neo4j_service == mock_services["neo4j_service"]
-    assert service_coordinator.repository_service == mock_services["repository_service"]
-
-
-def test_upload_local_repository(service_coordinator, mock_services):
-    """Test local repository upload process"""
-    test_path = Path("/test/path")
-
-    service_coordinator.upload_local_repository(test_path)
-
-    # Verify the sequence of operations
-    mock_services["knowledge_graph_service"].build_and_save_knowledge_graph.assert_called_once_with(
-        test_path
-    )
-
-
-def test_upload_github_repository(service_coordinator, mock_services):
-    """Test GitHub repository upload process"""
-    test_url = "https://github.com/test/repo"
-    test_commit = "abc123"
-    saved_path = Path("/saved/path")
-    mock_services["repository_service"].clone_github_repo.return_value = saved_path
-
-    service_coordinator.upload_github_repository(test_url, test_commit)
-
-    # Verify the sequence of operations
-    mock_services["repository_service"].clone_github_repo.assert_called_once_with(
-        mock_services["github_token"], test_url, test_commit
-    )
-    mock_services["knowledge_graph_service"].build_and_save_knowledge_graph.assert_called_once_with(
-        saved_path, test_url, test_commit
-    )
-
-
-def test_clear(service_coordinator, mock_services):
-    """Test clearing of services"""
-    service_coordinator.clear()
-
-    mock_services["knowledge_graph_service"].clear.assert_called_once()
-    mock_services["repository_service"].clean.assert_called_once()
-
-
-def test_close(service_coordinator, mock_services):
-    """Test proper closing of services"""
-    service_coordinator.close()
-
-    mock_services["neo4j_service"].close.assert_called_once()
-
-
-def test_exists_knowledge_graph(service_coordinator, mock_services):
-    """Test knowledge graph existence check"""
-    mock_services["knowledge_graph_service"].exists.return_value = True
-
-    result = service_coordinator.exists_knowledge_graph()
-
-    mock_services["knowledge_graph_service"].exists.assert_called_once()
-    assert result is True
diff --git a/tests/app/test_db.py b/tests/app/test_db.py
deleted file mode 100644
index 589fca1b..00000000
--- a/tests/app/test_db.py
+++ /dev/null
@@ -1,49 +0,0 @@
-import pytest
-from sqlmodel import Session, select
-
-from prometheus.app.db import create_superuser
-from prometheus.app.entity.user import User
-from tests.app.services.test_db_engine import test_engine  # noqa: F401
-from tests.test_utils.fixtures import postgres_container_fixture  # noqa: F401
-
-
-@pytest.mark.slow
-def test_create_superuser(postgres_container_fixture, test_engine):  # noqa: F811
-    username = "admin"
-    email = "admin@example.com"
-    password = "strongpassword"
-    github_token = "ghp_123456"
-
-    # Create superuser
-    create_superuser(
-        username=username,
-        email=email,
-        password=password,
-        github_token=github_token,
-    )
-
-    with Session(test_engine) as session:
-        user = session.exec(select(User).where(User.username == username)).first()
-
-        assert user is not None
-        assert user.email == email
-        assert user.is_superuser is True
-        assert user.issue_credit == 999999
-        assert user.github_token == github_token
-        assert user.password_hash != password  # Password must be hashed
-
-
-@pytest.mark.slow
-def test_duplicate_superuser_raises(postgres_container_fixture, test_engine):  # noqa: F811
-    username = "admin2"
-    email = "admin2@example.com"
-    password = "password"
-
-    create_superuser(username, email, password)
-
-    # Trying again with same username or email
-    with pytest.raises(ValueError, match="Username 'admin2' already exists"):
-        create_superuser(username, "different@example.com", "pass")
-
-    with pytest.raises(ValueError, match="Email 'admin2@example.com' already exists"):
-        create_superuser("different_user", email, "pass")
diff --git a/tests/app/test_main.py b/tests/app/test_main.py
index 8ad0c0c1..2a45d5f5 100644
--- a/tests/app/test_main.py
+++ b/tests/app/test_main.py
@@ -6,10 +6,10 @@
 
 @pytest.fixture
 def mock_dependencies():
-    """Mock the service coordinator dependencies"""
-    mock_coordinator = MagicMock()
-    with patch("prometheus.app.dependencies.initialize_services", return_value=mock_coordinator):
-        yield mock_coordinator
+    """Mock the service dependencies"""
+    mock_service = MagicMock()
+    with patch("prometheus.app.dependencies.initialize_services", return_value=mock_service):
+        yield mock_service
 
 
 @pytest.fixture
@@ -24,5 +24,5 @@ def test_client(mock_dependencies):
 
 def test_app_initialization(test_client, mock_dependencies):
     """Test that the app initializes correctly with mocked dependencies"""
-    assert test_client.app.state.service_coordinator is not None
-    assert test_client.app.state.service_coordinator == mock_dependencies
+    assert test_client.app.state.service is not None
+    assert test_client.app.state.service == mock_dependencies

From e7f9396825ad93a8b7da019b71b6ec15323f73c9 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 22:00:39 +0800
Subject: [PATCH 45/55] Fix formatting issue in test_issue.py by correcting
 indentation

---
 tests/app/api/test_issue.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/app/api/test_issue.py b/tests/app/api/test_issue.py
index 475b4607..5367c872 100644
--- a/tests/app/api/test_issue.py
+++ b/tests/app/api/test_issue.py
@@ -52,7 +52,7 @@ def test_answer_issue(mock_service):
             "passed_build": True,
             "passed_existing_test": True,
             "issue_response": "Issue fixed",
-        }
+        },
     }
 
 

From d2eed5892d027bfec36cff6c2f8a98b6618cff4e Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 22:08:01 +0800
Subject: [PATCH 46/55] Add database service tests and remove redundant port
 binding in fixtures

---
 tests/app/services/test_database_service.py | 17 +++++++++++++++++
 tests/test_utils/fixtures.py                |  1 -
 2 files changed, 17 insertions(+), 1 deletion(-)
 create mode 100644 tests/app/services/test_database_service.py

diff --git a/tests/app/services/test_database_service.py b/tests/app/services/test_database_service.py
new file mode 100644
index 00000000..5c7930b0
--- /dev/null
+++ b/tests/app/services/test_database_service.py
@@ -0,0 +1,17 @@
+import pytest
+
+from prometheus.app.services.database_service import DatabaseService
+from tests.test_utils.fixtures import postgres_container_fixture  # noqa: F401
+
+
+@pytest.mark.slow
+def test_database_service(postgres_container_fixture):  # noqa: F811
+    url = postgres_container_fixture.get_connection_url()
+    database_service = DatabaseService(url)
+    assert database_service.engine is not None
+
+    try:
+        database_service.engine.connect()
+        database_service.engine.dispose()  # Ensure connection is valid
+    except Exception as e:
+        pytest.fail(f"Connection verification failed: {e}")
diff --git a/tests/test_utils/fixtures.py b/tests/test_utils/fixtures.py
index 4073a844..b2b5cdd7 100644
--- a/tests/test_utils/fixtures.py
+++ b/tests/test_utils/fixtures.py
@@ -60,7 +60,6 @@ def postgres_container_fixture():
             port=5432,
         )
         .with_name(f"postgres_container_{uuid.uuid4().hex[:12]}")
-        .with_bind_ports(5432, 5432)  # Bind to a specific port for testing
     )
     with container as postgres_container:
         yield postgres_container

From 3b4a38a205e4a91c8132b7b796e9d1b5dd5d0f08 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 22:08:16 +0800
Subject: [PATCH 47/55] Refactor postgres container fixture for improved
 readability

---
 tests/test_utils/fixtures.py | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/tests/test_utils/fixtures.py b/tests/test_utils/fixtures.py
index b2b5cdd7..a0e7940a 100644
--- a/tests/test_utils/fixtures.py
+++ b/tests/test_utils/fixtures.py
@@ -51,16 +51,13 @@ def empty_neo4j_container_fixture():
 
 @pytest.fixture(scope="session")
 def postgres_container_fixture():
-    container = (
-        PostgresContainer(
-            image=POSTGRES_IMAGE,
-            username=POSTGRES_USERNAME,
-            password=POSTGRES_PASSWORD,
-            dbname=POSTGRES_DB,
-            port=5432,
-        )
-        .with_name(f"postgres_container_{uuid.uuid4().hex[:12]}")
-    )
+    container = PostgresContainer(
+        image=POSTGRES_IMAGE,
+        username=POSTGRES_USERNAME,
+        password=POSTGRES_PASSWORD,
+        dbname=POSTGRES_DB,
+        port=5432,
+    ).with_name(f"postgres_container_{uuid.uuid4().hex[:12]}")
     with container as postgres_container:
         yield postgres_container
 

From 04a0269aa3125f5347ae41c95d2df3d6de304e9e Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 22:25:30 +0800
Subject: [PATCH 48/55] Update test_issue_service.py to modify working
 directory path and adjust assertion results

---
 tests/app/services/test_issue_service.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tests/app/services/test_issue_service.py b/tests/app/services/test_issue_service.py
index 003bb978..6e8f2224 100644
--- a/tests/app/services/test_issue_service.py
+++ b/tests/app/services/test_issue_service.py
@@ -49,7 +49,7 @@ def issue_service(mock_kg_service, mock_repository_service, mock_neo4j_service,
         mock_neo4j_service,
         mock_llm_service,
         max_token_per_neo4j_result=1000,
-        working_directory="/test/working/dir",
+        working_directory="/tmp/working_dir/",
     )
 
 
@@ -78,6 +78,7 @@ def test_answer_issue_with_general_container(issue_service, monkeypatch):
 
     # Exercise
     result = issue_service.answer_issue(
+        issue_number=-1,
         issue_title="Test Issue",
         issue_body="Test Body",
         issue_comments=[],
@@ -102,7 +103,7 @@ def test_answer_issue_with_general_container(issue_service, monkeypatch):
         build_commands=None,
         test_commands=None,
     )
-    assert result == ("test_patch", True, True, True, "test_response")
+    assert result == (None, "test_patch", True, True, True, "test_response")
 
 
 def test_answer_issue_with_user_defined_container(issue_service, monkeypatch):
@@ -123,6 +124,7 @@ def test_answer_issue_with_user_defined_container(issue_service, monkeypatch):
 
     # Exercise
     result = issue_service.answer_issue(
+        issue_number=-1,
         issue_title="Test Issue",
         issue_body="Test Body",
         issue_comments=[],
@@ -146,4 +148,4 @@ def test_answer_issue_with_user_defined_container(issue_service, monkeypatch):
         "FROM python:3.8",
         "test-image",
     )
-    assert result == (None, False, False, False, "test_response")
+    assert result == (None, None, False, False, False, "test_response")

From a26660f025de077f8f7b0b5f9abb89cd318a6ca3 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 22:30:43 +0800
Subject: [PATCH 49/55] Update environment configuration for CORS and add JWT
 secret key

---
 .github/workflows/pytest_and_coverage.yml | 7 +++++++
 example.env                               | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pytest_and_coverage.yml b/.github/workflows/pytest_and_coverage.yml
index 15aa9547..c80effdc 100644
--- a/.github/workflows/pytest_and_coverage.yml
+++ b/.github/workflows/pytest_and_coverage.yml
@@ -14,6 +14,10 @@ jobs:
       # Logging
       PROMETHEUS_LOGGING_LEVEL: DEBUG
 
+      # General settings
+      PROMETHEUS_ENVIRONMENT: local
+      PROMETHEUS_BACKEND_CORS_ORIGINS: "[\"*\"]"
+
       # Neo4j settings
       PROMETHEUS_NEO4J_URI: bolt://localhost:7687
       PROMETHEUS_NEO4J_USERNAME: neo4j
@@ -48,6 +52,9 @@ jobs:
       # DATABASE settings
       PROMETHEUS_DATABASE_URL: postgresql://postgres:password@localhost:5432/postgres?sslmode=disable
 
+      # JWT settings
+      PROMETHEUS_JWT_SECRET_KEY: your_jwt_secret_key
+
     steps:
       - name: Check out code
         uses: actions/checkout@v4
diff --git a/example.env b/example.env
index 3283dffb..8699b7d4 100644
--- a/example.env
+++ b/example.env
@@ -3,7 +3,7 @@ PROMETHEUS_LOGGING_LEVEL=DEBUG
 
 # General settings
 PROMETHEUS_ENVIRONMENT=local
-PROMETHEUS_BACKEND_CORS_ORIGINS=["http://localhost:9002"]
+PROMETHEUS_BACKEND_CORS_ORIGINS=["*]
 
 # Neo4j settings
 PROMETHEUS_NEO4J_URI=bolt://neo4j:7687

From ce00bd865e5df4e2d53f77cca7e2af40cf344569 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 22:53:15 +0800
Subject: [PATCH 50/55] Add user service tests for superuser creation

---
 tests/app/services/test_user_service.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 tests/app/services/test_user_service.py

diff --git a/tests/app/services/test_user_service.py b/tests/app/services/test_user_service.py
new file mode 100644
index 00000000..80fb56bd
--- /dev/null
+++ b/tests/app/services/test_user_service.py
@@ -0,0 +1,25 @@
+import pytest
+
+from prometheus.app.services.database_service import DatabaseService
+from prometheus.app.services.user_service import UserService
+from tests.test_utils.fixtures import postgres_container_fixture
+
+
+@pytest.fixture
+def mock_database_service(postgres_container_fixture):
+    service = DatabaseService(postgres_container_fixture.get_connection_url())
+    service.start()
+    return service
+
+
+def test_create_superuser(mock_database_service):
+    # Exercise
+    service = UserService(mock_database_service)
+    service.create_superuser(
+        "testuser",
+        "test@gmail.com",
+        "password123",
+        github_token="gh_token"
+    )
+
+# TODO test login

From 1726289674174af92a8301ea4a0627f6d3a27aa2 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 22:54:12 +0800
Subject: [PATCH 51/55] Refactor superuser creation test for improved
 readability

---
 tests/app/services/test_user_service.py | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/tests/app/services/test_user_service.py b/tests/app/services/test_user_service.py
index 80fb56bd..42b74039 100644
--- a/tests/app/services/test_user_service.py
+++ b/tests/app/services/test_user_service.py
@@ -2,7 +2,6 @@
 
 from prometheus.app.services.database_service import DatabaseService
 from prometheus.app.services.user_service import UserService
-from tests.test_utils.fixtures import postgres_container_fixture
 
 
 @pytest.fixture
@@ -15,11 +14,7 @@ def mock_database_service(postgres_container_fixture):
 def test_create_superuser(mock_database_service):
     # Exercise
     service = UserService(mock_database_service)
-    service.create_superuser(
-        "testuser",
-        "test@gmail.com",
-        "password123",
-        github_token="gh_token"
-    )
+    service.create_superuser("testuser", "test@gmail.com", "password123", github_token="gh_token")
+
 
 # TODO test login

From a773c2c2d68f46a305563d8eabadff33e62a9111 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 23:01:15 +0800
Subject: [PATCH 52/55] Refactor mock_database_service fixture to use yield for
 resource management

---
 tests/app/services/test_user_service.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/app/services/test_user_service.py b/tests/app/services/test_user_service.py
index 42b74039..fbc24d78 100644
--- a/tests/app/services/test_user_service.py
+++ b/tests/app/services/test_user_service.py
@@ -2,13 +2,15 @@
 
 from prometheus.app.services.database_service import DatabaseService
 from prometheus.app.services.user_service import UserService
+from tests.test_utils.fixtures import postgres_container_fixture  # noqa: F401
 
 
 @pytest.fixture
-def mock_database_service(postgres_container_fixture):
+def mock_database_service(postgres_container_fixture):  # noqa: F811
     service = DatabaseService(postgres_container_fixture.get_connection_url())
     service.start()
-    return service
+    yield service
+    service.close()
 
 
 def test_create_superuser(mock_database_service):

From 63e2ce1f5c36fadfef57b1bdd594796c2b7d46c0 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Mon, 4 Aug 2025 23:58:37 +0800
Subject: [PATCH 53/55] Add login test and refactor user retrieval queries in
 UserService

---
 prometheus/app/services/user_service.py | 15 +++++++--------
 tests/app/services/test_user_service.py |  7 ++++++-
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/prometheus/app/services/user_service.py b/prometheus/app/services/user_service.py
index e865c943..32cc9124 100644
--- a/prometheus/app/services/user_service.py
+++ b/prometheus/app/services/user_service.py
@@ -2,7 +2,7 @@
 from typing import Optional
 
 from argon2 import PasswordHasher
-from sqlmodel import Session
+from sqlmodel import Session, or_, select
 
 from prometheus.app.entity.user import User
 from prometheus.app.services.base_service import BaseService
@@ -41,9 +41,11 @@ def create_user(
             User: The created superuser instance.
         """
         with Session(self.engine) as session:
-            if session.query(User).filter(User.username == username).first():
+            statement = select(User).where(User.username == username)
+            if session.exec(statement).first():
                 raise ValueError(f"Username '{username}' already exists")
-            if session.query(User).filter(User.email == email).first():
+            statement = select(User).where(User.email == email)
+            if session.exec(statement).first():
                 raise ValueError(f"Email '{email}' already exists")
 
             hashed_password = self.ph.hash(password)
@@ -70,11 +72,8 @@ def login(self, username: str, email: str, password: str) -> str:
             password (str): Plaintext password.
         """
         with Session(self.engine) as session:
-            user = (
-                session.query(User)
-                .filter((User.username == username) | (User.email == email))
-                .first()
-            )
+            statement = select(User).where(or_(User.username == username, User.email == email))
+            user = session.exec(statement).first()
 
             if not user:
                 raise ValueError("Invalid username or email")
diff --git a/tests/app/services/test_user_service.py b/tests/app/services/test_user_service.py
index fbc24d78..3136972f 100644
--- a/tests/app/services/test_user_service.py
+++ b/tests/app/services/test_user_service.py
@@ -19,4 +19,9 @@ def test_create_superuser(mock_database_service):
     service.create_superuser("testuser", "test@gmail.com", "password123", github_token="gh_token")
 
 
-# TODO test login
+def test_login(mock_database_service):
+    # Exercise
+    service = UserService(mock_database_service)
+    access_token = service.login("testuser", "test@gmail.com", "password123")
+    # Verify
+    assert access_token is not None

From 9bdf3a6ecdf98e4725ad08a30115bf85a4ae0844 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Tue, 5 Aug 2025 00:03:35 +0800
Subject: [PATCH 54/55] Refactor email validation method to use class method
 syntax

---
 prometheus/app/models/requests/auth.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/prometheus/app/models/requests/auth.py b/prometheus/app/models/requests/auth.py
index 96ef3fea..f0e8b8fa 100644
--- a/prometheus/app/models/requests/auth.py
+++ b/prometheus/app/models/requests/auth.py
@@ -17,8 +17,9 @@ class LoginRequest(BaseModel):
         max_length=30,
     )
 
+    @classmethod
     @field_validator("email", mode="after")
-    def validate_email_format(self, v: str) -> str:
+    def validate_email_format(cls, v: str) -> str:
         pattern = r"^[^@\s]+@[^@\s]+\.[^@\s]+$"
         if not re.match(pattern, v):
             raise ValueError("Invalid email format")

From 439a9e87440623c3fab6ec9b89e7c27043d793c8 Mon Sep 17 00:00:00 2001
From: Yue Pan <79363355+dcloud347@users.noreply.github.com>
Date: Tue, 5 Aug 2025 00:09:04 +0800
Subject: [PATCH 55/55] Add unit tests for authentication login endpoint

---
 tests/app/api/test_auth.py | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 tests/app/api/test_auth.py

diff --git a/tests/app/api/test_auth.py b/tests/app/api/test_auth.py
new file mode 100644
index 00000000..240cfe9e
--- /dev/null
+++ b/tests/app/api/test_auth.py
@@ -0,0 +1,38 @@
+from unittest import mock
+
+import pytest
+from fastapi import FastAPI
+from fastapi.testclient import TestClient
+
+from prometheus.app.api import auth
+from prometheus.app.exception_handler import register_exception_handlers
+
+app = FastAPI()
+register_exception_handlers(app)
+app.include_router(auth.router, prefix="/auth", tags=["auth"])
+client = TestClient(app)
+
+
+@pytest.fixture
+def mock_service():
+    service = mock.MagicMock()
+    app.state.service = service
+    yield service
+
+
+def test_login(mock_service):
+    mock_service["user_service"].login.return_value = "your_access_token"
+    response = client.post(
+        "/auth/login",
+        json={
+            "username": "testuser",
+            "email": "test@gmail.com",
+            "password": "passwordpassword",
+        },
+    )
+    assert response.status_code == 200
+    assert response.json() == {
+        "code": 200,
+        "message": "success",
+        "data": {"access_token": "your_access_token"},
+    }