autocoder/mcp_server/feature_mcp.py

#!/usr/bin/env python3
"""
MCP Server for Feature Management
==================================

Provides tools to manage features in the autonomous coding system.

Tools:
- feature_get_stats: Get progress statistics
- feature_get_by_id: Get a specific feature by ID
- feature_get_summary: Get minimal feature info (id, name, status, deps)
- feature_mark_passing: Mark a feature as passing
- feature_mark_failing: Mark a feature as failing (regression detected)
- feature_skip: Skip a feature (move to end of queue)
- feature_mark_in_progress: Mark a feature as in-progress
- feature_claim_and_get: Atomically claim and get feature details
- feature_clear_in_progress: Clear in-progress status
- feature_create_bulk: Create multiple features at once
- feature_create: Create a single feature
- feature_add_dependency: Add a dependency between features
- feature_remove_dependency: Remove a dependency
- feature_get_ready: Get features ready to implement
- feature_get_blocked: Get features blocked by dependencies (with limit)
- feature_get_graph: Get the dependency graph

Note: Feature selection (which feature to work on) is handled by the
orchestrator, not by agents. Agents receive pre-assigned feature IDs.
"""

import json
import os
import sys
import threading
from contextlib import asynccontextmanager
from pathlib import Path
from typing import Annotated

from mcp.server.fastmcp import FastMCP
from pydantic import BaseModel, Field

# Add parent directory to path so we can import from api module
sys.path.insert(0, str(Path(__file__).parent.parent))

from api.database import Feature, create_database
from api.dependency_resolver import (
    MAX_DEPENDENCIES_PER_FEATURE,
    compute_scheduling_scores,
    would_create_circular_dependency,
)
from api.migration import migrate_json_to_sqlite

# Configuration from environment
PROJECT_DIR = Path(os.environ.get("PROJECT_DIR", ".")).resolve()


# Pydantic models for input validation
class MarkPassingInput(BaseModel):
    """Input for marking a feature as passing."""
    feature_id: int = Field(..., description="The ID of the feature to mark as passing", ge=1)


class SkipFeatureInput(BaseModel):
    """Input for skipping a feature."""
    feature_id: int = Field(..., description="The ID of the feature to skip", ge=1)


class MarkInProgressInput(BaseModel):
    """Input for marking a feature as in-progress."""
    feature_id: int = Field(..., description="The ID of the feature to mark as in-progress", ge=1)


class ClearInProgressInput(BaseModel):
    """Input for clearing in-progress status."""
    feature_id: int = Field(..., description="The ID of the feature to clear in-progress status", ge=1)


class RegressionInput(BaseModel):
    """Input for getting regression features."""
    limit: int = Field(default=3, ge=1, le=10, description="Maximum number of passing features to return")


class FeatureCreateItem(BaseModel):
    """Schema for creating a single feature."""
    category: str = Field(..., min_length=1, max_length=100, description="Feature category")
    name: str = Field(..., min_length=1, max_length=255, description="Feature name")
    description: str = Field(..., min_length=1, description="Detailed description")
    steps: list[str] = Field(..., min_length=1, description="Implementation/test steps")


class BulkCreateInput(BaseModel):
    """Input for bulk creating features."""
    features: list[FeatureCreateItem] = Field(..., min_length=1, description="List of features to create")


# Global database session maker (initialized on startup)
_session_maker = None
_engine = None

# Lock for priority assignment to prevent race conditions
_priority_lock = threading.Lock()


@asynccontextmanager
async def server_lifespan(server: FastMCP):
    """Initialize database on startup, cleanup on shutdown."""
    global _session_maker, _engine

    # Create project directory if it doesn't exist
    PROJECT_DIR.mkdir(parents=True, exist_ok=True)

    # Initialize database
    _engine, _session_maker = create_database(PROJECT_DIR)

    # Run migration if needed (converts legacy JSON to SQLite)
    migrate_json_to_sqlite(PROJECT_DIR, _session_maker)

    yield

    # Cleanup
    if _engine:
        _engine.dispose()


# Initialize the MCP server
mcp = FastMCP("features", lifespan=server_lifespan)


def get_session():
    """Get a new database session."""
    if _session_maker is None:
        raise RuntimeError("Database not initialized")
    return _session_maker()


@mcp.tool()
def feature_get_stats() -> str:
    """Get statistics about feature completion progress.

    Returns the number of passing features, in-progress features, total features,
    and completion percentage. Use this to track overall progress of the implementation.

    Returns:
        JSON with: passing (int), in_progress (int), total (int), percentage (float)
    """
    from sqlalchemy import case, func

    session = get_session()
    try:
        # Single aggregate query instead of 3 separate COUNT queries
        result = session.query(
            func.count(Feature.id).label('total'),
            func.sum(case((Feature.passes == True, 1), else_=0)).label('passing'),
            func.sum(case((Feature.in_progress == True, 1), else_=0)).label('in_progress')
        ).first()

        total = result.total or 0
        passing = int(result.passing or 0)
        in_progress = int(result.in_progress or 0)
        percentage = round((passing / total) * 100, 1) if total > 0 else 0.0

        return json.dumps({
            "passing": passing,
            "in_progress": in_progress,
            "total": total,
            "percentage": percentage
        })
    finally:
        session.close()


@mcp.tool()
def feature_get_by_id(
    feature_id: Annotated[int, Field(description="The ID of the feature to retrieve", ge=1)]
) -> str:
    """Get a specific feature by its ID.

    Returns the full details of a feature including its name, description,
    verification steps, and current status.

    Args:
        feature_id: The ID of the feature to retrieve

    Returns:
        JSON with feature details, or error if not found.
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()

        if feature is None:
            return json.dumps({"error": f"Feature with ID {feature_id} not found"})

        return json.dumps(feature.to_dict())
    finally:
        session.close()


@mcp.tool()
def feature_get_summary(
    feature_id: Annotated[int, Field(description="The ID of the feature", ge=1)]
) -> str:
    """Get minimal feature info: id, name, status, and dependencies only.

    Use this instead of feature_get_by_id when you only need status info,
    not the full description and steps. This reduces response size significantly.

    Args:
        feature_id: The ID of the feature to retrieve

    Returns:
        JSON with: id, name, passes, in_progress, dependencies
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()
        if feature is None:
            return json.dumps({"error": f"Feature with ID {feature_id} not found"})
        return json.dumps({
            "id": feature.id,
            "name": feature.name,
            "passes": feature.passes,
            "in_progress": feature.in_progress,
            "dependencies": feature.dependencies or []
        })
    finally:
        session.close()


@mcp.tool()
def feature_mark_passing(
    feature_id: Annotated[int, Field(description="The ID of the feature to mark as passing", ge=1)]
) -> str:
    """Mark a feature as passing after successful implementation.

    Updates the feature's passes field to true and clears the in_progress flag.
    Use this after you have implemented the feature and verified it works correctly.

    Args:
        feature_id: The ID of the feature to mark as passing

    Returns:
        JSON with success confirmation: {success, feature_id, name}
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()

        if feature is None:
            return json.dumps({"error": f"Feature with ID {feature_id} not found"})

        feature.passes = True
        feature.in_progress = False
        session.commit()

        return json.dumps({"success": True, "feature_id": feature_id, "name": feature.name})
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to mark feature passing: {str(e)}"})
    finally:
        session.close()


@mcp.tool()
def feature_mark_failing(
    feature_id: Annotated[int, Field(description="The ID of the feature to mark as failing", ge=1)]
) -> str:
    """Mark a feature as failing after finding a regression.

    Updates the feature's passes field to false and clears the in_progress flag.
    Use this when a testing agent discovers that a previously-passing feature
    no longer works correctly (regression detected).

    After marking as failing, you should:
    1. Investigate the root cause
    2. Fix the regression
    3. Verify the fix
    4. Call feature_mark_passing once fixed

    Args:
        feature_id: The ID of the feature to mark as failing

    Returns:
        JSON with the updated feature details, or error if not found.
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()

        if feature is None:
            return json.dumps({"error": f"Feature with ID {feature_id} not found"})

        feature.passes = False
        feature.in_progress = False
        session.commit()
        session.refresh(feature)

        return json.dumps({
            "message": f"Feature #{feature_id} marked as failing - regression detected",
            "feature": feature.to_dict()
        })
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to mark feature failing: {str(e)}"})
    finally:
        session.close()


@mcp.tool()
def feature_skip(
    feature_id: Annotated[int, Field(description="The ID of the feature to skip", ge=1)]
) -> str:
    """Skip a feature by moving it to the end of the priority queue.

    Use this when a feature cannot be implemented yet due to:
    - Dependencies on other features that aren't implemented yet
    - External blockers (missing assets, unclear requirements)
    - Technical prerequisites that need to be addressed first

    The feature's priority is set to max_priority + 1, so it will be
    worked on after all other pending features. Also clears the in_progress
    flag so the feature returns to "pending" status.

    Args:
        feature_id: The ID of the feature to skip

    Returns:
        JSON with skip details: id, name, old_priority, new_priority, message
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()

        if feature is None:
            return json.dumps({"error": f"Feature with ID {feature_id} not found"})

        if feature.passes:
            return json.dumps({"error": "Cannot skip a feature that is already passing"})

        old_priority = feature.priority

        # Use lock to prevent race condition in priority assignment
        with _priority_lock:
            # Get max priority and set this feature to max + 1
            max_priority_result = session.query(Feature.priority).order_by(Feature.priority.desc()).first()
            new_priority = (max_priority_result[0] + 1) if max_priority_result else 1

            feature.priority = new_priority
            feature.in_progress = False
            session.commit()

        session.refresh(feature)

        return json.dumps({
            "id": feature.id,
            "name": feature.name,
            "old_priority": old_priority,
            "new_priority": new_priority,
            "message": f"Feature '{feature.name}' moved to end of queue"
        })
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to skip feature: {str(e)}"})
    finally:
        session.close()


@mcp.tool()
def feature_mark_in_progress(
    feature_id: Annotated[int, Field(description="The ID of the feature to mark as in-progress", ge=1)]
) -> str:
    """Mark a feature as in-progress.

    This prevents other agent sessions from working on the same feature.
    Call this after getting your assigned feature details with feature_get_by_id.

    Args:
        feature_id: The ID of the feature to mark as in-progress

    Returns:
        JSON with the updated feature details, or error if not found or already in-progress.
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()

        if feature is None:
            return json.dumps({"error": f"Feature with ID {feature_id} not found"})

        if feature.passes:
            return json.dumps({"error": f"Feature with ID {feature_id} is already passing"})

        if feature.in_progress:
            return json.dumps({"error": f"Feature with ID {feature_id} is already in-progress"})

        feature.in_progress = True
        session.commit()
        session.refresh(feature)

        return json.dumps(feature.to_dict())
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to mark feature in-progress: {str(e)}"})
    finally:
        session.close()


@mcp.tool()
def feature_claim_and_get(
    feature_id: Annotated[int, Field(description="The ID of the feature to claim", ge=1)]
) -> str:
    """Atomically claim a feature (mark in-progress) and return its full details.

    Combines feature_mark_in_progress + feature_get_by_id into a single operation.
    If already in-progress, still returns the feature details (idempotent).

    Args:
        feature_id: The ID of the feature to claim and retrieve

    Returns:
        JSON with feature details including claimed status, or error if not found.
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()

        if feature is None:
            return json.dumps({"error": f"Feature with ID {feature_id} not found"})

        if feature.passes:
            return json.dumps({"error": f"Feature with ID {feature_id} is already passing"})

        # Idempotent: if already in-progress, just return details
        already_claimed = feature.in_progress
        if not already_claimed:
            feature.in_progress = True
            session.commit()
            session.refresh(feature)

        result = feature.to_dict()
        result["already_claimed"] = already_claimed
        return json.dumps(result)
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to claim feature: {str(e)}"})
    finally:
        session.close()


@mcp.tool()
def feature_clear_in_progress(
    feature_id: Annotated[int, Field(description="The ID of the feature to clear in-progress status", ge=1)]
) -> str:
    """Clear in-progress status from a feature.

    Use this when abandoning a feature or manually unsticking a stuck feature.
    The feature will return to the pending queue.

    Args:
        feature_id: The ID of the feature to clear in-progress status

    Returns:
        JSON with the updated feature details, or error if not found.
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()

        if feature is None:
            return json.dumps({"error": f"Feature with ID {feature_id} not found"})

        feature.in_progress = False
        session.commit()
        session.refresh(feature)

        return json.dumps(feature.to_dict())
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to clear in-progress status: {str(e)}"})
    finally:
        session.close()


@mcp.tool()
def feature_create_bulk(
    features: Annotated[list[dict], Field(description="List of features to create, each with category, name, description, and steps")]
) -> str:
    """Create multiple features in a single operation.

    Features are assigned sequential priorities based on their order.
    All features start with passes=false.

    This is typically used by the initializer agent to set up the initial
    feature list from the app specification.

    Args:
        features: List of features to create, each with:
            - category (str): Feature category
            - name (str): Feature name
            - description (str): Detailed description
            - steps (list[str]): Implementation/test steps
            - depends_on_indices (list[int], optional): Array indices (0-based) of
              features in THIS batch that this feature depends on. Use this instead
              of 'dependencies' since IDs aren't known until after creation.
              Example: [0, 2] means this feature depends on features at index 0 and 2.

    Returns:
        JSON with: created (int) - number of features created, with_dependencies (int)
    """
    session = get_session()
    try:
        # Use lock to prevent race condition in priority assignment
        with _priority_lock:
            # Get the starting priority
            max_priority_result = session.query(Feature.priority).order_by(Feature.priority.desc()).first()
            start_priority = (max_priority_result[0] + 1) if max_priority_result else 1

            # First pass: validate all features and their index-based dependencies
            for i, feature_data in enumerate(features):
                # Validate required fields
                if not all(key in feature_data for key in ["category", "name", "description", "steps"]):
                    return json.dumps({
                        "error": f"Feature at index {i} missing required fields (category, name, description, steps)"
                    })

                # Validate depends_on_indices
                indices = feature_data.get("depends_on_indices", [])
                if indices:
                    # Check max dependencies
                    if len(indices) > MAX_DEPENDENCIES_PER_FEATURE:
                        return json.dumps({
                            "error": f"Feature at index {i} has {len(indices)} dependencies, max is {MAX_DEPENDENCIES_PER_FEATURE}"
                        })
                    # Check for duplicates
                    if len(indices) != len(set(indices)):
                        return json.dumps({
                            "error": f"Feature at index {i} has duplicate dependencies"
                        })
                    # Check for forward references (can only depend on earlier features)
                    for idx in indices:
                        if not isinstance(idx, int) or idx < 0:
                            return json.dumps({
                                "error": f"Feature at index {i} has invalid dependency index: {idx}"
                            })
                        if idx >= i:
                            return json.dumps({
                                "error": f"Feature at index {i} cannot depend on feature at index {idx} (forward reference not allowed)"
                            })

            # Second pass: create all features
            created_features: list[Feature] = []
            for i, feature_data in enumerate(features):
                db_feature = Feature(
                    priority=start_priority + i,
                    category=feature_data["category"],
                    name=feature_data["name"],
                    description=feature_data["description"],
                    steps=feature_data["steps"],
                    passes=False,
                    in_progress=False,
                )
                session.add(db_feature)
                created_features.append(db_feature)

            # Flush to get IDs assigned
            session.flush()

            # Third pass: resolve index-based dependencies to actual IDs
            deps_count = 0
            for i, feature_data in enumerate(features):
                indices = feature_data.get("depends_on_indices", [])
                if indices:
                    # Convert indices to actual feature IDs
                    dep_ids = [created_features[idx].id for idx in indices]
                    created_features[i].dependencies = sorted(dep_ids)
                    deps_count += 1

            session.commit()

        return json.dumps({
            "created": len(created_features),
            "with_dependencies": deps_count
        })
    except Exception as e:
        session.rollback()
        return json.dumps({"error": str(e)})
    finally:
        session.close()


@mcp.tool()
def feature_create(
    category: Annotated[str, Field(min_length=1, max_length=100, description="Feature category (e.g., 'Authentication', 'API', 'UI')")],
    name: Annotated[str, Field(min_length=1, max_length=255, description="Feature name")],
    description: Annotated[str, Field(min_length=1, description="Detailed description of the feature")],
    steps: Annotated[list[str], Field(min_length=1, description="List of implementation/verification steps")]
) -> str:
    """Create a single feature in the project backlog.

    Use this when the user asks to add a new feature, capability, or test case.
    The feature will be added with the next available priority number.

    Args:
        category: Feature category for grouping (e.g., 'Authentication', 'API', 'UI')
        name: Descriptive name for the feature
        description: Detailed description of what this feature should do
        steps: List of steps to implement or verify the feature

    Returns:
        JSON with the created feature details including its ID
    """
    session = get_session()
    try:
        # Use lock to prevent race condition in priority assignment
        with _priority_lock:
            # Get the next priority
            max_priority_result = session.query(Feature.priority).order_by(Feature.priority.desc()).first()
            next_priority = (max_priority_result[0] + 1) if max_priority_result else 1

            db_feature = Feature(
                priority=next_priority,
                category=category,
                name=name,
                description=description,
                steps=steps,
                passes=False,
                in_progress=False,
            )
            session.add(db_feature)
            session.commit()

        session.refresh(db_feature)

        return json.dumps({
            "success": True,
            "message": f"Created feature: {name}",
            "feature": db_feature.to_dict()
        })
    except Exception as e:
        session.rollback()
        return json.dumps({"error": str(e)})
    finally:
        session.close()


@mcp.tool()
def feature_add_dependency(
    feature_id: Annotated[int, Field(ge=1, description="Feature to add dependency to")],
    dependency_id: Annotated[int, Field(ge=1, description="ID of the dependency feature")]
) -> str:
    """Add a dependency relationship between features.

    The dependency_id feature must be completed before feature_id can be started.
    Validates: self-reference, existence, circular dependencies, max limit.

    Args:
        feature_id: The ID of the feature that will depend on another feature
        dependency_id: The ID of the feature that must be completed first

    Returns:
        JSON with success status and updated dependencies list, or error message
    """
    session = get_session()
    try:
        # Security: Self-reference check
        if feature_id == dependency_id:
            return json.dumps({"error": "A feature cannot depend on itself"})

        feature = session.query(Feature).filter(Feature.id == feature_id).first()
        dependency = session.query(Feature).filter(Feature.id == dependency_id).first()

        if not feature:
            return json.dumps({"error": f"Feature {feature_id} not found"})
        if not dependency:
            return json.dumps({"error": f"Dependency feature {dependency_id} not found"})

        current_deps = feature.dependencies or []

        # Security: Max dependencies limit
        if len(current_deps) >= MAX_DEPENDENCIES_PER_FEATURE:
            return json.dumps({"error": f"Maximum {MAX_DEPENDENCIES_PER_FEATURE} dependencies allowed per feature"})

        # Check if already exists
        if dependency_id in current_deps:
            return json.dumps({"error": "Dependency already exists"})

        # Security: Circular dependency check
        # would_create_circular_dependency(features, source_id, target_id)
        # source_id = feature gaining the dependency, target_id = feature being depended upon
        all_features = [f.to_dict() for f in session.query(Feature).all()]
        if would_create_circular_dependency(all_features, feature_id, dependency_id):
            return json.dumps({"error": "Cannot add: would create circular dependency"})

        # Add dependency
        current_deps.append(dependency_id)
        feature.dependencies = sorted(current_deps)
        session.commit()

        return json.dumps({
            "success": True,
            "feature_id": feature_id,
            "dependencies": feature.dependencies
        })
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to add dependency: {str(e)}"})
    finally:
        session.close()


@mcp.tool()
def feature_remove_dependency(
    feature_id: Annotated[int, Field(ge=1, description="Feature to remove dependency from")],
    dependency_id: Annotated[int, Field(ge=1, description="ID of dependency to remove")]
) -> str:
    """Remove a dependency from a feature.

    Args:
        feature_id: The ID of the feature to remove a dependency from
        dependency_id: The ID of the dependency to remove

    Returns:
        JSON with success status and updated dependencies list, or error message
    """
    session = get_session()
    try:
        feature = session.query(Feature).filter(Feature.id == feature_id).first()
        if not feature:
            return json.dumps({"error": f"Feature {feature_id} not found"})

        current_deps = feature.dependencies or []
        if dependency_id not in current_deps:
            return json.dumps({"error": "Dependency does not exist"})

        current_deps.remove(dependency_id)
        feature.dependencies = current_deps if current_deps else None
        session.commit()

        return json.dumps({
            "success": True,
            "feature_id": feature_id,
            "dependencies": feature.dependencies or []
        })
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to remove dependency: {str(e)}"})
    finally:
        session.close()


@mcp.tool()
def feature_get_ready(
    limit: Annotated[int, Field(default=10, ge=1, le=50, description="Max features to return")] = 10
) -> str:
    """Get all features ready to start (dependencies satisfied, not in progress).

    Useful for parallel execution - returns multiple features that can run simultaneously.
    A feature is ready if it is not passing, not in progress, and all dependencies are passing.

    Args:
        limit: Maximum number of features to return (1-50, default 10)

    Returns:
        JSON with: features (list), count (int), total_ready (int)
    """
    session = get_session()
    try:
        all_features = session.query(Feature).all()
        passing_ids = {f.id for f in all_features if f.passes}

        ready = []
        all_dicts = [f.to_dict() for f in all_features]
        for f in all_features:
            if f.passes or f.in_progress:
                continue
            deps = f.dependencies or []
            if all(dep_id in passing_ids for dep_id in deps):
                ready.append(f.to_dict())

        # Sort by scheduling score (higher = first), then priority, then id
        scores = compute_scheduling_scores(all_dicts)
        ready.sort(key=lambda f: (-scores.get(f["id"], 0), f["priority"], f["id"]))

        return json.dumps({
            "features": ready[:limit],
            "count": len(ready[:limit]),
            "total_ready": len(ready)
        })
    finally:
        session.close()


@mcp.tool()
def feature_get_blocked(
    limit: Annotated[int, Field(default=20, ge=1, le=100, description="Max features to return")] = 20
) -> str:
    """Get features that are blocked by unmet dependencies.

    Returns features that have dependencies which are not yet passing.
    Each feature includes a 'blocked_by' field listing the blocking feature IDs.

    Args:
        limit: Maximum number of features to return (1-100, default 20)

    Returns:
        JSON with: features (list with blocked_by field), count (int), total_blocked (int)
    """
    session = get_session()
    try:
        all_features = session.query(Feature).all()
        passing_ids = {f.id for f in all_features if f.passes}

        blocked = []
        for f in all_features:
            if f.passes:
                continue
            deps = f.dependencies or []
            blocking = [d for d in deps if d not in passing_ids]
            if blocking:
                blocked.append({
                    **f.to_dict(),
                    "blocked_by": blocking
                })

        return json.dumps({
            "features": blocked[:limit],
            "count": len(blocked[:limit]),
            "total_blocked": len(blocked)
        })
    finally:
        session.close()


@mcp.tool()
def feature_get_graph() -> str:
    """Get dependency graph data for visualization.

    Returns nodes (features) and edges (dependencies) for rendering a graph.
    Each node includes status: 'pending', 'in_progress', 'done', or 'blocked'.

    Returns:
        JSON with: nodes (list), edges (list of {source, target})
    """
    session = get_session()
    try:
        all_features = session.query(Feature).all()
        passing_ids = {f.id for f in all_features if f.passes}

        nodes = []
        edges = []

        for f in all_features:
            deps = f.dependencies or []
            blocking = [d for d in deps if d not in passing_ids]

            if f.passes:
                status = "done"
            elif blocking:
                status = "blocked"
            elif f.in_progress:
                status = "in_progress"
            else:
                status = "pending"

            nodes.append({
                "id": f.id,
                "name": f.name,
                "category": f.category,
                "status": status,
                "priority": f.priority,
                "dependencies": deps
            })

            for dep_id in deps:
                edges.append({"source": dep_id, "target": f.id})

        return json.dumps({
            "nodes": nodes,
            "edges": edges
        })
    finally:
        session.close()


@mcp.tool()
def feature_set_dependencies(
    feature_id: Annotated[int, Field(ge=1, description="Feature to set dependencies for")],
    dependency_ids: Annotated[list[int], Field(description="List of dependency feature IDs")]
) -> str:
    """Set all dependencies for a feature at once, replacing any existing dependencies.

    Validates: self-reference, existence of all dependencies, circular dependencies, max limit.

    Args:
        feature_id: The ID of the feature to set dependencies for
        dependency_ids: List of feature IDs that must be completed first

    Returns:
        JSON with success status and updated dependencies list, or error message
    """
    session = get_session()
    try:
        # Security: Self-reference check
        if feature_id in dependency_ids:
            return json.dumps({"error": "A feature cannot depend on itself"})

        # Security: Max dependencies limit
        if len(dependency_ids) > MAX_DEPENDENCIES_PER_FEATURE:
            return json.dumps({"error": f"Maximum {MAX_DEPENDENCIES_PER_FEATURE} dependencies allowed"})

        # Check for duplicates
        if len(dependency_ids) != len(set(dependency_ids)):
            return json.dumps({"error": "Duplicate dependencies not allowed"})

        feature = session.query(Feature).filter(Feature.id == feature_id).first()
        if not feature:
            return json.dumps({"error": f"Feature {feature_id} not found"})

        # Validate all dependencies exist
        all_feature_ids = {f.id for f in session.query(Feature).all()}
        missing = [d for d in dependency_ids if d not in all_feature_ids]
        if missing:
            return json.dumps({"error": f"Dependencies not found: {missing}"})

        # Check for circular dependencies
        all_features = [f.to_dict() for f in session.query(Feature).all()]
        # Temporarily update the feature's dependencies for cycle check
        test_features = []
        for f in all_features:
            if f["id"] == feature_id:
                test_features.append({**f, "dependencies": dependency_ids})
            else:
                test_features.append(f)

        for dep_id in dependency_ids:
            # source_id = feature_id (gaining dep), target_id = dep_id (being depended upon)
            if would_create_circular_dependency(test_features, feature_id, dep_id):
                return json.dumps({"error": f"Cannot add dependency {dep_id}: would create circular dependency"})

        # Set dependencies
        feature.dependencies = sorted(dependency_ids) if dependency_ids else None
        session.commit()

        return json.dumps({
            "success": True,
            "feature_id": feature_id,
            "dependencies": feature.dependencies or []
        })
    except Exception as e:
        session.rollback()
        return json.dumps({"error": f"Failed to set dependencies: {str(e)}"})
    finally:
        session.close()


if __name__ == "__main__":
    mcp.run()