virtuoso_mcp/virtuoso_mcp.py

import json
import logging
import os
import re
from datetime import datetime, timezone
from importlib import import_module
from pathlib import Path
from typing import Any, Callable, Dict, List, Optional

import requests
from requests.auth import HTTPDigestAuth
from fastapi import FastAPI, HTTPException, Request
from pydantic import BaseModel

LOG_LEVEL = os.getenv("MCP_LOG_LEVEL", "INFO").upper()
logging.basicConfig(level=getattr(logging, LOG_LEVEL, logging.INFO))
logger = logging.getLogger("virtuoso_mcp")

app = FastAPI(title="MCP Server")

# --- CONFIG ---
VIRTUOSO_ENDPOINT = os.getenv("VIRTUOSO_ENDPOINT") or os.getenv(
    "VIRTUOSO_SPARQL", "http://localhost:8891/sparql"
)
VIRTUOSO_USER = os.getenv("VIRTUOSO_USER")
VIRTUOSO_PASS = os.getenv("VIRTUOSO_PASS")
SPARQL_TIMEOUT = float(os.getenv("SPARQL_TIMEOUT", 10.0))
SPARQL_UPDATE_TIMEOUT = float(os.getenv("SPARQL_UPDATE_TIMEOUT", 15.0))
SPARQL_DEFAULT_LIMIT = int(os.getenv("SPARQL_DEFAULT_LIMIT", 100))
SPARQL_MAX_LIMIT = int(os.getenv("SPARQL_MAX_LIMIT", 500))
GRAPH_URI = os.getenv("GRAPH_URI", "http://example.org/catalog#")
EXAMPLES_DIR = Path(__file__).resolve().parent / "examples"
EXAMPLE_GRAPH = os.getenv(
    "EXAMPLE_GRAPH", "http://example.org/catalog#test"
)
ALLOW_EXAMPLE_LOAD = os.getenv("MCP_ALLOW_EXAMPLE_LOAD", "false").lower() == "true"
SESSION = requests.Session()
LOGS_DIR = Path(__file__).resolve().parent / "logs"
LOGS_DIR.mkdir(parents=True, exist_ok=True)
tool_logger = logging.getLogger("virtuoso_mcp.tools")
tool_handler = logging.FileHandler(LOGS_DIR / "tool_usage.log")
tool_handler.setFormatter(logging.Formatter("%(asctime)s %(message)s"))
tool_logger.addHandler(tool_handler)
tool_logger.setLevel(logging.INFO)
tool_logger.propagate = False

PREFIXES = f"""
PREFIX : <{GRAPH_URI}>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
""".strip()

# --- MODELS ---
class SparqlQueryRequest(BaseModel):
    query: str


class ToolRequest(BaseModel):
    tool: str
    input: Dict[str, Any] = {}


# --- MCP (minimal JSON-RPC 2.0) models ---

class JsonRpcRequest(BaseModel):
    jsonrpc: str = "2.0"
    id: Optional[Any] = None
    method: str
    params: Dict[str, Any] = {}


def mcp_error(id_value: Any, message: str, code: int = -32000) -> Dict[str, Any]:
    return {
        "jsonrpc": "2.0",
        "id": id_value,
        "error": {
            "code": code,
            "message": message,
        },
    }


def mcp_result(id_value: Any, result: Dict[str, Any]) -> Dict[str, Any]:
    return {
        "jsonrpc": "2.0",
        "id": id_value,
        "result": result,
    }


def _mcp_tool_definition(name: str) -> Dict[str, Any]:
    # Incremental compliance step: add explicit input schemas for the most-used tools.
    # We still keep `additionalProperties: True` so we don't break existing clients.
    base: Dict[str, Any] = {
        "name": name,
        "description": TOOL_DOCS.get(name, ""),
        "inputSchema": {
            "type": "object",
            "additionalProperties": True,
            "properties": {},
            "required": [],
        },
    }

    if name == "sparql_query":
        base["inputSchema"]["properties"] = {
            "query": {"type": "string", "description": "SPARQL SELECT query (bounded + guardrailed)"}
        }
        base["inputSchema"]["required"] = ["query"]
        return base

    if name == "search_label":
        base["inputSchema"]["properties"] = {
            "term": {"type": "string", "description": "Substring to search in rdfs:label"},
            "limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "Max results"},
        }
        base["inputSchema"]["required"] = ["term"]
        return base

    if name == "get_entities_by_type":
        base["inputSchema"]["properties"] = {
            "type_uri": {"type": "string", "description": "RDF type URI"},
            "limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "Max subjects"},
        }
        base["inputSchema"]["required"] = ["type_uri"]
        return base

    if name == "list_graphs":
        # No inputs.
        return base

    if name == "list_classes":
        base["inputSchema"]["properties"] = {
            "term": {"type": "string", "description": "Optional substring to match labels/comments"},
            "limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "Max results"},
        }
        base["inputSchema"]["required"] = []
        return base

    if name == "list_properties":
        base["inputSchema"]["properties"] = {
            "term": {"type": "string", "description": "Optional substring to match labels/comments"},
            "domain_uri": {"type": "string", "description": "Optional rdfs:domain class URI"},
            "range_uri": {"type": "string", "description": "Optional rdfs:range class URI"},
            "limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "Max results"},
        }
        base["inputSchema"]["required"] = []
        return base

    if name == "describe_class":
        base["inputSchema"]["properties"] = {
            "class_uri": {"type": "string", "description": "Class URI to describe"},
        }
        base["inputSchema"]["required"] = ["class_uri"]
        return base

    if name == "describe_property":
        base["inputSchema"]["properties"] = {
            "property_uri": {"type": "string", "description": "Property URI to describe"},
            "usage_limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "How many usage examples to include"},
        }
        base["inputSchema"]["required"] = ["property_uri"]
        return base

    # ---- Entity navigation batch (B) ----
    if name == "get_predicates_for_subject":
        base["inputSchema"]["properties"] = {
            "subject_uri": {"type": "string", "description": "Subject URI"},
            "limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "Max predicates"},
        }
        base["inputSchema"]["required"] = ["subject_uri"]
        return base

    if name == "get_labels_for_subject":
        base["inputSchema"]["properties"] = {
            "subject_uri": {"type": "string", "description": "Subject URI"},
        }
        base["inputSchema"]["required"] = ["subject_uri"]
        return base

    if name == "traverse_property":
        base["inputSchema"]["properties"] = {
            "subject_uri": {"type": "string", "description": "Starting subject URI"},
            "property_uri": {"type": "string", "description": "Predicate URI to traverse"},
            "direction": {
                "type": "string",
                "enum": ["outgoing", "incoming"],
                "description": "Traversal direction",
            },
            "limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "Max neighbors"},
        }
        base["inputSchema"]["required"] = ["subject_uri", "property_uri"]
        return base

    if name == "describe_subject":
        base["inputSchema"]["properties"] = {
            "subject_uri": {"type": "string", "description": "Subject URI"},
            "limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "Max outgoing predicate/object pairs"},
        }
        base["inputSchema"]["required"] = ["subject_uri"]
        return base

    if name == "path_traverse":
        base["inputSchema"]["properties"] = {
            "subject_uri": {"type": "string", "description": "Starting subject URI"},
            "property_path": {
                "type": "string",
                "description": "Comma-separated list of predicate URIs (alternative to 'properties')",
            },
            "properties": {
                "type": "array",
                "items": {"type": "string"},
                "description": "List of predicate URIs",
            },
            "direction": {
                "type": "string",
                "enum": ["outgoing", "incoming"],
                "description": "Traversal direction",
            },
            "limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "Max results"},
        }
        base["inputSchema"]["required"] = ["subject_uri"]
        return base

    # ---- Relationship analytics batch (C) ----
    if name == "property_usage_statistics":
        base["inputSchema"]["properties"] = {
            "property_uri": {"type": "string", "description": "Predicate URI"},
            "examples_limit": {"type": "integer", "minimum": 1, "maximum": SPARQL_MAX_LIMIT, "description": "How many usage examples to include"},
        }
        base["inputSchema"]["required"] = ["property_uri"]
        return base

    return base


# --- CORE SPARQL FUNCTION ---

def _build_auth() -> Optional[HTTPDigestAuth]:
    if VIRTUOSO_USER and VIRTUOSO_PASS:
        return HTTPDigestAuth(VIRTUOSO_USER, VIRTUOSO_PASS)
    return None


def _with_prefixes(query: str) -> str:
    if re.search(r"^\s*prefix\b", query, re.IGNORECASE):
        return query
    return f"{PREFIXES}\n{query}"


def run_sparql(query: str) -> Dict[str, Any]:
    """Execute a SPARQL query against Virtuoso and return the JSON payload."""
    logger.debug("Sending SPARQL query: %s", query)
    try:
        response = SESSION.post(
            VIRTUOSO_ENDPOINT,
            data=_with_prefixes(query).encode("utf-8"),
            headers={
                "Accept": "application/sparql-results+json",
                "Content-Type": "application/sparql-query",
            },
            timeout=SPARQL_TIMEOUT,
            auth=_build_auth(),
        )
        if not response.ok:
            logger.warning("SPARQL request failed: %s", response.status_code)
            response.raise_for_status()
        return response.json()
    except Exception as exc:  # pragma: no cover - propagate for FastAPI
        logger.warning("SPARQL request failed: %s", exc)
        raise HTTPException(status_code=500, detail=str(exc))


def run_sparql_update(query: str) -> Dict[str, Any]:
    """Execute a SPARQL UPDATE (INSERT/DELETE) against Virtuoso."""
    logger.debug("Sending SPARQL update: %s", query)
    try:
        response = SESSION.post(
            VIRTUOSO_ENDPOINT,
            data=_with_prefixes(query).encode("utf-8"),
            headers={"Content-Type": "application/sparql-update"},
            timeout=SPARQL_UPDATE_TIMEOUT,
            auth=_build_auth(),
        )
        if not response.ok:
            detail = (response.text or "").strip()
            logger.warning("SPARQL update failed: %s", response.status_code)
            raise HTTPException(
                status_code=500,
                detail=detail or f"SPARQL update failed with {response.status_code}",
            )
        return {"status": "ok"}
    except HTTPException:
        raise
    except Exception as exc:  # pragma: no cover - propagate for FastAPI
        logger.warning("SPARQL update failed: %s", exc)
        raise HTTPException(status_code=500, detail=str(exc))


# --- TOOL HELPERS ---

def escape_sparql_string(value: str) -> str:
    """Escape a string for SPARQL literal usage."""
    if value is None:
        return ""
    return (
        str(value)
        .replace("\\", "\\\\")
        .replace('"', "\\\"")
        .replace("\n", "\\n")
        .replace("\r", "")
    )


def sanitize_term(term: str) -> str:
    """Escape quotes inside label searches so we can safely interpolate strings."""
    return escape_sparql_string(term)


def _extract_limit(query: str) -> Optional[int]:
    match = re.search(r"\blimit\s+(\d+)\b", query, re.IGNORECASE)
    if not match:
        return None
    try:
        return int(match.group(1))
    except ValueError:
        return None


def _apply_limit(query: str, default_limit: int, max_limit: int) -> str:
    limit = _extract_limit(query)
    if limit is None:
        return f"{query.strip()}\nLIMIT {default_limit}"
    if limit > max_limit:
        return re.sub(
            r"\blimit\s+\d+\b",
            f"LIMIT {max_limit}",
            query,
            flags=re.IGNORECASE,
        )
    return query


def guard_select_query(query: str) -> str:
    """Enforce that raw queries are read-only and bounded by LIMIT."""
    lowered = query.lower()
    if re.search(r"\b(insert|delete|load|clear|drop|create|move|copy|add)\b", lowered):
        raise HTTPException(status_code=400, detail="SPARQL update operations are not allowed")
    if "select" not in lowered:
        raise HTTPException(status_code=400, detail="Only SELECT queries are allowed")
    return _apply_limit(query, SPARQL_DEFAULT_LIMIT, SPARQL_MAX_LIMIT)


def ttl_to_sparql_insert(ttl_text: str, graph: Optional[str]) -> str:
    prefix_lines: List[str] = []
    body_lines: List[str] = []
    for raw_line in ttl_text.splitlines():
        line = raw_line.strip()
        if not line:
            continue
        prefix_match = re.match(r"@prefix\s+([\w-]+):\s*<([^>]+)>\s*\.", line)
        if prefix_match:
            prefix_lines.append(
                f"PREFIX {prefix_match.group(1)}: <{prefix_match.group(2)}>"
            )
            continue
        if line.startswith("@base"):
            # Skip @base entries for now; they are rare in our exports.
            continue
        body_lines.append(raw_line)

    if not body_lines:
        raise HTTPException(status_code=400, detail="No RDF triples found in input")

    prefixes = "\n".join(prefix_lines)
    body = "\n".join(body_lines)
    if graph:
        insert_body = f"GRAPH <{graph}> {{\n{body}\n}}"
    else:
        insert_body = body
    return f"{prefixes}\nINSERT DATA {{\n{insert_body}\n}}"


# --- MCP TOOL IMPLEMENTATIONS ---

def tool_sparql_query(input_data: Dict[str, Any]) -> Dict[str, Any]:
    query = input_data.get("query")
    if not query:
        raise ValueError("Missing 'query' field")
    guarded = guard_select_query(query)
    return run_sparql(guarded)


def tool_list_graphs(_input: Dict[str, Any]) -> Dict[str, Any]:
    query = """
    SELECT DISTINCT ?g WHERE {
        GRAPH ?g { ?s ?p ?o }
    }
    LIMIT 50
    """
    return run_sparql(query)


def tool_search_label(input_data: Dict[str, Any]) -> Dict[str, Any]:
    term = input_data.get("term", "")
    sanitized = sanitize_term(term)
    limit = int(input_data.get("limit", 20))
    limit = min(max(limit, 1), SPARQL_MAX_LIMIT)
    query = f"""
    SELECT ?s ?label WHERE {{
        ?s rdfs:label ?label .
        FILTER(CONTAINS(LCASE(?label), LCASE(\"{sanitized}\")))
    }}
    LIMIT {limit}
    """
    return run_sparql(query)


def tool_get_entities_by_type(input_data: Dict[str, Any]) -> Dict[str, Any]:
    type_uri = input_data.get("type_uri")
    if not type_uri:
        raise ValueError("Missing 'type_uri' field")
    limit = int(input_data.get("limit", 50))
    limit = min(max(limit, 1), SPARQL_MAX_LIMIT)
    query = f"""
    SELECT ?s WHERE {{
        ?s rdf:type <{type_uri}> .
    }}
    LIMIT {limit}
    """
    return run_sparql(query)


def tool_get_predicates_for_subject(input_data: Dict[str, Any]) -> Dict[str, Any]:
    subject_uri = input_data.get("subject_uri")
    if not subject_uri:
        raise ValueError("Missing 'subject_uri' field")
    limit = int(input_data.get("limit", 50))
    limit = min(max(limit, 1), SPARQL_MAX_LIMIT)
    query = f"""
    SELECT DISTINCT ?p WHERE {{
        <{subject_uri}> ?p ?o .
    }}
    LIMIT {limit}
    """
    return run_sparql(query)


def tool_get_labels_for_subject(input_data: Dict[str, Any]) -> Dict[str, Any]:
    subject_uri = input_data.get("subject_uri")
    if not subject_uri:
        raise ValueError("Missing 'subject_uri' field")
    query = f"""
    SELECT ?label WHERE {{
        <{subject_uri}> rdfs:label ?label .
    }}
    LIMIT 20
    """
    return run_sparql(query)


def tool_traverse_property(input_data: Dict[str, Any]) -> Dict[str, Any]:
    subject_uri = input_data.get("subject_uri")
    property_uri = input_data.get("property_uri")
    if not subject_uri or not property_uri:
        raise ValueError("Missing 'subject_uri' or 'property_uri'")
    direction = input_data.get("direction", "outgoing")
    limit = int(input_data.get("limit", 50))
    limit = min(max(limit, 1), SPARQL_MAX_LIMIT)

    if direction not in {"outgoing", "incoming"}:
        raise ValueError("direction must be 'outgoing' or 'incoming'")

    if direction == "outgoing":
        triple = f"<{subject_uri}> <{property_uri}> ?neighbor ."
    else:
        triple = f"?neighbor <{property_uri}> <{subject_uri}> ."

    query = f"""
    SELECT ?neighbor ?label ?description WHERE {{
        {triple}
        OPTIONAL {{ ?neighbor rdfs:label ?label }}
        OPTIONAL {{ ?neighbor dc:description ?description }}
    }}
    LIMIT {limit}
    """
    return run_sparql(query)


def tool_list_classes(input_data: Dict[str, Any]) -> Dict[str, Any]:
    """List ontology classes (rdfs:Class and owl:Class) with optional term filtering."""
    term = sanitize_term(input_data.get("term", ""))
    limit = int(input_data.get("limit", 50))
    limit = min(max(limit, 1), SPARQL_MAX_LIMIT)

    term_filter = ""
    if term:
        term_filter = f"""
        FILTER(
            CONTAINS(LCASE(COALESCE(STR(?label), STR(?class))), LCASE(\"{term}\")) ||
            CONTAINS(LCASE(COALESCE(STR(?comment), \"\")), LCASE(\"{term}\"))
        )
        """

    query = f"""
    SELECT DISTINCT ?class ?label ?comment WHERE {{
        {{ ?class rdf:type rdfs:Class . }}
        UNION
        {{ ?class rdf:type <http://www.w3.org/2002/07/owl#Class> . }}
        OPTIONAL {{ ?class rdfs:label ?label }}
        OPTIONAL {{ ?class rdfs:comment ?comment }}
        {term_filter}
    }}
    LIMIT {limit}
    """
    return run_sparql(query)


def tool_list_properties(input_data: Dict[str, Any]) -> Dict[str, Any]:
    """List ontology properties with optional term/domain/range filtering."""
    term = sanitize_term(input_data.get("term", ""))
    domain_uri = input_data.get("domain_uri")
    range_uri = input_data.get("range_uri")
    limit = int(input_data.get("limit", 100))
    limit = min(max(limit, 1), SPARQL_MAX_LIMIT)

    filters = []
    if term:
        filters.append(
            f"""
            FILTER(
                CONTAINS(LCASE(COALESCE(STR(?label), STR(?property))), LCASE(\"{term}\")) ||
                CONTAINS(LCASE(COALESCE(STR(?comment), \"\")), LCASE(\"{term}\"))
            )
            """
        )
    if domain_uri:
        filters.append(f"FILTER(?domain = <{domain_uri}>)")
    if range_uri:
        filters.append(f"FILTER(?range = <{range_uri}>)")

    query = f"""
    SELECT DISTINCT ?property ?label ?comment ?domain ?range WHERE {{
        {{ ?property rdf:type rdf:Property . }}
        UNION
        {{ ?property rdf:type <http://www.w3.org/2002/07/owl#ObjectProperty> . }}
        UNION
        {{ ?property rdf:type <http://www.w3.org/2002/07/owl#DatatypeProperty> . }}
        OPTIONAL {{ ?property rdfs:label ?label }}
        OPTIONAL {{ ?property rdfs:comment ?comment }}
        OPTIONAL {{ ?property rdfs:domain ?domain }}
        OPTIONAL {{ ?property rdfs:range ?range }}
        {' '.join(filters)}
    }}
    LIMIT {limit}
    """
    return run_sparql(query)


def tool_describe_class(input_data: Dict[str, Any]) -> Dict[str, Any]:
    """Describe a class and include properties that declare it as rdfs:domain."""
    class_uri = input_data.get("class_uri")
    if not class_uri:
        raise ValueError("Missing 'class_uri' field")

    query = f"""
    SELECT ?label ?comment ?property ?propertyLabel ?propertyComment ?range WHERE {{
        OPTIONAL {{ <{class_uri}> rdfs:label ?label }}
        OPTIONAL {{ <{class_uri}> rdfs:comment ?comment }}
        OPTIONAL {{
            ?property rdfs:domain <{class_uri}> .
            OPTIONAL {{ ?property rdfs:label ?propertyLabel }}
            OPTIONAL {{ ?property rdfs:comment ?propertyComment }}
            OPTIONAL {{ ?property rdfs:range ?range }}
        }}
    }}
    LIMIT {SPARQL_MAX_LIMIT}
    """
    return run_sparql(query)


def tool_describe_property(input_data: Dict[str, Any]) -> Dict[str, Any]:
    """Describe a property and include usage examples from the graph."""
    property_uri = input_data.get("property_uri")
    if not property_uri:
        raise ValueError("Missing 'property_uri' field")

    usage_limit = int(input_data.get("usage_limit", 10))
    usage_limit = min(max(usage_limit, 1), SPARQL_MAX_LIMIT)

    metadata_query = f"""
    SELECT ?label ?comment ?domain ?range ?type WHERE {{
        OPTIONAL {{ <{property_uri}> rdfs:label ?label }}
        OPTIONAL {{ <{property_uri}> rdfs:comment ?comment }}
        OPTIONAL {{ <{property_uri}> rdfs:domain ?domain }}
        OPTIONAL {{ <{property_uri}> rdfs:range ?range }}
        OPTIONAL {{ <{property_uri}> rdf:type ?type }}
    }}
    LIMIT {SPARQL_MAX_LIMIT}
    """

    usage_query = f"""
    SELECT ?subject ?subjectLabel ?object ?objectLabel WHERE {{
        ?subject <{property_uri}> ?object .
        OPTIONAL {{ ?subject rdfs:label ?subjectLabel }}
        OPTIONAL {{ ?object rdfs:label ?objectLabel }}
    }}
    LIMIT {usage_limit}
    """

    return {
        "metadata": run_sparql(metadata_query),
        "usage": run_sparql(usage_query),
    }


def tool_describe_subject(input_data: Dict[str, Any]) -> Dict[str, Any]:
    subject_uri = input_data.get("subject_uri")
    if not subject_uri:
        raise ValueError("Missing 'subject_uri' field")
    limit = int(input_data.get("limit", 50))
    limit = min(max(limit, 1), SPARQL_MAX_LIMIT)
    query = f"""
    SELECT ?predicate ?object ?objectLabel WHERE {{
        <{subject_uri}> ?predicate ?object .
        OPTIONAL {{ ?object rdfs:label ?objectLabel }}
    }}
    LIMIT {limit}
    """
    return run_sparql(query)


def tool_path_traverse(input_data: Dict[str, Any]) -> Dict[str, Any]:
    subject_uri = input_data.get("subject_uri")
    property_path = input_data.get("property_path") or input_data.get("properties")
    if not subject_uri or not property_path:
        raise ValueError("Missing 'subject_uri' or 'property_path'")
    if isinstance(property_path, str):
        property_path = [p.strip() for p in property_path.split(",") if p.strip()]
    if not isinstance(property_path, list) or not property_path:
        raise ValueError("'property_path' must be a non-empty list of property URIs")
    direction = input_data.get("direction", "outgoing")
    limit = int(input_data.get("limit", 50))
    limit = min(max(limit, 1), SPARQL_MAX_LIMIT)

    statements = []
    optional_lines = []
    select_terms = []
    prev_subject = f"<{subject_uri}>"

    for idx, prop_uri in enumerate(property_path, start=1):
        step_var = f"?n{idx}"
        if direction == "outgoing":
            statements.append(f"{prev_subject} <{prop_uri}> {step_var} .")
        else:
            statements.append(f"{step_var} <{prop_uri}> {prev_subject} .")
        select_terms.append(step_var)
        optional_lines.append(f"OPTIONAL {{ {step_var} rdfs:label {step_var}Label }}")
        optional_lines.append(f"OPTIONAL {{ {step_var} dc:description {step_var}Description }}")
        prev_subject = step_var

    select_clause = " ".join(select_terms)
    query = f"""
    SELECT {select_clause} WHERE {{
        {'\n        '.join(statements)}
        {'\n        '.join(optional_lines)}
    }}
    LIMIT {limit}
    """
    return {
        "property_path": property_path,
        "direction": direction,
        "result": run_sparql(query),
    }


def tool_property_usage_statistics(input_data: Dict[str, Any]) -> Dict[str, Any]:
    property_uri = input_data.get("property_uri")
    if not property_uri:
        raise ValueError("Missing 'property_uri' field")
    examples_limit = int(input_data.get("examples_limit", 5))
    examples_limit = min(max(examples_limit, 1), SPARQL_MAX_LIMIT)

    count_query = f"""
    SELECT (COUNT(DISTINCT ?subject) AS ?usageCount) WHERE {{
        ?subject <{property_uri}> ?object .
    }}
    LIMIT {SPARQL_MAX_LIMIT}
    """
    usage_query = f"""
    SELECT ?subject ?subjectLabel ?object ?objectLabel WHERE {{
        ?subject <{property_uri}> ?object .
        OPTIONAL {{ ?subject rdfs:label ?subjectLabel }}
        OPTIONAL {{ ?object rdfs:label ?objectLabel }}
    }}
    LIMIT {examples_limit}
    """
    return {
        "count": run_sparql(count_query),
        "examples": run_sparql(usage_query),
    }


def tool_batch_insert(input_data: Dict[str, Any]) -> Dict[str, Any]:
    ttl_text = input_data.get("ttl")
    triples = input_data.get("triples")
    graph = input_data.get("graph") or GRAPH_URI

    if not ttl_text and not triples:
        raise ValueError("Provide either 'ttl' text or 'triples' list")

    def _format_object(obj_value: Any, obj_type: str, datatype: Optional[str], lang: Optional[str]) -> str:
        if obj_type == "uri":
            return f"<{obj_value}>"
        if obj_type == "literal":
            return f'"{escape_sparql_string(obj_value)}"'
        if obj_type == "typed_literal":
            if not datatype:
                raise ValueError("Missing datatype for typed_literal")
            return f'"{escape_sparql_string(obj_value)}"^^<{datatype}>'
        if obj_type == "lang_literal":
            if not lang:
                raise ValueError("Missing lang for lang_literal")
            return f'"{escape_sparql_string(obj_value)}"@{lang}'
        raise ValueError(f"Unknown object_type: {obj_type}")

    if ttl_text:
        query = ttl_to_sparql_insert(ttl_text, graph)
    else:
        lines = []
        for triple in triples:
            subj = triple.get("subject")
            pred = triple.get("predicate")
            obj_value = triple.get("object")
            if not subj or not pred or obj_value is None:
                raise ValueError("Each triple must provide subject, predicate, and object")
            obj_type = triple.get("object_type", "uri")
            datatype = triple.get("datatype")
            lang = triple.get("lang")
            obj_text = _format_object(obj_value, obj_type, datatype, lang)
            lines.append(f"<{subj}> <{pred}> {obj_text} .")
        ttl_bulk = "\n".join(lines)
        query = ttl_to_sparql_insert(ttl_bulk, graph)

    result = run_sparql_update(query)
    return {**result, "query": query}


def tool_load_examples(input_data: Dict[str, Any]) -> Dict[str, Any]:
    if not ALLOW_EXAMPLE_LOAD:
        raise HTTPException(status_code=403, detail="Example loading is disabled")

    requested = input_data.get("files") or []
    if isinstance(requested, str):
        requested = [requested]
    graph = input_data.get("graph") or EXAMPLE_GRAPH

    files_to_load = []
    if requested:
        files_to_load = requested
    else:
        files_to_load = sorted(p.name for p in EXAMPLES_DIR.glob("*.ttl"))

    if not files_to_load:
        raise HTTPException(status_code=404, detail="No example files available")

    results = []
    for filename in files_to_load:
        file_path = (EXAMPLES_DIR / filename).resolve()
        if not file_path.exists():
            raise HTTPException(status_code=400, detail=f"Missing example file: {filename}")
        if EXAMPLES_DIR not in file_path.parents and file_path != EXAMPLES_DIR:
            raise HTTPException(status_code=400, detail="Invalid example file path")
        ttl_text = file_path.read_text(encoding="utf-8")
        update_query = ttl_to_sparql_insert(ttl_text, graph)
        run_sparql_update(update_query)
        results.append({"file": filename, "graph": graph})

    return {"loaded": results}


def tool_insert_triple(input_data: Dict[str, Any]) -> Dict[str, Any]:
    subject = input_data.get("subject")
    predicate = input_data.get("predicate")
    obj = input_data.get("object")
    obj_type = input_data.get("object_type", "uri")
    graph = input_data.get("graph")

    if not subject or not predicate or obj is None:
        raise ValueError("Missing 'subject', 'predicate', or 'object' field")

    if obj_type == "uri":
        obj_value = f"<{obj}>"
    elif obj_type == "literal":
        obj_value = f"\"{escape_sparql_string(obj)}\""
    elif obj_type == "typed_literal":
        datatype = input_data.get("datatype")
        if not datatype:
            raise ValueError("Missing 'datatype' for typed_literal")
        obj_value = f"\"{escape_sparql_string(obj)}\"^^<{datatype}>"
    elif obj_type == "lang_literal":
        lang = input_data.get("lang")
        if not lang:
            raise ValueError("Missing 'lang' for lang_literal")
        obj_value = f"\"{escape_sparql_string(obj)}\"@{lang}"
    else:
        raise ValueError("Unknown object_type")

    ttl = f"<{subject}> <{predicate}> {obj_value} ."
    update_query = ttl_to_sparql_insert(ttl, graph)
    try:
        result = run_sparql_update(update_query)
    except HTTPException as exc:
        detail = f"{exc.detail}\n\nSPARQL:\n{update_query}"
        raise HTTPException(status_code=exc.status_code, detail=detail)
    return {**result, "query": update_query}


# --- TOOL REGISTRY ---
TOOLS = {
    "sparql_query": tool_sparql_query,
    "list_graphs": tool_list_graphs,
    "search_label": tool_search_label,
    "get_entities_by_type": tool_get_entities_by_type,
    "get_predicates_for_subject": tool_get_predicates_for_subject,
    "get_labels_for_subject": tool_get_labels_for_subject,
    "traverse_property": tool_traverse_property,
    "list_classes": tool_list_classes,
    "list_properties": tool_list_properties,
    "describe_class": tool_describe_class,
    "describe_property": tool_describe_property,
    "describe_subject": tool_describe_subject,
    "path_traverse": tool_path_traverse,
    "property_usage_statistics": tool_property_usage_statistics,
    "batch_insert": tool_batch_insert,
    "insert_triple": tool_insert_triple,
    "load_examples": tool_load_examples,
}


def load_domain_layers(tools: Dict[str, Callable[[Dict[str, Any]], Any]]) -> None:
    raw = os.getenv("DOMAIN_LAYERS", "garden_layer.plugin")
    modules = [item.strip() for item in raw.split(",") if item.strip()]
    if not modules:
        return
    for module_name in modules:
        module = None
        try:
            module = import_module(module_name)
        except ImportError as exc:
            base = module_name.split(".", 1)[0]
            if base != module_name:
                try:
                    module = import_module(base)
                    logger.info("Falling back to base module '%s' for domain layer '%s'", base, module_name)
                except ImportError:
                    logger.warning(
                        "Domain layer '%s' could not be imported and base module '%s' is missing: %s",
                        module_name,
                        base,
                        exc,
                    )
            else:
                logger.warning("Domain layer '%s' could not be imported: %s", module_name, exc)
        if module is None:
            continue
        register = getattr(module, "register_layer", None)
        if not callable(register):
            logger.warning("Domain layer '%s' does not expose register_layer", module_name)
            continue
        try:
            register(tools)
            logger.info("Loaded domain layer '%s'", module_name)
        except Exception as exc:
            logger.exception("Domain layer '%s' failed to register: %s", module_name, exc)

load_domain_layers(TOOLS)

TOOL_DOCS = {
    "sparql_query": "Execute a bounded SELECT query and return the JSON result.",
    "list_graphs": "List up to 50 active graph URIs.",
    "search_label": "Search rdfs:label values that contain a term (case-insensitive).",
    "get_entities_by_type": "List subjects of a given rdf:type.",
    "get_predicates_for_subject": "List distinct predicates used by a subject.",
    "get_labels_for_subject": "Fetch rdfs:label values for a subject.",
    "traverse_property": "Traverse a property (incoming or outgoing) for a subject and return labels/descriptions.",
    "list_classes": "List ontology classes with optional label/comment term filtering.",
    "list_properties": "List ontology properties with optional term/domain/range filters.",
    "describe_class": "Describe a class and list properties that use it as rdfs:domain.",
    "describe_property": "Describe a property (label/comment/domain/range/type) and sample usage.",
    "describe_subject": "Return subject predicates/objects (with labels) to inspect an individual node.",
    "path_traverse": "Follow a property path (list of predicates) from a subject, returning each step's nodes.",
    "property_usage_statistics": "Count how often a property is used and sample subjects/objects.",
    "batch_insert": "Insert multiple triples or TTL at once with a single guarded update.",
    "insert_triple": "Insert a single triple (useful for debugging updates).",
    "load_examples": "Load Turtle fixtures from the `examples/` directory when MCP_ALLOW_EXAMPLE_LOAD=true.",
}


# --- MCP ENDPOINT ---

@app.post("/mcp")
async def handle_mcp(http_request: Request):
    """Minimal MCP-ish JSON-RPC 2.0 endpoint on POST /mcp.

    Backward compatible legacy mode:
      {"tool": "search_label", "input": {...}}

    Minimal JSON-RPC mode (first step towards MCP compliance):
      {"jsonrpc":"2.0","id":1,"method":"initialize","params":{...}}
      {"jsonrpc":"2.0","id":2,"method":"tools/list","params":{...}}
      {"jsonrpc":"2.0","id":3,"method":"tools/call","params":{ "tool": "...", "params": {...} }}
    """

    body = None
    try:
        body = await http_request.json()
    except Exception:
        body = None

    # ---- Legacy mode ----
    if isinstance(body, dict) and "tool" in body:
        legacy = ToolRequest(**body)
        tool_name = legacy.tool
        input_data = legacy.input or {}

        client_host = http_request.client.host if http_request.client else "unknown"
        trimmed_input = json.dumps(input_data, ensure_ascii=False, default=str)
        if len(trimmed_input) > 1024:
            trimmed_input = f"{trimmed_input[:1024]}…"
        timestamp = datetime.now(timezone.utc).isoformat()
        tool_logger.info(
            "tool=%s client=%s time=%s input=%s",
            tool_name,
            client_host,
            timestamp,
            trimmed_input,
        )

        if tool_name not in TOOLS:
            raise HTTPException(status_code=400, detail=f"Unknown tool: {tool_name}")

        try:
            result = TOOLS[tool_name](input_data)
            return {
                "status": "ok",
                "tool": tool_name,
                "description": TOOL_DOCS.get(tool_name, ""),
                "result": result,
            }
        except Exception as exc:
            logger.error("Tool %s failed: %s", tool_name, exc)
            raise HTTPException(status_code=500, detail=str(exc))

    # ---- JSON-RPC 2.0 mode ----
    if not isinstance(body, dict):
        return mcp_error(None, "Invalid JSON-RPC request", code=-32600)

    try:
        rpc_req = JsonRpcRequest(**body)
    except Exception as exc:
        # If body is malformed, still surface the id if present.
        rpc_id = body.get("id")
        logger.warning("Invalid JSON-RPC request: %s", exc)
        return mcp_error(rpc_id, "Invalid JSON-RPC request", code=-32600)

    method = rpc_req.method
    rpc_id = rpc_req.id
    params = rpc_req.params or {}

    if method == "initialize":
        tools = [_mcp_tool_definition(name) for name in sorted(TOOLS.keys())]
        return mcp_result(
            rpc_id,
            {
                "protocolVersion": "0.1",
                "capabilities": {
                    "tools": True,
                    "list": True,
                    "call": True,
                },
                "tools": tools,
            },
        )

    if method in {"tools/list", "tools/listTools"}:
        tools = [_mcp_tool_definition(name) for name in sorted(TOOLS.keys())]
        return mcp_result(rpc_id, {"tools": tools})

    if method in {"tools/call", "tools/callTool"}:
        # Different clients sometimes wrap the call slightly differently.
        tool_name = (
            params.get("tool")
            or params.get("name")
            or params.get("toolName")
        )
        input_data = (
            params.get("params")
            or params.get("input")
            or params.get("arguments")
            or {}
        )
        if not tool_name:
            return mcp_error(rpc_id, "Missing tool name", code=-32602)
        if tool_name not in TOOLS:
            return mcp_error(rpc_id, f"Unknown tool: {tool_name}", code=-32601)
        try:
            result = TOOLS[tool_name](input_data)
            return mcp_result(rpc_id, {"result": result})
        except HTTPException as exc:
            return mcp_error(rpc_id, str(exc.detail), code=exc.status_code)
        except Exception as exc:
            logger.error("Tool %s failed: %s", tool_name, exc)
            return mcp_error(rpc_id, str(exc), code=-32000)

    return mcp_error(rpc_id, f"Method not found: {method}", code=-32601)


# --- HEALTH CHECK ---

@app.get("/")
def root():
    return {
        "status": "MCP server running",
        "tools": list(TOOLS.keys()),
        "virtuoso": VIRTUOSO_ENDPOINT,
        "guardrails": {
            "default_limit": SPARQL_DEFAULT_LIMIT,
            "max_limit": SPARQL_MAX_LIMIT,
            "allow_example_load": ALLOW_EXAMPLE_LOAD,
            "turtle_examples": True,
        },
    }


@app.get("/health")
def health():
    return root()