atlas-mcp/app/storage_service.py

"""Atlas persistence/read service via virtuoso-mcp (MCP transport).

We intentionally use the MCP SSE transport ("/mcp/sse") to match the standard across
our MCP servers and avoid legacy direct "/rpc" calls.
"""

from __future__ import annotations

import json
import logging
import os
import time
from typing import Any, Awaitable, Callable

from mcp import ClientSession
from mcp.client.sse import sse_client

from app.models import AtlasEntity
from app.triple_export import entity_to_turtle

logger = logging.getLogger(__name__)

ATLAS_GRAPH_IRI = os.getenv("ATLAS_GRAPH_IRI", "http://world.eu.org/atlas_data#")
VIRTUOSO_MCP_SSE_URL = os.getenv("ATLAS_VIRTUOSO_MCP_SSE_URL", "http://192.168.0.249:8501/mcp/sse")
VIRTUOSO_MCP_TIMEOUT = float(os.getenv("ATLAS_VIRTUOSO_MCP_TIMEOUT", "10"))
VIRTUOSO_MCP_SSE_READ_TIMEOUT = float(os.getenv("ATLAS_VIRTUOSO_MCP_SSE_READ_TIMEOUT", str(60 * 5)))

CallToolFn = Callable[[str, dict[str, Any]], Awaitable[dict[str, Any]]]


def _safe_fragment(value: str) -> str:
    value = (value or "").strip().lower()
    out = []
    for ch in value:
        if ch.isalnum() or ch in ["_", "-"]:
            out.append(ch)
        else:
            out.append("_")
    frag = "".join(out).strip("_")
    return frag or "entity"


def entity_iri(entity_id: str) -> str:
    return f"http://world.eu.org/atlas_data#entity_{_safe_fragment(entity_id)}"


class AtlasStorageService:
    def __init__(self, call_tool: CallToolFn | None = None):
        self._call_tool_override = call_tool
        self._tool_cache: dict[str, tuple[float, dict[str, Any]]] = {}
        self._tool_cache_ttl_seconds = float(os.getenv("ATLAS_VIRTUOSO_CALL_CACHE_TTL", "30"))

    def _cache_key(self, tool_name: str, payload: dict[str, Any]) -> str:
        return f"{tool_name}:{json.dumps(payload, sort_keys=True, separators=(',', ':'))}"

    def _cache_get(self, key: str) -> dict[str, Any] | None:
        item = self._tool_cache.get(key)
        if not item:
            return None
        expires_at, value = item
        if expires_at < time.time():
            self._tool_cache.pop(key, None)
            return None
        return value

    def _cache_set(self, key: str, value: dict[str, Any]) -> None:
        self._tool_cache[key] = (time.time() + self._tool_cache_ttl_seconds, value)

    async def _call_tool(self, tool_name: str, payload: dict[str, Any], *, cache_result: bool = True) -> dict[str, Any]:
        cache_key = self._cache_key(tool_name, payload)
        if cache_result:
            cached = self._cache_get(cache_key)
            if cached is not None:
                return cached

        if self._call_tool_override:
            result = await self._call_tool_override(tool_name, payload)
            if cache_result:
                self._cache_set(cache_key, result)
            return result

        try:
            async with sse_client(
                VIRTUOSO_MCP_SSE_URL,
                timeout=VIRTUOSO_MCP_TIMEOUT,
                sse_read_timeout=VIRTUOSO_MCP_SSE_READ_TIMEOUT,
            ) as (read_stream, write_stream):
                async with ClientSession(read_stream, write_stream) as session:
                    await session.initialize()
                    result = await session.call_tool(tool_name, {"input": payload})
                    if result.isError:
                        raise RuntimeError(f"Tool {tool_name} failed: {result.error}")
                    data = result.structuredContent if result.structuredContent is not None else result.content
                    if cache_result and isinstance(data, dict):
                        self._cache_set(cache_key, data)
                    return data
        except Exception as exc:
            raise RuntimeError(f"Virtuoso MCP call failed for {tool_name}: {exc}")

    async def write_entity(self, entity: AtlasEntity) -> dict[str, Any]:
        ttl = entity_to_turtle(entity)
        try:
            result = await self._call_tool(
                "batch_insert",
                {
                    "ttl": ttl,
                    "graph": ATLAS_GRAPH_IRI,
                },
                cache_result=False,
            )
            return {
                "status": "ok",
                "graph": ATLAS_GRAPH_IRI,
                "entity_id": entity.atlas_id,
                "result": result,
            }
        except Exception as exc:
            logger.warning(
                "Atlas persistence failed for %s into %s: %s",
                entity.atlas_id,
                ATLAS_GRAPH_IRI,
                exc,
            )
            return {
                "status": "unfinished",
                "message": "Persistence path not fully available yet",
                "error": str(exc),
                "entity_id": entity.atlas_id,
            }

    async def read_entity_claims(self, entity_id: str, include_superseded: bool = False) -> dict[str, Any]:
        iri = entity_iri(entity_id)
        status_filter = "" if include_superseded else 'FILTER(?status = "active")'
        query = f"""
	PREFIX atlas: <http://world.eu.org/atlas_ontology#>
	SELECT ?entity ?label ?canonType ?claim ?pred ?objIri ?objLit ?idVal ?idType ?layer ?status ?prov ?src ?method ?conf ?ts
	WHERE {{
	  VALUES ?entity {{ <{iri}> }}

	  ?entity a atlas:Entity ;
	          atlas:canonicalLabel ?label ;
	          atlas:hasCanonicalType ?canonType ;
	          atlas:hasClaim ?claim .

  ?claim atlas:claimSubjectIri ?entity ;
         atlas:claimPredicate ?pred ;
         atlas:claimLayer ?layer ;
         atlas:claimStatus ?status .

  OPTIONAL {{ ?claim atlas:claimObjectIri ?objIri . }}
  OPTIONAL {{ ?claim atlas:claimObjectLiteral ?objLit . }}
  OPTIONAL {{ ?objIri atlas:identifierValue ?idVal . }}
  OPTIONAL {{ ?objIri atlas:identifierType ?idType . }}

  OPTIONAL {{
    ?claim atlas:hasProvenance ?prov .
    ?prov atlas:provenanceSource ?src .
    OPTIONAL {{ ?prov atlas:retrievalMethod ?method . }}
    OPTIONAL {{ ?prov atlas:confidence ?conf . }}
    OPTIONAL {{ ?prov atlas:retrievedAt ?ts . }}
  }}

  {status_filter}
}}
ORDER BY ?claim
"""
        try:
            result = await self._call_tool("sparql_query", {"query": query})
            return {
                "status": "ok",
                "entity_id": entity_id,
                "query": query,
                "result": result,
            }
        except Exception as exc:
            return {
                "status": "unfinished",
                "message": "Read path not fully available yet",
                "error": str(exc),
                "entity_id": entity_id,
                "query": query,
            }

    async def sparql_update(self, query: str) -> dict[str, Any]:
        return await self._call_tool("sparql_update", {"query": query}, cache_result=False)

    async def supersede_claims(self, claim_iris: list[str]) -> None:
        if not claim_iris:
            return
        values = " ".join(f"<{uri}>" for uri in claim_iris)
        query = f"""
PREFIX atlas: <http://world.eu.org/atlas_ontology#>
WITH <{ATLAS_GRAPH_IRI}>
DELETE {{ ?claim atlas:claimStatus ?old . }}
INSERT {{ ?claim atlas:claimStatus "superseded" }}
WHERE {{
  VALUES ?claim {{ {values} }}
  OPTIONAL {{ ?claim atlas:claimStatus ?old . }}
}}
"""
        await self.sparql_update(query)

    async def replace_entity_core(self, entity_id: str, *, canonical_label: str, canonical_description: str | None, canonical_type: str | None) -> None:
        iri = entity_iri(entity_id)
        desc_insert = f'  <{iri}> atlas:canonicalDescription "{canonical_description.replace("\\", "\\\\").replace("\"", "\\\"")}" .\n' if canonical_description else ""
        type_insert = f"  <{iri}> atlas:hasCanonicalType atlas:{canonical_type} .\n" if canonical_type else ""
        query = f"""
PREFIX atlas: <http://world.eu.org/atlas_ontology#>
WITH <{ATLAS_GRAPH_IRI}>
DELETE {{
  <{iri}> atlas:canonicalLabel ?oldLabel .
  <{iri}> atlas:canonicalDescription ?oldDesc .
  <{iri}> atlas:hasCanonicalType ?oldType .
}}
INSERT {{
  <{iri}> atlas:canonicalLabel "{canonical_label.replace("\\", "\\\\").replace("\"", "\\\"")}" .
{desc_insert}{type_insert}}}
WHERE {{
  OPTIONAL {{ <{iri}> atlas:canonicalLabel ?oldLabel . }}
  OPTIONAL {{ <{iri}> atlas:canonicalDescription ?oldDesc . }}
  OPTIONAL {{ <{iri}> atlas:hasCanonicalType ?oldType . }}
}}
"""
        await self.sparql_update(query)