feat: ajout RAG CIM-10 avec FAISS + Ollama
Implémente un système RAG (Retrieval Augmented Generation) qui indexe les documents de référence ATIH (CIM-10 FR 2026, Guide Métho MCO, CCAM PMSI) et utilise Ollama (mistral-small3.2:24b) pour justifier et valider le codage CIM-10 des diagnostics. - Nouveaux modèles Pydantic : RAGSource, Diagnostic étendu (confidence, justification, sources_rag) — rétrocompatible - Module rag_index.py : chunking des 3 PDFs, embedding sentence-camembert-large, index FAISS IndexFlatIP (3630 vecteurs) - Module rag_search.py : recherche FAISS + appel Ollama avec fallback double - Flag CLI --no-rag pour désactiver l'enrichissement RAG - 18 nouveaux tests (88/88 passent) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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src/medical/rag_index.py
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src/medical/rag_index.py
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"""Indexation FAISS des documents de référence CIM-10 / Guide métho / CCAM."""
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from __future__ import annotations
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import json
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import logging
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import re
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from dataclasses import dataclass, asdict
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from pathlib import Path
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from typing import Optional
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import pdfplumber
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from ..config import RAG_INDEX_DIR, CIM10_PDF, GUIDE_METHODO_PDF, CCAM_PDF
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logger = logging.getLogger(__name__)
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# Singleton pour l'index chargé en mémoire
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_faiss_index = None
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_metadata: list[dict] = []
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@dataclass
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class Chunk:
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text: str
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document: str # "cim10", "guide_methodo", "ccam"
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page: Optional[int] = None
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code: Optional[str] = None
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# ---------------------------------------------------------------------------
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# Chunking CIM-10
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# ---------------------------------------------------------------------------
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def _chunk_cim10(pdf_path: Path) -> list[Chunk]:
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"""Découpe le PDF CIM-10 en chunks par code 3 caractères (ex: K80, K85)."""
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chunks: list[Chunk] = []
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current_code: str | None = None
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current_text: list[str] = []
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current_page: int | None = None
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# Pattern pour détecter un code CIM-10 à 3 caractères en début de ligne
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code3_pattern = re.compile(r"^([A-Z]\d{2})\s+(.+)")
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# Pattern pour les sous-codes (ex: K80.0, K80.1)
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subcode_pattern = re.compile(r"^([A-Z]\d{2}\.\d+)\s+(.+)")
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logger.info("Extraction des chunks CIM-10 depuis %s", pdf_path.name)
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with pdfplumber.open(pdf_path) as pdf:
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for page_num, page in enumerate(pdf.pages, start=1):
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text = page.extract_text()
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if not text:
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continue
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for line in text.split("\n"):
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line = line.strip()
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if not line:
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continue
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m = code3_pattern.match(line)
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if m and not subcode_pattern.match(line):
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# Nouveau code 3-char → sauvegarder le chunk précédent
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if current_code and current_text:
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chunk_text = "\n".join(current_text)
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if len(chunk_text.split()) >= 5:
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chunks.append(Chunk(
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text=chunk_text,
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document="cim10",
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page=current_page,
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code=current_code,
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))
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current_code = m.group(1)
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current_text = [line]
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current_page = page_num
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else:
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if current_code:
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current_text.append(line)
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# Dernier chunk
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if current_code and current_text:
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chunk_text = "\n".join(current_text)
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if len(chunk_text.split()) >= 5:
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chunks.append(Chunk(
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text=chunk_text,
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document="cim10",
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page=current_page,
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code=current_code,
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))
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logger.info("CIM-10 : %d chunks extraits", len(chunks))
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return chunks
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# ---------------------------------------------------------------------------
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# Chunking Guide Méthodologique MCO
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# ---------------------------------------------------------------------------
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def _chunk_guide_methodo(pdf_path: Path) -> list[Chunk]:
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"""Découpe le Guide Méthodologique MCO par sections/titres."""
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chunks: list[Chunk] = []
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current_title: str | None = None
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current_text: list[str] = []
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current_page: int | None = None
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# Patterns de titres de sections (chapitres, sous-chapitres)
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title_patterns = [
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re.compile(r"^((?:CHAPITRE|TITRE|PARTIE)\s+[IVXLCDM0-9]+.*)$", re.IGNORECASE),
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re.compile(r"^(\d+\.\d*\s+[A-ZÉÈÊÀÂÔÙÛÜ].{5,})$"),
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re.compile(r"^([A-ZÉÈÊÀÂÔÙÛÜ][A-ZÉÈÊÀÂÔÙÛÜ\s]{10,})$"),
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]
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logger.info("Extraction des chunks Guide Métho depuis %s", pdf_path.name)
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with pdfplumber.open(pdf_path) as pdf:
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for page_num, page in enumerate(pdf.pages, start=1):
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text = page.extract_text()
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if not text:
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continue
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for line in text.split("\n"):
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line = line.strip()
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if not line:
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continue
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is_title = False
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for pat in title_patterns:
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if pat.match(line):
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is_title = True
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break
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if is_title and len(line) > 8:
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# Sauvegarder le chunk précédent
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if current_title and current_text:
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chunk_text = current_title + "\n" + "\n".join(current_text)
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if len(chunk_text.split()) >= 20:
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chunks.append(Chunk(
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text=chunk_text,
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document="guide_methodo",
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page=current_page,
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))
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current_title = line
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current_text = []
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current_page = page_num
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else:
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current_text.append(line)
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# Dernier chunk
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if current_title and current_text:
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chunk_text = current_title + "\n" + "\n".join(current_text)
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if len(chunk_text.split()) >= 20:
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chunks.append(Chunk(
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text=chunk_text,
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document="guide_methodo",
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page=current_page,
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))
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# Si trop peu de chunks (le PDF ne suit pas les patterns de titre),
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# fallback : découper par pages groupées par 3
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if len(chunks) < 10:
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logger.info("Guide Métho : fallback découpe par pages (peu de titres détectés)")
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chunks = []
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with pdfplumber.open(pdf_path) as pdf:
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page_texts: list[str] = []
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start_page = 1
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for page_num, page in enumerate(pdf.pages, start=1):
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text = page.extract_text()
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if text:
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page_texts.append(text)
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if len(page_texts) >= 3:
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combined = "\n".join(page_texts)
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if len(combined.split()) >= 20:
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chunks.append(Chunk(
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text=combined,
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document="guide_methodo",
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page=start_page,
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))
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page_texts = []
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start_page = page_num + 1
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if page_texts:
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combined = "\n".join(page_texts)
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if len(combined.split()) >= 20:
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chunks.append(Chunk(
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text=combined,
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document="guide_methodo",
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page=start_page,
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))
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logger.info("Guide Métho : %d chunks extraits", len(chunks))
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return chunks
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# ---------------------------------------------------------------------------
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# Chunking CCAM
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# ---------------------------------------------------------------------------
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def _chunk_ccam(pdf_path: Path) -> list[Chunk]:
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"""Découpe le PDF CCAM en chunks par code d'acte."""
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chunks: list[Chunk] = []
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ccam_pattern = re.compile(r"([A-Z]{4}\d{3})\s+(.*)")
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logger.info("Extraction des chunks CCAM depuis %s", pdf_path.name)
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with pdfplumber.open(pdf_path) as pdf:
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for page_num, page in enumerate(pdf.pages, start=1):
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text = page.extract_text()
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if not text:
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continue
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current_code: str | None = None
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current_lines: list[str] = []
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for line in text.split("\n"):
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line = line.strip()
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if not line:
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continue
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m = ccam_pattern.match(line)
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if m:
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if current_code and current_lines:
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chunks.append(Chunk(
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text="\n".join(current_lines),
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document="ccam",
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page=page_num,
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code=current_code,
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))
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current_code = m.group(1)
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current_lines = [line]
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elif current_code:
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current_lines.append(line)
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if current_code and current_lines:
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chunks.append(Chunk(
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text="\n".join(current_lines),
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document="ccam",
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page=page_num,
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code=current_code,
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))
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# Fallback : si aucun code CCAM détecté, indexer par page
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if not chunks:
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logger.info("CCAM : aucun code détecté, fallback par page")
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with pdfplumber.open(pdf_path) as pdf:
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for page_num, page in enumerate(pdf.pages, start=1):
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text = page.extract_text()
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if text and len(text.split()) >= 10:
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chunks.append(Chunk(
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text=text,
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document="ccam",
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page=page_num,
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))
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logger.info("CCAM : %d chunks extraits", len(chunks))
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return chunks
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# ---------------------------------------------------------------------------
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# Construction de l'index FAISS
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# ---------------------------------------------------------------------------
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def build_index(force: bool = False) -> None:
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"""Construit l'index FAISS à partir des 3 PDFs de référence.
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Args:
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force: Si True, reconstruit même si l'index existe déjà.
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"""
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import faiss
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import numpy as np
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from sentence_transformers import SentenceTransformer
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index_path = RAG_INDEX_DIR / "faiss.index"
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meta_path = RAG_INDEX_DIR / "metadata.json"
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if not force and index_path.exists() and meta_path.exists():
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logger.info("Index FAISS déjà existant dans %s (use force=True pour reconstruire)", RAG_INDEX_DIR)
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return
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# Collecter tous les chunks
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all_chunks: list[Chunk] = []
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for pdf_path, chunk_fn in [
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(CIM10_PDF, _chunk_cim10),
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(GUIDE_METHODO_PDF, _chunk_guide_methodo),
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(CCAM_PDF, _chunk_ccam),
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]:
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if pdf_path.exists():
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all_chunks.extend(chunk_fn(pdf_path))
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else:
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logger.warning("PDF non trouvé : %s", pdf_path)
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if not all_chunks:
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logger.error("Aucun chunk extrait — vérifiez les chemins des PDFs")
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return
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logger.info("Total : %d chunks à indexer", len(all_chunks))
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# Embeddings — forcer CPU pour éviter les bugs CUDA avec ce modèle
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logger.info("Chargement du modèle d'embedding dangvantuan/sentence-camembert-large (CPU)...")
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model = SentenceTransformer("dangvantuan/sentence-camembert-large", device="cpu")
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model.max_seq_length = 512 # CamemBERT max position embeddings
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texts = [c.text[:2000] for c in all_chunks] # Tronquer les chunks trop longs
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logger.info("Calcul des embeddings pour %d chunks...", len(texts))
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embeddings = model.encode(
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texts, show_progress_bar=True, normalize_embeddings=True, batch_size=64,
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)
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embeddings = np.array(embeddings, dtype=np.float32)
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# Index FAISS (IndexFlatIP = cosine similarity avec vecteurs normalisés)
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dim = embeddings.shape[1]
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index = faiss.IndexFlatIP(dim)
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index.add(embeddings)
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# Sauvegarder
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RAG_INDEX_DIR.mkdir(parents=True, exist_ok=True)
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faiss.write_index(index, str(index_path))
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metadata = [asdict(c) for c in all_chunks]
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# Ne pas sauvegarder le texte complet dans metadata (trop lourd),
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# garder un extrait de 500 chars
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for m in metadata:
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m["extrait"] = m.pop("text")[:500]
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meta_path.write_text(json.dumps(metadata, ensure_ascii=False, indent=2), encoding="utf-8")
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logger.info("Index FAISS sauvegardé : %s (%d vecteurs, dim=%d)", index_path, len(all_chunks), dim)
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def get_index() -> tuple | None:
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"""Charge l'index FAISS et les métadonnées (singleton lazy-loaded).
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Returns:
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Tuple (faiss_index, metadata_list) ou None si l'index n'existe pas.
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"""
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global _faiss_index, _metadata
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if _faiss_index is not None:
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return _faiss_index, _metadata
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index_path = RAG_INDEX_DIR / "faiss.index"
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meta_path = RAG_INDEX_DIR / "metadata.json"
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if not index_path.exists() or not meta_path.exists():
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logger.warning("Index FAISS non trouvé dans %s — lancez build_index() d'abord", RAG_INDEX_DIR)
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return None
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import faiss
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_faiss_index = faiss.read_index(str(index_path))
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_metadata = json.loads(meta_path.read_text(encoding="utf-8"))
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logger.info("Index FAISS chargé : %d vecteurs", _faiss_index.ntotal)
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return _faiss_index, _metadata
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