4a12cd2676
Pipeline complet de traitement de documents médicaux PDF : - Extraction texte (pdfplumber) et classification (Trackare/CRH) - Anonymisation multi-couche (regex + NER CamemBERT + sweep) - Extraction médicale CIM-10 hybride : edsnlp (AP-HP) enrichit les diagnostics, médicaments (codes ATC via Romedi) et négation, avec fallback regex pour les patterns spécifiques - Fix sentencepiece pinné à <0.2.0 pour compatibilité CamemBERT Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
125 lines
4.1 KiB
Python
125 lines
4.1 KiB
Python
"""Tests d'intégration end-to-end sur les PDFs réels."""
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import json
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from pathlib import Path
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import pytest
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from src.config import INPUT_DIR, ANONYMIZED_DIR, STRUCTURED_DIR
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from src.main import process_pdf
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# Skip si les PDFs ne sont pas disponibles
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CRH_PDF = INPUT_DIR / "CRH 23042753.pdf"
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TRACKARE_PDF = INPUT_DIR / "trackare-01306172-23042753_01306172_23042753.pdf"
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needs_pdfs = pytest.mark.skipif(
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not CRH_PDF.exists() or not TRACKARE_PDF.exists(),
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reason="PDFs de test non disponibles dans input/",
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)
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# Données personnelles connues à vérifier
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PATIENT_PII = [
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"NARBAIS", "CLIER", "AUDREY", "01306172", "23042753",
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"23/02/1980", "IRREXELAIA", "BAIGORRY", "06.25.39.26.82",
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]
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SOIGNANT_NAMES = [
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"DUTREY", "MENDIBOURE", "PUJOS", "AUDEMAR", "MELLIN",
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"GUIRESSE", "GOYTINO", "SERRE", "NOVION",
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]
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@needs_pdfs
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class TestCRHIntegration:
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@pytest.fixture(autouse=True)
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def setup(self):
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self.anonymized, self.dossier, self.report = process_pdf(CRH_PDF)
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def test_no_patient_pii(self):
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text_upper = self.anonymized.upper()
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for pii in PATIENT_PII:
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assert pii.upper() not in text_upper, f"PII trouvé : {pii}"
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def test_medical_content_preserved(self):
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text_lower = self.anonymized.lower()
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for term in ["pancréatite", "cholécystectomie", "cholangiographie", "lithiase"]:
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assert term in text_lower, f"Terme médical manquant : {term}"
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def test_diagnostic_principal(self):
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dp = self.dossier.diagnostic_principal
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assert dp is not None
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assert dp.cim10_suggestion == "K85.1"
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def test_diagnostics_associes(self):
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codes = {d.cim10_suggestion for d in self.dossier.diagnostics_associes}
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assert "K80.5" in codes or "K80.2" in codes
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def test_sejour(self):
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s = self.dossier.sejour
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assert s.sexe == "F"
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assert s.age == 43
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assert s.date_entree == "25/02/2023"
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assert s.date_sortie == "03/03/2023"
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assert s.duree_sejour == 6
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def test_traitements_have_optional_atc(self):
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"""Vérifie que les traitements ont le champ code_atc (peut être None)."""
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for t in self.dossier.traitements_sortie:
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assert hasattr(t, "code_atc")
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@needs_pdfs
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class TestTrackareIntegration:
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@pytest.fixture(autouse=True)
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def setup(self):
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self.anonymized, self.dossier, self.report = process_pdf(TRACKARE_PDF)
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def test_no_patient_pii(self):
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text_upper = self.anonymized.upper()
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for pii in PATIENT_PII:
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assert pii.upper() not in text_upper, f"PII trouvé : {pii}"
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def test_no_soignant_names(self):
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# Ignorer "selles" qui contient "SELLE"
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text = self.anonymized
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for name in SOIGNANT_NAMES:
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# Chercher le nom comme mot complet
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import re
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pattern = re.compile(r"\b" + re.escape(name) + r"\b", re.IGNORECASE)
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matches = pattern.findall(text)
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assert len(matches) == 0, f"Nom soignant trouvé : {name} ({len(matches)} occurrences)"
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def test_medical_content_preserved(self):
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text_lower = self.anonymized.lower()
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for term in ["pancréatite", "cholécystectomie", "morphine", "paracétamol"]:
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assert term in text_lower, f"Terme médical manquant : {term}"
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def test_diagnostic_principal(self):
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dp = self.dossier.diagnostic_principal
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assert dp is not None
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assert dp.cim10_suggestion in ("K80.5", "K85.1")
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def test_sejour_with_vitals(self):
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s = self.dossier.sejour
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assert s.sexe == "F"
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assert s.age == 43
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assert s.imc is not None
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assert s.imc > 30
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assert s.poids is not None
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assert s.taille is not None
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def test_biologie(self):
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tests = {b.test for b in self.dossier.biologie_cle}
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assert "Lipasémie" in tests
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assert "CRP" in tests
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# Lipasémie doit être anormale
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for b in self.dossier.biologie_cle:
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if b.test == "Lipasémie":
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assert b.anomalie is True
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def test_report_counts(self):
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assert self.report.total_replacements > 100
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assert self.report.regex_replacements > 50
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