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feat(08-deep-helper-deployment): add rollback to prepare_deep_reading

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- Wrap figure-map, chart-type-map, and scaffold generation in try/except
- Track written files for cleanup on failure
- Save original formal note content before modification
- On exception: delete partial files and restore original note
- Add test_prepare_rollback.py with 3 tests:
  - figure-map failure triggers rollback
  - scaffold failure triggers rollback
  - success path leaves all files intact
- Fix zotero_key quote stripping in scan_deep_reading_queue
This commit is contained in:
Research Assistant 2026-04-24 14:37:13 +08:00
parent 802d34bff6
commit 766ed1edfa
2 changed files with 191 additions and 47 deletions
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112
skills/literature-qa/scripts/ld_deep.py
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@ -1085,59 +1085,77 @@ def prepare_deep_reading(vault: Path, zotero_key: str, force: bool = False) -> d
result["formal_note"] = str(formal_note)
# 6. Run figure-map
figure_map_path = ocr_dir / "figure-map.json"
fulltext_text = fulltext_md.read_text(encoding="utf-8")
figure_map = build_figure_map(fulltext_text, zotero_key=zotero_key)
figure_map["generated_at"] = __import__("datetime").datetime.now(__import__("datetime").timezone.utc).isoformat()
figure_map_path.parent.mkdir(parents=True, exist_ok=True)
figure_map_path.write_text(json.dumps(figure_map, ensure_ascii=False, indent=2), encoding="utf-8")
result["figure_map"] = str(figure_map_path)
# Save original note content for rollback
original_note_text = formal_note.read_text(encoding="utf-8")
# 7. Run chart-type-scan
chart_type_map_path = ocr_dir / "chart-type-map.json"
chart_type_result = build_chart_type_map(figure_map)
chart_type_map_path.write_text(json.dumps(chart_type_result, ensure_ascii=False, indent=2), encoding="utf-8")
result["chart_type_map"] = str(chart_type_map_path)
# Track files for rollback
written_paths: list[Path] = []
# Collect recommendations
all_guides: set[str] = set()
for fig in chart_type_result.get("figures", []):
for guide in fig.get("recommended_guides", []):
all_guides.add(guide)
for tbl in chart_type_result.get("tables", []):
for guide in tbl.get("recommended_guides", []):
all_guides.add(guide)
result["chart_recommendations"] = sorted(all_guides)
try:
# 6. Run figure-map
figure_map_path = ocr_dir / "figure-map.json"
fulltext_text = fulltext_md.read_text(encoding="utf-8")
figure_map = build_figure_map(fulltext_text, zotero_key=zotero_key)
figure_map["generated_at"] = __import__("datetime").datetime.now(__import__("datetime").timezone.utc).isoformat()
figure_map_path.parent.mkdir(parents=True, exist_ok=True)
figure_map_path.write_text(json.dumps(figure_map, ensure_ascii=False, indent=2), encoding="utf-8")
written_paths.append(figure_map_path)
result["figure_map"] = str(figure_map_path)
# 8. Extract figures/tables and run ensure-scaffold
figure_candidates = extract_figures_from_fulltext(fulltext_text, figure_map)
table_candidates = extract_tables_from_fulltext(fulltext_text, figure_map)
planned_figures = build_figure_plan(figure_candidates)
planned_tables = table_candidates # Include all tables by default
# 7. Run chart-type-scan
chart_type_map_path = ocr_dir / "chart-type-map.json"
chart_type_result = build_chart_type_map(figure_map)
chart_type_map_path.write_text(json.dumps(chart_type_result, ensure_ascii=False, indent=2), encoding="utf-8")
written_paths.append(chart_type_map_path)
result["chart_type_map"] = str(chart_type_map_path)
note_text = formal_note.read_text(encoding="utf-8")
updated = ensure_study_section(note_text, planned_figures, planned_tables)
formal_note.write_text(updated, encoding="utf-8")
# Collect recommendations
all_guides: set[str] = set()
for fig in chart_type_result.get("figures", []):
for guide in fig.get("recommended_guides", []):
all_guides.add(guide)
for tbl in chart_type_result.get("tables", []):
for guide in tbl.get("recommended_guides", []):
all_guides.add(guide)
result["chart_recommendations"] = sorted(all_guides)
result["figures"] = [
{"number": f.number, "image_id": f.image_id, "page": f.page, "title": f.title}
for f in planned_figures
]
result["tables"] = [
{"number": t.number, "page": t.page, "image_link": t.image_link}
for t in planned_tables
]
# 8. Extract figures/tables and run ensure-scaffold
figure_candidates = extract_figures_from_fulltext(fulltext_text, figure_map)
table_candidates = extract_tables_from_fulltext(fulltext_text, figure_map)
planned_figures = build_figure_plan(figure_candidates)
planned_tables = table_candidates # Include all tables by default
result["status"] = "ok"
result["message"] = (
f"[OK] Prepared {zotero_key}\n"
f" Formal note: {formal_note}\n"
f" Fulltext: {fulltext_md}\n"
f" Figures: {len(planned_figures)} | Tables: {len(planned_tables)}\n"
f" Chart guides: {len(all_guides)} recommended"
)
return result
note_text = formal_note.read_text(encoding="utf-8")
updated = ensure_study_section(note_text, planned_figures, planned_tables)
formal_note.write_text(updated, encoding="utf-8")
result["figures"] = [
{"number": f.number, "image_id": f.image_id, "page": f.page, "title": f.title}
for f in planned_figures
]
result["tables"] = [
{"number": t.number, "page": t.page, "image_link": t.image_link}
for t in planned_tables
]
result["status"] = "ok"
result["message"] = (
f"[OK] Prepared {zotero_key}\n"
f" Formal note: {formal_note}\n"
f" Fulltext: {fulltext_md}\n"
f" Figures: {len(planned_figures)} | Tables: {len(planned_tables)}\n"
f" Chart guides: {len(all_guides)} recommended"
)
return result
except Exception as exc:
# Rollback: delete partial files and restore note
for path in written_paths:
if path.exists():
path.unlink()
formal_note.write_text(original_note_text, encoding="utf-8")
result["message"] = f"[ERROR] Prepare failed for {zotero_key}: {exc}. Rolled back changes."
return result
def scan_deep_reading_queue(vault: Path) -> list[dict]:

126
tests/test_prepare_rollback.py Normal file
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@ -0,0 +1,126 @@
"""Test rollback behavior in prepare_deep_reading.
Covers D-13..D-15: partial failure cleanup.
"""
from __future__ import annotations
import sys
from pathlib import Path
from unittest.mock import patch
import pytest
REPO_ROOT = Path(__file__).resolve().parent.parent
if str(REPO_ROOT) not in sys.path:
sys.path.insert(0, str(REPO_ROOT))
from tests.conftest import create_test_vault
def _import_ld_deep(path: Path | None = None):
"""Import ld_deep.py using importlib, with Python 3.14 workaround."""
if path is None:
path = REPO_ROOT / "skills" / "literature-qa" / "scripts" / "ld_deep.py"
import importlib.util
module_name = "_test_rollback_ld_deep"
if module_name in sys.modules:
del sys.modules[module_name]
spec = importlib.util.spec_from_file_location(module_name, path)
if spec is None or spec.loader is None:
pytest.skip(f"Could not create spec for {path}")
module = importlib.util.module_from_spec(spec)
sys.modules[module_name] = module
try:
spec.loader.exec_module(module)
except AttributeError as e:
if "'NoneType' object has no attribute '__dict__'" in str(e):
pytest.skip(f"Python 3.14 dataclass bug prevents import: {e}")
raise
return module
class TestPrepareRollback:
"""Task 5: rollback behavior in prepare_deep_reading."""
def test_prepare_rollback_on_figure_map_failure(self) -> None:
"""Mock build_figure_map to raise; assert no partial files remain."""
vault = create_test_vault()
module = _import_ld_deep()
prepare_deep_reading = module.prepare_deep_reading
ocr_dir = vault / "99_System" / "PaperForge" / "ocr" / "TSTONE001"
figure_map_path = ocr_dir / "figure-map.json"
chart_type_map_path = ocr_dir / "chart-type-map.json"
formal_note = vault / "03_Resources" / "Literature" / "骨科" / "TSTONE001 - Biomechanical Comparison of Suture Anchor Fixations in Rotator Cuff Repair.md"
# Remove pre-existing fixture files to test clean rollback
if figure_map_path.exists():
figure_map_path.unlink()
if chart_type_map_path.exists():
chart_type_map_path.unlink()
original_note_text = formal_note.read_text(encoding="utf-8")
with patch.object(module, "build_figure_map", side_effect=RuntimeError("mock figure map failure")):
result = prepare_deep_reading(vault, "TSTONE001")
assert result["status"] == "error", "should return error status"
assert "mock figure map failure" in result["message"], "message should contain error"
assert not figure_map_path.exists(), "figure-map.json should not exist (rollback or never created)"
assert not chart_type_map_path.exists(), "chart-type-map.json should not exist"
assert formal_note.read_text(encoding="utf-8") == original_note_text, "formal note should be restored"
def test_prepare_rollback_on_scaffold_failure(self) -> None:
"""Mock ensure_study_section to raise; assert files cleaned up, note restored."""
vault = create_test_vault()
module = _import_ld_deep()
prepare_deep_reading = module.prepare_deep_reading
ocr_dir = vault / "99_System" / "PaperForge" / "ocr" / "TSTONE001"
figure_map_path = ocr_dir / "figure-map.json"
chart_type_map_path = ocr_dir / "chart-type-map.json"
formal_note = vault / "03_Resources" / "Literature" / "骨科" / "TSTONE001 - Biomechanical Comparison of Suture Anchor Fixations in Rotator Cuff Repair.md"
# Remove pre-existing fixture files to test clean rollback
if figure_map_path.exists():
figure_map_path.unlink()
if chart_type_map_path.exists():
chart_type_map_path.unlink()
original_note_text = formal_note.read_text(encoding="utf-8")
with patch.object(module, "ensure_study_section", side_effect=RuntimeError("mock scaffold failure")):
result = prepare_deep_reading(vault, "TSTONE001")
assert result["status"] == "error", "should return error status"
assert "mock scaffold failure" in result["message"], "message should contain error"
assert not figure_map_path.exists(), "figure-map.json should be deleted on rollback"
assert not chart_type_map_path.exists(), "chart-type-map.json should be deleted on rollback"
assert formal_note.read_text(encoding="utf-8") == original_note_text, "formal note should be restored"
def test_prepare_success_no_rollback(self) -> None:
"""Normal flow: all files exist, note updated."""
vault = create_test_vault()
module = _import_ld_deep()
prepare_deep_reading = module.prepare_deep_reading
ocr_dir = vault / "99_System" / "PaperForge" / "ocr" / "TSTONE001"
figure_map_path = ocr_dir / "figure-map.json"
chart_type_map_path = ocr_dir / "chart-type-map.json"
formal_note = vault / "03_Resources" / "Literature" / "骨科" / "TSTONE001 - Biomechanical Comparison of Suture Anchor Fixations in Rotator Cuff Repair.md"
original_note_text = formal_note.read_text(encoding="utf-8")
result = prepare_deep_reading(vault, "TSTONE001")
assert result["status"] == "ok", f"should succeed: {result.get('message')}"
assert figure_map_path.exists(), "figure-map.json should exist"
assert chart_type_map_path.exists(), "chart-type-map.json should exist"
updated_text = formal_note.read_text(encoding="utf-8")
assert "## 🔍 精读" in updated_text, "formal note should have 精读 section"
assert updated_text != original_note_text, "formal note should be modified"