mirror of
https://github.com/lllin000/PaperForge.git
synced 2026-07-22 06:50:53 +00:00
feat: runtime contract hardening + skill/command truth alignment (Package A+B)
Atomic snapshots, canonical index mutation serialization, sync post-clean truth, plugin path config-awareness, embed stop signal honesty, full snapshot bootstrap, pf_ prefix unification, workflow command/lifecycle/path corrections, mechanical/cognitive route separation with unknown-command guard.
This commit is contained in:
Research Assistant
parent
53736ab841
commit
ed95e0f565
26 changed files with 413 additions and 114 deletions
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@ -1,5 +1,5 @@
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{
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"vault": "<VAULT>",
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"worker_script": "<VAULT>/System/PaperForge/paperforge/worker",
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"ld_deep_script": "<VAULT>/.opencode/skills/literature-qa/scripts/ld_deep.py"
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"pf_deep_script": "<VAULT>/.opencode/skills/paperforge/scripts/pf_deep.py"
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}
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@ -14,12 +14,12 @@ COMMANDS = {
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"purpose": "Look up one paper's full status and recommended next action",
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},
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"search": {
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"usage": "paperforge search <query> --json [--collection NAME] [--domain NAME] [--ocr done|pending] [--year-from N] [--year-to N] [--limit N]",
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"purpose": "Full-text search with optional collection/domain/lifecycle filters",
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"usage": "paperforge search <query> --json [--domain NAME] [--ocr done|pending|failed|processing] [--year-from N] [--year-to N] [--limit N] [--lifecycle indexed|pdf_ready|fulltext_ready|deep_read_done]",
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"purpose": "Full-text search with optional domain and workflow-state filters",
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},
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"retrieve": {
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"usage": "paperforge retrieve <query> --json [--limit N]",
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"purpose": "Search OCR fulltext chunks for evidence paragraphs (coming soon)",
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"purpose": "Search OCR fulltext chunks for evidence paragraphs",
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},
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"deep": {
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"usage": "/pf-deep <zotero_key>",
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@ -1,6 +1,7 @@
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from __future__ import annotations
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import argparse
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import os
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import sys
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from pathlib import Path
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@ -78,15 +79,27 @@ def run(args: argparse.Namespace) -> int:
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import signal
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try:
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os.kill(pid, signal.SIGTERM)
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except Exception:
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pass
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except Exception as exc:
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result = PFResult(
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ok=False,
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command="embed stop",
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version=PF_VERSION,
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error=PFError(code=ErrorCode.INTERNAL_ERROR, message=f"Failed to stop embed build: {exc}"),
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data={"state": "running", "pid": pid},
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)
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if args.json:
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print(result.to_json())
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else:
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print(result.error.message, file=sys.stderr)
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return 1
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mark_vector_build_state(vault, status="stopping", message="Stop requested")
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result = PFResult(ok=True, command="embed stop", version=PF_VERSION,
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data={"state": "stopping" if pid else "idle"})
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result = PFResult(ok=True, command="embed stop", version=PF_VERSION, data={"state": "stopping", "pid": pid})
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else:
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result = PFResult(ok=True, command="embed stop", version=PF_VERSION, data={"state": "idle"})
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if args.json:
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print(result.to_json())
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else:
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print("Stop requested." if pid else "No active build.")
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print("Stop requested." if result.data["state"] == "stopping" else "No active build.")
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return 0
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# Build
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@ -331,7 +331,6 @@ def paperforge_paths(
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# ── v2.2: canonical locations below paperforge/ ──
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"config": paperforge / "config" / "domain-collections.json",
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"index": paperforge / "indexes" / "formal-library.json",
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"memory_db": paperforge / "indexes" / "paperforge.db",
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}
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@ -9,7 +9,14 @@ def read_json(path: Path):
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return json.loads(path.read_text(encoding="utf-8"))
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def write_json_atomic(path: Path, data) -> None:
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"""Write JSON atomically using a temp file and replace."""
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path.parent.mkdir(parents=True, exist_ok=True)
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tmp = path.with_suffix(f"{path.suffix}.tmp")
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tmp.write_text(json.dumps(data, ensure_ascii=False, indent=2), encoding="utf-8")
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tmp.replace(path)
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def write_json(path: Path, data) -> None:
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"""Write data as JSON, creating parent directories as needed."""
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path.parent.mkdir(parents=True, exist_ok=True)
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path.write_text(json.dumps(data, ensure_ascii=False, indent=2), encoding="utf-8")
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write_json_atomic(path, data)
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@ -9,10 +9,10 @@ from paperforge.config import paperforge_paths
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def get_memory_db_path(vault: Path) -> Path:
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"""Return the absolute path to paperforge.db."""
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paths = paperforge_paths(vault)
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db_path = paths.get("memory_db")
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if not db_path:
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raise FileNotFoundError("memory_db path not configured")
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return db_path
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index_path = paths.get("index")
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if not index_path:
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raise FileNotFoundError("index path not configured")
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return index_path.parent / "paperforge.db"
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def get_connection(db_path: Path, read_only: bool = False) -> sqlite3.Connection:
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@ -110,11 +110,11 @@ def _check_index(vault: Path) -> dict:
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if version:
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return _layer("ok", [f"Schema version: {version['value']}"])
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return _layer("degraded", ["Schema version unknown"],
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"Rebuild memory DB", "paperforge memory build --force")
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"Rebuild memory DB", "paperforge memory build")
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except Exception as e:
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return _layer("blocked", [f"DB query failed: {e}"],
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"Rebuild memory DB",
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"paperforge memory build --force")
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"paperforge memory build")
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def _check_vector(vault: Path) -> dict:
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@ -5,6 +5,7 @@ from datetime import datetime, timezone
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from pathlib import Path
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from paperforge.config import paperforge_paths
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from paperforge.core.io import write_json_atomic
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def _snapshot_dir(vault: Path) -> Path:
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@ -31,7 +32,7 @@ def write_memory_runtime(vault: Path, *, paper_count_db: int,
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"fts_ready": fts_ready,
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}
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path = _snapshot_dir(vault) / "memory-runtime-state.json"
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path.write_text(json.dumps(snap, ensure_ascii=False, indent=2), encoding="utf-8")
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write_json_atomic(path, snap)
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def write_vector_runtime(vault: Path, *, enabled: bool, mode: str, model: str,
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@ -53,9 +54,9 @@ def write_vector_runtime(vault: Path, *, enabled: bool, mode: str, model: str,
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"build_state": build_state or {},
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}
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path = _snapshot_dir(vault) / "vector-runtime-state.json"
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path.write_text(json.dumps(snap, ensure_ascii=False, indent=2), encoding="utf-8")
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write_json_atomic(path, snap)
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def write_runtime_health(vault: Path, health_data: dict) -> None:
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path = _snapshot_dir(vault) / "runtime-health.json"
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path.write_text(json.dumps(health_data, ensure_ascii=False, indent=2), encoding="utf-8")
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write_json_atomic(path, health_data)
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@ -40,7 +40,8 @@ def get_vector_db_path(vault: Path) -> Path:
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"""Return the ChromaDB persistence directory."""
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from paperforge.config import paperforge_paths
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paths = paperforge_paths(vault)
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return (paths.get("memory_db", paths.get("index", vault / "System" / "PaperForge"))).parent / "vectors"
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index_path = paths.get("index", vault / "System" / "PaperForge" / "indexes" / "formal-library.json")
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return index_path.parent / "vectors"
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def get_collection(vault: Path):
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@ -291,7 +292,7 @@ def get_vector_build_state_path(vault: Path) -> Path:
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"""Return path to vector-build-state.json."""
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from paperforge.config import paperforge_paths
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paths = paperforge_paths(vault)
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index_dir = (paths.get("memory_db", paths.get("index", vault / "System" / "PaperForge"))).parent
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index_dir = paths.get("index", vault / "System" / "PaperForge" / "indexes" / "formal-library.json").parent
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return index_dir / "vector-build-state.json"
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@ -10,8 +10,38 @@ const memoryState = (() => {
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const path = require('path');
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const { execFileSync } = require('node:child_process');
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function readPathConfig(vaultPath) {
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const pfPath = path.join(vaultPath, 'paperforge.json');
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const defaults = {
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system_dir: 'System',
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resources_dir: 'Resources',
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literature_dir: 'Literature',
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base_dir: 'Bases',
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};
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try {
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if (!fs.existsSync(pfPath)) {
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return { ...defaults, _warning: 'paperforge.json not found; using defaults' };
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}
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const raw = fs.readFileSync(pfPath, 'utf-8');
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const data = JSON.parse(raw);
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const vc = data.vault_config || {};
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return {
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system_dir: vc.system_dir || data.system_dir || defaults.system_dir,
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resources_dir: vc.resources_dir || data.resources_dir || defaults.resources_dir,
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literature_dir: vc.literature_dir || data.literature_dir || defaults.literature_dir,
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base_dir: vc.base_dir || data.base_dir || defaults.base_dir,
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_warning: null,
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};
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} catch (e) {
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console.warn('PaperForge: Failed to read paperforge.json, using defaults', e);
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return { ...defaults, _warning: 'paperforge.json invalid; using defaults' };
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}
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}
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function resolveVaultPaths(vaultPath) {
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const systemDir = path.join(vaultPath, 'System', 'PaperForge');
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const cfg = readPathConfig(vaultPath);
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const systemDir = path.join(vaultPath, cfg.system_dir, 'PaperForge');
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return {
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vault: vaultPath,
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systemDir,
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@ -22,8 +52,11 @@ const memoryState = (() => {
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vectorStatePath: path.join(systemDir, 'indexes', 'vector-runtime-state.json'),
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healthStatePath: path.join(systemDir, 'indexes', 'runtime-health.json'),
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buildStatePath: path.join(systemDir, 'indexes', 'vector-build-state.json'),
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exportsDir: path.join(systemDir, 'exports'),
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ocrDir: path.join(systemDir, 'ocr'),
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pluginDataPath: path.join(vaultPath, '.obsidian', 'plugins', 'paperforge', 'data.json'),
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pfJsonPath: path.join(vaultPath, 'paperforge.json'),
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configWarning: cfg._warning,
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};
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}
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@ -99,7 +132,7 @@ const memoryState = (() => {
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return _cachedPython;
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}
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}
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var sysCandidates = [{path:'python',extraArgs:[]},{path:'python3',extraArgs:[]}];
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var sysCandidates = [{path:'py',extraArgs:['-3']},{path:'python',extraArgs:[]},{path:'python3',extraArgs:[]}];
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for (var j = 0; j < sysCandidates.length; j++) {
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try {
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var c = sysCandidates[j];
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@ -170,6 +203,7 @@ function resolvePythonExecutable(vaultPath, settings, _fs, _execFileSync) {
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}
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const systemCandidates = [
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{ path: "py", extraArgs: ["-3"] },
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{ path: "python", extraArgs: [] },
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{ path: "python3", extraArgs: [] },
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];
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@ -242,7 +276,7 @@ function buildRuntimeInstallCommand(pythonExe, version, extraArgs) {
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const gitUrl = `git+https://github.com/LLLin000/PaperForge.git@v${version}`;
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const pypiArgs = [...extraArgs, "-m", "pip", "install", "--upgrade", pypiPkg];
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const gitArgs = [...extraArgs, "-m", "pip", "install", "--upgrade", gitUrl];
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return { cmd: pythonExe, pypiArgs, gitArgs, timeout: 120000 };
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return { cmd: pythonExe, url: gitUrl.replace('@v', '@'), args: gitArgs, pypiArgs, gitArgs, timeout: 120000 };
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}
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function parseRuntimeStatus(err, stdout, stderr) {
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@ -4618,7 +4652,7 @@ module.exports = class PaperForgePlugin extends Plugin {
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/* ── Auto-update PaperForge (deferred — don't slow startup) ── */
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if (this.settings.auto_update !== false && this.settings.setup_complete) {
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if (this.settings.auto_update_on_startup === true && this.settings.setup_complete) {
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setTimeout(() => this._autoUpdate(), 3000);
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}
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this._startFilePolling();
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@ -4627,14 +4661,22 @@ module.exports = class PaperForgePlugin extends Plugin {
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(() => {
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const vp = this.app.vault.adapter.basePath;
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if (!vp) return;
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const memSnap = require('path').join(vp, 'System', 'PaperForge', 'indexes', 'memory-runtime-state.json');
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const runtimePaths = memoryState.resolveVaultPaths(vp);
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const memSnap = runtimePaths.memoryStatePath;
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const fs = require('fs');
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if (!fs.existsSync(memSnap)) {
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// No snapshots — first launch or upgrade. Fire and forget.
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const py = resolvePythonExecutable(vp, this.settings);
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const { execFile } = require('node:child_process');
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const args = [...py.extraArgs, '-m', 'paperforge', '--vault', vp, 'runtime-health', '--json'];
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execFile(py.path, args, { cwd: vp, timeout: 60000, windowsHide: true }, () => {});
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const commands = [
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['runtime-health', '--json'],
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['memory', 'status', '--json'],
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['embed', 'status', '--json'],
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];
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commands.forEach((cmdArgs) => {
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const args = [...py.extraArgs, '-m', 'paperforge', '--vault', vp, ...cmdArgs];
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execFile(py.path, args, { cwd: vp, timeout: 60000, windowsHide: true }, () => {});
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});
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}
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})();
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}
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@ -4692,7 +4734,7 @@ module.exports = class PaperForgePlugin extends Plugin {
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_checkExports(vaultPath, fs, path, exec) {
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if (this._autoSyncRunning) return;
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const exportsDir = path.join(vaultPath, 'System', 'PaperForge', 'exports');
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const exportsDir = memoryState.resolveVaultPaths(vaultPath).exportsDir;
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if (!fs.existsSync(exportsDir)) return;
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let newestMtime = 0;
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@ -4728,7 +4770,7 @@ module.exports = class PaperForgePlugin extends Plugin {
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try {
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const fs = require('fs');
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const path = require('path');
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const exportsDir = path.join(vaultPath, 'System', 'PaperForge', 'exports');
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const exportsDir = memoryState.resolveVaultPaths(vaultPath).exportsDir;
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let newest = 0;
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fs.readdirSync(exportsDir).forEach(f => {
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if (!f.endsWith('.json')) return;
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@ -4741,7 +4783,7 @@ module.exports = class PaperForgePlugin extends Plugin {
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_checkOcr(vaultPath, fs, path, exec) {
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if (this._autoSyncRunning) return;
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const ocrDir = path.join(vaultPath, 'System', 'PaperForge', 'ocr');
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const ocrDir = memoryState.resolveVaultPaths(vaultPath).ocrDir;
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if (!fs.existsSync(ocrDir)) return;
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try {
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|
|
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|
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@ -6,6 +6,56 @@ const fs = require('fs');
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const path = require('path');
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const { execFile, spawn } = require('node:child_process');
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|
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function readPathConfig(vaultPath, _fs) {
|
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const f = _fs || fs;
|
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const pfPath = path.join(vaultPath, 'paperforge.json');
|
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const defaults = {
|
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system_dir: 'System',
|
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resources_dir: 'Resources',
|
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literature_dir: 'Literature',
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base_dir: 'Bases',
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};
|
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|
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try {
|
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if (!f.existsSync(pfPath)) {
|
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return { ...defaults, _warning: 'paperforge.json not found; using defaults' };
|
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}
|
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const raw = f.readFileSync(pfPath, 'utf-8');
|
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const data = JSON.parse(raw);
|
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const vc = data.vault_config || {};
|
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return {
|
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system_dir: vc.system_dir || data.system_dir || defaults.system_dir,
|
||||
resources_dir: vc.resources_dir || data.resources_dir || defaults.resources_dir,
|
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literature_dir: vc.literature_dir || data.literature_dir || defaults.literature_dir,
|
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base_dir: vc.base_dir || data.base_dir || defaults.base_dir,
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_warning: null,
|
||||
};
|
||||
} catch {
|
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return { ...defaults, _warning: 'paperforge.json invalid; using defaults' };
|
||||
}
|
||||
}
|
||||
|
||||
function resolveRuntimePaths(vaultPath, _fs) {
|
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const cfg = readPathConfig(vaultPath, _fs);
|
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const systemRoot = path.join(vaultPath, cfg.system_dir, 'PaperForge');
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return {
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vault: vaultPath,
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systemDir: systemRoot,
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indexesDir: path.join(systemRoot, 'indexes'),
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logsDir: path.join(systemRoot, 'logs'),
|
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dbPath: path.join(systemRoot, 'indexes', 'paperforge.db'),
|
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memoryStatePath: path.join(systemRoot, 'indexes', 'memory-runtime-state.json'),
|
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vectorStatePath: path.join(systemRoot, 'indexes', 'vector-runtime-state.json'),
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healthStatePath: path.join(systemRoot, 'indexes', 'runtime-health.json'),
|
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buildStatePath: path.join(systemRoot, 'indexes', 'vector-build-state.json'),
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exportsDir: path.join(systemRoot, 'exports'),
|
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ocrDir: path.join(systemRoot, 'ocr'),
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pluginDataPath: path.join(vaultPath, '.obsidian', 'plugins', 'paperforge', 'data.json'),
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pfJsonPath: path.join(vaultPath, 'paperforge.json'),
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configWarning: cfg._warning,
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};
|
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}
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|
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// ── Runtime helpers ──
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||||
|
||||
function resolvePythonExecutable(vaultPath, settings, _fs, _execFileSync) {
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|
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@ -33,6 +83,7 @@ function resolvePythonExecutable(vaultPath, settings, _fs, _execFileSync) {
|
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}
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|
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const systemCandidates = [
|
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{ path: "py", extraArgs: ["-3"] },
|
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{ path: "python", extraArgs: [] },
|
||||
{ path: "python3", extraArgs: [] },
|
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];
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|
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@ -107,7 +158,7 @@ function buildRuntimeInstallCommand(pythonExe, version, extraArgs) {
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const gitUrl = `git+https://github.com/LLLin000/PaperForge.git@v${version}`;
|
||||
const pypiArgs = [...extraArgs, "-m", "pip", "install", "--upgrade", pypiPkg];
|
||||
const gitArgs = [...extraArgs, "-m", "pip", "install", "--upgrade", gitUrl];
|
||||
return { cmd: pythonExe, pypiArgs, gitArgs, timeout: 120000 };
|
||||
return { cmd: pythonExe, url: gitUrl.replace('@v', '@'), args: gitArgs, pypiArgs, gitArgs, timeout: 120000 };
|
||||
}
|
||||
|
||||
function parseRuntimeStatus(err, stdout, stderr) {
|
||||
|
|
@ -211,6 +262,8 @@ function shouldRenderVectorReady(vectorDepsOk, embedStatusText) {
|
|||
}
|
||||
|
||||
module.exports = {
|
||||
readPathConfig,
|
||||
resolveRuntimePaths,
|
||||
resolvePythonExecutable,
|
||||
getPluginVersion,
|
||||
checkRuntimeVersion,
|
||||
|
|
|
|||
|
|
@ -7,11 +7,58 @@
|
|||
import { describe, it, expect, vi, beforeEach } from 'vitest';
|
||||
|
||||
const {
|
||||
readPathConfig,
|
||||
resolveRuntimePaths,
|
||||
resolvePythonExecutable,
|
||||
getPluginVersion,
|
||||
checkRuntimeVersion,
|
||||
} = await import('../src/testable.js');
|
||||
|
||||
describe('readPathConfig', () => {
|
||||
it('uses vault_config system_dir when present', () => {
|
||||
const mockFs = {
|
||||
existsSync: vi.fn(() => true),
|
||||
readFileSync: vi.fn(() => JSON.stringify({ vault_config: { system_dir: '99_System' } })),
|
||||
};
|
||||
const cfg = readPathConfig('/vault', mockFs);
|
||||
expect(cfg.system_dir).toBe('99_System');
|
||||
expect(cfg._warning).toBeNull();
|
||||
});
|
||||
|
||||
it('falls back to defaults with warning when config is missing', () => {
|
||||
const mockFs = {
|
||||
existsSync: vi.fn(() => false),
|
||||
readFileSync: vi.fn(),
|
||||
};
|
||||
const cfg = readPathConfig('/vault', mockFs);
|
||||
expect(cfg.system_dir).toBe('System');
|
||||
expect(cfg._warning).toContain('using defaults');
|
||||
});
|
||||
|
||||
it('falls back to defaults with warning when config is invalid', () => {
|
||||
const mockFs = {
|
||||
existsSync: vi.fn(() => true),
|
||||
readFileSync: vi.fn(() => '{bad json'),
|
||||
};
|
||||
const cfg = readPathConfig('/vault', mockFs);
|
||||
expect(cfg.system_dir).toBe('System');
|
||||
expect(cfg._warning).toContain('invalid');
|
||||
});
|
||||
});
|
||||
|
||||
describe('resolveRuntimePaths', () => {
|
||||
it('uses configured system_dir for runtime file paths', () => {
|
||||
const mockFs = {
|
||||
existsSync: vi.fn(() => true),
|
||||
readFileSync: vi.fn(() => JSON.stringify({ vault_config: { system_dir: '99_System' } })),
|
||||
};
|
||||
const paths = resolveRuntimePaths('/vault', mockFs);
|
||||
expect(paths.memoryStatePath).toContain('99_System');
|
||||
expect(paths.exportsDir).toContain('99_System');
|
||||
expect(paths.ocrDir).toContain('99_System');
|
||||
});
|
||||
});
|
||||
|
||||
describe('resolvePythonExecutable', () => {
|
||||
/** Create injected fs + execFileSync mocks */
|
||||
function mockDeps(existsSyncImpl, execFileSyncImpl) {
|
||||
|
|
|
|||
|
|
@ -288,6 +288,18 @@ class SyncService:
|
|||
orphaned = self.clean_orphaned_records(exports, paths, json_output=json_output)
|
||||
flat_cleaned = self.clean_flat_notes(paths, json_output=json_output)
|
||||
|
||||
if orphaned > 0 or flat_cleaned > 0:
|
||||
index_count = asset_index.build_index(self.vault, verbose)
|
||||
|
||||
try:
|
||||
from paperforge.memory.builder import build_from_index
|
||||
from paperforge.memory.db import get_memory_db_path
|
||||
|
||||
if get_memory_db_path(self.vault).exists():
|
||||
build_from_index(self.vault)
|
||||
except Exception:
|
||||
pass
|
||||
|
||||
if not json_output:
|
||||
print(f"index-refresh: {index_count} entries in index")
|
||||
total = sum(1 for _ in paths["literature"].rglob("*.md")) if paths["literature"].exists() else 0
|
||||
|
|
|
|||
|
|
@ -98,7 +98,17 @@ Reading-log 不是事实源。它记录的是**之前的关注点、解读和预
|
|||
|
||||
## 6. 意图路由
|
||||
|
||||
用户输入对应唯一一个 workflow 文件（打开并执行其完整流程）：
|
||||
用户输入分两类处理：
|
||||
|
||||
### A. 机械命令（直接执行并解读结果，不走研究 workflow）
|
||||
|
||||
| 用户说 | 动作 |
|
||||
| --- | --- |
|
||||
| `/pf-sync` | 执行 `paperforge sync`，检查结果并解释 |
|
||||
| `/pf-ocr` | 执行 `paperforge ocr`，检查结果并解释 |
|
||||
| `/pf-status` | 执行 `paperforge status --json` 或 `paperforge runtime-health --json`，解读状态 |
|
||||
|
||||
### B. 研究工作流（打开唯一 workflow 文件并执行完整流程）
|
||||
|
||||
| 用户说 | 打开 |
|
||||
| -------------------------------------------------------- | -------------------------------- |
|
||||
|
|
@ -108,10 +118,11 @@ Reading-log 不是事实源。它记录的是**之前的关注点、解读和预
|
|||
| "记一下" "记录阅读" "reading log" "读完这段记一下" | `workflows/reading-log.md` |
|
||||
| "总结会话" "工作记录" "项目记录" "project log" "记决策" | `workflows/project-log.md` |
|
||||
| "提取方法论" "总结规律" "存档写作规律" | `workflows/methodology.md` |
|
||||
| "branch" "代码审查" "feature" "dashboard" "memory layer" "用户反馈" "报错" "安装失败" "Git" "Zotero" "BetterBibTeX" "OCR" "插件" | `workflows/project-engineering.md` |
|
||||
| "branch" "代码审查" "feature" "dashboard" "memory layer" "用户反馈" "报错" "安装失败" "Git" "Zotero" "BetterBibTeX" "插件" | `workflows/project-engineering.md` |
|
||||
| 不确定 / 空输入 | 问用户：搜文献、精读、问答、记笔记、记工作、提方法论？ |
|
||||
|
||||
路由后如用户切换意图，重新判断并打开对应 workflow。
|
||||
未知或拼错的 `/pf-*` 命令不要静默掉进 `project-engineering`，必须明确提示用户命令不存在或请澄清意图。
|
||||
|
||||
---
|
||||
|
||||
|
|
|
|||
|
|
@ -120,7 +120,7 @@ $PYTHON "$SKILL_DIR/scripts/pf_deep.py" prepare --key <zotero_key> --vault "$VAU
|
|||
### Step 4: Postprocess（跑校验，修正问题）
|
||||
|
||||
```bash
|
||||
$PYTHON "$SKILL_DIR/scripts/pf_deep.py" postprocess-pass2 "<formal_note_path>" --figures <N> --vault "$VAULT"
|
||||
$PYTHON "$SKILL_DIR/scripts/pf_deep.py" postprocess-pass2 "<formal_note_path>" --figures <N>
|
||||
```
|
||||
|
||||
- 输出 `OK` → 继续 Step 5
|
||||
|
|
|
|||
|
|
@ -21,21 +21,29 @@
|
|||
|
||||
用户可能给 zotero_key、DOI、标题片段、作者+年份。按以下方式查找：
|
||||
|
||||
**优先用 paper-context（一次拿到全部信息）：**
|
||||
**如果用户给的是 zotero_key：**
|
||||
|
||||
```bash
|
||||
$PYTHON -m paperforge --vault "$VAULT" paper-context <query> --json
|
||||
$PYTHON -m paperforge --vault "$VAULT" paper-context <zotero_key> --json
|
||||
```
|
||||
|
||||
返回 JSON 包含 paper 元数据、OCR 状态、prior_notes 等。
|
||||
|
||||
**paper-context 无结果时的备选：**
|
||||
**如果用户给的是 DOI、标题片段、作者+年份，先解析成候选：**
|
||||
|
||||
```bash
|
||||
$PYTHON -m paperforge --vault "$VAULT" paper-status "<query>" --json
|
||||
```
|
||||
|
||||
如果 `paper-status` 直接唯一命中，取返回的 `zotero_key` 再调 `paper-context`。
|
||||
|
||||
**paper-status 无法唯一定位时的备选：**
|
||||
|
||||
```bash
|
||||
$PYTHON -m paperforge --vault "$VAULT" search "<query>" --json --limit 5
|
||||
```
|
||||
|
||||
如果多候选，列出让用户选（同 paper-search 的 Step 4-5 格式）。
|
||||
如果多候选，列出让用户选（同 paper-search 的 Step 4-5 格式）；用户选定后，再用选中的 `zotero_key` 调 `paper-context`。
|
||||
如果无结果，告知用户并停止。
|
||||
|
||||
### Step 2: 加载文献内容
|
||||
|
|
|
|||
|
|
@ -16,8 +16,8 @@
|
|||
|
||||
提取以下信息（缺什么就问用户）：
|
||||
- **搜索词**：关键词、作者名、年份
|
||||
- **范围**：domain（如"骨科"）、collection（如"DC"）、不指定=全库
|
||||
- **过滤条件**：OCR 状态（done/pending）、年份范围（--year-from/--year-to）、lifecycle
|
||||
- **范围**：domain（如"骨科"）、不指定=全库；如果用户说 collection，只把它当结果展示时的二级筛选条件
|
||||
- **过滤条件**：OCR 状态（done/pending/failed/processing）、年份范围（--year-from/--year-to）、lifecycle
|
||||
|
||||
### Step 2: 执行搜索
|
||||
|
||||
|
|
@ -25,8 +25,8 @@
|
|||
$PYTHON -m paperforge --vault "$VAULT" search <query> --json --limit 15 \
|
||||
[--domain "<domain>"] \
|
||||
[--year-from <N>] [--year-to <N>] \
|
||||
[--ocr <done|pending>] \
|
||||
[--lifecycle <active|archived>]
|
||||
[--ocr <done|pending|failed|processing>] \
|
||||
[--lifecycle <indexed|pdf_ready|fulltext_ready|deep_read_done>]
|
||||
```
|
||||
|
||||
返回 JSON 结构：
|
||||
|
|
@ -46,7 +46,7 @@ $PYTHON -m paperforge --vault "$VAULT" search <query> --json --limit 15 \
|
|||
"collection_path": "...",
|
||||
"ocr_status": "done",
|
||||
"deep_reading_status": "pending",
|
||||
"lifecycle": "active",
|
||||
"lifecycle": "pdf_ready",
|
||||
"has_pdf": true,
|
||||
"rank": "..."
|
||||
}
|
||||
|
|
@ -69,6 +69,7 @@ $PYTHON -m paperforge --vault "$VAULT" paper-context <zotero_key> --json
|
|||
```
|
||||
|
||||
目的：拿到 `ocr_status`、`prior_notes` 数量、`analyze` 状态，帮助用户判断哪些可以直接读。
|
||||
如果用户一开始明确要求 collection 范围，在这一步根据 `collection_path` 做结果后筛选，而不是给 `search` 传不存在的 `--collection` 参数。
|
||||
|
||||
### Step 4: 展示候选清单
|
||||
|
||||
|
|
|
|||
|
|
@ -79,7 +79,7 @@ Agent 按 JSON schema 写入 project-log.jsonl。
|
|||
展示给用户确认后再写入：
|
||||
|
||||
```
|
||||
即将记录到 Project/综述写作/project-log.md:
|
||||
即将记录到 Resources/Projects/综述写作/project-log.md:
|
||||
日期: 2026-05-14
|
||||
类型: session_summary
|
||||
标题: DC 段参数窗审计完成
|
||||
|
|
@ -111,7 +111,7 @@ $PYTHON -m paperforge --vault "$VAULT" project-log --write \
|
|||
$PYTHON -m paperforge --vault "$VAULT" project-log --render --project "<project>"
|
||||
```
|
||||
|
||||
输出到 `Project/<project>/project-log.md`。
|
||||
输出到 `Resources/Projects/<project>/project-log.md`。
|
||||
|
||||
---
|
||||
|
||||
|
|
|
|||
|
|
@ -100,7 +100,7 @@ $PYTHON -m paperforge --vault "$VAULT" reading-log --write <paper_id> \
|
|||
$PYTHON -m paperforge --vault "$VAULT" reading-log --render --project "<project>"
|
||||
```
|
||||
|
||||
输出到 `Project/<project>/reading-log.md`。
|
||||
输出到 `Resources/Projects/<project>/reading-log.md`。
|
||||
|
||||
---
|
||||
|
||||
|
|
|
|||
|
|
@ -59,6 +59,46 @@ LOCK_TIMEOUT = 10
|
|||
``filelock.Timeout``."""
|
||||
|
||||
|
||||
def _index_lock(path: Path) -> filelock.FileLock:
|
||||
return filelock.FileLock(path.with_suffix(".json.lock"), timeout=LOCK_TIMEOUT)
|
||||
|
||||
|
||||
def mutate_index(vault: Path, mutator) -> bool:
|
||||
"""Read, mutate, and write the canonical index under one lock."""
|
||||
path = get_index_path(vault)
|
||||
path.parent.mkdir(parents=True, exist_ok=True)
|
||||
|
||||
with _index_lock(path):
|
||||
if not path.exists():
|
||||
return False
|
||||
try:
|
||||
with open(path, encoding="utf-8") as fh:
|
||||
current = json.load(fh)
|
||||
except (json.JSONDecodeError, OSError) as exc:
|
||||
logger.warning("Corrupt index at %s during mutation: %s", path, exc)
|
||||
return False
|
||||
|
||||
updated = mutator(current)
|
||||
if updated is None:
|
||||
return False
|
||||
|
||||
tmp = tempfile.NamedTemporaryFile(mode="w", encoding="utf-8", delete=False, dir=path.parent)
|
||||
try:
|
||||
json.dump(updated, tmp, ensure_ascii=False, indent=2)
|
||||
tmp.flush()
|
||||
os.fsync(tmp.fileno())
|
||||
tmp.close()
|
||||
os.replace(tmp.name, path)
|
||||
except BaseException:
|
||||
tmp.close()
|
||||
try:
|
||||
os.unlink(tmp.name)
|
||||
except OSError:
|
||||
pass
|
||||
raise
|
||||
return True
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
# Path resolution
|
||||
# ---------------------------------------------------------------------------
|
||||
|
|
@ -123,10 +163,7 @@ def atomic_write_index(path: Path, data: dict) -> None:
|
|||
"""
|
||||
path.parent.mkdir(parents=True, exist_ok=True)
|
||||
|
||||
lock_path = path.with_suffix(".json.lock")
|
||||
lock = filelock.FileLock(lock_path, timeout=LOCK_TIMEOUT)
|
||||
|
||||
with lock:
|
||||
with _index_lock(path):
|
||||
tmp = None
|
||||
try:
|
||||
tmp = tempfile.NamedTemporaryFile(
|
||||
|
|
@ -587,9 +624,6 @@ def refresh_index_entry(vault: Path, key: str) -> bool:
|
|||
build_index(vault)
|
||||
return False
|
||||
|
||||
# Envelope format — incremental refresh
|
||||
items = existing.get("items", [])
|
||||
|
||||
# Find the export item for the requested key
|
||||
config = load_domain_config(paths)
|
||||
domain_lookup = {entry["export_file"]: entry["domain"] for entry in config["domains"]}
|
||||
|
|
@ -623,19 +657,24 @@ def refresh_index_entry(vault: Path, key: str) -> bool:
|
|||
except Exception:
|
||||
pass # memory DB refresh is best-effort
|
||||
|
||||
replaced = False
|
||||
for i, existing_entry in enumerate(items):
|
||||
if existing_entry.get("zotero_key") == key:
|
||||
items[i] = new_entry
|
||||
replaced = True
|
||||
break
|
||||
if not replaced:
|
||||
items.append(new_entry)
|
||||
def _apply(current):
|
||||
if is_legacy_format(current) or not isinstance(current, dict):
|
||||
return None
|
||||
items = list(current.get("items", []))
|
||||
replaced = False
|
||||
for i, existing_entry in enumerate(items):
|
||||
if existing_entry.get("zotero_key") == key:
|
||||
items[i] = new_entry
|
||||
replaced = True
|
||||
break
|
||||
if not replaced:
|
||||
items.append(new_entry)
|
||||
return build_envelope(items)
|
||||
|
||||
if not mutate_index(vault, _apply):
|
||||
build_index(vault)
|
||||
return False
|
||||
|
||||
# Write back atomically
|
||||
index_path = paths["index"]
|
||||
envelope = build_envelope(items)
|
||||
atomic_write_index(index_path, envelope)
|
||||
logger.info("refresh_index_entry: updated entry %s (%s)", key, found_domain)
|
||||
return True
|
||||
|
||||
|
|
|
|||
|
|
@ -287,25 +287,6 @@ def run_repair(vault: Path, paths: dict, verbose: bool = False, fix: bool = Fals
|
|||
if new_record_text != record_text:
|
||||
record_path.write_text(new_record_text, encoding="utf-8")
|
||||
fixed_formal_note_primary = True
|
||||
if index_ocr_status is not None:
|
||||
try:
|
||||
index_data = read_json(paths["index"])
|
||||
if isinstance(index_data, dict):
|
||||
idx_items = index_data.get("items", [])
|
||||
elif isinstance(index_data, list):
|
||||
idx_items = index_data
|
||||
else:
|
||||
idx_items = []
|
||||
for entry in idx_items:
|
||||
if isinstance(entry, dict) and entry.get("zotero_key") == zotero_key:
|
||||
entry["ocr_status"] = new_status
|
||||
break
|
||||
if isinstance(index_data, dict):
|
||||
index_data["items"] = idx_items
|
||||
write_json(paths["index"], index_data)
|
||||
fixed_index_entry = True
|
||||
except Exception as e:
|
||||
logger.warning("Failed to update index entry for %s: %s", zotero_key, e)
|
||||
if meta_validated_status is not None and meta_validated_status != "done":
|
||||
if meta_path.exists():
|
||||
try:
|
||||
|
|
@ -328,25 +309,6 @@ def run_repair(vault: Path, paths: dict, verbose: bool = False, fix: bool = Fals
|
|||
if new_record_text != record_text:
|
||||
record_path.write_text(new_record_text, encoding="utf-8")
|
||||
fixed_formal_note_primary = True
|
||||
if index_ocr_status is not None:
|
||||
try:
|
||||
index_data = read_json(paths["index"])
|
||||
if isinstance(index_data, dict):
|
||||
idx_items = index_data.get("items", [])
|
||||
elif isinstance(index_data, list):
|
||||
idx_items = index_data
|
||||
else:
|
||||
idx_items = []
|
||||
for entry in idx_items:
|
||||
if isinstance(entry, dict) and entry.get("zotero_key") == zotero_key:
|
||||
entry["ocr_status"] = new_status
|
||||
break
|
||||
if isinstance(index_data, dict):
|
||||
index_data["items"] = idx_items
|
||||
write_json(paths["index"], index_data)
|
||||
fixed_index_entry = True
|
||||
except Exception as e:
|
||||
logger.warning("Failed to update index entry for %s: %s", zotero_key, e)
|
||||
if meta_path.exists():
|
||||
try:
|
||||
meta = read_json(meta_path)
|
||||
|
|
@ -370,9 +332,14 @@ def run_repair(vault: Path, paths: dict, verbose: bool = False, fix: bool = Fals
|
|||
logger.info("fixed %d files for %s", fixed_count, zotero_key)
|
||||
if fixed_count > 0:
|
||||
try:
|
||||
refresh_index_entry(vault, zotero_key)
|
||||
fixed_index_entry = refresh_index_entry(vault, zotero_key)
|
||||
except Exception as e:
|
||||
logger.warning("Failed to refresh index for %s: %s", zotero_key, e)
|
||||
else:
|
||||
if fixed_index_entry:
|
||||
result["fixed"] += 1
|
||||
else:
|
||||
logger.warning("Failed to update index entry for %s via shared refresh", zotero_key)
|
||||
# Path error detection and repair
|
||||
path_errors = _detect_path_errors(paths, verbose)
|
||||
if path_errors["total"] > 0:
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@ from .test_contract_helpers import (
|
|||
class TestPathsJson:
|
||||
"""Contract: 'paperforge paths --json' returns valid JSON with correct value types."""
|
||||
|
||||
REQUIRED_KEYS = {"vault", "worker_script", "ld_deep_script"}
|
||||
REQUIRED_KEYS = {"vault", "worker_script", "pf_deep_script"}
|
||||
|
||||
def test_paths_json_value_semantics(self, cli_invoker):
|
||||
"""paths --json returns paths with correct value types (all non-empty strings)."""
|
||||
|
|
|
|||
|
|
@ -318,7 +318,7 @@ def test_paperforge_paths_returns_exact_keys(tmp_path: Path):
|
|||
"bases",
|
||||
"worker_script",
|
||||
"skill_dir",
|
||||
"ld_deep_script",
|
||||
"pf_deep_script",
|
||||
# ── v2.2: canonical locations below paperforge/ ──
|
||||
"config",
|
||||
"index",
|
||||
|
|
@ -370,8 +370,8 @@ def test_paperforge_paths_includes_worker_script(tmp_path: Path):
|
|||
assert paths["worker_script"].name == "__init__.py"
|
||||
|
||||
|
||||
def test_paperforge_paths_includes_ld_deep_script(tmp_path: Path):
|
||||
"""ld_deep_script key must point to ld_deep.py."""
|
||||
def test_paperforge_paths_includes_pf_deep_script(tmp_path: Path):
|
||||
"""pf_deep_script key must point to pf_deep.py."""
|
||||
from paperforge.config import paperforge_paths
|
||||
|
||||
vault = tmp_path / "vault_ld"
|
||||
|
|
@ -385,8 +385,8 @@ def test_paperforge_paths_includes_ld_deep_script(tmp_path: Path):
|
|||
(vault / ".opencode" / "command").mkdir(parents=True)
|
||||
|
||||
paths = paperforge_paths(vault)
|
||||
assert "ld_deep_script" in paths
|
||||
assert paths["ld_deep_script"].name == "ld_deep.py"
|
||||
assert "pf_deep_script" in paths
|
||||
assert paths["pf_deep_script"].name == "pf_deep.py"
|
||||
|
||||
|
||||
# ---------------------------------------------------------------------------
|
||||
|
|
@ -413,7 +413,7 @@ def test_paths_as_strings_returns_string_values():
|
|||
"bases": Path("/some/vault/05_Bases"),
|
||||
"worker_script": Path("/some/vault/99_System/PaperForge/worker/scripts/literature_pipeline.py"),
|
||||
"skill_dir": Path("/some/vault/.opencode/skills"),
|
||||
"ld_deep_script": Path("/some/vault/.opencode/skills/literature-qa/scripts/ld_deep.py"),
|
||||
"pf_deep_script": Path("/some/vault/.opencode/skills/paperforge/scripts/pf_deep.py"),
|
||||
}
|
||||
|
||||
result = paths_as_strings(paths)
|
||||
|
|
|
|||
|
|
@ -28,3 +28,36 @@ def test_embed_status_includes_build_state(tmp_path):
|
|||
mock_read.return_value = {"status": "running", "current": 3, "total": 10}
|
||||
result_code = run(args)
|
||||
assert result_code == 0
|
||||
|
||||
|
||||
def test_embed_stop_requests_signal_for_running_job(tmp_path):
|
||||
from argparse import Namespace
|
||||
|
||||
vault = tmp_path / "vault"
|
||||
vault.mkdir()
|
||||
args = Namespace(vault_path=vault, embed_subcommand="stop", json=True)
|
||||
|
||||
with patch("paperforge.commands.embed.read_vector_build_state") as mock_read:
|
||||
mock_read.return_value = {"status": "running", "pid": 12345}
|
||||
with patch("paperforge.commands.embed.os.kill") as mock_kill:
|
||||
with patch("paperforge.commands.embed.mark_vector_build_state") as mock_mark:
|
||||
result_code = run(args)
|
||||
|
||||
assert result_code == 0
|
||||
mock_kill.assert_called_once()
|
||||
mock_mark.assert_called_once()
|
||||
|
||||
|
||||
def test_embed_stop_returns_error_when_signal_fails(tmp_path):
|
||||
from argparse import Namespace
|
||||
|
||||
vault = tmp_path / "vault"
|
||||
vault.mkdir()
|
||||
args = Namespace(vault_path=vault, embed_subcommand="stop", json=True)
|
||||
|
||||
with patch("paperforge.commands.embed.read_vector_build_state") as mock_read:
|
||||
mock_read.return_value = {"status": "running", "pid": 12345}
|
||||
with patch("paperforge.commands.embed.os.kill", side_effect=OSError("denied")):
|
||||
result_code = run(args)
|
||||
|
||||
assert result_code == 1
|
||||
|
|
|
|||
33
tests/unit/core/test_io.py
Normal file
33
tests/unit/core/test_io.py
Normal file
|
|
@ -0,0 +1,33 @@
|
|||
from __future__ import annotations
|
||||
|
||||
import json
|
||||
|
||||
from paperforge.core.io import read_json, write_json, write_json_atomic
|
||||
|
||||
|
||||
def test_write_json_atomic_creates_parent_dirs(tmp_path):
|
||||
path = tmp_path / "nested" / "state.json"
|
||||
|
||||
write_json_atomic(path, {"ok": True})
|
||||
|
||||
assert path.exists()
|
||||
assert read_json(path) == {"ok": True}
|
||||
|
||||
|
||||
def test_write_json_atomic_replaces_existing_file(tmp_path):
|
||||
path = tmp_path / "state.json"
|
||||
path.write_text(json.dumps({"old": True}), encoding="utf-8")
|
||||
|
||||
write_json_atomic(path, {"new": True})
|
||||
|
||||
assert read_json(path) == {"new": True}
|
||||
assert not path.with_suffix(".json.tmp").exists()
|
||||
|
||||
|
||||
def test_write_json_uses_atomic_writer(tmp_path):
|
||||
path = tmp_path / "state.json"
|
||||
|
||||
write_json(path, {"value": 1})
|
||||
|
||||
assert read_json(path) == {"value": 1}
|
||||
assert not path.with_suffix(".json.tmp").exists()
|
||||
|
|
@ -15,3 +15,35 @@ def test_refresh_paper_returns_false_for_empty_key():
|
|||
|
||||
def test_refresh_paper_returns_false_for_missing_key():
|
||||
assert refresh_paper(Path("/nonexistent/vault"), {"title": "No Key"}) is False
|
||||
|
||||
|
||||
def test_refresh_paper_rebuild_from_index_removes_stale_rows(tmp_path):
|
||||
from paperforge.memory.builder import build_from_index
|
||||
from paperforge.memory.db import get_connection, get_memory_db_path
|
||||
from paperforge.worker.asset_index import build_envelope, get_index_path
|
||||
|
||||
vault = tmp_path / "vault"
|
||||
vault.mkdir()
|
||||
(vault / "paperforge.json").write_text(
|
||||
'{"vault_config":{"system_dir":"System","resources_dir":"Resources","literature_dir":"Literature","base_dir":"Bases","control_dir":"LiteratureControl"}}',
|
||||
encoding="utf-8",
|
||||
)
|
||||
|
||||
index_path = get_index_path(vault)
|
||||
index_path.parent.mkdir(parents=True, exist_ok=True)
|
||||
first = [{"zotero_key": "AAA", "title": "Paper A", "domain": "test", "has_pdf": False, "ocr_status": "pending", "analyze": False, "deep_reading_status": "pending", "pdf_path": "", "note_path": "", "main_note_path": "", "fulltext_path": "", "ocr_json_path": "", "ai_path": "", "paper_root": "", "citation_key": "", "doi": "", "journal": "", "first_author": "", "collection_path": "", "collections": [], "authors": [], "abstract": "", "zotero_storage_key": "", "attachment_count": 0, "supplementary": [], "recommend_analyze": False, "path_error": "", "analysis_note": "", "lifecycle": "indexed", "maturity": {"score": 0}, "next_step": "ready"}]
|
||||
index_path.write_text(__import__("json").dumps(build_envelope(first), ensure_ascii=False, indent=2), encoding="utf-8")
|
||||
|
||||
build_from_index(vault)
|
||||
|
||||
second = []
|
||||
index_path.write_text(__import__("json").dumps(build_envelope(second), ensure_ascii=False, indent=2), encoding="utf-8")
|
||||
build_from_index(vault)
|
||||
|
||||
conn = get_connection(get_memory_db_path(vault), read_only=True)
|
||||
try:
|
||||
count = conn.execute("SELECT COUNT(*) AS c FROM papers").fetchone()["c"]
|
||||
finally:
|
||||
conn.close()
|
||||
|
||||
assert count == 0
|
||||
|
|
|
|||
Loading…
Reference in a new issue