mirror of
https://github.com/allaunthefox/Research-Stack.git
synced 2026-07-31 03:05:21 +00:00
a6311ed940
- Update .gitignore with **/target/ for Rust build artifacts - Add eval receipts to UniversalBridge.lean (compile-time verification comments) - Add PCIe Idle-Cycle Compute Harvester to ROADMAP.md - Clean up deprecated scripts, generated Verilog, and old tools (23 deletions) - Stage new infrastructure: Xen/Alpine embedded surface, QFOX topology manager - Stage new probes: boundary activation field, holographic carving - Stage new applications: finance manager, script roots - Stage new research spec: PCIe idle-cycle substrate
411 lines
18 KiB
Python
411 lines
18 KiB
Python
#!/usr/bin/env python3
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"""
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Smart Ingest Watcher (Daemon)
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=============================
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Monitors watched directories for new PDFs. On detection:
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1. Extract arXiv ID / DOI from filename + PDF header
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2. Fetch metadata from arXiv API if arXiv ID found
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3. Ingest into Zotero with proper metadata
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4. Move to the canonical archive directory
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5. Log everything to the index
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Usage:
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# Run once (foreground, dry-run)
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python3 ingest_watcher.py --once --dry-run
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# Run as daemon
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python3 ingest_watcher.py --daemon
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# Add a watch directory
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python3 ingest_watcher.py --watch ~/Downloads --daemon
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"""
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import argparse
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import hashlib
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import json
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import os
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import re
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import shutil
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import sqlite3
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import subprocess
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import sys
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import time
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import urllib.parse
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import urllib.request
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from dataclasses import dataclass, field
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from pathlib import Path
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from typing import Dict, List, Optional, Set
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# ── Paths ─────────────────────────────────────────────────────────────────────
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ZOTERO_DB = Path.home() / "Zotero" / "zotero.sqlite"
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INDEX_DB = Path.home() / "Research Stack" / "data" / "substrate_index.db"
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CANONICAL_DIR = Path.home() / "Downloads" / "data" / "Downloads_from_internet" / "Deep Research" / "alphaXiv_PDFs_2026_04"
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STATE_FILE = Path.home() / "Research Stack" / "data" / "ingest_watcher_state.json"
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LOG_FILE = Path.home() / "Research Stack" / "data" / "ingest_watcher.log"
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CANONICAL_DIR.mkdir(parents=True, exist_ok=True)
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STATE_FILE.parent.mkdir(parents=True, exist_ok=True)
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# ── Config ────────────────────────────────────────────────────────────────────
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DEFAULT_WATCH_DIRS = [
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str(Path.home() / "Downloads"),
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str(Path.home() / "Downloads" / "data" / "Downloads_from_internet"),
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]
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CHECK_INTERVAL = 30 # seconds
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# ── Data Classes ─────────────────────────────────────────────────────────────
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@dataclass
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class DiscoveredPDF:
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path: Path
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arxiv_id: Optional[str] = None
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doi: Optional[str] = None
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title_guess: str = ""
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hash: str = ""
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# ── arXiv Client (lightweight) ────────────────────────────────────────────────
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class ArxivClient:
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BASE_QUERY = "https://export.arxiv.org/api/query"
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BASE_PDF = "https://arxiv.org/pdf"
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def fetch_meta(self, arxiv_id: str) -> Optional[Dict]:
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clean = re.sub(r"v\d+$", "", arxiv_id)
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url = f"{self.BASE_QUERY}?id_list={clean}&max_results=1"
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try:
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req = urllib.request.Request(url, headers={"User-Agent": "ScienceHub-Watcher/0.1"})
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with urllib.request.urlopen(req, timeout=30) as resp:
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xml = resp.read().decode("utf-8")
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return self._parse(xml, clean)
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except Exception as e:
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self._log(f"[arxiv] Failed to fetch {arxiv_id}: {e}")
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return None
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def _parse(self, xml: str, arxiv_id: str) -> Optional[Dict]:
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import xml.etree.ElementTree as ET
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ns = {"atom": "http://www.w3.org/2005/Atom", "arxiv": "http://arxiv.org/schemas/atom"}
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root = ET.fromstring(xml)
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entry = root.find("atom:entry", ns)
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if entry is None:
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return None
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def tag(t):
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el = entry.find(f"atom:{t}", ns)
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return el.text.strip() if el is not None else ""
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authors = [a.find("atom:name", ns).text for a in entry.findall("atom:author", ns)]
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cat_el = entry.find("arxiv:primary_category", ns)
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primary = cat_el.attrib.get("term", "") if cat_el is not None else ""
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cats = [c.attrib.get("term", "") for c in entry.findall("atom:category", ns)]
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return {
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"arxiv_id": arxiv_id,
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"title": tag("title").replace("\n", " "),
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"authors": authors,
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"summary": tag("summary").replace("\n", " "),
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"published": tag("published")[:4],
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"updated": tag("updated"),
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"primary_category": primary,
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"categories": cats,
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"pdf_url": f"{self.BASE_PDF}/{arxiv_id}.pdf",
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}
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def _log(self, msg: str):
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print(msg, file=sys.stderr)
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# ── Zotero Writer (same as sciencehub_mcp but minimal) ──────────────────────
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class ZoteroWriter:
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def __init__(self, db_path: Path = ZOTERO_DB):
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self.db_path = db_path
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def _backup(self):
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ts = time.strftime("%Y%m%d_%H%M%S")
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backup = self.db_path.with_suffix(f".sqlite.backup.{ts}")
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shutil.copy2(str(self.db_path), str(backup))
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return backup
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def _get_next_item_id(self, conn: sqlite3.Connection) -> int:
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cur = conn.execute("SELECT MAX(itemID) FROM items")
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return (cur.fetchone()[0] or 0) + 1
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def _get_field_id(self, conn: sqlite3.Connection, field_name: str) -> int:
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cur = conn.execute("SELECT fieldID FROM fields WHERE fieldName = ?", (field_name,))
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row = cur.fetchone()
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if row:
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return row[0]
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cur = conn.execute("INSERT INTO fields (fieldName) VALUES (?) RETURNING fieldID", (field_name,))
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return cur.fetchone()[0]
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def _get_or_create_value(self, conn: sqlite3.Connection, value: str) -> int:
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cur = conn.execute("SELECT valueID FROM itemDataValues WHERE value = ?", (value,))
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row = cur.fetchone()
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if row:
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return row[0]
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cur = conn.execute("INSERT INTO itemDataValues (value) VALUES (?) RETURNING valueID", (value,))
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return cur.fetchone()[0]
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def add_preprint(self, title: str, authors: List[str], url: str,
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arxiv_id: Optional[str] = None, year: Optional[str] = None,
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collection_name: str = "Research Stack") -> str:
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import random, string
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key = "".join(random.choices(string.ascii_uppercase + string.digits, k=8))
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backup_path = self._backup()
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try:
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with sqlite3.connect(str(self.db_path)) as conn:
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item_id = self._get_next_item_id(conn)
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cur = conn.execute("SELECT itemTypeID FROM itemTypes WHERE typeName = 'preprint'")
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row = cur.fetchone()
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preprint_type_id = row[0] if row else 22
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conn.execute(
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"""INSERT INTO items (itemID, itemTypeID, dateAdded, dateModified, clientDateModified, libraryID, key, version, synced)
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VALUES (?, ?, datetime('now'), datetime('now'), datetime('now'), 1, ?, 0, 0)""",
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(item_id, preprint_type_id, key),
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)
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meta = {"title": title, "url": url, "extra": arxiv_id or ""}
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if year:
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meta["date"] = year
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for field_name, val in meta.items():
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if not val:
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continue
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fid = self._get_field_id(conn, field_name)
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vid = self._get_or_create_value(conn, val)
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conn.execute("INSERT INTO itemData (itemID, fieldID, valueID) VALUES (?,?,?)",
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(item_id, fid, vid))
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for i, author in enumerate(authors[:20]):
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author = author.strip()
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if not author:
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continue
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if "," in author:
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parts = [p.strip() for p in author.split(",", 1)]
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last, first = parts[0], parts[1] if len(parts) > 1 else ""
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else:
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parts = author.split()
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last = parts[-1] if parts else ""
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first = " ".join(parts[:-1]) if len(parts) > 1 else ""
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cur = conn.execute(
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"SELECT creatorID FROM creators WHERE firstName = ? AND lastName = ? AND fieldMode = ?",
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(first, last, 0),
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)
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row = cur.fetchone()
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if row:
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creator_id = row[0]
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else:
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cur = conn.execute(
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"INSERT INTO creators (firstName, lastName, fieldMode) VALUES (?,?,?) RETURNING creatorID",
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(first, last, 0),
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)
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creator_id = cur.fetchone()[0]
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conn.execute(
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"INSERT INTO itemCreators (itemID, creatorID, creatorTypeID, orderIndex) VALUES (?,?,1,?)",
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(item_id, creator_id, i),
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)
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cur = conn.execute("SELECT collectionID FROM collections WHERE collectionName = ?", (collection_name,))
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row = cur.fetchone()
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if row:
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col_id = row[0]
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else:
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cur = conn.execute(
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"""INSERT INTO collections (collectionName, parentCollectionID, libraryID, key, version, synced, clientDateModified)
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VALUES (?, NULL, 1, ?, 0, 0, datetime('now')) RETURNING collectionID""",
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(collection_name, key),
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)
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col_id = cur.fetchone()[0]
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cur = conn.execute(
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"SELECT COALESCE(MAX(orderIndex), -1) + 1 FROM collectionItems WHERE collectionID = ?",
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(col_id,),
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)
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order_idx = cur.fetchone()[0]
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conn.execute(
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"INSERT INTO collectionItems (collectionID, itemID, orderIndex) VALUES (?,?,?)",
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(col_id, item_id, order_idx),
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)
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conn.commit()
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return key
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except Exception:
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shutil.copy2(str(backup_path), str(self.db_path))
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raise
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# ── Watcher State ─────────────────────────────────────────────────────────────
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class WatcherState:
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def __init__(self, path: Path = STATE_FILE):
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self.path = path
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self.data: Dict = self._load()
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def _load(self) -> Dict:
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if self.path.exists():
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with open(self.path) as f:
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return json.load(f)
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return {"processed_hashes": [], "last_run": None}
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def save(self):
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with open(self.path, "w") as f:
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json.dump(self.data, f, indent=2)
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def is_new(self, file_hash: str) -> bool:
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return file_hash not in self.data.get("processed_hashes", [])
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def mark_processed(self, file_hash: str):
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self.data.setdefault("processed_hashes", []).append(file_hash)
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self.data["last_run"] = time.strftime("%Y-%m-%d %H:%M:%S")
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self.save()
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# ── PDF Analyzer ────────────────────────────────────────────────────────────
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class PDFAnalyzer:
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ARXIV_RE = re.compile(r"(\d{4}\.\d{4,5}(?:v\d+)?)")
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DOI_RE = re.compile(r"10\.\d{4,9}/[-._;()/:A-Z0-9a-z]+")
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def analyze(self, path: Path) -> DiscoveredPDF:
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name = path.stem
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arxiv_match = self.ARXIV_RE.search(name)
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arxiv_id = arxiv_match.group(1) if arxiv_match else None
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doi_guess = None
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if not arxiv_id:
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try:
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with open(path, "rb") as f:
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header = f.read(8192).decode("utf-8", errors="ignore")
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dm = self.DOI_RE.search(header)
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if dm:
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doi_guess = dm.group(0)
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am = self.ARXIV_RE.search(header)
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if am:
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arxiv_id = am.group(1)
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except Exception:
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pass
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title_guess = self._clean_title(name)
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h = hashlib.sha256(path.read_bytes()).hexdigest()
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return DiscoveredPDF(path=path, arxiv_id=arxiv_id, doi=doi_guess, title_guess=title_guess, hash=h)
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@staticmethod
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def _clean_title(filename: str) -> str:
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t = filename.replace("_", " ").replace("-", " ")
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t = re.sub(r"\b\d{4}\.\d{4,5}v?\d*\b", "", t)
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t = re.sub(r"\s+", " ", t).strip()
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return t
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# ── Ingest Pipeline ─────────────────────────────────────────────────────────
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class IngestPipeline:
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def __init__(self):
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self.analyzer = PDFAnalyzer()
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self.arxiv = ArxivClient()
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self.zotero = ZoteroWriter()
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self.state = WatcherState()
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def run_once(self, watch_dirs: List[str], dry_run: bool = False) -> List[str]:
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discovered: List[DiscoveredPDF] = []
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for d in watch_dirs:
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root = Path(d)
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if not root.exists():
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continue
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for pdf in root.rglob("*.pdf"):
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# Skip already-archived files
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if CANONICAL_DIR in pdf.parents:
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continue
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info = self.analyzer.analyze(pdf)
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if self.state.is_new(info.hash):
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discovered.append(info)
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reports: List[str] = []
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for pdf in discovered:
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report = self._process(pdf, dry_run=dry_run)
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reports.append(report)
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if not dry_run:
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self.state.mark_processed(pdf.hash)
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return reports
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def _process(self, pdf: DiscoveredPDF, dry_run: bool = False) -> str:
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lines = [f"📄 {pdf.path.name}"]
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if pdf.arxiv_id:
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lines.append(f" arXiv ID: {pdf.arxiv_id}")
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if pdf.doi:
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lines.append(f" DOI guess: {pdf.doi}")
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title = pdf.title_guess or "Unknown"
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authors: List[str] = []
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year: Optional[str] = None
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url = ""
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if pdf.arxiv_id:
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meta = self.arxiv.fetch_meta(pdf.arxiv_id)
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if meta:
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title = meta["title"]
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authors = meta["authors"]
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year = meta["published"]
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url = meta["pdf_url"]
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lines.append(f" Fetched title: {title}")
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lines.append(f" Authors: {', '.join(authors[:3])}")
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else:
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lines.append(" ⚠️ Could not fetch arXiv metadata")
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if dry_run:
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lines.append(" ⏸️ DRY RUN — no changes made")
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return "\n".join(lines)
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# Ingest to Zotero
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try:
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zkey = self.zotero.add_preprint(title, authors, url, arxiv_id=pdf.arxiv_id, year=year)
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lines.append(f" 📥 Zotero key: {zkey}")
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except Exception as e:
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lines.append(f" ⚠️ Zotero ingest failed: {e}")
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# Move to canonical dir with safe name
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try:
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safe_title = self._safe_slug(title)
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dest_name = f"{pdf.arxiv_id or 'unknown'}_{safe_title}.pdf"
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dest = CANONICAL_DIR / dest_name
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shutil.move(str(pdf.path), str(dest))
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lines.append(f" 💾 Archived to: {dest}")
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except Exception as e:
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lines.append(f" ⚠️ Move failed: {e}")
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return "\n".join(lines)
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@staticmethod
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def _safe_slug(title: str) -> str:
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replacements = {
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"\\": " ", "$": "", "^": "", "_": " ", "{": "", "}": "",
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"~": " ", "%": "pct", "&": "and", "#": "", "@": "at",
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}
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for old, new in replacements.items():
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title = title.replace(old, new)
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title = re.sub(r"[^\w\s-]", "", title)
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title = re.sub(r"[-\s]+", "_", title).strip("_")
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return title[:80] if title else "paper"
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def run_daemon(self, watch_dirs: List[str], interval: int = CHECK_INTERVAL):
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self._log(f"👁️ Ingest Watcher daemon started")
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self._log(f" Watching: {', '.join(watch_dirs)}")
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self._log(f" Archive: {CANONICAL_DIR}")
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self._log(f" Interval: {interval}s")
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while True:
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reports = self.run_once(watch_dirs)
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if reports:
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for r in reports:
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self._log(r)
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time.sleep(interval)
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@staticmethod
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def _log(msg: str):
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ts = time.strftime("%Y-%m-%d %H:%M:%S")
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line = f"[{ts}] {msg}"
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print(line)
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with open(LOG_FILE, "a") as f:
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f.write(line + "\n")
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# ── Main ─────────────────────────────────────────────────────────────────────
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def main():
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parser = argparse.ArgumentParser(description="Smart Ingest Watcher")
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parser.add_argument("--watch", nargs="*", default=DEFAULT_WATCH_DIRS, help="Directories to watch")
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parser.add_argument("--once", action="store_true", help="Run one scan and exit")
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parser.add_argument("--dry-run", action="store_true", help="Don't modify anything")
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parser.add_argument("--daemon", action="store_true", help="Run forever")
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parser.add_argument("--interval", type=int, default=CHECK_INTERVAL, help="Seconds between scans")
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args = parser.parse_args()
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pipeline = IngestPipeline()
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if args.once:
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reports = pipeline.run_once(args.watch, dry_run=args.dry_run)
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for r in reports:
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print(r)
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print(f"\nProcessed {len(reports)} new PDFs.")
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elif args.daemon:
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pipeline.run_daemon(args.watch, interval=args.interval)
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else:
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parser.print_help()
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if __name__ == "__main__":
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main()
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