chore: track claude skills, tools, templates, reference code and research-wiki
- Add all claude skills (brainstorming, commit, debugging, TDD, etc.) - Add claude hooks (pre-commit-guard, post-edit-quality) - Add research templates (experiment plan, research brief, etc.) - Add claude tools (arxiv/semantic_scholar/openalex fetch, wiki, exa) - Add TRM4 reference implementation as algorithm fidelity baseline - Add research-wiki content (plans, index, graph, query_pack) - Update .gitignore to exclude .graphify_version runtime state
This commit is contained in:
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"""研究 Wiki 的初始化与日志工具。"""
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from __future__ import annotations
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import argparse
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import json
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import re
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import unicodedata
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from datetime import datetime, timezone
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from pathlib import Path
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from typing import Any
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from urllib.request import urlopen
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import xml.etree.ElementTree as ET
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ENTITY_TYPES = {
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"paper": "papers",
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"idea": "ideas",
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"experiment": "experiments",
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"claim": "claims",
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"gap": "gaps",
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"design": "designs",
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"finding": "findings",
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"adr": "adrs",
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"plan": "plans",
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"review": "reviews",
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"schema": "schemas",
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"metric": "metrics",
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}
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EDGE_TYPES = [
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"extends",
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"contradicts",
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"supersedes",
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"addresses_gap",
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"inspired_by",
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"tested_by",
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"supports",
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"invalidates",
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"implements",
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"reveals",
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"informs",
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"refines",
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"depends_on",
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"measures",
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"evaluates",
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]
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QUERY_PACK_BUDGET = 8000
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def slugify(text: str) -> str:
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"""将文本转换为 URL 安全的 slug。"""
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normalized = unicodedata.normalize("NFKD", text)
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normalized = re.sub(r"[^\w\s-]", "", normalized.lower())
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return re.sub(r"[-\s]+", "_", normalized).strip("_")[:60]
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def _write_if_missing(path: Path, content: str) -> None:
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"""仅在文件不存在时写入内容。
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参数:
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path: 目标文件路径。
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content: 需要写入的文本内容。
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"""
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if path.exists():
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return
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path.parent.mkdir(parents=True, exist_ok=True)
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path.write_text(content, encoding="utf-8")
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def append_log(wiki_dir: str, message: str) -> None:
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"""向 Wiki 变更日志追加一条记录。
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参数:
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wiki_dir: Wiki 根目录。
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message: 需要记录的消息。
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"""
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log_path = Path(wiki_dir) / "log.md"
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timestamp = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M UTC")
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with log_path.open("a", encoding="utf-8") as handle:
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handle.write(f"- [{timestamp}] {message}\n")
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def _render_frontmatter(data: dict[str, Any]) -> str:
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"""将字典渲染为 YAML frontmatter。"""
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lines = ["---"]
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for key, value in data.items():
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if isinstance(value, list):
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rendered_value = json.dumps(value, ensure_ascii=False)
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elif isinstance(value, str) and " " in value:
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rendered_value = f'"{value}"'
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else:
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rendered_value = str(value)
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lines.append(f"{key}: {rendered_value}")
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lines.append("---")
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return "\n".join(lines) + "\n"
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def _read_frontmatter(filepath: Path) -> dict[str, Any]:
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"""从 markdown 文件读取简易 frontmatter。"""
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text = filepath.read_text(encoding="utf-8")
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if not text.startswith("---\n"):
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return {}
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lines = text.splitlines()
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result: dict[str, Any] = {}
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for line in lines[1:]:
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if line == "---":
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break
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if ":" not in line:
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continue
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key, _, raw_value = line.partition(":")
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value = raw_value.strip()
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if value.startswith("[") and value.endswith("]"):
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try:
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result[key.strip()] = json.loads(value)
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continue
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except json.JSONDecodeError:
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pass
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if len(value) >= 2 and (
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(value.startswith('"') and value.endswith('"'))
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or (value.startswith("'") and value.endswith("'"))
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):
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value = value[1:-1]
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result[key.strip()] = value
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return result
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def _add_node_to_graph(
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wiki_dir: str, node_id: str, label: str, entity_type: str
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) -> None:
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"""向关系图中添加节点，若已存在则跳过。"""
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graph_path = Path(wiki_dir) / "graph" / "edges.json"
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graph = json.loads(graph_path.read_text(encoding="utf-8"))
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nodes = graph.setdefault("nodes", [])
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if not any(node.get("id") == node_id for node in nodes):
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nodes.append({"id": node_id, "label": label, "type": entity_type})
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graph_path.write_text(
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json.dumps(graph, ensure_ascii=False, indent=2), encoding="utf-8"
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)
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def add_edge(
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wiki_dir: str,
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from_id: str,
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to_id: str,
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edge_type: str,
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evidence: str = "",
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) -> None:
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"""向关系图中添加一条边。"""
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if edge_type not in EDGE_TYPES:
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raise ValueError(f"未知边类型: {edge_type}，合法值: {EDGE_TYPES}")
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graph_path = Path(wiki_dir) / "graph" / "edges.json"
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graph = json.loads(graph_path.read_text(encoding="utf-8"))
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links = graph.setdefault("links", [])
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for link in links:
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if (
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link.get("source") == from_id
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and link.get("target") == to_id
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and link.get("relation") == edge_type
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):
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return
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links.append(
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{
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"source": from_id,
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"target": to_id,
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"relation": edge_type,
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"evidence": evidence,
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"added": datetime.now(timezone.utc).isoformat(),
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}
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)
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graph_path.write_text(
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json.dumps(graph, ensure_ascii=False, indent=2), encoding="utf-8"
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)
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append_log(wiki_dir, f"新增边: {from_id} --{edge_type}--> {to_id}")
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def add_entity(
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wiki_dir: str,
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entity_type: str,
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entity_id: str,
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title: str,
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extra_frontmatter: dict[str, Any] | None = None,
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) -> Path:
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"""创建一个实体页面并同步到关系图。"""
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if entity_type not in ENTITY_TYPES:
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raise ValueError(f"未知实体类型: {entity_type}，合法值: {list(ENTITY_TYPES)}")
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root = Path(wiki_dir)
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entity_subdir = root / ENTITY_TYPES[entity_type]
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node_id = f"{entity_type}:{entity_id}"
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for existing_path in entity_subdir.glob("*.md"):
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frontmatter = _read_frontmatter(existing_path)
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if frontmatter.get("node_id") == node_id:
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return existing_path
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filepath = entity_subdir / f"{entity_id}.md"
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frontmatter: dict[str, Any] = {
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"type": entity_type,
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"node_id": node_id,
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"title": title,
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"date": datetime.now(timezone.utc).strftime("%Y-%m-%d"),
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}
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if extra_frontmatter:
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frontmatter.update(extra_frontmatter)
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content = _render_frontmatter(frontmatter) + f"\n# {title}\n\n"
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filepath.write_text(content, encoding="utf-8")
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_add_node_to_graph(wiki_dir, node_id, title, entity_type)
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append_log(wiki_dir, f"新增 {entity_type}: {title} ({node_id})")
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return filepath
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def _fetch_arxiv_metadata(arxiv_id: str) -> dict[str, Any] | None:
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"""通过 arXiv Atom API 拉取论文元数据。"""
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clean_id = (
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arxiv_id.removeprefix("arxiv:")
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.removeprefix("arXiv:")
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.removeprefix("ARXIV:")
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.strip()
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)
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url = f"http://export.arxiv.org/api/query?id_list={clean_id}"
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try:
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with urlopen(url) as response:
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root = ET.fromstring(response.read())
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except Exception:
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return None
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namespace = {"atom": "http://www.w3.org/2005/Atom"}
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entry = root.find("atom:entry", namespace)
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if entry is None:
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return None
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def _text(path: str) -> str:
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value = entry.findtext(path, default="", namespaces=namespace)
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return " ".join(value.split())
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authors = [
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" ".join(author.findtext("atom:name", default="", namespaces=namespace).split())
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for author in entry.findall("atom:author", namespace)
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]
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authors = [author for author in authors if author]
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published = _text("atom:published")
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year = published[:4] if len(published) >= 4 else ""
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return {
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"title": _text("atom:title"),
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"authors": authors,
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"year": year,
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"abstract": _text("atom:summary"),
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"arxiv_id": clean_id,
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}
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def _last_name(full_name: str) -> str:
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"""提取人名最后一个词作为姓氏。"""
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parts = full_name.strip().split()
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return parts[-1].lower() if parts else "unknown"
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def _markdown_body(text: str) -> str:
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"""提取 markdown 中 frontmatter 之后的正文。"""
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if not text.startswith("---\n"):
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return text
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lines = text.splitlines()
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for index, line in enumerate(lines[1:], start=1):
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if line == "---":
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return "\n".join(lines[index + 1 :])
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return ""
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def _iter_entity_pages(wiki_dir: str) -> list[tuple[str, Path, dict[str, Any], str]]:
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"""收集 Wiki 中所有实体页面。"""
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root = Path(wiki_dir)
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pages: list[tuple[str, Path, dict[str, Any], str]] = []
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for entity_type, subdir_name in ENTITY_TYPES.items():
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subdir = root / subdir_name
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for path in sorted(subdir.glob("*.md")):
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frontmatter = _read_frontmatter(path)
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body = _markdown_body(path.read_text(encoding="utf-8"))
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resolved_type = (
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str(frontmatter.get("type", entity_type)).strip() or entity_type
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)
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pages.append((resolved_type, path, frontmatter, body))
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return pages
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def rebuild_index(wiki_dir: str) -> None:
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"""按实体类型重建索引页。"""
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root = Path(wiki_dir)
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timestamp = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M UTC")
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pages = _iter_entity_pages(wiki_dir)
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grouped: dict[str, list[tuple[Path, dict[str, Any]]]] = {}
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for entity_type, path, frontmatter, _ in pages:
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grouped.setdefault(entity_type, []).append((path, frontmatter))
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lines = [
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"# Research Wiki 索引",
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"",
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f"> 自动生成，更新时间：{timestamp}",
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"",
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]
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for entity_type in ENTITY_TYPES:
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entries = grouped.get(entity_type, [])
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if not entries:
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continue
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entries = sorted(
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entries,
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key=lambda item: (
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str(item[1].get("title", item[0].stem)).casefold(),
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item[0].name,
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),
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)
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lines.append(f"## {entity_type} ({len(entries)})")
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for path, frontmatter in entries:
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title = str(frontmatter.get("title", path.stem)).strip() or path.stem
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node_id = str(
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frontmatter.get("node_id", f"{entity_type}:{path.stem}")
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).strip()
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relative_path = path.relative_to(root).as_posix()
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lines.append(f"- [{title}]({relative_path}) `{node_id}`")
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lines.append("")
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content = "\n".join(lines).rstrip() + "\n"
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(root / "index.md").write_text(content, encoding="utf-8")
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append_log(wiki_dir, f"重建索引: {len(pages)} 篇页面")
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def rebuild_query_pack(wiki_dir: str) -> None:
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"""基于 frontmatter 重新生成 Query Pack。"""
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pages = _iter_entity_pages(wiki_dir)
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failed_ideas: list[tuple[str, str]] = []
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open_gaps: list[str] = []
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core_papers: list[tuple[str, str, str]] = []
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for entity_type, path, frontmatter, _ in pages:
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title = str(frontmatter.get("title", path.stem)).strip() or path.stem
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if entity_type == "idea":
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outcome = str(frontmatter.get("outcome", "")).strip().lower()
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if outcome in {"negative", "failed"}:
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failure_reason = str(frontmatter.get("failure_reason", "")).strip()
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failed_ideas.append((title, failure_reason or "未填写"))
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if entity_type == "gap":
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status = str(frontmatter.get("status", "open")).strip().lower()
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if not status or status == "open":
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open_gaps.append(title)
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if entity_type == "paper":
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year = str(frontmatter.get("year", "")).strip()
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venue = str(frontmatter.get("venue", "")).strip()
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core_papers.append(
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(
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title,
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year or "未知年份",
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venue or "未知 venue",
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)
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)
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failed_ideas.sort(key=lambda item: item[0].casefold())
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open_gaps.sort(key=str.casefold)
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core_papers.sort(key=lambda item: (item[1], item[0].casefold(), item[2].casefold()))
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sections: list[tuple[str, list[str]]] = []
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if failed_ideas:
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sections.append(
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(
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"## 失败 Idea（禁区）",
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[f"- ❌ {title}: {reason}" for title, reason in failed_ideas[:10]],
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)
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)
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if open_gaps:
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sections.append(
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(
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"## 未解决空白",
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[f"- {title}" for title in open_gaps[:5]],
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)
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)
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if core_papers:
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sections.append(
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(
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"## 核心论文",
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[
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f"- [{title}] ({year}) {venue}"
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for title, year, venue in core_papers[:12]
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],
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)
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)
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content_parts = [
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"# Query Pack",
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"",
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"> 自动生成，请勿手动编辑。",
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"",
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"",
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]
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current_content = "\n".join(content_parts)
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for section_title, section_lines in sections:
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section_text = "\n".join([section_title, *section_lines, "", ""])
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candidate = current_content + section_text
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if len(candidate) > QUERY_PACK_BUDGET:
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break
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current_content = candidate
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content = current_content.rstrip() + "\n"
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(Path(wiki_dir) / "query_pack.md").write_text(content, encoding="utf-8")
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append_log(wiki_dir, f"重建 Query Pack: {len(content)} 字符")
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def get_stats(wiki_dir: str) -> str:
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"""统计 Wiki 规模与图谱信息。"""
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root = Path(wiki_dir)
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lines: list[str] = []
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for entity_type, subdir_name in ENTITY_TYPES.items():
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count = len(list((root / subdir_name).glob("*.md")))
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lines.append(f"{entity_type}: {count}")
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graph_path = root / "graph" / "edges.json"
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if graph_path.exists():
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graph = json.loads(graph_path.read_text(encoding="utf-8"))
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else:
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graph = {"nodes": [], "links": []}
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lines.append(f"nodes: {len(graph.get('nodes', []))}")
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lines.append(f"links: {len(graph.get('links', []))}")
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return "\n".join(lines)
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def lint_wiki(wiki_dir: str) -> list[str]:
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"""检查 Wiki 中的孤立节点与稀疏页面。"""
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root = Path(wiki_dir)
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issues: list[str] = []
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graph_path = root / "graph" / "edges.json"
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if graph_path.exists():
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graph = json.loads(graph_path.read_text(encoding="utf-8"))
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else:
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graph = {"nodes": [], "links": []}
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linked_node_ids = {
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str(link.get("source", "")).strip()
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for link in graph.get("links", [])
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if str(link.get("source", "")).strip()
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}
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linked_node_ids.update(
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str(link.get("target", "")).strip()
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||||
for link in graph.get("links", [])
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||||
if str(link.get("target", "")).strip()
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||||
)
|
||||
|
||||
for node in graph.get("nodes", []):
|
||||
node_id = str(node.get("id", "")).strip()
|
||||
if node_id and node_id not in linked_node_ids:
|
||||
label = str(node.get("label", "")).strip()
|
||||
issues.append(f"孤立节点: {node_id}" + (f" ({label})" if label else ""))
|
||||
|
||||
for _, path, _, body in _iter_entity_pages(wiki_dir):
|
||||
if len(body.strip()) < 50:
|
||||
relative_path = path.relative_to(root).as_posix()
|
||||
issues.append(f"稀疏页面: {relative_path} (正文 {len(body.strip())} 字符)")
|
||||
|
||||
return issues
|
||||
|
||||
|
||||
def ingest_paper(
|
||||
wiki_dir: str,
|
||||
arxiv_id: str | None = None,
|
||||
title: str | None = None,
|
||||
authors: str | None = None,
|
||||
year: str | None = None,
|
||||
venue: str = "arXiv",
|
||||
thesis: str = "",
|
||||
) -> Path | None:
|
||||
"""创建 paper 实体并补充标准化正文模板。"""
|
||||
abstract = ""
|
||||
authors_list: list[str]
|
||||
paper_title = title
|
||||
paper_year = year
|
||||
paper_arxiv_id = None
|
||||
|
||||
if arxiv_id:
|
||||
metadata = _fetch_arxiv_metadata(arxiv_id)
|
||||
if metadata is None:
|
||||
return None
|
||||
paper_title = metadata["title"]
|
||||
authors_list = metadata["authors"]
|
||||
paper_year = metadata["year"]
|
||||
abstract = metadata["abstract"]
|
||||
paper_arxiv_id = metadata["arxiv_id"]
|
||||
else:
|
||||
if not (title and authors and year):
|
||||
raise ValueError("非 arXiv 论文需提供 --title、--authors、--year")
|
||||
authors_list = [
|
||||
author.strip() for author in authors.split(",") if author.strip()
|
||||
]
|
||||
if not authors_list:
|
||||
raise ValueError("authors 不能为空")
|
||||
|
||||
if not paper_title:
|
||||
raise ValueError("论文标题不能为空")
|
||||
if not paper_year:
|
||||
raise ValueError("论文年份不能为空")
|
||||
if not authors_list:
|
||||
raise ValueError("论文作者不能为空")
|
||||
|
||||
slug = f"{_last_name(authors_list[0])}{paper_year}_{slugify(paper_title)[:30]}"
|
||||
extra_frontmatter: dict[str, Any] = {
|
||||
"authors": authors_list,
|
||||
"year": paper_year,
|
||||
"venue": venue,
|
||||
}
|
||||
if paper_arxiv_id is not None:
|
||||
extra_frontmatter["arxiv_id"] = paper_arxiv_id
|
||||
|
||||
path = add_entity(wiki_dir, "paper", slug, paper_title, extra_frontmatter)
|
||||
|
||||
content = path.read_text(encoding="utf-8")
|
||||
if "## 一句话论点" not in content:
|
||||
body = f"\n## 一句话论点\n\n{thesis or '待填写'}\n\n"
|
||||
if abstract:
|
||||
body += f"## 摘要\n\n> {' '.join(abstract.split())}\n\n"
|
||||
body += (
|
||||
"## 问题/空白\n\n"
|
||||
"## 方法\n\n"
|
||||
"## 关键结果\n\n"
|
||||
"## 局限性\n\n"
|
||||
"## 与本项目的相关性\n\n"
|
||||
)
|
||||
path.write_text(content + body, encoding="utf-8")
|
||||
|
||||
return path
|
||||
|
||||
|
||||
def init_wiki(wiki_dir: str) -> None:
|
||||
"""初始化研究 Wiki 的目录结构与基础文件。
|
||||
|
||||
参数:
|
||||
wiki_dir: Wiki 根目录。
|
||||
"""
|
||||
root = Path(wiki_dir)
|
||||
root.mkdir(parents=True, exist_ok=True)
|
||||
|
||||
for entity_dir in ENTITY_TYPES.values():
|
||||
(root / entity_dir).mkdir(parents=True, exist_ok=True)
|
||||
|
||||
graph_dir = root / "graph"
|
||||
graph_dir.mkdir(parents=True, exist_ok=True)
|
||||
|
||||
_write_if_missing(
|
||||
root / "index.md", "# Research Wiki 索引\n\n> 自动生成，请勿手动编辑。\n"
|
||||
)
|
||||
_write_if_missing(root / "log.md", "# Wiki 变更日志\n\n")
|
||||
_write_if_missing(root / "gap_map.md", "# 领域空白汇总\n\n")
|
||||
_write_if_missing(
|
||||
root / "query_pack.md",
|
||||
"# Query Pack\n\n> 尚无数据。运行 research-lit 或 idea-creator 后自动生成。\n",
|
||||
)
|
||||
_write_if_missing(
|
||||
graph_dir / "edges.json",
|
||||
json.dumps({"directed": True, "nodes": [], "links": []}, ensure_ascii=False),
|
||||
)
|
||||
|
||||
append_log(wiki_dir, "Wiki 初始化完成")
|
||||
|
||||
|
||||
def main() -> None:
|
||||
"""命令行入口。"""
|
||||
parser = argparse.ArgumentParser(description="研究 Wiki 工具")
|
||||
subparsers = parser.add_subparsers(dest="command", required=True)
|
||||
|
||||
init_parser = subparsers.add_parser("init", help="初始化 Wiki")
|
||||
init_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
|
||||
log_parser = subparsers.add_parser("log", help="追加日志")
|
||||
log_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
log_parser.add_argument("message", nargs="+", help="日志内容")
|
||||
|
||||
entity_parser = subparsers.add_parser("add_entity", help="创建实体")
|
||||
entity_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
entity_parser.add_argument(
|
||||
"--type", required=True, choices=list(ENTITY_TYPES), help="实体类型"
|
||||
)
|
||||
entity_parser.add_argument("--id", required=True, help="实体 ID")
|
||||
entity_parser.add_argument("--title", required=True, help="实体标题")
|
||||
|
||||
edge_parser = subparsers.add_parser("add_edge", help="创建关系边")
|
||||
edge_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
edge_parser.add_argument(
|
||||
"--from", dest="from_id", required=True, help="起点节点 ID"
|
||||
)
|
||||
edge_parser.add_argument("--to", dest="to_id", required=True, help="终点节点 ID")
|
||||
edge_parser.add_argument(
|
||||
"--type", required=True, choices=EDGE_TYPES, dest="edge_type", help="边类型"
|
||||
)
|
||||
edge_parser.add_argument("--evidence", default="", help="证据说明")
|
||||
|
||||
ingest_parser = subparsers.add_parser("ingest_paper", help="导入论文")
|
||||
ingest_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
ingest_parser.add_argument("--arxiv-id", dest="arxiv_id", help="arXiv ID")
|
||||
ingest_parser.add_argument("--title", help="论文标题")
|
||||
ingest_parser.add_argument("--authors", help="作者，逗号分隔")
|
||||
ingest_parser.add_argument("--year", help="年份")
|
||||
ingest_parser.add_argument("--venue", default="arXiv", help="发表 venue")
|
||||
ingest_parser.add_argument("--thesis", default="", help="一句话论点")
|
||||
|
||||
rebuild_query_pack_parser = subparsers.add_parser(
|
||||
"rebuild_query_pack", help="重建 Query Pack"
|
||||
)
|
||||
rebuild_query_pack_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
|
||||
rebuild_index_parser = subparsers.add_parser("rebuild_index", help="重建索引")
|
||||
rebuild_index_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
|
||||
stats_parser = subparsers.add_parser("stats", help="输出统计信息")
|
||||
stats_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
|
||||
lint_parser = subparsers.add_parser("lint", help="检查 Wiki 问题")
|
||||
lint_parser.add_argument("wiki_dir", help="Wiki 根目录")
|
||||
|
||||
args = parser.parse_args()
|
||||
|
||||
if args.command == "init":
|
||||
init_wiki(args.wiki_dir)
|
||||
return
|
||||
|
||||
if args.command == "log":
|
||||
append_log(args.wiki_dir, " ".join(args.message))
|
||||
return
|
||||
|
||||
if args.command == "add_entity":
|
||||
add_entity(args.wiki_dir, args.type, args.id, args.title)
|
||||
return
|
||||
|
||||
if args.command == "add_edge":
|
||||
add_edge(args.wiki_dir, args.from_id, args.to_id, args.edge_type, args.evidence)
|
||||
return
|
||||
|
||||
if args.command == "ingest_paper":
|
||||
ingest_paper(
|
||||
args.wiki_dir,
|
||||
arxiv_id=args.arxiv_id,
|
||||
title=args.title,
|
||||
authors=args.authors,
|
||||
year=args.year,
|
||||
venue=args.venue,
|
||||
thesis=args.thesis,
|
||||
)
|
||||
return
|
||||
|
||||
if args.command == "rebuild_query_pack":
|
||||
rebuild_query_pack(args.wiki_dir)
|
||||
return
|
||||
|
||||
if args.command == "rebuild_index":
|
||||
rebuild_index(args.wiki_dir)
|
||||
return
|
||||
|
||||
if args.command == "stats":
|
||||
print(get_stats(args.wiki_dir))
|
||||
return
|
||||
|
||||
if args.command == "lint":
|
||||
issues = lint_wiki(args.wiki_dir)
|
||||
print("\n".join(issues) if issues else "未发现问题")
|
||||
return
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
Reference in New Issue
Block a user