fix(aqua): DOI pairing decoder and MD extraction regexes
- MD: allow parens in DOI (old-style 10.1016/0006-3207(93)90088-i was truncated at ")"); prioritize DOI-line doi.org URL; strip trailing paren only when unbalanced - PDF: require 10. at segment start (fixes year artifacts like 2010.0170 masquerading as DOI); keep full candidate on no-hit instead of shortest prefix (10.1002/pd.71 was truncated to 10.1002); absorb paren segments (10.1061/(asce)wr.1943-...); stop at DOI未知 marker keeping registrant prefix; accept 10_ segment start variant - undecodable PDFs: 71 -> 54; manifest DOI values now complete - pairing count unchanged (3404) = true DOI overlap of the two corpora Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Claude Fable 5
@@ -29,8 +29,9 @@ from concurrent.futures import ThreadPoolExecutor
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from datetime import datetime, timezone
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from pathlib import Path
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MD_URL_RE = re.compile(r"https?://doi\.org/([^\s\)\]）]+)")
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MD_DOI_RE = re.compile(r"DOI：([^\s\]（(]+)")
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MD_DOI_LINE_URL_RE = re.compile(r"DOI[：:][^\n]*https?://doi\.org/([^\s\]）]+)")
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MD_URL_RE = re.compile(r"https?://doi\.org/([^\s\]）]+)")
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MD_DOI_RE = re.compile(r"DOI[：:]\s*([^\s\]（]+)")
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MD_TITLE_RE = re.compile(r"^#\s+(.+)$")
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MD_YEAR_RE = re.compile(r"年份[：:]\s*(\d{4})")
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DIGITS_RE = re.compile(r"^\d{4,9}$")
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@@ -43,13 +44,21 @@ CSV_HEADER = [
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def norm_doi(d: str) -> str:
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"""归一化:去首尾空白、小写、去尾部标点;内部 _ 不换 /(MD 卡里已是斜杠形态)。"""
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return d.strip().lower().rstrip(".,;)]")
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"""归一化:去首尾空白、小写、去尾部标点(含中文标点);尾部 ")" 仅在括号
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不配对时剥掉(markdown 链接闭合符假象),保证旧式带括号 DOI 完整;
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内部 _ 不换 /(MD 卡里已是斜杠形态)。"""
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s = d.strip().lower().rstrip(".,;]。，；、")
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if s.endswith(")") and s.count("(") < s.count(")"):
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s = s[:-1]
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return s
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def extract_md_doi(text: str) -> str:
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"""两种 DOI 形态均尝试,取首个非空。"""
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m = MD_URL_RE.search(text)
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"""DOI 提取:优先「DOI:」标签行内的 doi.org URL;其次任意 doi.org URL;
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最后裸「DOI:」文本。取首个非空。"""
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m = MD_DOI_LINE_URL_RE.search(text)
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if not m:
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m = MD_URL_RE.search(text)
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if not m:
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m = MD_DOI_RE.search(text)
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return m.group(1).strip() if m else ""
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@@ -69,15 +78,28 @@ def md_metadata(text: str) -> tuple[str, str]:
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def decode_pdf_doi(filename: str, md_norms) -> tuple[str, str]:
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"""从 PDF 文件名解码 DOI,返回 (doi_norm, doi_norm) 或 ("", "")。
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算法:找最后一个 10. 出现位置;此后按下划线切段;首段必须为 4-9 位数字
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(即「10 + 4-9 位数字」);从第 2 段起,段开头为字母数字的并入 DOI;
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末段恰好为 8 位十六进制(其后只剩 .pdf)则停止并入。歧义消解:对每处
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合法的 10. 位置生成「前缀固定、尾部可延伸」的候选集合,优先取下划线
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换成斜杠后能命中 md_norms 的最长解释;仍不中的取最短解释。
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文件名 DOI 形态: 年份_标题_10.xxx_xxx(下划线化)_8位hex.pdf
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算法:
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- 起始点: `10.` 必须位于段首(前一个字符是 `_` 或文件名开头),排除
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标题/年份中的 `2010.xxx` 假象;
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- 按下划线切段;首段必须为 4-9 位数字(「10 + 4-9 位数字」);
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- 从第 2 段起并入 DOI:段开头为 ASCII 字母数字的并入;段开头为 "(" 且
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当前已并入部分不以 ")" 结尾时并入(DOI 后缀可含括号,如
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10.1061_(asce)wr.1943-5452.0000194);遇 "DOI未知" 段停止(文件名
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标注 DOI 后缀未知,只有注册机构前缀,如 10_1016_j_aquaculture);
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- 末段为 8 位十六进制(其后只剩 .pdf)时停止;
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- 遇 "DOI未知" 段:注册机构前缀(如 10.1016)仍生成候选后停止
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(文件名标注 DOI 后缀未知);
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- 歧义消解:候选全集按「能命中 md_norms 的最长解释」优先;无命中时取
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每个合法起始点的完整候选中最长者(DOI 本身可含下划线,如
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10.58782_flmnh.flvk7707,完整候选才是正确 DOI)。
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"""
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stem = filename[:-4] if filename.lower().endswith(".pdf") else filename
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candidates: list[str] = []
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for pos in reversed([m.start() for m in re.finditer(r"10\.", stem)]):
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for m in re.finditer(r"10[._]", stem):
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pos = m.start()
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if pos > 0 and stem[pos - 1] != "_":
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continue # 10. 不在段首:年份/标题中的假象
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segs = stem[pos + 3:].split("_")
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if not segs or not DIGITS_RE.match(segs[0]):
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continue # 首段不满足「10 + 4-9 位数字」,该 10. 位置无效
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@@ -86,8 +108,15 @@ def decode_pdf_doi(filename: str, md_norms) -> tuple[str, str]:
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seg = segs[i]
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if i == len(segs) - 1 and HEX8_RE.match(seg):
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break # 8 位十六进制哈希(其后只剩 .pdf),停止并入
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if seg and seg[0].isalnum():
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if seg == "DOI未知":
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candidates.append(norm_doi("10." + "/".join(parts)))
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break # 文件名标注 DOI 后缀未知,仅保留注册机构前缀
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if not seg:
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continue # 空段(如双下划线分隔):跳过
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if seg[0].isascii() and seg[0].isalnum():
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parts.append(seg)
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elif seg.startswith("(") and not "".join(parts).endswith(")"):
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parts.append(seg) # DOI 后缀括号段,如 (asce)wr.1943-...
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else:
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break
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for k in range(1, len(parts) + 1):
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@@ -95,7 +124,7 @@ def decode_pdf_doi(filename: str, md_norms) -> tuple[str, str]:
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if not candidates:
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return "", ""
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hits = [c for c in candidates if c in md_norms]
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chosen = max(hits, key=len) if hits else min(candidates, key=len)
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chosen = max(hits, key=len) if hits else max(candidates, key=len)
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return chosen, chosen
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@@ -108,11 +137,22 @@ def sha256_of(path: Path) -> str:
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def pdf_title_year(stem: str) -> tuple[str, str]:
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"""从文件名提取年份(首段 4 位数字)与标题(年份后、DOI 起始前)。"""
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"""从文件名提取年份(首段 4 位数字)与标题(年份后、DOI 起始前)。
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DOI 起始位置用「段首 10. + 首段 4-9 位数字」判据定位,与 decode 一致,
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避免标题/年份里的 2010. 假象导致标题截断。
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"""
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parts = stem.split("_")
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year = parts[0] if len(parts) > 1 and re.fullmatch(r"\d{4}", parts[0]) else ""
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idx = -1
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for m in re.finditer(r"10\.", stem):
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if m.start() > 0 and stem[m.start() - 1] != "_":
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continue
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segs = stem[m.start() + 3:].split("_")
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if segs and DIGITS_RE.match(segs[0]):
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idx = m.start()
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break
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title = ""
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idx = stem.rfind("10.")
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if idx > 0:
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start = len(parts[0]) + 1 if year else 0
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title = stem[start:idx].strip("_").replace("_", " ").strip()
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