check-your-advisor 0.2.0__py3-none-any.whl

check_your_advisor/__init__.py

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+"""
+check-your-advisor — author-disambiguated PubMed harvesting and reference verification.
+
+Two entry points over one shared HTTP and normalisation layer:
+
+  fetch/download  Search PubMed, keep only the target researcher's papers via
+                  ORCID + affiliation + email verification, race 8 open-access
+                  sources for the PDF, then verify the downloaded file really
+                  is the requested paper.
+
+  verify          Check a bibliography against CrossRef and PubMed, including
+                  bidirectional DOI <-> PMID resolution.
+"""
+
+__version__ = "0.3.1"
+
+__all__ = ["__version__"]

check_your_advisor/__main__.py

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+"""Allow `python -m check_your_advisor ...`."""
+
+import sys
+
+from .cli import main
+
+if __name__ == "__main__":
+    sys.exit(main() or 0)

check_your_advisor/cache.py

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+"""
+缓存模块（SQLite）
+==================
+替代原代码中仅通过 os.path.exists(pdf_path) 检查的简陋缓存。
+
+改进：
+- 记录每篇论文的元数据（DOI、PMID、下载状态、来源、时间）
+- 支持过期清理
+- 支持查询命中/未命中统计
+"""
+
+import logging
+import sqlite3
+import threading
+import time
+from pathlib import Path
+
+logger = logging.getLogger("check_your_advisor.cache")
+
+CREATE_TABLE_SQL = """
+CREATE TABLE IF NOT EXISTS paper_cache (
+    doi TEXT,
+    pmid TEXT,
+    title TEXT,
+    pdf_path TEXT,
+    source TEXT,
+    status TEXT DEFAULT 'pending',
+    file_size_bytes INTEGER DEFAULT 0,
+    created_at REAL,
+    updated_at REAL,
+    PRIMARY KEY (pmid)
+);
+CREATE INDEX IF NOT EXISTS idx_doi ON paper_cache(doi);
+CREATE INDEX IF NOT EXISTS idx_status ON paper_cache(status);
+"""
+
+
+class PaperCache:
+    def __init__(self, db_path: str = "paper_cache.db"):
+        self.db_path = db_path
+        db_parent = Path(db_path).parent
+        if str(db_parent) not in {"", "."}:
+            db_parent.mkdir(parents=True, exist_ok=True)
+        # check_same_thread=False 允许跨线程使用；加锁保证串行访问
+        self._conn = sqlite3.connect(db_path, check_same_thread=False)
+        self._conn.row_factory = sqlite3.Row
+        self._lock = threading.Lock()
+        self._init_db()
+        self.hits = 0
+        self.misses = 0
+
+    def _init_db(self):
+        with self._lock:
+            cursor = self._conn.cursor()
+            cursor.executescript(CREATE_TABLE_SQL)
+            self._conn.commit()
+
+    def lookup(self, pmid: str) -> dict | None:
+        """查询缓存。返回 dict 或 None。"""
+        with self._lock:
+            cursor = self._conn.cursor()
+            cursor.execute("SELECT * FROM paper_cache WHERE pmid = ?", (pmid,))
+            row = cursor.fetchone()
+
+        if row and row["status"] == "downloaded" and row["pdf_path"]:
+            if Path(row["pdf_path"]).exists():
+                self.hits += 1
+                logger.debug("  缓存命中: PMID %s", pmid)
+                return dict(row)
+            else:
+                logger.warning("  缓存记录存在但文件丢失: %s", row["pdf_path"])
+                self.update(pmid, status="pending", pdf_path="")
+        self.misses += 1
+        return None
+
+    def update(self, pmid: str, **kwargs):
+        """更新或插入缓存记录"""
+        now = time.time()
+        with self._lock:
+            existing = self._conn.execute(
+                "SELECT pmid FROM paper_cache WHERE pmid = ?", (pmid,)
+            ).fetchone()
+
+            if existing:
+                sets = ", ".join(f"{k} = ?" for k in kwargs)
+                vals = list(kwargs.values()) + [now, pmid]
+                self._conn.execute(
+                    f"UPDATE paper_cache SET {sets}, updated_at = ? WHERE pmid = ?",
+                    vals,
+                )
+            else:
+                kwargs["pmid"] = pmid
+                kwargs["created_at"] = now
+                kwargs["updated_at"] = now
+                cols = ", ".join(kwargs.keys())
+                placeholders = ", ".join("?" for _ in kwargs)
+                self._conn.execute(
+                    f"INSERT INTO paper_cache ({cols}) VALUES ({placeholders})",
+                    list(kwargs.values()),
+                )
+            self._conn.commit()
+
+    def mark_downloaded(
+        self,
+        pmid: str,
+        pdf_path: str,
+        source: str,
+        file_size: int = 0,
+        doi: str = "",
+        title: str = "",
+    ):
+        self.update(
+            pmid,
+            doi=doi,
+            title=title,
+            status="downloaded",
+            pdf_path=pdf_path,
+            source=source,
+            file_size_bytes=file_size,
+        )
+
+    def mark_failed(self, pmid: str, doi: str = "", title: str = ""):
+        self.update(pmid, doi=doi, title=title, status="all_sources_failed")
+
+    def cleanup_expired(self, max_age_days: int = 90) -> int:
+        """清理超过指定天数的失败记录（下载成功的不清理）。返回删除条数。"""
+        cutoff = time.time() - max_age_days * 86400
+        with self._lock:
+            cursor = self._conn.cursor()
+            cursor.execute(
+                "DELETE FROM paper_cache WHERE status = 'all_sources_failed' AND updated_at < ?",
+                (cutoff,),
+            )
+            deleted = cursor.rowcount
+            self._conn.commit()
+        if deleted:
+            logger.info("  清理了 %d 条过期失败记录", deleted)
+        return deleted
+
+    def stats(self) -> dict:
+        with self._lock:
+            cursor = self._conn.cursor()
+            total = cursor.execute("SELECT COUNT(*) FROM paper_cache").fetchone()[0]
+            downloaded = cursor.execute(
+                "SELECT COUNT(*) FROM paper_cache WHERE status = 'downloaded'"
+            ).fetchone()[0]
+            failed = cursor.execute(
+                "SELECT COUNT(*) FROM paper_cache WHERE status = 'all_sources_failed'"
+            ).fetchone()[0]
+        return {
+            "total": total,
+            "downloaded": downloaded,
+            "failed": failed,
+            "session_hits": self.hits,
+            "session_misses": self.misses,
+        }
+
+    def close(self):
+        with self._lock:
+            self._conn.close()