Initial commit

2026-07-30 10:51:43 +09:00
commit 9e3b3ddc29
23 changed files with 4705 additions and 0 deletions
@@ -0,0 +1,161 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import argparse
+import sqlite3
+from pathlib import Path
+
+from common import CONFIG
+
+CATEGORIES = CONFIG.domain.categories
+
+SCHEMA = """
+PRAGMA foreign_keys = ON;
+
+CREATE TABLE IF NOT EXISTS categories (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    name TEXT NOT NULL UNIQUE,
+    description TEXT
+);
+
+CREATE TABLE IF NOT EXISTS papers (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    doi TEXT,
+    title TEXT NOT NULL,
+    title_normalized TEXT NOT NULL,
+    first_author TEXT,
+    year INTEGER,
+    journal TEXT,
+    volume TEXT,
+    issue TEXT,
+    pages TEXT,
+    publisher TEXT,
+    article_type TEXT,
+    language TEXT,
+    abstract TEXT,
+    summary_ja TEXT,
+    relevance INTEGER NOT NULL DEFAULT 0 CHECK (relevance BETWEEN 0 AND 5),
+    priority TEXT NOT NULL DEFAULT 'D' CHECK (priority IN ('A','B','C','D')),
+    review_status TEXT NOT NULL DEFAULT 'unreviewed',
+    category_id INTEGER,
+    pdf_path TEXT,
+    file_size INTEGER,
+    file_mtime TEXT,
+    file_sha256 TEXT,
+    source TEXT,
+    landing_url TEXT,
+    pdf_url TEXT,
+    url_source TEXT,
+    access_status TEXT,
+    url_checked_at TEXT,
+    created_at TEXT NOT NULL,
+    updated_at TEXT NOT NULL,
+    checked_at TEXT,
+    notes TEXT,
+    FOREIGN KEY (category_id) REFERENCES categories(id)
+);
+
+CREATE TABLE IF NOT EXISTS authors (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    name TEXT NOT NULL,
+    name_normalized TEXT NOT NULL,
+    orcid TEXT,
+    affiliation TEXT
+);
+
+CREATE TABLE IF NOT EXISTS paper_authors (
+    paper_id INTEGER NOT NULL,
+    author_id INTEGER NOT NULL,
+    author_order INTEGER NOT NULL,
+    is_corresponding INTEGER NOT NULL DEFAULT 0 CHECK (is_corresponding IN (0,1)),
+    PRIMARY KEY (paper_id, author_order),
+    UNIQUE (paper_id, author_id),
+    FOREIGN KEY (paper_id) REFERENCES papers(id) ON DELETE CASCADE,
+    FOREIGN KEY (author_id) REFERENCES authors(id) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS keywords (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    name TEXT NOT NULL,
+    name_normalized TEXT NOT NULL UNIQUE
+);
+
+CREATE TABLE IF NOT EXISTS paper_keywords (
+    paper_id INTEGER NOT NULL,
+    keyword_id INTEGER NOT NULL,
+    PRIMARY KEY (paper_id, keyword_id),
+    FOREIGN KEY (paper_id) REFERENCES papers(id) ON DELETE CASCADE,
+    FOREIGN KEY (keyword_id) REFERENCES keywords(id) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS processing_log (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    pdf_path TEXT,
+    paper_id INTEGER,
+    status TEXT NOT NULL CHECK (status IN ('registered','updated','duplicate','skipped','error')),
+    message TEXT,
+    processed_at TEXT NOT NULL,
+    FOREIGN KEY (paper_id) REFERENCES papers(id) ON DELETE SET NULL
+);
+
+CREATE UNIQUE INDEX IF NOT EXISTS idx_papers_doi
+ON papers(doi) WHERE doi IS NOT NULL AND doi <> '';
+
+CREATE UNIQUE INDEX IF NOT EXISTS idx_papers_sha256
+ON papers(file_sha256) WHERE file_sha256 IS NOT NULL AND file_sha256 <> '';
+
+CREATE INDEX IF NOT EXISTS idx_papers_title_normalized ON papers(title_normalized);
+CREATE INDEX IF NOT EXISTS idx_papers_year ON papers(year);
+CREATE INDEX IF NOT EXISTS idx_papers_relevance ON papers(relevance);
+CREATE INDEX IF NOT EXISTS idx_papers_priority ON papers(priority);
+CREATE INDEX IF NOT EXISTS idx_papers_category_id ON papers(category_id);
+CREATE INDEX IF NOT EXISTS idx_authors_name_normalized ON authors(name_normalized);
+CREATE INDEX IF NOT EXISTS idx_keywords_name_normalized ON keywords(name_normalized);
+"""
+
+URL_COLUMNS = {
+    "landing_url": "TEXT",
+    "pdf_url": "TEXT",
+    "url_source": "TEXT",
+    "access_status": "TEXT",
+    "url_checked_at": "TEXT",
+}
+
+
+def ensure_url_columns(con: sqlite3.Connection) -> None:
+    columns = {
+        row[1] for row in con.execute("PRAGMA table_info(papers)")
+    }
+    for name, column_type in URL_COLUMNS.items():
+        if name not in columns:
+            con.execute(
+                f'ALTER TABLE papers ADD COLUMN "{name}" {column_type}'
+            )
+
+
+def initialize(path: Path) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    with sqlite3.connect(path) as con:
+        con.executescript(SCHEMA)
+        ensure_url_columns(con)
+        con.executemany(
+            "INSERT OR IGNORE INTO categories(name, description) VALUES (?, NULL)",
+            [(name,) for name in CATEGORIES],
+        )
+        result = con.execute("PRAGMA integrity_check").fetchone()[0]
+        if result != "ok":
+            raise RuntimeError(result)
+
+def main() -> int:
+    p = argparse.ArgumentParser()
+    p.add_argument(
+        "database", nargs="?", default=str(CONFIG.path.database)
+    )
+    args = p.parse_args()
+    initialize(Path(args.database))
+    print(f"Initialized: {args.database}")
+    print("integrity_check: ok")
+    return 0
+
+if __name__ == "__main__":
+    raise SystemExit(main())