AstroResearch/migrations/00000000000000_init.sql

-- AstroResearch 完整数据库初始化迁移
-- 合并自 18 个开发期增量迁移文件，版本: 2026-06-25
--
-- 领域划分:
--   1. 文献与引用
--   2. 笔记与高亮
--   3. 批量同步
--   4. RAG 切片与天体目标
--   5. Agent 会话与消息
--   6. Agent 任务看板
--   7. Agent 审计日志
--   8. Agent 团队协作
--   9. 全文搜索 (FTS5)

-- ============================================================
-- 1. 文献与引用
-- ============================================================

CREATE TABLE IF NOT EXISTS papers (
    bibcode TEXT PRIMARY KEY,
    title TEXT NOT NULL,
    authors TEXT,          -- JSON array of author names
    year TEXT,
    pub TEXT,              -- journal / publisher
    keywords TEXT,         -- JSON array of keywords
    abstract TEXT,
    doi TEXT,
    arxiv_id TEXT,
    citation_count INTEGER DEFAULT 0,
    reference_count INTEGER DEFAULT 0,
    pdf_path TEXT,
    html_path TEXT,
    markdown_path TEXT,
    translation_path TEXT,
    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
    doctype TEXT
);

CREATE INDEX IF NOT EXISTS idx_papers_doi ON papers(doi);
CREATE INDEX IF NOT EXISTS idx_papers_arxiv_id ON papers(arxiv_id);

CREATE TABLE IF NOT EXISTS citations_references (
    source_bibcode TEXT NOT NULL,
    target_bibcode TEXT NOT NULL,
    PRIMARY KEY (source_bibcode, target_bibcode)
);

CREATE INDEX IF NOT EXISTS idx_citations_ref_source ON citations_references(source_bibcode);
CREATE INDEX IF NOT EXISTS idx_citations_ref_target ON citations_references(target_bibcode);

-- ============================================================
-- 2. 笔记与高亮
-- ============================================================

CREATE TABLE IF NOT EXISTS notes (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    bibcode TEXT NOT NULL,
    paragraph_index INTEGER NOT NULL,
    note_text TEXT NOT NULL DEFAULT '',
    highlight_color TEXT NOT NULL DEFAULT 'yellow',
    selected_text TEXT NOT NULL DEFAULT '',
    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
    FOREIGN KEY (bibcode) REFERENCES papers(bibcode) ON DELETE CASCADE
);

CREATE INDEX IF NOT EXISTS idx_notes_bibcode ON notes(bibcode);

-- ============================================================
-- 3. 批量同步
-- ============================================================

CREATE TABLE IF NOT EXISTS sync_queries (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    query TEXT NOT NULL,
    source TEXT NOT NULL,
    limit_count INTEGER NOT NULL,
    last_run DATETIME DEFAULT CURRENT_TIMESTAMP,
    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
    UNIQUE(query, source, limit_count)
);

-- ============================================================
-- 4. RAG 切片与天体目标
-- ============================================================

CREATE TABLE IF NOT EXISTS paper_chunks_content (
    rowid INTEGER PRIMARY KEY AUTOINCREMENT,
    bibcode TEXT,
    paragraph_index INTEGER,
    content TEXT,
    headings TEXT DEFAULT 'Document',
    section_index INTEGER DEFAULT 0,
    FOREIGN KEY(bibcode) REFERENCES papers(bibcode) ON DELETE CASCADE
);

CREATE TABLE IF NOT EXISTS paper_targets (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    bibcode TEXT,
    target_name TEXT,
    ra TEXT,
    dec TEXT,
    parallax REAL,
    spectral_type TEXT,
    v_magnitude REAL,
    aliases TEXT,
    created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
    otype TEXT,
    oname TEXT,
    pm_ra REAL,
    pm_de REAL,
    radial_velocity REAL,
    parallax_err REAL,
    photometry TEXT,
    FOREIGN KEY(bibcode) REFERENCES papers(bibcode) ON DELETE CASCADE,
    UNIQUE(bibcode, target_name)
);

CREATE INDEX IF NOT EXISTS idx_paper_targets_name ON paper_targets(target_name);

-- ============================================================
-- 5. Agent 会话与消息
-- ============================================================

CREATE TABLE IF NOT EXISTS agent_sessions (
    session_id TEXT PRIMARY KEY,
    title TEXT NOT NULL DEFAULT '',
    model TEXT NOT NULL DEFAULT '',
    turn_count INTEGER NOT NULL DEFAULT 0,
    last_error TEXT,
    summary TEXT,
    metadata TEXT,
    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
    updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
    deleted_at DATETIME,
    rewind_count INTEGER NOT NULL DEFAULT 0,
    parent_session_id TEXT REFERENCES agent_sessions(session_id),
    branch_metadata TEXT,
    mode TEXT NOT NULL DEFAULT 'default'
);

CREATE INDEX IF NOT EXISTS idx_agent_sessions_updated
    ON agent_sessions(updated_at) WHERE deleted_at IS NULL;

CREATE TABLE IF NOT EXISTS agent_messages (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    session_id TEXT NOT NULL,
    turn_index INTEGER NOT NULL DEFAULT 0,
    step_index INTEGER NOT NULL DEFAULT 0,
    role TEXT NOT NULL CHECK(role IN ('system', 'user', 'assistant', 'tool')),
    content TEXT NOT NULL DEFAULT '',
    thought TEXT,
    tool_calls TEXT,
    tool_call_id TEXT,
    token_count INTEGER NOT NULL DEFAULT 0,
    metadata TEXT,
    raw_json TEXT,
    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
    agent_name TEXT NOT NULL DEFAULT 'lead',
    active INTEGER NOT NULL DEFAULT 1,
    FOREIGN KEY (session_id) REFERENCES agent_sessions(session_id) ON DELETE CASCADE
);

CREATE INDEX IF NOT EXISTS idx_agent_messages_session ON agent_messages(session_id);
CREATE INDEX IF NOT EXISTS idx_agent_messages_turn ON agent_messages(session_id, turn_index);
CREATE INDEX IF NOT EXISTS idx_agent_messages_agent ON agent_messages(session_id, agent_name);
CREATE INDEX IF NOT EXISTS idx_agent_messages_active ON agent_messages(session_id, active);

-- ============================================================
-- 6. Agent 任务看板
-- ============================================================

CREATE TABLE IF NOT EXISTS agent_tasks (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    session_id TEXT NOT NULL,
    task_id TEXT NOT NULL,
    content TEXT NOT NULL DEFAULT '',
    status TEXT NOT NULL DEFAULT 'pending'
        CHECK(status IN ('pending', 'in_progress', 'completed')),
    blocked_by TEXT NOT NULL DEFAULT '[]',
    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
    updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
    owner TEXT NOT NULL DEFAULT '',
    FOREIGN KEY (session_id) REFERENCES agent_sessions(session_id) ON DELETE CASCADE
);

CREATE INDEX IF NOT EXISTS idx_agent_tasks_session ON agent_tasks(session_id);
CREATE INDEX IF NOT EXISTS idx_agent_tasks_status ON agent_tasks(session_id, status);
CREATE UNIQUE INDEX IF NOT EXISTS idx_agent_tasks_session_task ON agent_tasks(session_id, task_id);

-- ============================================================
-- 7. Agent 审计日志
-- ============================================================

CREATE TABLE IF NOT EXISTS agent_audit_log (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    session_id TEXT NOT NULL,
    step INTEGER NOT NULL DEFAULT 0,
    tool_name TEXT,
    status TEXT NOT NULL CHECK(status IN ('OK', 'FAIL', 'SESSION_STOP')),
    elapsed_ms INTEGER NOT NULL DEFAULT 0,
    output_preview TEXT,
    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
    agent_name TEXT NOT NULL DEFAULT 'lead',
    FOREIGN KEY (session_id) REFERENCES agent_sessions(session_id) ON DELETE CASCADE
);

CREATE INDEX IF NOT EXISTS idx_audit_log_session ON agent_audit_log(session_id);
CREATE INDEX IF NOT EXISTS idx_audit_log_created ON agent_audit_log(created_at);

-- ============================================================
-- 8. Agent 团队协作
-- ============================================================

CREATE TABLE IF NOT EXISTS agent_team_members (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    session_id TEXT NOT NULL,
    agent_name TEXT NOT NULL,
    agent_role TEXT NOT NULL,
    status TEXT NOT NULL DEFAULT 'active'
        CHECK(status IN ('spawning', 'active', 'idle', 'shutdown')),
    created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
    updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
    FOREIGN KEY (session_id) REFERENCES agent_sessions(session_id) ON DELETE CASCADE,
    UNIQUE(session_id, agent_name)
);

CREATE INDEX IF NOT EXISTS idx_team_members_session ON agent_team_members(session_id);
CREATE INDEX IF NOT EXISTS idx_team_members_status ON agent_team_members(session_id, status);

-- ============================================================
-- 9. 全文搜索 (FTS5)
-- ============================================================

-- 文献全文搜索
CREATE VIRTUAL TABLE IF NOT EXISTS papers_fts USING fts5(
    title,
    authors,
    keywords,
    abstract,
    pub,
    content='papers',
    content_rowid='rowid'
);

CREATE TRIGGER IF NOT EXISTS papers_fts_insert AFTER INSERT ON papers
BEGIN
    INSERT INTO papers_fts(rowid, title, authors, keywords, abstract, pub)
    VALUES (NEW.rowid, NEW.title, NEW.authors, NEW.keywords, NEW.abstract, NEW.pub);
END;

CREATE TRIGGER IF NOT EXISTS papers_fts_update AFTER UPDATE ON papers
BEGIN
    UPDATE papers_fts SET
        title = NEW.title,
        authors = NEW.authors,
        keywords = NEW.keywords,
        abstract = NEW.abstract,
        pub = NEW.pub
    WHERE rowid = OLD.rowid;
END;

CREATE TRIGGER IF NOT EXISTS papers_fts_delete AFTER DELETE ON papers
BEGIN
    DELETE FROM papers_fts WHERE rowid = OLD.rowid;
END;

-- Agent 会话全文搜索
CREATE VIRTUAL TABLE IF NOT EXISTS agent_sessions_fts USING fts5(
    session_id,
    title,
    summary,
    metadata,
    content='agent_sessions',
    content_rowid='rowid'
);

CREATE TRIGGER IF NOT EXISTS sessions_fts_insert AFTER INSERT ON agent_sessions
BEGIN
    INSERT INTO agent_sessions_fts(rowid, session_id, title, summary, metadata)
    VALUES (NEW.rowid, NEW.session_id, NEW.title, NEW.summary, NEW.metadata);
END;

CREATE TRIGGER IF NOT EXISTS sessions_fts_update AFTER UPDATE ON agent_sessions
BEGIN
    UPDATE agent_sessions_fts SET
        session_id = NEW.session_id,
        title = NEW.title,
        summary = NEW.summary,
        metadata = NEW.metadata
    WHERE rowid = OLD.rowid;
END;

CREATE TRIGGER IF NOT EXISTS sessions_fts_delete AFTER DELETE ON agent_sessions
BEGIN
    DELETE FROM agent_sessions_fts WHERE rowid = OLD.rowid;
END;

-- Agent 消息全文搜索
CREATE VIRTUAL TABLE IF NOT EXISTS agent_messages_fts USING fts5(
    session_id,
    role,
    content,
    thought,
    tool_calls,
    content='agent_messages',
    content_rowid='rowid'
);

CREATE TRIGGER IF NOT EXISTS messages_fts_insert AFTER INSERT ON agent_messages
BEGIN
    INSERT INTO agent_messages_fts(rowid, session_id, role, content, thought, tool_calls)
    VALUES (NEW.rowid, NEW.session_id, NEW.role, NEW.content, NEW.thought, NEW.tool_calls);
END;

CREATE TRIGGER IF NOT EXISTS messages_fts_update AFTER UPDATE ON agent_messages
BEGIN
    UPDATE agent_messages_fts SET
        session_id = NEW.session_id,
        role = NEW.role,
        content = NEW.content,
        thought = NEW.thought,
        tool_calls = NEW.tool_calls
    WHERE rowid = OLD.rowid;
END;

CREATE TRIGGER IF NOT EXISTS messages_fts_delete AFTER DELETE ON agent_messages
BEGIN
    DELETE FROM agent_messages_fts WHERE rowid = OLD.rowid;
END;

-- 段落切片全文搜索（配合 vec_paper_chunks 向量检索做混合搜索）
CREATE VIRTUAL TABLE IF NOT EXISTS paper_chunks_fts USING fts5(
    content,
    content='paper_chunks_content',
    content_rowid='rowid'
);

CREATE TRIGGER IF NOT EXISTS chunks_fts_insert AFTER INSERT ON paper_chunks_content
BEGIN
    INSERT INTO paper_chunks_fts(rowid, content) VALUES (NEW.rowid, NEW.content);
END;

CREATE TRIGGER IF NOT EXISTS chunks_fts_update AFTER UPDATE ON paper_chunks_content
BEGIN
    UPDATE paper_chunks_fts SET content = NEW.content WHERE rowid = OLD.rowid;
END;

CREATE TRIGGER IF NOT EXISTS chunks_fts_delete AFTER DELETE ON paper_chunks_content
BEGIN
    DELETE FROM paper_chunks_fts WHERE rowid = OLD.rowid;
END;

-- ============================================================
-- 注意: vec_paper_chunks 向量虚拟表由 main.rs 在运行时动态创建，
-- 维度由 EMBEDDING_DIM 环境变量控制 (默认 1536)。
-- ============================================================