Create a background Marker parse job for a PDF.

Search citation-ready evidence spans with exact locator metadata.

Returns span-level AssetRef JSON that can be passed to table_cite.

Verify a span-level AssetRef against the persisted citation index.

Export citation-ready evidence spans as a verified bundle.

Each entry carries AssetRef, exact quote/hash, locator metadata, context, conservative CRAAP scaffold, optional verification status, and Foam anchor metadata. Use output_format="foam" for a Foam-compatible evidence pack. Pass wiki_root to write the pack and optionally update an index note.

Process PDF files and create Document Manifests.

ETL Pipeline:

1. Extract text (to markdown) and images

2. Generate structured Document Manifest

3. Index in LightRAG (if enabled)

Args: file_paths: List of absolute paths to PDF files async_mode: Kept for backwards compatibility. PDF ingestion is routed to a background job from the MCP tool layer to keep stdio clients responsive. use_marker: If True, use Marker for structured parsing (slower but more accurate). Produces blocks.json with bbox/coordinates for precise source tracking. Default False uses PyMuPDF (faster but less structured). marker_max_pages_per_chunk: When using Marker, split PDFs into fixed-size page chunks. Set 0 to use the safe automatic strategy. extract_figures: When using Marker, control whether image crops are extracted and saved. Disable this first for image-heavy textbooks to reduce memory pressure. page_ranges: 1-indexed inclusive page ranges applied to every input file, e.g. ["1-50", "120-160"].

Returns: Job ID for tracking progress with get_job_status.

Example: # Async (recommended for large files): ingest_documents(["/papers/study1.pdf"]) # Then check status: get_job_status("job_xxx")

# With Marker for precise source tracking:
ingest_documents(["/papers/textbook.pdf"], use_marker=True)

List all processed documents with summaries.

Returns: List of documents with doc_id, title, and asset counts

Fetch specific content from a document with precision.

Asset Types:

• "table": Returns table as markdown (with page number)

• "figure": Returns image as base64 with page number for verification

• "section": Returns section text content

• "full_text": Returns entire document as markdown

Args: doc_id: Document identifier asset_type: One of "table", "figure", "section", "full_text" asset_id: Asset ID from manifest (e.g., "tab_1", "fig_1_1", "sec_methods") Use "full" for full_text type max_size: Maximum image dimension (longest edge) for figures. - None (default): Use default 1024px - 0: Return original size (no resize) - N: Resize to Npx longest edge (e.g., 512, 768, 2048)

Returns: For figures: ImageContent that vision AI can directly analyze For others: TextContent in markdown format

Example: # Get Table 1 from document fetch_document_asset("abc123", "table", "tab_1")

# Get figure with default resize (1024px)
fetch_document_asset("abc123", "figure", "fig_2_1")

# Get figure at specific size (512px for smaller context)
fetch_document_asset("abc123", "figure", "fig_2_1", max_size=512)

# Get original image (no resize)
fetch_document_asset("abc123", "figure", "fig_2_1", max_size=0)

Consolidated PDF document entrypoint.

Existing document tools stay registered and keep their original contracts.

Consolidated document asset and section entrypoint.

Consolidated citation evidence entrypoint.

Consolidated document conversion entrypoint.

Dispatches to the existing conversion tools so each source family keeps its established output-path containment policy.

攝入 .docx / .doc 文件，轉換為 DFM (Docx-Flavored Markdown) 格式。

將 docx 解析為中間表示 (IR)，再轉換為可在 VS Code 中編輯的 DFM 格式。 支援複雜元素：合併表格、圖表、頁首頁尾、巨集、目錄等。 支援舊版 .doc 格式（自動透過 LibreOffice 轉換為 .docx）。

輸出目錄結構：

data/{doc_id}/
├── content.dfm     # 可編輯的 Markdown + YAML 標注
├── ir.json          # IR 快照（用於回寫）
├── original.docx    # 原始檔案備份
├── parts/           # 保留的 XML 零件
└── assets/          # 圖片和二進位資產

Args: file_path: .docx 或 .doc 檔案的絕對路徑

Returns: 攝入結果摘要（doc_id、區塊數量等）

取得 docx 文件的可編輯 DFM 內容。

若指定 block_id，只回傳該區塊的內容；否則回傳完整 DFM。

Args: doc_id: 文件 ID（由 ingest_docx 產生） block_id: 可選，特定區塊 ID（如 p001, t001, h001）

Returns: DFM 內容或特定區塊資訊

將編輯後的內容存回 .docx 檔案。

支援兩種模式：

• DFM 模式（預設）：傳入 dfm_content（.dfm 格式全文）

• MD 模式（from_md=True）：從磁碟讀取 content.md + format.yaml

回寫流程：

1. 解析 DFM/MD → 提取修改

2. 載入原始 IR

3. 合併修改（格式合併策略）

4. 重建 .docx

安全機制：若內容萎縮 > 50%，預設拒絕輸出（疑似資料遺失）。 使用 force=True 強制輸出。

若 track_changes=True，會將 DFM 中的文字修改以真正 Word Track Changes (w:del/w:ins) 寫回，供使用者在 Word 中逐項審查。

Args: doc_id: 文件 ID dfm_content: 編輯後的 DFM 全文（from_md=True 時可省略） output_path: 輸出路徑（預設為 data/{doc_id}/output.docx） from_md: 若為 True，從磁碟讀取 content.md + format.yaml 而非使用 dfm_content force: 若為 True，即使偵測到嚴重內容萎縮仍強制輸出 track_changes: 若為 True，以 Word Track Changes 寫入文字 diff revision_author: 產生追蹤修訂時使用的作者名稱

Returns: 儲存結果

Consolidated DOCX/DFM entrypoint.

The legacy DOCX tools remain registered and keep their original parameters and output formats. This wrapper only adds an operation-based facade.

Plan a DOCX table write-back before applying structural changes.

The current DFM bridge is safest for same-shape cell text updates. This plan separates safe cell updates from row/column/header structural changes so the caller can review risk before docx_table_from_context.

Consolidated DOCX table bridge entrypoint.

Existing docx_table_* tools remain available for clients that rely on their names or generated allow-lists.

Get the status of an ETL job.

Use this to check progress of document ingestion started with ingest_documents.

Args: job_id: Job ID returned from ingest_documents

Returns: Job status including progress, phase, and result (if completed)

Example: get_job_status("job_20251226_143000_abc12345")

List ETL jobs.

Args: active_only: If True, only show pending/processing jobs

Returns: List of jobs with status and progress

Consolidated job entrypoint over get/list/cancel.

Existing job tools stay registered for backwards compatibility.

Consolidated knowledge-graph entrypoint.

Existing consult/export tools remain registered and keep their separate contracts for clients that prefer explicit tool names.

Consolidated ETL profile entrypoint.

Existing profile tools stay registered for backwards compatibility.

Consolidated section navigation entrypoint.

📋 表格規劃工具：Schema 設計、模板查詢、模板建表。

Operations:

• schema: 根據問題自動規劃表格結構

• templates: 列出內建表格模板

• from_template: 從模板快速建立表格

Args: operation: 操作類型 question: [schema] 使用者問題 doc_ids: [schema] 相關文件 ID hints: [schema] 結構提示 template_name: [from_template] 模板名稱 title_override: [from_template] 自訂標題

Examples: plan_table("schema", question="比較三種藥物副作用") plan_table("templates") plan_table("from_template", template_name="drug_comparison")

📊 表格管理工具：建立、刪除、列表、預覽、渲染、Schema 演進。

Operations:

• create: 建立新表格

• delete: 刪除表格

• list: 列出所有表格

• preview: Markdown 預覽

• resume: 恢復工作（Token-efficient）

• render: 渲染為 Excel/Markdown

• add_column: 新增欄位

• remove_column: 移除欄位

• rename_column: 重新命名欄位

Args: operation: 操作類型 intent: [create] comparison / citation / summary title: [create] 表格標題 columns: [create] 欄位列表 [{"name":"Drug","type":"text"}] source_description: [create] 資料來源 table_id: [大部分操作] 表格 ID limit: [preview] 預覽行數 format: [render] 輸出格式 filename: [render] 檔案名稱 column_name: [add/remove/rename_column] 欄位名 column_type: [add_column] 欄位類型 required: [add_column] 是否必填 default_value: [add_column] 預設值 enum_values: [add_column] enum 可選值 new_name: [rename_column] 新欄位名

Examples: table_manage("create", intent="comparison", title="Drug Compare", columns=[{"name":"Drug","type":"text"}]) table_manage("list") table_manage("preview", table_id="tbl_xxx") table_manage("add_column", table_id="tbl_xxx", column_name="Route", column_type="enum", enum_values=["IV","IM"])

📝 表格資料操作：新增/取得/更新/刪除 列 & 儲存格。

Operations:

• add_rows: 批次新增資料列

• get_row: 取得單列（含引用）

• update_row: 整列更新

• delete_row: 刪除列

• get_cell: 取得單格（含引用）

• update_cell: 更新單格

• clear_cell: 清除單格

Args: operation: 操作類型 table_id: 表格 ID rows: [add_rows] 資料列列表 row: [update_row] 新的列資料 row_index: [get/update/delete_row, cell ops] 列索引 (0-based) column_name: [cell ops] 欄位名 value: [update_cell] 新的值

Examples: table_data("add_rows", "tbl_xxx", rows=[{"Drug":"A","Dose":1}]) table_data("get_row", "tbl_xxx", row_index=0) table_data("update_cell", "tbl_xxx", row_index=0, column_name="Drug", value="B")

📎 表格引用管理：為儲存格附加、查詢、移除來源引用。

引用是「平行附加層」，不改變表格資料結構。 每個引用用 AssetRef 指向具體來源（PDF section、URL、使用者輸入等）。

Operations:

• add: 新增引用到儲存格

• get: 查詢引用（cell / row / table）

• remove: 移除引用

• cell_history: 查看儲存格變更歷史

Args: operation: 操作類型 table_id: 表格 ID row_index: 列索引 (0-based)，get 時可省略取得全表引用 column_name: 欄位名，get 時可省略取得整列引用 refs: [add] 引用列表，每項為 AssetRef dict [{"source_type":"section","doc_id":"doc_xxx","asset_id":"sec_01","excerpt":"..."}] [{"source_type":"external","url":"https://doi.org/...","label":"Smith 2024"}] [{"source_type":"user_input","excerpt":"Patient reported"}] confidence: [add] Agent 信心度 0.0~1.0 notes: [add] 備註 ref_index: [remove] 移除特定引用索引（不指定則移除整個 cell 引用）

Examples: table_cite("add", "tbl_xxx", row_index=0, column_name="Drug", refs=[{"source_type":"section","doc_id":"doc_a","asset_id":"sec_01", "excerpt":"dose was 5mg"}], confidence=0.9) table_cite("get", "tbl_xxx") # 全表引用 table_cite("get", "tbl_xxx", row_index=0) # 全列引用 table_cite("cell_history", "tbl_xxx", row_index=0, column_name="Drug")

📜 表格歷史與統計：變更紀錄、Token 估算。

Operations:

• changes: 查看表格變更歷史

• tokens: 估算 Token 消耗

Args: operation: 操作類型 table_id: 表格 ID [changes, tokens] limit: [changes] 最近 N 筆 draft_id: [tokens] 草稿 ID（可選） text: [tokens] 任意文字（可選）

Examples: table_history("changes", "tbl_xxx") table_history("tokens", "tbl_xxx")

📝 草稿工作流：建立、更新、新增資料、恢復、提交。

草稿會自動保存，即使對話中斷也能恢復。 適合長時間的表格建立流程。

Operations:

• create: 建立草稿

• update: 更新草稿

• add_rows: 批次新增資料到草稿

• resume: 恢復草稿（Token-efficient）

• commit: 草稿轉正式表格

• list: 列出草稿

• delete: 刪除草稿

Args: operation: 操作類型 draft_id: [大部分操作] 草稿 ID title: [create/update] 標題 intent: [create/update] comparison / citation / summary proposed_columns: [create/update] 欄位定義 extraction_plan: [create/update] 抽取計畫 source_doc_ids: [create/update] 來源文件 ID source_sections: [create/update] 來源章節 ID notes: [create/update] 工作筆記 rows: [add_rows] 資料列

Examples: table_draft("create", title="Drug Comparison", intent="comparison", proposed_columns=[{"name":"Drug","type":"text"}]) table_draft("add_rows", draft_id="draft_xxx", rows=[{"Drug":"A"}]) table_draft("commit", draft_id="draft_xxx")

🔍 資料來源探索：跨文件搜尋可用於表格的資料來源。

整合 Section、Figure、Table、Knowledge Graph 多個資料庫， 返回統一的 AssetRef 格式結果，可直接用於 table_cite。

Args: query: 搜尋關鍵字 doc_ids: 限定搜尋的文件（不指定則搜尋所有文件） include_kg: 是否包含知識圖譜搜尋 limit: 每類來源的最大結果數

Returns: 發現的資料來源（AssetRef 格式）

Example: discover_sources("remimazolam dosing") discover_sources("drug comparison", doc_ids=["doc_abc"])