endnote-cli

---

name: endnote-cli description: Interact with EndNote .enl libraries using the endnote-cli tool to read, search, export, and safely update references, groups, color tags, and attachments via direct SQLite access. Also handles batch-filling the translated_title field with user-specified translations, and auto-tagging references with their journal's CAS zone. Use when the user asks to work with EndNote libraries, .enl files, export BibTeX/RIS/CSV/XML/JSON, search or list references, rename PDFs, manage groups or color tags, write notes/keywords/ratings back, translate paper titles, fill translated_title / Translated Title, tag by journal zone / 分区, or start the EndNote MCP server. Trigger signals include: "EndNote", ".enl", "文献库", "参考文献管理", "Clarivate", "sdb.eni", "翻译标题", "Translated Title", "translated_title", "分区标签", "期刊分区", "新锐分区", "CAS 分区", "预印本标签".

EndNote CLI

Use the endnote-cli command to interact with EndNote .enl libraries via direct SQLite access. Works without EndNote running for reads; EndNote must be closed for writes (it locks the database files).

Command reference

Run endnote-cli --help or endnote-cli <command> --help for up-to-date usage. Full docs: https://github.com/TCMzhoutong/endnote-cli

Command	Subcommands	Purpose
app	ping, info	Check connectivity and library summary
item	list, get, count	List, inspect, and count references
group	list, tree, show	Browse GroupSet → Group hierarchy
tag	list, show	Browse color tags and tagged references
search	quick, advanced	Full-text and multi-field boolean search
export	bibtex, ris, json, csv, xml, pdf, citation	Export references
write	note, keyword, status, rating, label, tag, field, attach, clear, rename-pdf	Update safe fields, manage attachments
library	list, info, set-default, set-dir	Manage multiple .enl libraries
mcp	(none)	Start MCP server for Claude Code / Desktop

First-time setup

Before other commands work, point the CLI at a library directory and pick a default:

endnote-cli library set-dir "<path/to/your/EndNote/directory>"
endnote-cli library set-default MyLibrary.enl
endnote-cli app ping     # verify
endnote-cli app info     # library stats

Common patterns

# Search
endnote-cli search quick "knowledge graph"
endnote-cli search advanced -f title -o contains -v "RAG" -f year -o gte -v "2025" --bool and

# Browse
endnote-cli group tree
endnote-cli tag list
endnote-cli item list --limit 20

# Export
endnote-cli export bibtex --group "RAG" -o rag_papers.bib
endnote-cli export xml --group-set "Medical Cases"
endnote-cli export citation 296 --style apa

# Write (EndNote must be CLOSED)
endnote-cli write note 296 my_review.md
endnote-cli write keyword 296 "RAG,LLM,survey"
endnote-cli write tag 296 6                  # color tag ID
endnote-cli write rename-pdf --all --dry-run # always dry-run first
endnote-cli write rename-pdf --all

Safety rules

• Always dry-run destructive writes first (--dry-run on rename-pdf, bulk write ops).
• Close EndNote before any write subcommand — the app locks .enl and sdb.eni; writes while open corrupt state or silently fail.
• Never INSERT into refs — the table uses triggers calling EN_MAKE_SORT_KEY, a custom SQLite function only present inside the EndNote runtime. Only UPDATE of safe fields is supported; the CLI enforces this.
• Safe write fields: research_notes, notes, keywords, read_status, rating, label, caption, custom_1..custom_7, translated_title, translated_author. Other fields are not exposed by write.
• Dual-database sync: writes update both MyLibrary.enl and MyLibrary.Data/sdb/sdb.eni. The CLI handles this — do not hand-edit one side.
• Tag colors: only 7 presets render correctly (red, orange, yellow, green, blue, purple, gray). Custom hex renders as gray in the UI.

Auto-tag by journal zone → write journal-tags

endnote-cli write journal-tags assigns color tags based on each ref's journal zone. Tags applied per ref:

• 新锐N区 from XR2026 (New-Elite 2026) — red/orange/green/gray for N=1/2/3/4
• N区25年 from FQBJCR2025 (CAS upgraded 2025) — same colors
• 预印本 (gray) if secondary_title contains "arxiv"

Tags are created on first use (color baked in). Existing tags with matching names are reused, so subsequent runs are idempotent. --group <name> scopes to a group. --dry-run previews. --refresh strips and recomputes all zone/preprint tags (use when source data is refreshed via --refresh-data). Chinese-only journals and conference proceedings won't match (data covers SCI-scope only); that's expected.

Data source: github.com/hitfyd/ShowJCR, cached under ~/.endnote-cli/jcr_cache/.

Translate titles → translated_title

For refs whose title is in one language and translated_title is empty, translate the title and write it via EndnoteWriter.write_field(id, "translated_title", value).

• Ask the user for target language and domain up front if not obvious.
• Detect "foreign" titles by character-set heuristic on title; the language column is unreliable (often blank).
• Dry-run a preview list before writing. At write time, re-check the row's translated_title is still empty.
• After the real run, confirm both .enl and sdb.eni counts match and have the user spot-check in EndNote.

Multi-library

endnote-cli library list
endnote-cli library set-default OtherLibrary.enl
# or pass --library per-command if the CLI supports it (check --help)

MCP server

To expose EndNote capabilities to Claude Desktop or Claude Code as MCP tools:

{
  "mcpServers": {
    "endnote": { "command": "endnote-cli", "args": ["mcp"] }
  }
}