skill-endnote-research

name	skill-endnote-research
description	Use when the user gives a research idea and wants Codex to analyze possible research directions, search the local EndNote litlib index, create a literature list, copy matching PDFs, and generate a literature-review folder with a report. This skill is designed for the local EndNote workspace that contains litlib/index/papers.jsonl and My EndNote Library-Saved(1).Data/PDF.

Skill EndNote Research

Use this skill for Chinese or English research-idea prompts such as:

• "我要研究 流体与震群活动的关系。"
• "帮我从本地 EndNote 库找这个想法相关的文献并整理"
• "根据这个研究问题生成文献梳理文件夹"

Workflow

1. Identify two paths and keep them separate.
   • Output path: use the directory where the user invoked Codex as the project output location. Create 文献梳理/ there by default.
   • EndNote/litlib workspace: use the directory that contains litlib/index/papers.jsonl; for this user's local library, the usual path is /mnt/d/YIN/BaiduSyncdisk/endnote_file.
   • If the current directory is not the EndNote workspace, still keep output in the current project directory and pass the EndNote library path via --workspace.
2. Analyze the idea before searching.
   • State the likely research directions and why they matter.
   • For earthquake/seismology ideas, consider directions such as earthquake swarms, repeated earthquakes, induced seismicity, fluid triggering, fault activation, catalog statistics, migration patterns, focal mechanisms, stress transfer, geothermal/reservoir/wastewater contexts, and hazard implications.
3. Translate Chinese research ideas into English before searching.
   • If the user prompt is Chinese, write an English translation first. Example: 我要研究 流体与震群活动的关系。 -> I want to study the relationship between fluids and earthquake swarm activity.
   • Search both Chinese-language and English-language literature in the local library. Do not treat a Chinese prompt as Chinese-only retrieval.
4. Generate multiple Chinese and English search queries.
   • Include the original Chinese wording, the English translation, location names in Chinese and English, domain synonyms, mechanism terms, and method terms.
   • For the fluid-swarm example, include queries such as 流体 震群 活动 关系, fluid earthquake swarm activity relationship, fluid triggering earthquake swarm, pore pressure seismicity swarm, and hydrothermal fluids swarm seismicity.
   • Write these queries to a temporary text file when using the export script.
5. Run the bundled script to create the archive.
   • Script path: scripts/export_lit_review.py
   • Example:

python3 ~/.codex/skills/skill-endnote-research/scripts/export_lit_review.py \
  --workspace /mnt/d/YIN/BaiduSyncdisk/endnote_file \
  --question "我要研究 流体与震群活动的关系。" \
  --queries-file /tmp/litlib_queries.txt \
  --limit 20

6. Read 文献列表.md and 检索记录.json.
   • Use title/abstract matches as the primary retrieval evidence.
   • Use full-text snippets for confirmation and close-reading direction.
   • If the result set is weak, say so explicitly and suggest better query families.
7. Write or revise 总结报告.md in the created output folder.
   • Include: research-direction map, key literature groups, useful methods, initial research questions, likely data requirements, and next close-reading steps.
   • Distinguish what the literature supports from Codex interpretation.

Script Behavior

The script reads:

• litlib/index/papers.jsonl
• litlib/index/texts/*.txt
• each record's path field for the source PDF

It creates:

<directory where the command is run>/文献梳理/
  <timestamp>-<question-slug>/
    文献列表.md
    总结报告.md
    检索记录.json
    pdfs/

Default retrieval is title/abstract first, then full-text confirmation. It copies PDFs for matched records when the source files exist.

Output Guidance

When reporting back to the user, mention:

• the created folder path
• how many literature records were selected
• how many PDFs were copied
• any missing PDFs or weak-result caveats
• the main research directions found

Do not modify litlib/litlib.py unless the user explicitly asks to change the library tool itself.