Paper Folder Obsidian

Paper Folder Obsidian

Use this skill when the user wants an end-to-end paper reading workflow from a local paper folder into Obsidian.

Required user input

Ask for or confirm exactly these paths before doing any work:

paper_root: /absolute/path/to/A
output_root: /absolute/path/to/obsidian/subfolder

Interpret the input strictly:

• paper_root is the root folder A.
• Each first-level subfolder directly under A is one category.
• The number of first-level subfolders equals the number of output markdown files.
• Scan PDFs recursively inside each first-level subfolder.
• Ignore non-PDF files.
• If PDFs are placed directly under A, group them into a fallback category named root.

Important environment rule

Only claim that files were written when the runtime truly has filesystem access to those local paths.

• If the environment can access the local paths, write the markdown files and extracted images directly.
• If the environment cannot access the user's local filesystem, do not pretend the write succeeded. Instead, explain the limitation clearly and either:

1. ask the user to upload the folder contents, or
2. generate the markdown content as a deliverable they can save themselves.

Workflow

Follow this sequence.

1. Validate both absolute paths.
2. Run scripts/scan_paper_root.py to inventory PDFs and group them by first-level subfolder.
3. For each PDF in each category:

• read the PDF;
• extract bibliographic details from the first page and metadata when possible;
• create a concise, faithful paper summary using the sections below;
• run scripts/extract_pdf_assets.py to generate image assets:
• title_author_image: crop from the first page containing the paper title and author block;
• framework_image: search the early and mid paper pages for the figure that is most likely to describe the proposed method, pipeline, architecture, workflow, or overall framework. Do not default to the first-page figure. Score candidate figures using nearby captions/text such as Figure, pipeline, framework, architecture, overview, workflow, or proposed method, and prefer pages around the method section. If no figure passes the quality bar, omit it.

1. Write exactly one markdown file per category into output_root.
2. Store extracted images under a predictable sibling folder, for example:

• /assets/cat_01/cat_01_paper_001__title.png
• /assets/cat_01/cat_01_paper_001__framework.png

1. In the markdown, embed images with relative paths so Obsidian can render them.

Safe naming rule for markdown image links

Do not use the paper title, original PDF filename, or any user-provided Unicode text when naming extracted PNG files.

• Some PDFs have Chinese filenames, spaces, punctuation, or other characters that can break markdown rendering in some environments.
• Always use the safe, manifest-driven naming scheme from scan_paper_root.py:
• category asset directory: cat_
• per-paper base name: cat__paper_
• Example:
• assets/cat_02/cat_02_paper_003__title.png
• assets/cat_02/cat_02_paper_003__framework.png
• Keep the original paper title only inside the markdown content, never in the asset filename.
• When building markdown links, always use the generated relative path from this safe naming scheme.

Required paper fields

For every paper section, include:

• 标题
• 作者
• 年份
• 发表的期刊/会议
• github链接（如果有的话）
• 摘要式总结
• 核心贡献
• 方法
• 实验结论
• 局限性
• 你自己的启发
• Zotero 链接 / PDF 链接

Use 未找到 when a field is genuinely unavailable. For Zotero 链接, use 未提供 unless the user supplied a Zotero mapping. For PDF 链接, prefer the local absolute path or a vault-relative path if that is more useful.

Image rules

• Always include the title-authors image if extraction succeeded.
• Include the method/framework image only if extraction succeeded and looks plausibly relevant to the paper's method.
• Do not fabricate or hallucinate an image.
• If a framework image is missing, simply omit that image block.
• Prefer one framework image per paper.
• When uncertain, prefer omitting the framework image over using a likely wrong teaser, result chart, or first-page illustration.

Markdown format

Use the template in references/markdown_template.md. Add YAML frontmatter with category, sourceroot, and papercount. Use clear section headings so the note is readable in Obsidian.

Quality bar for summaries

• Base claims on the paper itself.
• Distinguish clearly between what the paper says and your own insight.
• Keep summaries concise but specific.
• Mention uncertainty when metadata or figure extraction is ambiguous.

Script usage

Inventory the paper tree:

python scripts/scan_paper_root.py "/path/to/A" --output-root "/path/to/output" --manifest /tmp/paper_manifest.json

Extract images for one PDF using a safe ASCII base name from the manifest:

python scripts/extract_pdf_assets.py "/path/to/paper.pdf" "/path/to/output/assets/cat_01" --base-name "cat_01_paper_001"

Example request

请读取下面这个论文目录，并把每个一级子文件夹汇总成一个 Obsidian markdown 文件，写入指定目录。

paper_root: /Users/qiqi/Documents/A
output_root: /Users/qiqi/Obsidian/MyVault/Paper Summaries

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: WindZh03
• Source: WindZh03/zotero-obsidian-skill
• License: MIT

Install and usage instructions live in the source repository linked above.