Mendeley Integration

A desktop-only Obsidian plugin that syncs your Mendeley library into reading notes in your vault, using the official Mendeley API (OAuth2 + REST).

(Una versión de este README en español está en README.es.md.)

Current status: Phase 1 (MVP).

• ✅ OAuth2 authentication with Mendeley (Authorization Code flow) with automatic token refresh.
• ✅ "Sync Mendeley library" command: creates/updates one note per reference.
• ✅ "Mendeley: full resync (ignore incremental progress)" command: forces a full resync, ignoring the incremental cursor. Useful the first time you change the note template, the target folder, or after updating the plugin to a version that changes how notes are organized (e.g. when the per-folder subfolders were introduced) — otherwise, documents that haven't changed in Mendeley since the last sync won't be reprocessed and will keep their old organization.
• ✅ Frontmatter with citekey, title, authors, year, journal, DOI, URL, abstract, tags, Mendeley folders, mendeley_id, and last-modified date.
• ✅ Citekey generation (uses Mendeley's citation_key if present; otherwise authorYear+firstTitleWord, with automatic disambiguation).
• ✅ Incremental sync (modified_since) and pagination.
• ✅ Notes are organized into subfolders inside the target folder, mirroring Mendeley's folder hierarchy (including nested subfolders). If a document belongs to several Mendeley folders at once, the note is placed under the alphabetically first one (the full folder list is still kept in mendeley_folders); if it's in no folder, it stays at the root.
• ✅ Generated content lives inside a delimited block (<!-- mendeley:start -->...<!-- mendeley:end -->); anything you write outside that block (e.g. under ## My notes) is never touched or deleted.
• 🔜 Phase 2: "Insert citation" command ([@citekey], Pandoc format), importing PDF annotations/highlights.
• 🔜 Phase 3: CSL JSON export, opening the attached PDF/DOI from the note, filtering by folder when syncing.

Known Phase 1 limitation: if you delete a document in Mendeley, the corresponding local note is not deleted automatically (by design: the plugin never deletes your content). You'll need to clean it up by hand if you want to.

1. Requirements

• Obsidian for desktop (Windows/macOS/Linux). The plugin is isDesktopOnly: true.
• A Mendeley account with access to dev.mendeley.com.
• Node.js 18+ only if you're going to build the plugin yourself (see the Development section).

2. Create a Mendeley application (Client ID / Secret)

1. Go to dev.mendeley.com and sign in with your Mendeley/Elsevier account.
2. Go to "My Apps" (dev.mendeley.com/myapps.html) and register a new application.
3. Fill out the form:
   • Name / Description: whatever you like, e.g. "Obsidian Mendeley Integration".
   • Redirect URL: copy the exact value shown in the plugin's settings tab (defaults to obsidian://mendeley-auth-callback). It must match character for character.
4. Save the app. Mendeley will show you a Client ID and a Client Secret — copy them, you'll need them in step 4.

⚠️ If the registration form rejects obsidian://mendeley-auth-callback (some OAuth providers only accept http(s) as a redirect URI for desktop apps): in practice we already confirmed Mendeley accepts this custom scheme end-to-end (authorization → token exchange → success), so this shouldn't come up. If it ever does for a different setup, the plugin's auth module is designed so the redirect URI can be swapped for a local loopback server (http://127.0.0.1:<port>/callback, the IETF-recommended mechanism for native apps) without reworking the rest of the plugin.

3. Install the plugin

This plugin is listed in Obsidian's official Community Plugins directory: in Obsidian, go to Settings → Community plugins → turn off "Restricted mode" if it's on → Browse → search for "Mendeley Integration" → install it → enable it.

Every user still needs to complete step 2 above (create your own Mendeley application) and step 4 below (configure and connect) — that part is the same for everyone, since each person needs their own Mendeley Client ID/Secret (see the security note in section 6 for why this can't be shared or bundled into the plugin).

4. Configure and connect

1. Go to Settings → Mendeley Integration.
2. Paste the Client ID and Client Secret you got in step 2.
3. Check that the Redirect URI shown matches the one you registered with Mendeley (use the copy button if you need to register it again).
4. Adjust the target folder (defaults to Mendeley) and, if you like, the note template.
5. Click "Connect to Mendeley": your browser will open to authorize the app. Once you accept, Mendeley redirects you to obsidian://mendeley-auth-callback?..., Obsidian activates itself, and the plugin captures the authorization code automatically.
6. Run the "Sync Mendeley library" command (Ctrl/Cmd+P → type "Mendeley").

5. What each note looks like

---
citekey: garcia2022microbiota
title: "Gut microbiota and cognitive decline"
authors:
  - "García, Ana"
  - "Smith, Jordan"
year: 2022
journal: "Journal of Neuroscience"
doi: "10.1000/xyz"
url: "https://example.com/paper"
abstract: "..."
tags: ["microbiota", "alzheimer"]
mendeley_folders: ["Thesis", "Alzheimer"]
mendeley_id: "abc-123"
mendeley_modified: "2024-01-01T00:00:00.000Z"
---

<!-- mendeley:start -->
## Gut microbiota and cognitive decline

**Authors:** García, Ana, Smith, Jordan
...
<!-- mendeley:end -->

## My notes

(write whatever you want here — it's never overwritten)

On every later sync, only the content inside <!-- mendeley:start -->...<!-- mendeley:end --> and the frontmatter keys the plugin manages (citekey, title, authors, year, journal, doi, url, abstract, tags, mendeley_folders, mendeley_id, mendeley_modified) get updated. Any other frontmatter key you add by hand is preserved.

6. Security and privacy

• The Client Secret and the access/refresh tokens are stored in data.json, inside the plugin's folder in your vault (.obsidian/plugins/mendeley-integration/data.json). They are not encrypted. Obsidian doesn't give community plugins access to the OS keychain, so this limitation is shared with most integration plugins (Google Calendar, GitHub Sync, etc.).
• If you share or sync your vault (e.g. with Git or another service), make sure to exclude .obsidian/plugins/mendeley-integration/data.json or avoid sharing that folder.
• The "Disconnect" button in the settings deletes the locally stored tokens (it doesn't revoke access on Mendeley's side; for that, check the authorized apps in your Mendeley account).

7. Development

npm install
npm run dev     # watch-mode build (esbuild)
npm run build   # type-check with tsc + minified production build
npm test        # run the unit tests (vitest)

Code layout in src/: auth/ (OAuth2), api/ (HTTP client + endpoints), sync/ (sync orchestration + delimited blocks), citekey/ (citekey generation), templates/ (frontmatter mapping + template rendering), settings/, and commands/.

The tests cover citekey generation, mapping Mendeley documents to frontmatter, and the delimited-block logic — the logic most prone to silent mistakes, since it runs on every sync against your real notes.

8. API reference used

• General docs: https://dev.mendeley.com/
• OAuth2 (Authorization Code): https://dev.mendeley.com/reference/topics/authorization_auth_code.html
• Methods/endpoints: https://dev.mendeley.com/methods/