ChemLocalLink

ChemLocalLink is a cross-platform application designed to manage and process Chemotion Files.

Key Features

• URL Handling: Handles chemotion-specific URLs to react with Chemotion.
• Structured Download Storage: Persistent per‑origin folder layout: <DownloadRoot>/<origin-host>/<optional/deep/link/path>/file.ext.
• Download & Edit Tracking: Checksums detect local edits; edited items flagged automatically (periodic scan).
• Folder Scan / Link External Files: Scan action links any new, untracked files placed manually inside the download tree.
• Upload Workflow (Keep or Delete): Upload edited files then either mark them as kept (retain on disk) or delete them (with recursive cleanup of now-empty folders).
• Session Export / Import: Portable .chemlocallink archive bundles transfer to another machine.
• Desktop Notifications: Progress + status notifications (download / upload / errors).
• History & State Persistence: downloads.json stored under application data, re‑hydrated on startup.

Installation

Windows

Prerequisites

• Windows 10 or later
• .NET 8.0 Desktop Runtime

Download and Install

1. Download the latest installer from the Releases page

   • Look for ChemLocalLink_x.x.x.exe

2. Install .NET 8.0 Desktop Runtime (if not already installed)

   • The installer will check and prompt you to install it if needed
   • Or download directly from Microsoft

3. Run the installer

   • Double-click the downloaded .exe file
   • Follow the installation wizard
   • A desktop shortcut and start menu entry will be created

Linux (Debian-based)

Prerequisites

• Debian-based System
• No additional runtime installation required (self-contained package)

Download and Install

1. Download the latest .deb package from the Releases page

   • For x64 systems: ChemLocalLink_x.x.x_amd64.deb
   • For ARM64 systems: ChemLocalLink_x.x.x_arm64.deb

2. Install the package

   Using apt (recommended)

   sudo apt update
   sudo apt install ./ChemLocalLink_x.x.x_amd64.deb

• The application will be available in your applications menu
• You can launch from terminal: chemlocallink

System Integration

The Debian package automatically:

• Installs the application to /usr/lib/ChemLocalLink/
• Creates a launcher script in /usr/bin/ChemLocalLink
• Registers the chemotion:// URL protocol handler
• Adds application icon to system icon themes
• Updates desktop database and MIME associations

Uninstallation

Windows

• Open Control Panel
• Go to Programs > Programs and Features
• Find "ChemLocalLink" in the list
• Right-click and select "Uninstall"

Linux (Debian-based)

sudo apt remove chemlocallink

Directory & Data Layout

Application data base path: (OS ApplicationData)/ChemLocalLink

Files created:

• downloads.json – persisted list of tracked downloads.
• config.json – app config.
• theme.json – theme config.

Default persistent download directory:

• Windows: %USERPROFILE%/Documents/ChemLocalLink
• macOS: ~/Documents/ChemLocalLink
• Linux: ~/Documents/ChemLocalLink if it exists, else ~/ChemLocalLink

Structure after processing a deep link (example):

ChemLocalLink/
  Origin/
    project/123/reactions/
      reaction_456.json

Session Export / Import

Archive extension: .chemlocallink

Contents:

manifest.json         // schemaVersion, appVersion, exportedAtUtc, fileCount
downloads.json        // portable metadata (relative file names)
files/                // actual files, preserving subfolder structure

Import rules:

• Skips entries whose checksum already exists.
• Recreates needed subdirectories relative to current download root.
• Adds non‑duplicate files to the top of history and rebuilds groups.

Typical Workflow

1. User clicks chemotion://... link (or pastes URL) in the app.
2. App resolves token + deep link path, downloads file to structured directory.
3. User edits file externally (double‑click to open).
4. App detects modification (checksum delta → IsEdited = true).
5. User uploads (single or bulk)
6. Optionally export session for transfer or backup.

Contributing

1. Fork the repository
2. Create a feature branch: git checkout -b feature/your-feature
3. Commit: git commit -m "feat: add your feature"
4. Push: git push origin feature/your-feature
5. Open a Pull Request

Please open issues for bugs, feature requests, or clarifications.

License

MIT License – see LICENSE for full text.

Contact

• Mostafa Mekky – mekky@kit.edu
• Issues: https://github.com/Chemotion/ChemLocalLink/issues

Chemotion

• https://chemotion.net/