fileglancer 2.1.0

Browse, share, and publish files on the Janelia file system

Fileglancer

Fileglancer is an intranet web application designed to allow researchers to easily browse, share, and manage large scientific imaging data using OME-NGFF (i.e. OME-Zarr). Our goal is to reduce the friction experienced by users who want to easily share their data with colleagues at their institution. Simply browse to your data, click on the Neuroglancer link, and send that link to your collaborator.

Core features:

• Browse and manage files on network file shares (NFS) using an intuitive web UI
• Create a "data link" for any file share path, allowing web-based anonymous access to your data
• Shareable links to Neuroglancer and other viewers
• Integration with our help desk (JIRA) for file conversion requests
• Integration with the x2s3 proxy service, to easily share data on the internet

See the documentation for more information.

Installation

Quick Start with pip

You can install and run Fileglancer using pip:

# Install from PyPI
pip install fileglancer

# Start the server
fileglancer start

The server will start on http://localhost:7878 by default. By default, users can browse their home directory (~/) without any additional configuration.

Configuration

Fileglancer can be configured using a YAML configuration file or environment variables. Create a config.yaml file in your working directory:

# Logging level
log_level: DEBUG

# Configure additional file share paths
file_share_mounts:
  - "~/"                    # User's home directory
  - "/data/shared"          # Additional shared directory

# Database configuration
db_url: "sqlite:///fileglancer.db"

Alternatively, you can use environment variables with the FGC_ prefix:

export FGC_LOG_LEVEL="DEBUG"
export FGC_FILE_SHARE_MOUNTS='["~/", "/data/shared"]'
export FGC_DB_URL="sqlite:///fileglancer.db"

For more configuration options, see the development docs.

Deployment @ Janelia Research Campus

If you are on the internal Janelia network navigate to "fileglancer.int.janelia.org" in your web browser and login with your Okta credentials. If you are outside of Janelia, you'll need to ask your System Administrator to install Fileglancer on a server on your institution's network.

Software Architecture

Fileglancer has a React front-end and a FastAPI backend. Uvicorn is used to manage the set of FastAPI workers. Inspired by JupyterHub's method of spinning up individual user servers using setuid, we use seteuid to change the effective user of each worker process as necessary to handling the incoming requests. This allows each logged in user to access their resources on the network file systems. The backend database access is managed by SQLAlchemy and supports many databases including Sqlite and Postgresql.

Documentation

• User guide
• Developer guide

Related repositories

• fileglancer-hub - Production deployment files
• fileglancer-janelia - Janelia-specific customizations
• fileglancer-docs - Documentation website