Configuration Schema

This document describes the configuration file schema for the Varvis Download CLI.

Overview

The configuration file is a JSON file that can contain any of the CLI options to avoid having to specify them on the command line each time. Command line arguments take precedence over configuration file values.

Default Configuration File

By default, the tool looks for a configuration file named .config.json in the current directory. You can specify a different configuration file using the --config option.

Schema

Property	Type	Required	Default	Description
username	string	No	-	Varvis API username
password	string	No	-	Varvis API password
target	string	No	-	Target for the Varvis API (can be full URL or alias)
destination	string	No	.	Destination folder for downloaded files
proxy	string	No	-	Proxy URL for HTTP requests
proxyUsername	string	No	-	Username for proxy authentication
proxyPassword	string	No	-	Password for proxy authentication
overwrite	boolean	No	false	Whether to overwrite existing files
filetypes	string	No	bam,bam.bai	Comma-separated list of file types to download
loglevel	string	No	info	Logging level (info, warn, error, debug)
logfile	string	No	-	Path to the log file
reportfile	string	No	-	Path to the report file
restoreArchived	string	No	ask	Restore archived files behavior ("no", "ask", "all", "force")
restorationFile	string	No	awaiting-restoration.json	Path for the restoration tracking file

Example Configuration Files

Basic Configuration

{
  "username": "your-username",
  "target": "https://your-varvis-instance.com",
  "destination": "/path/to/downloads"
}

Advanced Configuration

{
  "username": "your-username",
  "target": "production-server",
  "destination": "/data/downloads",
  "proxy": "http://proxy.company.com:8080",
  "proxyUsername": "proxy-user",
  "filetypes": "bam,bam.bai,vcf,vcf.gz.tbi",
  "overwrite": false,
  "loglevel": "debug",
  "logfile": "/var/log/varvis-download.log",
  "restoreArchived": "ask"
}

Minimal Configuration

{
  "username": "your-username",
  "target": "https://varvis.example.com"
}

File Types

The filetypes property accepts a comma-separated list of file extensions. Common values include:

• bam - Binary Alignment Map files
• bam.bai - BAM index files
• vcf - Variant Call Format files
• vcf.gz - Compressed VCF files
• vcf.gz.tbi - Tabix index files for compressed VCF
• bed - Browser Extensible Data files

Target Specification

The target property can be specified as:

• A full URL: https://varvis.example.com
• An alias that will be resolved by the application

Logging Levels

Available logging levels (from most to least verbose):

• debug - Detailed debugging information
• info - General information (default)
• warn - Warning messages only
• error - Error messages only

Archive Restoration Modes

The restoreArchived property controls how archived files are handled:

• no - Skip archived files entirely
• ask - Prompt for each archived file (default)
• all - Ask once, then restore all archived files
• force - Automatically restore all archived files without prompting