CLI Reference¶

Metaseed provides a command-line interface built with Typer.

Installation¶

The CLI is available after installing the package:

uv sync
uv run metaseed --help

Commands¶

version¶

Show the package version:

metaseed version

entities¶

List available MIAPPE entities for a version:

metaseed entities --version 1.1

validate¶

Validate a MIAPPE metadata file:

metaseed validate <file> --entity investigation --version 1.1

template¶

Generate an empty template for an entity:

metaseed template investigation --output my_investigation.yaml --format yaml

Options:

Option	Description
`--output`, `-o`	Output file path (prints to stdout if not specified)
`--format`, `-f`	Output format: `yaml` (default) or `json`
`--version`, `-v`	MIAPPE version (default: 1.1)

convert¶

Convert between YAML and JSON formats:

metaseed convert input.yaml output.json --entity investigation

The format is determined by file extension (.yaml, .yml, or .json).

ui¶

Launch the web interface:

metaseed ui --host 127.0.0.1 --port 8080

Options:

Option	Description
`--host`, `-h`	Host to bind to (default: 127.0.0.1)
`--port`, `-p`	Port to bind to (default: 8080)

The web interface provides:

Visual entity browser organized by hierarchy
Dynamic forms generated from YAML specifications
Nested entity creation (e.g., add Studies to an Investigation)
Validation feedback
Support for both MIAPPE and ISA profiles

profiles¶

List available profiles and their versions:

metaseed profiles

Output shows all installed profiles (miappe, isa, jerm, darwin-core, dissco, ena, etc.) with their available versions.

compare¶

Compare multiple profile specifications to see differences in entities, fields, and constraints:

# Compare two profiles (outputs markdown to stdout)
metaseed compare miappe/1.1 isa/1.0

# Compare with output file
metaseed compare miappe/1.1 isa/1.0 -o comparison.md

# Different output formats
metaseed compare miappe/1.1 isa/1.0 -f csv -o comparison.csv
metaseed compare miappe/1.1 isa/1.0 -f html -o comparison.html

# Compare multiple profiles
metaseed compare miappe/1.1 isa/1.0 jerm/1.0

Options:

Option	Description
`--output`, `-o`	Output file path (prints to stdout if not specified)
`--format`, `-f`	Output format: `markdown` (default), `csv`, or `html`

The comparison report shows:

Summary statistics (total entities, common, unique, modified, conflicts)
Entity-by-entity comparison with presence indicators
Field-level differences including type changes and constraint modifications

merge¶

Merge multiple profile specifications into a single combined profile:

# Basic merge (uses first_wins strategy)
metaseed merge miappe/1.1 isa/1.0 -o combined.yaml

# Merge with specific strategy
metaseed merge miappe/1.1 jerm/1.0 -s most_restrictive -o strict.yaml

# Custom name and version
metaseed merge miappe/1.1 isa/1.0 -n my-profile -v 2.0 -o my-profile.yaml

Options:

Option	Description
`--output`, `-o`	Output YAML file path (default: merged.yaml)
`--strategy`, `-s`	Merge strategy (default: first_wins)
`--name`, `-n`	Name for the merged profile
`--version`, `-v`	Version for the merged profile (default: 1.0)

Available merge strategies:

Strategy	Behavior
`first_wins`	Use the first profile's value for conflicts
`last_wins`	Use the last profile's value for conflicts
`most_restrictive`	required=True wins, tighter constraints
`least_restrictive`	required=False wins, looser constraints
`prefer_<profile>`	Always prefer a specific profile (e.g., `prefer_miappe/1.1`)

Global Options¶

Option	Description
`--version`	Show version and exit
`--help`	Show help message and exit

Configuration¶

The CLI reads configuration from:

Command-line arguments
Environment variables (prefixed with METASEED_)
Configuration file (metaseed.yaml in current directory)