Schema Commands

This document provides detailed information about the schema commands available in fairscape-cli.

Overview

The schema command group provides operations for creating, modifying, and working with data schemas. Schemas describe the structure and constraints of datasets, enabling validation and improved interoperability.

fairscape-cli schema [COMMAND] [OPTIONS]

Available Commands

Command Details

create-tabular

Create a new tabular schema definition.

fairscape-cli schema create-tabular [OPTIONS] SCHEMA_FILE

Options:

  • --name TEXT - Name of the schema [required]
  • --description TEXT - Description of the schema [required]
  • --guid TEXT - Optional custom identifier for the schema
  • --separator TEXT - Field separator character (e.g., , for CSV) [required]
  • --header BOOLEAN - Whether the data file has a header row (default: False)

Example:

fairscape-cli schema create-tabular \
    --name 'APMS Embedding Schema' \
    --description 'Tabular format for APMS music embeddings' \
    --separator ',' \
    --header False \
    ./schema_apms_music_embedding.json

add-property

This command group allows you to add different types of properties to an existing schema.

add-property string

Add a string property to a schema.

fairscape-cli schema add-property string [OPTIONS] SCHEMA_FILE

Options:

  • --name TEXT - Name of the property [required]
  • --index INTEGER - Column index in the data (0-based) [required]
  • --description TEXT - Description of the property [required]
  • --value-url TEXT - URL to a vocabulary term
  • --pattern TEXT - Regular expression pattern for validation

Example:

fairscape-cli schema add-property string \
    --name 'Gene Symbol' \
    --index 1 \
    --description 'Gene Symbol for the APMS bait protein' \
    --pattern '^[A-Za-z0-9\-]*$' \
    --value-url 'http://edamontology.org/data_1026' \
    ./schema_apms_music_embedding.json

add-property number

Add a number property to a schema.

fairscape-cli schema add-property number [OPTIONS] SCHEMA_FILE

Options:

  • --name TEXT - Name of the property [required]
  • --index INTEGER - Column index in the data (0-based) [required]
  • --description TEXT - Description of the property [required]
  • --maximum FLOAT - Maximum allowed value
  • --minimum FLOAT - Minimum allowed value
  • --value-url TEXT - URL to a vocabulary term

Example:

fairscape-cli schema add-property number \
    --name 'Measurement' \
    --index 2 \
    --description 'Sensor reading in units of X' \
    --minimum 0.0 \
    --maximum 100.0 \
    ./schema_apms_music_embedding.json

add-property integer

Add an integer property to a schema.

fairscape-cli schema add-property integer [OPTIONS] SCHEMA_FILE

Options:

  • --name TEXT - Name of the property [required]
  • --index INTEGER - Column index in the data (0-based) [required]
  • --description TEXT - Description of the property [required]
  • --maximum INTEGER - Maximum allowed value
  • --minimum INTEGER - Minimum allowed value
  • --value-url TEXT - URL to a vocabulary term

Example:

fairscape-cli schema add-property integer \
    --name 'Count' \
    --index 3 \
    --description 'Count of observations' \
    --minimum 0 \
    ./schema_apms_music_embedding.json

add-property boolean

Add a boolean property to a schema.

fairscape-cli schema add-property boolean [OPTIONS] SCHEMA_FILE

Options:

  • --name TEXT - Name of the property [required]
  • --index INTEGER - Column index in the data (0-based) [required]
  • --description TEXT - Description of the property [required]
  • --value-url TEXT - URL to a vocabulary term

Example:

fairscape-cli schema add-property boolean \
    --name 'IsValid' \
    --index 4 \
    --description 'Whether the observation is valid' \
    ./schema_apms_music_embedding.json

add-property array

Add an array property to a schema.

fairscape-cli schema add-property array [OPTIONS] SCHEMA_FILE

Options:

  • --name TEXT - Name of the property [required]
  • --index TEXT - Column index or range in the data (e.g., "5" or "2::") [required]
  • --description TEXT - Description of the property [required]
  • --value-url TEXT - URL to a vocabulary term
  • --items-datatype TEXT - Datatype of items in the array (string, number, integer, boolean) [required]
  • --min-items INTEGER - Minimum number of items in the array
  • --max-items INTEGER - Maximum number of items in the array
  • --unique-items BOOLEAN - Whether items must be unique

Example:

fairscape-cli schema add-property array \
    --name 'MUSIC APMS Embedding' \
    --index '2::' \
    --description 'Embedding Vector values' \
    --items-datatype 'number' \
    --unique-items False \
    --min-items 1024 \
    --max-items 1024 \
    ./schema_apms_music_embedding.json

infer

Infer a schema from a data file.

fairscape-cli schema infer [OPTIONS] INPUT_FILE SCHEMA_FILE

Options:

  • --name TEXT - Name for the schema [required]
  • --description TEXT - Description for the schema [required]
  • --guid TEXT - Optional custom identifier for the schema
  • --rocrate-path PATH - Optional path to an RO-Crate to append the schema to

Example:

fairscape-cli schema infer \
    --name 'Output Dataset Schema' \
    --description 'Inferred schema for output data' \
    --rocrate-path ./my_rocrate \
    ./my_rocrate/output.csv \
    ./my_rocrate/output_schema.json

add-to-crate

Add a schema to an RO-Crate.

fairscape-cli schema add-to-crate ROCRATE_PATH SCHEMA_FILE

Arguments:

  • ROCRATE_PATH - Path to the RO-Crate to add the schema to
  • SCHEMA_FILE - Path to the schema file

Example:

fairscape-cli schema add-to-crate \
    ./my_rocrate \
    ./schema_apms_music_embedding.json