validate

cli.validate

tvbo validate — sub-tree of validators (schema today; OMEX/SED-ML/BIDS later).

Attributes

Name	Description
app

Functions

Name	Description
all_	Recursively run validate schema on every YAML file under directory matching pattern.
bids	Validate a BIDS dataset directory using the bids_validator package.
omex	Shallow OMEX check — confirms the archive is a zip with manifest.xml at the root.
schema	Validate path against the shipped JSON Schema; auto-detects the target class.
sedml	Shallow SED-ML check — confirms the file has a <sedML> root element.

all_

cli.validate.all_(
    directory=typer.Argument(..., exists=True, file_okay=False, dir_okay=True, readable=True, help='Directory to walk.'),
    pattern=typer.Option('*.yaml', '--pattern', help="Glob pattern, e.g. '*.yml' or '**/*.yaml'."),
    fail_fast=typer.Option(False, '--fail-fast', help='Stop at first failure.'),
)

Recursively run validate schema on every YAML file under directory matching pattern.

bids

cli.validate.bids(
    path=typer.Argument(..., exists=True, file_okay=False, dir_okay=True, readable=True, help='BIDS dataset root.'),
)

Validate a BIDS dataset directory using the bids_validator package.

omex

cli.validate.omex(
    path=typer.Argument(..., exists=True, readable=True, help='OMEX archive (.omex / .zip).'),
)

Shallow OMEX check — confirms the archive is a zip with manifest.xml at the root.

Full COMBINE-archive validation is scheduled for the post-P3 milestone.

schema

cli.validate.schema(
    path=typer.Argument(..., exists=True, readable=True, help='YAML file.'),
    target_class=typer.Option(None, '--class', help='Target class (auto-detected from `class:` key when omitted).'),
)

Validate path against the shipped JSON Schema; auto-detects the target class.

Uses the lightweight jsonschema library against the pre-generated tvbo/datamodel/tvbo_datamodel.schema.json (produced from the LinkML schema at build time), so validation needs no runtime linkml. The file is parsed with TVBO’s loader so !include/merge-key extensions and slot aliases resolve exactly as they do when the model is loaded.

sedml

cli.validate.sedml(
    path=typer.Argument(..., exists=True, readable=True, help='SED-ML XML file.'),
)

Shallow SED-ML check — confirms the file has a <sedML> root element.

Full L1V4 validation is scheduled for the post-P3 milestone.