tvbo validate

Sub-tree of validators for TVB-O YAML and adjacent standards (BIDS, SED-ML, COMBINE/OMEX).

Synopsis

tvbo validate schema PATH [--class TARGET_CLASS]
tvbo validate bids   PATH
tvbo validate sedml  PATH
tvbo validate omex   PATH

validate schema — LinkML structural validation

Runs LinkML JSON-Schema validation against the shipped tvbo_datamodel.yaml.

Flag Default Purpose
PATH (required) YAML file.
--class auto-detected LinkML target class. The validator looks for a top-level class: key in the YAML; otherwise falls back to SimulationExperiment. 
tvbo validate schema ./study.yaml
tvbo validate schema ./model.yaml --class Dynamics

Exit code 0 = valid. Non-zero with one line per issue otherwise.

validate bids — BIDS dataset

Wraps bids_validator. Iterates every file under PATH, prints any that violate BIDS naming rules, and exits non-zero if any are invalid.

tvbo validate bids /data/derivatives/sub-01

Requires bids-validator:

uv pip install bids-validator

validate sedml — SED-ML (shallow stub)

Today this checks that the file:

  1. Is readable as text.
  2. Contains a <sedML> (or <sedml>) root element.

Full SED-ML L1V4 validation is scheduled for a post-P3 milestone. The stub is useful as a CI smoke test today.

tvbo validate sedml ./experiment.sedml

validate omex — COMBINE/OMEX archive (shallow stub)

Checks that the file:

  1. Is a valid zip archive.
  2. Contains manifest.xml at the archive root.

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

tvbo validate omex ./bundle.omex

Exit codes

Code Meaning
0 All checks passed
non-zero One or more failures (validator details on stderr)

See also