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Validating schemas

The validate command (also available as lint) checks LinkML schemas for structural and logical problems:

Terminal window
ohi linkml validate model.yaml

You can pass several schemas at once. Each one is checked, even if an earlier one has problems.

Severity levels

Section titled “Severity levels”

Each problem has one of three severity levels:

  • Fatal: the schema can’t be loaded. For example: unknown references, invalid range types, an undefined default range that is used, or invalid URIs or CURIEs.
  • Error: the schema loads, but breaks a structural rule. For example: several key or identifier slots in one class, several tree roots, or colliding identifiers.
  • Warning: the schema works, but something is probably wrong. For example: invalid slot usage, an undefined default range, no tree root, undeclared CURIE prefixes, or missing recommended slots such as description.

The generators refuse to run on a schema with fatal problems. Errors and warnings don’t stop them.

Exit code

Section titled “Exit code”

validate exits with code 1 if any schema has a fatal problem or an error, and with 0 otherwise. Add --strict to also fail on warnings, for example in CI.

Output formats

Section titled “Output formats”

Choose the format of the report with --format:

  • terminal (default): colored and grouped, for reading in a terminal.
  • plain: the same text without colors, for logs and other tools.
  • json: a machine-readable report, useful for editors, web UIs and scripts.

The JSON report follows the validation report schema.

Validating from code

Section titled “Validating from code”

The libraries return the same problems:

  • Python: schema.report, or schema.issues(severity) to filter it. See Python bindings.
  • JavaScript: the report returned by LinkML.loadFromString, or LinkML.lint(view). See the npm package README.

Both give the same report as --format json.

To load imported schemas from somewhere else while validating, see Import maps.