linkml validate

linkml validate

Validate data according to a LinkML Schema

linkml validate [OPTIONS] [DATA_SOURCES]...

Options

-s, --schema <schema>

Schema file to validate data against

-C, --target-class <target_class>

Class within the schema to validate data against

--config <config>

Validation configuration YAML file.

--exit-on-first-failure

Exit after the first validation failure is found. If not specified all validation failures are reported.

--legacy-mode

Use legacy linkml-validate behavior.

-m, --module <module>

[DEPRECATED: only used in legacy mode] Path to python datamodel module

-f, --input-format <input_format>

[DEPRECATED: only used in legacy mode] Input format. Inferred from input suffix if not specified

Options:

yml | yaml | json | rdf | ttl | json-ld | csv | tsv

-S, --index-slot <index_slot>

[DEPRECATED: only used in legacy mode] top level slot. Required for CSV dumping/loading

--include-range-class-descendants, --no-range-class-descendants

[DEPRECATED: only used in legacy mode] When handling range constraints, include all descendants of the range class instead of just the range class

-D, --include-context, --no-include-context

Include additional context when reporting of validation errors.

Default:

False

-V, --version

Show the version and exit.

Arguments

DATA_SOURCES

Optional argument(s)

Plugins

linkml validate jsonschema

Validates instance data

linkml validate jsonschema [OPTIONS] INPUT

Options

-m, --module <module>

Path to python datamodel module

-f, --input-format <input_format>

Input format. Inferred from input suffix if not specified

Options:

yml | yaml | json | rdf | ttl | json-ld | csv | tsv

-C, --target-class <target_class>

name of class in datamodel that the root node instantiates

-S, --index-slot <index_slot>

top level slot. Required for CSV dumping/loading

-s, --schema <schema>

Path to schema specified as LinkML yaml

--exit-on-first-failure, --no-exit-on-first-failure

Exit after the first validation failure is found. If not specified all validation failures are reported.

--include-range-class-descendants, --no-range-class-descendants

When handling range constraints, include all descendants of the range class instead of just the range class

-V, --version

Show the version and exit.

Arguments

INPUT

Required argument

linkml validate sparql

Validates sparql

Example:

linkml-sparql-validate -U http://sparql.hegroup.org/sparql -s tests/test_validation/input/omo.yaml

linkml validate sparql [OPTIONS]

Options

-G, --named-graph <named_graph>

Constrain query to a named graph

-i, --input <input>

Input file to validate

-U, --endpoint-url <endpoint_url>

URL of sparql endpoint

-L, --limit <limit>

Max results per query

-o, --output <output>

Path to report file

-f, --input-format <input_format>

Input format. Inferred from input suffix if not specified

Options:

yml | yaml | json | rdf | ttl | json-ld | csv | tsv

-t, --output-format <output_format>

Output format. Inferred from output suffix if not specified

Options:

yml | yaml | json | rdf | ttl | json-ld | csv | tsv

-s, --schema <schema>

Path to schema specified as LinkML yaml

-V, --version

Show the version and exit.