Hello,

When attempting to replicate the behavior described in the docs

https://linkml.io/linkml-validator/usage/#using-linkml-validator-as-a-module

with something like

from linkml.validator import Validator

my_dict={
    'species':'Homo sapiens'
}

schema_path='/Users/pgleasonbremer/coding_projects/altos/altos-labs-ontology/src/alo/schema/alo.yaml'

my_Validator=Validator(schema=schema_path)

my_Validator.validate(
    obj=my_dict,
    target_class='DataPackage'
)

I get

Traceback (most recent call last):
  File "/Users/pgleasonbremer/coding_projects/altos/linkml/mwe_validator_broken.py", line 12, in <module>
    my_Validator.validate(
TypeError: validate() got an unexpected keyword argument `obj`

however, I get no error when changing the keyword to instance

my_Validator.validate(
    instance=my_dict,
    target_class='DataPackage'
)

I would submit a PR to fix it, but i looked at the source and it looks like validate expects keyword obj, so i was a little confused, thanks.

convergent evolution between:

https://github.com/deepakunni3/linkml-validator/blob/main/linkml_validator/models.py

https://github.com/linkml/linkml-model/blob/main/linkml_model/model/schema/validation.yaml
(hmm, looks like there is no python expression of this yet)

the linkml-model one is itself based on the SHACL validation datamodel, and has URIs back to it

Almost as a finer grain extension of the benefits of the range plugin, it would be great to have a prefix checking plugin.

I can take a shot at implementing it, the one question I had @deepakunni3 is whether there's a way to control the strictness of a plugin? I think officially in linkml prefixes are only advisory and invalid prefixes should only be warnings, but there are situations (like, when kgx output is first generated as part of an ingest) where I might want to fail on a prefix error.

One approach I could see taking is to make the plugin available as two different modules, prefix_validation and prefix_validation_strict and just share the code between them.

I'm doing some development on Koza testing, and have run into an unexpected validation error against the Biolink model... I might be missing something obvious, but was hoping someone might have input.

Here's the error we're getting:

>       assert result.valid == True
E       assert False == True
E        +  where False = ValidationResult(plugin_name='JsonSchemaValidationPlugin', valid=False, validation_messages=[ValidationMessage(severit..., field=None, value=None, message="Additional properties are not allowed ('category', 'id', 'name' were unexpected)")]).valid

which seems to suggest that category, id, and name aren't valid slots for a named thing (?)

from pathlib import Path

import pytest
from linkml_validator.validator import Validator

valid_gene = {
    "id": "BOGUS:12345",
    "name": "Bogus Gene 12345",
    "category": ["biolink:NamedThing", "biolink:Gene"],
}

invalid_gene = {
        "name": "Bogus Gene 98765",
        "type": "biolink:NamedThing"
}

model_schema = Path(__file__).parent.parent / 'resources' / 'biolink-model.yaml'


@pytest.mark.parametrize("gene", [valid_gene])
def test_valid_input(gene):
    validator = Validator(schema="tests/resources/biolink-model.yaml")
    v = validator.validate(obj=gene, target_class="Entity")
    result = v.validation_results[0]
    assert result.valid == True


@pytest.mark.parametrize("gene", [invalid_gene])
def test_invalid_input(gene):
    validator = Validator(schema="tests/resources/biolink-model.yaml")
    v = validator.validate(obj=gene, target_class="NamedThing")
    result = v.validation_results[0]
    assert result.valid == False