LinkML Validator
Project description
LinkML Validator
The LinkML Validator is a library for performing validation on data objects that conform to a given LinkML schema.
The Validator is initialized using a LinkML schema YAML, and is designed to allow for flexible validation where each type of validation is done by a plugin.
For example, JSONSchema validation is performed by JsonSchemaValidationPlugin.
Motivation
The LinkML Validator is built with the following goals in mind:
- the Validator should respond with parseable validation messages
- the Validator should not break the validation process even if one object from a list of objects fail validation
- the Validator should provide the ability to perform more than one type of validation on an object
Installation
python setup.py install
To install development dependencies (like pytest
, mkdocs
, etc.):
pip install -e ".[dev]"
Running the LinkML Validator via CLI
To run the LinkML Validator,
linkml-validator --inputs <INPUT JSON> \
--schema <SCHEMA YAML> \
--output <OUTPUT>
You can pass filepath or a URL that points to the LinkML schema YAML.
Input data as a dictionary of objects
The input JSON can be a dictionary of objects keyed by the object type.
{
"<OBJECT_TYPE>": [
{
}
]
}
Where the <OBJECT_TYPE>
is the pythonic representation of a class defined in the schema YAML.
For example, consider examples/example_data1.json:
{
"NamedThing": [
{
"id": "obj1",
"name": "Object 1",
"type": "X"
},
{
"id": "obj2",
"name": "Object 2",
"type": "Y"
}
]
}
In the above example, the NamedThing
is the target_class
, which is the pythonic
representation of the class named thing
as defined in the
examples/example_schema.yaml.
You can run the validator on the above data as follows:
linkml-validator --inputs examples/example_data1.json \
--schema examples/example_schema.yaml \
--output examples/example_data1_validation_report.json
Input data as an array of objects
The input JSON can also be an array of objects:
[
{},
{}
]
In this case, one must also specify the object type via --target-class
argument in the CLI.
For example, consider examples/example_data2.json:
[
{
"id": "obj1",
"name": "Object 1",
"type": "X"
},
{
"id": "obj2",
"name": "Object 2",
"type": "Y"
}
]
You can run the validator on the above data as follows:
linkml-validator --inputs examples/example_data2.json \
--schema examples/example_schema.yaml \
--output examples/example_data2_validation_report.json \
--target-class NamedThing
Running selected plugins
To run only certain plugins as part of the validation,
linkml-validator --inputs data.json \
--schema schema.yaml \
--output validation_results.json \
--plugins JsonSchemaValidationPlugin
To perform strict validation,
linkml-validator --inputs data.json \
--schema schema.yaml \
--output validation_results.json \
--plugins JsonSchemaValidationPlugin \
--strict
Under normal (default) mode, the validator will run all the checks defined in all referenced plugins on a given object.
When in strict mode, the validator will stop the validation for an object if even one of the plugins report a failed validation.
Running your own plugins with the Validator (via CLI)
To run your custom plugin as part of the validation,
linkml-validator --inputs data.json \
--schema schema.yaml \
--output validation_results.json \
--plugins JsonSchemaValidationPlugin \
--plugins <CUSTOM_PLUGIN_CLASS>
where <CUSTOM_PLUGIN_CLASS>
the reference to a custom plugin class.
Note: The custom plugin class must be a subclass of linkml_validator.plugins.base.BasePlugin
and must implement all the methods defined in BasePlugin
class.
Using LinkML Validator as a module
You can use the linkml_validator.validator.Validator
class directly in your codebase
to perform validation on objects that you are working with.
The following code snippet provides a quick way of instantiating the Validator class and performing validation on an object:
from linkml_validator.validator import Validator
data_obj = {
"id": "obj1",
"name": "Object 1",
"type": "X"
}
validator = Validator(schema="examples/example_schema.yaml")
validator.validate(obj=data_obj, target_class="NamedThing")
Note: The above code makes the assumption that there is a class named thing
defined
in the examples/example_schema.yaml and that NamedThing
is its Pythonic representation.
You can also provide your own custom plugin class to run with the Validator,
from linkml_validator.validator import Validator
from linkml_validator.plugins.base import BasePlugin
from linkml_validator.models import ValidationResult
class MyCustomPlugin(BasePlugin):
NAME = "MyCustomPlugin"
def __init__(self, schema: str, **kwargs) -> None:
super().__init__(schema)
def process(self, obj: dict, **kwargs) -> ValidationResult:
# Add your custom logic for processing and validating the incoming object
valid = False
print("In MyCustomPlugin.process method")
result = ValidationResult(
plugin_name=self.NAME,
valid=valid,
validation_messages=[]
)
return result
data_obj = {
"id": "obj1",
"name": "Object 1",
"type": "X"
}
validator = Validator(schema="examples/example_schema.yaml", plugins=[{"plugin_class": "MyCustomPlugin", "args": {}])
validator.validate(obj=data_obj, target_class="NamedThing")
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