Validator¶

The Validator validates an instance of kgx.graph.base_graph.BaseGraph for Biolink Model compliance.

To validate a graph,

from kgx.validator import Validator
v = Validator()
v.validate(graph)

kgx.validator¶

class kgx.validator.ErrorType(value)[source]¶

Bases: enum.Enum

Validation error types

class kgx.validator.MessageLevel(value)[source]¶

Bases: enum.Enum

Message level for validation reports

class kgx.validator.ValidationError(entity: str, error_type: kgx.validator.ErrorType, message: str, message_level: kgx.validator.MessageLevel)[source]¶

Bases: object

ValidationError class that represents an error.

Parameters

entity (str) – The node or edge entity that is failing validation
error_type (kgx.validator.ErrorType) – The nature of the error
message (str) – The error message
message_level (kgx.validator.MessageLevel) – The message level

class kgx.validator.Validator(verbose: bool = False)[source]¶

Bases: object

Class for validating a property graph.

Parameters: verbose (bool) – Whether the generated report should be verbose or not (default: False)

static get_all_prefixes(jsonld: Optional[Dict] = None) → set[source]¶

Get all prefixes from Biolink Model JSON-LD context.

It also sets self.prefixes for subsequent access.

Parameters: jsonld (Optional[Dict]) – The JSON-LD context
Returns: A set of prefixes
Return type: Optional[Dict]

static get_required_edge_properties() → list[source]¶

Get all properties for an edge that are required, as defined by Biolink Model.

Returns: A list of required edge properties
Return type: list

static get_required_node_properties() → list[source]¶

Get all properties for a node that are required, as defined by Biolink Model.

Returns: A list of required node properties
Return type: list

static report(errors: List[kgx.validator.ValidationError]) → List[source]¶

Prepare error report.

Parameters: errors (List[ValidationError]) – List of kgx.validator.ValidationError
Returns: A list of formatted errors
Return type: List

validate(graph: kgx.graph.base_graph.BaseGraph) → list[source]¶

Validate nodes and edges in a graph. TODO: Support strict mode

Parameters: graph (kgx.graph.base_graph.BaseGraph) – The graph to validate
Returns: A list of errors for a given graph
Return type: list

static validate_categories(node: str, data: dict) → list[source]¶

Validate category field of a given node.

Parameters

node (str) – Node identifier
data (dict) – Node properties

Returns

A list of errors for a given node

Return type

list

static validate_edge_predicate(subject: str, object: str, data: dict) → list[source]¶

Validate edge_predicate field of a given edge.

Parameters

subject (str) – Subject identifier
object (str) – Object identifier
data (dict) – Edge properties

Returns

A list of errors for a given edge

Return type

list

static validate_edge_properties(subject: str, object: str, data: dict, required_properties: list) → list[source]¶

Checks if all the required edge properties exist for a given edge.

Parameters

subject (str) – Subject identifier
object (str) – Object identifier
data (dict) – Edge properties
required_properties (list) – Required edge properties

Returns

A list of errors for a given edge

Return type

list

static validate_edge_property_types(subject: str, object: str, data: dict) → list[source]¶

Checks if edge properties have the expected value type.

Parameters

subject (str) – Subject identifier
object (str) – Object identifier
data (dict) – Edge properties

Returns

A list of errors for a given edge

Return type

list

static validate_edge_property_values(subject: str, object: str, data: dict) → list[source]¶

Validate an edge property’s value.

Parameters

subject (str) – Subject identifier
object (str) – Object identifier
data (dict) – Edge properties

Returns

A list of errors for a given edge

Return type

list

validate_edges(graph: kgx.graph.base_graph.BaseGraph) → list[source]¶

Validate all the edges in a graph.

This method validates for the following, - Edge properties - Edge property type - Edge property value type - Edge label

Parameters: graph (kgx.graph.base_graph.BaseGraph) – The graph to validate
Returns: A list of errors for a given graph
Return type: list

static validate_node_properties(node: str, data: dict, required_properties: list) → list[source]¶

Checks if all the required node properties exist for a given node.

Parameters

node (str) – Node identifier
data (dict) – Node properties
required_properties (list) – Required node properties

Returns

A list of errors for a given node

Return type

list

static validate_node_property_types(node: str, data: dict) → list[source]¶

Checks if node properties have the expected value type.

Parameters

node (str) – Node identifier
data (dict) – Node properties

Returns

A list of errors for a given node

Return type

list

static validate_node_property_values(node: str, data: dict) → list[source]¶

Validate a node property’s value.

Parameters

node (str) – Node identifier
data (dict) – Node properties

Returns

A list of errors for a given node

Return type

list

validate_nodes(graph: kgx.graph.base_graph.BaseGraph) → list[source]¶

Validate all the nodes in a graph.

This method validates for the following, - Node properties - Node property type - Node property value type - Node categories

Parameters: graph (kgx.graph.base_graph.BaseGraph) – The graph to validate
Returns: A list of errors for a given graph
Return type: list

static write_report(errors: List[kgx.validator.ValidationError], outstream: TextIO) → None[source]¶

Write error report to a file

Parameters

errors (List[ValidationError]) – List of kgx.validator.ValidationError
outstream (TextIO) – The stream to write to