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)

Streaming Data Processing Mode¶

For very large graphs, the Validator operation may now successfully process graph data equally well using data streaming (command flag --stream=True) which significantly minimizes the memory footprint required to process such graphs.

Biolink Model Versioning¶

By default, the Validator validates against the latest Biolink Model release hosted by the current Biolink Model Toolkit; hwoever, one may override this default at the Validator class level using the Validator.set_biolink_model(version="#.#.#") where #.#.# is the major.minor.patch semantic versioning of the desired Biolink Model release.

Every instance of Validator() persistently assumes the most recently set class level Biolink Model version. Resetting the class level Biolink Model does not change the version of previously instantiated Validator() objects. In a multi-threaded environment instantiating multiple validator objects, it may be necessary to wrap the Validator.set_biolink_model and Validator() object instantiation together within a single thread locked block.

Note that the kgx validate CLI operation also has an optional biolink_release argument for the same purpose.

kgx.validator¶

class kgx.validator.ErrorType[source]¶

Bases: enum.Enum

Validation error types

class kgx.validator.MessageLevel[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, progress_monitor: Optional[Callable[[kgx.utils.kgx_utils.GraphEntityType, List], None]] = None, schema: Optional[str] = None)[source]¶

Bases: object

Class for validating a property graph.

The optional ‘progress_monitor’ for the validator should be a lightweight Callable which is injected into the class ‘inspector’ Callable, designed to intercepts node and edge records streaming through the Validator (inside a Transformer.process() call. The first (GraphEntityType) argument of the Callable tags the record as a NODE or an EDGE. The second argument given to the Callable is the current record itself. This Callable is strictly meant to be procedural and should not mutate the record. The intent of this Callable is to provide a hook to KGX applications wanting the namesake function of passively monitoring the graph data stream. As such, the Callable could simply tally up the number of times it is called with a NODE or an EDGE, then provide a suitable (quick!) report of that count back to the KGX application. The Callable (function/callable class) should not modify the record and should be of low complexity, so as not to introduce a large computational overhead to validation!

Parameters

verbose (bool) – Whether the generated report should be verbose or not (default: False)
progress_monitor (Optional[Callable[[GraphEntityType, List], None]]) – Function given a peek at the current record being processed by the class wrapped Callable.
schema (Optional[str]) – URL to (Biolink) Model Schema to be used for validated (default: None, use default Biolink Model Toolkit schema)

__call__(entity_type: kgx.utils.kgx_utils.GraphEntityType, rec: List)[source]¶: Transformer ‘inspector’ Callable

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]

get_error_messages()[source]¶

A direct Validator “instance” method version of report() that directly accesses the internal Validator self.errors list.

Returns: A list of formatted error messages.
Return type: List

static get_required_edge_properties(toolkit: Optional[bmt.toolkit.Toolkit] = None) → list[source]¶

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

Parameters: toolkit (Optional[Toolkit]) – Optional externally provided toolkit (default: use Validator class defined toolkit)
Returns: A list of required edge properties
Return type: list

static get_required_node_properties(toolkit: Optional[bmt.toolkit.Toolkit] = None) → list[source]¶

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

Parameters: toolkit (Optional[Toolkit]) – Optional externally provided toolkit (default: use Validator class defined toolkit)
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, toolkit: Optional[bmt.toolkit.Toolkit] = None) → list[source]¶

Validate category field of a given node.

Parameters

node (str) – Node identifier
data (dict) – Node properties
toolkit (Optional[Toolkit]) – Optional externally provided toolkit (default: use Validator class defined toolkit)

Returns

A list of errors for a given node

Return type

list

static validate_edge_predicate(subject: str, object: str, data: dict, toolkit: Optional[bmt.toolkit.Toolkit] = None) → list[source]¶

Validate edge_predicate field of a given edge.

Parameters

subject (str) – Subject identifier
object (str) – Object identifier
data (dict) – Edge properties
toolkit (Optional[Toolkit]) – Optional externally provided toolkit (default: use Validator class defined toolkit)

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, toolkit: Optional[bmt.toolkit.Toolkit] = None) → list[source]¶

Checks if edge properties have the expected value type.

Parameters

subject (str) – Subject identifier
object (str) – Object identifier
data (dict) – Edge properties
toolkit (Optional[Toolkit]) – Optional externally provided toolkit (default: use Validator class defined toolkit)

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 predicate

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, toolkit: Optional[bmt.toolkit.Toolkit] = None) → list[source]¶

Checks if node properties have the expected value type.

Parameters

node (str) – Node identifier
data (dict) – Node properties
toolkit (Optional[Toolkit]) – Optional externally provided toolkit (default: use Validator class defined toolkit)

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

write_report(outstream: TextIO) → None[source]¶

Write error report to a file

Parameters: outstream (TextIO) – The stream to write to