TRAPI Schema Validation

TRAPI Validation Functions.

exception reasoner_validator.trapi.TRAPIAccessError

Bases: RuntimeError

class reasoner_validator.trapi.TRAPISchemaValidator(default_test: str | None = None, default_target: str | None = None, trapi_version: str | None = None, strict_validation: bool | None = None)

Bases: ValidationReporter

TRAPI Validator is a wrapper class for validating conformance of JSON messages to the Translator Reasoner API.

Methods

add_messages(new_messages)	Batch addition of MESSAGES_BY_TARGET messages to a ValidationReporter instance. :param new_messages: MESSAGES_BY_TARGET, messages indexed by target, test and categories: one of "information", "skipped tests", "warnings", "errors" or "critical", with code-keyed dictionaries of (structured) message parameters.
apply_validation(validation_method, *args, ...)	Wrapper to allow validation_methods direct access to the ValidationReporter.
dump([title, id_rows, msg_rows, ...])	Dump all available messages captured by the ValidationReporter, printed as formatted human-readable text, on a specified file device.
dump_all_messages([test, target, flat])	Dump all messages for a given test from a given target, as JSON.
dump_critical([test, target, flat])	Dump critical error messages as JSON.
dump_errors([test, target, flat])	Dump 'error' messages as JSON.
dump_info([test, target, flat])	Dump 'information' messages as JSON.
dump_messages_type(message_type[, test, ...])	Dump ValidationReporter messages of type 'message_type' as JSON.
dump_skipped([test, target, flat])	Dump 'skipped test' messages as JSON.
dump_warnings([test, target, flat])	Dump 'warning' messages as JSON.
dumps([id_rows, msg_rows, compact_format])	Text string version of dump(): returns all available messages captured by the ValidationReporter, as a formatted human-readable text blob.
get_all_messages()	Get copy of all MESSAGES_BY_TARGET as a Python data structure.
get_all_messages_of_type(message_type)	Get MESSAGE_PARTITION dictionary of all ValidationReporter messages of a given 'message_type', harvested from all target and test contexts.
get_critical([test, target])	Get copy of all recorded 'critical' error messages, for a given test from a given target.
get_default_target()	Returns the current target of the ValidationReporter.
get_default_test()	Returns the current default test identifier of the ValidationReporter.
get_errors([test, target])	Get copy of all recorded 'error' messages, for a given test from a given target.
get_info([test, target])	Get copy of all recorded 'information' messages, for a given test from a given target.
get_message_type(code)	Get type of message code.
get_messages_by_target([target])	Returns a block of MESSAGES_BY_TEST corresponding to a given or default target.
get_messages_by_test([test, target])	Returns MESSAGE_CATALOG corresponding to a given or default target. Note that the dictionary returned is not a copy of the original thus caution should be taken not to mutate it! :param test: str, specified test (gets current 'default' test if not given) :param target: str, specified target (gets current 'default' test if not given) :return: MESSAGES_BY_TEST corresponding to a resolved target.
get_messages_of_type(message_type[, test, ...])	Get Python data dictionary of ValidationReporter messages of 'message_type', for a specified (or default?) target and test.
get_skipped([test, target])	Get copy of all recorded 'skipped test' messages, for a given test from a given target.
get_trapi_version()	return: str, TRAPI (SemVer) version currently targeted by the TRAPISchemaValidator.
get_warnings([test, target])	Get copy of all recorded 'warning' messages, for a given test from a given target.
has_critical([test, target])	Predicate to detect any recorded critical error messages.
has_errors([test, target])	Predicate to detect any recorded error messages.
has_information([test, target])	Predicate to detect any recorded information messages.
has_message_type(message_type[, test, target])	Predicate to detect if ValidationReporter has any non-empty messages of type 'message_type'.
has_messages([test, target])	Predicate to detect any recorded validation messages.
has_skipped([test, target])	Predicate to detect any recorded 'skipped test' messages.
has_warnings([test, target])	Predicate to detect any recorded warning messages.
is_strict_validation(graph_type)	Predicate to test if strict validation is to be applied.
is_valid_trapi_query(instance[, component])	Make sure that the Message is a syntactically valid TRAPI Query JSON object.
merge(reporter)	Merge all messages and metadata from a second TRAPISchemaValidator, into the calling TRAPISchemaValidator instance.
merge_coded_messages(aggregated, additions)	Merge additional MESSAGE_PARTITION content into an already aggregate MESSAGE_PARTITION.
minimum_required_trapi_version(version)	param version: simple 'major.minor.patch' TRAPI schema release SemVer
report(code[, test, target, source_trail])	Capture a single validation message, as per specified 'code' (with any code-specific contextual parameters). :param code: str, dot delimited validation path code :param test: str, specified test (gets current 'default' test if not given) :param target: str, specified target (gets current 'default' test if not given) :param source_trail, Optional[str], audit trail of knowledge source provenance for a given Edge, as a string. Defaults to "global" if not specified. :param message: **Dict, named parameters representing extra (str-formatted) context for the given code message :return: None (internally record the validation message).
report_header([title, compact_format])	Return a suitably generated report header. :param title: Optional[str], if title is None, then only the 'reasoner-validator' version is printed out in the header. If the title is an empty string (the default), then 'Validation Report' used. :param compact_format: bool, whether to print the header in compact format (default: True). Extra line feeds are otherwise provided to provide space around the header and control characters are output to underline the header. :return: str, generated header.
reset_default_target(name)	Resets the default target identifier of the ValidationReporter to a new string.
reset_default_test(name)	Resets the default test identifier of the ValidationReporter to a new string.
reset_trapi_version(version)	Reset TRAPI version tracked by the TRAPISchemaValidator.
test_case_has_validation_errors(tag, case)	Check if test case has validation errors.
to_dict()	Export TRAPISchemaValidator contents as a Python dictionary (including TRAPI version and parent class dictionary content) :return: Dict
validate(instance, component)	Validate instance against schema.

merge_identified_messages
merge_scoped_messages

default_target: str

default_test: str

get_trapi_version() → str

Returns:

str, TRAPI (SemVer) version currently targeted by the TRAPISchemaValidator.

is_valid_trapi_query(instance, component: str = 'Query')

Make sure that the Message is a syntactically valid TRAPI Query JSON object.

Parameters:

instance:

Dict, instance to validate

component:

str, TRAPI subschema to validate (e.g. ‘Query’, ‘QueryGraph’, ‘KnowledgeGraph’, ‘Result’; Default: ‘Query’)

Returns:

Validation (“information”, “warning” and “error”) messages are returned within the host TRAPIValidator instance.

Examples

>>> TRAPISchemaValidator(trapi_version="1.3.0").is_valid_trapi_query({"message": {}}, component="Query")

merge(reporter)

Merge all messages and metadata from a second TRAPISchemaValidator, into the calling TRAPISchemaValidator instance.

Parameters:

reporter – second TRAPISchemaValidator

messages: MESSAGES_BY_TARGET

minimum_required_trapi_version(version: str) → bool

Parameters:

version – simple ‘major.minor.patch’ TRAPI schema release SemVer

Returns:

True if current version is equal to, or newer than, a targeted ‘minimum_version’

report_header(title: str | None = None, compact_format: bool = True) → str

Return a suitably generated report header. :param title: Optional[str], if title is None, then only the ‘reasoner-validator’ version is printed out

in the header. If the title is an empty string (the default), then ‘Validation Report’ used.

Parameters:

compact_format – bool, whether to print the header in compact format (default: True). Extra line feeds are otherwise provided to provide space around the header and control characters are output to underline the header.

Returns:

str, generated header.

reset_trapi_version(version: str)

Reset TRAPI version tracked by the TRAPISchemaValidator. :param version: new version :return: None

strict_validation: bool | None

to_dict() → Dict

Export TRAPISchemaValidator contents as a Python dictionary (including TRAPI version and parent class dictionary content) :return: Dict

validate(instance, component)

Validate instance against schema.

Parameters:

instance

dict, instance to validate

componentstr

TRAPI subschema to validate (e.g. ‘Query’, ‘QueryGraph’, ‘KnowledgeGraph’, ‘Result’; Default: ‘Query’)

Raises:

`ValidationError

<https://python-jsonschema.readthedocs.io/en/latest/errors/#jsonschema.exceptions.ValidationError>`_ If the instance is invalid.

Examples

>>> TRAPISchemaValidator(trapi_version="1.3.0").validate({"message": {}}, "QGraph")

async reasoner_validator.trapi.call_trapi(url: str, trapi_message)

Given an url and a TRAPI message, post the message to the url and return the status and json response.

Parameters:

• url –

• trapi_message –

Returns:

reasoner_validator.trapi.fix_nullable(schema) → None

Fix nullable schema.

reasoner_validator.trapi.load_schema(target: str)

Load schema from GitHub release or branch, or from a locally specified YAML schema file. :param target: release semver, schema file path (with ‘.yaml’ file extension)

or a git branch name, all referencing a target TRAPI schema.

Returns:

loaded TRAPI schema

reasoner_validator.trapi.map_semver(version: str)

reasoner_validator.trapi.openapi_to_jsonschema(schema, version: str) → None

Convert OpenAPI schema to JSON schema. :param schema: Dict, in-memory representation of the OpenAPI schema to be validated. :param version: str, TRAPI version against which the schema is currently being validated. :return:

reasoner_validator.trapi.patch_schema(tag: str, schema: Dict, version: str)