Validator Reporter

Error and Warning Reporting Module

class reasoner_validator.report.ReportJsonEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Bases: JSONEncoder

Methods

default(o)

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

encode(o)

Return a JSON string representation of a Python data structure.

iterencode(o[, _one_shot])

Encode the given object and yield each string representation as available.
default(o)

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)
class reasoner_validator.report.TRAPIGraphType(value)

Bases: Enum

Enum type of Biolink Model compliant graph data being validated.

Input_Edge = 'Input Edge'
Knowledge_Graph = 'Knowledge Graph'
Query_Graph = 'Query Graph'
label() → str
class reasoner_validator.report.ValidationReporter(default_test: str | None = None, default_target: str | None = None, strict_validation: bool | None = None)

Bases: object

General wrapper for managing validation status messages: information, warnings, errors and ‘critical’ (errors). The TRAPI version and Biolink Model versions are also tracked for convenience at this abstract level although their application is within specific pertinent subclasses.

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_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.

merge(reporter)

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

merge_coded_messages(aggregated, additions)

Merge additional MESSAGE_PARTITION content into an already aggregate MESSAGE_PARTITION.

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.

test_case_has_validation_errors(tag, case)

Check if test case has validation errors.

to_dict()

Export ValidationReporter message contents as a Python dictionary.

merge_identified_messages

merge_scoped_messages
DEFAULT_TRAPI_VERSION = '1'
add_messages(new_messages: Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]]]])

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, **kwargs) → bool

Wrapper to allow validation_methods direct access to the ValidationReporter.

Parameters:

  • validation_method – function which accepts this instance of the ValidationReporter as its first argument, for use in reporting validation errors.

  • args – any positional arguments to the validation_method, after the initial ValidationReporter argument

  • kwargs – any (optional, additional) keyword arguments to the validation_method, after positional arguments

Returns:

bool, returns ‘False’ if validation method documented (critical) errors; True otherwise

dump(title: str | None = '', id_rows: int = 0, msg_rows: int = 0, compact_format: bool = False, file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Dump all available messages captured by the ValidationReporter, printed as formatted human-readable text, on a specified file device.

Parameters:

  • title – Optional[str], user supplied report title (default: autogenerated if not set or empty string; suppressed if an explicit argument of None is given); default: “” -> default title

  • id_rows – int >= 0, if set, maximum number of code-related identifiers to print per code (value of 0 means print all; default: 0)

  • msg_rows – int >= 0, if set, maximum number of parameterized code-related messages to print per identifier row (value of 0 means print all; default: 0)

  • compact_format – bool, if True, omit blank lines inserted by default for human readability; also, suppress character escapes (i.e. underlining of titles) (default: False)

  • file – target file device for output

Returns:

n/a

dump_all_messages(test: str | None = None, target: str | None = None, flat=False) → str

Dump all messages for a given test from a given target, as JSON. :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 flat: render output as ‘flat’ JSON (default: False) :return: str, JSON formatted string of all messages of test for target.

dump_critical(test: str | None = None, target: str | None = None, flat=False) → str

Dump critical error messages as JSON. :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 flat: render output as ‘flat’ JSON (default: False) :return: str, JSON formatted string of critical error messages.

dump_errors(test: str | None = None, target: str | None = None, flat=False) → str

Dump ‘error’ messages as JSON. :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 flat: render output as ‘flat’ JSON (default: False) :return: str, JSON formatted string of error messages.

dump_info(test: str | None = None, target: str | None = None, flat=False) → str

Dump ‘information’ messages as JSON. :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 flat: render output as ‘flat’ JSON (default: False) :return: str, JSON formatted string of information messages.

dump_messages_type(message_type: MessageType, test: str | None = None, target: str | None = None, flat=False) → str

Dump ValidationReporter messages of type ‘message_type’ as JSON. :param message_type: MessageType, type of message whose presence is to be detected. :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 flat: render output as ‘flat’ JSON (default: False) :return: bool, true only if ValidationReporter has any non-empty messages of type ‘message_type’.

dump_skipped(test: str | None = None, target: str | None = None, flat=False) → str

Dump ‘skipped test’ messages as JSON. :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 flat: render output as ‘flat’ JSON (default: False) :return: str, JSON formatted string of ‘skipped test’ messages.

dump_warnings(test: str | None = None, target: str | None = None, flat=False) → str

Dump ‘warning’ messages as JSON. :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 flat: render output as ‘flat’ JSON (default: False) :return: str, JSON formatted string of warning messages.

dumps(id_rows: int = 0, msg_rows: int = 0, compact_format: bool = True) → str

Text string version of dump(): returns all available messages captured by the ValidationReporter, as a formatted human-readable text blob.

Parameters:

  • id_rows – int >= 0, if set, maximum number of code-related identifiers to print per code (value of 0 means print all; default: 0)

  • msg_rows – int >= 0, if set, maximum number of parameterized code-related messages to print per identifier row (value of 0 means print all; default: 0)

  • compact_format – bool, if True, omit blank lines inserted by default for human readability (default: True)

Returns:

n/a

get_all_messages() → Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]]]]

Get copy of all MESSAGES_BY_TARGET as a Python data structure. :return: Dict (copy) of all validation messages in the ValidationReporter.

get_all_messages_of_type(message_type: MessageType) → Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]

Get MESSAGE_PARTITION dictionary of all ValidationReporter messages of a given ‘message_type’, harvested from all target and test contexts. :param message_type: MessageType, type of message whose presence is to be detected. :return: MESSAGE_PARTITION of aggregated messages of the specified MessageType.

get_critical(test: str | None = None, target: str | None = None) → Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]

Get copy of all recorded ‘critical’ error messages, for a given test from a given target. :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: Dict of all ‘critical error’ messages.

get_default_target() → str

Returns the current target of the ValidationReporter. :return: str, current target

get_default_test() → str

Returns the current default test identifier of the ValidationReporter. :return: str, current default test identifier

get_errors(test: str | None = None, target: str | None = None) → Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]

Get copy of all recorded ‘error’ messages, for a given test from a given target. :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: Dict of all ‘error’ messages.

get_info(test: str | None = None, target: str | None = None) → Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]

Get copy of all recorded ‘information’ messages, for a given test from a given target. :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: Dict of all ‘information’ messages.

static get_message_type(code: str) → MessageType

Get type of message code. :param code: message code :return: MessageType

get_messages_by_target(target: str | None = None) → Dict[str, Dict[str, Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]]]

Returns a block of MESSAGES_BY_TEST corresponding to a given or default target. :param target: str, specified target (gets current ‘default’ target if not given) :return: MESSAGES_BY_TEST corresponding to a resolved target

get_messages_by_test(test: str | None = None, target: str | None = None) → Dict[str, Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]]

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!

Parameters:

  • test – str, specified test (gets current ‘default’ test if not given)

  • target – str, specified target (gets current ‘default’ test if not given)

Returns:

MESSAGES_BY_TEST corresponding to a resolved target

get_messages_of_type(message_type: MessageType, test: str | None = None, target: str | None = None) → Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]

Get Python data dictionary of ValidationReporter messages of ‘message_type’, for a specified (or default?) target and test. :param message_type: MessageType, type of message whose presence is to be detected. :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: get copy of messages of type ‘message_type’.

get_skipped(test: str | None = None, target: str | None = None) → Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]

Get copy of all recorded ‘skipped test’ messages, for a given test from a given target. :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: Dict of all ‘skipped test’ messages.

get_warnings(test: str | None = None, target: str | None = None) → Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]]

Get copy of all recorded ‘warning’ messages, for a given test from a given target. :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: Dict of all ‘warning’ messages.

has_critical(test: str | None = None, target: str | None = None) → bool

Predicate to detect any recorded critical error messages. :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: bool, True if ValidationReporter has any ‘critical error’ messages.

has_errors(test: str | None = None, target: str | None = None) → bool

Predicate to detect any recorded error messages. :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: bool, True if ValidationReporter has any ‘error’ messages.

has_information(test: str | None = None, target: str | None = None) → bool

Predicate to detect any recorded information messages. :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: bool, True if ValidationReporter has any ‘information’ messages.

has_message_type(message_type: MessageType, test: str | None = None, target: str | None = None) → bool

Predicate to detect if ValidationReporter has any non-empty messages of type ‘message_type’. :param message_type: MessageType, type of message whose presence is to be detected. :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: bool, true only if ValidationReporter has any non-empty messages of type ‘message_type’.

has_messages(test: str | None = None, target: str | None = None) → bool

Predicate to detect any recorded validation messages. :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: bool, True if ValidationReporter has any non-empty messages.

has_skipped(test: str | None = None, target: str | None = None) → bool

Predicate to detect any recorded ‘skipped test’ messages. :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: bool, True if ValidationReporter has any ‘skipped tests’ messages.

has_warnings(test: str | None = None, target: str | None = None) → bool

Predicate to detect any recorded warning messages. :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: bool, True if ValidationReporter has any ‘warning’ messages.

is_strict_validation(graph_type: TRAPIGraphType) → bool

Predicate to test if strict validation is to be applied. If the internal ‘strict_validation’ flag is not set (i.e. None), then graph_type is to resolve strictness based on TRAPI graph type context.

Parameters:

graph_type – TRAPIGraphType, type of TRAPI graph component being validated

Returns:

bool, value of validation strictness set in the ValidationReporter.

merge(reporter)

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

Parameters:

reporter – second ValidationReporter

merge_coded_messages(aggregated: Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]], additions: Dict[str, Dict[str, Dict[str, List[Dict[str, str]] | None] | None]])

Merge additional MESSAGE_PARTITION content into an already aggregate MESSAGE_PARTITION. :param aggregated: MESSAGE_PARTITION of messages aggregated so far :param additions: MESSAGE_PARTITION of additional messages to be merged into the aggregated set. :return: None - mutable ‘aggregrated’ MESSAGE_PARTITION is updated as a side effect

static merge_identified_messages(aggregated: Dict[str, List[Dict[str, str]] | None], additions: Dict[str, List[Dict[str, str]] | None])
merge_scoped_messages(aggregated: Dict[str, Dict[str, List[Dict[str, str]] | None] | None], additions: Dict[str, Dict[str, List[Dict[str, str]] | None] | None])
report(code: str, test: str | None = None, target: str | None = None, source_trail: str | None = None, **message)

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.

Parameters:

message – **Dict, named parameters representing extra (str-formatted) context for the given code message

Returns:

None (internally record the validation message)

report_header(title: str | 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_default_target(name: str)

Resets the default target identifier of the ValidationReporter to a new string. :param name: str, new default target identifier (generally a URL, URI or CURIE) :return: None

reset_default_test(name: str)

Resets the default test identifier of the ValidationReporter to a new string. :param name: str, new default test identifier :return: None

static test_case_has_validation_errors(tag: str, case: Dict) → bool

Check if test case has validation errors.

Parameters:

  • tag – str, top level string key in the ‘case’ whose value is the validation messages ‘dictionary’

  • case – Dict, containing error messages in a structurally similar format to what is returned by the to_dict() method in this class.

Returns:

True if the case contains validation messages

to_dict() → Dict

Export ValidationReporter message contents as a Python dictionary. :return: Dict