Index

A

add_messages() (reasoner_validator.report.ValidationReporter method)

apply_validation() (reasoner_validator.report.ValidationReporter method)

B

BiolinkValidator (class in reasoner_validator.biolink) BMTWrapper (class in reasoner_validator.biolink)

build_source_trail() (reasoner_validator.biolink.BiolinkValidator static method) buildmetadata (reasoner_validator.versioning.SemVer attribute)

C

call_trapi() (in module reasoner_validator.trapi) CATEGORY_INCLUSIONS (reasoner_validator.biolink.BiolinkValidator attribute) category_matched() (reasoner_validator.validator.TRAPIResponseValidator method) check_biolink_model_compliance() (reasoner_validator.biolink.BiolinkValidator method) check_biolink_model_compliance_of_input_edge() (reasoner_validator.biolink.BiolinkValidator method) check_compliance_of_trapi_response() (reasoner_validator.validator.TRAPIResponseValidator method)

check_dangling_references() (reasoner_validator.trapi.mapping.MappingValidator method) check_node_edge_mappings() (in module reasoner_validator.trapi.mapping) code_dictionary (reasoner_validator.validation_codes.CodeDictionary attribute) CODE_DICTIONARY_FILE (reasoner_validator.validation_codes.CodeDictionary attribute) CodeDictionary (class in reasoner_validator.validation_codes) CONTEXT (reasoner_validator.validation_codes.CodeDictionary attribute) count_node() (reasoner_validator.biolink.BiolinkValidator method)

D

default() (reasoner_validator.report.ReportJsonEncoder method) default_target (reasoner_validator.trapi.mapping.MappingValidator attribute) (reasoner_validator.trapi.TRAPISchemaValidator attribute) default_test (reasoner_validator.trapi.mapping.MappingValidator attribute) (reasoner_validator.trapi.TRAPISchemaValidator attribute) DEFAULT_TRAPI_VERSION (reasoner_validator.report.ValidationReporter attribute) DESCRIPTION (reasoner_validator.validation_codes.CodeDictionary attribute) display() (reasoner_validator.validation_codes.CodeDictionary class method)

dump() (reasoner_validator.report.ValidationReporter method) dump_all_messages() (reasoner_validator.report.ValidationReporter method) dump_critical() (reasoner_validator.report.ValidationReporter method) dump_errors() (reasoner_validator.report.ValidationReporter method) dump_info() (reasoner_validator.report.ValidationReporter method) dump_messages_type() (reasoner_validator.report.ValidationReporter method) dump_skipped() (reasoner_validator.report.ValidationReporter method) dump_warnings() (reasoner_validator.report.ValidationReporter method) dumps() (reasoner_validator.report.ValidationReporter method)

F

filter_copy_by_facet() (reasoner_validator.validation_codes.CodeDictionary class method)

fix_nullable() (in module reasoner_validator.trapi) from_string() (reasoner_validator.versioning.SemVer class method)

G

get_aliases() (reasoner_validator.validator.TRAPIResponseValidator method) get_all_messages() (reasoner_validator.report.ValidationReporter method) get_all_messages_of_type() (reasoner_validator.report.ValidationReporter method) get_attribute_type_exclusions() (reasoner_validator.biolink.BiolinkValidator method) get_biolink_model_toolkit() (in module reasoner_validator.biolink) get_biolink_version() (reasoner_validator.biolink.BiolinkValidator method) (reasoner_validator.biolink.BMTWrapper method) get_bmt() (reasoner_validator.biolink.BMTWrapper method) get_code_entry() (reasoner_validator.validation_codes.CodeDictionary class method) get_code_subtree() (reasoner_validator.validation_codes.CodeDictionary class method) get_critical() (reasoner_validator.report.ValidationReporter method) get_default_target() (reasoner_validator.report.ValidationReporter method) get_default_test() (reasoner_validator.report.ValidationReporter method) get_description() (reasoner_validator.validation_codes.CodeDictionary class method) get_errors() (reasoner_validator.report.ValidationReporter method) get_info() (reasoner_validator.report.ValidationReporter method)

get_inverse_predicate() (reasoner_validator.biolink.BMTWrapper method) get_latest_version() (in module reasoner_validator.versioning) get_message_context() (reasoner_validator.validation_codes.CodeDictionary class method) get_message_template() (reasoner_validator.validation_codes.CodeDictionary class method) get_message_type() (reasoner_validator.report.ValidationReporter static method) (reasoner_validator.validation_codes.CodeDictionary static method) get_messages_by_target() (reasoner_validator.report.ValidationReporter method) get_messages_by_test() (reasoner_validator.report.ValidationReporter method) get_messages_of_type() (reasoner_validator.report.ValidationReporter method) get_node_categories() (reasoner_validator.biolink.BiolinkValidator method) get_node_identifiers() (reasoner_validator.biolink.BiolinkValidator method) get_reference() (in module reasoner_validator.biolink) get_result() (reasoner_validator.biolink.BiolinkValidator method) get_skipped() (reasoner_validator.report.ValidationReporter method) get_target_provenance() (reasoner_validator.biolink.BiolinkValidator method) get_trapi_version() (reasoner_validator.trapi.TRAPISchemaValidator method) get_warnings() (reasoner_validator.report.ValidationReporter method)

H

has_critical() (reasoner_validator.report.ValidationReporter method) has_dangling_nodes() (reasoner_validator.biolink.BiolinkValidator method) has_errors() (reasoner_validator.report.ValidationReporter method) has_information() (reasoner_validator.report.ValidationReporter method) has_message_type() (reasoner_validator.report.ValidationReporter method) has_messages() (reasoner_validator.report.ValidationReporter method)

has_skipped() (reasoner_validator.report.ValidationReporter method) has_valid_knowledge_graph() (reasoner_validator.validator.TRAPIResponseValidator method) has_valid_node_information() (reasoner_validator.biolink.BiolinkValidator method) has_valid_query_graph() (reasoner_validator.validator.TRAPIResponseValidator method) has_valid_results() (reasoner_validator.validator.TRAPIResponseValidator method) has_warnings() (reasoner_validator.report.ValidationReporter method)

I

Input_Edge (reasoner_validator.report.TRAPIGraphType attribute) is_curie() (in module reasoner_validator.biolink) is_strict_validation() (reasoner_validator.report.ValidationReporter method)

is_symmetric() (reasoner_validator.biolink.BMTWrapper method) is_trapi_1_4_or_later() (reasoner_validator.validator.TRAPIResponseValidator method) is_treats() (reasoner_validator.biolink.BiolinkValidator method) is_valid_trapi_query() (reasoner_validator.trapi.TRAPISchemaValidator method)

K

Knowledge_Graph (reasoner_validator.report.TRAPIGraphType attribute)

L

label() (reasoner_validator.report.TRAPIGraphType method)

load_schema() (in module reasoner_validator.trapi)

M

major (reasoner_validator.versioning.SemVer attribute) map_semver() (in module reasoner_validator.trapi) MappingValidator (class in reasoner_validator.trapi.mapping) markdown() (reasoner_validator.validation_codes.CodeDictionary class method) merge() (reasoner_validator.biolink.BiolinkValidator method) (reasoner_validator.report.ValidationReporter method) (reasoner_validator.trapi.TRAPISchemaValidator method) merge_coded_messages() (reasoner_validator.report.ValidationReporter method) merge_identified_messages() (reasoner_validator.report.ValidationReporter static method) merge_scoped_messages() (reasoner_validator.report.ValidationReporter method) MESSAGE (reasoner_validator.validation_codes.CodeDictionary attribute) messages (reasoner_validator.trapi.mapping.MappingValidator attribute) (reasoner_validator.trapi.TRAPISchemaValidator attribute)

minimum_required_biolink_version() (reasoner_validator.biolink.BiolinkValidator method) minimum_required_trapi_version() (reasoner_validator.trapi.TRAPISchemaValidator method) minor (reasoner_validator.versioning.SemVer attribute) module reasoner_validator.biolink reasoner_validator.report reasoner_validator.trapi reasoner_validator.trapi.mapping reasoner_validator.validation_codes reasoner_validator.validator reasoner_validator.versioning

O

openapi_to_jsonschema() (in module reasoner_validator.trapi)

P

patch (reasoner_validator.versioning.SemVer attribute) patch_schema() (in module reasoner_validator.trapi)

PREDICATE_INCLUSIONS (reasoner_validator.biolink.BiolinkValidator attribute) prefix (reasoner_validator.versioning.SemVer attribute) prerelease (reasoner_validator.versioning.SemVer attribute)

Q

Query_Graph (reasoner_validator.report.TRAPIGraphType attribute)

R

reasoner_validator.biolink module reasoner_validator.report module reasoner_validator.trapi module reasoner_validator.trapi.mapping module reasoner_validator.validation_codes module reasoner_validator.validator module reasoner_validator.versioning module

report() (reasoner_validator.report.ValidationReporter method) report_header() (reasoner_validator.biolink.BiolinkValidator method) (reasoner_validator.report.ValidationReporter method) (reasoner_validator.trapi.TRAPISchemaValidator method) ReportJsonEncoder (class in reasoner_validator.report) reset_biolink_version() (reasoner_validator.biolink.BiolinkValidator method) (reasoner_validator.biolink.BMTWrapper method) reset_default_target() (reasoner_validator.report.ValidationReporter method) reset_default_test() (reasoner_validator.report.ValidationReporter method) reset_node_info() (reasoner_validator.biolink.BiolinkValidator method) reset_trapi_version() (reasoner_validator.trapi.TRAPISchemaValidator method) resolve_testcase_node() (reasoner_validator.validator.TRAPIResponseValidator method)

S

sample_graph() (reasoner_validator.validator.TRAPIResponseValidator static method) sample_results() (reasoner_validator.validator.TRAPIResponseValidator static method) sanitize_workflow() (reasoner_validator.validator.TRAPIResponseValidator static method) SemVer (class in reasoner_validator.versioning)

SemVerError SemVerUnderspecified set_nodes() (reasoner_validator.biolink.BiolinkValidator method) strict_validation (reasoner_validator.trapi.mapping.MappingValidator attribute) (reasoner_validator.trapi.TRAPISchemaValidator attribute)

T

test_case_has_validation_errors() (reasoner_validator.report.ValidationReporter static method) testcase_edge_bindings() (reasoner_validator.validator.TRAPIResponseValidator static method) testcase_input_found_in_response() (reasoner_validator.validator.TRAPIResponseValidator method) testcase_node_bindings() (reasoner_validator.validator.TRAPIResponseValidator method) testcase_node_category_found() (reasoner_validator.validator.TRAPIResponseValidator method) testcase_node_found() (reasoner_validator.validator.TRAPIResponseValidator method) testcase_result_found() (reasoner_validator.validator.TRAPIResponseValidator method)

to_dict() (reasoner_validator.biolink.BiolinkValidator method) (reasoner_validator.report.ValidationReporter method) (reasoner_validator.trapi.TRAPISchemaValidator method) TRAPIAccessError TRAPIGraphType (class in reasoner_validator.report) TRAPIResponseValidator (class in reasoner_validator.validator) TRAPISchemaValidator (class in reasoner_validator.trapi)

V

validate() (reasoner_validator.trapi.TRAPISchemaValidator method) validate_agent_type() (reasoner_validator.biolink.BiolinkValidator method) validate_attribute_constraints() (reasoner_validator.biolink.BiolinkValidator method) validate_attributes() (reasoner_validator.biolink.BiolinkValidator method) validate_binding() (reasoner_validator.validator.TRAPIResponseValidator method) validate_biolink() (reasoner_validator.biolink.BiolinkValidator method) validate_category() (reasoner_validator.biolink.BiolinkValidator method) validate_element_status() (reasoner_validator.biolink.BiolinkValidator method) validate_graph_edge() (reasoner_validator.biolink.BiolinkValidator method) validate_graph_node() (reasoner_validator.biolink.BiolinkValidator method) validate_infores() (reasoner_validator.biolink.BiolinkValidator method)

validate_input_edge_node() (reasoner_validator.biolink.BiolinkValidator method) validate_knowledge_level() (reasoner_validator.biolink.BiolinkValidator method) validate_predicate() (reasoner_validator.biolink.BiolinkValidator method) validate_provenance() (reasoner_validator.biolink.BiolinkValidator method) validate_qualifier_constraints() (reasoner_validator.biolink.BiolinkValidator method) validate_qualifier_entry() (reasoner_validator.biolink.BiolinkValidator method) validate_qualifiers() (reasoner_validator.biolink.BiolinkValidator method) validate_slot_value() (reasoner_validator.biolink.BiolinkValidator method) validate_sources() (reasoner_validator.biolink.BiolinkValidator method) validation_code_tag() (reasoner_validator.validation_codes.CodeDictionary static method) ValidationReporter (class in reasoner_validator.report)