Validation Codes Dictionary
Critical Error
critical.trapi.validation
Message: Schema validation error
Context: identifier, component, json_path, reason
Description: Critical JSON Schema validation error reported for specified TRAPI query component at a specific JSON path location
critical.trapi.request.invalid
Message: Test could not generate a valid TRAPI query request object using identified element
Context: identifier, test, reason
Description: Specified TRAPI query unit ‘test’ query could not be prepared for the indicated reason, using the identified Biolink starting element
critical.trapi.response.unexpected_http_code
Message: Unexpected HTTP status code
Context: identifier
Description: TRAPI query attempt returned an abnormal (non-200) server HTTP status code as noted
Error
error.biolink.model.noncompliance
Message: S-P-O statement is not compliant to Biolink Model release
Context: identifier, biolink_release
Description: This knowledge statement is not compliant to the specified release of the Biolink Model. Review associated messages for underlying cause
error.trapi.response.empty
Message: TRAPI Response is missing
Description: TRAPI Response to be validated should not be totally empty but should have a Message body
error.trapi.response.message.empty
Message: TRAPI Response missing its Message
Description: TRAPI Response should at least have non-empty original TRAPI request Message in its reply
error.trapi.response.message.query_graph.missing
Message: TRAPI Message is missing its Query Graph
Description: TRAPI Response should generally have a TRAPI request message Query Graph key value in its reply
error.trapi.response.message.query_graph.empty
Message: Response returned an empty Message Query Graph
Description: TRAPI Response should at least have original non-empty TRAPI request message Query Graph in its reply
error.trapi.response.message.knowledge_graph.missing
Message: TRAPI Message is missing its Knowledge Graph component
Description: TRAPI Response should generally have a TRAPI request message Knowledge Graph key value in its reply
error.trapi.response.message.knowledge_graph.empty
Message: Response returned an empty Message Knowledge Graph, which is an error in this context
Description: An empty Knowledge Graph is considered an error in this validation context
error.trapi.response.message.knowledge_graph.node.missing
Message: Knowledge Graph of the TRAPI Response Message is missing an expected Node
Context: identifier
Description: The given TRAPI Response is expected to return specific node(s) related to the original input data used to prepare the TRAPI Request
error.trapi.response.message.knowledge_graph.node.category.unmatched
Message: The category of the knowledge graph node could not be matched against input node category
Context: identifier, expected_category, observed_categories
Description: The category of the knowledge graph node failed to match that of the specified input node
error.trapi.response.message.knowledge_graph.node.identifier.not_curie
Message: Node identifier is not a CURIE
Context: identifier
Description: A knowledge graph node identifier must be a CURIE
error.trapi.response.message.knowledge_graph.edge.missing
Message: Knowledge Graph of TRAPI Response Message Knowledge Graph is missing expected Edge
Context: identifier
Description: The given TRAPI Response is expected to return specific edge(s) related to the original input data used to prepare the TRAPI Request
error.trapi.response.message.result.missing
Message: TRAPI Response Message is missing expected knowledge graph edge mapping in its Results
Context: identifier
Description: The given TRAPI Response is expected to return a specified edge - in its list of Results - relating to the original input data used to prepare the TRAPI Request
error.trapi.response.message.result.node_binding.key.missing
Message: Node binding entry key of TRAPI Result is missing in Query Graph
Context: identifier
Description: The TRAPI Response Message Results entry has the specified node binding entry key missing in the corresponding TRAPI Message Query Graph
error.trapi.response.message.results.missing
Message: TRAPI Message is missing its Results component
Description: In this context, the TRAPI Response should generally have a non-empty TRAPI Response Message Results component
error.trapi.response.message.results.empty
Message: Response returned an empty Message Results, which is an error in this context
Description: An empty block of Results is considered an error in the specific validation context
error.trapi.response.message.results.not_array
Message: Response returned a non-array Message.Results
Description: TRAPI Message.Results must be an array data type (even if empty)
error.trapi.response.message.results.missing_bindings
Message: Result object IDs for output node binding did not return the original identifier nor aliases for input id
Context: identifier, output_node_binding
Description: TRAPI Message.Results cannot resolve its reported identifier mappings to the original query
error.input_edge.node.category.missing
Message: Category missing for node
Context: identifier
Description: Category value must be specified in an input test data edge
error.input_edge.node.category.not_a_category
Message: Asserted category is not a proper category class for node
Context: node_id, identifier
Description: Category specified in input test data edge node is not recorded as a category term in specified version of Biolink. Replace with a known category
error.input_edge.node.category.unknown
Message: Node has unknown category
Context: node_id, identifier
Description: Category specified in input test data edge node is not a model element recorded in specified version of Biolink. Replace with a known category
error.input_edge.node.id.missing
Message: Node identifier is missing for node
Context: identifier
Description: Input test data edge data needs to have a specific node identifier for testing
error.input_edge.predicate.missing
Message: Edge has missing or empty predicate
Context: identifier
Description: Input test edge data needs to have a specific edge predicate for testing
error.input_edge.predicate.unknown
Message: Edge has unknown predicate
Context: edge_id, identifier
Description: Predicate specified in input test data edge is not recorded in specified version of Biolink. Replace with a known predicate
error.input_edge.predicate.abstract
Message: Edge is not permitted to have ‘abstract’ predicate
Context: edge_id, identifier
Description: Edge data validation is currently strict: predicates cannot be ‘abstract’! Replace with a concrete predicate
error.input_edge.predicate.mixin
Message: Edge is not permitted to have an ‘mixin’ predicate
Context: edge_id, identifier
Description: Edge data validation is currently strict: predicates cannot be of type ‘mixin’! Replace with a concrete predicate
error.input_edge.predicate.invalid
Message: Edge has invalid predicate
Context: edge_id, identifier
Description: Predicate specified in Input Edge is not defined as a predicate in specified version of Biolink. Replace with a proper predicate
error.query_graph.nodes.uninformative
Message: Missing informative node information
Description: Query graph must have at least one node with identifiers and/or categories available for query
error.query_graph.node.category.missing
Message: Category is missing from node
Context: identifier
Description: Category value must be specified in an query graph edge
error.query_graph.node.category.not_a_category
Message: Node has invalid category
Context: node_id, identifier
Description: Category specified in query graph edge node is not recorded as a category term in specified version of Biolink. Replace with a known category
error.query_graph.node.category.unknown
Message: Node has unknown category
Context: node_id, identifier
Description: Category specified in query graph edge node is not a model element recorded in specified version of Biolink. Replace with a known category
error.query_graph.node.ids.not_array
Message: The ‘ids’ property value is not an array in node
Context: identifier
Description: Value of ‘ids’ property in Query Graph node must be an array data type (even if empty)
error.query_graph.node.categories.not_array
Message: The ‘categories’ property value is not an array in node
Context: identifier
Description: Value of ‘categories’ property in Query Graph node must be an array data type (even if empty)
error.query_graph.node.is_set.not_boolean
Message: The ‘is_set’ property is not a boolean value in node
Context: identifier
Description: The ‘is_set’ field in node of Query Graph, if present, must be a boolean value
error.query_graph.edge.subject.missing
Message: The ‘subject’ property value is missing or empty in Edge
Context: identifier
Description: Edge must have a ‘subject’ key with a non-empty associated value
error.query_graph.edge.subject.missing_from_nodes
Message: The nodes catalog of query graph for missing the subject id recorded on Edge
Context: edge_id, identifier
Description: Every ‘subject’ identifier of every edge in a Query Graph must also be recorded in the list of nodes for that graph
error.query_graph.edge.object.missing
Message: The ‘object’ property value is missing or empty in Edge
Context: identifier
Description: Edge must have a ‘object’ key with a non-empty associated value
error.query_graph.edge.object.missing_from_nodes
Message: The nodes catalog of query graph for missing the object id recorded on Edge
Context: edge_id, identifier
Description: Every ‘object’ identifier of every edge in a Query Graph must also be recorded in the list of nodes for that graph
error.query_graph.edge.predicate.missing
Message: Predicate is missing or empty for Edge
Context: identifier
Description: The predicate of Query Graph edge needs to specified using a ‘predicate’ key with an array list of one or more predicates
error.query_graph.edge.predicate.unknown
Message: Edge has unknown predicate
Context: edge_id, identifier
Description: Predicate specified in Query Graph edge is not defined in specified version of Biolink. Replace with a defined predicate
error.query_graph.edge.predicate.not_array
Message: Predicate property value is not an array for Edge
Context: identifier
Description: Value of ‘predicate’ property value in Query Graph must be an array data type
error.query_graph.edge.predicate.empty_array
Message: Predicate property value is an empty array for Edge
Context: identifier
Description: Value of ‘predicate’ array property value in Query Graph must contain one or more predicates
error.query_graph.edge.predicate.abstract
Message: Edge is not permitted to have an ‘abstract’ predicate
Context: edge_id, identifier
Description: Query Graph data validation is currently strict: cannot have ‘abstract’ predicates! Replace with a concrete predicate
error.query_graph.edge.predicate.mixin
Message: Edge is not permitted to have an ‘mixin’ predicate
Context: edge_id, identifier
Description: Query Graph data validation is currently strict: cannot have ‘mixin’ predicates! Replace with a concrete predicate
error.query_graph.edge.predicate.invalid
Message: Edge has invalid predicate
Context: edge_id, identifier
Description: Predicate specified in Query Graph edge is not defined as a predicate in specified version of Biolink. Replace with a proper predicate
error.query_graph.edge.attribute_constraints.not_array
Message: Attribute_constraints property value is not an array for Edge
Context: identifier
Description: Value of ‘attribute_constraints’ property value in a Query Graph must be an array data type
error.query_graph.edge.qualifier_constraints.qualifier_set.empty
Message: Qualifier_set property value is empty for Edge
Context: identifier
Description: Value of a ‘qualifier_constraints.qualifier_set’ property in a Query Graph must not be non-empty array
error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.type_id.unknown
Message: Edge has unknown qualifier_type_id
Context: edge_id, identifier
Description: A qualifier qualifier_type_id must be defined in the specified version of Biolink
error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.value.not_a_predicate
Message: Qualifier_type_id ‘biolink:qualified_predicate’ for edge has a qualifier_value which is not a Biolink predicate
Context: identifier, qualifier_value
Description: The ‘qualifier_value’ for ‘biolink:qualified_predicate’ should be a Biolink predicate term
error.query_graph.edge.qualifier_constraints.qualifier_set.qualifier.invalid
Message: Validation of qualifier in a qualifier_constraints qualifier_set threw an unexpected exception
Context: identifier, qualifier_type_id, qualifier_value, reason
Description: Validation of a specified ‘qualifier_type_id’ and ‘qualifier_value’ failed for a given exceptional reason
error.knowledge_graph.nodes.empty
Message: No nodes found
Description: Knowledge graph in TRAPI messages must have a ‘nodes’ key and non-empty associated value
error.knowledge_graph.nodes.uninformative
Message: Missing informative node information
Description: All nodes in a knowledge graph must have categories
error.knowledge_graph.edges.empty
Message: No edges found
Description: Knowledge graph in TRAPI messages must have a ‘edges’ key and non-empty associated value
error.knowledge_graph.node.id.missing
Message: Node identifier is missing for node
Context: identifier
Description: Knowledge graph node must have a ‘id’ key with a non-empty associated value
error.knowledge_graph.node.category.missing
Message: Category is missing for node
Context: identifier
Description: Category value must be specified in a knowledge graph node
error.knowledge_graph.node.category.not_a_category
Message: Node has invalid category
Context: node_id, identifier
Description: Category specified in knowledge graph edge node is not recorded as a category term in specified version of Biolink. Replace with a known category
error.knowledge_graph.node.category.unknown
Message: Node has unknown category
Context: node_id, identifier
Description: Category specified in knowledge graph edge node is not a model element recorded in specified version of Biolink. Replace with a known category
error.knowledge_graph.node.missing_categories
Message: Categories are missing for node
Context: identifier
Description: Knowledge graph node must have a ‘categories’ key with a non-empty associated value
error.knowledge_graph.node.ids.not_array
Message: The ‘ids’ property value is not an array for node
Context: identifier
Description: Value of ‘ids’ property in Query Graph node must be an array data type
error.knowledge_graph.node.empty_ids
Message: The ‘ids’ property array is empty for node
Context: identifier
Description: Value of ‘ids’ array property in Knowledge Graph node must contain one or more node identifiers
error.knowledge_graph.node.categories.not_array
Message: The categories property value is not an array for node
Context: identifier
Description: Value of ‘categories’ property in Knowledge Graph node must be an array data type
error.knowledge_graph.node.categories.not_concrete
Message: None of the asserted categories are concrete for node
Context: identifier, categories
Description: Categories specified in knowledge graph edge node may not resolve to any (non-abstract, non-mixin) category terms in the specified version of Biolink. Add at least one ‘concrete’ category (as the most specific category?)
error.knowledge_graph.node.empty_categories
Message: The ‘categories’ property array is empty for node
Context: identifier
Description: Value of ‘categories’ array property in Knowledge Graph node must contain one or more node category terms
error.knowledge_graph.node.is_set.not_boolean
Message: The ‘is_set’ property is not a boolean value for node
Context: identifier
Description: The ‘is_set’ field in node of Knowledge Graph, if present, must be a boolean value
error.knowledge_graph.edge.subject.missing
Message: The ‘subject’ property value is missing or empty for Edge
Context: identifier
Description: Edge must have a ‘subject’ key with a non-empty associated value
error.knowledge_graph.edge.subject.missing_from_nodes
Message: The nodes catalog of query graph for missing the subject id recorded on Edge
Context: edge_id, identifier
Description: Every ‘subject’ identifier of every edge in a Knowledge Graph must also be recorded in the list of nodes for that graph
error.knowledge_graph.edge.object.missing
Message: The ‘object’ property value is missing or empty for Edge
Context: identifier
Description: Edge must have a ‘object’ key with a non-empty associated value
error.knowledge_graph.edge.object.missing_from_nodes
Message: The nodes catalog of query graph for missing the object id recorded on Edge
Context: edge_id, identifier
Description: Every ‘object’ identifier of every edge in a Knowledge Graph must also be recorded in the list of nodes for that graph
error.knowledge_graph.edge.predicate.missing
Message: The predicate is missing or empty for Edge
Context: identifier
Description: Edge must have a ‘predicate’ key with a non-empty associated value
error.knowledge_graph.edge.predicate.unknown
Message: Edge has unknown predicate
Context: edge_id, identifier
Description: Predicate specified in Knowledge Graph edge is not defined in specified version of Biolink. Replace with a defined predicate
error.knowledge_graph.edge.predicate.invalid
Message: Edge has invalid predicate
Context: edge_id, identifier
Description: Predicate specified in Knowledge Graph edge is not defined as a predicate in specified version of Biolink. Replace with a defined predicate
error.knowledge_graph.edge.predicate.not_array
Message: The predicate property value is not an array for Edge
Context: identifier
Description: Value of the ‘predicate’ property in Knowledge Graph edge must be an array data type
error.knowledge_graph.edge.predicate.empty_array
Message: The predicate property value is an empty array for Edge
Context: identifier
Description: Value of the ‘predicate’ array property in Knowledge Graph edge must contain one or more predicates
error.knowledge_graph.edge.predicate.abstract
Message: Edge is not permitted to have an ‘abstract’ predicate
Context: edge_id, identifier
Description: Knowledge Graph data validation is currently strict: cannot have ‘abstract’ predicates! Replace with a concrete predicate
error.knowledge_graph.edge.predicate.mixin
Message: Edge is not permitted to have an ‘mixin’ predicate
Context: edge_id, identifier
Description: Knowledge Graph data validation is currently strict: cannot have ‘mixin’ predicates! Replace with a concrete predicate
error.knowledge_graph.edge.attribute.missing
Message: Missing ‘attributes’ key for Edge
Context: identifier
Description: Edge must have a ‘attributes’ key with a non-empty associated value
error.knowledge_graph.edge.attribute.empty
Message: Empty attributes in Edge
Context: identifier
Description: Value of ‘attributes’ property in Knowledge Graph edge must contain a list of one or more attributes
error.knowledge_graph.edge.attribute.not_array
Message: The attributes are not an array in Edge
Context: identifier
Description: Value of the ‘attributes’ property in Knowledge Graph edge must be an array of attributes
error.knowledge_graph.edge.attribute.type_id.unknown
Message: Edge has unknown attribute_type_id
Context: edge_id, identifier
Description: Edge Attribute type identifier specified in knowledge graph edge is not recorded in specified version of Biolink. Replace with a known term
error.knowledge_graph.edge.attribute.type_id.abstract
Message: Edge is not permitted to have an ‘abstract’ attribute_type_id
Context: edge_id, identifier
Description: Edge data validation is currently strict: attribute type identifiers cannot be ‘abstract’. Replace with a concrete attribute_type_id
error.knowledge_graph.edge.attribute.type_id.mixin
Message: Edge is not permitted to have an ‘mixin’ attribute_type_id
Context: edge_id, identifier
Description: Edge data validation is currently strict: attribute type identifiers cannot be of type ‘mixin’. Replace with a concrete attribute_type_id
error.knowledge_graph.edge.attribute.type_id.missing
Message: An attribute is missing its ‘attribute_type_id’ property in Edge
Context: identifier
Description: The attribute of a Knowledge graph edge must have a ‘attribute_type_id’ key with a non-empty associated value
error.knowledge_graph.edge.attribute.type_id.empty
Message: An attribute has empty ‘attribute_type_id’ property in Edge
Context: identifier
Description: The value of the ‘attribute_type_id’ of an attribute of a Knowledge graph edge must not be empty
error.knowledge_graph.edge.attribute.type_id.not_curie
Message: Edge has a value that is not a CURIE for attribute_type_id
Context: edge_id, identifier
Description: The ‘attribute_type_id’ of a Knowledge graph edge attribute must be a controlled vocabulary term specified by a CURIE
error.knowledge_graph.edge.attribute.value.missing
Message: An attribute is missing its ‘value’ property in Edge
Context: identifier, attribute_id
Description: An attribute of a Knowledge graph edge must have a ‘value’ key with a non-empty associated value
error.knowledge_graph.edge.attribute.value.empty
Message: An attribute has an empty value in Edge
Context: identifier, attribute_id
Description: The value of an attribute of a Knowledge graph edge must not be empty
error.knowledge_graph.edge.provenance.infores.missing
Message: Edge has provenance value which is not a well-formed InfoRes CURIE
Context: edge_id, identifier
Description: The value of an attribute specifying the provenance of a Knowledge graph edge must be the well-formed InfoRes CURIE of a knowledge source
error.knowledge_graph.edge.provenance.missing_primary
Message: A ‘primary’ knowledge source is missing for Edge
Context: identifier
Description: Edge attributes should record the ‘infores’ identifier of their primary knowledge source provenance with respect to KP
error.knowledge_graph.edge.qualifiers.not_array
Message: The ‘qualifiers’ property is not an array in Edge
Context: identifier
Description: Value of the ‘qualifiers’ property in Knowledge Graph edge must be an array of attributes
error.knowledge_graph.edge.qualifiers.empty
Message: The qualifiers property value is empty in Edge
Context: identifier
Description: Value of a ‘qualifiers’ property in a Knowledge Graph must not be non-empty array
error.knowledge_graph.edge.qualifiers.qualifier.type_id.unknown
Message: Edge has unknown qualifier_type_id
Context: edge_id, identifier
Description: A qualifier qualifier_type_id must be defined in the specified version of Biolink
error.knowledge_graph.edge.qualifiers.qualifier.value.not_a_predicate
Message: Qualifier_type_id ‘biolink:qualified_predicate’ for edge has a qualifier_value which is not a Biolink predicate
Context: identifier, qualifier_value
Description: The ‘qualifier_value’ for ‘biolink:qualified_predicate’ should be a Biolink predicate term
error.knowledge_graph.edge.qualifiers.qualifier.invalid
Message: Validation of qualifier in qualifiers threw an unexpected exception
Context: identifier, qualifier_type_id, qualifier_value, reason
Description: Validation of a specified ‘qualifier_type_id’ and ‘qualifier_value’ failed for a given exceptional reason
error.knowledge_graph.edge.knowledge_level.missing
Message: Edge is missing its required ‘knowledge_level’ property
Context: edge_id
Description: The ‘knowledge_level’ slot is required for all edges in knowledge graphs complying with the specified TRAPI and Biolink Model release
error.knowledge_graph.edge.knowledge_level.duplicated
Message: The ‘knowledge_level’ slot is duplicated for the given edge
Context: identifier, edge_id
Description: Each edge should only have one ‘knowledge_level’ attribute value. Additional ones are ignored
error.knowledge_graph.edge.knowledge_level.invalid
Message: The indicated ‘knowledge_level’ slot value is invalid for the given edge
Context: identifier, context
Description: Acceptable values of the ‘knowledge_level’ slot are only as enumerated in the specified Biolink Model
error.knowledge_graph.edge.agent_type.missing
Message: Edge is missing its required ‘agent_type’ property
Context: identifier
Description: The ‘agent_type’ slot is required for all edges in knowledge graphs complying with the specified Biolink Model release
error.knowledge_graph.edge.agent_type.duplicated
Message: The ‘agent_type’ slot is duplicated for the given edge
Context: identifier, edge_id
Description: Each edge should only have one ‘agent_type’ attribute value. Additional ones are ignored
error.knowledge_graph.edge.agent_type.invalid
Message: The indicated ‘agent_type’ slot value is invalid for the given edge
Context: identifier, context
Description: Acceptable values of the ‘agent_type’ slot are only as enumerated in the specified Biolink Model
error.knowledge_graph.edge.sources.missing
Message: Missing ‘sources’ key for Edge
Context: identifier
Description: Edge must have a ‘sources’ key with a non-empty associated value
error.knowledge_graph.edge.sources.empty
Message: Empty ‘sources’ property in Edge
Context: identifier
Description: Value of ‘sources’ property in Knowledge Graph edge must contain a list of one or more RetrievalSource entries
error.knowledge_graph.edge.sources.not_array
Message: The ‘sources’ are not an array in Edge
Context: identifier
Description: Value of the ‘sources’ property in Knowledge Graph edge must be an array of RetrievalSource entries
error.knowledge_graph.edge.sources.retrieval_source.resource_id.infores.missing
Message: RetrievalSource ‘resource_id’ identifier is missing
Context: edge_id
Description: A RetrievalSource ‘resource_id’ value should not be None or empty
error.knowledge_graph.edge.sources.retrieval_source.resource_id.infores.not_curie
Message: One (or more) Infores value(s) is not a valid well-formed CURIE
Context: edge_id, identifier
Description: A RetrievalSource ‘resource_id’ Infores value must be a well-formed CURIE
error.knowledge_graph.edge.sources.retrieval_source.resource_id.infores.invalid
Message: Invalid Infores namespace
Context: edge_id, identifier
Description: A RetrievalSource ‘resource_id’ Infores CURIE must come from the Infores namespace
error.knowledge_graph.edge.sources.retrieval_source.resource_id.infores.unknown
Message: Unregistered infores
Context: edge_id, identifier
Description: A ‘retrieval_source.resource_id’ value must be a registered Infores identifier
error.knowledge_graph.edge.sources.retrieval_source.resource_id.empty
Message: Empty ‘resource_id’ property in Edge
Context: identifier
Description: Value of the ‘resource_id’ property in the RetrievalSource of a Knowledge Graph Edge must be a non-empty Infores identifier
error.knowledge_graph.edge.sources.retrieval_source.upstream_resource_ids.infores.missing
Message: A RetrievalSource ‘upstream_resource_ids’ identifier is missing
Context: edge_id
Description: A RetrievalSource ‘upstream_resource_ids’ value should not be None or empty
error.knowledge_graph.edge.sources.retrieval_source.upstream_resource_ids.infores.not_curie
Message: One (or more) Infores value(s) is not a valid well-formed CURIE
Context: edge_id, identifier
Description: A RetrievalSource ‘upstream_resource_ids’ Infores value must be a well-formed CURIE
error.knowledge_graph.edge.sources.retrieval_source.upstream_resource_ids.infores.invalid
Message: Invalid Infores namespace
Context: edge_id, identifier
Description: A RetrievalSource ‘upstream_resource_ids’ Infores CURIE must come from the Infores namespace
error.knowledge_graph.edge.sources.retrieval_source.upstream_resource_ids.infores.unknown
Message: Unregistered Infores
Context: edge_id, identifier
Description: A ‘retrieval_source.upstream_resource_ids’ values must be registered infores identifiers
error.knowledge_graph.edge.sources.retrieval_source.resource_role.empty
Message: Empty ‘resource_role’ property in Edge
Context: identifier
Description: Value of the ‘resource_role’ property in the RetrievalSource of a Knowledge Graph Edge must be a non-empty ResourceRole enum value
Warning
warning.biolink.element.range.unspecified
Message: Undefined slot range specification
Context: identifier, context, value
Description: Biolink Model error: the range slot of the specified element is missing or its value is not a known enum
warning.trapi.response.status.unknown
Message: TRAPI Response has unrecognized status code
Context: identifier
Description: The TRAPI Response status code should be one of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable
warning.trapi.response.schema_version.missing
Message: TRAPI Response is missing its TRAPI schema version
Description: The TRAPI Response should specify its TRAPI version compliance
warning.trapi.response.biolink_version.missing
Message: TRAPI Response is missing its Biolink Model version
Description: The TRAPI Response should specify its Biolink Model version compliance
warning.trapi.response.message.knowledge_graph.empty
Message: Response returned an empty Message Knowledge Graph
Description: An empty Knowledge Graph is allowed but merits a boundary response warning
warning.trapi.response.message.knowledge_graph.node.category.imprecise
Message: The category of the knowledge graph node is imprecise
Context: identifier, expected_category, observed_categories
Description: The category of the knowledge graph node matching specified input node is more generic than expected
warning.trapi.response.message.knowledge_graph.node.identifier.unresolved
Message: Node identifier unresolved by node normalization
Context: identifier
Description: Node Normalizer didn’t return an identifier clique for the specified CURIE
warning.trapi.response.message.knowledge_graph.node.identifier.no_equivalent_identifiers
Message: No equivalent identifiers found for node identifier
Context: identifier
Description: Node Normalizer didn’t return any equivalent identifiers for the specified CURIE
warning.trapi.response.message.knowledge_graph.node.identifier.no_preferred_identifier
Message: Preferred identifier not provided for node identifier
Context: identifier
Description: Node Normalizer didn’t return a preferred identifier for the specified CURIE
warning.trapi.response.message.knowledge_graph.node.identifier.no_aliases
Message: Node identifier has no reported aliases
Context: identifier
Description: Node Normalizer didn’t return any aliases for the specified CURIE
warning.trapi.response.message.knowledge_graph.node.identifier.namespace.non_canonical
Message: Non-canonical node identifier namespace in aliases
Context: identifier
Description: The letter case of the namespace of the specified CURIE is not canonical to that reported by the Node Normalizer. Check the prefix map of the Biolink Model for correct version.
warning.trapi.response.message.knowledge_graph.node.identifier.namespace.missing
Message: CURIE missing from reported aliases
Context: identifier
Description: The list of aliases returned by the Node Normalizer didn’t include the specified CURIE
warning.trapi.response.message.results.empty
Message: Response returned empty Message.results
Description: Empty Results is allowed but merits a boundary response warning
warning.trapi.response.workflow.runner_parameters.missing
Message: TRAPI Response.workflow.runner_parameters property is missing
Description: If a ‘runner_parameters’ property value is given for a workflow step specification, it should not be null. This field will be ignored
warning.trapi.response.workflow.parameters.missing
Message: TRAPI Response.workflow.parameters property is missing
Description: If a ‘parameters’ property value is given for a workflow step specification, it should not be null. This field will be ignored
warning.graph.empty
Message: Empty graph
Context: identifier
Description: An empty graph in this particular context is allowed but merits a boundary response warning
warning.input_edge.node.category.deprecated
Message: Node category had deprecated category
Context: node_id, identifier
Description: Node category is deprecated in the current model, to be removed in the future. Review Biolink Model for suitable replacement
warning.input_edge.node.category.not_concrete
Message: Node has unknown, abstract or mixin category
Context: node_id, identifier
Description: Node category may be unknown, abstract or a mixin in the current model. TRAPI Responses using this edge may not resolve any Knowledge Graph nodes with this category. Review Biolink Model for ‘concrete’ replacement
warning.input_edge.node.id.unmapped_to_category
Message: Node identifier found unmapped to target categories for node
Context: identifier, unmapped_ids, categories
Description: The namespaces of Biolink model node of specified category may be incomplete with respect to identifiers being used in input edge data
warning.input_edge.predicate.deprecated
Message: Edge has deprecated predicate
Context: identifier
Description: Input data edge predicate is deprecated in the current model, to be removed in the future. Review Biolink Model for a suitable replacement
warning.input_edge.predicate.non_canonical
Message: Edge has non-canonical predicate
Context: edge_id, identifier
Description: A predicate selected for use as input data should preferably be tagged as ‘canonical’ in the specified Biolink Model release
warning.query_graph.nodes.dangling
Message: Dangling nodes
Context: identifier
Description: At least one query node is unused in the query graph
warning.query_graph.node.category.deprecated
Message: Node has deprecated category
Context: node_id, identifier
Description: Node category is deprecated in the current model, to be removed in the future. Review Biolink Model for suitable replacement
warning.query_graph.node.ids.unmapped_prefix
Message: Node identifiers found unmapped to target categories for node
Context: identifier, unmapped_ids, categories
Description: One or more node CURIE identifier namespaces are not found among any ‘id_prefix’ slot values in specified categories in the validating Biolink Model version
warning.query_graph.edge.predicate.deprecated
Message: Edge has deprecated predicate
Context: identifier
Description: Edge predicate is deprecated in the current model, to be removed in the future. Review Biolink Model for a suitable replacement
warning.query_graph.edge.predicate.non_canonical
Message: Edge has non-canonical predicate
Context: edge_id, identifier
Description: A predicate selected for use in a query graph should preferably be tagged as ‘canonical’ in the specified Biolink Model release
warning.query_graph.edge.qualifier_constraints.qualifier_set.qualifiers.qualifier.value.unresolved
Message: The ‘qualifier_type_id’ for edge has unresolved ‘qualifier_value’
Context: edge_id, identifier, qualifier_type_id
Description: A ‘qualifier_value’ for the specified ‘qualifier_type_id’ of a qualifier likely could not be resolved without knowledge of the edge category
warning.knowledge_graph.nodes.dangling
Message: Dangling nodes
Context: identifier
Description: At least one query node is unused in the knowledge graph
warning.knowledge_graph.node.name.missing
Message: Name is missing for node
Context: identifier
Description: Although TRAPI 1.4.0 states ‘nullable: True’, Translator user interface functionally requires that a non-empty ‘name’ property value ought to be specified in a knowledge graph node
warning.knowledge_graph.node.category.deprecated
Message: Node has deprecated category
Context: node_id, identifier
Description: Node category is deprecated in the current model, to be removed in the future. Review Biolink Model for a suitable replacement
warning.knowledge_graph.node.category.abstract_or_mixin
Message: Node has a abstract or mixin category
Context: node_id, identifier
Description: Node category is abstract or a mixin in the current model. Please consider selecting a more specific, concrete Biolink Model category
warning.knowledge_graph.node.id.unmapped_prefix
Message: Node identifier found unmapped to target categories for node
Context: identifier, node_id
Description: Node CURIE identifier namespace not found among any ‘id_prefix’ slot values in specified categories in the validating Biolink Model version
warning.knowledge_graph.edge.predicate.deprecated
Message: Edge has deprecated predicate
Context: identifier
Description: Edge predicate is deprecated in the current model, to be removed in the future. Review Biolink Model for a suitable replacement
warning.knowledge_graph.edge.predicate.non_canonical
Message: Edge has non-canonical predicate
Context: edge_id, identifier
Description: A predicate selected for use in a knowledge graph should preferably be tagged as ‘canonical’ in the specified Biolink Model release
warning.knowledge_graph.edge.qualifiers.qualifier.value.unresolved
Message: The ‘qualifier_type_id’ for edge has unresolved ‘qualifier_value’
Context: edge_id, identifier, qualifier_type_id
Description: A ‘qualifier_value’ for the specified ‘qualifier_type_id’ of a qualifier likely could not be resolved without knowledge of the edge category
warning.knowledge_graph.edge.attribute.type_id.is_category
Message: Edge has an ‘attribute_type_id’ that is a category
Context: edge_id, identifier
Description: Edge ‘attribute_type_id’ value is usually not drawn from the node category hierarchy
warning.knowledge_graph.edge.attribute.type_id.is_predicate
Message: Edge has an ‘attribute_type_id’ that is a predicate
Context: edge_id, identifier
Description: Edge ‘attribute_type_id’ value is usually not drawn from the node predicate hierarchy
warning.knowledge_graph.edge.attribute.type_id.not_association_slot
Message: Edge has an attribute_type_id that is not an association slot
Context: edge_id, identifier
Description: Edge ‘attribute_type_id’ value should generally be a term defined within the biolink:association_slot hierarchy
warning.knowledge_graph.edge.attribute.type_id.non_biolink_prefix
Message: Edge has an attribute_type_id that has a non-Biolink CURIE prefix mapped to Biolink
Context: edge_id, identifier
Description: Non-Biolink CURIEs are tolerated, but not preferred, as term value for the attribute_type_id properties of edge attributes
warning.knowledge_graph.edge.attribute.type_id.deprecated
Message: Edge has a deprecated ‘attribute_type_id’
Context: identifier
Description: Edge ‘attribute_type_id’ is deprecated in current model, to be removed in the future. Review Biolink Model for replacement
warning.knowledge_graph.edge.provenance.multiple_primary
Message: Edge has recorded multiple ‘primary’ knowledge sources
Context: identifier, sources
Description: Edge attributes should record only a single primary knowledge source provenance attribute value
warning.knowledge_graph.edge.provenance.ara.missing
Message: Edge is missing ARA knowledge source provenance
Context: edge_id, identifier
Description: Edge attributes ARAs should record the Infores identifier of their knowledge source provenance with respect to ARA
warning.knowledge_graph.edge.provenance.kp.missing
Message: Edge attribute values are missing expected Knowledge Provider provenance
Context: edge_id, identifier, kp_source_type
Description: Edge attributes of ARAs and KPs should record the infores identifier of their knowledge source provenance with respect to KP
warning.knowledge_graph.edge.knowledge_level.missing
Message: Edge is missing its required ‘knowledge_level’ property
Context: edge_id
Description: The ‘knowledge_level’ slot is currently optional but recommended for all edges in knowledge graphs complying with the specified TRAPI and Biolink Model release
warning.knowledge_graph.edge.agent_type.missing
Message: Edge is missing its required ‘agent_type’ property
Context: identifier
Description: The ‘agent_type’ slot is currently optional but recommended for all edges in knowledge graphs complying with the specified Biolink Model release
warning.knowledge_graph.edge.treats.support_graph.missing
Message: Edge with a treats-related predicate is missing its required ‘support_graph’ attribute
Context: identifier
Description: A ‘support_graph’ may be required as an explanation for a given ‘treats’ statement assertion
Information
info.trapi.response.message.knowledge_graph.node.parent.match
Message: Query node is ontological parent of its matching knowledge graph node
Context: identifier, query_id, context
Description: The knowledge graph node identifier was matched as an ontological subclass of the specified query node identifier
info.excluded
Message: All test case S-P-O triples from resource test location, or specific user excluded S-P-O triples
Context: identifier
Description: Check the JSON KP test edge data file for specific ‘exclude_tests’ directives, either global to the file, or on specific edges
info.compliant
Message: Biolink Model-compliant TRAPI Message
Description: Specified TRAPI message completely satisfies the target TRAPI schema and Biolink Model semantics for specified releases of these standards
info.input_edge.predicate.abstract
Message: Edge has an ‘abstract’ predicate
Context: edge_id, identifier
Description: Input edge data can have ‘abstract’ predicates, when the mode of validation is ‘non-strict’
info.input_edge.predicate.mixin
Message: Edge has an ‘mixin’ predicate
Context: edge_id, identifier
Description: Input edge data can have ‘mixin’ predicates, when the mode of validation is ‘non-strict’
info.query_graph.edge.predicate.abstract
Message: Edge has an ‘abstract’ predicate
Context: edge_id, identifier
Description: TRAPI Messages in Query Graphs can have ‘abstract’ predicates, when the mode of validation is ‘non-strict’
info.query_graph.edge.predicate.mixin
Message: Edge has an ‘mixin’ predicate
Context: edge_id, identifier
Description: TRAPI Messages in Query Graphs can have ‘mixin’ predicates, when the mode of validation is ‘non-strict’
info.knowledge_graph.edge.predicate.abstract
Message: Edge has an ‘abstract’ predicate
Context: edge_id, identifier
Description: TRAPI Messages in Knowledge Graphs can have ‘abstract’ predicates, when the mode of validation is ‘non-strict’
info.knowledge_graph.edge.predicate.mixin
Message: Edge has an ‘mixin’ predicate
Context: edge_id, identifier
Description: TRAPI Messages in Knowledge Graphs can have ‘mixin’ predicates, when the mode of validation is ‘non-strict’
info.knowledge_graph.edge.attribute.type_id.abstract
Message: Edge has an ‘abstract’ attribute_type_id
Context: edge_id, identifier
Description: TRAPI Messages in Knowledge Graphs can have ‘abstract’ attribute type identifiers, when the mode of validation is ‘non-strict’
info.knowledge_graph.edge.attribute.type_id.mixin
Message: Edge has an ‘mixin’ attribute_type_id
Context: edge_id, identifier
Description: TRAPI Messages in Knowledge Graphs can have ‘mixin’ attribute type identifiers, when the mode of validation is ‘non-strict’
Skipped Test
skipped.test
Message: Test case skipped for a test asset, for a specified reason
Context: identifier, context, reason
Description: Test was skipped for the documented ‘reason’, for the test specified by the ‘identifier’ in the ‘context’ indicated