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 locationy.
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 TRAPI Response Message Knowledge Graph 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.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.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.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!
Information
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.