From c8b0c98cca83882db690e5c547a84e48c107d650 Mon Sep 17 00:00:00 2001 From: vdancik Date: Tue, 28 Sep 2021 01:55:18 -0400 Subject: [PATCH] Add annotate-nodes operation to MolePro TRAPI 1.2.1 --- .../MolePro-TRAPI-1.2.yaml | 83 +++++++++++-------- 1 file changed, 49 insertions(+), 34 deletions(-) diff --git a/molecular_data_provider/MolePro-TRAPI-1.2.yaml b/molecular_data_provider/MolePro-TRAPI-1.2.yaml index 9d47bb5f..abad5852 100644 --- a/molecular_data_provider/MolePro-TRAPI-1.2.yaml +++ b/molecular_data_provider/MolePro-TRAPI-1.2.yaml @@ -1,7 +1,7 @@ openapi: 3.0.1 info: description: Molecular Data Provider for NCATS Biomedical Translator - version: 1.2.0.0 + version: 1.2.1.0 title: Molecular Data Provider for NCATS Biomedical Translator contact: email: translator@broadinstitute.org @@ -23,10 +23,11 @@ info: url: https://github.com/NCATSTranslator/translator_extensions/blob/\ production/x-translator/ x-trapi: - version: 1.2.0 + version: 1.2.1 asyncquery: false operations: - lookup + - annotate_nodes externalDocs: description: >- The values for version are restricted according to the regex in @@ -187,12 +188,16 @@ components: nullable: true workflow: description: List of workflow steps to be executed. - type: array - items: - type: object - properties: - id: - type: string + allOf: + - $ref: http://standards.ncats.io/workflow/1.0.0/schema + nullable: true + submitter: + type: string + description: >- + Any string for self-identifying the submitter of a query. The + purpose of this optional field is to aid in the tracking of + the source of queries for development and issue resolution. + nullable: true additionalProperties: true example: message: @@ -200,14 +205,14 @@ components: edges: e00: subject: n00 - predicate: 'biolink:affects' + predicates: ['biolink:affects'] object: n01 nodes: n00: - id: 'PUBCHEM.COMPOUND:2244' - category: 'biolink:ChemicalSubstance' + ids: ['PUBCHEM.COMPOUND:2244'] + categories: ['biolink:SmallMolecule'] n01: - category: 'biolink:Gene' + categories: ['biolink:Gene'] required: - message AsyncQuery: @@ -245,12 +250,16 @@ components: nullable: true workflow: description: List of workflow steps to be executed. - type: array - items: - type: object - properties: - id: - type: string + allOf: + - $ref: http://standards.ncats.io/workflow/1.0.0/schema + nullable: true + submitter: + type: string + description: >- + Any string for self-identifying the submitter of a query. The + purpose of this optional field is to aid in the tracking of + the source of queries for development and issue resolution. + nullable: true additionalProperties: true required: - callback @@ -291,12 +300,9 @@ components: nullable: true workflow: description: List of workflow steps that were executed. - type: array - items: - type: object - properties: - id: - type: string + allOf: + - $ref: http://standards.ncats.io/workflow/1.0.0/schema + nullable: true additionalProperties: true required: - message @@ -421,6 +427,7 @@ components: A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better. + nullable: true additionalProperties: true required: - node_bindings @@ -561,18 +568,18 @@ components: to AND) items: $ref: '#/components/schemas/QueryConstraint' - nullable: true + default: [] additionalProperties: true QEdge: type: object description: >- An edge in the QueryGraph used as an filter pattern specification in a - query. If optional predicate or relation properties are not specified, - they are assumed to be wildcard matches to the target knowledge space. + query. If the optional predicate property is not specified, + it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with - the terms provided is assumed, such that edge bindings returned may be - an exact match to the given QEdge predicate or relation term ('class'), - or to a term which is a subclass of the QEdge specified term. + the term provided is assumed, such that edge bindings returned may be + an exact match to the given QEdge predicate term, + or to a term that is a descendant of the QEdge predicate term. properties: predicates: type: array @@ -602,7 +609,7 @@ components: to AND) items: $ref: '#/components/schemas/QueryConstraint' - nullable: true + default: [] additionalProperties: true required: - subject @@ -879,7 +886,9 @@ components: for which the predicate is the most specific available. items: $ref: '#/components/schemas/MetaEdge' - minItems: 1 + required: + - nodes + - edges MetaNode: type: object description: >- @@ -900,6 +909,7 @@ components: Node attributes provided by this TRAPI web service. items: $ref: '#/components/schemas/MetaAttribute' + nullable: true required: - id_prefixes additionalProperties: false @@ -930,6 +940,7 @@ components: Edge attributes provided by this TRAPI web service. items: $ref: '#/components/schemas/MetaAttribute' + nullable: true required: - subject - predicate @@ -949,12 +960,15 @@ components: description: >- Source of an attribute provided by this TRAPI web service. example: infores:chembl + nullable: true original_attribute_names: type: array items: type: string description: >- Names of an the attribute as provided by the source. + nullable: true + minItems: 1 constraint_use: type: boolean description: >- @@ -967,6 +981,7 @@ components: Human-readable name or label for the constraint concept. Required whenever constraint_use is true. example: p-value + nullable: true required: - attribute_type_id QueryConstraint: @@ -985,7 +1000,6 @@ components: submit the new type for consideration by the appropriate authority. example: EDAM:data_0844 - nullable: false name: type: string description: >- @@ -994,7 +1008,6 @@ components: as the 'id'. This is redundant but required for human readability. example: molecular mass - nullable: false not: type: boolean default: false @@ -1035,6 +1048,7 @@ components: property. The Units of Measurement Ontology (UO) should be used if possible. The unit_id MUST be provided for (lists of) numerical values that correspond to a quantity that has units. + nullable: true unit_name: example: kilodalton description: >- @@ -1043,6 +1057,7 @@ components: property. The Units of Measurement Ontology (UO) SHOULD be used if possible. This property SHOULD be provided if a unit_id is provided. This is redundant but recommended for human readability. + nullable: true required: - name - id