rcsb-api-tools

RCSB Saguaro Web API is an open-source library that includes different tools to validate and request data from the Sequence Coordinates Server, the RCSB Data API and the RCSB Search Service.

Node Module Instalation

npm install @rcsb/rcsb-api-tools

Requesting RCSB GraphQL data

import {GraphQLRequest} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/GraphQLRequest"

const client = new GraphQLRequest("data-api"|"sequence-coordinates"|url);

client.request(query_params, query_string);

Example

query_params

const query_params = {
  queryId: "P01112",
  from: "UNIPROT",
  to: "PDB_ENTITY"
}

query_string

query QueryAlignment($queryId: String!, $from: String!, $to: String!, $range:[Int!]){
     alignments(
         queryId:$queryId
         from:$from
         to:$to
         range:$range
     ){
         query_sequence
         target_alignments {
             target_id
             orientation
             target_sequence
             coverage {
                 query_coverage
                 query_length
                 target_coverage
                 target_length
             }
             aligned_regions {
                 query_begin
                 query_end
                 target_begin
                 target_end
                 exon_shift
             }
         }
 
     }
 }

Importing RCSB GraphQL interfaces

data-api/yosemite server

E.g. import type {CoreEntry, RcsbEntryContainerIdentifiers} from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Yosemite/GqlTypes";

sequence-coordinates/borrego server

E.g. import type {Query, SequenceAnnotations, SequenceAlignments} from '@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes';

GraphQL query validation

import {validateQueries} from "@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Generator/GeneratorTools";
validateQueries(graphql_schema_url, "path_to_queries/my_query.graphql");

Requesting RCSB Search data

import {SearchRequest} from "@rcsb/rcsb-api-tools/lib/RcsbSearch/SearchRequest";

const client = new SearchRequest();

client.request(query_object);

Example

import type {SearchQuery} from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchQueryInterface";
import {LogicalOperator, ReturnType, Service, Type} from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";
import {RcsbSearchMetadata} from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata";

const search_query = {
    query: {
        type: Type.Group,
        nodes:[{
            type:Type.Terminal,
            service: Service.FullText,
            parameters:{
                attribute:RcsbSearchMetadata.RcsbEntryInfo.DiffrnResolutionHigh.Value.path,
                operator:RcsbSearchMetadata.RcsbEntryInfo.DiffrnResolutionHigh.Value.operator.Greater,
                value: 2
            }
        },{
            type: Type.Terminal,
            service: Service.FullText,
            parameters: {
                attribute: RcsbSearchMetadata.RcsbEntitySourceOrganism.TaxonomyLineage.Name.path,
                operator: RcsbSearchMetadata.RcsbEntitySourceOrganism.TaxonomyLineage.Name.operator.ExactMatch,
                value: "Homo sapiens"
            }
        }],
        logical_operator: LogicalOperator.And,
    },
    return_type: ReturnType.PolymerEntity
};
const search = new SearchRequest();
search.request(search_query);

Importing RCSB Search classes/interfaces

Search metadata class

Search metadata class provides the searchable paths and methods for the RCSB Search API

import {RcsbSearchMetadata} from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchMetadata";

Utility examples

E.g. RcsbSearchMetadata.RcsbEntryInfo.DiffrnResolutionHigh.Value.path attribute contains the string "rcsb_entry_info.diffrn_resolution_high.value"

E.g. RcsbSearchMetadata.RcsbEntryInfo.DiffrnResolutionHigh.Value.operator enumerates the possible comparison operations (i.e. Equals, Greater, Range, ...)

Search enums

Search enums provide a collection of enums/classes that provide a controlled vocabulary to build the RCSB Search queries. The name of each enum/class (camel cased) matches with the RCSB search schema field name in snake case format. E.g. import {AggregationType, Operator, ReturnType, Service} from "@rcsb/rcsb-api-tools/lib/RcsbSearch/Types/SearchEnums";

AggregationType encodes the possible values of the schema field "aggregation_type", i.e. AggregationType.Terms = "terms", AggregationType.Histogram = "histogram", ...

Building GraphQL types from specific URLs

• GraphQL types can be generated from specific URLs. By default, production server are used
  • E.g. npm run buildGraphQLInterfaces -- --data-api http://132.249.210.199/graphql --1d-service http://132.249.213.161/graphql

External schemas

• DW schemas are collected from rcsb-mojave-model project released in maven.
  • rcsb-mojave-model:target/generated-sources/schema/core
• Search API schemas are collected from the rcsb-arches git repo.
  • rcsb-arches:src/main/resources/schema

Download external schemas

• DW schemas
  • npm run downloadDwSchemas -- --schema-version <VERSION-TAG>
  • E.g. npm run downloadDwSchemas -- --schema-version 1.32.1-MODELS-SNAPSHOT
• Search schemas
  • npm run downloadSearchSchemas -- --branch-name <GIT-REMOTE-BRANCH-NAME>
  • E.g. npm run downloadSearchSchemas -- --branch-name dev-computed-models