diff --git a/packages/genome-nexus-ts-api-client/package.json b/packages/genome-nexus-ts-api-client/package.json deleted file mode 100644 index 94d02dde6c0..00000000000 --- a/packages/genome-nexus-ts-api-client/package.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "name": "genome-nexus-ts-api-client", - "description": "Genome Nexus API Client for TypeScript", - "version": "1.1.32", - "main": "dist/index.js", - "module": "dist/index.es.js", - "jsnext:main": "dist/index.es.js", - "typings": "dist/index.d.ts", - "styles": "dist/styles.css", - "engines": { - "node": "15.2.1", - "yarn": "1.22.5" - }, - "files": [ - "dist" - ], - "author": "cBioPortal", - "license": "AGPL-3.0-or-later", - "repository": "cBioPortal/cbioportal-frontend", - "scripts": { - "build": "cross-env NODE_ENV=production NODE_OPTIONS=--max-old-space-size=2048 yarn run rollup", - "start": "yarn run watch", - "watch": "yarn run rollup:watch", - "watchSSL": "yarn run watch", - "rollup": "rollup -c rollup.config.ts", - "rollup:watch": "rollup -c rollup.config.ts -w", - "prepare": "yarn run build", - "test": "cross-env jest $GREP --env=jsdom --runInBand --ci --reporters=default --reporters=jest-junit --passWithNoTests", - "test:watch": "yarn run test --watch" - }, - "dependencies": { - "superagent": "^3.8.3", - "typescript": "4.0.3" - } -} diff --git a/packages/genome-nexus-ts-api-client/rollup.config.ts b/packages/genome-nexus-ts-api-client/rollup.config.ts deleted file mode 100644 index 055d595f7e2..00000000000 --- a/packages/genome-nexus-ts-api-client/rollup.config.ts +++ /dev/null @@ -1,9 +0,0 @@ -import getRollupOptions from '../config/rollup.config'; -import pkg from './package.json'; - -export default getRollupOptions( - 'src/index.tsx', - pkg.main, - pkg.module, - pkg.styles -); diff --git a/packages/genome-nexus-ts-api-client/src/generated/Genome2StructureAPI-docs.json b/packages/genome-nexus-ts-api-client/src/generated/Genome2StructureAPI-docs.json deleted file mode 100644 index e69de29bb2d..00000000000 diff --git a/packages/genome-nexus-ts-api-client/src/generated/Genome2StructureAPI.ts b/packages/genome-nexus-ts-api-client/src/generated/Genome2StructureAPI.ts deleted file mode 100644 index 06cf509bd60..00000000000 --- a/packages/genome-nexus-ts-api-client/src/generated/Genome2StructureAPI.ts +++ /dev/null @@ -1,1053 +0,0 @@ -import * as request from "superagent"; - -type CallbackHandler = (err: any, res ? : request.Response) => void; -export type Alignment = { - 'alignmentId': number - - 'bitscore': number - - 'chain': string - - 'evalue': string - - 'identity': number - - 'identityPositive': number - - 'midlineAlign': string - - 'pdbAlign': string - - 'pdbFrom': number - - 'pdbId': string - - 'pdbNo': string - - 'pdbSeg': string - - 'pdbTo': number - - 'residueMapping': Array < ResidueMapping > - - 'segStart': string - - 'seqAlign': string - - 'seqFrom': number - - 'seqId': string - - 'seqTo': number - - 'updateDate': string - -}; -export type ResidueMapping = { - 'pdbAminoAcid': string - - 'pdbPosition': number - - 'queryAminoAcid': string - - 'queryPosition': number - -}; - -/** - * A Genome to Strucure (G2S) API Supports Automated Mapping and Annotating Genomic Variants in 3D Protein Structures. Supports Inputs from Human Genome Position, Uniprot and Human Ensembl Names. - * @class Genome2StructureAPI - * @param {(string)} [domainOrOptions] - The project domain. - */ -export default class Genome2StructureAPI { - - private domain: string = ""; - private errorHandlers: CallbackHandler[] = []; - - constructor(domain ? : string) { - if (domain) { - this.domain = domain; - } - } - - getDomain() { - return this.domain; - } - - addErrorHandler(handler: CallbackHandler) { - this.errorHandlers.push(handler); - } - - private request(method: string, url: string, body: any, headers: any, queryParameters: any, form: any, reject: CallbackHandler, resolve: CallbackHandler, errorHandlers: CallbackHandler[]) { - let req = (new(request as any).Request(method, url) as request.Request) - .query(queryParameters); - Object.keys(headers).forEach(key => { - req.set(key, headers[key]); - }); - - if (body) { - req.send(body); - } - - if (typeof(body) === 'object' && !(body.constructor.name === 'Buffer')) { - req.set('Content-Type', 'application/json'); - } - - if (Object.keys(form).length > 0) { - req.type('form'); - req.send(form); - } - - req.end((error, response) => { - if (error || !response.ok) { - reject(error); - errorHandlers.forEach(handler => handler(error)); - } else { - resolve(response); - } - }); - } - - getPdbAlignmentBySequenceUsingGETURL(parameters: { - 'sequence': string, - 'paramList' ? : Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments'; - if (parameters['sequence'] !== undefined) { - queryParameters['sequence'] = parameters['sequence']; - } - - if (parameters['paramList'] !== undefined) { - queryParameters['paramList'] = parameters['paramList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Get PDB Alignments by Protein Sequence - * @method - * @name Genome2StructureAPI#getPdbAlignmentBySequenceUsingGET - * @param {string} sequence - Input Protein Sequence: ETGQSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPP - * @param {array} paramList - Default Blast Parameters: - Evalue=1e-10,Wordsize=3,Gapopen=11,Gapextend=1, - Matrix=BLOSUM62,Comp_based_stats=2, - Threshold=11,Windowsize=40 - */ - getPdbAlignmentBySequenceUsingGET(parameters: { - 'sequence': string, - 'paramList' ? : Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['sequence'] !== undefined) { - queryParameters['sequence'] = parameters['sequence']; - } - - if (parameters['sequence'] === undefined) { - reject(new Error('Missing required parameter: sequence')); - return; - } - - if (parameters['paramList'] !== undefined) { - queryParameters['paramList'] = parameters['paramList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - getPdbAlignmentBySequenceUsingPOSTURL(parameters: { - 'sequence': string, - 'paramList' ? : Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments'; - if (parameters['sequence'] !== undefined) { - queryParameters['sequence'] = parameters['sequence']; - } - - if (parameters['paramList'] !== undefined) { - queryParameters['paramList'] = parameters['paramList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Get PDB Alignments by Protein Sequence - * @method - * @name Genome2StructureAPI#getPdbAlignmentBySequenceUsingPOST - * @param {string} sequence - Input Protein Sequence: ETGQSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPP - * @param {array} paramList - Default Blast Parameters: - Evalue=1e-10,Wordsize=3,Gapopen=11,Gapextend=1, - Matrix=BLOSUM62,Comp_based_stats=2, - Threshold=11,Windowsize=40 - */ - getPdbAlignmentBySequenceUsingPOST(parameters: { - 'sequence': string, - 'paramList' ? : Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['sequence'] !== undefined) { - queryParameters['sequence'] = parameters['sequence']; - } - - if (parameters['sequence'] === undefined) { - reject(new Error('Missing required parameter: sequence')); - return; - } - - if (parameters['paramList'] !== undefined) { - queryParameters['paramList'] = parameters['paramList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - getPdbAlignmentReisudeBySequenceUsingGETURL(parameters: { - 'sequence': string, - 'positionList' ? : Array < string > , - 'paramList' ? : Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments/residueMapping'; - if (parameters['sequence'] !== undefined) { - queryParameters['sequence'] = parameters['sequence']; - } - - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters['paramList'] !== undefined) { - queryParameters['paramList'] = parameters['paramList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Get PDB Residue Mapping by Protein Sequence and Residue position - * @method - * @name Genome2StructureAPI#getPdbAlignmentReisudeBySequenceUsingGET - * @param {string} sequence - Input Protein Sequence: ETGQSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPP - * @param {array} positionList - Input Residue Positions e.g. 10,20 - * @param {array} paramList - Default Blast Parameters: - Evalue=1e-10,Wordsize=3,Gapopen=11,Gapextend=1, - Matrix=BLOSUM62,Comp_based_stats=2, - Threshold=11,Windowsize=40 - */ - getPdbAlignmentReisudeBySequenceUsingGET(parameters: { - 'sequence': string, - 'positionList' ? : Array < string > , - 'paramList' ? : Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments/residueMapping'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['sequence'] !== undefined) { - queryParameters['sequence'] = parameters['sequence']; - } - - if (parameters['sequence'] === undefined) { - reject(new Error('Missing required parameter: sequence')); - return; - } - - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters['paramList'] !== undefined) { - queryParameters['paramList'] = parameters['paramList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - getPdbAlignmentReisudeBySequenceUsingPOSTURL(parameters: { - 'sequence': string, - 'positionList' ? : Array < string > , - 'paramList' ? : Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments/residueMapping'; - if (parameters['sequence'] !== undefined) { - queryParameters['sequence'] = parameters['sequence']; - } - - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters['paramList'] !== undefined) { - queryParameters['paramList'] = parameters['paramList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Get PDB Residue Mapping by Protein Sequence and Residue position - * @method - * @name Genome2StructureAPI#getPdbAlignmentReisudeBySequenceUsingPOST - * @param {string} sequence - Input Protein Sequence: ETGQSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPP - * @param {array} positionList - Input Residue Positions e.g. 10,20 - * @param {array} paramList - Default Blast Parameters: - Evalue=1e-10,Wordsize=3,Gapopen=11,Gapextend=1, - Matrix=BLOSUM62,Comp_based_stats=2, - Threshold=11,Windowsize=40 - */ - getPdbAlignmentReisudeBySequenceUsingPOST(parameters: { - 'sequence': string, - 'positionList' ? : Array < string > , - 'paramList' ? : Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments/residueMapping'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['sequence'] !== undefined) { - queryParameters['sequence'] = parameters['sequence']; - } - - if (parameters['sequence'] === undefined) { - reject(new Error('Missing required parameter: sequence')); - return; - } - - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters['paramList'] !== undefined) { - queryParameters['paramList'] = parameters['paramList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - getAlignmentUsingGETURL(parameters: { - 'idType': string, - 'id': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments/{id_type}/{id}'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - path = path.replace('{id}', parameters['id'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Get PDB Alignments by ProteinId - * @method - * @name Genome2StructureAPI#getAlignmentUsingGET - * @param {string} idType - Input id_type: ensembl; uniprot; uniprot_isoform - * @param {string} id - Input id e.g. - ensembl:ENSP00000484409.1/ENSG00000141510.16/ENST00000504290.5; uniprot:P04637/P53_HUMAN; uniprot_isoform:P04637_9/P53_HUMAN_9 - */ - getAlignmentUsingGET(parameters: { - 'idType': string, - 'id': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments/{id_type}/{id}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - if (parameters['idType'] === undefined) { - reject(new Error('Missing required parameter: idType')); - return; - } - - path = path.replace('{id}', parameters['id'] + ''); - - if (parameters['id'] === undefined) { - reject(new Error('Missing required parameter: id')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - getAlignmentByPDBUsingGETURL(parameters: { - 'idType': string, - 'id': string, - 'pdbId': string, - 'chainId': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments/{id_type}/{id}/pdb/{pdb_id}_{chain_id}'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - path = path.replace('{id}', parameters['id'] + ''); - - path = path.replace('{pdb_id}', parameters['pdbId'] + ''); - - path = path.replace('{chain_id}', parameters['chainId'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Get PDB Alignments by ProteinId, PDBId and Chain - * @method - * @name Genome2StructureAPI#getAlignmentByPDBUsingGET - * @param {string} idType - Input id_type: ensembl; uniprot; uniprot_isoform - * @param {string} id - Input id e.g. - ensembl:ENSP00000484409.1/ENSG00000141510.16/ENST00000504290.5; uniprot:P04637/P53_HUMAN; uniprot_isoform:P04637_9/P53_HUMAN_9 - * @param {string} pdbId - Input PDB Id e.g. 2fej - * @param {string} chainId - Input Chain e.g. A - */ - getAlignmentByPDBUsingGET(parameters: { - 'idType': string, - 'id': string, - 'pdbId': string, - 'chainId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments/{id_type}/{id}/pdb/{pdb_id}_{chain_id}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - if (parameters['idType'] === undefined) { - reject(new Error('Missing required parameter: idType')); - return; - } - - path = path.replace('{id}', parameters['id'] + ''); - - if (parameters['id'] === undefined) { - reject(new Error('Missing required parameter: id')); - return; - } - - path = path.replace('{pdb_id}', parameters['pdbId'] + ''); - - if (parameters['pdbId'] === undefined) { - reject(new Error('Missing required parameter: pdbId')); - return; - } - - path = path.replace('{chain_id}', parameters['chainId'] + ''); - - if (parameters['chainId'] === undefined) { - reject(new Error('Missing required parameter: chainId')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - postResidueMappingByPDBUsingGETURL(parameters: { - 'idType': string, - 'id': string, - 'pdbId': string, - 'chainId': string, - 'positionList' ? : Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments/{id_type}/{id}/pdb/{pdb_id}_{chain_id}/residueMapping'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - path = path.replace('{id}', parameters['id'] + ''); - - path = path.replace('{pdb_id}', parameters['pdbId'] + ''); - - path = path.replace('{chain_id}', parameters['chainId'] + ''); - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Post Residue Mapping by ProteinId, PDBId and Chain - * @method - * @name Genome2StructureAPI#postResidueMappingByPDBUsingGET - * @param {string} idType - Input id_type: ensembl; uniprot; uniprot_isoform; hgvs; hgvs38 - * @param {string} id - Input id e.g. - ensembl:ENSP00000484409.1/ENSG00000141510.16/ENST00000504290.5; - uniprot:P04637/P53_HUMAN; - uniprot_isoform:P04637_9/P53_HUMAN_9; - hgvs:17:g.79478130C>G; - hgvs38:17:g.7676594T>G - * @param {string} pdbId - Input PDB Id e.g. 2fej - * @param {string} chainId - Input Chain e.g. A - * @param {array} positionList - Input Residue Positions e.g. 10,100 (Anynumber for hgvs); - Return all residue mappings if none - */ - postResidueMappingByPDBUsingGET(parameters: { - 'idType': string, - 'id': string, - 'pdbId': string, - 'chainId': string, - 'positionList' ? : Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments/{id_type}/{id}/pdb/{pdb_id}_{chain_id}/residueMapping'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - if (parameters['idType'] === undefined) { - reject(new Error('Missing required parameter: idType')); - return; - } - - path = path.replace('{id}', parameters['id'] + ''); - - if (parameters['id'] === undefined) { - reject(new Error('Missing required parameter: id')); - return; - } - - path = path.replace('{pdb_id}', parameters['pdbId'] + ''); - - if (parameters['pdbId'] === undefined) { - reject(new Error('Missing required parameter: pdbId')); - return; - } - - path = path.replace('{chain_id}', parameters['chainId'] + ''); - - if (parameters['chainId'] === undefined) { - reject(new Error('Missing required parameter: chainId')); - return; - } - - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - postResidueMappingByPDBUsingPOSTURL(parameters: { - 'idType': string, - 'id': string, - 'pdbId': string, - 'chainId': string, - 'positionList' ? : Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments/{id_type}/{id}/pdb/{pdb_id}_{chain_id}/residueMapping'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - path = path.replace('{id}', parameters['id'] + ''); - - path = path.replace('{pdb_id}', parameters['pdbId'] + ''); - - path = path.replace('{chain_id}', parameters['chainId'] + ''); - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Post Residue Mapping by ProteinId, PDBId and Chain - * @method - * @name Genome2StructureAPI#postResidueMappingByPDBUsingPOST - * @param {string} idType - Input id_type: ensembl; uniprot; uniprot_isoform; hgvs; hgvs38 - * @param {string} id - Input id e.g. - ensembl:ENSP00000484409.1/ENSG00000141510.16/ENST00000504290.5; - uniprot:P04637/P53_HUMAN; - uniprot_isoform:P04637_9/P53_HUMAN_9; - hgvs:17:g.79478130C>G; - hgvs38:17:g.7676594T>G - * @param {string} pdbId - Input PDB Id e.g. 2fej - * @param {string} chainId - Input Chain e.g. A - * @param {array} positionList - Input Residue Positions e.g. 10,100 (Anynumber for hgvs); - Return all residue mappings if none - */ - postResidueMappingByPDBUsingPOST(parameters: { - 'idType': string, - 'id': string, - 'pdbId': string, - 'chainId': string, - 'positionList' ? : Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments/{id_type}/{id}/pdb/{pdb_id}_{chain_id}/residueMapping'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - if (parameters['idType'] === undefined) { - reject(new Error('Missing required parameter: idType')); - return; - } - - path = path.replace('{id}', parameters['id'] + ''); - - if (parameters['id'] === undefined) { - reject(new Error('Missing required parameter: id')); - return; - } - - path = path.replace('{pdb_id}', parameters['pdbId'] + ''); - - if (parameters['pdbId'] === undefined) { - reject(new Error('Missing required parameter: pdbId')); - return; - } - - path = path.replace('{chain_id}', parameters['chainId'] + ''); - - if (parameters['chainId'] === undefined) { - reject(new Error('Missing required parameter: chainId')); - return; - } - - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - postResidueMappingUsingGETURL(parameters: { - 'idType': string, - 'id': string, - 'positionList' ? : Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments/{id_type}/{id}/residueMapping'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - path = path.replace('{id}', parameters['id'] + ''); - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * POST PDB Residue Mapping by ProteinId - * @method - * @name Genome2StructureAPI#postResidueMappingUsingGET - * @param {string} idType - Input id_type: ensembl; uniprot; - uniprot_isoform; hgvs; hgvs38 - * @param {string} id - Input id e.g. - ensembl:ENSP00000484409.1/ENSG00000141510.16/ENST00000504290.5; - uniprot:P04637/P53_HUMAN; - uniprot_isoform:P04637_9/P53_HUMAN_9; - hgvs:17:g.79478130C>G; - hgvs38:17:g.7676594T>G - * @param {array} positionList - Input Residue Positions e.g. 10,100; Anynumber for hgvs; - Return all residue mappings if none - */ - postResidueMappingUsingGET(parameters: { - 'idType': string, - 'id': string, - 'positionList' ? : Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments/{id_type}/{id}/residueMapping'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - if (parameters['idType'] === undefined) { - reject(new Error('Missing required parameter: idType')); - return; - } - - path = path.replace('{id}', parameters['id'] + ''); - - if (parameters['id'] === undefined) { - reject(new Error('Missing required parameter: id')); - return; - } - - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - - postResidueMappingUsingPOSTURL(parameters: { - 'idType': string, - 'id': string, - 'positionList' ? : Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/api/alignments/{id_type}/{id}/residueMapping'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - path = path.replace('{id}', parameters['id'] + ''); - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * POST PDB Residue Mapping by ProteinId - * @method - * @name Genome2StructureAPI#postResidueMappingUsingPOST - * @param {string} idType - Input id_type: ensembl; uniprot; - uniprot_isoform; hgvs; hgvs38 - * @param {string} id - Input id e.g. - ensembl:ENSP00000484409.1/ENSG00000141510.16/ENST00000504290.5; - uniprot:P04637/P53_HUMAN; - uniprot_isoform:P04637_9/P53_HUMAN_9; - hgvs:17:g.79478130C>G; - hgvs38:17:g.7676594T>G - * @param {array} positionList - Input Residue Positions e.g. 10,100; Anynumber for hgvs; - Return all residue mappings if none - */ - postResidueMappingUsingPOST(parameters: { - 'idType': string, - 'id': string, - 'positionList' ? : Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Alignment > - > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/api/alignments/{id_type}/{id}/residueMapping'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{id_type}', parameters['idType'] + ''); - - if (parameters['idType'] === undefined) { - reject(new Error('Missing required parameter: idType')); - return; - } - - path = path.replace('{id}', parameters['id'] + ''); - - if (parameters['id'] === undefined) { - reject(new Error('Missing required parameter: id')); - return; - } - - if (parameters['positionList'] !== undefined) { - queryParameters['positionList'] = parameters['positionList']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }).then(function(response: request.Response) { - return response.body; - }); - }; - -} \ No newline at end of file diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json deleted file mode 100644 index 1c2683aeb99..00000000000 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json +++ /dev/null @@ -1,3872 +0,0 @@ -{ - "swagger": "2.0", - "info": { - "description": "This page shows how to use HTTP requests to access the Genome Nexus API. There are more high level clients available in Python, R, JavaScript, TypeScript and various other languages as well as a command line client to annotate MAF and VCF. See https://docs.genomenexus.org/api.\n\nAside from programmatic clients there are web based tools to annotate variants, see https://docs.genomenexus.org/tools.\n\n We currently only provide long-term support for the '/annotation' endpoint. The other endpoints might change.", - "version": "2.0", - "title": "Genome Nexus API", - "license": { - "name": "MIT License", - "url": "https://github.com/genome-nexus/genome-nexus/blob/master/LICENSE" - } - }, - "tags": [ - { - "name": "info-controller", - "description": "Info Controller" - }, - { - "name": "pdb-controller", - "description": "PDB Controller" - }, - { - "name": "annotation-controller", - "description": "Annotation Controller" - }, - { - "name": "ptm-controller", - "description": "PTM Controller" - }, - { - "name": "pfam-controller", - "description": "PFAM Controller" - }, - { - "name": "ensembl-controller", - "description": "Ensembl Controller" - } - ], - "schemes": [ - "http", - "https" - ], - "paths": { - "/annotation": { - "post": { - "tags": [ - "annotation-controller" - ], - "summary": "Retrieves VEP annotation for the provided list of variants", - "operationId": "fetchVariantAnnotationPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "variants", - "description": "List of variants. For example [\"X:g.66937331T>A\",\"17:g.41242962_41242963insGA\"] (GRCh37) or [\"1:g.182712A>C\", \"2:g.265023C>T\", \"3:g.319781del\", \"19:g.110753dup\", \"1:g.1385015_1387562del\"] (GRCh38)", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string" - }, - { - "name": "token", - "in": "query", - "description": "Map of tokens. For example {\"source1\":\"put-your-token1-here\",\"source2\":\"put-your-token2-here\"}", - "required": false, - "type": "string" - }, - { - "name": "fields", - "in": "query", - "description": "Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to \"annotation_summary\" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal}", - "required": false, - "type": "array", - "items": { - "type": "string", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - }, - "collectionFormat": "multi", - "default": "annotation_summary", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/VariantAnnotation" - } - } - } - } - } - }, - "/annotation/dbsnp/": { - "post": { - "tags": [ - "annotation-controller" - ], - "summary": "Retrieves VEP annotation for the provided list of dbSNP ids", - "operationId": "fetchVariantAnnotationByIdPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "variantIds", - "description": "List of variant IDs. For example [\"rs116035550\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string" - }, - { - "name": "token", - "in": "query", - "description": "Map of tokens. For example {\"source1\":\"put-your-token1-here\",\"source2\":\"put-your-token2-here\"}", - "required": false, - "type": "string" - }, - { - "name": "fields", - "in": "query", - "description": "Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to \"annotation_summary\" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal}", - "required": false, - "type": "array", - "items": { - "type": "string", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - }, - "collectionFormat": "multi", - "default": "annotation_summary", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/VariantAnnotation" - } - } - } - } - } - }, - "/annotation/dbsnp/{variantId}": { - "get": { - "tags": [ - "annotation-controller" - ], - "summary": "Retrieves VEP annotation for the give dbSNP id", - "operationId": "fetchVariantAnnotationByIdGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "variantId", - "in": "path", - "description": "dbSNP id. For example rs116035550.", - "required": true, - "type": "string" - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string" - }, - { - "name": "token", - "in": "query", - "description": "Map of tokens. For example {\"source1\":\"put-your-token1-here\",\"source2\":\"put-your-token2-here\"}", - "required": false, - "type": "string" - }, - { - "name": "fields", - "in": "query", - "description": "Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to \"annotation_summary\" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal}", - "required": false, - "type": "array", - "items": { - "type": "string", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - }, - "collectionFormat": "multi", - "default": "annotation_summary", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/VariantAnnotation" - } - } - } - } - }, - "/annotation/genomic": { - "post": { - "tags": [ - "annotation-controller" - ], - "summary": "Retrieves VEP annotation for the provided list of genomic locations", - "operationId": "fetchVariantAnnotationByGenomicLocationPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "genomicLocations", - "description": "List of Genomic Locations", - "required": true, - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/GenomicLocation" - } - } - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string" - }, - { - "name": "token", - "in": "query", - "description": "Map of tokens. For example {\"source1\":\"put-your-token1-here\",\"source2\":\"put-your-token2-here\"}", - "required": false, - "type": "string" - }, - { - "name": "fields", - "in": "query", - "description": "Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to \"annotation_summary\" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal}", - "required": false, - "type": "array", - "items": { - "type": "string", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - }, - "collectionFormat": "multi", - "default": "annotation_summary", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/VariantAnnotation" - } - } - } - } - } - }, - "/annotation/genomic/{genomicLocation}": { - "get": { - "tags": [ - "annotation-controller" - ], - "summary": "Retrieves VEP annotation for the provided genomic location", - "operationId": "fetchVariantAnnotationByGenomicLocationGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "genomicLocation", - "in": "path", - "description": "A genomic location. For example 7,140453136,140453136,A,T", - "required": true, - "type": "string" - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string" - }, - { - "name": "token", - "in": "query", - "description": "Map of tokens. For example {\"source1\":\"put-your-token1-here\",\"source2\":\"put-your-token2-here\"}", - "required": false, - "type": "string" - }, - { - "name": "fields", - "in": "query", - "description": "Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to \"annotation_summary\" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal}", - "required": false, - "type": "array", - "items": { - "type": "string", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - }, - "collectionFormat": "multi", - "default": "annotation_summary", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/VariantAnnotation" - } - } - } - } - }, - "/annotation/{variant}": { - "get": { - "tags": [ - "annotation-controller" - ], - "summary": "Retrieves VEP annotation for the provided variant", - "operationId": "fetchVariantAnnotationGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "variant", - "in": "path", - "description": "Variant. For example 17:g.41242962_41242963insGA", - "required": true, - "type": "string" - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string" - }, - { - "name": "token", - "in": "query", - "description": "Map of tokens. For example {\"source1\":\"put-your-token1-here\",\"source2\":\"put-your-token2-here\"}", - "required": false, - "type": "string" - }, - { - "name": "fields", - "in": "query", - "description": "Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to \"annotation_summary\" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal}", - "required": false, - "type": "array", - "items": { - "type": "string", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - }, - "collectionFormat": "multi", - "default": "annotation_summary", - "enum": [ - "annotation_summary", - "clinvar", - "hotspots", - "mutation_assessor", - "my_variant_info", - "nucleotide_context", - "oncokb", - "ptms", - "signal" - ] - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/VariantAnnotation" - } - } - } - } - }, - "/ensembl/canonical-gene/entrez": { - "post": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves canonical Ensembl Gene ID by Entrez Gene Ids", - "operationId": "fetchCanonicalEnsemblGeneIdByEntrezGeneIdsPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "entrezGeneIds", - "description": "List of Entrez Gene Ids. For example [\"23140\",\"26009\",\"100131879\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/EnsemblGene" - } - } - } - } - } - }, - "/ensembl/canonical-gene/entrez/{entrezGeneId}": { - "get": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves Ensembl canonical gene id by Entrez Gene Id", - "operationId": "fetchCanonicalEnsemblGeneIdByEntrezGeneIdGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "entrezGeneId", - "in": "path", - "description": "An Entrez Gene Id. For example 23140", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/EnsemblGene" - } - } - } - } - }, - "/ensembl/canonical-gene/hgnc": { - "post": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves canonical Ensembl Gene ID by Hugo Symbols", - "operationId": "fetchCanonicalEnsemblGeneIdByHugoSymbolsPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "hugoSymbols", - "description": "List of Hugo Symbols. For example [\"TP53\",\"PIK3CA\",\"BRCA1\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/EnsemblGene" - } - } - } - } - } - }, - "/ensembl/canonical-gene/hgnc/{hugoSymbol}": { - "get": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves Ensembl canonical gene id by Hugo Symbol", - "operationId": "fetchCanonicalEnsemblGeneIdByHugoSymbolGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "hugoSymbol", - "in": "path", - "description": "A Hugo Symbol. For example TP53", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/EnsemblGene" - } - } - } - } - }, - "/ensembl/canonical-transcript/hgnc": { - "post": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves Ensembl canonical transcripts by Hugo Symbols", - "operationId": "fetchCanonicalEnsemblTranscriptsByHugoSymbolsPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "hugoSymbols", - "description": "List of Hugo Symbols. For example [\"TP53\",\"PIK3CA\",\"BRCA1\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string", - "default": "uniprot" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/EnsemblTranscript" - } - } - } - } - } - }, - "/ensembl/canonical-transcript/hgnc/{hugoSymbol}": { - "get": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves Ensembl canonical transcript by Hugo Symbol", - "operationId": "fetchCanonicalEnsemblTranscriptByHugoSymbolGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "hugoSymbol", - "in": "path", - "description": "A Hugo Symbol. For example TP53", - "required": true, - "type": "string" - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string", - "default": "uniprot" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/EnsemblTranscript" - } - } - } - } - }, - "/ensembl/transcript": { - "get": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves Ensembl Transcripts by protein ID, and gene ID. Retrieves all transcripts in case no query parameter provided", - "operationId": "fetchEnsemblTranscriptsGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "geneId", - "in": "query", - "description": "An Ensembl gene ID. For example ENSG00000136999", - "required": false, - "type": "string" - }, - { - "name": "proteinId", - "in": "query", - "description": "An Ensembl protein ID. For example ENSP00000439985", - "required": false, - "type": "string" - }, - { - "name": "hugoSymbol", - "in": "query", - "description": "A Hugo Symbol For example ARF5", - "required": false, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/EnsemblTranscript" - } - } - } - } - }, - "post": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves Ensembl Transcripts by Ensembl transcript IDs, hugo Symbols, protein IDs, or gene IDs", - "operationId": "fetchEnsemblTranscriptsByEnsemblFilterPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "ensemblFilter", - "description": "List of Ensembl transcript IDs. For example [\"ENST00000361390\", \"ENST00000361453\", \"ENST00000361624\"]
OR
List of Hugo Symbols. For example [\"TP53\", \"PIK3CA\", \"BRCA1\"]
OR
List of Ensembl protein IDs. For example [\"ENSP00000439985\", \"ENSP00000478460\", \"ENSP00000346196\"]
OR
List of Ensembl gene IDs. For example [\"ENSG00000136999\", \"ENSG00000272398\", \"ENSG00000198695\"]", - "required": true, - "schema": { - "$ref": "#/definitions/EnsemblFilter" - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/EnsemblTranscript" - } - } - } - } - } - }, - "/ensembl/transcript/{transcriptId}": { - "get": { - "tags": [ - "ensembl-controller" - ], - "summary": "Retrieves the transcript by an Ensembl transcript ID", - "operationId": "fetchEnsemblTranscriptByTranscriptIdGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "transcriptId", - "in": "path", - "description": "An Ensembl transcript ID. For example ENST00000361390", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/EnsemblTranscript" - } - } - } - } - }, - "/ensembl/xrefs": { - "get": { - "tags": [ - "ensembl-controller" - ], - "summary": "Perform lookups of Ensembl identifiers and retrieve their external references in other databases", - "operationId": "fetchGeneXrefsGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "accession", - "in": "query", - "description": "Ensembl gene accession. For example ENSG00000169083", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/GeneXref" - } - } - } - } - } - }, - "/pdb/header": { - "post": { - "tags": [ - "pdb-controller" - ], - "summary": "Retrieves PDB header info by a PDB id", - "operationId": "fetchPdbHeaderPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "pdbIds", - "description": "List of pdb ids, for example [\"1a37\",\"1a4o\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/PdbHeader" - } - } - } - } - } - }, - "/pdb/header/{pdbId}": { - "get": { - "tags": [ - "pdb-controller" - ], - "summary": "Retrieves PDB header info by a PDB id", - "operationId": "fetchPdbHeaderGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "pdbId", - "in": "path", - "description": "PDB id, for example 1a37", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/PdbHeader" - } - } - } - } - }, - "/pfam/domain": { - "post": { - "tags": [ - "pfam-controller" - ], - "summary": "Retrieves PFAM domains by PFAM domain accession IDs", - "operationId": "fetchPfamDomainsByPfamAccessionPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "pfamAccessions", - "description": "List of PFAM domain accession IDs. For example [\"PF02827\",\"PF00093\",\"PF15276\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/PfamDomain" - } - } - } - } - } - }, - "/pfam/domain/{pfamAccession}": { - "get": { - "tags": [ - "pfam-controller" - ], - "summary": "Retrieves a PFAM domain by a PFAM domain ID", - "operationId": "fetchPfamDomainsByAccessionGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "pfamAccession", - "in": "path", - "description": "A PFAM domain accession ID. For example PF02827", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/PfamDomain" - } - } - } - } - }, - "/ptm/experimental": { - "get": { - "tags": [ - "ptm-controller" - ], - "summary": "Retrieves PTM entries by Ensembl Transcript ID", - "operationId": "fetchPostTranslationalModificationsGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "ensemblTranscriptId", - "in": "query", - "description": "Ensembl Transcript ID. For example ENST00000646891", - "required": false, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/PostTranslationalModification" - } - } - } - } - }, - "post": { - "tags": [ - "ptm-controller" - ], - "summary": "Retrieves PTM entries by Ensembl Transcript IDs", - "operationId": "fetchPostTranslationalModificationsByPtmFilterPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "ptmFilter", - "description": "List of Ensembl transcript IDs. For example [\"ENST00000420316\", \"ENST00000646891\", \"ENST00000371953\"]", - "required": true, - "schema": { - "$ref": "#/definitions/PtmFilter" - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/PostTranslationalModification" - } - } - } - } - } - }, - "/version": { - "get": { - "tags": [ - "info-controller" - ], - "summary": "Retrieve Genome Nexus Version", - "operationId": "fetchVersionGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/AggregateSourceInfo" - } - } - } - } - } - }, - "definitions": { - "AggregateSourceInfo": { - "type": "object", - "properties": { - "annotationSourcesInfo": { - "type": "array", - "items": { - "$ref": "#/definitions/SourceVersionInfo" - } - }, - "genomeNexus": { - "$ref": "#/definitions/GenomeNexusInfo" - }, - "vep": { - "$ref": "#/definitions/VEPInfo" - } - } - }, - "AlleleCount": { - "type": "object", - "required": [ - "ac", - "ac_afr", - "ac_amr", - "ac_asj", - "ac_eas", - "ac_fin", - "ac_nfe", - "ac_oth", - "ac_sas" - ], - "properties": { - "ac": { - "type": "integer", - "format": "int32" - }, - "ac_afr": { - "type": "integer", - "format": "int32" - }, - "ac_amr": { - "type": "integer", - "format": "int32" - }, - "ac_asj": { - "type": "integer", - "format": "int32" - }, - "ac_eas": { - "type": "integer", - "format": "int32" - }, - "ac_fin": { - "type": "integer", - "format": "int32" - }, - "ac_nfe": { - "type": "integer", - "format": "int32" - }, - "ac_oth": { - "type": "integer", - "format": "int32" - }, - "ac_sas": { - "type": "integer", - "format": "int32" - } - } - }, - "AlleleFrequency": { - "type": "object", - "required": [ - "af", - "af_afr", - "af_amr", - "af_asj", - "af_eas", - "af_fin", - "af_nfe", - "af_oth", - "af_sas" - ], - "properties": { - "af": { - "type": "number", - "format": "double" - }, - "af_afr": { - "type": "number", - "format": "double" - }, - "af_amr": { - "type": "number", - "format": "double" - }, - "af_asj": { - "type": "number", - "format": "double" - }, - "af_eas": { - "type": "number", - "format": "double" - }, - "af_fin": { - "type": "number", - "format": "double" - }, - "af_nfe": { - "type": "number", - "format": "double" - }, - "af_oth": { - "type": "number", - "format": "double" - }, - "af_sas": { - "type": "number", - "format": "double" - } - } - }, - "AlleleNumber": { - "type": "object", - "required": [ - "an", - "an_afr", - "an_amr", - "an_asj", - "an_eas", - "an_fin", - "an_nfe", - "an_oth", - "an_sas" - ], - "properties": { - "an": { - "type": "integer", - "format": "int32" - }, - "an_afr": { - "type": "integer", - "format": "int32" - }, - "an_amr": { - "type": "integer", - "format": "int32" - }, - "an_asj": { - "type": "integer", - "format": "int32" - }, - "an_eas": { - "type": "integer", - "format": "int32" - }, - "an_fin": { - "type": "integer", - "format": "int32" - }, - "an_nfe": { - "type": "integer", - "format": "int32" - }, - "an_oth": { - "type": "integer", - "format": "int32" - }, - "an_sas": { - "type": "integer", - "format": "int32" - } - } - }, - "Alleles": { - "type": "object", - "properties": { - "allele": { - "type": "string", - "description": "allele" - } - } - }, - "ArticleAbstract": { - "type": "object", - "properties": { - "abstract": { - "type": "string" - }, - "link": { - "type": "string" - } - } - }, - "Citations": { - "type": "object", - "properties": { - "abstracts": { - "type": "array", - "items": { - "$ref": "#/definitions/ArticleAbstract" - } - }, - "pmids": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "Clinvar": { - "type": "object", - "properties": { - "alternateAllele": { - "type": "string" - }, - "chromosome": { - "type": "string" - }, - "clinicalSignificance": { - "type": "string" - }, - "clinvarId": { - "type": "integer", - "format": "int32" - }, - "conflictingClinicalSignificance": { - "type": "string" - }, - "endPosition": { - "type": "integer", - "format": "int32" - }, - "referenceAllele": { - "type": "string" - }, - "startPosition": { - "type": "integer", - "format": "int32" - } - } - }, - "ClinvarAnnotation": { - "type": "object", - "properties": { - "annotation": { - "$ref": "#/definitions/Clinvar" - } - } - }, - "ColocatedVariant": { - "type": "object", - "required": [ - "gnomad_afr_allele", - "gnomad_afr_maf", - "gnomad_eas_allele", - "gnomad_eas_maf", - "gnomad_nfe_allele", - "gnomad_nfe_maf" - ], - "properties": { - "dbSnpId": { - "type": "string" - }, - "gnomad_nfe_allele": { - "type": "string", - "description": "GnomAD Non-Finnish European Allele" - }, - "gnomad_nfe_maf": { - "type": "string", - "description": "GnomAD Non-Finnish European MAF" - }, - "gnomad_afr_allele": { - "type": "string", - "description": "GnomAD African/African American Allele" - }, - "gnomad_afr_maf": { - "type": "string", - "description": "GnomAD African/African American MAF" - }, - "gnomad_eas_allele": { - "type": "string", - "description": "GnomAD East Asian Allele" - }, - "gnomad_eas_maf": { - "type": "string", - "description": "GnomAD East Asian MAF" - } - } - }, - "Cosmic": { - "type": "object", - "properties": { - "alt": { - "type": "string", - "description": "alt" - }, - "chrom": { - "type": "string", - "description": "chrom" - }, - "cosmicId": { - "type": "string", - "description": "cosmic_id" - }, - "hg19": { - "description": "hg19", - "$ref": "#/definitions/Hg19" - }, - "license": { - "type": "string", - "description": "_license" - }, - "mutFreq": { - "type": "number", - "format": "double", - "description": "mut_freq" - }, - "mutNt": { - "type": "string", - "description": "mut_nt" - }, - "ref": { - "type": "string", - "description": "ref" - }, - "tumorSite": { - "type": "string", - "description": "tumor_site" - } - } - }, - "CountByTumorType": { - "type": "object", - "properties": { - "tumorType": { - "type": "string", - "description": "Tumor Type" - }, - "tumorTypeCount": { - "type": "integer", - "format": "int32", - "description": "Sample count for Tumor Type" - }, - "variantCount": { - "type": "integer", - "format": "int32", - "description": "Variant count for Tumor Type" - } - } - }, - "Dbsnp": { - "type": "object", - "properties": { - "_class": { - "type": "string", - "description": "class" - }, - "alleleOrigin": { - "type": "string", - "description": "allele_origin" - }, - "alleles": { - "type": "array", - "description": "alleles", - "items": { - "$ref": "#/definitions/Alleles" - } - }, - "alt": { - "type": "string", - "description": "alt" - }, - "chrom": { - "type": "string", - "description": "chrom" - }, - "dbsnpBuild": { - "type": "integer", - "format": "int32", - "description": "dbsnp_build" - }, - "flags": { - "type": "array", - "description": "flags", - "items": { - "type": "string" - } - }, - "hg19": { - "description": "hg19", - "$ref": "#/definitions/Hg19" - }, - "license": { - "type": "string", - "description": "_license" - }, - "ref": { - "type": "string", - "description": "ref" - }, - "rsid": { - "type": "string", - "description": "rsid" - }, - "validated": { - "type": "boolean", - "example": false, - "description": "validated" - }, - "varSubtype": { - "type": "string", - "description": "var_subtype" - }, - "vartype": { - "type": "string", - "description": "vartype" - } - } - }, - "Drug": { - "type": "object", - "properties": { - "drugName": { - "type": "string" - }, - "ncitCode": { - "type": "string" - } - } - }, - "EnsemblFilter": { - "type": "object", - "properties": { - "geneIds": { - "type": "array", - "description": "List of Ensembl gene IDs. For example [\"ENSG00000136999\", \"ENSG00000272398\", \"ENSG00000198695\"]", - "items": { - "type": "string" - } - }, - "hugoSymbols": { - "type": "array", - "description": "List of Hugo Symbols. For example [\"TP53\", \"PIK3CA\", \"BRCA1\"]", - "items": { - "type": "string" - } - }, - "proteinIds": { - "type": "array", - "description": "List of Ensembl protein IDs. For example [\"ENSP00000439985\", \"ENSP00000478460\", \"ENSP00000346196\"]", - "items": { - "type": "string" - } - }, - "transcriptIds": { - "type": "array", - "description": "List of Ensembl transcript IDs. For example [\"ENST00000361390\", \"ENST00000361453\", \"ENST00000361624\"]", - "items": { - "type": "string" - } - } - } - }, - "EnsemblGene": { - "type": "object", - "required": [ - "geneId", - "hugoSymbol" - ], - "properties": { - "geneId": { - "type": "string", - "description": "Ensembl gene id" - }, - "hugoSymbol": { - "type": "string", - "description": "Approved Hugo symbol" - }, - "synonyms": { - "type": "array", - "description": "Hugo symbol synonyms", - "items": { - "type": "string" - } - }, - "previousSymbols": { - "type": "array", - "description": "Previous Hugo symbols", - "items": { - "type": "string" - } - }, - "entrezGeneId": { - "type": "string", - "description": "Entrez Gene Id" - } - } - }, - "EnsemblTranscript": { - "type": "object", - "required": [ - "geneId", - "proteinId", - "transcriptId" - ], - "properties": { - "uniprotId": { - "type": "string" - }, - "transcriptId": { - "type": "string", - "description": "Ensembl transcript id" - }, - "geneId": { - "type": "string", - "description": "Ensembl gene id" - }, - "proteinId": { - "type": "string", - "description": "Ensembl protein id" - }, - "proteinLength": { - "type": "integer", - "format": "int32", - "description": "Length of protein" - }, - "pfamDomains": { - "type": "array", - "description": "Pfam domains", - "items": { - "$ref": "#/definitions/PfamDomainRange" - } - }, - "hugoSymbols": { - "type": "array", - "description": "Hugo symbols", - "items": { - "type": "string" - } - }, - "refseqMrnaId": { - "type": "string", - "description": "RefSeq mRNA ID" - }, - "ccdsId": { - "type": "string", - "description": "Consensus CDS (CCDS) ID" - }, - "exons": { - "type": "array", - "description": "Exon information", - "items": { - "$ref": "#/definitions/Exon" - } - }, - "utrs": { - "type": "array", - "description": "UTR information", - "items": { - "$ref": "#/definitions/UntranslatedRegion" - } - } - } - }, - "Exon": { - "type": "object", - "required": [ - "exonEnd", - "exonId", - "exonStart", - "rank", - "strand", - "version" - ], - "properties": { - "exonId": { - "type": "string", - "description": "Exon id" - }, - "exonStart": { - "type": "integer", - "format": "int32", - "description": "Start position of exon" - }, - "exonEnd": { - "type": "integer", - "format": "int32", - "description": "End position of exon" - }, - "rank": { - "type": "integer", - "format": "int32", - "description": "Number of exon in transcript" - }, - "strand": { - "type": "integer", - "format": "int32", - "description": "Strand exon is on, -1 for - and 1 for +" - }, - "version": { - "type": "integer", - "format": "int32", - "description": "Exon version" - } - } - }, - "Gene": { - "type": "object", - "properties": { - "geneId": { - "type": "string", - "description": "geneid" - }, - "symbol": { - "type": "string", - "description": "symbol" - } - } - }, - "GeneXref": { - "type": "object", - "required": [ - "db_display_name", - "dbname", - "description", - "display_id", - "primary_id", - "version" - ], - "properties": { - "db_display_name": { - "type": "string", - "description": "Database display name" - }, - "dbname": { - "type": "string", - "description": "Database name" - }, - "description": { - "type": "string", - "description": "Description" - }, - "display_id": { - "type": "string", - "description": "Display id" - }, - "ensemblGeneId": { - "type": "string" - }, - "info_text": { - "type": "string", - "description": "Database info text" - }, - "info_types": { - "type": "string", - "description": "Database info type" - }, - "primary_id": { - "type": "string", - "description": "Primary id" - }, - "synonyms": { - "type": "array", - "description": "Synonyms", - "items": { - "type": "string" - } - }, - "version": { - "type": "string", - "description": "Version" - } - } - }, - "GeneralPopulationStats": { - "type": "object", - "properties": { - "counts": { - "description": "Counts", - "$ref": "#/definitions/SignalPopulationStats" - }, - "frequencies": { - "description": "Frequencies", - "$ref": "#/definitions/SignalPopulationStats" - } - } - }, - "GenomeNexusInfo": { - "type": "object", - "properties": { - "database": { - "$ref": "#/definitions/Version" - }, - "server": { - "$ref": "#/definitions/Version" - } - } - }, - "GenomicLocation": { - "type": "object", - "required": [ - "chromosome", - "end", - "referenceAllele", - "start", - "variantAllele" - ], - "properties": { - "chromosome": { - "type": "string", - "description": "Chromosome" - }, - "start": { - "type": "integer", - "format": "int32", - "description": "Start Position" - }, - "end": { - "type": "integer", - "format": "int32", - "description": "End Position" - }, - "referenceAllele": { - "type": "string", - "description": "Reference Allele" - }, - "variantAllele": { - "type": "string", - "description": "Variant Allele" - } - } - }, - "Gnomad": { - "type": "object", - "properties": { - "alleleCount": { - "description": "ac", - "$ref": "#/definitions/AlleleCount" - }, - "alleleFrequency": { - "description": "af", - "$ref": "#/definitions/AlleleFrequency" - }, - "alleleNumber": { - "description": "an", - "$ref": "#/definitions/AlleleNumber" - }, - "homozygotes": { - "description": "hom", - "$ref": "#/definitions/Homozygotes" - } - } - }, - "Hg19": { - "type": "object", - "properties": { - "end": { - "type": "integer", - "format": "int32", - "description": "end" - }, - "start": { - "type": "integer", - "format": "int32", - "description": "start" - } - } - }, - "Hg38": { - "type": "object", - "properties": { - "end": { - "type": "string", - "description": "end" - }, - "start": { - "type": "string", - "description": "start" - } - } - }, - "Hgvs": { - "type": "object", - "properties": { - "coding": { - "type": "array", - "items": { - "type": "string" - } - }, - "genomic": { - "type": "array", - "items": { - "type": "string" - } - }, - "protein": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "Homozygotes": { - "type": "object", - "required": [ - "hom", - "hom_afr", - "hom_amr", - "hom_asj", - "hom_eas", - "hom_fin", - "hom_nfe", - "hom_oth", - "hom_sas" - ], - "properties": { - "hom": { - "type": "integer", - "format": "int32" - }, - "hom_afr": { - "type": "integer", - "format": "int32" - }, - "hom_amr": { - "type": "integer", - "format": "int32" - }, - "hom_asj": { - "type": "integer", - "format": "int32" - }, - "hom_eas": { - "type": "integer", - "format": "int32" - }, - "hom_fin": { - "type": "integer", - "format": "int32" - }, - "hom_nfe": { - "type": "integer", - "format": "int32" - }, - "hom_oth": { - "type": "integer", - "format": "int32" - }, - "hom_sas": { - "type": "integer", - "format": "int32" - } - } - }, - "Hotspot": { - "type": "object", - "properties": { - "hugoSymbol": { - "type": "string", - "description": "Hugo gene symbol" - }, - "inframeCount": { - "type": "integer", - "format": "int32", - "description": "Inframe mutation count" - }, - "missenseCount": { - "type": "integer", - "format": "int32", - "description": "Missense mutation count" - }, - "residue": { - "type": "string", - "description": "Hotspot residue" - }, - "spliceCount": { - "type": "integer", - "format": "int32", - "description": "Splice mutation count" - }, - "transcriptId": { - "type": "string", - "description": "Ensembl Transcript Id" - }, - "truncatingCount": { - "type": "integer", - "format": "int32", - "description": "Truncation mutation count" - }, - "tumorCount": { - "type": "integer", - "format": "int32", - "description": "Tumor count" - }, - "type": { - "type": "string", - "description": "Hotspot type" - } - } - }, - "HotspotAnnotation": { - "type": "object", - "properties": { - "annotation": { - "type": "array", - "items": { - "type": "array", - "items": { - "$ref": "#/definitions/Hotspot" - } - } - }, - "license": { - "type": "string" - } - } - }, - "HrdScore": { - "type": "object", - "properties": { - "fractionLoh": { - "type": "number", - "format": "double", - "description": "Median HRD Fraction LOH" - }, - "lst": { - "type": "number", - "format": "double", - "description": "Median HRD LST" - }, - "ntelomericAi": { - "type": "number", - "format": "double", - "description": "Median HRD ntelomeric AI" - } - } - }, - "Implication": { - "type": "object", - "properties": { - "abstracts": { - "type": "array", - "items": { - "$ref": "#/definitions/ArticleAbstract" - } - }, - "alterations": { - "type": "array", - "items": { - "type": "string" - } - }, - "description": { - "type": "string" - }, - "levelOfEvidence": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - }, - "pmids": { - "type": "array", - "items": { - "type": "string" - } - }, - "tumorType": { - "$ref": "#/definitions/TumorType" - } - } - }, - "IndicatorQueryResp": { - "type": "object", - "properties": { - "alleleExist": { - "type": "boolean", - "example": false - }, - "dataVersion": { - "type": "string" - }, - "diagnosticImplications": { - "type": "array", - "items": { - "$ref": "#/definitions/Implication" - } - }, - "diagnosticSummary": { - "type": "string" - }, - "geneExist": { - "type": "boolean", - "example": false - }, - "geneSummary": { - "type": "string" - }, - "highestDiagnosticImplicationLevel": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - }, - "highestFdaLevel": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - }, - "highestPrognosticImplicationLevel": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - }, - "highestResistanceLevel": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - }, - "highestSensitiveLevel": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - }, - "hotspot": { - "type": "boolean", - "example": false - }, - "lastUpdate": { - "type": "string" - }, - "mutationEffect": { - "$ref": "#/definitions/MutationEffectResp" - }, - "oncogenic": { - "type": "string" - }, - "otherSignificantResistanceLevels": { - "type": "array", - "items": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - } - }, - "otherSignificantSensitiveLevels": { - "type": "array", - "items": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - } - }, - "prognosticImplications": { - "type": "array", - "items": { - "$ref": "#/definitions/Implication" - } - }, - "prognosticSummary": { - "type": "string" - }, - "query": { - "$ref": "#/definitions/Query" - }, - "treatments": { - "type": "array", - "items": { - "$ref": "#/definitions/IndicatorQueryTreatment" - } - }, - "tumorTypeSummary": { - "type": "string" - }, - "variantExist": { - "type": "boolean", - "example": false - }, - "variantSummary": { - "type": "string" - }, - "vus": { - "type": "boolean", - "example": false - } - } - }, - "IndicatorQueryTreatment": { - "type": "object", - "properties": { - "abstracts": { - "type": "array", - "items": { - "$ref": "#/definitions/ArticleAbstract" - } - }, - "alterations": { - "type": "array", - "items": { - "type": "string" - } - }, - "approvedIndications": { - "type": "array", - "items": { - "type": "string" - } - }, - "description": { - "type": "string" - }, - "drugs": { - "type": "array", - "items": { - "$ref": "#/definitions/Drug" - } - }, - "fdaLevel": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - }, - "level": { - "type": "string", - "enum": [ - "LEVEL_1", - "LEVEL_2", - "LEVEL_3A", - "LEVEL_3B", - "LEVEL_4", - "LEVEL_R1", - "LEVEL_R2", - "LEVEL_Px1", - "LEVEL_Px2", - "LEVEL_Px3", - "LEVEL_Dx1", - "LEVEL_Dx2", - "LEVEL_Dx3", - "LEVEL_Fda1", - "LEVEL_Fda2", - "LEVEL_Fda3", - "NO" - ] - }, - "levelAssociatedCancerType": { - "$ref": "#/definitions/TumorType" - }, - "levelExcludedCancerTypes": { - "type": "array", - "items": { - "$ref": "#/definitions/TumorType" - } - }, - "pmids": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "IntegerRange": { - "type": "object", - "properties": { - "end": { - "type": "integer", - "format": "int32" - }, - "start": { - "type": "integer", - "format": "int32" - } - } - }, - "IntergenicConsequences": { - "type": "object", - "required": [ - "consequenceTerms", - "impact", - "variantAllele" - ], - "properties": { - "impact": { - "type": "string", - "description": "impact" - }, - "variantAllele": { - "type": "string", - "description": "variant_allele" - }, - "consequenceTerms": { - "type": "array", - "description": "consequence_terms", - "items": { - "type": "string" - } - } - } - }, - "MainType": { - "type": "object", - "properties": { - "id": { - "type": "integer", - "format": "int32" - }, - "name": { - "type": "string" - }, - "tumorForm": { - "type": "string", - "enum": [ - "SOLID", - "LIQUID", - "MIXED" - ] - } - }, - "description": "OncoTree Cancer Type" - }, - "MutationAssessor": { - "type": "object", - "required": [ - "input" - ], - "properties": { - "codonStartPosition": { - "type": "string", - "description": "Codon start position" - }, - "cosmicCount": { - "type": "integer", - "format": "int32", - "description": "Number of mutations in COSMIC for this protein" - }, - "functionalImpact": { - "type": "string", - "description": "Functional impact" - }, - "functionalImpactScore": { - "type": "number", - "format": "double", - "description": "Functional impact score" - }, - "hgvs": { - "type": "string" - }, - "hugoSymbol": { - "type": "string", - "description": "Hugo gene symbol" - }, - "input": { - "type": "string", - "description": "User-input variants" - }, - "mappingIssue": { - "type": "string", - "description": "Mapping issue info" - }, - "msaGaps": { - "type": "number", - "format": "double", - "description": "Portion of gaps in variant position in multiple sequence alignment" - }, - "msaHeight": { - "type": "integer", - "format": "int32", - "description": "Number of diverse sequences in multiple sequence alignment (identical or highly similar sequences filtered out)" - }, - "msaLink": { - "type": "string", - "description": "Link to multiple sequence alignment" - }, - "pdbLink": { - "type": "string", - "description": "Link to 3d structure browser" - }, - "referenceGenomeVariant": { - "type": "string", - "description": "Reference genome variant" - }, - "referenceGenomeVariantType": { - "type": "string", - "description": "Reference genome variant type" - }, - "refseqId": { - "type": "string", - "description": "Refseq protein ID" - }, - "refseqPosition": { - "type": "integer", - "format": "int32", - "description": "Variant position in Refseq protein, can be different from the one in Uniprot" - }, - "refseqResidue": { - "type": "string", - "description": "Reference residue in Refseq protein, can be different from the one in Uniprot" - }, - "snpCount": { - "type": "integer", - "format": "int32", - "description": "Number of SNPs in dbSNP for this protein" - }, - "uniprotId": { - "type": "string", - "description": "Uniprot protein accession ID" - }, - "uniprotPosition": { - "type": "integer", - "format": "int32", - "description": "Variant position in Uniprot protein, can be different from the one in Refseq" - }, - "uniprotResidue": { - "type": "string", - "description": "Reference residue in Uniprot protein, can be different from the one in Refseq" - }, - "variant": { - "type": "string", - "description": "Amino acid substitution" - }, - "variantConservationScore": { - "type": "number", - "format": "double", - "description": "Variant conservation score" - }, - "variantSpecificityScore": { - "type": "number", - "format": "double", - "description": "Variant specificity score" - } - } - }, - "MutationAssessorAnnotation": { - "type": "object", - "properties": { - "annotation": { - "$ref": "#/definitions/MutationAssessor" - }, - "license": { - "type": "string" - } - } - }, - "MutationEffectResp": { - "type": "object", - "properties": { - "citations": { - "$ref": "#/definitions/Citations" - }, - "description": { - "type": "string" - }, - "knownEffect": { - "type": "string" - } - } - }, - "Mutdb": { - "type": "object", - "properties": { - "alt": { - "type": "string", - "description": "alt" - }, - "chrom": { - "type": "string", - "description": "chrom" - }, - "cosmicId": { - "type": "string", - "description": "cosmic_id" - }, - "hg19": { - "description": "hg19", - "$ref": "#/definitions/Hg19" - }, - "mutpredScore": { - "type": "number", - "format": "double", - "description": "mutpred_score" - }, - "ref": { - "type": "string", - "description": "ref" - }, - "rsid": { - "type": "string", - "description": "rsid" - }, - "uniprotId": { - "type": "string", - "description": "uniprot_id" - } - } - }, - "MyVariantInfo": { - "type": "object", - "properties": { - "clinVar": { - "description": "clinvar", - "$ref": "#/definitions/MyVariantInfoClinVar" - }, - "cosmic": { - "description": "cosmic", - "$ref": "#/definitions/Cosmic" - }, - "dbsnp": { - "description": "dbsnp", - "$ref": "#/definitions/Dbsnp" - }, - "gnomadExome": { - "description": "gnomad_exome", - "$ref": "#/definitions/Gnomad" - }, - "gnomadGenome": { - "description": "gnomad_genome", - "$ref": "#/definitions/Gnomad" - }, - "hgvs": { - "type": "string", - "description": "hgvs" - }, - "mutdb": { - "$ref": "#/definitions/Mutdb" - }, - "query": { - "type": "string" - }, - "snpeff": { - "description": "snpeff", - "$ref": "#/definitions/Snpeff" - }, - "variant": { - "type": "string", - "description": "variant" - }, - "vcf": { - "description": "vcf", - "$ref": "#/definitions/Vcf" - }, - "version": { - "type": "integer", - "format": "int32", - "description": "version" - } - } - }, - "MyVariantInfoAnnotation": { - "type": "object", - "properties": { - "annotation": { - "$ref": "#/definitions/MyVariantInfo" - }, - "license": { - "type": "string" - } - } - }, - "MyVariantInfoClinVar": { - "type": "object", - "properties": { - "alleleId": { - "type": "integer", - "format": "int32", - "description": "allele_id" - }, - "alt": { - "type": "string", - "description": "alt" - }, - "chrom": { - "type": "string", - "description": "chrom" - }, - "cytogenic": { - "type": "string", - "description": "cytogenic" - }, - "gene": { - "description": "gene", - "$ref": "#/definitions/Gene" - }, - "hg19": { - "description": "hg19", - "$ref": "#/definitions/Hg19" - }, - "hg38": { - "description": "hg38", - "$ref": "#/definitions/Hg38" - }, - "hgvs": { - "description": "hgvs", - "$ref": "#/definitions/Hgvs" - }, - "license": { - "type": "string", - "description": "license" - }, - "rcv": { - "type": "array", - "items": { - "$ref": "#/definitions/Rcv" - } - }, - "variantId": { - "type": "integer", - "format": "int32", - "description": "variant_id" - } - } - }, - "NucleotideContext": { - "type": "object", - "required": [ - "seq" - ], - "properties": { - "hgvs": { - "type": "string" - }, - "id": { - "type": "string" - }, - "molecule": { - "type": "string" - }, - "query": { - "type": "string" - }, - "seq": { - "type": "string", - "description": "Nucleotide context sequence" - } - } - }, - "NucleotideContextAnnotation": { - "type": "object", - "properties": { - "annotation": { - "$ref": "#/definitions/NucleotideContext" - }, - "license": { - "type": "string" - } - } - }, - "OncokbAnnotation": { - "type": "object", - "properties": { - "annotation": { - "$ref": "#/definitions/IndicatorQueryResp" - }, - "license": { - "type": "string" - } - } - }, - "PdbHeader": { - "type": "object", - "required": [ - "pdbId", - "title" - ], - "properties": { - "compound": { - "type": "object" - }, - "pdbId": { - "type": "string", - "description": "PDB id" - }, - "source": { - "type": "object" - }, - "title": { - "type": "string", - "description": "PDB description" - } - } - }, - "PfamDomain": { - "type": "object", - "required": [ - "name", - "pfamAccession" - ], - "properties": { - "description": { - "type": "string", - "description": "PFAM domain description" - }, - "name": { - "type": "string", - "description": "PFAM domain name" - }, - "pfamAccession": { - "type": "string", - "description": "PFAM domain accession" - } - } - }, - "PfamDomainRange": { - "type": "object", - "required": [ - "pfamDomainEnd", - "pfamDomainId", - "pfamDomainStart" - ], - "properties": { - "pfamDomainId": { - "type": "string", - "description": "Pfam domain id" - }, - "pfamDomainStart": { - "type": "integer", - "format": "int32", - "description": "Pfam domain start amino acid" - }, - "pfamDomainEnd": { - "type": "integer", - "format": "int32", - "description": "Pfam domain end amino acid" - } - } - }, - "PostTranslationalModification": { - "type": "object", - "properties": { - "ensemblTranscriptIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "position": { - "type": "integer", - "format": "int32" - }, - "pubmedIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "sequence": { - "type": "string" - }, - "type": { - "type": "string" - }, - "uniprotAccession": { - "type": "string" - }, - "uniprotEntry": { - "type": "string" - } - } - }, - "PtmAnnotation": { - "type": "object", - "properties": { - "annotation": { - "type": "array", - "items": { - "type": "array", - "items": { - "$ref": "#/definitions/PostTranslationalModification" - } - } - }, - "license": { - "type": "string" - } - } - }, - "PtmFilter": { - "type": "object", - "properties": { - "transcriptIds": { - "type": "array", - "description": "List of Ensembl transcript IDs. For example [\"ENST00000361390\", \"ENST00000361453\", \"ENST00000361624\"]", - "items": { - "type": "string" - } - } - } - }, - "Query": { - "type": "object", - "properties": { - "alteration": { - "type": "string" - }, - "alterationType": { - "type": "string" - }, - "consequence": { - "type": "string" - }, - "entrezGeneId": { - "type": "integer", - "format": "int32" - }, - "hgvs": { - "type": "string" - }, - "hugoSymbol": { - "type": "string" - }, - "id": { - "type": "string" - }, - "proteinEnd": { - "type": "integer", - "format": "int32" - }, - "proteinStart": { - "type": "integer", - "format": "int32" - }, - "referenceGenome": { - "type": "string", - "enum": [ - "GRCh37", - "GRCh38" - ] - }, - "svType": { - "type": "string", - "enum": [ - "DELETION", - "TRANSLOCATION", - "DUPLICATION", - "INSERTION", - "INVERSION", - "FUSION", - "UNKNOWN" - ] - }, - "tumorType": { - "type": "string" - } - } - }, - "Rcv": { - "type": "object", - "properties": { - "accession": { - "type": "string", - "description": "accession" - }, - "clinicalSignificance": { - "type": "string", - "description": "clinical_significance" - }, - "origin": { - "type": "string", - "description": "origin" - }, - "preferredName": { - "type": "string", - "description": "preferred_name" - } - } - }, - "SignalAnnotation": { - "type": "object", - "properties": { - "annotation": { - "type": "array", - "items": { - "$ref": "#/definitions/SignalMutation" - } - }, - "license": { - "type": "string" - } - } - }, - "SignalMutation": { - "type": "object", - "properties": { - "biallelicCountsByTumorType": { - "type": "array", - "description": "Biallelic Counts by Tumor Type", - "items": { - "$ref": "#/definitions/CountByTumorType" - } - }, - "chromosome": { - "type": "string", - "description": "Chromosome" - }, - "countsByTumorType": { - "type": "array", - "description": "Counts by Tumor Type", - "items": { - "$ref": "#/definitions/CountByTumorType" - } - }, - "endPosition": { - "type": "integer", - "format": "int64", - "description": "End Position" - }, - "generalPopulationStats": { - "description": "General Population Stats", - "$ref": "#/definitions/GeneralPopulationStats" - }, - "hugoGeneSymbol": { - "type": "string", - "description": "Hugo Gene Symbol" - }, - "mskExperReview": { - "type": "boolean", - "example": false, - "description": "Msk Expert Review" - }, - "mutationStatus": { - "type": "string", - "description": "Mutation Status" - }, - "overallNumberOfGermlineHomozygous": { - "type": "integer", - "format": "int32" - }, - "pathogenic": { - "type": "string", - "description": "Pathogenic" - }, - "penetrance": { - "type": "string", - "description": "Penetrance" - }, - "qcPassCountsByTumorType": { - "type": "array", - "description": "QC Pass Counts by Tumor Type", - "items": { - "$ref": "#/definitions/CountByTumorType" - } - }, - "referenceAllele": { - "type": "string", - "description": "Reference Allele" - }, - "startPosition": { - "type": "integer", - "format": "int64", - "description": "Start Position" - }, - "statsByTumorType": { - "type": "array", - "description": "Stats By Tumor Type", - "items": { - "$ref": "#/definitions/StatsByTumorType" - } - }, - "variantAllele": { - "type": "string", - "description": "Variant Allele" - } - } - }, - "SignalPopulationStats": { - "type": "object", - "properties": { - "afr": { - "type": "number", - "format": "double", - "description": "African/African American" - }, - "asj": { - "type": "number", - "format": "double", - "description": "Ashkenazi Jewish" - }, - "asn": { - "type": "number", - "format": "double", - "description": "Asian" - }, - "eur": { - "type": "number", - "format": "double", - "description": "European" - }, - "impact": { - "type": "number", - "format": "double", - "description": "Impact" - }, - "oth": { - "type": "number", - "format": "double", - "description": "Other" - } - } - }, - "Snpeff": { - "type": "object", - "properties": { - "license": { - "type": "string", - "description": "license" - } - } - }, - "SourceVersionInfo": { - "type": "object", - "properties": { - "description": { - "type": "string" - }, - "id": { - "type": "string" - }, - "name": { - "type": "string" - }, - "type": { - "type": "string" - }, - "url": { - "type": "string" - }, - "version": { - "type": "string" - } - } - }, - "StatsByTumorType": { - "type": "object", - "properties": { - "ageAtDx": { - "type": "integer", - "format": "int32", - "description": "Median Age at Dx" - }, - "fBiallelic": { - "type": "number", - "format": "double", - "description": "Frequency Of Biallelic" - }, - "fCancerTypeCount": { - "type": "number", - "format": "double", - "description": "Frequency Of Cancer Type Count" - }, - "hrdScore": { - "description": "Hrd Score", - "$ref": "#/definitions/HrdScore" - }, - "msiScore": { - "type": "number", - "format": "double", - "description": "Msi Score" - }, - "nCancerTypeCount": { - "type": "integer", - "format": "int32", - "description": "Number Of Cancer Type Count" - }, - "numberOfGermlineHomozygous": { - "type": "integer", - "format": "int32", - "description": "Number Of Germline Homozygous Per Tumor Type" - }, - "numberWithSig": { - "type": "integer", - "format": "int32", - "description": "Number of Variants with Signature" - }, - "tmb": { - "type": "number", - "format": "double", - "description": "Median TMB" - }, - "tumorType": { - "type": "string", - "description": "Tumor Type" - } - } - }, - "TranscriptConsequence": { - "type": "object", - "required": [ - "transcript_id" - ], - "properties": { - "amino_acids": { - "type": "string", - "description": "Amino acids" - }, - "canonical": { - "type": "string", - "description": "Canonical transcript indicator" - }, - "codons": { - "type": "string", - "description": "Codons" - }, - "consequence_terms": { - "type": "array", - "description": "List of consequence terms", - "items": { - "type": "string" - } - }, - "exon": { - "type": "string" - }, - "gene_id": { - "type": "string", - "description": "Ensembl gene id" - }, - "gene_symbol": { - "type": "string", - "description": "Hugo gene symbol" - }, - "hgnc_id": { - "type": "string", - "description": "HGNC id" - }, - "hgvsc": { - "type": "string", - "description": "HGVSc" - }, - "hgvsg": { - "type": "string", - "description": "HGVSg" - }, - "hgvsp": { - "type": "string", - "description": "HGVSp" - }, - "polyphen_prediction": { - "type": "string", - "description": "Polyphen Prediction" - }, - "polyphen_score": { - "type": "number", - "format": "double", - "description": "Polyphen Score" - }, - "protein_end": { - "type": "integer", - "format": "int32", - "description": "Protein end position" - }, - "protein_id": { - "type": "string", - "description": "Ensembl protein id" - }, - "protein_start": { - "type": "integer", - "format": "int32", - "description": "Protein start position" - }, - "refseq_transcript_ids": { - "type": "array", - "description": "List of RefSeq transcript ids", - "items": { - "type": "string" - } - }, - "sift_prediction": { - "type": "string", - "description": "Sift Prediction" - }, - "sift_score": { - "type": "number", - "format": "double", - "description": "Sift Score" - }, - "transcript_id": { - "type": "string", - "description": "Ensembl transcript id" - }, - "uniprotId": { - "type": "string" - }, - "variant_allele": { - "type": "string", - "description": "Variant allele" - } - } - }, - "TranscriptConsequenceSummary": { - "type": "object", - "required": [ - "transcriptId" - ], - "properties": { - "aminoAcidAlt": { - "type": "string", - "description": "Alt Amino Acid" - }, - "aminoAcidRef": { - "type": "string", - "description": "Reference Amino Acid" - }, - "aminoAcids": { - "type": "string", - "description": "Amino acids change" - }, - "codonChange": { - "type": "string", - "description": "Codon change" - }, - "consequenceTerms": { - "type": "string", - "description": "Consequence terms (comma separated)" - }, - "entrezGeneId": { - "type": "string", - "description": "Entrez gene id" - }, - "exon": { - "type": "string" - }, - "hgvsc": { - "type": "string", - "description": "HGVSc" - }, - "hgvsp": { - "type": "string", - "description": "HGVSp" - }, - "hgvspShort": { - "type": "string", - "description": "HGVSp short" - }, - "hugoGeneSymbol": { - "type": "string", - "description": "Hugo gene symbol" - }, - "isVue": { - "type": "boolean" - }, - "polyphenPrediction": { - "type": "string", - "description": "Polyphen Prediction" - }, - "polyphenScore": { - "type": "number", - "format": "double", - "description": "Polyphen Score" - }, - "proteinPosition": { - "description": "Protein position (start and end)", - "$ref": "#/definitions/IntegerRange" - }, - "refSeq": { - "type": "string", - "description": "RefSeq id" - }, - "siftPrediction": { - "type": "string", - "description": "Sift Prediction" - }, - "siftScore": { - "type": "number", - "format": "double", - "description": "Sift Score" - }, - "transcriptId": { - "type": "string", - "description": "Transcript id" - }, - "uniprotId": { - "type": "string", - "description": "Uniprot ID" - }, - "variantClassification": { - "type": "string", - "description": "Variant classification" - } - } - }, - "TumorType": { - "type": "object", - "properties": { - "children": { - "type": "object", - "additionalProperties": { - "$ref": "#/definitions/TumorType" - } - }, - "code": { - "type": "string" - }, - "color": { - "type": "string" - }, - "id": { - "type": "integer", - "format": "int32" - }, - "level": { - "type": "integer", - "format": "int32" - }, - "mainType": { - "$ref": "#/definitions/MainType" - }, - "name": { - "type": "string" - }, - "parent": { - "type": "string" - }, - "tissue": { - "type": "string" - }, - "tumorForm": { - "type": "string", - "enum": [ - "SOLID", - "LIQUID", - "MIXED" - ] - } - }, - "description": "OncoTree Detailed Cancer Type" - }, - "UntranslatedRegion": { - "type": "object", - "required": [ - "end", - "start", - "strand", - "type" - ], - "properties": { - "type": { - "type": "string", - "description": "UTR Type" - }, - "start": { - "type": "integer", - "format": "int32", - "description": "Start position of UTR" - }, - "end": { - "type": "integer", - "format": "int32", - "description": "End position of UTR" - }, - "strand": { - "type": "integer", - "format": "int32", - "description": "Strand UTR is on, -1 for - and 1 for +" - } - } - }, - "VEPInfo": { - "type": "object", - "properties": { - "cache": { - "$ref": "#/definitions/Version" - }, - "comment": { - "type": "string" - }, - "server": { - "$ref": "#/definitions/Version" - } - } - }, - "VariantAnnotation": { - "type": "object", - "required": [ - "id", - "intergenic_consequences", - "originalVariantQuery", - "variant" - ], - "properties": { - "allele_string": { - "type": "string", - "description": "Allele string (e.g: A/T)" - }, - "annotationJSON": { - "type": "string", - "description": "Annotation data as JSON string" - }, - "annotation_summary": { - "description": "Variant Annotation Summary", - "$ref": "#/definitions/VariantAnnotationSummary" - }, - "assembly_name": { - "type": "string", - "description": "NCBI build number" - }, - "clinvar": { - "description": "MyVariantInfoClinVar", - "$ref": "#/definitions/ClinvarAnnotation" - }, - "colocatedVariants": { - "type": "array", - "items": { - "$ref": "#/definitions/ColocatedVariant" - } - }, - "end": { - "type": "integer", - "format": "int32", - "description": "End position" - }, - "errorMessage": { - "type": "string" - }, - "genomicLocationExplanation": { - "type": "string" - }, - "hgvsg": { - "type": "string" - }, - "hotspots": { - "description": "Hotspot Annotation", - "$ref": "#/definitions/HotspotAnnotation" - }, - "id": { - "type": "string", - "description": "Variant id" - }, - "intergenic_consequences": { - "type": "array", - "description": "intergenicConsequences", - "items": { - "$ref": "#/definitions/IntergenicConsequences" - } - }, - "most_severe_consequence": { - "type": "string", - "description": "Most severe consequence" - }, - "mutation_assessor": { - "description": "Mutation Assessor Annotation", - "$ref": "#/definitions/MutationAssessorAnnotation" - }, - "my_variant_info": { - "description": "My Variant Info Annotation", - "$ref": "#/definitions/MyVariantInfoAnnotation" - }, - "nucleotide_context": { - "description": "Nucleotide Context Annotation", - "$ref": "#/definitions/NucleotideContextAnnotation" - }, - "oncokb": { - "description": "Oncokb", - "$ref": "#/definitions/OncokbAnnotation" - }, - "originalVariantQuery": { - "type": "string", - "description": "Original variant query" - }, - "ptms": { - "description": "Post Translational Modifications", - "$ref": "#/definitions/PtmAnnotation" - }, - "seq_region_name": { - "type": "string", - "description": "Chromosome" - }, - "signalAnnotation": { - "$ref": "#/definitions/SignalAnnotation" - }, - "start": { - "type": "integer", - "format": "int32", - "description": "Start position" - }, - "strand": { - "type": "integer", - "format": "int32", - "description": "Strand (negative or positive)" - }, - "successfully_annotated": { - "type": "boolean", - "example": false, - "description": "Status flag indicating whether variant was succesfully annotated" - }, - "transcript_consequences": { - "type": "array", - "description": "List of transcripts", - "items": { - "$ref": "#/definitions/TranscriptConsequence" - } - }, - "variant": { - "type": "string", - "description": "Variant key" - } - } - }, - "VariantAnnotationSummary": { - "type": "object", - "required": [ - "transcriptConsequenceSummaries", - "transcriptConsequenceSummary", - "transcriptConsequences", - "variant" - ], - "properties": { - "assemblyName": { - "type": "string", - "description": "Assembly name" - }, - "canonicalTranscriptId": { - "type": "string", - "description": "Canonical transcript id" - }, - "genomicLocation": { - "description": "Genomic location", - "$ref": "#/definitions/GenomicLocation" - }, - "strandSign": { - "type": "string", - "description": "Strand (- or +)" - }, - "transcriptConsequenceSummaries": { - "type": "array", - "description": "All transcript consequence summaries", - "items": { - "$ref": "#/definitions/TranscriptConsequenceSummary" - } - }, - "transcriptConsequenceSummary": { - "description": "Most impactful transcript consequence of canonical transcript or if non-existent any transcript", - "$ref": "#/definitions/TranscriptConsequenceSummary" - }, - "transcriptConsequences": { - "type": "array", - "description": "(Deprecated) Transcript consequence summaries (list of one when using annotation/, multiple when using annotation/summary/", - "items": { - "$ref": "#/definitions/TranscriptConsequenceSummary" - } - }, - "variant": { - "type": "string", - "description": "Variant key" - }, - "variantType": { - "type": "string", - "description": "Variant type" - }, - "vues": { - "$ref": "#/definitions/Vues" - } - } - }, - "Vcf": { - "type": "object", - "properties": { - "alt": { - "type": "string", - "description": "alt" - }, - "position": { - "type": "string", - "description": "position" - }, - "ref": { - "type": "string", - "description": "ref" - } - } - }, - "Version": { - "type": "object", - "properties": { - "static": { - "type": "boolean" - }, - "version": { - "type": "string" - } - } - }, - "VueReference": { - "type": "object", - "properties": { - "pubmedId": { - "type": "integer", - "format": "int32" - }, - "referenceText": { - "type": "string" - } - } - }, - "Vues": { - "type": "object", - "properties": { - "comment": { - "type": "string" - }, - "confirmed": { - "type": "boolean" - }, - "context": { - "type": "string" - }, - "defaultEffect": { - "type": "string" - }, - "genomicLocation": { - "type": "string" - }, - "genomicLocationDescription": { - "type": "string" - }, - "hugoGeneSymbol": { - "type": "string" - }, - "mutationOrigin": { - "type": "string" - }, - "references": { - "type": "array", - "items": { - "$ref": "#/definitions/VueReference" - } - }, - "revisedProteinEffect": { - "type": "string" - }, - "revisedVariantClassification": { - "type": "string" - }, - "revisedVariantClassificationStandard": { - "type": "string" - }, - "transcriptId": { - "type": "string" - }, - "variant": { - "type": "string" - }, - "vepPredictedProteinEffect": { - "type": "string" - }, - "vepPredictedVariantClassification": { - "type": "string" - } - } - } - } -} diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts deleted file mode 100644 index 58dba3d740f..00000000000 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts +++ /dev/null @@ -1,3191 +0,0 @@ -import * as request from "superagent"; - -type CallbackHandler = (err: any, res ? : request.Response) => void; -export type AggregateSourceInfo = { - 'annotationSourcesInfo': Array < SourceVersionInfo > - - 'genomeNexus': GenomeNexusInfo - - 'vep': VEPInfo - -}; -export type AlleleCount = { - 'ac': number - - 'ac_afr': number - - 'ac_amr': number - - 'ac_asj': number - - 'ac_eas': number - - 'ac_fin': number - - 'ac_nfe': number - - 'ac_oth': number - - 'ac_sas': number - -}; -export type AlleleFrequency = { - 'af': number - - 'af_afr': number - - 'af_amr': number - - 'af_asj': number - - 'af_eas': number - - 'af_fin': number - - 'af_nfe': number - - 'af_oth': number - - 'af_sas': number - -}; -export type AlleleNumber = { - 'an': number - - 'an_afr': number - - 'an_amr': number - - 'an_asj': number - - 'an_eas': number - - 'an_fin': number - - 'an_nfe': number - - 'an_oth': number - - 'an_sas': number - -}; -export type Alleles = { - 'allele': string - -}; -export type ArticleAbstract = { - 'abstract': string - - 'link': string - -}; -export type Citations = { - 'abstracts': Array < ArticleAbstract > - - 'pmids': Array < string > - -}; -export type Clinvar = { - 'alternateAllele': string - - 'chromosome': string - - 'clinicalSignificance': string - - 'clinvarId': number - - 'conflictingClinicalSignificance': string - - 'endPosition': number - - 'referenceAllele': string - - 'startPosition': number - -}; -export type ClinvarAnnotation = { - 'annotation': Clinvar - -}; -export type ColocatedVariant = { - 'dbSnpId': string - - 'gnomad_nfe_allele': string - - 'gnomad_nfe_maf': string - - 'gnomad_afr_allele': string - - 'gnomad_afr_maf': string - - 'gnomad_eas_allele': string - - 'gnomad_eas_maf': string - -}; -export type Cosmic = { - 'alt': string - - 'chrom': string - - 'cosmicId': string - - 'hg19': Hg19 - - 'license': string - - 'mutFreq': number - - 'mutNt': string - - 'ref': string - - 'tumorSite': string - -}; -export type CountByTumorType = { - 'tumorType': string - - 'tumorTypeCount': number - - 'variantCount': number - -}; -export type Dbsnp = { - '_class': string - - 'alleleOrigin': string - - 'alleles': Array < Alleles > - - 'alt': string - - 'chrom': string - - 'dbsnpBuild': number - - 'flags': Array < string > - - 'hg19': Hg19 - - 'license': string - - 'ref': string - - 'rsid': string - - 'validated': boolean - - 'varSubtype': string - - 'vartype': string - -}; -export type Drug = { - 'drugName': string - - 'ncitCode': string - -}; -export type EnsemblFilter = { - 'geneIds': Array < string > - - 'hugoSymbols': Array < string > - - 'proteinIds': Array < string > - - 'transcriptIds': Array < string > - -}; -export type EnsemblGene = { - 'geneId': string - - 'hugoSymbol': string - - 'synonyms': Array < string > - - 'previousSymbols': Array < string > - - 'entrezGeneId': string - -}; -export type EnsemblTranscript = { - 'uniprotId': string - - 'transcriptId': string - - 'geneId': string - - 'proteinId': string - - 'proteinLength': number - - 'pfamDomains': Array < PfamDomainRange > - - 'hugoSymbols': Array < string > - - 'refseqMrnaId': string - - 'ccdsId': string - - 'exons': Array < Exon > - - 'utrs': Array < UntranslatedRegion > - -}; -export type Exon = { - 'exonId': string - - 'exonStart': number - - 'exonEnd': number - - 'rank': number - - 'strand': number - - 'version': number - -}; -export type Gene = { - 'geneId': string - - 'symbol': string - -}; -export type GeneXref = { - 'db_display_name': string - - 'dbname': string - - 'description': string - - 'display_id': string - - 'ensemblGeneId': string - - 'info_text': string - - 'info_types': string - - 'primary_id': string - - 'synonyms': Array < string > - - 'version': string - -}; -export type GeneralPopulationStats = { - 'counts': SignalPopulationStats - - 'frequencies': SignalPopulationStats - -}; -export type GenomeNexusInfo = { - 'database': Version - - 'server': Version - -}; -export type GenomicLocation = { - 'chromosome': string - - 'start': number - - 'end': number - - 'referenceAllele': string - - 'variantAllele': string - -}; -export type Gnomad = { - 'alleleCount': AlleleCount - - 'alleleFrequency': AlleleFrequency - - 'alleleNumber': AlleleNumber - - 'homozygotes': Homozygotes - -}; -export type Hg19 = { - 'end': number - - 'start': number - -}; -export type Hg38 = { - 'end': string - - 'start': string - -}; -export type Hgvs = { - 'coding': Array < string > - - 'genomic': Array < string > - - 'protein': Array < string > - -}; -export type Homozygotes = { - 'hom': number - - 'hom_afr': number - - 'hom_amr': number - - 'hom_asj': number - - 'hom_eas': number - - 'hom_fin': number - - 'hom_nfe': number - - 'hom_oth': number - - 'hom_sas': number - -}; -export type Hotspot = { - 'hugoSymbol': string - - 'inframeCount': number - - 'missenseCount': number - - 'residue': string - - 'spliceCount': number - - 'transcriptId': string - - 'truncatingCount': number - - 'tumorCount': number - - 'type': string - -}; -export type HotspotAnnotation = { - 'annotation': Array < Array < Hotspot > - > - - 'license': string - -}; -export type HrdScore = { - 'fractionLoh': number - - 'lst': number - - 'ntelomericAi': number - -}; -export type Implication = { - 'abstracts': Array < ArticleAbstract > - - 'alterations': Array < string > - - 'description': string - - 'levelOfEvidence': "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" - - 'pmids': Array < string > - - 'tumorType': TumorType - -}; -export type IndicatorQueryResp = { - 'alleleExist': boolean - - 'dataVersion': string - - 'diagnosticImplications': Array < Implication > - - 'diagnosticSummary': string - - 'geneExist': boolean - - 'geneSummary': string - - 'highestDiagnosticImplicationLevel': "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" - - 'highestFdaLevel': "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" - - 'highestPrognosticImplicationLevel': "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" - - 'highestResistanceLevel': "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" - - 'highestSensitiveLevel': "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" - - 'hotspot': boolean - - 'lastUpdate': string - - 'mutationEffect': MutationEffectResp - - 'oncogenic': string - - 'otherSignificantResistanceLevels': Array < "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" > - - 'otherSignificantSensitiveLevels': Array < "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" > - - 'prognosticImplications': Array < Implication > - - 'prognosticSummary': string - - 'query': Query - - 'treatments': Array < IndicatorQueryTreatment > - - 'tumorTypeSummary': string - - 'variantExist': boolean - - 'variantSummary': string - - 'vus': boolean - -}; -export type IndicatorQueryTreatment = { - 'abstracts': Array < ArticleAbstract > - - 'alterations': Array < string > - - 'approvedIndications': Array < string > - - 'description': string - - 'drugs': Array < Drug > - - 'fdaLevel': "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" - - 'level': "LEVEL_1" | "LEVEL_2" | "LEVEL_3A" | "LEVEL_3B" | "LEVEL_4" | "LEVEL_R1" | "LEVEL_R2" | "LEVEL_Px1" | "LEVEL_Px2" | "LEVEL_Px3" | "LEVEL_Dx1" | "LEVEL_Dx2" | "LEVEL_Dx3" | "LEVEL_Fda1" | "LEVEL_Fda2" | "LEVEL_Fda3" | "NO" - - 'levelAssociatedCancerType': TumorType - - 'levelExcludedCancerTypes': Array < TumorType > - - 'pmids': Array < string > - -}; -export type IntegerRange = { - 'end': number - - 'start': number - -}; -export type IntergenicConsequences = { - 'impact': string - - 'variantAllele': string - - 'consequenceTerms': Array < string > - -}; -export type MainType = { - 'id': number - - 'name': string - - 'tumorForm': "SOLID" | "LIQUID" | "MIXED" - -}; -export type MutationAssessor = { - 'codonStartPosition': string - - 'cosmicCount': number - - 'functionalImpact': string - - 'functionalImpactScore': number - - 'hgvs': string - - 'hugoSymbol': string - - 'input': string - - 'mappingIssue': string - - 'msaGaps': number - - 'msaHeight': number - - 'msaLink': string - - 'pdbLink': string - - 'referenceGenomeVariant': string - - 'referenceGenomeVariantType': string - - 'refseqId': string - - 'refseqPosition': number - - 'refseqResidue': string - - 'snpCount': number - - 'uniprotId': string - - 'uniprotPosition': number - - 'uniprotResidue': string - - 'variant': string - - 'variantConservationScore': number - - 'variantSpecificityScore': number - -}; -export type MutationAssessorAnnotation = { - 'annotation': MutationAssessor - - 'license': string - -}; -export type MutationEffectResp = { - 'citations': Citations - - 'description': string - - 'knownEffect': string - -}; -export type Mutdb = { - 'alt': string - - 'chrom': string - - 'cosmicId': string - - 'hg19': Hg19 - - 'mutpredScore': number - - 'ref': string - - 'rsid': string - - 'uniprotId': string - -}; -export type MyVariantInfo = { - 'clinVar': MyVariantInfoClinVar - - 'cosmic': Cosmic - - 'dbsnp': Dbsnp - - 'gnomadExome': Gnomad - - 'gnomadGenome': Gnomad - - 'hgvs': string - - 'mutdb': Mutdb - - 'query': string - - 'snpeff': Snpeff - - 'variant': string - - 'vcf': Vcf - - 'version': number - -}; -export type MyVariantInfoAnnotation = { - 'annotation': MyVariantInfo - - 'license': string - -}; -export type MyVariantInfoClinVar = { - 'alleleId': number - - 'alt': string - - 'chrom': string - - 'cytogenic': string - - 'gene': Gene - - 'hg19': Hg19 - - 'hg38': Hg38 - - 'hgvs': Hgvs - - 'license': string - - 'rcv': Array < Rcv > - - 'variantId': number - -}; -export type NucleotideContext = { - 'hgvs': string - - 'id': string - - 'molecule': string - - 'query': string - - 'seq': string - -}; -export type NucleotideContextAnnotation = { - 'annotation': NucleotideContext - - 'license': string - -}; -export type OncokbAnnotation = { - 'annotation': IndicatorQueryResp - - 'license': string - -}; -export type PdbHeader = { - 'compound': {} - - 'pdbId': string - - 'source': {} - - 'title': string - -}; -export type PfamDomain = { - 'description': string - - 'name': string - - 'pfamAccession': string - -}; -export type PfamDomainRange = { - 'pfamDomainId': string - - 'pfamDomainStart': number - - 'pfamDomainEnd': number - -}; -export type PostTranslationalModification = { - 'ensemblTranscriptIds': Array < string > - - 'position': number - - 'pubmedIds': Array < string > - - 'sequence': string - - 'type': string - - 'uniprotAccession': string - - 'uniprotEntry': string - -}; -export type PtmAnnotation = { - 'annotation': Array < Array < PostTranslationalModification > - > - - 'license': string - -}; -export type PtmFilter = { - 'transcriptIds': Array < string > - -}; -export type Query = { - 'alteration': string - - 'alterationType': string - - 'consequence': string - - 'entrezGeneId': number - - 'hgvs': string - - 'hugoSymbol': string - - 'id': string - - 'proteinEnd': number - - 'proteinStart': number - - 'referenceGenome': "GRCh37" | "GRCh38" - - 'svType': "DELETION" | "TRANSLOCATION" | "DUPLICATION" | "INSERTION" | "INVERSION" | "FUSION" | "UNKNOWN" - - 'tumorType': string - -}; -export type Rcv = { - 'accession': string - - 'clinicalSignificance': string - - 'origin': string - - 'preferredName': string - -}; -export type SignalAnnotation = { - 'annotation': Array < SignalMutation > - - 'license': string - -}; -export type SignalMutation = { - 'biallelicCountsByTumorType': Array < CountByTumorType > - - 'chromosome': string - - 'countsByTumorType': Array < CountByTumorType > - - 'endPosition': number - - 'generalPopulationStats': GeneralPopulationStats - - 'hugoGeneSymbol': string - - 'mskExperReview': boolean - - 'mutationStatus': string - - 'overallNumberOfGermlineHomozygous': number - - 'pathogenic': string - - 'penetrance': string - - 'qcPassCountsByTumorType': Array < CountByTumorType > - - 'referenceAllele': string - - 'startPosition': number - - 'statsByTumorType': Array < StatsByTumorType > - - 'variantAllele': string - -}; -export type SignalPopulationStats = { - 'afr': number - - 'asj': number - - 'asn': number - - 'eur': number - - 'impact': number - - 'oth': number - -}; -export type Snpeff = { - 'license': string - -}; -export type SourceVersionInfo = { - 'description': string - - 'id': string - - 'name': string - - 'type': string - - 'url': string - - 'version': string - -}; -export type StatsByTumorType = { - 'ageAtDx': number - - 'fBiallelic': number - - 'fCancerTypeCount': number - - 'hrdScore': HrdScore - - 'msiScore': number - - 'nCancerTypeCount': number - - 'numberOfGermlineHomozygous': number - - 'numberWithSig': number - - 'tmb': number - - 'tumorType': string - -}; -export type TranscriptConsequence = { - 'amino_acids': string - - 'canonical': string - - 'codons': string - - 'consequence_terms': Array < string > - - 'exon': string - - 'gene_id': string - - 'gene_symbol': string - - 'hgnc_id': string - - 'hgvsc': string - - 'hgvsg': string - - 'hgvsp': string - - 'polyphen_prediction': string - - 'polyphen_score': number - - 'protein_end': number - - 'protein_id': string - - 'protein_start': number - - 'refseq_transcript_ids': Array < string > - - 'sift_prediction': string - - 'sift_score': number - - 'transcript_id': string - - 'uniprotId': string - - 'variant_allele': string - -}; -export type TranscriptConsequenceSummary = { - 'aminoAcidAlt': string - - 'aminoAcidRef': string - - 'aminoAcids': string - - 'codonChange': string - - 'consequenceTerms': string - - 'entrezGeneId': string - - 'exon': string - - 'hgvsc': string - - 'hgvsp': string - - 'hgvspShort': string - - 'hugoGeneSymbol': string - - 'isVue': boolean - - 'polyphenPrediction': string - - 'polyphenScore': number - - 'proteinPosition': IntegerRange - - 'refSeq': string - - 'siftPrediction': string - - 'siftScore': number - - 'transcriptId': string - - 'uniprotId': string - - 'variantClassification': string - -}; -export type TumorType = { - 'children': {} - - 'code': string - - 'color': string - - 'id': number - - 'level': number - - 'mainType': MainType - - 'name': string - - 'parent': string - - 'tissue': string - - 'tumorForm': "SOLID" | "LIQUID" | "MIXED" - -}; -export type UntranslatedRegion = { - 'type': string - - 'start': number - - 'end': number - - 'strand': number - -}; -export type VEPInfo = { - 'cache': Version - - 'comment': string - - 'server': Version - -}; -export type VariantAnnotation = { - 'allele_string': string - - 'annotationJSON': string - - 'annotation_summary': VariantAnnotationSummary - - 'assembly_name': string - - 'clinvar': ClinvarAnnotation - - 'colocatedVariants': Array < ColocatedVariant > - - 'end': number - - 'errorMessage': string - - 'genomicLocationExplanation': string - - 'hgvsg': string - - 'hotspots': HotspotAnnotation - - 'id': string - - 'intergenic_consequences': Array < IntergenicConsequences > - - 'most_severe_consequence': string - - 'mutation_assessor': MutationAssessorAnnotation - - 'my_variant_info': MyVariantInfoAnnotation - - 'nucleotide_context': NucleotideContextAnnotation - - 'oncokb': OncokbAnnotation - - 'originalVariantQuery': string - - 'ptms': PtmAnnotation - - 'seq_region_name': string - - 'signalAnnotation': SignalAnnotation - - 'start': number - - 'strand': number - - 'successfully_annotated': boolean - - 'transcript_consequences': Array < TranscriptConsequence > - - 'variant': string - -}; -export type VariantAnnotationSummary = { - 'assemblyName': string - - 'canonicalTranscriptId': string - - 'genomicLocation': GenomicLocation - - 'strandSign': string - - 'transcriptConsequenceSummaries': Array < TranscriptConsequenceSummary > - - 'transcriptConsequenceSummary': TranscriptConsequenceSummary - - 'transcriptConsequences': Array < TranscriptConsequenceSummary > - - 'variant': string - - 'variantType': string - - 'vues': Vues - -}; -export type Vcf = { - 'alt': string - - 'position': string - - 'ref': string - -}; -export type Version = { - 'static': boolean - - 'version': string - -}; -export type VueReference = { - 'pubmedId': number - - 'referenceText': string - -}; -export type Vues = { - 'comment': string - - 'confirmed': boolean - - 'context': string - - 'defaultEffect': string - - 'genomicLocation': string - - 'genomicLocationDescription': string - - 'hugoGeneSymbol': string - - 'mutationOrigin': string - - 'references': Array < VueReference > - - 'revisedProteinEffect': string - - 'revisedVariantClassification': string - - 'revisedVariantClassificationStandard': string - - 'transcriptId': string - - 'variant': string - - 'vepPredictedProteinEffect': string - - 'vepPredictedVariantClassification': string - -}; - -/** - * This page shows how to use HTTP requests to access the Genome Nexus API. There are more high level clients available in Python, R, JavaScript, TypeScript and various other languages as well as a command line client to annotate MAF and VCF. See https://docs.genomenexus.org/api. - -Aside from programmatic clients there are web based tools to annotate variants, see https://docs.genomenexus.org/tools. - - We currently only provide long-term support for the '/annotation' endpoint. The other endpoints might change. - * @class GenomeNexusAPI - * @param {(string)} [domainOrOptions] - The project domain. - */ -export default class GenomeNexusAPI { - - private domain: string = ""; - private errorHandlers: CallbackHandler[] = []; - - constructor(domain ? : string) { - if (domain) { - this.domain = domain; - } - } - - getDomain() { - return this.domain; - } - - addErrorHandler(handler: CallbackHandler) { - this.errorHandlers.push(handler); - } - - private request(method: string, url: string, body: any, headers: any, queryParameters: any, form: any, reject: CallbackHandler, resolve: CallbackHandler, errorHandlers: CallbackHandler[]) { - let req = (new(request as any).Request(method, url) as request.Request) - .query(queryParameters); - Object.keys(headers).forEach(key => { - req.set(key, headers[key]); - }); - - if (body) { - req.send(body); - } - - if (typeof(body) === 'object' && !(body.constructor.name === 'Buffer')) { - req.set('Content-Type', 'application/json'); - } - - if (Object.keys(form).length > 0) { - req.type('form'); - req.send(form); - } - - req.end((error, response) => { - if (error || !response.ok) { - reject(error); - errorHandlers.forEach(handler => handler(error)); - } else { - resolve(response); - } - }); - } - - fetchVariantAnnotationPOSTURL(parameters: { - 'variants': Array < string > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/annotation'; - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves VEP annotation for the provided list of variants - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationPOST - * @param {} variants - List of variants. For example ["X:g.66937331T>A","17:g.41242962_41242963insGA"] (GRCh37) or ["1:g.182712A>C", "2:g.265023C>T", "3:g.319781del", "19:g.110753dup", "1:g.1385015_1387562del"] (GRCh38) - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationPOSTWithHttpInfo(parameters: { - 'variants': Array < string > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/annotation'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['variants'] !== undefined) { - body = parameters['variants']; - } - - if (parameters['variants'] === undefined) { - reject(new Error('Missing required parameter: variants')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves VEP annotation for the provided list of variants - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationPOST - * @param {} variants - List of variants. For example ["X:g.66937331T>A","17:g.41242962_41242963insGA"] (GRCh37) or ["1:g.182712A>C", "2:g.265023C>T", "3:g.319781del", "19:g.110753dup", "1:g.1385015_1387562del"] (GRCh38) - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationPOST(parameters: { - 'variants': Array < string > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < VariantAnnotation > - > { - return this.fetchVariantAnnotationPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchVariantAnnotationByIdPOSTURL(parameters: { - 'variantIds': Array < string > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/annotation/dbsnp/'; - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves VEP annotation for the provided list of dbSNP ids - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationByIdPOST - * @param {} variantIds - List of variant IDs. For example ["rs116035550"] - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationByIdPOSTWithHttpInfo(parameters: { - 'variantIds': Array < string > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/annotation/dbsnp/'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['variantIds'] !== undefined) { - body = parameters['variantIds']; - } - - if (parameters['variantIds'] === undefined) { - reject(new Error('Missing required parameter: variantIds')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves VEP annotation for the provided list of dbSNP ids - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationByIdPOST - * @param {} variantIds - List of variant IDs. For example ["rs116035550"] - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationByIdPOST(parameters: { - 'variantIds': Array < string > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < VariantAnnotation > - > { - return this.fetchVariantAnnotationByIdPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchVariantAnnotationByIdGETURL(parameters: { - 'variantId': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/annotation/dbsnp/{variantId}'; - - path = path.replace('{variantId}', parameters['variantId'] + ''); - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves VEP annotation for the give dbSNP id - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationByIdGET - * @param {string} variantId - dbSNP id. For example rs116035550. - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationByIdGETWithHttpInfo(parameters: { - 'variantId': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/annotation/dbsnp/{variantId}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{variantId}', parameters['variantId'] + ''); - - if (parameters['variantId'] === undefined) { - reject(new Error('Missing required parameter: variantId')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves VEP annotation for the give dbSNP id - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationByIdGET - * @param {string} variantId - dbSNP id. For example rs116035550. - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationByIdGET(parameters: { - 'variantId': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < VariantAnnotation > { - return this.fetchVariantAnnotationByIdGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchVariantAnnotationByGenomicLocationPOSTURL(parameters: { - 'genomicLocations': Array < GenomicLocation > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/annotation/genomic'; - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves VEP annotation for the provided list of genomic locations - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationByGenomicLocationPOST - * @param {} genomicLocations - List of Genomic Locations - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationByGenomicLocationPOSTWithHttpInfo(parameters: { - 'genomicLocations': Array < GenomicLocation > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/annotation/genomic'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['genomicLocations'] !== undefined) { - body = parameters['genomicLocations']; - } - - if (parameters['genomicLocations'] === undefined) { - reject(new Error('Missing required parameter: genomicLocations')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves VEP annotation for the provided list of genomic locations - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationByGenomicLocationPOST - * @param {} genomicLocations - List of Genomic Locations - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationByGenomicLocationPOST(parameters: { - 'genomicLocations': Array < GenomicLocation > , - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < VariantAnnotation > - > { - return this.fetchVariantAnnotationByGenomicLocationPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchVariantAnnotationByGenomicLocationGETURL(parameters: { - 'genomicLocation': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/annotation/genomic/{genomicLocation}'; - - path = path.replace('{genomicLocation}', parameters['genomicLocation'] + ''); - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves VEP annotation for the provided genomic location - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationByGenomicLocationGET - * @param {string} genomicLocation - A genomic location. For example 7,140453136,140453136,A,T - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationByGenomicLocationGETWithHttpInfo(parameters: { - 'genomicLocation': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/annotation/genomic/{genomicLocation}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{genomicLocation}', parameters['genomicLocation'] + ''); - - if (parameters['genomicLocation'] === undefined) { - reject(new Error('Missing required parameter: genomicLocation')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves VEP annotation for the provided genomic location - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationByGenomicLocationGET - * @param {string} genomicLocation - A genomic location. For example 7,140453136,140453136,A,T - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationByGenomicLocationGET(parameters: { - 'genomicLocation': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < VariantAnnotation > { - return this.fetchVariantAnnotationByGenomicLocationGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchVariantAnnotationGETURL(parameters: { - 'variant': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/annotation/{variant}'; - - path = path.replace('{variant}', parameters['variant'] + ''); - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves VEP annotation for the provided variant - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationGET - * @param {string} variant - Variant. For example 17:g.41242962_41242963insGA - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationGETWithHttpInfo(parameters: { - 'variant': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/annotation/{variant}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters['variant'] === undefined) { - reject(new Error('Missing required parameter: variant')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['token'] !== undefined) { - queryParameters['token'] = parameters['token']; - } - - if (parameters['fields'] !== undefined) { - queryParameters['fields'] = parameters['fields']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves VEP annotation for the provided variant - * @method - * @name GenomeNexusAPI#fetchVariantAnnotationGET - * @param {string} variant - Variant. For example 17:g.41242962_41242963insGA - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} token - Map of tokens. For example {"source1":"put-your-token1-here","source2":"put-your-token2-here"} - * @param {array} fields - Comma separated list of fields to include in the annotation (case-sensitive!). Defaults to "annotation_summary" if no value passed. Valid values: {annotation_summary, clinvar, hotspots, mutation_assessor, my_variant_info, nucleotide_context, oncokb, ptms, signal} - */ - fetchVariantAnnotationGET(parameters: { - 'variant': string, - 'isoformOverrideSource' ? : string, - 'token' ? : string, - 'fields' ? : "annotation_summary" | "clinvar" | "hotspots" | "mutation_assessor" | "my_variant_info" | "nucleotide_context" | "oncokb" | "ptms" | "signal", - $queryParameters ? : any, - $domain ? : string - }): Promise < VariantAnnotation > { - return this.fetchVariantAnnotationGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchCanonicalEnsemblGeneIdByEntrezGeneIdsPOSTURL(parameters: { - 'entrezGeneIds': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/canonical-gene/entrez'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves canonical Ensembl Gene ID by Entrez Gene Ids - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblGeneIdByEntrezGeneIdsPOST - * @param {} entrezGeneIds - List of Entrez Gene Ids. For example ["23140","26009","100131879"] - */ - fetchCanonicalEnsemblGeneIdByEntrezGeneIdsPOSTWithHttpInfo(parameters: { - 'entrezGeneIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/canonical-gene/entrez'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['entrezGeneIds'] !== undefined) { - body = parameters['entrezGeneIds']; - } - - if (parameters['entrezGeneIds'] === undefined) { - reject(new Error('Missing required parameter: entrezGeneIds')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves canonical Ensembl Gene ID by Entrez Gene Ids - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblGeneIdByEntrezGeneIdsPOST - * @param {} entrezGeneIds - List of Entrez Gene Ids. For example ["23140","26009","100131879"] - */ - fetchCanonicalEnsemblGeneIdByEntrezGeneIdsPOST(parameters: { - 'entrezGeneIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < EnsemblGene > - > { - return this.fetchCanonicalEnsemblGeneIdByEntrezGeneIdsPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchCanonicalEnsemblGeneIdByEntrezGeneIdGETURL(parameters: { - 'entrezGeneId': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/canonical-gene/entrez/{entrezGeneId}'; - - path = path.replace('{entrezGeneId}', parameters['entrezGeneId'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves Ensembl canonical gene id by Entrez Gene Id - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblGeneIdByEntrezGeneIdGET - * @param {string} entrezGeneId - An Entrez Gene Id. For example 23140 - */ - fetchCanonicalEnsemblGeneIdByEntrezGeneIdGETWithHttpInfo(parameters: { - 'entrezGeneId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/canonical-gene/entrez/{entrezGeneId}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{entrezGeneId}', parameters['entrezGeneId'] + ''); - - if (parameters['entrezGeneId'] === undefined) { - reject(new Error('Missing required parameter: entrezGeneId')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves Ensembl canonical gene id by Entrez Gene Id - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblGeneIdByEntrezGeneIdGET - * @param {string} entrezGeneId - An Entrez Gene Id. For example 23140 - */ - fetchCanonicalEnsemblGeneIdByEntrezGeneIdGET(parameters: { - 'entrezGeneId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < EnsemblGene > { - return this.fetchCanonicalEnsemblGeneIdByEntrezGeneIdGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchCanonicalEnsemblGeneIdByHugoSymbolsPOSTURL(parameters: { - 'hugoSymbols': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/canonical-gene/hgnc'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves canonical Ensembl Gene ID by Hugo Symbols - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblGeneIdByHugoSymbolsPOST - * @param {} hugoSymbols - List of Hugo Symbols. For example ["TP53","PIK3CA","BRCA1"] - */ - fetchCanonicalEnsemblGeneIdByHugoSymbolsPOSTWithHttpInfo(parameters: { - 'hugoSymbols': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/canonical-gene/hgnc'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['hugoSymbols'] !== undefined) { - body = parameters['hugoSymbols']; - } - - if (parameters['hugoSymbols'] === undefined) { - reject(new Error('Missing required parameter: hugoSymbols')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves canonical Ensembl Gene ID by Hugo Symbols - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblGeneIdByHugoSymbolsPOST - * @param {} hugoSymbols - List of Hugo Symbols. For example ["TP53","PIK3CA","BRCA1"] - */ - fetchCanonicalEnsemblGeneIdByHugoSymbolsPOST(parameters: { - 'hugoSymbols': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < EnsemblGene > - > { - return this.fetchCanonicalEnsemblGeneIdByHugoSymbolsPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchCanonicalEnsemblGeneIdByHugoSymbolGETURL(parameters: { - 'hugoSymbol': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/canonical-gene/hgnc/{hugoSymbol}'; - - path = path.replace('{hugoSymbol}', parameters['hugoSymbol'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves Ensembl canonical gene id by Hugo Symbol - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblGeneIdByHugoSymbolGET - * @param {string} hugoSymbol - A Hugo Symbol. For example TP53 - */ - fetchCanonicalEnsemblGeneIdByHugoSymbolGETWithHttpInfo(parameters: { - 'hugoSymbol': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/canonical-gene/hgnc/{hugoSymbol}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{hugoSymbol}', parameters['hugoSymbol'] + ''); - - if (parameters['hugoSymbol'] === undefined) { - reject(new Error('Missing required parameter: hugoSymbol')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves Ensembl canonical gene id by Hugo Symbol - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblGeneIdByHugoSymbolGET - * @param {string} hugoSymbol - A Hugo Symbol. For example TP53 - */ - fetchCanonicalEnsemblGeneIdByHugoSymbolGET(parameters: { - 'hugoSymbol': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < EnsemblGene > { - return this.fetchCanonicalEnsemblGeneIdByHugoSymbolGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchCanonicalEnsemblTranscriptsByHugoSymbolsPOSTURL(parameters: { - 'hugoSymbols': Array < string > , - 'isoformOverrideSource' ? : string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/canonical-transcript/hgnc'; - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves Ensembl canonical transcripts by Hugo Symbols - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblTranscriptsByHugoSymbolsPOST - * @param {} hugoSymbols - List of Hugo Symbols. For example ["TP53","PIK3CA","BRCA1"] - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - */ - fetchCanonicalEnsemblTranscriptsByHugoSymbolsPOSTWithHttpInfo(parameters: { - 'hugoSymbols': Array < string > , - 'isoformOverrideSource' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/canonical-transcript/hgnc'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['hugoSymbols'] !== undefined) { - body = parameters['hugoSymbols']; - } - - if (parameters['hugoSymbols'] === undefined) { - reject(new Error('Missing required parameter: hugoSymbols')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves Ensembl canonical transcripts by Hugo Symbols - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblTranscriptsByHugoSymbolsPOST - * @param {} hugoSymbols - List of Hugo Symbols. For example ["TP53","PIK3CA","BRCA1"] - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - */ - fetchCanonicalEnsemblTranscriptsByHugoSymbolsPOST(parameters: { - 'hugoSymbols': Array < string > , - 'isoformOverrideSource' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < EnsemblTranscript > - > { - return this.fetchCanonicalEnsemblTranscriptsByHugoSymbolsPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchCanonicalEnsemblTranscriptByHugoSymbolGETURL(parameters: { - 'hugoSymbol': string, - 'isoformOverrideSource' ? : string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/canonical-transcript/hgnc/{hugoSymbol}'; - - path = path.replace('{hugoSymbol}', parameters['hugoSymbol'] + ''); - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves Ensembl canonical transcript by Hugo Symbol - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblTranscriptByHugoSymbolGET - * @param {string} hugoSymbol - A Hugo Symbol. For example TP53 - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - */ - fetchCanonicalEnsemblTranscriptByHugoSymbolGETWithHttpInfo(parameters: { - 'hugoSymbol': string, - 'isoformOverrideSource' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/canonical-transcript/hgnc/{hugoSymbol}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{hugoSymbol}', parameters['hugoSymbol'] + ''); - - if (parameters['hugoSymbol'] === undefined) { - reject(new Error('Missing required parameter: hugoSymbol')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves Ensembl canonical transcript by Hugo Symbol - * @method - * @name GenomeNexusAPI#fetchCanonicalEnsemblTranscriptByHugoSymbolGET - * @param {string} hugoSymbol - A Hugo Symbol. For example TP53 - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - */ - fetchCanonicalEnsemblTranscriptByHugoSymbolGET(parameters: { - 'hugoSymbol': string, - 'isoformOverrideSource' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < EnsemblTranscript > { - return this.fetchCanonicalEnsemblTranscriptByHugoSymbolGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchEnsemblTranscriptsGETURL(parameters: { - 'geneId' ? : string, - 'proteinId' ? : string, - 'hugoSymbol' ? : string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/transcript'; - if (parameters['geneId'] !== undefined) { - queryParameters['geneId'] = parameters['geneId']; - } - - if (parameters['proteinId'] !== undefined) { - queryParameters['proteinId'] = parameters['proteinId']; - } - - if (parameters['hugoSymbol'] !== undefined) { - queryParameters['hugoSymbol'] = parameters['hugoSymbol']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves Ensembl Transcripts by protein ID, and gene ID. Retrieves all transcripts in case no query parameter provided - * @method - * @name GenomeNexusAPI#fetchEnsemblTranscriptsGET - * @param {string} geneId - An Ensembl gene ID. For example ENSG00000136999 - * @param {string} proteinId - An Ensembl protein ID. For example ENSP00000439985 - * @param {string} hugoSymbol - A Hugo Symbol For example ARF5 - */ - fetchEnsemblTranscriptsGETWithHttpInfo(parameters: { - 'geneId' ? : string, - 'proteinId' ? : string, - 'hugoSymbol' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/transcript'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['geneId'] !== undefined) { - queryParameters['geneId'] = parameters['geneId']; - } - - if (parameters['proteinId'] !== undefined) { - queryParameters['proteinId'] = parameters['proteinId']; - } - - if (parameters['hugoSymbol'] !== undefined) { - queryParameters['hugoSymbol'] = parameters['hugoSymbol']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves Ensembl Transcripts by protein ID, and gene ID. Retrieves all transcripts in case no query parameter provided - * @method - * @name GenomeNexusAPI#fetchEnsemblTranscriptsGET - * @param {string} geneId - An Ensembl gene ID. For example ENSG00000136999 - * @param {string} proteinId - An Ensembl protein ID. For example ENSP00000439985 - * @param {string} hugoSymbol - A Hugo Symbol For example ARF5 - */ - fetchEnsemblTranscriptsGET(parameters: { - 'geneId' ? : string, - 'proteinId' ? : string, - 'hugoSymbol' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < EnsemblTranscript > - > { - return this.fetchEnsemblTranscriptsGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchEnsemblTranscriptsByEnsemblFilterPOSTURL(parameters: { - 'ensemblFilter': EnsemblFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/transcript'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves Ensembl Transcripts by Ensembl transcript IDs, hugo Symbols, protein IDs, or gene IDs - * @method - * @name GenomeNexusAPI#fetchEnsemblTranscriptsByEnsemblFilterPOST - * @param {} ensemblFilter - List of Ensembl transcript IDs. For example ["ENST00000361390", "ENST00000361453", "ENST00000361624"]
OR
List of Hugo Symbols. For example ["TP53", "PIK3CA", "BRCA1"]
OR
List of Ensembl protein IDs. For example ["ENSP00000439985", "ENSP00000478460", "ENSP00000346196"]
OR
List of Ensembl gene IDs. For example ["ENSG00000136999", "ENSG00000272398", "ENSG00000198695"] - */ - fetchEnsemblTranscriptsByEnsemblFilterPOSTWithHttpInfo(parameters: { - 'ensemblFilter': EnsemblFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/transcript'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['ensemblFilter'] !== undefined) { - body = parameters['ensemblFilter']; - } - - if (parameters['ensemblFilter'] === undefined) { - reject(new Error('Missing required parameter: ensemblFilter')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves Ensembl Transcripts by Ensembl transcript IDs, hugo Symbols, protein IDs, or gene IDs - * @method - * @name GenomeNexusAPI#fetchEnsemblTranscriptsByEnsemblFilterPOST - * @param {} ensemblFilter - List of Ensembl transcript IDs. For example ["ENST00000361390", "ENST00000361453", "ENST00000361624"]
OR
List of Hugo Symbols. For example ["TP53", "PIK3CA", "BRCA1"]
OR
List of Ensembl protein IDs. For example ["ENSP00000439985", "ENSP00000478460", "ENSP00000346196"]
OR
List of Ensembl gene IDs. For example ["ENSG00000136999", "ENSG00000272398", "ENSG00000198695"] - */ - fetchEnsemblTranscriptsByEnsemblFilterPOST(parameters: { - 'ensemblFilter': EnsemblFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < EnsemblTranscript > - > { - return this.fetchEnsemblTranscriptsByEnsemblFilterPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchEnsemblTranscriptByTranscriptIdGETURL(parameters: { - 'transcriptId': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/transcript/{transcriptId}'; - - path = path.replace('{transcriptId}', parameters['transcriptId'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves the transcript by an Ensembl transcript ID - * @method - * @name GenomeNexusAPI#fetchEnsemblTranscriptByTranscriptIdGET - * @param {string} transcriptId - An Ensembl transcript ID. For example ENST00000361390 - */ - fetchEnsemblTranscriptByTranscriptIdGETWithHttpInfo(parameters: { - 'transcriptId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/transcript/{transcriptId}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{transcriptId}', parameters['transcriptId'] + ''); - - if (parameters['transcriptId'] === undefined) { - reject(new Error('Missing required parameter: transcriptId')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves the transcript by an Ensembl transcript ID - * @method - * @name GenomeNexusAPI#fetchEnsemblTranscriptByTranscriptIdGET - * @param {string} transcriptId - An Ensembl transcript ID. For example ENST00000361390 - */ - fetchEnsemblTranscriptByTranscriptIdGET(parameters: { - 'transcriptId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < EnsemblTranscript > { - return this.fetchEnsemblTranscriptByTranscriptIdGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchGeneXrefsGETURL(parameters: { - 'accession': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ensembl/xrefs'; - if (parameters['accession'] !== undefined) { - queryParameters['accession'] = parameters['accession']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Perform lookups of Ensembl identifiers and retrieve their external references in other databases - * @method - * @name GenomeNexusAPI#fetchGeneXrefsGET - * @param {string} accession - Ensembl gene accession. For example ENSG00000169083 - */ - fetchGeneXrefsGETWithHttpInfo(parameters: { - 'accession': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ensembl/xrefs'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['accession'] !== undefined) { - queryParameters['accession'] = parameters['accession']; - } - - if (parameters['accession'] === undefined) { - reject(new Error('Missing required parameter: accession')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Perform lookups of Ensembl identifiers and retrieve their external references in other databases - * @method - * @name GenomeNexusAPI#fetchGeneXrefsGET - * @param {string} accession - Ensembl gene accession. For example ENSG00000169083 - */ - fetchGeneXrefsGET(parameters: { - 'accession': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < GeneXref > - > { - return this.fetchGeneXrefsGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchPdbHeaderPOSTURL(parameters: { - 'pdbIds': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/pdb/header'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves PDB header info by a PDB id - * @method - * @name GenomeNexusAPI#fetchPdbHeaderPOST - * @param {} pdbIds - List of pdb ids, for example ["1a37","1a4o"] - */ - fetchPdbHeaderPOSTWithHttpInfo(parameters: { - 'pdbIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/pdb/header'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['pdbIds'] !== undefined) { - body = parameters['pdbIds']; - } - - if (parameters['pdbIds'] === undefined) { - reject(new Error('Missing required parameter: pdbIds')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves PDB header info by a PDB id - * @method - * @name GenomeNexusAPI#fetchPdbHeaderPOST - * @param {} pdbIds - List of pdb ids, for example ["1a37","1a4o"] - */ - fetchPdbHeaderPOST(parameters: { - 'pdbIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < PdbHeader > - > { - return this.fetchPdbHeaderPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchPdbHeaderGETURL(parameters: { - 'pdbId': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/pdb/header/{pdbId}'; - - path = path.replace('{pdbId}', parameters['pdbId'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves PDB header info by a PDB id - * @method - * @name GenomeNexusAPI#fetchPdbHeaderGET - * @param {string} pdbId - PDB id, for example 1a37 - */ - fetchPdbHeaderGETWithHttpInfo(parameters: { - 'pdbId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/pdb/header/{pdbId}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{pdbId}', parameters['pdbId'] + ''); - - if (parameters['pdbId'] === undefined) { - reject(new Error('Missing required parameter: pdbId')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves PDB header info by a PDB id - * @method - * @name GenomeNexusAPI#fetchPdbHeaderGET - * @param {string} pdbId - PDB id, for example 1a37 - */ - fetchPdbHeaderGET(parameters: { - 'pdbId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < PdbHeader > { - return this.fetchPdbHeaderGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchPfamDomainsByPfamAccessionPOSTURL(parameters: { - 'pfamAccessions': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/pfam/domain'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves PFAM domains by PFAM domain accession IDs - * @method - * @name GenomeNexusAPI#fetchPfamDomainsByPfamAccessionPOST - * @param {} pfamAccessions - List of PFAM domain accession IDs. For example ["PF02827","PF00093","PF15276"] - */ - fetchPfamDomainsByPfamAccessionPOSTWithHttpInfo(parameters: { - 'pfamAccessions': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/pfam/domain'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['pfamAccessions'] !== undefined) { - body = parameters['pfamAccessions']; - } - - if (parameters['pfamAccessions'] === undefined) { - reject(new Error('Missing required parameter: pfamAccessions')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves PFAM domains by PFAM domain accession IDs - * @method - * @name GenomeNexusAPI#fetchPfamDomainsByPfamAccessionPOST - * @param {} pfamAccessions - List of PFAM domain accession IDs. For example ["PF02827","PF00093","PF15276"] - */ - fetchPfamDomainsByPfamAccessionPOST(parameters: { - 'pfamAccessions': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < PfamDomain > - > { - return this.fetchPfamDomainsByPfamAccessionPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchPfamDomainsByAccessionGETURL(parameters: { - 'pfamAccession': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/pfam/domain/{pfamAccession}'; - - path = path.replace('{pfamAccession}', parameters['pfamAccession'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves a PFAM domain by a PFAM domain ID - * @method - * @name GenomeNexusAPI#fetchPfamDomainsByAccessionGET - * @param {string} pfamAccession - A PFAM domain accession ID. For example PF02827 - */ - fetchPfamDomainsByAccessionGETWithHttpInfo(parameters: { - 'pfamAccession': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/pfam/domain/{pfamAccession}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{pfamAccession}', parameters['pfamAccession'] + ''); - - if (parameters['pfamAccession'] === undefined) { - reject(new Error('Missing required parameter: pfamAccession')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves a PFAM domain by a PFAM domain ID - * @method - * @name GenomeNexusAPI#fetchPfamDomainsByAccessionGET - * @param {string} pfamAccession - A PFAM domain accession ID. For example PF02827 - */ - fetchPfamDomainsByAccessionGET(parameters: { - 'pfamAccession': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < PfamDomain > { - return this.fetchPfamDomainsByAccessionGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchPostTranslationalModificationsGETURL(parameters: { - 'ensemblTranscriptId' ? : string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ptm/experimental'; - if (parameters['ensemblTranscriptId'] !== undefined) { - queryParameters['ensemblTranscriptId'] = parameters['ensemblTranscriptId']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves PTM entries by Ensembl Transcript ID - * @method - * @name GenomeNexusAPI#fetchPostTranslationalModificationsGET - * @param {string} ensemblTranscriptId - Ensembl Transcript ID. For example ENST00000646891 - */ - fetchPostTranslationalModificationsGETWithHttpInfo(parameters: { - 'ensemblTranscriptId' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ptm/experimental'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['ensemblTranscriptId'] !== undefined) { - queryParameters['ensemblTranscriptId'] = parameters['ensemblTranscriptId']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves PTM entries by Ensembl Transcript ID - * @method - * @name GenomeNexusAPI#fetchPostTranslationalModificationsGET - * @param {string} ensemblTranscriptId - Ensembl Transcript ID. For example ENST00000646891 - */ - fetchPostTranslationalModificationsGET(parameters: { - 'ensemblTranscriptId' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < PostTranslationalModification > - > { - return this.fetchPostTranslationalModificationsGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchPostTranslationalModificationsByPtmFilterPOSTURL(parameters: { - 'ptmFilter': PtmFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/ptm/experimental'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves PTM entries by Ensembl Transcript IDs - * @method - * @name GenomeNexusAPI#fetchPostTranslationalModificationsByPtmFilterPOST - * @param {} ptmFilter - List of Ensembl transcript IDs. For example ["ENST00000420316", "ENST00000646891", "ENST00000371953"] - */ - fetchPostTranslationalModificationsByPtmFilterPOSTWithHttpInfo(parameters: { - 'ptmFilter': PtmFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/ptm/experimental'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['ptmFilter'] !== undefined) { - body = parameters['ptmFilter']; - } - - if (parameters['ptmFilter'] === undefined) { - reject(new Error('Missing required parameter: ptmFilter')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves PTM entries by Ensembl Transcript IDs - * @method - * @name GenomeNexusAPI#fetchPostTranslationalModificationsByPtmFilterPOST - * @param {} ptmFilter - List of Ensembl transcript IDs. For example ["ENST00000420316", "ENST00000646891", "ENST00000371953"] - */ - fetchPostTranslationalModificationsByPtmFilterPOST(parameters: { - 'ptmFilter': PtmFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < PostTranslationalModification > - > { - return this.fetchPostTranslationalModificationsByPtmFilterPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchVersionGETURL(parameters: { - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/version'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieve Genome Nexus Version - * @method - * @name GenomeNexusAPI#fetchVersionGET - */ - fetchVersionGETWithHttpInfo(parameters: { - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/version'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieve Genome Nexus Version - * @method - * @name GenomeNexusAPI#fetchVersionGET - */ - fetchVersionGET(parameters: { - $queryParameters ? : any, - $domain ? : string - }): Promise < AggregateSourceInfo > { - return this.fetchVersionGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; -} \ No newline at end of file diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json deleted file mode 100644 index 9fa1a4d7329..00000000000 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json +++ /dev/null @@ -1,2442 +0,0 @@ -{ - "swagger": "2.0", - "info": { - "description": "This page shows how to use HTTP requests to access the Genome Nexus API. There are more high level clients available in Python, R, JavaScript, TypeScript and various other languages as well as a command line client to annotate MAF and VCF. See https://docs.genomenexus.org/api.\n\nAside from programmatic clients there are web based tools to annotate variants, see https://docs.genomenexus.org/tools.\n\n We currently only provide long-term support for the '/annotation' endpoint. The other endpoints might change.", - "version": "2.0", - "title": "Genome Nexus API", - "license": { - "name": "MIT License", - "url": "https://github.com/genome-nexus/genome-nexus/blob/master/LICENSE" - } - }, - "tags": [ - { - "name": "cross-reference-controller", - "description": "Cross Reference Controller" - }, - { - "name": "signal-mutation-controller", - "description": "Signal Mutation Controller" - }, - { - "name": "search-controller", - "description": "Search Controller" - }, - { - "name": "cancer-hotspots-controller", - "description": "Cancer Hotspots Controller" - }, - { - "name": "mutation-assessor-controller", - "description": "Mutation Assessor Controller" - }, - { - "name": "annotation-summary-controller", - "description": "Annotation Summary Controller" - }, - { - "name": "curious-cases-controller", - "description": "Curious Cases Controller" - }, - { - "name": "signal-query-controller", - "description": "Signal Query Controller" - }, - { - "name": "my-variant-info-controller", - "description": "My Variant Info Controller" - }, - { - "name": "nucleotide-context-controller", - "description": "Nucleotide Context Controller" - } - ], - "schemes": [ - "http", - "https" - ], - "paths": { - "/annotation/summary": { - "post": { - "tags": [ - "annotation-summary-controller" - ], - "summary": "Retrieves VEP annotation summary for the provided list of variants", - "operationId": "fetchVariantAnnotationSummaryPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "variants", - "description": "List of variants. For example [\"X:g.66937331T>A\",\"17:g.41242962_41242963insGA\"] (GRCh37) or [\"1:g.182712A>C\", \"2:g.265023C>T\", \"3:g.319781del\", \"19:g.110753dup\", \"1:g.1385015_1387562del\"] (GRCh38)", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string" - }, - { - "name": "projection", - "in": "query", - "description": "Indicates whether to return summary for all transcripts or only for canonical transcript", - "required": false, - "type": "string", - "default": "ALL", - "enum": [ - "ALL", - "CANONICAL" - ] - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/VariantAnnotationSummary" - } - } - } - } - } - }, - "/annotation/summary/{variant}": { - "get": { - "tags": [ - "annotation-summary-controller" - ], - "summary": "Retrieves VEP annotation summary for the provided variant", - "operationId": "fetchVariantAnnotationSummaryGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "variant", - "in": "path", - "description": "Variant. For example 17:g.41242962_41242963insGA", - "required": true, - "type": "string" - }, - { - "name": "isoformOverrideSource", - "in": "query", - "description": "Isoform override source. For example uniprot", - "required": false, - "type": "string" - }, - { - "name": "projection", - "in": "query", - "description": "Indicates whether to return summary for all transcripts or only for canonical transcript", - "required": false, - "type": "string", - "default": "ALL", - "enum": [ - "ALL", - "CANONICAL" - ] - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/VariantAnnotationSummary" - } - } - } - } - }, - "/cancer_hotspots/genomic": { - "post": { - "tags": [ - "cancer-hotspots-controller" - ], - "summary": "Retrieves hotspot annotations for the provided list of genomic locations", - "operationId": "fetchHotspotAnnotationByGenomicLocationPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "genomicLocations", - "description": "List of genomic locations.", - "required": true, - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/GenomicLocation" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/AggregatedHotspots" - } - } - } - } - } - }, - "/cancer_hotspots/genomic/{genomicLocation}": { - "get": { - "tags": [ - "cancer-hotspots-controller" - ], - "summary": "Retrieves hotspot annotations for a specific genomic location", - "operationId": "fetchHotspotAnnotationByGenomicLocationGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "genomicLocation", - "in": "path", - "description": "A genomic location. For example 7,140453136,140453136,A,T", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/Hotspot" - } - } - } - } - } - }, - "/cancer_hotspots/hgvs": { - "post": { - "tags": [ - "cancer-hotspots-controller" - ], - "summary": "Retrieves hotspot annotations for the provided list of variants", - "operationId": "fetchHotspotAnnotationByHgvsPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "variants", - "description": "List of variants. For example [\"7:g.140453136A>T\",\"12:g.25398285C>A\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/AggregatedHotspots" - } - } - } - } - } - }, - "/cancer_hotspots/hgvs/{variant}": { - "get": { - "tags": [ - "cancer-hotspots-controller" - ], - "summary": "Retrieves hotspot annotations for a specific variant", - "operationId": "fetchHotspotAnnotationByHgvsGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "variant", - "in": "path", - "description": "A variant. For example 7:g.140453136A>T", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/Hotspot" - } - } - } - } - } - }, - "/cancer_hotspots/proteinLocations": { - "post": { - "tags": [ - "cancer-hotspots-controller" - ], - "summary": "Retrieves hotspot annotations for the provided list of transcript id, protein location and mutation type", - "operationId": "fetchHotspotAnnotationByProteinLocationsPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "proteinLocations", - "description": "List of transcript id, protein start location, protein end location, mutation type. \bThe mutation types are limited to 'Missense_Mutation', 'In_Frame_Ins', 'In_Frame_Del', 'Splice_Site', and 'Splice_Region'", - "required": true, - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/ProteinLocation" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/AggregatedHotspots" - } - } - } - } - } - }, - "/cancer_hotspots/transcript": { - "post": { - "tags": [ - "cancer-hotspots-controller" - ], - "summary": "Retrieves hotspot annotations for the provided list of transcript ID", - "operationId": "fetchHotspotAnnotationByTranscriptIdPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "transcriptIds", - "description": "List of transcript Id. For example [\"ENST00000288602\",\"ENST00000256078\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/AggregatedHotspots" - } - } - } - } - } - }, - "/cancer_hotspots/transcript/{transcriptId}": { - "get": { - "tags": [ - "cancer-hotspots-controller" - ], - "summary": "Retrieves hotspot annotations for the provided transcript ID", - "operationId": "fetchHotspotAnnotationByTranscriptIdGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "transcriptId", - "in": "path", - "description": "A Transcript Id. For example ENST00000288602", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/Hotspot" - } - } - } - } - } - }, - "/curious_cases/{genomicLocation}": { - "get": { - "tags": [ - "curious-cases-controller" - ], - "summary": "Retrieves Curious Cases info by a genomic location", - "operationId": "fetchCuriousCasesGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "genomicLocation", - "in": "path", - "description": "Genomic location, for example: 7,116411883,116411905,TTCTTTCTCTCTGTTTTAAGATC,-", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/CuriousCases" - } - } - } - } - }, - "/mutation_assessor": { - "post": { - "tags": [ - "mutation-assessor-controller" - ], - "summary": "Retrieves mutation assessor information for the provided list of variants", - "operationId": "postMutationAssessorAnnotation", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "variants", - "description": "List of variants. For example [\"7:g.140453136A>T\",\"12:g.25398285C>A\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/MutationAssessor" - } - } - } - } - } - }, - "/mutation_assessor/{variant}": { - "get": { - "tags": [ - "mutation-assessor-controller" - ], - "summary": "Retrieves mutation assessor information for the provided list of variants", - "operationId": "fetchMutationAssessorAnnotationGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "variant", - "in": "path", - "description": "A variant. For example 7:g.140453136A>T", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/MutationAssessor" - } - } - } - } - }, - "/my_variant_info/variant": { - "post": { - "tags": [ - "my-variant-info-controller" - ], - "summary": "Retrieves myvariant information for the provided list of variants", - "operationId": "postMyVariantInfoAnnotation", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "variants", - "description": "List of variants. For example [\"7:g.140453136A>T\",\"12:g.25398285C>A\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/MyVariantInfo" - } - } - } - } - } - }, - "/my_variant_info/variant/{variant}": { - "get": { - "tags": [ - "my-variant-info-controller" - ], - "summary": "Retrieves myvariant information for the provided list of variants", - "operationId": "fetchMyVariantInfoAnnotationGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "variant", - "in": "path", - "description": ". For example 7:g.140453136A>T", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/MyVariantInfo" - } - } - } - } - }, - "/nucleotide_context": { - "post": { - "tags": [ - "nucleotide-context-controller" - ], - "summary": "Retrieves nucleotide context information for the provided list of variants", - "operationId": "postNucleotideContextAnnotation", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "variants", - "description": "List of variants. For example [\"7:g.140453136A>T\",\"12:g.25398285C>A\"]", - "required": true, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/NucleotideContext" - } - } - } - } - } - }, - "/nucleotide_context/{variant}": { - "get": { - "tags": [ - "nucleotide-context-controller" - ], - "summary": "Retrieves nucleotide context information for the provided list of variants", - "operationId": "fetchNucleotideContextAnnotationGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "variant", - "in": "path", - "description": "A variant. For example 7:g.140453136A>T", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "$ref": "#/definitions/NucleotideContext" - } - } - } - } - }, - "/search": { - "get": { - "tags": [ - "search-controller" - ], - "summary": "Performs index search.", - "operationId": "searchAnnotationByKeywordGETUsingGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "keyword", - "in": "query", - "description": "keyword. For example 13:g.32890665G>A, TP53 p.R273C, BRAF c.1799T>A", - "required": true, - "type": "string" - }, - { - "name": "limit", - "in": "query", - "description": "Max number of matching results to return", - "required": false, - "type": "integer", - "format": "int32" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/IndexSearch" - } - } - } - } - } - }, - "/signal/mutation": { - "get": { - "tags": [ - "signal-mutation-controller" - ], - "summary": "Retrieves SignalDB mutations by Hugo Gene Symbol", - "operationId": "fetchSignalMutationsByHugoSymbolGETUsingGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "hugoGeneSymbol", - "in": "query", - "description": "Hugo Symbol. For example BRCA1", - "required": false, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/SignalMutation" - } - } - } - } - }, - "post": { - "tags": [ - "signal-mutation-controller" - ], - "summary": "Retrieves SignalDB mutations by Mutation Filter", - "operationId": "fetchSignalMutationsByMutationFilterPOSTUsingPOST", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "in": "body", - "name": "mutationFilter", - "description": "List of Hugo Gene Symbols. For example [\"TP53\", \"PIK3CA\", \"BRCA1\"]", - "required": true, - "schema": { - "$ref": "#/definitions/SignalMutationFilter" - } - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/SignalMutation" - } - } - } - } - } - }, - "/signal/mutation/hgvs/{variant}": { - "get": { - "tags": [ - "signal-mutation-controller" - ], - "summary": "Retrieves SignalDB mutations by hgvgs variant", - "operationId": "fetchSignalMutationsByHgvsgGETUsingGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "variant", - "in": "path", - "description": "A variant. For example 13:g.32890665G>A", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/SignalMutation" - } - } - } - } - } - }, - "/signal/search": { - "get": { - "tags": [ - "signal-query-controller" - ], - "summary": "Performs search by gene, protein change, variant or region.", - "operationId": "searchSignalByKeywordGETUsingGET", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "keyword", - "in": "query", - "description": "keyword. For example BRCA; BRAF V600; 13:32906640-32906640; 13:g.32890665G>A", - "required": true, - "type": "string" - }, - { - "name": "limit", - "in": "query", - "description": "Max number of matching results to return", - "required": false, - "type": "integer", - "format": "int32" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/SignalQuery" - } - } - } - } - } - }, - "/xrefs/{accession}": { - "get": { - "tags": [ - "cross-reference-controller" - ], - "summary": "Perform lookups of Ensembl identifiers and retrieve their external references in other databases", - "operationId": "fetchGeneXrefsGET_1", - "consumes": [ - "application/json" - ], - "produces": [ - "application/json" - ], - "parameters": [ - { - "name": "accession", - "in": "path", - "description": "Ensembl gene accession. For example ENSG00000169083", - "required": true, - "type": "string" - } - ], - "responses": { - "200": { - "description": "OK", - "schema": { - "type": "array", - "items": { - "$ref": "#/definitions/GeneXref" - } - } - } - }, - "deprecated": true - } - } - }, - "definitions": { - "AggregatedHotspots": { - "type": "object", - "required": [ - "genomicLocation", - "hotspots", - "variant" - ], - "properties": { - "genomicLocation": { - "description": "Genomic Location", - "$ref": "#/definitions/GenomicLocation" - }, - "hotspots": { - "type": "array", - "description": "Hotspots", - "items": { - "$ref": "#/definitions/Hotspot" - } - }, - "proteinLocation": { - "$ref": "#/definitions/ProteinLocation" - }, - "transcriptId": { - "type": "string" - }, - "variant": { - "type": "string", - "description": "HGVS notation" - } - } - }, - "AlleleCount": { - "type": "object", - "required": [ - "ac", - "ac_afr", - "ac_amr", - "ac_asj", - "ac_eas", - "ac_fin", - "ac_nfe", - "ac_oth", - "ac_sas" - ], - "properties": { - "ac": { - "type": "integer", - "format": "int32" - }, - "ac_afr": { - "type": "integer", - "format": "int32" - }, - "ac_amr": { - "type": "integer", - "format": "int32" - }, - "ac_asj": { - "type": "integer", - "format": "int32" - }, - "ac_eas": { - "type": "integer", - "format": "int32" - }, - "ac_fin": { - "type": "integer", - "format": "int32" - }, - "ac_nfe": { - "type": "integer", - "format": "int32" - }, - "ac_oth": { - "type": "integer", - "format": "int32" - }, - "ac_sas": { - "type": "integer", - "format": "int32" - } - } - }, - "AlleleFrequency": { - "type": "object", - "required": [ - "af", - "af_afr", - "af_amr", - "af_asj", - "af_eas", - "af_fin", - "af_nfe", - "af_oth", - "af_sas" - ], - "properties": { - "af": { - "type": "number", - "format": "double" - }, - "af_afr": { - "type": "number", - "format": "double" - }, - "af_amr": { - "type": "number", - "format": "double" - }, - "af_asj": { - "type": "number", - "format": "double" - }, - "af_eas": { - "type": "number", - "format": "double" - }, - "af_fin": { - "type": "number", - "format": "double" - }, - "af_nfe": { - "type": "number", - "format": "double" - }, - "af_oth": { - "type": "number", - "format": "double" - }, - "af_sas": { - "type": "number", - "format": "double" - } - } - }, - "AlleleNumber": { - "type": "object", - "required": [ - "an", - "an_afr", - "an_amr", - "an_asj", - "an_eas", - "an_fin", - "an_nfe", - "an_oth", - "an_sas" - ], - "properties": { - "an": { - "type": "integer", - "format": "int32" - }, - "an_afr": { - "type": "integer", - "format": "int32" - }, - "an_amr": { - "type": "integer", - "format": "int32" - }, - "an_asj": { - "type": "integer", - "format": "int32" - }, - "an_eas": { - "type": "integer", - "format": "int32" - }, - "an_fin": { - "type": "integer", - "format": "int32" - }, - "an_nfe": { - "type": "integer", - "format": "int32" - }, - "an_oth": { - "type": "integer", - "format": "int32" - }, - "an_sas": { - "type": "integer", - "format": "int32" - } - } - }, - "Alleles": { - "type": "object", - "properties": { - "allele": { - "type": "string", - "description": "allele" - } - } - }, - "Cosmic": { - "type": "object", - "properties": { - "alt": { - "type": "string", - "description": "alt" - }, - "chrom": { - "type": "string", - "description": "chrom" - }, - "cosmicId": { - "type": "string", - "description": "cosmic_id" - }, - "hg19": { - "description": "hg19", - "$ref": "#/definitions/Hg19" - }, - "license": { - "type": "string", - "description": "_license" - }, - "mutFreq": { - "type": "number", - "format": "double", - "description": "mut_freq" - }, - "mutNt": { - "type": "string", - "description": "mut_nt" - }, - "ref": { - "type": "string", - "description": "ref" - }, - "tumorSite": { - "type": "string", - "description": "tumor_site" - } - } - }, - "CountByTumorType": { - "type": "object", - "properties": { - "tumorType": { - "type": "string", - "description": "Tumor Type" - }, - "tumorTypeCount": { - "type": "integer", - "format": "int32", - "description": "Sample count for Tumor Type" - }, - "variantCount": { - "type": "integer", - "format": "int32", - "description": "Variant count for Tumor Type" - } - } - }, - "CuriousCases": { - "type": "object", - "properties": { - "comment": { - "type": "string" - }, - "genomicLocation": { - "type": "string" - }, - "hugoGeneSymbol": { - "type": "string" - }, - "pubmedIds": { - "type": "array", - "items": { - "type": "integer", - "format": "int32" - } - } - } - }, - "Dbsnp": { - "type": "object", - "properties": { - "_class": { - "type": "string", - "description": "class" - }, - "alleleOrigin": { - "type": "string", - "description": "allele_origin" - }, - "alleles": { - "type": "array", - "description": "alleles", - "items": { - "$ref": "#/definitions/Alleles" - } - }, - "alt": { - "type": "string", - "description": "alt" - }, - "chrom": { - "type": "string", - "description": "chrom" - }, - "dbsnpBuild": { - "type": "integer", - "format": "int32", - "description": "dbsnp_build" - }, - "flags": { - "type": "array", - "description": "flags", - "items": { - "type": "string" - } - }, - "hg19": { - "description": "hg19", - "$ref": "#/definitions/Hg19" - }, - "license": { - "type": "string", - "description": "_license" - }, - "ref": { - "type": "string", - "description": "ref" - }, - "rsid": { - "type": "string", - "description": "rsid" - }, - "validated": { - "type": "boolean", - "example": false, - "description": "validated" - }, - "varSubtype": { - "type": "string", - "description": "var_subtype" - }, - "vartype": { - "type": "string", - "description": "vartype" - } - } - }, - "Gene": { - "type": "object", - "properties": { - "geneId": { - "type": "string", - "description": "geneid" - }, - "symbol": { - "type": "string", - "description": "symbol" - } - } - }, - "GeneXref": { - "type": "object", - "required": [ - "db_display_name", - "dbname", - "description", - "display_id", - "primary_id", - "version" - ], - "properties": { - "db_display_name": { - "type": "string", - "description": "Database display name" - }, - "dbname": { - "type": "string", - "description": "Database name" - }, - "description": { - "type": "string", - "description": "Description" - }, - "display_id": { - "type": "string", - "description": "Display id" - }, - "ensemblGeneId": { - "type": "string" - }, - "info_text": { - "type": "string", - "description": "Database info text" - }, - "info_types": { - "type": "string", - "description": "Database info type" - }, - "primary_id": { - "type": "string", - "description": "Primary id" - }, - "synonyms": { - "type": "array", - "description": "Synonyms", - "items": { - "type": "string" - } - }, - "version": { - "type": "string", - "description": "Version" - } - } - }, - "GeneralPopulationStats": { - "type": "object", - "properties": { - "counts": { - "description": "Counts", - "$ref": "#/definitions/SignalPopulationStats" - }, - "frequencies": { - "description": "Frequencies", - "$ref": "#/definitions/SignalPopulationStats" - } - } - }, - "GenomicLocation": { - "type": "object", - "required": [ - "chromosome", - "end", - "referenceAllele", - "start", - "variantAllele" - ], - "properties": { - "chromosome": { - "type": "string", - "description": "Chromosome" - }, - "start": { - "type": "integer", - "format": "int32", - "description": "Start Position" - }, - "end": { - "type": "integer", - "format": "int32", - "description": "End Position" - }, - "referenceAllele": { - "type": "string", - "description": "Reference Allele" - }, - "variantAllele": { - "type": "string", - "description": "Variant Allele" - } - } - }, - "Gnomad": { - "type": "object", - "properties": { - "alleleCount": { - "description": "ac", - "$ref": "#/definitions/AlleleCount" - }, - "alleleFrequency": { - "description": "af", - "$ref": "#/definitions/AlleleFrequency" - }, - "alleleNumber": { - "description": "an", - "$ref": "#/definitions/AlleleNumber" - }, - "homozygotes": { - "description": "hom", - "$ref": "#/definitions/Homozygotes" - } - } - }, - "Hg19": { - "type": "object", - "properties": { - "end": { - "type": "integer", - "format": "int32", - "description": "end" - }, - "start": { - "type": "integer", - "format": "int32", - "description": "start" - } - } - }, - "Hg38": { - "type": "object", - "properties": { - "end": { - "type": "string", - "description": "end" - }, - "start": { - "type": "string", - "description": "start" - } - } - }, - "Hgvs": { - "type": "object", - "properties": { - "coding": { - "type": "array", - "items": { - "type": "string" - } - }, - "genomic": { - "type": "array", - "items": { - "type": "string" - } - }, - "protein": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "Homozygotes": { - "type": "object", - "required": [ - "hom", - "hom_afr", - "hom_amr", - "hom_asj", - "hom_eas", - "hom_fin", - "hom_nfe", - "hom_oth", - "hom_sas" - ], - "properties": { - "hom": { - "type": "integer", - "format": "int32" - }, - "hom_afr": { - "type": "integer", - "format": "int32" - }, - "hom_amr": { - "type": "integer", - "format": "int32" - }, - "hom_asj": { - "type": "integer", - "format": "int32" - }, - "hom_eas": { - "type": "integer", - "format": "int32" - }, - "hom_fin": { - "type": "integer", - "format": "int32" - }, - "hom_nfe": { - "type": "integer", - "format": "int32" - }, - "hom_oth": { - "type": "integer", - "format": "int32" - }, - "hom_sas": { - "type": "integer", - "format": "int32" - } - } - }, - "Hotspot": { - "type": "object", - "properties": { - "hugoSymbol": { - "type": "string", - "description": "Hugo gene symbol" - }, - "inframeCount": { - "type": "integer", - "format": "int32", - "description": "Inframe mutation count" - }, - "missenseCount": { - "type": "integer", - "format": "int32", - "description": "Missense mutation count" - }, - "residue": { - "type": "string", - "description": "Hotspot residue" - }, - "spliceCount": { - "type": "integer", - "format": "int32", - "description": "Splice mutation count" - }, - "transcriptId": { - "type": "string", - "description": "Ensembl Transcript Id" - }, - "truncatingCount": { - "type": "integer", - "format": "int32", - "description": "Truncation mutation count" - }, - "tumorCount": { - "type": "integer", - "format": "int32", - "description": "Tumor count" - }, - "type": { - "type": "string", - "description": "Hotspot type" - } - } - }, - "HrdScore": { - "type": "object", - "properties": { - "fractionLoh": { - "type": "number", - "format": "double", - "description": "Median HRD Fraction LOH" - }, - "lst": { - "type": "number", - "format": "double", - "description": "Median HRD LST" - }, - "ntelomericAi": { - "type": "number", - "format": "double", - "description": "Median HRD ntelomeric AI" - } - } - }, - "Index": { - "type": "object", - "properties": { - "cdna": { - "type": "array", - "items": { - "type": "string" - } - }, - "hgvsc": { - "type": "array", - "items": { - "type": "string" - } - }, - "hgvsp": { - "type": "array", - "items": { - "type": "string" - } - }, - "hgvspShort": { - "type": "array", - "items": { - "type": "string" - } - }, - "hugoSymbol": { - "type": "array", - "items": { - "type": "string" - } - }, - "rsid": { - "type": "array", - "items": { - "type": "string" - } - }, - "variant": { - "type": "string" - } - } - }, - "IndexSearch": { - "type": "object", - "properties": { - "queryType": { - "type": "string", - "enum": [ - "GENE_HGVSPSHORT", - "GENE_CDNA", - "GENE_HGVSP", - "HGVSG", - "HGVSC" - ] - }, - "results": { - "type": "array", - "items": { - "$ref": "#/definitions/Index" - } - } - } - }, - "IntegerRange": { - "type": "object", - "properties": { - "end": { - "type": "integer", - "format": "int32" - }, - "start": { - "type": "integer", - "format": "int32" - } - } - }, - "MutationAssessor": { - "type": "object", - "required": [ - "input" - ], - "properties": { - "codonStartPosition": { - "type": "string", - "description": "Codon start position" - }, - "cosmicCount": { - "type": "integer", - "format": "int32", - "description": "Number of mutations in COSMIC for this protein" - }, - "functionalImpact": { - "type": "string", - "description": "Functional impact" - }, - "functionalImpactScore": { - "type": "number", - "format": "double", - "description": "Functional impact score" - }, - "hgvs": { - "type": "string" - }, - "hugoSymbol": { - "type": "string", - "description": "Hugo gene symbol" - }, - "input": { - "type": "string", - "description": "User-input variants" - }, - "mappingIssue": { - "type": "string", - "description": "Mapping issue info" - }, - "msaGaps": { - "type": "number", - "format": "double", - "description": "Portion of gaps in variant position in multiple sequence alignment" - }, - "msaHeight": { - "type": "integer", - "format": "int32", - "description": "Number of diverse sequences in multiple sequence alignment (identical or highly similar sequences filtered out)" - }, - "msaLink": { - "type": "string", - "description": "Link to multiple sequence alignment" - }, - "pdbLink": { - "type": "string", - "description": "Link to 3d structure browser" - }, - "referenceGenomeVariant": { - "type": "string", - "description": "Reference genome variant" - }, - "referenceGenomeVariantType": { - "type": "string", - "description": "Reference genome variant type" - }, - "refseqId": { - "type": "string", - "description": "Refseq protein ID" - }, - "refseqPosition": { - "type": "integer", - "format": "int32", - "description": "Variant position in Refseq protein, can be different from the one in Uniprot" - }, - "refseqResidue": { - "type": "string", - "description": "Reference residue in Refseq protein, can be different from the one in Uniprot" - }, - "snpCount": { - "type": "integer", - "format": "int32", - "description": "Number of SNPs in dbSNP for this protein" - }, - "uniprotId": { - "type": "string", - "description": "Uniprot protein accession ID" - }, - "uniprotPosition": { - "type": "integer", - "format": "int32", - "description": "Variant position in Uniprot protein, can be different from the one in Refseq" - }, - "uniprotResidue": { - "type": "string", - "description": "Reference residue in Uniprot protein, can be different from the one in Refseq" - }, - "variant": { - "type": "string", - "description": "Amino acid substitution" - }, - "variantConservationScore": { - "type": "number", - "format": "double", - "description": "Variant conservation score" - }, - "variantSpecificityScore": { - "type": "number", - "format": "double", - "description": "Variant specificity score" - } - } - }, - "Mutdb": { - "type": "object", - "properties": { - "alt": { - "type": "string", - "description": "alt" - }, - "chrom": { - "type": "string", - "description": "chrom" - }, - "cosmicId": { - "type": "string", - "description": "cosmic_id" - }, - "hg19": { - "description": "hg19", - "$ref": "#/definitions/Hg19" - }, - "mutpredScore": { - "type": "number", - "format": "double", - "description": "mutpred_score" - }, - "ref": { - "type": "string", - "description": "ref" - }, - "rsid": { - "type": "string", - "description": "rsid" - }, - "uniprotId": { - "type": "string", - "description": "uniprot_id" - } - } - }, - "MyVariantInfo": { - "type": "object", - "properties": { - "clinVar": { - "description": "clinvar", - "$ref": "#/definitions/MyVariantInfoClinVar" - }, - "cosmic": { - "description": "cosmic", - "$ref": "#/definitions/Cosmic" - }, - "dbsnp": { - "description": "dbsnp", - "$ref": "#/definitions/Dbsnp" - }, - "gnomadExome": { - "description": "gnomad_exome", - "$ref": "#/definitions/Gnomad" - }, - "gnomadGenome": { - "description": "gnomad_genome", - "$ref": "#/definitions/Gnomad" - }, - "hgvs": { - "type": "string", - "description": "hgvs" - }, - "mutdb": { - "$ref": "#/definitions/Mutdb" - }, - "query": { - "type": "string" - }, - "snpeff": { - "description": "snpeff", - "$ref": "#/definitions/Snpeff" - }, - "variant": { - "type": "string", - "description": "variant" - }, - "vcf": { - "description": "vcf", - "$ref": "#/definitions/Vcf" - }, - "version": { - "type": "integer", - "format": "int32", - "description": "version" - } - } - }, - "MyVariantInfoClinVar": { - "type": "object", - "properties": { - "alleleId": { - "type": "integer", - "format": "int32", - "description": "allele_id" - }, - "alt": { - "type": "string", - "description": "alt" - }, - "chrom": { - "type": "string", - "description": "chrom" - }, - "cytogenic": { - "type": "string", - "description": "cytogenic" - }, - "gene": { - "description": "gene", - "$ref": "#/definitions/Gene" - }, - "hg19": { - "description": "hg19", - "$ref": "#/definitions/Hg19" - }, - "hg38": { - "description": "hg38", - "$ref": "#/definitions/Hg38" - }, - "hgvs": { - "description": "hgvs", - "$ref": "#/definitions/Hgvs" - }, - "license": { - "type": "string", - "description": "license" - }, - "rcv": { - "type": "array", - "items": { - "$ref": "#/definitions/Rcv" - } - }, - "variantId": { - "type": "integer", - "format": "int32", - "description": "variant_id" - } - } - }, - "NucleotideContext": { - "type": "object", - "required": [ - "seq" - ], - "properties": { - "hgvs": { - "type": "string" - }, - "id": { - "type": "string" - }, - "molecule": { - "type": "string" - }, - "query": { - "type": "string" - }, - "seq": { - "type": "string", - "description": "Nucleotide context sequence" - } - } - }, - "ProteinLocation": { - "type": "object", - "required": [ - "end", - "mutationType", - "start", - "transcriptId" - ], - "properties": { - "transcriptId": { - "type": "string", - "description": "Ensembl Transcript ID" - }, - "start": { - "type": "integer", - "format": "int32", - "description": "Start Position Residue" - }, - "end": { - "type": "integer", - "format": "int32", - "description": "End Position Residue" - }, - "mutationType": { - "type": "string", - "description": "Mutation Type e.g. Missense_Mutation" - } - } - }, - "Rcv": { - "type": "object", - "properties": { - "accession": { - "type": "string", - "description": "accession" - }, - "clinicalSignificance": { - "type": "string", - "description": "clinical_significance" - }, - "origin": { - "type": "string", - "description": "origin" - }, - "preferredName": { - "type": "string", - "description": "preferred_name" - } - } - }, - "SignalMutation": { - "type": "object", - "properties": { - "biallelicCountsByTumorType": { - "type": "array", - "description": "Biallelic Counts by Tumor Type", - "items": { - "$ref": "#/definitions/CountByTumorType" - } - }, - "chromosome": { - "type": "string", - "description": "Chromosome" - }, - "countsByTumorType": { - "type": "array", - "description": "Counts by Tumor Type", - "items": { - "$ref": "#/definitions/CountByTumorType" - } - }, - "endPosition": { - "type": "integer", - "format": "int64", - "description": "End Position" - }, - "generalPopulationStats": { - "description": "General Population Stats", - "$ref": "#/definitions/GeneralPopulationStats" - }, - "hugoGeneSymbol": { - "type": "string", - "description": "Hugo Gene Symbol" - }, - "mskExperReview": { - "type": "boolean", - "example": false, - "description": "Msk Expert Review" - }, - "mutationStatus": { - "type": "string", - "description": "Mutation Status" - }, - "overallNumberOfGermlineHomozygous": { - "type": "integer", - "format": "int32" - }, - "pathogenic": { - "type": "string", - "description": "Pathogenic" - }, - "penetrance": { - "type": "string", - "description": "Penetrance" - }, - "qcPassCountsByTumorType": { - "type": "array", - "description": "QC Pass Counts by Tumor Type", - "items": { - "$ref": "#/definitions/CountByTumorType" - } - }, - "referenceAllele": { - "type": "string", - "description": "Reference Allele" - }, - "startPosition": { - "type": "integer", - "format": "int64", - "description": "Start Position" - }, - "statsByTumorType": { - "type": "array", - "description": "Stats By Tumor Type", - "items": { - "$ref": "#/definitions/StatsByTumorType" - } - }, - "variantAllele": { - "type": "string", - "description": "Variant Allele" - } - } - }, - "SignalMutationFilter": { - "type": "object", - "properties": { - "hugoSymbols": { - "type": "array", - "description": "List of Hugo Symbols. For example [\"TP53\", \"PIK3CA\", \"BRCA1\"]", - "items": { - "type": "string" - } - } - } - }, - "SignalPopulationStats": { - "type": "object", - "properties": { - "afr": { - "type": "number", - "format": "double", - "description": "African/African American" - }, - "asj": { - "type": "number", - "format": "double", - "description": "Ashkenazi Jewish" - }, - "asn": { - "type": "number", - "format": "double", - "description": "Asian" - }, - "eur": { - "type": "number", - "format": "double", - "description": "European" - }, - "impact": { - "type": "number", - "format": "double", - "description": "Impact" - }, - "oth": { - "type": "number", - "format": "double", - "description": "Other" - } - } - }, - "SignalQuery": { - "type": "object", - "properties": { - "alteration": { - "type": "string", - "description": "Matching Alteration (e.g: V600E)" - }, - "description": { - "type": "string", - "description": "Optional free-form text" - }, - "hugoSymbol": { - "type": "string", - "description": "Matching Hugo Gene Symbol (e.g: BRCA2, BRAF)" - }, - "matchType": { - "type": "string", - "description": "Match Type", - "enum": [ - "EXACT", - "STARTS_WITH", - "PARTIAL", - "NO_MATCH" - ] - }, - "queryType": { - "type": "string", - "description": "Query Type", - "enum": [ - "GENE", - "ALTERATION", - "VARIANT", - "REGION" - ] - }, - "region": { - "type": "string", - "description": "Matching Region (e.g: 13:32968940-32968940)" - }, - "variant": { - "type": "string", - "description": "Matching HGVSG Variant (e.g: 17:g.37880220T>C)" - } - } - }, - "Snpeff": { - "type": "object", - "properties": { - "license": { - "type": "string", - "description": "license" - } - } - }, - "StatsByTumorType": { - "type": "object", - "properties": { - "ageAtDx": { - "type": "integer", - "format": "int32", - "description": "Median Age at Dx" - }, - "fBiallelic": { - "type": "number", - "format": "double", - "description": "Frequency Of Biallelic" - }, - "fCancerTypeCount": { - "type": "number", - "format": "double", - "description": "Frequency Of Cancer Type Count" - }, - "hrdScore": { - "description": "Hrd Score", - "$ref": "#/definitions/HrdScore" - }, - "msiScore": { - "type": "number", - "format": "double", - "description": "Msi Score" - }, - "nCancerTypeCount": { - "type": "integer", - "format": "int32", - "description": "Number Of Cancer Type Count" - }, - "numberOfGermlineHomozygous": { - "type": "integer", - "format": "int32", - "description": "Number Of Germline Homozygous Per Tumor Type" - }, - "numberWithSig": { - "type": "integer", - "format": "int32", - "description": "Number of Variants with Signature" - }, - "tmb": { - "type": "number", - "format": "double", - "description": "Median TMB" - }, - "tumorType": { - "type": "string", - "description": "Tumor Type" - } - } - }, - "TranscriptConsequenceSummary": { - "type": "object", - "required": [ - "transcriptId" - ], - "properties": { - "aminoAcidAlt": { - "type": "string", - "description": "Alt Amino Acid" - }, - "aminoAcidRef": { - "type": "string", - "description": "Reference Amino Acid" - }, - "aminoAcids": { - "type": "string", - "description": "Amino acids change" - }, - "codonChange": { - "type": "string", - "description": "Codon change" - }, - "consequenceTerms": { - "type": "string", - "description": "Consequence terms (comma separated)" - }, - "entrezGeneId": { - "type": "string", - "description": "Entrez gene id" - }, - "exon": { - "type": "string" - }, - "hgvsc": { - "type": "string", - "description": "HGVSc" - }, - "hgvsp": { - "type": "string", - "description": "HGVSp" - }, - "hgvspShort": { - "type": "string", - "description": "HGVSp short" - }, - "hugoGeneSymbol": { - "type": "string", - "description": "Hugo gene symbol" - }, - "isVue": { - "type": "boolean" - }, - "polyphenPrediction": { - "type": "string", - "description": "Polyphen Prediction" - }, - "polyphenScore": { - "type": "number", - "format": "double", - "description": "Polyphen Score" - }, - "proteinPosition": { - "description": "Protein position (start and end)", - "$ref": "#/definitions/IntegerRange" - }, - "refSeq": { - "type": "string", - "description": "RefSeq id" - }, - "siftPrediction": { - "type": "string", - "description": "Sift Prediction" - }, - "siftScore": { - "type": "number", - "format": "double", - "description": "Sift Score" - }, - "transcriptId": { - "type": "string", - "description": "Transcript id" - }, - "uniprotId": { - "type": "string", - "description": "Uniprot ID" - }, - "variantClassification": { - "type": "string", - "description": "Variant classification" - } - } - }, - "VariantAnnotationSummary": { - "type": "object", - "required": [ - "transcriptConsequenceSummaries", - "transcriptConsequenceSummary", - "transcriptConsequences", - "variant" - ], - "properties": { - "assemblyName": { - "type": "string", - "description": "Assembly name" - }, - "canonicalTranscriptId": { - "type": "string", - "description": "Canonical transcript id" - }, - "genomicLocation": { - "description": "Genomic location", - "$ref": "#/definitions/GenomicLocation" - }, - "strandSign": { - "type": "string", - "description": "Strand (- or +)" - }, - "transcriptConsequenceSummaries": { - "type": "array", - "description": "All transcript consequence summaries", - "items": { - "$ref": "#/definitions/TranscriptConsequenceSummary" - } - }, - "transcriptConsequenceSummary": { - "description": "Most impactful transcript consequence of canonical transcript or if non-existent any transcript", - "$ref": "#/definitions/TranscriptConsequenceSummary" - }, - "transcriptConsequences": { - "type": "array", - "description": "(Deprecated) Transcript consequence summaries (list of one when using annotation/, multiple when using annotation/summary/", - "items": { - "$ref": "#/definitions/TranscriptConsequenceSummary" - } - }, - "variant": { - "type": "string", - "description": "Variant key" - }, - "variantType": { - "type": "string", - "description": "Variant type" - }, - "vues": { - "$ref": "#/definitions/Vues" - } - } - }, - "Vcf": { - "type": "object", - "properties": { - "alt": { - "type": "string", - "description": "alt" - }, - "position": { - "type": "string", - "description": "position" - }, - "ref": { - "type": "string", - "description": "ref" - } - } - }, - "VueReference": { - "type": "object", - "properties": { - "pubmedId": { - "type": "integer", - "format": "int32" - }, - "referenceText": { - "type": "string" - } - } - }, - "Vues": { - "type": "object", - "properties": { - "comment": { - "type": "string" - }, - "confirmed": { - "type": "boolean" - }, - "context": { - "type": "string" - }, - "defaultEffect": { - "type": "string" - }, - "genomicLocation": { - "type": "string" - }, - "genomicLocationDescription": { - "type": "string" - }, - "hugoGeneSymbol": { - "type": "string" - }, - "mutationOrigin": { - "type": "string" - }, - "references": { - "type": "array", - "items": { - "$ref": "#/definitions/VueReference" - } - }, - "revisedProteinEffect": { - "type": "string" - }, - "revisedVariantClassification": { - "type": "string" - }, - "revisedVariantClassificationStandard": { - "type": "string" - }, - "transcriptId": { - "type": "string" - }, - "variant": { - "type": "string" - }, - "vepPredictedProteinEffect": { - "type": "string" - }, - "vepPredictedVariantClassification": { - "type": "string" - } - } - } - } -} diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts deleted file mode 100644 index 3f0b07b07be..00000000000 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts +++ /dev/null @@ -1,2487 +0,0 @@ -import * as request from "superagent"; - -type CallbackHandler = (err: any, res ? : request.Response) => void; -export type AggregatedHotspots = { - 'genomicLocation': GenomicLocation - - 'hotspots': Array < Hotspot > - - 'proteinLocation': ProteinLocation - - 'transcriptId': string - - 'variant': string - -}; -export type AlleleCount = { - 'ac': number - - 'ac_afr': number - - 'ac_amr': number - - 'ac_asj': number - - 'ac_eas': number - - 'ac_fin': number - - 'ac_nfe': number - - 'ac_oth': number - - 'ac_sas': number - -}; -export type AlleleFrequency = { - 'af': number - - 'af_afr': number - - 'af_amr': number - - 'af_asj': number - - 'af_eas': number - - 'af_fin': number - - 'af_nfe': number - - 'af_oth': number - - 'af_sas': number - -}; -export type AlleleNumber = { - 'an': number - - 'an_afr': number - - 'an_amr': number - - 'an_asj': number - - 'an_eas': number - - 'an_fin': number - - 'an_nfe': number - - 'an_oth': number - - 'an_sas': number - -}; -export type Alleles = { - 'allele': string - -}; -export type Cosmic = { - 'alt': string - - 'chrom': string - - 'cosmicId': string - - 'hg19': Hg19 - - 'license': string - - 'mutFreq': number - - 'mutNt': string - - 'ref': string - - 'tumorSite': string - -}; -export type CountByTumorType = { - 'tumorType': string - - 'tumorTypeCount': number - - 'variantCount': number - -}; -export type CuriousCases = { - 'comment': string - - 'genomicLocation': string - - 'hugoGeneSymbol': string - - 'pubmedIds': Array < number > - -}; -export type Dbsnp = { - '_class': string - - 'alleleOrigin': string - - 'alleles': Array < Alleles > - - 'alt': string - - 'chrom': string - - 'dbsnpBuild': number - - 'flags': Array < string > - - 'hg19': Hg19 - - 'license': string - - 'ref': string - - 'rsid': string - - 'validated': boolean - - 'varSubtype': string - - 'vartype': string - -}; -export type Gene = { - 'geneId': string - - 'symbol': string - -}; -export type GeneXref = { - 'db_display_name': string - - 'dbname': string - - 'description': string - - 'display_id': string - - 'ensemblGeneId': string - - 'info_text': string - - 'info_types': string - - 'primary_id': string - - 'synonyms': Array < string > - - 'version': string - -}; -export type GeneralPopulationStats = { - 'counts': SignalPopulationStats - - 'frequencies': SignalPopulationStats - -}; -export type GenomicLocation = { - 'chromosome': string - - 'start': number - - 'end': number - - 'referenceAllele': string - - 'variantAllele': string - -}; -export type Gnomad = { - 'alleleCount': AlleleCount - - 'alleleFrequency': AlleleFrequency - - 'alleleNumber': AlleleNumber - - 'homozygotes': Homozygotes - -}; -export type Hg19 = { - 'end': number - - 'start': number - -}; -export type Hg38 = { - 'end': string - - 'start': string - -}; -export type Hgvs = { - 'coding': Array < string > - - 'genomic': Array < string > - - 'protein': Array < string > - -}; -export type Homozygotes = { - 'hom': number - - 'hom_afr': number - - 'hom_amr': number - - 'hom_asj': number - - 'hom_eas': number - - 'hom_fin': number - - 'hom_nfe': number - - 'hom_oth': number - - 'hom_sas': number - -}; -export type Hotspot = { - 'hugoSymbol': string - - 'inframeCount': number - - 'missenseCount': number - - 'residue': string - - 'spliceCount': number - - 'transcriptId': string - - 'truncatingCount': number - - 'tumorCount': number - - 'type': string - -}; -export type HrdScore = { - 'fractionLoh': number - - 'lst': number - - 'ntelomericAi': number - -}; -export type Index = { - 'cdna': Array < string > - - 'hgvsc': Array < string > - - 'hgvsp': Array < string > - - 'hgvspShort': Array < string > - - 'hugoSymbol': Array < string > - - 'rsid': Array < string > - - 'variant': string - -}; -export type IndexSearch = { - 'queryType': "GENE_HGVSPSHORT" | "GENE_CDNA" | "GENE_HGVSP" | "HGVSG" | "HGVSC" - - 'results': Array < Index > - -}; -export type IntegerRange = { - 'end': number - - 'start': number - -}; -export type MutationAssessor = { - 'codonStartPosition': string - - 'cosmicCount': number - - 'functionalImpact': string - - 'functionalImpactScore': number - - 'hgvs': string - - 'hugoSymbol': string - - 'input': string - - 'mappingIssue': string - - 'msaGaps': number - - 'msaHeight': number - - 'msaLink': string - - 'pdbLink': string - - 'referenceGenomeVariant': string - - 'referenceGenomeVariantType': string - - 'refseqId': string - - 'refseqPosition': number - - 'refseqResidue': string - - 'snpCount': number - - 'uniprotId': string - - 'uniprotPosition': number - - 'uniprotResidue': string - - 'variant': string - - 'variantConservationScore': number - - 'variantSpecificityScore': number - -}; -export type Mutdb = { - 'alt': string - - 'chrom': string - - 'cosmicId': string - - 'hg19': Hg19 - - 'mutpredScore': number - - 'ref': string - - 'rsid': string - - 'uniprotId': string - -}; -export type MyVariantInfo = { - 'clinVar': MyVariantInfoClinVar - - 'cosmic': Cosmic - - 'dbsnp': Dbsnp - - 'gnomadExome': Gnomad - - 'gnomadGenome': Gnomad - - 'hgvs': string - - 'mutdb': Mutdb - - 'query': string - - 'snpeff': Snpeff - - 'variant': string - - 'vcf': Vcf - - 'version': number - -}; -export type MyVariantInfoClinVar = { - 'alleleId': number - - 'alt': string - - 'chrom': string - - 'cytogenic': string - - 'gene': Gene - - 'hg19': Hg19 - - 'hg38': Hg38 - - 'hgvs': Hgvs - - 'license': string - - 'rcv': Array < Rcv > - - 'variantId': number - -}; -export type NucleotideContext = { - 'hgvs': string - - 'id': string - - 'molecule': string - - 'query': string - - 'seq': string - -}; -export type ProteinLocation = { - 'transcriptId': string - - 'start': number - - 'end': number - - 'mutationType': string - -}; -export type Rcv = { - 'accession': string - - 'clinicalSignificance': string - - 'origin': string - - 'preferredName': string - -}; -export type SignalMutation = { - 'biallelicCountsByTumorType': Array < CountByTumorType > - - 'chromosome': string - - 'countsByTumorType': Array < CountByTumorType > - - 'endPosition': number - - 'generalPopulationStats': GeneralPopulationStats - - 'hugoGeneSymbol': string - - 'mskExperReview': boolean - - 'mutationStatus': string - - 'overallNumberOfGermlineHomozygous': number - - 'pathogenic': string - - 'penetrance': string - - 'qcPassCountsByTumorType': Array < CountByTumorType > - - 'referenceAllele': string - - 'startPosition': number - - 'statsByTumorType': Array < StatsByTumorType > - - 'variantAllele': string - -}; -export type SignalMutationFilter = { - 'hugoSymbols': Array < string > - -}; -export type SignalPopulationStats = { - 'afr': number - - 'asj': number - - 'asn': number - - 'eur': number - - 'impact': number - - 'oth': number - -}; -export type SignalQuery = { - 'alteration': string - - 'description': string - - 'hugoSymbol': string - - 'matchType': "EXACT" | "STARTS_WITH" | "PARTIAL" | "NO_MATCH" - - 'queryType': "GENE" | "ALTERATION" | "VARIANT" | "REGION" - - 'region': string - - 'variant': string - -}; -export type Snpeff = { - 'license': string - -}; -export type StatsByTumorType = { - 'ageAtDx': number - - 'fBiallelic': number - - 'fCancerTypeCount': number - - 'hrdScore': HrdScore - - 'msiScore': number - - 'nCancerTypeCount': number - - 'numberOfGermlineHomozygous': number - - 'numberWithSig': number - - 'tmb': number - - 'tumorType': string - -}; -export type TranscriptConsequenceSummary = { - 'aminoAcidAlt': string - - 'aminoAcidRef': string - - 'aminoAcids': string - - 'codonChange': string - - 'consequenceTerms': string - - 'entrezGeneId': string - - 'exon': string - - 'hgvsc': string - - 'hgvsp': string - - 'hgvspShort': string - - 'hugoGeneSymbol': string - - 'isVue': boolean - - 'polyphenPrediction': string - - 'polyphenScore': number - - 'proteinPosition': IntegerRange - - 'refSeq': string - - 'siftPrediction': string - - 'siftScore': number - - 'transcriptId': string - - 'uniprotId': string - - 'variantClassification': string - -}; -export type VariantAnnotationSummary = { - 'assemblyName': string - - 'canonicalTranscriptId': string - - 'genomicLocation': GenomicLocation - - 'strandSign': string - - 'transcriptConsequenceSummaries': Array < TranscriptConsequenceSummary > - - 'transcriptConsequenceSummary': TranscriptConsequenceSummary - - 'transcriptConsequences': Array < TranscriptConsequenceSummary > - - 'variant': string - - 'variantType': string - - 'vues': Vues - -}; -export type Vcf = { - 'alt': string - - 'position': string - - 'ref': string - -}; -export type VueReference = { - 'pubmedId': number - - 'referenceText': string - -}; -export type Vues = { - 'comment': string - - 'confirmed': boolean - - 'context': string - - 'defaultEffect': string - - 'genomicLocation': string - - 'genomicLocationDescription': string - - 'hugoGeneSymbol': string - - 'mutationOrigin': string - - 'references': Array < VueReference > - - 'revisedProteinEffect': string - - 'revisedVariantClassification': string - - 'revisedVariantClassificationStandard': string - - 'transcriptId': string - - 'variant': string - - 'vepPredictedProteinEffect': string - - 'vepPredictedVariantClassification': string - -}; - -/** - * This page shows how to use HTTP requests to access the Genome Nexus API. There are more high level clients available in Python, R, JavaScript, TypeScript and various other languages as well as a command line client to annotate MAF and VCF. See https://docs.genomenexus.org/api. - -Aside from programmatic clients there are web based tools to annotate variants, see https://docs.genomenexus.org/tools. - - We currently only provide long-term support for the '/annotation' endpoint. The other endpoints might change. - * @class GenomeNexusAPIInternal - * @param {(string)} [domainOrOptions] - The project domain. - */ -export default class GenomeNexusAPIInternal { - - private domain: string = ""; - private errorHandlers: CallbackHandler[] = []; - - constructor(domain ? : string) { - if (domain) { - this.domain = domain; - } - } - - getDomain() { - return this.domain; - } - - addErrorHandler(handler: CallbackHandler) { - this.errorHandlers.push(handler); - } - - private request(method: string, url: string, body: any, headers: any, queryParameters: any, form: any, reject: CallbackHandler, resolve: CallbackHandler, errorHandlers: CallbackHandler[]) { - let req = (new(request as any).Request(method, url) as request.Request) - .query(queryParameters); - Object.keys(headers).forEach(key => { - req.set(key, headers[key]); - }); - - if (body) { - req.send(body); - } - - if (typeof(body) === 'object' && !(body.constructor.name === 'Buffer')) { - req.set('Content-Type', 'application/json'); - } - - if (Object.keys(form).length > 0) { - req.type('form'); - req.send(form); - } - - req.end((error, response) => { - if (error || !response.ok) { - reject(error); - errorHandlers.forEach(handler => handler(error)); - } else { - resolve(response); - } - }); - } - - fetchVariantAnnotationSummaryPOSTURL(parameters: { - 'variants': Array < string > , - 'isoformOverrideSource' ? : string, - 'projection' ? : "ALL" | "CANONICAL", - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/annotation/summary'; - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['projection'] !== undefined) { - queryParameters['projection'] = parameters['projection']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves VEP annotation summary for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchVariantAnnotationSummaryPOST - * @param {} variants - List of variants. For example ["X:g.66937331T>A","17:g.41242962_41242963insGA"] (GRCh37) or ["1:g.182712A>C", "2:g.265023C>T", "3:g.319781del", "19:g.110753dup", "1:g.1385015_1387562del"] (GRCh38) - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} projection - Indicates whether to return summary for all transcripts or only for canonical transcript - */ - fetchVariantAnnotationSummaryPOSTWithHttpInfo(parameters: { - 'variants': Array < string > , - 'isoformOverrideSource' ? : string, - 'projection' ? : "ALL" | "CANONICAL", - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/annotation/summary'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['variants'] !== undefined) { - body = parameters['variants']; - } - - if (parameters['variants'] === undefined) { - reject(new Error('Missing required parameter: variants')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['projection'] !== undefined) { - queryParameters['projection'] = parameters['projection']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves VEP annotation summary for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchVariantAnnotationSummaryPOST - * @param {} variants - List of variants. For example ["X:g.66937331T>A","17:g.41242962_41242963insGA"] (GRCh37) or ["1:g.182712A>C", "2:g.265023C>T", "3:g.319781del", "19:g.110753dup", "1:g.1385015_1387562del"] (GRCh38) - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} projection - Indicates whether to return summary for all transcripts or only for canonical transcript - */ - fetchVariantAnnotationSummaryPOST(parameters: { - 'variants': Array < string > , - 'isoformOverrideSource' ? : string, - 'projection' ? : "ALL" | "CANONICAL", - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < VariantAnnotationSummary > - > { - return this.fetchVariantAnnotationSummaryPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchVariantAnnotationSummaryGETURL(parameters: { - 'variant': string, - 'isoformOverrideSource' ? : string, - 'projection' ? : "ALL" | "CANONICAL", - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/annotation/summary/{variant}'; - - path = path.replace('{variant}', parameters['variant'] + ''); - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['projection'] !== undefined) { - queryParameters['projection'] = parameters['projection']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves VEP annotation summary for the provided variant - * @method - * @name GenomeNexusAPIInternal#fetchVariantAnnotationSummaryGET - * @param {string} variant - Variant. For example 17:g.41242962_41242963insGA - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} projection - Indicates whether to return summary for all transcripts or only for canonical transcript - */ - fetchVariantAnnotationSummaryGETWithHttpInfo(parameters: { - 'variant': string, - 'isoformOverrideSource' ? : string, - 'projection' ? : "ALL" | "CANONICAL", - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/annotation/summary/{variant}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters['variant'] === undefined) { - reject(new Error('Missing required parameter: variant')); - return; - } - - if (parameters['isoformOverrideSource'] !== undefined) { - queryParameters['isoformOverrideSource'] = parameters['isoformOverrideSource']; - } - - if (parameters['projection'] !== undefined) { - queryParameters['projection'] = parameters['projection']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves VEP annotation summary for the provided variant - * @method - * @name GenomeNexusAPIInternal#fetchVariantAnnotationSummaryGET - * @param {string} variant - Variant. For example 17:g.41242962_41242963insGA - * @param {string} isoformOverrideSource - Isoform override source. For example uniprot - * @param {string} projection - Indicates whether to return summary for all transcripts or only for canonical transcript - */ - fetchVariantAnnotationSummaryGET(parameters: { - 'variant': string, - 'isoformOverrideSource' ? : string, - 'projection' ? : "ALL" | "CANONICAL", - $queryParameters ? : any, - $domain ? : string - }): Promise < VariantAnnotationSummary > { - return this.fetchVariantAnnotationSummaryGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchHotspotAnnotationByGenomicLocationPOSTURL(parameters: { - 'genomicLocations': Array < GenomicLocation > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/cancer_hotspots/genomic'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves hotspot annotations for the provided list of genomic locations - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByGenomicLocationPOST - * @param {} genomicLocations - List of genomic locations. - */ - fetchHotspotAnnotationByGenomicLocationPOSTWithHttpInfo(parameters: { - 'genomicLocations': Array < GenomicLocation > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/cancer_hotspots/genomic'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['genomicLocations'] !== undefined) { - body = parameters['genomicLocations']; - } - - if (parameters['genomicLocations'] === undefined) { - reject(new Error('Missing required parameter: genomicLocations')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves hotspot annotations for the provided list of genomic locations - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByGenomicLocationPOST - * @param {} genomicLocations - List of genomic locations. - */ - fetchHotspotAnnotationByGenomicLocationPOST(parameters: { - 'genomicLocations': Array < GenomicLocation > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < AggregatedHotspots > - > { - return this.fetchHotspotAnnotationByGenomicLocationPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchHotspotAnnotationByGenomicLocationGETURL(parameters: { - 'genomicLocation': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/cancer_hotspots/genomic/{genomicLocation}'; - - path = path.replace('{genomicLocation}', parameters['genomicLocation'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves hotspot annotations for a specific genomic location - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByGenomicLocationGET - * @param {string} genomicLocation - A genomic location. For example 7,140453136,140453136,A,T - */ - fetchHotspotAnnotationByGenomicLocationGETWithHttpInfo(parameters: { - 'genomicLocation': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/cancer_hotspots/genomic/{genomicLocation}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{genomicLocation}', parameters['genomicLocation'] + ''); - - if (parameters['genomicLocation'] === undefined) { - reject(new Error('Missing required parameter: genomicLocation')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves hotspot annotations for a specific genomic location - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByGenomicLocationGET - * @param {string} genomicLocation - A genomic location. For example 7,140453136,140453136,A,T - */ - fetchHotspotAnnotationByGenomicLocationGET(parameters: { - 'genomicLocation': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Hotspot > - > { - return this.fetchHotspotAnnotationByGenomicLocationGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchHotspotAnnotationByHgvsPOSTURL(parameters: { - 'variants': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/cancer_hotspots/hgvs'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves hotspot annotations for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByHgvsPOST - * @param {} variants - List of variants. For example ["7:g.140453136A>T","12:g.25398285C>A"] - */ - fetchHotspotAnnotationByHgvsPOSTWithHttpInfo(parameters: { - 'variants': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/cancer_hotspots/hgvs'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['variants'] !== undefined) { - body = parameters['variants']; - } - - if (parameters['variants'] === undefined) { - reject(new Error('Missing required parameter: variants')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves hotspot annotations for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByHgvsPOST - * @param {} variants - List of variants. For example ["7:g.140453136A>T","12:g.25398285C>A"] - */ - fetchHotspotAnnotationByHgvsPOST(parameters: { - 'variants': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < AggregatedHotspots > - > { - return this.fetchHotspotAnnotationByHgvsPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchHotspotAnnotationByHgvsGETURL(parameters: { - 'variant': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/cancer_hotspots/hgvs/{variant}'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves hotspot annotations for a specific variant - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByHgvsGET - * @param {string} variant - A variant. For example 7:g.140453136A>T - */ - fetchHotspotAnnotationByHgvsGETWithHttpInfo(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/cancer_hotspots/hgvs/{variant}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters['variant'] === undefined) { - reject(new Error('Missing required parameter: variant')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves hotspot annotations for a specific variant - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByHgvsGET - * @param {string} variant - A variant. For example 7:g.140453136A>T - */ - fetchHotspotAnnotationByHgvsGET(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Hotspot > - > { - return this.fetchHotspotAnnotationByHgvsGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchHotspotAnnotationByProteinLocationsPOSTURL(parameters: { - 'proteinLocations': Array < ProteinLocation > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/cancer_hotspots/proteinLocations'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves hotspot annotations for the provided list of transcript id, protein location and mutation type - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByProteinLocationsPOST - * @param {} proteinLocations - List of transcript id, protein start location, protein end location, mutation type. The mutation types are limited to 'Missense_Mutation', 'In_Frame_Ins', 'In_Frame_Del', 'Splice_Site', and 'Splice_Region' - */ - fetchHotspotAnnotationByProteinLocationsPOSTWithHttpInfo(parameters: { - 'proteinLocations': Array < ProteinLocation > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/cancer_hotspots/proteinLocations'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['proteinLocations'] !== undefined) { - body = parameters['proteinLocations']; - } - - if (parameters['proteinLocations'] === undefined) { - reject(new Error('Missing required parameter: proteinLocations')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves hotspot annotations for the provided list of transcript id, protein location and mutation type - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByProteinLocationsPOST - * @param {} proteinLocations - List of transcript id, protein start location, protein end location, mutation type. The mutation types are limited to 'Missense_Mutation', 'In_Frame_Ins', 'In_Frame_Del', 'Splice_Site', and 'Splice_Region' - */ - fetchHotspotAnnotationByProteinLocationsPOST(parameters: { - 'proteinLocations': Array < ProteinLocation > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < AggregatedHotspots > - > { - return this.fetchHotspotAnnotationByProteinLocationsPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchHotspotAnnotationByTranscriptIdPOSTURL(parameters: { - 'transcriptIds': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/cancer_hotspots/transcript'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves hotspot annotations for the provided list of transcript ID - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByTranscriptIdPOST - * @param {} transcriptIds - List of transcript Id. For example ["ENST00000288602","ENST00000256078"] - */ - fetchHotspotAnnotationByTranscriptIdPOSTWithHttpInfo(parameters: { - 'transcriptIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/cancer_hotspots/transcript'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['transcriptIds'] !== undefined) { - body = parameters['transcriptIds']; - } - - if (parameters['transcriptIds'] === undefined) { - reject(new Error('Missing required parameter: transcriptIds')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves hotspot annotations for the provided list of transcript ID - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByTranscriptIdPOST - * @param {} transcriptIds - List of transcript Id. For example ["ENST00000288602","ENST00000256078"] - */ - fetchHotspotAnnotationByTranscriptIdPOST(parameters: { - 'transcriptIds': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < AggregatedHotspots > - > { - return this.fetchHotspotAnnotationByTranscriptIdPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchHotspotAnnotationByTranscriptIdGETURL(parameters: { - 'transcriptId': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/cancer_hotspots/transcript/{transcriptId}'; - - path = path.replace('{transcriptId}', parameters['transcriptId'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves hotspot annotations for the provided transcript ID - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByTranscriptIdGET - * @param {string} transcriptId - A Transcript Id. For example ENST00000288602 - */ - fetchHotspotAnnotationByTranscriptIdGETWithHttpInfo(parameters: { - 'transcriptId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/cancer_hotspots/transcript/{transcriptId}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{transcriptId}', parameters['transcriptId'] + ''); - - if (parameters['transcriptId'] === undefined) { - reject(new Error('Missing required parameter: transcriptId')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves hotspot annotations for the provided transcript ID - * @method - * @name GenomeNexusAPIInternal#fetchHotspotAnnotationByTranscriptIdGET - * @param {string} transcriptId - A Transcript Id. For example ENST00000288602 - */ - fetchHotspotAnnotationByTranscriptIdGET(parameters: { - 'transcriptId': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < Hotspot > - > { - return this.fetchHotspotAnnotationByTranscriptIdGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchCuriousCasesGETURL(parameters: { - 'genomicLocation': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/curious_cases/{genomicLocation}'; - - path = path.replace('{genomicLocation}', parameters['genomicLocation'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves Curious Cases info by a genomic location - * @method - * @name GenomeNexusAPIInternal#fetchCuriousCasesGET - * @param {string} genomicLocation - Genomic location, for example: 7,116411883,116411905,TTCTTTCTCTCTGTTTTAAGATC,- - */ - fetchCuriousCasesGETWithHttpInfo(parameters: { - 'genomicLocation': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/curious_cases/{genomicLocation}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{genomicLocation}', parameters['genomicLocation'] + ''); - - if (parameters['genomicLocation'] === undefined) { - reject(new Error('Missing required parameter: genomicLocation')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves Curious Cases info by a genomic location - * @method - * @name GenomeNexusAPIInternal#fetchCuriousCasesGET - * @param {string} genomicLocation - Genomic location, for example: 7,116411883,116411905,TTCTTTCTCTCTGTTTTAAGATC,- - */ - fetchCuriousCasesGET(parameters: { - 'genomicLocation': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < CuriousCases > { - return this.fetchCuriousCasesGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - postMutationAssessorAnnotationURL(parameters: { - 'variants': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/mutation_assessor'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves mutation assessor information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#postMutationAssessorAnnotation - * @param {} variants - List of variants. For example ["7:g.140453136A>T","12:g.25398285C>A"] - */ - postMutationAssessorAnnotationWithHttpInfo(parameters: { - 'variants': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/mutation_assessor'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['variants'] !== undefined) { - body = parameters['variants']; - } - - if (parameters['variants'] === undefined) { - reject(new Error('Missing required parameter: variants')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves mutation assessor information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#postMutationAssessorAnnotation - * @param {} variants - List of variants. For example ["7:g.140453136A>T","12:g.25398285C>A"] - */ - postMutationAssessorAnnotation(parameters: { - 'variants': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < MutationAssessor > - > { - return this.postMutationAssessorAnnotationWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchMutationAssessorAnnotationGETURL(parameters: { - 'variant': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/mutation_assessor/{variant}'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves mutation assessor information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchMutationAssessorAnnotationGET - * @param {string} variant - A variant. For example 7:g.140453136A>T - */ - fetchMutationAssessorAnnotationGETWithHttpInfo(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/mutation_assessor/{variant}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters['variant'] === undefined) { - reject(new Error('Missing required parameter: variant')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves mutation assessor information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchMutationAssessorAnnotationGET - * @param {string} variant - A variant. For example 7:g.140453136A>T - */ - fetchMutationAssessorAnnotationGET(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < MutationAssessor > { - return this.fetchMutationAssessorAnnotationGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - postMyVariantInfoAnnotationURL(parameters: { - 'variants': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/my_variant_info/variant'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves myvariant information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#postMyVariantInfoAnnotation - * @param {} variants - List of variants. For example ["7:g.140453136A>T","12:g.25398285C>A"] - */ - postMyVariantInfoAnnotationWithHttpInfo(parameters: { - 'variants': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/my_variant_info/variant'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['variants'] !== undefined) { - body = parameters['variants']; - } - - if (parameters['variants'] === undefined) { - reject(new Error('Missing required parameter: variants')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves myvariant information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#postMyVariantInfoAnnotation - * @param {} variants - List of variants. For example ["7:g.140453136A>T","12:g.25398285C>A"] - */ - postMyVariantInfoAnnotation(parameters: { - 'variants': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < MyVariantInfo > - > { - return this.postMyVariantInfoAnnotationWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchMyVariantInfoAnnotationGETURL(parameters: { - 'variant': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/my_variant_info/variant/{variant}'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves myvariant information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchMyVariantInfoAnnotationGET - * @param {string} variant - . For example 7:g.140453136A>T - */ - fetchMyVariantInfoAnnotationGETWithHttpInfo(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/my_variant_info/variant/{variant}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters['variant'] === undefined) { - reject(new Error('Missing required parameter: variant')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves myvariant information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchMyVariantInfoAnnotationGET - * @param {string} variant - . For example 7:g.140453136A>T - */ - fetchMyVariantInfoAnnotationGET(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < MyVariantInfo > { - return this.fetchMyVariantInfoAnnotationGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - postNucleotideContextAnnotationURL(parameters: { - 'variants': Array < string > , - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/nucleotide_context'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves nucleotide context information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#postNucleotideContextAnnotation - * @param {} variants - List of variants. For example ["7:g.140453136A>T","12:g.25398285C>A"] - */ - postNucleotideContextAnnotationWithHttpInfo(parameters: { - 'variants': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/nucleotide_context'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['variants'] !== undefined) { - body = parameters['variants']; - } - - if (parameters['variants'] === undefined) { - reject(new Error('Missing required parameter: variants')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves nucleotide context information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#postNucleotideContextAnnotation - * @param {} variants - List of variants. For example ["7:g.140453136A>T","12:g.25398285C>A"] - */ - postNucleotideContextAnnotation(parameters: { - 'variants': Array < string > , - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < NucleotideContext > - > { - return this.postNucleotideContextAnnotationWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchNucleotideContextAnnotationGETURL(parameters: { - 'variant': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/nucleotide_context/{variant}'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves nucleotide context information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchNucleotideContextAnnotationGET - * @param {string} variant - A variant. For example 7:g.140453136A>T - */ - fetchNucleotideContextAnnotationGETWithHttpInfo(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/nucleotide_context/{variant}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters['variant'] === undefined) { - reject(new Error('Missing required parameter: variant')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves nucleotide context information for the provided list of variants - * @method - * @name GenomeNexusAPIInternal#fetchNucleotideContextAnnotationGET - * @param {string} variant - A variant. For example 7:g.140453136A>T - */ - fetchNucleotideContextAnnotationGET(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < NucleotideContext > { - return this.fetchNucleotideContextAnnotationGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - searchAnnotationByKeywordGETUsingGETURL(parameters: { - 'keyword': string, - 'limit' ? : number, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/search'; - if (parameters['keyword'] !== undefined) { - queryParameters['keyword'] = parameters['keyword']; - } - - if (parameters['limit'] !== undefined) { - queryParameters['limit'] = parameters['limit']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Performs index search. - * @method - * @name GenomeNexusAPIInternal#searchAnnotationByKeywordGETUsingGET - * @param {string} keyword - keyword. For example 13:g.32890665G>A, TP53 p.R273C, BRAF c.1799T>A - * @param {integer} limit - Max number of matching results to return - */ - searchAnnotationByKeywordGETUsingGETWithHttpInfo(parameters: { - 'keyword': string, - 'limit' ? : number, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/search'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['keyword'] !== undefined) { - queryParameters['keyword'] = parameters['keyword']; - } - - if (parameters['keyword'] === undefined) { - reject(new Error('Missing required parameter: keyword')); - return; - } - - if (parameters['limit'] !== undefined) { - queryParameters['limit'] = parameters['limit']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Performs index search. - * @method - * @name GenomeNexusAPIInternal#searchAnnotationByKeywordGETUsingGET - * @param {string} keyword - keyword. For example 13:g.32890665G>A, TP53 p.R273C, BRAF c.1799T>A - * @param {integer} limit - Max number of matching results to return - */ - searchAnnotationByKeywordGETUsingGET(parameters: { - 'keyword': string, - 'limit' ? : number, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < IndexSearch > - > { - return this.searchAnnotationByKeywordGETUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchSignalMutationsByHugoSymbolGETUsingGETURL(parameters: { - 'hugoGeneSymbol' ? : string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/signal/mutation'; - if (parameters['hugoGeneSymbol'] !== undefined) { - queryParameters['hugoGeneSymbol'] = parameters['hugoGeneSymbol']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves SignalDB mutations by Hugo Gene Symbol - * @method - * @name GenomeNexusAPIInternal#fetchSignalMutationsByHugoSymbolGETUsingGET - * @param {string} hugoGeneSymbol - Hugo Symbol. For example BRCA1 - */ - fetchSignalMutationsByHugoSymbolGETUsingGETWithHttpInfo(parameters: { - 'hugoGeneSymbol' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/signal/mutation'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['hugoGeneSymbol'] !== undefined) { - queryParameters['hugoGeneSymbol'] = parameters['hugoGeneSymbol']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves SignalDB mutations by Hugo Gene Symbol - * @method - * @name GenomeNexusAPIInternal#fetchSignalMutationsByHugoSymbolGETUsingGET - * @param {string} hugoGeneSymbol - Hugo Symbol. For example BRCA1 - */ - fetchSignalMutationsByHugoSymbolGETUsingGET(parameters: { - 'hugoGeneSymbol' ? : string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < SignalMutation > - > { - return this.fetchSignalMutationsByHugoSymbolGETUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchSignalMutationsByMutationFilterPOSTUsingPOSTURL(parameters: { - 'mutationFilter': SignalMutationFilter, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/signal/mutation'; - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves SignalDB mutations by Mutation Filter - * @method - * @name GenomeNexusAPIInternal#fetchSignalMutationsByMutationFilterPOSTUsingPOST - * @param {} mutationFilter - List of Hugo Gene Symbols. For example ["TP53", "PIK3CA", "BRCA1"] - */ - fetchSignalMutationsByMutationFilterPOSTUsingPOSTWithHttpInfo(parameters: { - 'mutationFilter': SignalMutationFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/signal/mutation'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['mutationFilter'] !== undefined) { - body = parameters['mutationFilter']; - } - - if (parameters['mutationFilter'] === undefined) { - reject(new Error('Missing required parameter: mutationFilter')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('POST', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves SignalDB mutations by Mutation Filter - * @method - * @name GenomeNexusAPIInternal#fetchSignalMutationsByMutationFilterPOSTUsingPOST - * @param {} mutationFilter - List of Hugo Gene Symbols. For example ["TP53", "PIK3CA", "BRCA1"] - */ - fetchSignalMutationsByMutationFilterPOSTUsingPOST(parameters: { - 'mutationFilter': SignalMutationFilter, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < SignalMutation > - > { - return this.fetchSignalMutationsByMutationFilterPOSTUsingPOSTWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchSignalMutationsByHgvsgGETUsingGETURL(parameters: { - 'variant': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/signal/mutation/hgvs/{variant}'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Retrieves SignalDB mutations by hgvgs variant - * @method - * @name GenomeNexusAPIInternal#fetchSignalMutationsByHgvsgGETUsingGET - * @param {string} variant - A variant. For example 13:g.32890665G>A - */ - fetchSignalMutationsByHgvsgGETUsingGETWithHttpInfo(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/signal/mutation/hgvs/{variant}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{variant}', parameters['variant'] + ''); - - if (parameters['variant'] === undefined) { - reject(new Error('Missing required parameter: variant')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Retrieves SignalDB mutations by hgvgs variant - * @method - * @name GenomeNexusAPIInternal#fetchSignalMutationsByHgvsgGETUsingGET - * @param {string} variant - A variant. For example 13:g.32890665G>A - */ - fetchSignalMutationsByHgvsgGETUsingGET(parameters: { - 'variant': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < SignalMutation > - > { - return this.fetchSignalMutationsByHgvsgGETUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - searchSignalByKeywordGETUsingGETURL(parameters: { - 'keyword': string, - 'limit' ? : number, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/signal/search'; - if (parameters['keyword'] !== undefined) { - queryParameters['keyword'] = parameters['keyword']; - } - - if (parameters['limit'] !== undefined) { - queryParameters['limit'] = parameters['limit']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Performs search by gene, protein change, variant or region. - * @method - * @name GenomeNexusAPIInternal#searchSignalByKeywordGETUsingGET - * @param {string} keyword - keyword. For example BRCA; BRAF V600; 13:32906640-32906640; 13:g.32890665G>A - * @param {integer} limit - Max number of matching results to return - */ - searchSignalByKeywordGETUsingGETWithHttpInfo(parameters: { - 'keyword': string, - 'limit' ? : number, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/signal/search'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - if (parameters['keyword'] !== undefined) { - queryParameters['keyword'] = parameters['keyword']; - } - - if (parameters['keyword'] === undefined) { - reject(new Error('Missing required parameter: keyword')); - return; - } - - if (parameters['limit'] !== undefined) { - queryParameters['limit'] = parameters['limit']; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Performs search by gene, protein change, variant or region. - * @method - * @name GenomeNexusAPIInternal#searchSignalByKeywordGETUsingGET - * @param {string} keyword - keyword. For example BRCA; BRAF V600; 13:32906640-32906640; 13:g.32890665G>A - * @param {integer} limit - Max number of matching results to return - */ - searchSignalByKeywordGETUsingGET(parameters: { - 'keyword': string, - 'limit' ? : number, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < SignalQuery > - > { - return this.searchSignalByKeywordGETUsingGETWithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; - fetchGeneXrefsGET_1URL(parameters: { - 'accession': string, - $queryParameters ? : any - }): string { - let queryParameters: any = {}; - let path = '/xrefs/{accession}'; - - path = path.replace('{accession}', parameters['accession'] + ''); - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - let keys = Object.keys(queryParameters); - return this.domain + path + (keys.length > 0 ? '?' + (keys.map(key => key + '=' + encodeURIComponent(queryParameters[key])).join('&')) : ''); - }; - - /** - * Perform lookups of Ensembl identifiers and retrieve their external references in other databases - * @method - * @name GenomeNexusAPIInternal#fetchGeneXrefsGET_1 - * @param {string} accession - Ensembl gene accession. For example ENSG00000169083 - */ - fetchGeneXrefsGET_1WithHttpInfo(parameters: { - 'accession': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < request.Response > { - const domain = parameters.$domain ? parameters.$domain : this.domain; - const errorHandlers = this.errorHandlers; - const request = this.request; - let path = '/xrefs/{accession}'; - let body: any; - let queryParameters: any = {}; - let headers: any = {}; - let form: any = {}; - return new Promise(function(resolve, reject) { - headers['Accept'] = 'application/json'; - headers['Content-Type'] = 'application/json'; - - path = path.replace('{accession}', parameters['accession'] + ''); - - if (parameters['accession'] === undefined) { - reject(new Error('Missing required parameter: accession')); - return; - } - - if (parameters.$queryParameters) { - Object.keys(parameters.$queryParameters).forEach(function(parameterName) { - var parameter = parameters.$queryParameters[parameterName]; - queryParameters[parameterName] = parameter; - }); - } - - request('GET', domain + path, body, headers, queryParameters, form, reject, resolve, errorHandlers); - - }); - }; - - /** - * Perform lookups of Ensembl identifiers and retrieve their external references in other databases - * @method - * @name GenomeNexusAPIInternal#fetchGeneXrefsGET_1 - * @param {string} accession - Ensembl gene accession. For example ENSG00000169083 - */ - fetchGeneXrefsGET_1(parameters: { - 'accession': string, - $queryParameters ? : any, - $domain ? : string - }): Promise < Array < GeneXref > - > { - return this.fetchGeneXrefsGET_1WithHttpInfo(parameters).then(function(response: request.Response) { - return response.body; - }); - }; -} \ No newline at end of file diff --git a/packages/genome-nexus-ts-api-client/src/index.tsx b/packages/genome-nexus-ts-api-client/src/index.tsx deleted file mode 100644 index b07add4772e..00000000000 --- a/packages/genome-nexus-ts-api-client/src/index.tsx +++ /dev/null @@ -1,8 +0,0 @@ -export * from './generated/Genome2StructureAPI'; -export { default as Genome2StructureAPI } from './generated/Genome2StructureAPI'; -export * from './generated/GenomeNexusAPI'; -export { default as GenomeNexusAPI } from './generated/GenomeNexusAPI'; -export { - // only export default, otherwise we have namespace conflict with GenomeNexusAPI - default as GenomeNexusAPIInternal, -} from './generated/GenomeNexusAPIInternal'; diff --git a/packages/genome-nexus-ts-api-client/tsconfig.json b/packages/genome-nexus-ts-api-client/tsconfig.json deleted file mode 100644 index 9b9dd502377..00000000000 --- a/packages/genome-nexus-ts-api-client/tsconfig.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "extends": "../config/tsconfig.json", - "include": [ - "src", - "../typings/**/*" - ] -} diff --git a/src/pages/resultsView/mutation/ResultsViewMutationTable.tsx b/src/pages/resultsView/mutation/ResultsViewMutationTable.tsx index 1498e8bb3a5..1f37762ae39 100644 --- a/src/pages/resultsView/mutation/ResultsViewMutationTable.tsx +++ b/src/pages/resultsView/mutation/ResultsViewMutationTable.tsx @@ -77,6 +77,7 @@ export default class ResultsViewMutationTable extends MutationTable< MutationTableColumnType.CLINVAR, MutationTableColumnType.DBSNP, MutationTableColumnType.SIGNAL, + MutationTableColumnType.ALPHAMISSENSE, ], columnVisibilityProps: {}, }; @@ -257,6 +258,7 @@ export default class ResultsViewMutationTable extends MutationTable< this._columns[MutationTableColumnType.CLINVAR].order = 270; this._columns[MutationTableColumnType.DBSNP].order = 280; this._columns[MutationTableColumnType.SIGNAL].order = 290; + this._columns[MutationTableColumnType.ALPHAMISSENSE].order = 29; // exclude this._columns[ diff --git a/src/pages/staticPages/tools/mutationMapper/StandaloneMutationTable.tsx b/src/pages/staticPages/tools/mutationMapper/StandaloneMutationTable.tsx index a8576cf605a..3371af74819 100644 --- a/src/pages/staticPages/tools/mutationMapper/StandaloneMutationTable.tsx +++ b/src/pages/staticPages/tools/mutationMapper/StandaloneMutationTable.tsx @@ -47,6 +47,7 @@ export default class StandaloneMutationTable extends MutationTable< MutationTableColumnType.TUMOR_ALLELE_FREQ, MutationTableColumnType.NORMAL_ALLELE_FREQ, MutationTableColumnType.EXON, + MutationTableColumnType.ALPHAMISSENSE, MutationTableColumnType.HGVSC, MutationTableColumnType.GNOMAD, MutationTableColumnType.CLINVAR, @@ -68,7 +69,6 @@ export default class StandaloneMutationTable extends MutationTable< this._columns[columnName] = column; } ); - // override default visibility for some columns this._columns[ MutationTableColumnType.TUMOR_ALLELE_FREQ @@ -95,6 +95,7 @@ export default class StandaloneMutationTable extends MutationTable< this._columns[MutationTableColumnType.ANNOTATION].order = 30; this._columns[MutationTableColumnType.FUNCTIONAL_IMPACT].order = 38; this._columns[MutationTableColumnType.MUTATION_TYPE].order = 40; + this._columns[MutationTableColumnType.ALPHAMISSENSE].order = 41; this._columns[MutationTableColumnType.VARIANT_TYPE].order = 45; //this._columns[MutationTableColumnType.COPY_NUM].order = 50; //this._columns[MutationTableColumnType.COSMIC].order = 60; diff --git a/src/shared/components/mutationTable/MutationTable.tsx b/src/shared/components/mutationTable/MutationTable.tsx index ffe8ecfb5bb..2791456aba9 100644 --- a/src/shared/components/mutationTable/MutationTable.tsx +++ b/src/shared/components/mutationTable/MutationTable.tsx @@ -13,6 +13,7 @@ import { Mutation, ClinicalData, } from 'cbioportal-ts-api-client'; +import AlphaMissenseColumnFormatter from './column/AlphaMissenseColumnFormatter'; import SampleColumnFormatter from './column/SampleColumnFormatter'; import TumorAlleleFreqColumnFormatter from './column/TumorAlleleFreqColumnFormatter'; import NormalAlleleFreqColumnFormatter from './column/NormalAlleleFreqColumnFormatter'; @@ -198,6 +199,7 @@ export enum MutationTableColumnType { NORMAL_ALLELE_FREQ = 'Allele Freq (N)', FUNCTIONAL_IMPACT = 'Functional Impact', ANNOTATION = 'Annotation', + ALPHAMISSENSE = 'AlphaMissense', CUSTOM_DRIVER = 'Custom Driver', CUSTOM_DRIVER_TIER = 'Custom Driver Tier', HGVSG = 'HGVSg', @@ -470,6 +472,53 @@ export default class MutationTable< truncateOnResize: true, }; + this._columns[MutationTableColumnType.ALPHAMISSENSE] = { + name: MutationTableColumnType.ALPHAMISSENSE, + render: (d: Mutation[]) => + this.props.genomeNexusCache ? ( + AlphaMissenseColumnFormatter.renderFunction( + d, + this.props.genomeNexusCache + ) + ) : ( + + ), + download: (d: Mutation[]) => + AlphaMissenseColumnFormatter.download( + d, + this.props.genomeNexusCache as GenomeNexusCache + ), + sortBy: (d: Mutation[]) => + AlphaMissenseColumnFormatter.getSortValue( + d, + this.props.genomeNexusCache as GenomeNexusCache + ), + visible: false, + tooltip: ( + + {' '} + AlphaMissense is a feature within the VEP plugin used to + predict the pathogenicity of missense variants. Missense + variants refer to changes in a single base of the gene that + result in a change in the encoded amino acid, potentially + affecting the function of the protein. AlphaMissense + utilizes deep learning algorithms to assess the potential + impact of these variants, aiding researchers in better + understanding the relationship between the variant, gene + function, and disease. Pathogenic: Score > 0.564; + significant impact; may cause disease. + Benign: Score < 0.34; minor impact; unlikely to + cause disease. + Ambiguous: Score between 0.34 and 0.564; intermediate + score; insufficient data.-{' '} + + Read Paper + + + ), + defaultSortDirection: 'desc', + }; + this._columns[MutationTableColumnType.SAMPLE_ID] = { name: MutationTableColumnType.SAMPLE_ID, render: (d: Mutation[]) => diff --git a/src/shared/components/mutationTable/column/AlphaMissenseColumnFormatter.tsx b/src/shared/components/mutationTable/column/AlphaMissenseColumnFormatter.tsx new file mode 100644 index 00000000000..87a51c22ffb --- /dev/null +++ b/src/shared/components/mutationTable/column/AlphaMissenseColumnFormatter.tsx @@ -0,0 +1,170 @@ +import * as React from 'react'; +import { Circle } from 'better-react-spinkit'; +import 'rc-tooltip/assets/bootstrap_white.css'; +import { Mutation } from 'cbioportal-ts-api-client'; +import { + TableCellStatusIndicator, + TableCellStatus, + DefaultTooltip, +} from 'cbioportal-frontend-commons'; +import GenomeNexusCache, { + GenomeNexusCacheDataType, +} from 'shared/cache/GenomeNexusCache'; +import styles from './exon.module.scss'; +import { AlphaMissense } from 'genome-nexus-ts-api-client'; + +export default class AlphaMissenseColumnFormatter { + public static renderFunction( + data: Mutation[], + genomeNexusCache: GenomeNexusCache | undefined + ) { + const genomeNexusCacheData = AlphaMissenseColumnFormatter.getGenomeNexusDataFromCache( + data, + genomeNexusCache + ); + + return ( +
+ + {AlphaMissenseColumnFormatter.getAlphaMissenseDataViz( + genomeNexusCacheData + )} + +
+ ); + } + + private static getGenomeNexusDataFromCache( + data: Mutation[], + cache: GenomeNexusCache | undefined + ): GenomeNexusCacheDataType | null { + if (data.length === 0 || !cache) { + return null; + } + return cache.get(data[0]); + } + + private static getAlphaMissenseDataViz( + genomeNexusCacheData: GenomeNexusCacheDataType | null + ) { + let status: TableCellStatus | null = null; + if (genomeNexusCacheData === null) { + status = TableCellStatus.LOADING; + } else if ( + genomeNexusCacheData.status === 'error' || + genomeNexusCacheData.data?.successfully_annotated === false + ) { + status = TableCellStatus.ERROR; + } else if (genomeNexusCacheData.data === null) { + status = TableCellStatus.NA; + } else { + let alphamissenseData = AlphaMissenseColumnFormatter.getData( + genomeNexusCacheData + ); + let pathogenicity = alphamissenseData?.pathogenicity || ''; + let score = alphamissenseData?.score || 0.0; + if (alphamissenseData == null) { + return alphamissenseData; + } else { + return ( + ( +
{score}
+ )} + placement="topLeft" + > + + {pathogenicity} + + + ); + } + } + + if (status !== null) { + if (status === TableCellStatus.LOADING) { + return ( + + ); + } else { + return ; + } + } + } + + public static getData( + genomeNexusCache: GenomeNexusCacheDataType | null + ): AlphaMissense | null { + let alphaMissenseData: AlphaMissense | null = { + pathogenicity: 'N/A', + score: 0, + }; + if (genomeNexusCache?.data) { + const genomeNexusData = genomeNexusCache.data; + const alphaMissense = + genomeNexusData.annotation_summary?.transcriptConsequenceSummary + ?.alphaMissense; + if (alphaMissense) { + alphaMissenseData = alphaMissense; + } + } + return alphaMissenseData; + } + + public static download( + data: Mutation[], + genomeNexusCache: GenomeNexusCache + ): string { + const genomeNexusCacheData = AlphaMissenseColumnFormatter.getGenomeNexusDataFromCache( + data, + genomeNexusCache + ); + const alphamissenseData = + genomeNexusCacheData && + AlphaMissenseColumnFormatter.getData(genomeNexusCacheData); + + if (!alphamissenseData) { + return ''; + } else { + return ( + alphamissenseData.pathogenicity + + ' (' + + alphamissenseData.score + + ')' + ); + } + } + + public static getSortValue( + data: Mutation[], + genomeNexusCache: GenomeNexusCache + ): number | null { + const genomeNexusCacheData = AlphaMissenseColumnFormatter.getGenomeNexusDataFromCache( + data, + genomeNexusCache + ); + if (genomeNexusCacheData) { + let alphamissenseData = AlphaMissenseColumnFormatter.getData( + genomeNexusCacheData + ); + if (alphamissenseData == null) { + return null; + } else { + return alphamissenseData.score; + } + } else { + return null; + } + } +} diff --git a/yarn.lock b/yarn.lock index 840732ddb91..fcb069fe5bc 100644 --- a/yarn.lock +++ b/yarn.lock @@ -11536,6 +11536,14 @@ genfun@^5.0.0: resolved "https://registry.yarnpkg.com/genfun/-/genfun-5.0.0.tgz#9dd9710a06900a5c4a5bf57aca5da4e52fe76537" integrity sha512-KGDOARWVga7+rnB3z9Sd2Letx515owfk0hSxHGuqjANb1M+x2bGZGqHLiozPsYMdM2OubeMni/Hpwmjq6qIUhA== +genome-nexus-ts-api-client@^1.1.32: + version "1.1.33" + resolved "https://registry.yarnpkg.com/genome-nexus-ts-api-client/-/genome-nexus-ts-api-client-1.1.33.tgz#aea3eafe6ca59e0187c25c487b7fb9f9b704bdde" + integrity sha512-wrbDKoVjw9etDChfacrNStlORqWlS/k2dA5DzlxFEfen3WYO7QtXAFLVSxpjanA/3sGQnVqaxreZzjTPDXhs1A== + dependencies: + superagent "^3.8.3" + typescript "4.0.3" + gensync@^1.0.0-beta.2: version "1.0.0-beta.2" resolved "https://registry.yarnpkg.com/gensync/-/gensync-1.0.0-beta.2.tgz#32a6ee76c3d7f52d46b2b1ae5d93fea8580a25e0"