WikiPathways Webservices

/**
 * WikiPathwaysWebservices - generated by OmniStream from WikiPathways Webservices's OpenAPI spec.
 * One typed method per endpoint. A single Omni key reaches the API.
 */
const DEFAULT_BASE = "https://grid.skinvaults.online/v1/proxy/wikipathways";

export class WikiPathwaysWebservicesError extends Error {
  status: number;
  code?: string;
  constructor(status: number, code: string | undefined, message?: string) {
    super(message || `WikiPathwaysWebservices error ${status}`);
    this.name = "WikiPathwaysWebservicesError";
    this.status = status;
    this.code = code;
  }
}

export interface WikiPathwaysWebservicesOptions {
  baseUrl?: string;
  fetch?: typeof fetch;
  timeoutMs?: number;
}

export class WikiPathwaysWebservices {
  /** @param token Your OmniStream key (one key for every API). */
  constructor(private token: string, private opts: WikiPathwaysWebservicesOptions = {}) {
    if (!token) throw new Error("WikiPathwaysWebservices: token is required");
  }
  rateLimit: { remainingMinute?: number; remainingDay?: number } | null = null;

  private async _request(method: string, path: string, { params, body }: { params?: Record<string, unknown>; body?: unknown } = {}): Promise<any> {
    const f = this.opts.fetch ?? globalThis.fetch;
    const url = new URL((this.opts.baseUrl ?? DEFAULT_BASE).replace(/\/+$/, "") + path);
    if (params) for (const [k, v] of Object.entries(params)) if (v != null) url.searchParams.set(k, String(v));
    const headers: Record<string, string> = { "x-omni-key": this.token };
    if (body !== undefined) headers["content-type"] = "application/json";
    const res = await f(url, { method, headers, body: body !== undefined ? JSON.stringify(body) : undefined });
    this.rateLimit = {
      remainingMinute: Number(res.headers.get("x-ratelimit-remaining-minute")) || undefined,
      remainingDay: Number(res.headers.get("x-ratelimit-remaining-day")) || undefined,
    };
    const data = await res.json().catch(() => ({}));
    if (!res.ok) throw new WikiPathwaysWebservicesError(res.status, data?.error?.code, data?.error?.message);
    return data.data ?? data;
  }

  /** createPathwayCreate a new pathway on the wiki with the given GPML code.<br>Note: To create/modify pathways via the web service, you need to have an account with web service write permissions. Please contact us to request write access for the web service. */
  postcreatepathway(params: { "gpml": string; "auth": string; "username": string; "format"?: string }): Promise<any> {
    return this._request("POST", "/createPathway", { params });
  }

  /** findInteractionsFind interactions defined in WikiPathways pathways. */
  getfindinteractions(params: { "query": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/findInteractions", { params });
  }

  /** findPathwaysByLiterature */
  getfindpathwaysbyliterature(params: { "query": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/findPathwaysByLiterature", { params });
  }

  /** findPathwaysByText */
  getfindpathwaysbytext(params: { "query": string; "species"?: string; "format"?: string }): Promise<any> {
    return this._request("GET", "/findPathwaysByText", { params });
  }

  /** findPathwaysByXref */
  getfindpathwaysbyxref(params: { "ids": unknown[]; "codes"?: unknown[]; "format"?: string }): Promise<any> {
    return this._request("GET", "/findPathwaysByXref", { params });
  }

  /** getColoredPathwayGet a colored image version of the pathway. */
  getgetcoloredpathway(params: { "pwId": string; "revision": string; "graphId": unknown[]; "color": unknown[]; "fileType": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getColoredPathway", { params });
  }

  /** getCurationTagHistory */
  getgetcurationtaghistory(params: { "pwId": string; "timestamp"?: string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getCurationTagHistory", { params });
  }

  /** getCurationTagsGet all curation tags for the given tag name. Use this method if you want to find all pathways that are tagged with a specific curation tag. */
  getgetcurationtags(params: { "pwId": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getCurationTags", { params });
  }

  /** getCurationTagsByNameGet all curation tags for the given tag name. Use this method if you want to find all pathways that are tagged with a specific curation tag. */
  getgetcurationtagsbyname(params: { "tagName": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getCurationTagsByName", { params });
  }

  /** getOntologyTermsByPathway */
  getgetontologytermsbypathway(params: { "pwId": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getOntologyTermsByPathway", { params });
  }

  /** getPathway */
  getgetpathway(params: { "pwId": string; "revision"?: number; "format"?: string }): Promise<any> {
    return this._request("GET", "/getPathway", { params });
  }

  /** getPathwayAsDownload a pathway in the specified file format. */
  getgetpathwayas(params: { "fileType": string; "pwId": string; "revision"?: number; "format"?: string }): Promise<any> {
    return this._request("GET", "/getPathwayAs", { params });
  }

  /** getPathwayHistoryGet the revision history of a pathway. */
  getgetpathwayhistory(params: { "pwId": string; "timestamp": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getPathwayHistory", { params });
  }

  /** getPathwayInfoGet some general info about the pathway, such as the name, species, without downloading the GPML. */
  getgetpathwayinfo(params: { "pwId": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getPathwayInfo", { params });
  }

  /** getPathwaysByOntologyTerm */
  getgetpathwaysbyontologyterm(params: { "term": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getPathwaysByOntologyTerm", { params });
  }

  /** getPathwaysByParentOntologyTerm */
  getgetpathwaysbyparentontologyterm(params: { "term": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getPathwaysByParentOntologyTerm", { params });
  }

  /** getRecentChangesGet the recently changed pathways.<br>Note: the recent changes table only retains items for a limited time (2 months), so there is no guarantee that you will get all changes when the timestamp points to a date that is more than 2 months in the past. */
  getgetrecentchanges(params: { "timestamp": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getRecentChanges", { params });
  }

  /** getUserByOrcid */
  getgetuserbyorcid(params: { "orcid": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getUserByOrcid", { params });
  }

  /** getXrefList */
  getgetxreflist(params: { "pwId": string; "code": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/getXrefList", { params });
  }

  /** listOrganisms */
  getlistorganisms(params: { "format"?: string }): Promise<any> {
    return this._request("GET", "/listOrganisms", { params });
  }

  /** listPathways */
  getlistpathways(params: { "organism"?: string; "format"?: string }): Promise<any> {
    return this._request("GET", "/listPathways", { params });
  }

  /** loginStart a logged in session, using an existing WikiPathways account. This function will return an authentication code that can be used to excecute methods that need authentication (e.g. updatePathway). */
  getlogin(params: { "name": string; "pass": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/login", { params });
  }

  /** removeCurationTagRemove a curation tag from a pathway. */
  getremovecurationtag(params: { "pwId": string; "tagName": string; "auth": string; "username": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/removeCurationTag", { params });
  }

  /** removeOntologyTag */
  getremoveontologytag(params: { "pwId": string; "termId": string; "auth": string; "user": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/removeOntologyTag", { params });
  }

  /** saveCurationTag */
  getsavecurationtag(params: { "pwId": string; "tagName": string; "text": string; "revision": number; "auth": string; "username": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/saveCurationTag", { params });
  }

  /** saveOntologyTag */
  getsaveontologytag(params: { "pwId": string; "term": string; "termId": string; "auth": string; "user": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/saveOntologyTag", { params });
  }

  /** updatePathwayUpdate a pathway on the wiki with the given GPML code.<br>Note: To create/modify pathways via the web service, you need to have an account with web service write permissions. Please contact us to request write access for the web service. */
  getupdatepathway(params: { "pwId": string; "description": string; "gpml": string; "revision": number; "auth": string; "username": string; "format"?: string }): Promise<any> {
    return this._request("GET", "/updatePathway", { params });
  }
}

export default WikiPathwaysWebservices;