@datagrok-libraries/utils 0.0.8 → 0.0.9

package/src/spe.ts

@@ -1,172 +0,0 @@
-import {Options, Coordinates, Vectors, DistanceMetric} from './type_declarations';
-import {calculateEuclideanDistance, calcDistanceMatrix, fillRandomMatrix, vectorAdd, randomInt} from './operations';
-
-/**
- * Implements stochastic proximity embedding.
- *
- * @export
- * @class SPEBase
- * @link doi:10.1016/S1093-3263(03)00155-4
- */
-export class SPEBase {
-  protected static dimension = 2;
-  protected steps: number;
-  protected cycles: number;
-  protected cutoff: number;
-  protected lambda: number;
-  protected dlambda: number;
-  protected lambda2: number;
-  protected dlambda2: number;
-  protected epsilon: number;
-  protected distanceFunction: DistanceMetric;
-  protected distance: Coordinates;
-
-  /**
-   * Creates an instance of SPEBase.
-   * @param {Options} [options] Options to pass to the constructor.
-   * @memberof SPEBase
-   */
-  constructor(options?: Options) {
-    this.steps = options?.steps ?? 0;
-    this.cycles = options?.cycles ?? 1e6;
-    // Select a cutoff distance {cutoff} and ...
-    this.cutoff = options?.cutoff ?? 0;
-    // ... an initial learning rate {lambda} > 0
-    this.lambda = options?.lambda ?? 2.0;
-    this.dlambda = options?.dlambda ?? 0.01;
-    this.lambda2 = this.lambda/2.;
-    this.dlambda2 = this.dlambda/2.;
-    this.epsilon = options?.epsilon ?? 1e-10;
-    // eslint-disable-next-line brace-style
-    this.distanceFunction = options?.distance ?? calculateEuclideanDistance;
-    this.distance = [];
-  }
-
-  /**
-   * Initializes distance matrix.
-   *
-   * @protected
-   * @param {Vectors} vectors Input vectors to calculate distance between.
-   * @memberof SPEBase
-   */
-  protected initDistance(vectors: Vectors) {
-    this.distance = calcDistanceMatrix(vectors, this.distanceFunction);
-  }
-
-  /**
-   * Calculates distance between the two vectors given.
-   * 
-   * @param {Vectors} vectors Set of vectors to calculate distances between.
-   * @param {number} index1 Index of the first vector of the pair.
-   * @param {number} index2 Index of the second vector of the pair.
-   * @return {number} Distance between these two vectors.
-   */
-  protected calcDistance(vectors: Vectors, index1: number, index2: number): number {
-    return this.distance[index1][index2];
-  }
-
-  /**
-   * Embeds the vectors given into a two-dimensional space.
-   * 
-   * @param {Vectors} vectors D-dimensional coordinates.
-   * @return {Coordinates} SPE coordinates in D space.
-   */
-  public embed(vectors: Vectors): Coordinates {
-    const nItems = vectors.length;
-    const areaWidth = 40;
-    // Initialize the D-dimensional coordinates of the N points.
-    const coordinates = fillRandomMatrix(nItems, SPEBase.dimension, areaWidth);
-
-    let lambda2 = this.lambda2;
-
-    if (this.steps == 0) {
-      this.steps = vectors.length-1;
-    }
-
-    this.initDistance(vectors);
-
-    for (let cycle = 0; cycle < this.cycles; ++cycle) {
-      for (let step = 0; step < this.steps; ++step) {
-        // Select two points, i and j, at random, ...
-        const i = randomInt(nItems); let j = randomInt(nItems);
-        while (i == j) j = randomInt(nItems);
-
-        const rowi = coordinates[i]; const rowj = coordinates[j];
-
-        // ... retrieve (or evaluate) their proximity in the input space, rij and ...
-        const r = this.calcDistance(vectors, i, j);
-        // ... compute their Euclidean distance on the D-dimensional map, dij.
-        const d = calculateEuclideanDistance(rowi, rowj);
-
-        // If rij <= rc, or if rij > rc and dij < rij ...
-        if ((this.cutoff == 0) || (r <= this.cutoff) || (d < r)) {
-          const multiplier = lambda2*(r-d)/(d+this.epsilon);
-          // ... update the coordinates xi and xj.
-          const diffIJ = vectorAdd(rowi, rowj, -1);
-          coordinates[i] = vectorAdd(rowi, diffIJ, multiplier);
-          coordinates[j] = vectorAdd(rowj, diffIJ, -multiplier);
-        }
-      }
-      // Decrease the learning rate {lambda} by a prescribed {dlambda}.
-      lambda2 -= this.dlambda2;
-      if (lambda2 <= 0.) {
-        break;
-      }
-    }
-    return coordinates;
-  }
-}
-
-/**
- * Implements modified stochastic proximity embedding.
- *
- * @export
- * @class PSPEBase
- * @link doi:10.1016/S1093-3263(03)00155-4
- */
- export class PSPEBase extends SPEBase {
-  /**
-   * Embeds the vectors given into a two-dimensional space using a modified update rule.
-   * 
-   * @param {Vectors} vectors D-dimensional coordinates.
-   * @return {Coordinates} SPE coordinates in D space.
-   */
-  public embed(vectors: Vectors): Coordinates {
-    const nItems = vectors.length;
-    const areaWidth = 40;
-    //  Initialize the D-dimensional coordinates of the N points.
-    const coordinates = fillRandomMatrix(nItems, PSPEBase.dimension, areaWidth);
-    let lambda = this.lambda;
-
-    this.initDistance(vectors);
-
-    for (let cycle = 0; cycle < this.cycles; ++cycle) {
-      // Select a point, i, at random (pivot).
-      const i: number = randomInt(nItems);
-      const rowi = coordinates[i];
-
-      // For every point j != i ...
-      for (let j = 0; j < nItems; ++j) {
-        if (i == j) continue;
-        const rowj = coordinates[j];
-        // ... retrieve (or evaluate) its proximity to i in the input space, rij ...
-        const r = this.calcDistance(vectors, i, j);
-        // ... and compute their Euclidean distance on the D-dimensional map, dij.
-        const d = calculateEuclideanDistance(rowi, rowj);
-        // If rij <= rc, or if rij > rc and dij < rij ...
-        if ((this.cutoff == 0) || (r <= this.cutoff) || (d < r)) {
-          const multiplier = lambda*(r-d)/(d+this.epsilon);
-          const diffIJ = vectorAdd(rowi, rowj, -1);
-          // ... update the coordinates xj.
-          coordinates[j] = vectorAdd(rowj, diffIJ, -multiplier);
-        }
-      }
-      // Decrease the learning rate {lambda} by a prescribed {dlambda}.
-      lambda -= this.dlambda;
-      if (lambda <= 0.) {
-        break;
-      }
-    }
-    return coordinates;
-  }
-}

package/src/string-measure.ts

@@ -1,54 +0,0 @@
-import * as fl from 'fastest-levenshtein';
-import {jaroWinkler} from 'jaro-winkler-typescript';
-
-import {DistanceMetric} from './type_declarations';
-import {assert} from './operations';
-
-/**
- * Unified class implementing the different string measures.
- *
- * @export
- * @class Measurer
- */
-export class Measurer {
-    protected method: string;
-    public static receipt: {[name: string]: DistanceMetric} = {
-      'Levenshtein': fl.distance,
-      'Jaro-Winkler': jaroWinkler,
-    };
-
-    /**
-     * Creates an instance of Measurer.
-     * @param {string} method Method to calculate distance between strings.
-     * @memberof Measurer
-     */
-    constructor(method: string) {
-      assert(Measurer.availableMeasures.includes(method), 'The ${method} was not found.')
-      this.method = method;
-    }
-
-    /**
-     * Returns custom string distance function specified.
-     * @return {DistanceMetric} Callback of the measure chosen.
-     */
-    public getMeasure(): DistanceMetric {
-      return Measurer.receipt[this.method];
-    }
-
-    /**
-     * Returns available string distance metrics.
-     *
-     * @readonly
-     * @type {string[]}
-     * @memberof Measurer
-     */
-    public static get availableMeasures() : string[] {
-      let keys = [];
-
-      for (let key in Measurer.receipt) {
-        keys.push(key);
-      }
-      return keys;
-    }
-    
-}

package/src/string-utils.ts

@@ -1,8 +0,0 @@
-export function tryParseJson(s: string) : any {
-    try {
-        return JSON.parse(s);
-    }
-    catch (_) {
-        return null;
-    }
-}

package/src/table-validation.ts

@@ -1,67 +0,0 @@
-/* Do not change these import lines. Datagrok will import API library in exactly the same manner */
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from "datagrok-api/dg";
-
-interface Rule {
-  column: string;
-  type: string;
-  pattern: string;
-  matcher?: any;
-}
-
-interface RuleSet {
-  name: string;
-  rules: Rule[];
-}
-
-// @ts-ignore
-let ruleSet: RuleSet = {
-  name: 'SDTM DM rules',
-  rules: [
-    {
-      column: 'age',
-      type: 'int',
-      pattern: '18-90'
-    },
-    {
-      column: 'height',
-      type: 'numerical',
-      pattern: '18-90'
-    },
-    {
-      column: 'sex',
-      type: 'string',
-      pattern: 'in (F, M)'
-    },
-    {
-      column: 'started',
-      type: 'datetime',
-      pattern: '> 1/1/1900'
-    }
-  ]
-};
-
-/** Returns error message, or null if valid. */
-function validateCell(cell: any, ruleset: RuleSet) : string | null {
-  let name = cell.column.name.toLowerCase();
-
-  for (let rule of ruleset.rules)
-    if (rule.column == name) {
-      rule.matcher = rule.matcher ?? DG.ValueMatcher.forColumn(cell.column, rule.pattern);
-      let error = rule.matcher.validate(cell.value);
-      if (error !== null)
-        return error;
-    }
-
-  return null;
-}
-
-function main() : void {
-  console.log('foo');
-}
-
-let cell = {column: { name: 'age' }, value: 999 };
-validateCell(cell, ruleSet);
-
-console.log('ddd');

package/src/test-utils.ts

@@ -1,97 +0,0 @@
-import * as path from "path";
-import * as os from "os";
-import * as fs from "fs";
-// @ts-ignore
-import * as yaml from 'js-yaml';
-const fetch = require('node-fetch');
-
-export async function getToken(url: string, key: string) {
-  let response = await fetch(`${url}/users/login/dev/${key}`, {method: 'POST'});
-  let json = await response.json();
-  if (json.isSuccess == true)
-    return json.token;
-  else
-    throw 'Unable to login to server. Check your dev key';
-}
-
-export async function getWebUrl(url: string, token: string) {
-  let response = await fetch(`${url}/admin/plugins/admin/settings`, {headers: {Authorization: token}});
-  let json = await response.json();
-  return json.settings.webRoot;
-}
-
-const grokDir = path.join(os.homedir(), '.grok');
-const confPath = path.join(grokDir, 'config.yaml');
-
-function mapURL(conf: Config): Indexable {
-  let urls: Indexable = {};
-  for (let server in conf.servers) {
-    urls[conf['servers'][server]['url']] = conf['servers'][server];
-  }
-  return urls;
-}
-
-export function getDevKey(hostKey: string): {url: string, key: string} {
-  let config = yaml.load(fs.readFileSync(confPath, 'utf8')) as any;
-  let host = hostKey == '' ? config.default : hostKey;
-  host = host.trim();
-  let urls = mapURL(config);
-  let key = '';
-  let url = '';
-  try {
-    let url = new URL(host).href;
-    if (url.endsWith('/')) url = url.slice(0, -1);
-    if (url in urls) key = config['servers'][urls[url]]['key'];
-  } catch (error) {
-    if (config['servers'][host] == null)
-      throw `Unknown server alias. Please add it to ${confPath}`;
-    url = config['servers'][host]['url'];
-    key = config['servers'][host]['key'];
-  }
-  return {url, key};
-}
-
-export async function getBrowserPage(puppeteer: any): Promise<{browser: any, page: any}> {
-  let url:string = process.env.HOST ?? '';
-  let cfg = getDevKey(url);
-  url = cfg.url;
-
-  let key = cfg.key;
-  let token = await getToken(url, key);
-  url = await getWebUrl(url, token);
-  console.log(`Using web root: ${url}`);
-
-  let browser = await puppeteer.launch({
-    args: ['--disable-dev-shm-usage', '--disable-features=site-per-process'],
-    ignoreHTTPSErrors: true,
-  });
-
-  let page = await browser.newPage();
-  await page.goto(`${url}/oauth/`);
-  await page.setCookie({name: 'auth', value: token});
-  await page.evaluate((token: any) => {
-    window.localStorage.setItem('auth', token);
-  }, token);
-  await page.goto(url);
-  try {
-    await page.waitForSelector('.grok-preloader');
-    console.log('got preloader');
-    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 100000});
-  } catch (error) {
-    throw error;
-  }
-  return {browser, page};
-}
-
-
-interface Config {
-  servers: {
-    [alias: string]: {
-      url: string,
-      key: string
-    }
-  },
-  default: string,
-}
-
-interface Indexable { [key: string]: any }

package/src/type_declarations.ts

@@ -1,54 +0,0 @@
-/**
- * Denotes a vector of floating poit values.
- *
- * @export
- * @class Vector
- * @extends {Float32Array}
- */
-export class Vector extends Float32Array {}
-
-/**
- * Denotes a two-dimensional matrix.
- *
- * @export
- * @class Matrix
- * @extends {Array<Vector>}
- */
-export class Matrix extends Array<Vector> {}
-
-/**
- * Denotes cartesian coordinates.
- *
- * @export
- * @class Coordinates
- * @extends {Matrix}
- */
-export class Coordinates extends Matrix {}
-
-/**
- * Denotes an array of arbitrary-typed vectors.
- *
- * @export
- * @class Vectors
- * @extends {Array<any>}
- */
-export class Vectors extends Array<any> {}
-
-/**
- * Denotes a dictionary containing function options.
- *
- * @export
- * @type Options
- */
-export type Options = {[name: string]: any};
-
-/**
- * Denotes custom distance metric between the two given vectors.
- *
- * @export
- * @type DistanceMetric
- * @param {any} v1 The first vector.
- * @param {any} v2 The second vector.
- * @return {number} Distance between these two vectors.
- */
- export type DistanceMetric = (v1: any, v2: any) => (number);