@datagrok/peptides 1.5.1 → 1.7.1

package/src/widgets/distribution.ts

@@ -7,6 +7,8 @@ import $ from 'cash-dom';
 import * as C from '../utils/constants';
 import {getStats, MaskInfo, Stats} from '../utils/statistics';
 import {PeptidesModel} from '../model';
+import {wrapDistroAndStatsDefault} from '../utils/misc';
+import wu from 'wu';
 
 const allConst = 'All';
 const otherConst = 'Other';
@@ -17,13 +19,9 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
   const selectionObject = model.mutationCliffsSelection;
   const clustersColName = model.settings.clustersColumnName;
   let clustersProcessedObject: string[] = [];
-  if (clustersColName) {
-    const clustersRawObject = model.logoSummarySelection;
-    const clustersColCategories = table.getCol(model.settings.clustersColumnName!).categories;
-    clustersProcessedObject = new Array(clustersRawObject.length);
-    for (let i = 0; i < clustersRawObject.length; ++i)
-      clustersProcessedObject[i] = clustersColCategories[clustersRawObject[i]];
-  }
+  if (clustersColName)
+    clustersProcessedObject = model.logoSummarySelection;
+
   const positions = Object.keys(selectionObject);
   const positionsLen = positions.length;
   let aarStr = allConst;
@@ -43,18 +41,28 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
           continue;
 
         for (const aar of aarList) {
+          const indexes: number[] = [];
           aarStr = `${position} : ${aar}`;
-          const splitCol = DG.Column.bool(C.COLUMNS_NAMES.SPLIT_COL, rowCount).init((i) => posCol.get(i) == aar);
-
+          const splitCol = DG.Column.bool(C.COLUMNS_NAMES.SPLIT_COL, rowCount).init((i) => {
+            const flag = posCol.get(i) == aar;
+            if (flag)
+              indexes.push(i);
+          });
           const distributionTable = DG.DataFrame.fromColumns([activityScaledCol, splitCol]);
-          const currentStatsDf = model.monomerPositionStatsDf.rows.match({Pos: position, AAR: aar}).toDataFrame();
-          const stats: Stats = {
-            count: currentStatsDf.get(C.COLUMNS_NAMES.COUNT, 0),
-            ratio: currentStatsDf.get(C.COLUMNS_NAMES.RATIO, 0),
-            pValue: currentStatsDf.get(C.COLUMNS_NAMES.P_VALUE, 0),
-            meanDifference: currentStatsDf.get(C.COLUMNS_NAMES.MEAN_DIFFERENCE, 0),
-          };
-          const distributionRoot = getDistributionAndStats(distributionTable, stats, aarStr, otherStr, true);
+
+          const colResults: {[colName: string]: number} = {};
+          for (const [col, agg] of Object.entries(model.settings.columns || {})) {
+            const currentCol = table.getCol(col);
+            const currentColData = currentCol.getRawData();
+            const tempCol = DG.Column.float('', indexes.length);
+            tempCol.init((i) => currentColData[indexes[i]]);
+            colResults[`${agg}(${col})`] = tempCol.stats[agg as keyof DG.Stats] as number;
+          }
+
+          const stats = model.monomerPositionStats[position][aar];
+          const das = getDistributionAndStats(distributionTable, stats, aarStr, otherStr, true);
+          const resultMap: {[key: string]: any} = {...das.tableMap, ...colResults};
+          const distributionRoot = wrapDistroAndStatsDefault(das.labels, das.histRoot, resultMap);
           $(distributionRoot).addClass('d4-flex-col');
 
           res.push(distributionRoot);
@@ -81,7 +89,20 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
         const stats = getStats(activityScaledData, maskInfo);
         const splitCol = DG.Column.fromBitSet(C.COLUMNS_NAMES.SPLIT_COL, mask);
         const distributionTable = DG.DataFrame.fromColumns([activityScaledCol, splitCol]);
-        const distributionRoot = getDistributionAndStats(distributionTable, stats, aarStr, otherStr, true);
+
+        const indexes = mask.getSelectedIndexes();
+        const colResults: {[colName: string]: number} = {};
+        for (const [col, agg] of Object.entries(model.settings.columns || {})) {
+          const currentCol = table.getCol(col);
+          const currentColData = currentCol.getRawData();
+          const tempCol = DG.Column.float('', indexes.length);
+          tempCol.init((i) => currentColData[indexes[i]]);
+          colResults[`${agg}(${col})`] = tempCol.stats[agg as keyof DG.Stats] as number;
+        }
+
+        const das = getDistributionAndStats(distributionTable, stats, aarStr, otherStr, true);
+        const resultMap: {[key: string]: any} = {...das.tableMap, ...colResults};
+        const distributionRoot = wrapDistroAndStatsDefault(das.labels, das.histRoot, resultMap);
         $(distributionRoot).addClass('d4-flex-col');
 
         res.push(distributionRoot);
@@ -124,7 +145,20 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
         const stats = getStats(activityScaledData, maskInfo);
         const splitCol = DG.Column.fromBitSet(C.COLUMNS_NAMES.SPLIT_COL, mask);
         const distributionTable = DG.DataFrame.fromColumns([activityScaledCol, splitCol]);
-        const distributionRoot = getDistributionAndStats(distributionTable, stats, aarStr, otherStr, true);
+
+        const indexes = mask.getSelectedIndexes();
+        const colResults: {[colName: string]: number} = {};
+        for (const [col, agg] of Object.entries(model.settings.columns || {})) {
+          const currentCol = table.getCol(col);
+          const currentColData = currentCol.getRawData();
+          const tempCol = DG.Column.float('', indexes.length);
+          tempCol.init((i) => currentColData[indexes[i]]);
+          colResults[`${agg}(${col})`] = tempCol.stats[agg as keyof DG.Stats] as number;
+        }
+
+        const das = getDistributionAndStats(distributionTable, stats, aarStr, otherStr, true);
+        const resultMap: {[key: string]: any} = {...das.tableMap, ...colResults};
+        const distributionRoot = wrapDistroAndStatsDefault(das.labels, das.histRoot, resultMap);
         $(distributionRoot).addClass('d4-flex-col');
 
         res.push(distributionRoot);
@@ -151,13 +185,27 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
         }
 
         const distributionTable = DG.DataFrame.fromColumns([activityScaledCol, splitCol]);
+        // distributionTable.filter.copyFrom(table.filter);
+
+        const indexes = model.getCompoundBitest().getSelectedIndexes();
+        const colResults: {[colName: string]: number} = {};
+        for (const [col, agg] of Object.entries(model.settings.columns || {})) {
+          const currentCol = table.getCol(col);
+          const currentColData = currentCol.getRawData();
+          const tempCol = DG.Column.float('', indexes.length);
+          tempCol.init((i) => currentColData[indexes[i]]);
+          colResults[`${agg}(${col})`] = tempCol.stats[agg as keyof DG.Stats] as number;
+        }
+
         const maskInfo: MaskInfo = {
           mask: table.selection.getBuffer(),
           trueCount: table.selection.trueCount,
           falseCount: table.selection.falseCount,
         };
         const stats = getStats(activityScaledCol.getRawData(), maskInfo);
-        const distributionRoot = getDistributionAndStats(distributionTable, stats, aarStr, otherStr);
+        const das = getDistributionAndStats(distributionTable, stats, aarStr, otherStr);
+        const resultMap: {[key: string]: any} = {...das.tableMap, ...colResults};
+        const distributionRoot = wrapDistroAndStatsDefault(das.labels, das.histRoot, resultMap);
         $(distributionRoot).addClass('d4-flex-col');
 
         res.push(distributionRoot);
@@ -194,9 +242,10 @@ export function getDistributionWidget(table: DG.DataFrame, model: PeptidesModel)
   return new DG.Widget(ui.divV([controlsHost, distributionHost]));
 }
 
-export function getDistributionAndStats(
-  table: DG.DataFrame, stats: Stats, thisLabel: string, otherLabel: string = '', isTooltip: boolean = false,
-): HTMLDivElement {
+type DistroAndStats = {labels: HTMLDivElement, histRoot: HTMLElement, tableMap: StringDictionary};
+
+export function getDistributionAndStats(table: DG.DataFrame, stats: Stats, thisLabel: string, otherLabel: string = '',
+  isTooltip: boolean = false, splitColName?: string): DistroAndStats {
   const labels = ui.divV([
     ui.label(thisLabel, {style: {color: DG.Color.toHtml(otherLabel == '' ? DG.Color.blue : DG.Color.orange)}}),
     ui.label(otherLabel, {style: {color: DG.Color.toHtml(DG.Color.blue)}})]);
@@ -204,7 +253,7 @@ export function getDistributionAndStats(
   const histRoot = table.plot.histogram({
     filteringEnabled: false,
     valueColumnName: C.COLUMNS_NAMES.ACTIVITY_SCALED,
-    splitColumnName: C.COLUMNS_NAMES.SPLIT_COL,
+    splitColumnName: splitColName ?? C.COLUMNS_NAMES.SPLIT_COL,
     legendVisibility: 'Never',
     showXAxis: true,
     showColumnSelector: false,
@@ -222,9 +271,5 @@ export function getDistributionAndStats(
     'Mean difference': stats.meanDifference.toFixed(2),
   };
 
-  const result = ui.divV([labels, histRoot, ui.tableFromMap(tableMap)]);
-  result.style.minWidth = '200px';
-  if (isTooltip)
-    histRoot.style.maxHeight = '150px';
-  return result;
+  return {labels: labels, histRoot: histRoot, tableMap: tableMap};
 }

package/src/widgets/manual-alignment.ts

@@ -5,7 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import $ from 'cash-dom';
 import '../styles.css';
 import {PeptidesModel} from '../model';
-import {splitAlignedSequences} from '@datagrok-libraries/bio';
+import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
 
 /** Manual sequence alignment widget.
  *
@@ -31,7 +31,7 @@ export function manualAlignmentWidget(alignedSequenceCol: DG.Column<string>, cur
     grok.shell.o = temp;
 
     const peptidesController = PeptidesModel.getInstance(currentDf);
-    peptidesController.updateDefault();
+    peptidesController.updateGrid();
   });
 
   const resetBtn = ui.button(

package/src/widgets/mutation-cliffs.ts

@@ -6,6 +6,7 @@ import {PeptidesModel} from '../model';
 import {getSeparator} from '../utils/misc';
 
 export function mutationCliffsWidget(table: DG.DataFrame, model: PeptidesModel): DG.Widget {
+  const currentFilter = table.filter.getSelectedIndexes();
   const substInfo = model.substitutionsInfo;
   const currentCell = model.mutationCliffsSelection;
   const positions = Object.keys(currentCell);
@@ -28,12 +29,15 @@ export function mutationCliffsWidget(table: DG.DataFrame, model: PeptidesModel):
 
       const posCol = table.getCol(pos);
       for (const [referenceIdx, indexArray] of substitutionsMap.entries()) {
-        const forbiddentIndexes = seenIndexes.has(referenceIdx) ? seenIndexes.get(referenceIdx)! : [];
+        if (!currentFilter.includes(referenceIdx))
+          continue;
+
+        const forbiddentIndexes = seenIndexes.get(referenceIdx) ?? [];
         const baseSequence = alignedSeqCol.get(referenceIdx);
         const baseActivity = activityScaledCol.get(referenceIdx);
 
         for (const subIdx of indexArray) {
-          if (forbiddentIndexes.includes(subIdx))
+          if (forbiddentIndexes.includes(subIdx) || !currentFilter.includes(subIdx))
             continue;
 
           if (!seenIndexes.has(subIdx))

package/src/widgets/peptides.ts

@@ -2,13 +2,15 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
+import * as uuid from 'uuid';
+
 import '../styles.css';
 import * as C from '../utils/constants';
 import * as type from '../utils/types';
 import {PeptidesModel} from '../model';
 import $ from 'cash-dom';
 import {scaleActivity} from '../utils/misc';
-import * as bio from '@datagrok-libraries/bio';
+import {ALIGNMENT, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
 /** Peptide analysis widget.
  *
@@ -16,7 +18,7 @@ import * as bio from '@datagrok-libraries/bio';
  * @param {DG.Column} col Aligned sequence column
  * @return {Promise<DG.Widget>} Widget containing peptide analysis */
 export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
-{host: HTMLElement, callback: () => Promise<boolean>} {
+  { host: HTMLElement, callback: () => Promise<boolean> } {
   const logoHost = ui.div();
   // logoHost.style.alignContent = 'center';
   let seqColInput: DG.InputBase | null = null;
@@ -38,8 +40,8 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
         return viewer.root;
       }));
     });
-  } else if (!(col.getTag(bio.TAGS.aligned) == bio.ALIGNMENT.SEQ_MSA) &&
-             col.getTag(DG.TAGS.UNITS) !== bio.NOTATION.HELM) {
+  } else if (!(col.getTag(bioTAGS.aligned) == ALIGNMENT.SEQ_MSA) &&
+    col.getTag(DG.TAGS.UNITS) !== NOTATION.HELM) {
     return {
       host: ui.label('Peptides analysis only works with aligned sequences'),
       callback: async (): Promise<boolean> => false,
@@ -65,7 +67,8 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
   let scaledCol: DG.Column<number>;
 
   const defaultActivityColumn: DG.Column<number> | null =
-    df.col('activity') || df.col('IC50') || DG.Utils.firstOrNull(df.columns.numerical); ;
+    df.col('activity') || df.col('IC50') || DG.Utils.firstOrNull(df.columns.numerical);
+  ;
   const histogramHost = ui.div([], {id: 'pep-hist-host'});
 
   const activityScalingMethod = ui.choiceInput(
@@ -94,6 +97,7 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
   };
   const activityColumnChoice = ui.columnInput('Activity', df, defaultActivityColumn, activityScalingMethodState);
   const clustersColumnChoice = ui.columnInput('Clusters', df, null);
+  clustersColumnChoice.nullable = true;
   activityColumnChoice.fireChanged();
   activityScalingMethod.fireChanged();
 
@@ -118,12 +122,14 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
     return false;
   };
 
+  let bottomHeight = 'auto';
   const inputElements: HTMLElement[] = [ui.inputs(inputsList)];
   $(inputElements[0]).find('label').css('width', 'unset');
   if (typeof col !== 'undefined') {
     const startBtn = ui.button('Launch SAR', startAnalysisCallback);
     startBtn.style.alignSelf = 'center';
     inputElements.push(startBtn);
+    bottomHeight = '215px';
   }
 
   $(logoHost).empty().append(ui.wait(async () => {
@@ -137,7 +143,7 @@ export function analyzePeptidesUI(df: DG.DataFrame, col?: DG.Column<string>):
     ui.splitH([
       ui.splitV(inputElements),
       histogramHost,
-    ], {style: {height: '215px'}}),
+    ], {style: {height: bottomHeight}}),
   ]);
   mainHost.style.maxWidth = '400px';
   return {host: mainHost, callback: startAnalysisCallback};
@@ -164,22 +170,23 @@ export async function startAnalysis(activityColumn: DG.Column<number>, peptidesC
     };
     if (clustersColumn) {
       const clusterCol = newDf.getCol(clustersColumn.name);
-      newDf.columns.replace(clusterCol, clusterCol.convertTo(DG.COLUMN_TYPE.STRING));
+      if (clusterCol.type != DG.COLUMN_TYPE.STRING)
+        newDfCols.replace(clusterCol, clusterCol.convertTo(DG.COLUMN_TYPE.STRING));
       settings.clustersColumnName = clustersColumn.name;
     }
     newDf.setTag(C.TAGS.SETTINGS, JSON.stringify(settings));
 
     let monomerType = 'HELM_AA';
-    if (peptidesCol.getTag(DG.TAGS.UNITS) == bio.NOTATION.HELM) {
+    if (peptidesCol.getTag(DG.TAGS.UNITS) == NOTATION.HELM) {
       const sampleSeq = peptidesCol.get(0)!;
       monomerType = sampleSeq.startsWith('PEPTIDE') ? 'HELM_AA' : 'HELM_BASE';
     } else {
       const alphabet = peptidesCol.tags[C.TAGS.ALPHABET];
       monomerType = alphabet == 'DNA' || alphabet == 'RNA' ? 'HELM_BASE' : 'HELM_AA';
     }
-
+    const dfUuid = uuid.v4();
+    newDf.setTag(C.TAGS.UUID, dfUuid);
     newDf.setTag('monomerType', monomerType);
-    newDf.setTag('newAnalysis', '1');
     model = PeptidesModel.getInstance(newDf);
     await model.addViewers();
   } else

package/jest.config.js

@@ -1,33 +0,0 @@
-module.exports = {
-  "roots": [
-    "<rootDir>/src"
-  ],
-  "testMatch": [
-    "**/__jest__/**/*.test.+(ts|tsx)"
-  ],
-  moduleFileExtensions: [
-    'ts',
-    'js',
-  ],
-  "transform": {
-    "^.+\\.(ts|tsx)$": "ts-jest"
-  },
-  transformIgnorePatterns: ['^.+\\.js$'],
-  globals: {
-    'ts-jest': {
-      'tsconfig': {
-          "target": "es6",
-          "module": "es2020",
-      }
-    }
-  },
-  reporters: [
-    "default",
-    [
-      "./node_modules/jest-html-reporter",
-      {
-        "includeConsoleLog": true
-      }
-    ]
-  ]
-}

package/src/__jest__/remote.test.ts

@@ -1,76 +0,0 @@
-/**
- * @jest-environment jsdom
- */
-
-import * as utils from './test-node';
-import puppeteer from 'puppeteer';
-
-const P_START_TIMEOUT: number = 3600000;
-let browser: puppeteer.Browser;
-let page: puppeteer.Page;
-
-beforeAll(async () => {
-  const out = await utils.getBrowserPage(puppeteer);
-  browser = out.browser;
-  page = out.page;
-}, P_START_TIMEOUT);
-
-afterAll(async () => {
-  await browser?.close();
-});
-
-expect.extend({
-  checkOutput(received, expected, context) {
-    if (received === expected) {
-      return {
-        message: () => context,
-        pass: true,
-      };
-    } else {
-      return {
-        message: () => context,
-        pass: false,
-      };
-    }
-  },
-});
-
-it('TEST', async () => {
-  const targetPackage:string = process.env.TARGET_PACKAGE ?? 'Peptides';
-  console.log(`Testing ${targetPackage} package`);
-
-  const r = await page.evaluate((targetPackage):Promise<object> => {
-    return new Promise<object>((resolve, reject) => {
-      (<any>window).grok.functions.eval(targetPackage + ':test()').then((df: any) => {
-        const cStatus = df.columns.byName('success');
-        const cSkipped = df.columns.byName('skipped');
-        const cMessage = df.columns.byName('result');
-        const cCat = df.columns.byName('category');
-        const cName = df.columns.byName('name');
-        const cTime = df.columns.byName('ms');
-        let failed = false;
-        let skipReport = '';
-        let passReport = '';
-        let failReport = '';
-        for (let i = 0; i < df.rowCount; i++) {
-          if (cStatus.get(i)) {
-            if (cSkipped.get(i))
-              skipReport += `Test result : Skipped : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-            else
-              passReport += `Test result : Success : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-          } else {
-            failed = true;
-            failReport += `Test result : Failed : ${cTime.get(i)} : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
-          }
-        }
-        resolve({failReport, skipReport, passReport, failed});
-      }).catch((e: any) => reject(e));
-    });
-  }, targetPackage);
-  // @ts-ignore
-  console.log(r.passReport);
-  // @ts-ignore
-  console.log(r.skipReport);
-  // @ts-ignore
-  expect(r.failed).checkOutput(false, r.failReport);
-}, 7200000);

package/src/__jest__/test-node.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) {
-  const response = await fetch(`${url}/users/login/dev/${key}`, {method: 'POST'});
-  const 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) {
-  const response = await fetch(`${url}/admin/plugins/admin/settings`, {headers: {Authorization: token}});
-  const 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 {
-  const urls: Indexable = {};
-  for (const server in conf.servers)
-    urls[conf['servers'][server]['url']] = conf['servers'][server];
-
-  return urls;
-}
-
-export function getDevKey(hostKey: string): {url: string, key: string} {
-  const config = yaml.load(fs.readFileSync(confPath, 'utf8')) as any;
-  let host = hostKey == '' ? config.default : hostKey;
-  host = host.trim();
-  const 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 ?? '';
-  const cfg = getDevKey(url);
-  url = cfg.url;
-
-  const key = cfg.key;
-  const token = await getToken(url, key);
-  url = await getWebUrl(url, token);
-  console.log(`Using web root: ${url}`);
-
-  const browser = await puppeteer.launch({
-    args: ['--disable-dev-shm-usage', '--disable-features=site-per-process'],
-    ignoreHTTPSErrors: true,
-  });
-
-  const page = await browser.newPage();
-  await page.setDefaultNavigationTimeout(0);
-  await page.goto(`${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', {timeout: 1800000});
-    await page.waitForFunction(() => document.querySelector('.grok-preloader') == null, {timeout: 3600000});
-  } catch (error) {
-    throw error;
-  }
-  return {browser, page};
-}
-
-
-interface Config {
-  servers: {
-    [alias: string]: {
-      url: string,
-      key: string
-    }
-  },
-  default: string,
-}
-
-interface Indexable { [key: string]: any }