@datagrok/peptides 1.3.1 → 1.3.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@datagrok/peptides",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "author": {
     "name": "Volodymyr Dyma",
     "email": "vdyma@datagrok.ai"
@@ -12,10 +12,10 @@
     "directory": "packages/Peptides"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^3.3.0",
+    "@datagrok-libraries/bio": "^5.1.0",
     "@datagrok-libraries/ml": "^2.0.1",
     "@datagrok-libraries/statistics": "^0.1.6",
-    "@datagrok-libraries/utils": "^0.4.1",
+    "@datagrok-libraries/utils": "^1.10.1",
     "cash-dom": "latest",
     "datagrok-api": "^1.6.0",
     "file-loader": "^6.2.0",

package/setup-unlink-clean.cmd

@@ -0,0 +1,19 @@
+set package_dir=%cd%
+
+set dirs=^
+\..\..\js-api\ ^
+\..\..\libraries\utils\ ^
+\..\..\libraries\ml\ ^
+\..\..\libraries\bio\ ^
+\
+
+call npm uninstall -g ^
+    datagrok-api ^
+    @datagrok-libraries/utils ^
+    @datagrok-libraries/ml ^
+    @datagrok-libraries/bio ^
+
+for %%p in (%dirs%) do cd %package_dir%\%%p & rmdir /s /q node_modules
+for %%p in (%dirs%) do cd %package_dir%\%%p & rmdir /s /q dist
+
+for %%p in (%dirs%) do cd %package_dir%\%%p & del "package-lock.json"

package/setup.cmd

@@ -1,18 +1,15 @@
-call npm unlink datagrok-api
-call npm unlink @datagrok-libraries/utils
-call npm unlink @datagrok-libraries/ml
-cd ../../js-api
-call npm install
-call npm link
-cd ../libraries/utils
-call npm install
-call npm link
-call npm link datagrok-api
-cd ../../libraries/ml
-call npm install
-call npm link
-call npm link @datagrok-libraries/utils
-cd ../../packages/Peptides
-call npm install
-call npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/ml
-webpack
+call setup-unlink-clean.cmd
+
+set package_dir=%cd%
+
+set dirs=^
+\..\..\js-api\ ^
+\..\..\libraries\utils\ ^
+\..\..\libraries\ml\ ^
+\..\..\libraries\bio\ ^
+\
+
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm install
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm link
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm run link-all
+for %%p in (%dirs%) do cd %package_dir%\%%p & call npm run build

package/src/model.ts

@@ -452,6 +452,8 @@ export class PeptidesModel {
       ratioCol.set(i, stats.ratio);
     }
 
+    const monomerCol = matrixDf.getCol(C.COLUMNS_NAMES.MONOMER);
+    matrixDf = matrixDf.clone(DG.BitSet.create(matrixDf.rowCount, (i) => monomerCol.get(i) ? true : false));
     return matrixDf as DG.DataFrame;
   }
 
@@ -916,6 +918,8 @@ export class PeptidesModel {
 
   initMonomerPositionSelection(aar: string, position: string, isInvariantMapSelection: boolean): void {
     const tempSelection = isInvariantMapSelection ? this.invariantMapSelection : this.mutationCliffsSelection;
+    for (const key of Object.keys(tempSelection))
+      tempSelection[key] = [];
     tempSelection[position] = [aar];
 
     if (isInvariantMapSelection)

package/src/utils/cell-renderer.ts

@@ -1,8 +1,7 @@
-import {SeqPaletteBase} from '@datagrok-libraries/bio/src/seq-palettes';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
 
 import * as C from './constants';
-import {getPalleteByType} from './misc';
 import * as types from './types';
 
 function renderCellSelection(canvasContext: CanvasRenderingContext2D, bound: DG.Rect): void {
@@ -104,7 +103,7 @@ export function renderLogoSummaryCell(canvasContext: CanvasRenderingContext2D, c
 export function renderBarchart(ctx: CanvasRenderingContext2D, col: DG.Column, monomerColStats: types.MonomerColStats,
   bounds: DG.Rect, max: number): types.BarCoordinates {
   let sum = col.length - (monomerColStats['-']?.count ?? 0);
-  const colorPalette = getPalleteByType(col.tags[C.TAGS.ALPHABET]);
+  const colorPalette = bio.getPaletteByType(col.tags[C.TAGS.ALPHABET]);
   const name = col.name;
   const colNameSize = ctx.measureText(name);
   const margin = 0.2;
@@ -144,7 +143,7 @@ export function renderBarchart(ctx: CanvasRenderingContext2D, col: DG.Column, mo
     ctx.fillStyle = color;
 
     if (textSize.width <= subBarHeight) {
-      if (color != SeqPaletteBase.undefinedColor)
+      if (color != bio.SeqPaletteBase.undefinedColor)
         ctx.fillRect(xStart, yStart, barWidth, subBarHeight);
       else {
         ctx.strokeRect(xStart + 0.5, yStart, barWidth - 1, subBarHeight);

package/src/utils/misc.ts

@@ -7,20 +7,6 @@ import {NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
 import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 
-export function getPalleteByType(paletteType: string): SeqPalette {
-  switch (paletteType) {
-  case 'PT':
-    return AminoacidsPalettes.GrokGroups;
-  case 'NT':
-  case 'DNA':
-  case 'RNA':
-    return NucleotidesPalettes.Chromatogram;
-    // other
-  default:
-    return UnknownSeqPalettes.Color;
-  }
-}
-
 export function getTypedArrayConstructor(
   maxNum: number): Uint8ArrayConstructor | Uint16ArrayConstructor | Uint32ArrayConstructor {
   return maxNum < 256 ? Uint8Array :

package/src/widgets/manual-alignment.ts

@@ -1,8 +1,7 @@
 import * as ui from 'datagrok-api/ui';
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
-
-import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter';
+import * as bio from '@datagrok-libraries/bio';
 
 import $ from 'cash-dom';
 import '../styles.css';
@@ -20,7 +19,7 @@ export function manualAlignmentWidget(alignedSequenceCol: DG.Column<string>, cur
   const applyChangesBtn = ui.button('Apply', async () => {
     const newSequence = sequenceInput.value;
     const affectedRowIndex = currentDf.currentRowIdx;
-    const splitSequence = splitAlignedSequences(DG.Column.fromStrings('splitSequence', [newSequence]));
+    const splitSequence = bio.splitAlignedSequences(DG.Column.fromStrings('splitSequence', [newSequence]));
 
     alignedSequenceCol.set(affectedRowIndex, newSequence);
     for (const part of splitSequence.columns) {

package/src/widgets/peptides.ts

@@ -1,8 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import * as bio from '@datagrok-libraries/bio';
 
 import '../styles.css';
 import * as C from '../utils/constants';
@@ -84,7 +83,7 @@ export async function analyzePeptidesWidget(df: DG.DataFrame, col: DG.Column): P
   });
   startBtn.style.alignSelf = 'center';
 
-  const viewer = await df.plot.fromType('WebLogo') as WebLogo;
+  const viewer = await df.plot.fromType('WebLogo') as bio.WebLogo;
   viewer.root.style.setProperty('height', '130px');
   const logoHost = ui.div();
   $(logoHost).empty().append(viewer.root);
@@ -109,7 +108,7 @@ export async function startAnalysis(activityColumn: DG.Column<number> | null, pe
     const f = currentDf.filter;
     //prepare new DF
     const newDf = DG.DataFrame.create(f.trueCount);
-    const getIndex = indexes.length !== 0 ? (i: number) : number => indexes[i] : (i: number): number => i;
+    const getIndex = indexes.length !== 0 ? (i: number): number => indexes[i] : (i: number): number => i;
     let activityCol: DG.Column<number> | null = null;
     for (const col of currentDf.columns.toList()) {
       let virtualCol: DG.Column<any>;

package/{test-Peptides-8408d9b6ee67-ca232121.html → test-Peptides-916a90d7d48b-44350c85.html}

@@ -1,4 +1,4 @@
-<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=8408d9b6ee67. Commit ca232121.</title><style type="text/css">html,
+<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit 44350c85.</title><style type="text/css">html,
 body {
   font-family: Arial, Helvetica, sans-serif;
   font-size: 1rem;
@@ -229,11 +229,14 @@ header {
   font-size: 1rem;
   padding: 0 0.5rem;
 }
-</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=8408d9b6ee67. Commit ca232121.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-11 15:08:32</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">127.821s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">112.749s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Evaluation failed: TypeError: Cannot read properties of null (reading 'get')
-    at __puppeteer_evaluation_script__:17:71
-    at ExecutionContext._evaluateInternal (/home/runner/work/public/public/packages/Peptides/node_modules/puppeteer/src/common/ExecutionContext.ts:273:13)
-    at processTicksAndRejections (internal/process/task_queues.js:97:5)
-    at ExecutionContext.evaluate (/home/runner/work/public/public/packages/Peptides/node_modules/puppeteer/src/common/ExecutionContext.ts:140:12)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:62:11)
+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:latest SHA=916a90d7d48b. Commit 44350c85.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-10-14 10:11:35</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">96.64s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">76.108s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 610 : Peptides.Core.Start analysis: simple : Unable to get project asset "getMonomerLib"
+Test result : Failed : 372 : Peptides.Core.Start analysis: сomplex : Unable to get project asset "getMonomerLib"
+Test result : Failed : 382 : Peptides.Core.Save and load project : Unable to get project asset "getMonomerLib"
+
+    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:68:20
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:62:11)
     at Generator.next (&lt;anonymous&gt;)
     at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/test-node.ts:28:58)
     at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:40:11
@@ -243,4 +246,31 @@ header {
     at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:30:12)
     at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:38:23)
     at Promise.then.completed (/home/runner/work/public/public/packages/Peptides/node_modules/jest-circus/build/utils.js:391:28)
-    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div></div></div></div></body></html>
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:66:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 0 : Peptides.Peptide space.test_table.is_not_empty : OK
+Test result : Success : 6368 : Peptides.Peptide space.PeptideSimilaritySpaceWidget.is_drawing : OK
+Test result : Success : 2 : Peptides.Peptide space.test_deminsionality_reducer : OK
+Test result : Success : 1 : Peptides.Peptide space.test_peptide_similarity_space_viewer : OK
+Test result : Success : 2945 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Levenshtein.is_numeric : OK
+Test result : Success : 3009 : Peptides.Peptide space.peptide_space.DimensinalityReducer.UMAP.Jaro-Winkler.is_numeric : OK
+Test result : Success : 3394 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Levenshtein.is_numeric : OK
+Test result : Success : 3685 : Peptides.Peptide space.peptide_space.DimensinalityReducer.t-SNE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 205 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Levenshtein.is_numeric : OK
+Test result : Success : 629 : Peptides.Peptide space.peptide_space.DimensinalityReducer.SPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 174 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Levenshtein.is_numeric : OK
+Test result : Success : 731 : Peptides.Peptide space.peptide_space.DimensinalityReducer.pSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 7686 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Levenshtein.is_numeric : OK
+Test result : Success : 9316 : Peptides.Peptide space.peptide_space.DimensinalityReducer.OriginalSPE.Jaro-Winkler.is_numeric : OK
+Test result : Success : 1837 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Levenshtein.is_proper : OK
+Test result : Success : 2670 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Jaro-Winkler.is_proper : OK
+Test result : Success : 3278 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Levenshtein.is_proper : OK
+Test result : Success : 4073 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Jaro-Winkler.is_proper : OK
+Test result : Success : 244 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Levenshtein.is_proper : OK
+Test result : Success : 666 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.SPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 578 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Levenshtein.is_proper : OK
+Test result : Success : 612 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Jaro-Winkler.is_proper : OK
+Test result : Success : 9654 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Levenshtein.is_proper : OK
+Test result : Success : 9749 : Peptides.Peptide space.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Jaro-Winkler.is_proper : OK
+</pre></div></div></div></div></body></html>