@datagrok/bio 1.7.23 → 1.7.24

package/package.json

@@ -1,12 +1,11 @@
 {
   "name": "@datagrok/bio",
-  "beta": false,
   "friendlyName": "Bio",
   "author": {
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "1.7.23",
+  "version": "1.7.24",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -15,9 +14,9 @@
   },
   "dependencies": {
     "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "^3.0.2",
-    "@datagrok-libraries/ml": "^3.0.0",
-    "@datagrok-libraries/utils": "^1.4.0",
+    "@datagrok-libraries/bio": "^3.0.3",
+    "@datagrok-libraries/ml": "^3.0.3",
+    "@datagrok-libraries/utils": "^1.5.4",
     "cash-dom": "latest",
     "datagrok-api": "^1.5.0",
     "dayjs": "^1.11.4",

package/src/__jest__/remote.test.ts

@@ -51,10 +51,10 @@ it('TEST', async () => {
         let failReport = '';
         for (let i = 0; i < df.rowCount; i++) {
           if (cStatus.get(i)) {
-            passReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+            passReport += `Test result : Success : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
           } else {
             failed = true;
-            failReport += `Test result : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
+            failReport += `Test result : Failed : ${targetPackage}.${cCat.get(i)}.${cName.get(i)} : ${cMessage.get(i)}\n`;
           }
         }
         resolve({failReport, passReport, failed});

package/src/package.ts

@@ -24,6 +24,7 @@ import {lru} from './utils/cell-renderer';
 import {representationsWidget} from './widgets/representations';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {FastaFileHandler} from '@datagrok-libraries/bio/src/utils/fasta-handler';
+import {removeEmptyStringRows} from '@datagrok-libraries/utils/src/dataframe-utils'
 
 
 //tags: init
@@ -161,16 +162,22 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, macroMolecule: D
   if (!encodedCol)
     return;
   const embedColsNames = getEmbeddingColsNames(table);
+  const withoutEmptyValues = DG.DataFrame.fromColumns([macroMolecule]).clone();
+  const emptyValsIdxs = removeEmptyStringRows(withoutEmptyValues, encodedCol);
+
   const chemSpaceParams = {
-    seqCol: encodedCol,
+    seqCol: withoutEmptyValues.col(macroMolecule.name)!,
     methodName: methodName,
     similarityMetric: similarityMetric,
     embedAxesNames: embedColsNames
   };
   const sequenceSpaceRes = await sequenceSpace(chemSpaceParams);
   const embeddings = sequenceSpaceRes.coordinates;
-  for (const col of embeddings)
-    table.columns.add(col);
+  for (const col of embeddings) {
+      const listValues = col.toList();
+      emptyValsIdxs.forEach((ind: number) => listValues.splice(ind, 0, null));
+      table.columns.add(DG.Column.fromFloat32Array(col.name, listValues));
+  }   
   if (plotEmbeddings) {
     for (const v of grok.shell.views) {
       if (v.name === table.name)

package/src/utils/cell-renderer.ts

@@ -66,7 +66,7 @@ function printLeftOrCentered(
   x: number, y: number, w: number, h: number,
   g: CanvasRenderingContext2D, s: string, color = undefinedColor,
   pivot: number = 0, left = false, transparencyRate: number = 1.0,
-  separator: string = '', last: boolean = false, drawStyle: string = 'classic', maxWord:any={}, maxWordIdx:number=0, gridCell:any = {}): number {
+  separator: string = '', last: boolean = false, drawStyle: string = 'classic', maxWord: any = {}, maxWordIdx: number = 0, gridCell: any = {}): number {
   g.textAlign = 'start';
   const colorPart = s.substring(0);
   let grayPart = last ? '' : separator;
@@ -212,8 +212,10 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       const separator = gridCell.cell.column.getTag('separator') ?? '';
       const splitterFunc: SplitterFunc = WebLogo.getSplitter(units, gridCell.cell.column.getTag('separator'));
 
-      // обработка новых елементов
       const columns = gridCell.cell.column.categories;
+      let monomerToShortFunction: (amino: string, maxLengthOfMonomer: number) => string = WebLogo.monomerToShort;
+      let maxLengthOfMonomer = 8;
+
       let maxLengthWords = {};
       // check if gridCell.cell.column.temp is array
       if (gridCell.cell.column.getTag('.calculatedCellRender') !== 'exist') {
@@ -221,7 +223,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
           let subParts: string[] = splitterFunc(columns[i]);
           subParts.forEach((amino, index) => {
             //@ts-ignore
-            let textSizeWidth = g.measureText(WebLogo.monomerToText(amino) + ' ');
+            let textSizeWidth = g.measureText(monomerToShortFunction(amino, maxLengthOfMonomer));
             //@ts-ignore
             if (textSizeWidth.width > (maxLengthWords[index] ?? 0)) {
               //@ts-ignore
@@ -240,23 +242,15 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
       let color = undefinedColor;
       // get max length word in subParts
       let tagUnits = gridCell.cell.column.getTag(DG.TAGS.UNITS);
-      let maxLength = 0;
-      let maxWord = '';
       let drawStyle = 'classic';
       if (tagUnits.includes('MSA')) {
-        subParts.forEach(part => {
-          if (part.length > maxLength) {
-            maxLength = part.length;
-            maxWord = part;
-            drawStyle = 'msa';
-          }
-        });
+        drawStyle = 'msa';
       }
       subParts.forEach((amino, index) => {
         color = palette.get(amino);
         g.fillStyle = undefinedColor;
         let last = index === subParts.length - 1;
-        x1 = printLeftOrCentered(x1, y, w, h, g, WebLogo.monomerToText(amino), color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell);
+        x1 = printLeftOrCentered(x1, y, w, h, g, monomerToShortFunction(amino, maxLengthOfMonomer), color, 0, true, 1.0, separator, last, drawStyle, maxLengthWords, index, gridCell);
       });
 
       g.restore();

package/src/utils/sequence-activity-cliffs.ts

@@ -8,7 +8,7 @@ export async function sequenceGetSimilarities(col: DG.Column, seq: string): Prom
   const stringArray = col.toList();
   const distances = new Array(stringArray.length).fill(0.0);
   for (let i = 0; i < stringArray.length; ++i)
-    distances[i] = getSimilarityFromDistance(AvailableMetrics['String']['Levenshtein'](stringArray[i], seq));
+    distances[i] = stringArray[i] ? getSimilarityFromDistance(AvailableMetrics['String']['Levenshtein'](stringArray[i], seq)) : 0;
   return DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'distances', distances);
 }
 

package/test-Bio-4f0c8bae6479-367602e1.html

@@ -0,0 +1,358 @@
+<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit 367602e1.</title><style type="text/css">html,
+body {
+  font-family: Arial, Helvetica, sans-serif;
+  font-size: 1rem;
+  margin: 0;
+  padding: 0;
+  color: #333;
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+  padding: 2rem 1rem;
+  font-size: 0.85rem;
+}
+#jesthtml-content {
+  margin: 0 auto;
+  max-width: 70rem;
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+#timestamp {
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+
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+  display: flex;
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+  font-size: 1rem;
+}
+#summary > div {
+  margin-right: 2rem;
+  background: #eee;
+  padding: 1rem;
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+#summary > div:last-child {
+  margin-right: 0;
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+@media only screen and (max-width: 720px) {
+  #summary {
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+  #summary > div {
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+  padding: 1rem;
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+  color: #d8000c;
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+.suite-info .suite-time.warn {
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+
+/* CONSOLE LOGS */
+.suite-consolelog {
+  margin-bottom: 0.25rem;
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+/* OBSOLETE SNAPSHOTS */
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+</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=4f0c8bae6479. Commit 367602e1.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-08-05 13:35:35</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/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">237.34s</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">221.518s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : Bio.WebLogo-positions.allPositions : Error: Expected "12", got "0"
+
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:67:20
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
+    at runMicrotasks (&lt;anonymous&gt;)
+    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/Bio/src/__jest__/test-node.ts:63:11)
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/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/Bio/src/__jest__/remote.test.ts:40:11
+    at Generator.next (&lt;anonymous&gt;)
+    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
+    at new Promise (&lt;anonymous&gt;)
+    at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
+    at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:23)
+    at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
+    at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Bio package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin">    at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:65:11
+    at Generator.next (&lt;anonymous&gt;)
+    at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
+    at runMicrotasks (&lt;anonymous&gt;)
+    at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : Bio.WebLogo.testGetStats : OK
+Test result : Success : Bio.WebLogo.testGetAlphabetSimilarity : OK
+Test result : Success : Bio.WebLogo.testPickupPaletteN1 : OK
+Test result : Success : Bio.WebLogo.testPickupPaletteN1e : OK
+Test result : Success : Bio.WebLogo.testPickupPaletteAA1 : OK
+Test result : Success : Bio.WebLogo.testPickupPaletteX : OK
+Test result : Success : Bio.WebLogo.monomerToText.longMonomerSingle : OK
+Test result : Success : Bio.WebLogo.monomerToText.longMonomerShort : OK
+Test result : Success : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
+Test result : Success : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
+Test result : Success : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
+Test result : Success : Bio.Palettes.testPaletteN : OK
+Test result : Success : Bio.Palettes.testPaletteAA : OK
+Test result : Success : Bio.detectors.NegativeEmpty : OK
+Test result : Success : Bio.detectors.Negative1 : OK
+Test result : Success : Bio.detectors.Negative2 : OK
+Test result : Success : Bio.detectors.Negative3 : OK
+Test result : Success : Bio.detectors.NegativeSmiles : OK
+Test result : Success : Bio.detectors.Dna1 : OK
+Test result : Success : Bio.detectors.Rna1 : OK
+Test result : Success : Bio.detectors.AA1 : OK
+Test result : Success : Bio.detectors.MsaDna1 : OK
+Test result : Success : Bio.detectors.MsaAA1 : OK
+Test result : Success : Bio.detectors.SepDna : OK
+Test result : Success : Bio.detectors.SepRna : OK
+Test result : Success : Bio.detectors.SepPt : OK
+Test result : Success : Bio.detectors.SepUn1 : OK
+Test result : Success : Bio.detectors.SepUn2 : OK
+Test result : Success : Bio.detectors.SepMsaN1 : OK
+Test result : Success : Bio.detectors.SamplesFastaCsvPt : OK
+Test result : Success : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
+Test result : Success : Bio.detectors.SamplesFastaCsvNegativeLength : OK
+Test result : Success : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
+Test result : Success : Bio.detectors.SamplesFastaFastaPt : OK
+Test result : Success : Bio.detectors.samplesPeptidesComplexNegativeID : OK
+Test result : Success : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
+Test result : Success : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
+Test result : Success : Bio.detectors.samplesMsaComplexUn : OK
+Test result : Success : Bio.detectors.samplesMsaComplexNegativeActivity : OK
+Test result : Success : Bio.detectors.samplesIdCsvNegativeID : OK
+Test result : Success : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
+Test result : Success : Bio.detectors.samplesHelmCsvHELM : OK
+Test result : Success : Bio.detectors.samplesHelmCsvNegativeActivity : OK
+Test result : Success : Bio.detectors.samplesTestHelmNegativeID : OK
+Test result : Success : Bio.detectors.samplesTestHelmNegativeTestType : OK
+Test result : Success : Bio.detectors.samplesTestHelmPositiveHelmString : OK
+Test result : Success : Bio.detectors.samplesTestHelmNegativeValid : OK
+Test result : Success : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
+Test result : Success : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
+Test result : Success : Bio.detectors.samplesTestHelmNegativeSmiles : OK
+Test result : Success : Bio.detectors.samplesTestDemogNegativeAll : OK
+Test result : Success : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
+Test result : Success : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
+Test result : Success : Bio.detectors.samplesFastaPtPosSequence : OK
+Test result : Success : Bio.detectors.samplesTestCerealNegativeCerealName : OK
+Test result : Success : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
+Test result : Success : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
+Test result : Success : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
+Test result : Success : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
+Test result : Success : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
+Test result : Success : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
+Test result : Success : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
+Test result : Success : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
+Test result : Success : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
+Test result : Success : Bio.MSA.isCorrect : OK
+Test result : Success : Bio.MSA.isCorrectLong : OK
+Test result : Success : Bio.sequenceSpace.sequenceSpaceOpens : OK
+Test result : Success : Bio.activityCliffs.activityCliffsOpen : OK
+Test result : Success : Bio.splitters.helm1 : OK
+Test result : Success : Bio.splitters.helm2 : OK
+Test result : Success : Bio.splitters.helm3-multichar : OK
+Test result : Success : Bio.splitters.testHelm1 : OK
+Test result : Success : Bio.splitters.testHelm2 : OK
+Test result : Success : Bio.splitters.testHelm3 : OK
+Test result : Success : Bio.renderers.afterMsa : OK
+Test result : Success : Bio.renderers.afterConvert : OK
+Test result : Success : Bio.converters.testFastaPtToSeparator : OK
+Test result : Success : Bio.converters.testFastaDnaToSeparator : OK
+Test result : Success : Bio.converters.testFastaRnaToSeparator : OK
+Test result : Success : Bio.converters.testFastaGapsToSeparator : OK
+Test result : Success : Bio.converters.testFastaPtToHelm : OK
+Test result : Success : Bio.converters.testFastaDnaToHelm : OK
+Test result : Success : Bio.converters.testFastaRnaToHelm : OK
+Test result : Success : Bio.converters.testFastaGapsToHelm : OK
+Test result : Success : Bio.converters.testSeparatorPtToFasta : OK
+Test result : Success : Bio.converters.testSeparatorDnaToFasta : OK
+Test result : Success : Bio.converters.testSeparatorRnaToFasta : OK
+Test result : Success : Bio.converters.testSeparatorGapsToFasta : OK
+Test result : Success : Bio.converters.testSeparatorPtToHelm : OK
+Test result : Success : Bio.converters.testSeparatorDnaToHelm : OK
+Test result : Success : Bio.converters.testSeparatorRnaToHelm : OK
+Test result : Success : Bio.converters.testSeparatorGapsToHelm : OK
+Test result : Success : Bio.converters.testHelmDnaToFasta : OK
+Test result : Success : Bio.converters.testHelmRnaToFasta : OK
+Test result : Success : Bio.converters.testHelmPtToFasta : OK
+Test result : Success : Bio.converters.testHelmDnaToSeparator : OK
+Test result : Success : Bio.converters.testHelmRnaToSeparator : OK
+Test result : Success : Bio.converters.testHelmPtToSeparator : OK
+Test result : Success : Bio.converters.testHelmLoneRibose : OK
+Test result : Success : Bio.converters.testHelmLoneDeoxyribose : OK
+Test result : Success : Bio.converters.testHelmLonePhosphorus : OK
+Test result : Success : Bio.fastaFileHandler.testNormalFormatting : OK
+Test result : Success : Bio.fastaFileHandler.testExtraSpaces : OK
+Test result : Success : Bio.fastaFileHandler.testExtraNewlines : OK
+Test result : Success : Bio.WebLogo-positions.positions with shrinkEmptyTail option : OK
+Test result : Success : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
+</pre></div></div></div></div></body></html>