@datagrok/bio 2.5.0 → 2.6.1

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.5.0",
+  "version": "2.6.1",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -22,11 +22,11 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.33.0",
+    "@datagrok-libraries/bio": "^5.33.2",
     "@datagrok-libraries/chem-meta": "^1.0.1",
     "@datagrok-libraries/ml": "^6.3.39",
     "@datagrok-libraries/tutorials": "^1.3.2",
-    "@datagrok-libraries/utils": "^4.0.11",
+    "@datagrok-libraries/utils": "^4.0.17",
     "cash-dom": "^8.0.0",
     "css-loader": "^6.7.3",
     "datagrok-api": "^1.13.3",

package/src/package-test.ts

@@ -8,9 +8,7 @@ import './tests/detectors-tests';
 import './tests/detectors-weak-and-likely-tests';
 import './tests/detectors-benchmark-tests';
 import './tests/msa-tests';
-
-import './tests/splitters-test'; //Unhandled exceptions.exceptions : Cannot read properties of null (reading 'f')
-
+import './tests/splitters-test';
 import './tests/monomer-libraries-tests';
 import './tests/renderers-test';
 import './tests/renderers-monomer-placer';

package/src/tests/WebLogo-positions-test.ts

@@ -1,8 +1,8 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
-import {ALPHABET, NOTATION, SplitterFunc, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {category, expect, expectArray, test, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
+import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {
   countForMonomerAtPosition,
   PositionInfo as PI,
@@ -19,14 +19,6 @@ ATC-G-TTGC--
 -TC-GCTTGC--
 -TC-GCTTGC--`;
 
-
-  before(async () => {
-  });
-
-  after(async () => {
-    // Closing opened views causes the error 'Cannot read properties of null (reading 'f')'
-  });
-
   test('allPositions', async () => {
     const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDf1);
     const tv: DG.TableView = grok.shell.addTableView(df);
@@ -40,6 +32,7 @@ ATC-G-TTGC--
     const wlViewer: WebLogoViewer = (await df.plot.fromType('WebLogo')) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
+    await awaitCheck(() => wlViewer.Length > 0, 'WebLogo.Length is zero', 100);
     const positions: PI[] = wlViewer['positions'];
 
     const resAllDf1: PI[] = [
@@ -64,7 +57,7 @@ ATC-G-TTGC--
       for (const m of positions[i].getMonomers())
         expect(positions[i].getFreq(m).count, resAllDf1[i].getFreq(m).count);
     }
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('positions with shrinkEmptyTail option true (filtered)', async () => {
     const csvDf2 = `seq
@@ -91,6 +84,7 @@ ATC-G-TTGC--
       {'shrinkEmptyTail': true})) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
+    await awaitCheck(() => wlViewer.Length > 0, 'WebLogo.Length is zero', 100);
     const positions: PI[] = wlViewer['positions'];
 
     const resAllDf1: PI[] = [
@@ -112,7 +106,7 @@ ATC-G-TTGC--
       for (const m of positions[i].getMonomers())
         expect(positions[i].getFreq(m).count, resAllDf1[i].getFreq(m).count);
     }
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('positions with skipEmptyPositions option', async () => {
     const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDf1);
@@ -128,6 +122,7 @@ ATC-G-TTGC--
       {'skipEmptyPositions': true})) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
+    await awaitCheck(() => wlViewer.Length > 0, 'WebLogo.Length is zero');
     const resPosList: PI[] = wlViewer['positions'];
 
     const tgtPosList: PI[] = [
@@ -148,7 +143,7 @@ ATC-G-TTGC--
       const tgtPos = tgtPosList[posI];
       expectPositionInfo(resPos, tgtPos);
     }
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('count sequences for monomer at position', async () => {
     const df: DG.DataFrame = buildDfWithSeqCol(csvDf1, NOTATION.FASTA, ALPHABET.DNA, 'SEQ.MSA');
@@ -163,6 +158,7 @@ ATC-G-TTGC--
     })) as WebLogoViewer;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
+    await awaitCheck(() => wlViewer.Length > 0, 'WebLogo.Length is zero', 100);
     const resPosList: PI[] = wlViewer['positions'];
     const tgtPosList: PI[] = [
       new PI(2, '3', {'C': new PMI(5)}),
@@ -182,7 +178,7 @@ ATC-G-TTGC--
     const uh = UnitsHandler.getOrCreate(seqCol);
     const countAt1 = countForMonomerAtPosition(df, uh, df.filter, 'G', atPI1);
     expect(countAt1, 5);
-  }, {skipReason: 'GROK-13300'});
+  });
 });
 
 function expectPositionInfo(actualPos: PI, expectedPos: PI): void {

package/src/tests/detectors-benchmark-tests.ts

@@ -21,19 +21,19 @@ category('detectorsBenchmark', () => {
   // -- fasta --
 
   test('fastaDnaShorts50Few50', async () => {
-      await detectMacromoleculeBenchmark(10, NOTATION.FASTA, ALPHABET.DNA, 50, 50);
-    },
-    {skipReason: '#1192'});
+    await detectMacromoleculeBenchmark(10, NOTATION.FASTA, ALPHABET.DNA, 50, 50);
+  },
+  {skipReason: '#1192'});
 
   test('fastaDnaShorts50Many1E6', async () => {
-      await detectMacromoleculeBenchmark(10, NOTATION.FASTA, ALPHABET.DNA, 50, 1E6);
-    },
-    {skipReason: '#1192'});
+    await detectMacromoleculeBenchmark(10, NOTATION.FASTA, ALPHABET.DNA, 50, 1E6);
+  },
+  {skipReason: '#1192'});
 
   test('fastaDnaLong1e6Few50', async () => {
-      await detectMacromoleculeBenchmark(10, NOTATION.FASTA, ALPHABET.DNA, 1E6, 50);
-    },
-    {skipReason: '#1192'});
+    await detectMacromoleculeBenchmark(10, NOTATION.FASTA, ALPHABET.DNA, 1E6, 50);
+  },
+  {skipReason: '#1192'});
 
   // -- separator --
 

package/src/tests/detectors-tests.ts

@@ -225,6 +225,11 @@ MWRSWY-CKHP`;
     await _testPos(readCsv(csvTests.fastaPt1), 'seq',
       NOTATION.FASTA, ALIGNMENT.SEQ, ALPHABET.PT, 20, false);
   });
+  test('FastaPtGaps', () => _testPosList(['FW-PH-EYY', 'FYNRQWYV-', 'FKP-Q-SEYV'],
+    NOTATION.FASTA, ALIGNMENT.SEQ, ALPHABET.PT, 20, false));
+  test('FastaPtGapsMsa', () => _testPosList(['FW-PH-EYY', 'FYNRQWYV-', 'FKP-Q-SEY'],
+    NOTATION.FASTA, ALIGNMENT.SEQ_MSA, ALPHABET.PT, 20, false));
+
   test('FastaUn', async () => {
     await _testPos(readCsv(csvTests.fastaUn), 'seq',
       NOTATION.FASTA, ALIGNMENT.SEQ_MSA, ALPHABET.UN, 12, true);
@@ -387,6 +392,31 @@ export async function _testNeg(readDf: DfReaderFunc, colName: string) {
   }
 }
 
+export async function _testPosList(list: string[], units: NOTATION,
+  aligned: ALIGNMENT, alphabet: ALPHABET, alphabetSize: number, alphabetIsMultichar: boolean,
+  separator: string | null = null
+): Promise<void> {
+  const col: DG.Column = DG.Column.fromList(DG.TYPE.STRING, 'seq', list);
+  const semType: string = await grok.functions.call('Bio:detectMacromolecule', {col: col});
+  if (semType)
+    col.semType = semType;
+
+  expect(col.semType, DG.SEMTYPE.MACROMOLECULE);
+  expect(col.getTag(DG.TAGS.UNITS), units);
+  expect(col.getTag(bioTAGS.aligned), aligned);
+  expect(col.getTag(bioTAGS.alphabet), alphabet);
+  if (separator)
+    expect(col.getTag(bioTAGS.separator), separator);
+
+  const uh = UnitsHandler.getOrCreate(col);
+  expect(uh.getAlphabetSize(), alphabetSize);
+  expect(uh.getAlphabetIsMultichar(), alphabetIsMultichar);
+  if (!uh.isHelm()) {
+    expect(uh.aligned, aligned);
+    expect(uh.alphabet, alphabet);
+  }
+}
+
 export async function _testPos(
   readDf: DfReaderFunc, colName: string, units: string,
   aligned: string | null, alphabet: string | null, alphabetSize: number, alphabetIsMultichar: boolean,

package/src/tests/msa-tests.ts

@@ -73,11 +73,11 @@ MWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHP
 
   test('isCorrect', async () => {
     await _testMsaIsCorrect(fromCsv, toCsv);
-  }, {skipReason: 'GROK-13221'});
+  });
 
   test('isCorrectLong', async () => {
     await _testMsaIsCorrect(longFromCsv, longToCsv);
-  }, {skipReason: 'GROK-13221'});
+  });
 
   test('isCorrectHelm', async () => {
     await awaitContainerStart();
@@ -93,13 +93,13 @@ MWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHP
     await _testMSAOnColumn(
       SeparatorFromCsv, SeparatorToCsv, NOTATION.SEPARATOR, NOTATION.FASTA, ALPHABET.PT,
     );
-  }, {skipReason: 'GROK-13221'});
+  });
 
   test('isCorrectSeparatorLong', async () => {
     await _testMSAOnColumn(
       SeparatorLongFromCsv, SeparatorLongToCsv, NOTATION.SEPARATOR, NOTATION.FASTA, ALPHABET.PT,
     );
-  }, {skipReason: 'GROK-13221'});
+  });
 });
 
 async function _testMsaIsCorrect(srcCsv: string, tgtCsv: string): Promise<void> {

package/src/tests/renderers-test.ts

@@ -1,7 +1,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, delay, expect, test} from '@datagrok-libraries/utils/src/test';
+import {category, expect, test, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
 
 import {importFasta} from '../package';
 import {convertDo} from '../utils/convert';
@@ -12,54 +12,40 @@ import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {multipleSequenceAlignmentUI} from '../utils/multiple-sequence-alignment-ui';
 
 category('renderers', () => {
-  let tvList: DG.TableView[];
-  let dfList: DG.DataFrame[];
-
-  before(async () => {
-    tvList = [];
-    dfList = [];
-  });
-
-  after(async () => {
-    // Closing viewes and data frames leads to exception
-    // dfList.forEach((df: DG.DataFrame) => { grok.shell.closeTable(df); });
-    // tvList.forEach((tv: DG.TableView) => tv.close());
-  });
-
   test('long sequence performance ', async () => {
-    performanceTest(generateLongSequence, 'Long sequences');
-  }, {skipReason: 'GROK-13300'});
+    await performanceTest(generateLongSequence, 'Long sequences');
+  });
 
   test('many sequence performance', async () => {
-    performanceTest(generateManySequences, 'Many sequences');
-  }, {skipReason: 'GROK-13300'});
+    await performanceTest(generateManySequences, 'Many sequences');
+  });
   test('many sequence performance', async () => {
-    performanceTest(generateManySequences, 'Many sequences');
-  }, {skipReason: 'GROK-13300'});
+    await performanceTest(generateManySequences, 'Many sequences');
+  });
 
   test('rendererMacromoleculeFasta', async () => {
     await _rendererMacromoleculeFasta();
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('rendererMacromoleculeSeparator', async () => {
     await _rendererMacromoleculeSeparator();
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('rendererMacromoleculeDifference', async () => {
     await _rendererMacromoleculeDifference();
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('afterMsa', async () => {
     await _testAfterMsa();
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('afterConvert', async () => {
     await _testAfterConvert();
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('selectRendererBySemType', async () => {
     await _selectRendererBySemType();
-  }, {skipReason: 'GROK-13300'});
+  });
 
   test('setRendererManually', async () => {
     await _setRendererManually();
@@ -78,8 +64,8 @@ category('renderers', () => {
     // call to calculate 'cell.renderer' tag
     await grok.data.detectSemanticTypes(df);
 
-    dfList.push(df);
-    tvList.push(tv);
+    await awaitCheck(() => { return tv.grid.dataFrame != df; },
+      'View grid has wrong data frame', 100);
 
     const resCellRenderer = seqCol.getTag(DG.TAGS.CELL_RENDERER);
     expect(resCellRenderer, 'sequence');
@@ -98,8 +84,8 @@ category('renderers', () => {
     // call to calculate 'cell.renderer' tag
     await grok.data.detectSemanticTypes(df);
 
-    dfList.push(df);
-    tvList.push(tv);
+    await awaitCheck(() => { return tv.grid.dataFrame != df; },
+      'View grid has wrong data frame', 100);
 
     const resCellRenderer = seqCol.getTag(DG.TAGS.CELL_RENDERER);
     expect(resCellRenderer, 'sequence');
@@ -120,8 +106,8 @@ category('renderers', () => {
     // call to calculate 'cell.renderer' tag
     await grok.data.detectSemanticTypes(df);
 
-    dfList.push(df);
-    tvList.push(tv);
+    await awaitCheck(() => { return tv.grid.dataFrame != df; },
+      'View grid has wrong data frame', 100);
 
     const resCellRenderer = seqDiffCol.getTag(DG.TAGS.CELL_RENDERER);
     expect(resCellRenderer, C.SEM_TYPES.MACROMOLECULE_DIFFERENCE);
@@ -141,6 +127,8 @@ category('renderers', () => {
     await grok.data.detectSemanticTypes(df);
 
     console.log('Bio: tests/renderers/afterMsa, table view');
+    await awaitCheck(() => { return tv.grid.dataFrame != df; },
+      'View grid has wrong data frame', 100);
 
     console.log('Bio: tests/renderers/afterMsa, src before test ' +
       `semType="${srcSeqCol!.semType}", units="${srcSeqCol!.getTag(DG.TAGS.UNITS)}", ` +
@@ -153,6 +141,8 @@ category('renderers', () => {
 
     const msaSeqCol = await multipleSequenceAlignmentUI({col: srcSeqCol});
     tv.grid.invalidate();
+    await awaitCheck(() => { return tv.grid.dataFrame != df; },
+      'View grid has wrong data frame', 100);
 
     expect(msaSeqCol.semType, DG.SEMTYPE.MACROMOLECULE);
     expect(msaSeqCol.getTag(DG.TAGS.UNITS), NOTATION.FASTA);
@@ -162,9 +152,6 @@ category('renderers', () => {
 
     // check newColumn with UnitsHandler constructor
     const _uh: UnitsHandler = UnitsHandler.getOrCreate(msaSeqCol);
-
-    dfList.push(df);
-    tvList.push(tv);
   }
 
   async function _testAfterConvert() {
@@ -180,10 +167,9 @@ category('renderers', () => {
     // call to calculate 'cell.renderer' tag
     await grok.data.detectSemanticTypes(df);
 
-    tvList.push(tv);
-    dfList.push(df);
-
     const tgtCol: DG.Column = await convertDo(srcCol, NOTATION.SEPARATOR, '/');
+    await awaitCheck(() => { return tv.grid.dataFrame != df; },
+      'View grid has wrong data frame', 100);
 
     const resCellRenderer = tgtCol.getTag(DG.TAGS.CELL_RENDERER);
     expect(resCellRenderer, 'sequence');
@@ -206,8 +192,6 @@ category('renderers', () => {
     seqDiffCol.semType = C.SEM_TYPES.MACROMOLECULE_DIFFERENCE;
     const df = DG.DataFrame.fromColumns([seqDiffCol]);
     const tv = grok.shell.addTableView(df);
-    dfList.push(df);
-    tvList.push(tv);
 
     await delay(100);
     const renderer = seqDiffCol.getTag(DG.TAGS.CELL_RENDERER);
@@ -234,10 +218,8 @@ category('renderers', () => {
     const df = DG.DataFrame.fromColumns([seqDiffCol]);
     await grok.data.detectSemanticTypes(df);
     const tv = grok.shell.addTableView(df);
-    dfList.push(df);
-    tvList.push(tv);
+    await awaitCheck(() => document.querySelector('canvas') !== null, 'cannot load table', 3000);
 
-    await delay(100);
     const resCellRenderer = seqDiffCol.getTag(DG.TAGS.CELL_RENDERER);
     if (resCellRenderer !== tgtCellRenderer) { // this is value of MacromoleculeDifferenceCR.cellType
       throw new Error(`Tag 'cell.renderer' has been manually set to '${tgtCellRenderer}' for column ` +

package/src/tests/similarity-diversity-tests.ts

@@ -1,18 +1,10 @@
-import {after, before, category, test, expect, awaitCheck} from '@datagrok-libraries/utils/src/test';
+import {category, test, expect, awaitCheck} from '@datagrok-libraries/utils/src/test';
 import * as DG from 'datagrok-api/dg';
 import {createTableView} from './utils';
 import * as grok from 'datagrok-api/grok';
 import {SequenceSimilarityViewer} from '../analysis/sequence-similarity-viewer';
 
 category('similarity/diversity', async () => {
-  before(async () => {
-    // grok.shell.closeAll();
-  });
-
-  after(async () => {
-    grok.shell.closeAll();
-  });
-
   test('similaritySearchViewer', async () => {
     await _testSimilaritySearchViewer();
   });
@@ -23,51 +15,43 @@ category('similarity/diversity', async () => {
 });
 
 async function _testSimilaritySearchViewer() {
-  try {
-    const molecules = await createTableView('tests/sample_MSA_data.csv');
-    const viewer = molecules.addViewer('Sequence Similarity Search');
-    await awaitCheck(() => getSearchViewer(viewer, 'Sequence Similarity Search') !== undefined,
-      'Sequence Similarity Search has not been created', 5000);
-    const similaritySearchViewer: SequenceSimilarityViewer = getSearchViewer(viewer, 'Sequence Similarity Search');
-    await awaitCheck(() => similaritySearchViewer.root.getElementsByClassName('d4-grid').length !== 0,
-      'Sequence Similarity Search has not been created', 5000);
-    expect(similaritySearchViewer.fingerprint, 'Morgan');
-    expect(similaritySearchViewer.distanceMetric, 'Tanimoto');
-    expect(similaritySearchViewer.scores!.get(0), DG.FLOAT_NULL);
-    expect(similaritySearchViewer.idxs!.get(0), 0);
-    expect(similaritySearchViewer.molCol!.get(0),
-      'D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me');
-    expect(similaritySearchViewer.scores!.get(1), 0.4722222089767456);
-    expect(similaritySearchViewer.idxs!.get(1), 11);
-    expect(similaritySearchViewer.molCol!.get(1),
-      'meI/hHis//Aca/meM/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me');
-    molecules.dataFrame.currentRowIdx = 1;
-    await awaitCheck(() => similaritySearchViewer.targetMoleculeIdx === 1, 'Target molecule has not been changed', 5000);
-    await awaitCheck(() => similaritySearchViewer.molCol!.get(0) ===
-        'meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me',
-      'Incorrect first similar molecule', 5000);
-
-  } finally {
-    grok.shell.closeAll();
-  }
+  const molecules = await createTableView('tests/sample_MSA_data.csv');
+  const viewer = molecules.addViewer('Sequence Similarity Search');
+  await awaitCheck(() => getSearchViewer(viewer, 'Sequence Similarity Search') !== undefined,
+    'Sequence Similarity Search has not been created', 5000);
+  const similaritySearchViewer: SequenceSimilarityViewer = getSearchViewer(viewer, 'Sequence Similarity Search');
+  await awaitCheck(() => similaritySearchViewer.root.getElementsByClassName('d4-grid').length !== 0,
+    'Sequence Similarity Search has not been created', 5000);
+  expect(similaritySearchViewer.fingerprint, 'Morgan');
+  expect(similaritySearchViewer.distanceMetric, 'Tanimoto');
+  expect(similaritySearchViewer.scores!.get(0), DG.FLOAT_NULL);
+  expect(similaritySearchViewer.idxs!.get(0), 0);
+  expect(similaritySearchViewer.molCol!.get(0),
+    'D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me');
+  expect(similaritySearchViewer.scores!.get(1), 0.4722222089767456);
+  expect(similaritySearchViewer.idxs!.get(1), 11);
+  expect(similaritySearchViewer.molCol!.get(1),
+    'meI/hHis//Aca/meM/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me');
+  molecules.dataFrame.currentRowIdx = 1;
+  await awaitCheck(() => similaritySearchViewer.targetMoleculeIdx === 1,
+    'Target molecule has not been changed', 5000);
+  await awaitCheck(() => similaritySearchViewer.molCol!.get(0) ===
+      'meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me',
+  'Incorrect first similar molecule', 5000);
 }
 
 async function _testDiversitySearchViewer() {
-  try {
-    const molecules = await createTableView('tests/sample_MSA_data.csv');
-    const viewer = molecules.addViewer('Sequence Diversity Search');
-    await awaitCheck(() => getSearchViewer(viewer, 'Sequence Diversity Search') !== undefined,
-      'Sequence Diversity Search has not been created', 5000);
-    const diversitySearchviewer = getSearchViewer(viewer, 'Sequence Diversity Search');
-    await awaitCheck(() => diversitySearchviewer.root.getElementsByClassName('d4-grid').length !== 0,
-      'Sequence Diversity Search has not been created', 5000);
-    expect(diversitySearchviewer.fingerprint, 'Morgan');
-    expect(diversitySearchviewer.distanceMetric, 'Tanimoto');
-    expect(diversitySearchviewer.initialized, true);
-    expect(diversitySearchviewer.renderMolIds.length > 0, true);
-  } finally {
-    grok.shell.closeAll();
-  }
+  const molecules = await createTableView('tests/sample_MSA_data.csv');
+  const viewer = molecules.addViewer('Sequence Diversity Search');
+  await awaitCheck(() => getSearchViewer(viewer, 'Sequence Diversity Search') !== undefined,
+    'Sequence Diversity Search has not been created', 5000);
+  const diversitySearchviewer = getSearchViewer(viewer, 'Sequence Diversity Search');
+  await awaitCheck(() => diversitySearchviewer.root.getElementsByClassName('d4-grid').length !== 0,
+    'Sequence Diversity Search has not been created', 5000);
+  expect(diversitySearchviewer.fingerprint, 'Morgan');
+  expect(diversitySearchviewer.distanceMetric, 'Tanimoto');
+  expect(diversitySearchviewer.initialized, true);
+  expect(diversitySearchviewer.renderMolIds.length > 0, true);
 }
 
 function getSearchViewer(viewer: DG.Viewer, name: string) {
@@ -77,4 +61,3 @@ function getSearchViewer(viewer: DG.Viewer, name: string) {
       return v;
   }
 }
-

package/src/tests/splitters-test.ts

@@ -2,7 +2,16 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {after, before, category, test, expect, expectArray, delay} from '@datagrok-libraries/utils/src/test';
+import {
+  after,
+  before,
+  category,
+  test,
+  expect,
+  expectArray,
+  delay,
+  awaitCheck
+} from '@datagrok-libraries/utils/src/test';
 import * as C from '../utils/constants';
 import {_package, getHelmMonomers} from '../package';
 import {TAGS as bioTAGS, splitterAsFasta, splitterAsHelm} from '@datagrok-libraries/bio/src/utils/macromolecule';
@@ -80,13 +89,14 @@ category('splitters', async () => {
 
     const newDf = await splitToMonomersUI(df, seqCol);
     expect(newDf.columns.names().includes('17'), true);
+    // call to calculate 'cell.renderer' tag
+    await grok.data.detectSemanticTypes(newDf);
 
     // TODO: Check cell.renderer for columns of monomers
-    // const _tv: DG.TableView = grok.shell.addTableView(df);
-    // await delay(500); // needed to account for table adding
-    // // call to calculate 'cell.renderer' tag
-    // await grok.data.detectSemanticTypes(df);
-  }, {skipReason: 'GROK-13300'});
+    const tv: DG.TableView = grok.shell.addTableView(newDf);
+    await awaitCheck(() => { return tv.grid.dataFrame != df; },
+      'View grid has wrong data frame', 100);
+  });
 
   test('getHelmMonomers', async () => {
     const df: DG.DataFrame = DG.DataFrame.fromCsv(

package/src/tests/utils/sequences-generators.ts

@@ -2,6 +2,7 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {awaitCheck} from '@datagrok-libraries/utils/src/test';
 
 
 export function generateManySequences(): DG.Column[] {
@@ -23,13 +24,16 @@ export function generateLongSequence(): DG.Column[] {
   return columns;
 }
 
-export function performanceTest(generateFunc: () => DG.Column[], testName: string) {
+export async function performanceTest(generateFunc: () => DG.Column[], testName: string) {
   const columns = generateFunc();
   const df: DG.DataFrame = DG.DataFrame.fromColumns(columns);
-  grok.data.detectSemanticTypes(df);
+  await grok.data.detectSemanticTypes(df);
   const startTime: number = Date.now();
   const col: DG.Column = df.columns.byName('MSA');
-  grok.shell.addTableView(df);
+  const view: DG.TableView = grok.shell.addTableView(df);
+
+  await awaitCheck(() => { return view.grid.dataFrame !== df; },
+    'View grid has wrong data frame ', 100);
 
   const endTime: number = Date.now();
   const elapsedTime: number = endTime - startTime;

package/src/tests/viewers.ts

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 //import * as ui from 'datagrok-api/ui';
 
-import {category, delay, test} from '@datagrok-libraries/utils/src/test';
+import {category, test, testViewer} from '@datagrok-libraries/utils/src/test';
 import {readDataframe} from './utils';
 
 
@@ -11,11 +11,7 @@ category('viewers', () => {
   for (const v of viewers) {
     test(v, async () => {
       const df = await readDataframe('data/sample_FASTA_DNA.csv');
-      const tv = grok.shell.addTableView(df);
-      await grok.data.detectSemanticTypes(df);
-      tv.addViewer(v);
-      await delay(2000);
-      // await testViewer(v, df, {detectSemanticTypes: true});
-    });
+      await testViewer(v, df, {detectSemanticTypes: true});
+    }, v === 'Sequence Similarity Search' ? {skipReason: 'GROK-13162'} : undefined);
   }
 });

package/src/utils/cell-renderer.ts

@@ -88,11 +88,16 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
     if (left !== null && left < seqMonList.length) {
       const monomerSymbol: string = seqMonList[left];
       const tooltipElements: HTMLElement[] = [ui.div(monomerSymbol)];
-      const monomer = seqColTemp.getMonomer(monomerSymbol);
-      if (monomer) {
-        const options = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
-        const monomerSVG = grok.chem.svgMol(monomer.smiles, undefined, undefined, options);
-        tooltipElements.push(monomerSVG);
+      if (seqColTemp._monomerStructureMap[monomerSymbol]) {
+        tooltipElements.push(seqColTemp._monomerStructureMap[monomerSymbol]);
+      } else {
+        const monomer = seqColTemp.getMonomer(monomerSymbol);
+        if (monomer) {
+          const options = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
+          const monomerSVG = grok.chem.svgMol(monomer.smiles, undefined, undefined, options);
+          tooltipElements.push(monomerSVG);
+          seqColTemp._monomerStructureMap[monomerSymbol] = monomerSVG;
+        }
       }
       ui.tooltip.show(ui.divV(tooltipElements), e.x + 16, e.y + 16);
     } else {
@@ -122,7 +127,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
     // TODO: Store temp data to GridColumn
     // Now the renderer requires data frame table Column underlying GridColumn
-    const view = gridCell.grid.view;
+    const grid = gridCell.grid;
     const tableCol: DG.Column = gridCell.cell.column;
     const tableColTemp: TempType = tableCol.temp;
 
@@ -135,7 +140,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
     let seqColTemp: MonomerPlacer = tableCol.temp[tempTAGS.bioSeqCol];
     if (!seqColTemp) {
-      seqColTemp = new MonomerPlacer(view, tableCol,
+      seqColTemp = new MonomerPlacer(grid, tableCol,
         () => {
           const uh = UnitsHandler.getOrCreate(tableCol);
           return {
@@ -236,7 +241,7 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
         /*x1 = */
         printLeftOrCentered(x + this.padding, y, w, h,
           g, amino, color, 0, true, 1.0, separator, last, drawStyle,
-          maxLengthWordsSum, index, gridCell, referenceSequence, maxLengthOfMonomer);
+          maxLengthWordsSum, index, gridCell, referenceSequence, maxLengthOfMonomer, seqColTemp._monomerLengthMap);
         if (minDistanceRenderer > w) break;
       }
     } catch (err: any) {