@datagrok/bio 2.0.16 → 2.0.18

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.0.16",
+  "version": "2.0.18",
   "description": "Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the [Datagrok](https://datagrok.ai) platform",
   "repository": {
     "type": "git",
@@ -13,18 +13,18 @@
     "directory": "packages/Bio"
   },
   "dependencies": {
-    "@biowasm/aioli": ">=2.4.0",
-    "@datagrok-libraries/bio": "^4.4.3",
-    "@datagrok-libraries/chem-meta": "1.0.0",
+    "@biowasm/aioli": "^3.1.0",
+    "@datagrok-libraries/bio": "^5.0.0",
+    "@datagrok-libraries/chem-meta": "1.0.1",
     "@datagrok-libraries/ml": "^6.2.0",
-    "@datagrok-libraries/utils": "^1.6.2",
+    "@datagrok-libraries/utils": "^1.10.1",
     "@deck.gl/core": "^8.7.5",
     "@deck.gl/layers": "^8.7.5",
     "@luma.gl/constants": "^8.5.10",
     "@luma.gl/core": "^8.5.10",
-    "@phylocanvas/phylocanvas.gl": "^1.43.0",
-    "cash-dom": "latest",
-    "datagrok-api": "^1.6.12",
+    "@phylocanvas/phylocanvas.gl": "^1.44.0",
+    "cash-dom": "^8.0.0",
+    "datagrok-api": "^1.7.0",
     "dayjs": "^1.11.4",
     "openchemlib": "6.0.1",
     "rxjs": "^6.5.5",
@@ -36,9 +36,9 @@
     "@types/node": "^17.0.24",
     "@types/node-fetch": "^2.6.2",
     "@types/wu": "latest",
-    "@typescript-eslint/eslint-plugin": "latest",
-    "@typescript-eslint/parser": "latest",
-    "eslint": "latest",
+    "@typescript-eslint/eslint-plugin": "^4.20.0",
+    "@typescript-eslint/parser": "^4.20.0",
+    "eslint": "^7.23.0",
     "eslint-config-google": "latest",
     "jest": "^27.5.1",
     "jest-html-reporter": "^3.6.0",
@@ -47,9 +47,9 @@
     "puppeteer": "^13.7.0",
     "ts-jest": "^27.0.0",
     "ts-loader": "^9.2.5",
-    "typescript": "^4.5.4",
-    "webpack": "latest",
-    "webpack-cli": "^4.10.0"
+    "typescript": "^4.2.3",
+    "webpack": "^5.64.1",
+    "webpack-cli": "^4.6.0"
   },
   "scripts": {
     "link-api": "npm link datagrok-api",

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

@@ -1,12 +1,12 @@
-import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
-import * as DG from 'datagrok-api/dg';
+import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+
+import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {getSimilarityFromDistance} from '@datagrok-libraries/utils/src/similarity-metrics';
 import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
-import * as grok from 'datagrok-api/grok';
-import {SplitterFunc, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {SEM_TYPES, TAGS} from '../utils/constants';
+import {TAGS} from '../utils/constants';
 import {drawMoleculeDifferenceOnCanvas} from '../utils/cell-renderer';
 
 export async function getDistances(col: DG.Column, seq: string): Promise<Array<number>> {
@@ -14,7 +14,7 @@ export async function getDistances(col: DG.Column, seq: string): Promise<Array<n
   const distances = new Array(stringArray.length).fill(0);
   for (let i = 0; i < stringArray.length; ++i) {
     const distance = stringArray[i] ? AvailableMetrics['String']['Levenshtein'](stringArray[i], seq) : null;
-    distances[i] = distance ? distance/Math.max((stringArray[i] as string).length, seq.length) : null;
+    distances[i] = distance ? distance / Math.max((stringArray[i] as string).length, seq.length) : null;
   }
   return distances;
 }
@@ -61,7 +61,7 @@ export function createTooltipElement(params: ITooltipAndPanelParams): HTMLDivEle
 }
 
 function moleculeInfo(df: DG.DataFrame, idx: number, seqColName: string): HTMLElement {
-  const dict: {[key: string]: string} = {};
+  const dict: { [key: string]: string } = {};
   for (const col of df.columns) {
     if (col.name !== seqColName)
       dict[col.name] = df.get(col.name, idx);
@@ -82,10 +82,10 @@ export function createPropPanelElement(params: ITooltipAndPanelParams): HTMLDivE
     activitiesArray[idx] = params.activityCol.get(molIdx);
   });
 
-  const molDifferences: {[key: number]: HTMLCanvasElement} = {};
+  const molDifferences: { [key: number]: HTMLCanvasElement } = {};
   const units = params.seqCol.getTag(DG.TAGS.UNITS);
   const separator = params.seqCol.getTag(TAGS.SEPARATOR);
-  const splitter = WebLogo.getSplitter(units, separator);
+  const splitter = bio.getSplitter(units, separator);
   const subParts1 = splitter(sequencesArray[0]);
   const subParts2 = splitter(sequencesArray[1]);
   const canvas = createDifferenceCanvas(subParts1, subParts2, units, molDifferences);

package/src/analysis/sequence-similarity-viewer.ts

@@ -1,14 +1,15 @@
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+
 import {SequenceSearchBaseViewer} from './sequence-search-base-viewer';
 import {getMonomericMols} from '../calculations/monomerLevelMols';
 import * as C from '../utils/constants';
 import {createDifferenceCanvas, createDifferencesWithPositions} from './sequence-activity-cliffs';
 import {updateDivInnerHTML} from '../utils/ui-utils';
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {TableView} from 'datagrok-api/dg';
-import { Subject } from 'rxjs';
+import {Subject} from 'rxjs';
 
 export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   hotSearch: boolean;
@@ -84,7 +85,7 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
     const molDifferences: { [key: number]: HTMLCanvasElement } = {};
     const units = resDf.col('sequence')!.getTag(DG.TAGS.UNITS);
     const separator = resDf.col('sequence')!.getTag(C.TAGS.SEPARATOR);
-    const splitter = WebLogo.getSplitter(units, separator);
+    const splitter = bio.getSplitter(units, separator);
     const subParts1 = splitter(this.moleculeColumn!.get(this.targetMoleculeIdx));
     const subParts2 = splitter(resDf.get('sequence', resDf.currentRowIdx));
     const canvas = createDifferenceCanvas(subParts1, subParts2, units, molDifferences);

package/src/calculations/monomerLevelMols.ts

@@ -1,19 +1,21 @@
 import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
+
 import * as C from '../utils/constants';
 import {getHelmMonomers} from '../package';
-import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
 
 const V2000_ATOM_NAME_POS = 31;
 
 export async function getMonomericMols(mcol: DG.Column, pattern: boolean = false): Promise<DG.Column> {
   const separator: string = mcol.tags[C.TAGS.SEPARATOR];
   const units: string = mcol.tags[DG.TAGS.UNITS];
-  const splitter = WebLogo.getSplitter(units, separator);
+  const splitter = bio.getSplitter(units, separator);
   let molV3000Array;
   const monomersDict = new Map();
   const monomers = units === 'helm' ?
-    getHelmMonomers(mcol) : Object.keys(WebLogo.getStats(mcol, 0, splitter).freq).filter((it) => it !== '');
+    getHelmMonomers(mcol) : Object.keys(bio.getStats(mcol, 0, splitter).freq).filter((it) => it !== '');
 
   for (let i = 0; i < monomers.length; i++)
     monomersDict.set(monomers[i], `${i + 1}`);

package/src/package-test.ts

@@ -12,6 +12,7 @@ import './tests/splitters-test';
 import './tests/renderers-test';
 import './tests/convert-test';
 import './tests/fasta-handler-test';
+import './tests/fasta-export-tests';
 import './tests/WebLogo-positions-test';
 import './tests/checkInputColumn-tests';
 import './tests/similarity-diversity-tests';

package/src/package.ts

@@ -2,18 +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 bio from '@datagrok-libraries/bio';
 
 export const _package = new DG.Package();
 
 import {MacromoleculeDifferenceCellRenderer, MonomerCellRenderer} from './utils/cell-renderer';
-import {WebLogo, SeqColStats} from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {VdRegionsViewer} from './viewers/vd-regions-viewer';
 import {runKalign, testMSAEnoughMemory} from './utils/multiple-sequence-alignment';
 import {SequenceAlignment, Aligned} from './seq_align';
-import {Nucleotides} from '@datagrok-libraries/bio/src/nucleotides';
-import {Aminoacids} from '@datagrok-libraries/bio/src/aminoacids';
 import {getEmbeddingColsNames, sequenceSpace} from './analysis/sequence-space';
-import {AvailableMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getActivityCliffs} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
 import {createPropPanelElement, createTooltipElement, getSimilaritiesMarix} from './analysis/sequence-activity-cliffs';
 import {createJsonMonomerLibFromSdf, encodeMonomers, getMolfilesFromSeq, HELM_CORE_LIB_FILENAME} from './utils/utils';
@@ -21,8 +18,6 @@ import {getMacroMol} from './utils/atomic-works';
 import {MacromoleculeSequenceCellRenderer} from './utils/cell-renderer';
 import {convert} from './utils/convert';
 import {getMacroMolColumnPropertyPanel, 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';
 import {
   generateManySequences,
@@ -34,7 +29,8 @@ import {splitAlignedSequences} from '@datagrok-libraries/bio/src/utils/splitter'
 import * as C from './utils/constants';
 import {SequenceSimilarityViewer} from './analysis/sequence-similarity-viewer';
 import {SequenceDiversityViewer} from './analysis/sequence-diversity-viewer';
-import { substructureSearchDialog } from './substructure-search/substructure-search';
+import {substructureSearchDialog} from './substructure-search/substructure-search';
+import {saveAsFastaUI} from './utils/save-as-fasta';
 
 //tags: init
 export async function initBio() {
@@ -91,7 +87,7 @@ export function checkInputColumn(
   let res: boolean = true;
   let msg: string = '';
 
-  const uh = new UnitsHandler(col);
+  const uh = new bio.UnitsHandler(col);
   if (col.semType !== DG.SEMTYPE.MACROMOLECULE) {
     grok.shell.warning(name + ' analysis is allowed for Macromolecules semantic type');
     res = false;
@@ -141,7 +137,7 @@ export function sequenceAlignment(alignType: string, alignTable: string, gap: nu
 //tags: viewer, panel
 //output: viewer result
 export function webLogoViewer() {
-  return new WebLogo();
+  return new bio.WebLogo();
 }
 
 //name: VdRegions
@@ -307,7 +303,7 @@ export async function compositionAnalysis(): Promise<void> {
     if (col.semType != DG.SEMTYPE.MACROMOLECULE)
       return false;
 
-    const colUH = new UnitsHandler(col);
+    const colUH = new bio.UnitsHandler(col);
     // TODO: prevent for cyclic, branched or multiple chains in Helm
     return true;
   });
@@ -326,7 +322,7 @@ export async function compositionAnalysis(): Promise<void> {
     return;
   } else if (colList.length > 1) {
     const colListNames: string [] = colList.map((col) => col.name);
-    const selectedCol = colList.find((c) => { return (new UnitsHandler(c)).isMsa(); });
+    const selectedCol = colList.find((c) => { return (new bio.UnitsHandler(c)).isMsa(); });
     const colInput: DG.InputBase = ui.choiceInput(
       'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
     ui.dialog({
@@ -378,7 +374,7 @@ export async function peptideMolecule(macroMolecule: DG.Cell): Promise<DG.Widget
 //input: string fileContent
 //output: list tables
 export function importFasta(fileContent: string): DG.DataFrame [] {
-  const ffh = new FastaFileHandler(fileContent);
+  const ffh = new bio.FastaFileHandler(fileContent);
   return ffh.importFasta();
 }
 
@@ -453,7 +449,7 @@ export async function testDetectMacromolecule(path: string): Promise<DG.DataFram
 //tags: panel, bio
 //input: column col {semType: Macromolecule}
 export function splitToMonomers(col: DG.Column<string>): void {
-  if (!col.getTag(UnitsHandler.TAGS.aligned).includes(C.MSA))
+  if (!col.getTag(bio.UnitsHandler.TAGS.aligned).includes(C.MSA))
     return grok.shell.error('Splitting is applicable only for aligned sequences');
 
   const tempDf = splitAlignedSequences(col);
@@ -470,7 +466,7 @@ export function splitToMonomers(col: DG.Column<string>): void {
 //name: Bio: getHelmMonomers
 //input: column col {semType: Macromolecule}
 export function getHelmMonomers(seqCol: DG.Column<string>): string[] {
-  const stats = WebLogo.getStats(seqCol, 1, WebLogo.splitterAsHelm);
+  const stats = bio.getStats(seqCol, 1, bio.splitterAsHelm);
   return Object.keys(stats.freq);
 }
 
@@ -516,3 +512,9 @@ export function bioSubstructureSearch(col: DG.Column): void {
   substructureSearchDialog(col);
 }
 
+//name: saveAsFasta
+//description: As FASTA...
+//tags: fileExporter
+export function saveAsFasta() {
+  saveAsFastaUI();
+}

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

@@ -1,9 +1,9 @@
-import {after, before, category, test, expect, expectObject, delay} from '@datagrok-libraries/utils/src/test';
-
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-import {PositionInfo, PositionMonomerInfo, WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import * as bio from '@datagrok-libraries/bio';
+
+import {after, before, category, test, expect, expectObject, delay} from '@datagrok-libraries/utils/src/test';
 import {Column} from 'datagrok-api/dg';
 import {ALPHABET, NOTATION, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
@@ -41,27 +41,27 @@ ATC-G-TTGC--
     seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
     seqCol.setTag(UnitsHandler.TAGS.alphabet, ALPHABET.DNA);
 
-    const wlViewer: WebLogo = await df.plot.fromType('WebLogo') as unknown as WebLogo;
+    const wlViewer: bio.WebLogo = (await df.plot.fromType('WebLogo')) as bio.WebLogo;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    const positions: PositionInfo[] = wlViewer['positions'];
-
-    const resAllDf1: PositionInfo[] = [
-      new PositionInfo('1', {'A': new PositionMonomerInfo(2), '-': new PositionMonomerInfo(3)}),
-      new PositionInfo('2', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('3', {'C': new PositionMonomerInfo(5)}),
-      new PositionInfo('4', {'-': new PositionMonomerInfo(5)}),
-      new PositionInfo('5', {'G': new PositionMonomerInfo(5)}),
-      new PositionInfo('6', {'-': new PositionMonomerInfo(3), 'C': new PositionMonomerInfo(2)}),
-      new PositionInfo('7', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('8', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('9', {'G': new PositionMonomerInfo(5)}),
-      new PositionInfo('10', {'C': new PositionMonomerInfo(5)}),
-      new PositionInfo('11', {'-': new PositionMonomerInfo(5)}),
-      new PositionInfo('12', {'-': new PositionMonomerInfo(5)})
+    const positions: bio.PositionInfo[] = wlViewer['positions'];
+
+    const resAllDf1: bio.PositionInfo[] = [
+      new bio.PositionInfo('1', {'A': new bio.PositionMonomerInfo(2), '-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('2', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('3', {'C': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('4', {'-': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('5', {'G': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('6', {'-': new bio.PositionMonomerInfo(3), 'C': new bio.PositionMonomerInfo(2)}),
+      new bio.PositionInfo('7', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('8', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('9', {'G': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('10', {'C': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('11', {'-': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('12', {'-': new bio.PositionMonomerInfo(5)}),
     ];
 
     expect(positions.length, resAllDf1.length);
@@ -94,25 +94,25 @@ ATC-G-TTGC--
       return i > 2;
     });
     df.filter.fireChanged();
-    const wlViewer: WebLogo = await df.plot.fromType('WebLogo', {'shrinkEmptyTail': true}) as unknown as WebLogo;
-
+    const wlViewer: bio.WebLogo = (await df.plot.fromType('WebLogo',
+      {'shrinkEmptyTail': true})) as bio.WebLogo;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    const positions: PositionInfo[] = wlViewer['positions'];
-
-    const resAllDf1: PositionInfo[] = [
-      new PositionInfo('1', {'-': new PositionMonomerInfo(3)}),
-      new PositionInfo('2', {'T': new PositionMonomerInfo(3)}),
-      new PositionInfo('3', {'-': new PositionMonomerInfo(3)}),
-      new PositionInfo('4', {'-': new PositionMonomerInfo(3)}),
-      new PositionInfo('5', {'C': new PositionMonomerInfo(3)}),
-      new PositionInfo('6', {'-': new PositionMonomerInfo(2), 'C': new PositionMonomerInfo(1)}),
-      new PositionInfo('7', {'G': new PositionMonomerInfo(3)}),
-      new PositionInfo('8', {'T': new PositionMonomerInfo(3)}),
-      new PositionInfo('9', {'-': new PositionMonomerInfo(3)}),
+    const positions: bio.PositionInfo[] = wlViewer['positions'];
+
+    const resAllDf1: bio.PositionInfo[] = [
+      new bio.PositionInfo('1', {'-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('2', {'T': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('3', {'-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('4', {'-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('5', {'C': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('6', {'-': new bio.PositionMonomerInfo(2), 'C': new bio.PositionMonomerInfo(1)}),
+      new bio.PositionInfo('7', {'G': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('8', {'T': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('9', {'-': new bio.PositionMonomerInfo(3)}),
     ];
 
     expect(positions.length, resAllDf1.length);
@@ -134,24 +134,25 @@ ATC-G-TTGC--
     seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
     seqCol.setTag(UnitsHandler.TAGS.alphabet, ALPHABET.DNA);
 
-    const wlViewer: WebLogo = await df.plot.fromType('WebLogo', {'skipEmptyPositions': true}) as unknown as WebLogo;
+    const wlViewer: bio.WebLogo = (await df.plot.fromType('WebLogo',
+      {'skipEmptyPositions': true})) as bio.WebLogo;
     tv.dockManager.dock(wlViewer.root, DG.DOCK_TYPE.DOWN);
 
     tvList.push(tv);
     dfList.push(df);
 
-    const positions: PositionInfo[] = wlViewer['positions'];
-
-    const resAllDf1: PositionInfo[] = [
-      new PositionInfo('1', {'A': new PositionMonomerInfo(2), '-': new PositionMonomerInfo(3)}),
-      new PositionInfo('2', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('3', {'C': new PositionMonomerInfo(5)}),
-      new PositionInfo('5', {'G': new PositionMonomerInfo(5)}),
-      new PositionInfo('6', {'-': new PositionMonomerInfo(3), 'C': new PositionMonomerInfo(2)}),
-      new PositionInfo('7', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('8', {'T': new PositionMonomerInfo(5)}),
-      new PositionInfo('9', {'G': new PositionMonomerInfo(5)}),
-      new PositionInfo('10', {'C': new PositionMonomerInfo(5)})
+    const positions: bio.PositionInfo[] = wlViewer['positions'];
+
+    const resAllDf1: bio.PositionInfo[] = [
+      new bio.PositionInfo('1', {'A': new bio.PositionMonomerInfo(2), '-': new bio.PositionMonomerInfo(3)}),
+      new bio.PositionInfo('2', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('3', {'C': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('5', {'G': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('6', {'-': new bio.PositionMonomerInfo(3), 'C': new bio.PositionMonomerInfo(2)}),
+      new bio.PositionInfo('7', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('8', {'T': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('9', {'G': new bio.PositionMonomerInfo(5)}),
+      new bio.PositionInfo('10', {'C': new bio.PositionMonomerInfo(5)})
     ];
 
     expect(positions.length, resAllDf1.length);

package/src/tests/WebLogo-test.ts

@@ -1,9 +1,9 @@
-import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
-
 import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
+import * as bio from '@datagrok-libraries/bio';
 
+import {after, before, category, test, expect, expectObject} from '@datagrok-libraries/utils/src/test';
 import {Nucleotides, NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
 import {Aminoacids, AminoacidsPalettes} from '@datagrok-libraries/bio/src/aminoacids';
 import {WebLogo} from '@datagrok-libraries/bio/src/viewers/web-logo';
@@ -63,19 +63,19 @@ XZJ{}2
 
 category('WebLogo.monomerToShort', () => {
   test('longMonomerSingle', async () => {
-    await expect(WebLogo.monomerToShort('S', 5), 'S');
+    await expect(bio.monomerToShort('S', 5), 'S');
   });
   test('longMonomerShort', async () => {
-    await expect(WebLogo.monomerToShort('Short', 5), 'Short');
+    await expect(bio.monomerToShort('Short', 5), 'Short');
   });
   test('longMonomerLong56', async () => {
-    await expect(WebLogo.monomerToShort('Long56', 5), 'Long5…');
+    await expect(bio.monomerToShort('Long56', 5), 'Long5…');
   });
   test('longMonomerComplexFirstPartShort', async () => {
-    await expect(WebLogo.monomerToShort('Long-long', 5), 'Long…');
+    await expect(bio.monomerToShort('Long-long', 5), 'Long…');
   });
   test('longMonomerComplexFirstPartLong56', async () => {
-    await expect(WebLogo.monomerToShort('Long56-long', 5), 'Long5…');
+    await expect(bio.monomerToShort('Long56-long', 5), 'Long5…');
   });
 });
 
@@ -83,7 +83,7 @@ category('WebLogo.monomerToShort', () => {
 export async function _testGetStats(csvDfN1: string) {
   const dfN1: DG.DataFrame = DG.DataFrame.fromCsv(csvDfN1);
   const seqCol: DG.Column = dfN1.col('seq')!;
-  const stats = WebLogo.getStats(seqCol, 5, WebLogo.splitterAsFasta);
+  const stats = bio.getStats(seqCol, 5, bio.splitterAsFasta);
 
   expectObject(stats.freq, {
     'A': 4,
@@ -103,7 +103,7 @@ export async function _testGetAlphabetSimilarity() {
     '-': 1000
   };
   const alphabet: Set<string> = new Set(Object.keys(Nucleotides.Names));
-  const res = WebLogo.getAlphabetSimilarity(freq, alphabet);
+  const res = bio.getAlphabetSimilarity(freq, alphabet);
 
   expect(res > 0.6, true);
 }
@@ -111,7 +111,7 @@ export async function _testGetAlphabetSimilarity() {
 export async function _testPickupPaletteN1(csvDfN1: string) {
   const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDfN1);
   const col: DG.Column = df.col('seq')!;
-  const cp = WebLogo.pickUpPalette(col);
+  const cp = bio.pickUpPalette(col);
 
   expect(cp instanceof NucleotidesPalettes, true);
 }
@@ -119,7 +119,7 @@ export async function _testPickupPaletteN1(csvDfN1: string) {
 export async function _testPickupPaletteN1e(csvDfN1e: string) {
   const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDfN1e);
   const col: DG.Column = df.col('seq')!;
-  const cp = WebLogo.pickUpPalette(col);
+  const cp = bio.pickUpPalette(col);
 
   expect(cp instanceof NucleotidesPalettes, true);
 }
@@ -127,7 +127,7 @@ export async function _testPickupPaletteN1e(csvDfN1e: string) {
 export async function _testPickupPaletteAA1(csvDfAA1: string) {
   const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDfAA1);
   const col: DG.Column = df.col('seq')!;
-  const cp = WebLogo.pickUpPalette(col);
+  const cp = bio.pickUpPalette(col);
 
   expect(cp instanceof AminoacidsPalettes, true);
 }
@@ -135,14 +135,14 @@ export async function _testPickupPaletteAA1(csvDfAA1: string) {
 export async function _testPickupPaletteX(csvDfX: string) {
   const df: DG.DataFrame = DG.DataFrame.fromCsv(csvDfX);
   const col: DG.Column = df.col('seq')!;
-  const cp = WebLogo.pickUpPalette(col);
+  const cp = bio.pickUpPalette(col);
 
   expect(cp instanceof UnknownSeqPalette, true);
 }
 
 export async function _testPickupPaletteAA2(dfAA2: DG.DataFrame) {
   const seqCol: DG.Column = dfAA2.col('seq')!;
-  const cp = WebLogo.pickUpPalette(seqCol);
+  const cp = bio.pickUpPalette(seqCol);
 
   expect(cp instanceof AminoacidsPalettes, true);
 }

package/src/tests/convert-test.ts

@@ -1,7 +1,8 @@
-import {category, expectArray, test} from '@datagrok-libraries/utils/src/test';
-
-import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
+import * as ui from 'datagrok-api/ui';
+import * as grok from 'datagrok-api/grok';
+
+import {category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
 
 import {ConverterFunc} from './types';
 import {NotationConverter} from '@datagrok-libraries/bio/src/utils/notation-converter';
@@ -139,6 +140,7 @@ RNA1{P.R(U)P.R(U)P.R(C)P.R(A)P.R(A)P.R(C)P.P.P}$$$
     return function(srcCol: DG.Column): DG.Column {
       const converter = new NotationConverter(srcCol);
       const resCol = converter.convert(tgtNotation, tgtSeparator);
+      expect(resCol.getTag('units'), tgtNotation);
       return resCol;
     };
   };

package/src/tests/fasta-export-tests.ts

@@ -0,0 +1,110 @@
+import * as DG from 'datagrok-api/dg';
+import * as ui from 'datagrok-api/ui';
+import * as grok from 'datagrok-api/grok';
+import * as bio from '@datagrok-libraries/bio';
+
+import {category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
+import {saveAsFastaDo, wrapSequence} from '../utils/save-as-fasta';
+
+type SaveAsFastaTestArgs = { srcCsv: string, idCols: string [], seqCol: string, lineWidth: number, tgtFasta: string };
+
+category('fastaExport', () => {
+
+  enum WrapDataTest {
+    single = 'single',
+    multi = 'multi'
+  }
+
+  const wrapData: { [key: string]: { src: string, tgt: string[] } } = {
+    [WrapDataTest.single]: {
+      src: 'MDYKETLLMPKTDFPMRGGLP',
+      tgt: ['MDYKETLLMP', 'KTDFPMRGGL', 'P'],
+    },
+    [WrapDataTest.multi]: {
+      src: 'M[MeI]YKETLL[MeF]PKTDFPMRGGL[MeA]',
+      tgt: ['M[MeI]YKETLL[MeF]P', 'KTDFPMRGGL', '[MeA]'],
+    },
+  };
+
+  enum SaveAsFastaTests {
+    test1 = 'test1',
+    test2 = 'test2'
+  }
+
+  const saveAsFastaData: {
+    [key: string]: SaveAsFastaTestArgs
+  } = {
+    [SaveAsFastaTests.test1]: {
+      srcCsv: `id,seq
+1,MDYKETLLMP
+2,KTDFPMRGGL
+3,P`,
+      idCols: ['id'],
+      seqCol: 'seq',
+      lineWidth: 10,
+      tgtFasta: `>1
+MDYKETLLMP
+>2
+KTDFPMRGGL
+>3
+P
+`
+    },
+    [SaveAsFastaTests.test2]: {
+      srcCsv: `id,id2,seq
+1,seqA,M[MeI]YKETLL[MeF]P
+2,seqB,KTDFPMRGGL
+3,seqC,[MeA]
+`,
+      idCols: ['id2', 'id'],
+      seqCol: 'seq',
+      lineWidth: 5,
+      tgtFasta: `>seqA|1
+M[MeI]YKE
+TLL[MeF]P
+>seqB|2
+KTDFP
+MRGGL
+>seqC|3
+[MeA]
+`
+    }
+  };
+
+  test('wrapSequenceSingle', async () => {
+    _testWrapSequence(WrapDataTest.single, 10);
+  });
+
+  test('wrapSequenceMulti', async () => {
+    _testWrapSequence(WrapDataTest.multi, 10);
+  });
+
+  test('saveAsFastaTest1', async () => {
+    _testSaveAsFasta(saveAsFastaData[SaveAsFastaTests.test1]);
+  });
+
+  test('saveAsFastaTest2', async () => {
+    _testSaveAsFasta(saveAsFastaData[SaveAsFastaTests.test2]);
+  });
+
+  function _testWrapSequence(testKey: string, lineWidth: number = 10) {
+    const splitter = bio.splitterAsFasta;
+
+    const srcSeq: string = wrapData[testKey].src;
+    const wrapRes: string[] = wrapSequence(srcSeq, splitter, lineWidth);
+    const wrapTgt: string[] = wrapData[testKey].tgt;
+
+    expectArray(wrapRes, wrapTgt);
+  }
+
+  async function _testSaveAsFasta(args: SaveAsFastaTestArgs) {
+    const df: DG.DataFrame = DG.DataFrame.fromCsv(args.srcCsv);
+
+    const seqCol: DG.Column = df.getCol(args.seqCol);
+    const idCols: DG.Column[] = args.idCols.map((colName) => df.getCol(colName));
+
+    const fastaRes: string = saveAsFastaDo(idCols, seqCol, args.lineWidth);
+    expect(fastaRes, args.tgtFasta);
+  }
+});
+