@datagrok/bio 2.11.8 → 2.11.11

package/files/tests/to-atomic-level-pt-fasta-2.mol

@@ -0,0 +1,45 @@
+
+Datagrok macromolecule handler
+
+  0  0  0  0  0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 17 16 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 0.7144 -1.2375  0.000000 0
+M  V30 2 C 0.7144 -0.4125  0.000000 0
+M  V30 3 N 0 0  0.000000 0
+M  V30 4 C 1.4289 0  0.000000 0
+M  V30 5 O 2.1434 -0.4126  0.000000 0
+M  V30 6 N 4.2867 4.9501  0.000000 0
+M  V30 7 C 3.5722 4.5376  0.000000 0
+M  V30 8 N 2.8578 4.95  0.000000 0
+M  V30 9 N 3.5723 3.7126  0.000000 0
+M  V30 10 C 2.8578 3.3001  0.000000 0
+M  V30 11 C 2.8578 2.475  0.000000 0
+M  V30 12 C 2.1433 2.0626  0.000000 0
+M  V30 13 C 2.1433 1.2375  0.000000 0
+M  V30 14 N 1.4289 0.825  0.000000 0
+M  V30 15 C 2.8578 0.8251  0.000000 0
+M  V30 16 O 3.5723 1.2376  0.000000 0
+M  V30 17 O 2.8578 0 0.000000 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 2 1 CFG=3
+M  V30 2 1 2 3
+M  V30 3 1 2 4
+M  V30 4 2 4 5
+M  V30 5 1 4 14
+M  V30 6 1 6 7
+M  V30 7 2 7 8 CFG=3
+M  V30 8 1 7 9
+M  V30 9 1 9 10
+M  V30 10 1 10 11
+M  V30 11 1 11 12
+M  V30 12 1 13 12 CFG=1
+M  V30 13 1 13 14
+M  V30 14 1 13 15
+M  V30 15 2 15 16
+M  V30 16 1 15 17
+M  V30 END BOND
+M  V30 END CTAB
+M  END

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.8",
+  "version": "2.11.11",
   "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",
@@ -34,7 +34,7 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.39.5",
+    "@datagrok-libraries/bio": "^5.39.6",
     "@datagrok-libraries/chem-meta": "^1.0.1",
     "@datagrok-libraries/ml": "^6.3.55",
     "@datagrok-libraries/tutorials": "^1.3.6",
@@ -64,9 +64,9 @@
     "webpack": "^5.76.3",
     "webpack-bundle-analyzer": "latest",
     "webpack-cli": "^4.9.1",
-    "@datagrok/chem": "1.7.2",
-    "@datagrok/helm": "2.1.17",
-    "@datagrok/dendrogram": "^1.2.20"
+    "@datagrok/chem": "^1.8.4",
+    "@datagrok/helm": "^2.1.21",
+    "@datagrok/dendrogram": "^1.2.21"
   },
   "scripts": {
     "link-api": "npm link datagrok-api",

package/src/package.ts

@@ -409,7 +409,7 @@ export async function activityCliffs(df: DG.DataFrame, macroMolecule: DG.Column<
     'alphabet': macroMolecule.getTag(bioTAGS.alphabet),
   };
   let cliffsEncodeFunction: (seqCol: DG.Column, similarityMetric: MmDistanceFunctionsNames | BitArrayMetrics) => any =
-     getEncodedSeqSpaceCol;
+    getEncodedSeqSpaceCol;
   const ncUH = UnitsHandler.getOrCreate(macroMolecule);
   const columnDistanceMetric: MmDistanceFunctionsNames | BitArrayMetrics = similarityMetric;
   const seqCol = macroMolecule;
@@ -671,8 +671,11 @@ export async function sequenceSpaceTopMenu(
 //input: bool nonlinear=false { description: Slower mode for cycling/branching HELM structures }
 export async function toAtomicLevel(df: DG.DataFrame, macroMolecule: DG.Column, nonlinear: boolean): Promise<void> {
   const pi = DG.TaskBarProgressIndicator.create('Converting to atomic level ...');
-  sequenceToMolfile(df, macroMolecule, nonlinear);
-  pi.close();
+  try {
+    await sequenceToMolfile(df, macroMolecule, nonlinear);
+  } finally {
+    pi.close();
+  }
 }
 
 //top-menu: Bio | Analyze | MSA...

package/src/substructure-search/substructure-search.ts

@@ -148,11 +148,14 @@ export async function helmSubstructureSearch(substructure: string, col: DG.Colum
 
 export async function invalidateMols(col: DG.Column<string>, pattern: boolean) {
   const progressBar = DG.TaskBarProgressIndicator.create(`Invalidating molfiles for ${col.name}`);
-  await delay(10);
-  const monomersDict = new Map();
-  const monomericMolsCol = await getMonomericMols(col, pattern, monomersDict);
-  col.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS] = monomericMolsCol;
-  col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT] = monomersDict;
-  col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION] = col.version;
-  progressBar.close();
+  try {
+    await delay(10);
+    const monomersDict = new Map();
+    const monomericMolsCol = await getMonomericMols(col, pattern, monomersDict);
+    col.temp[MONOMERIC_COL_TAGS.MONOMERIC_MOLS] = monomericMolsCol;
+    col.temp[MONOMERIC_COL_TAGS.MONOMERS_DICT] = monomersDict;
+    col.temp[MONOMERIC_COL_TAGS.LAST_INVALIDATED_VERSION] = col.version;
+  } finally {
+    progressBar.close();
+  }
 }

package/src/tests/activity-cliffs-tests.ts

@@ -10,25 +10,28 @@ import {DimReductionMethods} from '@datagrok-libraries/ml/src/reduce-dimensional
 import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {BitArrayMetricsNames} from '@datagrok-libraries/ml/src/typed-metrics';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {LIB_DEFAULT, LIB_STORAGE_NAME} from '../utils/monomer-lib';
+import {
+  getUserLibSettings, LibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 import {_package} from '../package-test';
 
+
 category('activityCliffs', async () => {
   let viewList: DG.ViewBase[] = [];
   let dfList: DG.DataFrame[] = [];
 
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
-  let userLibrariesSettings: {};
+  let userLibSettings: LibSettings;
 
 
   before(async () => {
     monomerLibHelper = await getMonomerLibHelper();
-    userLibrariesSettings = await grok.dapi.userDataStorage.get(LIB_STORAGE_NAME, true);
+    userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await grok.dapi.userDataStorage.post(LIB_STORAGE_NAME, LIB_DEFAULT, true);
+    await setUserLibSettingsForTests();
     await monomerLibHelper.loadLibraries(true); // load default libraries
 
     viewList = [];
@@ -40,7 +43,7 @@ category('activityCliffs', async () => {
     // for (const view of viewList) view.close();
 
     // UserDataStorage.put() replaces existing data
-    await grok.dapi.userDataStorage.put(LIB_STORAGE_NAME, userLibrariesSettings, true);
+    await setUserLibSettings(userLibSettings);
     await monomerLibHelper.loadLibraries(true); // load user settings libraries
   });
 

package/src/tests/monomer-libraries-tests.ts

@@ -5,7 +5,10 @@ import * as ui from 'datagrok-api/ui';
 import {test, after, before, category, expect} from '@datagrok-libraries/utils/src/test';
 
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {getLibFileNameList, getUserLibSettings, LIB_STORAGE_NAME, setUserLibSetting} from '../utils/monomer-lib';
+import {
+  getUserLibSettings, LibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {getLibFileNameList} from '../utils/monomer-lib';
 
 
 category('monomerLibraries', () => {
@@ -15,16 +18,16 @@ category('monomerLibraries', () => {
 
   before(async () => {
     monomerLibHelper = await getMonomerLibHelper();
-    userLibrariesSettings = await grok.dapi.userDataStorage.get(LIB_STORAGE_NAME, true);
+    userLibrariesSettings = getUserLibSettings();
   });
 
   after(async () => {
-    await grok.dapi.userDataStorage.put(LIB_STORAGE_NAME, userLibrariesSettings, true);
+    await setUserLibSettings(userLibrariesSettings);
   });
 
   test('default', async () => {
     // Clear settings to test default
-    await grok.dapi.userDataStorage.put(LIB_STORAGE_NAME, {}, true);
+    await setUserLibSettings({exclude: [], explicit: []});
     await monomerLibHelper.loadLibraries(true); // test defaultLib
 
     // Currently default monomer lib set is of all files at LIB_PATH (at least HELMCoreLibrary.json)
@@ -32,12 +35,25 @@ category('monomerLibraries', () => {
     expect(currentMonomerLib.getPolymerTypes().length > 0, true);
   });
 
+  test('forTests', async () => {
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.loadLibraries(true); // test defaultLib
+
+    // Currently default monomer lib set is of all files at LIB_PATH (at least HELMCoreLibrary.json)
+    const currentMonomerLib = monomerLibHelper.getBioLib();
+    // HELMCoreLibrary.json checks
+    expect(currentMonomerLib.getPolymerTypes().length, 2);
+    expect(currentMonomerLib.getMonomerSymbolsByType('PEPTIDE').length, 322);
+    expect(currentMonomerLib.getMonomerSymbolsByType('RNA').length, 383);
+  });
+
   test('empty', async () => {
     // exclude all monomer libraries for empty set
     const libSettings = await getUserLibSettings();
     const libFnList = await getLibFileNameList();
     libSettings.exclude = libFnList;
-    await setUserLibSetting(libSettings);
+    libSettings.explicit = [];
+    await setUserLibSettings(libSettings);
 
     await monomerLibHelper.loadLibraries(true);
     const currentMonomerLib = monomerLibHelper.getBioLib();

package/src/tests/renderers-test.ts

@@ -49,14 +49,6 @@ category('renderers', () => {
     await _selectRendererBySemType();
   });
 
-  test('setRendererManuallyBeforeAddColumn', async () => {
-    await _setRendererManuallyBeforeAddColumn();
-  }, {skipReason: 'GROK-11212'});
-
-  test('setRendererManuallyAfterAddColumn', async () => {
-    await _setRendererManuallyAfterAddColumn();
-  }, {skipReason: 'GROK-11212'});
-
   async function _rendererMacromoleculeFasta() {
     const csv: string = await grok.dapi.files.readAsText('System:AppData/Bio/samples/FASTA.csv');
     const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
@@ -207,58 +199,4 @@ category('renderers', () => {
         `view renderer has set to '${renderer}' instead of correct 'MacromoleculeDifference'.`);
     }
   }
-
-  /** GROK-11212 Do not overwrite / recalculate 'cell.renderer' tag that has been set programmatically
-   * https://reddata.atlassian.net/browse/GROK-11212 */
-  async function _setRendererManuallyBeforeAddColumn() {
-    const seqDiffCol: DG.Column = DG.Column.fromStrings('SequencesDiff',
-      ['meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca#D-Tyr_Et/Tyr_ab-dehydroMe/meN/E/N/dV']);
-    seqDiffCol.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
-    seqDiffCol.setTag(bioTAGS.separator, '/');
-    seqDiffCol.setTag(bioTAGS.aligned, 'SEQ');
-    seqDiffCol.setTag(bioTAGS.alphabet, 'UN');
-    seqDiffCol.setTag(bioTAGS.alphabetIsMultichar, 'true');
-    seqDiffCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    const tgtCellRenderer = 'MacromoleculeDifference';
-    seqDiffCol.setTag(DG.TAGS.CELL_RENDERER, tgtCellRenderer);
-    const df = DG.DataFrame.fromColumns([seqDiffCol]);
-    await grok.data.detectSemanticTypes(df);
-    const tv = grok.shell.addTableView(df);
-    await awaitCheck(() => document.querySelector('canvas') !== null, 'cannot load table', 3000);
-
-    const resCellRenderer = seqDiffCol.getTag(DG.TAGS.CELL_RENDERER);
-    if (resCellRenderer !== tgtCellRenderer) { // this is value of MacromoleculeDifferenceCR.cellType
-      throw new Error(`Tag 'cell.renderer' has been manually set to '${tgtCellRenderer}' for column ` +
-        `but after df was added as table, tag 'cell.renderer' has reset to '${resCellRenderer}' ` +
-        `instead of manual '${tgtCellRenderer}'.`);
-    }
-  }
-
-  /** GROK-11212 Do not overwrite / recalculate 'cell.renderer' tag that has been set programmatically
-   * https://reddata.atlassian.net/browse/GROK-11212 */
-  async function _setRendererManuallyAfterAddColumn() {
-    const seqDiffCol: DG.Column = DG.Column.fromStrings('SequencesDiff',
-      ['meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca#D-Tyr_Et/Tyr_ab-dehydroMe/meN/E/N/dV']);
-    seqDiffCol.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
-    seqDiffCol.setTag(bioTAGS.separator, '/');
-    seqDiffCol.setTag(bioTAGS.aligned, 'SEQ');
-    seqDiffCol.setTag(bioTAGS.alphabet, 'UN');
-    seqDiffCol.setTag(bioTAGS.alphabetIsMultichar, 'true');
-    seqDiffCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    const tgtCellRenderer = 'MacromoleculeDifference';
-    const df = DG.DataFrame.fromColumns([seqDiffCol]);
-    await grok.data.detectSemanticTypes(df);
-    const tv = grok.shell.addTableView(df);
-    await awaitCheck(() => $(tv.root).find('.d4-grid canvas').length > 0, 'View grid canvas not found', 200);
-
-    seqDiffCol.setTag(DG.TAGS.CELL_RENDERER, tgtCellRenderer);
-    await awaitCheck(() => $(tv.root).find('.d4-grid canvas').length > 0, 'View grid canvas not found', 200);
-
-    const resCellRenderer = seqDiffCol.getTag(DG.TAGS.CELL_RENDERER);
-    if (resCellRenderer !== tgtCellRenderer) { // this is value of MacromoleculeDifferenceCR.cellType
-      throw new Error(`Tag 'cell.renderer' has been manually set to '${tgtCellRenderer}' for column ` +
-        `but after df was added as table, tag 'cell.renderer' has reset to '${resCellRenderer}' ` +
-        `instead of manual '${tgtCellRenderer}'.`);
-    }
-  }
 });

package/src/tests/scoring.ts

@@ -1,27 +1,48 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {category, test, expectFloat, before} from '@datagrok-libraries/utils/src/test';
+import {category, test, expectFloat, before, after} from '@datagrok-libraries/utils/src/test';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+
 import {sequenceIdentityScoring, sequenceSimilarityScoring} from '../package';
-import {getMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {
+  LibSettings, getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
 
 category('Scoring', () => {
   const sequence = 'sequence';
   const expectedSimilarity = 'expected_similarity';
   const expectedIdentity = 'expected_identity';
+  /* eslint-disable max-len */
   const table = DG.DataFrame.fromCsv(`${sequence},${expectedSimilarity},${expectedIdentity}
-  PEPTIDE1{Aca.Orn.gGlu.Pqa.D-His_1Bn.dH.hHis.4Abz.D-Tic.D-Dap.Y.Iva.meS.F.P.F.D-1Nal}$$$$,1.0,1.0
-  PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC}$$$$,0.68,0.53
-  PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal]}$$$$V2.0,0.34,0.0
-  `);
+PEPTIDE1{Aca.Orn.gGlu.Pqa.D-His_1Bn.dH.hHis.4Abz.D-Tic.D-Dap.Y.Iva.meS.F.P.F.D-1Nal}$$$$,1.0,1.0
+PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC}$$$$,0.68,0.53
+PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal]}$$$$V2.0,0.34,0.0`
+  );
+  /* eslint-enable max-len */
   const seqCol: DG.Column<string> = table.getCol(sequence);
   seqCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
   seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
   const reference = seqCol.get(0)!;
 
+  let monomerLibHelper: IMonomerLibHelper;
+  /** Backup actual user's monomer libraries settings */
+  let userLibSettings: LibSettings;
+
   before(async () => {
-    const monomerLibHelper = await getMonomerLibHelper();
-    await monomerLibHelper.loadLibraries(true);
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.loadLibraries(true); // load default libraries
+  });
+
+  after(async () => {
+    // UserDataStorage.put() replaces existing data
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true); // load user settings libraries
   });
 
   test('Identity', async () => {

package/src/tests/substructure-filters-tests.ts

@@ -1,30 +1,35 @@
-import {after, before, category, test, expect, delay} from '@datagrok-libraries/utils/src/test';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 
-import {readDataframe} from './utils';
-import {BioSubstructureFilter, HelmFilter, SeparatorFilter} from '../widgets/bio-substructure-filter';
+import {after, before, category, test, expect, delay, testEvent} from '@datagrok-libraries/utils/src/test';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {LIB_DEFAULT, LIB_STORAGE_NAME} from '../utils/monomer-lib';
+import {
+  LibSettings, getUserLibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+
+import {awaitGrid, readDataframe} from './utils';
+import {BioSubstructureFilter, HelmFilter, SeparatorFilter} from '../widgets/bio-substructure-filter';
+
+import {_package} from '../package-test';
 
 
 category('substructureFilters', async () => {
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
-  let userLibrariesSettings: {};
+  let userLibSettings: LibSettings;
 
   before(async () => {
     monomerLibHelper = await getMonomerLibHelper();
-    userLibrariesSettings = await grok.dapi.userDataStorage.get(LIB_STORAGE_NAME, true);
+    userLibSettings = await getUserLibSettings();
 
     // Test 'helm' requires default monomer library loaded
-    await grok.dapi.userDataStorage.post(LIB_STORAGE_NAME, LIB_DEFAULT, true);
+    await setUserLibSettingsForTests();
     await monomerLibHelper.loadLibraries(true); // load default libraries
   });
 
   after(async () => {
     // UserDataStorage.put() replaces existing data
-    await grok.dapi.userDataStorage.put(LIB_STORAGE_NAME, userLibrariesSettings, true);
+    await setUserLibSettings(userLibSettings);
     await monomerLibHelper.loadLibraries(true); // load user settings libraries
   });
 
@@ -66,30 +71,30 @@ category('substructureFilters', async () => {
     const helmTableView = grok.shell.addTableView(helm);
     const filter = new BioSubstructureFilter();
     await grok.data.detectSemanticTypes(helm);
+
+    _package.logger.debug('Bio/substructureFilters/helm, filter attaching.');
     filter.attach(helm);
+    _package.logger.debug('Bio/substructureFilters/helm, filter attached.');
 
-    const helmFilterChanged = new Promise((resolve, reject) => {
-      helm.onFilterChanged.subscribe(async (_: any) => {
-        try {
-          resolve(true);
-        } catch (error) {
-          reject(error);
-        }
-      });
-    });
+    _package.logger.debug('Bio/substructureFilters/helm, filter 1 changing.');
     (filter.bioFilter! as HelmFilter).helmSubstructure = 'PEPTIDE1{C}$$$$V2.0';
-    filter.bioFilter!.onChanged.next();
-    await helmFilterChanged;
 
-    //await delay(3000);
+    _package.logger.debug('Bio/substructureFilters/helm, filter 1 change awaiting.');
+    await testEvent(helm.onRowsFiltered, () => {},
+      () => { filter.bioFilter!.onChanged.next(); }, 20000);
+    _package.logger.debug('Bio/substructureFilters/helm, filter 1 changed.');
     expect(filter.dataFrame!.filter.trueCount, 2);
     expect(filter.dataFrame!.filter.get(0), true);
     expect(filter.dataFrame!.filter.get(3), true);
+
+    _package.logger.debug('Bio/substructureFilters/helm, filter 2 changing.');
     (filter.bioFilter! as HelmFilter).helmSubstructure = 'PEPTIDE1{A.C}$$$$V2.0';
-    filter.bioFilter!.onChanged.next();
-    await delay(100);
+    _package.logger.debug('Bio/substructureFilters/helm, filter 2 change awaiting.');
+    await testEvent(helm.onRowsFiltered, () => {},
+      () => { filter.bioFilter!.onChanged.next(); }, 20000);
+    await awaitGrid(helmTableView.grid);
+    _package.logger.debug('Bio/substructureFilters/helm, filter 2 changed.');
     expect(filter.dataFrame!.filter.trueCount, 1);
     expect(filter.dataFrame!.filter.get(3), true);
-    helmTableView.close();
-  }, {skipReason: 'GROK-12779'});
+  }, {timeout: 30000});
 });

package/src/tests/to-atomic-level-tests.ts

@@ -3,13 +3,20 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {before, after, category, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import wu from 'wu';
 
-import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {toAtomicLevel} from '../package';
+import {before, after, category, test, expectArray, expect} from '@datagrok-libraries/utils/src/test';
 import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomic-level';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types/index';
-import {LIB_STORAGE_NAME, LIB_DEFAULT, getUserLibSettings} from '../utils/monomer-lib';
+import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {
+  getUserLibSettings, LibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+
+import {toAtomicLevel} from '../package';
+import {_package} from '../package-test';
 
 const appPath = 'System:AppData/Bio';
 const fileSource = new DG.FileSource(appPath);
@@ -27,9 +34,9 @@ const inputPath: { [k: string]: string } = {
 };
 
 const outputPath: { [k: string]: string } = {
-  PT: 'tests/to-atomic-level-peptides-output.csv',
-  DNA: 'tests/to-atomic-level-dna-output.csv',
-  MSA: 'tests/to-atomic-level-msa-output.csv',
+  PT: 'tests/to-atomic-level-peptides-fasta-output.csv',
+  DNA: 'tests/to-atomic-level-dna-fasta-output.csv',
+  MSA: 'tests/to-atomic-level-msa-separator-output.csv',
 };
 
 const inputColName = 'sequence';
@@ -41,24 +48,24 @@ category('toAtomicLevel', async () => {
 
   let monomerLibHelper: IMonomerLibHelper;
   /** Backup actual user's monomer libraries settings */
-  let userLibrariesSettings: any = null;
+  let userLibSettings: LibSettings;
 
   before(async () => {
     monomerLibHelper = await getMonomerLibHelper();
-    userLibrariesSettings = {...await grok.dapi.userDataStorage.get(LIB_STORAGE_NAME, true)};
-    const defaultLib = Object.values(LIB_DEFAULT)[0];
-    await monomerLibHelper.selectSpecifiedLibraries([defaultLib]);
-    monomerLibHelper.loadLibraries(true);
+    userLibSettings = await getUserLibSettings();
+    // Clear settings to test default
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.loadLibraries(true);
 
     for (const key in testNames) {
-      sourceDf[key] = await fileSource.readCsv(inputPath[key]);
+      sourceDf[key] = DG.DataFrame.fromCsv((await fileSource.readAsText(inputPath[key])).replace(/\n$/, ''));
       await grok.data.detectSemanticTypes(sourceDf[key]);
-      targetDf[key] = await fileSource.readCsv(outputPath[key]);
+      targetDf[key] = DG.DataFrame.fromCsv((await fileSource.readAsText(outputPath[key])).replace(/\n$/, ''));
     }
   });
 
   after(async () => {
-    await grok.dapi.userDataStorage.put(LIB_STORAGE_NAME, userLibrariesSettings, true);
+    await setUserLibSettings(userLibSettings);
     await monomerLibHelper.loadLibraries(true);
   });
 
@@ -67,15 +74,15 @@ category('toAtomicLevel', async () => {
     await toAtomicLevel(source, inputCol, false);
     const obtainedCol = source.getCol(outputColName);
     const expectedCol = target.getCol(outputColName);
-    const obtainedArray = [...obtainedCol.values()];
-    const expectedArray = [...expectedCol.values()];
+    const obtainedArray: string[] = wu(obtainedCol.values()).map((mol) => polishMolfile(mol)).toArray();
+    const expectedArray: string[] = wu(expectedCol.values()).map((mol) => polishMolfile(mol)).toArray();
     expectArray(obtainedArray, expectedArray);
   }
 
   for (const key in testNames) {
     test(`${testNames[key]}`, async () => {
       await getTestResult(sourceDf[key], targetDf[key]);
-    }, {skipReason: 'GROK-13100'});
+    });
   }
 
   enum csvTests {
@@ -93,38 +100,38 @@ category('toAtomicLevel', async () => {
 
   const csvData: { [key in csvTests]: string } = {
     [csvTests.fastaDna]: `seq
-ACGTC
-CAGTGT
-TTCAAC`,
+ACGTCACGTC
+CAGTGTCAGTGT
+TTCAACTTCAAC`,
     [csvTests.fastaRna]: `seq
-ACGUC
-CAGUGU
-UUCAAC`,
+ACGUCACGUC
+CAGUGUCAGUGU
+UUCAACUUCAAC`,
     [csvTests.fastaPt]: `seq
-FWPHEY
-YNRQWYV
-MKPSEYV`,
+FWPHEYFWPHEY
+YNRQWYVYNRQWYV
+MKPSEYVMKPSEYV`,
     [csvTests.separatorDna]: `seq
-A/C/G/T/C
-C/A/G/T/G/T
-T/T/C/A/A/C`,
+A/C/G/T/C/A/C/G/T/C
+C/A/G/T/G/T/C/A/G/T/G/T
+T/T/C/A/A/C/T/T/C/A/A/C`,
     [csvTests.separatorRna]: `seq
-A*C*G*U*C
-C*A*G*U*G*U
-U*U*C*A*A*C`,
+A*C*G*U*C*A*C*G*U*C
+C*A*G*U*G*U*C*A*G*U*G*U
+U*U*C*A*A*C*U*U*C*A*A*C`,
     [csvTests.separatorPt]: `seq
-F-W-P-H-E-Y
-Y-N-R-Q-W-Y-V
-M-K-P-S-E-Y-V`,
+F-W-P-H-E-Y-F-W-P-H-E-Y
+Y-N-R-Q-W-Y-V-Y-N-R-Q-W-Y-V
+M-K-P-S-E-Y-V-M-K-P-S-E-Y-V`,
     [csvTests.separatorUn]: `seq
-meI-hHis-Aca-N-T-dE-Thr_PO3H2-Aca-D
-meI-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2
-Lys_Boc-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2`,
+meI-hHis-Aca-N-T-dE-Thr_PO3H2-Aca-D-meI-hHis-Aca-N-T-dE-Thr_PO3H2-Aca-D
+meI-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2-meI-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2
+Lys_Boc-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2-Lys_Boc-hHis-Aca-Cys_SEt-T-dK-Thr_PO3H2-Aca-Tyr_PO3H2`,
 
     [csvTests.helm]: `seq
-PEPTIDE1{meI.D-gGlu.Aca.N.T.dE.Thr_PO3H2.Aca.D}$$$
-PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$
-PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$`,
+PEPTIDE1{meI.D-gGlu.Aca.N.T.dE.Thr_PO3H2.Aca.D.Thr_PO3H2.Aca.D}$$$
+PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.Thr_PO3H2.Aca.Tyr_PO3H2}$$$
+PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.Thr_PO3H2.Aca.Tyr_PO3H2}$$$`,
   };
 
   /** Also detects semantic types
@@ -134,7 +141,7 @@ PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$`,
   async function readCsv(key: csvTests): Promise<DG.DataFrame> {
     // Always recreate test data frame from CSV for reproducible detector behavior in tests.
     const csv: string = csvData[key];
-    const df: DG.DataFrame = DG.DataFrame.fromCsv(csv);
+    const df: DG.DataFrame = DG.DataFrame.fromCsv(csv.replace(/\n$/, ''));
     await grok.data.detectSemanticTypes(df);
     return df;
   }
@@ -170,10 +177,35 @@ PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$`,
   test('helm', async () => {
     await _testToAtomicLevel(await readCsv(csvTests.helm), 'seq', monomerLibHelper);
   });
+
+  test('ptFasta2', async () => {
+    const srcCsv: string = `seq\nAR`;
+    const tgtMol: string = await _package.files.readAsText('tests/to-atomic-level-pt-fasta-2.mol');
+
+    const srcDf = DG.DataFrame.fromCsv(srcCsv);
+    const seqCol = srcDf.getCol('seq');
+    seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
+    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+    seqCol.setTag(bioTAGS.alphabet, ALPHABET.PT);
+    const uh = UnitsHandler.getOrCreate(seqCol);
+    const resCol = (await _testToAtomicLevel(srcDf, 'seq', monomerLibHelper))!;
+    expect(polishMolfile(resCol.get(0)), polishMolfile(tgtMol));
+  });
 });
 
-async function _testToAtomicLevel(df: DG.DataFrame, seqColName: string = 'seq', monomerLibHelper: IMonomerLibHelper) {
+async function _testToAtomicLevel(
+  df: DG.DataFrame, seqColName: string = 'seq', monomerLibHelper: IMonomerLibHelper
+): Promise<DG.Column | null> {
   const seqCol: DG.Column<string> = df.getCol(seqColName);
   const monomerLib: IMonomerLib = monomerLibHelper.getBioLib();
-  const _resCol = await _toAtomicLevel(df, seqCol, monomerLib);
+  const res = await _toAtomicLevel(df, seqCol, monomerLib);
+  if (res.warnings.length > 0)
+    _package.logger.warning(`_toAtomicLevel() warnings ${res.warnings.join('\n')}`);
+  return res.col;
+}
+
+function polishMolfile(mol: string): string {
+  return mol.replaceAll('\r\n', '\n')
+    .replace(/\n$/, '')
+    .split('\n').map((l) => l.trimEnd()).join('\n');
 }