@datagrok/bio 2.11.36 → 2.11.37

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.36",
+  "version": "2.11.37",
   "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",

package/src/tests/msa-tests.ts

@@ -81,12 +81,12 @@ MWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHPMWRSWYCKHP
   test('isCorrectHelm', async () => {
     await awaitContainerStart();
     await _testMSAOnColumn(helmFromCsv, helmToCsv, NOTATION.HELM, NOTATION.SEPARATOR, undefined, 'mafft');
-  }, {timeout: 60000});
+  }, {timeout: 60000 /* docker */});
 
   test('isCorrectHelmLong', async () => {
     await awaitContainerStart();
     await _testMSAOnColumn(longHelmFromCsv, longHelmToCsv, NOTATION.HELM, NOTATION.SEPARATOR, undefined, 'mafft');
-  }, {timeout: 60000});
+  }, {timeout: 60000 /* docker */});
 
   test('isCorrectSeparator', async () => {
     await _testMSAOnColumn(

package/src/tests/pepsea-tests.ts

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 
-import {category, expect, test} from '@datagrok-libraries/utils/src/test';
+import {before, category, expect, test} from '@datagrok-libraries/utils/src/test';
 import {runPepsea} from '../utils/pepsea';
 import {awaitContainerStart} from './utils';
 
@@ -12,13 +12,16 @@ category('PepSeA', () => {
   "PEPTIDE1{F.L.R.G.Y.[MeF].Y.W.S.N.D.C}$$$$","F.L.R.G.Y.MeF.Y.W.S.N.D.C"
   "PEPTIDE1{F.V.R.G.Y.[MeF].Y.W.S.N.C}$$$$","F.V.R.G.Y.MeF.Y.W.S..N.C"`;
 
-  test('Basic alignment', async () => {
+  before(async () => {
     await awaitContainerStart();
+  });
+
+  test('Basic alignment', async () => {
     const table = DG.DataFrame.fromCsv(testCsv);
     const alignedCol = await runPepsea(table.getCol('HELM'), 'msa(HELM)');
     expect(alignedCol !== null, true, 'PepSeA container has not started');
     const alignedTestCol = table.getCol('MSA');
     for (let i = 0; i < alignedCol!.length; ++i)
       expect(alignedCol!.get(i) == alignedTestCol.get(i), true);
-  }, {timeout: 60000});
+  }, {timeout: 60000 /* docker */});
 });

package/src/utils/helm-to-molfile.ts

@@ -106,7 +106,9 @@ export class HelmToMolfileConverter {
     return DG.Column.fromStrings(columnName, beautifiedMols.map((mol) => {
       if (mol === null)
         return '';
-      return mol.get_molblock();
+      const molBlock = mol.get_v3Kmolblock();
+      mol!.delete();
+      return molBlock;
     }));
   }