@datagrok/helm 2.1.21 → 2.1.22

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/helm",
   "friendlyName": "Helm",
-  "version": "2.1.21",
+  "version": "2.1.22",
   "author": {
     "name": "Oleksandra Serhiienko",
     "email": "oserhiienko@datagrok.ai"
@@ -16,6 +16,7 @@
   ],
   "dependencies": {
     "@datagrok-libraries/bio": "^5.39.6",
+    "@datagrok-libraries/chem-meta": "^1.2.1",
     "@datagrok-libraries/utils": "^4.0.17",
     "cash-dom": "^8.1.1",
     "datagrok-api": "^1.10.2",

package/src/package-test.ts

@@ -1,10 +1,12 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
+
 import {runTests, tests, TestContext} from '@datagrok-libraries/utils/src/test';
 
 import './tests/helm-tests.ts';
 import './tests/findMonomers-tests';
 import './tests/renderers-tests';
+import './tests/get-molfiles';
 
 export const _package = new DG.Package();
 export {tests};

package/src/tests/findMonomers-tests.ts

@@ -2,33 +2,33 @@ import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 
-import {_package} from '../package-test';
 import {after, before, category, delay, expect, expectObject, test} from '@datagrok-libraries/utils/src/test';
-import {findMonomers, parseHelm} from '../utils';
 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';
 
-const LIB_STORAGE_NAME = 'Libraries';
-export const LIB_DEFAULT: { [fileName: string]: string } = {'HELMCoreLibrary.json': 'HELMCoreLibrary.json'};
+import {findMonomers, parseHelm} from '../utils';
 
 
 /** Tests with default monomer library */
 category('findMonomers', () => {
-
   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);
+    userLibSettings = await getUserLibSettings();
 
     // Tests 'findMonomers' requires default monomer library loaded
-    await grok.dapi.userDataStorage.post(LIB_STORAGE_NAME, LIB_DEFAULT, true);
-    await monomerLibHelper.loadLibraries(true); // load default libraries
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.loadLibraries(true); // load default libraries for tests
   });
 
   after(async () => {
-    await grok.dapi.userDataStorage.put(LIB_STORAGE_NAME, userLibrariesSettings, true);
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true);
   });
 
   const tests: { [testName: string]: { test: string, tgt: Set<string> } } = {

package/src/tests/get-molfiles.ts

@@ -0,0 +1,49 @@
+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, delay, expect, test, expectArray, testEvent} from '@datagrok-libraries/utils/src/test';
+import {
+  getUserLibSettings, LibSettings, setUserLibSettings, setUserLibSettingsForTests
+} from '@datagrok-libraries/bio/src/monomer-works/lib-settings';
+import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
+import {MolfileHandler} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler';
+import {MolfileHandlerBase} from '@datagrok-libraries/chem-meta/src/parsing-utils/molfile-handler-base';
+
+category('getMolfiles', () => {
+  let monomerLibHelper: IMonomerLibHelper;
+  let userLibSettings: LibSettings;
+
+  before(async () => {
+    monomerLibHelper = await getMonomerLibHelper();
+    userLibSettings = await getUserLibSettings();
+    await setUserLibSettingsForTests();
+    await monomerLibHelper.loadLibraries(true);
+  });
+
+  after(async () => {
+    await setUserLibSettings(userLibSettings);
+    await monomerLibHelper.loadLibraries(true);
+  });
+
+  const csv = `Helm, atoms, bonds
+PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV}$$$$,11,10
+PEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV}$$$$,11,10
+PEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$,9,8`;
+
+  test('linear1', async () => {
+    const df = DG.DataFrame.fromCsv(csv);
+    const helmCol = df.getCol('Helm');
+    const view = grok.shell.addTableView(df);
+    const resCol: DG.Column<string> = await grok.functions.call('Helm:getMolfiles', {col: helmCol});
+
+    await delay(100);
+    await testEvent(view.grid.onAfterDrawContent, () => {}, () => {
+      view.grid.invalidate();
+    });
+    expect(resCol.length, helmCol.length);
+    const resMolfileList: MolfileHandlerBase[] = resCol.toList().map((molfile) => MolfileHandler.getInstance(molfile));
+    expectArray(resMolfileList.map((mf) => mf.atomCount), df.getCol('atoms').toList());
+    expectArray(resMolfileList.map((mf) => mf.bondCount), df.getCol('bonds').toList());
+  });
+});

package/src/{utils.ts → utils/index.ts}

@@ -1,4 +1,5 @@
 import * as DG from 'datagrok-api/dg';
+
 import {
   RGROUP_CAP_GROUP_NAME,
   RGROUP_CAP_GROUP_SMILES,
@@ -8,7 +9,7 @@ import {
   RGROUPS,
   RGROUP_LABEL,
   SDF_MONOMER_NAME
-} from './constants';
+} from '../constants';
 
 export function getParts(subParts: string[], s: string): string[] {
   const j = 0;