@datagrok/sequence-translator 1.3.11 → 1.3.13

package/src/tests/polytool-enumerate-tests.ts

@@ -0,0 +1,95 @@
+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, expect, test, expectArray} from '@datagrok-libraries/utils/src/test';
+import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+
+import {PolyToolEnumeratorParams, PolyToolEnumeratorTypes} from '../polytool/types';
+import {getPtEnumeratorHelm} from '../polytool/pt-enumeration-helm';
+
+category('PolyTool', () => {
+  let helmHelper: IHelmHelper;
+
+  before(async () => {
+    helmHelper = await getHelmHelper(); // initialize JSDraw2 and org
+  });
+
+  after(async () => {
+
+  });
+
+  const tests: {
+    [testName: string]: { src: string, params: PolyToolEnumeratorParams, tgt: [string, string][] }
+  } = {
+    'single1': {
+      src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
+      params: {
+        type: PolyToolEnumeratorTypes.Single,
+        placeholders: {
+          [4]: ['K', 'P', 'F4COO'],
+          [6]: ['Y', 'T'],
+        },
+      },
+      tgt: [
+        ['PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5K'],
+        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5P'],
+        ['PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5[F4COO]'],
+        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-[Tic]7Y'],
+        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', '-[Tic]7T'],
+      ]
+    },
+    'single-with-original': {
+      src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
+      params: {
+        type: PolyToolEnumeratorTypes.Single,
+        placeholders: {
+          [4]: ['K', 'P', 'F4COO'],
+          [6]: ['Y', 'T'],
+        },
+        keepOriginal: true,
+      },
+      tgt: [
+        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', ''],
+        ['PEPTIDE1{[Ac(1)].F.W.G.K.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5K'],
+        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5P'],
+        ['PEPTIDE1{[Ac(1)].F.W.G.[F4COO].L.[Tic].[C(1)].G.[NH2]}$$$$V2.0', '-P5[F4COO]'],
+        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0', '-[Tic]7Y'],
+        ['PEPTIDE1{[Ac(1)].F.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0', '-[Tic]7T'],
+      ]
+    },
+    'matrix1': {
+      src: 'PEPTIDE1{[Ac(1)].F.W.G.P.L.[Tic].[C(1)].G.[NH2]}$$$$V2.0',
+      params:
+        {
+          type: PolyToolEnumeratorTypes.Matrix,
+          placeholders: {
+            [1]: ['D', 'L'],
+            [4]: ['K', 'P', 'F4COO'],
+            [6]: ['Y', 'T'],
+          }
+        },
+      tgt: [
+        ["PEPTIDE1{[Ac(1)].D.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0", "-F2D-P5K-[Tic]7Y"],
+        ["PEPTIDE1{[Ac(1)].D.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0", "-F2D-P5K-[Tic]7T"],
+        ["PEPTIDE1{[Ac(1)].D.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0", "-F2D-P5P-[Tic]7Y"],
+        ["PEPTIDE1{[Ac(1)].D.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0", "-F2D-P5P-[Tic]7T"],
+        ["PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0", "-F2D-P5[F4COO]-[Tic]7Y"],
+        ["PEPTIDE1{[Ac(1)].D.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0", "-F2D-P5[F4COO]-[Tic]7T"],
+        ["PEPTIDE1{[Ac(1)].L.W.G.K.L.Y.[C(1)].G.[NH2]}$$$$V2.0", "-F2L-P5K-[Tic]7Y"],
+        ["PEPTIDE1{[Ac(1)].L.W.G.K.L.T.[C(1)].G.[NH2]}$$$$V2.0", "-F2L-P5K-[Tic]7T"],
+        ["PEPTIDE1{[Ac(1)].L.W.G.P.L.Y.[C(1)].G.[NH2]}$$$$V2.0", "-F2L-P5P-[Tic]7Y"],
+        ["PEPTIDE1{[Ac(1)].L.W.G.P.L.T.[C(1)].G.[NH2]}$$$$V2.0", "-F2L-P5P-[Tic]7T"],
+        ["PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.Y.[C(1)].G.[NH2]}$$$$V2.0", "-F2L-P5[F4COO]-[Tic]7Y"],
+        ["PEPTIDE1{[Ac(1)].L.W.G.[F4COO].L.T.[C(1)].G.[NH2]}$$$$V2.0", "-F2L-P5[F4COO]-[Tic]7T"],
+      ],
+    }
+  };
+
+  for (const [testName, testData] of Object.entries(tests)) {
+    test(`enumerator-${testName}`, async () => {
+      const res = getPtEnumeratorHelm(testData.src, '', testData.params);
+      expectArray(res, testData.tgt);
+    });
+  }
+});

package/src/utils/context-menu.ts

@@ -2,11 +2,13 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import * as ui from 'datagrok-api/ui';
 
-import {defaultErrorHandler} from './err-info';
-import {_package, addContextMenu} from '../package';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {polyToolEnumerateHelmUI} from '../polytool/pt-dialog';
+
+import {defaultErrorHandler} from './err-info';
+import {polyToolEnumerateHelmUI} from '../polytool/pt-enumeration-helm-dialog';
+
+import {_package} from '../package';
 
 export type SequenceTranslatorWindowType = Window & {
   $sequenceTranslator?: {

package/src/utils/err-info.ts

@@ -6,8 +6,9 @@ import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 
 import {_package} from '../package';
 
-export function defaultErrorHandler(err: any): void {
+export function defaultErrorHandler(err: any, shell: boolean = true): [string, string | undefined] {
   const [errMsg, errStack] = errInfo(err);
   _package.logger.error(errMsg, undefined, errStack);
-  grok.shell.error(errMsg);
+  if (shell) grok.shell.error(errMsg);
+  return [errMsg, errStack];
 }

package/webpack.config.js

@@ -17,16 +17,9 @@ module.exports = {
   },
   module: {
     rules: [
-      {
-        test: /\.ts(x?)$/,
-        use: 'ts-loader',
-        exclude: /node_modules/,
-      },
-      {
-        test: /\.css$/,
-        use: ['style-loader', 'css-loader'],
-        exclude: /node_modules/,
-      },
+      {test: /\.js$/, enforce: 'pre', use: ['source-map-loader'], exclude: [/node_modules/]},
+      {test: /\.ts(x?)$/, use: 'ts-loader', exclude: [/node_modules/]},
+      {test: /\.css$/, use: ['style-loader', 'css-loader'], exclude: [/node_modules/]},
     ],
   },
   devtool: 'source-map',