#4495 - Macro: UI support for IDT import/export

ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-idt.spec.ts

@@ -0,0 +1,126 @@
+import { test, expect } from '@playwright/test';
+import {
+  TopPanelButton,
+  openFileAndAddToCanvasMacro,
+  selectTopPanelButton,
+  takeEditorScreenshot,
+  waitForPageInit,
+  saveToFile,
+  openFile,
+  receiveFileComparisonData,
+  // selectOptionInDropdown,
+  // pressButton,
+  chooseFileFormat,
+  readFileContents,
+  // moveMouseAway,
+  getIdt,
+} from '@utils';
+import { turnOnMacromoleculesEditor } from '@utils/macromolecules';
+
+function removeNotComparableData(file: string) {
+  return file.replaceAll('\r', '');
+}
+test.describe('Import-Saving .idt Files', () => {
+  test.beforeEach(async ({ page }) => {
+    await waitForPageInit(page);
+    await turnOnMacromoleculesEditor(page);
+  });
+
+  // TODO: uncomment after solving Indigo issue
+  // test(`Import .idt file`, async ({ page }) => {
+  //   await openFileAndAddToCanvasMacro('IDT/idt-rna-a.idt', page);
+  //   await moveMouseAway(page);
+  //   await takeEditorScreenshot(page);
+  // });
+
+  // TODO: uncomment after solving Indigo issue
+  // test('Import incorrect data', async ({ page }) => {
+  //   const randomText = '!+%45#asjfnsalkfl';
+  //   await selectTopPanelButton(TopPanelButton.Open, page);
+  //   await page.getByTestId('paste-from-clipboard-button').click();
+  //   await page.getByTestId('open-structure-textarea').fill(randomText);
+  //   await chooseFileFormat(page, 'IDT');
+  //   await page.getByTestId('add-to-canvas-button').click();
+  //   await takeEditorScreenshot(page);
+  // });
+
+  test('Check import of .ket file and save in .idt format', async ({
+    page,
+  }) => {
+    await openFileAndAddToCanvasMacro('KET/rna-a.ket', page);
+    const expectedFile = await getIdt(page);
+    await saveToFile('IDT/idt-rna-a-expected.idt', expectedFile);
+
+    const METADATA_STRING_INDEX = [1];
+
+    const { fileExpected: idtFileExpected, file: idtFile } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName: 'tests/test-data/IDT/idt-rna-a-expected.idt',
+        metaDataIndexes: METADATA_STRING_INDEX,
+      });
+
+    expect(idtFile).toEqual(idtFileExpected);
+
+    await takeEditorScreenshot(page);
+  });
+
+  test('Check that empty file can be saved in .idt format', async ({
+    page,
+  }) => {
+    const expectedFile = await getIdt(page);
+    await saveToFile('IDT/idt-empty.idt', expectedFile);
+
+    const METADATA_STRING_INDEX = [1];
+
+    const { fileExpected: idtFileExpected, file: idtFile } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName: 'tests/test-data/IDT/idt-empty.idt',
+        metaDataIndexes: METADATA_STRING_INDEX,
+      });
+
+    expect(idtFile).toEqual(idtFileExpected);
+  });
+
+  test('Check that system does not let importing empty .idt file', async ({
+    page,
+  }) => {
+    await selectTopPanelButton(TopPanelButton.Open, page);
+    await openFile('IDT/idt-empty.idt', page);
+    await page.getByText('Add to Canvas').isDisabled();
+  });
+
+  // TODO: uncomment after solving Indigo issue
+  // test('Check that system does not let uploading corrupted .idt file', async ({
+  //   page,
+  // }) => {
+  //   await selectTopPanelButton(TopPanelButton.Open, page);
+  //
+  //   const filename = 'IDT/idt-corrupted.idt';
+  //   await openFile(filename, page);
+  //   await selectOptionInDropdown(filename, page);
+  //   await pressButton(page, 'Add to Canvas');
+  //   await takeEditorScreenshot(page);
+  // });
+
+  test('Should open .ket file and modify to .idt format in save modal textarea', async ({
+    page,
+  }) => {
+    await openFileAndAddToCanvasMacro('KET/rna-a.ket', page);
+    await selectTopPanelButton(TopPanelButton.Save, page);
+    await chooseFileFormat(page, 'IDT');
+    await page
+      .getByTestId('dropdown-select')
+      .getByRole('combobox')
+      .allInnerTexts();
+
+    const textArea = page.getByTestId('preview-area-text');
+    const file = await readFileContents('tests/test-data/IDT/idt-rna-a.idt');
+    const expectedData = removeNotComparableData(file);
+    const valueInTextarea = removeNotComparableData(
+      await textArea.inputValue(),
+    );
+    expect(valueInTextarea).toBe(expectedData);
+  });
+});

ketcher-autotests/tests/test-data/IDT/idt-corrupted.idt

@@ -0,0 +1 @@
+!+-$#12w12r23e32e33

ketcher-autotests/tests/test-data/IDT/idt-rna-a-expected.idt

@@ -0,0 +1 @@
+rA/3Phos/

ketcher-autotests/tests/test-data/IDT/idt-rna-a.idt

@@ -0,0 +1 @@
+rA/3Phos/

ketcher-autotests/tests/utils/files/receiveFileComparisonData.ts

@@ -18,6 +18,7 @@ const GetFileMethod: Record<string, keyof Ketcher> = {
   sdf: 'getSdf',
   fasta: 'getFasta',
   seq: 'getSequence',
+  idt: 'getIdt',
 } as const;
 
 type KetcherApiFunction = (format?: string) => Promise<string>;

ketcher-autotests/tests/utils/formats/formats.ts

@@ -9,6 +9,10 @@ export async function getFasta(page: Page): Promise<string> {
   return await page.evaluate(() => window.ketcher.getFasta());
 }
 
+export async function getIdt(page: Page): Promise<string> {
+  return await page.evaluate(() => window.ketcher.getIdt());
+}
+
 export async function getSequence(page: Page): Promise<string> {
   return await page.evaluate(() => window.ketcher.getSequence());
 }

ketcher-autotests/tests/utils/macromolecules/index.ts

@@ -44,7 +44,7 @@ export async function scrollDown(page: Page, scrollDelta: number) {
 
 export async function chooseFileFormat(
   page: Page,
-  fileFomat: 'Ket' | 'MDL Molfile V3000' | 'FASTA' | 'Sequence',
+  fileFomat: 'Ket' | 'MDL Molfile V3000' | 'FASTA' | 'Sequence' | 'IDT',
 ) {
   await page.getByTestId('dropdown-select').click();
   await waitForSpinnerFinishedWork(page, async () => {

packages/ketcher-core/src/application/formatters/formatProperties.ts

@@ -132,6 +132,12 @@ const formatProperties: FormatPropertiesMap = {
     ['.fasta'],
     true,
   ),
+  idt: new SupportedFormatProperties(
+    'IDT',
+    ChemicalMimeType.IDT,
+    ['.idt'],
+    false,
+  ),
   sequence: new SupportedFormatProperties(
     'SEQUENCE',
     ChemicalMimeType.SEQUENCE,

packages/ketcher-core/src/application/formatters/structFormatter.types.ts

@@ -51,6 +51,7 @@ export enum SupportedFormat {
   sdfV3000 = 'sdfV3000',
   fasta = 'fasta',
   sequence = 'sequence',
+  idt = 'idt',
   unknown = 'unknown',
 }
 

packages/ketcher-core/src/application/ketcher.ts

@@ -162,6 +162,15 @@ export class Ketcher {
     return molfile;
   }
 
+  getIdt(): Promise<string> {
+    return getStructure(
+      SupportedFormat.idt,
+      this.#formatterFactory,
+      this.#editor.struct(),
+      CoreEditor.provideEditorInstance()?.drawingEntitiesManager,
+    );
+  }
+
   async getRxn(molfileFormat: MolfileFormat = 'v2000'): Promise<string> {
     if (window.isPolymerEditorTurnedOn) {
       throw new Error('RXN format is not available in macro mode');

packages/ketcher-core/src/domain/services/struct/structService.types.ts

@@ -34,6 +34,7 @@ export enum ChemicalMimeType {
   RNA = 'chemical/x-rna-sequence',
   DNA = 'chemical/x-dna-sequence',
   PEPTIDE = 'chemical/x-peptide-sequence',
+  IDT = 'chemical/x-idt',
 }
 
 export interface WithStruct {

packages/ketcher-macromolecules/src/components/modal/Open/Open.tsx

@@ -95,6 +95,7 @@ const options: Array<Option> = [
   { id: 'mol', label: 'MDL Molfile V3000' },
   { id: 'seq', label: 'Sequence' },
   { id: 'fasta', label: 'FASTA' },
+  { id: 'idt', label: 'IDT' },
 ];
 
 const additionalOptions: Array<Option> = [

packages/ketcher-macromolecules/src/components/modal/save/Save.tsx

@@ -49,12 +49,14 @@ const options: Array<Option> = [
   { id: 'mol', label: 'MDL Molfile V3000' },
   { id: 'sequence', label: 'Sequence' },
   { id: 'fasta', label: 'FASTA' },
+  { id: 'idt', label: 'IDT' },
 ];
 
 const formatDetector = {
   mol: ChemicalMimeType.Mol,
   fasta: ChemicalMimeType.FASTA,
   sequence: ChemicalMimeType.SEQUENCE,
+  idt: ChemicalMimeType.IDT,
 };
 
 const StyledModal = styled(Modal)({

packages/ketcher-macromolecules/src/helpers/formats/formatProperties.ts

@@ -19,7 +19,7 @@ import {
   SupportedFormatProperties,
 } from './supportedFormatProperties';
 
-export type SupportedFormats = 'mol' | 'ket' | 'fasta' | 'sequence';
+export type SupportedFormats = 'mol' | 'ket' | 'fasta' | 'sequence' | 'idt';
 
 type FormatProperties = {
   [key in SupportedFormats]: SupportedFormatProperties;
@@ -54,6 +54,13 @@ const formatProperties: FormatProperties = {
     false,
     {},
   ),
+  idt: new SupportedFormatProperties(
+    'IDT',
+    ChemicalMimeType.Idt,
+    ['.idt'],
+    false,
+    {},
+  ),
 };
 
 export const getPropertiesByFormat = (format: SupportedFormats) => {

packages/ketcher-macromolecules/src/helpers/formats/supportedFormatProperties.ts

@@ -20,6 +20,7 @@ export enum ChemicalMimeType {
   Helm = 'chemical/x-helm',
   Fasta = 'chemical/x-fasta',
   Sequence = 'chemical/x-sequence',
+  Idt = 'chemical/x-idt',
 }
 
 interface SupportedFormatPropertiesOptions {

packages/ketcher-standalone/src/infrastructure/services/struct/indigoWorker.types.ts

@@ -65,6 +65,7 @@ export enum SupportedFormat {
   SDF = 'sdf',
   FASTA = 'fasta',
   SEQUENCE = 'sequence',
+  IDT = 'idt',
 }
 
 export interface WithStruct {

packages/ketcher-standalone/src/infrastructure/services/struct/standaloneStructService.ts

@@ -137,6 +137,10 @@ function convertMimeTypeToOutputFormat(
       format = SupportedFormat.SEQUENCE;
       break;
     }
+    case ChemicalMimeType.IDT: {
+      format = SupportedFormat.IDT;
+      break;
+    }
     case ChemicalMimeType.UNKNOWN:
     default: {
       throw new Error('Unsupported chemical mime type');
@@ -271,6 +275,7 @@ class IndigoService implements StructService {
       struct,
     } = data;
     const format = convertMimeTypeToOutputFormat(outputFormat);
+    console.log('convert format', format);
 
     return new Promise((resolve, reject) => {
       const action = ({ data }: OutputMessageWrapper) => {
@@ -308,6 +313,7 @@ class IndigoService implements StructService {
       this.EE.removeListener(WorkerEvent.Convert, action);
       this.EE.addListener(WorkerEvent.Convert, action);
 
+      console.log('convert worker.postMessage', inputMessage);
       this.worker.postMessage(inputMessage);
     });
   }