Backmerge: #4109 - Macro: UI support export sequence (#4294)

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

@@ -0,0 +1,190 @@
+import { test, expect } from '@playwright/test';
+import {
+  TopPanelButton,
+  openFileAndAddToCanvasMacro,
+  selectTopPanelButton,
+  takeEditorScreenshot,
+  waitForPageInit,
+  saveToFile,
+  openFile,
+  receiveFileComparisonData,
+  selectOptionInDropdown,
+  pressButton,
+  selectSnakeLayoutModeTool,
+  chooseFileFormat,
+  readFileContents,
+  getSequence,
+  moveMouseAway,
+} from '@utils';
+import { turnOnMacromoleculesEditor } from '@utils/macromolecules';
+
+test.describe('Import-Saving .seq Files', () => {
+  test.beforeEach(async ({ page }) => {
+    await waitForPageInit(page);
+    await turnOnMacromoleculesEditor(page);
+  });
+
+  const sequenceFileTypes = ['DNA', 'RNA', 'Peptide'] as const;
+
+  for (const fileType of sequenceFileTypes) {
+    test(`Import .seq ${fileType} file`, async ({ page }) => {
+      await openFileAndAddToCanvasMacro(
+        `Sequence/sequence-${fileType.toLowerCase()}.seq`,
+        page,
+        fileType,
+      );
+      await moveMouseAway(page);
+      await takeEditorScreenshot(page);
+    });
+  }
+
+  test('Import incorrect data', async ({ page }) => {
+    const randomText = '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, 'Sequence');
+    await page.getByTestId('add-to-canvas-button').click();
+    await takeEditorScreenshot(page);
+  });
+
+  test('Check import of .ket file and save in .seq format', async ({
+    page,
+  }) => {
+    await openFileAndAddToCanvasMacro('KET/rna-a.ket', page);
+    const expectedFile = await getSequence(page);
+    await saveToFile('Sequence/sequence-rna-a-expected.seq', expectedFile);
+
+    const METADATA_STRING_INDEX = [1];
+
+    const { fileExpected: sequenceFileExpected, file: sequenceFile } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName:
+          'tests/test-data/Sequence/sequence-rna-a-expected.seq',
+        metaDataIndexes: METADATA_STRING_INDEX,
+      });
+
+    expect(sequenceFile).toEqual(sequenceFileExpected);
+
+    await takeEditorScreenshot(page);
+  });
+
+  test('Check that empty file can be saved in .seq format', async ({
+    page,
+  }) => {
+    const expectedFile = await getSequence(page);
+    await saveToFile('Sequence/sequence-empty.seq', expectedFile);
+
+    const METADATA_STRING_INDEX = [1];
+
+    const { fileExpected: sequenceFileExpected, file: sequenceFile } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName: 'tests/test-data/Sequence/sequence-empty.seq',
+        metaDataIndexes: METADATA_STRING_INDEX,
+      });
+
+    expect(sequenceFile).toEqual(sequenceFileExpected);
+  });
+
+  test('Check that system does not let importing empty .seq file', async ({
+    page,
+  }) => {
+    await selectTopPanelButton(TopPanelButton.Open, page);
+    await openFile('Sequence/sequence-empty.seq', page);
+    await page.getByText('Add to Canvas').isDisabled();
+  });
+
+  test('Check that system does not let uploading corrupted .seq file', async ({
+    page,
+  }) => {
+    await selectTopPanelButton(TopPanelButton.Open, page);
+
+    const filename = 'Sequence/sequence-corrupted.seq';
+    await openFile(filename, page);
+    await selectOptionInDropdown(filename, page);
+    await pressButton(page, 'Add to Canvas');
+    await takeEditorScreenshot(page);
+  });
+
+  test('Validate correct displaying of snake viewed RNA chain loaded from .seq file format', async ({
+    page,
+  }) => {
+    await openFileAndAddToCanvasMacro(
+      'Sequence/sequence-snake-mode-rna.seq',
+      page,
+    );
+    await selectSnakeLayoutModeTool(page);
+    await takeEditorScreenshot(page);
+  });
+
+  test('Check that you can save snake viewed chain of peptides in a .seq file', async ({
+    page,
+  }) => {
+    await openFileAndAddToCanvasMacro(
+      'Sequence/sequence-snake-mode-rna.seq',
+      page,
+    );
+    await selectSnakeLayoutModeTool(page);
+    const expectedFile = await getSequence(page);
+    await saveToFile(
+      'Sequence/sequence-snake-mode-rna-expected.seq',
+      expectedFile,
+    );
+
+    const METADATA_STRING_INDEX = [1];
+
+    const { fileExpected: sequenceFileExpected, file: sequenceFile } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName:
+          'tests/test-data/Sequence/sequence-snake-mode-rna-expected.seq',
+        metaDataIndexes: METADATA_STRING_INDEX,
+      });
+
+    expect(sequenceFile).toEqual(sequenceFileExpected);
+  });
+
+  test('Should open .ket file and modify to .seq format in save modal textarea', async ({
+    page,
+  }) => {
+    await openFileAndAddToCanvasMacro('KET/rna-a.ket', page);
+    await selectTopPanelButton(TopPanelButton.Save, page);
+    await chooseFileFormat(page, 'Sequence');
+    await page
+      .getByTestId('dropdown-select')
+      .getByRole('combobox')
+      .allInnerTexts();
+
+    const textArea = page.getByTestId('preview-area-text');
+    const file = await readFileContents(
+      'tests/test-data/Sequence/sequence-rna-a.seq',
+    );
+    const expectedData = file;
+    const valueInTextarea = await textArea.inputValue();
+    expect(valueInTextarea).toBe(expectedData);
+  });
+
+  // Should not convert to Sequence type in case of there are more than one monomer type
+  test('Should not convert .ket file with RNA and Peptide to .seq format in save modal', async ({
+    page,
+  }) => {
+    await openFileAndAddToCanvasMacro('KET/rna-and-peptide.ket', page);
+    await selectTopPanelButton(TopPanelButton.Save, page);
+    await chooseFileFormat(page, 'Sequence');
+
+    await takeEditorScreenshot(page);
+  });
+
+  // Should not convert to Sequence type in case of there is any CHEM
+  test('Should not convert .ket file with CHEMs to .seq format in save modal', async ({
+    page,
+  }) => {
+    await openFileAndAddToCanvasMacro('KET/chems-not-connected.ket', page);
+    await selectTopPanelButton(TopPanelButton.Save, page);
+    await chooseFileFormat(page, 'Sequence');
+
+    await takeEditorScreenshot(page);
+  });
+});

ketcher-autotests/tests/test-data/Sequence/sequence-corrupted.seq

@@ -0,0 +1 @@
+12w12r23e32e33

ketcher-autotests/tests/test-data/Sequence/sequence-dna.seq

@@ -0,0 +1 @@
+TCCAGCCATTGTGATTGCATGTTCCCAGGTTGAGGTAGTAGGTTGTATAGTTTAGAATTACATCAAGGGAGATAACTGTACAGCCTCCTAGCTTTCCTTGGGTCTTGCACAAAGCAACATGGCGAGA

ketcher-autotests/tests/test-data/Sequence/sequence-peptide.seq

@@ -0,0 +1 @@
+MIIGYVIGQATTQEALILAERPVRLGTYVVLEYDNVKALGLITNVTRGSPLLDDNMNDIEIVQRLKQFNNSIPVYTKAKVKLLCDMNNHFLMPDIPPFAGTPAREAEDEELKSIYSQDGQIRIGSLIGKNVEVKLNINSFARHLAILAATGSGKSNTVAVLSQRISELGGSVLIFDYHGEYYDSDIKNLNRIEPKLNPLYMTPREFSTLLEIRENAIIQYRILRRAFIKVTNGIRAALAAGQIPFSTLNSQFYELMADALETQGNSDKKSSAKDEVLNKFEEFMDRYSNVIDLTSSDIIEKVKRGKVNVVSLTQLDEDSMDAVVSHYLRRILDSRKDFKRSKNSGLKFPIIAVIEEAHVFLSKNENTLTKYWASRIAREGRKFGVGLTIVSQRPKGLDENILSQMTNKIILKIIEPTDKKYILESSDNLSEDLAEQLSSLDVGEAIIIGKIVKLPAVVKIDMFEGKLLGSDPDMIGEWKKVAASEKIAKGFADFGTEIGD

ketcher-autotests/tests/test-data/Sequence/sequence-rna-a-expected.seq

@@ -0,0 +1 @@
+A

ketcher-autotests/tests/test-data/Sequence/sequence-rna-a.seq

@@ -0,0 +1 @@
+A

ketcher-autotests/tests/test-data/Sequence/sequence-rna.seq

@@ -0,0 +1 @@
+UCCAGCCAUUGUGAUUGCAUGUUCCCAGGUUGAGGUAGUAGGUUGUAUAGUUUAGAAUUACAUCAAGGGAGAUAACUGUACAGCCUCCUAGCUUUCCUUGGGUCUUGCACAAAGCAACAUGGCGAGA

ketcher-autotests/tests/test-data/Sequence/sequence-snake-mode-rna-expected.seq

@@ -0,0 +1 @@
+CCCCCCCCCCCCCCCCCCCCCCCCCCC

ketcher-autotests/tests/test-data/Sequence/sequence-snake-mode-rna.seq

@@ -0,0 +1 @@
+CCCCCCCCCCCCCCCCCCCCCCCCCCC

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

@@ -17,6 +17,7 @@ const GetFileMethod: Record<string, keyof Ketcher> = {
   inchi: 'getInchi',
   sdf: 'getSdf',
   fasta: 'getFasta',
+  seq: 'getSequence',
 } 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 getSequence(page: Page): Promise<string> {
+  return await page.evaluate(() => window.ketcher.getSequence());
+}
+
 export async function getCml(page: Page): Promise<string> {
   return await page.evaluate(() => window.ketcher.getCml());
 }

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',
+  fileFomat: 'Ket' | 'MDL Molfile V3000' | 'FASTA' | 'Sequence',
 ) {
   await page.getByTestId('dropdown-select').click();
   await waitForSpinnerFinishedWork(page, async () => {

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

@@ -132,6 +132,13 @@ const formatProperties: FormatPropertiesMap = {
     ['.fasta'],
     true,
   ),
+  sequence: new SupportedFormatProperties(
+    'SEQUENCE',
+    ChemicalMimeType.SEQUENCE,
+    ['.seq'],
+    false,
+    {},
+  ),
   unknown: new SupportedFormatProperties(
     'Unknown',
     ChemicalMimeType.UNKNOWN,

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

@@ -50,6 +50,7 @@ export enum SupportedFormat {
   sdf = 'sdf',
   sdfV3000 = 'sdfV3000',
   fasta = 'fasta',
+  sequence = 'sequence',
   unknown = 'unknown',
 }
 

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

@@ -201,6 +201,15 @@ export class Ketcher {
     );
   }
 
+  getSequence(): Promise<string> {
+    return getStructure(
+      SupportedFormat.sequence,
+      this.#formatterFactory,
+      this.#editor.struct(),
+      CoreEditor.provideEditorInstance()?.drawingEntitiesManager,
+    );
+  }
+
   getSmarts(): Promise<string> {
     if (window.isPolymerEditorTurnedOn) {
       throw new Error('SMARTS format is not available in macro mode');

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

@@ -30,6 +30,7 @@ export enum ChemicalMimeType {
   UNKNOWN = 'chemical/x-unknown',
   SDF = 'chemical/x-sdf',
   FASTA = 'fasta',
+  SEQUENCE = 'chemical/x-sequence',
 }
 
 export interface WithStruct {

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

@@ -64,7 +64,7 @@ const LoadContainer = styled.div`
   }
 `;
 export const LoadingCircles = () => (
-  <LoadContainer>
+  <LoadContainer className="loading-spinner">
     <span />
     <span />
     <span />

packages/ketcher-macromolecules/src/components/modal/Open/AnalyzingFile/LoadingCircles/__snapshots__/LoadingCircles.test.tsx.snap

@@ -6,7 +6,7 @@ Object {
   "baseElement": <body>
     <div>
       <div
-        class="css-rmxyg7"
+        class="loading-spinner css-rmxyg7"
       >
         <span />
         <span />
@@ -16,7 +16,7 @@ Object {
   </body>,
   "container": <div>
     <div
-      class="css-rmxyg7"
+      class="loading-spinner css-rmxyg7"
     >
       <span />
       <span />

packages/ketcher-macromolecules/src/components/modal/Open/AnalyzingFile/__snapshots__/AnalyzingFile.test.tsx.snap

@@ -9,7 +9,7 @@ Object {
         class="css-1ro7qq4"
       >
         <div
-          class="css-rmxyg7"
+          class="loading-spinner css-rmxyg7"
         >
           <span />
           <span />
@@ -23,7 +23,7 @@ Object {
       class="css-1ro7qq4"
     >
       <div
-        class="css-rmxyg7"
+        class="loading-spinner css-rmxyg7"
       >
         <span />
         <span />

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

@@ -47,12 +47,14 @@ import { openErrorModal } from 'state/modal';
 const options: Array<Option> = [
   { id: 'ket', label: 'Ket' },
   { id: 'mol', label: 'MDL Molfile V3000' },
+  { id: 'sequence', label: 'Sequence' },
   { id: 'fasta', label: 'FASTA' },
 ];
 
 const formatDetector = {
   mol: ChemicalMimeType.Mol,
   fasta: ChemicalMimeType.FASTA,
+  sequence: ChemicalMimeType.SEQUENCE,
 };
 
 const StyledModal = styled(Modal)({
@@ -95,7 +97,7 @@ export const Save = ({
 
     try {
       setIsLoading(true);
-      if (fileFormat === 'fasta') {
+      if (fileFormat === 'fasta' || fileFormat === 'sequence') {
         const isValid =
           editor.drawingEntitiesManager.validateIfApplicableForFasta();
         if (!isValid) {

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

@@ -19,7 +19,7 @@ import {
   SupportedFormatProperties,
 } from './supportedFormatProperties';
 
-export type SupportedFormats = 'mol' | 'ket' | 'fasta';
+export type SupportedFormats = 'mol' | 'ket' | 'fasta' | 'sequence';
 
 type FormatProperties = {
   [key in SupportedFormats]: SupportedFormatProperties;
@@ -44,7 +44,14 @@ const formatProperties: FormatProperties = {
     'FASTA',
     ChemicalMimeType.Fasta,
     ['.fasta'],
-    true,
+    false,
+    {},
+  ),
+  sequence: new SupportedFormatProperties(
+    'SEQUENCE',
+    ChemicalMimeType.Sequence,
+    ['.seq'],
+    false,
     {},
   ),
 };

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

@@ -19,6 +19,7 @@ export enum ChemicalMimeType {
   Mol = 'chemical/x-mdl-molfile',
   Helm = 'chemical/x-helm',
   Fasta = 'fasta',
+  Sequence = 'sequence',
 }
 
 interface SupportedFormatPropertiesOptions {

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

@@ -64,6 +64,7 @@ export enum SupportedFormat {
   CDXML = 'cdxml',
   SDF = 'sdf',
   FASTA = 'fasta',
+  SEQUENCE = 'sequence',
 }
 
 export interface WithStruct {