Merge branch 'master' of https://github.com/epam/ketcher into 3475-ma…

…cro-change-rna-preset-configuration

ketcher-autotests/tests/File-Management/Open-And-Save-Files/MOL-Files/mol-files.spec.ts

@@ -261,7 +261,10 @@ test('Open and Save file - Open/Save file contains Heteroatoms 1/2 - open', asyn
    */
   await waitForPageInit(page);
 
-  await openFileAndAddToCanvas('Heteroatoms.mol', page);
+  await openFileAndAddToCanvas(
+    'Molfiles-V2000/heteroatoms-structure.mol',
+    page,
+  );
   // check that structure opened from file is displayed correctly
   await takeEditorScreenshot(page);
 });
@@ -275,7 +278,10 @@ test('Open and Save file - Open/Save file contains Heteroatoms 2/2 - save', asyn
    */
   await waitForPageInit(page);
 
-  await openFileAndAddToCanvas('Heteroatoms.mol', page);
+  await openFileAndAddToCanvas(
+    'Molfiles-V2000/heteroatoms-structure.mol',
+    page,
+  );
   const expectedFile = await getMolfile(page, 'v2000');
   await saveToFile('heteroatoms-expected.mol', expectedFile);
   const METADATA_STRING_INDEX = [1];

ketcher-autotests/tests/File-Management/Open-And-Save-Files/cdxml-files.spec.ts

@@ -29,7 +29,7 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
      * Test case: EPMLSOPKET-2956
      * Description: Open/Import structure while openning a CDXML file
      */
-    await openFileAndAddToCanvas('cdxml-2956.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-2956.cdxml', page);
     // check that structure opened from file is displayed correctly
   });
 
@@ -38,7 +38,7 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
      * Test case: EPMLSOPKET-3086
      * Description: Open/Import structure while openning a CDXML file
      */
-    await openFileAndAddToCanvas('cdxml-3086.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-3086.cdxml', page);
     // check that structure opened from file is displayed correctly
   });
 
@@ -68,15 +68,15 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
      * Test case: EPMLSOPKET-4713
      * Description: Open/Import structure while openning a CDXML file
      */
-    await openFileAndAddToCanvas('cdxml-4713.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-4713.cdxml', page);
   });
 
   test('Text tool - Save as .cdxml file', async ({ page }) => {
     /**
      * Test case: EPMLSOPKET-4714
      * Description: Open/Import structure while openning a CDXML file
      */
-    await openFileAndAddToCanvas('cdxml-4714.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-4714.cdxml', page);
     await page.keyboard.press('Control+a');
     await page.keyboard.press('Delete');
   });
@@ -86,7 +86,7 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
      * Test case: EPMLSOPKET-4715
      * Description: Open/Import structure while openning a CDXML file
      */
-    await openFileAndAddToCanvas('cdxml-4715.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-4715.cdxml', page);
     await page.keyboard.press('Control+a');
     await page.keyboard.press('Delete');
   });
@@ -98,7 +98,7 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
      * Test case: EPMLSOPKET-4716
      * Description: Open/Import structure while openning a CDXML file
      */
-    await openFileAndAddToCanvas('cdxml-4716.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-4716.cdxml', page);
 
     await selectTopPanelButton(TopPanelButton.Clear, page);
     await takeEditorScreenshot(page);
@@ -114,7 +114,7 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
      * Test case: EPMLSOPKET-4717
      * Description: Open/Import structure while openning a CDXML file
      */
-    await openFileAndAddToCanvas('cdxml-4717.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-4717.cdxml', page);
     // check that structure opened from file is displayed correctly
   });
 
@@ -123,7 +123,7 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
      * Test case: EPMLSOPKET-4718
      * Description: Open/Import structure while openning a CDXML file
      */
-    await openFileAndAddToCanvas('cdxml-4718-structures.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-4718-structures.cdxml', page);
     // check that structure opened from file is displayed correctly
   });
 

ketcher-autotests/tests/File-Management/Smile-Files/smile-files.spec.ts

@@ -13,6 +13,7 @@ import {
   waitForLoad,
   waitForPageInit,
   nonEmptyString,
+  pasteFromClipboardAndAddToCanvas,
 } from '@utils';
 import { getSmiles } from '@utils/formats';
 
@@ -137,7 +138,10 @@ test.describe('SMILES files', () => {
     Description: SmileString is correctly generated from structure and
     vise versa structure is correctly generated from SmileString.
     */
-    await openFileAndAddToCanvas('Heteroatoms.mol', page);
+    await openFileAndAddToCanvas(
+      'Molfiles-V2000/heteroatoms-structure.mol',
+      page,
+    );
     await getAndCompareSmiles(
       page,
       'tests/test-data/smiles-heteroatoms-expected.json',
@@ -314,4 +318,58 @@ test.describe('SMILES files', () => {
 
     await clearCanvasAndPasteSmiles(page, 'C1C=CC=CC=1>N>C1C=CC=CC=1');
   });
+
+  test('Open SMILE file with S-Group Properties', async ({ page }) => {
+    /*
+    Test case: https://github.com/epam/Indigo/issues/1040
+    Description: SMILE file opens and have S-Group Properties
+    */
+    await openFileAndAddToCanvas(
+      'SMILES/structure-with-s-group-properties.smi',
+      page,
+    );
+    await getAndCompareSmiles(
+      page,
+      'tests/test-data/SMILES/structure-with-s-group-properties.smi',
+    );
+    await page.getByText('info2').dblclick();
+    await takeEditorScreenshot(page);
+
+    await clearCanvasAndPasteSmiles(page, 'CCC |SgD:1:atropisomer:info2::::|');
+  });
+
+  test('Stereobond is preserved after pasting a SMILES structure', async ({
+    page,
+  }) => {
+    /*
+    Test case: https://github.com/epam/Indigo/issues/1300
+    Description: The Single Down stereo bond is on the structure
+    */
+    await pasteFromClipboardAndAddToCanvas(page, 'C1=C(C)C(=O)C[S@]1=O');
+  });
+
+  test('Single Up, Single Down and Single Up/Down stereobonds is preserved after pasting a SMILES structure', async ({
+    page,
+  }) => {
+    /*
+    Test case: https://github.com/epam/Indigo/issues/1300
+    Description: The Single Up, Single Down and Single Up/Down  stereo bonds is on the structure
+    The test result is not what it should be. The behavior requires further clarification.
+    Single Down bond changes to Single Up and two other stereobonds dissapear.
+    */
+    await pasteFromClipboardAndAddToCanvas(page, 'C1[S@](=O)CC(=O)[C@@]=1C');
+  });
+
+  test('Enhanced stereo labels on atropisomers are not lost when opening saved Extended SMILES', async ({
+    page,
+  }) => {
+    /*
+    Test case: https://github.com/epam/Indigo/issues/1257
+    Description: Stereo information for bond and atom is kept
+    */
+    await openFileAndAddToCanvas(
+      'Extended-SMILES/atropoisomer-enhanced-stereo.cxsmi',
+      page,
+    );
+  });
 });

ketcher-autotests/tests/Indigo-Tools/Calculated-Values-Tool/calculated-values.spec.ts

@@ -72,7 +72,10 @@ test.describe('Calculated Values Tools', () => {
     The number of decimal places in the 'Molecular Weight' and 'Exact Mass'
     changes according to the selected values in the fields for the decimal places count.
     */
-    await openFileAndAddToCanvas('calculated-values-rings.mol', page);
+    await openFileAndAddToCanvas(
+      'Molfiles-V2000/calculated-values-rings.mol',
+      page,
+    );
     await selectTopPanelButton(TopPanelButton.Calculated, page);
 
     await takeEditorScreenshot(page);
@@ -101,7 +104,7 @@ test.describe('Calculated Values Tools', () => {
     The number of decimal places in the 'Molecular Weight' and 'Exact Mass'
     changes according to the selected values in the fields for the decimal places count.
     */
-    await openFileAndAddToCanvas('calcvalues-reaction.rxn', page);
+    await openFileAndAddToCanvas('Rxn-V2000/calcvalues-reaction.rxn', page);
     await selectTopPanelButton(TopPanelButton.Calculated, page);
 
     await takeEditorScreenshot(page);
@@ -569,7 +572,7 @@ test.describe('Calculated Values Tools', () => {
     Elemental Analysis:
     C 60.1 H 4.1 Br 35.8
     */
-    await openFileAndAddToCanvas('c14napthylbromide.mol', page);
+    await openFileAndAddToCanvas('Molfiles-V2000/c14napthylbromide.mol', page);
     await selectTopPanelButton(TopPanelButton.Calculated, page);
   });
 

ketcher-autotests/tests/Macromolecule-editor/Chem-monomers/chem-add-to-canvas.spec.ts

@@ -5,6 +5,7 @@ import {
   waitForPageInit,
 } from '@utils';
 import { POLYMER_TOGGLER } from '../../../constants/testIdConstants';
+import { hideMonomerPreview } from '@utils/macromolecules';
 
 /* 
 Test case: #2497 - Add chem to canvas
@@ -23,6 +24,7 @@ test('Select chem and drag it to canvas', async ({ page }) => {
 
   // Click on <svg> #polymer-editor-canvas
   await clickInTheMiddleOfTheScreen(page);
+  await hideMonomerPreview(page);
 
   await takeEditorScreenshot(page);
 });

ketcher-autotests/tests/Macromolecule-editor/Favorites/favorites-add-to-canvas.spec.ts

@@ -8,7 +8,10 @@ import {
   ALANINE,
   getFavoriteButtonSelector,
 } from '@utils/selectors/macromoleculeEditor';
-import { turnOnMacromoleculesEditor } from '@utils/macromolecules';
+import {
+  hideMonomerPreview,
+  turnOnMacromoleculesEditor,
+} from '@utils/macromolecules';
 
 test('Add molecule to favorites, switch to Favorites tab and drag it to the canvas', async ({
   page,
@@ -20,6 +23,7 @@ test('Add molecule to favorites, switch to Favorites tab and drag it to the canv
   await page.getByText('Favorites').click();
   await page.click(ALANINE);
   await clickInTheMiddleOfTheScreen(page);
+  await hideMonomerPreview(page);
 
   await takeEditorScreenshot(page);
 });

ketcher-autotests/tests/Macromolecule-editor/Peptides/peptides-add-to-canvas.spec.ts

@@ -7,7 +7,10 @@ import {
   waitForPageInit,
 } from '@utils';
 import { ALANINE } from '@utils/selectors/macromoleculeEditor';
-import { turnOnMacromoleculesEditor } from '@utils/macromolecules';
+import {
+  hideMonomerPreview,
+  turnOnMacromoleculesEditor,
+} from '@utils/macromolecules';
 
 /* 
 Test case: #3063 - Add e2e tests for Macromolecule editor
@@ -26,6 +29,7 @@ test.describe('Peptide', () => {
   test('Select peptide and drag it to canvas', async ({ page }) => {
     await page.click(ALANINE);
     await clickInTheMiddleOfTheScreen(page);
+    await hideMonomerPreview(page);
   });
 
   test('Add monomer preview on canvas', async ({ page }) => {

ketcher-autotests/tests/Macromolecule-editor/RNAEditor/delete-preset.spec.ts

@@ -34,10 +34,16 @@ test.describe('Macromolecules delete RNA presets', () => {
     await page.getByTestId('A_Copy_A_R_P').click();
     await page.getByTestId('A_Copy_A_R_P').click({ button: 'right' });
 
-    await page.getByTestId('deletepreset').click();
+    const deletePresetButton = await page.getByTestId('deletepreset');
+    await deletePresetButton.waitFor({ state: 'visible' });
+    await deletePresetButton.click();
+
+    await page.waitForSelector('[role=dialog]', { state: 'visible' });
 
     await takePageScreenshot(page);
 
     await page.getByTitle('Delete').click();
+
+    await page.waitForSelector('[role=dialog]', { state: 'hidden' });
   });
 });

ketcher-autotests/tests/Reagents/CDX-Format/reagents-cdx-format.spec.ts

@@ -0,0 +1,84 @@
+import { Page, expect, test } from '@playwright/test';
+import {
+  takeEditorScreenshot,
+  openFileAndAddToCanvas,
+  waitForPageInit,
+  saveToFile,
+  receiveFileComparisonData,
+  pasteFromClipboardAndAddToCanvas,
+  FILE_TEST_DATA,
+  clickInTheMiddleOfTheScreen,
+  selectTopPanelButton,
+  TopPanelButton,
+} from '@utils';
+import { getCdx } from '@utils/formats';
+
+async function saveFileAsCdxFormat(page: Page) {
+  await selectTopPanelButton(TopPanelButton.Save, page);
+  await page.getByRole('button', { name: 'MDL Rxnfile V2000' }).click();
+  await page.getByRole('option', { name: 'CDX', exact: true }).click();
+}
+
+test.describe('Reagents CDX format', () => {
+  test.beforeEach(async ({ page }) => {
+    await waitForPageInit(page);
+  });
+
+  test.afterEach(async ({ page }) => {
+    await takeEditorScreenshot(page);
+  });
+
+  test('File saves in "CDX" format', async ({ page }) => {
+    /*
+    Test case: EPMLSOPKET-4709
+    Description: File saved in format (e.g. "ketcher.cdx")
+    */
+
+    await openFileAndAddToCanvas('KET/two-reagents-above-and-below.ket', page);
+    const expectedFile = await getCdx(page);
+    await saveToFile(
+      'CDX/two-reagents-above-and-below-expected.cdx',
+      expectedFile,
+    );
+
+    const { fileExpected: cdxFileExpected, file: cdxFile } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName:
+          'tests/test-data/CDX/two-reagents-above-and-below-expected.cdx',
+      });
+
+    expect(cdxFile).toEqual(cdxFileExpected);
+  });
+
+  test('Open file in "CDX" format', async ({ page }) => {
+    /*
+    Test case: EPMLSOPKET-4711
+    Description: File open in CDX format.
+    */
+    await openFileAndAddToCanvas('CDX/two-reagents.cdx', page);
+  });
+
+  test('Paste from clipboard in "CDX" format', async ({ page }) => {
+    /*
+      Test case: EPMLSOPKET-4710
+      Description: Reagents 'NH3' displays above reaction arrow and HCl below.
+      */
+    await pasteFromClipboardAndAddToCanvas(
+      page,
+      FILE_TEST_DATA.reagentsBelowAndAboveArrowCdx,
+    );
+    await clickInTheMiddleOfTheScreen(page);
+  });
+
+  test('Detection molecule as reagent and write reagent information in CDX format in "Preview" tab', async ({
+    page,
+  }) => {
+    /*
+    Test case: EPMLSOPKET-4707, EPMLSOPKET-4708
+    Description: 'Can not display binary content' in Preview window.
+    */
+    await openFileAndAddToCanvas('CDX/two-reagents.cdx', page);
+    await saveFileAsCdxFormat(page);
+  });
+});

ketcher-autotests/tests/Reagents/CDXML-Format/reagents-cdxml-format.spec.ts

@@ -152,6 +152,6 @@ test.describe('Reagents CDXML format', () => {
       Description: The structure opens as it was saved with all structural elements: 
       plus and two reaction arrows NH3 molecule above first arrow and HCl below second arrow
     */
-    await openFileAndAddToCanvas('cdxml-multistep.cdxml', page);
+    await openFileAndAddToCanvas('CDXML/cdxml-multistep.cdxml', page);
   });
 });