Backmerge: #5634 - ketcher.getMolfile() stopped working for macro can…

…vas with peptides (#5750)

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

@@ -109,34 +109,31 @@ test.describe('CML files', () => {
     expect(cmlFile).toEqual(cmlFileExpected);
   });
 
-  test.fail(
-    'Open and Save file - CML - CML for R-group and other features',
-    async ({ page }) => {
-      /**
-       * Test case: EPMLSOPKET-1948
-       * Description: Saved cml file with structure is compering with paste R-group from a mol file
-       * It needs to be investigated why the test is failing.
-       * We have bug https://github.com/epam/Indigo/issues/2497
-       */
-
-      await openFileAddToCanvasTakeScreenshot(
-        page,
-        'Molfiles-V2000/cml-1948-R-group.mol',
-      );
-      // check that structure opened from file is displayed correctly
+  test('Open and Save file - CML - CML for R-group and other features', async ({
+    page,
+  }) => {
+    /**
+     * Test case: EPMLSOPKET-1948
+     * Description: Saved cml file with structure is compering with paste R-group from a mol file
+     */
 
-      const expectedFile = await getCml(page);
-      await saveToFile('CML/cml-1948-r-group-expected.cml', expectedFile);
-      const { file: cmlFile, fileExpected: cmlFileExpected } =
-        await receiveFileComparisonData({
-          page,
-          expectedFileName: 'tests/test-data/CML/cml-1948-r-group-expected.cml',
-        });
-      // comparing cml file with golden cml file
+    await openFileAddToCanvasTakeScreenshot(
+      page,
+      'Molfiles-V2000/cml-1948-R-group.mol',
+    );
+    // check that structure opened from file is displayed correctly
 
-      expect(cmlFile).toEqual(cmlFileExpected);
-    },
-  );
+    const expectedFile = await getCml(page);
+    await saveToFile('CML/cml-1948-r-group-expected.cml', expectedFile);
+    const { file: cmlFile, fileExpected: cmlFileExpected } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName: 'tests/test-data/CML/cml-1948-r-group-expected.cml',
+      });
+    // comparing cml file with golden cml file
+
+    expect(cmlFile).toEqual(cmlFileExpected);
+  });
 
   test('Validate that unsplit nucleotides connected with peptides could be saved to CML file and loaded back', async ({
     page,

ketcher-autotests/tests/File-Management/Open-And-Save-Files/Save-File/save-file.spec.ts

@@ -178,35 +178,33 @@ test.describe('Save files', () => {
     },
   );
 
-  test.fail(
-    'Automatic selection of MDL Molfile v3000 encoding is work if the number of atoms (or bonds) exceeds 999',
-    async ({ page }) => {
-      /**
-       * IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2494
-       * Test case: EPMLSOPKET-5260
-       * Description: Structure is saved according to automated selected format MDL Molfile v3000
-       */
-
-      await openFileAndAddToCanvas(
-        'Molfiles-V3000/structure-where-atoms-exceeds999.mol',
+  test('Automatic selection of MDL Molfile v3000 encoding is work if the number of atoms (or bonds) exceeds 999', async ({
+    page,
+  }) => {
+    /**
+     * Test case: EPMLSOPKET-5260
+     * Description: Structure is saved according to automated selected format MDL Molfile v3000
+     */
+
+    await openFileAndAddToCanvas(
+      'Molfiles-V3000/structure-where-atoms-exceeds999.mol',
+      page,
+    );
+    const expectedFile = await getMolfile(page);
+    await saveToFile(
+      'Molfiles-V3000/structure-where-atoms-exceeds999-expected.mol',
+      expectedFile,
+    );
+    const METADATA_STRING_INDEX = [1];
+    const { fileExpected: molFileExpected, file: molFile } =
+      await receiveFileComparisonData({
         page,
-      );
-      const expectedFile = await getMolfile(page);
-      await saveToFile(
-        'Molfiles-V3000/structure-where-atoms-exceeds999-expected.mol',
-        expectedFile,
-      );
-      const METADATA_STRING_INDEX = [1];
-      const { fileExpected: molFileExpected, file: molFile } =
-        await receiveFileComparisonData({
-          page,
-          expectedFileName:
-            'tests/test-data/Molfiles-V3000/structure-where-atoms-exceeds999-expected.mol',
-          metaDataIndexes: METADATA_STRING_INDEX,
-        });
-      expect(molFile).toEqual(molFileExpected);
-    },
-  );
+        expectedFileName:
+          'tests/test-data/Molfiles-V3000/structure-where-atoms-exceeds999-expected.mol',
+        metaDataIndexes: METADATA_STRING_INDEX,
+      });
+    expect(molFile).toEqual(molFileExpected);
+  });
 
   test('The file formats in the Save Structure window match the mockup', async ({
     page,

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

@@ -380,40 +380,36 @@ test.describe('Import-Saving .mol Files', () => {
     await turnOnMacromoleculesEditor(page);
   });
 
-  test.fail(
-    'Check that you can save snake viewed chain of peptides in a Mol v3000 file',
-    { tag: ['@IncorrectResultBecauseOfBug'] },
-    async () => {
-      /*
+  test('Check that you can save snake viewed chain of peptides in a Mol v3000 file', async () => {
+    /*
     Test case: Import/Saving files
     Description: Snake viewed chain of peptides saved in a Mol v3000 file
 
     Test fails because we have bug https://github.com/epam/ketcher/issues/5634
     */
-      await openFileAndAddToCanvasMacro(
-        'Molfiles-V3000/snake-mode-peptides.mol',
-        page,
-      );
-      await selectSnakeLayoutModeTool(page);
-      const expectedFile = await getMolfile(page);
-      await saveToFile(
-        'Molfiles-V3000/snake-mode-peptides-expected.mol',
-        expectedFile,
-      );
+    await openFileAndAddToCanvasMacro(
+      'Molfiles-V3000/snake-mode-peptides.mol',
+      page,
+    );
+    await selectSnakeLayoutModeTool(page);
+    const expectedFile = await getMolfile(page);
+    await saveToFile(
+      'Molfiles-V3000/snake-mode-peptides-expected.mol',
+      expectedFile,
+    );
 
-      const METADATA_STRING_INDEX = [1];
+    const METADATA_STRING_INDEX = [1];
 
-      const { fileExpected: molFileExpected, file: molFile } =
-        await receiveFileComparisonData({
-          page,
-          expectedFileName:
-            'tests/test-data/Molfiles-V3000/snake-mode-peptides-expected.mol',
-          metaDataIndexes: METADATA_STRING_INDEX,
-        });
+    const { fileExpected: molFileExpected, file: molFile } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName:
+          'tests/test-data/Molfiles-V3000/snake-mode-peptides-expected.mol',
+        metaDataIndexes: METADATA_STRING_INDEX,
+      });
 
-      expect(molFile).toEqual(molFileExpected);
-    },
-  );
+    expect(molFile).toEqual(molFileExpected);
+  });
 
   test('Check that .mol file with macro structures is imported correctly in macro mode when saving it in micro mode', async () => {
     /*

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

@@ -82,4 +82,5 @@ export interface Editor {
   macromoleculeConvertionError: string | null | undefined;
   setMacromoleculeConvertionError: (errorMessage: string) => void;
   clearMacromoleculeConvertionError: () => void;
+  serverSettings: object;
 }

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

@@ -113,12 +113,15 @@ export class Indigo {
     });
   }
 
-  layout(struct: StructOrString): Promise<Struct> {
+  layout(struct: StructOrString, options): Promise<Struct> {
     return this.#structService
-      .layout({
-        struct: convertStructToString(struct, this.#ketSerializer),
-        output_format: ChemicalMimeType.KET,
-      })
+      .layout(
+        {
+          struct: convertStructToString(struct, this.#ketSerializer),
+          output_format: ChemicalMimeType.KET,
+        },
+        options,
+      )
       .then((data) => this.#ketSerializer.deserialize(data.struct));
   }
 

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

@@ -413,7 +413,10 @@ export class Ketcher {
     }
 
     runAsyncAction<void>(async () => {
-      const struct = await this._indigo.layout(this.#editor.struct());
+      const struct = await this._indigo.layout(
+        this.#editor.struct(),
+        this.editor.serverSettings,
+      );
       const ketSerializer = new KetSerializer();
       this.setMolecule(ketSerializer.serialize(struct));
     }, this.eventBus);
@@ -480,11 +483,12 @@ export class Ketcher {
         meta = 'image/png';
         options.outputFormat = 'png';
     }
+    const serverSettings = this.editor.serverSettings;
 
-    const base64 = await this.structService.generateImageAsBase64(
-      data,
-      options,
-    );
+    const base64 = await this.structService.generateImageAsBase64(data, {
+      ...serverSettings,
+      ...options,
+    });
     const byteCharacters = atob(base64);
     const byteNumbers = new Array(byteCharacters.length);
     for (let i = 0; i < byteCharacters.length; i++) {

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

@@ -36,7 +36,9 @@ export function getStructure(
   drawingEntitiesManager?: DrawingEntitiesManager,
   selection?: EditorSelection,
 ): Promise<string> {
-  const formatter = formatterFactory.create(structureFormat);
+  const serverSettings = ketcherProvider.getKetcher().editor.serverSettings;
+  const formatter = formatterFactory.create(structureFormat, serverSettings);
+
   return formatter.getStructureFromStructAsync(
     struct,
     drawingEntitiesManager,

packages/ketcher-react/src/script/editor/Editor.ts

@@ -162,10 +162,12 @@ class Editor implements KetcherEditor {
     updateFloatingTools: Subscription<FloatingToolsParams>;
   };
 
+  public serverSettings = {};
+
   lastEvent: any;
   macromoleculeConvertionError: string | null | undefined;
 
-  constructor(clientArea, options) {
+  constructor(clientArea, options, serverSettings) {
     this.render = new Render(
       clientArea,
       Object.assign(
@@ -186,6 +188,7 @@ class Editor implements KetcherEditor {
     this.renderAndRecoordinateStruct =
       this.renderAndRecoordinateStruct.bind(this);
     this.setOptions = this.setOptions.bind(this);
+    this.setServerSettings(serverSettings);
 
     this.lastCursorPosition = {
       x: 0,
@@ -339,6 +342,10 @@ class Editor implements KetcherEditor {
     return this.render.options;
   }
 
+  public setServerSettings(serverSettings) {
+    this.serverSettings = serverSettings;
+  }
+
   private updateToolAfterOptionsChange(wasViewOnlyEnabled: boolean) {
     const isViewOnlyEnabled = this.render.options.viewOnlyMode;
     if (

packages/ketcher-react/src/script/editor/tool/rotate-controller.test.ts

@@ -57,7 +57,7 @@ describe('Rotate controller', () => {
    * 2. click Rotate Tool
    */
   it('hides when active tool is not SelectTool', () => {
-    const editor = new Editor(document, {});
+    const editor = new Editor(document, {}, {});
     const NonSelectTool = new RotateTool(editor, undefined);
     const paper = jest.fn();
     const visibleAtoms = [0, 1];
@@ -89,7 +89,7 @@ describe('Rotate controller', () => {
    * Click `zoom in` or press `Ctrl+=`
    */
   it('rerenders while zooming', () => {
-    const editor = new Editor(document, {});
+    const editor = new Editor(document, {}, {});
     editor.rotateController.rerender = jest.fn();
 
     editor.zoom(2);
@@ -203,7 +203,7 @@ describe('Rotate controller', () => {
    * 2. Undo
    */
   it(`cancels rotation without modifying history stack`, () => {
-    const editor = new Editor(document, {});
+    const editor = new Editor(document, {}, {});
     editor.render.ctab.molecule.getSelectedVisibleAtoms = () => [];
     // @ts-ignore
     editor.rotateController.rotateTool.dragCtx = {

packages/ketcher-react/src/script/ui/views/Editor.jsx

@@ -35,12 +35,14 @@ const mapDispatchToProps = (dispatch) => {
   };
 };
 
-const Editor = connect(
-  (state) => ({
+const Editor = connect((state) => {
+  const serverSettings = state.options.getServerSettings();
+
+  return {
     options: state.options.settings,
+    serverSettings,
     indigoVerification: state.requestsStatuses.indigoVerification,
-  }),
-  mapDispatchToProps,
-)(StructEditor);
+  };
+}, mapDispatchToProps)(StructEditor);
 
 export default Editor;

packages/ketcher-react/src/script/ui/views/components/StructEditor/StructEditor.jsx

@@ -41,7 +41,10 @@ function setupEditor(editor, props, oldProps = {}) {
     }
   }
 
-  if (oldProps.options && options !== oldProps.options) editor.options(options);
+  if (oldProps.options && options !== oldProps.options) {
+    editor.options(options);
+    editor.setServerSettings(props.serverSettings);
+  }
 
   Object.keys(editor.event).forEach((name) => {
     const eventName = `on${upperFirst(name)}`;
@@ -147,9 +150,13 @@ class StructEditor extends Component {
   }
 
   componentDidMount() {
-    this.editor = new Editor(this.editorRef.current, {
-      ...this.props.options,
-    });
+    this.editor = new Editor(
+      this.editorRef.current,
+      {
+        ...this.props.options,
+      },
+      { ...this.props.serverSettings },
+    );
     const ketcher = ketcherProvider.getKetcher();
     if (ketcher?.editor.macromoleculeConvertionError) {
       this.props.onShowMacromoleculesErrorMessage(
@@ -287,6 +294,7 @@ class StructEditor extends Component {
       showAttachmentPoints = true,
       onUpdateFloatingTools,
       onShowMacromoleculesErrorMessage,
+      serverSettings,
       /* eslint-enable @typescript-eslint/no-unused-vars */
       ...props
     } = this.props;