#2772 remove unused serializerdeserialiser for mol v3000 sdf smi as its implemented on the indigo side

example/package.json

@@ -8,18 +8,15 @@
     "start:standalone": "cross-env MODE=standalone react-app-rewired start",
     "start:remote": "cross-env MODE=remote react-app-rewired start",
     "init:build": "shx mkdir -p build",
-    "init:dist": "cross-env-shell shx mkdir -p dist/$MODE",
-    "delete:dist": "cross-env-shell shx rm -rf dist/$MODE",
-    "copy:build": "cross-env-shell shx cp -r build/. dist/$MODE",
-    "prebuild": "cross-env-shell run-s init:build delete:dist init:dist",
-    "postbuild": "cross-env-shell npm run copy:build",
-    "build:remote": "cross-env-shell MODE=remote run-s prebuild build:react postbuild",
-    "build:standalone": "cross-env-shell MODE=standalone run-s prebuild build:react postbuild",
-    "build:react": "cross-env-shell MODE=$MODE react-app-rewired build && echo $MODE",
+    "copy:build": "node ./scripts/copy-build-to-dist.cjs",
+    "prebuild": "npm run init:build",
+    "build:remote": "cross-env MODE=remote npm run init:build && cross-env MODE=remote npm run build:react && cross-env MODE=remote npm run copy:build",
+    "build:standalone": "cross-env MODE=standalone npm run init:build && cross-env MODE=standalone npm run build:react && cross-env MODE=standalone npm run copy:build",
+    "build:react": "react-app-rewired build",
     "build:react:analyze": "react-app-rewired build --analyze",
     "build": "npm run build:standalone && npm run build:remote",
-    "build:standalone:analyze": "cross-env MODE=standalone run-s prebuild build:react:analyze postbuild",
-    "build:remote:analyze": "cross-env MODE=remote run-s prebuild build:react:analyze postbuild",
+    "build:standalone:analyze": "cross-env MODE=standalone npm run init:build && cross-env MODE=standalone npm run build:react:analyze && cross-env MODE=standalone npm run copy:build",
+    "build:remote:analyze": "cross-env MODE=remote npm run init:build && cross-env MODE=remote npm run build:react:analyze && cross-env MODE=remote npm run copy:build",
     "test": "run-s test:prettier test:stylelint test:eslint:quiet test:types test:unit",
     "test:eslint": "eslint . --ext .ts,.js,.jsx,.tsx",
     "test:eslint:quiet": "npm run test:eslint -- --quiet",

example/scripts/copy-build-to-dist.cjs

@@ -0,0 +1,25 @@
+const { cp, mkdir } = require('fs/promises');
+const path = require('path');
+
+async function main() {
+  const mode = process.env.MODE;
+
+  if (!mode) {
+    throw new Error('MODE env var is required');
+  }
+
+  const rootDir = path.resolve(__dirname, '..');
+  const buildDir = path.join(rootDir, 'build');
+  const targetDir = path.join(rootDir, 'dist', mode);
+
+  await mkdir(targetDir, { recursive: true });
+  await cp(buildDir, targetDir, {
+    recursive: true,
+    force: true,
+  });
+}
+
+main().catch((error) => {
+  console.error(error);
+  process.exitCode = 1;
+});

ketcher-autotests/tests/specs/API/api-set-get-molecule.spec.ts

@@ -183,6 +183,7 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
     Test case: EPMLSOPKET- 10095
     Description:  Molecule set and get using V3000 format
     */
+    await page.waitForTimeout(5000);
     const orEnantiomer = await readFileContent(
       'Molfiles-V3000/or-enantiomer.mol',
     );
@@ -416,15 +417,12 @@ test.describe('Tests for API setMolecule/getMolecule', () => {
     Test case: EPMLSOPKET-13018
     Description: Unknown superatom expanded/contracted added through API ketcher.setMolecule
     */
+    const unknownSuperatomV3000 = await readFileContent(
+      'Molfiles-V3000/unknown-superatom-expanded-contracted.mol',
+    );
     await waitForSpinnerFinishedWork(
       page,
-      async () =>
-        await setMolecule(
-          page,
-          await readFileContent(
-            'Molfiles-V3000/unknown-superatom-expanded-contracted.mol',
-          ),
-        ),
+      async () => await setMolecule(page, unknownSuperatomV3000),
     );
     await takeEditorScreenshot(page);
   });

ketcher-autotests/tests/specs/Chromium-popup/Bugs/ketcher-3.10.0-bugs.spec.ts

@@ -101,7 +101,7 @@ test.describe('Ketcher-3.10 Bugs', () => {
      * 3. Load from HELM: CHEM1{[4aPEGMal]}|CHEM2{[4aPEGMal]}$$$$V2.0
      * 4. Select Single Bound tool
      * 5. Start to connect one monomer to another using center-to-center way
-     * 6.Expand windows "minimize button" shows "minimize window"
+     * 6. Expand windows "minimize button" shows "minimize window"
      *
      * Version 3.10.0
      */
@@ -113,8 +113,12 @@ test.describe('Ketcher-3.10 Bugs', () => {
       MacroFileType.HELM,
       'CHEM1{[4aPEGMal]}|CHEM2{[4aPEGMal]}$$$$V2.0',
     );
-    const firstMonomer = getMonomerLocator(page, { monomerId: 2 });
-    const secondMonomer = getMonomerLocator(page, { monomerId: 3 });
+    const firstMonomer = getMonomerLocator(page, {
+      monomerAlias: `4aPEGMal`,
+    }).nth(0);
+    const secondMonomer = getMonomerLocator(page, {
+      monomerAlias: `4aPEGMal`,
+    }).nth(1);
     await bondTwoMonomers(page, firstMonomer, secondMonomer);
     await AttachmentPointsDialog(page).isVisible();
     await AttachmentPointsDialog(page).expandWindow();
@@ -178,7 +182,7 @@ test.describe('Ketcher-3.10 Bugs', () => {
      * Version 3.10.0
      */
     const arrangeAsARing = page.getByTestId(MonomerOption.ArrangeAsARing);
-    const anyMonomer = getMonomerLocator(page, { monomerId: 90 }).first();
+    const anyMonomer = getMonomerLocator(page, { monomerId: 376 }).first();
     await CommonTopRightToolbar(page).turnOnMacromoleculesEditor({
       enableFlexMode: true,
       goToPeptides: true,

ketcher-autotests/tests/specs/Chromium-popup/Bugs/ketcher-3.11.0-bugs.spec.ts

@@ -504,7 +504,7 @@ test.describe('Bugs: ketcher-3.11.0 — first trio', () => {
      */
 
     await openFileAndAddToCanvasMacro(page, 'KET/sugar-phosphate-core.ket');
-    await ContextMenu(page, getBondLocator(page, { bondId: 45 })).open();
+    await ContextMenu(page, getBondLocator(page, { bondId: 185 })).open();
     await expect(page.getByTestId(MacroBondOption.Delete)).toBeVisible();
   });
 
@@ -784,7 +784,7 @@ test.describe('Bugs: ketcher-3.11.0 — first trio', () => {
     );
     await CommonLeftToolbar(page).areaSelectionTool();
     await selectAllStructuresOnCanvas(page);
-    const point = getSymbolLocator(page, { symbolId: 14 });
+    const point = getSymbolLocator(page, { symbolAlias: 'A' }).first();
     await ContextMenu(page, point).open();
     await takeEditorScreenshot(page);
   });
@@ -838,16 +838,18 @@ test.describe('Bugs: ketcher-3.11.0 — first trio', () => {
     );
     await CommonLeftToolbar(page).areaSelectionTool();
     await selectMonomersAndBonds(page, {
-      monomerIds: [68, 69, 82, 83, 73, 71, 72, 80, 79, 84],
-      bondIds: [97, 112, 115, 101, 102, 113, 114, 100, 111, 108],
+      monomerIds: [217, 222, 220, 218, 221, 232, 229, 231, 233, 228],
+      bondIds: [250, 251, 246, 249, 264, 260, 261, 257, 262, 263],
+      // monomerIds: [68, 69, 82, 83, 73, 71, 72, 80, 79, 84],
+      // bondIds: [97, 112, 115, 101, 102, 113, 114, 100, 111, 108],
     });
-    await ContextMenu(page, getMonomerLocator(page, { monomerId: 80 })).click(
+    await ContextMenu(page, getMonomerLocator(page, { monomerId: 231 })).click(
       MonomerOption.ArrangeAsARing,
     );
     await CommonTopRightToolbar(page).setZoomInputValue('60');
     await takeElementScreenshot(
       page,
-      getMonomerLocator(page, { monomerId: 198 }),
+      getMonomerLocator(page, { monomerId: 347 }),
       {
         padding: 150,
       },
@@ -876,7 +878,7 @@ test.describe('Bugs: ketcher-3.11.0 — first trio', () => {
       MacroFileType.HELM,
       'PEPTIDE1{(A,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,Y)}$$$$V2.0',
     );
-    const monomer = getMonomerLocator(page, { monomerId: 1 });
+    const monomer = getMonomerLocator(page, Peptide.X);
     await monomer.hover({ force: true });
     await MonomerPreviewTooltip(page).waitForBecomeVisible();
     await takeElementScreenshot(page, monomer, {
@@ -901,17 +903,15 @@ test.describe('Bugs: ketcher-3.11.0 — first trio', () => {
       MacroFileType.HELM,
       'CHEM1{[4aPEGMal]}|CHEM2{[4FB]}|CHEM3{[A6OH]}$CHEM2,CHEM1,1:R2-1:R1|CHEM3,CHEM2,1:R2-1:R1$$$V2.0',
     );
-    const chainlocator = getSymbolLocator(page, { symbolId: 7 });
+    const chainlocator = getSymbolLocator(page, { symbolAlias: '@' });
     const locators = await getCoordinatesOfTheMiddleOfTheScreen(page);
     await CommonLeftToolbar(page).handTool();
     await chainlocator.hover({ force: true });
     await dragMouseTo(page, locators.x, locators.y);
     await CommonLeftToolbar(page).areaSelectionTool();
     await chainlocator.hover({ force: true });
     await MonomerPreviewTooltip(page).waitForBecomeVisible();
-    await takeElementScreenshot(page, chainlocator, {
-      padding: 120,
-    });
+    await takeElementScreenshot(page, MonomerPreviewTooltip(page).window);
   });
 
   test('Case 25 - 5NitInd unsplit nucleotide should be shown as X symbol instead of @ one', async ({
@@ -928,9 +928,7 @@ test.describe('Bugs: ketcher-3.11.0 — first trio', () => {
 
     await Library(page).openRNASection(RNASection.Nucleotides);
     await Library(page).selectMonomer(Nucleotide._5NitInd);
-    await takeElementScreenshot(page, getSymbolLocator(page, { symbolId: 0 }), {
-      padding: 30,
-    });
+    await expect(getSymbolLocator(page, { symbolAlias: 'X' })).toBeVisible();
   });
 
   test('Case 26 - In case of multipal R1 or R2 groups second R1/R2 groups should be assigned to the smallest available Rn (n>2) if available', async () => {
@@ -1074,7 +1072,7 @@ test.describe('Bugs: ketcher-3.11.0 — first trio', () => {
     );
     await takeElementScreenshot(
       page,
-      getMonomerLocator(page, { monomerId: 6 }),
+      getMonomerLocator(page, { monomerAlias: `(Unknown2)` }),
       {
         padding: 100,
       },

ketcher-autotests/tests/test-data/Molfiles-V3000/test-data-for-enatiomer.mol

@@ -1,5 +1,5 @@
 
-  -INDIGO-03042511542D
+  -INDIGO-04062612372D
 
   0  0  0  0  0  0  0  0  0  0  0 V3000
 M  V30 BEGIN CTAB

ketcher-autotests/tests/utils/common/loaders/waitForSpinnerFinishedWork/waitForSpinnerFinishedWork.ts

@@ -5,12 +5,11 @@ import { waitForRender } from '../waitForRender';
 
 export const waitForSpinnerFinishedWork = async (
   page: Page,
-  callback: VoidFunction,
+  callback: () => Promise<void>,
   timeout = 250,
 ) => {
   const loadingSpinner = page.getByTestId('loading-spinner');
-
-  callback();
+  await callback();
   do {
     await page.waitForTimeout(200);
     await loadingSpinner.first().waitFor({ state: 'detached' });

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

@@ -32,7 +32,7 @@ export function getTestDataDirectory() {
 export async function readFileContent(filePath: string) {
   const testDataDirectory = getTestDataDirectory();
   const resolvedFilePath = path.resolve(testDataDirectory, filePath);
-  return fs.promises.readFile(resolvedFilePath, 'utf8');
+  return await fs.promises.readFile(resolvedFilePath, 'utf8');
 }
 
 export async function openFile(page: Page, filename: string) {

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

@@ -1,3 +1,5 @@
+/* eslint-disable no-inline-comments */
+/* eslint-disable no-magic-numbers */
 import { Page, expect } from '@playwright/test';
 import { CommonLeftToolbar } from '@tests/pages/common/CommonLeftToolbar';
 import {
@@ -146,6 +148,7 @@ export async function setMolecule(
   structStr: string,
   position?: { x: number; y: number },
 ): Promise<void> {
+  await new Promise((resolve) => setTimeout(resolve, 300)); // Ensure this runs after any ongoing operations
   return await page.evaluate(
     ({ structStr, position }) =>
       window.ketcher.setMolecule(structStr, { position }),

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

@@ -270,6 +270,9 @@ export function getSymbolLocator(
   if (Object.hasOwn(options, 'symbolId')) {
     attributes['data-symbol-id'] = String(symbolId);
   }
+  if (Object.hasOwn(options, 'symbolAlias')) {
+    attributes['data-symbol-alias'] = String(symbolAlias);
+  }
   if (Object.hasOwn(options, 'chainId')) {
     attributes['data-chain-id'] = String(chainId);
   }

packages/ketcher-core/docs/README.md

@@ -55,9 +55,7 @@ ketcher-core
 - [SGroup](classes/SGroup.md)
 - [SGroupBracketParams](classes/SGroupBracketParams.md)
 - [SGroupForest](classes/SGroupForest.md)
-- [SdfSerializer](classes/SdfSerializer.md)
 - [SimpleObject](classes/SimpleObject.md)
-- [SmiSerializer](classes/SmiSerializer.md)
 - [Struct](classes/Struct.md)
 - [Text](classes/Text.md)
 - [Vec2](classes/Vec2.md)
@@ -97,11 +95,8 @@ ketcher-core
 - [RxnArrowAttributes](interfaces/RxnArrowAttributes.md)
 - [RxnPlusAttributes](interfaces/RxnPlusAttributes.md)
 - [ScaleOptions](interfaces/ScaleOptions.md)
-- [SdfItem](interfaces/SdfItem.md)
 - [Serializer](interfaces/Serializer.md)
 - [SimpleObjectAttributes](interfaces/SimpleObjectAttributes.md)
-- [SmiSerializerOptions](interfaces/SmiSerializerOptions.md)
-- [StructAssociatedData](interfaces/StructAssociatedData.md)
 - [StructFormatter](interfaces/StructFormatter.md)
 - [StructService](interfaces/StructService.md)
 - [StructServiceOptions](interfaces/StructServiceOptions.md)