#5651 – The reaction can't save to MDL RXN V3000 (returns RXN V2000 i…

…nstead) (#5706) * #5651 - Add support for MOL V3000, SDF V3000, MDL RXN V3000 on structure save * Update tests
epam · Oct 10, 2024 · cb22a2f · cb22a2f
1 parent 94e546c
commit cb22a2f
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Showing 15 changed files with 349 additions and 407 deletions.
diff --git a/ketcher-autotests/tests/File-Management/Open-And-Save-Files/MOL-Files/mol-files.spec.ts b/ketcher-autotests/tests/File-Management/Open-And-Save-Files/MOL-Files/mol-files.spec.ts
@@ -199,39 +199,34 @@ test('Open and Save file - Open/Save V3000 *.mol file contains abbreviation 1/2
   await takeEditorScreenshot(page);
 });
 
-test.fail(
-  'Open and Save file - Open/Save V3000 *.mol file contains abbreviation 2/2 - save',
-  async ({ page }) => {
-    /*
-     * IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2490
-     * Test case: EPMLSOPKET-1859(2)
-     * Description: v3000 mol file with abbreviation is opened and saved correctly
-     */
-    await waitForPageInit(page);
+test('Open and Save file - Open/Save V3000 *.mol file contains abbreviation 2/2 - save', async ({
+  page,
+}) => {
+  /*
+   * Test case: EPMLSOPKET-1859(2)
+   * Description: v3000 mol file with abbreviation is opened and saved correctly
+   */
+  await waitForPageInit(page);
 
-    await openFileAndAddToCanvas(
-      'Molfiles-V3000/sec-butyl-abr-V3000.mol',
-      page,
-    );
-    const expectedFile = await getMolfile(page, 'v3000');
-    await saveToFile(
-      'Molfiles-V3000/sec_butyl_abr_V3000-expected.mol',
-      expectedFile,
-    );
-    const METADATA_STRING_INDEX = [1];
+  await openFileAndAddToCanvas('Molfiles-V3000/sec-butyl-abr-V3000.mol', page);
+  const expectedFile = await getMolfile(page, 'v3000');
+  await saveToFile(
+    'Molfiles-V3000/sec_butyl_abr_V3000-expected.mol',
+    expectedFile,
+  );
+  const METADATA_STRING_INDEX = [1];
 
-    const { fileExpected: molFileExpected, file: molFile } =
-      await receiveFileComparisonData({
-        page,
-        expectedFileName:
-          'tests/test-data/Molfiles-V3000/sec_butyl_abr_V3000-expected.mol',
-        fileFormat: 'v3000',
-        metaDataIndexes: METADATA_STRING_INDEX,
-      });
+  const { fileExpected: molFileExpected, file: molFile } =
+    await receiveFileComparisonData({
+      page,
+      expectedFileName:
+        'tests/test-data/Molfiles-V3000/sec_butyl_abr_V3000-expected.mol',
+      fileFormat: 'v3000',
+      metaDataIndexes: METADATA_STRING_INDEX,
+    });
 
-    expect(molFile).toEqual(molFileExpected);
-  },
-);
+  expect(molFile).toEqual(molFileExpected);
+});
 
 test('Open and Save file - Open/Save file with R-Groups 1/2 - open', async ({
   page,
@@ -332,39 +327,34 @@ test('Open and Save file - Open/Save V3000 mol file contains attached data 1/2 -
   await takeEditorScreenshot(page);
 });
 
-test.fail(
-  'Open and Save file - Open/Save V3000 mol file contains attached data 2/2 - save',
-  async ({ page }) => {
-    /*
-     * IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2490
-     * Test case: EPMLSOPKET-1882(2)
-     * Description: Structure with attached data is saved to mol file correctly
-     */
-    await waitForPageInit(page);
+test('Open and Save file - Open/Save V3000 mol file contains attached data 2/2 - save', async ({
+  page,
+}) => {
+  /*
+   * Test case: EPMLSOPKET-1882(2)
+   * Description: Structure with attached data is saved to mol file correctly
+   */
+  await waitForPageInit(page);
 
-    await openFileAndAddToCanvas(
-      'Molfiles-V3000/attached-data-V3000.mol',
-      page,
-    );
-    const expectedFile = await getMolfile(page, 'v3000');
-    await saveToFile(
-      'Molfiles-V3000/attached-data-V3000-expected.mol',
-      expectedFile,
-    );
-    const METADATA_STRING_INDEX = [1];
+  await openFileAndAddToCanvas('Molfiles-V3000/attached-data-V3000.mol', page);
+  const expectedFile = await getMolfile(page, 'v3000');
+  await saveToFile(
+    'Molfiles-V3000/attached-data-V3000-expected.mol',
+    expectedFile,
+  );
+  const METADATA_STRING_INDEX = [1];
 
-    const { fileExpected: molFileExpected, file: molFile } =
-      await receiveFileComparisonData({
-        page,
-        expectedFileName:
-          'tests/test-data/Molfiles-V3000/attached-data-V3000-expected.mol',
-        fileFormat: 'v3000',
-        metaDataIndexes: METADATA_STRING_INDEX,
-      });
+  const { fileExpected: molFileExpected, file: molFile } =
+    await receiveFileComparisonData({
+      page,
+      expectedFileName:
+        'tests/test-data/Molfiles-V3000/attached-data-V3000-expected.mol',
+      fileFormat: 'v3000',
+      metaDataIndexes: METADATA_STRING_INDEX,
+    });
 
-    expect(molFile).toEqual(molFileExpected);
-  },
-);
+  expect(molFile).toEqual(molFileExpected);
+});
 
 test('Open and Save file - V3000 *.mol file contains Heteroatoms 1/2 - open', async ({
   page,
@@ -380,36 +370,34 @@ test('Open and Save file - V3000 *.mol file contains Heteroatoms 1/2 - open', as
   await takeEditorScreenshot(page);
 });
 
-test.fail(
-  'Open and Save file - V3000 *.mol file contains Heteroatoms 2/2 - save',
-  async ({ page }) => {
-    /**
-     * IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2490
-     * Test case: EPMLSOPKET-1879(2)
-     * Description: Structure with heteroatoms is saved correctly to mol file
-     */
-    await waitForPageInit(page);
+test('Open and Save file - V3000 *.mol file contains Heteroatoms 2/2 - save', async ({
+  page,
+}) => {
+  /**
+   * Test case: EPMLSOPKET-1879(2)
+   * Description: Structure with heteroatoms is saved correctly to mol file
+   */
+  await waitForPageInit(page);
 
-    await openFileAndAddToCanvas('Molfiles-V3000/heteroatoms-V3000.mol', page);
-    const expectedFile = await getMolfile(page, 'v3000');
-    await saveToFile(
-      'Molfiles-V3000/heteroatoms-V3000-expected.mol',
-      expectedFile,
-    );
-    const METADATA_STRING_INDEX = [1];
+  await openFileAndAddToCanvas('Molfiles-V3000/heteroatoms-V3000.mol', page);
+  const expectedFile = await getMolfile(page, 'v3000');
+  await saveToFile(
+    'Molfiles-V3000/heteroatoms-V3000-expected.mol',
+    expectedFile,
+  );
+  const METADATA_STRING_INDEX = [1];
 
-    const { fileExpected: molFileExpected, file: molFile } =
-      await receiveFileComparisonData({
-        page,
-        expectedFileName:
-          'tests/test-data/Molfiles-V3000/heteroatoms-V3000-expected.mol',
-        fileFormat: 'v3000',
-        metaDataIndexes: METADATA_STRING_INDEX,
-      });
+  const { fileExpected: molFileExpected, file: molFile } =
+    await receiveFileComparisonData({
+      page,
+      expectedFileName:
+        'tests/test-data/Molfiles-V3000/heteroatoms-V3000-expected.mol',
+      fileFormat: 'v3000',
+      metaDataIndexes: METADATA_STRING_INDEX,
+    });
 
-    expect(molFile).toEqual(molFileExpected);
-  },
-);
+  expect(molFile).toEqual(molFileExpected);
+});
 
 test('Open and Save file - Open/Save file with Attached data 1/2 - open', async ({
   page,
@@ -504,61 +492,56 @@ test('Open and Save file - Open/Save V3000 mol file contains abs stereochemistry
   await takeEditorScreenshot(page);
 });
 
-test.fail(
-  'Open and Save file - Open/Save V3000 mol file contains abs stereochemistry 2/2 - save',
-  async ({ page }) => {
-    /*
-     * IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2490
-     * Test case: EPMLSOPKET-1884(2)
-     * Description: Structure with abs stereochemistry is saved correctly to mol file
-     */
-    await waitForPageInit(page);
+test('Open and Save file - Open/Save V3000 mol file contains abs stereochemistry 2/2 - save', async ({
+  page,
+}) => {
+  /*
+   * Test case: EPMLSOPKET-1884(2)
+   * Description: Structure with abs stereochemistry is saved correctly to mol file
+   */
+  await waitForPageInit(page);
 
-    await openFileAndAddToCanvas('Molfiles-V3000/V3000-abs.mol', page);
-    const expectedFile = await getMolfile(page, 'v3000');
-    await saveToFile('Molfiles-V3000/V3000-abs-expected.mol', expectedFile);
-    const METADATA_STRING_INDEX = [1];
+  await openFileAndAddToCanvas('Molfiles-V3000/V3000-abs.mol', page);
+  const expectedFile = await getMolfile(page, 'v3000');
+  await saveToFile('Molfiles-V3000/V3000-abs-expected.mol', expectedFile);
+  const METADATA_STRING_INDEX = [1];
 
-    const { fileExpected: molFileExpected, file: molFile } =
-      await receiveFileComparisonData({
-        page,
-        expectedFileName:
-          'tests/test-data/Molfiles-V3000/V3000-abs-expected.mol',
-        fileFormat: 'v3000',
-        metaDataIndexes: METADATA_STRING_INDEX,
-      });
+  const { fileExpected: molFileExpected, file: molFile } =
+    await receiveFileComparisonData({
+      page,
+      expectedFileName: 'tests/test-data/Molfiles-V3000/V3000-abs-expected.mol',
+      fileFormat: 'v3000',
+      metaDataIndexes: METADATA_STRING_INDEX,
+    });
 
-    expect(molFile).toEqual(molFileExpected);
-  },
-);
+  expect(molFile).toEqual(molFileExpected);
+});
 
-test.fail(
-  'Open and Save file - Save V2000 molfile as V3000 molfile',
-  async ({ page }) => {
-    /*
-     * IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2490
-     * Test case: EPMLSOPKET-1985
-     * Description: Structure opened from V2000 molfile can be saved to V3000 molfile
-     */
-    await waitForPageInit(page);
+test('Open and Save file - Save V2000 molfile as V3000 molfile', async ({
+  page,
+}) => {
+  /*
+   * Test case: EPMLSOPKET-1985
+   * Description: Structure opened from V2000 molfile can be saved to V3000 molfile
+   */
+  await waitForPageInit(page);
 
-    await openFileAndAddToCanvas('Molfiles-V2000/spiro2.mol', page);
-    const expectedFile = await getMolfile(page, 'v3000');
-    await saveToFile('Molfiles-V3000/spiro-expected.mol', expectedFile);
+  await openFileAndAddToCanvas('Molfiles-V2000/spiro2.mol', page);
+  const expectedFile = await getMolfile(page, 'v3000');
+  await saveToFile('Molfiles-V3000/spiro-expected.mol', expectedFile);
 
-    const METADATA_STRINGS_INDEXES = [1, 3];
+  const METADATA_STRINGS_INDEXES = [1, 3];
 
-    const { fileExpected: molFileExpected, file: molFile } =
-      await receiveFileComparisonData({
-        page,
-        expectedFileName: 'tests/test-data/Molfiles-V3000/spiro-expected.mol',
-        metaDataIndexes: METADATA_STRINGS_INDEXES,
-        fileFormat: 'v3000',
-      });
+  const { fileExpected: molFileExpected, file: molFile } =
+    await receiveFileComparisonData({
+      page,
+      expectedFileName: 'tests/test-data/Molfiles-V3000/spiro-expected.mol',
+      metaDataIndexes: METADATA_STRINGS_INDEXES,
+      fileFormat: 'v3000',
+    });
 
-    expect(molFile).toEqual(molFileExpected);
-  },
-);
+  expect(molFile).toEqual(molFileExpected);
+});
 
 test('Open and Save file - Save V3000 molfile as V2000 molfile', async ({
   page,
@@ -730,8 +713,6 @@ test.describe('Open and Save file', () => {
 
     for (const file of files) {
       test(`${file.testName}`, async ({ page }) => {
-        // IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2490
-        if (file.format === 'v3000') test.fail();
         await openFileAndAddToCanvas(file.pathToOpen, page);
 
         const expectedFile = await getMolfile(

diff --git a/ketcher-autotests/tests/File-Management/Open-And-Save-Files/Rxn-Files/rxn-files.spec.ts b/ketcher-autotests/tests/File-Management/Open-And-Save-Files/Rxn-Files/rxn-files.spec.ts
@@ -356,36 +356,31 @@ test.describe('Tests for Open and Save RXN file operations', () => {
     await takeEditorScreenshot(page);
   });
 
-  test.fail(
-    'Open and Save file - V3000 rxn file contains Rgroup 2/2 - save',
-    async ({ page }) => {
-      /**
-       * * IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2476
-       * Test case: EPMLSOPKET-1902(2)
-       * Description: Reaction can be saved correctly to rxn V3000 file
-       */
-      await openFileAndAddToCanvas('Rxn-V3000/r-group-V3000.rxn', page);
-      const expectedFile = await getRxn(page, 'v3000');
-      await saveToFile(
-        'Rxn-V3000/r-group-V3000-expectedV3000.rxn',
-        expectedFile,
-      );
+  test('Open and Save file - V3000 rxn file contains Rgroup 2/2 - save', async ({
+    page,
+  }) => {
+    /**
+     * Test case: EPMLSOPKET-1902(2)
+     * Description: Reaction can be saved correctly to rxn V3000 file
+     */
+    await openFileAndAddToCanvas('Rxn-V3000/r-group-V3000.rxn', page);
+    const expectedFile = await getRxn(page, 'v3000');
+    await saveToFile('Rxn-V3000/r-group-V3000-expectedV3000.rxn', expectedFile);
 
-      // eslint-disable-next-line no-magic-numbers
-      const METADATA_STRINGS_INDEXES = [2];
+    // eslint-disable-next-line no-magic-numbers
+    const METADATA_STRINGS_INDEXES = [2];
 
-      const { fileExpected: rxnFileExpected, file: rxnFile } =
-        await receiveFileComparisonData({
-          page,
-          expectedFileName:
-            'tests/test-data/Rxn-V3000/r-group-V3000-expectedV3000.rxn',
-          metaDataIndexes: METADATA_STRINGS_INDEXES,
-          fileFormat: 'v3000',
-        });
+    const { fileExpected: rxnFileExpected, file: rxnFile } =
+      await receiveFileComparisonData({
+        page,
+        expectedFileName:
+          'tests/test-data/Rxn-V3000/r-group-V3000-expectedV3000.rxn',
+        metaDataIndexes: METADATA_STRINGS_INDEXES,
+        fileFormat: 'v3000',
+      });
 
-      expect(rxnFile).toEqual(rxnFileExpected);
-    },
-  );
+    expect(rxnFile).toEqual(rxnFileExpected);
+  });
 
   test('Validate that unsplit nucleotides connected with phosphates could be saved to rxn2000 file and loaded back', async ({
     page,

diff --git a/ketcher-autotests/tests/File-Management/Open-And-Save-Files/SDF-Files/sdf-files.spec.ts b/ketcher-autotests/tests/File-Management/Open-And-Save-Files/SDF-Files/sdf-files.spec.ts
@@ -40,10 +40,7 @@ test.describe('CDF files', () => {
     await takeEditorScreenshot(page);
   });
 
-  test.fail('Open SDF v3000 file and save it', async ({ page }) => {
-    /*
-     * IMPORTANT: Test fails because we have bug https://github.com/epam/Indigo/issues/2477
-     */
+  test('Open SDF v3000 file and save it', async ({ page }) => {
     await openFileAndAddToCanvas('SDF/sdf-v3000-to-open.sdf', page);
     try {
       const expectedFile = await getSdf(page, 'v3000');