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Prevent invalid modificationTypes from loading monomers #9071

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Initial plan
Copilot Feb 1, 2026
2d2e668
Validate modificationTypes on monomer library update
Copilot Feb 1, 2026
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114 changes: 114 additions & 0 deletions packages/ketcher-core/__tests__/application/editor/Editor.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -161,5 +161,119 @@ describe('CoreEditor', () => {
);
expect(editor.monomersLibrary.length).toBe(initialLibrarySize + 1);
});

it('should reject monomer with empty modificationTypes value', () => {
const monomerWithEmptyModificationTypes = {
root: {
templates: [
{
$ref: 'monomerTemplate-TEST_MOD_EMPTY',
},
],
},
'monomerTemplate-TEST_MOD_EMPTY': {
type: 'monomerTemplate',
id: 'TEST_MOD_EMPTY',
class: 'CHEM',
classHELM: 'CHEM',
fullName: 'Test Mod Empty',
name: 'TEST_MOD_EMPTY',
naturalAnalogShort: 'X',
props: {
MonomerName: 'TEST_MOD_EMPTY',
MonomerClass: 'CHEM',
Name: 'TEST_MOD_EMPTY',
MonomerNaturalAnalogCode: 'X',
modificationTypes: [' '],
},
},
};

const initialLibrarySize = editor.monomersLibrary.length;
editor.updateMonomersLibrary(
JSON.stringify(monomerWithEmptyModificationTypes),
);

expect(errorSpy).toHaveBeenCalledWith(
'Load of "TEST_MOD_EMPTY" monomer has failed, monomer definition contains invalid modificationTypes value. The modificationTypes couldn\'t be empty',
);
expect(editor.monomersLibrary.length).toBe(initialLibrarySize);
});

it('should reject monomer with formatting characters in modificationTypes', () => {
const monomerWithFormattingCharacters = {
root: {
templates: [
{
$ref: 'monomerTemplate-TEST_MOD_FORMAT',
},
],
},
'monomerTemplate-TEST_MOD_FORMAT': {
type: 'monomerTemplate',
id: 'TEST_MOD_FORMAT',
class: 'CHEM',
classHELM: 'CHEM',
fullName: 'Test Mod Format',
name: 'TEST_MOD_FORMAT',
naturalAnalogShort: 'X',
props: {
MonomerName: 'TEST_MOD_FORMAT',
MonomerClass: 'CHEM',
Name: 'TEST_MOD_FORMAT',
MonomerNaturalAnalogCode: 'X',
modificationTypes: ['Bad\tType'],
},
},
};

const initialLibrarySize = editor.monomersLibrary.length;
editor.updateMonomersLibrary(
JSON.stringify(monomerWithFormattingCharacters),
);

expect(errorSpy).toHaveBeenCalledWith(
'Load of "TEST_MOD_FORMAT" monomer has failed, monomer definition contains invalid modificationTypes value. The modificationTypes value contains formatting characters',
);
expect(editor.monomersLibrary.length).toBe(initialLibrarySize);
});

it('should accept monomer with valid modificationTypes', () => {
const monomerWithValidModificationTypes = {
root: {
templates: [
{
$ref: 'monomerTemplate-TEST_MOD_VALID',
},
],
},
'monomerTemplate-TEST_MOD_VALID': {
type: 'monomerTemplate',
id: 'TEST_MOD_VALID',
class: 'CHEM',
classHELM: 'CHEM',
fullName: 'Test Mod Valid',
name: 'TEST_MOD_VALID',
naturalAnalogShort: 'X',
props: {
MonomerName: 'TEST_MOD_VALID',
MonomerClass: 'CHEM',
Name: 'TEST_MOD_VALID',
MonomerNaturalAnalogCode: 'X',
modificationTypes: ['Natural amino acid'],
},
},
};

const initialLibrarySize = editor.monomersLibrary.length;
editor.updateMonomersLibrary(
JSON.stringify(monomerWithValidModificationTypes),
);

expect(errorSpy).not.toHaveBeenCalledWith(
expect.stringContaining('invalid modificationTypes value'),
);
expect(editor.monomersLibrary.length).toBe(initialLibrarySize + 1);
});
});
});
34 changes: 34 additions & 0 deletions packages/ketcher-core/src/application/editor/Editor.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -361,6 +361,30 @@ export class CoreEditor {
monomersLibrary: newMonomersLibraryChunk,
} = parseMonomersLibrary(monomersDataRaw);

const getModificationTypesError = (
modificationTypes?: string[],
): string | null => {
if (!modificationTypes) {
return null;
}

for (const modificationType of modificationTypes) {
if (!modificationType.trim()) {
return "The modificationTypes couldn't be empty";
}

if (/[\t\n\r]/.test(modificationType)) {
return 'The modificationTypes value contains formatting characters';
}

if (modificationType.length > 200) {
return 'The modificationTypes value exceeds 200 characters';
}
}

return null;
};

// handle monomer templates
newMonomersLibraryChunk.forEach((newMonomer) => {
const aliasCollisionExists = this._monomersLibrary.some(
Expand Down Expand Up @@ -396,6 +420,16 @@ export class CoreEditor {
return;
}

const modificationTypesError = getModificationTypesError(
newMonomer.props?.modificationTypes,
);
if (modificationTypesError) {
KetcherLogger.error(
`Load of "${newMonomer.props.MonomerName}" monomer has failed, monomer definition contains invalid modificationTypes value. ${modificationTypesError}`,
);
return;
}

const existingMonomerIndex = this._monomersLibrary.findIndex(
(monomer) => {
return (
Expand Down