Skip to content

#8143 System allow to load monomers with invalid HELM aliases (spaces are not allowed) #9073

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Copilot wants to merge 7 commits into
base: master
Choose a base branch
from
+48 −0
Open

#8143 System allow to load monomers with invalid HELM aliases (spaces are not allowed) #9073

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
4e3c8cc
Initial plan
Copilot Feb 1, 2026
a78d25d
Validate HELM alias on monomer load
Copilot Feb 1, 2026
1d6ba55
Handle top-level HELM alias validation
Copilot Feb 1, 2026
ce3aa25
Harden HELM alias validation logging
Copilot Feb 1, 2026
45d3dd1
Align HELM alias validation with props
Copilot Feb 1, 2026
def0ab8
Escape asterisk in HELM alias regex
Copilot Feb 1, 2026
c74058d
Simplify HELM alias regex
Copilot Feb 1, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
36 changes: 36 additions & 0 deletions packages/ketcher-core/__tests__/application/editor/Editor.test.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -161,5 +161,41 @@ describe('CoreEditor', () => {
);
expect(editor.monomersLibrary.length).toBe(initialLibrarySize + 1);
});

it('should reject monomer with invalid aliasHELM', () => {
const monomerWithInvalidAlias = {
root: {
templates: [
{
$ref: 'monomerTemplate-CHEM4',
},
],
},
'monomerTemplate-CHEM4': {
type: 'monomerTemplate',
id: 'CHEM4',
class: 'CHEM',
classHELM: 'CHEM',
fullName: 'Test Chem 4',
name: 'CHEM4',
naturalAnalogShort: 'X',
props: {
MonomerName: 'CHEM4',
MonomerClass: 'CHEM',
Name: 'CHEM4',
MonomerNaturalAnalogCode: 'X',
aliasHELM: 'INV ALID',
},
},
};

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

expect(errorSpy).toHaveBeenCalledWith(
'Load of "CHEM4" monomer has failed, monomer definition contains invalid HELM alias value. The HELM alias must consist only of uppercase and lowercase letters, numbers, hyphens (-), underscores (_), and asterisks (*), spaces prohibited.',
);
expect(editor.monomersLibrary.length).toBe(initialLibrarySize);
});
});
});
12 changes: 12 additions & 0 deletions packages/ketcher-core/src/application/editor/Editor.ts
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -363,6 +363,18 @@ export class CoreEditor {

// handle monomer templates
newMonomersLibraryChunk.forEach((newMonomer) => {
const aliasHELM = newMonomer.props?.aliasHELM;
const monomerName = newMonomer.props?.MonomerName ?? 'Unknown';
if (
aliasHELM !== undefined &&
/[^A-Za-z0-9_*\-]/.test(aliasHELM)
) {
KetcherLogger.error(
`Load of "${monomerName}" monomer has failed, monomer definition contains invalid HELM alias value. The HELM alias must consist only of uppercase and lowercase letters, numbers, hyphens (-), underscores (_), and asterisks (*), spaces prohibited.`,
);
return;
}

const aliasCollisionExists = this._monomersLibrary.some(
(monomer) =>
(Boolean(newMonomer.props?.aliasHELM) &&
Expand Down
Loading