fix: Avoid overflows when saving files with large outputs

src/notebooks/deepnote/deepnoteDataConverter.ts

@@ -243,9 +243,9 @@ export class DeepnoteDataConverter {
                 } else if (item.mime === 'application/json') {
                     data['application/json'] = JSON.parse(new TextDecoder().decode(item.data));
                 } else if (item.mime === 'image/png') {
-                    data['image/png'] = btoa(String.fromCharCode(...new Uint8Array(item.data)));
+                    data['image/png'] = this.uint8ArrayToBase64(item.data);
                 } else if (item.mime === 'image/jpeg') {
-                    data['image/jpeg'] = btoa(String.fromCharCode(...new Uint8Array(item.data)));
+                    data['image/jpeg'] = this.uint8ArrayToBase64(item.data);
                 } else if (item.mime === 'application/vnd.deepnote.dataframe.v3+json') {
                     data['application/vnd.deepnote.dataframe.v3+json'] = JSON.parse(
                         new TextDecoder().decode(item.data)
@@ -523,4 +523,21 @@ export class DeepnoteDataConverter {
             return new NotebookCellOutput([]);
         });
     }
+
+    /**
+     * Converts a Uint8Array to a base64 string without causing stack overflow.
+     * Uses chunked processing to avoid call stack limits with large arrays.
+     */
+    private uint8ArrayToBase64(data: Uint8Array): string {
+        // Process in chunks to avoid stack overflow from spread operator
+        const chunkSize = 8192;
+        let binaryString = '';
+
+        for (let i = 0; i < data.length; i += chunkSize) {
+            const chunk = data.subarray(i, Math.min(i + chunkSize, data.length));
+            binaryString += String.fromCharCode(...chunk);
+        }
+
+        return btoa(binaryString);
+    }
 }

src/notebooks/deepnote/deepnoteDataConverter.unit.test.ts

@@ -1,5 +1,5 @@
 import { assert } from 'chai';
-import { NotebookCellKind, type NotebookCellData } from 'vscode';
+import { NotebookCellKind, NotebookCellOutput, NotebookCellOutputItem, type NotebookCellData } from 'vscode';
 
 import { DeepnoteDataConverter } from './deepnoteDataConverter';
 import type { DeepnoteBlock, DeepnoteOutput } from '../../platform/deepnote/deepnoteTypes';
@@ -797,4 +797,51 @@ suite('DeepnoteDataConverter', () => {
             assert.deepStrictEqual(roundTripBlocks, originalBlocks);
         });
     });
+
+    suite('large data handling', () => {
+        test('should handle cells with large image data without stack overflow', () => {
+            // Create a large image data buffer (1MB) - this reproduces the bug where
+            // saving fails with "Maximum call stack size exceeded" because
+            // btoa(String.fromCharCode(...largeArray)) causes stack overflow
+            const largeImageSize = 1000000; // 1MB
+            const largeImageData = new Uint8Array(largeImageSize);
+
+            for (let i = 0; i < largeImageSize; i++) {
+                largeImageData[i] = i % 256;
+            }
+
+            const cellWithLargeImage: NotebookCellData = {
+                kind: NotebookCellKind.Code,
+                value: 'display_image()',
+                languageId: 'python',
+                metadata: {
+                    __deepnotePocket: {
+                        type: 'code',
+                        sortingKey: 'a0'
+                    },
+                    id: 'block-1'
+                },
+                outputs: [
+                    new NotebookCellOutput([new NotebookCellOutputItem(largeImageData, 'image/png')], {
+                        cellId: 'block-1',
+                        cellIndex: 0
+                    })
+                ]
+            };
+
+            // This should not throw - it should handle large data gracefully
+            const blocks = converter.convertCellsToBlocks([cellWithLargeImage]);
+
+            assert.strictEqual(blocks.length, 1);
+            assert.strictEqual(blocks[0].type, 'code');
+            assert.isDefined(blocks[0].outputs);
+            assert.strictEqual(blocks[0].outputs!.length, 1);
+
+            // Verify the output data is properly base64 encoded
+            const output = blocks[0].outputs![0] as { data?: Record<string, unknown> };
+            assert.isDefined(output.data);
+            assert.isDefined(output.data!['image/png']);
+            assert.isString(output.data!['image/png']);
+        });
+    });
 });

src/notebooks/deepnote/deepnoteSerializer.ts

@@ -5,10 +5,43 @@ import { l10n, workspace, type CancellationToken, type NotebookData, type Notebo
 import { logger } from '../../platform/logging';
 import { IDeepnoteNotebookManager } from '../types';
 import { DeepnoteDataConverter } from './deepnoteDataConverter';
-import type { DeepnoteFile, DeepnoteNotebook } from '../../platform/deepnote/deepnoteTypes';
+import type { DeepnoteBlock, DeepnoteFile, DeepnoteNotebook } from '../../platform/deepnote/deepnoteTypes';
 
 export { DeepnoteBlock, DeepnoteNotebook, DeepnoteOutput, DeepnoteFile } from '../../platform/deepnote/deepnoteTypes';
 
+/**
+ * Deep clones an object while removing circular references.
+ * Uses a recursion stack pattern to only drop true cycles, preserving shared references.
+ */
+function cloneWithoutCircularRefs<T>(obj: T, seen = new WeakSet<object>()): T {
+    if (obj === null || typeof obj !== 'object') {
+        return obj;
+    }
+
+    if (seen.has(obj as object)) {
+        // True circular reference on the current path - drop it
+        return undefined as T;
+    }
+
+    seen.add(obj as object);
+
+    try {
+        if (Array.isArray(obj)) {
+            return obj.map((item) => cloneWithoutCircularRefs(item, seen)) as T;
+        }
+
+        const clone: Record<string, unknown> = {};
+
+        for (const key of Object.keys(obj as Record<string, unknown>)) {
+            clone[key] = cloneWithoutCircularRefs((obj as Record<string, unknown>)[key], seen);
+        }
+
+        return clone as T;
+    } finally {
+        seen.delete(obj as object);
+    }
+}
+
 /**
  * Serializer for converting between Deepnote YAML files and VS Code notebook format.
  * Handles reading/writing .deepnote files and manages project state persistence.
@@ -108,49 +141,63 @@ export class DeepnoteNotebookSerializer implements NotebookSerializer {
         }
 
         try {
+            logger.debug('SerializeNotebook: Starting serialization');
+
             const projectId = data.metadata?.deepnoteProjectId;
 
             if (!projectId) {
                 throw new Error('Missing Deepnote project ID in notebook metadata');
             }
 
+            logger.debug(`SerializeNotebook: Project ID: ${projectId}`);
+
             const originalProject = this.notebookManager.getOriginalProject(projectId) as DeepnoteFile | undefined;
 
             if (!originalProject) {
                 throw new Error('Original Deepnote project not found. Cannot save changes.');
             }
 
+            logger.debug('SerializeNotebook: Got original project');
+
             const notebookId =
                 data.metadata?.deepnoteNotebookId || this.notebookManager.getTheSelectedNotebookForAProject(projectId);
 
             if (!notebookId) {
                 throw new Error('Cannot determine which notebook to save');
             }
 
-            const notebookIndex = originalProject.project.notebooks.findIndex(
-                (nb: { id: string }) => nb.id === notebookId
-            );
+            logger.debug(`SerializeNotebook: Notebook ID: ${notebookId}`);
+
+            const notebook = originalProject.project.notebooks.find((nb: { id: string }) => nb.id === notebookId);
 
-            if (notebookIndex === -1) {
+            if (!notebook) {
                 throw new Error(`Notebook with ID ${notebookId} not found in project`);
             }
 
-            const updatedProject = JSON.parse(JSON.stringify(originalProject)) as DeepnoteFile;
+            logger.debug(`SerializeNotebook: Found notebook, converting ${data.cells.length} cells to blocks`);
+
+            // Clone blocks while removing circular references that may have been
+            // introduced by VS Code's notebook cell/output handling
+            const blocks = this.converter.convertCellsToBlocks(data.cells);
+
+            logger.debug(`SerializeNotebook: Converted to ${blocks.length} blocks, now cloning without circular refs`);
+
+            notebook.blocks = cloneWithoutCircularRefs<DeepnoteBlock[]>(blocks);
 
-            const updatedBlocks = this.converter.convertCellsToBlocks(data.cells);
+            logger.debug('SerializeNotebook: Cloned blocks, updating modifiedAt');
 
-            updatedProject.project.notebooks[notebookIndex].blocks = updatedBlocks;
+            originalProject.metadata.modifiedAt = new Date().toISOString();
 
-            updatedProject.metadata.modifiedAt = new Date().toISOString();
+            logger.debug('SerializeNotebook: Starting yaml.dump');
 
-            const yamlString = yaml.dump(updatedProject, {
+            const yamlString = yaml.dump(originalProject, {
                 indent: 2,
                 lineWidth: -1,
                 noRefs: true,
                 sortKeys: false
             });
 
-            this.notebookManager.storeOriginalProject(projectId, updatedProject, notebookId);
+            logger.debug(`SerializeNotebook: yaml.dump complete, ${yamlString.length} chars`);
 
             return new TextEncoder().encode(yamlString);
         } catch (error) {

src/notebooks/deepnote/deepnoteSerializer.unit.test.ts

@@ -325,6 +325,77 @@ project:
         });
     });
 
+    suite('circular reference handling', () => {
+        test('should serialize notebook with circular references in output metadata', async () => {
+            // Create output with circular reference - this reproduces the bug
+            // where saving fails with "Maximum call stack size exceeded"
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            const circularOutput: any = {
+                output_type: 'execute_result',
+                execution_count: 1,
+                data: { 'text/plain': 'test' },
+                metadata: {}
+            };
+            // Create circular reference
+            circularOutput.metadata.self = circularOutput;
+
+            const projectWithCircularRef: DeepnoteFile = {
+                version: '1.0',
+                metadata: {
+                    createdAt: '2023-01-01T00:00:00Z',
+                    modifiedAt: '2023-01-02T00:00:00Z'
+                },
+                project: {
+                    id: 'project-circular',
+                    name: 'Circular Test',
+                    notebooks: [
+                        {
+                            id: 'notebook-1',
+                            name: 'Test Notebook',
+                            blocks: [
+                                {
+                                    blockGroup: 'group-1',
+                                    id: 'block-1',
+                                    content: 'test',
+                                    sortingKey: 'a0',
+                                    type: 'code',
+                                    outputs: [circularOutput]
+                                }
+                            ],
+                            executionMode: 'block',
+                            isModule: false
+                        }
+                    ],
+                    settings: {}
+                }
+            };
+
+            manager.storeOriginalProject('project-circular', projectWithCircularRef, 'notebook-1');
+
+            const notebookData = {
+                cells: [
+                    {
+                        kind: 2, // NotebookCellKind.Code
+                        value: 'test',
+                        languageId: 'python',
+                        metadata: {}
+                    }
+                ],
+                metadata: {
+                    deepnoteProjectId: 'project-circular',
+                    deepnoteNotebookId: 'notebook-1'
+                }
+            };
+
+            // Should successfully serialize even with circular references
+            const result = await serializer.serializeNotebook(notebookData as any, {} as any);
+
+            assert.instanceOf(result, Uint8Array);
+            const yamlString = new TextDecoder().decode(result);
+            assert.include(yamlString, 'project-circular');
+        });
+    });
+
     suite('integration scenarios', () => {
         test('should maintain independence between serializer instances', () => {
             const manager1 = new DeepnoteNotebookManager();