AI-assisted knowledge graph auto-linking by d-oit · Pull Request #291 · d-oit/do-knowledge-studio

d-oit · 2026-06-08T14:36:04Z

Implemented AI-assisted knowledge graph auto-linking. This feature uses LLMs to analyze note content, extract named entities (people, orgs, tech, etc.), and suggest relationships between them. Users can review these suggestions through a dedicated dialog and selectively add them to the knowledge graph.

Key components:

src/lib/ai/entity-extractor.ts: LLM prompt and extraction logic.
src/lib/ai/graph-linker.ts: Service for applying entities/links to the DB with deduplication and metadata tagging.
src/features/ai/EntityReviewDialog.tsx: Review interface with checkboxes for entities and relationships.
src/features/editor/Editor.tsx: Integrated "AI Extract" button and auto-trigger logic after saving a note.
src/features/graph/GraphControls.tsx: New "Analyze All Notes" batch processing mode.

The implementation ensures that:

Entities are deduplicated by name.
Relationships are not duplicated if they already exist.
New entities store the sourceNoteId in their metadata for traceability.
Unit and integration tests cover the core extraction and linking logic.

Fixes #285

PR created automatically by Jules for task 9896207610745298301 started by @d-oit

Implemented LLM-powered entity extraction and relationship discovery from notes. Added a review UI for users to selectively add extracted entities and edges to the graph. Integrated extraction into the editor (manual and auto-trigger) and added batch analysis to graph controls. Includes duplicate checking and backlinks to source notes in metadata. Co-authored-by: d-oit <6849456+d-oit@users.noreply.github.com>

google-labs-jules · 2026-06-08T14:36:05Z

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deepsource-io · 2026-06-08T14:36:21Z

DeepSource Code Review

We reviewed changes in 89efe1b...eab8399 on this pull request. Below is the summary for the review, and you can see the individual issues we found as inline review comments.

See full review on DeepSource ↗

Important

Some issues found as part of this review are outside of the diff in this pull request and aren't shown in the inline review comments due to GitHub's API limitations. You can see those issues on the DeepSource dashboard.

PR Report Card

Overall Grade	Security Reliability Complexity Hygiene

Code Review Summary

Analyzer	Updated (UTC)	Details
JavaScript	Jun 9, 2026 8:21a.m.	Review ↗
Python	Jun 9, 2026 8:21a.m.	Review ↗
Shell	Jun 9, 2026 8:21a.m.	Review ↗
SQL	Jun 9, 2026 8:21a.m.	Review ↗

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codacy-production · 2026-06-08T14:36:57Z

Not up to standards ⛔

🔴 Issues 12 high · 6 medium

Alerts:
⚠ 18 issues (≤ 0 issues of at least minor severity)

Results:
18 new issues

Category Results

BestPractice 6 high

ErrorProne 6 medium
6 high

View in Codacy

🟢 Metrics 77 complexity · 5 duplication

Metric Results

Complexity 77

Duplication 5

View in Codacy

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_{TIP This summary will be updated as you push new changes.}

deepsource-io · 2026-06-08T14:36:59Z

+  };
+
+  return (
+    <div className="modal-overlay" onClick={(e) => e.target === e.currentTarget && onClose()}>


JSX tree is too deeply nested. Found 5 levels of nesting

Nesting JSX elements too deeply can confuse developers reading the code. To make maintenance and refactoring easier, DeepSource recommends limiting the maximum JSX tree depth to 4.

deepsource-io · 2026-06-08T14:36:59Z

+            </h4>
+            <div className="entity-list" style={{ display: 'flex', flexDirection: 'column', gap: '8px' }}>
+              {result.entities.map((entity, idx) => (
+                <label key={idx} style={{


Do not use Array index in keys

When rendering a list of items in React, it is necessary to pass a "key" prop.
This key is used by React to identify which items have changed, are added, or are removed and should be stable.
It is not recommended to use the index of an element as key because it doesn't uniquely identify the element.
When elements are added/removed from an array, the index of an element may change, which will result in unnecessary re-renders.

deepsource-io · 2026-06-08T14:36:59Z

+              {result.relationships.map((rel, idx) => {
+                const key = `${rel.from}->${rel.to}`;
+                return (
+                  <label key={idx} style={{


Do not use Array index in keys

When rendering a list of items in React, it is necessary to pass a "key" prop.
This key is used by React to identify which items have changed, are added, or are removed and should be stable.
It is not recommended to use the index of an element as key because it doesn't uniquely identify the element.
When elements are added/removed from an array, the index of an element may change, which will result in unnecessary re-renders.

deepsource-io · 2026-06-08T14:36:59Z

+  const [isExtracting, setIsExtracting] = useState(false);
+  const [extractionResult, setExtractionResult] = useState<EntityExtractionResult | null>(null);
+  const [showExtractionReview, setShowExtractionReview] = useState(false);
+  const [extractionSourceId, setExtractionSourceId] = useState<string | undefined>(undefined);


Remove redundant `undefined` from function call

When an argument is omitted from a function call, it will default to undefined. It is therefore redundant to explicitly pass an undefined literal as the last argument.

deepsource-io · 2026-06-08T14:36:59Z

    setSourceUrl(e.target.value);
  }, []);

+  const handleExtractEntities = useCallback(async (entityId?: string, forceContent?: string) => {


Function has a cyclomatic complexity of 10 with "medium" risk

A function with high cyclomatic complexity can be hard to understand and
maintain. Cyclomatic complexity is a software metric that measures the number of
independent paths through a function. A higher cyclomatic complexity indicates
that the function has more decision points and is more complex.

deepsource-io · 2026-06-08T14:36:59Z

+export async function applyEntitiesToGraph(
+  result: EntityExtractionResult,
+  repository: IRepository,
+  selectedEntities: string[],
+  selectedRelationships: string[],
+  sourceNoteId?: string
+): Promise<void> {
+  const nameToId = new Map<string, string>();
+
+  // 1. Process selected entities
+  for (const entity of result.entities) {
+    if (!selectedEntities.includes(entity.name)) continue;
+
+    let existing = await repository.getEntityByName(entity.name);
+    if (!existing) {
+      // Create new entity if it doesn't exist
+      const created = await repository.createEntity({
+        name: entity.name,
+        type: entity.type,
+        description: entity.description,
+        metadata: {
+          sourceNoteId,
+          aiExtracted: true
+        }
+      });
+      nameToId.set(entity.name, created.id!);
+    } else {
+      nameToId.set(entity.name, existing.id!);
+    }
+  }
+
+  // 2. Fetch existing links once if doing batch to avoid N+1 check?
+  // For now, simple check for each relationship
+  const existingLinks = await repository.getAllLinks();
+
+  for (const rel of result.relationships) {
+    const relKey = `${rel.from}->${rel.to}`;
+    if (!selectedRelationships.includes(relKey)) continue;
+
+    // Resolve IDs for the from and to entities
+    const fromId = nameToId.get(rel.from) || (await repository.getEntityByName(rel.from))?.id;
+    const toId = nameToId.get(rel.to) || (await repository.getEntityByName(rel.to))?.id;
+
+    if (fromId && toId) {
+      // Check if link already exists to avoid duplicates
+      const exists = existingLinks.some(l =>
+        l.source_id === fromId &&
+        l.target_id === toId &&
+        l.relation === rel.label
+      );
+
+      if (!exists) {
+        await repository.createLink({
+          source_id: fromId,
+          target_id: toId,
+          relation: rel.label,
+          metadata: {
+            sourceNoteId,
+            aiExtracted: true
+          }
+        });
+      }
+    }
+  }
+}


Unexpected function declaration in the global scope, wrap in an IIFE for a local variable, assign as global property for a global variable

It is considered a best practice to avoid 'polluting' the global scope with variables that are intended to be local to the script. Global variables created from a script can produce name collisions with global variables created from another script, which will usually lead to runtime errors or unexpected behavior. It is mostly useful for browser scripts.

deepsource-io · 2026-06-08T14:36:59Z

+/**
+ * Applies the selected entities and relationships from an AI extraction result to the graph.
+ */
+export async function applyEntitiesToGraph(


`applyEntitiesToGraph` has a cyclomatic complexity of 11 with "medium" risk

A function with high cyclomatic complexity can be hard to understand and
maintain. Cyclomatic complexity is a software metric that measures the number of
independent paths through a function. A higher cyclomatic complexity indicates
that the function has more decision points and is more complex.

deepsource-io · 2026-06-08T14:37:00Z

+          aiExtracted: true
+        }
+      });
+      nameToId.set(entity.name, created.id!);


Forbidden non-null assertion

Using non-null assertions cancels out the benefits of strict null-checking, and introduces the possibility of runtime errors. Avoid non-null assertions unless absolutely necessary. If you still need to use one, write a skipcq comment to explain why it is safe.

deepsource-io · 2026-06-08T14:37:00Z

+      });
+      nameToId.set(entity.name, created.id!);
+    } else {
+      nameToId.set(entity.name, existing.id!);


Forbidden non-null assertion

Using non-null assertions cancels out the benefits of strict null-checking, and introduces the possibility of runtime errors. Avoid non-null assertions unless absolutely necessary. If you still need to use one, write a skipcq comment to explain why it is safe.

Implemented LLM-powered entity extraction and relationship discovery from notes. Added a review UI for users to selectively add extracted entities and edges to the graph. Integrated extraction into the editor (manual and auto-trigger) and added batch analysis to graph controls. Includes duplicate checking and backlinks to source notes in metadata. Fixed CI failures: - Added Sparkles and X icons to lucide-react mock in tests. - Fixed missing imports and initialized repository in GraphControls.tsx and Editor.tsx. - Resolved lint errors (unused vars, explicit any, prefer-const). Co-authored-by: d-oit <6849456+d-oit@users.noreply.github.com>

deepsource-io · 2026-06-08T15:02:25Z

 import { useMediaQuery } from '../../hooks/useMediaQuery';
 import { MEDIA_QUERIES } from '../../lib/constants';
 import type { GraphSnapshot } from '../../lib/validation';
 import { repository, type GraphSnapshotDiff } from '../../db/repository';


'repository' is defined but never used

Unused variables are generally considered a code smell and should be avoided.

deepsource-io · 2026-06-08T15:02:26Z

+import { applyEntitiesToGraph } from '../graph-linker';
+import { IRepository } from '../../../db/repository/types';
+import { EntityExtractionResult } from '../entity-extractor';
+import { Entity } from '../../../lib/validation';


Useless path segments for "../../../lib/validation", should be "../../validation"

Unnecessarily complex import statements can be simplified. Complex imports usually result in confusing code. This usually happens as a result of refactoring.

deepsource-io · 2026-06-08T15:02:26Z

+  it('creates new entities and links if they do not exist', async () => {
+    const mockRepository: Partial<IRepository> = {
+      getEntityByName: vi.fn().mockResolvedValue(null),
+      createEntity: vi.fn().mockImplementation((e: Omit<Entity, 'id' | 'created_at' | 'updated_at'>) => Promise.resolve({ ...e, id: 'new-id-' + e.name, rowid: 1 })),


Unexpected string concatenation

In ES2015 (ES6), we can use template literals instead of string concatenation.

Implemented LLM-powered entity extraction and relationship discovery from notes. Added a review UI for users to selectively add extracted entities and edges to the graph. Integrated extraction into the editor (manual and auto-trigger) and added batch analysis to graph controls. Includes duplicate checking and backlinks to source notes in metadata. Fixed CI failures: - Added Sparkles and X icons to lucide-react mock in tests. - Fixed missing imports and initialized repository in GraphControls.tsx and Editor.tsx. - Fixed GraphControls.test.tsx to use renderWithDb. - Resolved lint errors (unused vars, explicit any, prefer-const). Co-authored-by: d-oit <6849456+d-oit@users.noreply.github.com>

deepsource-io · 2026-06-08T15:33:24Z


  it('triggers focus mode toggle', () => {
-    render(<GraphControls {...defaultProps} hasSelection={true} />);
+    renderWithDb(<GraphControls {...defaultProps} hasSelection={true} />, { repository });


Value must be omitted for boolean attribute `hasSelection`

When using a boolean attribute in JSX, you can set the attribute value to true or omit the value. This helps to keep consistency in code.

google-labs-jules Bot mentioned this pull request Jun 8, 2026

feat: AI-assisted knowledge graph auto-linking — entity extraction and edge suggestion from notes #285

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8 tasks

github-actions Bot added config tests Related to automated/manual tests labels Jun 8, 2026

deepsource-io Bot reviewed Jun 8, 2026

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Merge branch 'main' into feat/ai-graph-linking-9896207610745298301

eab8399

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Not up to standards ⛔

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JSX tree is too deeply nested. Found 5 levels of nesting

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Do not use Array index in keys

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Do not use Array index in keys

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Remove redundant `undefined` from function call

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Function has a cyclomatic complexity of 10 with "medium" risk

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Unexpected function declaration in the global scope, wrap in an IIFE for a local variable, assign as global property for a global variable

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`applyEntitiesToGraph` has a cyclomatic complexity of 11 with "medium" risk

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Forbidden non-null assertion

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Forbidden non-null assertion

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'repository' is defined but never used

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Useless path segments for "../../../lib/validation", should be "../../validation"

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Unexpected string concatenation

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Value must be omitted for boolean attribute `hasSelection`

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deepsource-io Bot commented Jun 8, 2026 •

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