fix: use dict spread to avoid shallow copy mutation in index_data_points

[nightcityblade]

Description

When a DataPoint has multiple index_fields, the for loop in index_data_points() only processes the first field. This happens because model_copy() performs a shallow copy, so indexed_data_point.metadata and data_point.metadata reference the same dict. Setting indexed_data_point.metadata["index_fields"] = [field_name] mutates the original, truncating the iteration list.

The fix replaces the direct dict mutation with a dict spread ({**data_point.metadata, "index_fields": [field_name]}), creating a new dict for each copy so the original is never modified.

Acceptance Criteria

• Multiple index_fields are all processed and embedded correctly
• Original data_point.metadata["index_fields"] is not mutated during iteration

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Code refactoring
• Other (please specify):

Screenshots

N/A — single-line logic fix verified via manual simulation.

Pre-submission Checklist

• I have tested my changes thoroughly before submitting this PR
• This PR contains minimal changes necessary to address the issue/feature
• My code follows the project's coding standards and style guidelines
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if applicable)
• All new and existing tests pass
• I have searched existing PRs to ensure this change hasn't been submitted already
• I have linked any relevant issues in the description
• My commits have clear and descriptive messages

DCO Affirmation

I affirm that all code in every commit of this pull request conforms to the terms of the Topoteretes Developer Certificate of Origin.

Fixes #2529

Summary by CodeRabbit

• Bug Fixes
  • Fixed metadata preservation during data point indexing to ensure all metadata fields are properly retained while correctly managing index field information.

[pull-checklist]

Please make sure all the checkboxes are checked:

• I have tested these changes locally.
• I have reviewed the code changes.
• I have added end-to-end and unit tests (if applicable).
• I have updated the documentation and README.md file (if necessary).
• I have removed unnecessary code and debug statements.
• PR title is clear and follows the convention.
• I have tagged reviewers or team members for feedback.

[github-actions]

Hello @nightcityblade, thank you for submitting a PR! We will respond as soon as possible.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

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📥 Commits

Reviewing files that changed from the base of the PR and between 4dff60e and 71c73f1.

📒 Files selected for processing (1)

• cognee/tasks/storage/index_data_points.py

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Walkthrough

Fixed a shallow copy metadata mutation bug in the index data points task. Replaced direct field assignment with dictionary unpacking to ensure each indexed data point receives a proper copy of metadata while maintaining only the relevant index field.

Changes

Cohort / File(s)	Summary
Metadata Copy Fix cognee/tasks/storage/index_data_points.py	Changed metadata assignment from mutating the shallow-copied dict to using dictionary unpacking ({**data_point.metadata, "index_fields": [field_name]}) to create an isolated metadata object per indexed copy, preventing truncation of the original index_fields list during iteration.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: using dict spread operator to avoid shallow copy mutation in index_data_points function.
Description check	✅ Passed	The PR description comprehensively explains the bug, root cause, fix approach, acceptance criteria, and includes all required template sections with proper checkbox completion.
Linked Issues check	✅ Passed	The code change directly addresses issue #2529 by implementing dict spread to create new metadata per copy, preventing mutation of the original index_fields list during iteration.
Out of Scope Changes check	✅ Passed	The single-line change is tightly scoped to fixing the shallow copy mutation issue in index_data_points.py with no extraneous modifications.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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[dexters1]

PR is made towards wrong branch. Check CONTRIBUTING.md

https://github.com/topoteretes/cognee/blob/main/CONTRIBUTING.md

[nightcityblade]

Thanks @dexters1! Updated the base branch to dev as per CONTRIBUTING.md. Sorry about that!

[nightcityblade]

Thanks for the feedback! The PR currently targets dev as the base branch, which aligns with CONTRIBUTING.md's guidance to branch from dev. Could you clarify which branch I should target instead? Happy to update it.