chore: remove stale TODO and legacy comments (#2316)

[ajuijas]

Description

This PR resolves issue #2316 by fully auditing and triaging the TODO comments across the codebase.

Changes:

1. Removes Stale TODOs: Deleted 6 outdated TODO comments related to legacy caching and exception handling that were no longer relevant.
2. References New GitHub Issues: For the 9 remaining actionable TODOs, we created dedicated GitHub issues. I then updated the inline comments in the Python files to reference these new issue IDs (e.g., changing TODO: to TODO(#2350):).

This cleans up the code and makes sure all pending work is tracked in GitHub issues instead.

Acceptance Criteria

• Requirement: Audit and triage all TODO/FIXME comments in the codebase (issue Audit and triage TODO/FIXME comments into actionable issues or removal #2316).
• Proof: Stale comments are removed without altering any functional logic. All actionable comments have been updated to reference their corresponding GitHub issues.

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):

Pre-submission Checklist

• I have tested my changes thoroughly before submitting this PR (See CONTRIBUTING.md)
• 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.

[coderabbitai]

Walkthrough

Mostly comment/TODO text updates across multiple modules and tests; one behavioral-affecting change: removal of the base-class initializer call from EntityNotFoundError.init in exceptions.py.

Changes

Cohort / File(s)	Summary
Comment/TODO updates (multiple modules) cognee/api/v1/cognify/cognify.py, cognee/context_global_variables.py, cognee/infrastructure/databases/graph/neo4j_driver/.../Neo4jAuraDevDatasetDatabaseHandler.py, cognee/infrastructure/databases/hybrid/neptune_analytics/NeptuneAnalyticsAdapter.py, cognee/infrastructure/databases/vector/chromadb/ChromaDBAdapter.py, cognee/infrastructure/llm/structured_output_framework/.../openai/adapter.py, cognee/tests/integration/retrieval/test_rag_completion_retriever.py, cognee/tests/test_cognee_server_start.py, cognee/tests/unit/entity_extraction/regex_entity_extraction_test.py, examples/pocs/single_add_datapoints/single_add_datapoints_pipeline.py	Updated inline comments / TODOs to reference issue numbers or reformat text; no functional or signature changes.
Cache interface documentation cognee/infrastructure/databases/cache/cache_db_interface.py	Removed backward-compatibility ":TODO: delete when retrievers are updated" notes from three docstrings; behavior unchanged.
Exception constructor change cognee/infrastructure/databases/exceptions/exceptions.py	Removed super().__init__(message, name, status_code) call from EntityNotFoundError.init; initializer now only assigns instance attributes (possible behavioral/initialization impact).
Test comment cleanup cognee/tests/unit/infrastructure/databases/cache/test_fs_adapter_crud.py, cognee/tests/unit/infrastructure/databases/cache/test_redis_adapter_crud.py	Deleted backward-compatibility header comment lines; test logic unchanged.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

• Merge main vol7 #1891: Touches cognee/api/v1/cognify/cognify.py's get_default_tasks (related to TODO/comment edits in same function).

Suggested labels

run-checks

Suggested reviewers

• lxobr
• dexters1
• Vasilije1990

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The PR title 'chore: remove stale TODO and legacy comments (#2316)' clearly and concisely summarizes the main change: removing outdated TODO comments to address issue #2316.
Docstring Coverage	✅ Passed	Docstring coverage is 82.35% which is sufficient. The required threshold is 80.00%.
Description check	✅ Passed	The PR description is complete and follows the template structure with all required sections filled out, including clear explanation of changes, acceptance criteria, type of change, pre-submission checklist confirmation, and DCO affirmation.

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• Post copyable unit tests in a comment

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[coderabbitai]

🧹 Nitpick comments (1)

cognee/infrastructure/databases/cache/cache_db_interface.py (1)

56-56: LGTM! TODO cleanup aligns with PR objectives.

The removal of stale TODO comments from these backward-compatibility wrapper docstrings is appropriate and keeps the documentation concise. The functional delegation logic remains unchanged.

---

Optional enhancement for future consideration:

These backward-compatibility wrapper methods could benefit from more complete docstrings documenting their parameters and return values, similar to the abstract methods they delegate to (e.g., create_qa_entry, get_latest_qa_entries, get_all_qa_entries). However, this is out of scope for this cleanup PR.

As per coding guidelines: "undocumented function definitions and class definitions in the project's Python code are assumed incomplete. Please consider suggesting a short summary of the code for any of these incomplete definitions as docstrings when reviewing."

Also applies to: 85-85, 96-96

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@cognee/infrastructure/databases/cache/cache_db_interface.py` at line 56, Add
brief, properly formatted docstrings to the backward-compatibility wrapper
methods that currently lack documentation (the wrapper that delegates to
create_qa_entry and the similar wrappers for get_latest_qa_entries and
get_all_qa_entries) describing their parameters, return value, and that they
delegate to the corresponding abstract methods; reference the wrapper method
names (the create_qa_entry wrapper, get_latest_qa_entries wrapper,
get_all_qa_entries wrapper) and mirror the essential param/return info from the
delegated abstract methods to satisfy the project's undocumented-definition
guideline.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@cognee/infrastructure/databases/cache/cache_db_interface.py`:
- Line 56: Add brief, properly formatted docstrings to the
backward-compatibility wrapper methods that currently lack documentation (the
wrapper that delegates to create_qa_entry and the similar wrappers for
get_latest_qa_entries and get_all_qa_entries) describing their parameters,
return value, and that they delegate to the corresponding abstract methods;
reference the wrapper method names (the create_qa_entry wrapper,
get_latest_qa_entries wrapper, get_all_qa_entries wrapper) and mirror the
essential param/return info from the delegated abstract methods to satisfy the
project's undocumented-definition guideline.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro

Run ID: 3c3d756d-0d69-4736-a41c-e69675e4b917

📥 Commits

Reviewing files that changed from the base of the PR and between c9370a8 and df8c437.

📒 Files selected for processing (4)

• cognee/infrastructure/databases/cache/cache_db_interface.py
• cognee/infrastructure/databases/exceptions/exceptions.py
• cognee/tests/unit/infrastructure/databases/cache/test_fs_adapter_crud.py
• cognee/tests/unit/infrastructure/databases/cache/test_redis_adapter_crud.py

💤 Files with no reviewable changes (3)

• cognee/tests/unit/infrastructure/databases/cache/test_redis_adapter_crud.py
• cognee/infrastructure/databases/exceptions/exceptions.py
• cognee/tests/unit/infrastructure/databases/cache/test_fs_adapter_crud.py

[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.