Cherry-pick: Fix cypher search (#1739)

[pazone]

Description

Resolve issue with cypher search by encoding the return value from the cypher query into JSON. Uses fastapi json encoder

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update
• Code refactoring
• Performance improvement
• Other (please specify):

Screenshots/Videos (if applicable)

Example of result now with Cypher search with the following query "MATCH (src)-[rel]->(nbr) RETURN src, rel" on Simple example:

{
   "search_result":[
      [
         [
            {
               "_id":{
                  "offset":0,
                  "table":0
               },
               "_label":"Node",
               "id":"87372381-a9fe-5b82-9c92-3f5dbab1bc35",
               "name":"",
               "type":"DocumentChunk",
               "created_at":"2025-11-05T14:12:46.707597",
               "updated_at":"2025-11-05T14:12:54.801747",
               "properties":"{\"created_at\": 1762351945009, \"updated_at\": 1762351945009, \"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"text\"]}, \"belongs_to_set\": null, \"text\": \"\\n    Natural language processing (NLP) is an interdisciplinary\\n    subfield of computer science and information retrieval.\\n    \", \"chunk_size\": 48, \"chunk_index\": 0, \"cut_type\": \"paragraph_end\"}"
            },
            {
               "_src":{
                  "offset":0,
                  "table":0
               },
               "_dst":{
                  "offset":1,
                  "table":0
               },
               "_label":"EDGE",
               "_id":{
                  "offset":0,
                  "table":1
               },
               "relationship_name":"contains",
               "created_at":"2025-11-05T14:12:47.217590",
               "updated_at":"2025-11-05T14:12:55.193003",
               "properties":"{\"source_node_id\": \"87372381-a9fe-5b82-9c92-3f5dbab1bc35\", \"target_node_id\": \"bc338a39-64d6-549a-acec-da60846dd90d\", \"relationship_name\": \"contains\", \"updated_at\": \"2025-11-05 14:12:54\", \"relationship_type\": \"contains\", \"edge_text\": \"relationship_name: contains; entity_name: natural language processing (nlp); entity_description: An interdisciplinary subfield of computer science and information retrieval concerned with interactions between computers and human (natural) languages.\"}"
            }
         ]
      ]
   ],
   "dataset_id":"UUID(""af4b1c1c-90fc-59b7-952c-1da9bbde370c"")",
   "dataset_name":"main_dataset",
   "graphs":"None"
}

Relates to #1725 Issue: #1723

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.

Description

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update
• Code refactoring
• Performance improvement
• Other (please specify):

Screenshots/Videos (if applicable)

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.

[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.

[coderabbitai]

Walkthrough

The retrieval module's query results are now JSON-serializable. A new import of jsonable_encoder from fastapi.encoders wraps the graph engine query output to ensure proper encoding without affecting existing control flow or error handling.

Changes

Cohort / File(s)	Summary
JSON Serialization Enhancement cognee/modules/retrieval/cypher_search_retriever.py	Added import of jsonable_encoder from fastapi.encoders; wrapped graph_engine.query(query) result with jsonable_encoder for JSON serialization.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Poem

🐰 A tiny hop, a gentle wrap,
JSON flows without a gap,
The encoder guards the data's way,
Serialized and bright today! ✨

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'Cherry-pick: Fix cypher search (#1739)' is related to the changeset and refers to fixing a bug in cypher search, which matches the bug fix nature of the changes, though it could be more descriptive.
Description check	✅ Passed	The description includes required sections (Description, Type of Change, Pre-submission Checklist, DCO Affirmation) with the bug fix clearly identified, a detailed example output provided, and relevant issue/PR references linked, though most pre-submission checklist items remain unchecked.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix_cypher_cherrypick

---

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Reviewing files that changed from the base of the PR and between 26c18e9 and 007c7d4.

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• cognee/modules/retrieval/cypher_search_retriever.py (2 hunks)

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{cognee,cognee-mcp,distributed,examples,alembic}/**/*.py

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{cognee,cognee-mcp,distributed,examples,alembic}/**/*.py: Use 4-space indentation; name modules and functions in snake_case; name classes in PascalCase (Python)
Adhere to ruff rules, including import hygiene and configured line length (100)
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Files:

• cognee/modules/retrieval/cypher_search_retriever.py

cognee/**/*.py

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cognee/**/*.py: Public APIs in the core library should be type-annotated where practical
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Files:

• cognee/modules/retrieval/cypher_search_retriever.py

🧬 Code graph analysis (1)

cognee/modules/retrieval/cypher_search_retriever.py (2)

cognee/infrastructure/databases/graph/kuzu/adapter.py (1)

• query (210-278)

cognee/infrastructure/databases/graph/neo4j_driver/adapter.py (1)

• query (100-128)

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🔇 Additional comments (2)

cognee/modules/retrieval/cypher_search_retriever.py (2)

2-3: FastAPI is already a core project dependency; this change does not introduce new coupling.

The concern in the original review comment is based on an incorrect premise. FastAPI is already declared as a core dependency in pyproject.toml ("fastapi>=0.116.2,<1.0.0"), and CypherSearchRetriever is already integrated into the search pipeline that serves API endpoints. Using jsonable_encoder here is appropriate for ensuring query results are JSON-serializable before being returned through the API.

Likely an incorrect or invalid review comment.

---

55-55: Type annotation improvement recommended; JSON encoding change is appropriate.

The jsonable_encoder wrapping is correct for API serialization. Graph engines return List[Dict[str, Any]] (Neo4j) or List[Tuple] (Kuzu), and encoding ensures consistent JSON-serializable output for API consumers.

However, improve the return type annotation from Any to List[Dict[str, Any]] to accurately reflect the JSON-encoded output structure and provide clarity to callers.

---

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