<!-- .github/pull_request_template.md -->
## Description
This PR introduces several configuration improvements to enhance the
application's flexibility and reliability. The changes make JWT token
expiration and cookie domain configurable via environment variables,
improve CORS configuration, and add container restart policies for
better uptime.
**JWT Token Expiration Configuration:**
- Added `JWT_LIFETIME_SECONDS` environment variable to configure JWT
token expiration time
- Set default expiration to 3600 seconds (1 hour) for both API and
client authentication backends
- Removed hardcoded expiration values in favor of environment-based
configuration
- Added documentation comments explaining the JWT strategy configuration
**Cookie Domain Configuration:**
- Added `AUTH_TOKEN_COOKIE_DOMAIN` environment variable to configure
cookie domain
- When not set or empty, cookie domain defaults to `None` allowing
cross-domain usage
- Added documentation explaining cookie expiration is handled by JWT
strategy
- Updated default_transport to use environment-based cookie domain
**CORS Configuration Enhancement:**
- Added `CORS_ALLOWED_ORIGINS` environment variable with default value
of `'*'`
- Configured frontend to use `NEXT_PUBLIC_BACKEND_API_URL` environment
variable
- Set default backend API URL to `http://localhost:8000`
**Docker Service Reliability:**
- Added `restart: always` policy to all services (cognee, frontend,
neo4j, chromadb, and postgres)
- This ensures services automatically restart on failure or system
reboot
- Improves container reliability and uptime in production and
development environments
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->
## Type of Change
<!-- Please check the relevant option -->
- [x] Bug fix (non-breaking change that fixes an issue)
- [x] 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)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Services now automatically restart on failure for improved
reliability.
* **Configuration**
* Cookie domain for authentication is now configurable via environment
variable, defaulting to None if not set.
* JWT token lifetime is now configurable via environment variable, with
a 3600-second default.
* CORS allowed origins are now configurable with a default of all
origins (*).
* Frontend backend API URL is now configurable, defaulting to
http://localhost:8000.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
fix(embeddings): handle empty API key in LiteLLMEmbeddingEngine
- Add conditional check for empty API key to prevent authentication
errors- Set default API key to "EMPTY" when no valid key is provided-
This ensures proper fallback behavior when API key is not configured
```
<!-- .github/pull_request_template.md -->
## Description
This PR fixes an issue where the `LiteLLMEmbeddingEngine` throws an authentication error when the `EMBEDDING_API_KEY` environment variable is empty or not set. The error message indicated `"api_key client option must be set either by passing api_key to the client or by setting the OPENAI_API_KEY environment variable"`.
Log Error: 2025-12-23T11:36:58.220908 [error ] Error embedding text: litellm.AuthenticationError: AuthenticationError: OpenAIException - The api_key client option must be set either by passing api_key to the client or by setting the OPENAI_API_KEY environment variable [LiteLLMEmbeddingEngine]
**Root Cause**: When initializing the embedding engine, if the `api_key` parameter is an empty string, the underlying LiteLLM client doesn't treat it as "no key provided" but instead uses this empty string to make API requests, triggering authentication failure.
**Solution**: Added a conditional check in the code that creates the `LiteLLMEmbeddingEngine` instance. If the `EMBEDDING_API_KEY` read from configuration is empty (`None` or empty string), we explicitly set the `api_key` parameter passed to the engine constructor to a non-empty placeholder string `"EMPTY"`. This aligns with LiteLLM's handling of optional authentication and prevents exceptions in scenarios where keys are not required or need to be obtained from other sources
**How to Reproduce**:
Configure the application with the following settings (as shown in the error log):
EMBEDDING_PROVIDER="custom"
EMBEDDING_MODEL="openai/Qwen/Qwen3-Embedding-xxx"
EMBEDDING_ENDPOINT="xxxxx"
EMBEDDING_API_VERSION=""
EMBEDDING_DIMENSIONS=1024
EMBEDDING_MAX_TOKENS=16384
EMBEDDING_BATCH_SIZE=10
# If embedding key is not provided same key set for LLM_API_KEY will be used
EMBEDDING_API_KEY=""
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to test it locally;
* Proof that it's sufficiently tested.
-->
## Type of Change
<!-- Please check the relevant option -->
- [x] 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)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] I have tested my changes thoroughly before submitting this PR
- [x] 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
- [x] 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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
* **Bug Fixes**
* Improved API key validation for the embedding service to properly handle blank or missing API keys, ensuring more reliable embedding generation and preventing potential service errors.
<sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
This PR addresses a runtime error where the application fails because
ChromaDB is not installed. The error message `"ChromaDB is not
installed. Please install it with 'pip install chromadb'"` occurs when
attempting to use features that depend on ChromaDB.
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->
## Type of Change
<!-- Please check the relevant option -->
- [ ] 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)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Chores**
* Updated dependency management to include chromadb in the build
configuration.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
feat(Dockerfile): add chromadb support and China mirror option
- Add chromadb extra dependency to uv sync commands in Dockerfile- Include optional aliyun mirror configuration for users in China- Update dependency installation to include chromadb extra```
fix(embeddings): handle empty API key in LiteLLMEmbeddingEngine
- Add conditional check for empty API key to prevent authentication errors- Set default API key to "EMPTY" when no valid key is provided- This ensures proper fallback behavior when API key is not configured
```
fix(auth): add error handling for JWT lifetime configuration
- Add try-catch block to handle invalid JWT_LIFETIME_SECONDS environment variable
- Default to 360 seconds when environment variable is not a valid integer
- Apply same fix to both API and client authentication backendsdocs(docker): add security warning for CORS configuration
- Add comment warning about default CORS_ALLOWED_ORIGINS setting
- Emphasize need to override wildcard with specific domains in production
```
refactor(auth): remove redundant comments from JWT strategy configurationRemove duplicate comments that were explaining the JWT lifetime configuration
in both API and client authentication backends. The code remains functionallyunchanged but comments are cleaned up for better maintainability.
```
feat(auth): make JWT token expiration configurable via environment variable- Add JWT_LIFETIME_SECONDS environment variable to configure token expiration
- Set default expiration to3600 seconds (1 hour) for both API and client auth backends
- Remove hardcoded expiration values in favor of environment-based configuration
- Add documentation comments explaining the JWT strategy configuration
feat(auth): make cookie domain configurable via environment variable
- Add AUTH_TOKEN_COOKIE_DOMAIN environment variable to configure cookie domain
- When not set or empty, cookie domain defaults to None allowing cross-domain usage
- Add documentation explaining cookie expiration is handled by JWT strategy
- Update default_transport to use environment-based cookie domainfeat(docker): add CORS_ALLOWED_ORIGINS environment variable
- Add CORS_ALLOWED_ORIGINS environment variable with default value of '*'
- Configure frontend to use NEXT_PUBLIC_BACKEND_API_URL environment variable
- Set default backend API URL to http://localhost:8000
feat(docker): add restart policy to all services
- Add restart: always policy to cognee, frontend, neo4j, chromadb, and postgres services
- This ensures services automatically restart on failure or system reboot
- Improves container reliability and uptime```
<!-- .github/pull_request_template.md -->
## Description
<!--
Please provide a clear, human-generated description of the changes in
this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->
## Type of Change
<!-- Please check the relevant option -->
- [ ] 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)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Two interactive tutorial notebooks added (Cognee Basics, Python
Development) with runnable code and rich markdown; MarkdownPreview for
rendered markdown; instance-aware notebook support and cloud proxy with
API key handling; notebook CRUD (create, save, run, delete).
* **Bug Fixes**
* Improved authentication handling to treat 401/403 consistently.
* **Improvements**
* Auto-expanding text areas; better error propagation from dataset
operations; migration to allow toggling deletability for legacy tutorial
notebooks.
* **Tests**
* Expanded tests for tutorial creation and loading.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
This PR adds support for structured outputs with llama cpp using litellm
and instructor. It returns a Pydantic instance. Based on the github
issue described
[here](https://github.com/topoteretes/cognee/issues/1947).
It features the following:
- works for both local and server modes (OpenAI api compatible)
- defaults to `JSON` mode (**not JSON schema mode, which is too rigid**)
- uses existing patterns around logging & tenacity decorator consistent
with other adapters
- Respects max_completion_tokens / max_tokens
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->
I used the script below to test it with the [Phi-3-mini-4k-instruct
model](https://huggingface.co/microsoft/Phi-3-mini-4k-instruct-gguf).
This tests a basic structured data extraction and a more complex one
locally, then verifies that data extraction works in server mode.
There are instructors in the script on how to set up the models. If you
are testing this on a mac, run `brew install llama.cpp` to get llama cpp
working locally. If you don't have Apple silicon chips, you will need to
alter the script or the configs to run this on GPU.
```
"""
Comprehensive test script for LlamaCppAPIAdapter - Tests LOCAL and SERVER modes
SETUP INSTRUCTIONS:
===================
1. Download a small model (pick ONE):
# Phi-3-mini (2.3GB, recommended - best balance)
wget https://huggingface.co/microsoft/Phi-3-mini-4k-instruct-gguf/resolve/main/Phi-3-mini-4k-instruct-q4.gguf
# OR TinyLlama (1.1GB, smallest but lower quality)
wget https://huggingface.co/TheBloke/TinyLlama-1.1B-Chat-v1.0-GGUF/resolve/main/tinyllama-1.1b-chat-v1.0.Q4_K_M.gguf
2. For SERVER mode tests, start a server:
python -m llama_cpp.server --model ./Phi-3-mini-4k-instruct-q4.gguf --port 8080 --n_gpu_layers -1
"""
import asyncio
import os
from pydantic import BaseModel
from cognee.infrastructure.llm.structured_output_framework.litellm_instructor.llm.llama_cpp.adapter import (
LlamaCppAPIAdapter,
)
class Person(BaseModel):
"""Simple test model for person extraction"""
name: str
age: int
class EntityExtraction(BaseModel):
"""Test model for entity extraction"""
entities: list[str]
summary: str
# Configuration - UPDATE THESE PATHS
MODEL_PATHS = [
"./Phi-3-mini-4k-instruct-q4.gguf",
"./tinyllama-1.1b-chat-v1.0.Q4_K_M.gguf",
]
def find_model() -> str:
"""Find the first available model file"""
for path in MODEL_PATHS:
if os.path.exists(path):
return path
return None
async def test_local_mode():
"""Test LOCAL mode (in-process, no server needed)"""
print("=" * 70)
print("Test 1: LOCAL MODE (In-Process)")
print("=" * 70)
model_path = find_model()
if not model_path:
print("❌ No model found! Download a model first:")
print()
return False
print(f"Using model: {model_path}")
try:
adapter = LlamaCppAPIAdapter(
name="LlamaCpp-Local",
model_path=model_path, # Local mode parameter
max_completion_tokens=4096,
n_ctx=2048,
n_gpu_layers=-1, # 0 for CPU, -1 for all GPU layers
)
print(f"✓ Adapter initialized in {adapter.mode_type.upper()} mode")
print(" Sending request...")
result = await adapter.acreate_structured_output(
text_input="John Smith is 30 years old",
system_prompt="Extract the person's name and age.",
response_model=Person,
)
print(f"✅ Success!")
print(f" Name: {result.name}")
print(f" Age: {result.age}")
print()
return True
except ImportError as e:
print(f"❌ ImportError: {e}")
print(" Install llama-cpp-python: pip install llama-cpp-python")
print()
return False
except Exception as e:
print(f"❌ Failed: {e}")
print()
return False
async def test_server_mode():
"""Test SERVER mode (localhost HTTP endpoint)"""
print("=" * 70)
print("Test 3: SERVER MODE (Localhost HTTP)")
print("=" * 70)
try:
adapter = LlamaCppAPIAdapter(
name="LlamaCpp-Server",
endpoint="http://localhost:8080/v1", # Server mode parameter
api_key="dummy",
model="Phi-3-mini-4k-instruct-q4.gguf",
max_completion_tokens=1024,
chat_format="phi-3"
)
print(f"✓ Adapter initialized in {adapter.mode_type.upper()} mode")
print(f" Endpoint: {adapter.endpoint}")
print(" Sending request...")
result = await adapter.acreate_structured_output(
text_input="Sarah Johnson is 25 years old",
system_prompt="Extract the person's name and age.",
response_model=Person,
)
print(f"✅ Success!")
print(f" Name: {result.name}")
print(f" Age: {result.age}")
print()
return True
except Exception as e:
print(f"❌ Failed: {e}")
print(" Make sure llama-cpp-python server is running on port 8080:")
print(" python -m llama_cpp.server --model your-model.gguf --port 8080")
print()
return False
async def test_entity_extraction_local():
"""Test more complex extraction with local mode"""
print("=" * 70)
print("Test 2: Complex Entity Extraction (Local Mode)")
print("=" * 70)
model_path = find_model()
if not model_path:
print("❌ No model found!")
print()
return False
try:
adapter = LlamaCppAPIAdapter(
name="LlamaCpp-Local",
model_path=model_path,
max_completion_tokens=1024,
n_ctx=2048,
n_gpu_layers=-1,
)
print(f"✓ Adapter initialized")
print(" Sending complex extraction request...")
result = await adapter.acreate_structured_output(
text_input="Natural language processing (NLP) is a subfield of artificial intelligence (AI) and computer science.",
system_prompt="Extract all technical entities mentioned and provide a brief summary.",
response_model=EntityExtraction,
)
print(f"✅ Success!")
print(f" Entities: {', '.join(result.entities)}")
print(f" Summary: {result.summary}")
print()
return True
except Exception as e:
print(f"❌ Failed: {e}")
print()
return False
async def main():
"""Run all tests"""
print("\n" + "🦙" * 35)
print("Llama CPP Adapter - Comprehensive Test Suite")
print("Testing LOCAL and SERVER modes")
print("🦙" * 35 + "\n")
results = {}
# Test 1: Local mode (no server needed)
print("=" * 70)
print("PHASE 1: Testing LOCAL mode (in-process)")
print("=" * 70)
print()
results["local_basic"] = await test_local_mode()
results["local_complex"] = await test_entity_extraction_local()
# Test 2: Server mode (requires server on 8080)
print("\n" + "=" * 70)
print("PHASE 2: Testing SERVER mode (requires server running)")
print("=" * 70)
print()
results["server"] = await test_server_mode()
# Summary
print("\n" + "=" * 70)
print("TEST SUMMARY")
print("=" * 70)
for test_name, passed in results.items():
status = "✅ PASSED" if passed else "❌ FAILED"
print(f" {test_name:20s}: {status}")
passed_count = sum(results.values())
total_count = len(results)
print()
print(f"Total: {passed_count}/{total_count} tests passed")
if passed_count == total_count:
print("\n🎉 All tests passed! The adapter is working correctly.")
elif results.get("local_basic"):
print("\n✓ Local mode works! Server/cloud tests need llama-cpp-python server running.")
else:
print("\n⚠️ Please check setup instructions at the top of this file.")
if __name__ == "__main__":
asyncio.run(main())
```
**The following screenshots show the tests passing**
<img width="622" height="149" alt="image"
src="https://github.com/user-attachments/assets/9df02f66-39a9-488a-96a6-dc79b47e3001"
/>
Test 1
<img width="939" height="750" alt="image"
src="https://github.com/user-attachments/assets/87759189-8fd2-450f-af7f-0364101a5690"
/>
Test 2
<img width="938" height="746" alt="image"
src="https://github.com/user-attachments/assets/61e423c0-3d41-4fde-acaf-ae77c3463d66"
/>
Test 3
<img width="944" height="232" alt="image"
src="https://github.com/user-attachments/assets/f7302777-2004-447c-a2fe-b12762241ba9"
/>
**note** I also tried to test it with the `TinyLlama-1.1B-Chat` model
but such a small model is bad at producing structured JSON consistently.
## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [ X] 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)
see above
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [X] **I have tested my changes thoroughly before submitting this PR**
- [X] **This PR contains minimal changes necessary to address the
issue/feature**
- [X] My code follows the project's coding standards and style
guidelines
- [X] I have added tests that prove my fix is effective or that my
feature works
- [X] I have added necessary documentation (if applicable)
- [X] All new and existing tests pass
- [X] I have searched existing PRs to ensure this change hasn't been
submitted already
- [X] I have linked any relevant issues in the description
- [X] 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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Llama CPP integration supporting local (in-process) and server
(OpenAI‑compatible) modes.
* Selectable provider with configurable model path, context size, GPU
layers, and chat format.
* Asynchronous structured-output generation with rate limiting,
retries/backoff, and debug logging.
* **Chores**
* Added llama-cpp-python dependency and bumped project version.
* **Documentation**
* CONTRIBUTING updated with a “Running Simple Example” walkthrough for
local/server usage.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
<!--
Please provide a clear, human-generated description of the changes in
this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->
- `map_vector_distances_to_graph_nodes` and
`map_vector_distances_to_graph_edges` accept both single-query (flat
list) and multi-query (nested list) inputs.
- `query_list_length` controls the mode: omit it for single-query
behavior, or provide it to enable multi-query mode with strict length
validation and per-query results.
- `vector_distance` on `Node` and `Edge` is now a list (one distance per
query). Constructors set it to `None`, and `reset_distances` initializes
it at the start of each search.
- `Node.update_distance_for_query` and `Edge.update_distance_for_query`
are the only methods that write to `vector_distance`. They ensure the
list has enough elements and keep unmatched queries at the penalty
value.
- `triplet_distance_penalty` is the default distance value used
everywhere. Unmatched nodes/edges and missing scores all use this same
penalty for consistency.
- `edges_by_distance_key` is an index mapping edge labels to matching
edges. This lets us update all edges with the same label at once,
instead of scanning the full edge list repeatedly.
- `calculate_top_triplet_importances` returns `List[Edge]` for
single-query mode and `List[List[Edge]]` for multi-query mode.
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->
## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [x] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [x] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] 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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Multi-query support for mapping/scoring node and edge distances and a
configurable triplet distance penalty.
* Distance-keyed edge indexing for more accurate distance-to-edge
matching.
* **Refactor**
* Vector distance metadata changed from scalars to per-query lists;
added reset/normalization and per-query update flows.
* Node/edge distance initialization now supports deferred/listed
distances.
* **Tests**
* Updated and expanded tests for multi-query flows, list-based
distances, edge-key handling, and related error cases.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
<!--
Please provide a clear, human-generated description of the changes in
this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->
## Type of Change
<!-- Please check the relevant option -->
- [ ] 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
- [x] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Documentation**
* Deprecated legacy examples and added a migration guide mapping old
paths to new locations
* Added a comprehensive new-examples README detailing configurations,
pipelines, demos, and migration notes
* **New Features**
* Added many runnable examples and demos: database configs,
embedding/LLM setups, permissions and access-control, custom pipelines
(organizational, product recommendation, code analysis, procurement),
multimedia, visualization, temporal/ontology demos, and a local UI
starter
* **Chores**
* Updated CI/test entrypoints to use the new-examples layout
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: lxobr <122801072+lxobr@users.noreply.github.com>
<!-- .github/pull_request_template.md -->
## Description
This PR covers the higher level search.py logic with unit tests. As a
part of the implementation we fully cover the following core logic:
- search.py
- get_search_type_tools (with all the core search types)
- search - prepare_search_results contract (testing behavior from
search.py interface)
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->
## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [x] 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)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] 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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Tests**
* Added comprehensive unit test coverage for search functionality,
including search type tool selection, search operations, and result
preparation workflows across multiple scenarios and edge cases.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
This PR changes the permission test in e2e tests to use pytest.
Introduces:
- fixtures for the environment setup
- one eventloop for all pytest tests
- mocking for acreate_structured_output answer generation (for search)
- Asserts in permission test (before we use the example only)
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->
## Type of Change
<!-- Please check the relevant option -->
- [ ] 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
- [x] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] 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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Entity model now includes description and metadata fields for richer
entity information and indexing.
* **Tests**
* Expanded and restructured permission tests covering multi-tenant and
role-based access flows; improved test scaffolding and stability.
* E2E test workflow now runs pytest with verbose output and INFO logs.
* **Bug Fixes**
* Access-tracking updates now commit transactions so access timestamps
persist.
* **Chores**
* General formatting, cleanup, and refactoring across modules and
maintenance scripts.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
This PR implements a data deletion system for unused DataPoint models
based on last access tracking. The system tracks when data is accessed
during search operations and provides cleanup functionality to remove
data that hasn't been accessed within a configurable time threshold.
**Key Changes:**
1. Added `last_accessed` timestamp field to the SQL `Data` model
2. Added `last_accessed_at` timestamp field to the graph `DataPoint`
model
3. Implemented `update_node_access_timestamps()` function that updates
both graph nodes and SQL records during search operations
4. Created `cleanup_unused_data()` function with SQL-based deletion mode
for whole document cleanup
5. Added Alembic migration to add `last_accessed` column to the `data`
table
6. Integrated timestamp tracking into in retrievers
7. Added comprehensive end-to-end test for the cleanup functionality
## Related Issues
Fixes #[issue_number]
## Type of Change
- [x] New feature (non-breaking change that adds functionality)
- [ ] Bug fix (non-breaking change that fixes an issue)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
## Database Changes
- [x] This PR includes database schema changes
- [x] Alembic migration included: `add_last_accessed_to_data`
- [x] Migration adds `last_accessed` column to `data` table
- [x] Migration includes backward compatibility (nullable column)
- [x] Migration tested locally
## Implementation Details
### Files Modified:
1. **cognee/modules/data/models/Data.py** - Added `last_accessed` column
2. **cognee/infrastructure/engine/models/DataPoint.py** - Added
`last_accessed_at` field
3. **cognee/modules/retrieval/chunks_retriever.py** - Integrated
timestamp tracking in `get_context()`
4. **cognee/modules/retrieval/utils/update_node_access_timestamps.py**
(new file) - Core tracking logic
5. **cognee/tasks/cleanup/cleanup_unused_data.py** (new file) - Cleanup
implementation
6. **alembic/versions/[revision]_add_last_accessed_to_data.py** (new
file) - Database migration
7. **cognee/tests/test_cleanup_unused_data.py** (new file) - End-to-end
test
### Key Functions:
- `update_node_access_timestamps(items)` - Updates timestamps in both
graph and SQL
- `cleanup_unused_data(minutes_threshold, dry_run, text_doc)` - Main
cleanup function
- SQL-based cleanup mode uses `cognee.delete()` for proper document
deletion
## Testing
- [x] Added end-to-end test: `test_textdocument_cleanup_with_sql()`
- [x] Test covers: add → cognify → search → timestamp verification →
aging → cleanup → deletion verification
- [x] Test verifies cleanup across all storage systems (SQL, graph,
vector)
- [x] All existing tests pass
- [x] Manual testing completed
## Screenshots/Videos
N/A - Backend functionality
## Pre-submission Checklist
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] My commits have clear and descriptive messages
## Breaking Changes
None - This is a new feature that doesn't affect existing functionality.
## 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.
Resolves#1335
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Added access timestamp tracking to monitor when data is last
retrieved.
* Introduced automatic cleanup of unused data based on configurable time
thresholds and access history.
* Retrieval operations now update access timestamps to ensure accurate
tracking of data usage.
* **Tests**
* Added integration test validating end-to-end cleanup workflow across
storage layers.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
<!--
Please provide a clear, human-generated description of the changes in
this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->
Added tests that just run scripts we have in the docs, in our guides
section (Essentials and Customizing Cognee). This is a start of a test
suite regarding docs, to make sure new releases don't break the scripts
we have written in our docs.
The new workflow only runs on releases, and is part of the Release Test
Workflow we have.
## Type of Change
<!-- Please check the relevant option -->
- [ ] Bug fix (non-breaking change that fixes an issue)
- [x] 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)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Chores**
* Enhanced release workflow automation with improved coordination
between repositories.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- .github/pull_request_template.md -->
## Description
This PR fixes get_raw_data endpoint in get_dataset_router
- Fixes local path access
- Adds s3 access
- Covers new fixed functionality with unit tests
## Acceptance Criteria
<!--
* Key requirements to the new feature or modification;
* Proof that the changes work and meet the requirements;
* Include instructions on how to verify the changes. Describe how to
test it locally;
* Proof that it's sufficiently tested.
-->
## Type of Change
<!-- Please check the relevant option -->
- [x] 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)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [x] **I have tested my changes thoroughly before submitting this PR**
- [x] **This PR contains minimal changes necessary to address the
issue/feature**
- [x] My code follows the project's coding standards and style
guidelines
- [x] I have added tests that prove my fix is effective or that my
feature works
- [x] I have added necessary documentation (if applicable)
- [x] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
- [x] I have linked any relevant issues in the description
- [x] 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.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Streaming support for remote S3 data locations so large dataset files
can be retrieved efficiently.
* Improved handling of local and remote file paths for downloads.
* **Improvements**
* Standardized error responses for missing datasets or data files.
* **Tests**
* Added unit tests covering local file downloads and S3 streaming,
including content and attachment header verification.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
