<!-- .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 -->
<!-- .github/pull_request_template.md -->
## Description
Resolve issue with special characters like '#' and '@' in passwords for
Postgres
## 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
* **Refactor**
* Improved internal database connection handling for relational and
vector databases to enhance system stability and code maintainability.
<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
Add ability to define custom labels for Data in Cognee. Initial PR by
contributor: apenade
## 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**
* Added support for labeling individual data items during ingestion
workflows
* Expanded the add API to accept data items with optional custom labels
for better organization
* Labels are persisted and retrievable when accessing dataset
information
* Enhanced data retrieval to include label information in API responses
* **Tests**
* Added comprehensive end-to-end tests validating custom data labeling
functionality
<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 -->
This PR restructures/adds unittests for the retrieval module. (STEP 2)
-Added missing unit tests for all core retrieval business logic
## 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**
* Expanded and refactored retrieval module test suites with
comprehensive unit test coverage for ChunksRetriever,
SummariesRetriever, RagCompletionRetriever, TripletRetriever,
GraphCompletionRetriever, TemporalRetriever, and related components.
* Added new test modules for completion utilities, graph summary
retrieval, and user feedback functionality.
* Improved test robustness with edge case handling and error scenario
coverage.
<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
