<!-- .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.
-->
Recently a few cases cryptic errors like in issue #1721 have occurred
across cognee use cases.
Debugging #1721 however, I found out that if LLM_API_KEY happens to have
`"` quotation marks as part of it's value, for example, when already
part of the ENV
<img width="1014" height="507" alt="Screenshot 2025-11-07 at 16 58 22"
src="https://github.com/user-attachments/assets/54b7cbb0-5bdc-4b40-b2b1-aed6c5d3d886"
/>
Then it makes it's way into Cognee and gets treated as part of the API
key.
By default, we do not do sanitization nor cleanup.
While most of the time quotation marks get handled for us:
1. `export KEY="VALUE"` will strip it
2. python dotenv will strip it if read from `.env`
But issues like https://github.com/docker/cli/issues/3630 and #1721
demonstrate that we have to have some handling on our end instead of
assuming it's stripped.
## This PR
This PR sets up a list of string params we want to strip + some that we
may want to.
We may want to avoid doing this for all params, which is why I went with
selective approach.
TODO: add testing
## 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
* **Bug Fixes**
* Configuration values with surrounding quotes are now automatically
normalized and cleaned during system initialization, ensuring consistent
and predictable data handling across all configuration parameters.
* **Tests**
* Added comprehensive unit tests to validate automatic quote removal
from configuration values, covering various scenarios including quoted,
unquoted, empty, and edge cases with mixed and internal quotes.
<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 -->
- [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 -->
- [ ] **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**
* Enhanced Node.js and npm environment management for improved system
compatibility on Unix-like platforms.
* **Chores**
* Updated Next.js to v16, React to v19.2, and Auth0 SDK to v4.13.1 for
compatibility and performance improvements.
* Removed CrewAI workflow trigger component.
* Removed user feedback submission form.
<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
Fixes lancedb batch handling issue. Duplicated elements could appear in
the collections when duplicates happen in the same insert
batch.
## 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
* **Bug Fixes**
* Improved data integrity by implementing deduplication logic to
eliminate duplicate entries and ensure only the latest version is
retained.
<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.
-->
This PR removes codify, and the code graph pipeline, out of the
repository. It also introduces a Custom Pipeline interface, which can be
used in the future to define custom pipelines.
## 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.
<!-- .github/pull_request_template.md -->
## Description
This PR introduces triplet embeddings via a new
create_triplet_embeddings memify pipeline.
The pipeline reads the graph in batches, extracts properties from graph
elements based on their datapoint types, and generates combined triplet
embeddings. These embeddings are stored in the vector database as a new
collection.
Changes in This PR:
-Added a new create_triplet_embeddings memify pipeline.
-Added a new get_triplet_datapoints memify task.
-Introduced a new triplet_completion search type.
-Added full test coverage
--Unit tests: memify task, pipeline, and retriever
--Integration tests: memify task, pipeline, and retriever
--End-to-end tests: updated session history tests and multi-DB search
tests; added tests for triplet_completion and memify pipeline execution
Acceptance Criteria and Testing
Scenario 1:
-Run default add, cognify pipelines
-Run create triplet embeddings memify pipeline
-Verify the vector DB contains a non empty Triplet_text collection.
-Use the new triplet_completion search type and confirm it works
correctly.
Scenario 2:
-Run the default add and cognify pipelines.
-Do not run the triplet embeddings memify pipeline.
-Attempt to use the triplet_completion search type.
-You should receive an error indicating that the triplet embeddings
memify pipeline must be executed first.
## 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
* **New Features**
* Triplet-based search with LLM-powered completions (TRIPLET_COMPLETION)
* Batch triplet retrieval and a triplet embeddings pipeline for
extraction, indexing, and optional background processing
* Context retrieval from triplet embeddings with optional caching and
conversation-history support
* New Triplet data type exposed for indexing and search
* **Examples**
* End-to-end example demonstrating triplet embeddings extraction and
TRIPLET_COMPLETION search
* **Tests**
* Unit and integration tests covering triplet extraction, retrieval,
embedding pipeline, and completion flows
<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: Pavel Zorin <pazonec@yandex.ru>
<!-- .github/pull_request_template.md -->
This PR introduces wide vector and graph structure filtering
capabilities. With these changes, the graph completion retriever and all
retrievers that inherit from it will now filter relevant vector elements
and subgraphs based on the query. This improvement significantly
increases search speed for large graphs while maintaining—and in some
cases slightly improving—accuracy.
Changes in This PR:
-Introduced new wide_search_top_k parameter: Controls the initial search
space size
-Added graph adapter level filtering method: Enables relevant subgraph
filtering while maintaining backward compatibility. For community or
custom graph adapters that don't implement this method, the system
gracefully falls back to the original search behavior.
-Updated modal dashboard and evaluation framework: Fixed compatibility
issues.
Added comprehensive unit tests: Introduced unit tests for
brute_force_triplet_search (previously untested) and expanded the
CogneeGraph test suite.
Integration tests: Existing integration tests verify end-to-end search
functionality (no changes required).
Acceptance Criteria and Testing
To verify the new search behavior, run search queries with different
wide_search_top_k parameters while logging is enabled:
None: Triggers a full graph search (default behavior)
1: Projects a minimal subgraph (demonstrates maximum filtering)
Custom values: Test intermediate levels of filtering
Internal Testing and results:
Performance and accuracy benchmarks are available upon request. The
implementation demonstrates measurable improvements in query latency for
large graphs without sacrificing result quality.
## 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
- [x] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
None
## 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.
---------
Co-authored-by: Pavel Zorin <pazonec@yandex.ru>
<!-- .github/pull_request_template.md -->
## Description
This PR fixes the failing CI tests related to the new ontology api
endpoint.
<!--
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 -->
- [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.
<!-- .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
- [ ] 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.
## Description
This PR resolves#1446 by adding support to upload ontology files and
refer to them in the cognee POST request.
Implementation Details:
- New endpoint: POST /api/v1/ontologies for ontology file upload with a
simple key parameter
that can be referenced in POST cognify requests
- File storage: Ontology files are stored in /tmp/ontologies/{user_id}/
with metadata
management
- New service: OntologyService created for file management and metadata
handling
- Resolver: RDFLibOntologyResolver modified to handle file-like objects.
## 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.
<!-- .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.
-->
Create a dedicated CSV ingestion path with a custom loader and custom
chunker that preserves row-column relationships in the produced chunks.
#1348
## 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)
- [x] Breaking change (fix or feature that would cause existing
functionality to change)
- [x] Documentation update
- [x] Code refactoring
- [x] Performance improvement
- [x] 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.
<!-- .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 a variable to control which instructor mode we use. The defaults
for each adapter are used, but a user can override this if the set the
`LLM_INSTRUCTOR_MODE` env variable.
## 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.
<!-- .github/pull_request_template.md -->
Updates crawler test url to avoid blocking and unavailable sites in CI.
## 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
- [ ] 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.
The OllamaEmbeddingEngine is compatible with OpenAI
<!-- .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
- [ ] 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.
