- Added AdvancedPdfLoader class for enhanced PDF processing using the unstructured library.
- Integrated fallback mechanism to PyPdfLoader in case of unstructured library import failure or exceptions.
- Updated supported loaders to include AdvancedPdfLoader.
- Added unit tests for AdvancedPdfLoader to ensure functionality and error handling.
- Updated poetry.lock and pyproject.toml to include new dependencies and versions.
Signed-off-by: EricXiao <taoiaox@gmail.com>
<!-- .github/pull_request_template.md -->
## Description
<!--
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this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
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I Implemented Lexical Chunk Retriever In the LexicalRetriever class is
Inherite the BaseRetriever and The DocumentChunk are lazy loaded when
first time query is made because it save time during object
initialization
and the function get_context and the get_completion are Implemented same
as the ChunksRetriever the only diffrence is that the DocumentChunk are
converted to match the output type of the ChunksRetriever using function
get_own_properties in the utils.
## 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):
## Changes Made
<!-- List the specific changes made in this PR -->
- Added LexicalRetriever base class with customizable tokenizer & scorer
- Implemented caching of DocumentChunk tokens and payloads
- Added robust initialization with error handling and logging -
Implemented get_context with top_k ranking and optional scores
- Implemented get_completion consistent with BaseRetriever interface
- Added JaccardChunksRetriever demo using set/multiset Jaccard
similarity
- Support for stopwords and multiset frequency-aware similarity -
Integrated logging for initialization, scoring, and retrieval
## Testing
- Manual tests: initialized retriever, retrieved chunks with toy corpus
- Edge cases: empty corpus, empty query, scorer/tokenizer errors
- Verified Jaccard similarity results for single/multiset cases
- Code formatted and linted
## 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
## Related Issues
<!-- Link any related issues using "Fixes #issue_number" or "Relates to
#issue_number" -->
Relates to #1392
## Additional Notes
<!-- Add any additional notes, concerns, or context for reviewers -->
Int the cognee/modules/chunking/models/DocumentChunk.py
don't remove the optional from is_part_of attributes.
## 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: Andrej Milicevic <milicevicandrej@yahoo.com>
Co-authored-by: Igor Ilic <30923996+dexters1@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
Co-authored-by: Igor Ilic <igorilic03@gmail.com>
Co-authored-by: Vasilije <8619304+Vasilije1990@users.noreply.github.com>
Co-authored-by: Boris <boris@topoteretes.com>
Co-authored-by: lxobr <122801072+lxobr@users.noreply.github.com>
<!-- .github/pull_request_template.md -->
## Description
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process and reasoning.
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## Type of Change
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- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
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- [ ] Performance improvement
- [ ] Other (please specify):
## Changes Made
<!-- List the specific changes made in this PR -->
-
-
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## Testing
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## Screenshots/Videos (if applicable)
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## Additional Notes
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## Description
Ontology notebook fix
## Type of Change
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- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
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- [ ] Code refactoring
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## Changes Made
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Ontology notebook fix
## Testing
manual
## Screenshots/Videos (if applicable)
None
## Pre-submission Checklist
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feature works
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- [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
## Related Issues
None
## Additional Notes
None
## 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
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this PR.
Adds abstraction for OntologyResolvers and matching mechanism
## Type of Change
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- [x] 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):
## Changes Made
<!-- List the specific changes made in this PR -->
Adds ontology abstraction + matching resolver logic to support multiple
solutions
## Testing
Testing of changes is done using manual testing and ci/cd tests
## Screenshots/Videos (if applicable)
None
## Pre-submission Checklist
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feature works
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- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
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- [ ] My commits have clear and descriptive messages
## Related Issues
None
## Additional Notes
None
## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
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## Description
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process and reasoning.
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## Type of Change
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- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
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- [ ] Performance improvement
- [ ] Other (please specify):
## Changes Made
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-
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-
## Testing
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## Screenshots/Videos (if applicable)
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#issue_number" -->
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## Description
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this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
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Update default tutorial:
1. Use tutorial from [notebook_tutorial
branch](https://github.com/topoteretes/cognee/blob/notebook_tutorial/notebooks/tutorial.ipynb),
specifically - it's .zip version with all necessary data files
2. Use Jupyter Notebook `Notebook` abstractions to read, and map `ipynb`
into our Notebook model
3. Dynamically update starter notebook code blocks that reference
starter data files, and swap them with local paths to downloaded copies
4. Test coverage
| Before | After (storage backend = local) | After (s3) |
|--------|---------------------------------|------------|
| <img width="613" height="546" alt="Screenshot 2025-09-17 at 01 00 58"
src="https://github.com/user-attachments/assets/20b59021-96c1-4a83-977f-e064324bd758"
/> | <img width="1480" height="262" alt="Screenshot 2025-09-18 at 13 01
57"
src="https://github.com/user-attachments/assets/bd56ea78-7c6a-42e3-ae3f-4157da231b2d"
/> | <img width="1485" height="307" alt="Screenshot 2025-09-18 at 12 56
08"
src="https://github.com/user-attachments/assets/248ae720-4c78-445a-ba8b-8a2991ed3f80"
/> |
## File Replacements
### S3 Demo
https://github.com/user-attachments/assets/bd46eec9-ef77-4f69-9ef0-e7d1612ff9b3
---
### Local FS Demo
https://github.com/user-attachments/assets/8251cea0-81b3-4cac-a968-9576c358f334
## 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)
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- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Changes Made
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-
-
-
## Testing
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## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
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submitted already
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- [ ] My commits have clear and descriptive messages
## Related Issues
<!-- Link any related issues using "Fixes #issue_number" or "Relates to
#issue_number" -->
## Additional Notes
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## DCO Affirmation
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## Description
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## Type of Change
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- [ ] New feature (non-breaking change that adds functionality)
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functionality to change)
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- [ ] Other (please specify):
## Changes Made
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## Testing
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## Screenshots/Videos (if applicable)
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## Description
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## Type of Change
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- [x] New feature (non-breaking change that adds functionality)
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## Changes Made
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## Summary
The `root_dir.py/ensure_absolute_path` validation in the `GraphConfig`
model currently enforces that all paths start with `/`.
This works for local file system paths but breaks when using S3 storage,
since S3 paths do not begin with `/` and fail validation.
## Fix
This PR updates the `ensure_absolute_path` method to recognize and treat
S3 paths as valid.
## Logs before
```
(.venv) daulet@Mac cognee-claude % cognee-cli -ui
2025-09-18T01:30:39.768877 [info ] Deleted old log file: /Users/daulet/Desktop/dev/cognee-claude/logs/2025-09-18_02-15-14.log [cognee.shared.logging_utils]
2025-09-18T01:30:40.391407 [error ] Exception [cognee.shared.logging_utils] exception_message="1 validation error for GraphConfig\n Value error, Path must be absolute. Got relative path: s3://daulet-personal-dev/cognee/data [type=value_error, input_value={'data_root_directory': '...45daea63bc5392d85746fb'}, input_type=dict]\n For further information visit https://errors.pydantic.dev/2.11/v/value_error" traceback=True
```
## Logs after
```
(.venv) daulet@Mac cognee-claude % cognee-cli -ui
2025-09-18T01:34:34.404642 [info ] Deleted old log file: /Users/daulet/Desktop/dev/cognee-claude/logs/2025-09-18_02-17-55.log [cognee.shared.logging_utils]
2025-09-18T01:34:35.026078 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.4.dev1-local database_path=s3://daulet-personal-dev/cognee/system/databases graph_database_name= os_info='Darwin 24.5.0 (Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132)' python_version=3.10.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-09-18T01:34:35.026223 [info ] Database storage: s3://daulet-personal-dev/cognee/system/databases [cognee.shared.logging_utils]
Starting cognee UI...
2025-09-18T01:34:36.105617 [info ] Starting cognee UI... [cognee.shared.logging_utils]
2025-09-18T01:34:36.105756 [info ] Starting cognee backend API server... [cognee.shared.logging_utils]
2025-09-18T01:34:37.522194 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.4.dev1-local database_path=s3://daulet-personal-dev/cognee/system/databases graph_database_name= os_info='Darwin 24.5.0 (Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132)' python_version=3.10.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-09-18T01:34:37.522376 [info ] Database storage: s3://daulet-personal-dev/cognee/system/databases [cognee.shared.logging_utils]
2025-09-18T01:34:38.115247 [info ] ✓ Backend API started at http://localhost:8000 [cognee.shared.logging_utils]
2025-09-18T01:34:38.198637 [info ] Starting frontend server at http://localhost:3000 [cognee.shared.logging_utils]
2025-09-18T01:34:38.198879 [info ] This may take a moment to compile and start... [cognee.shared.logging_utils]
INFO: Started server process [83608]
INFO: Waiting for application startup.
2025-09-18T01:34:39.781430 [warning ] Kuzu S3 storage file not found: s3://daulet-personal-dev/cognee/system/databases/cognee_graph_kuzu [cognee.shared.logging_utils]
2025-09-18T01:34:39.802516 [info ] Loaded JSON extension [cognee.shared.logging_utils]
2025-09-18T01:34:40.197857 [info ] Deleted Kuzu database files at s3://daulet-personal-dev/cognee/system/databases/cognee_graph_kuzu [cognee.shared.logging_utils]
2025-09-18T01:34:41.211523 [info ] ✓ Cognee UI is starting up... [cognee.shared.logging_utils]
2025-09-18T01:34:41.212561 [info ] ✓ Open your browser to: http://localhost:3000 [cognee.shared.logging_utils]
2025-09-18T01:34:41.212814 [info ] ✓ The UI will be available once Next.js finishes compiling [cognee.shared.logging_utils]
Success: UI server started successfully!
The interface is available at: http://localhost:3000
The API backend is available at: http://localhost:8000
Note: Press Ctrl+C to stop the server...
```
## Description
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this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
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## Type of Change
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functionality to change)
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- [ ] Other (please specify):
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## Testing
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## Screenshots/Videos (if applicable)
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issue/feature**
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## Description
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Added docs that were missing from permission related functions in the
code.
## Type of Change
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- [ ] New feature (non-breaking change that adds functionality)
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functionality to change)
- [x] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Changes Made
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## Description
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Updated very little docs, since the two files I was supposed to look at
already have docs written. Expanding these would be unnecessary imo, not
a lot of value can be added.
## Type of Change
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## Description
Fixes infinite loop introduced in combined search refactor
## 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):
## Changes Made
<!-- List the specific changes made in this PR -->
Fixes infinite loop introduced in combined search refactor
## Testing
Manual
## 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
## Related Issues
https://github.com/topoteretes/cognee/pull/1341
## Additional Notes
None
## 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.
