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## Description
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Added a CI test to make sure fastembed works as intended.
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## Description
Ontology notebook fix
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Ontology notebook fix
## Testing
manual
## Screenshots/Videos (if applicable)
None
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## Description
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Adds abstraction for OntologyResolvers and matching mechanism
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Adds ontology abstraction + matching resolver logic to support multiple
solutions
## Testing
Testing of changes is done using manual testing and ci/cd tests
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None
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## Description
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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
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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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## Screenshots/Videos (if applicable)
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## Description
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Added docs that were missing from permission related functions in the
code.
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- [ ] Code refactoring
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- [ ] Other (please specify):
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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.
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## Description
Fixes infinite loop introduced in combined search refactor
## Type of Change
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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.
