<!-- .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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- Added an `edge_text` field to edges that auto-fills from
`relationship_type` if not provided.
- Containts edges now store descriptions for better embedding
- Updated and refactored indexing so that edge_text gets embedded and
exposed
- Updated retrieval to use the new embeddings
- Added a test to verify edge_text exists in the graph with the correct
format.
## 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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- [x] Performance improvement
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## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
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issue/feature**
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guidelines
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feature works
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- [ ] All new and existing tests pass
- [x] I have searched existing PRs to ensure this change hasn't been
submitted already
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## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
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<!-- .github/pull_request_template.md -->
## Description
Update cognee version and lock files
## Type of Change
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## Description
Remove custom text file resolution, it sometimes wrongly marks other
file types as txt
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## Description
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this PR.
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Fixes https://github.com/topoteretes/cognee/issues/1681
We do not support AWS out of the box in MCP right now.
This PR enables users to select what extras they want to start their
`cognee-mcp` with, so users can extend MCP if need be.
## Testing
1. Added `AWS_REGION`, `AWS_ACCESS_KEY_ID`, and `AWS_SECRET_ACCESS_KEY`
into `.env`
2. Uploaded completely [generated
story](https://github.com/topoteretes/cognee-community/blob/main/packages/hybrid/duckdb/examples/simple_document_example/data/generated_story.txt)
into S3
3. Started mcp, using MCP inspector called `cognify` with s3 path to the
generated story
<img width="780" height="703" alt="Screenshot 2025-10-29 at 17 08 10"
src="https://github.com/user-attachments/assets/47157591-7243-4e87-befb-fb7ca6f3cf61"
/>
4. Called "search" tool with story-specific question
<img width="776" height="717" alt="Screenshot 2025-10-29 at 17 08 34"
src="https://github.com/user-attachments/assets/64ab25f4-80d6-4f8a-a982-17c2191c6503"
/>
### Logs
<details>
```
daulet@Mac cognee-claude % docker run \
-e TRANSPORT_MODE=sse \
-e EXTRAS=aws,postgres,neo4j \
--env-file ./.env \
-p 8121:8000 \
--rm -it cognee/cognee-mcp:custom-deps
Debug mode:
Environment:
Installing optional dependencies: aws,postgres,neo4j
Current cognee version: 0.3.7
Installing cognee with extras: aws,postgres,neo4j
Running: uv pip install 'cognee[aws,postgres,neo4j]==0.3.7'
Resolved 137 packages in 679ms
Prepared 7 packages in 484ms
Installed 7 packages in 86ms
+ aiobotocore==2.25.1
+ aioitertools==0.12.0
+ boto3==1.40.61
+ botocore==1.40.61
+ jmespath==1.0.1
+ s3fs==2025.3.2
+ s3transfer==0.14.0
✓ Optional dependencies installation completed
Transport mode: sse
Debug port: 5678
HTTP port: 8000
Direct mode: Using local cognee instance
Running database migrations...
2025-10-29T16:56:01.562650 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.7 database_path=/app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases graph_database_name= os_info='Linux 6.12.5-linuxkit (#1 SMP Tue Jan 21 10:23:32 UTC 2025)' python_version=3.12.12 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-10-29T16:56:01.562816 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils]
2025-10-29T16:56:01.782204 [warning ] Failed to import protego, make sure to install using pip install protego>=0.1 [cognee.shared.logging_utils]
2025-10-29T16:56:01.782403 [warning ] Failed to import playwright, make sure to install using pip install playwright>=1.9.0 [cognee.shared.logging_utils]
Database migrations done.
Starting Cognee MCP Server with transport mode: sse
2025-10-29T16:56:06.184893 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.7 database_path=/app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases graph_database_name= os_info='Linux 6.12.5-linuxkit (#1 SMP Tue Jan 21 10:23:32 UTC 2025)' python_version=3.12.12 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb
2025-10-29T16:56:06.185069 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils]
2025-10-29T16:56:06.245181 [warning ] Failed to import protego, make sure to install using pip install protego>=0.1 [cognee.shared.logging_utils]
2025-10-29T16:56:06.245327 [warning ] Failed to import playwright, make sure to install using pip install playwright>=1.9.0 [cognee.shared.logging_utils]
2025-10-29T16:56:06.582115 [info ] Cognee client initialized in direct mode [cognee.shared.logging_utils]
2025-10-29T16:56:06.582268 [info ] Starting MCP server with transport: sse [cognee.shared.logging_utils]
2025-10-29T16:56:06.582618 [info ] Running MCP server with SSE transport on 0.0.0.0:8000 [cognee.shared.logging_utils]
INFO: Started server process [1]
INFO: Waiting for application startup.
INFO: Application startup complete.
INFO: Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
INFO: 192.168.65.1:54572 - "GET /sse HTTP/1.1" 200 OK
INFO: 192.168.65.1:57034 - "GET /sse HTTP/1.1" 200 OK
INFO: 192.168.65.1:57104 - "GET /sse HTTP/1.1" 200 OK
INFO: 192.168.65.1:55411 - "POST /messages/?session_id=33fc2c041d184f3ab62597c69259d036 HTTP/1.1" 202 Accepted
INFO: 192.168.65.1:55411 - "POST /messages/?session_id=33fc2c041d184f3ab62597c69259d036 HTTP/1.1" 202 Accepted
INFO: 192.168.65.1:22986 - "POST /messages/?session_id=33fc2c041d184f3ab62597c69259d036 HTTP/1.1" 202 Accepted
Processing request of type CallToolRequest
2025-10-29T16:57:52.864665 [info ] Cognify process starting. [cognee.shared.logging_utils]
2025-10-29T16:57:58.159329 [info ] Pipeline run started: `469d4729-328a-542d-aac1-3ea4167d9b83` [run_tasks_with_telemetry()]
2025-10-29T16:57:58.332811 [info ] Coroutine task started: `resolve_data_directories` [run_tasks_base]
2025-10-29T16:57:58.604008 [info ] Coroutine task started: `ingest_data` [run_tasks_base]
2025-10-29T16:57:58.899181 [info ] Registered loader: pypdf_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.899637 [info ] Registered loader: text_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.899817 [info ] Registered loader: image_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.899964 [info ] Registered loader: audio_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.900103 [info ] Registered loader: unstructured_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.900197 [info ] Registered loader: advanced_pdf_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:58.900321 [info ] Registered loader: beautiful_soup_loader [cognee.infrastructure.loaders.LoaderEngine]
2025-10-29T16:57:59.022385 [info ] Coroutine task completed: `ingest_data` [run_tasks_base]
2025-10-29T16:57:59.183862 [info ] Coroutine task completed: `resolve_data_directories` [run_tasks_base]
2025-10-29T16:57:59.347932 [info ] Pipeline run completed: `469d4729-328a-542d-aac1-3ea4167d9b83` [run_tasks_with_telemetry()]
2025-10-29T16:57:59.600721 [info ] Loaded JSON extension [cognee.shared.logging_utils]
2025-10-29T16:57:59.616370 [info ] Ontology file 'None' not found. No owl ontology will be attached to the graph. [OntologyAdapter]
2025-10-29T16:57:59.633495 [info ] Pipeline run started: `21372a56-1d44-5e19-a024-209d03a99218` [run_tasks_with_telemetry()]
2025-10-29T16:57:59.784198 [info ] Coroutine task started: `classify_documents` [run_tasks_base]
2025-10-29T16:57:59.933817 [info ] Coroutine task started: `check_permissions_on_dataset` [run_tasks_base]
2025-10-29T16:58:00.147315 [info ] Async Generator task started: `extract_chunks_from_documents` [run_tasks_base]
2025-10-29T16:58:00.366572 [info ] Coroutine task started: `extract_graph_from_data` [run_tasks_base]
2025-10-29T16:58:51.639973 [info ] No close match found for 'person' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.642293 [info ] No close match found for 'khaélith orun' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.642456 [info ] No close match found for 'location' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.642551 [info ] No close match found for 'vorrxundra' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.642632 [info ] No close match found for 'creature' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.642739 [info ] No close match found for 'thirvalque' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.642823 [info ] No close match found for 'ossaryn' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.642928 [info ] No close match found for 'fyrneloch' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.643126 [info ] No close match found for 'mirror-river' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.643237 [info ] No close match found for 'zyrrhalin' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.643325 [info ] No close match found for 'artifact' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.643410 [info ] No close match found for 'crystal plates' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:51.643468 [info ] No close match found for 'concept' in category 'classes' [OntologyAdapter]
2025-10-29T16:58:51.643551 [info ] No close match found for 'forgotten futures' in category 'individuals' [OntologyAdapter]
2025-10-29T16:58:52.968522 [info ] Coroutine task started: `summarize_text` [run_tasks_base]
2025-10-29T16:59:03.982055 [info ] Coroutine task started: `add_data_points` [run_tasks_base]
2025-10-29T16:59:04.884215 [info ] Coroutine task completed: `add_data_points` [run_tasks_base]
2025-10-29T16:59:05.038833 [info ] Coroutine task completed: `summarize_text` [run_tasks_base]
2025-10-29T16:59:05.200412 [info ] Coroutine task completed: `extract_graph_from_data` [run_tasks_base]
2025-10-29T16:59:05.361403 [info ] Async Generator task completed: `extract_chunks_from_documents` [run_tasks_base]
2025-10-29T16:59:05.529879 [info ] Coroutine task completed: `check_permissions_on_dataset` [run_tasks_base]
2025-10-29T16:59:05.694801 [info ] Coroutine task completed: `classify_documents` [run_tasks_base]
2025-10-29T16:59:05.852353 [info ] Pipeline run completed: `21372a56-1d44-5e19-a024-209d03a99218` [run_tasks_with_telemetry()]
2025-10-29T16:59:06.042754 [info ] Cognify process finished. [cognee.shared.logging_utils]
INFO: 192.168.65.1:25778 - "POST /messages/?session_id=33fc2c041d184f3ab62597c69259d036 HTTP/1.1" 202 Accepted
Processing request of type CallToolRequest
2025-10-29T17:01:03.372413 [info ] Graph projection completed: 17 nodes, 33 edges in 0.01s [CogneeGraph]
2025-10-29T17:01:03.790022 [info ] Vector collection retrieval completed: Retrieved distances from 6 collections in 0.07s [cognee.shared.logging_utils]
```
</details>
## 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)
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- [ ] 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
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submitted already
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## 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.
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## Description
Fix issue with logs
## 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)
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## Screenshots/Videos (if applicable)
<!-- Add screenshots or videos to help explain your changes -->
## Pre-submission Checklist
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- [ ] **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.
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## Description
Remove custom PDF handling and let filetype handle PDF documents
## 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)
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- [ ] **I have tested my changes thoroughly before submitting this PR**
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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
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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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## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
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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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## Type of Change
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- [ ] 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)
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- [ ] Other (please specify):
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guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
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submitted already
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## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
Remove fallback when provided vector adapter is not reckognized to use
LanceDB. When no adapter provider info is provided LanceDB will still be
used.
## 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 -->
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feature works
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submitted already
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## DCO Affirmation
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the terms of the Topoteretes Developer Certificate of Origin.
<!-- .github/pull_request_template.md -->
## Description
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## Type of Change
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- [ ] New feature (non-breaking change that adds functionality)
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## Description
In case of a read-only file system handle the inability to create an
.anon_id file
## Type of Change
<!-- Please check the relevant option -->
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## Pre-submission Checklist
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- [ ] **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
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- [ ] All new and existing tests pass
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submitted already
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## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
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## Description
Adds the concept of now to the qa for temporal queries
## 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)
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## 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.
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## Description
Adds multifile ontology support
## 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
- [x] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):
## Screenshots/Videos (if applicable)
None
## 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
- [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.
…de ID
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## Description
Update description of relational database column to use relational
database ID value instead of graph node ID value
## 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.
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## Description
Enable Cognee to work on read only file systems by avoiding use of file
handler when logging if log file location is read only
## 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.
