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Vasilije1990
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Oct 27, 2024
Fixed Broken Link in Readme
borisarzentar
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hajdul88
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Jun 25, 2025
…nt-neo4j-memgraph-1749615699 feat: make authentication optional for Neo4j and Memgraph connections
dexters1
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Sep 10, 2025
…-token-support feat: add support for AWS session token in S3 configuration
Vasilije1990
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Sep 28, 2025
<!-- .github/pull_request_template.md --> ## Description Running cognee-mcp as a docker container currently fails when using latest main version: ``` (cognee-mcp) daulet@Mac cognee-claude % docker run -e TRANSPORT_MODE=sse -p 8001:8000 cognee/cognee-mcp:main Debug mode: Environment: Transport mode: sse Debug port: 5678 HTTP port: 8000 Running database migrations... 2025-09-25T21:15:17.065171 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.2 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=3.12.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb 2025-09-25T21:15:17.065330 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils] generated new fontManager Database migrations done. Starting Cognee MCP Server with transport mode: sse 2025-09-25T21:15:24.204708 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.2 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=3.12.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb 2025-09-25T21:15:24.204863 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils] Usage: cognee [-h] [--version] [--debug] [-ui] {add,search,cognify,delete,config} ... cognee: error: argument command: invalid choice: 'sse' (choose from add, search, cognify, delete, config) (cognee-mcp) daulet@Mac cognee-claude % ``` This is due to both `cognee-mcp` and `cognee` (v0.3.2) projects defining their CLI script aliases as `cognee`. `entrypoint.sh` uses `cognee` cli, assuming it's `cognee-mcp`, which is failing (see logs above). While in later version of cognee we define `cognee-cli` instead of `cognee`, it's still important to be safer and be more explicit in `cognee-mcp` cli alias. ## Testing the fix ``` (cognee-mcp) daulet@Mac cognee-claude % docker run -e TRANSPORT_MODE=sse -p 8001:8000 cognee/cognee-mcp:daulet-dev Debug mode: Environment: Transport mode: sse Debug port: 5678 HTTP port: 8000 Running database migrations... 2025-09-25T21:18:45.855092 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.2 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=3.12.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb 2025-09-25T21:18:45.855270 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils] generated new fontManager Database migrations done. Starting Cognee MCP Server with transport mode: sse 2025-09-25T21:18:53.188498 [info ] Logging initialized [cognee.shared.logging_utils] cognee_version=0.3.2 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=3.12.11 relational_config=cognee_db structlog_version=25.4.0 vector_config=lancedb 2025-09-25T21:18:53.188665 [info ] Database storage: /app/.venv/lib/python3.12/site-packages/cognee/.cognee_system/databases [cognee.shared.logging_utils] 2025-09-25T21:18:54.272533 [info ] Starting MCP server with transport: sse [cognee.shared.logging_utils] 2025-09-25T21:18:54.272661 [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) ``` <!-- 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.
Vasilije1990
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Oct 22, 2025
fix: Update code for Ollama API compatibility with newer version
Vasilije1990
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Oct 29, 2025
<!-- .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. --> Fixes #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) - [ ] 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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