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Description
I have completed the first two steps and configured the DeepSeek API. Why am I getting a 405 error: {"detail":"Method Not Allowed"}?
python main.py --phase code_generation
`(cellforge) xxxxxxx scAgents % python main.py --phase code_generation
✅ Loaded environment variables from /Users/xxxxxx/Documents/cellforge/scAgents/.env
✅ Sentence transformer encoder initialized
✅ CellForge Qdrant client initialized
✅ cellforge_tmp Qdrant client initialized
✅ Collection task_analysis_papers exists in CellForge
✅ Collection task_analysis_experimental_designs exists in CellForge
✅ Collection task_analysis_implementation_guides exists in CellForge
✅ Collection task_analysis_evaluation_frameworks exists in CellForge
✅ Collection task_analysis_decision_support exists in CellForge
✅ Collection task_analysis_papers exists in cellforge_tmp
✅ Collection task_analysis_experimental_designs exists in cellforge_tmp
✅ Collection task_analysis_implementation_guides exists in cellforge_tmp
✅ Collection task_analysis_evaluation_frameworks exists in cellforge_tmp
✅ Collection task_analysis_decision_support exists in cellforge_tmp
✅ Dataset loaded successfully: /Users/xxxxxx/Documents/cellforge/scAgents/cellforge/data/datasets/NormanWeissman2019_filtered.h5ad
DATASET INFORMATION
Shape: (111445, 33694)
Number of cells: 111445
Number of genes: 33694
Observation (cells) columns:
['guide_id', 'read_count', 'UMI_count', 'coverage', 'gemgroup', 'good_coverage', 'number_of_cells', 'tissue_type', 'cell_line', 'cancer', 'disease', 'perturbation_type', 'celltype', 'organism', 'perturbation', 'nperts', 'ngenes', 'ncounts', 'percent_mito', 'percent_ribo']
Variable (genes) columns:
['ensemble_id', 'ncounts', 'ncells']
Loaded .env from: /Users/xxxxxxDocuments/cellforge/scAgents/.env
Loaded .env from: /Users/xxxxxx/Documents/cellforge/scAgents/.env
Loaded .env from: /Users/xxxxxx/Documents/cellforge/scAgents/.env
============================================================
PHASE 3: CODE GENERATION
📋 Found research plan: cellforge/data/results/research_plan_20251109_035634.json
🔧 Generating code from research plan...
INFO:cellforge.Code_Generation:Loaded environment from: /Users/xxxxxx/Documents/cellforge/scAgents/.env
INFO:cellforge.Code_Generation:Using API configuration: deepseek
INFO:cellforge.Code_Generation:=== Starting Code Generation with OpenHands ===
INFO:cellforge.Code_Generation:Starting OpenHands Docker container...
INFO:cellforge.Code_Generation:Docker available: Docker version 28.5.1, build e180ab8
INFO:cellforge.Code_Generation:Docker Compose available: Docker Compose version v2.40.2-desktop.1
INFO:cellforge.Code_Generation:Stopping any existing OpenHands containers...
INFO:cellforge.Code_Generation:Prepared environment variables for deepseek
INFO:cellforge.Code_Generation:Building and starting OpenHands container...
INFO:cellforge.Code_Generation:OpenHands Docker container started successfully
INFO:cellforge.Code_Generation:Container output: #1 [internal] load local bake definitions
#1 reading from stdin 639B done
#1 DONE 0.0s
#2 [internal] load build definition from Dockerfile
#2 transferring dockerfile: 3.33kB done
#2 DONE 0.0s
#3 [internal] load metadata for docker.io/library/node:24.8-trixie-slim
#3 DONE 0.0s
#4 [internal] load metadata for docker.io/library/python:3.13.7-slim-trixie
#4 DONE 0.0s
#5 [internal] load .dockerignore
#5 transferring context: 335B done
#5 DONE 0.0s
#6 [base 1/1] FROM docker.io/library/python:3.13.7-slim-trixie@sha256:5f55cdf0c5d9dc1a415637a5ccc4a9e18663ad203673173b8cda8f8dcacef689
#6 resolve docker.io/library/python:3.13.7-slim-trixie@sha256:5f55cdf0c5d9dc1a415637a5ccc4a9e18663ad203673173b8cda8f8dcacef689 done
#6 DONE 0.0s
#7 [frontend-builder 1/6] FROM docker.io/library/node:24.8-trixie-slim@sha256:a7f91166324d17fa1029718c876f3b02fb542e64d3cf40208ae6d31ff33c90c9
#7 resolve docker.io/library/node:24.8-trixie-slim@sha256:a7f91166324d17fa1029718c876f3b02fb542e64d3cf40208ae6d31ff33c90c9 done
#7 DONE 0.0s
#8 [internal] load build context
#8 transferring context: 118.91kB 0.0s done
#8 DONE 0.0s
#9 [backend-builder 2/5] RUN apt-get update -y && apt-get install -y curl make git build-essential jq gettext && python3 -m pip install poetry --break-system-packages
#9 CACHED
#10 [openhands-app 2/20] RUN mkdir -p /.openhands
#10 CACHED
#11 [backend-builder 3/5] COPY pyproject.toml poetry.lock ./
#11 CACHED
#12 [backend-builder 4/5] RUN touch README.md
#12 CACHED
#13 [frontend-builder 5/6] COPY frontend ./
#13 CACHED
#14 [openhands-app 10/20] RUN sudo chown -R openhands:openhands /opt/workspace_base && sudo chmod -R 770 /opt/workspace_base
#14 CACHED
#15 [openhands-app 5/20] RUN sed -i 's/^UID_MIN.*/UID_MIN 499/' /etc/login.defs
#15 CACHED
#16 [openhands-app 18/20] COPY --chown=openhands:openhands --chmod=770 --from=frontend-builder /app/build ./frontend/build
#16 CACHED
#17 [openhands-app 16/20] RUN python openhands/core/download.py # No-op to download assets
#17 CACHED
#18 [openhands-app 8/20] RUN useradd -l -m -u 42420 --gid 42420 -s /bin/bash openhands && usermod -aG openhands openhands && usermod -aG sudo openhands && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
#18 CACHED
#19 [openhands-app 3/20] RUN mkdir -p /opt/workspace_base
#19 CACHED
#20 [openhands-app 7/20] RUN groupadd --gid 42420 openhands
#20 CACHED
#21 [openhands-app 17/20] RUN find /app ! -group openhands -exec chgrp openhands {} +
#21 CACHED
#22 [openhands-app 15/20] COPY --chown=openhands:openhands pyproject.toml poetry.lock README.md MANIFEST.in LICENSE ./
#22 CACHED
#23 [frontend-builder 4/6] RUN npm ci
#23 CACHED
#24 [backend-builder 5/5] RUN export POETRY_CACHE_DIR && poetry install --no-root && rm -rf /tmp/poetry_cache
#24 CACHED
#25 [openhands-app 12/20] COPY --chown=openhands:openhands --chmod=770 ./microagents ./microagents
#25 CACHED
#26 [openhands-app 11/20] COPY --chown=openhands:openhands --chmod=770 --from=backend-builder /app/.venv /app/.venv
#26 CACHED
#27 [backend-builder 1/5] WORKDIR /app
#27 CACHED
#28 [frontend-builder 3/6] COPY frontend/package.json frontend/package-lock.json ./
#28 CACHED
#29 [openhands-app 13/20] COPY --chown=openhands:openhands --chmod=770 ./openhands ./openhands
#29 CACHED
#30 [openhands-app 9/20] RUN chown -R openhands:openhands /app && chmod -R 770 /app
#30 CACHED
#31 [frontend-builder 2/6] WORKDIR /app
#31 CACHED
#32 [openhands-app 6/20] RUN sed -i 's/^UID_MAX.*/UID_MAX 1000000/' /etc/login.defs
#32 CACHED
#33 [openhands-app 4/20] RUN apt-get update -y && apt-get install -y curl ssh sudo && rm -rf /var/lib/apt/lists/*
#33 CACHED
#34 [frontend-builder 6/6] RUN npm run build
#34 CACHED
#35 [openhands-app 19/20] COPY --chown=openhands:openhands --chmod=770 ./containers/app/entrypoint.sh /app/entrypoint.sh
#35 CACHED
#36 [openhands-app 14/20] COPY --chown=openhands:openhands --chmod=777 ./openhands/runtime/plugins ./openhands/runtime/plugins
#36 CACHED
#37 [openhands-app 20/20] WORKDIR /app
#37 CACHED
#38 exporting to image
#38 exporting layers done
#38 exporting manifest sha256:020dc0d708a881ae8dd0ea94a8ed5f8afc5c15b4ab9f5dafe8c07726b27397df done
#38 exporting config sha256:a169f00afffd104ff29bab86e8af5124a31df7882798ebce946ef612418fe02a done
#38 exporting attestation manifest sha256:c423e269e84f9d6e98ce6b84a1d755e4acd1fd9886e949513e5800b4bc776880 done
#38 exporting manifest list sha256:7a022c17df380ebe8be4f6bbaaf666f5e0e818305bacdc1d94ae616520d284ef done
#38 naming to docker.io/library/openhands:latest done
#38 unpacking to docker.io/library/openhands:latest done
#38 DONE 0.0s
#39 resolving provenance for metadata file
#39 DONE 0.0s
INFO:cellforge.Code_Generation:Waiting for OpenHands to be ready...
INFO:cellforge.Code_Generation:OpenHands is ready!
INFO:cellforge.Code_Generation:Large research plan detected (27241 characters), ensuring complete input...
INFO:cellforge.Code_Generation:Waiting for complete JSON input...
INFO:cellforge.Code_Generation:JSON content is complete and valid
INFO:cellforge.Code_Generation:Sending request to OpenHands API...
INFO:cellforge.Code_Generation:Detected large JSON content, ensuring complete input...
INFO:cellforge.Code_Generation:Waiting for complete JSON input...
INFO:cellforge.Code_Generation:JSON content is complete and valid
INFO:cellforge.Code_Generation:Sending request to: http://localhost:3000/api/chat
INFO:cellforge.Code_Generation:Using model: deepseek-chat
INFO:cellforge.Code_Generation:Response status: 405
ERROR:cellforge.Code_Generation:OpenHands API error: 405 - {"detail":"Method Not Allowed"}
ERROR:cellforge.Code_Generation:Failed to generate code
INFO:cellforge.Code_Generation:Stopping OpenHands Docker container...
INFO:cellforge.Code_Generation:OpenHands Docker container stopped successfully
❌ Code generation failed
`