modelseed-api/Dockerfile.standalone at main · ModelSEED/modelseed-api · GitHub

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# ModelSEED API: self-contained image for standalone use
#
# Unlike the production Dockerfile (which COPYs sibling repos from the
# build host), this image clones all dependency repos from GitHub during
# the build. Result: a single self-contained image that anyone can pull
# from ghcr.io and run without setting up a local development environment.
#
# Build (CI): GitHub Actions builds + pushes to ghcr.io/modelseed/modelseed-api
# Build (local, for testing):
#     docker build -f Dockerfile.standalone -t modelseed-api:standalone .
# Run:
#     docker run -p 8000:8000 ghcr.io/modelseed/modelseed-api:latest
#     # then hit http://localhost:8000/demo/
#
# The image includes ModelSEEDDatabase and ModelSEEDTemplates baked in;
# total size ~1.5-2 GB. Larger than typical web-app images but eliminates
# the need for separate data downloads.
#
# Defaults to local-storage mode (no PATRIC account needed). All ANL-
# specific endpoints (workspace, RAST jobs, RAST genome) cleanly return
# 503 unless their env vars are configured. See docs/STANDALONE.md.

FROM python:3.11-slim

# System deps: GLPK for cobra's linear solver, git for cloning, gcc/g++
# for Python wheel builds that need compilation.
RUN apt-get update && apt-get install -y --no-install-recommends \
        glpk-utils \
        libglpk-dev \
        libexpat1 \
        gcc \
        g++ \
        git \
    && rm -rf /var/lib/apt/lists/*

WORKDIR /deps

# Clone dependency repos. Using `--depth 1` keeps the image smaller by
# skipping git history. Pin to specific commits later if reproducible
# builds become important; HEAD of each branch is fine for now.
RUN git clone --depth 1 --branch master https://github.com/Fxe/cobrakbase.git && \
    git clone --depth 1 --branch main https://github.com/cshenry/ModelSEEDpy.git && \
    git clone --depth 1 --branch main https://github.com/cshenry/KBUtilLib.git && \
    git clone --depth 1 --branch main https://github.com/kbaseapps/cb_annotation_ontology_api.git && \
    git clone --depth 1 --branch dev https://github.com/ModelSEED/ModelSEEDDatabase.git && \
    git clone --depth 1 --branch main https://github.com/ModelSEED/ModelSEEDTemplates.git

# Install dependency packages in the order they expect.
# cobrakbase first (no deps on others), then ModelSEEDpy, then KBUtilLib.
RUN pip install --no-cache-dir -e /deps/cobrakbase && \
    pip install --no-cache-dir -e /deps/ModelSEEDpy && \
    pip install --no-cache-dir -e /deps/KBUtilLib

WORKDIR /app

# Copy modelseed-api source from build context. With CI, the context is
# this repo's checkout; locally, run from the repo root.
COPY src/ /app/src/
COPY data/ /app/data/
COPY pyproject.toml /app/

# Install modelseed-api with the modeling+celery extras.
RUN pip install --no-cache-dir -e ".[modeling,celery]"

# numpy/scikit-learn occasionally end up at mismatched ABI versions
# after the editable installs; force-reinstall to a coherent pair.
# Then pre-download the ~25MB genome classifier files so the first
# model build is fast.
RUN pip install --no-cache-dir --force-reinstall numpy scikit-learn && \
    python -c "from modelseedpy.helpers import get_classifier; get_classifier('knn_ACNP_RAST_filter_01_17_2023')"

# Default configuration.
ENV MODELSEED_MODELSEED_DB_PATH=/deps/ModelSEEDDatabase \
    MODELSEED_TEMPLATES_PATH=/deps/ModelSEEDTemplates/templates/v7.0 \
    MODELSEED_CB_ANNOTATION_ONTOLOGY_API_PATH=/deps/cb_annotation_ontology_api \
    MODELSEED_JOB_STORE_DIR=/tmp/modelseed-jobs \
    MODELSEED_HOST=0.0.0.0 \
    MODELSEED_PORT=8000 \
    MODELSEED_STORAGE_BACKEND=local \
    MODELSEED_LOCAL_DATA_DIR=/data/modelseed
# Local-storage by default: no PATRIC account needed, models persist
# under MODELSEED_LOCAL_DATA_DIR. Users who want PATRIC-workspace mode
# can override MODELSEED_STORAGE_BACKEND=workspace at run time.

# WORKAROUND: cobrakbase.KBaseAPI() reads a token from ~/.kbase/token
# even when not connecting to KBase. Required by MSReconstructionUtils
# init. Dummy value is fine.
ENV KB_AUTH_TOKEN=unused
RUN mkdir -p /root/.kbase && echo "unused" > /root/.kbase/token

# Make sure the default local-data dir exists so first-run writes work
# without the user pre-creating + bind-mounting it.
RUN mkdir -p /data/modelseed && chmod 777 /data/modelseed
VOLUME /data/modelseed

EXPOSE 8000

WORKDIR /app/src
CMD ["python", "-m", "uvicorn", "modelseed_api.main:app", "--host", "0.0.0.0", "--port", "8000"]