diff --git a/Dockerfile b/Dockerfile index 2878f1a2..784a7193 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,49 +1,40 @@ -# To run: docker run -v /path/to/wsgi.py:/var/www/indexd/wsgi.py --name=indexd -p 81:80 indexd -# To check running container: docker exec -it indexd /bin/bash +ARG AZLINUX_BASE_VERSION=master -FROM quay.io/cdis/python:python3.9-buster-2.0.0 +# Base stage with python-build-base +FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base ENV appname=indexd -RUN pip install --upgrade pip poetry -RUN apt-get update && apt-get install -y --no-install-recommends \ - build-essential libffi-dev musl-dev gcc libxml2-dev libxslt-dev \ - curl bash git vim +WORKDIR /${appname} -RUN mkdir -p /var/www/$appname \ - && mkdir -p /var/www/.cache/Python-Eggs/ \ - && mkdir /run/nginx/ \ - && ln -sf /dev/stdout /var/log/nginx/access.log \ - && ln -sf /dev/stderr /var/log/nginx/error.log \ - && chown nginx -R /var/www/.cache/Python-Eggs/ \ - && chown nginx /var/www/$appname +RUN chown -R gen3:gen3 /${appname} -EXPOSE 80 +# Builder stage +FROM base AS builder -WORKDIR /$appname +USER gen3 -# copy ONLY poetry artifact, install the dependencies but not indexd -# this will make sure than the dependencies is cached -COPY poetry.lock pyproject.toml /$appname/ -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-root --no-dev --no-interaction \ - && poetry show -v +COPY poetry.lock pyproject.toml /${appname}/ -# copy source code ONLY after installing dependencies -COPY . /$appname -COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini -COPY ./deployment/uwsgi/wsgi.py /$appname/wsgi.py -COPY clear_prometheus_multiproc /$appname/clear_prometheus_multiproc +RUN poetry install -vv --without dev --no-interaction -# install indexd -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-dev --no-interaction \ - && poetry show -v +COPY --chown=gen3:gen3 . /${appname} +COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /${appname}/wsgi.py -RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/index/version_data.py \ - && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/index/version_data.py +# Run poetry again so this app itself gets installed too +RUN poetry install --without dev --no-interaction -# directory where the app can find Alembic files -WORKDIR /indexd +RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /${appname}/version_data.py \ + && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /${appname}/version_data.py -CMD ["/dockerrun.sh"] +# Final stage +FROM base + +COPY --from=builder /${appname} /${appname} + +# Switch to non-root user 'gen3' for the serving process +USER gen3 + +WORKDIR /${appname} + +CMD ["/bin/bash", "-c", "/indexd/dockerrun.bash"] diff --git a/deployment/scripts/indexd/indexd_setup.sh b/deployment/scripts/indexd/indexd_setup.sh deleted file mode 100644 index e6d02cd7..00000000 --- a/deployment/scripts/indexd/indexd_setup.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash -# entrypoint bash script for indexd - -## try to install python util, or else fallback to environment variables. - -# activate virtual env -pushd /indexd -# TODO: check if poetry can install globally -python -m venv py-venv && . py-venv/bin/activate && source $HOME/.poetry/env -poetry install -vv --no-dev --no-interaction && poetry show -v -python3 -m pip install cdispyutils -popd - -/dockerrun.sh \ No newline at end of file diff --git a/deployment/uwsgi/uwsgi.ini b/deployment/uwsgi/uwsgi.ini deleted file mode 100644 index 7e2d7969..00000000 --- a/deployment/uwsgi/uwsgi.ini +++ /dev/null @@ -1,36 +0,0 @@ -[uwsgi] -protocol = uwsgi -socket = /var/run/gen3/uwsgi.sock -buffer-size = 32768 -uid = nginx -gid = nginx -chown-socket = nginx:nginx -chmod-socket = 666 -master = true -harakiri-verbose = true -# No global HARAKIRI, using only user HARAKIRI, because export overwrites it -# Cannot overwrite global HARAKIRI with user's: https://git.io/fjYuD -# harakiri = 45 -; If VIRTUAL_ENV is set then use its value to specify the virtualenv directory -if-env = VIRTUAL_ENV -virtualenv = %(_) -endif = -http-timeout = 45 -socket-timeout = 45 -worker-reload-mercy = 45 -reload-mercy = 45 -mule-reload-mercy = 45 -disable-logging = true -wsgi-file=/indexd/wsgi.py -plugins = python3 -vacuum = true -pythonpath = /indexd/ -stats = 127.0.0.1:9191 -stats-http = true -env = prometheus_multiproc_dir=/var/tmp/uwsgi_flask_metrics -exec-asap = /indexd/clear_prometheus_multiproc /var/tmp/uwsgi_flask_metrics -# Initialize application in worker processes, not master. This prevents the -# workers from all trying to open the same database connections at startup. -lazy = true -lazy-apps = true -listen = 4096 diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py new file mode 100644 index 00000000..64092ba3 --- /dev/null +++ b/deployment/wsgi/gunicorn.conf.py @@ -0,0 +1,9 @@ +wsgi_app = "deployment.wsgi.wsgi:application" +bind = "0.0.0.0:8000" +workers = 1 +preload_app = True +user = "gen3" +group = "gen3" +timeout = 300 +keepalive = 2 +keepalive_timeout = 5 diff --git a/deployment/uwsgi/wsgi.py b/deployment/wsgi/wsgi.py similarity index 100% rename from deployment/uwsgi/wsgi.py rename to deployment/wsgi/wsgi.py diff --git a/dockerrun.bash b/dockerrun.bash new file mode 100755 index 00000000..aee1b22d --- /dev/null +++ b/dockerrun.bash @@ -0,0 +1,4 @@ +#!/bin/bash + +nginx +poetry run gunicorn -c "/indexd/deployment/wsgi/gunicorn.conf.py" diff --git a/poetry.lock b/poetry.lock index 27b4eb29..122a37eb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. [[package]] name = "alembic" -version = "1.13.3" +version = "1.14.0" description = "A database migration tool for SQLAlchemy." optional = false python-versions = ">=3.8" files = [ - {file = "alembic-1.13.3-py3-none-any.whl", hash = "sha256:908e905976d15235fae59c9ac42c4c5b75cfcefe3d27c0fbf7ae15a37715d80e"}, - {file = "alembic-1.13.3.tar.gz", hash = "sha256:203503117415561e203aa14541740643a611f641517f0209fcae63e9fa09f1a2"}, + {file = "alembic-1.14.0-py3-none-any.whl", hash = "sha256:99bd884ca390466db5e27ffccff1d179ec5c05c965cfefc0607e69f9e411cb25"}, + {file = "alembic-1.14.0.tar.gz", hash = "sha256:b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b"}, ] [package.dependencies] @@ -21,13 +21,13 @@ tz = ["backports.zoneinfo"] [[package]] name = "anyio" -version = "4.6.0" +version = "4.6.2.post1" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" files = [ - {file = "anyio-4.6.0-py3-none-any.whl", hash = "sha256:c7d2e9d63e31599eeb636c8c5c03a7e108d73b345f064f1c19fdc87b79036a9a"}, - {file = "anyio-4.6.0.tar.gz", hash = "sha256:137b4559cbb034c477165047febb6ff83f390fc3b20bf181c1fc0a728cb8beeb"}, + {file = "anyio-4.6.2.post1-py3-none-any.whl", hash = "sha256:6d170c36fba3bdd840c73d3868c1e777e33676a69c3a72cf0a0d5d6d8009b61d"}, + {file = "anyio-4.6.2.post1.tar.gz", hash = "sha256:4c8bc31ccdb51c7f7bd251f51c609e038d63e34219b44aa86e47576389880b4c"}, ] [package.dependencies] @@ -38,7 +38,7 @@ typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.21.0b1)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"] trio = ["trio (>=0.26.1)"] [[package]] @@ -121,13 +121,13 @@ files = [ [[package]] name = "blinker" -version = "1.8.2" +version = "1.9.0" description = "Fast, simple object-to-object and broadcast signaling" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"}, - {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"}, + {file = "blinker-1.9.0-py3-none-any.whl", hash = "sha256:ba0efaa9080b619ff2f3459d1d500c57bddea4a6b424b60a91141db6fd2f08bc"}, + {file = "blinker-1.9.0.tar.gz", hash = "sha256:b4ce2265a7abece45e7cc896e98dbebe6cead56bcf805a3d23136d145f5445bf"}, ] [[package]] @@ -260,101 +260,116 @@ pycparser = "*" [[package]] name = "charset-normalizer" -version = "3.3.2" +version = "3.4.0" description = "The Real First Universal Charset Detector. 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