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MIDRC-927 Amazon Linux 2 image #2

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MIDRC-927 Amazon Linux 2 image #2

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b0054fb
AL2
paulineribeyre Jan 31, 2025
69bc1c0
postgres 13 instead of 16
paulineribeyre Feb 5, 2025
0735a39
postgres 15.10 and libpq 15.8-1
paulineribeyre Feb 5, 2025
9f64853
revert libpq change, keep postgres 15.10
paulineribeyre Feb 5, 2025
4387f78
clean up + postgres 16.5
paulineribeyre Feb 14, 2025
08b6ce0
fix runtime
paulineribeyre Feb 14, 2025
73b6f1a
Merge branch 'tag-24.3.5' of github.com:uc-cdis/orthanc-builder into …
paulineribeyre Feb 21, 2025
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138 changes: 50 additions & 88 deletions docker/orthanc/AmazonLinux2Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,92 +1,55 @@
# ===> https://github.com/orthanc-server/orthanc-builder/blob/11d6930/docker/orthanc/Dockerfile.runner-base

########################## orthanc-runner-base
##################
# The dockerfile below is copied+adapted from docker/orthanc/Dockerfile.runner-base
##################

# base image to build and execute orthanc.
# This image should contain only the packages that are common to both !
# The purpose of this intermediate image is to benefit from Docker cache.
ARG BASE_DEBIAN_IMAGE=bookworm-20250113-slim
FROM debian:$BASE_DEBIAN_IMAGE AS orthanc-runner-base

# we had some issues with one of the mirror -> force it to the Belgian mirror
# RUN rm /etc/apt/sources.list.d/debian.sources
# RUN echo "deb http://ftp.be.debian.org/debian/ bookworm main" | tee /etc/apt/sources.list.d/belgium.mirror.list

RUN export DEBIAN_FRONTEND=noninteractive && \
apt-get --assume-yes update && \
apt-get --assume-yes install python3 && \
apt-get --assume-yes install python3-pip && \
apt-get --assume-yes install ca-certificates && \
apt-get --assume-yes install tzdata && \
apt-get --assume-yes install locales && \
apt-get --assume-yes install libcurl4 && \
apt-get --assume-yes install libdcmtk17 && \
apt-get --assume-yes install libboost-log1.74.0 libboost-filesystem1.74.0 libboost-locale1.74.0 libboost-regex1.74.0 libboost-system1.74.0 libboost-thread1.74.0 libboost-iostreams1.74.0 && \
apt-get --assume-yes install libjpeg62-turbo && \
apt-get --assume-yes install libjsoncpp25 && \
apt-get --assume-yes install liblua5.4 && \
apt-get --assume-yes install libpng16-16 && \
apt-get --assume-yes install libpugixml1v5 && \
apt-get --assume-yes install libsqlite3-0 && \
apt-get --assume-yes install libssl3 && \
apt-get --assume-yes install libuuid1 && \
apt-get --assume-yes install lsb-base && \
apt-get --assume-yes install zlib1g && \
apt-get --assume-yes install libpq5 && \
apt-get --assume-yes install libmariadb3 && \
apt-get --assume-yes install unixodbc && \
apt-get --assume-yes install libopenslide0 && \
apt-get --assume-yes install libcrypto++ && \
apt-get --assume-yes install libcpprest && \
apt-get --assume-yes install libprotobuf32 && \
apt-get --assume-yes clean && \
rm --recursive --force /var/lib/apt/lists/*
FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/amazonlinux-base:master AS orthanc-runner-base

RUN dnf -y update && \
dnf -y install python3.11-devel \
ca-certificates tzdata \
libcurl-devel boost-devel libjpeg-turbo-devel \
jsoncpp-devel lua-devel libpng-devel sqlite-devel \
openssl-devel libuuid-devel unixODBC-devel \
protobuf-devel && \
dnf clean all

# Make sure the en_US locale has been generated (required for
# case-insensitive comparison of strings with accents)
RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen
RUN locale-gen
# (pauline 02/2025) The lines below don't work, but everything seems to work fine without this
# RUN dnf -y install glibc-locale-source glibc-langpack-en
# RUN localedef -i en_US -f UTF-8 en_US.UTF-8

# ===> https://github.com/orthanc-server/orthanc-builder/blob/11d6930/docker/orthanc/Dockerfile.builder-base
##################
# The dockerfile below is copied+adapted from docker/orthanc/Dockerfile.builder-base
##################

########################## Orthanc builder base
# image to compile Orthanc and its plugins dynamically
FROM orthanc-runner-base AS orthanc-builder-base

RUN export DEBIAN_FRONTEND=noninteractive
RUN apt-get --assume-yes update
RUN apt-get --assume-yes install wget
RUN apt-get --assume-yes install build-essential
RUN apt-get --assume-yes install unzip
RUN apt-get --assume-yes install uuid-dev
RUN apt-get --assume-yes install apt-utils
RUN apt-get --assume-yes install libcurl4-openssl-dev
RUN apt-get --assume-yes install curl
RUN apt-get --assume-yes install apt-transport-https
RUN apt-get --assume-yes install liblua5.4-dev
RUN apt-get --assume-yes install libgtest-dev
RUN apt-get --assume-yes install libpng-dev
RUN apt-get --assume-yes install libsqlite3-dev
RUN apt-get --assume-yes install libjpeg-dev zlib1g-dev libdcmtk-dev libboost-all-dev libwrap0-dev libcharls-dev libjsoncpp-dev libpugixml-dev
RUN apt-get --assume-yes install git
RUN apt-get --assume-yes install mercurial
RUN apt-get --assume-yes install zip
RUN apt-get --assume-yes install libpq-dev postgresql-server-dev-all
RUN apt-get --assume-yes install python3-dev
RUN apt-get --assume-yes install unixodbc-dev
RUN apt-get --assume-yes install libgmock-dev
RUN apt-get --assume-yes install protobuf-compiler
# on recent Debian, the libmysql-dev package is not available anymore
# and the MariaDbConfiguration.cmake does not handle it correctly -> use the downloaded mariadb_client
RUN apt-get --assume-yes install default-libmysqlclient-dev
# RUN apt-get --assume-yes install libmariadb-dev

RUN apt-get --assume-yes install cmake
RUN apt-get --assume-yes install awscli
# for orthanc-stl plugin:
RUN apt-get --assume-yes install libgl1-mesa-dev libxt-dev

RUN apt-get --assume-yes install default-jdk
RUN dnf -y update && \
dnf -y install wget unzip gcc gcc-c++ make cmake libuuid-devel \
ca-certificates tzdata libcurl-devel boost-devel \
libjpeg-turbo-devel zlib-devel git mercurial zip \
libpq libpq-devel postgresql-libs postgresql-devel \
protobuf-compiler aws-cli libpng-devel sqlite-devel \
lua-devel \
unixODBC-devel \
tar python-pip \
readline-devel libicu-devel openssl-devel \
java-11-amazon-corretto \
patch gtest gtest-devel && \
dnf clean all

RUN wget https://ftp.postgresql.org/pub/source/v16.5/postgresql-16.5.tar.gz && tar -zxvf postgresql-16.5.tar.gz && cd postgresql-16.5 && ./configure --bindir=/usr/bin --with-openssl && make -C src/bin install && make -C src/include install && make -C src/interfaces install

# install googletest, pugixml and cryptopp from source because the packages are not available
# in this amazon linux 2 base image
RUN git clone https://github.com/google/googletest.git && cd googletest && mkdir build && cd build && cmake .. && make && make install
RUN git clone https://github.com/zeux/pugixml.git && cd pugixml && mkdir build && cd build && cmake .. && make && make install
RUN git clone https://github.com/weidai11/cryptopp.git && cd cryptopp && make && make install

# # install a recent cmake version (required later by recent vcpkg versions that we don't use now !)
# WORKDIR /tmp
Expand Down Expand Up @@ -153,7 +116,9 @@ COPY build-or-download.sh /scripts

# ARG STONE_INTERMEDIATE_TARGET=build-stone-viewer-amd64

# ===> https://github.com/orthanc-server/orthanc-builder/blob/11d6930/docker/orthanc/Dockerfile
##################
# The dockerfile below is copied+adapted from docker/orthanc/Dockerfile
##################

# FROM orthanc-builder-base
ARG ARG_AWS_ACCESS_KEY_ID
Expand Down Expand Up @@ -201,8 +166,6 @@ RUN /scripts/build-or-download.sh version=$STABLE_OR_UNSTABLE target=orthanc-gdc
FROM orthanc-builder-base AS build-plugin-pg

ARG ORTHANC_PG_COMMIT_ID
# RUN echo debughere
# RUN hg --debug clone "https://bitbucket.org/sjodogne/orthanc"
RUN /scripts/build-or-download.sh version=$STABLE_OR_UNSTABLE target=orthanc-pg commitId=$ORTHANC_PG_COMMIT_ID baseImage=$PLATFORM/$BASE_IMAGE_TAG preferDownloads=$PREFER_DOWNLOADS enableUploads=$ENABLE_UPLOAD

########################## Orthanc MySQL
Expand Down Expand Up @@ -470,7 +433,10 @@ RUN if [[ ! -z "$TARGETPLATFORM" ]] && [[ "$TARGETPLATFORM" != "linux/amd64" ]];
RUN chmod +x /usr/share/orthanc/plugins-available/*
RUN chmod +x /usr/local/bin/*

RUN pip install envsubst==0.1.5 --break-system-packages
RUN dnf -y update && \
dnf -y install python-pip vim git libpq && \
dnf clean all
RUN pip install envsubst==0.1.5

# configure SSL for azure rest sdk (azure object storage plugin)
ENV SSL_CERT_DIR=/etc/ssl/certs
Expand All @@ -489,16 +455,12 @@ COPY *.lua /lua-scripts/
COPY test-aliveness.py /probes/


# cleanup unnecessary packages that can trigger errors during security scan
RUN apt purge --assume-yes build-essential perl bzip2 gnupg xdg-user-dirs && apt --assume-yes autoremove


# always create an 'orthanc' group (gid=999) and an orthanc user (uid=999)
# always create an 'orthanc' group (gid=1000) and an orthanc user (uid=1000)
# and grants him all permissions on files that can be modified by the docker-entrypoint.sh
# The default root users can still access these files too.
# for the /etc/hostid -> we must make sure the file exists to grant the permission
RUN groupadd --system orthanc --gid=999; \
useradd --system --gid=orthanc --uid=999 --home-dir=/var/lib/orthanc --shell=/bin/false orthanc; \
RUN groupadd --system orthanc --gid=1000; \
useradd --system --gid=orthanc --uid=1000 --home-dir=/var/lib/orthanc --shell=/bin/false orthanc; \
mkdir -p /var/lib/orthanc; \
chown -R orthanc:orthanc /var/lib/orthanc; \
chown -R orthanc:orthanc /tmp; \
Expand Down
12 changes: 9 additions & 3 deletions docker/orthanc/build-or-download.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -95,9 +95,12 @@ if [[ $target == "orthanc" ]]; then

# note: building with static DCMTK while waiting for Debian bullseye to update to latest DCMTK issues (we need DCMTK 3.6.7: https://www.hipaajournal.com/warning-issued-about-3-high-severity-vulnerabilities-in-offis-dicom-software/)
# also force latest OpenSSL (and therefore, we need to force static libcurl)
cmake -DALLOW_DOWNLOADS=ON -DCMAKE_BUILD_TYPE:STRING=Release -DSTANDALONE_BUILD=ON -DUSE_GOOGLE_TEST_DEBIAN_PACKAGE=ON -DUSE_SYSTEM_CIVETWEB=OFF -DUSE_SYSTEM_DCMTK=OFF -DUSE_SYSTEM_OPENSSL=OFF -DUSE_SYSTEM_CURL=OFF $sourcesRootPath/OrthancServer
# (pauline 02/2025) Setting `DUSE_GOOGLE_TEST_DEBIAN_PACKAGE` to `OFF` to fix error when
# the CI runs the tests: `Please install the libgtest-dev package`
cmake -DALLOW_DOWNLOADS=ON -DCMAKE_BUILD_TYPE:STRING=Release -DSTANDALONE_BUILD=ON -DUSE_GOOGLE_TEST_DEBIAN_PACKAGE=OFF -DUSE_SYSTEM_CIVETWEB=OFF -DUSE_SYSTEM_DCMTK=OFF -DUSE_SYSTEM_OPENSSL=OFF -DUSE_SYSTEM_CURL=OFF $sourcesRootPath/OrthancServer
make -j 4
# HttpClient.Ssl and HttpClient.SslNoVerification are failing
# (pauline 02/2025) Commenting out unit tests to fix error when the CI runs the tests:
# `HttpClient.Ssl and HttpClient.SslNoVerification are failing`
# $buildRootPath/UnitTests

upload Orthanc
Expand Down Expand Up @@ -165,7 +168,10 @@ elif [[ $target == "orthanc-pg" ]]; then

hg clone https://orthanc.uclouvain.be/hg/orthanc-databases/ -r $commitId $sourcesRootPath
pushd $buildRootPath
cmake -DALLOW_DOWNLOADS=ON -DCMAKE_BUILD_TYPE:STRING=Release -DUSE_SYSTEM_GOOGLE_TEST=ON -DUSE_SYSTEM_ORTHANC_SDK=OFF $sourcesRootPath/PostgreSQL
# (pauline 02/2025) Adding "-D PostgreSQL_TYPE_INCLUDE_DIR=`pg_config --includedir-server`"
# to fix error: `CMake Error: The following variables are used in this project, but they
# are set to NOTFOUND. PostgreSQL_TYPE_INCLUDE_DIR`
cmake -DALLOW_DOWNLOADS=ON -DCMAKE_BUILD_TYPE:STRING=Release -DUSE_SYSTEM_GOOGLE_TEST=ON -DUSE_SYSTEM_ORTHANC_SDK=OFF -D PostgreSQL_TYPE_INCLUDE_DIR=`pg_config --includedir-server` $sourcesRootPath/PostgreSQL
make -j 4

upload libOrthancPostgreSQLIndex.so
Expand Down
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