FROM ubuntu:18.04

RUN apt-get update && apt-get install -y --no-install-recommends \
		bzip2 \
		unzip \
		xz-utils \
	&& rm -rf /var/lib/apt/lists/*

# Default to UTF-8 file.encoding
ENV LANG C.UTF-8

# add a simple script that can auto-detect the appropriate JAVA_HOME value
# based on whether the JDK or only the JRE is installed
RUN { \
		echo '#!/bin/sh'; \
		echo 'set -e'; \
		echo; \
		echo 'dirname "$(dirname "$(readlink -f "$(which javac || which java)")")"'; \
	} > /usr/local/bin/docker-java-home \
	&& chmod +x /usr/local/bin/docker-java-home

# do some fancy footwork to create a JAVA_HOME that's cross-architecture-safe
RUN ln -svT "/usr/lib/jvm/java-8-openjdk-$(dpkg --print-architecture)" /docker-java-home
ENV JAVA_HOME /docker-java-home

ENV JAVA_VERSION 8u171

# see https://bugs.debian.org/775775
# and https://github.com/docker-library/java/issues/19#issuecomment-70546872
#ENV CA_CERTIFICATES_JAVA_VERSION 20161107~bpo8+1

# deal with slim variants not having man page directories (which causes "update-alternatives" to fail)
RUN set -ex; \
	if [ ! -d /usr/share/man/man1 ]; then \
		mkdir -p /usr/share/man/man1; \
	fi; \
#	echo 'deb http://ftp.se.debian.org/debian/ stretch main contrib non-free' > /etc/apt/sources.list.d/stretch.list && \
#	echo 'deb http://ftp.se.debian.org/debian/ stretch-backports main contrib non-free' > /etc/apt/sources.list.d/stretch-backports.list && \
	apt-get update && \
	apt-get install -y --no-install-recommends \
		openjdk-8-jdk-headless \
		ca-certificates-java \
		ca-certificates \
		openssl \
		wget \
		libapr1-dev \
		coreutils \
		dpkg-dev dpkg \
		gcc \
		libc-dev \
		make \
#		libssl1.1.0 \
		libssl-dev \
		apache2 ;\
	rm -rf /var/lib/apt/lists/*

#RUN apt-mark auto libssl1.0.0

# set default java version
RUN update-java-alternatives --set /usr/lib/jvm/java-1.8.0-openjdk-amd64

# verify that "docker-java-home" returns what we expect
# update-alternatives so that future installs of other OpenJDK versions don't change /usr/bin/java
# ... and verify that it actually worked for one of the alternatives we care about
RUN	set -ex; \
#    apt-get purge -y openjdk-7-jre-headless ; \
#	[ "$(readlink -f "$JAVA_HOME")" = "$(docker-java-home)" ]; \
	update-alternatives --get-selections | awk -v home="$(readlink -f "$JAVA_HOME")" 'index($3, home) == 1 { $2 = "manual"; print | "update-alternatives --set-selections" }'; \
	update-alternatives --query java | grep -q 'Status: manual'

# see CA_CERTIFICATES_JAVA_VERSION notes above
RUN /var/lib/dpkg/info/ca-certificates-java.postinst configure
RUN apt-get update && apt-get install -y apt-transport-https ca-certificates

RUN echo "deb [trusted=yes] https://cloud.r-project.org/bin/linux/ubuntu/ bionic-cran35/" > /etc/apt/sources.list.d/debian-r-3.5.list 

ENV R_BASE_VERSION 3.5.0

# If you're reading this and have any feedback on how this image could be
# improved, please open an issue or a pull request so we can discuss it!
#
#   https://github.com/docker-library/openjdk/issues

ENV DEBIAN_FRONTEND noninteractive
RUN set -e \
    && apt-get update \
    && apt-get install -y --no-install-recommends supervisor sasl2-bin vim mc rsyslog \
    build-essential libssl-dev curl telnet

## Now install R and littler, and create a link for littler in /usr/local/bin
## Also set a default CRAN repo, and make sure littler knows about it too
## NB '-t unstable' paused to allow drr35 repo to supply current ones
RUN apt-get update \
	&& apt-get install -y \
		littler \
                r-cran-littler \
		r-base=${R_BASE_VERSION}-* \
		r-base-dev=${R_BASE_VERSION}-* \
		r-recommended=${R_BASE_VERSION}-* \
        && echo 'options(repos = c(CRAN = "https://cloud.r-project.org/"), download.file.method = "libcurl")' >> /etc/R/Rprofile.site \
        && echo 'source("/etc/R/Rprofile.site")' >> /etc/littler.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
	&& install.r docopt beeswarm car caret circlize clinfun coxme dplyr echarts4r edgebundleR emmeans EnvStats factoextra FactoMineR flux GGally gganimate ggcorrplot ggdendro ggforce ggplot2 ggpubr ggraph ggrepel ggridges ggthemes glmnet highcharter igraph lme4 logNormReg lubridate migest multcomp NMF patchwork pheatmap plotly plotROC pROC psych quantreg randomForest RColorBrewer reshape2 Rtsne scales stringr survminer tidyr tsne umap \
    # BiocManager has to be installed this way, or R -e won't pick it up. 'fgsea' can only be installed using BiocManager.
    && R -e "install.packages('BiocManager')" && R -e "BiocManager::install('fgsea')" \
    # The ComplexHeatmap, GSVA, limma, NormqPCR, org.Hs.eg.db also require the BiocManager
    && R -e "BiocManager::install('ComplexHeatmap')" && R -e "BiocManager::install('GSVA')" && R -e "BiocManager::install('limma')" && R -e "BiocManager::install('NormqPCR')" && R -e "BiocManager::install('org.Hs.eg.db')" \
	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
	&& rm -rf /var/lib/apt/lists/*

# RUN echo "install.packages('Rserve')" | R --save
RUN echo "install.packages('Rserve',,'http://www.rforge.net/')" | R --save

RUN apt-get update && apt-get install libcurl4-openssl-dev
RUN R -e "install.packages('heatmaply')"
RUN R -e "install.packages('irlba')"
RUN R -e "install.packages('lmerTest')"

# uses to convert sh scripts created on Windows OS or building container under Windows OS
RUN apt-get update && apt-get install -y dos2unix

RUN set -e \
    && mkdir -p /usr/local/pluto/distrib

# # install java 12 for visualization service
# RUN wget https://download.java.net/java/GA/jdk12.0.2/e482c34c86bd4bf8b56c0b35558996b9/10/GPL/openjdk-12.0.2_linux-x64_bin.tar.gz
# RUN mkdir /usr/local/pluto/distrib/java12
# RUN mv openjdk-12.0.2_linux-x64_bin.tar.gz /usr/local/pluto/distrib/java12
# RUN tar -xzvf /usr/local/pluto/distrib/java12/openjdk-12.0.2_linux-x64_bin.tar.gz -C /usr/local/pluto/distrib/java12

WORKDIR /usr/local/pluto
VOLUME /usr/local/pluto/distrib
EXPOSE 80
EXPOSE 22
EXPOSE 443
EXPOSE 6311
EXPOSE 9092

ENV BASE_HREF -

ENV VERSION 1

ADD assets/install.sh /opt/install.sh
#ADD assets/deploy.sh /usr/local/pluto/deploy.sh
ADD assets/000-default.conf /etc/apache2/sites-available/000-default.conf
RUN set -e && a2enmod proxy && a2enmod proxy_http && a2enmod rewrite && dos2unix /opt/install.sh && chmod 755 /opt/install.sh && ls -l /opt


ADD target/front.zip /usr/local/pluto/distrib/front.zip
ADD target/Pluto-0.0.1-SNAPSHOT.jar /usr/local/pluto/Pluto.jar
ADD target/worker.jar /usr/local/pluto/worker.jar
ADD target/visualization.jar /usr/local/pluto/visualization.jar
ADD target/visualization-application.properties /usr/local/pluto/visualization-application.properties
ADD target/conf /usr/local/pluto/conf

RUN unzip distrib/*.zip -d front


CMD /opt/install.sh; /usr/bin/supervisord -c /etc/supervisor/supervisord.conf