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medco-deployment/i2b2-web/Dockerfile
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FROM debian:jessie
# variables
ARG I2B2_DOMAIN_NAME_ARG="i2b2demo"
ENV I2B2_VERSION="v1.7.08a" \
I2B2_WEB_DIR="/opt/i2b2-webclient" \
SHRINE_SRC_DIR="/opt/shrine-src" \
SHRINE_VERSION="fork/1.22.8-medco" \
I2B2_DOMAIN_NAME="$I2B2_DOMAIN_NAME_ARG" \
LIGHTTPD_WEB_ROOT="/var/www/html" \
DB_PASSWORD="pFjy3EjDVwLfT2rB9xkK" \
CONF_DIR="/opt/medco-configuration"
# requirements
RUN echo "deb http://httpredir.debian.org/debian jessie-backports main contrib non-free" >> /etc/apt/sources.list && \
apt-get -y update && \
apt-get -y install lighttpd php5-cgi curl libcurl3 php5-common php5-cli php5-curl git php5-pgsql wget tar && \
apt-get -y -t jessie-backports install postgresql-client && \
apt-get -y clean && \
lighttpd-enable-mod fastcgi-php ssl
# phpPgAdmin
WORKDIR "$LIGHTTPD_WEB_ROOT"
RUN wget http://downloads.sourceforge.net/phppgadmin/phpPgAdmin-5.1.tar.gz?download && \
tar xvzf phpPgAdmin-5.1.tar.gz?download && \
rm phpPgAdmin-5.1.tar.gz\?download && \
mv phpPgAdmin-5.1 phppgadmin && \
sed -i "s/'host'] = ''/'host'] = 'i2b2-database'/" phppgadmin/conf/config.inc.php && \
sed -i "s/ = 'PostgreSQL'/ = '$I2B2_DOMAIN_NAME PostgreSQL Server'/" phppgadmin/conf/config.inc.php && \
sed -i "s/'extra_login_security'] = true/'extra_login_security'] = false/" phppgadmin/conf/config.inc.php && \
sed -i "/\$cmd = \$exe/c\$cmd = \$exe;" phppgadmin/dbexport.php
# download i2b2 webclient
WORKDIR "$I2B2_WEB_DIR"
RUN git clone https://github.com/i2b2/i2b2-webclient.git . && \
git checkout tags/$I2B2_VERSION && \
chmod -R 777 .
# download shrine webclient
ENV NOCACHE="12"
WORKDIR "$SHRINE_SRC_DIR"
RUN git clone https://c4science.ch/source/shrine-medco.git . && \
git checkout $SHRINE_VERSION && \
cp "$I2B2_WEB_DIR"/index.php "$SHRINE_SRC_DIR"/shrine-webclient/src/main/html/ && \
chmod -R 777 .
# copy clients
RUN cp -R "$I2B2_WEB_DIR" "$LIGHTTPD_WEB_ROOT/i2b2-admin" && \
cp -R "$I2B2_WEB_DIR" "$LIGHTTPD_WEB_ROOT/i2b2-client" && \
cp -R "$SHRINE_SRC_DIR/shrine-webclient/src/main/html" "$LIGHTTPD_WEB_ROOT/shrine-client"
# copy and apply settings
ARG NODE_IDX_ARG="0"
ENV NODE_IDX="$NODE_IDX_ARG"
COPY i2b2-web-writeconfig.sh .
RUN chmod -R +x ./i2b2-web-writeconfig.sh && sleep 1 && /bin/bash -c ./i2b2-web-writeconfig.sh
# todo: phpmyadmin https://files.phpmyadmin.net/phpMyAdmin/4.7.4/phpMyAdmin-4.7.4-all-languages.zip
# RUN wget http://downloads.sourceforge.net/phppgadmin/phpPgAdmin-5.1.tar.gz?download && \
# /phpMyAdmin-4.7.4-all-languages/
# fix permissions + bug fix
RUN chown -R www-data:www-data "$LIGHTTPD_WEB_ROOT" && \
chmod -R +r "$LIGHTTPD_WEB_ROOT" && \
chmod -R +x "$LIGHTTPD_WEB_ROOT" && \
install -d -o www-data -g www-data -m 0750 "/var/run/lighttpd"
# run
EXPOSE 80
CMD ["lighttpd", "-D", "-f", "/etc/lighttpd/lighttpd.conf"]
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