Dockerfile.local

#
# Copyright (c) 2016 The Hyve B.V.
# This code is licensed under the GNU Affero General Public License (AGPL),
# version 3, or (at your option) any later version.
#

#
# Dockerfile to test local, unreleased source code in Docker images.
#
# See https://github.com/thehyve/cbioportal-docker/blob/master/docs/development.md
#

FROM tomcat:8-jre8
MAINTAINER Fedde Schaeffer <fedde@thehyve.nl>

# install build and runtime dependencies and configure Tomcat for production
RUN apt-get update && apt-get install -y --no-install-recommends \
		git \
		libmysql-java \
		maven \
		openjdk-8-jdk \
		patch \
		python3 \
		python3-jinja2 \
		python3-mysqldb \
		python3-requests \
		python3-yaml \
	&& rm -rf /var/lib/apt/lists/* \
	&& ln -s /usr/share/java/mysql-connector-java.jar "$CATALINA_HOME"/lib/ \
	&& rm -rf $CATALINA_HOME/webapps/*m* 

# include Maven configs to fetch additional Java dependencies listed there
# starting with the dependencies of the backend projects, which change
# significantly less often than the externally maintained frontend code
ENV PORTAL_HOME=/cbioportal
COPY pom.xml                                     $PORTAL_HOME/
WORKDIR $PORTAL_HOME
# list of subproject POM files:
# find . -mindepth 2 -not \( -path '*/target/*' -or -path '*/frontend-cbioportal/*' \)  -name pom.xml \
# | sed -e 's/^\.\/\(.*\)\/pom.xml$/COPY \1\/pom.xml#\1\//' | column -ts '#'
COPY business/pom.xml                         business/
COPY core/pom.xml                             core/
COPY db-scripts/pom.xml                       db-scripts/
COPY model/pom.xml                            model/
COPY persistence/pom.xml                      persistence/
COPY persistence/persistence-api/pom.xml      persistence/persistence-api/
COPY persistence/persistence-mybatis/pom.xml  persistence/persistence-mybatis/
COPY scripts/pom.xml                          scripts/
COPY security/pom.xml                         security/
COPY security/security-spring/pom.xml         security/security-spring/
COPY service/pom.xml                          service/
COPY web/pom.xml                              web/
RUN for subproject in */.; do cd "$subproject"; mvn dependency:go-offline --fail-never; cd ..; done
COPY portal/pom.xml                           portal/
RUN mvn dependency:go-offline --fail-never

# include the rest of the cBioPortal sources
COPY . $PORTAL_HOME

# install default config files, build and install, placing the scripts jar back
# in the target folder where import scripts expect it after cleanup
RUN mv ./portal.properties src/main/resources/portal.properties \
	&& mv ./log4j.properties src/main/resources/log4j.properties \
	&& mvn -Pdefault,heroku -DskipTests clean install \
	&& unzip portal/target/cbioportal*.war -d $CATALINA_HOME/webapps/cbioportal \
	&& mv scripts/target/scripts-*.jar /root/ \
	&& mvn clean \
	&& mkdir scripts/target/ \
	&& mv /root/scripts-*.jar scripts/target/

# add runtime plumbing to Tomcat config:
# - make cBioPortal honour db config in portal.properties
# temporarily add session.service.url here since it does not work in portal.properties
RUN echo 'CATALINA_OPTS="-Dauthenticate=false -Dsession.service.url=http://cbio-session-service:8080/api/sessions/main_session/ $CATALINA_OPTS -Ddbconnector=dbcp"' >>$CATALINA_HOME/bin/setenv.sh
# - tweak server-wide config file
RUN patch $CATALINA_HOME/conf/server.xml <catalina_server.xml.patch

# add importer scripts to PATH for easy running in containers
RUN find $PWD/core/src/main/scripts/ -type f -executable \! -name '*.pl'  -print0 | xargs -0 -- ln -st /usr/local/bin
# TODO: fix the workdir-dependent references to '../scripts/env.pl' and do this:
# RUN find $PWD/core/src/main/scripts/ -type f -executable \! \( -name env.pl -o -name envSimple.pl \)  -print0 | xargs -0 -- ln -st /usr/local/bin