add docker Dockerfile in data/docker

data/docker/Dockerfile.partons

+# start from debian jessie
+FROM debian:stretch
+
+# PARTONS version
+ENV PARTONSTAG="v1.0"
+
+# set WORKSPACE env. variable
+ENV WORKSPACE="/root/workspace"
+
+# set working directory
+WORKDIR ${WORKSPACE}
+
+# install git
+# install cmake, build and runtime libraries
+RUN apt-get update && \ 
+    apt-get install -y --no-install-recommends git && \
+    apt-get install -y --no-install-recommends cmake build-essential libeigen3-dev libcln-dev libsfml-dev libqt4-dev libqt4-sql-mysql && \ 
+    apt-get clean && \
+    apt-get autoclean && \
+    rm -rf /var/lib/apt/lists/*
+
+# pull and install elem-utils
+RUN cd ${WORKSPACE} && \
+    git config --global http.sslVerify false && \
+    git clone --single-branch --depth 1 --branch ${PARTONSTAG} https://drf-gitlab.cea.fr/partons/core/elementary-utils.git && \
+    cd ${WORKSPACE}/elementary-utils/build && \
+    cmake -G"Unix Makefiles" ../ -DCMAKE_BUILD_TYPE=Release && \
+    make 
+
+# pull and install numa
+RUN cd ${WORKSPACE} && \
+    git config --global http.sslVerify false && \
+    git clone --single-branch --depth 1 --branch ${PARTONSTAG} https://drf-gitlab.cea.fr/partons/core/numa.git && \
+    cd ${WORKSPACE}/numa/build && \
+    cmake -G"Unix Makefiles" ../ -DCMAKE_BUILD_TYPE=Release && \
+    make 
+
+# pull and install partons
+RUN cd ${WORKSPACE} && \
+    git config --global http.sslVerify false && \
+    git clone --single-branch --depth 1 --branch ${PARTONSTAG} https://drf-gitlab.cea.fr/partons/core/partons.git && \
+    cd ${WORKSPACE}/partons/build && \
+    cmake -G"Unix Makefiles" ../ -DCMAKE_BUILD_TYPE=Release && \
+    make
+
+# pull and compile partons-example
+RUN cd ${WORKSPACE} && \
+    git config --global http.sslVerify false && \
+    git clone --single-branch --depth 1 --branch ${PARTONSTAG} https://drf-gitlab.cea.fr/partons/core/partons-example.git && \
+    cd ${WORKSPACE}/partons-example/build && \
+    cmake -G"Unix Makefiles" ../ -DCMAKE_BUILD_TYPE=Release && \
+    make 
+
+# creare directories and copy scripts
+RUN mkdir ${WORKSPACE}/.docker && \
+    mkdir ${WORKSPACE}/partons-example/scenarios
+
+COPY ./Dockerfile.partons.mysql ${WORKSPACE}/.docker 
+COPY ./Dockerfile.partons.startup ${WORKSPACE}/.docker 
+
+RUN chmod u+x ${WORKSPACE}/.docker/Dockerfile.partons.mysql && \
+    chmod u+x ${WORKSPACE}/.docker/Dockerfile.partons.startup
+
+# set up database
+RUN echo "mysql-server mysql-server/root_password password partons" | debconf-set-selections && \
+    echo "mysql-server mysql-server/root_password_again password partons" | debconf-set-selections && \
+    apt-get update && \ 
+    apt-get install -y --no-install-recommends mysql-server && \ 
+    apt-get clean && \
+    apt-get autoclean && \
+    rm -rf /var/lib/apt/lists/* && \
+    ${WORKSPACE}/.docker/Dockerfile.partons.mysql && \
+    rm ${WORKSPACE}/.docker/Dockerfile.partons.mysql
+
+# start mysql server each time container is used
+# due to issue: https://github.com/docker/for-linux/issues/72 
+ENTRYPOINT [".docker/Dockerfile.partons.startup"] 

data/docker/Dockerfile.partons.mysql

+#!/bin/bash
+
+# start 
+find /var/lib/mysql -type f -exec touch {} \;
+service mysql start &> /dev/null
+
+# set env.
+__mysql_database="partons"
+__mysql_root="root"
+__mysql_root_password="partons"
+__mysql_user="partons"
+__mysql_user_password="partons"
+
+#define functioni to execute queries 
+function sql_exec() {
+  mysql -u "${__mysql_root}" -D "${__mysql_database}" -p${__mysql_root_password} -e "${1}"
+}
+
+# go to directory with schema
+cd /root/workspace/partons/data/database/sql_schema 
+
+# create database and add user
+mysql -u "${__mysql_root}" -p"${__mysql_root_password}" -e "create database ${__mysql_database}"
+sql_exec "CREATE USER '${__mysql_user}'@'localhost' IDENTIFIED BY '${__mysql_user_password}';"
+sql_exec "GRANT SELECT, INSERT, UPDATE, DELETE ON ${__mysql_database}.* TO '${__mysql_user}'@'localhost';"
+sql_exec "GRANT FILE ON *.* TO '${__mysql_user}'@'localhost';"
+
+# excecute scripts
+#  TODO: if scripts are going to be enumerated this piece of the code
+#+       can be automated, therefore will need less further involvement
+#+       of anyone.
+#+
+#+       Desirable naming might look like following:
+#+       mysql5_common.sql                      -> mysql5_001_common.sql
+#+       mysql5_gpd_layer.sql                   -> mysql5_002_gpd_layer.sql
+#+       mysql5_convol_coeff_function_layer.sql -> mysql5_003_convol_coeff_function_layer.sql
+#+       mysql5_observable_layer.sql            -> mysql5_004_observable_layer.sql
+sql_exec "SOURCE mysql5_common.sql"
+sql_exec "SOURCE mysql5_gpd_layer.sql"
+sql_exec "SOURCE mysql5_convol_coeff_function_layer.sql"
+sql_exec "SOURCE mysql5_observable_layer.sql"

data/docker/Dockerfile.partons.startup

+#!/bin/bash
+
+
+echo "Welcome to PARTONS" 
+echo "See http://partons.cea.fr for description and technical documentation"
+
+#mysql
+find /var/lib/mysql -type f -exec touch {} \;
+service mysql start &> /dev/null
+
+if [ $# -eq 0 ]; then
+   /bin/bash  
+else
+
+   cd /root/workspace/partons-example
+
+   for i in $@; do
+      ./bin/PARTONS_example scenarios/$i 
+   done
+fi

data/docker/README

+to create new image: 
+1) select PARTONS version (code tag) in Dockerfile.partons
+2) execute (remamber to change vX.Y): 
+   docker build . -f Dockerfile.partons -t pawelsznajder/partons:vX.Y