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specmicp/scripts/analyser/reactmicp_unsaturated_analyse.sh
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reactmicp_unsaturated_analyse.sh
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#! /usr/bin/env bash
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Fabien Georget <fabieng@princeton.edu>,
# Princeton University
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software without
# specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# -----------------------------------------------------------------------------
# This file is a wrapper script to analyse a hdf5 file produced by the
# unsaturated system of ReactMiCP
# It calls a python interpreter in interactive mode and loads a module
# The module where the useful functions are defined
python_script=analyse_unsaturated_hdf5.py
# Return codes
RETCODE_NO_FILE=1
RETCODE_NO_PYTHON=2
RETCODE_FILE_DOESNT_EXIST=3
RETCODE_BAD_OPTION=4
RETCODE_BAD_PYTHON_MODULE=5
echo "
===================================
ReactMiCP
===========
Unsaturated HDF5 output analyser
--------------------------------
===================================
Copyright (c) 2015 F. Georget <fabieng@princeton.edu>
"
function check_file_arg {
# check that the file argument exist
if [[ ! $1 || -z $1 ]]
then
echo "Error : one argument required. Aborting" >&2;
exit ${RETCODE_NO_FILE};
fi
}
function print_help {
echo "
Analyse hdf5 file produced by the unsaturated system of ReactMiCP.
The analyser is a script which open a python interpreter and load useful functions.
Usage : $0 [options] <file>
<file> : hdf5 file
Options :
-m, --module <module> alternative python module to use
-p, --python <interpreter> python interpreter to use
-h, --h : print this help"
exit 0
}
check_file_arg $1
# Options
# -------
while [[ $# > 1 ]]
do
key="$1"
case ${key} in
-h|--help)
print_help
;;
-m|--module)
python_script="$2"
shift
;;
-p|--python)
python_shell="$2"
shift
;;
*)
echo "Unknow option '$1'. Aborting" >&2
exit ${RETCODE_BAD_OPTION}
;;
esac
shift
done
check_file_arg $1
if [[ $1 = "-h" || $1 = "--help" ]]
then
print_help
fi
# check that the HDF5 file exist
# no point going further if it doesn't
if [[ ! -f $1 ]]
then
echo "Error : no such file : '$1'. Aborting" >&2;
exit ${RETCODE_FILE_DOESNT_EXIST}
fi
# copy file parameter
filepath=$1
shift
# Find the python script
if [[ ! -f ${python_script} ]]
then
# Find the true directory of this bash script
# https://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
test_src=${DIR}/${python_script}
if [[ ! -f ${test_src} ]]
then
echo "Unable to find python module. Aborting" >&2;
exit ${RETCODE_BAD_PYTHON_MODULE};
else
python_script=${test_src}
fi
fi
# find the python shell
if [[ -z ${python_shell} ]]
then
python_shell=$(command -v ipython)
if [[ $? ]]
then
echo " * python shell detected : ipython (${python_shell})"
else
python_shell=$(command -v python)
if [[ $1 ]]
then
echo " * python shell detected : python (${python_shell})"
else
echo "Error : A python interpreter is required. Aborting\n" >&2;
exit ${RETCODE_NO_PYTHON};
fi
fi
fi
# Don't print the python banner if possible
# it makes thing just more confusing
basename_python=$(basename ${python_shell})
if [[ ${basename_python} = ipython* ]]
then
no_banner="--no-banner"
elif [[ ${basename_python} = python* ]]
then
python_version=$(${python_shell} -V 2>&1 | cut -d' ' -f2 | cut -d'.' -f1 -)
if [[ $python_version -ge 3 ]]
then
no_banner="-q"
fi
fi
# run the analysis
exec ${python_shell} -i ${no_banner} ${python_script} ${filepath}
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