stylus

#!/bin/bash
#--------------------------------------------------------------------------------
# Recognized arguments - these must precede all other arguments:
#   r -- Select the local release version
#   d -- Select the local debug version
#   p -- Select the local profile version
#
# 	i -- Do not set argument environment variables
# 
#   l -- Select the local web server for genes and Han definitions
#   t -- Select the local sample directory for genes and Han definitions
#   x -- Select the xgrid configuration for genes and Han definitions
# 
# All other arguments are passed unmodified to the stgrid.py script
#
# The following variables will be set if not present in the local environment:
# 
# STYLUS_GRIDARGS  - The default grid argument string (command-line overrides duplicate arguments)
# STYLUS_EXECARGS  - The default execution argument string (command-line overrides duplicate arguments)
# STYLUS_RPTARGS   - The default report argument string (command-line overrides duplicate arguments)
#
# STYLUS_DATAPATH  - The default path for experiment data (to which non-absolute experiment names are appended)
# STYLUS_RPTPATH   - The default path for reports (to which non-absolute experiment names are appended)
#
# STYLUS_GENOMEURL - The URL from which to obtain genome files
# STYLUS_HANURL    - The URL from which to obtain Han definition files
# STYLUS_HTMLURL   - The URL from which to obtain XHTML-related files (e.g., stylus.css)
# STYLUS_PLANURL   - The URL from which to obtain plan files
# STYLUS_SCHEMAURL - The URL from which to obtain XML schemas
# 
# STYLUS_AUTHOR    - Experiment author
#
# SYTLUS_XGRID_VOLUME	- The absolute root path for an Xgrid configuration
# STYLUS_XGRID_EMAIL	- E-mail address to which to send job completion notification 
# STYLUS_XGRID_SHELL	- Shell in which to spawn the Stylus command
# 
# XGRID_CONTROLLER_HOSTNAME - Xgrid to use (IP address or DNS name) (Apple defined variable)
# XGRID_CONTROLLER_PASSWORD - Xgrid password to use (Apple defined variable)
# 
# The following variables are modified:
# PYTHONPATH        - Path to Python modules
# DYLD_LIBRARY_PATH - Mac OS X path to dynamically loaded libraries
# LD_LIBRARY_PATH   - Linux path to dynamically loaded libraries
# 
# Stylus, Copyright 2006-2009 Biologic Institute
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#     http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#--------------------------------------------------------------------------------

task=stylus
version=release
setenv=1
config=

# Parse incoming arguments
until [ -z "$1" ]
do
  case $1 in
	r ) version=release; shift;;
	d ) version=debug; shift;;
	p ) version=profile; shift;;
	i ) setenv=0; shift;;
	l ) config=local; shift;;
	t ) config=test; shift;;
	x ) config=xgrid; shift;;
	* ) break;;
  esac
done

# Obtain Stylus home directory (assumed to be location of this script)
STYLUS_HOME="$PWD/`dirname $0`"			# Obtain current directory
STYLUS_HOME=${STYLUS_HOME%.}			# Strip off trailing period
STYLUS_HOME=${STYLUS_HOME%\/}			# Strip off trailing slash
STYLUS_HOME=${STYLUS_HOME/\/\/\//\/}	# Reduce any initial /// to /

# Set Stylus-related environment variables
if [ -z "$STYLUS_XGRID_VOLUME" ] ; then
	export STYLUS_XGRID_VOLUME=/Volumes/Grid/Biologic
fi

if [[ $setenv = 1 ]] ; then
	if [ -z "$STYLUS_GRIDARGS" ] ; then
		export STYLUS_GRIDARGS=""
	fi

	if [ -z "$STYLUS_EXECARGS" ] ; then
		export STYLUS_EXECARGS="-g 52DC.gene -p nosteps.xml -l ,debug,log,echo,long"
	fi

	if [ -z "$STYLUS_RPTARGS" ] ; then
		export STYLUS_RPTARGS="-g 52DC.gene -p nosteps.xml -x d,d"
	fi
fi

if [ -z "$STYLUS_DATAPATH" ] ; then
	if [[ $config = xgrid ]] ; then
		export STYLUS_DATAPATH="$STYLUS_XGRID_VOLUME"/results/data/
	else
		export STYLUS_DATAPATH="$STYLUS_HOME/sample/data/"
	fi
fi

if [ -z "$STYLUS_RPTPATH" ] ; then
	if [[ $config = xgrid ]] ; then
		export STYLUS_RPTPATH="$STYLUS_XGRID_VOLUME"/results/reports/
	else
		export STYLUS_RPTPATH="$STYLUS_HOME/sample/reports/"
	fi
fi

if [ -z "$STYLUS_GENOMEURL" ] ; then
	if [[ $config = test ]] ; then
		export STYLUS_GENOMEURL=file://$STYLUS_HOME/sample/
	elif [[ $config = local ]] ; then
		export STYLUS_GENOMEURL=http://localhost/genes/
	elif [[ $config = xgrid ]] ; then
		export STYLUS_GENOMEURL=file://$STYLUS_XGRID_VOLUME/genes/
	else
		export STYLUS_GENOMEURL=http://bioserve.bi010gic.net/genes/
	fi
fi

if [ -z "$STYLUS_HANURL" ] ; then
	if [[ $config = test ]] ; then
		export STYLUS_HANURL=file://$STYLUS_HOME/sample/
	elif [[ $config = local ]] ; then
		export STYLUS_HANURL=http://localhost/archetypes/
	else
		export STYLUS_HANURL=http://bioserve.bi010gic.net/archetypes/
	fi
fi

if [ -z "$STYLUS_HTMLURL" ] ; then
	export STYLUS_HTMLURL=file://$STYLUS_HOME/html/
fi

if [ -z "$STYLUS_PLANURL" ] ; then
	if [[ $config = xgrid ]] ; then
		export STYLUS_PLANURL=file://$STYLUS_XGRID_VOLUME/plans/
	else
		export STYLUS_PLANURL=file://$STYLUS_HOME/sample/plans/
	fi
fi

if [ -z "$STYLUS_SCHEMAURL" ] ; then
	export STYLUS_SCHEMAURL=file://$STYLUS_HOME/schemas/
fi

if [ -z "$STYLUS_AUTHOR" ] ; then
	export STYLUS_AUTHOR="D. Axe, Biologic Institute"
fi

if [ -z "$STYLUS_XGRID_SHELL" ] ; then
	export STYLUS_XGRID_SHELL=/bin/bash
fi

if [ -z $XGRID_CONTROLLER_HOSTNAME ] ; then
	export XGRID_CONTROLLER_HOSTNAME=bioserve.bi010gic.net
fi

if [ -z $XGRID_CONTROLLER_PASSWORD ] ; then
	export XGRID_CONTROLLER_PASSWORD=""
fi

export PYTHONPATH="$STYLUS_HOME/lib":$PYTHONPATH

# Prepare the Xgrid client environment or launch Stylus as requested
cc=0
python "$STYLUS_HOME/scripts/stgrid.py" "$@"
cc=$?
exit $cc