#!/bin/sh


#Function to print help to the user:
usage() {
	cat 1>&2 << EOF

	Usage: $0 [--useJava <true or false>] input.xml

	This script will apply an XSLT transformation to Beast 2 input files, setting them up for multithreaded execution. (Which is not the default.)
	It is really only meant for CIPRES, but my be useful to others.

	OPTIONS:
		--useJava <boolean>	This sets whether ThreadedTreeLikelihood objects should use java or not(beagle). Apparently version 2.1.3 of BEAST 2 defaults this to "true" regardless of what is set at the command-line. Highly inconvenient. This script defaults to using false for this.

EOF
}

#bash command line parameter 
USEJAVA=false

#Parse the command line
PARSINGARGS=1

while [[ "$PARSINGARGS" == "1" && "$1" ]]
do
        case $1 in
                -h|--help)
                        usage; exit 0;;
                --useJava|--usejava)
                        shift; USEJAVA=$1; shift;;
                *)
			PARSINGARGS=0;;
        esac
done

if [[ "$USEJAVA" != "true" && "$USEJAVA" != "false" ]]
then
	echo Invalid choice for --useJava option: $USEJAVA 1>&2
	exit 1
fi


#Begin XSLT transformation
xsltproc -stringparam usejavain ${USEJAVA} - ${1} << EOF
<?xml version="1.0"?>

<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">

<xsl:param name="usejavain" select="'false'"/>

<xsl:template match="@*|node()">
        <xsl:copy>
                <xsl:apply-templates select="@*|node()"/>
        </xsl:copy>
</xsl:template>

<!-- XSLT 1.0 does not provide an "ends-with()" function, but we can make one:
http://stackoverflow.com/questions/11848780/use-ends-with-in-xslt-v1-0

to check ends-with($s, $t)

do
	$t = substring($s, string-length() - string-length($t) +1)
-->

<!-- replace single threaded tree likelihoods with multithreaded ones. -->
<!-- We use the fully qualified name because we don't know if the XML file imports that or not. -->
<!-- Apparently the default for useJava is true, and only if we explicitly set it to false can we get BEAGLE to work. -->
<xsl:template match="distribution[@spec='TreeLikelihood' or @spec='ThreadedTreeLikelihood' or substring(@spec, string-length(@spec) - string-length('.TreeLikelihood')+1)='.TreeLikelihood' or substring(@spec, string-length(@spec) - string-length('.ThreadedTreeLikelihood')+1)='.ThreadedTreeLikelihood']">
	<xsl:copy>
		<xsl:copy-of select="@*" />
		<xsl:attribute name="spec">beast.evolution.likelihood.ThreadedTreeLikelihood</xsl:attribute>
		<xsl:attribute name="useJava"><xsl:value-of select="\$usejavain"/></xsl:attribute>
                <xsl:apply-templates />
	</xsl:copy>

</xsl:template>


<!-- Deal with threading / thread-safety in CompundDistributions. -->
<xsl:template match="distribution[@spec='CompoundDistribution' or substring(@spec,string-length(@spec) - string-length('.CompoundDistribution') + 1) = '.CompoundDistribution']/@useThreads">
        <xsl:attribute name="useThreads">
                <xsl:value-of select="'false'"/>
        </xsl:attribute>
</xsl:template>

<!-- This was for turning threading on in CompoundDistributions, in that case, I think that it's only the "likelihood" one that we want to turn on
     Now we want to turn it off for the thread safety issue, and in that case we want it off on all of them.
     Once thread-safety is fixed, maybe we'll want to ensure threading is off in most and turn it on only in "likelihood".
     -->
<!--
<xsl:template match="distribution[@id='likelihood']">
        <xsl:copy>
                <xsl:copy-of select="@*" />
                <xsl:attribute name="useThreads">true</xsl:attribute>
                <xsl:apply-templates />
        </xsl:copy>
</xsl:template>
-->

<!-- You can just replace the content of this template with the appropriate script to run ParticleFilter -->
<!-- See http://www.beast2.org/wiki/index.php/Performance_Suggestions#Particle_Filter -->
<xsl:template match="run[@spec='ParticleFilter' or @spec='inference.ParticleFilter' or @spec='beast.inference.ParticleFilter']/text()">
        <contact-CIPRES-admins-if-you-absolutely-need-particlefilter>
        Please do not use ParticleFilter on CIPRES.
        Contact CIPRES administrators if this is absolutely necessary for your science.
        </contact-CIPRES-admins-if-you-absolutely-need-particlefilter>
</xsl:template>

<xsl:template match="run[@spec='PathSampler' or @spec='inference.PathSampler' or @spec='beast.inference.PathSampler']/text()">
	<contact-CIPRES-admins-if-you-absolutely-need-pathsampling>
	Please do not use PathSampler on CIPRES.
	Contact CIPRES administrators if this is absolutely necessary for your science.
	</contact-CIPRES-admins-if-you-absolutely-need-pathsampling>
</xsl:template>

</xsl:stylesheet>

EOF
#END XSLT
exit $?