<commit_before><?xml version="1.0"?>
<!--

Targets for checking out dependencies for the healthchecks.

Use

	ant clean

to delete the directory with the checkouts.

-->
<project name="checkoutDependencies" default="checkoutPerlDependencies" basedir="..">

	<property file="buildfiles/build.properties" />

	<!--
		Directory where checkout will be placed
	-->
	<property name="perlDependencyCheckoutDir" value="perlcode" />

        <target 
		name        = "checkoutPerlDependencies" 
		description = "" 
		depends     = "checkoutBioperlDependency, checkoutEnsemblDependency"
	/>

	<!--
		All checkouts go into this directory
	-->
        <target name="createPerlDependencyDir" description="">
		<mkdir dir="${perlDependencyCheckoutDir}" />
	</target>

	<!--
		Deletes the directory with the checkouts
	-->
        <target name="clean" description="">
		<delete dir="${perlDependencyCheckoutDir}"/>
	</target>

	<!--
		Checkouts of the Ensembl API
	-->
        <target name="checkoutEnsemblDependency" description="" depends="createPerlDependencyDir">

		<property name="ensemblRevisionOption"     value="-r branch-ensembl-61" />
		<property name="ensemblCvsRoot"            value=":pserver:cvsuser:<EMAIL>:/cvsroot/ensembl" />

		<cvs 
			cvsRoot="${ensemblCvsRoot}" 
			command="checkout -d ${perlDependencyCheckoutDir}/ensembl ${ensemblRevisionOption} ensembl"
		/>
		<cvs 
			cvsRoot="${ensemblCvsRoot}" 
			command="checkout -d ${perlDependencyCheckoutDir}/ensembl-variation ${ensemblRevisionOption} ensembl-variation"
		/>
	</target>

	<!--
		Checkouts of Bioperl<commit_msg>Branch 62 does not exist yet, corrected this. Also sets executable permissions for ./perl/run_healthcheck.pl<commit_after><?xml version="1.0"?>
<!--

Targets for checking out dependencies for the healthchecks.

Use

	ant clean

to delete the directory with the checkouts.

-->
<project name="checkoutDependencies" default="checkoutPerlDependencies" basedir="..">

	<property file="buildfiles/build.properties" />

	<!--
		Directory where checkout will be placed
	-->
	<property name="perlDependencyCheckoutDir" value="perlcode" />

        <target 
		name        = "setPermissions" 
		description = "Adds run permissions to th perl/run_healthcheck.pl program which is necessary for running perl based healthchecks." 
	>
		<chmod file="./perl/run_healthcheck.pl" perm="u+x" />
	</target>

        <target 
		name        = "checkoutPerlDependencies" 
		description = "" 
		depends     = "checkoutBioperlDependency, checkoutEnsemblDependency, setPermissions"
	/>

	<!--
		All checkouts go into this directory
	-->
        <target name="createPerlDependencyDir" description="">
		<mkdir dir="${perlDependencyCheckoutDir}" />
	</target>

	<!--
		Deletes the directory with the checkouts
	-->
        <target name="clean" description="">
		<delete dir="${perlDependencyCheckoutDir}"/>
	</target>

	<!--
		Checkouts of the Ensembl API
	-->
        <target name="checkoutEnsemblDependency" description="" depends="createPerlDependencyDir">

		<property name="ensemblRevisionOption"     value="-r branch-ensembl-62" />
		<property name="ensemblCvsRoot"            value=":pserver:cvsuser:<EMAIL>:/cvsroot/ensembl" />

		<cvs 
			cvsRoot="${ensemblCvsRoot}" 
			command="checkout -d ${perlDependencyCheckoutDir}/ensembl ${ensemblRevisionOption} ensembl"
		/>
		<cvs 
			cvsRoot="${ensemblCvsRoot}" 
			command="checkout -d ${perlDependencyCheckoutDir}/ensembl-variation ${ensemblRevisionOption} ensembl-variation"
		/>
	</target>

	<!--
		Checkouts of Bioperl
{'fraction_non_alphanumeric': 0.13452279807419995, 'fraction_numerical': 0.002832058906825262, 'mean_word_length': 3.9816643159379406, 'pattern_counts': {'":': 2, '<': 54, '<?xml version=': 2, '>': 52, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7236845', 'n_tokens_mistral': 1187, 'n_tokens_neox': 1062, 'n_words': 236}