build.checkoutDependencies.xml

<?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">

        <exec dir="." executable="git" os="Linux,Mac OS X">
          <arg line="clone --branch master https://github.com/Ensembl/ensembl-variation ${perlDependencyCheckoutDir}/ensembl-variation" />
        </exec>
        <exec dir="." executable="git" os="Linux,Mac OS X">
          <arg line="clone --branch master https://github.com/Ensembl/ensembl-funcgen ${perlDependencyCheckoutDir}/ensembl-funcgen" />
        </exec>
        <exec dir="." executable="git" os="Linux,Mac OS X">
          <arg line="clone --branch master https://github.com/Ensembl/ensembl ${perlDependencyCheckoutDir}/ensembl" />
        </exec>
	</target>

	<!--
		Checkouts of Bioperl
	-->
        <target name="checkoutBioperlDependency" description="" depends="createPerlDependencyDir">

		<mkdir dir="${perlDependencyCheckoutDir}/bioperl"/>

		<exec dir="." executable="git" os="Linux,Mac OS X">
		  <arg line="clone --branch v1.6.x https://github.com/bioperl/bioperl-live ${perlDependencyCheckoutDir}/bioperl" />
		</exec>

	</target>

</project>

build.configurable_testrunner.properties

name           = ensj-healthcheck
version        =
build.name     = ${name}
build.compiler = modern

src    = src/
target = target/
build  = ${target}/build/
dist   = ${target}/dist/
doc    = doc/
lib    = lib/
images = images/
test   = test/

src.java.dir             = ${src}

test.class.dir           = ${build}
class.dir                = ${build}

lib.dir.runtime          = ${lib}
lib.dir.devel            = ${lib}

test.dir                 = ${test}
test.class.dir           = ${test.dir}classes
test.report.dir          = ${test.dir}report
test.checkstyle.dir      = ${test.dir}checkstyle
test.java.dir            = ${test.dir}src

#
# The next two (logConfig, resources.runtime) are also in the 
# ./run-configurable-testrunner.sh If changed here, must be changed there as 
# well.
#
logConfig                = config/logger/logging.properties
resources.runtime        = resources/runtime
resources.docs           = resources/docs
automatic_documentation  = doc/

build.configurable_testrunner.xml

<?xml version="1.0"?>
<project name="ConfigurableTestRunner" default="compile" basedir="..">

	<property file="buildfiles/build.properties" />
	<import   file = "build.checkoutDependencies.xml"       />

        <path id="compile.classpath">
                <pathelement location="${class.dir}" />
                <pathelement location="${lib.dir.devel}/stringtemplate-3.2.1.jar" />
                <pathelement location="${lib.dir.devel}/antlr-2.7.7.jar" />
                <fileset dir="${lib.dir.runtime}" includes="*.jar" />
        </path>

        <path id="run.classpath">
                <pathelement location="${resources.runtime}" />
                <path refid="compile.classpath" />
        </path>

        <path id="test.classpath">
                <path refid="compile.classpath" />
                <pathelement location="${test.class.dir}" />
                <pathelement location="${test.dir}/testData" />
        </path>

        <path id="sourcepath.code">
                <pathelement location="${src.java.dir}"     />
        </path>

        <target 
		name        = "docs" 
		description = "Creates technical documentation for the testgroups."
		depends     = "doc_overview, javadoc.api"
	/>	

        <target name="javadoc.api" description="Creates javadoc documentation.">	
		<mkdir dir="${automatic_documentation}/api"/>
		<javadoc
			destdir       = "${automatic_documentation}/api"
			author        = "true"
			version       = "true"
			use           = "true"
			sourcepathref = "sourcepath.code"
			classpathref  = "compile.classpath"
			excludepackagenames = "org.ensembl.healthcheck.test.*"
			windowtitle   = "EG Healthchecks">
			<fileset dir="${src.java.dir}" defaultexcludes="yes" />
		</javadoc>
	</target>

        <target name="javadoc.uml.api" description="An alternative to javadoc.api that creates javadoc documentation with uml inheritance diagrams. Requires the program dot to be installed.">
		<mkdir dir="${automatic_documentation}/api"/>
		<javadoc
			destdir       = "docs/api"
			author        = "true"
			version       = "true"
			use           = "true"
			sourcepathref = "sourcepath.code"
			classpathref  = "compile.classpath"
			excludepackagenames = "org.ensembl.healthcheck.test.*"
			windowtitle   = "EG Healthchecks">
			<fileset dir="${src.java.dir}" defaultexcludes="yes" />
			<doclet  name="org.umlgraph.doclet.UmlGraphDoc" path="${lib.dir.devel}/UmlGraph-5.3.jar" >
				<param name="-inferrel" />
				<param name="-inferdep" />
				<param name="-hide"         value="java.*"      />
				<param name="-collpackages" value="java.util.*" />
				<param name="-postfixpackage" />
				<param name="-qualify" />
				<param name="-attributes" />
				<param name="-operations" />
				<param name="-enumerations" />
				<param name="-enumconstants" />
				<param name="-visibility" />
			</doclet>
		</javadoc>
	</target>

        <target name="doc_overview" description="Copies static content for the docs.">	
		<copy 
			todir = "${automatic_documentation}">
			<fileset dir="${resources.docs}/static/"/>
		</copy>
	</target>

        <target name="init">
                <mkdir dir="${class.dir}"/>
                <mkdir dir="${test.class.dir}"/>
        </target>

        <target name="clean" description="Erases contents of classes dir">
                <delete dir="${class.dir}"               />
                <delete dir="${test.class.dir}"          />
                <delete dir="${automatic_documentation}" />
        </target>

        <target name="run" depends="compile" description="Runs the ConfigurableTestRunner using the command line arguments stored in cmdline.">
		<echo>Running ${cmdline}</echo>
		<echo>Logging to ${logConfig}</echo>
                <java 
                        classname    = "org.ensembl.healthcheck.ConfigurableTestRunner" 
                        fork         = "true"
                        classpathref = "run.classpath"
                >
			<arg    line = "${cmdline}" />
			<jvmarg line = "-Djava.util.logging.config.file=${logConfig}" />

                </java>
        </target>

        <target name="run.createTestGroupsFromScratch" depends="compile" description="Builds testgroups from the groups as which testcases register">
                <java 
                        classname    = "org.ensembl.healthcheck.TestsInGroups" 
                        fork         = "true"
                        classpathref = "compile.classpath"
                >
			<arg    line = "org.ensembl.healthcheck.testcase src/ org.ensembl.healthcheck.testgroup" />
			<jvmarg line = "-Djava.util.logging.config.file=${logConfig}" />
                </java>
        </target>
</project>

build.configurable_testrunner_devel.xml

<?xml version="1.0"?>
<project name="ConfigurableTestRunnerDevel" default="compile" basedir=".">

	<!--
		Configure the command line here in the cmdline property, if 
		you want to run the tests using ant. This is passed to the 
		org.ensembl.healthcheck.ConfigurableTestRunner when it is run.

		Start the testrunner by typing "ant" on the command line.
	-->
        <property name="cmdline"          value="

		--group 
			testgroup.AllComparaTests
		--less
			testgroup.ProblemTests
			testgroup.ExpectedToFailOnEGComparaBacteria
		--conf 
			config/healthchecks/database.external_db.properties
			config/healthchecks/database.secondary.external_db.properties
		--output.databases
			ensembl_compara_bacteria_5_58
		--output.database
			healthchecks_mnuhn
		--reporterType
			Database

	"/>
	<!-- Not used by ant, just a repository for copy and paste operations. -->
        <property name="OldCmdline"          value="

		-group 
			testgroup.AllVariationTests
		-less
			testgroup.ProblemTests
			testgroup.ExpectedToFailOnEGComparaBacteria
		-output.databases
			arabidopsis_thaliana_variation_5_58_9

		-group 
			testgroup.AllComparaTests
		-less
			testgroup.ProblemTests
			testgroup.ExpectedToFailOnEGComparaBacteria
		-conf 
			database.mnuhn.properties 
			configfiles/database.external_db.properties
			configfiles/database.secondary.external_db.properties
CheckTaxon

		-group 
			testgroup.AllEGCore
		-test 
			org.ensembl.healthcheck.testcase.compara.CheckTopLevelDnaFrag
		-less
			testgroup.ExpectedToFailOnEGComparaBacteria

		-conf 
			database.mnuhn.properties 
			configfiles/database.cp3.properties
			configfiles/database.secondary.ensmirror.properties

	"/>

	<property file="build.properties" />

        <path id="compile.classpath">
                <pathelement location="${class.dir}" />
                <pathelement location="${lib.dir.devel}/stringtemplate-3.2.1.jar" />
                <pathelement location="${lib.dir.devel}/antlr-2.7.7.jar" />
                <fileset dir="${lib.dir.runtime}" includes="*.jar" />
        </path>

        <path id="run.classpath">
                <pathelement location="${resources.runtime}" />
                <path refid="compile.classpath" />
        </path>

        <path id="test.classpath">
                <path refid="compile.classpath" />
                <pathelement location="${test.class.dir}" />
                <pathelement location="${test.dir}/testData" />
        </path>

        <path id="sourcepath.code">
                <pathelement location="${src.java.dir}"     />
                <pathelement location="${src_new.java.dir}" />
                <pathelement location="${src.healthcheck.groups}" />
                <pathelement location="${src.testcases}" />
        </path>
        <path id="sourcepath.test">
                <pathelement location="${src.healthcheck.groups}" />
        </path>

        <target 
		name        = "docs" 
		description = "Creates technical documentation for the testgroups."
		depends     = "doc_overview, javadoc.testgroups, javadoc.testcases, javadoc.api"
	/>	

        <target name="javadoc.api" description="Creates javadoc documentation.">	
		<mkdir dir="docs/api"/>
		<javadoc
			destdir       = "docs/api"
			author        = "true"
			version       = "true"
			use           = "true"
			sourcepathref = "sourcepath.code"
			classpathref  = "compile.classpath"
			excludepackagenames = "org.ensembl.healthcheck.test.*"
			windowtitle   = "EG Healthchecks">
			<fileset dir="${src_new.java.dir}" defaultexcludes="yes" />
			<doclet  name="org.umlgraph.doclet.UmlGraphDoc" path="${lib.dir.devel}/UmlGraph-5.3.jar" >
				<param name="-inferrel" />
				<param name="-inferdep" />
				<param name="-hide"         value="java.*"      />
				<param name="-collpackages" value="java.util.*" />
				<param name="-postfixpackage" />
				<param name="-qualify" />
				<param name="-attributes" />
				<param name="-operations" />
				<param name="-enumerations" />
				<param name="-enumconstants" />
				<param name="-visibility" />
			</doclet>
		</javadoc>
	</target>

        <target name="javadoc.testcases" description="Creates javadoc files for the testgroups.">	
		<mkdir dir="docs/testcases"/>
		<javadoc
			destdir             = "docs/testcases"
			author              = "true"
			version             = "true"
			use                 = "true"
			sourcepath          = "${src.testcases}"
			classpathref        = "compile.classpath"
			packagenames        = "org.ensembl.healthcheck.testcase.*"
			windowtitle         = "Test groups"
                >
		<!--
			sourcepathref       = "sourcepath.code"
		-->
			<doclet  name="org.umlgraph.doclet.UmlGraphDoc" path="${lib.dir.devel}/UmlGraph-5.3.jar" />
		</javadoc>
	</target>

        <target name="doc_overview" description="Copies static content for the docs.">	
		<copy 
			todir = "${automatic_documentation}">
			<fileset dir="${resources.docs}/static/"/>
		</copy>
	</target>

        <target name="javadoc.testgroups" description="Creates javadoc files for the testgroups.">	
		<mkdir dir="docs/testgroups"/>
		<javadoc
			destdir             = "docs/testgroups"
			author              = "true"
			version             = "true"
			use                 = "true"
			sourcepathref       = "sourcepath.code"
			classpathref        = "compile.classpath"
			packagenames        = "testgroup.*"
                        overview            = "${resources.docs}/testgroups/overview.html"
			excludepackagenames = "org.*"
                        linksource          = "yes"
			windowtitle         = "Test groups"
                >
			<doclet  name="org.umlgraph.doclet.UmlGraphDoc" path="${lib.dir.devel}/UmlGraph-5.3.jar" />
		</javadoc>
	</target>

        <target name="publish" description="Copies this directory to the public_html directory. More a kind of backup.">
		<delete dir="/homes/mnuhn/public_html/configurableTestRunner.old" />
		<move 
			file   = "/homes/mnuhn/public_html/configurableTestRunner" 
			tofile = "/homes/mnuhn/public_html/configurableTestRunner.old" 
		/>
		<copy todir="/homes/mnuhn/public_html/configurableTestRunner">
		    <fileset dir="."/>
		  </copy>
	</target>

        <target name="createTestDB" description="Creates an empty database with the test database schema. For developmental purposes only.">

		<sql
			driver       = "org.gjt.mm.mysql.Driver"
			url          = "jdbc:mysql://mysql-cluster-eg-prod-1.ebi.ac.uk:4238/"
			userid       = "ensrw"
			password     = "writ3rp1"
                        classpathref = "compile.classpath"
		>
			drop database if exists healthchecks_mnuhn;
			create database healthchecks_mnuhn;
		</sql>
		<sql
			driver       = "org.gjt.mm.mysql.Driver"
			url          = "jdbc:mysql://mysql-cluster-eg-prod-1.ebi.ac.uk:4238/healthchecks_mnuhn"
			userid       = "ensrw"
			password     = "writ3rp1"
                        classpathref = "compile.classpath"
			src = "${resources.runtime}/table.sql"
		>
		</sql>
        </target>

        <target name="compile" depends="init" description="Compiles all source code. Use this for compiling your test groups.">
                <javac 
                        srcdir       = "${src.java.dir}" 
                        destdir      = "${class.dir}"
                        classpathref = "compile.classpath"
                        debug        = "true" 
                        debuglevel   = "lines,vars,source"
                 >
                 </javac>
                <javac 
                        srcdir       = "${src.testcases}" 
                        destdir      = "${class.dir}"
                        classpathref = "compile.classpath"
                        debug        = "true" 
                        debuglevel   = "lines,vars,source"
                 >
                 </javac>
                <javac 
                        srcdir       = "${src_new.java.dir}" 
                        destdir      = "${class.dir}"
                        classpathref = "compile.classpath"
                        debug        = "true" 
                        debuglevel   = "lines,vars,source"
                 >
                 </javac>
                <javac 
                        srcdir       = "${test.class.dir}" 
                        destdir      = "${class.dir}"
                        classpathref = "compile.classpath"
                        debug        = "true" 
                        debuglevel   = "lines,vars,source"
                 >
                 </javac>
                <javac 
                        srcdir       = "${src.healthcheck.groups}" 
                        destdir      = "${class.dir}"
                        classpathref = "compile.classpath"
                        debug        = "true" 
                        debuglevel   = "lines,vars,source"
                 >
                 </javac>
        </target>

        <target name="init">
                <mkdir dir="${class.dir}"/>
                <mkdir dir="${test.class.dir}"/>
        </target>

        <target name="clean" description="Erases contents of classes dir">
                <delete dir="${class.dir}"               />
                <delete dir="${test.class.dir}"          />
                <delete dir="${automatic_documentation}" />
        </target>

        <target name="compile-tests" depends="compile" description="Compiles tests code.">
                <javac 
                        srcdir       = "${test.java.dir}" 
                        destdir      = "${test.class.dir}"
                        classpathref = "test.classpath"
                 >
                 </javac>
        </target>

        <target name="test" depends="compile-tests" description="Runs the tests.">
                <junit
                        printsummary  = "true"
                        haltonfailure = "true"
                        fork          = "true"
                >
                        <classpath refid="test.classpath" />
                        <formatter type="plain" usefile="false" />

                        <batchtest
                                fork  = "yes"
                                todir = "${test.report.dir}"
                        >
                                <fileset dir="${test.java.dir}">
                                        <include name="**/*" />
                                </fileset>
                        </batchtest>

                </junit>
        </target>

        <target name="run" depends="compile" description="Runs the ConfigurableTestRunner using the command line arguments stored in cmdline.">
		<echo>Running ${cmdline}</echo>
		<echo>Logging to ${logConfig}</echo>
                <java 
                        classname    = "org.ensembl.healthcheck.ConfigurableTestRunner" 
                        fork         = "true"
                        classpathref = "run.classpath"
                >
			<arg    line = "${cmdline}" />
			<jvmarg line = "-Djava.util.logging.config.file=${logConfig}" />

                </java>
        </target>

        <target name="run.createTestGroupsFromScratch" depends="compile" description="Builds testgroups from the groups as which testcases register">
                <java 
                        classname    = "org.ensembl.healthcheck.TestsInGroups" 
                        fork         = "true"
                        classpathref = "compile.classpath"
                >
			<arg    line = "org.ensembl.healthcheck.testcase src/testgroups testgroup.autogeneratedlegacy" />
			<jvmarg line = "-Djava.util.logging.config.file=${logConfig}" />
                </java>
        </target>
</project>

build.setPermissions.xml

<?xml version="1.0"?>
<!--
-->
<project name="setPermissions" default="setPermissions" basedir="..">

	<!--
	-->
        <target name="setPermissions" description="" depends="">

		<chmod file="perl/run_healthcheck.pl" perm="u+x"/>

	</target>
</project>