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build.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- WARNING: Eclipse auto-generated file.
Any modifications will be overwritten.
To include a user specific buildfile here, simply create one in the same
directory with the processing instruction <?eclipse.ant.import?>
as the first entry and export the buildfile again. -->
<project name="EntityGenerator" basedir="." default="build">
<property environment="env"/>
<property name="debuglevel" value="source,lines,vars"/>
<property name="target" value="1.8"/>
<property name="source" value="1.8"/>
<path id="classpath">
<pathelement location="src"/>
<pathelement location="resources/log4j2.xml"/>
<pathelement location="resources/commons-collections4-4.3.jar"/>
<pathelement location="resources/commons-lang3-3.8.jar"/>
<pathelement location="resources/gson-2.3.1.jar"/>
<pathelement location="resources/guava-r05.jar"/>
<pathelement location="resources/jackson-annotations-2.8.8.jar"/>
<pathelement location="resources/jackson-core-2.8.8.jar"/>
<pathelement location="resources/jackson-databind-2.8.8.jar"/>
<pathelement location="resources/java-sizeof-0.0.3.jar"/>
<pathelement location="resources/javacsv-2.1.jar"/>
<pathelement location="resources/jdom-2.0.2.jar"/>
<pathelement location="resources/joda-time-2.1.jar"/>
<pathelement location="resources/json-20160810.jar"/>
<pathelement location="resources/json-simple.jar"/>
<pathelement location="resources/log4j-api-2.11.0.jar"/>
<pathelement location="resources/log4j-core-2.11.0.jar"/>
<pathelement location="resources/opencsv-2.3.jar"/>
<pathelement location="resources/opencsv-4.2.jar"/>
<pathelement location="resources/reflections-0.9.8.jar"/>
</path>
<target name="init">
<mkdir dir="bin"/>
<copy includeemptydirs="false" todir="bin">
<fileset dir="src">
<exclude name="**/*.java"/>
</fileset>
</copy>
<copy includeemptydirs="false" todir="bin">
<fileset dir="resources">
<exclude name="**/*.java"/>
</fileset>
</copy>
</target>
<target name="clean">
<delete dir="bin"/>
</target>
<target depends="clean" name="cleanall"/>
<target depends="build-subprojects,build-project" name="build"/>
<target name="build-subprojects"/>
<target depends="init" name="build-project">
<echo message="${ant.project.name}: ${ant.file}"/>
<javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="true" source="${source}" target="${target}">
<src path="src"/>
<src path="resources"/>
<classpath refid="classpath"/>
</javac>
<!--
<jar destfile="ConceptGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.ConceptGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="CountGenerator3.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.CountGenerator3"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="CountGenerator2.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.CountGenerator2"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="CountGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.CountGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="DataCleanUp.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.DataCleanUp"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="DataCurator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.DataCurator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="DataEvaluation.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.DataEvaluation"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="FactGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.FactGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="FillInTree.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.FillInTree"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="MetadataGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.MetadataGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="Partitioner.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.Partitioner"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="PatientGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.PatientGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="PatientSequencer.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.PatientSequencer"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="Sequencer.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.Seqeuncer"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="EntityGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.EntityGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="DataMerge.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.DataMerge"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="FixPaths.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.FixPaths"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
-->
<jar destfile="GenericGlobalConceptsGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.GenericGlobalConceptsGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="GenericMappingGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.GenericMappingGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="DbgapTreeBuilder3.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.DbgapTreeBuilder3"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="StudiesConsentsGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.StudiesConsentsGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="RemoveConsentZeroPatients.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.RemoveConsentZeroPatients"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="VariantPatientIdentifier.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.VariantPatientIdentifier"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="UpdateCountsInJsonMetadata.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.UpdateCountsInJsonMetadata"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="HarmonizedPatientMappingGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.HarmonizedPatientMappingGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="ValidatePatientMappings.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.ValidatePatientMappings"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="CleanupPatientNums.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.CleanupPatientNums"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="MergeGlobalAllConcepts.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.MergeGlobalAllConcepts"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="SortGlobal.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.SortGlobal"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="BDCValidations.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.BDCValidations"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="HPDSPatientNumTracker.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.HPDSPatientNumTracker"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="CollectIdentifiers.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.CollectIdentifiers"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="BuildCounts.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.BuildCounts"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="PurgePatients.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.PurgePatients"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="AllConceptsInsertStudy.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.AllConceptsInsertStudy"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="BDCShareTreeBuilder.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.BDCShareTreeBuilder"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<!--<jar destfile="RootNodeConcept.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.RootNodeConcept"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="AddStartDateFix.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.AddStartDateFix"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar> -->
<jar destfile="SampleIdGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.SampleIdGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="Partitioner.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.Partitioner"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="DataAnalyzer.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.DataAnalyzer"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<!--<jar destfile="MergeMappings.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.MergeMappings"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>-
<jar destfile="DbgapTreeBuilder.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.DbgapTreeBuilder"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>-->
<jar destfile="DbgapTreeBuilder2.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.DbgapTreeBuilder2"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<!--<jar destfile="HarmonizedConsentsGenerator.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.HarmonizedConsentsGenerator"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>-->
<jar destfile="VcfIndexSync.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.VcfIndexSync"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="GenerateAllConcepts.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.GenerateAllConcepts"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="DbGapDataMerge.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.DbGapDataMerge"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<!--<jar destfile="SwapValuefix.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.SwapValuefix"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar> -->
<jar destfile="AllConceptValidation.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.AllConceptValidation"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="HarmonizedSyncPatients.jar">
<manifest>
<attribute name="Main-Class" value="etl.jobs.csv.bdc.HarmonizedSyncPatients2"/>
</manifest>
<fileset dir="bin" includes="**/*.class" />
<fileset dir="bin" includes="*.xml"></fileset>
<zipgroupfileset dir="bin" includes="**/*.jar" />
</jar>
<jar destfile="JSONToAllConcepts.jar">
<manifest>
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<jar destfile="JsonMetadataGenerator.jar">
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