agr.gradle

def env = System.getenv()
def log4jConfig = env['SOURCEROOT'] + "/home/WEB-INF/conf/log4j2.xml"
tasks.withType(JavaExec) {
    systemProperty "log4j2.configurationFile", log4jConfig
    systemProperty "com.mchange.v2.log.MLog", "log4j2"
}

task createBasicGeneInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicGeneInfo'
}
task createBasicGeneInfoFileTest(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicGeneInfo'
    args '5'
}

task createConstructFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicConstructInfo'
}

task createHtpdatasetFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicRNASeqMetaDatasetInfo'
}

task createHtpdatasampleFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicRNASeqMetaDatasampleInfo'
}

task createBasicFishInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicFishInfo'
}

task createBasicSTRInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicSTRInfo'
}

task createBasicVariantInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicVariantInfo'
}

task createZfinExpressionInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.ZFINExpressionInfo'
}

task createBasicAlleleInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicAlleleInfo'
}
task createBasicResourceInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicResourceInfo'
}


task createGPIFile(type: JavaExec) {
    description 'Generates tab delimited file for GO/Noctua'
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.GPIFile'
}

task createGPI2File(type: JavaExec) {
    description 'Generates tab delimited file for GO/Noctua(Ver 2.0)'
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.GPIFileVer2'
}

task createDiseaseInfoLinkMLFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.DiseaseAnnotationLinkMLInfo'
    doFirst {
        args linkMLVersion
    }
}

task createDiseaseInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.DiseaseInfo'
}

task createDiseaseInfoFileTest(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.DiseaseInfo'
    args '100'
}

task createBasicPhenotypeInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicPhenotypeInfo'
}

task createBasicWTExpressionInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicExpressionInfo'
}

task createReferenceInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicReferenceInfo'
}

task createReferenceExchangeInfoFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.BasicReferenceExchangeInfo'
}

task createAllelesLinkMLFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.AlleleLinkMLInfo'
    doFirst {
        args linkMLVersion
    }
}

task createGenesLinkMLFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.GeneLinkMLInfo'
    doFirst {
        args linkMLVersion
    }
}

task createConstructLinkMLFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.ConstructLinkMLInfo'
    doFirst {
        args linkMLVersion
    }
}

task createVariantLinkMLFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.VariantLinkMLInfo'
    doFirst {
        args linkMLVersion
    }
}

task createFishLinkMLFile(type: JavaExec) {
    classpath = sourceSets.main.runtimeClasspath
    main = 'org.zfin.marker.agr.FishLinkMLInfo'
    doFirst {
        args linkMLVersion
    }
}

task createAllianceLinkMLFiles {
    dependsOn createGenesLinkMLFile
    dependsOn createAllelesLinkMLFile
    dependsOn createFishLinkMLFile
    dependsOn createDiseaseInfoLinkMLFile
    dependsOn createConstructLinkMLFile
    dependsOn createVariantLinkMLFile
}

task createAllianceFiles {
    dependsOn createDiseaseInfoFile
    dependsOn createBasicPhenotypeInfoFile
    dependsOn createBasicWTExpressionInfoFile
    dependsOn createBasicAlleleInfoFile
    dependsOn createBasicGeneInfoFile
    dependsOn createBasicFishInfoFile
    dependsOn createBasicSTRInfoFile
    dependsOn createZfinExpressionInfoFile
    dependsOn createConstructFile
    dependsOn createHtpdatasetFile
    dependsOn createHtpdatasampleFile
    dependsOn createBasicVariantInfoFile
    dependsOn createBasicResourceInfoFile
    dependsOn createReferenceInfoFile
    dependsOn createReferenceExchangeInfoFile

}