build.gradle

buildscript {
    dependencies {
        classpath 'org.postgresql:postgresql:42.2.18'
    }
}

plugins {
    id "org.liquibase.gradle" version "2.1.1"
}

apply plugin: 'java'
apply plugin: 'groovy'
apply from: 'agr.gradle'
apply from: 'console.gradle'


//apply from: file('setupTestsReports.gradle')

sourceCompatibility = 17
targetCompatibility = 17

//apply from : '../zfinGradle/build.gradle'

def env = System.getenv()
def dbname = env['DBNAME']
def sourceroot = env['SOURCEROOT']
def pgbindir = env['PGBINDIR']
def pgdata = env['PGDATA']
def pghost = env['PGHOST']
def dbunloadspath = env['DB_UNLOADS_PATH']
def solrunloadspath = env['SOLR_UNLOADS_PATH']
def downloaddirectory = env['DOWNLOAD_DIRECTORY']
String targetroot = env['TARGETROOT']

/*
dependencies {
    implementation 'org.liquibase:liquibase-core:3.4.1'
    implementation "org.liquibase:liquibase-gradle-plugin:1.1.1"
    implementation gradleApi()
    implementation localGroovy()
}
*/

task deployPostgres(dependsOn: ['deployPostgresFunctions',
                                'deployPostgresTrigger']) {
    description "Deploy all postgres code"
}

defaultTasks 'make'

project.ext.set("dbname", dbname)
project.ext.set("sourceroot", sourceroot)
project.ext.set("pgdata", pgdata)
project.ext.set("pgbindir", pgbindir)
project.ext.set("targetroot", targetroot)

task loadDatabase() {
    doLast {
        File unloads = file(dbunloadspath)
        String unloadPath
        if (unloads.exists()) {
            def files = unloads.listFiles()
            Arrays.sort(files, new Comparator<File>() {
                int compare(File f1, File f2) {
                    return Long.valueOf(f2.lastModified()).compareTo(f1.lastModified())
                }
            })
            File latest = files[0]
            File latestBakDump = latest.listFiles().last()
            unloadPath = latestBakDump.getPath()
        }

        //use -DB=... path if specified, also, yes, I'm being cute so that it will be -DB=...
        //rather than -Ddb=...
        if (System.getProperty("B")) {
            unloadPath = System.getProperty("B")
        }

        //might as well support -Dunload also
        if (System.getProperty("unload")) {
            unloadPath = System.getProperty("unload")
        }

        println "Loading $unloadPath into $dbname"
        exec {
            ignoreExitValue = true
            commandLine "bash", "-c", "echo 'select pg_terminate_backend(pg_stat_activity.pid) from pg_stat_activity where pid <> pg_backend_pid();' | psql -v ON_ERROR_STOP=1 $dbname"
        }
        exec {
            ignoreExitValue = true
            commandLine 'dropdb', dbname
        }
        exec {
            ignoreExitValue = true
            commandLine 'createdb', dbname
        }
        exec {
            ignoreExitValue = true
            commandLine "bash", "-c", "pg_restore -j 8 -d $dbname $unloadPath"
        }
        exec {
            ignoreExitValue = true
            commandLine "bash", "-c", "echo 'vacuum (analyze)' | psql -v ON_ERROR_STOP=1 $dbname"
        }
        exec {
            // do an "upsert" in the developer_data table to record the time of the last loaddb
            ignoreExitValue = true
            commandLine "bash", "-c", "echo \$'insert into developer_data (dd_key, dd_value)" +
                    " values (\\'loaddb completed\\', \\'$unloadPath\\') ON CONFLICT (dd_key) " +
                    "DO UPDATE SET dd_value = EXCLUDED.dd_value;' | psql -v ON_ERROR_STOP=1 $dbname"
        }

    }
}

task loadDb(type: GradleBuild) {
    tasks = ['loadDatabase']
}

task downloadDB(type: GradleBuild) {
    tasks = ['getLatestDatabaseUnload']
}

task downloadSolrIndex(type: GradleBuild) {
    tasks = ['getLatestSolrUnload']
}

task loadSolrIndex(type: GradleBuild) {
    tasks = ['getLatestSolrIndex']
}

task getdb(dependsOn: downloadDB) //alias for downloadDB (aka getLatestDatabaseUnload)
task loaddb(dependsOn: loadDb) //just an alias, since we're used to loaddb.pl


task buildDatabase(type: GradleBuild) {
    tasks = ['liquibasePreBuild']
}

task buildPostGmakeDatabase(type: GradleBuild) {
    tasks = ['liquibasePostBuild']
}

task reload(type: GradleBuild) {
    tasks = ['loadDatabase', 'liquibasePreBuild', 'liquibasePostBuild']
}

String preChangeLog = "source/org/zfin/db/load/db.changelog.master.xml"

task liquibasePreBuild() {
    doLast {
        liquibase {
            activities {
                main {
                    println preChangeLog
                    changeLogFile preChangeLog
                    url 'jdbc:postgresql://' + pghost + ':5432/' + dbname
                }
            }
        }
    }
}

liquibasePreBuild.finalizedBy(update)

String postChangeLog = "source/org/zfin/db/postGmakePostloaddb/db.changelog.master.xml"
task liquibasePostBuild() {
    doLast {

        liquibase {
            activities {
                main {
                    changeLogFile preChangeLog
                    Properties properties = new Properties()
                    properties.setProperty("SOURCEROOT", ".")
                    changeLogFile postChangeLog
                    url 'jdbc:postgresql://' + pghost + ':5432/' + dbname
                }
            }
        }
    }
}

liquibasePostBuild.finalizedBy(update)

// variables used for translation of keys in files in SOURCEROOT copied into TARGETROOT
def translateVariableSet = [
        'CATALINA_HOME',
        'CGI_BIN_DIR_NAME',
        'DB_NAME',
        'PGHOST',
        'DEFAULT_EMAIL',
        'ENVIRONMENT',
        'FTP_ROOT',
        'GBROWSE_PATH_FROM_ROOT',
        'GENBANK_DAILY_EMAIL',
        'GO_EMAIL_ERR',
        'GO_EMAIL_CURATOR',
        'GROOVY_CLASSPATH',
        'INSTANCE',
        'JAVA_HOME',
        'JBROWSE_PATH_FROM_ROOT',
        'LOADUP_FULL_PATH',
        'MOVE_BLAST_FILES_TO_DEVELOPMENT',
        'MUTANT_NAME',
        'PARTNER_DBNAME',
        'PARTNER_INTERNAL_INSTANCE',
        'ROOT_PATH',
        'SHARED_DOMAIN_NAME',
        'SOURCEROOT',
        'SQLHOSTS_FILE',
        'SWISSPROT_EMAIL_REPORT',
        'SWISSPROT_EMAIL_CURATOR',
        'SWISSPROT_EMAIL_ERR',
        'TARGETROOT',
        'USER',
        'VALIDATION_EMAIL_DBA',
        'WEBHOST_BLASTDB_TO_COPY',
        'WEBHOST_FASTA_FILE_PATH',
]

// load properties into gradle
task setup {
    project.ext.ttNameMap = new Properties()
    file("home/WEB-INF/zfin.properties").withInputStream {
        ttNameMap.load(it)
    }
    Map filteredMap = new HashMap()
    project.ext.ttNameMap.each { name, value ->
        if (translateVariableSet.contains(name)) {
            filteredMap.put(name, value)
        }
    }
    project.ext.ttNameMap = filteredMap
}

/*
    allprojects.findAll { it.path.startsWith(":server_apps:data_transfer:") }.each { p ->
        println p.path
    }
*/

task printProp() {
    doLast {
        println 'All Properties'
        ttNameMap.each { name, value ->
            println name + ' = ' + value
        }
    }
}

project(':home') {
    task deployFiles {
        doLast {
            def sourceFiles = [file('robots.txt'), file('favicon.ico')]
            def targetDir = file("${targetroot}/home")

            if (!targetDir.exists()) {
                targetDir.mkdirs()
            }

            sourceFiles.each { sourceFile ->
                def targetFile = new File(targetDir, sourceFile.name)
                targetFile.bytes = sourceFile.bytes
            }

            println "Copied ${sourceFiles.size()} files to ${targetDir}"
        }
    }
}

task "home;zf_info;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'home/zf_info'
    excludes = ['Makefile']
}

task "home;ZFIN;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'home/ZFIN'
    excludes = ['Makefile']
}

task "server_apps;sysexecs;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'server_apps/sysexecs'
    excludes = ['Makefile', 'build.gradle']
}

task "server_apps;apache;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'server_apps/apache'
    excludes = ['Makefile', 'build.gradle']
}

task "server_apps;Reports;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'server_apps/Reports'
    excludes = ['Makefile', 'build.gradle']
}

task "server_apps;DB_maintenance;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'server_apps/DB_maintenance'
    excludes = ['Makefile', 'build.gradle']
    excludeDirs = ['postgres/liquibase']
}

task "cgi-bin;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'cgi-bin'
    excludes = ['Makefile', 'build.gradle']
}

task "server_apps;perl_lib;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'server_apps/perl_lib'
}

task deployGitInfoFile() {
    description 'Deploy git-info.txt file into TARGETROOT'
    group 'ZFIN Deployment'
    def packageFiles = 'git-info.txt'
    doLast {
        exec {
            commandLine 'bash', './generate-git-info.sh'
        }
        copy {
            from(packageFiles)
            into(targetroot + "/home/WEB-INF/classes")
        }
    }
}

task "server_apps;data_transfer;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'server_apps/data_transfer'
    excludes = ['Makefile', 'build.gradle', '.gitignore', '.DS_Store']
    excludeDirs = ['SangerMutants', 'Ensembl']
}

task "server_apps;data_transfer;Ensembl;deployFiles" (type: SimpleDirectoryCopyTask) {
    sourcePath = 'server_apps/data_transfer/Ensembl'
    includes = ['sh', 'sql', 'groovy']
}

project(':server_apps:data_transfer:Downloads') {
    task "createSymlink"() {
        doLast {
            if (!file(downloaddirectory).exists()) {
                exec {
                    commandLine "mkdir", "-p", downloaddirectory
                }
            }
            String datatransferpath = targetroot + "/home/data-transfer"
            if (!file(datatransferpath).exists()) {
                exec {
                    commandLine "ln", "-s", downloaddirectory, datatransferpath
                }
            }
        }
    }
}

task make(type: GradleBuild) {
    tasks = ['deployPostgresFunctions',
             'deployPostgresTriggers',
             'createEmptyDirsIfNotExists',
             'home:deployFiles',
             'home;zf_info;deployFiles',
             'home;ZFIN;deployFiles',
             'server_apps;apache;deployFiles',
             'server_apps;sysexecs;deployFiles',
             'server_apps;DB_maintenance;deployFiles',
             'server_apps;data_transfer;deployFiles',
             ':server_apps:data_transfer:Downloads:createSymlink',
             'server_apps;data_transfer;Ensembl;deployFiles',
             'server_apps;Reports;deployFiles',
             'deployGitInfoFile',
             'cgi-bin;deployFiles',
             'server_apps;perl_lib;deployFiles',
    ]
}

task createEmptyDirsIfNotExists() {
    doLast {
        exec {
            commandLine "mkdir", "-p", targetroot + "/home/data_transfer/Downloads/"
        }
        exec {
            commandLine "mkdir", "-p", targetroot + "/server_apps/data_transfer/Downloads/GFF3/knockdown_reagents/"
        }
        exec {
            commandLine "mkdir", "-p", downloaddirectory + "/current/"
        }
    }
}

task getLatestSolrUnload() {
    doLast {
        if (solrunloadspath != '/research/zunloads/solr/zfindb') {
            def command = "ssh " + env['SSH_USER'] + "@" + env['SSH_HOST'] + " " + 'ls -d /research/zunloads/solr/zfindb/20??.??.??-??:?? | sort -n |tail -n 1'
            def filepath = command.execute().text
            println "Getting " + filepath
            exec {
                ignoreExitValue = true
                commandLine "scp", "-r", env['SSH_USER'] + "@" + env['SSH_HOST'] + ":" + filepath, solrunloadspath
            }
        } else {
            println 'SOLR_UNLOADS_PATH is set to ' + solrunloadspath + '. Please change before attempting to copy.'
        }
    }
}

task getLatestSolrIndexFilesTrunk() {
    doLast {
        exec {
            ignoreExitValue = true
            commandLine "bash", "-c", "scp -r " + env['SSH_USER'] + "@" + env['SSH_HOST'] + ":/research/zunloads/solr/trunkdb/current current.solr.dump"
        }
    }
}

task getLatestDatabaseUnload() {
    doLast {
        if (dbunloadspath != '/research/zunloads/databases/zfindb') {
            def command = "ssh " + env['SSH_USER'] + "@" + env['SSH_HOST'] + " " + 'ls -d /research/zunloads/databases/zfindb/20??.??.??.? | sort -n |tail -n 1'
            def filepath = command.execute().text
            println "Getting " + filepath
            exec {
                ignoreExitValue = true
                commandLine "scp", "-r", env['SSH_USER'] + "@" + env['SSH_HOST'] + ":"  + filepath, dbunloadspath
            }
        } else {
            println 'DB_UNLOADS_PATH is set to ' + dbunloadspath + '. Please change before attempting to copy.'
        }
    }
}

task getLatestPostgresFilesTrunk() {
    doLast {
        exec {
            ignoreExitValue = true
            commandLine "bash", "-c", "scp " + env['SSH_USER'] + "@" + env['SSH_HOST'] + ":/research/zunloads/databases/trunkdb/current current.postgres.dump"
        }
    }
}

task getLatestSolrIndex() {
    doLast {
        println 'Upgrade Solr index to the latest production one...'
        println "latest index: " + "find ./* -type d -prune -exec ls -d ".execute().text

        def folder = solrunloadspath
        def baseDir = new File(folder)
        def files = baseDir.listFiles()
        Arrays.sort(files, new Comparator<File>() {
            int compare(File f1, File f2) {
                return Long.valueOf(f2.lastModified()).compareTo(f1.lastModified())
            }
        })
        def latestIndex = files[0]
        println latestIndex
        def sout = new StringBuilder(), serr = new StringBuilder()
        def procString = "ant restore-solr-core -DRESTORE_FROM=" + latestIndex.getAbsolutePath()
        def proc = procString.execute()
        def b = new StringBuffer()
        proc.consumeProcessErrorStream(b)

        println proc.text
        println b.toString()

    }
}

//getsolr as alias for getLatestSolrUnload
task getsolr(dependsOn: getLatestSolrUnload)

//loadsolr as alias for getLatestSolrIndex
task loadsolr(dependsOn: getLatestSolrIndex)

task getBlastAllDatabases() {
    doLast {
        exec {
            ignoreExitValue = true
            commandLine "rsync", "-av", env['SSH_USER'] + "@" + env['SSH_HOST'] + ":/research/zfin.org/blastdb/Current", "/opt/zfin/blastdb/"
        }
    }
}

task getBlastSmallDatabases() {
    doLast {
        exec {
            ignoreExitValue = true
            commandLine "rsync", "-av", "--max-size=100m", env['SSH_USER'] + "@" + env['SSH_HOST'] + ":/research/zfin.org/blastdb/Current", "/opt/zfin/blastdb/"
        }
    }
}

task getBlastBinaries() {
    doLast {
        exec {
            ignoreExitValue = true
            commandLine "rsync", "-av", env['SSH_USER'] + "@" + env['SSH_HOST'] + ":/opt/ab-blast", "/opt/zfin/blastdb/"
        }
    }
}

task getBlast(type: GradleBuild) {
    tasks = ['getBlastSmallDatabases',
             'getBlastBinaries'
    ]
}

task createSchemaSpy() {
    doLast {
        println 'Creating ER diagram for ' + ttNameMap.get('DB_NAME') + ' ...'
        javaexec {
            main = "-jar"
            args = [
                    "lib/Java/schemaSpy_5.0.0.jar",
                    "-t",
                    "pgsql",
                    "-db",
                    ttNameMap.get('DB_NAME'),
                    "-u",
                    ttNameMap.get('USER'),
                    "-host",
                    pghost,
                    "-dp",
                    "lib/Java/postgresql-42.2.18.jar",
                    "-s",
                    "public",
                    "-o",
                    ttNameMap.get('TARGETROOT') + "/home/schemaSpy",
            ]
        }
    }
}

repositories {
    mavenCentral()
}

dependencies {
    liquibaseRuntime("org.liquibase:liquibase-core:4.7.1")
    liquibaseRuntime("info.picocli:picocli:4.6.3")
    liquibaseRuntime("org.postgresql:postgresql:42.2.18")
    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.8.11'
    implementation group: 'commons-collections', name: 'commons-collections', version: '3.2.1'
    implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.17.1'
    implementation group: 'net.bytebuddy', name: 'byte-buddy', version: '1.12.7'
    implementation group: 'org.hibernate', name: 'hibernate-core', version: '6.4.4.Final'
    implementation group: 'org.hibernate', name: 'hibernate-validator', version: '6.0.13.Final'
    implementation group: 'org.hibernate.search', name: 'hibernate-search-engine', version: '6.1.1.Final'
    implementation group: 'org.hibernate.search', name: 'hibernate-search-mapper-pojo-base', version: '6.1.1.Final'
    implementation group: 'org.springframework', name: 'spring-orm', version: '6.1.1'
    implementation group: 'org.springframework', name: 'spring-core', version: '6.1.1'
    implementation group: 'org.springframework.security', name: 'spring-security-core', version: '6.1.1'
    implementation group: 'org.springframework.security', name: 'spring-security-config', version: '6.1.1'
    implementation group: 'org.springframework', name: 'spring-webmvc', version: '6.1.1'
    implementation group: 'org.springframework', name: 'spring-web', version: '6.1.1'
    implementation group: 'org.springframework', name: 'spring-context-support', version: '6.1.1'
    implementation group: 'org.springframework.security', name: 'spring-security-web', version: '6.1.1'
    implementation group: 'org.springframework.security', name: 'spring-security-crypto', version: '6.1.1'
    implementation group: 'org.springframework.integration', name: 'spring-integration-core', version: '6.1.1'

    implementation group: 'jakarta.validation', name: 'jakarta.validation-api', version: '3.0.2'
    implementation group: 'commons-lang', name: 'commons-lang', version: '2.6'
    implementation 'org.junit.jupiter:junit-jupiter:5.4.2'
    implementation group: 'jakarta.servlet', name: 'jakarta.servlet-api', version: '6.0.0'
    //runtimeOnly group: 'com.google.gwt', name: 'gwt-servlet', version: '2.9.0'
//    implementation('org.gwtproject:gwt-user:2.11.0')
    implementation files("lib/Java/gwt/gwt-user-2.11.0.jar")

    implementation group: 'org.jboss.resteasy', name: 'resteasy-client', version: '3.9.1.Final'
    implementation group: 'org.jboss.resteasy', name: 'resteasy-jaxrs', version: '3.9.1.Final'
    implementation group: 'org.jboss.resteasy', name: 'resteasy-jackson2-provider', version: '3.9.1.Final'
    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.15.2'
    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.15.2'
    implementation group: 'com.fasterxml.jackson.module', name: 'jackson-module-parameter-names', version: '2.15.2'
    implementation files("home/WEB-INF/lib/rescu-2.1.0-eclipse-transformed.jar")
    implementation 'jakarta.transaction:jakarta.transaction-api:2.0.0'




//Thanks for using https://jar-download.com

    /*
    implementation group: 'org.jboss.resteasy', name: 'resteasy-jackson-provider', version: '3.15.2.Final'
    implementation group: 'org.codehaus.jackson', name: 'jackson-core-asl', version: '1.9.13'
    implementation group: 'org.codehaus.jackson', name: 'jackson-xc', version: '1.9.13'
    implementation group: 'org.codehaus.jackson', name: 'jackson-jaxrs', version: '1.9.13'
    implementation group: 'org.codehaus.jackson', name: 'jackson-mapper-asl', version: '1.9.13'
*/
    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.15.2'
/*
    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.0'
    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-core', version: '2.15.2'
    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.13.0'
     //implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jdk8', version: '2.13.0'
*/
    //implementation group: 'com.fasterxml.jackson.module', name: 'jackson-module-parameter-names', version: '2.13.0'
    implementation group: 'org.eclipse.microprofile.openapi', name: 'microprofile-openapi-api', version: '2.0.1-RC1'
    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.3.1'
    implementation group: 'org.projectlombok', name: 'lombok', version: '1.18.20'
    implementation group: 'org.apache.httpcomponents', name: 'httpcore', version: '4.4.1'
    implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.4.1'
    implementation group: 'jakarta.annotation', name: 'jakarta.annotation-api', version: '2.0.0'
    implementation group: 'com.google.code.gson', name: 'gson', version: '2.2.4'
//    implementation group: 'org.fusesource.restygwt', name: 'restygwt', version: '2.2.7'
    implementation files('home/WEB-INF/lib/restygwt-2.2.7-eclipse-transformed.jar')
    implementation group: 'jakarta.ws.rs', name: 'jakarta.ws.rs-api', version: '3.1.0'
    implementation group: 'org.apache.solr', name: 'solr-solrj', version: '8.6.3'
    implementation group: 'commons-beanutils', name: 'commons-beanutils', version: '1.9.1'
    implementation group: 'commons-cli', name: 'commons-cli', version: '1.2'
    implementation group: 'org.freemarker', name: 'freemarker', version: '2.3.20'
    implementation group: 'org.apache.lucene', name: 'lucene-core', version: '2.3.1'
    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '3.0.1'
//    implementation('org.glassfish.jaxb:jaxb-runtime:2.3.0')
    implementation group: 'com.mchange', name: 'c3p0', version: '0.9.5.5'
    implementation group: 'com.sun.activation', name: 'jakarta.activation', version: '2.0.1'
    implementation group: 'com.sun.mail', name: 'jakarta.mail', version: '2.0.1'
    implementation group: 'org.apache.commons', name: 'commons-exec', version: '1.0'
    implementation group: 'taglibs', name: 'standard', version: '1.1.2'

    implementation files('home/WEB-INF/lib/AnalyticsReportingApp-1.0.2.jar') //From repo: https://github.com/rtaylorzfin/google-analytics-reporting-app/
    implementation files('home/WEB-INF/lib/agr_curation_api-v0.36.1.jar')
    implementation files('home/WEB-INF/lib/patricia-trie-0.2.jar')
    implementation files('home/WEB-INF/lib/cvu.jar')
    implementation files('home/WEB-INF/lib/commons-configuration-ant-task-0.9.6.jar')
    implementation files('home/WEB-INF/lib/obo.jar')
    implementation files('home/WEB-INF/lib/bbop.jar')
    implementation files('home/WEB-INF/lib/blast-serialization-1.0-eclipse-transformed.jar')
    implementation files('home/WEB-INF/lib/text-table-formatter-1.0.jar')
    implementation files('home/WEB-INF/lib/commons-collections4-4.4.jar')
    implementation files('home/WEB-INF/lib/commons-lang3-3.1.jar')
    // maven reference does not have version 1.0, so using the plain jar file
    //implementation group: 'org.nocrala.tools.texttablefmt', name: 'text-table-formatter', version: '1.2.4'
    implementation files('home/WEB-INF/lib/slf4j-api-1.7.26.jar')
    implementation files('home/WEB-INF/lib/jakarta.persistence-api-3.1.0.jar')
    implementation files('home/WEB-INF/lib/jakarta.annotation-api-2.0.0.jar')

    implementation files('home/WEB-INF/lib/log4j-api-2.17.1.jar')
    implementation files('home/WEB-INF/lib/log4j-core-2.17.1.jar')
    implementation files('home/WEB-INF/lib/log4j-slf4j-impl-2.13.3.jar')

    implementation group: 'net.sourceforge.htmlunit', name: 'htmlunit', version: '2.62.0'
    implementation group: 'commons-configuration', name: 'commons-configuration', version: '1.6'
    implementation group: 'commons-net', name: 'commons-net', version: '1.4.1'
    implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.4'
    implementation group: 'com.github.samtools', name: 'htsjdk', version: '2.20.3'
    implementation group: 'org.jdom', name: 'jdom', version: '1.1'
    implementation group: 'org.springframework.ws', name: 'spring-ws-core', version: '4.0.10'

    implementation group: 'org.codehaus.castor', name: 'castor-xml', version: '1.3'
    implementation group: 'com.googlecode.owasp-java-html-sanitizer', name: 'owasp-java-html-sanitizer', version: '20200713.1'
    implementation group: 'org.imgscalr', name: 'imgscalr-lib', version: '4.2'
    implementation group: 'org.biojava', name: 'core', version: '1.9.4'
    //implementation group: 'org.apache.tomcat', name: 'tomcat-servlet-api', version: '9.0.39'
    implementation group: 'org.apache.ant', name: 'ant', version: '1.8.2'
    implementation group: 'org.apache.logging.log4j', name: 'log4j-web', version: '2.17.1'
    implementation group: 'org.postgresql', name: 'postgresql', version: '42.2.18'
    implementation group: 'com.google.guava', name: 'guava', version: '27.1-jre'
    implementation group: 'org.apache.cxf', name: 'cxf-rt-rs-client', version: '3.4.2'
    implementation group: 'com.fasterxml.jackson.jaxrs', name: 'jackson-jaxrs-json-provider', version: '2.12.2'
    implementation group: 'org.json', name: 'json', version: '20210307'

    annotationProcessor 'org.projectlombok:lombok:1.18.20'
    //implementation group: 'log4j', name: 'log4j', version: '1.2.15'

//Thanks for using https://jar-download.com


    //implementation group: 'org.apache.commons', name: 'commons-collections4', version: '4.4'
    implementation("com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.9.4")
    implementation 'junit:junit:4.11'
    implementation group: 'org.hibernate', name: 'hibernate-gradle-plugin', version: '5.6.5.Final'
    testImplementation group: 'xerces', name: 'xercesImpl', version: '2.12.1'
    testImplementation("org.junit.jupiter:junit-jupiter-api:5.4.2")
    testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.4.2")
    testRuntimeOnly("org.junit.vintage:junit-vintage-engine:5.4.2")
    testImplementation group: 'org.junit.platform', name: 'junit-platform-suite-api', version: '1.7.0'
    testImplementation group: 'commons-discovery', name: 'commons-discovery', version: '0.5'
    testImplementation group: 'wsdl4j', name: 'wsdl4j', version: '1.6.3'
    implementation group: 'org.javassist', name: 'javassist', version: '3.27.0-GA'
    implementation group: 'log4j', name: 'log4j', version: '1.2.17'

//    testCompile group: 'org.junit.jupiter', name: 'junit-jupiter-engine', version: '5.7.0'
    testImplementation group: 'org.hamcrest', name: 'hamcrest-all', version: '1.3'
    testImplementation group: 'net.sourceforge.jwebunit', name: 'jwebunit-core', version: '2.4'

    testImplementation group: 'org.gebish', name: 'geb-ast', version: '6.0'
    testImplementation group: 'org.gebish', name: 'geb-core', version: '6.0'
    testImplementation group: 'org.gebish', name: 'geb-spock', version: '6.0'
    testImplementation group: 'org.gebish', name: 'geb-waiting', version: '6.0'
    testImplementation group: 'oauth.signpost', name: 'signpost-core', version: '2.1.1'


//    testCompile group: 'org.openqa.selenium', name: 'selenium', version: '0.8.1'

    //testImplementation('org.codehaus.groovy:groovy-all:3.0.6')
    testImplementation group: 'org.spockframework', name: 'spock-junit4', version: '2.3-groovy-3.0'
    testImplementation group: 'org.spockframework', name: 'spock-spring', version: '2.3-groovy-3.0'
    //changed this from groovy-2.4
    testImplementation 'org.spockframework:spock-core:2.3-groovy-3.0'
    testImplementation group: 'org.gwtproject', name: 'gwt-servlet-jakarta', version: '2.11.0'


    testImplementation group: 'net.sourceforge.htmlunit', name: 'htmlunit', version: '2.62.0'
    testImplementation group: 'org.slf4j', name: 'slf4j-log4j12', version: '1.7.30'
    testImplementation group: 'org.javassist', name: 'javassist', version: '3.27.0-GA'

    implementation group: 'org.apache.commons', name: 'commons-math', version: '2.2'

    // not working: odd
    //testCompile group: 'org.jenkins-ci.plugins', name: 'testInProgress-client', version: '1.1'
    implementation files('lib/Java/testInProgress-client-1.1.jar')
    implementation files('lib/Java/selenium-api-2.35.0.jar')
    implementation files('lib/Java/selenium-htmlunit-driver-2.35.0.jar')
    implementation files('lib/Java/selenium-remote-driver-2.35.0.jar')
    implementation files('lib/Java/spring-test-6.1.1.jar')
    implementation files('lib/Java/servlet-api-5.0.0.jar')
    implementation files('lib/Java/jakarta.servlet.jsp-api-3.1.1.jar')
    implementation files('lib/Java/jakarta.servlet.jsp.jstl-api-3.0.0.jar')
    implementation files('home/WEB-INF/lib/gwt-servlet-jakarta-2.11.0.jar')
    // not working :(
    //testImplementation group: 'org.seleniumhq.selenium', name: 'htmlunit-driver', version: '2.35'
//    implementation group: 'org.springframework.boot', name: 'spring-boot-starter'


    testAnnotationProcessor "org.projectlombok:lombok:1.18.20"
    implementation 'org.jooq:jool:0.9.15'
}

sourceSets {
    main {
        java.srcDirs = ['source']
        resources.srcDirs = ['home']
    }

    test {
        //java.srcDirs = ['test']
        groovy.srcDirs = ['test']
        resources.srcDirs = ['test']
    }
}

test {
    maxHeapSize = "2048m"
    useJUnitPlatform()
    jvmArgs('--add-opens', 'java.base/jdk.internal.loader=ALL-UNNAMED',
            '--add-opens', 'java.base/java.util=ALL-UNNAMED',
            '--add-opens', 'java.base/java.lang=ALL-UNNAMED',
            '--add-opens', 'java.base/java.lang.invoke=ALL-UNNAMED',
            '--add-opens', 'java.base/java.util=ALL-UNNAMED',
            '--add-opens', 'java.prefs/java.util.prefs=ALL-UNNAMED',
            '--add-opens', 'java.base/java.nio.charset=ALL-UNNAMED',
            '--add-opens', 'java.base/java.net=ALL-UNNAMED',
            '--add-opens', 'java.base/java.util.concurrent.atomic=ALL-UNNAMED')
    testLogging {
        //showStandardStreams = true
    }

    def includeSmokeTests = project.hasProperty('smokeTests')
    def includeNonSmokeTests = project.hasProperty('nonSmokeTests')
    if (!includeSmokeTests && !includeNonSmokeTests) {
        //if neither flag is set, run all tests
        includeSmokeTests = true
        includeNonSmokeTests = true
    }

    filter {

        if (includeNonSmokeTests) {
            includeTestsMatching "org.zfin.UnitTests"
            //spock tests

            includeTestsMatching "org.zfin.publication.MeshHeadingSpec"

            includeTestsMatching "org.zfin.publication.presentation.PublicationValidatorSpec"
            includeTestsMatching "org.zfin.publication.repository.PublicationRepositorySpec"
            includeTestsMatching "org.zfin.feature.service.MutationDetailsConversionServiceSpec"
            includeTestsMatching "org.zfin.util.ReportGeneratorSpec"
            includeTestsMatching "org.zfin.search.service.SolrServiceSpec"
            includeTestsMatching "org.zfin.search.service.SolrQueryFacadeSpec"
            includeTestsMatching "org.zfin.search.service.MarkerSearchServiceSpec"
            includeTestsMatching "org.zfin.search.service.SearchSuggestionServiceSpec"

            includeTestsMatching "org.zfin.ontology.service.RibbonServiceIntegrationSpec"
            includeTestsMatching "org.zfin.uniquery.RelatedLinksSpec"

//      Failing tests that we may want to bring back: (ZFIN-8271)
//        includeTestsMatching "org.zfin.uniquery.CategoriesAndFacetsSpec"
//        includeTestsMatching "org.zfin.uniquery.QuerySpec"
//        includeTestsMatching "org.zfin.uniquery.ResultAttributesSpec"

            includeTestsMatching "org.zfin.sequence.repository.SequenceRepositorySpec"
            includeTestsMatching "org.zfin.feature.FeatureServiceSpec"
            includeTestsMatching "org.zfin.curation.service.CurationDTOConversionServiceSpec"
            includeTestsMatching "org.zfin.expression.ExpressionSearchSpec"
            includeTestsMatching "org.zfin.marker.presentation.GeneAddFormBeanValidatorSpec"
            includeTestsMatching "org.zfin.marker.presentation.MarkerGoServiceIntegrationSpec"
            includeTestsMatching "org.zfin.marker.presentation.SequenceTargetingReagentAddBeanValidatorSpec"
            includeTestsMatching "org.zfin.figure.repository.FigureRepositorySpec"
            includeTestsMatching "org.zfin.gbrowse.presentation.GBrowseImageSpec"
            includeTestsMatching "org.zfin.figure.service.ImageServiceSpec"

            /*need to figure out ..all tests fail here
        includeTestsMatching "org.zfin.figure.service.FigureViewServiceSpec"*/

            //includeTestsMatching "org.zfin.publication.PublicationServiceSpec"
            // PublicationServiceSpec > #authorString should bring back #author FAILED
            //org.spockframework.runtime.SpockAssertionError at UnrollIterationNameProvider.java:80


            /*includeTestsMatching "org.zfin.figure.service.ImageServiceSpec" (needs fixing..null pointer here:  tempDir.newFolder(ZfinPropertiesEnum.IMAGE_LOAD.toString(), "medium"))
        includeTestsMatching "org.zfin.figure.service.VideoServiceSpec"*/

            /*//following use geb..likely not to fix

        includeTestsMatching "org.zfin.figure.presentation.FigureViewWebSpec" (geb test)
        includeTestsMatching "org.zfin.marker.MarkerselectWebSpec" (geb test)
        includeTestsMatching "org.zfin.framework.GroovyWebSpec"(geb test)
        includeTestsMatching "org.zfin.ontology.service.RibbonServiceIntegrationSpec"(geb test)*/

            // db unit tests
            includeTestsMatching "org.zfin.DbUnitTests"
            includeTestsMatching "org.zfin.infrastructure.EnumValidationTest"
            includeTestsMatching "org.zfin.DbControllerTests"
            includeTestsMatching "org.zfin.ThirdPartyServiceTests"
        }

        if (includeSmokeTests) {
            includeTestsMatching "org.zfin.anatomy.AnatomySmokeTest"
            includeTestsMatching "org.zfin.antibody.smoketest.AntibodySmokeTest"
            includeTestsMatching "org.zfin.sequence.blast.smoketest.BlastSmokeTest"
            includeTestsMatching "org.zfin.datatransfer.smoketests.DownloadSmokeTest"
            includeTestsMatching "org.zfin.feature.presentation.FeatureDetailSmokeTest"
            includeTestsMatching "org.zfin.feature.presentation.GenotypeDetailSmokeTest"
            includeTestsMatching "org.zfin.expression.presentation.FigureSummarySmokeTest"
            includeTestsMatching "org.zfin.fish.smoketest.FishSmokeTest"
            includeTestsMatching "org.zfin.fish.smoketest.PhenotypeSummarySmokeTest"
            includeTestsMatching "org.zfin.httpunittest.MarkerViewSmokeTest"
            includeTestsMatching "org.zfin.sebservice.MarkerRestSmokeTest"
            //include specific method in any of the tests
    //        includeTestsMatching "*ActiveDataTest"
        }
    }

    reports {
        junitXml.required = true
        html.required = true
    }
}
tasks.withType(Test) {
    testLogging {
        // set options for log level LIFECYCLE
        showExceptions true
        showCauses true
        showStackTraces true

        info.events = debug.events

        afterSuite { desc, result ->
            if (!desc.parent) { // will match the outermost suite
                def output = "Results: ${result.resultType} (${result.testCount} tests, ${result.successfulTestCount} successes, ${result.failedTestCount} failures, ${result.skippedTestCount} skipped)"
                def startItem = '|  ', endItem = '  |'
                def repeatLength = startItem.length() + output.length() + endItem.length()
                println('\n' + ('-' * repeatLength) + '\n' + startItem + output + endItem + '\n' + ('-' * repeatLength))
            }
        }
    }
}

reporting.baseDir = "reports/gradle"
testResultsDirName = "reports/test-results"

task showDirs {
    doLast {
        logger.quiet(rootDir.toPath().relativize(project.reportsDir.toPath()).toString())
        logger.quiet(rootDir.toPath().relativize(project.testResultsDir.toPath()).toString())
    }
}