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build.gradle
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plugins {
id 'java'
id 'war'
id "io.swagger.core.v3.swagger-gradle-plugin" version "2.1.9"
}
compileJava {
options.compilerArgs << '-parameters'
}
// build API endpoint and stores in swagger directory
resolve {
outputFileName = 'geomeAPI'
outputFormat = 'JSON'
prettyPrint = 'TRUE'
classpath = sourceSets.main.runtimeClasspath
resourcePackages = ['biocode.fims']
outputDir = file('swagger')
}
repositories {
mavenCentral()
}
apply plugin: "application"
dependencies {
compile 'jstl:jstl:1.2'
compile group: 'org.springframework', name: 'spring-web', version: '4.3.14.RELEASE'
compile group: 'org.glassfish.jersey.bundles.repackaged', name: 'jersey-guava', version: '2.25.1'
// this version is temporary until https://github.com/dhatim/fastexcel/pull/75 is merged & released
// we can remove the above maven-dev-releases as well
//compile group: 'org.dhatim', name: 'fastexcel', version: '41c4f50-SNAPSHOT'
// https://mvnrepository.com/artifact/org.dhatim/fastexcel
compile group: 'com.github.rzymek', name: 'opczip', version: '1.0.1'
compile group: 'com.opencsv', name: 'opencsv', version: '4.2'
compile 'org.glassfish.jersey.media:jersey-media-json-jackson:2.27'
compile group: 'org.glassfish.jersey.containers', name: 'jersey-container-servlet', version: '2.27'
compile 'org.apache.poi:poi:4.0.0'
compile 'org.apache.poi:poi-ooxml:4.0.0'
compile 'com.sun.mail:javax.mail:1.5.5'
compile 'joda-time:joda-time:2.1' // TODO replace with java 8 Date/Times
compile 'org.apache.httpcomponents:httpcore:4.2.1'
compile 'org.apache.httpcomponents:httpclient:4.2.1'
compile 'com.ibm.icu:icu4j:3.4.4'
compile group: 'org.parboiled', name: 'parboiled-java', version: '1.1.8'
compile group: 'com.auth0', name: 'java-jwt', version: '3.8.1'
compile group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.8.11'
compile group: 'com.fasterxml.jackson.module', name: 'jackson-module-parameter-names', version: '2.9.6'
// aspectj
runtime group: 'org.aspectj', name: 'aspectjweaver', version: '1.8.9'
compile group: 'org.springframework', name: 'spring-aop', version: '4.3.14.RELEASE'
compile group: 'org.imgscalr', name: 'imgscalr-lib', version: '4.2'
compile 'org.glassfish.jersey.media:jersey-media-multipart:2.27'
compile group: 'org.glassfish.jersey.media', name: 'jersey-media-moxy', version: '2.27'
compile group: 'org.glassfish.jersey.ext', name: 'jersey-spring4', version: '2.27'
compile group: 'org.springframework', name: 'spring-context', version: '4.3.6.RELEASE'
compile 'org.springframework:spring-jdbc:4.3.14.RELEASE'
compile 'commons-validator:commons-validator:1.5.0'
// needed for apache-poi to evaluate array/matrix functions
compile group: 'org.apache.commons', name: 'commons-math3', version: '3.0'
compile 'org.apache.commons:commons-dbcp2:2.1.1'
// https://mvnrepository.com/artifact/org.apache.commons/commons-text
compile group: 'org.apache.commons', name: 'commons-text', version: '1.4'
compile 'org.apache.commons:commons-lang3:3.8'
compile group: 'commons-collections', name: 'commons-collections', version: '3.2.2'
compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.2.11'
compile group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '2.2.11'
compile group: 'com.sun.xml.bind', name: 'jaxb-core', version: '2.2.11'
compile group: 'javax.el', name: 'javax.el-api', version: '3.0.0'
// https://mvnrepository.com/artifact/commons-net/commons-net
compile group: 'commons-net', name: 'commons-net', version: '3.6'
compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.9.6'
// https://mvnrepository.com/artifact/com.fasterxml.jackson.datatype/jackson-datatype-jsr310
compile group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.10.1'
compile 'com.fasterxml.jackson.datatype:jackson-datatype-hibernate5:2.8.4'
compile 'org.springframework.data:spring-data-jpa:1.10.1.RELEASE'
compile group: 'org.hibernate.javax.persistence', name: 'hibernate-jpa-2.1-api', version: '1.0.0.Final'
// https://mvnrepository.com/artifact/org.eclipse.persistence/org.eclipse.persistence.moxy
compile group: 'org.hibernate', name: 'hibernate-java8', version: '5.1.0.Final'
compile group: 'org.eclipse.persistence', name: 'org.eclipse.persistence.moxy', version: '2.7.6'
compile 'org.hibernate:hibernate-entitymanager:5.1.0.Final'
compile group: 'org.postgresql', name: 'postgresql', version: '42.2.1'
compile 'javax.servlet:javax.servlet-api:4.0.1'
compile 'org.slf4j:slf4j-log4j12:1.7.19'
compile 'com.googlecode.json-simple:json-simple:1.1.1'
compile 'commons-cli:commons-cli:1.4'
compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
testCompile "junit:junit-dep:4.10"
testCompile group: 'org.springframework', name: 'spring-test', version: '4.3.14.RELEASE'
testCompile 'org.mockito:mockito-all:1.9.5'
testCompile 'org.powermock:powermock-module-junit4:1.5.6'
testCompile 'org.powermock:powermock-api-mockito:1.5.6'
// tried 0.12.11 failed
// tried 0.7.5 failed
// tried 0.8.7 failed
implementation group: 'org.dhatim', name: 'fastexcel', version: '0.9.13'
}
//=============================
//= application configuration
//=============================
mainClassName = ''
task harvestSraBioSamples(type: JavaExec) {
classpath = configurations.compile + sourceSets.main.runtimeClasspath
main = "biocode.fims.run.SraAccessionHarvesterRunner"
}
task reportSraSubmissions(type: JavaExec) {
classpath = configurations.compile + sourceSets.main.runtimeClasspath
main = "biocode.fims.run.SraSubmissionReporterRunner"
}
startScripts {
classpath = files(jar.archivePath, configurations.compile, configurations.runtime)
}
task copyEnvironmentProps(type: Copy) {
from('src/main/environment/' + project.findProperty("environment")) {
include '**/*.properties'
include '**/*.props'
}
into 'build/resources/main'
}
tasks.war.dependsOn("copyEnvironmentProps")
war {
enabled = true
webXml = file('src/main/environment/' + project.findProperty("environment") + '/web.xml')
from 'swagger/'
from('src/main/web/'){
include 'docs/**'
into ''
}
from('docs/'){
include 'helpDocumentation.pdf'
into 'docs'
}
from('src/main/web/'){
include 'apidocs/**'
into ''
}
}