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build.gradle
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build.gradle
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buildscript {
ext {
springBootVersion = '2.7.17'
// Remove this line to see what version is favored by springBootVersion
// and the version brought in by spring-data-elasticsearch
set('elasticsearch.version', '7.12.1')
}
repositories {
jcenter()
maven { url "https://repo.spring.io/release" }
maven { url "https://repo.spring.io/milestone" }
maven { url "https://repo.spring.io/snapshot" }
mavenCentral()
}
dependencies {
classpath "org.springframework.boot:spring-boot-gradle-plugin:${springBootVersion}"
}
}
plugins {
id 'java'
id 'eclipse'
id 'war'
id 'org.springframework.boot' version "${springBootVersion}"
id 'io.spring.dependency-management' version '1.1.3'
id 'maven-publish'
// google java format gradle plugin
id "com.diffplug.spotless" version "6.25.0"
}
repositories {
mavenLocal()
jcenter()
maven { url "https://repo.spring.io/release" }
maven { url "https://repo.spring.io/milestone" }
maven { url "https://repo.spring.io/snapshot" }
mavenCentral()
}
ext['log4j2.version'] = '2.17.1'
// Extra Properties
ext {
// Parameters
if (!project.hasProperty("inputPath")) {
inputPath = "na"
}
if (!project.hasProperty("listFile")) {
listFile = "na"
}
if (!project.hasProperty("terminology")) {
terminology = "na"
}
}
/* Version info */
group = "gov.nih.nci.evs.api"
version = "2.0.0.RELEASE"
sourceCompatibility = 17
targetCompatibility = 17
springBoot {
// generate file META-INF/build-info.properties during the build
buildInfo()
}
// Java Toolchain to detect which version of Java to use, if not present
// it will automatically download and install the required version of Java
java {
toolchain {
languageVersion = JavaLanguageVersion.of(17)
}
}
dependencies {
// Use version 2 with spring boot 3
// custom location => springdoc.swagger-ui.path=/swagger-ui/index.html
implementation("org.springdoc:springdoc-openapi-ui:1.8.0") {
exclude group: "org.webjars", module: "swagger-ui"
}
implementation 'org.springframework.boot:spring-boot-starter-web'
implementation 'org.springframework.boot:spring-boot-devtools'
implementation 'org.springframework.boot:spring-boot-starter-actuator'
implementation 'org.springframework.boot:spring-boot-starter-cache'
implementation 'org.springframework.boot:spring-boot-properties-migrator'
implementation 'org.springframework:spring-aop'
implementation 'org.springframework.data:spring-data-elasticsearch:4.2.12'
//Java Mail Sender dependency
implementation 'org.springframework.boot:spring-boot-starter-mail'
implementation 'com.google.guava:guava:32.1.3-jre'
implementation 'org.aspectj:aspectjweaver:1.9.2'
implementation 'org.apache.commons:commons-text:1.10.0'
implementation 'org.apache.opennlp:opennlp-tools:2.2.0'
implementation 'org.ehcache:ehcache:3.8.1'
implementation 'javax.cache:cache-api:1.1.1'
implementation 'commons-io:commons-io:2.14.0'
implementation 'commons-cli:commons-cli:1.4'
implementation 'cglib:cglib:3.3.0'
//implementation 'com.maxmind.geoip2:geoip2:2.15.0'
// fhir dependencies
implementation('ca.uhn.hapi.fhir:hapi-fhir-base:6.8.3') {
exclude group: 'com.google.guava', module: 'guava'
}
implementation('com.fasterxml.jackson.core:jackson-core:2.15.2') {
exclude group: 'com.google.guava', module: 'guava'
}
implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.8.3") {
exclude group: "com.google.guava", module: "guava"
}
implementation("ca.uhn.hapi.fhir:hapi-fhir-server:6.8.3") {
exclude group: "com.google.guava", module: "guava"
}
implementation('ca.uhn.hapi.fhir:hapi-fhir-jpaserver-base:6.8.3') {
exclude group: 'ca.uhn.hapi.fhir', module: 'hapi-fhir-sql-migrate'
exclude group: 'org.elasticsearch.client', module: 'elasticsearch-rest-high-level-client'
exclude group: 'org.hibernate.search'
exclude group: 'org.apache.lucene'
exclude group: 'com.github.jsonld-java', module: 'jsonld-java'
exclude group: 'com.graphql-java', module: 'graphql-java'
exclude group: 'org.glassfish', module: 'javax.el'
exclude group: 'org.apache.logging.log4j', module: 'log4j-to-slf4j'
exclude group: 'com.google.guava', module: 'guava'
}
implementation('ca.uhn.hapi.fhir:hapi-fhir-server-openapi:6.8.3') {
exclude group: 'com.google.guava', module: 'guava'
}
// Lombok dependencies
implementation 'org.projectlombok:lombok:1.18.32'
compileOnly 'org.projectlombok:lombok:1.18.32'
compileOnly 'jakarta.servlet:jakarta.servlet-api:6.0.0'
annotationProcessor 'org.projectlombok:lombok:1.18.32'
providedRuntime 'org.springframework.boot:spring-boot-starter-tomcat'
/*
* Test Dependencies
*/
testImplementation 'org.springframework.boot:spring-boot-starter-test'
testImplementation 'org.junit.jupiter:junit-jupiter-params:5.9.3'
testImplementation 'org.junit.jupiter:junit-jupiter-api:5.9.3'
testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.9.3'
testRuntimeOnly 'org.junit.platform:junit-platform-commons:1.9.3'
testRuntimeOnly 'org.junit.platform:junit-platform-runner:1.9.3'
testCompileOnly 'org.projectlombok:lombok:1.18.32'
testAnnotationProcessor 'org.projectlombok:lombok:1.18.32'
}
test {
useJUnitPlatform{}
// Args to pass when running the tests to ensure the cglib can be accessed and avoid InaccessibleObjectException
jvmArgs('-Xmx8G', '--add-opens', 'java.base/java.lang=ALL-UNNAMED')
// Set the active profile to use our application-test.yml file from test resources
systemProperty("spring.profiles.active", "test")
/*
* Configure gradle to show standard out and standard error
* of the test JVM(s) on the console
*/
testLogging.showStandardStreams = true
}
// Format the code using google-java-format: https://github.com/diffplug/spotless/blob/main/plugin-gradle/README.md
// Use ./gradlew spotlessCheck to run checks
// Use ./gradlew spotlessApply to perform fixes
spotless {
format 'misc', {
// define the files to apply `misc` to
target '*.gradle', '.gitattributes', '.gitignore'
// define the steps to apply to those files
trimTrailingWhitespace()
indentWithSpaces(2) // or spaces. Takes an integer argument if you don't like 4
endWithNewline()
}
java {
target 'src/main/java/**/*.java', 'src/test/java/**/*.java'
// apply a specific flavor of google-java-format
googleJavaFormat('1.22.0').reflowLongStrings().formatJavadoc(true).reorderImports(true).groupArtifact('com.google.googlejavaformat:google-java-format')
removeUnusedImports()
// fix formatting of type annotations
// formatAnnotations()
}
}
// # for this, the cuis with listed sources will have hierarchies computed
// ./gradlew rrfSample -Pterminology=NCIMTH,ICD10CM,ICD9CM,SNOMEDCT_US,RXNORM,LNC,MDR,RADLEX -PlistFile=src/main/resources/cuis.txt -PinputPath=../data/NCIM
tasks.register('rrfSample', JavaExec) {
classpath = sourceSets.main.runtimeClasspath
main = "gov.nih.nci.evs.api.service.SamplingApplication"
systemProperties System.getProperties()
// arguments to pass to the application
args("rrfSample", inputPath, listFile, terminology)
jvmArgs "-Xmx8G"
}
tasks.register('zipFile', Zip) {
def zipFileRootDirectory = "${project.name}-${project.version}"
from('src/main/bin') {
fileMode = 0755
into "$zipFileRootDirectory/bin"
}
from("$buildDir/main/bin") {
fileMode = 0755
include '**/createDirectoriesForWorkspace.pl'
into "$zipFileRootDirectory/bin"
}
from('src/main/config') {
into "${archiveBaseName}-${project.version}/config"
into "$zipFileRootDirectory/config"
}
from("$buildDir/main/config") {
include '**/createDirectories.properties'
into "$zipFileRootDirectory/config"
}
from("$buildDir/libs") {
include '*.*'
into "$zipFileRootDirectory/lib"
}
rename { String fileName ->
fileName.replace("-${project.version}", "")
}
}
// NOTE: this causes LoaderServiceImpl to launch when run via -jar
bootJar {
manifest {
attributes 'Start-Class': 'gov.nih.nci.evs.api.service.LoaderServiceImpl'
}
// Handle duplicate copying more than one file to the same destination
// https://docs.gradle.org/8.2.1/dsl/org.gradle.api.tasks.Copy.html#org.gradle.api.tasks.Copy:duplicatesStrategy
duplicatesStrategy(DuplicatesStrategy.EXCLUDE)
}
zipFile.dependsOn = [bootWar, bootJar]
build.dependsOn = [spotlessCheck, test, bootWar, bootJar, zipFile]
publishToMavenLocal.dependsOn = [bootWar, bootJar, zipFile]
dependencyLocking {
lockAllConfigurations()
}