build.gradle

/*
 * This file was generated by the Gradle 'init' task.
 */

plugins {
	id 'java'
	id 'war'
	id 'jacoco'
	id 'org.ajoberstar.grgit' version '4.1.1'
}

repositories {
	mavenCentral()
	
	maven {
		name = "Clojars"
		url = "https://repo.clojars.org/"
	}
	maven {
		name = "JitPack" 
		url = 'https://jitpack.io'
	}
}
task buildGitCommitFile {
	doLast {
		def commitId = grgit.head().id
		// is there a variable for builddir/classes/java/main?
		file("$buildDir/classes/java/main/us/kbase/assemblyhomology/gitcommit").text = commitId
	}
}

compileJava {
	// TODO BUILD remove when we no longer support java 8, use `options.release = 11` if needed
	java.sourceCompatibility = JavaVersion.VERSION_1_8
	java.targetCompatibility = JavaVersion.VERSION_1_8
	finalizedBy buildGitCommitFile
}

test {
	/* 
	 * TODO TEST Figure out why tests fail without this and remove. Might have something to do
	 * with the stfuLoggers() call in many of the tests, might kill logging for tests that
	 * require it
	 * Although it seems to make Mongo start up correctly as well which is odd
	 */
	forkEvery = 1
	/*
	  * TODO TEST split tests into mongo wrapper tests & all other tests (incl. integration).
	  * Set up GHA to run the non-mongo tests with a single version of mongo and run the
	  * mongo tests with matrixed mongo versions. Combine coverage at the end somehow
	*/
	systemProperty "ASSEMHOMOL_TEST_CONFIG", "./test.cfg"
	testLogging {
		exceptionFormat = 'full'
		showStandardStreams = true
	}
	finalizedBy jacocoTestReport
}

// TODO TEST add a test that starts the server in a docker container and checks some simple cmds

jacocoTestReport {
	reports {
		xml.required = true
		csv.required = true
	}
}

javadoc {
	options {
		// I don't know why this isn't working, but it's not worth spending time on right now
		links "https://docs.oracle.com/javase/8/docs/api/"
	}
}

war {
	webXml = file('war/web.xml')
}

configurations {
	// can't directly access testImplementation, so extend and access
	testimpl.extendsFrom testImplementation
}

task generateCLIScript {
	dependsOn compileJava
	doLast {
		def dependencies = configurations.runtimeClasspath.collect { File file ->
			file.absolutePath
		}
	
		def classpath = dependencies.join(':')
	
		def scriptContent = """#!/bin/sh

CLASSPATH=$classpath

java -cp build/classes/java/main:\$CLASSPATH us.kbase.assemblyhomology.cli.AssemblyHomologyCLI \$@
"""

		file("$buildDir/assembly_homology").text = scriptContent
		file("$buildDir/assembly_homology").setExecutable(true)
	}
}

task buildAll {
	dependsOn generateCLIScript
	dependsOn war
	dependsOn javadoc
}

dependencies {

	implementation 'org.ini4j:ini4j:0.5.2'
	implementation 'commons-io:commons-io:2.4'
	implementation 'com.beust:jcommander:1.72'
	implementation 'org.mongodb:mongodb-driver-core:4.11.1'
	implementation 'org.mongodb:mongodb-driver-sync:4.11.1'
	implementation 'org.mongodb:bson-record-codec:4.11.1'
	implementation 'org.mongodb:bson:4.11.1'
	implementation 'com.google.guava:guava:18.0'
	implementation "com.github.kbase:auth2_client_java:0.5.0"
	implementation('com.github.kbase:java_common:0.3.0') {
		exclude group: 'net.java.dev.jna' // breaks mac builds, not needed
		exclude group: 'org.eclipse.jetty.aggregate'  // ugh, java common pollutes everything
		exclude group: 'com.fasterxml.jackson.core'  // breaks everything if we upgrade
		exclude group: 'javax.servlet', module: 'servlet-api'  // 2.5 vs 3.1 below
	}
	implementation('com.github.kbase.workspace_deluxe:workspace-client:0.15.0') {
		exclude group: 'net.java.dev.jna' // breaks mac builds, not needed
		exclude group: 'org.eclipse.jetty.aggregate'  // ugh, java common pollutes everything
		exclude group: 'com.fasterxml.jackson.core'  // breaks everything if we upgrade
		exclude group: 'javax.servlet', module: 'servlet-api'  // 2.5 vs 3.0.1 below
	}
	implementation 'com.github.zafarkhaja:java-semver:0.9.0'
	implementation 'org.yaml:snakeyaml:1.18'
	implementation 'ch.qos.logback:logback-classic:1.1.2'
	implementation 'org.slf4j:slf4j-api:1.7.25'
	// TODO DEPS Need to rework the java common logger to not use syslog4j at all since it's
	// abandonware and has a ton of CVEs, even in the newer versions.
	implementation "org.syslog4j:syslog4j:0.9.46"
	implementation 'com.fasterxml.jackson.core:jackson-annotations:2.5.4'
	implementation 'com.fasterxml.jackson.core:jackson-databind:2.5.4'
	implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.5.4'
	implementation 'org.glassfish.jersey.containers:jersey-container-servlet:2.23.2'
	implementation 'org.glassfish.jersey.media:jersey-media-json-jackson:2.23.2'
	implementation 'javax.servlet:javax.servlet-api:3.0.1'
	implementation 'javax.xml.bind:jaxb-api:2.4.0-b180830.0359'
	
	testImplementation "com.github.kbase:auth2:0.7.1"
	testImplementation 'com.github.kbase.workspace_deluxe:workspace_deluxe-test-shadow-all:0.15.0'
	testImplementation 'nl.jqno.equalsverifier:equalsverifier:3.1.10'
	testImplementation 'junit:junit:4.12'
	testImplementation('org.eclipse.jetty:jetty-servlet:9.3.11.v20160721') {
		exclude group: "javax.servlet", module: "javax.servlet-api" // upgrading breaks tests
	}
	testImplementation 'org.mockito:mockito-core:3.0.0'
	testImplementation 'org.apache.commons:commons-lang3:3.5'
	testImplementation('com.github.kbase:java_test_utilities:0.1.0') {
		exclude group: 'com.fasterxml.jackson.core'  // upgrading breaks stuff
	}
}

task showTestClassPath {
	doLast {
		configurations.testimpl.each { println it }
	}
}