build.gradle

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

plugins {
	id 'java'
	id 'war'
	id 'jacoco'
}

group = 'com.github.kbase'

var VER_JAVA_COMMON = "0.3.0"
var VER_AUTH2_CLIENT = "0.5.0"

var DEFAULT_URL = "https://ci.kbase.us/services/narrative_method_store/rpc"

var LOC_NMS_SPEC = "$rootDir/NarrativeMethodStore.spec"
var LOC_DOC_HTML = "$rootDir/docshtml"

repositories {
	mavenCentral()
	maven {
		name = "Jitpack"
		url = 'https://jitpack.io'
	}
	maven {
		name = "Clojars"
		url = "https://repo.clojars.org/"
	}
}

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
}

javadoc {
	/* We don't actually need the full javadoc for anything, so just hijack this task for
	 * building the client javadocs. If we ever need the full javadocs make a new task for the
	 * client java docs
	 */
	failOnError = false  // fixing this would be a lot of work
	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/"
		links "https://javadoc.jitpack.io/com/github/kbase/auth2_client_java/$VER_AUTH2_CLIENT/javadoc/"
		links "https://javadoc.jitpack.io/com/github/kbase/java_common/$VER_JAVA_COMMON/javadoc/"
	}
	include "**/narrativemethodstore/*.java"
	exclude "**/narrativemethodstore/NarrativeMethodStoreServer.java"
	exclude "**/narrativemethodstore/ImageServlet.java"
	include "**/common/service/Tuple*.java"
}

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
	systemProperty "test.cfg", "./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
	}
}

jar {
	// Much like javadoc, we hijack this task to build the client jar, since we don't need
	// a service jar
	include "us/kbase/narrativemethodstore/*.class"
	exclude "us/kbase/narrativemethodstore/NarrativeMethodStoreServer*.class"  // exclude anonymous classes
	exclude "us/kbase/narrativemethodstore/ImageServlet*.class"  // exclude anonymous classes
	include "us/kbase/common/service/Tuple*.class"
	archiveAppendix = 'client'
}

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

/* SDK compile notes:
 * kb-sdk starts a docker container in interactive mode. Gradle's commandLine doesn't allocate
 * a tty so the command fails.
 * I tried using a ProcessBuilder and
 * https://docs.oracle.com/en%2Fjava%2Fjavase%2F11%2Fdocs%2Fapi%2F%2F/java.base/java/lang/ProcessBuilder.html#inheritIO()
 * but that failed also with no useful output.
 * 
 * The current solution is to precede the kb-sdk call with a script call, which either
 * allocates a tty or fools kb-sdk into thinking there is one - not quite sure.
 * https://man7.org/linux/man-pages/man1/script.1.html
 * I tried to redirect the script log file  to /dev/null with -O and --log-out but script didn't
 * recognize either option, hence the delete.
 *
 * This is, generally speaking, a janky mess and if someone can find a better way to do this
 * that'd be fantastic.
 */
 
 var LOC_SCRIPT_TYPESCRIPT = "$rootDir/typescript"

// TODO GRADLE is there some way to DRY these 3 compile tasks up? Not a huge deal
task sdkCompileHTML {
	// We want to check in the HTML so we don't put it in the build dir
	var cmd = "kb-sdk compile --html --out $LOC_DOC_HTML $LOC_NMS_SPEC"
	doLast {
		exec {
			commandLine "script", "-qefc", cmd
		}
		delete LOC_SCRIPT_TYPESCRIPT
	}
}

task sdkCompileLibs {
	var cmd = "kb-sdk compile " +
				"--out lib " +
				"--jsclname javascript/NarrativeMethodStore/Client " +
				"--plclname Bio::KBase::NarrativeMethodStore::Client " +
				"--pyclname biokbase.narrative_method_store.client " +
				"--url $DEFAULT_URL " + 
				LOC_NMS_SPEC
	doLast {
		exec {
			commandLine "script", "-qefc", cmd
		}
		delete LOC_SCRIPT_TYPESCRIPT
		delete "$rootDir/lib/biokbase/narrative_method_store/authclient.py"
	}
}

task sdkCompileJava {
	// TODO GRADLE is there a variable for src/main/java?
	var cmd = "kb-sdk compile " +
				"--java " +
				"--javasrc $rootDir/src/main/java " +
				"--javasrv " +
				"--out . " +
				"--url $DEFAULT_URL " + 
				LOC_NMS_SPEC
	doLast {
		exec {
			commandLine "script", "-qefc", cmd
		}
		delete LOC_SCRIPT_TYPESCRIPT
	}
}

task sdkCompile {
	dependsOn sdkCompileHTML
	dependsOn sdkCompileJava
	dependsOn sdkCompileLibs
}

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

dependencies {

	implementation("com.github.kbase:auth2_client_java:$VER_AUTH2_CLIENT") {
		exclude group: 'com.fasterxml.jackson.core'  // breaks everything if we upgrade
	}
	implementation("com.github.kbase:java_common:$VER_JAVA_COMMON") {
		exclude group: 'com.fasterxml.jackson.core'  // breaks everything if we upgrade
	}
	implementation 'org.ini4j:ini4j:0.5.2'
	implementation 'com.fasterxml.jackson.core:jackson-annotations:2.2.3'
	implementation 'com.fasterxml.jackson.core:jackson-databind:2.2.3'
	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 'org.yaml:snakeyaml:1.11'
	implementation 'org.apache.velocity:velocity:1.7'
	implementation 'commons-io:commons-io:2.4'
	implementation 'com.google.guava:guava:14.0.1'
	implementation 'javax.annotation:javax.annotation-api:1.2'
	implementation 'javax.servlet:servlet-api:2.5'
	// this is OOOOOOLD. But that probably means updating java_common
	implementation 'org.eclipse.jetty.aggregate:jetty-all:7.0.0.v20091005'

	testImplementation 'junit:junit:4.12'
	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 }
	}
}