update build/test dependencies

build.gradle.kts

@@ -1,8 +1,13 @@
 import com.jfrog.bintray.gradle.BintrayExtension
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
+import org.gradle.kotlin.dsl.registering
+import org.gradle.api.tasks.bundling.Jar
+import org.gradle.api.publish.maven.MavenPublication
+import org.gradle.kotlin.dsl.create
+import org.gradle.kotlin.dsl.get
 
 plugins {
-    kotlin("jvm") version "1.3.41"
+    kotlin("jvm") version "1.7.0"
     id("maven-publish")
     id("com.jfrog.bintray") version "1.8.1"
 }
@@ -11,35 +16,35 @@ group = "io.krews"
 version = "0.14.0"
 
 repositories {
-    maven { setUrl("http://dl.bintray.com/kotlin/kotlin-eap") }
+    maven { setUrl("https://dl.bintray.com/kotlin/kotlin-eap") }
     mavenCentral()
     jcenter()
 }
 
 dependencies {
-    compile(kotlin("stdlib-jdk8"))
-    compile(kotlin("reflect"))
-    compile("io.github.microutils","kotlin-logging","1.6.10")
-    compile("ch.qos.logback", "logback-classic","1.2.3")
-    compile("io.projectreactor", "reactor-core", "3.2.6.RELEASE")
-    compile("com.github.docker-java", "docker-java", "3.1.5")
+    implementation(kotlin("stdlib-jdk8"))
+    implementation(kotlin("reflect"))
+    implementation("io.github.microutils","kotlin-logging","1.6.10")
+    implementation("ch.qos.logback", "logback-classic","1.2.3")
+    implementation("io.projectreactor", "reactor-core", "3.2.6.RELEASE")
+    implementation("com.github.docker-java", "docker-java", "3.3.0")
     // This one is needed to fix a warning from docker-java
-    compile("javax.activation", "activation", "1.1.1")
-    compile( "org.apache.commons", "commons-lang3", "3.8.1")
-    compile("com.typesafe", "config", "1.2.1")
-    compile("com.fasterxml.jackson.module", "jackson-module-kotlin", "2.9.7")
-    compile("org.jetbrains.exposed", "exposed", "0.10.5")
-    compile("org.xerial", "sqlite-jdbc", "3.25.2")
-    compile("org.flywaydb", "flyway-core", "5.2.0")
-    compile("com.zaxxer", "HikariCP", "3.1.0")
-    compile("com.google.apis", "google-api-services-lifesciences", "v2beta-rev20200220-1.30.9")
-    compile("com.google.apis", "google-api-services-storage", "v1-rev20200326-1.30.9")
-    compile("com.google.auth", "google-auth-library-oauth2-http", "0.20.0")
-    compile("com.github.ajalt","clikt", "1.5.0")
-    compile( "org.jetbrains.kotlinx", "kotlinx-html-jvm", "0.6.11")
-    compile( "org.jetbrains.kotlinx", "kotlinx-coroutines-core", "1.1.1")
+    implementation("javax.activation", "activation", "1.1.1")
+    implementation( "org.apache.commons", "commons-lang3", "3.8.1")
+    implementation("com.typesafe", "config", "1.2.1")
+    implementation("com.fasterxml.jackson.module", "jackson-module-kotlin", "2.9.7")
+    implementation("org.jetbrains.exposed", "exposed", "0.10.5")
+    implementation("org.xerial", "sqlite-jdbc", "3.25.2")
+    implementation("org.flywaydb", "flyway-core", "5.2.0")
+    implementation("com.zaxxer", "HikariCP", "3.1.0")
+    implementation("com.google.apis", "google-api-services-lifesciences", "v2beta-rev20200220-1.30.9")
+    implementation("com.google.apis", "google-api-services-storage", "v1-rev20200326-1.30.9")
+    implementation("com.google.auth", "google-auth-library-oauth2-http", "0.20.0")
+    implementation("com.github.ajalt","clikt", "1.5.0")
+    implementation( "org.jetbrains.kotlinx", "kotlinx-html-jvm", "0.6.11")
+    implementation( "org.jetbrains.kotlinx", "kotlinx-coroutines-core", "1.1.1")
     testImplementation("org.junit.jupiter", "junit-jupiter", "5.4.0")
-    testCompile("org.assertj", "assertj-core", "3.11.1")
+    testImplementation("org.assertj", "assertj-core", "3.11.1")
     testImplementation("io.mockk", "mockk", "1.9.3")
 }
 
@@ -54,28 +59,28 @@ tasks.withType<KotlinCompile> {
     kotlinOptions.jvmTarget = "1.8"
 }
 
-val sourcesJar by tasks.creating(Jar::class) {
-    classifier = "sources"
-    from(java.sourceSets["main"].allSource)
+val sourcesJar = tasks.register<Jar>("sourcesJar") {
+    archiveClassifier.set("sources")
+    from(sourceSets["main"].allSource)
 }
 
 val publicationName = "krews"
 publishing {
-    publications.invoke {
-        publicationName(MavenPublication::class) {
+    publications {
+        create<MavenPublication>(publicationName) {
             from(components["java"])
-            artifact(sourcesJar)
+            artifact(sourcesJar.get())
         }
     }
     repositories {
         maven {
-	    name = "GitHubPackages"
-	    url = uri("https://maven.pkg.github.com/weng-lab/krews")
-	    credentials {
+            name = "GitHubPackages"
+            url = uri("https://maven.pkg.github.com/weng-lab/krews")
+            credentials {
                 username = System.getenv("GITHUB_ACTOR")
-		password = System.getenv("GITHUB_TOKEN")
+                password = System.getenv("GITHUB_TOKEN")
             }
-	}
+        }
     }
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,5 @@
-#Thu Mar 14 15:32:43 EDT 2019
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.8-all.zip

src/main/kotlin/krews/config/BaseConfig.kt

@@ -7,6 +7,8 @@ data class TaskConfig (
     val google: GoogleTaskConfig? = null,
     // Task level Slurm executor configuration
     val slurm: SlurmTaskConfig? = null,
+    // Task level Slurm executor configuration
+    val bsub: SlurmTaskConfig? = null,
     // The maximum allowed parallelism for this task
     val parallelism: Parallelism = UnlimitedParallelism,
     // The number of tasks "executions" that will be run with the same job / vm.
@@ -26,6 +28,8 @@ data class WorkflowConfig (
     val google: GoogleWorkflowConfig? = null,
     // Slurm executor configuration
     val slurm: SlurmWorkflowConfig? = null,
+    // BSUB executor configuration
+    val bsub: SlurmWorkflowConfig? = null,
     // The maximum allowed parallelism for the system as a whole. Also see per-task parallelism
     val parallelism: Parallelism = UnlimitedParallelism,
     // The concurrency for task setup, status checking, and cleanup

src/main/kotlin/krews/config/BsubConfig.kt

@@ -0,0 +1,24 @@
+package krews.config
+
+import krews.core.Capacity
+
+data class BsubWorkflowConfig(
+    // Interval in seconds between checks for pipeline job completion
+    val jobCompletionPollInterval: Int = 10,
+    // Optional ssh configuration. Will cause all slurm command to be passed through ssh.
+    // Only available for password-less login.
+    val ssh: SshConfig? = null
+)
+
+data class BsubTaskConfig(
+    // Number of cpus. Can be used to override the runtime value.
+    val cpus: Int? = null,
+    // Memory capacity. Can be used to override the runtime value.
+    val mem: Capacity? = null,
+    // Time limit on the run time for the job in minutes.
+    val time: Int? = null,
+    // SBatch partition to use.
+    val partition: String? = null,
+    // Additional sbatch arguments
+    val sbatchArgs: Map<String, String>? = null
+)

src/main/kotlin/krews/config/ConfigUtils.kt

@@ -144,7 +144,7 @@ fun createTaskConfigs(rawTaskConfigs: Map<String, Map<String, Any>>, tasks: Coll
  * "MySampleValue_te5t test*&test" should become "mysamplevalue-te5t-test--test"
  */
 private fun kebabify(value: String): String {
-    return Regex("[^a-z0-9]").replace(value.toLowerCase(), "-")
+    return Regex("[^a-z0-9]").replace(value.lowercase(), "-")
 }
 
 /**

src/main/kotlin/krews/config/Parallelism.kt

@@ -21,7 +21,7 @@ class ParallelismDeserializer : StdDeserializer<Parallelism>(Parallelism::class.
     override fun deserialize(p: JsonParser, ctxt: DeserializationContext): Parallelism {
         val mapper = p.codec as ObjectMapper
         val obj = mapper.readTree<TreeNode>(p) as JsonNode
-        if (obj.nodeType == JsonNodeType.STRING && obj.asText().toLowerCase() == "unlimited") return UnlimitedParallelism
+        if (obj.nodeType == JsonNodeType.STRING && obj.asText().lowercase() == "unlimited") return UnlimitedParallelism
         if (obj.nodeType == JsonNodeType.NUMBER) return LimitedParallelism(obj.asInt())
         throw JsonMappingException(p, "Invalid parallelism. Must be either a number or \"unlimited\"")
     }

src/main/kotlin/krews/config/SlurmConfig.kt

@@ -27,4 +27,4 @@ data class SlurmTaskConfig(
     val partition: String? = null,
     // Additional sbatch arguments
     val sbatchArgs: Map<String, String>? = null
-)
+)

src/main/kotlin/krews/core/Capacity.kt

@@ -41,7 +41,7 @@ val Number.TB: Capacity get() = Capacity(this, CapacityType.TB)
 
 internal fun stringToCapacity(str: String): Capacity {
     val regex = """(\d+)\s*([KMGT]?B)""".toRegex()
-    val matchResult = regex.find(str.toUpperCase())
+    val matchResult = regex.find(str.uppercase())
     val (value, type) = matchResult!!.destructured
     return Capacity(value.toDouble(), CapacityType.valueOf(type))
 }

src/main/kotlin/krews/executor/bsub/BsubExecutor.kt

@@ -85,7 +85,7 @@ class BsubExecutor(private val workflowConfig: WorkflowConfig) : LocallyDirected
         appendBsubParam(bsubScript, "W", time)
         appendBsubParam(bsubScript, "q", taskConfig.bsub?.partition)
         for ((argName, argVal) in taskConfig.bsub?.sbatchArgs ?: mapOf()) {
-            appendSbatchParam(bsubScript, argName, argVal)
+            appendBsubParam(bsubScript, argName, argVal)
         }
 
         bsubScript.append("\n")
@@ -235,7 +235,7 @@ class BsubExecutor(private val workflowConfig: WorkflowConfig) : LocallyDirected
         delay(kotlin.random.Random.nextLong(0, 5000))
 
         val bsubCommand = "echo $bsubScriptAsBase64 | base64 --decode | bsub"
-        val bsubResponse = commandExecutor.exec(bsubScript)
+        val bsubResponse = commandExecutor.exec(bsubCommand)
         val jobId = "\\d+\$".toRegex().find(bsubResponse)?.value
             ?: throw Exception("JobID not found in response for bsub command")
 

src/main/kotlin/krews/executor/google/GoogleLocalExecutor.kt

@@ -75,15 +75,15 @@ class GoogleLocalExecutor(workflowConfig: WorkflowConfig) : LocallyDirectedExecu
         val maxMemory = taskRunContexts.map { it.memory }.maxBy { it?.bytes ?: -1 } ?: taskConfig.google?.mem
         virtualMachine.machineType = googleMachineType(taskConfig.google, maxCpus, maxMemory)
         if (taskConfig.google?.bootDiskSizeGb != null)
-            virtualMachine.setBootDiskSizeGb(taskConfig.google?.bootDiskSizeGb)
+            virtualMachine.setBootDiskSizeGb(taskConfig.google.bootDiskSizeGb)
 
         if (taskConfig.google?.gpus != null) {
             val acceleratorConfig = Accelerator()
-            acceleratorConfig.type = taskConfig.google?.gpus!!.gpuType
-            acceleratorConfig.count = taskConfig.google?.gpus!!.gpuCount
+            acceleratorConfig.type = taskConfig.google.gpus.gpuType
+            acceleratorConfig.count = taskConfig.google.gpus.gpuCount
             virtualMachine.accelerators = listOf(acceleratorConfig)
-            if (taskConfig.google?.gpus!!.bootImage != null)
-                virtualMachine.bootImage = taskConfig.google?.gpus!!.bootImage
+            if (taskConfig.google.gpus.bootImage != null)
+                virtualMachine.bootImage = taskConfig.google.gpus.bootImage
         }
 
         val serviceAccount = ServiceAccount()