add test module

.gitignore

@@ -1,3 +1,5 @@
 .gradle/
 .idea/
-/build/
+/build/
+/lib/build/
+/test/build/

build.gradle.kts

@@ -1,127 +1,18 @@
-import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
-
 plugins {
   kotlin("jvm") version "1.8.0"
-  id("org.jetbrains.dokka") version "1.7.20"
-  java
-  `maven-publish`
-}
-
-group = "org.veupathdb.lib"
-version = "1.3.6"
-
-repositories {
-  mavenLocal()
-  mavenCentral()
-  maven {
-    name = "GitHubPackages"
-    url  = uri("https://maven.pkg.github.com/veupathdb/maven-packages")
-    credentials {
-      username = if (extra.has("gpr.user")) extra["gpr.user"] as String? else System.getenv("GITHUB_USERNAME")
-      password = if (extra.has("gpr.key")) extra["gpr.key"] as String? else System.getenv("GITHUB_TOKEN")
-    }
-  }
-}
-
-dependencies {
-
-  // Logging
-  implementation("org.slf4j:slf4j-api:1.7.36")
-
-  // Jackson
-  implementation(platform("com.fasterxml.jackson:jackson-bom:2.14.2"))
-  implementation("com.fasterxml.jackson.core:jackson-databind")
-  implementation("org.veupathdb.lib:jackson-singleton:3.0.0")
-
-  // DB
-  implementation("com.zaxxer:HikariCP:5.0.1")
-  implementation("org.postgresql:postgresql:42.5.1")
-
-  // S3
-  implementation("org.veupathdb.lib.s3:s34k-minio:0.4.0+s34k-0.8.0")
-  implementation("org.veupathdb.lib.s3:workspaces:4.1.0")
-
-  // Rabbit
-  implementation("org.veupathdb.lib:rabbit-job-queue:1.2.0")
-
-  // Metrics
-  implementation("io.prometheus:simpleclient:0.16.0")
-  implementation("io.prometheus:simpleclient_common:0.16.0")
-
-  // Misc & Utils
-  api("org.veupathdb.lib:hash-id:1.0.2")
-
-  // Testing
-  testImplementation(kotlin("test"))
-}
-
-tasks.test {
-  useJUnitPlatform()
 }
 
-tasks.withType<KotlinCompile> {
-  kotlinOptions.jvmTarget = "17"
-}
-
-java {
-  sourceCompatibility = JavaVersion.VERSION_17
-  targetCompatibility = JavaVersion.VERSION_17
-
-  withJavadocJar()
-  withSourcesJar()
-}
-
-tasks.javadoc {
-  // This is required to generate the javadoc jar when publishing a release.
-  exclude("module-info.java")
-}
-
-tasks.dokkaHtml {
-  outputDirectory.set(file("build/docs/dokka"))
-}
-
-tasks.dokkaJavadoc {
-  outputDirectory.set(file("build/docs/javadoc"))
-}
-
-task("docs") {
-  dependsOn("dokkaHtml", "dokkaJavadoc")
-}
-
-publishing {
+allprojects {
   repositories {
+    mavenLocal()
+    mavenCentral()
     maven {
-      name = "GitHub"
-      url = uri("https://maven.pkg.github.com/VEuPathDB/lib-compute-platform")
+      name = "GitHubPackages"
+      url  = uri("https://maven.pkg.github.com/veupathdb/maven-packages")
       credentials {
-        username = project.findProperty("gpr.user") as String? ?: System.getenv("USERNAME")
-        password = project.findProperty("gpr.key") as String? ?: System.getenv("TOKEN")
+        username = if (extra.has("gpr.user")) extra["gpr.user"] as String? else System.getenv("GITHUB_USERNAME")
+        password = if (extra.has("gpr.key")) extra["gpr.key"] as String? else System.getenv("GITHUB_TOKEN")
       }
     }
   }
-
-  publications {
-    create<MavenPublication>("gpr") {
-      from(components["java"])
-      pom {
-        name.set("S3 Workspaces")
-        description.set("Workspaces backed by an S3 object store.")
-        url.set("https://github.com/VEuPathDB/lib-compute-platform")
-        developers {
-          developer {
-            id.set("epharper")
-            name.set("Elizabeth Paige Harper")
-            email.set("epharper@upenn.edu")
-            url.set("https://github.com/foxcapades")
-            organization.set("VEuPathDB")
-          }
-        }
-        scm {
-          connection.set("scm:git:git://github.com/VEuPathDB/lib-compute-platform.git")
-          developerConnection.set("scm:git:ssh://github.com/VEuPathDB/lib-compute-platform.git")
-          url.set("https://github.com/VEuPathDB/lib-compute-platform")
-        }
-      }
-    }
-  }
-}
+}

lib/build.gradle.kts

@@ -0,0 +1,112 @@
+import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
+
+plugins {
+  kotlin("jvm")
+  id("org.jetbrains.dokka") version "1.7.20"
+  java
+  `maven-publish`
+}
+
+group = "org.veupathdb.lib"
+version = "1.3.6"
+
+
+dependencies {
+
+  // Logging
+  implementation("org.slf4j:slf4j-api:1.7.36")
+
+  // Jackson
+  implementation(platform("com.fasterxml.jackson:jackson-bom:2.14.2"))
+  implementation("com.fasterxml.jackson.core:jackson-databind")
+  implementation("org.veupathdb.lib:jackson-singleton:3.0.0")
+
+  // DB
+  implementation("com.zaxxer:HikariCP:5.0.1")
+  implementation("org.postgresql:postgresql:42.5.1")
+
+  // S3
+  implementation("org.veupathdb.lib.s3:s34k-minio:0.4.1+s34k-0.8.0")
+  implementation("org.veupathdb.lib.s3:workspaces:4.1.1")
+
+  // Rabbit
+  implementation("org.veupathdb.lib:rabbit-job-queue:1.2.0")
+
+  // Metrics
+  implementation("io.prometheus:simpleclient:0.16.0")
+  implementation("io.prometheus:simpleclient_common:0.16.0")
+
+  // Misc & Utils
+  api("org.veupathdb.lib:hash-id:1.0.2")
+
+  // Testing
+  testImplementation(kotlin("test"))
+}
+
+tasks.test {
+  useJUnitPlatform()
+}
+
+kotlin {
+  jvmToolchain(17)
+}
+
+java {
+  withJavadocJar()
+  withSourcesJar()
+}
+
+tasks.javadoc {
+  // This is required to generate the javadoc jar when publishing a release.
+  exclude("module-info.java")
+}
+
+tasks.dokkaHtml {
+  outputDirectory.set(file("build/docs/dokka"))
+}
+
+tasks.dokkaJavadoc {
+  outputDirectory.set(file("build/docs/javadoc"))
+}
+
+task("docs") {
+  dependsOn("dokkaHtml", "dokkaJavadoc")
+}
+
+publishing {
+  repositories {
+    maven {
+      name = "GitHub"
+      url = uri("https://maven.pkg.github.com/VEuPathDB/lib-compute-platform")
+      credentials {
+        username = project.findProperty("gpr.user") as String? ?: System.getenv("USERNAME")
+        password = project.findProperty("gpr.key") as String? ?: System.getenv("TOKEN")
+      }
+    }
+  }
+
+  publications {
+    create<MavenPublication>("gpr") {
+      from(components["java"])
+      pom {
+        name.set("S3 Workspaces")
+        description.set("Workspaces backed by an S3 object store.")
+        url.set("https://github.com/VEuPathDB/lib-compute-platform")
+        developers {
+          developer {
+            id.set("epharper")
+            name.set("Elizabeth Paige Harper")
+            email.set("epharper@upenn.edu")
+            url.set("https://github.com/foxcapades")
+            organization.set("VEuPathDB")
+          }
+        }
+        scm {
+          connection.set("scm:git:git://github.com/VEuPathDB/lib-compute-platform.git")
+          developerConnection.set("scm:git:ssh://github.com/VEuPathDB/lib-compute-platform.git")
+          url.set("https://github.com/VEuPathDB/lib-compute-platform")
+        }
+      }
+    }
+  }
+}

src/main/kotlin/org/veupathdb/lib/compute/platform/intern/db/DatabaseMigrator.kt → lib/src/main/kotlin/org/veupathdb/lib/compute/platform/intern/db/DatabaseMigrator.kt

@@ -2,6 +2,8 @@ package org.veupathdb.lib.compute.platform.intern.db
 
 import org.slf4j.LoggerFactory
 import java.util.zip.ZipInputStream
+import kotlin.io.path.isRegularFile
+import kotlin.io.path.toPath
 
 private const val MigrationPath = "db/migrations/"
 
@@ -27,7 +29,7 @@ internal class DatabaseMigrator : Runnable {
     Log.debug("Found {} migrations", migs.size)
 
     if (migs.isNotEmpty()) {
-      QueueDB.ds!!.connection.use { con ->
+      QueueDB.ds.connection.use { con ->
         migs.forEach {
           Log.info("Executing database migration script: {}", it)
           con.createStatement().use { stmt -> stmt.execute(loadSQL(it)) }
@@ -37,6 +39,8 @@ internal class DatabaseMigrator : Runnable {
   }
 
   private fun listMigrations(version: String): List<String> {
+    Log.trace("listMigrations(version={})", version)
+
     val jarStream  = ZipInputStream(thisJar.openStream())
     val migrations = ArrayList<String>(10)
 
@@ -49,6 +53,8 @@ internal class DatabaseMigrator : Runnable {
       if (migVersion(entry) <= version)
         continue
 
+      Log.debug("found migration entry {}", entry)
+
       migrations.add(entry)
     }
 

src/main/kotlin/org/veupathdb/lib/compute/platform/intern/db/queries/select/list-all-jobs.kt → lib/src/main/kotlin/org/veupathdb/lib/compute/platform/intern/db/queries/select/list-all-jobs.kt

@@ -6,12 +6,14 @@ import java.sql.Connection
 import java.sql.ResultSet
 import java.util.stream.Stream
 
+// language=postgresql
 private const val SQL = """
   SELECT
     job_id
   , status
   , queue
   , config
+  , input_files
   , created
   , last_accessed
   , grabbed

src/main/kotlin/org/veupathdb/lib/compute/platform/intern/db/queries/select/list-queued-jobs.kt → lib/src/main/kotlin/org/veupathdb/lib/compute/platform/intern/db/queries/select/list-queued-jobs.kt

@@ -12,6 +12,7 @@ private const val SQL = """
   , status
   , queue
   , config
+  , input_files
   , created
   , last_accessed
   , grabbed

src/main/kotlin/org/veupathdb/lib/compute/platform/intern/s3/S3.kt → lib/src/main/kotlin/org/veupathdb/lib/compute/platform/intern/s3/S3.kt

@@ -286,10 +286,20 @@ internal object S3 {
   fun listJobIDs(): Sequence<HashID> {
     return s3.buckets[BucketName(config.bucket)]!!
       .objects
-      .listSubPaths(config.rootPath)
+      .listSubPaths(config.rootPath.appendSlash())
       .commonPrefixes()
       .asSequence()
+      .map { it.getJobID() }
       .map { try { HashID(it) } catch (e: Throwable) { null } }
       .filterNotNull()
   }
+
+  private fun String.appendSlash() =
+    if (!endsWith('/'))
+      "$this/"
+    else
+      this
+
+  private fun String.getJobID() =
+    substring(lastIndexOf('/', length - 2) + 1, length - 1)
 }

makefile

@@ -17,3 +17,7 @@ publish-local:
 .PHONY: docs
 docs:
 	@gradle docs
+
+run-test:
+	@./gradlew :test:shadowJar
+	@java -jar test/build/libs/test.jar

settings.gradle.kts

@@ -1,3 +1,7 @@
-
 rootProject.name = "compute-platform"
 
+include(":lib")
+project(":lib").name = "compute-platform"
+
+include(":test")
+project(":test").name = "test"

test/build.gradle.kts

@@ -0,0 +1,20 @@
+plugins {
+  kotlin("jvm")
+  id("com.github.johnrengelman.shadow") version "7.1.2"
+}
+
+dependencies {
+  implementation(project(":compute-platform"))
+
+  implementation("org.slf4j:slf4j-api:1.7.36")
+  implementation("org.apache.logging.log4j:log4j-core:2.19.0")
+  runtimeOnly("org.apache.logging.log4j:log4j-slf4j-impl:2.19.0")
+}
+
+tasks.shadowJar {
+  archiveFileName.set("test.jar")
+
+  manifest {
+    attributes["Main-Class"] = "lcp.MainKt"
+  }
+}