update dependency

build.gradle.kts

@@ -1,5 +1,5 @@
 plugins {
-  kotlin("jvm") version "1.9.20"
+  kotlin("jvm") version "1.9.23"
 }
 
 allprojects {

lib/build.gradle.kts

@@ -1,8 +1,6 @@
-import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
-
 plugins {
   kotlin("jvm")
-  id("org.jetbrains.dokka") version "1.9.10"
+  id("org.jetbrains.dokka") version "1.9.20"
   java
   `maven-publish`
 }
@@ -15,7 +13,7 @@ dependencies {
   implementation(kotlin("stdlib-jdk8"))
 
   // Logging
-  implementation("org.slf4j:slf4j-api:1.7.36")
+  api("org.slf4j:slf4j-api:1.7.36")
 
   // Jackson
   implementation(platform("com.fasterxml.jackson:jackson-bom:2.16.0"))
@@ -27,8 +25,8 @@ dependencies {
   implementation("org.postgresql:postgresql:42.7.3")
 
   // S3
-  api("org.veupathdb.lib.s3:s34k-minio:0.7.2+s34k-0.11.0")
-  api("org.veupathdb.lib.s3:workspaces:4.1.2")
+  api("org.veupathdb.lib.s3:s34k:0.11.0")
+  api("org.veupathdb.lib.s3:workspaces-java:5.1.0")
 
   // Rabbit
   implementation("org.veupathdb.lib:rabbit-job-queue:2.0.0")

lib/src/main/kotlin/module-info.java

@@ -17,8 +17,8 @@
   requires hash.id;
   requires s34k;
   requires rabbit.job.queue;
-  requires workspaces;
   requires jackson.singleton;
   requires com.github.benmanes.caffeine;
+  requires workspaces.java;
 
 }

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

@@ -1,15 +1,15 @@
 package org.veupathdb.lib.compute.platform.intern.s3
 
 import org.veupathdb.lib.compute.platform.job.JobFileReference
-import org.veupathdb.lib.s3.workspaces.WorkspaceFile
+import org.veupathdb.lib.s3.workspaces.java.WorkspaceFile
 import java.io.InputStream
 
 internal data class JobFileReferenceImpl(private val raw: WorkspaceFile) : JobFileReference {
   override val name: String
     get() = raw.name
 
   override val size: Long
-    get() = raw.size
+    get() = raw.size()
 
   override fun open(): InputStream {
     return raw.open()

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

@@ -10,8 +10,8 @@ import org.veupathdb.lib.s3.s34k.S3Api
 import org.veupathdb.lib.s3.s34k.S3Client
 import org.veupathdb.lib.s3.s34k.S3Config
 import org.veupathdb.lib.s3.s34k.fields.BucketName
-import org.veupathdb.lib.s3.workspaces.S3Workspace
-import org.veupathdb.lib.s3.workspaces.S3WorkspaceFactory
+import org.veupathdb.lib.s3.workspaces.java.S3Workspace
+import org.veupathdb.lib.s3.workspaces.java.S3WorkspaceFactory
 import java.io.File
 import java.io.InputStream
 import java.nio.file.Path
@@ -74,7 +74,7 @@ internal object S3 {
   @JvmStatic
   fun getJob(jobID: HashID): AsyncS3Job? {
     Log.debug("Fetching workspace {} from S3", jobID)
-    return wsf[jobID]?.let(::XS3Workspace)?.let(::AsyncS3Job)
+    return wsf.get(jobID)?.let(::XS3Workspace)?.let(::AsyncS3Job)
   }
 
 
@@ -89,7 +89,7 @@ internal object S3 {
   fun persistFiles(jobID: HashID, files: List<Path>) {
     Log.debug("persisting {} files to workspace {} in S3", files.size, jobID)
 
-    val ws = wsf[jobID] ?: throw IllegalStateException("Attempted to write result files to nonexistent workspace $jobID")
+    val ws = wsf.get(jobID) ?: throw IllegalStateException("Attempted to write result files to nonexistent workspace $jobID")
 
     files.forEach {
       persistFile(ws, it.toFile())
@@ -120,7 +120,7 @@ internal object S3 {
   @JvmOverloads
   fun deleteWorkspace(jobID: HashID, throwOnNotExists: Boolean = true) {
     Log.info("Deleting workspace with ID {}.", jobID)
-    val ws = wsf[jobID]
+    val ws = wsf.get(jobID)
 
     if (ws == null && throwOnNotExists) {
       throw IllegalStateException("Attempted to delete nonexistent workspace $jobID")
@@ -168,7 +168,7 @@ internal object S3 {
     Log.debug("Fetching result files from workspace {} in S3", jobID)
 
     // Load the workspace
-    val ws = wsf[jobID] ?: throw IllegalStateException("Attempted to lookup result files from nonexistent workspace $jobID")
+    val ws = wsf.get(jobID) ?: throw IllegalStateException("Attempted to lookup result files from nonexistent workspace $jobID")
 
     // Fetch the list of files from the workspace
     val files = ws.files()
@@ -208,7 +208,7 @@ internal object S3 {
     Log.debug("fetching target file \"{}\" for job {} in S3", fileName, jobID)
 
     // Load the workspace
-    val ws = wsf[jobID] ?: throw IllegalStateException("attempted to fetch target file from nonexistent workspace $jobID")
+    val ws = wsf.get(jobID) ?: throw IllegalStateException("attempted to fetch target file from nonexistent workspace $jobID")
 
     // Sift through the files for one matching the target file name and return
     // it (or null if none were found).
@@ -232,7 +232,7 @@ internal object S3 {
     Log.debug("Expiring workspace for job {} in S3", jobID)
 
     // Load the workspace
-    val ws = wsf[jobID] ?: throw IllegalStateException("Attempted to expire nonexistent workspace $jobID")
+    val ws = wsf.get(jobID) ?: throw IllegalStateException("Attempted to expire nonexistent workspace $jobID")
 
     // Iterate through the files in the workspace
     ws.files().forEach {
@@ -288,28 +288,28 @@ internal object S3 {
   fun markWorkspaceAsInProgress(jobID: HashID) {
     Log.debug("marking workspace for job {} as in-progress in s3", jobID)
 
-    val ws = wsf[jobID] ?: throw IllegalStateException("Attempted to mark nonexistent workspace $jobID as in-progress")
+    val ws = wsf.get(jobID) ?: throw IllegalStateException("Attempted to mark nonexistent workspace $jobID as in-progress")
     ws.touch(FlagInProgress)
   }
 
   fun markWorkspaceAsQueued(jobID: HashID) {
     Log.debug("marking workspace for job {} as queued in S3", jobID)
 
-    val ws = wsf[jobID] ?: throw IllegalStateException("Attempted to mark nonexistent workspace $jobID as queued")
+    val ws = wsf.get(jobID) ?: throw IllegalStateException("Attempted to mark nonexistent workspace $jobID as queued")
     ws.touch(FlagQueued)
   }
 
   fun markWorkspaceAsFailed(jobID: HashID) {
     Log.debug("marking workspace for job {} as failed in s3", jobID)
 
-    val ws = wsf[jobID] ?: throw IllegalStateException("Attempted to mark nonexistent workspace $jobID as failed")
+    val ws = wsf.get(jobID) ?: throw IllegalStateException("Attempted to mark nonexistent workspace $jobID as failed")
     ws.touch(FlagFailed)
   }
 
   fun markWorkspaceAsComplete(jobID: HashID) {
     Log.debug("marking workspace for job {} as complete in s3", jobID)
 
-    val ws = wsf[jobID] ?: throw IllegalStateException("Attempted to mark nonexistent workspace $jobID as complete")
+    val ws = wsf.get(jobID) ?: throw IllegalStateException("Attempted to mark nonexistent workspace $jobID as complete")
     ws.touch(FlagComplete)
   }
 

lib/src/main/kotlin/org/veupathdb/lib/compute/platform/intern/s3/XS3Workspace.kt

@@ -5,7 +5,7 @@ import org.veupathdb.lib.compute.platform.intern.*
 import org.veupathdb.lib.compute.platform.job.JobStatus
 import org.veupathdb.lib.jackson.Json
 import org.veupathdb.lib.s3.s34k.errors.S34KError
-import org.veupathdb.lib.s3.workspaces.S3Workspace
+import org.veupathdb.lib.s3.workspaces.java.S3Workspace
 
 /**
  * Extended S3 Workspace

test/build.gradle.kts

@@ -6,7 +6,7 @@ plugins {
 dependencies {
   implementation(project(":compute-platform"))
 
-  implementation("org.slf4j:slf4j-api:1.7.36")
+  implementation("org.veupathdb.lib.s3:s34k-minio:0.7.2+s34k-0.11.0")
   implementation("org.apache.logging.log4j:log4j-core:2.19.0")
   runtimeOnly("org.apache.logging.log4j:log4j-slf4j-impl:2.19.0")
 }