fix timeout

Author: Foxcapades

lib/build.gradle.kts

@@ -9,8 +9,6 @@ version = "1.8.4"
 
 
 dependencies {
-  implementation(kotlin("stdlib-jdk8"))
-
   // Logging
   api("org.slf4j:slf4j-api:1.7.36")
 

lib/src/main/kotlin/org/veupathdb/lib/compute/platform/intern/queues/QueueWrapper.kt

@@ -99,9 +99,12 @@ internal class QueueWrapper(conf: AsyncQueueConfig) {
         PlatformJobResultStatus.Failure -> handler.sendError(ErrorNotification(job.jobID, 1))
         PlatformJobResultStatus.Aborted -> { /* Job was aborted, send no notifications. */ }
       }
+    } catch (e: InterruptedException) {
+      Log.error("job execution for ${job.jobID} was interrupted; likely timed out", e)
+      handler.sendError(ErrorNotification(jobID = job.jobID, code = 1, message = e.message ?: "job timed out"))
     } catch (e: Throwable) {
       Log.error("job execution failed with an exception for job ${job.jobID}", e)
       handler.sendError(ErrorNotification(jobID = job.jobID, code = 1, message = e.message))
     }
   }
-}
+}

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

@@ -162,7 +162,9 @@ internal object S3 {
     val sleepMillis = 1000L
     val maxSleeps = 15  // 15 seconds
 
-    var sleepCounter = 0
+    Thread.sleep(sleepMillis)
+
+    var sleepCounter = 1
 
     // while MinIO is still reporting that the object exists, sleep on it.
     while (obj.exists()) {