fix issue with path - need refinement

henriqueribeiro · Jun 3, 2024 · aff0349 · aff0349
1 parent e0c9474
commit aff0349
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Showing 2 changed files with 17 additions and 14 deletions.
diff --git a/.../aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala b/.../aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala
@@ -428,12 +428,14 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     val wfid = standardParams.jobDescriptor.toString.split(":")(0)
     val globName = GlobFunctions.globName(s"${womFile.value}-${wfid}")
     val globbedDir = Paths.get(womFile.value).getParent match {
-      case path: Path => path.toString
-      case _ => "./"
+      // remove ./ so it does not appear on s3 path
+      case path: Path => path.toString.stripPrefix("./")
+      case _ => ""
     }
     // generalize folder and list file
-    val globDirectory = DefaultPathBuilder.get(globbedDir + "/." + globName + "/")
-    val globListFile = DefaultPathBuilder.get(globbedDir + "/." + globName + ".list")
+    val globDirPrefix = s"${globbedDir}/.${globName}".stripPrefix("/");
+    val globDirectory = DefaultPathBuilder.get(globDirPrefix + "/")
+    val globListFile = DefaultPathBuilder.get(globDirPrefix +  ".list")
 
     // locate the disk where the globbed data resides
     val (_, globDirectoryDisk) = relativePathAndVolume(womFile.value, runtimeAttributes.disks)
@@ -461,14 +463,14 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
   private def generateAwsBatchGlobFileOutputs(womFile: WomGlobFile): List[AwsBatchFileOutput] = {
 
     val (globName, globbedDir, globDirectoryDisk, globDirectoryDestinationPath, globListFileDestinationPath) = generateGlobPaths(womFile)
-    val (relpathDir,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + "/" + "*").toString,runtimeAttributes.disks)
-    val (relpathList,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + ".list").toString,runtimeAttributes.disks)
+    val (relpathDir,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + "/" + "*").toString.stripPrefix("/"),runtimeAttributes.disks)
+    val (relpathList,_) = relativePathAndVolume(DefaultPathBuilder.get(globbedDir + "/." + globName + ".list").toString.stripPrefix("/"),runtimeAttributes.disks)
     // We need both the glob directory and the glob list:
     List(
       // The glob directory:.
-      AwsBatchFileOutput(DefaultPathBuilder.get(globbedDir.toString + "/." + globName + "/" + "*").toString,globDirectoryDestinationPath, relpathDir, globDirectoryDisk),
+      AwsBatchFileOutput(DefaultPathBuilder.get(globbedDir.toString + "/." + globName + "/" + "*").toString.stripPrefix("/"),globDirectoryDestinationPath, relpathDir, globDirectoryDisk),
       // The glob list file:
-      AwsBatchFileOutput(DefaultPathBuilder.get(globbedDir.toString + "/." + globName + ".list").toString, globListFileDestinationPath, relpathList, globDirectoryDisk)
+      AwsBatchFileOutput(DefaultPathBuilder.get(globbedDir.toString + "/." + globName + ".list").toString.stripPrefix("/"), globListFileDestinationPath, relpathList, globDirectoryDisk)
     )
   }
 
@@ -865,8 +867,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     val (globName, globbedDir, _, _, _) = generateGlobPaths(globFile) 
     val controlFileName = "cromwell_glob_control_file"
     val absoluteGlobValue = commandDirectory.resolve(globFile.value).pathAsString
-    val globDirectory = globbedDir + "/." + globName + "/"
-    val globList = globbedDir + "/." + globName + ".list"
+    val globDirectory = (globbedDir + "/." + globName + "/").stripPrefix("/")
+    val globList = (globbedDir + "/." + globName + ".list").stripPrefix("/")
     val globLinkCommand: String = (if (configuration.globLinkCommand.isDefined) {
        "( " + configuration.globLinkCommand.getOrElse("").toString + " )"
 

diff --git a/...ortedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala b/...ortedBackends/aws/src/main/scala/cromwell/backend/impl/aws/io/AwsBatchGlobFunctions.scala
@@ -69,8 +69,9 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
     val wfid = callContext.root.toString.split("/").toList.filter(element => wfid_regex.pattern.matcher(element).matches()).lastOption.getOrElse("")
     val globPatternName = globName(s"${pattern}-${wfid}")
     val globbedDir = Paths.get(pattern).getParent match {
-      case x: Path => x.toString
-      case _  => "./"
+      // remove "./" to avoid it from appearing in s3 path
+      case x: Path => x.toString.stripPrefix("./")
+      case _  => ""
     }
     val listFilePath = if (pattern.startsWith("/mnt/efs/")) {
         DefaultPathBuilder.get(globbedDir + "/." + globPatternName + ".list")
@@ -81,9 +82,9 @@ trait AwsBatchGlobFunctions extends GlobFunctions {
       lines.toList map { fileName =>
         // again : this should be config based...
         if (pattern.startsWith("/mnt/efs/")) {
-            s"${globbedDir}/.${globPatternName}/${fileName}"
+            s"${globbedDir}/.${globPatternName}/${fileName}".stripPrefix("/")
         } else {
-            callContext.root.resolve(s"${globbedDir}/.${globPatternName}/${fileName}".stripPrefix("/")).pathAsString
+            callContext.root.resolve(s"${globbedDir}/.${globPatternName}/${fileName}".stripPrefix("/")).pathAsString.stripPrefix("/")
         }
       }
     }