WX-1015 Override glob behavior for TES to use absolute path (#7120)

broadinstitute · Apr 18, 2023 · b568fac · b568fac
1 parent 037f1d0
commit b568fac
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Showing 3 changed files with 12 additions and 4 deletions.
diff --git a/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala b/backend/src/main/scala/cromwell/backend/io/GlobFunctions.scala
@@ -38,7 +38,7 @@ trait GlobFunctions extends IoFunctionSet with AsyncIoFunctions {
     import GlobFunctions._
     val globPatternName = globName(pattern)
     val listFilePath = callContext.root.resolve(s"${globName(pattern)}.list")
-    asyncIo.readLinesAsync(listFilePath.toRealPath()) map { lines =>
+    asyncIo.readLinesAsync(listFilePath.getSymlinkSafePath()) map { lines =>
       lines.toList map { fileName =>
         (callContext.root /  globPatternName  / fileName).pathAsString
       }

diff --git a/core/src/main/scala/cromwell/core/path/NioPathMethods.scala b/core/src/main/scala/cromwell/core/path/NioPathMethods.scala
@@ -2,7 +2,6 @@ package cromwell.core.path
 
 import java.nio.file.WatchEvent.{Kind, Modifier}
 import java.nio.file.{LinkOption, WatchKey, WatchService}
-
 import scala.jdk.CollectionConverters._
 
 /**
@@ -68,4 +67,11 @@ trait NioPathMethods {
   final def startsWith(other: String): Boolean = nioPathPrivate.startsWith(other)
 
   final def toRealPath(options: LinkOption*): Path = newPath(nioPathPrivate.toRealPath(options: _*))
+
+  /**
+    * Get a valid path object that resolves symlinks if supported
+    * Default implementation assumes symlinks are supported, and that toRealPath may return a valid path.
+    * This implementation may be overridden for NIO implementations that do not support symbolic links (For example the Azure NIO library)
+    */
+  def getSymlinkSafePath(options: LinkOption*): Path  = toRealPath(options: _*)
 }
diff --git a/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala b/filesystems/blob/src/main/scala/cromwell/filesystems/blob/BlobPathBuilder.scala
@@ -1,14 +1,14 @@
 package cromwell.filesystems.blob
 
-import com.azure.storage.blob.nio.{AzureBlobFileAttributes}
+import com.azure.storage.blob.nio.AzureBlobFileAttributes
 import com.google.common.net.UrlEscapers
 import cromwell.core.path.{NioPath, Path, PathBuilder}
 import cromwell.filesystems.blob.BlobPathBuilder._
 
 import java.net.{MalformedURLException, URI}
+import java.nio.file.{Files, LinkOption}
 import scala.language.postfixOps
 import scala.util.{Failure, Success, Try}
-import java.nio.file.Files
 
 object BlobPathBuilder {
 
@@ -119,4 +119,6 @@ case class BlobPath private[blob](pathString: String, endpoint: EndpointURL, con
       }
     )
   }
+
+  override def getSymlinkSafePath(options: LinkOption*): Path  = toAbsolutePath
 }