Pivotal ID # 186496317: Too Many Open Files (#774)

https://www.pivotaltracker.com/story/show/186496317

- Improve method signature
- Close InputStream after using it

commons/commons-util/src/main/kotlin/ebi/ac/uk/io/FileUtils.kt

@@ -10,6 +10,7 @@ import ebi.ac.uk.io.ext.isEmpty
 import ebi.ac.uk.io.ext.notExist
 import ebi.ac.uk.io.ext.size
 import org.apache.commons.codec.digest.DigestUtils
+import org.springframework.core.io.InputStreamSource
 import java.io.File
 import java.io.InputStream
 import java.nio.file.FileAlreadyExistsException
@@ -44,10 +45,12 @@ object FileUtils {
     }
 
     fun copyOrReplaceFile(
-        source: InputStream,
+        source: InputStreamSource,
         target: File,
         permissions: Permissions,
-    ) = FileUtilsHelper.copyFile(source, target.toPath(), permissions)
+    ) {
+        source.inputStream.use { FileUtilsHelper.copyFile(it, target.toPath(), permissions) }
+    }
 
     fun getOrCreateFolder(
         folder: Path,

submission/submission-webapp/src/main/kotlin/ac/uk/ebi/biostd/files/utils/MultipartFileUtils.kt

@@ -11,7 +11,7 @@ internal fun transferTo(basePath: Path, file: MultipartFile) {
     val expectedFilePath = basePath.resolve(file.originalFilename!!)
     FileUtils.createParentFolders(expectedFilePath, RWXRWX___)
     FileUtils.copyOrReplaceFile(
-        source = file.inputStream,
+        source = file,
         target = expectedFilePath.toFile(),
         permissions = Permissions(RW_RW____, RWXRWX___)
     )