Cleanup

Author: labkey-jeckels

ms2/src/org/labkey/ms2/pipeline/MS2PipelineManager.java

@@ -65,9 +65,9 @@ public boolean accept(File file)
 
             if (TPPTask.isPepXMLFile(file))
             {
-                File parent = file.getParentFile();
+                FileLike parent = FileSystemLike.wrapFile(file.getParentFile());
                 String basename = TPPTask.FT_PEP_XML.getBaseName(file);
-                return !fileExists(TPPTask.getProtXMLFile(FileSystemLike.wrapFile(parent), basename)) &&
+                return !fileExists(TPPTask.getProtXMLFile(parent, basename)) &&
                         !fileExists(AbstractMS2SearchProtocol.FT_SEARCH_XAR.newFile(parent, basename));
             }
 

ms2/src/org/labkey/ms2/pipeline/ProteinProphetPipelineProvider.java

@@ -24,6 +24,7 @@
 import org.labkey.api.module.Module;
 import org.labkey.api.security.permissions.InsertPermission;
 import org.labkey.ms2.MS2Controller;
+import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 
@@ -65,7 +66,7 @@ public boolean accept(File f)
                 File parent = f.getParentFile();
                 String basename = fileType.getBaseName(f);
 
-                return !fileExists(AbstractMS2SearchProtocol.FT_SEARCH_XAR.newFile(parent, basename));
+                return !fileExists(AbstractMS2SearchProtocol.FT_SEARCH_XAR.newFile(FileSystemLike.wrapFile(parent), basename));
             }
 
             return false;