More file path improvements, mostly around pipeline jobs

Author: labkey-jeckels

src/org/labkey/targetedms/TargetedMSController.java

@@ -276,6 +276,7 @@
 import org.labkey.targetedms.view.spectrum.LibrarySpectrumMatch;
 import org.labkey.targetedms.view.spectrum.LibrarySpectrumMatchGetter;
 import org.labkey.targetedms.view.spectrum.PeptideSpectrumView;
+import org.labkey.vfs.FileLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -3936,18 +3937,6 @@ public void setPeptideRepresentative(String[] peptideRepresentative)
         {
             _peptideRepresentative = peptideRepresentative;
         }
-
-        @Override
-        public List<File> getValidatedFiles(Container c)
-        {
-            List<File> files = super.getValidatedFiles(c);
-            List<File> resolvedFiles = new ArrayList<>(files.size());
-            for(File file: files)
-            {
-                resolvedFiles.add(FileUtil.resolveFile(file));  // Strips out ".." and "." from the path
-            }
-            return resolvedFiles;
-        }
     }
 
     @RequiresPermission(InsertPermission.class)

src/org/labkey/targetedms/TargetedMSManager.java

@@ -116,6 +116,7 @@
 import org.labkey.targetedms.query.PeptideManager;
 import org.labkey.targetedms.query.PrecursorManager;
 import org.labkey.targetedms.query.RepresentativeStateManager;
+import org.labkey.vfs.FileLike;
 
 import java.io.IOException;
 import java.net.URI;
@@ -666,7 +667,7 @@ public static Long addRunToQueue(ViewBackgroundInfo info,
             XarSource source = new AbstractFileXarSource("Wrap Targeted MS Run", container, user)
             {
                 @Override
-                public Path getLogFilePath()
+                public FileLike getLogFilePath()
                 {
                     throw new UnsupportedOperationException();
                 }

src/org/labkey/targetedms/view/confirmImport.jsp

@@ -18,6 +18,7 @@
 <%@ page import="org.labkey.api.view.ActionURL"%>
 <%@ page import="org.labkey.api.view.HttpView"%>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
+<%@ page import="org.labkey.vfs.FileLike" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
@@ -51,7 +52,7 @@
     </tr>
     <labkey:form action="<%=targetURL%>" method="POST">
         <input type="hidden" name="path" value="<%= h(form.getPath() )%>" />
-        <% for (java.io.File file : form.getValidatedFiles(getContainer()))
+        <% for (FileLike file : form.getValidatedFiles(getContainer()))
         { %>
             <tr style="border:1px solid;">
                 <td>