From 287eda36dadd33c600d9f62cd2917e2de0b2dce0 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Sun, 5 Oct 2025 12:52:15 -0700
Subject: [PATCH 01/15] Checkpoint FileLike migration

---
 .../api/assay/AbstractAssayProvider.java      | 31 ++++++++++--------
 .../assay/AbstractTempDirDataCollector.java   | 32 +------------------
 .../labkey/api/assay/AssayDataCollector.java  |  2 +-
 .../org/labkey/api/assay/AssayFileWriter.java |  4 +--
 .../org/labkey/api/assay/AssayProvider.java   | 14 +-------
 .../api/assay/FileUploadDataCollector.java    | 13 ++++----
 .../api/assay/PipelineDataCollector.java      |  7 ++--
 .../PreviouslyUploadedDataCollector.java      | 11 +++----
 .../api/assay/actions/AssayRunUploadForm.java |  4 +--
 api/src/org/labkey/api/assay/fileUpload.jsp   |  3 +-
 .../labkey/assay/TextAreaDataCollector.java   | 15 +--------
 .../org/labkey/assay/TsvAssayProvider.java    |  4 +--
 .../src/org/labkey/assay/view/dataUpload.jsp  |  2 +-
 13 files changed, 44 insertions(+), 98 deletions(-)

diff --git a/api/src/org/labkey/api/assay/AbstractAssayProvider.java b/api/src/org/labkey/api/assay/AbstractAssayProvider.java
index 6a6c72f562b..bf070724392 100644
--- a/api/src/org/labkey/api/assay/AbstractAssayProvider.java
+++ b/api/src/org/labkey/api/assay/AbstractAssayProvider.java
@@ -115,6 +115,7 @@
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.ViewContext;
+import org.labkey.vfs.FileLike;
 import org.labkey.vfs.FileSystemLike;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
@@ -612,7 +613,7 @@ public List<Pair<Domain, Map<DomainProperty, Object>>> createDefaultDomains(Cont
     }
 
     @Override
-    public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, File> uploadedFiles, AssayRunUploadForm context)
+    public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, org.labkey.vfs.FileLike> uploadedFiles, AssayRunUploadForm context)
     {
         return getDataCollectors(uploadedFiles, context, true);
     }
@@ -623,7 +624,7 @@ public String getResourceName()
         return getName();
     }
 
-    public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, File> uploadedFiles, AssayRunUploadForm<?> context, boolean allowFileReuseOnReRun)
+    public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, org.labkey.vfs.FileLike> uploadedFiles, AssayRunUploadForm<?> context, boolean allowFileReuseOnReRun)
     {
         List<AssayDataCollector> result = new ArrayList<>();
         if (!PipelineDataCollector.getFileQueue(context).isEmpty())
@@ -636,7 +637,8 @@ public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, File> up
             {
                 // In the re-run scenario, figure out what files to offer up for reuse
 
-                Map<String, File> reusableFiles = new HashMap<>();
+//                Map<String, File> reusableFiles = new HashMap<>();
+                Map<String, org.labkey.vfs.FileLike> reusableFiles = new HashMap<>();
                 // Include any files that were uploaded as part of this request
                 if (uploadedFiles != null && !uploadedFiles.isEmpty())
                 {
@@ -674,14 +676,15 @@ else if (inputDatas.size() > 1)
                 // Filter out any files that aren't under the current pipeline root, since we won't be able to resolve
                 // them successfully due to security restrictions for what's an allowable input to the new run. See issue 18387.
                 PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(context.getContainer());
-                for (Iterator<Map.Entry<String, File>> iter = reusableFiles.entrySet().iterator(); iter.hasNext(); )
+                for (Iterator<Map.Entry<String, FileLike>> iter = reusableFiles.entrySet().iterator(); iter.hasNext(); )
                 {
-                    Map.Entry<String, File> entry = iter.next();
+                    Map.Entry<String, FileLike> entry = iter.next();
                     // If it's not under the current pipeline root
-                    if (pipeRoot == null || !pipeRoot.isUnderRoot(entry.getValue()))
+                    if (pipeRoot == null || !pipeRoot.isUnderRoot(entry.getValue().toNioPathForRead()))
                     {
-                        // Remove it from the collection
+                        // Remove it from both collections
                         iter.remove();
+                        reusableFiles.remove(entry.getKey());
                     }
                 }
 
@@ -691,8 +694,7 @@ else if (inputDatas.size() > 1)
                     // to reuse or re-upload
                     if (!reusableFiles.isEmpty())
                     {
-                        var reusableFileLike = FileSystemLike.wrapFiles(reusableFiles);
-                        result.add(new PreviouslyUploadedDataCollector<>(reusableFileLike));
+                        result.add(new PreviouslyUploadedDataCollector<>(reusableFiles));
                     }
                     result.add(new FileUploadDataCollector<>(getMaxFileInputs()));
                 }
@@ -708,8 +710,7 @@ else if (inputDatas.size() > 1)
                 // Normal (non-rerun) scenario
                 if (uploadedFiles != null)
                 {
-                    var uploadedFileLikes = FileSystemLike.wrapFiles(uploadedFiles);
-                    result.add(new PreviouslyUploadedDataCollector<>(uploadedFileLikes));
+                    result.add(new PreviouslyUploadedDataCollector<>(uploadedFiles));
                 }
                 result.add(new FileUploadDataCollector<>(getMaxFileInputs()));
             }
@@ -717,12 +718,14 @@ else if (inputDatas.size() > 1)
         return result;
     }
 
-    private void addReusableData(Map<String, File> reusableFiles, ExpData inputData)
+    private void addReusableData(Map<String, org.labkey.vfs.FileLike> reusableFiles, ExpData inputData)
     {
         // Not all datas are associated with a file
         if (inputData.getFile() != null)
         {
-            reusableFiles.put(AssayDataCollector.PRIMARY_FILE + (reusableFiles.isEmpty() ? "" : Integer.toString(reusableFiles.size())), inputData.getFile());
+            String key = AssayDataCollector.PRIMARY_FILE + (reusableFiles.isEmpty() ? "" : Integer.toString(reusableFiles.size()));
+            File f = inputData.getFile();
+            reusableFiles.put(key, org.labkey.vfs.FileSystemLike.wrapFile(f));
         }
     }
 
@@ -733,7 +736,7 @@ public AssayRunCreator getRunCreator()
     }
 
     @Override
-    public ExpProtocol createAssayDefinition(User user, Container container, String name, String description, ExpProtocol.Status status, XarContext context)
+    public ExpProtocol createAssayDefinition(User user, Container container, String name, String description, ExpProtocol.Status status, @NotNull XarContext context)
             throws ExperimentException
     {
         String protocolLsid = getAssayProtocolLsid(container, name, context);
diff --git a/api/src/org/labkey/api/assay/AbstractTempDirDataCollector.java b/api/src/org/labkey/api/assay/AbstractTempDirDataCollector.java
index 904bdfea196..cca1e9fd544 100644
--- a/api/src/org/labkey/api/assay/AbstractTempDirDataCollector.java
+++ b/api/src/org/labkey/api/assay/AbstractTempDirDataCollector.java
@@ -47,31 +47,7 @@ public abstract class AbstractTempDirDataCollector<ContextType extends AssayRunU
     protected boolean _uploadComplete = false;
 
     private static final Logger LOG = LogHelper.getLogger(AbstractTempDirDataCollector.class, "Activity related to data collection into a temporary directory");
-
-    private void removeTempDir(ContextType context) throws ExperimentException
-    {
-        // TODO: remove this instanceof check
-        if (!(context instanceof AssayRunUploadForm))
-            return;
-
-        String uploadAttemptID = ((AssayRunUploadForm<?>) context).getUploadAttemptID();
-
-        // Cleanup files other than input generated by transform scripts
-        FileLike tempDir = ensureSubdirectory(context.getContainer(), TEMP_DIR_NAME);
-        FileLike uploadAttemptDir = tempDir.resolveChild(uploadAttemptID);
-        if (NetworkDrive.exists(uploadAttemptDir))
-        {
-            try
-            {
-                FileUtils.deleteDirectory(uploadAttemptDir.toNioPathForWrite().toFile());
-            }
-            catch (IOException e)
-            {
-                // Delete quietly
-            }
-        }
-    }
-
+    
     @Override
     public void initDir(ContextType context) throws ExperimentException
     {
@@ -234,12 +210,6 @@ public Map<String, FileLike> uploadComplete(ContextType context, @Nullable ExpRu
         return result;
     }
 
-    /** @return the preferred name for the run given the primary data file */
-    protected String getPreferredAssayId(File primaryFile)
-    {
-        return primaryFile.getName();
-    }
-
     protected String getPreferredAssayId(FileLike primaryFile)
     {
         return primaryFile.getName();
diff --git a/api/src/org/labkey/api/assay/AssayDataCollector.java b/api/src/org/labkey/api/assay/AssayDataCollector.java
index d713cc9cf10..36774c90c65 100644
--- a/api/src/org/labkey/api/assay/AssayDataCollector.java
+++ b/api/src/org/labkey/api/assay/AssayDataCollector.java
@@ -57,7 +57,7 @@ public String getButtonText()
     }
 
     /** @return the UI to plug into the import wizard for the user to somehow select/upload the file */
-    HttpView getView(ContextType context) throws ExperimentException;
+    HttpView<?> getView(ContextType context) throws ExperimentException;
 
     /** @return the name for this AssayDataCollector. Needs to be unique within the set of data collectors for any given import attempt */
     String getShortName();
diff --git a/api/src/org/labkey/api/assay/AssayFileWriter.java b/api/src/org/labkey/api/assay/AssayFileWriter.java
index 327151f9b62..d2130887aaa 100644
--- a/api/src/org/labkey/api/assay/AssayFileWriter.java
+++ b/api/src/org/labkey/api/assay/AssayFileWriter.java
@@ -232,7 +232,7 @@ public String getFileName(MultipartFile file)
         return file.getOriginalFilename();
     }
 
-    public Map<String, FileLike> savePostedFiles(ContextType context, Set<String> parameterNames, boolean allowMultiple, boolean ensureExpData) throws ExperimentException, IOException
+    public Map<String, FileLike> savePostedFiles(ContextType context, @NotNull Set<String> parameterNames, boolean allowMultiple, boolean ensureExpData) throws ExperimentException, IOException
     {
         Map<String, FileLike> files = CollectionUtils.enforceValueClass(new TreeMap<>(), FileLike.class);
         Set<String> originalFileNames = new HashSet<>();
@@ -244,7 +244,7 @@ public Map<String, FileLike> savePostedFiles(ContextType context, Set<String> pa
             while (iter.hasNext())
             {
                 Map.Entry<String, List<MultipartFile>> entry = iter.next();
-                if (parameterNames == null || parameterNames.contains(entry.getKey()))
+                if (parameterNames.contains(entry.getKey()))
                 {
                     List<MultipartFile> multipartFiles = entry.getValue();
                     boolean isAfterFirstFile = false;
diff --git a/api/src/org/labkey/api/assay/AssayProvider.java b/api/src/org/labkey/api/assay/AssayProvider.java
index 1e8dd43ecd3..d94874809db 100644
--- a/api/src/org/labkey/api/assay/AssayProvider.java
+++ b/api/src/org/labkey/api/assay/AssayProvider.java
@@ -59,10 +59,8 @@
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.Controller;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.Collection;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -116,17 +114,7 @@ enum ReRunSupport
     AssayRunCreator getRunCreator();
 
     /** @return all the legal data collectors that the user can choose from for the current import attempt */
-    // TODO File->FileLike
-    List<AssayDataCollector> getDataCollectors(Map<String, File> uploadedFiles, AssayRunUploadForm context);
-
-    default List<AssayDataCollector> getDataCollectorsFileObject(Map<String, FileLike> uploadedFileObjects, AssayRunUploadForm context)
-    {
-        Map<String,File> map = new HashMap<>();
-        if (uploadedFileObjects != null)
-            for (var entry : uploadedFileObjects.entrySet())
-                map.put(entry.getKey(), entry.getValue().toNioPathForRead().toFile());
-        return getDataCollectors(map, context);
-    }
+    List<AssayDataCollector> getDataCollectors(Map<String, FileLike> uploadedFileObjects, AssayRunUploadForm context);
 
     /**
      * @return the name of the assay provider.
diff --git a/api/src/org/labkey/api/assay/FileUploadDataCollector.java b/api/src/org/labkey/api/assay/FileUploadDataCollector.java
index 2f018065ee8..98551e1df12 100644
--- a/api/src/org/labkey/api/assay/FileUploadDataCollector.java
+++ b/api/src/org/labkey/api/assay/FileUploadDataCollector.java
@@ -23,7 +23,6 @@
 import org.labkey.api.view.JspView;
 import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.Collections;
 import java.util.HashMap;
@@ -38,7 +37,7 @@
 public class FileUploadDataCollector<ContextType extends AssayRunUploadContext<? extends AssayProvider>> extends AbstractTempDirDataCollector<ContextType>
 {
     private final int _maxFileInputs;
-    private final Map<String, File> _reusableFiles;
+    private final Map<String, FileLike> _reusableFiles;
     // Name of the form <input> for the file.
     private final String _fileInputName;
 
@@ -52,12 +51,12 @@ public FileUploadDataCollector(int maxFileInputs)
         this(maxFileInputs, Collections.emptyMap());
     }
 
-    public FileUploadDataCollector(int maxFileInputs, Map<String, File> reusableFiles)
+    public FileUploadDataCollector(int maxFileInputs, Map<String, FileLike> reusableFiles)
     {
         this(maxFileInputs, reusableFiles, PRIMARY_FILE);
     }
 
-    public FileUploadDataCollector(int maxFileInputs, Map<String, File> reusableFiles, String fileInputName)
+    public FileUploadDataCollector(int maxFileInputs, Map<String, FileLike> reusableFiles, String fileInputName)
     {
         _maxFileInputs = maxFileInputs;
         _reusableFiles = Collections.unmodifiableMap(reusableFiles);
@@ -69,12 +68,12 @@ public FileUploadDataCollector(int maxFileInputs, Map<String, File> reusableFile
     }
 
     @Override
-    public HttpView getView(ContextType context)
+    public HttpView<?> getView(ContextType context)
     {
-        return new JspView<FileUploadDataCollector>("/org/labkey/api/assay/fileUpload.jsp", this);
+        return new JspView<>("/org/labkey/api/assay/fileUpload.jsp", this);
     }
 
-    public Map<String, File> getReusableFiles()
+    public Map<String, FileLike> getReusableFiles()
     {
         return _reusableFiles;
     }
diff --git a/api/src/org/labkey/api/assay/PipelineDataCollector.java b/api/src/org/labkey/api/assay/PipelineDataCollector.java
index b484d562181..1db558acd23 100644
--- a/api/src/org/labkey/api/assay/PipelineDataCollector.java
+++ b/api/src/org/labkey/api/assay/PipelineDataCollector.java
@@ -22,6 +22,7 @@
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExpRun;
+import org.labkey.api.util.DOM;
 import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.HtmlStringBuilder;
 import org.labkey.api.util.Pair;
@@ -41,8 +42,6 @@
 import java.util.List;
 import java.util.Map;
 
-import static org.labkey.api.util.HtmlString.unsafe;
-
 /**
  * Data collector that supplies files the user previously selected through the pipeline/file browser.
  *
@@ -58,7 +57,7 @@ public PipelineDataCollector()
     private File _originalFileLocation = null;
 
     @Override
-    public HttpView getView(ContextType context) throws ExperimentException
+    public HttpView<?> getView(ContextType context) throws ExperimentException
     {
         return new HtmlView(getHTML(context));
     }
@@ -68,7 +67,7 @@ public HtmlString getHTML(ContextType context)
         Map<String, File> files = getCurrentFilesForDisplay(context);
         if (files.isEmpty())
         {
-            return unsafe("<div class=\"labkey-error\">No files have been selected.</div>");
+            return DOM.createHtml(DOM.DIV(DOM.at(DOM.cl("labkey-error")), "No files have been selected."));
         }
 
         HtmlStringBuilder html = HtmlStringBuilder.of();
diff --git a/api/src/org/labkey/api/assay/PreviouslyUploadedDataCollector.java b/api/src/org/labkey/api/assay/PreviouslyUploadedDataCollector.java
index 11588d03805..293b90fb64b 100644
--- a/api/src/org/labkey/api/assay/PreviouslyUploadedDataCollector.java
+++ b/api/src/org/labkey/api/assay/PreviouslyUploadedDataCollector.java
@@ -16,7 +16,7 @@
 
 package org.labkey.api.assay;
 
-import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.collections.CollectionUtils;
 import org.labkey.api.data.Container;
@@ -27,7 +27,6 @@
 import org.labkey.api.view.InsertView;
 import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.Collections;
 import java.util.LinkedHashMap;
@@ -100,19 +99,19 @@ public HtmlView getView(ContextType context)
             sb.append(separator);
             separator = ", ";
             sb.append(entry.getValue().getName());
-            sb.append(getHiddenFormElementHTML(context.getContainer(), entry.getKey(), entry.getValue().toNioPathForRead().toFile()));
+            sb.append(getHiddenFormElementHTML(context.getContainer(), entry.getKey(), entry.getValue()));
         }
         return new HtmlView(sb);
     }
 
-    public HtmlString getHiddenFormElementHTML(Container container, String formElementName, File file)
+    public HtmlString getHiddenFormElementHTML(Container container, String formElementName, FileLike file)
     {
         PipeRoot pipeRoot = getPipelineRoot(container);
         HtmlStringBuilder sb = HtmlStringBuilder.of();
         sb.unsafeAppend("<input name=\"");
         sb.append(_type.getPathFormElementName());
         sb.unsafeAppend("\" type=\"hidden\" value=\"");
-        sb.append(pipeRoot.relativePath(file).replace('\\', '/'));
+        sb.append(pipeRoot.relativePath(file.toNioPathForRead()).replace('\\', '/'));
         sb.unsafeAppend("\"/><input type=\"hidden\" name=\"");
         sb.append(_type.getNameFormElementName());
         sb.unsafeAppend("\" value=\"");
@@ -174,7 +173,7 @@ private Map<String, FileLike> getFilesFromRequest(ContextType context, Type type
         Map<String, FileLike> result = CollectionUtils.enforceValueClass(new LinkedHashMap<>(), FileLike.class);
         for (int i = 0; i < paths.length; i++)
         {
-            result.put(names[i], pipelineRoot.resolvePathToFileLike(StringUtils.replace(paths[i],"\\","/")));
+            result.put(names[i], pipelineRoot.resolvePathToFileLike(Strings.CS.replace(paths[i],"\\","/")));
         }
         return result;
     }
diff --git a/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java b/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java
index 534f7193b44..88caae0db1d 100644
--- a/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java
+++ b/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java
@@ -356,14 +356,14 @@ public Map<DomainProperty, FileLike> getAdditionalPostedFiles(List<? extends Dom
                     // Hidden values in form containing previously uploaded files if previous upload resulted in error
                     for (String fileParam : filePdNames)
                     {
-                        if (request instanceof MultipartHttpServletRequest && null != request.getParameter(fileParam))
+                        if (request instanceof MultipartHttpServletRequest mhsr && null != request.getParameter(fileParam))
                         {
                             String previousFileName = request.getParameter(fileParam);
                             if (null != previousFileName)
                             {
                                 previousFile = FileUtil.appendName(getAssayDirectory(getContainer(), null), previousFileName);
 
-                                MultipartFile multiFile = ((MultipartHttpServletRequest)request).getFileMap().get(UploadWizardAction.getInputName(fileParameters.get(fileParam)));
+                                MultipartFile multiFile = mhsr.getFileMap().get(UploadWizardAction.getInputName(fileParameters.get(fileParam)));
 
                                 // If file is removed from form after error, override hidden file name with empty file
                                 if (null != multiFile && multiFile.getOriginalFilename().isEmpty())
diff --git a/api/src/org/labkey/api/assay/fileUpload.jsp b/api/src/org/labkey/api/assay/fileUpload.jsp
index 1297dba469a..b37889d112e 100644
--- a/api/src/org/labkey/api/assay/fileUpload.jsp
+++ b/api/src/org/labkey/api/assay/fileUpload.jsp
@@ -26,6 +26,7 @@
 <%@ page import="java.io.File" %>
 <%@ page import="java.util.Collections" %>
 <%@ page import="java.util.Map" %>
+<%@ page import="org.labkey.vfs.FileLike" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%!
@@ -99,7 +100,7 @@
         // Add an entry for all file groups that can be reused from a previous upload
         <%
         PreviouslyUploadedDataCollector reuseDataCollector = new PreviouslyUploadedDataCollector(Collections.emptyMap(), PreviouslyUploadedDataCollector.Type.ReRun);
-        for (Map.Entry<String, File> entry : bean.getReusableFiles().entrySet()) { %>
+        for (Map.Entry<String, FileLike> entry : bean.getReusableFiles().entrySet()) { %>
             addFileUploadInputRow(null, <%= q(entry.getValue().getName())%>, <%= q(reuseDataCollector.getHiddenFormElementHTML(getContainer(), entry.getKey(), entry.getValue()))%>);
         <% } %>
 
diff --git a/assay/src/org/labkey/assay/TextAreaDataCollector.java b/assay/src/org/labkey/assay/TextAreaDataCollector.java
index 78e4f0ce6d0..2e3eff2528d 100644
--- a/assay/src/org/labkey/assay/TextAreaDataCollector.java
+++ b/assay/src/org/labkey/assay/TextAreaDataCollector.java
@@ -27,7 +27,6 @@
 import org.labkey.vfs.FileLike;
 
 import java.io.ByteArrayInputStream;
-import java.io.File;
 import java.io.IOException;
 import java.util.Collections;
 import java.util.Map;
@@ -41,7 +40,7 @@ public class TextAreaDataCollector<ContextType extends AssayRunUploadContext<? e
     private static final String FORM_ELEMENT_NAME = "TextAreaDataCollector.textArea";
 
     @Override
-    public HttpView getView(ContextType context)
+    public HtmlView getView(ContextType context)
     {
         return HtmlView.unsafe("<textarea id=\"" + FORM_ELEMENT_NAME + "\" name=\"" + FORM_ELEMENT_NAME + "\" rows=\"10\" cols=\"80\"></textarea>\n" +
                 "<script type=\"text/javascript\" nonce=\"" + HttpView.currentPageConfig().getScriptNonce()+ "\">\n" +
@@ -88,16 +87,4 @@ public Map<String, FileLike> createData(ContextType context) throws IOException,
         writeFile(bIn, file.toNioPathForRead().toFile());
         return Collections.singletonMap(PRIMARY_FILE, file);
     }
-
-    @Override
-    protected String getPreferredAssayId(File primaryFile)
-    {
-        // Strip off the .tmp extension if present
-        String result = primaryFile.getName();
-        if (result.toLowerCase().endsWith(".tmp"))
-        {
-            result = result.substring(0, result.length() - ".tmp".length());
-        }
-        return result;
-    }
 }
diff --git a/assay/src/org/labkey/assay/TsvAssayProvider.java b/assay/src/org/labkey/assay/TsvAssayProvider.java
index 15166da8126..2a4b8c6a0ef 100644
--- a/assay/src/org/labkey/assay/TsvAssayProvider.java
+++ b/assay/src/org/labkey/assay/TsvAssayProvider.java
@@ -163,7 +163,7 @@ protected TsvAssayProvider(String protocolLSIDPrefix, String runLSIDPrefix, Stri
     }
 
     @Override
-    public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, File> uploadedFiles, AssayRunUploadForm context)
+    public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, org.labkey.vfs.FileLike> uploadedFiles, AssayRunUploadForm context)
     {
         List<AssayDataCollector> result = super.getDataCollectors(uploadedFiles, context);
         if (PipelineDataCollector.getFileQueue(context).isEmpty())
@@ -909,7 +909,7 @@ public void testReshowDataCollectorList()
             }});
 
             TsvAssayProvider provider = new TsvAssayProvider();
-            List<AssayDataCollector> dataCollectors = provider.getDataCollectors(Collections.singletonMap(AssayDataCollector.PRIMARY_FILE, new File("/mockFile")), _uploadContext);
+            List<AssayDataCollector> dataCollectors = provider.getDataCollectors(Collections.singletonMap(AssayDataCollector.PRIMARY_FILE, org.labkey.vfs.FileSystemLike.wrapFile(new File("/mockFile"))), _uploadContext);
             assertEquals(3, dataCollectors.size());
             assertEquals(TextAreaDataCollector.class, dataCollectors.get(0).getClass());
             assertEquals(PreviouslyUploadedDataCollector.class, dataCollectors.get(1).getClass());
diff --git a/assay/src/org/labkey/assay/view/dataUpload.jsp b/assay/src/org/labkey/assay/view/dataUpload.jsp
index a7e42694c6a..13e04bd5f53 100644
--- a/assay/src/org/labkey/assay/view/dataUpload.jsp
+++ b/assay/src/org/labkey/assay/view/dataUpload.jsp
@@ -45,7 +45,7 @@
         {
         }
 
-        for (AssayDataCollector collector : bean.getProvider().getDataCollectorsFileObject(uploadedData, bean))
+        for (AssayDataCollector collector : bean.getProvider().getDataCollectors(uploadedData, bean))
         {
             if (collector.isVisible())
             {

From caf207f35488daa150719695122e9da5653470ce Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Sun, 5 Oct 2025 13:38:28 -0700
Subject: [PATCH 02/15] Null check

---
 api/src/org/labkey/api/assay/AbstractAssayProvider.java | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/api/src/org/labkey/api/assay/AbstractAssayProvider.java b/api/src/org/labkey/api/assay/AbstractAssayProvider.java
index bf070724392..b54000c8f56 100644
--- a/api/src/org/labkey/api/assay/AbstractAssayProvider.java
+++ b/api/src/org/labkey/api/assay/AbstractAssayProvider.java
@@ -725,7 +725,10 @@ private void addReusableData(Map<String, org.labkey.vfs.FileLike> reusableFiles,
         {
             String key = AssayDataCollector.PRIMARY_FILE + (reusableFiles.isEmpty() ? "" : Integer.toString(reusableFiles.size()));
             File f = inputData.getFile();
-            reusableFiles.put(key, org.labkey.vfs.FileSystemLike.wrapFile(f));
+            if (f != null)
+            {
+                reusableFiles.put(key, org.labkey.vfs.FileSystemLike.wrapFile(f));
+            }
         }
     }
 

From c0229f86518fc7b47d7047e974a0b177bf568265 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Mon, 6 Oct 2025 07:18:28 -0700
Subject: [PATCH 03/15] scriptDir

---
 .../assay/transform/DataTransformService.java | 23 +++++++++----------
 api/src/org/labkey/vfs/FileSystemLike.java    |  2 +-
 .../pipeline/analysis/CommandTaskImpl.java    |  3 ++-
 .../labkey/pipeline/api/ScriptTaskImpl.java   |  9 ++++----
 4 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/api/src/org/labkey/api/assay/transform/DataTransformService.java b/api/src/org/labkey/api/assay/transform/DataTransformService.java
index 5b65275fc45..0b46f8387c8 100644
--- a/api/src/org/labkey/api/assay/transform/DataTransformService.java
+++ b/api/src/org/labkey/api/assay/transform/DataTransformService.java
@@ -94,7 +94,7 @@ public TransformResult transformAndValidate(
                 continue;
 
             // read the contents of the script file
-            File scriptFile = analysisScript.getScript().toNioPathForRead().toFile();
+            FileLike scriptFile = analysisScript.getScript();
             if (scriptFile.exists())
             {
                 if (operation == TransformOperation.UPDATE)
@@ -104,7 +104,7 @@ public TransformResult transformAndValidate(
 
                 // TODO: don't bother slurping the contents of binary scripts
                 StringBuilder sb = new StringBuilder();
-                try (BufferedReader br = Readers.getReader(scriptFile))
+                try (BufferedReader br = Readers.getReader(scriptFile.openInputStream()))
                 {
                     String l;
                     while ((l = br.readLine()) != null)
@@ -115,7 +115,7 @@ public TransformResult transformAndValidate(
                     throw new ValidationException(e.getMessage());
                 }
                 ScriptEngine engine = null;
-                String ext = FileUtil.getExtension(scriptFile);
+                String ext = FileUtil.getExtension(scriptFile.getName());
                 if (ext != null)
                 {
                     engine = LabKeyScriptEngineManager.get()
@@ -143,7 +143,7 @@ public TransformResult transformAndValidate(
                         FileLike runInfo = files.getKey();
 
                         bindings.put(ExternalScriptEngine.WORKING_DIRECTORY, scriptDir.toNioPathForWrite().toString());
-                        bindings.put(ExternalScriptEngine.SCRIPT_PATH, scriptFile.getAbsolutePath());
+                        bindings.put(ExternalScriptEngine.SCRIPT_PATH, scriptFile.toNioPathForRead().toFile().getAbsolutePath());
 
                         Map<String, String> paramMap = new HashMap<>();
 
@@ -168,7 +168,7 @@ public TransformResult transformAndValidate(
                         }
                         else
                         {
-                            rewrittenScriptFile = FileSystemLike.wrapFile(scriptFile);
+                            rewrittenScriptFile = scriptFile;
                         }
 
                         // process any output from the transformation script
@@ -228,20 +228,20 @@ public TransformResult transformAndValidate(
             }
             else
             {
-                throw new ValidationException("The transform script, " + scriptFile.getAbsolutePath() + ", configured for this assay does not exist. Please check " +
+                throw new ValidationException("The transform script, " + scriptFile + ", configured for this assay does not exist. Please check " +
                         "the configuration for this assay design.");
             }
         }
         return result;
     }
 
-    public void addStandardParameters(@Nullable HttpServletRequest request, @Nullable Container container, @Nullable File scriptFile, @Nullable String apiKey, @NotNull Map<String, String> paramMap)
+    public void addStandardParameters(@Nullable HttpServletRequest request, @Nullable Container container, @Nullable FileLike scriptFile, @Nullable String apiKey, @NotNull Map<String, String> paramMap)
     {
         if (scriptFile != null)
         {
-            File srcDir = scriptFile.getParentFile();
+            FileLike srcDir = scriptFile.getParent();
             if (srcDir != null && srcDir.exists())
-                paramMap.put(SRC_DIR_REPLACEMENT, srcDir.getAbsolutePath().replaceAll("\\\\", "/"));
+                paramMap.put(SRC_DIR_REPLACEMENT, srcDir.toNioPathForRead().toFile().getAbsolutePath().replaceAll("\\\\", "/"));
         }
         paramMap.put(R_SESSIONID_REPLACEMENT, getSessionInfo(request, apiKey));
         paramMap.put(LEGACY_SESSION_COOKIE_NAME_REPLACEMENT, getSessionCookieName(request));
@@ -263,15 +263,14 @@ private String getSessionCookieName(@Nullable HttpServletRequest request)
         return SecurityManager.TRANSFORM_SESSION_ID;
     }
 
-    private FileLike getScriptDir(ExpProtocol protocol, File scriptFile, boolean isDefault) throws IOException
+    private FileLike getScriptDir(ExpProtocol protocol, FileLike scriptFile, boolean isDefault) throws IOException
     {
         FileLike tempDir = FileUtil.getTempDirectoryFileLike();
         FileLike tempRoot = tempDir.resolveChild(ExternalScriptEngine.DEFAULT_WORKING_DIRECTORY);
 
         if (isDefault && scriptFile.exists())
         {
-            // TODO getScriptDir(FileLike scriptFile);
-            tempDir = new FileSystemLike.Builder(scriptFile.getParentFile()).readwrite().root();
+            tempDir = scriptFile.getParent();
             tempRoot = tempDir.resolveChild("TransformAndValidationFiles");
         }
 
diff --git a/api/src/org/labkey/vfs/FileSystemLike.java b/api/src/org/labkey/vfs/FileSystemLike.java
index 7fc22bef58a..d52f93c578a 100644
--- a/api/src/org/labkey/vfs/FileSystemLike.java
+++ b/api/src/org/labkey/vfs/FileSystemLike.java
@@ -45,7 +45,7 @@
  *
  * <p/>
  * implementation notes:
- * - This is meant to be a wrapper over java.nio.file.Path, java.io.File or org.apache.commons.vfs2.FileObject or other implementaions.
+ * - This is meant to be a wrapper over java.nio.file.Path, java.io.File or org.apache.commons.vfs2.FileObject or other implementations.
  *   However, it is still lower level than Resource.  For instance, it does not know about Permissions or ContentType, etc.
  * <br>
  * - FileLike objects always present String path and util.Path relative to the FileSystemLike root.
diff --git a/pipeline/src/org/labkey/pipeline/analysis/CommandTaskImpl.java b/pipeline/src/org/labkey/pipeline/analysis/CommandTaskImpl.java
index 9d1503aab75..43105dc53c8 100644
--- a/pipeline/src/org/labkey/pipeline/analysis/CommandTaskImpl.java
+++ b/pipeline/src/org/labkey/pipeline/analysis/CommandTaskImpl.java
@@ -50,6 +50,7 @@
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.NetworkDrive;
 import org.labkey.api.util.Path;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -521,7 +522,7 @@ private void inputFile(TaskPath tp, String role, RecordedAction action) throws I
      * to replace tokens the script or the command line before executing it.
      * The replaced paths will be resolved to paths in the work directory.
      */
-    protected Map<String, String> createReplacements(@Nullable File scriptFile, @Nullable String apiKey, @Nullable Container container) throws IOException
+    protected Map<String, String> createReplacements(@Nullable FileLike scriptFile, @Nullable String apiKey, @Nullable Container container) throws IOException
     {
         Map<String, String> replacements = new HashMap<>();
 
diff --git a/pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java b/pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java
index 2f958af4298..4d5128496c8 100644
--- a/pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java
+++ b/pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java
@@ -42,6 +42,8 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.pipeline.analysis.CommandTaskImpl;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import javax.script.Bindings;
 import javax.script.ScriptContext;
@@ -110,7 +112,7 @@ protected boolean runCommand(RecordedAction action, @Nullable String apiKey, @Nu
 
         try
         {
-            @Nullable File scriptFile = null;
+            @Nullable FileLike scriptFile = null;
             String scriptSource;
             if (factory._scriptInline != null)
             {
@@ -123,9 +125,9 @@ else if (factory._scriptPath != null)
                     throw new PipelineJobException("Script path not found: " + factory._scriptPath);
 
                 String path = paths[0];
-                scriptFile = new File(path);
+                scriptFile = FileSystemLike.wrapFile(new File(path));
 
-                scriptSource = PageFlowUtil.getFileContentsAsString(scriptFile);
+                scriptSource = PageFlowUtil.getStreamContentsAsString(scriptFile.openInputStream());
             }
             else
             {
@@ -264,7 +266,6 @@ protected void writeTaskInfo(File file, RecordedAction action) throws IOExceptio
         rows.add(factory.getRowMap("containerId", getJob().getContainer().getEntityId()));
         rows.add(factory.getRowMap("user", getJob().getUser().getEmail()));
 
-        PipeRoot pipeRoot = getJob().getPipeRoot();
         rows.add(factory.getRowMap("pipeRoot", getJob().getPipeRoot().getRootPath()));
 
         // FileAnalysisJobSupport properties

From 9ca56ac4813ee296230536fc74f4fc77d64c3fed Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Wed, 8 Oct 2025 11:41:05 -0700
Subject: [PATCH 04/15] Test fix

---
 api/src/org/labkey/vfs/FileSystemLike.java       | 2 ++
 assay/src/org/labkey/assay/TsvAssayProvider.java | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/api/src/org/labkey/vfs/FileSystemLike.java b/api/src/org/labkey/vfs/FileSystemLike.java
index d52f93c578a..953c002553e 100644
--- a/api/src/org/labkey/vfs/FileSystemLike.java
+++ b/api/src/org/labkey/vfs/FileSystemLike.java
@@ -196,6 +196,8 @@ public FileLike root()
     /** Helper for partially converted code. Parent dir must exist. */
     static FileLike wrapFile(File f)
     {
+        if (f == null)
+            return null;
         FileLike p = new Builder(f.getParentFile()).root();
         return p.resolveChild(f.getName());
     }
diff --git a/assay/src/org/labkey/assay/TsvAssayProvider.java b/assay/src/org/labkey/assay/TsvAssayProvider.java
index 2a4b8c6a0ef..7eb30f8252c 100644
--- a/assay/src/org/labkey/assay/TsvAssayProvider.java
+++ b/assay/src/org/labkey/assay/TsvAssayProvider.java
@@ -848,7 +848,7 @@ public void testReRunDataNotUnderRootCollectorList()
                 will(returnValue(Collections.singletonList(_data)));
                 allowing(_data).getFile();
                 // Use a file that's not under the pipeline root for the folder
-                will(returnValue(new File("mockFile")));
+                will(returnValue(new File("mockParent/mockFile")));
             }});
 
             TsvAssayProvider provider = new TsvAssayProvider();

From b63a84184e684c67764fb18ea1440f7ecefd595b Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Wed, 8 Oct 2025 11:46:16 -0700
Subject: [PATCH 05/15] Code cleanup

---
 assay/src/org/labkey/assay/TsvAssayProvider.java | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/assay/src/org/labkey/assay/TsvAssayProvider.java b/assay/src/org/labkey/assay/TsvAssayProvider.java
index 7eb30f8252c..35ddc3f43a3 100644
--- a/assay/src/org/labkey/assay/TsvAssayProvider.java
+++ b/assay/src/org/labkey/assay/TsvAssayProvider.java
@@ -120,7 +120,6 @@ public class TsvAssayProvider extends AbstractTsvAssayProvider
 
     public static final String NAME = "General";
     public static final String PLATE_TEMPLATE_PROPERTY_NAME = "PlateTemplate";
-    public static final String PLATE_TEMPLATE_PROPERTY_CAPTION = "Plate Template";
 
     private static final Set<String> participantImportAliases;
     private static final Set<String> specimenImportAliases;
@@ -168,7 +167,7 @@ public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, org.labk
         List<AssayDataCollector> result = super.getDataCollectors(uploadedFiles, context);
         if (PipelineDataCollector.getFileQueue(context).isEmpty())
         {
-            result.add(0, new TextAreaDataCollector());
+            result.add(0, new TextAreaDataCollector<>());
         }
         return result;
     }
@@ -784,7 +783,7 @@ public static class TestCase extends Assert
         private ExpProtocol _protocol;
         private ExpRun _run;
         private ExpData _data;
-        private AssayRunUploadForm _uploadContext;
+        private AssayRunUploadForm<?> _uploadContext;
 
         @Before
         public void setUp()
@@ -818,7 +817,7 @@ public void testReRunDataCollectorList()
             // data or reusing the existing file
             _context.checking(new Expectations(){{
                 allowing(_session).getAttribute(PipelineDataCollector.class.getName());
-                will(returnValue(new HashMap()));
+                will(returnValue(new HashMap<>()));
                 allowing(_uploadContext).getReRun();
                 will(returnValue(_run));
                 allowing(_run).getInputDatas(ExpDataRunInput.DEFAULT_ROLE, ExpProtocol.ApplicationType.ExperimentRunOutput);
@@ -841,7 +840,7 @@ public void testReRunDataNotUnderRootCollectorList()
             // data or reusing the existing file
             _context.checking(new Expectations(){{
                 allowing(_session).getAttribute(PipelineDataCollector.class.getName());
-                will(returnValue(new HashMap()));
+                will(returnValue(new HashMap<>()));
                 allowing(_uploadContext).getReRun();
                 will(returnValue(_run));
                 allowing(_run).getInputDatas(ExpDataRunInput.DEFAULT_ROLE, ExpProtocol.ApplicationType.ExperimentRunOutput);
@@ -865,7 +864,7 @@ public void testDataCollectorList()
             // Simulate a regular upload wizard
             _context.checking(new Expectations(){{
                 allowing(_session).getAttribute(PipelineDataCollector.class.getName());
-                will(returnValue(new HashMap()));
+                will(returnValue(new HashMap<>()));
                 allowing(_uploadContext).getReRun();
                 will(returnValue(null));
             }});
@@ -884,7 +883,7 @@ public void testPipelineDataCollectorList()
             _context.checking(new Expectations()
             {{
                 allowing(_session).getAttribute(PipelineDataCollector.class.getName());
-                Map<Pair<Container, Long>, Collection> map = new HashMap<>();
+                Map<Pair<Container, Long>, Collection<?>> map = new HashMap<>();
                 map.put(new Pair<>(_container, _protocol.getRowId()), Collections.singletonList(Collections.singletonMap(AssayDataCollector.PRIMARY_FILE, new File("mockFile"))));
                 will(returnValue(map));
                 allowing(_uploadContext).getReRun();
@@ -903,7 +902,7 @@ public void testReshowDataCollectorList()
             // Simulate an error reshow, where the user should be able to reuse the existing file or upload a replacement
             _context.checking(new Expectations(){{
                 allowing(_session).getAttribute(PipelineDataCollector.class.getName());
-                will(returnValue(new HashMap()));
+                will(returnValue(new HashMap<>()));
                 allowing(_uploadContext).getReRun();
                 will(returnValue(null));
             }});

From da15a2753492dd292a830ee5145928eda3d37b26 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Wed, 8 Oct 2025 12:14:20 -0700
Subject: [PATCH 06/15] Lots of FileUtil.appendName()

---
 .../labkey/api/data/FileSqlScriptProvider.java | 13 +++++++------
 api/src/org/labkey/api/data/TSVGridWriter.java |  3 ++-
 .../org/labkey/api/data/TempTableTracker.java  |  4 ++--
 .../labkey/api/data/WorkbookContainerType.java |  6 +++---
 .../api/files/FileSystemWatcherImpl.java       | 14 +++++++-------
 api/src/org/labkey/api/jsp/JspClassLoader.java |  4 +++-
 .../org/labkey/api/module/DefaultModule.java   |  6 +++---
 api/src/org/labkey/api/module/MockModule.java  |  2 +-
 api/src/org/labkey/api/module/Module.java      |  2 +-
 .../org/labkey/api/module/ModuleLoader.java    |  2 +-
 .../labkey/api/pipeline/LocalDirectory.java    | 10 +++++-----
 .../org/labkey/api/pipeline/PipelineJob.java   |  2 +-
 .../api/pipeline/PipelineProtocolFactory.java  |  4 ++--
 .../AbstractFileAnalysisProtocolFactory.java   |  6 +++---
 .../org/labkey/api/reader/ExcelFactory.java    |  7 ++++---
 api/src/org/labkey/api/reader/ExcelLoader.java | 18 +++++++++---------
 .../api/reports/ExternalScriptEngine.java      |  6 +++---
 .../report/ExternalScriptEngineReport.java     |  6 +++---
 .../api/reports/report/ScriptReport.java       |  2 +-
 .../api/reports/report/r/RReportJob.java       | 11 ++++-------
 .../report/r/view/DownloadOutputView.java      |  2 +-
 .../r/view/DownloadParamReplacement.java       |  2 +-
 .../api/reports/report/r/view/ImageOutput.java |  2 +-
 .../api/reports/report/r/view/ROutputView.java |  4 ++--
 .../org/labkey/api/settings/AppPropsImpl.java  |  3 ++-
 api/src/org/labkey/api/util/DotRunner.java     |  2 +-
 .../api/util/MaintenancePipelineJob.java       |  3 +--
 .../org/labkey/api/writer/FileSystemFile.java  |  2 +-
 api/src/org/labkey/vfs/vfsTestCase.jsp         |  8 ++++----
 core/src/org/labkey/core/CoreController.java   | 16 +++-------------
 .../core/attachment/AttachmentServiceImpl.java | 18 +++++++++---------
 .../core/notification/EmailServiceImpl.java    |  3 ++-
 .../org/labkey/core/vcs/VcsServiceImpl.java    |  5 +++--
 .../org/labkey/core/webdav/DavController.java  |  2 +-
 .../org/labkey/devtools/ToolsController.java   |  2 +-
 35 files changed, 98 insertions(+), 104 deletions(-)

diff --git a/api/src/org/labkey/api/data/FileSqlScriptProvider.java b/api/src/org/labkey/api/data/FileSqlScriptProvider.java
index 092ac063ae6..016e5c0a61b 100644
--- a/api/src/org/labkey/api/data/FileSqlScriptProvider.java
+++ b/api/src/org/labkey/api/data/FileSqlScriptProvider.java
@@ -31,6 +31,7 @@
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.resource.Resource;
 import org.labkey.api.settings.AppProps;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Path;
 import org.labkey.api.vcs.Vcs;
@@ -164,7 +165,7 @@ Returned set can be empty (i.e., schemas that have no scripts)
     // Returns all script file names listed in the specified file
     private @NotNull Collection<String> getScriptsFromFile(SqlDialect dialect, String filename) throws IOException
     {
-        Path path = Path.parse(_module.getSqlScriptsPath(dialect)).append(filename);
+        Path path = _module.getSqlScriptsPath(dialect).append(filename);
         Resource r = _module.getModuleResource(path);
 
         return null != r ? PageFlowUtil.getStreamContentsAsList(r.getInputStream(), true) : Collections.emptyList();
@@ -205,7 +206,7 @@ protected String getContents(DbSchema schema, String filename) throws SqlScriptE
     {
         try
         {
-            Path path = Path.parse(_module.getSqlScriptsPath(schema.getSqlDialect())).append(filename);
+            Path path = _module.getSqlScriptsPath(schema.getSqlDialect()).append(filename);
             Resource r = _module.getModuleResource(path);
             if (null == r || !r.isFile())
                 throw new SqlScriptException("File not found: " + path, filename);
@@ -249,7 +250,7 @@ public void saveScript(DbSchema schema, String description, String contents, boo
         if (!scriptsDir.exists())
             throw new IllegalStateException("SQL scripts directory not found");
 
-        File file = new File(scriptsDir, description);
+        File file = FileUtil.appendName(scriptsDir, description);
         boolean exists = file.exists();
 
         if (exists && !overwrite)
@@ -279,12 +280,12 @@ public File getScriptDirectory(SqlDialect dialect)
         if (isBlank(_module.getSourcePath()))
             return null;
 
-        String scriptsPath = _module.getSqlScriptsPath(dialect);
-        File scriptsDir = new File(new File(_module.getSourcePath(), "resources"), scriptsPath);
+        Path scriptsPath = _module.getSqlScriptsPath(dialect);
+        File scriptsDir = FileUtil.appendPath(FileUtil.appendName(new File(_module.getSourcePath()), "resources"), scriptsPath);
 
         // Handle file structure of old file-based modules, e.g., reagent
         if (!scriptsDir.exists())
-            scriptsDir = new File(_module.getSourcePath(), scriptsPath);
+            scriptsDir = FileUtil.appendPath(new File(_module.getSourcePath()), scriptsPath);
 
         return scriptsDir;
     }
diff --git a/api/src/org/labkey/api/data/TSVGridWriter.java b/api/src/org/labkey/api/data/TSVGridWriter.java
index 043b44cf9a8..a678c886d39 100644
--- a/api/src/org/labkey/api/data/TSVGridWriter.java
+++ b/api/src/org/labkey/api/data/TSVGridWriter.java
@@ -22,6 +22,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.ResultSetRowMapFactory;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.view.HttpView;
 
 import java.io.File;
@@ -266,7 +267,7 @@ private List<File> writeResultSetBatches(Results results, File outputDir, String
     private File startBatchFile(File outputDir, String baseName, String extension, int batchSize, int totalBatches) throws IOException
     {
         String batchId = batchSize == 0 ? "" : "-" + totalBatches;
-        File file = new File(outputDir, baseName + batchId + extension);
+        File file = FileUtil.appendName(outputDir, baseName + batchId + extension);
         prepare(file);
         writeFileHeader();
         if (isHeaderRowVisible())
diff --git a/api/src/org/labkey/api/data/TempTableTracker.java b/api/src/org/labkey/api/data/TempTableTracker.java
index bc9d62e0709..3ce1c067499 100644
--- a/api/src/org/labkey/api/data/TempTableTracker.java
+++ b/api/src/org/labkey/api/data/TempTableTracker.java
@@ -212,7 +212,7 @@ static void synchronizeLog(boolean loadFile)
             try
             {
                 if (null == tempTableLog)
-                    tempTableLog = new RandomAccessFile(new File(FileUtil.getTempDirectory(), LOGFILE), "rwd");
+                    tempTableLog = new RandomAccessFile(FileUtil.appendName(FileUtil.getTempDirectory(), LOGFILE), "rwd");
 
                 if (loadFile)
                 {
@@ -344,7 +344,7 @@ public void shutdownStarted()
             {
                 join(5000);
             }
-            catch (InterruptedException e) {}
+            catch (InterruptedException ignored) {}
             synchronizeLog(false);
         }
     }
diff --git a/api/src/org/labkey/api/data/WorkbookContainerType.java b/api/src/org/labkey/api/data/WorkbookContainerType.java
index 24e17d4c27d..b3796ae673e 100644
--- a/api/src/org/labkey/api/data/WorkbookContainerType.java
+++ b/api/src/org/labkey/api/data/WorkbookContainerType.java
@@ -435,7 +435,7 @@ public void testFileRootOverride() throws Exception
             File parentRoot = FileContentService.get().getFileRoot(parent);
             File origSubRoot = FileContentService.get().getFileRoot(sub);
             File origWbRoot = FileContentService.get().getFileRoot(wbOverride);
-            File wbOverrideRoot = new File(FileContentService.get().getSiteDefaultRoot(), "_foo");
+            File wbOverrideRoot = FileUtil.appendName(FileContentService.get().getSiteDefaultRoot(), "_foo");
 
             FileContentService.get().setFileRoot(wbOverride, wbOverrideRoot);
 
@@ -448,9 +448,9 @@ public void testFileRootOverride() throws Exception
             Assert.assertEquals("Incorrect file root", wbOverrideRoot, FileContentService.get().getFileRoot(wbOverride));
             Assert.assertEquals("Should not have changed", origWbRoot, FileContentService.get().getDefaultRoot(wbOverride, false));
 
-            Assert.assertEquals("Incorrect file root", new File(parentRoot, wbDefaultRoot.getName()), FileContentService.get().getFileRoot(wbDefaultRoot));
+            Assert.assertEquals("Incorrect file root", FileUtil.appendName(parentRoot, wbDefaultRoot.getName()), FileContentService.get().getFileRoot(wbDefaultRoot));
 
-            File test = new File(FileContentService.get().getFileRoot(wbOverride), "/@files/test.txt");
+            File test = FileUtil.appendPath(FileContentService.get().getFileRoot(wbOverride), Path.parse("/@files/test.txt"));
             if (!test.getParentFile().exists())
             {
                 FileUtil.mkdirs(test.getParentFile());
diff --git a/api/src/org/labkey/api/files/FileSystemWatcherImpl.java b/api/src/org/labkey/api/files/FileSystemWatcherImpl.java
index 880074aaa2a..5f8339d4352 100644
--- a/api/src/org/labkey/api/files/FileSystemWatcherImpl.java
+++ b/api/src/org/labkey/api/files/FileSystemWatcherImpl.java
@@ -489,7 +489,7 @@ public static class TestCase extends Assert
         public void testFileWatchers() throws IOException, InterruptedException
         {
             File root = FileUtil.createTempDirectory("fileWatcherTest").toFile(); //Conversion should be safe as temp dir should be on a local URI //TODO should convert to Path for consistencies sake
-            File testFolder = new File(root, "test");
+            File testFolder = FileUtil.appendName(root, "test");
 
             // Do it twice to ensure that everything gets cleaned up on directory delete and a new watcher can be added
             // to a new version of the same directory
@@ -553,13 +553,13 @@ public void overflow()
             assertNotNull(plm);
             assertEquals(1, plm._list.size());
 
-            File a = new File(testFolder, "a");
-            File b = new File(testFolder, "b");
-            File c = new File(testFolder, "c");
+            File a = FileUtil.appendName(testFolder, "a");
+            File b = FileUtil.appendName(testFolder, "b");
+            File c = FileUtil.appendName(testFolder, "c");
 
-            assertTrue(a.createNewFile());
-            assertTrue(b.createNewFile());
-            assertTrue(c.createNewFile());
+            assertTrue(FileUtil.createNewFile(a));
+            assertTrue(FileUtil.createNewFile(b));
+            assertTrue(FileUtil.createNewFile(c));
 
             waitForEvents(events, 3);
 
diff --git a/api/src/org/labkey/api/jsp/JspClassLoader.java b/api/src/org/labkey/api/jsp/JspClassLoader.java
index 7f00130da8a..3df284ef7c6 100644
--- a/api/src/org/labkey/api/jsp/JspClassLoader.java
+++ b/api/src/org/labkey/api/jsp/JspClassLoader.java
@@ -22,6 +22,8 @@
 import org.labkey.api.util.ConfigurationException;
 
 import jakarta.servlet.ServletContext;
+import org.labkey.api.util.FileUtil;
+
 import java.io.File;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -71,7 +73,7 @@ private boolean scanForJspJars()
         {
             // use m.getExplodedPath() instead of getModuleResource() otherwise, we will look for the
             // jars in the source directory on dev machines
-            var libDir = new File(m.getExplodedPath(), "lib");
+            var libDir = FileUtil.appendName(m.getExplodedPath(), "lib");
             if (!libDir.exists())
                 continue;
             var listing = libDir.listFiles((dir, name) -> name.contains("_jsp") && name.endsWith(".jar"));
diff --git a/api/src/org/labkey/api/module/DefaultModule.java b/api/src/org/labkey/api/module/DefaultModule.java
index 8935a9d88df..e654802bb8d 100644
--- a/api/src/org/labkey/api/module/DefaultModule.java
+++ b/api/src/org/labkey/api/module/DefaultModule.java
@@ -1029,7 +1029,7 @@ public final Set<String> getSqlScripts(@NotNull DbSchema schema)
     {
         SqlDialect dialect = schema.getSqlDialect();
 
-        String sqlScriptsPath = getSqlScriptsPath(dialect);
+        Path sqlScriptsPath = getSqlScriptsPath(dialect);
         Resource dir = getModuleResource(sqlScriptsPath);
         if (dir == null || !dir.isCollection())
             return Collections.emptySet();
@@ -1046,9 +1046,9 @@ public final Set<String> getSqlScripts(@NotNull DbSchema schema)
     }
 
     @Override
-    public final String getSqlScriptsPath(@NotNull SqlDialect dialect)
+    public final Path getSqlScriptsPath(@NotNull SqlDialect dialect)
     {
-        return "schemas/dbscripts/" + dialect.getSQLScriptPath() + "/";
+        return Path.parse("schemas/dbscripts/" + dialect.getSQLScriptPath() + "/");
     }
 
     @Override
diff --git a/api/src/org/labkey/api/module/MockModule.java b/api/src/org/labkey/api/module/MockModule.java
index 84e7b1215d4..ee2c70dbc23 100644
--- a/api/src/org/labkey/api/module/MockModule.java
+++ b/api/src/org/labkey/api/module/MockModule.java
@@ -367,7 +367,7 @@ public Set<String> getSqlScripts(@Nullable DbSchema schema)
     }
 
     @Override
-    public String getSqlScriptsPath(@NotNull SqlDialect dialect)
+    public Path getSqlScriptsPath(@NotNull SqlDialect dialect)
     {
         return null;
     }
diff --git a/api/src/org/labkey/api/module/Module.java b/api/src/org/labkey/api/module/Module.java
index cf938f6e959..e64bb9fe929 100644
--- a/api/src/org/labkey/api/module/Module.java
+++ b/api/src/org/labkey/api/module/Module.java
@@ -355,7 +355,7 @@ default String getBuildTime()
      * @param dialect The sql dialect for the scripts
      * @return The script file path
      */
-    String getSqlScriptsPath(@NotNull SqlDialect dialect);
+    Path getSqlScriptsPath(@NotNull SqlDialect dialect);
 
     /**
      * handle a http request
diff --git a/api/src/org/labkey/api/module/ModuleLoader.java b/api/src/org/labkey/api/module/ModuleLoader.java
index a3f8f5b9f91..1dfd255e7c0 100644
--- a/api/src/org/labkey/api/module/ModuleLoader.java
+++ b/api/src/org/labkey/api/module/ModuleLoader.java
@@ -1214,7 +1214,7 @@ else if (!moduleNamePattern.matcher(module.getName()).matches())
     private Module loadModuleFromProperties(ApplicationContext parentContext, File moduleDir) throws ClassNotFoundException, InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException
     {
         //check for simple .properties file
-        File modulePropsFile = new File(moduleDir, "config/module.properties");
+        File modulePropsFile = FileUtil.appendPath(moduleDir, Path.parse("config/module.properties"));
         Map<String, String> props = Collections.emptyMap();
         if (modulePropsFile.exists())
         {
diff --git a/api/src/org/labkey/api/pipeline/LocalDirectory.java b/api/src/org/labkey/api/pipeline/LocalDirectory.java
index c614f3f5470..f537ce2e94f 100644
--- a/api/src/org/labkey/api/pipeline/LocalDirectory.java
+++ b/api/src/org/labkey/api/pipeline/LocalDirectory.java
@@ -102,7 +102,7 @@ public LocalDirectory(Container container, String moduleName, PipeRoot pipeRoot,
         try
         {
             File containerDir = ensureContainerDir(container);
-            _localDirectoryFile = new File(containerDir, FileUtil.makeFileNameWithTimestamp("_temp_"));
+            _localDirectoryFile = FileUtil.appendName(containerDir, FileUtil.makeFileNameWithTimestamp("_temp_"));
 
             ensureLocalDirectory();
         }
@@ -179,7 +179,7 @@ public File copyToLocalDirectory(String url, Logger log)
                 String filename = FileUtil.getFileName(path);
                 try
                 {
-                    File tempFile = new File(_localDirectoryFile, filename);
+                    File tempFile = FileUtil.appendName(_localDirectoryFile, filename);
                     if (!Files.exists(tempFile.toPath()))
                     {
                         Files.copy(path, tempFile.toPath(), StandardCopyOption.COPY_ATTRIBUTES);
@@ -214,7 +214,7 @@ public static File copyToContainerDirectory(@NotNull Container container, @NotNu
         try
         {
             File containerDir = ensureContainerDir(container);
-            File tempFile = new File(containerDir, tempFileName);
+            File tempFile = FileUtil.appendName(containerDir, tempFileName);
             if (!Files.exists(tempFile.toPath()))
             {
                 log.debug("Copying file to container's temp directory: "+ FileUtil.pathToString(remotePath));
@@ -295,12 +295,12 @@ private void deleteDirectory(Path dir)
     private static File getModuleLocalTempDirectory()
     {
         File tempDir = FileUtil.getTempDirectory();   // tomcat/temp or similar
-        return new File(tempDir, FileUtil.makeLegalName(PipelineService.MODULE_NAME + "_temp"));
+        return FileUtil.appendName(tempDir, FileUtil.makeLegalName(PipelineService.MODULE_NAME + "_temp"));
     }
 
     public static File getContainerLocalTempDirectory(Container container)
     {
-        return new File(getModuleLocalTempDirectory(), FileUtil.makeLegalName(container.getName() + "_" + container.getId()));
+        return FileUtil.appendName(getModuleLocalTempDirectory(), FileUtil.makeLegalName(container.getName() + "_" + container.getId()));
     }
 
     public Path getRemoteLogFilePath()
diff --git a/api/src/org/labkey/api/pipeline/PipelineJob.java b/api/src/org/labkey/api/pipeline/PipelineJob.java
index 18e595703a3..e872a09ce1f 100644
--- a/api/src/org/labkey/api/pipeline/PipelineJob.java
+++ b/api/src/org/labkey/api/pipeline/PipelineJob.java
@@ -476,7 +476,7 @@ public static File findUniqueLogFile(File primaryFile, String baseName)
         String validBaseName = FileUtil.makeLegalName(baseName);
         // need to look in current and archived dirs for any unused log file names (issue 20987)
         File fileLog = FT_LOG.newFile(primaryFile.getParentFile(), validBaseName);
-        File archivedDir = new File(primaryFile.getParentFile(), AssayFileWriter.ARCHIVED_DIR_NAME);
+        File archivedDir = FileUtil.appendName(primaryFile.getParentFile(), AssayFileWriter.ARCHIVED_DIR_NAME);
         File fileLogArchived = FT_LOG.newFile(archivedDir, validBaseName);
 
         int index = 1;
diff --git a/api/src/org/labkey/api/pipeline/PipelineProtocolFactory.java b/api/src/org/labkey/api/pipeline/PipelineProtocolFactory.java
index 20a29692af8..97e4d4dcba6 100644
--- a/api/src/org/labkey/api/pipeline/PipelineProtocolFactory.java
+++ b/api/src/org/labkey/api/pipeline/PipelineProtocolFactory.java
@@ -52,8 +52,8 @@ public static Path getProtocolRootDir(PipeRoot root)
 
     public static File locateProtocolRootDir(File rootDir, File systemDir)
     {
-        File protocolRootDir = new File(systemDir, _pipelineProtocolDir);
-        File protocolRootDirLegacy = new File(rootDir, _pipelineProtocolDir);
+        File protocolRootDir = FileUtil.appendName(systemDir, _pipelineProtocolDir);
+        File protocolRootDirLegacy = FileUtil.appendName(rootDir, _pipelineProtocolDir);
         if (NetworkDrive.exists(protocolRootDirLegacy))
             protocolRootDirLegacy.renameTo(protocolRootDir);
         return protocolRootDir;
diff --git a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocolFactory.java b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocolFactory.java
index 12b60e2c06e..28fe1bf96e7 100644
--- a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocolFactory.java
+++ b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocolFactory.java
@@ -178,11 +178,11 @@ public void initSystemDirectory(File rootDir, File systemDir)
         File protocolRootDir = locateProtocolRootDir(rootDir, systemDir);
 
         // Make sure the defaults for this particular protocol are in the right place.
-        File fileLegacyDefaults = new File(rootDir, getLegacyDefaultParametersFileName());
+        File fileLegacyDefaults = FileUtil.appendName(rootDir, getLegacyDefaultParametersFileName());
         if (NetworkDrive.exists(fileLegacyDefaults))
         {
-            File protocolDir = new File(protocolRootDir, getName());
-            fileLegacyDefaults.renameTo(new File(protocolDir, getDefaultParametersFileName()));
+            File protocolDir = FileUtil.appendName(protocolRootDir, getName());
+            fileLegacyDefaults.renameTo(FileUtil.appendName(protocolDir, getDefaultParametersFileName()));
         }
     }
 
diff --git a/api/src/org/labkey/api/reader/ExcelFactory.java b/api/src/org/labkey/api/reader/ExcelFactory.java
index 0d344340d3e..9bb65e35935 100644
--- a/api/src/org/labkey/api/reader/ExcelFactory.java
+++ b/api/src/org/labkey/api/reader/ExcelFactory.java
@@ -57,6 +57,7 @@
 import org.labkey.api.data.ExcelWriter;
 import org.labkey.api.reader.jxl.JxlWorkbook;
 import org.labkey.api.settings.AppProps;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.JunitUtil;
 import org.labkey.api.util.logging.LogHelper;
 import org.openxmlformats.schemas.spreadsheetml.x2006.main.CTSheet;
@@ -919,9 +920,9 @@ public void testExcelFileImportShouldFail() throws Exception
         {
             File dataloading = JunitUtil.getSampleData(null, "dataLoading/excel");
 
-            attemptImportExpectError(new File(dataloading, "doesntexist.xls"), FileNotFoundException.class);
-            attemptImportExpectError(new File(dataloading, ""), FileNotFoundException.class);
-            attemptImportExpectError(new File(dataloading, "notreallyexcel.xls"), InvalidFormatException.class);
+            attemptImportExpectError(FileUtil.appendName(dataloading, "doesntexist.xls"), FileNotFoundException.class);
+            attemptImportExpectError(FileUtil.appendName(dataloading, ""), FileNotFoundException.class);
+            attemptImportExpectError(FileUtil.appendName(dataloading, "notreallyexcel.xls"), InvalidFormatException.class);
         }
 
         private void attemptImportExpectError(File excelFile, Class<? extends Throwable> exceptionClass)
diff --git a/api/src/org/labkey/api/reader/ExcelLoader.java b/api/src/org/labkey/api/reader/ExcelLoader.java
index c2dc153bdd0..456d4d921b7 100644
--- a/api/src/org/labkey/api/reader/ExcelLoader.java
+++ b/api/src/org/labkey/api/reader/ExcelLoader.java
@@ -804,11 +804,11 @@ public void detect() throws Exception
         {
             File excelSamplesRoot = JunitUtil.getSampleData(null, "dataLoading/excel");
 
-            assertTrue(isExcel(new File(excelSamplesRoot, "ExcelLoaderTest.xls")));
-            assertTrue(isExcel(new File(excelSamplesRoot, "SimpleExcelFile.xls")));
-            assertTrue(isExcel(new File(excelSamplesRoot, "SimpleExcelFile.xlsx")));
-            assertTrue(isExcel(new File(excelSamplesRoot, "fruits.xls")));
-            assertTrue(isExcel(new File(excelSamplesRoot, "DatesWithSeconds.xlsx")));
+            assertTrue(isExcel(FileUtil.appendName(excelSamplesRoot, "ExcelLoaderTest.xls")));
+            assertTrue(isExcel(FileUtil.appendName(excelSamplesRoot, "SimpleExcelFile.xls")));
+            assertTrue(isExcel(FileUtil.appendName(excelSamplesRoot, "SimpleExcelFile.xlsx")));
+            assertTrue(isExcel(FileUtil.appendName(excelSamplesRoot, "fruits.xls")));
+            assertTrue(isExcel(FileUtil.appendName(excelSamplesRoot, "DatesWithSeconds.xlsx")));
 
             // Issue 22153: detect xls file without extension
             assertTrue(isExcel(JunitUtil.getSampleData(null, "Nab/seaman/MS010407")));
@@ -821,9 +821,9 @@ public void detect() throws Exception
                 assertTrue(factory instanceof ExcelLoader.Factory);
             }
 
-            assertFalse(isExcel(new File(excelSamplesRoot, "notreallyexcel.xls")));
-            assertFalse(isExcel(new File(excelSamplesRoot, "notreallyexcel.xlsx")));
-            assertFalse(isExcel(new File(excelSamplesRoot, "fruits.tsv")));
+            assertFalse(isExcel(FileUtil.appendName(excelSamplesRoot, "notreallyexcel.xls")));
+            assertFalse(isExcel(FileUtil.appendName(excelSamplesRoot, "notreallyexcel.xlsx")));
+            assertFalse(isExcel(FileUtil.appendName(excelSamplesRoot, "fruits.tsv")));
         }
 
         @Test
@@ -958,7 +958,7 @@ private ExcelLoader getExcelLoader(String filename) throws IOException
             if (!excelSamplesRoot.canRead())
                 throw new IOException("Could not read excel samples in: " + excelSamplesRoot);
 
-            File excelFile = new File(excelSamplesRoot, filename);
+            File excelFile = FileUtil.appendName(excelSamplesRoot, filename);
 
             return new ExcelLoader(excelFile, true);
         }
diff --git a/api/src/org/labkey/api/reports/ExternalScriptEngine.java b/api/src/org/labkey/api/reports/ExternalScriptEngine.java
index 8ea29e50c61..0f1fec57695 100644
--- a/api/src/org/labkey/api/reports/ExternalScriptEngine.java
+++ b/api/src/org/labkey/api/reports/ExternalScriptEngine.java
@@ -191,7 +191,7 @@ protected File getWorkingDir(ScriptContext context)
             else
             {
                 File tempDir = new File(System.getProperty("java.io.tmpdir"));
-                _workingDirectory = new File(tempDir, DEFAULT_WORKING_DIRECTORY);
+                _workingDirectory = FileUtil.appendName(tempDir, DEFAULT_WORKING_DIRECTORY);
             }
 
             if (!_workingDirectory.exists())
@@ -440,10 +440,10 @@ protected File writeScriptFile(String script, ScriptContext context, List<String
             if (isBinaryScript)
                 scriptFile = path;
             else
-                scriptFile = new File(getWorkingDir(context), path.getName());
+                scriptFile = FileUtil.appendName(getWorkingDir(context), path.getName());
         }
         else
-            scriptFile = new File(getWorkingDir(context), "script." + extensions.get(0));
+            scriptFile = FileUtil.appendName(getWorkingDir(context), "script." + extensions.get(0));
 
         bindings.put(REWRITTEN_SCRIPT_FILE, scriptFile);
 
diff --git a/api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java b/api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java
index b9ba97d6643..ae77e2e53b8 100644
--- a/api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java
+++ b/api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java
@@ -419,14 +419,14 @@ protected void cacheResults(ViewContext context, List<ParamReplacement> replacem
                     return;
 
                 try {
-                    File mapFile = new File(cacheDir, SUBSTITUTION_MAP);
+                    File mapFile = FileUtil.appendName(cacheDir, SUBSTITUTION_MAP);
 
                     for (ParamReplacement param : replacements)
                     {
                         List<Pair<File, File>> changes = new ArrayList<>();
                         for (File src : param.getFiles())
                         {
-                            File dst = new File(cacheDir, src.getName());
+                            File dst = FileUtil.appendName(cacheDir, src.getName());
                             if (src.exists() && FileUtil.createTempFile(dst))
                             {
                                 FileUtil.copyFile(src, dst);
@@ -482,7 +482,7 @@ protected boolean getCachedReport(ViewContext context, List<ParamReplacement> re
 
                 try
                 {
-                    replacements.addAll(ParamReplacementSvc.get().fromFile(new File(cacheDir, SUBSTITUTION_MAP)));
+                    replacements.addAll(ParamReplacementSvc.get().fromFile(FileUtil.appendName(cacheDir, SUBSTITUTION_MAP)));
                     return !replacements.isEmpty();
                 }
                 catch (Exception e)
diff --git a/api/src/org/labkey/api/reports/report/ScriptReport.java b/api/src/org/labkey/api/reports/report/ScriptReport.java
index 774fc97f2f5..42278885423 100644
--- a/api/src/org/labkey/api/reports/report/ScriptReport.java
+++ b/api/src/org/labkey/api/reports/report/ScriptReport.java
@@ -279,7 +279,7 @@ public static File getTempRoot(ReportDescriptor descriptor)
     public static File getDefaultTempRoot()
     {
         File tempDir = new File(System.getProperty("java.io.tmpdir"));
-        return new File(tempDir, REPORT_DIR);
+        return FileUtil.appendName(tempDir, REPORT_DIR);
     }
 
     public static FileLike getTempRootFileLike(ReportDescriptor descriptor)
diff --git a/api/src/org/labkey/api/reports/report/r/RReportJob.java b/api/src/org/labkey/api/reports/report/r/RReportJob.java
index 8e96dbbfd93..79c220902a5 100644
--- a/api/src/org/labkey/api/reports/report/r/RReportJob.java
+++ b/api/src/org/labkey/api/reports/report/r/RReportJob.java
@@ -18,8 +18,6 @@
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.JdbcType;
 import org.labkey.api.exp.PropertyType;
@@ -61,7 +59,6 @@
  */
 public class RReportJob extends PipelineJob implements Serializable
 {
-    private static final Logger _log = LogManager.getLogger(RReportJob.class);
     private static final ThreadLocal<String> _jobIdentifier = new ThreadLocal<>();
 
     public static final String PROCESSING_STATUS = "Processing";
@@ -300,7 +297,7 @@ protected void processOutputs(RReport report, List<ParamReplacement> outputSubst
                         List<File> newFiles = new ArrayList<>();
                         for (File file : replacement.getFiles())
                         {
-                            File newFile = new File(parentDir, file.getName());
+                            File newFile = FileUtil.appendName(parentDir, file.getName());
                             FileUtils.moveFile(file, newFile);
                             newFiles.add(newFile);
                         }
@@ -315,7 +312,7 @@ protected void processOutputs(RReport report, List<ParamReplacement> outputSubst
                     // move the remaining files and delete the pipeline specific directory
                     for (File file : reportDir.listFiles())
                     {
-                        File newFile = new File(parentDir, file.getName());
+                        File newFile = FileUtil.appendName(parentDir, file.getName());
                         // special handling for log file
                         if (LOG_FILE_NAME.equalsIgnoreCase(file.getName()))
                         {
@@ -341,10 +338,10 @@ protected void processOutputs(RReport report, List<ParamReplacement> outputSubst
                         }
                     }
                     FileUtils.deleteDirectory(reportDir);
-                    substitutionMap = new File(reportDir.getParent(), RReport.SUBSTITUTION_MAP);
+                    substitutionMap = FileUtil.appendName(reportDir.getParentFile(), RReport.SUBSTITUTION_MAP);
                 }
                 else
-                    substitutionMap = new File(reportDir, RReport.SUBSTITUTION_MAP);
+                    substitutionMap = FileUtil.appendName(reportDir, RReport.SUBSTITUTION_MAP);
                 ParamReplacementSvc.get().toFile(outputSubst, substitutionMap);
             }
         }
diff --git a/api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java b/api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java
index 31a0027933c..3ee179b603b 100644
--- a/api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java
+++ b/api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java
@@ -62,7 +62,7 @@ protected String renderInternalAsString(File file)
 
         if (file != null && file.exists() && (file.length() > 0))
         {
-            File newFile = moveToTemp(file, "RReportPdf");
+            File newFile = moveToTemp(file);
             // file hasn't been saved yet
             String key = ImageUtil.setFileInSession(getViewContext().getRequest(), newFile);
             downloadUrl = PageFlowUtil.urlProvider(ReportUrls.class).urlStreamFile(getViewContext().getContainer()).
diff --git a/api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java b/api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java
index 7d85234bb7a..10bff2618d2 100644
--- a/api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java
+++ b/api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java
@@ -49,7 +49,7 @@ protected final File getSubstitution(File directory, String extension)
                 fileName = getName().concat(extension);
 
             if (directory != null)
-                file = new File(directory, fileName);
+                file = FileUtil.appendName(directory, fileName);
         }
         if (file != null)
             addFile(file);
diff --git a/api/src/org/labkey/api/reports/report/r/view/ImageOutput.java b/api/src/org/labkey/api/reports/report/r/view/ImageOutput.java
index fee09049e6c..b89061204d9 100644
--- a/api/src/org/labkey/api/reports/report/r/view/ImageOutput.java
+++ b/api/src/org/labkey/api/reports/report/r/view/ImageOutput.java
@@ -128,7 +128,7 @@ protected String renderInternalAsString(File file)
                 if (!_deleteFile)
                     imgFile = file;
                 else
-                    imgFile = moveToTemp(file, "RReportImg");
+                    imgFile = moveToTemp(file);
 
                 if (imgFile != null)
                 {
diff --git a/api/src/org/labkey/api/reports/report/r/view/ROutputView.java b/api/src/org/labkey/api/reports/report/r/view/ROutputView.java
index 45598777218..a20d34d6ffb 100644
--- a/api/src/org/labkey/api/reports/report/r/view/ROutputView.java
+++ b/api/src/org/labkey/api/reports/report/r/view/ROutputView.java
@@ -148,11 +148,11 @@ protected void renderTitle(Object model, PrintWriter out)
         out.write(sb.toString());
     }
 
-    protected File moveToTemp(File file, String prefix)
+    protected File moveToTemp(File file)
     {
         File root = ScriptEngineReport.getTempRoot(ReportService.get().createDescriptorInstance(RReportDescriptor.TYPE));
 
-        File newFile = new File(root, FileUtil.makeFileNameWithTimestamp(FileUtil.getBaseName(file.getName()), FileUtil.getExtension(file)));
+        File newFile = FileUtil.appendName(root, FileUtil.makeFileNameWithTimestamp(FileUtil.getBaseName(file.getName()), FileUtil.getExtension(file)));
         newFile.delete();
 
         LOG.debug("Moving '" + file.getAbsolutePath() + "' to '" + newFile.getAbsolutePath() + "'");
diff --git a/api/src/org/labkey/api/settings/AppPropsImpl.java b/api/src/org/labkey/api/settings/AppPropsImpl.java
index 8a134521ca2..82833c35df5 100644
--- a/api/src/org/labkey/api/settings/AppPropsImpl.java
+++ b/api/src/org/labkey/api/settings/AppPropsImpl.java
@@ -33,6 +33,7 @@
 import org.labkey.api.security.UserManager;
 import org.labkey.api.security.UserPrincipal;
 import org.labkey.api.util.ExceptionReportingLevel;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.MothershipReport;
 import org.labkey.api.util.PageFlowUtil;
@@ -267,7 +268,7 @@ public String getPipelineToolsDirectory()
     {
         @SuppressWarnings("ConstantConditions")
         File webappDir = new File(ModuleLoader.getServletContext().getRealPath(""));
-        File binDir = new File(webappDir.getParentFile(), "bin");
+        File binDir = FileUtil.appendName(webappDir.getParentFile(), "bin");
 
         return lookupStringValue(pipelineToolsDirectory, binDir.getAbsolutePath());
     }
diff --git a/api/src/org/labkey/api/util/DotRunner.java b/api/src/org/labkey/api/util/DotRunner.java
index aa3a8296dd8..b975a34b2b7 100644
--- a/api/src/org/labkey/api/util/DotRunner.java
+++ b/api/src/org/labkey/api/util/DotRunner.java
@@ -88,7 +88,7 @@ public static void testDotPath(File baseDirectory) throws ExperimentException
     {
         try
         {
-            File testVersion = new File(baseDirectory, "dottest.txt");
+            File testVersion = FileUtil.appendName(baseDirectory, "dottest.txt");
             if (testVersion.exists())
                 return;
 
diff --git a/api/src/org/labkey/api/util/MaintenancePipelineJob.java b/api/src/org/labkey/api/util/MaintenancePipelineJob.java
index c0ccf7ba091..eaee550dffe 100644
--- a/api/src/org/labkey/api/util/MaintenancePipelineJob.java
+++ b/api/src/org/labkey/api/util/MaintenancePipelineJob.java
@@ -22,7 +22,6 @@
 import org.labkey.api.util.SystemMaintenance.MaintenanceTask;
 import org.labkey.api.view.ViewBackgroundInfo;
 
-import java.io.File;
 import java.util.Collection;
 
 /**
@@ -43,7 +42,7 @@ protected MaintenancePipelineJob(@JsonProperty("_tasks") Collection<MaintenanceT
     MaintenancePipelineJob(ViewBackgroundInfo info, PipeRoot pipeRoot, Collection<MaintenanceTask> tasks)
     {
         super("SystemMaintenance", info, pipeRoot);
-        setLogFile(new File(pipeRoot.getLogDirectory(), FileUtil.makeFileNameWithTimestamp("system_maintenance", "log")).toPath());
+        setLogFile(pipeRoot.getLogDirectoryFileLike(true).resolveChild(FileUtil.makeFileNameWithTimestamp("system_maintenance", "log")).toNioPathForWrite());
         _tasks = tasks;
     }
 
diff --git a/api/src/org/labkey/api/writer/FileSystemFile.java b/api/src/org/labkey/api/writer/FileSystemFile.java
index dce4ee72d14..298c2f0b42f 100644
--- a/api/src/org/labkey/api/writer/FileSystemFile.java
+++ b/api/src/org/labkey/api/writer/FileSystemFile.java
@@ -81,7 +81,7 @@ public String getLocation()
     @Override
     public PrintWriter getPrintWriter(String filename) throws IOException
     {
-        File file = new File(_root.toFile(), makeLegalName(filename));
+        File file = FileUtil.appendName(_root.toFile(), makeLegalName(filename));
 
         return PrintWriters.getPrintWriter(file);
     }
diff --git a/api/src/org/labkey/vfs/vfsTestCase.jsp b/api/src/org/labkey/vfs/vfsTestCase.jsp
index 68de7c6dd93..1c60019ccc6 100644
--- a/api/src/org/labkey/vfs/vfsTestCase.jsp
+++ b/api/src/org/labkey/vfs/vfsTestCase.jsp
@@ -229,8 +229,8 @@
         fs = fs.getCachingFileSystem();
         FileLike root = fs.getRoot();
         File ROOT = root.toNioPathForWrite().toFile();
-        File DIR = new File(ROOT,"caching");
-        FileUtil.deleteDir(new File(ROOT,"caching"));
+        File DIR = FileUtil.appendName(ROOT,"caching");
+        FileUtil.deleteDir(DIR);
 
         FileLike dir = root.resolveChild("caching");
         assertFalse(dir.exists());
@@ -243,12 +243,12 @@
         assertTrue(dir.isDirectory());
         assertTrue(dir.getChildren().isEmpty());
 
-        File FILE = new File(DIR, "a.txt");
+        File FILE = FileUtil.appendName(DIR, "a.txt");
         FileLike file = dir.resolveChild("a.txt");
         assertFalse(file.exists());
         assertFalse(file.isFile());
         assertTrue(dir.getChildren().isEmpty());
-        FILE.createNewFile();
+        FileUtil.createNewFile(FILE);
         assertFalse(file.exists());
         assertFalse(file.isFile());
         assertTrue(dir.getChildren().isEmpty());
diff --git a/core/src/org/labkey/core/CoreController.java b/core/src/org/labkey/core/CoreController.java
index b7435ac5c3f..96068322b9a 100644
--- a/core/src/org/labkey/core/CoreController.java
+++ b/core/src/org/labkey/core/CoreController.java
@@ -2133,18 +2133,8 @@ public Object execute(LoadLibraryForm form, BindException errors)
     // use of illegal filename chars is intentional
     private static final String TOKEN_PREFIX = "upload://";
 
-    static File getUploadDir(User user, String session) throws IOException
-    {
-        if (user.isGuest())
-            throw new UnauthorizedException();
-        File tmpDir = FileUtil.getTempDirectory();
-        File userDir = new File(tmpDir,"loadingDock/" + session);
-        FileUtil.mkdirs(userDir);
-        return userDir;
-    }
-
     @RequiresNoPermission
-    public static class StyleGuideAction extends SimpleViewAction
+    public static class StyleGuideAction extends SimpleViewAction<Object>
     {
         @Override
         public ModelAndView getView(Object o, BindException errors)
@@ -2160,7 +2150,7 @@ public void addNavTrail(NavTree root)
     }
 
     @AdminConsoleAction(AdminOperationsPermission.class)
-    public static class ConfigureReportsAndScriptsAction extends SimpleViewAction
+    public static class ConfigureReportsAndScriptsAction extends SimpleViewAction<Object>
     {
         @Override
         public ModelAndView getView(Object o, BindException errors)
@@ -2177,7 +2167,7 @@ public void addNavTrail(NavTree root)
     }
 
     @AdminConsoleAction(AdminOperationsPermission.class)
-    public static class ScriptEnginesSummaryAction extends ReadOnlyApiAction
+    public static class ScriptEnginesSummaryAction extends ReadOnlyApiAction<Object>
     {
         @Override
         public ApiResponse execute(Object o, BindException errors)
diff --git a/core/src/org/labkey/core/attachment/AttachmentServiceImpl.java b/core/src/org/labkey/core/attachment/AttachmentServiceImpl.java
index b6e72f8779f..38bf73075b4 100644
--- a/core/src/org/labkey/core/attachment/AttachmentServiceImpl.java
+++ b/core/src/org/labkey/core/attachment/AttachmentServiceImpl.java
@@ -591,9 +591,9 @@ public int moveAttachments(Container newContainer, List<AttachmentParent> parent
 
         for (Attachment attachment : attachments)
         {
-            if (parent instanceof AttachmentDirectory)
+            if (parent instanceof AttachmentDirectory adParent)
             {
-                File f = new File(((AttachmentDirectory)parent).getFileSystemDirectory(), attachment.getName());
+                File f = new File((adParent).getFileSystemDirectory(), attachment.getName());
                 files.add(new FileAttachmentFile(f));
             }
             else
@@ -1788,9 +1788,9 @@ public void testDirectories() throws IOException
             svc.renameAttachment(attachParent, newName, oldName, user);
 
 
-            assertTrue(new File(attachDir, UPLOAD_LOG).exists());
+            assertTrue(FileUtil.appendName(attachDir, UPLOAD_LOG).exists());
 
-            File otherDir = new File(attachDir, "subdir");
+            File otherDir = FileUtil.appendName(attachDir, "subdir");
             otherDir.mkdir();
             AttachmentDirectory namedParent = fileService.registerDirectory(folder, "test", otherDir.getCanonicalPath(), false);
 
@@ -1802,14 +1802,14 @@ public void testDirectories() throws IOException
             att = svc.getAttachments(namedParent);
             assertEquals(1, att.size());
             assertTrue(att.get(0).getFile().exists());
-            assertSameFile(new File(otherDir, "file.txt"), att.get(0).getFile());
-            assertTrue(new File(otherDir, UPLOAD_LOG).exists());
+            assertSameFile(FileUtil.appendName(otherDir, "file.txt"), att.get(0).getFile());
+            assertTrue(FileUtil.appendName(otherDir, UPLOAD_LOG).exists());
 
             fileService.unregisterDirectory(folder, "test");
             namedParentTest = fileService.getRegisteredDirectory(folder, "test");
             assertNull(namedParentTest);
 
-            File relativeDir = new File(attachDir, "subdir2");
+            File relativeDir = FileUtil.appendName(attachDir, "subdir2");
             relativeDir.mkdirs();
             AttachmentDirectory relativeParent = fileService.registerDirectory(folder, "relative", FileUtil.getAbsoluteCaseSensitiveFile(relativeDir).getAbsolutePath(), false);
             
@@ -1822,10 +1822,10 @@ public void testDirectories() throws IOException
             assertEquals(1, att.size());
 
             File expectedFile1 = att.get(0).getFile();
-            File expectedFile2 = new File(relativeDir, UPLOAD_LOG);
+            File expectedFile2 = FileUtil.appendName(relativeDir, UPLOAD_LOG);
 
             assertTrue(expectedFile1.exists());
-            assertEquals(new File(relativeDir, "file.txt"), expectedFile1);
+            assertEquals(FileUtil.appendName(relativeDir, "file.txt"), expectedFile1);
             assertTrue(expectedFile2.exists());
 
 
diff --git a/core/src/org/labkey/core/notification/EmailServiceImpl.java b/core/src/org/labkey/core/notification/EmailServiceImpl.java
index 98d685f3fc1..767794155ee 100644
--- a/core/src/org/labkey/core/notification/EmailServiceImpl.java
+++ b/core/src/org/labkey/core/notification/EmailServiceImpl.java
@@ -43,6 +43,7 @@
 import org.labkey.api.notification.EmailPref;
 import org.labkey.api.notification.EmailService;
 import org.labkey.api.security.User;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.JunitUtil;
 import org.labkey.api.util.MailHelper;
 import org.labkey.api.util.MailHelper.BulkEmailer;
@@ -374,7 +375,7 @@ private void testAttachmentExceptions(String name) throws IOException
             EmailMessage msg = getBaseMessage();
             File studySampleData = JunitUtil.getSampleData(module, "study");
 
-            List<File> attachmentList = Collections.singletonList(new File(studySampleData, name));
+            List<File> attachmentList = Collections.singletonList(FileUtil.appendName(studySampleData, name));
 
             exception.expect(IllegalArgumentException.class);
             msg.setFiles(attachmentList);
diff --git a/core/src/org/labkey/core/vcs/VcsServiceImpl.java b/core/src/org/labkey/core/vcs/VcsServiceImpl.java
index a19e7761c2c..eef8701044f 100644
--- a/core/src/org/labkey/core/vcs/VcsServiceImpl.java
+++ b/core/src/org/labkey/core/vcs/VcsServiceImpl.java
@@ -3,6 +3,7 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.vcs.Vcs;
 import org.labkey.api.vcs.VcsService;
 
@@ -50,9 +51,9 @@ private static VcsType determine(File dir)
         {
             while (null != dir)
             {
-                if (new File(dir, ".git").exists())
+                if (FileUtil.appendName(dir, ".git").exists())
                     return git;
-                if (new File(dir, ".svn").exists())
+                if (FileUtil.appendName(dir, ".svn").exists())
                     return svn;
                 dir = dir.getParentFile();
             }
diff --git a/core/src/org/labkey/core/webdav/DavController.java b/core/src/org/labkey/core/webdav/DavController.java
index 7fa4980be9d..58c7bbb0112 100644
--- a/core/src/org/labkey/core/webdav/DavController.java
+++ b/core/src/org/labkey/core/webdav/DavController.java
@@ -3779,7 +3779,7 @@ WebdavStatus doMethod() throws DavException, IOException
                     if (destFile.exists())
                     {
                         WebdavResource parent = (WebdavResource)dest.parent();
-                        tmp = new File(parent.getFile(), "~rename" + GUID.makeHash() + "~" + dest.getName());
+                        tmp = FileUtil.appendName(parent.getFile(), "~rename" + GUID.makeHash() + "~" + dest.getName());
                         markTempFile(tmp);
                         if (!destFile.renameTo(tmp))
                             throw new ConfigurationException("Could not remove destination: " + dest.getPath());
diff --git a/devtools/src/org/labkey/devtools/ToolsController.java b/devtools/src/org/labkey/devtools/ToolsController.java
index 1d3902d05b9..dc1041fb97e 100644
--- a/devtools/src/org/labkey/devtools/ToolsController.java
+++ b/devtools/src/org/labkey/devtools/ToolsController.java
@@ -286,7 +286,7 @@ public void handle(Path gaPath, Stream<String> stream)
                     @Override
                     public void handle(Path gaPath, Stream<String> stream)
                     {
-                        try (PrintWriter output = PrintWriters.getPrintWriter(new File(gaPath.getParent().toFile(), "gitattributes.temp")))
+                        try (PrintWriter output = PrintWriters.getPrintWriter(FileUtil.appendName(gaPath.getParent().toFile(), "gitattributes.temp")))
                         {
                             stream
                                 .filter(o -> !missingFiles.contains(o))

From cc85424550cbc428eb8a9add3f183ed86585224f Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Wed, 8 Oct 2025 13:06:37 -0700
Subject: [PATCH 07/15] Lots of FileUtil.appendName()

---
 .../labkey/api/data/bigiron/AbstractClrInstallationManager.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/api/src/org/labkey/api/data/bigiron/AbstractClrInstallationManager.java b/api/src/org/labkey/api/data/bigiron/AbstractClrInstallationManager.java
index 25bd23681ed..e001dc1f1ef 100644
--- a/api/src/org/labkey/api/data/bigiron/AbstractClrInstallationManager.java
+++ b/api/src/org/labkey/api/data/bigiron/AbstractClrInstallationManager.java
@@ -231,7 +231,7 @@ private String getEnableClrStatements(SqlDialect dialect) throws SqlScriptExcept
         {
             Module core = ModuleLoader.getInstance().getCoreModule();
             String enableClrFilename = "enable_clr.sql";
-            Path path = Path.parse(core.getSqlScriptsPath(dialect)).append(enableClrFilename);
+            Path path = core.getSqlScriptsPath(dialect).append(enableClrFilename);
             Resource r = core.getModuleResource(path);
 
             try

From f069dade1b1eeaae83ec1d5070fd5f6d5ef283e8 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Wed, 8 Oct 2025 15:34:43 -0700
Subject: [PATCH 08/15] Lots of FileUtil.appendName()

---
 .../api/jsp/RecompilingJspClassLoader.java    |  4 +++-
 api/src/org/labkey/api/util/JunitUtil.java    |  2 +-
 .../attachment/AttachmentServiceImpl.java     | 22 ++++++++++++++-----
 .../pipeline/AbstractStudyPipelineJob.java    |  3 ++-
 .../publish/PublishController.java            |  3 +--
 .../visitmanager/PurgeParticipantsJob.java    |  3 +--
 .../labkey/test/tests/study/AssayTest.java    |  3 ++-
 .../test/tests/study/AutoLinkToStudyTest.java |  9 ++++----
 .../tests/study/LinkAssayToStudyTest.java     |  3 ++-
 .../test/tests/study/SharedStudyTest.java     |  8 ++++---
 .../test/tests/study/StudyVisitTagTest.java   |  9 ++++----
 .../test/tests/study/TargetStudyTest.java     |  6 ++---
 12 files changed, 47 insertions(+), 28 deletions(-)

diff --git a/api/src/org/labkey/api/jsp/RecompilingJspClassLoader.java b/api/src/org/labkey/api/jsp/RecompilingJspClassLoader.java
index bd4101ceb70..dfff873721a 100644
--- a/api/src/org/labkey/api/jsp/RecompilingJspClassLoader.java
+++ b/api/src/org/labkey/api/jsp/RecompilingJspClassLoader.java
@@ -31,6 +31,8 @@
 
 import jakarta.servlet.ServletContext;
 import jakarta.servlet.ServletException;
+import org.labkey.api.util.Path;
+
 import javax.tools.JavaCompiler;
 import javax.tools.ToolProvider;
 import java.io.ByteArrayOutputStream;
@@ -70,7 +72,7 @@ public Class loadClass(ServletContext context, String jspFilename) throws ClassN
         {
             File jspJavaFileBuildDirectory = new File(finder.getBuildPath() + JSP_JAVA_PATH);
             File jspClassesFileBuildDirectory = new File(finder.getBuildPath() + JSP_CLASSES_DIR);
-            File classFile = new File(jspClassesFileBuildDirectory, JSP_PACKAGE_PATH + compiledJspPath + ".class");
+            File classFile = FileUtil.appendPath(jspClassesFileBuildDirectory, Path.parse(JSP_PACKAGE_PATH + compiledJspPath + ".class"));
             File sourceFile = null;
             if (null != finder.getSourcePath())
                 sourceFile = new File(getCompleteSourcePath(finder.getSourcePath(), getSourceJspPath(jspFilename)));
diff --git a/api/src/org/labkey/api/util/JunitUtil.java b/api/src/org/labkey/api/util/JunitUtil.java
index 24575abe785..f2b5d2c0731 100644
--- a/api/src/org/labkey/api/util/JunitUtil.java
+++ b/api/src/org/labkey/api/util/JunitUtil.java
@@ -236,7 +236,7 @@ public static void createRaces(final Runnable runnable, final int threads, final
             }
         }
 
-        File file = new File(sampleDataDir, relativePath);
+        File file = FileUtil.appendPath(sampleDataDir, Path.parse(relativePath));
         if (file.exists())
             return file;
 
diff --git a/core/src/org/labkey/core/attachment/AttachmentServiceImpl.java b/core/src/org/labkey/core/attachment/AttachmentServiceImpl.java
index 38bf73075b4..7fb16ff2852 100644
--- a/core/src/org/labkey/core/attachment/AttachmentServiceImpl.java
+++ b/core/src/org/labkey/core/attachment/AttachmentServiceImpl.java
@@ -119,6 +119,7 @@
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
@@ -1146,17 +1147,28 @@ public InputStream getInputStream(AttachmentParent parent, String name) throws F
 
             rs = stmt.executeQuery();
 
-            if (parent instanceof AttachmentDirectory)
+            if (parent instanceof AttachmentDirectory adParent)
             {
-                File parentDir = ((AttachmentDirectory) parent).getFileSystemDirectory();
-                if (!parentDir.exists())
+                java.nio.file.Path parentDir = adParent.getFileSystemDirectoryPath();
+                if (!Files.exists(parentDir))
                     throw new FileNotFoundException("No parent directory for downloaded file " + name + ". Please contact an administrator.");
-                File file = new File(parentDir, name);
+                java.nio.file.Path file = FileUtil.appendName(parentDir, name);
                 stmt.close();
                 stmt = null;
                 rs.close();
                 rs = null;
-                return new FileInputStream(file);
+                try
+                {
+                    return Files.newInputStream(file);
+                }
+                catch (FileNotFoundException e)
+                {
+                    throw e;
+                }
+                catch (IOException e)
+                {
+                    throw new FileNotFoundException(e.getMessage());
+                }
             }
             else
             {
diff --git a/study/api-src/org/labkey/api/study/pipeline/AbstractStudyPipelineJob.java b/study/api-src/org/labkey/api/study/pipeline/AbstractStudyPipelineJob.java
index faba426be8a..2555366289e 100644
--- a/study/api-src/org/labkey/api/study/pipeline/AbstractStudyPipelineJob.java
+++ b/study/api-src/org/labkey/api/study/pipeline/AbstractStudyPipelineJob.java
@@ -38,6 +38,7 @@
 import org.labkey.study.xml.StudyDocument;
 
 import java.io.File;
+import java.nio.file.Path;
 
 // Allows some sharing of code between study publication and specimen refresh
 public abstract class AbstractStudyPipelineJob extends PipelineJob
@@ -54,7 +55,7 @@ public AbstractStudyPipelineJob(String provider, Container source, Container des
 
         setDstContainer(destination);
 
-        File tempLogFile = new File(root.getLogDirectory(), FileUtil.makeFileNameWithTimestamp(getLogName(), "log"));
+        Path tempLogFile = root.getLogDirectoryFileLike(true).resolveChild(FileUtil.makeFileNameWithTimestamp(getLogName(), "log")).toNioPathForWrite();
         setLogFile(tempLogFile);
     }
 
diff --git a/study/src/org/labkey/study/controllers/publish/PublishController.java b/study/src/org/labkey/study/controllers/publish/PublishController.java
index 761f8ecd54f..16a5e29c0e9 100644
--- a/study/src/org/labkey/study/controllers/publish/PublishController.java
+++ b/study/src/org/labkey/study/controllers/publish/PublishController.java
@@ -50,7 +50,6 @@
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 
-import java.io.File;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -315,7 +314,7 @@ public AutoLinkPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot pipeRoot,
             _runIds = form.getRunId();
             _autoLinkCategory = form.getAutoLinkCategory();
 
-            setLogFile(new File(pipeRoot.getRootPath(), FileUtil.makeFileNameWithTimestamp("auto_link_to_study", "log")).toPath());
+            setLogFile(FileUtil.appendName(pipeRoot.getRootPath(), FileUtil.makeFileNameWithTimestamp("auto_link_to_study", "log")).toPath());
         }
 
         @Override
diff --git a/study/src/org/labkey/study/visitmanager/PurgeParticipantsJob.java b/study/src/org/labkey/study/visitmanager/PurgeParticipantsJob.java
index 9ad589b0bd5..118dc10328a 100644
--- a/study/src/org/labkey/study/visitmanager/PurgeParticipantsJob.java
+++ b/study/src/org/labkey/study/visitmanager/PurgeParticipantsJob.java
@@ -13,7 +13,6 @@
 import org.labkey.study.model.StudyImpl;
 import org.labkey.study.model.StudyManager;
 
-import java.io.File;
 import java.util.Iterator;
 import java.util.Map;
 import java.util.Set;
@@ -30,7 +29,7 @@ public PurgeParticipantsJob()
     PurgeParticipantsJob(ViewBackgroundInfo info, PipeRoot pipeRoot)
     {
         super("StudyParticipantPurge", info, pipeRoot);
-        setLogFile(new File(pipeRoot.getLogDirectory(), FileUtil.makeFileNameWithTimestamp("purge_participants", "log")).toPath());
+        setLogFile(pipeRoot.getLogDirectoryFileLike(true).resolveChild(FileUtil.makeFileNameWithTimestamp("purge_participants", "log")).toNioPathForWrite());
     }
 
     @Override
diff --git a/study/test/src/org/labkey/test/tests/study/AssayTest.java b/study/test/src/org/labkey/test/tests/study/AssayTest.java
index fc612123a4f..88329c00103 100644
--- a/study/test/src/org/labkey/test/tests/study/AssayTest.java
+++ b/study/test/src/org/labkey/test/tests/study/AssayTest.java
@@ -18,6 +18,7 @@
 
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.remoteapi.CommandException;
 import org.labkey.remoteapi.assay.AssayListCommand;
 import org.labkey.remoteapi.assay.AssayListResponse;
@@ -131,7 +132,7 @@ public void testAssaySecurity() throws Exception
         log("Starting Assay security scenario tests");
         setupEnvironment();
         setupPipeline(getProjectName());
-        SpecimenImporter importer = new SpecimenImporter(TestFileUtils.getTestTempDir(), StudyHelper.SPECIMEN_ARCHIVE_A, new File(TestFileUtils.getTestTempDir(), "specimensSubDir"), TEST_ASSAY_FLDR_STUDY2, 1);
+        SpecimenImporter importer = new SpecimenImporter(TestFileUtils.getTestTempDir(), StudyHelper.SPECIMEN_ARCHIVE_A, FileUtil.appendName(TestFileUtils.getTestTempDir(), "specimensSubDir"), TEST_ASSAY_FLDR_STUDY2, 1);
         importer.importAndWaitForComplete();
         defineAssay();
         uploadRuns(TEST_ASSAY_FLDR_LAB1, TEST_ASSAY_USR_TECH1);
diff --git a/study/test/src/org/labkey/test/tests/study/AutoLinkToStudyTest.java b/study/test/src/org/labkey/test/tests/study/AutoLinkToStudyTest.java
index 631dae2a881..a477916f7e7 100644
--- a/study/test/src/org/labkey/test/tests/study/AutoLinkToStudyTest.java
+++ b/study/test/src/org/labkey/test/tests/study/AutoLinkToStudyTest.java
@@ -5,6 +5,7 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.TestFileUtils;
@@ -100,7 +101,7 @@ public void testAutoLinkInSameFolder()
                 .setAutoLinkCategory(categoryName)
                 .clickSave();
 
-        File runFile = new File(TestFileUtils.getSampleData("AssayImportExport"), "GenericAssay_Run1.xls");
+        File runFile = FileUtil.appendName(TestFileUtils.getSampleData("AssayImportExport"), "GenericAssay_Run1.xls");
         importAssayRun(runFile, ASSAY_NAME, runName);
 
         log("Verifying data is auto imported in study");
@@ -181,7 +182,7 @@ public void testPredefinedDatasetCategories()
         _assayHelper.clickEditAssayDesign().setAutoLinkTarget("").clickSave();
 
         goToProjectHome();
-        File runFile = new File(TestFileUtils.getSampleData("AssayImportExport"), "GenericAssay_Run3.xls");
+        File runFile = FileUtil.appendName(TestFileUtils.getSampleData("AssayImportExport"), "GenericAssay_Run3.xls");
         importAssayRun(runFile, ASSAY_NAME, runName);
 
         linkToStudy(runName, STUDY1, 1, categoryName); // Category exists in Study 1
@@ -212,7 +213,7 @@ public void testOverWritingDatasetCategory()
                 .clickSave();
 
         goToProjectHome();
-        File runFile = new File(TestFileUtils.getSampleData("AssayImportExport"), "GenericAssay_Run4.xls");
+        File runFile = FileUtil.appendName(TestFileUtils.getSampleData("AssayImportExport"), "GenericAssay_Run4.xls");
         importAssayRun(runFile, ASSAY_NAME, runName);
 
         linkToStudy(runName, STUDY1, 1, categoryName);
@@ -240,7 +241,7 @@ public void testReaderRoleLinkToStudy()
                 .clickSave();
 
         goToProjectHome();
-        File runFile = new File(TestFileUtils.getSampleData("AssayImportExport"), "GenericAssay_Run4.xls");
+        File runFile = FileUtil.appendName(TestFileUtils.getSampleData("AssayImportExport"), "GenericAssay_Run4.xls");
         importAssayRun(runFile, ASSAY_NAME, runName);
 
         goToProjectHome(STUDY1);
diff --git a/study/test/src/org/labkey/test/tests/study/LinkAssayToStudyTest.java b/study/test/src/org/labkey/test/tests/study/LinkAssayToStudyTest.java
index 55a0f30bec6..5739c5813d7 100644
--- a/study/test/src/org/labkey/test/tests/study/LinkAssayToStudyTest.java
+++ b/study/test/src/org/labkey/test/tests/study/LinkAssayToStudyTest.java
@@ -19,6 +19,7 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.test.Locator;
 import org.labkey.test.TestFileUtils;
 import org.labkey.test.TestTimeoutException;
@@ -75,7 +76,7 @@ private void doSetup() throws IOException
         {
             SpecimenImporter importer = new SpecimenImporter(TestFileUtils.getTestTempDir(),
                     StudyHelper.SPECIMEN_ARCHIVE_A,
-                    new File(TestFileUtils.getTestTempDir(), "specimensSubDir"), TEST_ASSAY_FLDR_STUDY2, 1);
+                    FileUtil.appendName(TestFileUtils.getTestTempDir(), "specimensSubDir"), TEST_ASSAY_FLDR_STUDY2, 1);
             importer.importAndWaitForComplete();
         }
         defineAssay();
diff --git a/study/test/src/org/labkey/test/tests/study/SharedStudyTest.java b/study/test/src/org/labkey/test/tests/study/SharedStudyTest.java
index 9f3aceeffd9..d54c8b68973 100644
--- a/study/test/src/org/labkey/test/tests/study/SharedStudyTest.java
+++ b/study/test/src/org/labkey/test/tests/study/SharedStudyTest.java
@@ -23,6 +23,8 @@
 import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.Path;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.Locators;
@@ -114,7 +116,7 @@ private void doSetup()
                 .setDatasetId(SHARED_DEMOGRAPHICS_ID)
                 .shareDemographics("Share by PandaId")
                 .clickApply();
-        datasetDesignerPage.getFieldsPanel().setInferFieldFile(new File(STUDY_DIR, "study/datasets/dataset5001.tsv"));
+        datasetDesignerPage.getFieldsPanel().setInferFieldFile(FileUtil.appendPath(STUDY_DIR, Path.parse("study/datasets/dataset5001.tsv")));
         // leave the 'visits' column unmapped, make sure it doesn't have a value/only has a placeholder
         // (this dataset doesn't have a meaningful visit field)
         assertEquals("", datasetDesignerPage.getPreviewMappedColumnValue("Visits"));
@@ -131,8 +133,8 @@ private void doSetup()
         setFormElement(Locator.name("subjectColumnName"), "PandaId");
         clickButton("Create Study");
         beginAt(WebTestHelper.buildURL("study", getProjectName() + "/" + STUDY2, "dataset", Maps.of("datasetId", SHARED_DEMOGRAPHICS_ID)));
-        _listHelper.importDataFromFile(new File(STUDY_DIR, "study/datasets/extra_demographics.txt"));
-        _studyHelper.importDataset(STUDY2_DATASET, getProjectName() + "/" + STUDY2, STUDY2_DATASET_ID, new File(STUDY_DIR, "study/datasets/extra_dataset.txt"));
+        _listHelper.importDataFromFile(FileUtil.appendPath(STUDY_DIR, Path.parse("study/datasets/extra_demographics.txt")));
+        _studyHelper.importDataset(STUDY2_DATASET, getProjectName() + "/" + STUDY2, STUDY2_DATASET_ID, FileUtil.appendPath(STUDY_DIR, Path.parse("study/datasets/extra_dataset.txt")));
     }
 
     @Before
diff --git a/study/test/src/org/labkey/test/tests/study/StudyVisitTagTest.java b/study/test/src/org/labkey/test/tests/study/StudyVisitTagTest.java
index 3dcafa3ece7..a5222287b78 100644
--- a/study/test/src/org/labkey/test/tests/study/StudyVisitTagTest.java
+++ b/study/test/src/org/labkey/test/tests/study/StudyVisitTagTest.java
@@ -18,6 +18,7 @@
 import org.apache.commons.collections4.Bag;
 import org.apache.commons.collections4.bag.HashBag;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.TestFileUtils;
@@ -98,26 +99,26 @@ protected void importStudies()
     {
         File visitTagsPath = TestFileUtils.getSampleData("VisitTags");
         goToProjectHome();
-        startImportStudyFromZip(new File(visitTagsPath, PARENT_FOLDER_STUDY + ".folder.zip"), false, false);
+        startImportStudyFromZip(FileUtil.appendName(visitTagsPath, PARENT_FOLDER_STUDY + ".folder.zip"), false, false);
 
         for (String study : DATE_BASED_STUDIES)
         {
             clickFolder(study);
-            startImportStudyFromZip(new File(visitTagsPath, study + ".folder.zip"), false, false);
+            startImportStudyFromZip(FileUtil.appendName(visitTagsPath, study + ".folder.zip"), false, false);
             waitForPipelineJobsToComplete(1, "Study import", false);
         }
 
         for (String study : VISIT_BASED_STUDIES)
         {
             clickFolder(study);
-            startImportStudyFromZip(new File(visitTagsPath, study + ".folder.zip"), false, false);
+            startImportStudyFromZip(FileUtil.appendName(visitTagsPath, study + ".folder.zip"), false, false);
             waitForPipelineJobsToComplete(1, "Study import", false);
         }
 
         for (String study : SINGLE_USE_TAG_ERRORS)
         {
             clickFolder(study);
-            startImportStudyFromZip(new File(visitTagsPath, study + ".folder.zip"), false, false);
+            startImportStudyFromZip(FileUtil.appendName(visitTagsPath, study + ".folder.zip"), false, false);
             waitForPipelineJobsToComplete(1, "Study import", true /* expect error */);
             checkExpectedErrors(1);
         }
diff --git a/study/test/src/org/labkey/test/tests/study/TargetStudyTest.java b/study/test/src/org/labkey/test/tests/study/TargetStudyTest.java
index 144a5e1e6bf..f88217e037a 100644
--- a/study/test/src/org/labkey/test/tests/study/TargetStudyTest.java
+++ b/study/test/src/org/labkey/test/tests/study/TargetStudyTest.java
@@ -18,6 +18,7 @@
 
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.SortDirection;
@@ -32,7 +33,6 @@
 import org.labkey.test.util.StudyHelper;
 import org.openqa.selenium.By;
 
-import java.io.File;
 import java.util.Random;
 
 import static org.junit.Assert.assertEquals;
@@ -101,10 +101,10 @@ protected void setupSpecimens() throws Exception
     {
         log("** Import specimens into Study 1 and Study 2");
         setupPipeline(TEST_ASSAY_PRJ_SECURITY);
-        SpecimenImporter importer1 = new SpecimenImporter(TestFileUtils.getTestTempDir(), StudyHelper.SPECIMEN_ARCHIVE_A, new File(TestFileUtils.getTestTempDir(), "specimensSubDir"), TEST_ASSAY_FLDR_STUDY1, 1);
+        SpecimenImporter importer1 = new SpecimenImporter(TestFileUtils.getTestTempDir(), StudyHelper.SPECIMEN_ARCHIVE_A, FileUtil.appendName(TestFileUtils.getTestTempDir(), "specimensSubDir"), TEST_ASSAY_FLDR_STUDY1, 1);
         importer1.startImport();
 
-        SpecimenImporter importer2 = new SpecimenImporter(TestFileUtils.getTestTempDir(), StudyHelper.SPECIMEN_ARCHIVE_A, new File(TestFileUtils.getTestTempDir(), "specimensSubDir"), TEST_ASSAY_FLDR_STUDY2, 1);
+        SpecimenImporter importer2 = new SpecimenImporter(TestFileUtils.getTestTempDir(), StudyHelper.SPECIMEN_ARCHIVE_A, FileUtil.appendName(TestFileUtils.getTestTempDir(), "specimensSubDir"), TEST_ASSAY_FLDR_STUDY2, 1);
         importer2.startImport();
 
         importer1.waitForComplete();

From 1a717fef342b00b80c3781126d75643331c8c337 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Wed, 8 Oct 2025 17:04:11 -0700
Subject: [PATCH 09/15] More FileUtil.appendName()

---
 .../org/labkey/devtools/ToolsController.java  |    2 +-
 .../org/labkey/experiment/XarExporter.java    |    4 +-
 .../experiment/api/ExpDataTableImpl.java      | 1900 ++++++++---------
 .../experiment/pipeline/MoveRunsTask.java     |  568 ++---
 .../experiment/pipeline/SampleReloadTask.java |    2 +-
 5 files changed, 1238 insertions(+), 1238 deletions(-)

diff --git a/devtools/src/org/labkey/devtools/ToolsController.java b/devtools/src/org/labkey/devtools/ToolsController.java
index dc1041fb97e..f6a077a417a 100644
--- a/devtools/src/org/labkey/devtools/ToolsController.java
+++ b/devtools/src/org/labkey/devtools/ToolsController.java
@@ -230,7 +230,7 @@ private List<String> getMissingFiles(Path gaPath, Stream<String> filepaths)
             .filter(line -> {
                 int idx = line.indexOf(' ');
                 String filename = line.substring(0, idx);
-                File file = new File(gaDirFile, filename);
+                File file = FileUtil.appendPath(gaDirFile, org.labkey.api.util.Path.parse(filename));
 
                 return !file.exists();
             })
diff --git a/experiment/src/org/labkey/experiment/XarExporter.java b/experiment/src/org/labkey/experiment/XarExporter.java
index 9a184ee17a2..1af4efb740e 100644
--- a/experiment/src/org/labkey/experiment/XarExporter.java
+++ b/experiment/src/org/labkey/experiment/XarExporter.java
@@ -1590,7 +1590,7 @@ public void writeAsDirectory(File dir) throws IOException
         {
             if (_includeXML)
             {
-                File xmlEntry = new File(dir, _xarXmlFileName);
+                File xmlEntry = FileUtil.appendName(dir, _xarXmlFileName);
                 logProgress("Writing XAR XML file");
                 try (FileOutputStream os = new FileOutputStream(xmlEntry))
                 {
@@ -1615,7 +1615,7 @@ public void writeAsDirectory(File dir) throws IOException
         catch (Exception e)
         {
             // insert the stack trace into the zip file
-            File errorEntry = new File(dir,"error.log");
+            File errorEntry = FileUtil.appendName(dir,"error.log");
 
             try (FileOutputStream os = new FileOutputStream(errorEntry); PrintStream ps = new PrintStream(os))
             {
diff --git a/experiment/src/org/labkey/experiment/api/ExpDataTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpDataTableImpl.java
index 232ff1029ab..f6e90b5b05b 100644
--- a/experiment/src/org/labkey/experiment/api/ExpDataTableImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExpDataTableImpl.java
@@ -1,950 +1,950 @@
-/*
- * Copyright (c) 2008-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.labkey.experiment.api;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.jetbrains.annotations.NotNull;
-import org.json.JSONObject;
-import org.junit.AfterClass;
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.labkey.api.action.ApiJsonWriter;
-import org.labkey.api.action.ApiResponseWriter;
-import org.labkey.api.action.ExtendedApiQueryResponse;
-import org.labkey.api.action.NullSafeBindException;
-import org.labkey.api.compliance.TableRules;
-import org.labkey.api.compliance.TableRulesManager;
-import org.labkey.api.data.ColumnInfo;
-import org.labkey.api.data.Container;
-import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerManager;
-import org.labkey.api.data.ExcelWriter;
-import org.labkey.api.data.JdbcType;
-import org.labkey.api.data.MutableColumnInfo;
-import org.labkey.api.data.RenderContext;
-import org.labkey.api.data.SQLFragment;
-import org.labkey.api.data.SimpleFilter;
-import org.labkey.api.exp.DomainDescriptor;
-import org.labkey.api.exp.OntologyManager;
-import org.labkey.api.exp.PropertyColumn;
-import org.labkey.api.exp.api.DataType;
-import org.labkey.api.exp.api.ExpData;
-import org.labkey.api.exp.api.ExpDataClass;
-import org.labkey.api.exp.api.ExpExperiment;
-import org.labkey.api.exp.api.ExpProtocol;
-import org.labkey.api.exp.api.ExpRun;
-import org.labkey.api.exp.api.ExpSampleType;
-import org.labkey.api.exp.api.ExperimentService;
-import org.labkey.api.exp.property.Domain;
-import org.labkey.api.exp.property.DomainProperty;
-import org.labkey.api.exp.property.PropertyService;
-import org.labkey.api.exp.query.ExpDataTable;
-import org.labkey.api.exp.query.ExpSchema;
-import org.labkey.api.exp.query.SamplesSchema;
-import org.labkey.api.files.FileContentService;
-import org.labkey.api.pipeline.PipeRoot;
-import org.labkey.api.pipeline.PipelineService;
-import org.labkey.api.query.DetailsURL;
-import org.labkey.api.query.ExprColumn;
-import org.labkey.api.query.FieldKey;
-import org.labkey.api.query.QueryForeignKey;
-import org.labkey.api.query.QueryService;
-import org.labkey.api.query.QuerySettings;
-import org.labkey.api.query.QueryUpdateService;
-import org.labkey.api.query.QueryView;
-import org.labkey.api.query.RowIdForeignKey;
-import org.labkey.api.query.UserSchema;
-import org.labkey.api.query.column.BuiltInColumnTypes;
-import org.labkey.api.reader.ExcelLoader;
-import org.labkey.api.security.User;
-import org.labkey.api.security.permissions.InsertPermission;
-import org.labkey.api.security.permissions.UpdatePermission;
-import org.labkey.api.util.ConfigurationException;
-import org.labkey.api.util.FileUtil;
-import org.labkey.api.util.HtmlString;
-import org.labkey.api.util.LinkBuilder;
-import org.labkey.api.util.TestContext;
-import org.labkey.api.view.ActionURL;
-import org.labkey.api.writer.HtmlWriter;
-import org.labkey.api.writer.MemoryVirtualFile;
-import org.labkey.api.writer.VirtualFile;
-import org.labkey.experiment.controllers.exp.ExperimentController;
-import org.labkey.experiment.lineage.LineageMethod;
-import org.springframework.beans.MutablePropertyValues;
-import org.springframework.validation.BindException;
-
-import java.io.File;
-import java.io.OutputStream;
-import java.io.StringWriter;
-import java.io.Writer;
-import java.net.URI;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-import java.util.stream.Collectors;
-
-import static org.labkey.api.exp.query.ExpSchema.TableType.DataClasses;
-
-public class ExpDataTableImpl extends ExpRunItemTableImpl<ExpDataTable.Column> implements ExpDataTable
-{
-    protected ExpExperiment _experiment;
-    protected boolean _runSpecified;
-    protected ExpRun _run;
-    protected DataType _type;
-    protected ExpDataClass _dataClass;
-
-    public ExpDataTableImpl(String name, UserSchema schema, ContainerFilter cf)
-    {
-        super(name, ExperimentServiceImpl.get().getTinfoData(), schema, cf);
-
-        addAllowablePermission(UpdatePermission.class);
-        addAllowablePermission(InsertPermission.class);
-    }
-
-    @Override
-    protected void populateColumns()
-    {
-        addColumn(Column.RowId).setHidden(true);
-        addColumn(Column.Name);
-        addColumn(Column.Description);
-        var aliasCol = addColumn(Column.Alias);
-        aliasCol.setHidden(true);
-        addColumn(Column.DataClass);
-        ExpSchema schema = getExpSchema();
-        addColumn(Column.Run).setFk(schema.getRunIdForeignKey(getContainerFilter()));
-        addColumn(Column.Created);
-        addColumn(Column.CreatedBy);
-        addColumn(Column.Modified);
-        addColumn(Column.ModifiedBy);
-
-        addColumn(Column.ContentLink);
-        addColumn(Column.Thumbnail);
-        addColumn(Column.InlineThumbnail);
-        addColumn(Column.SourceProtocolApplication);
-        addColumn(Column.Protocol);
-        addContainerColumn(Column.Folder, null);
-        addColumn(Column.ViewOrDownload);
-        addColumn(Column.Generated);
-        addColumn(Column.LastIndexed);
-
-        addFileColumns(false);
-
-        setDefaultColumns();
-        setTitleColumn("Name");
-
-        // Only include the dataClassId parameter if the ExpData row has a DataClass
-        DetailsURL detailsURL = DetailsURL.fromString("/experiment/showData.view?rowId=${rowId}${dataClass:prefix('%26dataClassId=')}");
-
-        setDetailsURL(detailsURL);
-        getMutableColumn(Column.RowId).setURL(detailsURL);
-        getMutableColumn(Column.Name).setURL(detailsURL);
-
-        ActionURL deleteUrl = ExperimentController.ExperimentUrlsImpl.get().getDeleteDatasURL(getContainer(), null);
-        setDeleteURL(new DetailsURL(deleteUrl));
-
-        addVocabularyDomains();
-        addColumn(Column.Properties);
-
-        var colInputs = addColumn(Column.Inputs);
-        addMethod("Inputs", new LineageMethod(colInputs, true), Set.of(colInputs.getFieldKey()));
-
-        var colOutputs = addColumn(Column.Outputs);
-        addMethod("Outputs", new LineageMethod(colOutputs, false), Set.of(colOutputs.getFieldKey()));
-
-        MutableColumnInfo lineageLookup = ClosureQueryHelper.createAncestorLookupColumnInfo("Ancestors", this, _rootTable.getColumn("rowid"), null, false);
-        addColumn(lineageLookup);
-
-        addExpObjectMethod();
-    }
-
-    @Override
-    public ColumnInfo getExpObjectColumn()
-    {
-        var ret = wrapColumn("_ExpDataTableImpl_object_", _rootTable.getColumn("objectid"));
-        ret.setConceptURI(BuiltInColumnTypes.EXPOBJECTID_CONCEPT_URI);
-        return ret;
-    }
-
-    public List<String> addFileColumns(boolean isFilesTable)
-    {
-        List<String> customProps = new ArrayList<>();
-        var lsidColumn = addColumn(Column.LSID);
-        lsidColumn.setHidden(true);
-        if (!isFilesTable)
-            addColumn(Column.DataFileUrl);
-
-        addColumn(Column.DownloadLink);
-        addColumn(Column.ViewFileLink);
-        addColumn(Column.FileExists);
-        addColumn(Column.FileSize);
-        addColumn(Column.FileExtension);
-        addColumn(Column.WebDavUrl);
-        addColumn(Column.WebDavUrlRelative);
-        var flagCol = addColumn(Column.Flag);
-        if (isFilesTable)
-            flagCol.setLabel("Description");
-
-        FileContentService svc = FileContentService.get();
-        String domainURI = svc.getDomainURI(getContainer());
-        DomainDescriptor dd = OntologyManager.getDomainDescriptor(domainURI, getContainer());
-
-        if (dd != null)
-        {
-            Domain domain = PropertyService.get().getDomain(dd.getDomainId());
-            if (domain != null)
-            {
-                for (DomainProperty prop : domain.getProperties())
-                {
-                    // don't set container on property column so that inherited domain properties work
-                    var projectColumn = new PropertyColumn(prop.getPropertyDescriptor(), lsidColumn, getContainer(), _userSchema.getUser(), false);
-                    addColumn(projectColumn);
-                    customProps.add(projectColumn.getAlias().getId());
-                }
-                setDomain(domain);
-            }
-        }
-
-        return customProps;
-    }
-
-    @Override
-    public boolean supportTableRules() // intentional override
-    {
-        return true;
-    }
-
-    @Override
-    protected @NotNull TableRules findTableRules()
-    {
-        Container definitionContainer = getUserSchema().getContainer();
-        if (null != getDomain())
-            definitionContainer = getDomain().getContainer();
-        return TableRulesManager.get().getTableRules(definitionContainer, getUserSchema().getUser(), getUserSchema().getContainer());
-    }
-
-    public void setDefaultColumns()
-    {
-        checkLocked();
-        List<FieldKey> defaultCols = new ArrayList<>();
-        defaultCols.add(FieldKey.fromParts(Column.Name));
-        defaultCols.add(FieldKey.fromParts(Column.Run));
-        defaultCols.add(FieldKey.fromParts(Column.DataFileUrl));
-        setDefaultVisibleColumns(defaultCols);
-    }
-
-    @Override
-    public QueryUpdateService getUpdateService()
-    {
-        return FileContentService.get().getFilePropsUpdateService(this, getContainer());
-    }
-
-    @Override
-    protected ColumnInfo resolveColumn(String name)
-    {
-        return super.resolveColumn(name);
-    }
-
-    @Override
-    public MutableColumnInfo createColumn(String alias, Column column)
-    {
-        switch (column)
-        {
-            case Folder:
-                return wrapColumn(alias, _rootTable.getColumn("Container"));
-            case Created:
-                return wrapColumn(alias, _rootTable.getColumn("Created"));
-            case CreatedBy:
-                return createUserColumn(alias, _rootTable.getColumn("CreatedBy"));
-            case Modified:
-                return wrapColumn(alias, _rootTable.getColumn("Modified"));
-            case ModifiedBy:
-                return createUserColumn(alias, _rootTable.getColumn("ModifiedBy"));
-            case DataFileUrl:
-                var dataFileUrl = wrapColumn(alias, _rootTable.getColumn("DataFileUrl"));
-                dataFileUrl.setUserEditable(false);
-                return dataFileUrl;
-            case LSID:
-                var lsid = wrapColumn(alias, _rootTable.getColumn("LSID"));
-                lsid.setUserEditable(false);
-                return lsid;
-            case Name:
-                return wrapColumn(alias, _rootTable.getColumn("Name"));
-            case Description:
-                return wrapColumn(alias, _rootTable.getColumn("Description"));
-            case LastIndexed:
-                SQLFragment lastIndexedSql = new SQLFragment("(SELECT LastIndexed FROM ").
-                        append(ExperimentServiceImpl.get().getTinfoDataIndexed(), "di").
-                        append(" WHERE di.DataId = ").
-                        append(ExprColumn.STR_TABLE_ALIAS).append(".RowId)");
-                var lastIndexed = new ExprColumn(this, "LastIndexed", lastIndexedSql, JdbcType.TIMESTAMP);
-                lastIndexed.setUserEditable(false);
-                return lastIndexed;
-            case DataClass:
-            {
-                var c = wrapColumn(alias, _rootTable.getColumn("classId"));
-                c.setUserEditable(false);
-                var fk = QueryForeignKey.from(getUserSchema(), getContainerFilter())
-                        .to(DataClasses.name(), "RowId", "Name");
-                c.setFk( fk );
-                return c;
-            }
-            case Protocol:
-            {
-                ExprColumn col = new ExprColumn(this, Column.Protocol.toString(), new SQLFragment(
-                        "(SELECT ProtocolLSID FROM " + ExperimentServiceImpl.get().getTinfoProtocolApplication() + " pa " +
-                        " WHERE pa.RowId = " + ExprColumn.STR_TABLE_ALIAS + ".SourceApplicationId)"), JdbcType.VARCHAR, getColumn(Column.SourceProtocolApplication));
-                col.setFk(getExpSchema().getProtocolForeignKey(getContainerFilter(),"LSID"));
-                col.setSqlTypeName("lsidtype");
-                col.setHidden(true);
-                return col;
-            }
-            case SourceProtocolApplication:
-            {
-                var columnInfo = wrapColumn(alias, _rootTable.getColumn("SourceApplicationId"));
-                columnInfo.setFk(getExpSchema().getProtocolApplicationForeignKey(getContainerFilter()));
-                columnInfo.setUserEditable(false);
-                columnInfo.setHidden(true);
-                return columnInfo;
-            }
-
-            case SourceApplicationInput:
-            {
-                var col = createEdgeColumn(alias, Column.SourceProtocolApplication, ExpSchema.TableType.DataInputs);
-                col.setDescription("Contains a reference to the DataInput row between this ExpData and it's SourceProtocolApplication");
-                col.setHidden(true);
-                return col;
-            }
-
-            case RunApplication:
-            {
-                SQLFragment sql = new SQLFragment("(SELECT pa.rowId FROM ")
-                        .append(ExperimentService.get().getTinfoProtocolApplication(), "pa")
-                        .append(" WHERE pa.runId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".runId")
-                        .append(" AND pa.cpasType = '").append(ExpProtocol.ApplicationType.ExperimentRunOutput.name()).append("'")
-                        .append(")");
-
-                var col = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
-                col.setFk(getExpSchema().getProtocolApplicationForeignKey(getContainerFilter()));
-                col.setDescription("Contains a reference to the ExperimentRunOutput protocol application of the run that created this data");
-                col.setUserEditable(false);
-                col.setReadOnly(true);
-                col.setHidden(true);
-                return col;
-            }
-
-            case RunApplicationOutput:
-            {
-                var col = createEdgeColumn(alias, Column.RunApplication, ExpSchema.TableType.DataInputs);
-                col.setDescription("Contains a reference to the DataInput row between this ExpData and it's RunOutputApplication");
-                return col;
-            }
-            case RowId:
-            {
-                var ret = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                ret.setFk(new RowIdForeignKey(ret));
-                ret.setHidden(true);
-                return ret;
-            }
-            case Run:
-                var runId = wrapColumn(alias, _rootTable.getColumn("RunId"));
-                runId.setUserEditable(false);
-                return runId;
-            case Flag:
-                return createFlagColumn(alias);
-            case Alias:
-                return createAliasColumn(alias, ExperimentService.get()::getTinfoDataAliasMap);
-            case DownloadLink:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(DownloadFileDataLinkColumn::new);
-                result.setDescription("A link to download the file");
-                return result;
-            }
-            case ViewFileLink:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(ViewFileDataLinkColumn::new);
-                result.setDescription("A link to view the file directly on the web site");
-                return result;
-            }
-            case ContentLink:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(ViewContentDataLinkColumn::new);
-                result.setDescription("A link to view the imported contents of the file on the web site");
-                return result;
-            }
-            case Thumbnail:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(ThumbnailDataLinkColumn::new);
-                result.setDescription("A popup thumbnail of the file if it is an image");
-                return result;
-            }
-            case InlineThumbnail:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(InlineThumbnailDataLinkColumn::new);
-                result.setDescription("An inline thumbnail of the file if it is an image");
-                return result;
-            }
-            case FileSize:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setTextAlign("left");
-                result.setJdbcType(JdbcType.VARCHAR);
-                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
-                {
-                    @Override
-                    protected void renderData(HtmlWriter out, ExpData data)
-                    {
-                        String val = ((String)getJsonValue(data));
-                        out.write(val);
-                    }
-
-                    @Override
-                    public Object getJsonValue(ExpData data)
-                    {
-                        if (data == null || data.getFile() == null)
-                            return "";
-                        else if (!data.getFile().exists())
-                            return "File Not Found";
-                        else
-                        {
-                            long size = data.getFile().length();
-                            return FileUtils.byteCountToDisplaySize(size);
-                        }
-                    }
-                });
-                result.setUserEditable(false);
-                result.setShownInUpdateView(false);
-                result.setShownInInsertView(false);
-
-                return result;
-            }
-            case FileExists:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setJdbcType(JdbcType.BOOLEAN);
-                result.setTextAlign("left");
-                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
-                {
-                    @Override
-                    protected void renderData(HtmlWriter out, ExpData data)
-                    {
-                        Boolean val = (Boolean)getJsonValue(data);
-                        out.write(val.toString());
-                    }
-
-                    @Override
-                    protected Object getJsonValue(ExpData data)
-                    {
-                        if (data == null)
-                        {
-                            return false;
-                        }
-                        Path path = data.getFilePath();
-                        return path != null && Files.exists(path);
-                    }
-                });
-                result.setUserEditable(false);
-                result.setShownInUpdateView(false);
-                result.setShownInInsertView(false);
-                return result;
-            }
-            case FileExtension:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setJdbcType(JdbcType.VARCHAR);
-                result.setTextAlign("left");
-                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
-                {
-                    @Override
-                    protected void renderData(HtmlWriter out, ExpData data)
-                    {
-                        Object val = getJsonValue(data);
-                        out.write(val);
-                    }
-
-                    @Override
-                    protected Object getJsonValue(ExpData data)
-                    {
-                        return data.getFile() == null ? null : FileUtil.getExtension(data.getFile());
-                    }
-                });
-                result.setUserEditable(false);
-                result.setShownInUpdateView(false);
-                result.setShownInInsertView(false);
-                return result;
-            }
-            case ViewOrDownload:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setLabel("View/Download");
-                result.setDisplayColumnFactory(ViewOrDownloadDataColumn::new);
-                result.setDescription("Displays links to either download the file or view directly on the web site");
-                return result;
-            }
-            case WebDavUrl:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setJdbcType(JdbcType.VARCHAR);
-                result.setLabel("WebDAV URL");
-                result.setDescription("This is the full WebDAV URL to this file");
-                result.setDisplayColumnFactory(colInfo -> new WebDavUrlColumn(colInfo, false));
-                return result;
-            }
-            case WebDavUrlRelative:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setJdbcType(JdbcType.VARCHAR);
-                result.setLabel("Relative WebDAV URL");
-                result.setDescription("This is the WebDAV path of this file, relative to the file root of this container");
-                result.setDisplayColumnFactory(colInfo -> new WebDavUrlColumn(colInfo, true));
-                return result;
-            }
-            case Generated:
-                return wrapColumn(alias, _rootTable.getColumn("Generated"));
-
-            case Inputs:
-                return createLineageColumn(this, alias, true, false);
-
-            case Outputs:
-                return createLineageColumn(this, alias, false, false);
-
-            case Properties:
-                return createPropertiesColumn(alias);
-
-            default:
-                throw new IllegalArgumentException("Unknown column " + column);
-        }
-    }
-
-    @Override
-    public void setExperiment(ExpExperiment experiment)
-    {
-        checkLocked();
-        if (getExperiment() != null)
-            throw new IllegalArgumentException("Attempt to unset experiment");
-        if (experiment == null)
-            return;
-        SQLFragment condition = new SQLFragment("exp.Data.RunId IN "
-                + " ( SELECT ExperimentRunId FROM exp.RunList "
-                + " WHERE ExperimentId = ? )");
-        condition.add(experiment.getRowId());
-        addCondition(condition);
-        _experiment = experiment;
-    }
-
-    @Override
-    public ExpExperiment getExperiment()
-    {
-        return _experiment;
-    }
-
-    @Override
-    public void setRun(ExpRun run)
-    {
-        checkLocked();
-        if (_runSpecified)
-            throw new IllegalArgumentException("Cannot unset run");
-        _runSpecified = true;
-        _run = run;
-        if (run == null)
-        {
-            addCondition(new SQLFragment("(RunId IS NULL)"), FieldKey.fromParts("RunId"));
-        }
-        else
-        {
-            addCondition(_rootTable.getColumn("RunId"), run.getRowId());
-        }
-    }
-
-    @Override
-    public ExpRun getRun()
-    {
-        return _run;
-    }
-
-    @Override
-    public MutableColumnInfo addDataInputColumn(String alias, String role)
-    {
-        SQLFragment sql = new SQLFragment("(SELECT MIN(exp.datainput.dataid)" +
-                "\nFROM exp.datainput" +
-                "\nWHERE " + ExprColumn.STR_TABLE_ALIAS +  ".SourceApplicationId = exp.datainput.TargetApplicationId" +
-                "\nAND ");
-        if (role == null)
-        {
-            sql.append("1 = 0");
-        }
-        else
-        {
-            sql.append("exp.datainput.role = ?");
-            sql.add(role);
-        }
-        sql.append(")");
-        ExprColumn ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
-        return doAdd(ret);
-    }
-
-    @Override
-    public MutableColumnInfo addMaterialInputColumn(String alias, SamplesSchema schema, String pdRole, final ExpSampleType sampleType)
-    {
-        SQLFragment sql = new SQLFragment("(SELECT MIN(InputMaterial.RowId)" +
-            "\nFROM exp.materialInput" +
-            "\nINNER JOIN exp.material AS InputMaterial ON exp.materialInput.materialId = InputMaterial.RowId" +
-            "\nWHERE " + ExprColumn.STR_TABLE_ALIAS + ".SourceApplicationId = exp.materialInput.TargetApplicationId");
-        if (sampleType != null)
-        {
-            sql.append("\nAND InputMaterial.CPASType = ?");
-            sql.add(sampleType.getLSID());
-        }
-        sql.append(")");
-        ExprColumn ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
-        ret.setFk(schema.materialIdForeignKey(sampleType, null));
-        return doAdd(ret);
-    }
-
-    @Override
-    public DataType getDataType()
-    {
-        return _type;
-    }
-
-    @Override
-    public void setDataType(DataType type)
-    {
-        checkLocked();
-        _type = type;
-        getFilter().deleteConditions(FieldKey.fromParts("LSID"));
-        if (_type != null)
-        {
-            addCondition(new SQLFragment("LSID LIKE " + getSqlDialect().concatenate("'urn:lsid:%:'", "?", "'%'"), _type.getNamespacePrefix()), FieldKey.fromParts("LSID"));
-        }
-    }
-
-    public void setDataClass(ExpDataClass dataClass)
-    {
-        checkLocked();
-        _dataClass = dataClass;
-        getFilter().deleteConditions(FieldKey.fromParts("classId"));
-        if (_dataClass != null)
-        {
-            addCondition(getColumn("classId"), _dataClass.getRowId());
-        }
-    }
-
-    @Override
-    public MutableColumnInfo addInputRunCountColumn(String alias)
-    {
-        SQLFragment sql = new SQLFragment("(SELECT COUNT(DISTINCT exp.ProtocolApplication.RunId) " +
-                "FROM exp.ProtocolApplication INNER JOIN Exp.DataInput ON exp.ProtocolApplication.RowId = Exp.DataInput.TargetApplicationId " +
-                "WHERE Exp.DataInput.DataId = " + ExprColumn.STR_TABLE_ALIAS + ".RowId)");
-        var ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
-        return doAdd(ret);
-    }
-
-    private static class ThumbnailDataLinkColumn extends ViewFileDataLinkColumn
-    {
-        public ThumbnailDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected void renderData(HtmlWriter out, ExpData data)
-        {
-            renderThumbnailPopup(out, data, getURL(data));
-        }
-    }
-
-    private static class InlineThumbnailDataLinkColumn extends ViewFileDataLinkColumn
-    {
-        public InlineThumbnailDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected void renderData(HtmlWriter out, ExpData data)
-        {
-            out.write(renderThumbnailImg(data, getURL(data)));
-        }
-    }
-
-    private static class DownloadFileDataLinkColumn extends DataLinkColumn
-    {
-        public DownloadFileDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected ActionURL getURL(ExpData data)
-        {
-            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, false);
-        }
-    }
-
-    private static class ViewFileDataLinkColumn extends DataLinkColumn
-    {
-        public ViewFileDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected ActionURL getURL(ExpData data)
-        {
-            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true);
-        }
-    }
-
-    private static class ViewContentDataLinkColumn extends DataLinkColumn
-    {
-        public ViewContentDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected ActionURL getURL(ExpData data)
-        {
-            return data.findDataHandler().getContentURL(data);
-        }
-    }
-
-    private static class ViewOrDownloadDataColumn extends DataLinkColumn
-    {
-        public ViewOrDownloadDataColumn (ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected ActionURL getURL(ExpData data)
-        {
-            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true);
-        }
-
-        @Override
-        public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
-        {
-            ExpData data = getData(ctx, getColumnInfo());
-            if (data != null)
-            {
-                if (data.isFileOnDisk())
-                {
-                    out.write(LinkBuilder.labkeyLink("View File", ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true)));
-                    out.write(HtmlString.BR);
-                    out.write(LinkBuilder.labkeyLink("Download", ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, false)));
-                }
-                else
-                {
-                    out.write("File not available");
-                }
-            }
-        }
-    }
-
-    private static class WebDavUrlColumn extends ExpDataFileColumn
-    {
-        private final boolean _relative;
-
-        public WebDavUrlColumn (ColumnInfo colInfo, boolean relative)
-        {
-            super(colInfo);
-            setTextAlign("left");
-            _relative = relative;
-        }
-
-        @Override
-        public Object getJsonValue(ExpData data)
-        {
-            if (data == null)
-                return null;
-
-            return Objects.toString(data.getWebDavURL(_relative ? FileContentService.PathType.folderRelative : FileContentService.PathType.serverRelative), null);
-        }
-
-        @Override
-        protected void renderData(HtmlWriter out, ExpData data)
-        {
-            Object val = getJsonValue(data);
-            out.write(val);
-        }
-    }
-
-    public static class TestCase extends Assert
-    {
-        public static final String PROJECT_NAME = "ExptDataTableImplIntegrationTest";
-
-        @BeforeClass
-        public static void initialSetUp()
-        {
-            doInitialSetUp(PROJECT_NAME);
-        }
-
-        @AfterClass
-        public static void cleanup()
-        {
-            doCleanup(PROJECT_NAME);
-        }
-
-        private class WebDavTestCase
-        {
-            private final ExpData _data;
-            private final String _relativePath;
-
-            public WebDavTestCase(String name, File file, String relativePath)
-            {
-                _data = ExperimentService.get().createData(getProject(), new DataType("TestData"));
-                _data.setDataFileURI(file.toURI());
-                _data.setName(name);
-                _data.save(getUser());
-
-                _relativePath = relativePath;
-            }
-
-            public String getUrl()
-            {
-                if (_relativePath == null)
-                {
-                    return null;
-                }
-
-                PipeRoot pr = PipelineService.get().getPipelineRootSetting(getProject());
-
-                URI uri = pr.getWebdavURL().resolve(getUrlRelative());
-                return uri == null ? null : uri.toString();
-            }
-
-            public String getUrlRelative()
-            {
-                return _relativePath;
-            }
-        }
-
-        @Test
-        public void testWebDavColumns() throws Exception
-        {
-            PipeRoot pr = PipelineService.get().getPipelineRootSetting(getProject());
-            if (pr == null)
-            {
-                throw new ConfigurationException("File root is not set");
-            }
-
-            List<WebDavTestCase> testCases = new ArrayList<>();
-
-            final String PATH1 = "webDavTest.txt";
-            testCases.add(new WebDavTestCase("TestData1", new File(pr.getRootPath(), PATH1), PATH1));
-            testCases.add(new WebDavTestCase("TestData2", new File(pr.getRootPath(), "subfolder/webDavTest.txt"), "subfolder/webDavTest.txt"));
-            testCases.add(new WebDavTestCase("TestData3", new File(pr.getRootPath(), "subfolder/webD  avT est.txt"), "subfolder/webD%20%20avT%20est.txt"));
-
-            PipeRoot prHome = PipelineService.get().getPipelineRootSetting(ContainerManager.getHomeContainer());
-            testCases.add(new WebDavTestCase("NotUnderFolderRoot", new File(prHome.getRootPath(), PATH1), null));
-
-            testCases.add(new WebDavTestCase("NotUnderFileRoot", new File("/", PATH1), null));
-
-            UserSchema us = QueryService.get().getUserSchema(getUser(), getProject(), ExpSchema.SCHEMA_NAME);
-
-            for (final WebDavTestCase tc : testCases)
-            {
-                BindException errors = new NullSafeBindException(new Object(), "command");
-                MutablePropertyValues mpv = new MutablePropertyValues();
-                mpv.addPropertyValue("schemaName", ExpSchema.SCHEMA_NAME);
-                mpv.addPropertyValue("query.queryName", ExpSchema.TableType.Data.name());
-                List<FieldKey> fieldKeys = Arrays.asList("RowId", "Name", Column.WebDavUrl.name(), Column.WebDavUrlRelative.name()).stream().map(FieldKey::fromString).collect(Collectors.toList());
-                mpv.addPropertyValue("query.columns", StringUtils.join(fieldKeys, ","));
-
-                QuerySettings qs = us.getSettings(mpv, "query");
-
-                qs.setBaseFilter(new SimpleFilter(FieldKey.fromString("RowId"), tc._data.getRowId()));
-                QueryView view = new QueryView(us, qs, errors);
-
-                ExtendedApiQueryResponse resp = new ExtendedApiQueryResponse(view, false, false, "auditLog", "ContainerAuditEvent", 0, fieldKeys, false, false, false);
-                Writer writer = new StringWriter();
-                ApiResponseWriter apiWriter = new ApiJsonWriter(writer);
-                resp.render(apiWriter);
-                JSONObject json = new JSONObject(writer.toString());
-                JSONObject row = json.getJSONArray("rows").getJSONObject(0);
-
-                String webDavUrl = row.getJSONObject("WebDavUrl").optString("value", null);
-                String webDavUrlRelative = row.getJSONObject("WebDavUrlRelative").optString("value", null);
-
-                assertEquals("Incorrect WebDavUrlRelative", tc.getUrlRelative(), webDavUrlRelative);
-                assertEquals("Incorrect WebDavUrl", tc.getUrl(), webDavUrl);
-
-                ExcelWriter excel = view.getExcelWriter(ExcelWriter.ExcelDocumentType.xlsx, null);
-                try (VirtualFile f = new MemoryVirtualFile())
-                {
-                    try (OutputStream os = f.getOutputStream("excel.xlsx"))
-                    {
-                        excel.renderWorkbook(os);
-                    }
-
-                    try (ExcelLoader loader = new ExcelLoader(f.getInputStream("excel.xlsx"), true, getProject()))
-                    {
-                        loader.iterator().forEachRemaining(map -> {
-                            Object excelWebdavUrl = map.get("WebDAV URL");
-                            Object excelWebdavUrlRelative = map.get("Relative WebDAV URL");
-                            assertEquals("Incorrect WebDavUrl", tc.getUrl(), excelWebdavUrl);
-                            assertEquals("Incorrect WebDavUrlRelative", tc.getUrlRelative(), excelWebdavUrlRelative);
-                        });
-                    }
-                }
-            }
-        }
-
-        protected static void doInitialSetUp(String projectName)
-        {
-            //pre-clean
-            doCleanup(projectName);
-
-            Container project = ContainerManager.getForPath(projectName);
-            if (project == null)
-            {
-                ContainerManager.createContainer(ContainerManager.getRoot(), projectName, TestContext.get().getUser());
-            }
-        }
-
-        protected static void doCleanup(String projectName)
-        {
-            Container project = ContainerManager.getForPath(projectName);
-            if (project != null)
-            {
-                ContainerManager.delete(project, getUser());
-            }
-        }
-
-        protected static User getUser()
-        {
-            return TestContext.get().getUser();
-        }
-
-        protected Container getProject()
-        {
-            return ContainerManager.getForPath(PROJECT_NAME);
-        }
-    }
-}
+/*
+ * Copyright (c) 2008-2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.labkey.experiment.api;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.NotNull;
+import org.json.JSONObject;
+import org.junit.AfterClass;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.labkey.api.action.ApiJsonWriter;
+import org.labkey.api.action.ApiResponseWriter;
+import org.labkey.api.action.ExtendedApiQueryResponse;
+import org.labkey.api.action.NullSafeBindException;
+import org.labkey.api.compliance.TableRules;
+import org.labkey.api.compliance.TableRulesManager;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.ExcelWriter;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.MutableColumnInfo;
+import org.labkey.api.data.RenderContext;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.exp.DomainDescriptor;
+import org.labkey.api.exp.OntologyManager;
+import org.labkey.api.exp.PropertyColumn;
+import org.labkey.api.exp.api.DataType;
+import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.exp.api.ExpDataClass;
+import org.labkey.api.exp.api.ExpExperiment;
+import org.labkey.api.exp.api.ExpProtocol;
+import org.labkey.api.exp.api.ExpRun;
+import org.labkey.api.exp.api.ExpSampleType;
+import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.exp.property.Domain;
+import org.labkey.api.exp.property.DomainProperty;
+import org.labkey.api.exp.property.PropertyService;
+import org.labkey.api.exp.query.ExpDataTable;
+import org.labkey.api.exp.query.ExpSchema;
+import org.labkey.api.exp.query.SamplesSchema;
+import org.labkey.api.files.FileContentService;
+import org.labkey.api.pipeline.PipeRoot;
+import org.labkey.api.pipeline.PipelineService;
+import org.labkey.api.query.DetailsURL;
+import org.labkey.api.query.ExprColumn;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryForeignKey;
+import org.labkey.api.query.QueryService;
+import org.labkey.api.query.QuerySettings;
+import org.labkey.api.query.QueryUpdateService;
+import org.labkey.api.query.QueryView;
+import org.labkey.api.query.RowIdForeignKey;
+import org.labkey.api.query.UserSchema;
+import org.labkey.api.query.column.BuiltInColumnTypes;
+import org.labkey.api.reader.ExcelLoader;
+import org.labkey.api.security.User;
+import org.labkey.api.security.permissions.InsertPermission;
+import org.labkey.api.security.permissions.UpdatePermission;
+import org.labkey.api.util.ConfigurationException;
+import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.HtmlString;
+import org.labkey.api.util.LinkBuilder;
+import org.labkey.api.util.TestContext;
+import org.labkey.api.view.ActionURL;
+import org.labkey.api.writer.HtmlWriter;
+import org.labkey.api.writer.MemoryVirtualFile;
+import org.labkey.api.writer.VirtualFile;
+import org.labkey.experiment.controllers.exp.ExperimentController;
+import org.labkey.experiment.lineage.LineageMethod;
+import org.springframework.beans.MutablePropertyValues;
+import org.springframework.validation.BindException;
+
+import java.io.File;
+import java.io.OutputStream;
+import java.io.StringWriter;
+import java.io.Writer;
+import java.net.URI;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static org.labkey.api.exp.query.ExpSchema.TableType.DataClasses;
+
+public class ExpDataTableImpl extends ExpRunItemTableImpl<ExpDataTable.Column> implements ExpDataTable
+{
+    protected ExpExperiment _experiment;
+    protected boolean _runSpecified;
+    protected ExpRun _run;
+    protected DataType _type;
+    protected ExpDataClass _dataClass;
+
+    public ExpDataTableImpl(String name, UserSchema schema, ContainerFilter cf)
+    {
+        super(name, ExperimentServiceImpl.get().getTinfoData(), schema, cf);
+
+        addAllowablePermission(UpdatePermission.class);
+        addAllowablePermission(InsertPermission.class);
+    }
+
+    @Override
+    protected void populateColumns()
+    {
+        addColumn(Column.RowId).setHidden(true);
+        addColumn(Column.Name);
+        addColumn(Column.Description);
+        var aliasCol = addColumn(Column.Alias);
+        aliasCol.setHidden(true);
+        addColumn(Column.DataClass);
+        ExpSchema schema = getExpSchema();
+        addColumn(Column.Run).setFk(schema.getRunIdForeignKey(getContainerFilter()));
+        addColumn(Column.Created);
+        addColumn(Column.CreatedBy);
+        addColumn(Column.Modified);
+        addColumn(Column.ModifiedBy);
+
+        addColumn(Column.ContentLink);
+        addColumn(Column.Thumbnail);
+        addColumn(Column.InlineThumbnail);
+        addColumn(Column.SourceProtocolApplication);
+        addColumn(Column.Protocol);
+        addContainerColumn(Column.Folder, null);
+        addColumn(Column.ViewOrDownload);
+        addColumn(Column.Generated);
+        addColumn(Column.LastIndexed);
+
+        addFileColumns(false);
+
+        setDefaultColumns();
+        setTitleColumn("Name");
+
+        // Only include the dataClassId parameter if the ExpData row has a DataClass
+        DetailsURL detailsURL = DetailsURL.fromString("/experiment/showData.view?rowId=${rowId}${dataClass:prefix('%26dataClassId=')}");
+
+        setDetailsURL(detailsURL);
+        getMutableColumn(Column.RowId).setURL(detailsURL);
+        getMutableColumn(Column.Name).setURL(detailsURL);
+
+        ActionURL deleteUrl = ExperimentController.ExperimentUrlsImpl.get().getDeleteDatasURL(getContainer(), null);
+        setDeleteURL(new DetailsURL(deleteUrl));
+
+        addVocabularyDomains();
+        addColumn(Column.Properties);
+
+        var colInputs = addColumn(Column.Inputs);
+        addMethod("Inputs", new LineageMethod(colInputs, true), Set.of(colInputs.getFieldKey()));
+
+        var colOutputs = addColumn(Column.Outputs);
+        addMethod("Outputs", new LineageMethod(colOutputs, false), Set.of(colOutputs.getFieldKey()));
+
+        MutableColumnInfo lineageLookup = ClosureQueryHelper.createAncestorLookupColumnInfo("Ancestors", this, _rootTable.getColumn("rowid"), null, false);
+        addColumn(lineageLookup);
+
+        addExpObjectMethod();
+    }
+
+    @Override
+    public ColumnInfo getExpObjectColumn()
+    {
+        var ret = wrapColumn("_ExpDataTableImpl_object_", _rootTable.getColumn("objectid"));
+        ret.setConceptURI(BuiltInColumnTypes.EXPOBJECTID_CONCEPT_URI);
+        return ret;
+    }
+
+    public List<String> addFileColumns(boolean isFilesTable)
+    {
+        List<String> customProps = new ArrayList<>();
+        var lsidColumn = addColumn(Column.LSID);
+        lsidColumn.setHidden(true);
+        if (!isFilesTable)
+            addColumn(Column.DataFileUrl);
+
+        addColumn(Column.DownloadLink);
+        addColumn(Column.ViewFileLink);
+        addColumn(Column.FileExists);
+        addColumn(Column.FileSize);
+        addColumn(Column.FileExtension);
+        addColumn(Column.WebDavUrl);
+        addColumn(Column.WebDavUrlRelative);
+        var flagCol = addColumn(Column.Flag);
+        if (isFilesTable)
+            flagCol.setLabel("Description");
+
+        FileContentService svc = FileContentService.get();
+        String domainURI = svc.getDomainURI(getContainer());
+        DomainDescriptor dd = OntologyManager.getDomainDescriptor(domainURI, getContainer());
+
+        if (dd != null)
+        {
+            Domain domain = PropertyService.get().getDomain(dd.getDomainId());
+            if (domain != null)
+            {
+                for (DomainProperty prop : domain.getProperties())
+                {
+                    // don't set container on property column so that inherited domain properties work
+                    var projectColumn = new PropertyColumn(prop.getPropertyDescriptor(), lsidColumn, getContainer(), _userSchema.getUser(), false);
+                    addColumn(projectColumn);
+                    customProps.add(projectColumn.getAlias().getId());
+                }
+                setDomain(domain);
+            }
+        }
+
+        return customProps;
+    }
+
+    @Override
+    public boolean supportTableRules() // intentional override
+    {
+        return true;
+    }
+
+    @Override
+    protected @NotNull TableRules findTableRules()
+    {
+        Container definitionContainer = getUserSchema().getContainer();
+        if (null != getDomain())
+            definitionContainer = getDomain().getContainer();
+        return TableRulesManager.get().getTableRules(definitionContainer, getUserSchema().getUser(), getUserSchema().getContainer());
+    }
+
+    public void setDefaultColumns()
+    {
+        checkLocked();
+        List<FieldKey> defaultCols = new ArrayList<>();
+        defaultCols.add(FieldKey.fromParts(Column.Name));
+        defaultCols.add(FieldKey.fromParts(Column.Run));
+        defaultCols.add(FieldKey.fromParts(Column.DataFileUrl));
+        setDefaultVisibleColumns(defaultCols);
+    }
+
+    @Override
+    public QueryUpdateService getUpdateService()
+    {
+        return FileContentService.get().getFilePropsUpdateService(this, getContainer());
+    }
+
+    @Override
+    protected ColumnInfo resolveColumn(String name)
+    {
+        return super.resolveColumn(name);
+    }
+
+    @Override
+    public MutableColumnInfo createColumn(String alias, Column column)
+    {
+        switch (column)
+        {
+            case Folder:
+                return wrapColumn(alias, _rootTable.getColumn("Container"));
+            case Created:
+                return wrapColumn(alias, _rootTable.getColumn("Created"));
+            case CreatedBy:
+                return createUserColumn(alias, _rootTable.getColumn("CreatedBy"));
+            case Modified:
+                return wrapColumn(alias, _rootTable.getColumn("Modified"));
+            case ModifiedBy:
+                return createUserColumn(alias, _rootTable.getColumn("ModifiedBy"));
+            case DataFileUrl:
+                var dataFileUrl = wrapColumn(alias, _rootTable.getColumn("DataFileUrl"));
+                dataFileUrl.setUserEditable(false);
+                return dataFileUrl;
+            case LSID:
+                var lsid = wrapColumn(alias, _rootTable.getColumn("LSID"));
+                lsid.setUserEditable(false);
+                return lsid;
+            case Name:
+                return wrapColumn(alias, _rootTable.getColumn("Name"));
+            case Description:
+                return wrapColumn(alias, _rootTable.getColumn("Description"));
+            case LastIndexed:
+                SQLFragment lastIndexedSql = new SQLFragment("(SELECT LastIndexed FROM ").
+                        append(ExperimentServiceImpl.get().getTinfoDataIndexed(), "di").
+                        append(" WHERE di.DataId = ").
+                        append(ExprColumn.STR_TABLE_ALIAS).append(".RowId)");
+                var lastIndexed = new ExprColumn(this, "LastIndexed", lastIndexedSql, JdbcType.TIMESTAMP);
+                lastIndexed.setUserEditable(false);
+                return lastIndexed;
+            case DataClass:
+            {
+                var c = wrapColumn(alias, _rootTable.getColumn("classId"));
+                c.setUserEditable(false);
+                var fk = QueryForeignKey.from(getUserSchema(), getContainerFilter())
+                        .to(DataClasses.name(), "RowId", "Name");
+                c.setFk( fk );
+                return c;
+            }
+            case Protocol:
+            {
+                ExprColumn col = new ExprColumn(this, Column.Protocol.toString(), new SQLFragment(
+                        "(SELECT ProtocolLSID FROM " + ExperimentServiceImpl.get().getTinfoProtocolApplication() + " pa " +
+                        " WHERE pa.RowId = " + ExprColumn.STR_TABLE_ALIAS + ".SourceApplicationId)"), JdbcType.VARCHAR, getColumn(Column.SourceProtocolApplication));
+                col.setFk(getExpSchema().getProtocolForeignKey(getContainerFilter(),"LSID"));
+                col.setSqlTypeName("lsidtype");
+                col.setHidden(true);
+                return col;
+            }
+            case SourceProtocolApplication:
+            {
+                var columnInfo = wrapColumn(alias, _rootTable.getColumn("SourceApplicationId"));
+                columnInfo.setFk(getExpSchema().getProtocolApplicationForeignKey(getContainerFilter()));
+                columnInfo.setUserEditable(false);
+                columnInfo.setHidden(true);
+                return columnInfo;
+            }
+
+            case SourceApplicationInput:
+            {
+                var col = createEdgeColumn(alias, Column.SourceProtocolApplication, ExpSchema.TableType.DataInputs);
+                col.setDescription("Contains a reference to the DataInput row between this ExpData and it's SourceProtocolApplication");
+                col.setHidden(true);
+                return col;
+            }
+
+            case RunApplication:
+            {
+                SQLFragment sql = new SQLFragment("(SELECT pa.rowId FROM ")
+                        .append(ExperimentService.get().getTinfoProtocolApplication(), "pa")
+                        .append(" WHERE pa.runId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".runId")
+                        .append(" AND pa.cpasType = '").append(ExpProtocol.ApplicationType.ExperimentRunOutput.name()).append("'")
+                        .append(")");
+
+                var col = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
+                col.setFk(getExpSchema().getProtocolApplicationForeignKey(getContainerFilter()));
+                col.setDescription("Contains a reference to the ExperimentRunOutput protocol application of the run that created this data");
+                col.setUserEditable(false);
+                col.setReadOnly(true);
+                col.setHidden(true);
+                return col;
+            }
+
+            case RunApplicationOutput:
+            {
+                var col = createEdgeColumn(alias, Column.RunApplication, ExpSchema.TableType.DataInputs);
+                col.setDescription("Contains a reference to the DataInput row between this ExpData and it's RunOutputApplication");
+                return col;
+            }
+            case RowId:
+            {
+                var ret = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                ret.setFk(new RowIdForeignKey(ret));
+                ret.setHidden(true);
+                return ret;
+            }
+            case Run:
+                var runId = wrapColumn(alias, _rootTable.getColumn("RunId"));
+                runId.setUserEditable(false);
+                return runId;
+            case Flag:
+                return createFlagColumn(alias);
+            case Alias:
+                return createAliasColumn(alias, ExperimentService.get()::getTinfoDataAliasMap);
+            case DownloadLink:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(DownloadFileDataLinkColumn::new);
+                result.setDescription("A link to download the file");
+                return result;
+            }
+            case ViewFileLink:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(ViewFileDataLinkColumn::new);
+                result.setDescription("A link to view the file directly on the web site");
+                return result;
+            }
+            case ContentLink:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(ViewContentDataLinkColumn::new);
+                result.setDescription("A link to view the imported contents of the file on the web site");
+                return result;
+            }
+            case Thumbnail:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(ThumbnailDataLinkColumn::new);
+                result.setDescription("A popup thumbnail of the file if it is an image");
+                return result;
+            }
+            case InlineThumbnail:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(InlineThumbnailDataLinkColumn::new);
+                result.setDescription("An inline thumbnail of the file if it is an image");
+                return result;
+            }
+            case FileSize:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setTextAlign("left");
+                result.setJdbcType(JdbcType.VARCHAR);
+                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
+                {
+                    @Override
+                    protected void renderData(HtmlWriter out, ExpData data)
+                    {
+                        String val = ((String)getJsonValue(data));
+                        out.write(val);
+                    }
+
+                    @Override
+                    public Object getJsonValue(ExpData data)
+                    {
+                        if (data == null || data.getFile() == null)
+                            return "";
+                        else if (!data.getFile().exists())
+                            return "File Not Found";
+                        else
+                        {
+                            long size = data.getFile().length();
+                            return FileUtils.byteCountToDisplaySize(size);
+                        }
+                    }
+                });
+                result.setUserEditable(false);
+                result.setShownInUpdateView(false);
+                result.setShownInInsertView(false);
+
+                return result;
+            }
+            case FileExists:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setJdbcType(JdbcType.BOOLEAN);
+                result.setTextAlign("left");
+                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
+                {
+                    @Override
+                    protected void renderData(HtmlWriter out, ExpData data)
+                    {
+                        Boolean val = (Boolean)getJsonValue(data);
+                        out.write(val.toString());
+                    }
+
+                    @Override
+                    protected Object getJsonValue(ExpData data)
+                    {
+                        if (data == null)
+                        {
+                            return false;
+                        }
+                        Path path = data.getFilePath();
+                        return path != null && Files.exists(path);
+                    }
+                });
+                result.setUserEditable(false);
+                result.setShownInUpdateView(false);
+                result.setShownInInsertView(false);
+                return result;
+            }
+            case FileExtension:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setJdbcType(JdbcType.VARCHAR);
+                result.setTextAlign("left");
+                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
+                {
+                    @Override
+                    protected void renderData(HtmlWriter out, ExpData data)
+                    {
+                        Object val = getJsonValue(data);
+                        out.write(val);
+                    }
+
+                    @Override
+                    protected Object getJsonValue(ExpData data)
+                    {
+                        return data.getFile() == null ? null : FileUtil.getExtension(data.getFile());
+                    }
+                });
+                result.setUserEditable(false);
+                result.setShownInUpdateView(false);
+                result.setShownInInsertView(false);
+                return result;
+            }
+            case ViewOrDownload:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setLabel("View/Download");
+                result.setDisplayColumnFactory(ViewOrDownloadDataColumn::new);
+                result.setDescription("Displays links to either download the file or view directly on the web site");
+                return result;
+            }
+            case WebDavUrl:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setJdbcType(JdbcType.VARCHAR);
+                result.setLabel("WebDAV URL");
+                result.setDescription("This is the full WebDAV URL to this file");
+                result.setDisplayColumnFactory(colInfo -> new WebDavUrlColumn(colInfo, false));
+                return result;
+            }
+            case WebDavUrlRelative:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setJdbcType(JdbcType.VARCHAR);
+                result.setLabel("Relative WebDAV URL");
+                result.setDescription("This is the WebDAV path of this file, relative to the file root of this container");
+                result.setDisplayColumnFactory(colInfo -> new WebDavUrlColumn(colInfo, true));
+                return result;
+            }
+            case Generated:
+                return wrapColumn(alias, _rootTable.getColumn("Generated"));
+
+            case Inputs:
+                return createLineageColumn(this, alias, true, false);
+
+            case Outputs:
+                return createLineageColumn(this, alias, false, false);
+
+            case Properties:
+                return createPropertiesColumn(alias);
+
+            default:
+                throw new IllegalArgumentException("Unknown column " + column);
+        }
+    }
+
+    @Override
+    public void setExperiment(ExpExperiment experiment)
+    {
+        checkLocked();
+        if (getExperiment() != null)
+            throw new IllegalArgumentException("Attempt to unset experiment");
+        if (experiment == null)
+            return;
+        SQLFragment condition = new SQLFragment("exp.Data.RunId IN "
+                + " ( SELECT ExperimentRunId FROM exp.RunList "
+                + " WHERE ExperimentId = ? )");
+        condition.add(experiment.getRowId());
+        addCondition(condition);
+        _experiment = experiment;
+    }
+
+    @Override
+    public ExpExperiment getExperiment()
+    {
+        return _experiment;
+    }
+
+    @Override
+    public void setRun(ExpRun run)
+    {
+        checkLocked();
+        if (_runSpecified)
+            throw new IllegalArgumentException("Cannot unset run");
+        _runSpecified = true;
+        _run = run;
+        if (run == null)
+        {
+            addCondition(new SQLFragment("(RunId IS NULL)"), FieldKey.fromParts("RunId"));
+        }
+        else
+        {
+            addCondition(_rootTable.getColumn("RunId"), run.getRowId());
+        }
+    }
+
+    @Override
+    public ExpRun getRun()
+    {
+        return _run;
+    }
+
+    @Override
+    public MutableColumnInfo addDataInputColumn(String alias, String role)
+    {
+        SQLFragment sql = new SQLFragment("(SELECT MIN(exp.datainput.dataid)" +
+                "\nFROM exp.datainput" +
+                "\nWHERE " + ExprColumn.STR_TABLE_ALIAS +  ".SourceApplicationId = exp.datainput.TargetApplicationId" +
+                "\nAND ");
+        if (role == null)
+        {
+            sql.append("1 = 0");
+        }
+        else
+        {
+            sql.append("exp.datainput.role = ?");
+            sql.add(role);
+        }
+        sql.append(")");
+        ExprColumn ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
+        return doAdd(ret);
+    }
+
+    @Override
+    public MutableColumnInfo addMaterialInputColumn(String alias, SamplesSchema schema, String pdRole, final ExpSampleType sampleType)
+    {
+        SQLFragment sql = new SQLFragment("(SELECT MIN(InputMaterial.RowId)" +
+            "\nFROM exp.materialInput" +
+            "\nINNER JOIN exp.material AS InputMaterial ON exp.materialInput.materialId = InputMaterial.RowId" +
+            "\nWHERE " + ExprColumn.STR_TABLE_ALIAS + ".SourceApplicationId = exp.materialInput.TargetApplicationId");
+        if (sampleType != null)
+        {
+            sql.append("\nAND InputMaterial.CPASType = ?");
+            sql.add(sampleType.getLSID());
+        }
+        sql.append(")");
+        ExprColumn ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
+        ret.setFk(schema.materialIdForeignKey(sampleType, null));
+        return doAdd(ret);
+    }
+
+    @Override
+    public DataType getDataType()
+    {
+        return _type;
+    }
+
+    @Override
+    public void setDataType(DataType type)
+    {
+        checkLocked();
+        _type = type;
+        getFilter().deleteConditions(FieldKey.fromParts("LSID"));
+        if (_type != null)
+        {
+            addCondition(new SQLFragment("LSID LIKE " + getSqlDialect().concatenate("'urn:lsid:%:'", "?", "'%'"), _type.getNamespacePrefix()), FieldKey.fromParts("LSID"));
+        }
+    }
+
+    public void setDataClass(ExpDataClass dataClass)
+    {
+        checkLocked();
+        _dataClass = dataClass;
+        getFilter().deleteConditions(FieldKey.fromParts("classId"));
+        if (_dataClass != null)
+        {
+            addCondition(getColumn("classId"), _dataClass.getRowId());
+        }
+    }
+
+    @Override
+    public MutableColumnInfo addInputRunCountColumn(String alias)
+    {
+        SQLFragment sql = new SQLFragment("(SELECT COUNT(DISTINCT exp.ProtocolApplication.RunId) " +
+                "FROM exp.ProtocolApplication INNER JOIN Exp.DataInput ON exp.ProtocolApplication.RowId = Exp.DataInput.TargetApplicationId " +
+                "WHERE Exp.DataInput.DataId = " + ExprColumn.STR_TABLE_ALIAS + ".RowId)");
+        var ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
+        return doAdd(ret);
+    }
+
+    private static class ThumbnailDataLinkColumn extends ViewFileDataLinkColumn
+    {
+        public ThumbnailDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected void renderData(HtmlWriter out, ExpData data)
+        {
+            renderThumbnailPopup(out, data, getURL(data));
+        }
+    }
+
+    private static class InlineThumbnailDataLinkColumn extends ViewFileDataLinkColumn
+    {
+        public InlineThumbnailDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected void renderData(HtmlWriter out, ExpData data)
+        {
+            out.write(renderThumbnailImg(data, getURL(data)));
+        }
+    }
+
+    private static class DownloadFileDataLinkColumn extends DataLinkColumn
+    {
+        public DownloadFileDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected ActionURL getURL(ExpData data)
+        {
+            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, false);
+        }
+    }
+
+    private static class ViewFileDataLinkColumn extends DataLinkColumn
+    {
+        public ViewFileDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected ActionURL getURL(ExpData data)
+        {
+            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true);
+        }
+    }
+
+    private static class ViewContentDataLinkColumn extends DataLinkColumn
+    {
+        public ViewContentDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected ActionURL getURL(ExpData data)
+        {
+            return data.findDataHandler().getContentURL(data);
+        }
+    }
+
+    private static class ViewOrDownloadDataColumn extends DataLinkColumn
+    {
+        public ViewOrDownloadDataColumn (ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected ActionURL getURL(ExpData data)
+        {
+            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true);
+        }
+
+        @Override
+        public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
+        {
+            ExpData data = getData(ctx, getColumnInfo());
+            if (data != null)
+            {
+                if (data.isFileOnDisk())
+                {
+                    out.write(LinkBuilder.labkeyLink("View File", ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true)));
+                    out.write(HtmlString.BR);
+                    out.write(LinkBuilder.labkeyLink("Download", ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, false)));
+                }
+                else
+                {
+                    out.write("File not available");
+                }
+            }
+        }
+    }
+
+    private static class WebDavUrlColumn extends ExpDataFileColumn
+    {
+        private final boolean _relative;
+
+        public WebDavUrlColumn (ColumnInfo colInfo, boolean relative)
+        {
+            super(colInfo);
+            setTextAlign("left");
+            _relative = relative;
+        }
+
+        @Override
+        public Object getJsonValue(ExpData data)
+        {
+            if (data == null)
+                return null;
+
+            return Objects.toString(data.getWebDavURL(_relative ? FileContentService.PathType.folderRelative : FileContentService.PathType.serverRelative), null);
+        }
+
+        @Override
+        protected void renderData(HtmlWriter out, ExpData data)
+        {
+            Object val = getJsonValue(data);
+            out.write(val);
+        }
+    }
+
+    public static class TestCase extends Assert
+    {
+        public static final String PROJECT_NAME = "ExptDataTableImplIntegrationTest";
+
+        @BeforeClass
+        public static void initialSetUp()
+        {
+            doInitialSetUp(PROJECT_NAME);
+        }
+
+        @AfterClass
+        public static void cleanup()
+        {
+            doCleanup(PROJECT_NAME);
+        }
+
+        private class WebDavTestCase
+        {
+            private final ExpData _data;
+            private final String _relativePath;
+
+            public WebDavTestCase(String name, File file, String relativePath)
+            {
+                _data = ExperimentService.get().createData(getProject(), new DataType("TestData"));
+                _data.setDataFileURI(file.toURI());
+                _data.setName(name);
+                _data.save(getUser());
+
+                _relativePath = relativePath;
+            }
+
+            public String getUrl()
+            {
+                if (_relativePath == null)
+                {
+                    return null;
+                }
+
+                PipeRoot pr = PipelineService.get().getPipelineRootSetting(getProject());
+
+                URI uri = pr.getWebdavURL().resolve(getUrlRelative());
+                return uri == null ? null : uri.toString();
+            }
+
+            public String getUrlRelative()
+            {
+                return _relativePath;
+            }
+        }
+
+        @Test
+        public void testWebDavColumns() throws Exception
+        {
+            PipeRoot pr = PipelineService.get().getPipelineRootSetting(getProject());
+            if (pr == null)
+            {
+                throw new ConfigurationException("File root is not set");
+            }
+
+            List<WebDavTestCase> testCases = new ArrayList<>();
+
+            final String PATH1 = "webDavTest.txt";
+            testCases.add(new WebDavTestCase("TestData1", FileUtil.appendName(pr.getRootPath(), PATH1), PATH1));
+            testCases.add(new WebDavTestCase("TestData2", FileUtil.appendPath(pr.getRootPath(), org.labkey.api.util.Path.parse("subfolder/webDavTest.txt")), "subfolder/webDavTest.txt"));
+            testCases.add(new WebDavTestCase("TestData3", FileUtil.appendPath(pr.getRootPath(), org.labkey.api.util.Path.parse("subfolder/webD  avT est.txt")), "subfolder/webD%20%20avT%20est.txt"));
+
+            PipeRoot prHome = PipelineService.get().getPipelineRootSetting(ContainerManager.getHomeContainer());
+            testCases.add(new WebDavTestCase("NotUnderFolderRoot", FileUtil.appendName(prHome.getRootPath(), PATH1), null));
+
+            testCases.add(new WebDavTestCase("NotUnderFileRoot", new File("/", PATH1), null));
+
+            UserSchema us = QueryService.get().getUserSchema(getUser(), getProject(), ExpSchema.SCHEMA_NAME);
+
+            for (final WebDavTestCase tc : testCases)
+            {
+                BindException errors = new NullSafeBindException(new Object(), "command");
+                MutablePropertyValues mpv = new MutablePropertyValues();
+                mpv.addPropertyValue("schemaName", ExpSchema.SCHEMA_NAME);
+                mpv.addPropertyValue("query.queryName", ExpSchema.TableType.Data.name());
+                List<FieldKey> fieldKeys = Arrays.asList("RowId", "Name", Column.WebDavUrl.name(), Column.WebDavUrlRelative.name()).stream().map(FieldKey::fromString).collect(Collectors.toList());
+                mpv.addPropertyValue("query.columns", StringUtils.join(fieldKeys, ","));
+
+                QuerySettings qs = us.getSettings(mpv, "query");
+
+                qs.setBaseFilter(new SimpleFilter(FieldKey.fromString("RowId"), tc._data.getRowId()));
+                QueryView view = new QueryView(us, qs, errors);
+
+                ExtendedApiQueryResponse resp = new ExtendedApiQueryResponse(view, false, false, "auditLog", "ContainerAuditEvent", 0, fieldKeys, false, false, false);
+                Writer writer = new StringWriter();
+                ApiResponseWriter apiWriter = new ApiJsonWriter(writer);
+                resp.render(apiWriter);
+                JSONObject json = new JSONObject(writer.toString());
+                JSONObject row = json.getJSONArray("rows").getJSONObject(0);
+
+                String webDavUrl = row.getJSONObject("WebDavUrl").optString("value", null);
+                String webDavUrlRelative = row.getJSONObject("WebDavUrlRelative").optString("value", null);
+
+                assertEquals("Incorrect WebDavUrlRelative", tc.getUrlRelative(), webDavUrlRelative);
+                assertEquals("Incorrect WebDavUrl", tc.getUrl(), webDavUrl);
+
+                ExcelWriter excel = view.getExcelWriter(ExcelWriter.ExcelDocumentType.xlsx, null);
+                try (VirtualFile f = new MemoryVirtualFile())
+                {
+                    try (OutputStream os = f.getOutputStream("excel.xlsx"))
+                    {
+                        excel.renderWorkbook(os);
+                    }
+
+                    try (ExcelLoader loader = new ExcelLoader(f.getInputStream("excel.xlsx"), true, getProject()))
+                    {
+                        loader.iterator().forEachRemaining(map -> {
+                            Object excelWebdavUrl = map.get("WebDAV URL");
+                            Object excelWebdavUrlRelative = map.get("Relative WebDAV URL");
+                            assertEquals("Incorrect WebDavUrl", tc.getUrl(), excelWebdavUrl);
+                            assertEquals("Incorrect WebDavUrlRelative", tc.getUrlRelative(), excelWebdavUrlRelative);
+                        });
+                    }
+                }
+            }
+        }
+
+        protected static void doInitialSetUp(String projectName)
+        {
+            //pre-clean
+            doCleanup(projectName);
+
+            Container project = ContainerManager.getForPath(projectName);
+            if (project == null)
+            {
+                ContainerManager.createContainer(ContainerManager.getRoot(), projectName, TestContext.get().getUser());
+            }
+        }
+
+        protected static void doCleanup(String projectName)
+        {
+            Container project = ContainerManager.getForPath(projectName);
+            if (project != null)
+            {
+                ContainerManager.delete(project, getUser());
+            }
+        }
+
+        protected static User getUser()
+        {
+            return TestContext.get().getUser();
+        }
+
+        protected Container getProject()
+        {
+            return ContainerManager.getForPath(PROJECT_NAME);
+        }
+    }
+}
diff --git a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java
index 06d7786d6d5..6fe26125a61 100644
--- a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java
+++ b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java
@@ -1,284 +1,284 @@
-/*
- * Copyright (c) 2008-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.experiment.pipeline;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.apache.xmlbeans.XmlException;
-import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument;
-import org.fhcrc.cpas.exp.xml.ExperimentArchiveType;
-import org.jetbrains.annotations.NotNull;
-import org.labkey.api.data.Container;
-import org.labkey.api.data.DbScope;
-import org.labkey.api.exp.ExperimentDataHandler;
-import org.labkey.api.exp.ExperimentException;
-import org.labkey.api.exp.XarSource;
-import org.labkey.api.exp.api.ExpData;
-import org.labkey.api.exp.api.ExperimentService;
-import org.labkey.api.pipeline.PipelineJob;
-import org.labkey.api.pipeline.RecordedActionSet;
-import org.labkey.api.util.DateUtil;
-import org.labkey.api.util.FileUtil;
-import org.labkey.api.util.XmlBeansUtil;
-import org.labkey.experiment.DataURLRelativizer;
-import org.labkey.api.exp.xar.LSIDRelativizer;
-import org.labkey.experiment.XarExporter;
-import org.labkey.experiment.XarReader;
-import org.labkey.experiment.api.ExpRunImpl;
-import org.labkey.experiment.api.ExperimentServiceImpl;
-
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-import java.nio.file.Path;
-import java.sql.BatchUpdateException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-/**
- * User: jeckels
- * Date: Sep 8, 2008
- */
-public class MoveRunsTask extends PipelineJob.Task<MoveRunsTaskFactory>
-{
-    public MoveRunsTask(MoveRunsTaskFactory factory, PipelineJob job)
-    {
-        super(factory, job);
-    }
-
-    @Override
-    @NotNull
-    public RecordedActionSet run()
-    {
-        MoveRunsPipelineJob job = (MoveRunsPipelineJob)getJob();
-
-        try
-        {
-            for (long runId : job.getRunIds())
-            {
-                ExpRunImpl experimentRun = ExperimentServiceImpl.get().getExpRun(runId);
-                if (experimentRun != null)
-                {
-                    moveRun(job, experimentRun);
-                }
-                else
-                {
-                    job.info("Run with id " + runId + " is no longer available in the system");
-                }
-            }
-        }
-        catch (Throwable t)
-        {
-            job.error("Exception during move", t);
-            job.error("Move FAILED");
-            if (t instanceof BatchUpdateException)
-            {
-                job.error("Underlying exception", ((BatchUpdateException)t).getNextException());
-            }
-        }
-        return new RecordedActionSet();
-    }
-
-    private void moveRun(MoveRunsPipelineJob job, ExpRunImpl experimentRun) throws ExperimentException, IOException
-    {
-        XarExporter exporter = new XarExporter(LSIDRelativizer.PARTIAL_FOLDER_RELATIVE, DataURLRelativizer.ORIGINAL_FILE_LOCATION.createURLRewriter(), getJob().getUser(), getJob().getContainer());
-        exporter.addExperimentRun(experimentRun);
-
-        ByteArrayOutputStream bOut = new ByteArrayOutputStream();
-        exporter.dumpXML(bOut);
-
-        try (DbScope.Transaction transaction = ExperimentService.get().getSchema().getScope().ensureTransaction())
-        {
-            Map<String,Long> dataFiles = new HashMap<>();
-
-            for (ExpData oldData : experimentRun.getAllDataUsedByRun())
-            {
-                ExperimentDataHandler handler = oldData.findDataHandler();
-                handler.beforeMove(oldData, experimentRun.getContainer(), job.getUser());
-            }
-
-            for (ExpData data : ExperimentService.get().deleteExperimentRunForMove(experimentRun.getRowId(), job.getUser()))
-            {
-                if (data.getDataFileUrl() != null)
-                {
-                    dataFiles.put(data.getDataFileUrl(), data.getRowId());
-                }
-            }
-
-            MoveRunsXarSource xarSource = new MoveRunsXarSource(bOut.toString(), experimentRun.getFilePathRootPath(), job);
-            XarReader reader = new XarReader(xarSource, job);
-            reader.parseAndLoad(false, null);
-
-            List<String> runLSIDs = reader.getProcessedRunsLSIDs();
-            assert runLSIDs.size() == 1 : "Expected a single run to be loaded";
-
-            for (String dataURL : dataFiles.keySet())
-            {
-                ExpData newData = ExperimentService.get().getExpDataByURL(xarSource.getCanonicalDataFileURL(dataURL), job.getSourceContainer());
-                if (newData != null)
-                {
-                    ExperimentDataHandler handler = newData.findDataHandler();
-                    handler.runMoved(newData, experimentRun.getContainer(), job.getContainer(), experimentRun.getLSID(), runLSIDs.get(0), job.getUser(), dataFiles.get(dataURL));
-                }
-            }
-            transaction.commit();
-        }
-    }
-
-    public static class MoveRunsXarSource extends XarSource
-    {
-        private static final Logger _log = LogManager.getLogger(MoveRunsXarSource.class);
-
-        private final String _xml;
-        private File _logFile;
-        private File _logFileDir;
-
-        private final String _uploadTime;
-
-        private String _experimentName;
-        private final String _root;
-        private final Container _sourceContainer;
-
-        public MoveRunsXarSource(String xml, Path root, MoveRunsPipelineJob job) throws ExperimentException
-        {
-            super(job);
-            _xml = xml;
-            if (null == root)
-                throw new ExperimentException("File path root is null");
-
-            _root = FileUtil.getAbsolutePath(job.getSourceContainer(), root);
-            if (null == _root)
-                throw new ExperimentException("Unable to create absolute file path for root");
-
-            _sourceContainer = job.getSourceContainer();
-
-            int retry = 0;
-            while (_logFileDir == null)
-            {
-                try
-                {
-                    _logFileDir = FileUtil.createTempFile("xarupload", "");
-                }
-                catch (IOException e)
-                {
-                    if (++retry > 10)
-                    {
-                        throw new ExperimentException("Unable to create a log file", e);
-                    }
-                    _log.warn("Failed to create log file, retrying...", e);
-                }
-            }
-
-            _logFileDir.delete();
-            try
-            {
-                FileUtil.mkdir(_logFileDir);
-            }
-            catch (IOException e)
-            {
-                throw new ExperimentException("Unable to create log file directory", e);
-            }
-            _logFileDir.deleteOnExit();
-            _logFile = new File(_logFileDir, "upload.xar.log");
-            _logFile.deleteOnExit();
-            _uploadTime = DateUtil.formatDateTime(job.getContainer());
-        }
-
-        @Override
-        public ExperimentArchiveDocument getDocument() throws XmlException
-        {
-            ExperimentArchiveDocument doc = ExperimentArchiveDocument.Factory.parse(_xml, XmlBeansUtil.getDefaultParseOptions());
-            ExperimentArchiveType ea = doc.getExperimentArchive();
-            if (ea != null)
-            {
-                if (ea.getExperimentArray() != null && ea.getExperimentArray().length > 0)
-                {
-                    _experimentName = ea.getExperimentArray()[0].getName();
-                }
-            }
-            return doc;
-        }
-
-        @Override
-        public Path getRootPath()
-        {
-            return FileUtil.stringToPath(_sourceContainer, _root);
-        }
-
-        @Override
-        public Path getJobRootPath()
-        {
-            var pipelineJob = getXarContext().getJob();
-            return pipelineJob != null
-                    ? pipelineJob.getPipeRoot().getRootFileLike().toNioPathForRead()
-                    : super.getJobRootPath();
-        }
-
-        @Override
-        public boolean shouldIgnoreDataFiles()
-        {
-            return true;
-        }
-
-        @Override
-        public String canonicalizeDataFileURL(String dataFileURL)
-        {
-            URI uri = FileUtil.createUri(dataFileURL);
-            Path dataFilePath;
-            if (!uri.isAbsolute())
-            {
-                dataFilePath = getRootPath().resolve(dataFileURL);
-            }
-            else
-            {
-                dataFilePath = FileUtil.getPath(_sourceContainer, uri);
-            }
-            return FileUtil.getAbsoluteCaseSensitivePathString(_sourceContainer, dataFilePath.toUri());
-        }
-
-        @Override
-        public Path getLogFilePath()
-        {
-            return _logFile.toPath();
-        }
-
-        public String toString()
-        {
-            String result = "Uploaded file: " + _uploadTime;
-            if (_experimentName != null)
-            {
-                result += _experimentName;
-            }
-            return result;
-        }
-
-        public void cleanup()
-        {
-            if (_logFile != null)
-            {
-                _logFile.delete();
-                _logFile = null;
-            }
-            if (_logFileDir != null)
-            {
-                _logFileDir.delete();
-                _logFileDir = null;
-            }
-        }
-    }
-}
+/*
+ * Copyright (c) 2008-2018 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.experiment.pipeline;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.xmlbeans.XmlException;
+import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument;
+import org.fhcrc.cpas.exp.xml.ExperimentArchiveType;
+import org.jetbrains.annotations.NotNull;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.exp.ExperimentDataHandler;
+import org.labkey.api.exp.ExperimentException;
+import org.labkey.api.exp.XarSource;
+import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.pipeline.PipelineJob;
+import org.labkey.api.pipeline.RecordedActionSet;
+import org.labkey.api.util.DateUtil;
+import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.XmlBeansUtil;
+import org.labkey.experiment.DataURLRelativizer;
+import org.labkey.api.exp.xar.LSIDRelativizer;
+import org.labkey.experiment.XarExporter;
+import org.labkey.experiment.XarReader;
+import org.labkey.experiment.api.ExpRunImpl;
+import org.labkey.experiment.api.ExperimentServiceImpl;
+
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.nio.file.Path;
+import java.sql.BatchUpdateException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * User: jeckels
+ * Date: Sep 8, 2008
+ */
+public class MoveRunsTask extends PipelineJob.Task<MoveRunsTaskFactory>
+{
+    public MoveRunsTask(MoveRunsTaskFactory factory, PipelineJob job)
+    {
+        super(factory, job);
+    }
+
+    @Override
+    @NotNull
+    public RecordedActionSet run()
+    {
+        MoveRunsPipelineJob job = (MoveRunsPipelineJob)getJob();
+
+        try
+        {
+            for (long runId : job.getRunIds())
+            {
+                ExpRunImpl experimentRun = ExperimentServiceImpl.get().getExpRun(runId);
+                if (experimentRun != null)
+                {
+                    moveRun(job, experimentRun);
+                }
+                else
+                {
+                    job.info("Run with id " + runId + " is no longer available in the system");
+                }
+            }
+        }
+        catch (Throwable t)
+        {
+            job.error("Exception during move", t);
+            job.error("Move FAILED");
+            if (t instanceof BatchUpdateException)
+            {
+                job.error("Underlying exception", ((BatchUpdateException)t).getNextException());
+            }
+        }
+        return new RecordedActionSet();
+    }
+
+    private void moveRun(MoveRunsPipelineJob job, ExpRunImpl experimentRun) throws ExperimentException, IOException
+    {
+        XarExporter exporter = new XarExporter(LSIDRelativizer.PARTIAL_FOLDER_RELATIVE, DataURLRelativizer.ORIGINAL_FILE_LOCATION.createURLRewriter(), getJob().getUser(), getJob().getContainer());
+        exporter.addExperimentRun(experimentRun);
+
+        ByteArrayOutputStream bOut = new ByteArrayOutputStream();
+        exporter.dumpXML(bOut);
+
+        try (DbScope.Transaction transaction = ExperimentService.get().getSchema().getScope().ensureTransaction())
+        {
+            Map<String,Long> dataFiles = new HashMap<>();
+
+            for (ExpData oldData : experimentRun.getAllDataUsedByRun())
+            {
+                ExperimentDataHandler handler = oldData.findDataHandler();
+                handler.beforeMove(oldData, experimentRun.getContainer(), job.getUser());
+            }
+
+            for (ExpData data : ExperimentService.get().deleteExperimentRunForMove(experimentRun.getRowId(), job.getUser()))
+            {
+                if (data.getDataFileUrl() != null)
+                {
+                    dataFiles.put(data.getDataFileUrl(), data.getRowId());
+                }
+            }
+
+            MoveRunsXarSource xarSource = new MoveRunsXarSource(bOut.toString(), experimentRun.getFilePathRootPath(), job);
+            XarReader reader = new XarReader(xarSource, job);
+            reader.parseAndLoad(false, null);
+
+            List<String> runLSIDs = reader.getProcessedRunsLSIDs();
+            assert runLSIDs.size() == 1 : "Expected a single run to be loaded";
+
+            for (String dataURL : dataFiles.keySet())
+            {
+                ExpData newData = ExperimentService.get().getExpDataByURL(xarSource.getCanonicalDataFileURL(dataURL), job.getSourceContainer());
+                if (newData != null)
+                {
+                    ExperimentDataHandler handler = newData.findDataHandler();
+                    handler.runMoved(newData, experimentRun.getContainer(), job.getContainer(), experimentRun.getLSID(), runLSIDs.get(0), job.getUser(), dataFiles.get(dataURL));
+                }
+            }
+            transaction.commit();
+        }
+    }
+
+    public static class MoveRunsXarSource extends XarSource
+    {
+        private static final Logger _log = LogManager.getLogger(MoveRunsXarSource.class);
+
+        private final String _xml;
+        private File _logFile;
+        private File _logFileDir;
+
+        private final String _uploadTime;
+
+        private String _experimentName;
+        private final String _root;
+        private final Container _sourceContainer;
+
+        public MoveRunsXarSource(String xml, Path root, MoveRunsPipelineJob job) throws ExperimentException
+        {
+            super(job);
+            _xml = xml;
+            if (null == root)
+                throw new ExperimentException("File path root is null");
+
+            _root = FileUtil.getAbsolutePath(job.getSourceContainer(), root);
+            if (null == _root)
+                throw new ExperimentException("Unable to create absolute file path for root");
+
+            _sourceContainer = job.getSourceContainer();
+
+            int retry = 0;
+            while (_logFileDir == null)
+            {
+                try
+                {
+                    _logFileDir = FileUtil.createTempFile("xarupload", "");
+                }
+                catch (IOException e)
+                {
+                    if (++retry > 10)
+                    {
+                        throw new ExperimentException("Unable to create a log file", e);
+                    }
+                    _log.warn("Failed to create log file, retrying...", e);
+                }
+            }
+
+            _logFileDir.delete();
+            try
+            {
+                FileUtil.mkdir(_logFileDir);
+            }
+            catch (IOException e)
+            {
+                throw new ExperimentException("Unable to create log file directory", e);
+            }
+            _logFileDir.deleteOnExit();
+            _logFile = FileUtil.appendName(_logFileDir, "upload.xar.log");
+            _logFile.deleteOnExit();
+            _uploadTime = DateUtil.formatDateTime(job.getContainer());
+        }
+
+        @Override
+        public ExperimentArchiveDocument getDocument() throws XmlException
+        {
+            ExperimentArchiveDocument doc = ExperimentArchiveDocument.Factory.parse(_xml, XmlBeansUtil.getDefaultParseOptions());
+            ExperimentArchiveType ea = doc.getExperimentArchive();
+            if (ea != null)
+            {
+                if (ea.getExperimentArray() != null && ea.getExperimentArray().length > 0)
+                {
+                    _experimentName = ea.getExperimentArray()[0].getName();
+                }
+            }
+            return doc;
+        }
+
+        @Override
+        public Path getRootPath()
+        {
+            return FileUtil.stringToPath(_sourceContainer, _root);
+        }
+
+        @Override
+        public Path getJobRootPath()
+        {
+            var pipelineJob = getXarContext().getJob();
+            return pipelineJob != null
+                    ? pipelineJob.getPipeRoot().getRootFileLike().toNioPathForRead()
+                    : super.getJobRootPath();
+        }
+
+        @Override
+        public boolean shouldIgnoreDataFiles()
+        {
+            return true;
+        }
+
+        @Override
+        public String canonicalizeDataFileURL(String dataFileURL)
+        {
+            URI uri = FileUtil.createUri(dataFileURL);
+            Path dataFilePath;
+            if (!uri.isAbsolute())
+            {
+                dataFilePath = getRootPath().resolve(dataFileURL);
+            }
+            else
+            {
+                dataFilePath = FileUtil.getPath(_sourceContainer, uri);
+            }
+            return FileUtil.getAbsoluteCaseSensitivePathString(_sourceContainer, dataFilePath.toUri());
+        }
+
+        @Override
+        public Path getLogFilePath()
+        {
+            return _logFile.toPath();
+        }
+
+        public String toString()
+        {
+            String result = "Uploaded file: " + _uploadTime;
+            if (_experimentName != null)
+            {
+                result += _experimentName;
+            }
+            return result;
+        }
+
+        public void cleanup()
+        {
+            if (_logFile != null)
+            {
+                _logFile.delete();
+                _logFile = null;
+            }
+            if (_logFileDir != null)
+            {
+                _logFileDir.delete();
+                _logFileDir = null;
+            }
+        }
+    }
+}
diff --git a/experiment/src/org/labkey/experiment/pipeline/SampleReloadTask.java b/experiment/src/org/labkey/experiment/pipeline/SampleReloadTask.java
index 6a19f3e780b..5237faa9b48 100644
--- a/experiment/src/org/labkey/experiment/pipeline/SampleReloadTask.java
+++ b/experiment/src/org/labkey/experiment/pipeline/SampleReloadTask.java
@@ -65,7 +65,7 @@ public RecordedActionSet run()
     {
         PipelineJob job = getJob();
         FileAnalysisJobSupport support = job.getJobSupport(FileAnalysisJobSupport.class);
-        job.setLogFile(new File(support.getDataDirectory(), FileUtil.makeFileNameWithTimestamp("triggered_sample_reload", "log")));
+        job.setLogFile(FileUtil.appendName(support.getDataDirectory(), FileUtil.makeFileNameWithTimestamp("triggered_sample_reload", "log")));
         Map<String, String> params = support.getParameters();
 
         job.setStatus("RELOADING", "Job started at: " + DateUtil.nowISO());

From 39cb430c1ed4023ebd9b8469c32d3b28b7b4907b Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Thu, 9 Oct 2025 17:18:59 -0700
Subject: [PATCH 10/15] Fix tests using files

---
 api/src/org/labkey/api/util/JunitUtil.java | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/api/src/org/labkey/api/util/JunitUtil.java b/api/src/org/labkey/api/util/JunitUtil.java
index f2b5d2c0731..7ec4478f7da 100644
--- a/api/src/org/labkey/api/util/JunitUtil.java
+++ b/api/src/org/labkey/api/util/JunitUtil.java
@@ -201,7 +201,8 @@ public static void createRaces(final Runnable runnable, final int threads, final
             {
                 // Modules might have null sourcePath on TeamCity, so crawl for test/sampledata directories and populate
                 // a map the first time, then stash the map for future lookups.
-                String name = module.getExplodedFileLike().getName();
+                // Convert to a Path since this is the root for the FileLike so asking for its name returns an empty string
+                String name = module.getExplodedFileLike().toNioPathForRead().getFileName().toString();
 
                 synchronized (MAP_LOCK)
                 {

From 06c246cc53b159b14b48164ffd9ea2f7c4ea7138 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Fri, 10 Oct 2025 09:47:08 -0700
Subject: [PATCH 11/15] Fix tests using files

---
 .../org/labkey/core/notification/EmailServiceImpl.java   | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/core/src/org/labkey/core/notification/EmailServiceImpl.java b/core/src/org/labkey/core/notification/EmailServiceImpl.java
index 767794155ee..ed6105f5067 100644
--- a/core/src/org/labkey/core/notification/EmailServiceImpl.java
+++ b/core/src/org/labkey/core/notification/EmailServiceImpl.java
@@ -48,6 +48,7 @@
 import org.labkey.api.util.MailHelper;
 import org.labkey.api.util.MailHelper.BulkEmailer;
 import org.labkey.api.util.MimeMap.MimeType;
+import org.labkey.api.util.Path;
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.WebPartView;
@@ -330,8 +331,8 @@ public static class TestCase extends Assert
         public ExpectedException exception = ExpectedException.none();
 
         private static final String PROTOCOL_ATTACHMENT_PATH = "study/Protocol.txt";
-        private static final String NON_EXISTENT_ATTACHMENT_NAME = "fake_file.txt";
-        private static final String FAKE_DIRECTORY_NAME = "/path/to/fake/directory";
+        private static final Path NON_EXISTENT_ATTACHMENT_NAME = Path.parse("fake_file.txt");
+        private static final Path FAKE_DIRECTORY_NAME = Path.parse("./path/to/fake/directory");
 
         private final Module module = ModuleLoader.getInstance().getModule("Study");
 
@@ -370,12 +371,12 @@ public void testDirectoryAttachment() throws IOException
             testAttachmentExceptions(FAKE_DIRECTORY_NAME);
         }
 
-        private void testAttachmentExceptions(String name) throws IOException
+        private void testAttachmentExceptions(Path childPath) throws IOException
         {
             EmailMessage msg = getBaseMessage();
             File studySampleData = JunitUtil.getSampleData(module, "study");
 
-            List<File> attachmentList = Collections.singletonList(FileUtil.appendName(studySampleData, name));
+            List<File> attachmentList = Collections.singletonList(FileUtil.appendPath(studySampleData, childPath));
 
             exception.expect(IllegalArgumentException.class);
             msg.setFiles(attachmentList);

From 957b0c50c23cbbc4551d46bb3885d77775bae930 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Fri, 10 Oct 2025 16:13:12 -0700
Subject: [PATCH 12/15] Newlines

---
 .../experiment/api/ExpDataTableImpl.java      | 1900 ++++++++---------
 .../experiment/pipeline/MoveRunsTask.java     |  568 ++---
 2 files changed, 1234 insertions(+), 1234 deletions(-)

diff --git a/experiment/src/org/labkey/experiment/api/ExpDataTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpDataTableImpl.java
index f6e90b5b05b..1896b1eb5b6 100644
--- a/experiment/src/org/labkey/experiment/api/ExpDataTableImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExpDataTableImpl.java
@@ -1,950 +1,950 @@
-/*
- * Copyright (c) 2008-2019 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.labkey.experiment.api;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.jetbrains.annotations.NotNull;
-import org.json.JSONObject;
-import org.junit.AfterClass;
-import org.junit.Assert;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.labkey.api.action.ApiJsonWriter;
-import org.labkey.api.action.ApiResponseWriter;
-import org.labkey.api.action.ExtendedApiQueryResponse;
-import org.labkey.api.action.NullSafeBindException;
-import org.labkey.api.compliance.TableRules;
-import org.labkey.api.compliance.TableRulesManager;
-import org.labkey.api.data.ColumnInfo;
-import org.labkey.api.data.Container;
-import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerManager;
-import org.labkey.api.data.ExcelWriter;
-import org.labkey.api.data.JdbcType;
-import org.labkey.api.data.MutableColumnInfo;
-import org.labkey.api.data.RenderContext;
-import org.labkey.api.data.SQLFragment;
-import org.labkey.api.data.SimpleFilter;
-import org.labkey.api.exp.DomainDescriptor;
-import org.labkey.api.exp.OntologyManager;
-import org.labkey.api.exp.PropertyColumn;
-import org.labkey.api.exp.api.DataType;
-import org.labkey.api.exp.api.ExpData;
-import org.labkey.api.exp.api.ExpDataClass;
-import org.labkey.api.exp.api.ExpExperiment;
-import org.labkey.api.exp.api.ExpProtocol;
-import org.labkey.api.exp.api.ExpRun;
-import org.labkey.api.exp.api.ExpSampleType;
-import org.labkey.api.exp.api.ExperimentService;
-import org.labkey.api.exp.property.Domain;
-import org.labkey.api.exp.property.DomainProperty;
-import org.labkey.api.exp.property.PropertyService;
-import org.labkey.api.exp.query.ExpDataTable;
-import org.labkey.api.exp.query.ExpSchema;
-import org.labkey.api.exp.query.SamplesSchema;
-import org.labkey.api.files.FileContentService;
-import org.labkey.api.pipeline.PipeRoot;
-import org.labkey.api.pipeline.PipelineService;
-import org.labkey.api.query.DetailsURL;
-import org.labkey.api.query.ExprColumn;
-import org.labkey.api.query.FieldKey;
-import org.labkey.api.query.QueryForeignKey;
-import org.labkey.api.query.QueryService;
-import org.labkey.api.query.QuerySettings;
-import org.labkey.api.query.QueryUpdateService;
-import org.labkey.api.query.QueryView;
-import org.labkey.api.query.RowIdForeignKey;
-import org.labkey.api.query.UserSchema;
-import org.labkey.api.query.column.BuiltInColumnTypes;
-import org.labkey.api.reader.ExcelLoader;
-import org.labkey.api.security.User;
-import org.labkey.api.security.permissions.InsertPermission;
-import org.labkey.api.security.permissions.UpdatePermission;
-import org.labkey.api.util.ConfigurationException;
-import org.labkey.api.util.FileUtil;
-import org.labkey.api.util.HtmlString;
-import org.labkey.api.util.LinkBuilder;
-import org.labkey.api.util.TestContext;
-import org.labkey.api.view.ActionURL;
-import org.labkey.api.writer.HtmlWriter;
-import org.labkey.api.writer.MemoryVirtualFile;
-import org.labkey.api.writer.VirtualFile;
-import org.labkey.experiment.controllers.exp.ExperimentController;
-import org.labkey.experiment.lineage.LineageMethod;
-import org.springframework.beans.MutablePropertyValues;
-import org.springframework.validation.BindException;
-
-import java.io.File;
-import java.io.OutputStream;
-import java.io.StringWriter;
-import java.io.Writer;
-import java.net.URI;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-import java.util.stream.Collectors;
-
-import static org.labkey.api.exp.query.ExpSchema.TableType.DataClasses;
-
-public class ExpDataTableImpl extends ExpRunItemTableImpl<ExpDataTable.Column> implements ExpDataTable
-{
-    protected ExpExperiment _experiment;
-    protected boolean _runSpecified;
-    protected ExpRun _run;
-    protected DataType _type;
-    protected ExpDataClass _dataClass;
-
-    public ExpDataTableImpl(String name, UserSchema schema, ContainerFilter cf)
-    {
-        super(name, ExperimentServiceImpl.get().getTinfoData(), schema, cf);
-
-        addAllowablePermission(UpdatePermission.class);
-        addAllowablePermission(InsertPermission.class);
-    }
-
-    @Override
-    protected void populateColumns()
-    {
-        addColumn(Column.RowId).setHidden(true);
-        addColumn(Column.Name);
-        addColumn(Column.Description);
-        var aliasCol = addColumn(Column.Alias);
-        aliasCol.setHidden(true);
-        addColumn(Column.DataClass);
-        ExpSchema schema = getExpSchema();
-        addColumn(Column.Run).setFk(schema.getRunIdForeignKey(getContainerFilter()));
-        addColumn(Column.Created);
-        addColumn(Column.CreatedBy);
-        addColumn(Column.Modified);
-        addColumn(Column.ModifiedBy);
-
-        addColumn(Column.ContentLink);
-        addColumn(Column.Thumbnail);
-        addColumn(Column.InlineThumbnail);
-        addColumn(Column.SourceProtocolApplication);
-        addColumn(Column.Protocol);
-        addContainerColumn(Column.Folder, null);
-        addColumn(Column.ViewOrDownload);
-        addColumn(Column.Generated);
-        addColumn(Column.LastIndexed);
-
-        addFileColumns(false);
-
-        setDefaultColumns();
-        setTitleColumn("Name");
-
-        // Only include the dataClassId parameter if the ExpData row has a DataClass
-        DetailsURL detailsURL = DetailsURL.fromString("/experiment/showData.view?rowId=${rowId}${dataClass:prefix('%26dataClassId=')}");
-
-        setDetailsURL(detailsURL);
-        getMutableColumn(Column.RowId).setURL(detailsURL);
-        getMutableColumn(Column.Name).setURL(detailsURL);
-
-        ActionURL deleteUrl = ExperimentController.ExperimentUrlsImpl.get().getDeleteDatasURL(getContainer(), null);
-        setDeleteURL(new DetailsURL(deleteUrl));
-
-        addVocabularyDomains();
-        addColumn(Column.Properties);
-
-        var colInputs = addColumn(Column.Inputs);
-        addMethod("Inputs", new LineageMethod(colInputs, true), Set.of(colInputs.getFieldKey()));
-
-        var colOutputs = addColumn(Column.Outputs);
-        addMethod("Outputs", new LineageMethod(colOutputs, false), Set.of(colOutputs.getFieldKey()));
-
-        MutableColumnInfo lineageLookup = ClosureQueryHelper.createAncestorLookupColumnInfo("Ancestors", this, _rootTable.getColumn("rowid"), null, false);
-        addColumn(lineageLookup);
-
-        addExpObjectMethod();
-    }
-
-    @Override
-    public ColumnInfo getExpObjectColumn()
-    {
-        var ret = wrapColumn("_ExpDataTableImpl_object_", _rootTable.getColumn("objectid"));
-        ret.setConceptURI(BuiltInColumnTypes.EXPOBJECTID_CONCEPT_URI);
-        return ret;
-    }
-
-    public List<String> addFileColumns(boolean isFilesTable)
-    {
-        List<String> customProps = new ArrayList<>();
-        var lsidColumn = addColumn(Column.LSID);
-        lsidColumn.setHidden(true);
-        if (!isFilesTable)
-            addColumn(Column.DataFileUrl);
-
-        addColumn(Column.DownloadLink);
-        addColumn(Column.ViewFileLink);
-        addColumn(Column.FileExists);
-        addColumn(Column.FileSize);
-        addColumn(Column.FileExtension);
-        addColumn(Column.WebDavUrl);
-        addColumn(Column.WebDavUrlRelative);
-        var flagCol = addColumn(Column.Flag);
-        if (isFilesTable)
-            flagCol.setLabel("Description");
-
-        FileContentService svc = FileContentService.get();
-        String domainURI = svc.getDomainURI(getContainer());
-        DomainDescriptor dd = OntologyManager.getDomainDescriptor(domainURI, getContainer());
-
-        if (dd != null)
-        {
-            Domain domain = PropertyService.get().getDomain(dd.getDomainId());
-            if (domain != null)
-            {
-                for (DomainProperty prop : domain.getProperties())
-                {
-                    // don't set container on property column so that inherited domain properties work
-                    var projectColumn = new PropertyColumn(prop.getPropertyDescriptor(), lsidColumn, getContainer(), _userSchema.getUser(), false);
-                    addColumn(projectColumn);
-                    customProps.add(projectColumn.getAlias().getId());
-                }
-                setDomain(domain);
-            }
-        }
-
-        return customProps;
-    }
-
-    @Override
-    public boolean supportTableRules() // intentional override
-    {
-        return true;
-    }
-
-    @Override
-    protected @NotNull TableRules findTableRules()
-    {
-        Container definitionContainer = getUserSchema().getContainer();
-        if (null != getDomain())
-            definitionContainer = getDomain().getContainer();
-        return TableRulesManager.get().getTableRules(definitionContainer, getUserSchema().getUser(), getUserSchema().getContainer());
-    }
-
-    public void setDefaultColumns()
-    {
-        checkLocked();
-        List<FieldKey> defaultCols = new ArrayList<>();
-        defaultCols.add(FieldKey.fromParts(Column.Name));
-        defaultCols.add(FieldKey.fromParts(Column.Run));
-        defaultCols.add(FieldKey.fromParts(Column.DataFileUrl));
-        setDefaultVisibleColumns(defaultCols);
-    }
-
-    @Override
-    public QueryUpdateService getUpdateService()
-    {
-        return FileContentService.get().getFilePropsUpdateService(this, getContainer());
-    }
-
-    @Override
-    protected ColumnInfo resolveColumn(String name)
-    {
-        return super.resolveColumn(name);
-    }
-
-    @Override
-    public MutableColumnInfo createColumn(String alias, Column column)
-    {
-        switch (column)
-        {
-            case Folder:
-                return wrapColumn(alias, _rootTable.getColumn("Container"));
-            case Created:
-                return wrapColumn(alias, _rootTable.getColumn("Created"));
-            case CreatedBy:
-                return createUserColumn(alias, _rootTable.getColumn("CreatedBy"));
-            case Modified:
-                return wrapColumn(alias, _rootTable.getColumn("Modified"));
-            case ModifiedBy:
-                return createUserColumn(alias, _rootTable.getColumn("ModifiedBy"));
-            case DataFileUrl:
-                var dataFileUrl = wrapColumn(alias, _rootTable.getColumn("DataFileUrl"));
-                dataFileUrl.setUserEditable(false);
-                return dataFileUrl;
-            case LSID:
-                var lsid = wrapColumn(alias, _rootTable.getColumn("LSID"));
-                lsid.setUserEditable(false);
-                return lsid;
-            case Name:
-                return wrapColumn(alias, _rootTable.getColumn("Name"));
-            case Description:
-                return wrapColumn(alias, _rootTable.getColumn("Description"));
-            case LastIndexed:
-                SQLFragment lastIndexedSql = new SQLFragment("(SELECT LastIndexed FROM ").
-                        append(ExperimentServiceImpl.get().getTinfoDataIndexed(), "di").
-                        append(" WHERE di.DataId = ").
-                        append(ExprColumn.STR_TABLE_ALIAS).append(".RowId)");
-                var lastIndexed = new ExprColumn(this, "LastIndexed", lastIndexedSql, JdbcType.TIMESTAMP);
-                lastIndexed.setUserEditable(false);
-                return lastIndexed;
-            case DataClass:
-            {
-                var c = wrapColumn(alias, _rootTable.getColumn("classId"));
-                c.setUserEditable(false);
-                var fk = QueryForeignKey.from(getUserSchema(), getContainerFilter())
-                        .to(DataClasses.name(), "RowId", "Name");
-                c.setFk( fk );
-                return c;
-            }
-            case Protocol:
-            {
-                ExprColumn col = new ExprColumn(this, Column.Protocol.toString(), new SQLFragment(
-                        "(SELECT ProtocolLSID FROM " + ExperimentServiceImpl.get().getTinfoProtocolApplication() + " pa " +
-                        " WHERE pa.RowId = " + ExprColumn.STR_TABLE_ALIAS + ".SourceApplicationId)"), JdbcType.VARCHAR, getColumn(Column.SourceProtocolApplication));
-                col.setFk(getExpSchema().getProtocolForeignKey(getContainerFilter(),"LSID"));
-                col.setSqlTypeName("lsidtype");
-                col.setHidden(true);
-                return col;
-            }
-            case SourceProtocolApplication:
-            {
-                var columnInfo = wrapColumn(alias, _rootTable.getColumn("SourceApplicationId"));
-                columnInfo.setFk(getExpSchema().getProtocolApplicationForeignKey(getContainerFilter()));
-                columnInfo.setUserEditable(false);
-                columnInfo.setHidden(true);
-                return columnInfo;
-            }
-
-            case SourceApplicationInput:
-            {
-                var col = createEdgeColumn(alias, Column.SourceProtocolApplication, ExpSchema.TableType.DataInputs);
-                col.setDescription("Contains a reference to the DataInput row between this ExpData and it's SourceProtocolApplication");
-                col.setHidden(true);
-                return col;
-            }
-
-            case RunApplication:
-            {
-                SQLFragment sql = new SQLFragment("(SELECT pa.rowId FROM ")
-                        .append(ExperimentService.get().getTinfoProtocolApplication(), "pa")
-                        .append(" WHERE pa.runId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".runId")
-                        .append(" AND pa.cpasType = '").append(ExpProtocol.ApplicationType.ExperimentRunOutput.name()).append("'")
-                        .append(")");
-
-                var col = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
-                col.setFk(getExpSchema().getProtocolApplicationForeignKey(getContainerFilter()));
-                col.setDescription("Contains a reference to the ExperimentRunOutput protocol application of the run that created this data");
-                col.setUserEditable(false);
-                col.setReadOnly(true);
-                col.setHidden(true);
-                return col;
-            }
-
-            case RunApplicationOutput:
-            {
-                var col = createEdgeColumn(alias, Column.RunApplication, ExpSchema.TableType.DataInputs);
-                col.setDescription("Contains a reference to the DataInput row between this ExpData and it's RunOutputApplication");
-                return col;
-            }
-            case RowId:
-            {
-                var ret = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                ret.setFk(new RowIdForeignKey(ret));
-                ret.setHidden(true);
-                return ret;
-            }
-            case Run:
-                var runId = wrapColumn(alias, _rootTable.getColumn("RunId"));
-                runId.setUserEditable(false);
-                return runId;
-            case Flag:
-                return createFlagColumn(alias);
-            case Alias:
-                return createAliasColumn(alias, ExperimentService.get()::getTinfoDataAliasMap);
-            case DownloadLink:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(DownloadFileDataLinkColumn::new);
-                result.setDescription("A link to download the file");
-                return result;
-            }
-            case ViewFileLink:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(ViewFileDataLinkColumn::new);
-                result.setDescription("A link to view the file directly on the web site");
-                return result;
-            }
-            case ContentLink:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(ViewContentDataLinkColumn::new);
-                result.setDescription("A link to view the imported contents of the file on the web site");
-                return result;
-            }
-            case Thumbnail:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(ThumbnailDataLinkColumn::new);
-                result.setDescription("A popup thumbnail of the file if it is an image");
-                return result;
-            }
-            case InlineThumbnail:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setDisplayColumnFactory(InlineThumbnailDataLinkColumn::new);
-                result.setDescription("An inline thumbnail of the file if it is an image");
-                return result;
-            }
-            case FileSize:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setTextAlign("left");
-                result.setJdbcType(JdbcType.VARCHAR);
-                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
-                {
-                    @Override
-                    protected void renderData(HtmlWriter out, ExpData data)
-                    {
-                        String val = ((String)getJsonValue(data));
-                        out.write(val);
-                    }
-
-                    @Override
-                    public Object getJsonValue(ExpData data)
-                    {
-                        if (data == null || data.getFile() == null)
-                            return "";
-                        else if (!data.getFile().exists())
-                            return "File Not Found";
-                        else
-                        {
-                            long size = data.getFile().length();
-                            return FileUtils.byteCountToDisplaySize(size);
-                        }
-                    }
-                });
-                result.setUserEditable(false);
-                result.setShownInUpdateView(false);
-                result.setShownInInsertView(false);
-
-                return result;
-            }
-            case FileExists:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setJdbcType(JdbcType.BOOLEAN);
-                result.setTextAlign("left");
-                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
-                {
-                    @Override
-                    protected void renderData(HtmlWriter out, ExpData data)
-                    {
-                        Boolean val = (Boolean)getJsonValue(data);
-                        out.write(val.toString());
-                    }
-
-                    @Override
-                    protected Object getJsonValue(ExpData data)
-                    {
-                        if (data == null)
-                        {
-                            return false;
-                        }
-                        Path path = data.getFilePath();
-                        return path != null && Files.exists(path);
-                    }
-                });
-                result.setUserEditable(false);
-                result.setShownInUpdateView(false);
-                result.setShownInInsertView(false);
-                return result;
-            }
-            case FileExtension:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setJdbcType(JdbcType.VARCHAR);
-                result.setTextAlign("left");
-                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
-                {
-                    @Override
-                    protected void renderData(HtmlWriter out, ExpData data)
-                    {
-                        Object val = getJsonValue(data);
-                        out.write(val);
-                    }
-
-                    @Override
-                    protected Object getJsonValue(ExpData data)
-                    {
-                        return data.getFile() == null ? null : FileUtil.getExtension(data.getFile());
-                    }
-                });
-                result.setUserEditable(false);
-                result.setShownInUpdateView(false);
-                result.setShownInInsertView(false);
-                return result;
-            }
-            case ViewOrDownload:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setLabel("View/Download");
-                result.setDisplayColumnFactory(ViewOrDownloadDataColumn::new);
-                result.setDescription("Displays links to either download the file or view directly on the web site");
-                return result;
-            }
-            case WebDavUrl:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setJdbcType(JdbcType.VARCHAR);
-                result.setLabel("WebDAV URL");
-                result.setDescription("This is the full WebDAV URL to this file");
-                result.setDisplayColumnFactory(colInfo -> new WebDavUrlColumn(colInfo, false));
-                return result;
-            }
-            case WebDavUrlRelative:
-            {
-                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
-                result.setJdbcType(JdbcType.VARCHAR);
-                result.setLabel("Relative WebDAV URL");
-                result.setDescription("This is the WebDAV path of this file, relative to the file root of this container");
-                result.setDisplayColumnFactory(colInfo -> new WebDavUrlColumn(colInfo, true));
-                return result;
-            }
-            case Generated:
-                return wrapColumn(alias, _rootTable.getColumn("Generated"));
-
-            case Inputs:
-                return createLineageColumn(this, alias, true, false);
-
-            case Outputs:
-                return createLineageColumn(this, alias, false, false);
-
-            case Properties:
-                return createPropertiesColumn(alias);
-
-            default:
-                throw new IllegalArgumentException("Unknown column " + column);
-        }
-    }
-
-    @Override
-    public void setExperiment(ExpExperiment experiment)
-    {
-        checkLocked();
-        if (getExperiment() != null)
-            throw new IllegalArgumentException("Attempt to unset experiment");
-        if (experiment == null)
-            return;
-        SQLFragment condition = new SQLFragment("exp.Data.RunId IN "
-                + " ( SELECT ExperimentRunId FROM exp.RunList "
-                + " WHERE ExperimentId = ? )");
-        condition.add(experiment.getRowId());
-        addCondition(condition);
-        _experiment = experiment;
-    }
-
-    @Override
-    public ExpExperiment getExperiment()
-    {
-        return _experiment;
-    }
-
-    @Override
-    public void setRun(ExpRun run)
-    {
-        checkLocked();
-        if (_runSpecified)
-            throw new IllegalArgumentException("Cannot unset run");
-        _runSpecified = true;
-        _run = run;
-        if (run == null)
-        {
-            addCondition(new SQLFragment("(RunId IS NULL)"), FieldKey.fromParts("RunId"));
-        }
-        else
-        {
-            addCondition(_rootTable.getColumn("RunId"), run.getRowId());
-        }
-    }
-
-    @Override
-    public ExpRun getRun()
-    {
-        return _run;
-    }
-
-    @Override
-    public MutableColumnInfo addDataInputColumn(String alias, String role)
-    {
-        SQLFragment sql = new SQLFragment("(SELECT MIN(exp.datainput.dataid)" +
-                "\nFROM exp.datainput" +
-                "\nWHERE " + ExprColumn.STR_TABLE_ALIAS +  ".SourceApplicationId = exp.datainput.TargetApplicationId" +
-                "\nAND ");
-        if (role == null)
-        {
-            sql.append("1 = 0");
-        }
-        else
-        {
-            sql.append("exp.datainput.role = ?");
-            sql.add(role);
-        }
-        sql.append(")");
-        ExprColumn ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
-        return doAdd(ret);
-    }
-
-    @Override
-    public MutableColumnInfo addMaterialInputColumn(String alias, SamplesSchema schema, String pdRole, final ExpSampleType sampleType)
-    {
-        SQLFragment sql = new SQLFragment("(SELECT MIN(InputMaterial.RowId)" +
-            "\nFROM exp.materialInput" +
-            "\nINNER JOIN exp.material AS InputMaterial ON exp.materialInput.materialId = InputMaterial.RowId" +
-            "\nWHERE " + ExprColumn.STR_TABLE_ALIAS + ".SourceApplicationId = exp.materialInput.TargetApplicationId");
-        if (sampleType != null)
-        {
-            sql.append("\nAND InputMaterial.CPASType = ?");
-            sql.add(sampleType.getLSID());
-        }
-        sql.append(")");
-        ExprColumn ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
-        ret.setFk(schema.materialIdForeignKey(sampleType, null));
-        return doAdd(ret);
-    }
-
-    @Override
-    public DataType getDataType()
-    {
-        return _type;
-    }
-
-    @Override
-    public void setDataType(DataType type)
-    {
-        checkLocked();
-        _type = type;
-        getFilter().deleteConditions(FieldKey.fromParts("LSID"));
-        if (_type != null)
-        {
-            addCondition(new SQLFragment("LSID LIKE " + getSqlDialect().concatenate("'urn:lsid:%:'", "?", "'%'"), _type.getNamespacePrefix()), FieldKey.fromParts("LSID"));
-        }
-    }
-
-    public void setDataClass(ExpDataClass dataClass)
-    {
-        checkLocked();
-        _dataClass = dataClass;
-        getFilter().deleteConditions(FieldKey.fromParts("classId"));
-        if (_dataClass != null)
-        {
-            addCondition(getColumn("classId"), _dataClass.getRowId());
-        }
-    }
-
-    @Override
-    public MutableColumnInfo addInputRunCountColumn(String alias)
-    {
-        SQLFragment sql = new SQLFragment("(SELECT COUNT(DISTINCT exp.ProtocolApplication.RunId) " +
-                "FROM exp.ProtocolApplication INNER JOIN Exp.DataInput ON exp.ProtocolApplication.RowId = Exp.DataInput.TargetApplicationId " +
-                "WHERE Exp.DataInput.DataId = " + ExprColumn.STR_TABLE_ALIAS + ".RowId)");
-        var ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
-        return doAdd(ret);
-    }
-
-    private static class ThumbnailDataLinkColumn extends ViewFileDataLinkColumn
-    {
-        public ThumbnailDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected void renderData(HtmlWriter out, ExpData data)
-        {
-            renderThumbnailPopup(out, data, getURL(data));
-        }
-    }
-
-    private static class InlineThumbnailDataLinkColumn extends ViewFileDataLinkColumn
-    {
-        public InlineThumbnailDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected void renderData(HtmlWriter out, ExpData data)
-        {
-            out.write(renderThumbnailImg(data, getURL(data)));
-        }
-    }
-
-    private static class DownloadFileDataLinkColumn extends DataLinkColumn
-    {
-        public DownloadFileDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected ActionURL getURL(ExpData data)
-        {
-            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, false);
-        }
-    }
-
-    private static class ViewFileDataLinkColumn extends DataLinkColumn
-    {
-        public ViewFileDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected ActionURL getURL(ExpData data)
-        {
-            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true);
-        }
-    }
-
-    private static class ViewContentDataLinkColumn extends DataLinkColumn
-    {
-        public ViewContentDataLinkColumn(ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected ActionURL getURL(ExpData data)
-        {
-            return data.findDataHandler().getContentURL(data);
-        }
-    }
-
-    private static class ViewOrDownloadDataColumn extends DataLinkColumn
-    {
-        public ViewOrDownloadDataColumn (ColumnInfo colInfo)
-        {
-            super(colInfo);
-        }
-
-        @Override
-        protected ActionURL getURL(ExpData data)
-        {
-            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true);
-        }
-
-        @Override
-        public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
-        {
-            ExpData data = getData(ctx, getColumnInfo());
-            if (data != null)
-            {
-                if (data.isFileOnDisk())
-                {
-                    out.write(LinkBuilder.labkeyLink("View File", ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true)));
-                    out.write(HtmlString.BR);
-                    out.write(LinkBuilder.labkeyLink("Download", ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, false)));
-                }
-                else
-                {
-                    out.write("File not available");
-                }
-            }
-        }
-    }
-
-    private static class WebDavUrlColumn extends ExpDataFileColumn
-    {
-        private final boolean _relative;
-
-        public WebDavUrlColumn (ColumnInfo colInfo, boolean relative)
-        {
-            super(colInfo);
-            setTextAlign("left");
-            _relative = relative;
-        }
-
-        @Override
-        public Object getJsonValue(ExpData data)
-        {
-            if (data == null)
-                return null;
-
-            return Objects.toString(data.getWebDavURL(_relative ? FileContentService.PathType.folderRelative : FileContentService.PathType.serverRelative), null);
-        }
-
-        @Override
-        protected void renderData(HtmlWriter out, ExpData data)
-        {
-            Object val = getJsonValue(data);
-            out.write(val);
-        }
-    }
-
-    public static class TestCase extends Assert
-    {
-        public static final String PROJECT_NAME = "ExptDataTableImplIntegrationTest";
-
-        @BeforeClass
-        public static void initialSetUp()
-        {
-            doInitialSetUp(PROJECT_NAME);
-        }
-
-        @AfterClass
-        public static void cleanup()
-        {
-            doCleanup(PROJECT_NAME);
-        }
-
-        private class WebDavTestCase
-        {
-            private final ExpData _data;
-            private final String _relativePath;
-
-            public WebDavTestCase(String name, File file, String relativePath)
-            {
-                _data = ExperimentService.get().createData(getProject(), new DataType("TestData"));
-                _data.setDataFileURI(file.toURI());
-                _data.setName(name);
-                _data.save(getUser());
-
-                _relativePath = relativePath;
-            }
-
-            public String getUrl()
-            {
-                if (_relativePath == null)
-                {
-                    return null;
-                }
-
-                PipeRoot pr = PipelineService.get().getPipelineRootSetting(getProject());
-
-                URI uri = pr.getWebdavURL().resolve(getUrlRelative());
-                return uri == null ? null : uri.toString();
-            }
-
-            public String getUrlRelative()
-            {
-                return _relativePath;
-            }
-        }
-
-        @Test
-        public void testWebDavColumns() throws Exception
-        {
-            PipeRoot pr = PipelineService.get().getPipelineRootSetting(getProject());
-            if (pr == null)
-            {
-                throw new ConfigurationException("File root is not set");
-            }
-
-            List<WebDavTestCase> testCases = new ArrayList<>();
-
-            final String PATH1 = "webDavTest.txt";
-            testCases.add(new WebDavTestCase("TestData1", FileUtil.appendName(pr.getRootPath(), PATH1), PATH1));
-            testCases.add(new WebDavTestCase("TestData2", FileUtil.appendPath(pr.getRootPath(), org.labkey.api.util.Path.parse("subfolder/webDavTest.txt")), "subfolder/webDavTest.txt"));
-            testCases.add(new WebDavTestCase("TestData3", FileUtil.appendPath(pr.getRootPath(), org.labkey.api.util.Path.parse("subfolder/webD  avT est.txt")), "subfolder/webD%20%20avT%20est.txt"));
-
-            PipeRoot prHome = PipelineService.get().getPipelineRootSetting(ContainerManager.getHomeContainer());
-            testCases.add(new WebDavTestCase("NotUnderFolderRoot", FileUtil.appendName(prHome.getRootPath(), PATH1), null));
-
-            testCases.add(new WebDavTestCase("NotUnderFileRoot", new File("/", PATH1), null));
-
-            UserSchema us = QueryService.get().getUserSchema(getUser(), getProject(), ExpSchema.SCHEMA_NAME);
-
-            for (final WebDavTestCase tc : testCases)
-            {
-                BindException errors = new NullSafeBindException(new Object(), "command");
-                MutablePropertyValues mpv = new MutablePropertyValues();
-                mpv.addPropertyValue("schemaName", ExpSchema.SCHEMA_NAME);
-                mpv.addPropertyValue("query.queryName", ExpSchema.TableType.Data.name());
-                List<FieldKey> fieldKeys = Arrays.asList("RowId", "Name", Column.WebDavUrl.name(), Column.WebDavUrlRelative.name()).stream().map(FieldKey::fromString).collect(Collectors.toList());
-                mpv.addPropertyValue("query.columns", StringUtils.join(fieldKeys, ","));
-
-                QuerySettings qs = us.getSettings(mpv, "query");
-
-                qs.setBaseFilter(new SimpleFilter(FieldKey.fromString("RowId"), tc._data.getRowId()));
-                QueryView view = new QueryView(us, qs, errors);
-
-                ExtendedApiQueryResponse resp = new ExtendedApiQueryResponse(view, false, false, "auditLog", "ContainerAuditEvent", 0, fieldKeys, false, false, false);
-                Writer writer = new StringWriter();
-                ApiResponseWriter apiWriter = new ApiJsonWriter(writer);
-                resp.render(apiWriter);
-                JSONObject json = new JSONObject(writer.toString());
-                JSONObject row = json.getJSONArray("rows").getJSONObject(0);
-
-                String webDavUrl = row.getJSONObject("WebDavUrl").optString("value", null);
-                String webDavUrlRelative = row.getJSONObject("WebDavUrlRelative").optString("value", null);
-
-                assertEquals("Incorrect WebDavUrlRelative", tc.getUrlRelative(), webDavUrlRelative);
-                assertEquals("Incorrect WebDavUrl", tc.getUrl(), webDavUrl);
-
-                ExcelWriter excel = view.getExcelWriter(ExcelWriter.ExcelDocumentType.xlsx, null);
-                try (VirtualFile f = new MemoryVirtualFile())
-                {
-                    try (OutputStream os = f.getOutputStream("excel.xlsx"))
-                    {
-                        excel.renderWorkbook(os);
-                    }
-
-                    try (ExcelLoader loader = new ExcelLoader(f.getInputStream("excel.xlsx"), true, getProject()))
-                    {
-                        loader.iterator().forEachRemaining(map -> {
-                            Object excelWebdavUrl = map.get("WebDAV URL");
-                            Object excelWebdavUrlRelative = map.get("Relative WebDAV URL");
-                            assertEquals("Incorrect WebDavUrl", tc.getUrl(), excelWebdavUrl);
-                            assertEquals("Incorrect WebDavUrlRelative", tc.getUrlRelative(), excelWebdavUrlRelative);
-                        });
-                    }
-                }
-            }
-        }
-
-        protected static void doInitialSetUp(String projectName)
-        {
-            //pre-clean
-            doCleanup(projectName);
-
-            Container project = ContainerManager.getForPath(projectName);
-            if (project == null)
-            {
-                ContainerManager.createContainer(ContainerManager.getRoot(), projectName, TestContext.get().getUser());
-            }
-        }
-
-        protected static void doCleanup(String projectName)
-        {
-            Container project = ContainerManager.getForPath(projectName);
-            if (project != null)
-            {
-                ContainerManager.delete(project, getUser());
-            }
-        }
-
-        protected static User getUser()
-        {
-            return TestContext.get().getUser();
-        }
-
-        protected Container getProject()
-        {
-            return ContainerManager.getForPath(PROJECT_NAME);
-        }
-    }
-}
+/*
+ * Copyright (c) 2008-2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.labkey.experiment.api;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.NotNull;
+import org.json.JSONObject;
+import org.junit.AfterClass;
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.labkey.api.action.ApiJsonWriter;
+import org.labkey.api.action.ApiResponseWriter;
+import org.labkey.api.action.ExtendedApiQueryResponse;
+import org.labkey.api.action.NullSafeBindException;
+import org.labkey.api.compliance.TableRules;
+import org.labkey.api.compliance.TableRulesManager;
+import org.labkey.api.data.ColumnInfo;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.ExcelWriter;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.MutableColumnInfo;
+import org.labkey.api.data.RenderContext;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.exp.DomainDescriptor;
+import org.labkey.api.exp.OntologyManager;
+import org.labkey.api.exp.PropertyColumn;
+import org.labkey.api.exp.api.DataType;
+import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.exp.api.ExpDataClass;
+import org.labkey.api.exp.api.ExpExperiment;
+import org.labkey.api.exp.api.ExpProtocol;
+import org.labkey.api.exp.api.ExpRun;
+import org.labkey.api.exp.api.ExpSampleType;
+import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.exp.property.Domain;
+import org.labkey.api.exp.property.DomainProperty;
+import org.labkey.api.exp.property.PropertyService;
+import org.labkey.api.exp.query.ExpDataTable;
+import org.labkey.api.exp.query.ExpSchema;
+import org.labkey.api.exp.query.SamplesSchema;
+import org.labkey.api.files.FileContentService;
+import org.labkey.api.pipeline.PipeRoot;
+import org.labkey.api.pipeline.PipelineService;
+import org.labkey.api.query.DetailsURL;
+import org.labkey.api.query.ExprColumn;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryForeignKey;
+import org.labkey.api.query.QueryService;
+import org.labkey.api.query.QuerySettings;
+import org.labkey.api.query.QueryUpdateService;
+import org.labkey.api.query.QueryView;
+import org.labkey.api.query.RowIdForeignKey;
+import org.labkey.api.query.UserSchema;
+import org.labkey.api.query.column.BuiltInColumnTypes;
+import org.labkey.api.reader.ExcelLoader;
+import org.labkey.api.security.User;
+import org.labkey.api.security.permissions.InsertPermission;
+import org.labkey.api.security.permissions.UpdatePermission;
+import org.labkey.api.util.ConfigurationException;
+import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.HtmlString;
+import org.labkey.api.util.LinkBuilder;
+import org.labkey.api.util.TestContext;
+import org.labkey.api.view.ActionURL;
+import org.labkey.api.writer.HtmlWriter;
+import org.labkey.api.writer.MemoryVirtualFile;
+import org.labkey.api.writer.VirtualFile;
+import org.labkey.experiment.controllers.exp.ExperimentController;
+import org.labkey.experiment.lineage.LineageMethod;
+import org.springframework.beans.MutablePropertyValues;
+import org.springframework.validation.BindException;
+
+import java.io.File;
+import java.io.OutputStream;
+import java.io.StringWriter;
+import java.io.Writer;
+import java.net.URI;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static org.labkey.api.exp.query.ExpSchema.TableType.DataClasses;
+
+public class ExpDataTableImpl extends ExpRunItemTableImpl<ExpDataTable.Column> implements ExpDataTable
+{
+    protected ExpExperiment _experiment;
+    protected boolean _runSpecified;
+    protected ExpRun _run;
+    protected DataType _type;
+    protected ExpDataClass _dataClass;
+
+    public ExpDataTableImpl(String name, UserSchema schema, ContainerFilter cf)
+    {
+        super(name, ExperimentServiceImpl.get().getTinfoData(), schema, cf);
+
+        addAllowablePermission(UpdatePermission.class);
+        addAllowablePermission(InsertPermission.class);
+    }
+
+    @Override
+    protected void populateColumns()
+    {
+        addColumn(Column.RowId).setHidden(true);
+        addColumn(Column.Name);
+        addColumn(Column.Description);
+        var aliasCol = addColumn(Column.Alias);
+        aliasCol.setHidden(true);
+        addColumn(Column.DataClass);
+        ExpSchema schema = getExpSchema();
+        addColumn(Column.Run).setFk(schema.getRunIdForeignKey(getContainerFilter()));
+        addColumn(Column.Created);
+        addColumn(Column.CreatedBy);
+        addColumn(Column.Modified);
+        addColumn(Column.ModifiedBy);
+
+        addColumn(Column.ContentLink);
+        addColumn(Column.Thumbnail);
+        addColumn(Column.InlineThumbnail);
+        addColumn(Column.SourceProtocolApplication);
+        addColumn(Column.Protocol);
+        addContainerColumn(Column.Folder, null);
+        addColumn(Column.ViewOrDownload);
+        addColumn(Column.Generated);
+        addColumn(Column.LastIndexed);
+
+        addFileColumns(false);
+
+        setDefaultColumns();
+        setTitleColumn("Name");
+
+        // Only include the dataClassId parameter if the ExpData row has a DataClass
+        DetailsURL detailsURL = DetailsURL.fromString("/experiment/showData.view?rowId=${rowId}${dataClass:prefix('%26dataClassId=')}");
+
+        setDetailsURL(detailsURL);
+        getMutableColumn(Column.RowId).setURL(detailsURL);
+        getMutableColumn(Column.Name).setURL(detailsURL);
+
+        ActionURL deleteUrl = ExperimentController.ExperimentUrlsImpl.get().getDeleteDatasURL(getContainer(), null);
+        setDeleteURL(new DetailsURL(deleteUrl));
+
+        addVocabularyDomains();
+        addColumn(Column.Properties);
+
+        var colInputs = addColumn(Column.Inputs);
+        addMethod("Inputs", new LineageMethod(colInputs, true), Set.of(colInputs.getFieldKey()));
+
+        var colOutputs = addColumn(Column.Outputs);
+        addMethod("Outputs", new LineageMethod(colOutputs, false), Set.of(colOutputs.getFieldKey()));
+
+        MutableColumnInfo lineageLookup = ClosureQueryHelper.createAncestorLookupColumnInfo("Ancestors", this, _rootTable.getColumn("rowid"), null, false);
+        addColumn(lineageLookup);
+
+        addExpObjectMethod();
+    }
+
+    @Override
+    public ColumnInfo getExpObjectColumn()
+    {
+        var ret = wrapColumn("_ExpDataTableImpl_object_", _rootTable.getColumn("objectid"));
+        ret.setConceptURI(BuiltInColumnTypes.EXPOBJECTID_CONCEPT_URI);
+        return ret;
+    }
+
+    public List<String> addFileColumns(boolean isFilesTable)
+    {
+        List<String> customProps = new ArrayList<>();
+        var lsidColumn = addColumn(Column.LSID);
+        lsidColumn.setHidden(true);
+        if (!isFilesTable)
+            addColumn(Column.DataFileUrl);
+
+        addColumn(Column.DownloadLink);
+        addColumn(Column.ViewFileLink);
+        addColumn(Column.FileExists);
+        addColumn(Column.FileSize);
+        addColumn(Column.FileExtension);
+        addColumn(Column.WebDavUrl);
+        addColumn(Column.WebDavUrlRelative);
+        var flagCol = addColumn(Column.Flag);
+        if (isFilesTable)
+            flagCol.setLabel("Description");
+
+        FileContentService svc = FileContentService.get();
+        String domainURI = svc.getDomainURI(getContainer());
+        DomainDescriptor dd = OntologyManager.getDomainDescriptor(domainURI, getContainer());
+
+        if (dd != null)
+        {
+            Domain domain = PropertyService.get().getDomain(dd.getDomainId());
+            if (domain != null)
+            {
+                for (DomainProperty prop : domain.getProperties())
+                {
+                    // don't set container on property column so that inherited domain properties work
+                    var projectColumn = new PropertyColumn(prop.getPropertyDescriptor(), lsidColumn, getContainer(), _userSchema.getUser(), false);
+                    addColumn(projectColumn);
+                    customProps.add(projectColumn.getAlias().getId());
+                }
+                setDomain(domain);
+            }
+        }
+
+        return customProps;
+    }
+
+    @Override
+    public boolean supportTableRules() // intentional override
+    {
+        return true;
+    }
+
+    @Override
+    protected @NotNull TableRules findTableRules()
+    {
+        Container definitionContainer = getUserSchema().getContainer();
+        if (null != getDomain())
+            definitionContainer = getDomain().getContainer();
+        return TableRulesManager.get().getTableRules(definitionContainer, getUserSchema().getUser(), getUserSchema().getContainer());
+    }
+
+    public void setDefaultColumns()
+    {
+        checkLocked();
+        List<FieldKey> defaultCols = new ArrayList<>();
+        defaultCols.add(FieldKey.fromParts(Column.Name));
+        defaultCols.add(FieldKey.fromParts(Column.Run));
+        defaultCols.add(FieldKey.fromParts(Column.DataFileUrl));
+        setDefaultVisibleColumns(defaultCols);
+    }
+
+    @Override
+    public QueryUpdateService getUpdateService()
+    {
+        return FileContentService.get().getFilePropsUpdateService(this, getContainer());
+    }
+
+    @Override
+    protected ColumnInfo resolveColumn(String name)
+    {
+        return super.resolveColumn(name);
+    }
+
+    @Override
+    public MutableColumnInfo createColumn(String alias, Column column)
+    {
+        switch (column)
+        {
+            case Folder:
+                return wrapColumn(alias, _rootTable.getColumn("Container"));
+            case Created:
+                return wrapColumn(alias, _rootTable.getColumn("Created"));
+            case CreatedBy:
+                return createUserColumn(alias, _rootTable.getColumn("CreatedBy"));
+            case Modified:
+                return wrapColumn(alias, _rootTable.getColumn("Modified"));
+            case ModifiedBy:
+                return createUserColumn(alias, _rootTable.getColumn("ModifiedBy"));
+            case DataFileUrl:
+                var dataFileUrl = wrapColumn(alias, _rootTable.getColumn("DataFileUrl"));
+                dataFileUrl.setUserEditable(false);
+                return dataFileUrl;
+            case LSID:
+                var lsid = wrapColumn(alias, _rootTable.getColumn("LSID"));
+                lsid.setUserEditable(false);
+                return lsid;
+            case Name:
+                return wrapColumn(alias, _rootTable.getColumn("Name"));
+            case Description:
+                return wrapColumn(alias, _rootTable.getColumn("Description"));
+            case LastIndexed:
+                SQLFragment lastIndexedSql = new SQLFragment("(SELECT LastIndexed FROM ").
+                        append(ExperimentServiceImpl.get().getTinfoDataIndexed(), "di").
+                        append(" WHERE di.DataId = ").
+                        append(ExprColumn.STR_TABLE_ALIAS).append(".RowId)");
+                var lastIndexed = new ExprColumn(this, "LastIndexed", lastIndexedSql, JdbcType.TIMESTAMP);
+                lastIndexed.setUserEditable(false);
+                return lastIndexed;
+            case DataClass:
+            {
+                var c = wrapColumn(alias, _rootTable.getColumn("classId"));
+                c.setUserEditable(false);
+                var fk = QueryForeignKey.from(getUserSchema(), getContainerFilter())
+                        .to(DataClasses.name(), "RowId", "Name");
+                c.setFk( fk );
+                return c;
+            }
+            case Protocol:
+            {
+                ExprColumn col = new ExprColumn(this, Column.Protocol.toString(), new SQLFragment(
+                        "(SELECT ProtocolLSID FROM " + ExperimentServiceImpl.get().getTinfoProtocolApplication() + " pa " +
+                        " WHERE pa.RowId = " + ExprColumn.STR_TABLE_ALIAS + ".SourceApplicationId)"), JdbcType.VARCHAR, getColumn(Column.SourceProtocolApplication));
+                col.setFk(getExpSchema().getProtocolForeignKey(getContainerFilter(),"LSID"));
+                col.setSqlTypeName("lsidtype");
+                col.setHidden(true);
+                return col;
+            }
+            case SourceProtocolApplication:
+            {
+                var columnInfo = wrapColumn(alias, _rootTable.getColumn("SourceApplicationId"));
+                columnInfo.setFk(getExpSchema().getProtocolApplicationForeignKey(getContainerFilter()));
+                columnInfo.setUserEditable(false);
+                columnInfo.setHidden(true);
+                return columnInfo;
+            }
+
+            case SourceApplicationInput:
+            {
+                var col = createEdgeColumn(alias, Column.SourceProtocolApplication, ExpSchema.TableType.DataInputs);
+                col.setDescription("Contains a reference to the DataInput row between this ExpData and it's SourceProtocolApplication");
+                col.setHidden(true);
+                return col;
+            }
+
+            case RunApplication:
+            {
+                SQLFragment sql = new SQLFragment("(SELECT pa.rowId FROM ")
+                        .append(ExperimentService.get().getTinfoProtocolApplication(), "pa")
+                        .append(" WHERE pa.runId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".runId")
+                        .append(" AND pa.cpasType = '").append(ExpProtocol.ApplicationType.ExperimentRunOutput.name()).append("'")
+                        .append(")");
+
+                var col = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
+                col.setFk(getExpSchema().getProtocolApplicationForeignKey(getContainerFilter()));
+                col.setDescription("Contains a reference to the ExperimentRunOutput protocol application of the run that created this data");
+                col.setUserEditable(false);
+                col.setReadOnly(true);
+                col.setHidden(true);
+                return col;
+            }
+
+            case RunApplicationOutput:
+            {
+                var col = createEdgeColumn(alias, Column.RunApplication, ExpSchema.TableType.DataInputs);
+                col.setDescription("Contains a reference to the DataInput row between this ExpData and it's RunOutputApplication");
+                return col;
+            }
+            case RowId:
+            {
+                var ret = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                ret.setFk(new RowIdForeignKey(ret));
+                ret.setHidden(true);
+                return ret;
+            }
+            case Run:
+                var runId = wrapColumn(alias, _rootTable.getColumn("RunId"));
+                runId.setUserEditable(false);
+                return runId;
+            case Flag:
+                return createFlagColumn(alias);
+            case Alias:
+                return createAliasColumn(alias, ExperimentService.get()::getTinfoDataAliasMap);
+            case DownloadLink:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(DownloadFileDataLinkColumn::new);
+                result.setDescription("A link to download the file");
+                return result;
+            }
+            case ViewFileLink:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(ViewFileDataLinkColumn::new);
+                result.setDescription("A link to view the file directly on the web site");
+                return result;
+            }
+            case ContentLink:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(ViewContentDataLinkColumn::new);
+                result.setDescription("A link to view the imported contents of the file on the web site");
+                return result;
+            }
+            case Thumbnail:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(ThumbnailDataLinkColumn::new);
+                result.setDescription("A popup thumbnail of the file if it is an image");
+                return result;
+            }
+            case InlineThumbnail:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setDisplayColumnFactory(InlineThumbnailDataLinkColumn::new);
+                result.setDescription("An inline thumbnail of the file if it is an image");
+                return result;
+            }
+            case FileSize:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setTextAlign("left");
+                result.setJdbcType(JdbcType.VARCHAR);
+                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
+                {
+                    @Override
+                    protected void renderData(HtmlWriter out, ExpData data)
+                    {
+                        String val = ((String)getJsonValue(data));
+                        out.write(val);
+                    }
+
+                    @Override
+                    public Object getJsonValue(ExpData data)
+                    {
+                        if (data == null || data.getFile() == null)
+                            return "";
+                        else if (!data.getFile().exists())
+                            return "File Not Found";
+                        else
+                        {
+                            long size = data.getFile().length();
+                            return FileUtils.byteCountToDisplaySize(size);
+                        }
+                    }
+                });
+                result.setUserEditable(false);
+                result.setShownInUpdateView(false);
+                result.setShownInInsertView(false);
+
+                return result;
+            }
+            case FileExists:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setJdbcType(JdbcType.BOOLEAN);
+                result.setTextAlign("left");
+                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
+                {
+                    @Override
+                    protected void renderData(HtmlWriter out, ExpData data)
+                    {
+                        Boolean val = (Boolean)getJsonValue(data);
+                        out.write(val.toString());
+                    }
+
+                    @Override
+                    protected Object getJsonValue(ExpData data)
+                    {
+                        if (data == null)
+                        {
+                            return false;
+                        }
+                        Path path = data.getFilePath();
+                        return path != null && Files.exists(path);
+                    }
+                });
+                result.setUserEditable(false);
+                result.setShownInUpdateView(false);
+                result.setShownInInsertView(false);
+                return result;
+            }
+            case FileExtension:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setJdbcType(JdbcType.VARCHAR);
+                result.setTextAlign("left");
+                result.setDisplayColumnFactory(colInfo -> new ExpDataFileColumn(colInfo)
+                {
+                    @Override
+                    protected void renderData(HtmlWriter out, ExpData data)
+                    {
+                        Object val = getJsonValue(data);
+                        out.write(val);
+                    }
+
+                    @Override
+                    protected Object getJsonValue(ExpData data)
+                    {
+                        return data.getFile() == null ? null : FileUtil.getExtension(data.getFile());
+                    }
+                });
+                result.setUserEditable(false);
+                result.setShownInUpdateView(false);
+                result.setShownInInsertView(false);
+                return result;
+            }
+            case ViewOrDownload:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setLabel("View/Download");
+                result.setDisplayColumnFactory(ViewOrDownloadDataColumn::new);
+                result.setDescription("Displays links to either download the file or view directly on the web site");
+                return result;
+            }
+            case WebDavUrl:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setJdbcType(JdbcType.VARCHAR);
+                result.setLabel("WebDAV URL");
+                result.setDescription("This is the full WebDAV URL to this file");
+                result.setDisplayColumnFactory(colInfo -> new WebDavUrlColumn(colInfo, false));
+                return result;
+            }
+            case WebDavUrlRelative:
+            {
+                var result = wrapColumn(alias, _rootTable.getColumn("RowId"));
+                result.setJdbcType(JdbcType.VARCHAR);
+                result.setLabel("Relative WebDAV URL");
+                result.setDescription("This is the WebDAV path of this file, relative to the file root of this container");
+                result.setDisplayColumnFactory(colInfo -> new WebDavUrlColumn(colInfo, true));
+                return result;
+            }
+            case Generated:
+                return wrapColumn(alias, _rootTable.getColumn("Generated"));
+
+            case Inputs:
+                return createLineageColumn(this, alias, true, false);
+
+            case Outputs:
+                return createLineageColumn(this, alias, false, false);
+
+            case Properties:
+                return createPropertiesColumn(alias);
+
+            default:
+                throw new IllegalArgumentException("Unknown column " + column);
+        }
+    }
+
+    @Override
+    public void setExperiment(ExpExperiment experiment)
+    {
+        checkLocked();
+        if (getExperiment() != null)
+            throw new IllegalArgumentException("Attempt to unset experiment");
+        if (experiment == null)
+            return;
+        SQLFragment condition = new SQLFragment("exp.Data.RunId IN "
+                + " ( SELECT ExperimentRunId FROM exp.RunList "
+                + " WHERE ExperimentId = ? )");
+        condition.add(experiment.getRowId());
+        addCondition(condition);
+        _experiment = experiment;
+    }
+
+    @Override
+    public ExpExperiment getExperiment()
+    {
+        return _experiment;
+    }
+
+    @Override
+    public void setRun(ExpRun run)
+    {
+        checkLocked();
+        if (_runSpecified)
+            throw new IllegalArgumentException("Cannot unset run");
+        _runSpecified = true;
+        _run = run;
+        if (run == null)
+        {
+            addCondition(new SQLFragment("(RunId IS NULL)"), FieldKey.fromParts("RunId"));
+        }
+        else
+        {
+            addCondition(_rootTable.getColumn("RunId"), run.getRowId());
+        }
+    }
+
+    @Override
+    public ExpRun getRun()
+    {
+        return _run;
+    }
+
+    @Override
+    public MutableColumnInfo addDataInputColumn(String alias, String role)
+    {
+        SQLFragment sql = new SQLFragment("(SELECT MIN(exp.datainput.dataid)" +
+                "\nFROM exp.datainput" +
+                "\nWHERE " + ExprColumn.STR_TABLE_ALIAS +  ".SourceApplicationId = exp.datainput.TargetApplicationId" +
+                "\nAND ");
+        if (role == null)
+        {
+            sql.append("1 = 0");
+        }
+        else
+        {
+            sql.append("exp.datainput.role = ?");
+            sql.add(role);
+        }
+        sql.append(")");
+        ExprColumn ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
+        return doAdd(ret);
+    }
+
+    @Override
+    public MutableColumnInfo addMaterialInputColumn(String alias, SamplesSchema schema, String pdRole, final ExpSampleType sampleType)
+    {
+        SQLFragment sql = new SQLFragment("(SELECT MIN(InputMaterial.RowId)" +
+            "\nFROM exp.materialInput" +
+            "\nINNER JOIN exp.material AS InputMaterial ON exp.materialInput.materialId = InputMaterial.RowId" +
+            "\nWHERE " + ExprColumn.STR_TABLE_ALIAS + ".SourceApplicationId = exp.materialInput.TargetApplicationId");
+        if (sampleType != null)
+        {
+            sql.append("\nAND InputMaterial.CPASType = ?");
+            sql.add(sampleType.getLSID());
+        }
+        sql.append(")");
+        ExprColumn ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
+        ret.setFk(schema.materialIdForeignKey(sampleType, null));
+        return doAdd(ret);
+    }
+
+    @Override
+    public DataType getDataType()
+    {
+        return _type;
+    }
+
+    @Override
+    public void setDataType(DataType type)
+    {
+        checkLocked();
+        _type = type;
+        getFilter().deleteConditions(FieldKey.fromParts("LSID"));
+        if (_type != null)
+        {
+            addCondition(new SQLFragment("LSID LIKE " + getSqlDialect().concatenate("'urn:lsid:%:'", "?", "'%'"), _type.getNamespacePrefix()), FieldKey.fromParts("LSID"));
+        }
+    }
+
+    public void setDataClass(ExpDataClass dataClass)
+    {
+        checkLocked();
+        _dataClass = dataClass;
+        getFilter().deleteConditions(FieldKey.fromParts("classId"));
+        if (_dataClass != null)
+        {
+            addCondition(getColumn("classId"), _dataClass.getRowId());
+        }
+    }
+
+    @Override
+    public MutableColumnInfo addInputRunCountColumn(String alias)
+    {
+        SQLFragment sql = new SQLFragment("(SELECT COUNT(DISTINCT exp.ProtocolApplication.RunId) " +
+                "FROM exp.ProtocolApplication INNER JOIN Exp.DataInput ON exp.ProtocolApplication.RowId = Exp.DataInput.TargetApplicationId " +
+                "WHERE Exp.DataInput.DataId = " + ExprColumn.STR_TABLE_ALIAS + ".RowId)");
+        var ret = new ExprColumn(this, alias, sql, JdbcType.INTEGER);
+        return doAdd(ret);
+    }
+
+    private static class ThumbnailDataLinkColumn extends ViewFileDataLinkColumn
+    {
+        public ThumbnailDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected void renderData(HtmlWriter out, ExpData data)
+        {
+            renderThumbnailPopup(out, data, getURL(data));
+        }
+    }
+
+    private static class InlineThumbnailDataLinkColumn extends ViewFileDataLinkColumn
+    {
+        public InlineThumbnailDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected void renderData(HtmlWriter out, ExpData data)
+        {
+            out.write(renderThumbnailImg(data, getURL(data)));
+        }
+    }
+
+    private static class DownloadFileDataLinkColumn extends DataLinkColumn
+    {
+        public DownloadFileDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected ActionURL getURL(ExpData data)
+        {
+            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, false);
+        }
+    }
+
+    private static class ViewFileDataLinkColumn extends DataLinkColumn
+    {
+        public ViewFileDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected ActionURL getURL(ExpData data)
+        {
+            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true);
+        }
+    }
+
+    private static class ViewContentDataLinkColumn extends DataLinkColumn
+    {
+        public ViewContentDataLinkColumn(ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected ActionURL getURL(ExpData data)
+        {
+            return data.findDataHandler().getContentURL(data);
+        }
+    }
+
+    private static class ViewOrDownloadDataColumn extends DataLinkColumn
+    {
+        public ViewOrDownloadDataColumn (ColumnInfo colInfo)
+        {
+            super(colInfo);
+        }
+
+        @Override
+        protected ActionURL getURL(ExpData data)
+        {
+            return ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true);
+        }
+
+        @Override
+        public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
+        {
+            ExpData data = getData(ctx, getColumnInfo());
+            if (data != null)
+            {
+                if (data.isFileOnDisk())
+                {
+                    out.write(LinkBuilder.labkeyLink("View File", ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, true)));
+                    out.write(HtmlString.BR);
+                    out.write(LinkBuilder.labkeyLink("Download", ExperimentController.ExperimentUrlsImpl.get().getShowFileURL(data, false)));
+                }
+                else
+                {
+                    out.write("File not available");
+                }
+            }
+        }
+    }
+
+    private static class WebDavUrlColumn extends ExpDataFileColumn
+    {
+        private final boolean _relative;
+
+        public WebDavUrlColumn (ColumnInfo colInfo, boolean relative)
+        {
+            super(colInfo);
+            setTextAlign("left");
+            _relative = relative;
+        }
+
+        @Override
+        public Object getJsonValue(ExpData data)
+        {
+            if (data == null)
+                return null;
+
+            return Objects.toString(data.getWebDavURL(_relative ? FileContentService.PathType.folderRelative : FileContentService.PathType.serverRelative), null);
+        }
+
+        @Override
+        protected void renderData(HtmlWriter out, ExpData data)
+        {
+            Object val = getJsonValue(data);
+            out.write(val);
+        }
+    }
+
+    public static class TestCase extends Assert
+    {
+        public static final String PROJECT_NAME = "ExptDataTableImplIntegrationTest";
+
+        @BeforeClass
+        public static void initialSetUp()
+        {
+            doInitialSetUp(PROJECT_NAME);
+        }
+
+        @AfterClass
+        public static void cleanup()
+        {
+            doCleanup(PROJECT_NAME);
+        }
+
+        private class WebDavTestCase
+        {
+            private final ExpData _data;
+            private final String _relativePath;
+
+            public WebDavTestCase(String name, File file, String relativePath)
+            {
+                _data = ExperimentService.get().createData(getProject(), new DataType("TestData"));
+                _data.setDataFileURI(file.toURI());
+                _data.setName(name);
+                _data.save(getUser());
+
+                _relativePath = relativePath;
+            }
+
+            public String getUrl()
+            {
+                if (_relativePath == null)
+                {
+                    return null;
+                }
+
+                PipeRoot pr = PipelineService.get().getPipelineRootSetting(getProject());
+
+                URI uri = pr.getWebdavURL().resolve(getUrlRelative());
+                return uri == null ? null : uri.toString();
+            }
+
+            public String getUrlRelative()
+            {
+                return _relativePath;
+            }
+        }
+
+        @Test
+        public void testWebDavColumns() throws Exception
+        {
+            PipeRoot pr = PipelineService.get().getPipelineRootSetting(getProject());
+            if (pr == null)
+            {
+                throw new ConfigurationException("File root is not set");
+            }
+
+            List<WebDavTestCase> testCases = new ArrayList<>();
+
+            final String PATH1 = "webDavTest.txt";
+            testCases.add(new WebDavTestCase("TestData1", FileUtil.appendName(pr.getRootPath(), PATH1), PATH1));
+            testCases.add(new WebDavTestCase("TestData2", FileUtil.appendPath(pr.getRootPath(), org.labkey.api.util.Path.parse("subfolder/webDavTest.txt")), "subfolder/webDavTest.txt"));
+            testCases.add(new WebDavTestCase("TestData3", FileUtil.appendPath(pr.getRootPath(), org.labkey.api.util.Path.parse("subfolder/webD  avT est.txt")), "subfolder/webD%20%20avT%20est.txt"));
+
+            PipeRoot prHome = PipelineService.get().getPipelineRootSetting(ContainerManager.getHomeContainer());
+            testCases.add(new WebDavTestCase("NotUnderFolderRoot", FileUtil.appendName(prHome.getRootPath(), PATH1), null));
+
+            testCases.add(new WebDavTestCase("NotUnderFileRoot", new File("/", PATH1), null));
+
+            UserSchema us = QueryService.get().getUserSchema(getUser(), getProject(), ExpSchema.SCHEMA_NAME);
+
+            for (final WebDavTestCase tc : testCases)
+            {
+                BindException errors = new NullSafeBindException(new Object(), "command");
+                MutablePropertyValues mpv = new MutablePropertyValues();
+                mpv.addPropertyValue("schemaName", ExpSchema.SCHEMA_NAME);
+                mpv.addPropertyValue("query.queryName", ExpSchema.TableType.Data.name());
+                List<FieldKey> fieldKeys = Arrays.asList("RowId", "Name", Column.WebDavUrl.name(), Column.WebDavUrlRelative.name()).stream().map(FieldKey::fromString).collect(Collectors.toList());
+                mpv.addPropertyValue("query.columns", StringUtils.join(fieldKeys, ","));
+
+                QuerySettings qs = us.getSettings(mpv, "query");
+
+                qs.setBaseFilter(new SimpleFilter(FieldKey.fromString("RowId"), tc._data.getRowId()));
+                QueryView view = new QueryView(us, qs, errors);
+
+                ExtendedApiQueryResponse resp = new ExtendedApiQueryResponse(view, false, false, "auditLog", "ContainerAuditEvent", 0, fieldKeys, false, false, false);
+                Writer writer = new StringWriter();
+                ApiResponseWriter apiWriter = new ApiJsonWriter(writer);
+                resp.render(apiWriter);
+                JSONObject json = new JSONObject(writer.toString());
+                JSONObject row = json.getJSONArray("rows").getJSONObject(0);
+
+                String webDavUrl = row.getJSONObject("WebDavUrl").optString("value", null);
+                String webDavUrlRelative = row.getJSONObject("WebDavUrlRelative").optString("value", null);
+
+                assertEquals("Incorrect WebDavUrlRelative", tc.getUrlRelative(), webDavUrlRelative);
+                assertEquals("Incorrect WebDavUrl", tc.getUrl(), webDavUrl);
+
+                ExcelWriter excel = view.getExcelWriter(ExcelWriter.ExcelDocumentType.xlsx, null);
+                try (VirtualFile f = new MemoryVirtualFile())
+                {
+                    try (OutputStream os = f.getOutputStream("excel.xlsx"))
+                    {
+                        excel.renderWorkbook(os);
+                    }
+
+                    try (ExcelLoader loader = new ExcelLoader(f.getInputStream("excel.xlsx"), true, getProject()))
+                    {
+                        loader.iterator().forEachRemaining(map -> {
+                            Object excelWebdavUrl = map.get("WebDAV URL");
+                            Object excelWebdavUrlRelative = map.get("Relative WebDAV URL");
+                            assertEquals("Incorrect WebDavUrl", tc.getUrl(), excelWebdavUrl);
+                            assertEquals("Incorrect WebDavUrlRelative", tc.getUrlRelative(), excelWebdavUrlRelative);
+                        });
+                    }
+                }
+            }
+        }
+
+        protected static void doInitialSetUp(String projectName)
+        {
+            //pre-clean
+            doCleanup(projectName);
+
+            Container project = ContainerManager.getForPath(projectName);
+            if (project == null)
+            {
+                ContainerManager.createContainer(ContainerManager.getRoot(), projectName, TestContext.get().getUser());
+            }
+        }
+
+        protected static void doCleanup(String projectName)
+        {
+            Container project = ContainerManager.getForPath(projectName);
+            if (project != null)
+            {
+                ContainerManager.delete(project, getUser());
+            }
+        }
+
+        protected static User getUser()
+        {
+            return TestContext.get().getUser();
+        }
+
+        protected Container getProject()
+        {
+            return ContainerManager.getForPath(PROJECT_NAME);
+        }
+    }
+}
diff --git a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java
index 6fe26125a61..acc6a3ec7ee 100644
--- a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java
+++ b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java
@@ -1,284 +1,284 @@
-/*
- * Copyright (c) 2008-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.experiment.pipeline;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.apache.xmlbeans.XmlException;
-import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument;
-import org.fhcrc.cpas.exp.xml.ExperimentArchiveType;
-import org.jetbrains.annotations.NotNull;
-import org.labkey.api.data.Container;
-import org.labkey.api.data.DbScope;
-import org.labkey.api.exp.ExperimentDataHandler;
-import org.labkey.api.exp.ExperimentException;
-import org.labkey.api.exp.XarSource;
-import org.labkey.api.exp.api.ExpData;
-import org.labkey.api.exp.api.ExperimentService;
-import org.labkey.api.pipeline.PipelineJob;
-import org.labkey.api.pipeline.RecordedActionSet;
-import org.labkey.api.util.DateUtil;
-import org.labkey.api.util.FileUtil;
-import org.labkey.api.util.XmlBeansUtil;
-import org.labkey.experiment.DataURLRelativizer;
-import org.labkey.api.exp.xar.LSIDRelativizer;
-import org.labkey.experiment.XarExporter;
-import org.labkey.experiment.XarReader;
-import org.labkey.experiment.api.ExpRunImpl;
-import org.labkey.experiment.api.ExperimentServiceImpl;
-
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-import java.nio.file.Path;
-import java.sql.BatchUpdateException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-/**
- * User: jeckels
- * Date: Sep 8, 2008
- */
-public class MoveRunsTask extends PipelineJob.Task<MoveRunsTaskFactory>
-{
-    public MoveRunsTask(MoveRunsTaskFactory factory, PipelineJob job)
-    {
-        super(factory, job);
-    }
-
-    @Override
-    @NotNull
-    public RecordedActionSet run()
-    {
-        MoveRunsPipelineJob job = (MoveRunsPipelineJob)getJob();
-
-        try
-        {
-            for (long runId : job.getRunIds())
-            {
-                ExpRunImpl experimentRun = ExperimentServiceImpl.get().getExpRun(runId);
-                if (experimentRun != null)
-                {
-                    moveRun(job, experimentRun);
-                }
-                else
-                {
-                    job.info("Run with id " + runId + " is no longer available in the system");
-                }
-            }
-        }
-        catch (Throwable t)
-        {
-            job.error("Exception during move", t);
-            job.error("Move FAILED");
-            if (t instanceof BatchUpdateException)
-            {
-                job.error("Underlying exception", ((BatchUpdateException)t).getNextException());
-            }
-        }
-        return new RecordedActionSet();
-    }
-
-    private void moveRun(MoveRunsPipelineJob job, ExpRunImpl experimentRun) throws ExperimentException, IOException
-    {
-        XarExporter exporter = new XarExporter(LSIDRelativizer.PARTIAL_FOLDER_RELATIVE, DataURLRelativizer.ORIGINAL_FILE_LOCATION.createURLRewriter(), getJob().getUser(), getJob().getContainer());
-        exporter.addExperimentRun(experimentRun);
-
-        ByteArrayOutputStream bOut = new ByteArrayOutputStream();
-        exporter.dumpXML(bOut);
-
-        try (DbScope.Transaction transaction = ExperimentService.get().getSchema().getScope().ensureTransaction())
-        {
-            Map<String,Long> dataFiles = new HashMap<>();
-
-            for (ExpData oldData : experimentRun.getAllDataUsedByRun())
-            {
-                ExperimentDataHandler handler = oldData.findDataHandler();
-                handler.beforeMove(oldData, experimentRun.getContainer(), job.getUser());
-            }
-
-            for (ExpData data : ExperimentService.get().deleteExperimentRunForMove(experimentRun.getRowId(), job.getUser()))
-            {
-                if (data.getDataFileUrl() != null)
-                {
-                    dataFiles.put(data.getDataFileUrl(), data.getRowId());
-                }
-            }
-
-            MoveRunsXarSource xarSource = new MoveRunsXarSource(bOut.toString(), experimentRun.getFilePathRootPath(), job);
-            XarReader reader = new XarReader(xarSource, job);
-            reader.parseAndLoad(false, null);
-
-            List<String> runLSIDs = reader.getProcessedRunsLSIDs();
-            assert runLSIDs.size() == 1 : "Expected a single run to be loaded";
-
-            for (String dataURL : dataFiles.keySet())
-            {
-                ExpData newData = ExperimentService.get().getExpDataByURL(xarSource.getCanonicalDataFileURL(dataURL), job.getSourceContainer());
-                if (newData != null)
-                {
-                    ExperimentDataHandler handler = newData.findDataHandler();
-                    handler.runMoved(newData, experimentRun.getContainer(), job.getContainer(), experimentRun.getLSID(), runLSIDs.get(0), job.getUser(), dataFiles.get(dataURL));
-                }
-            }
-            transaction.commit();
-        }
-    }
-
-    public static class MoveRunsXarSource extends XarSource
-    {
-        private static final Logger _log = LogManager.getLogger(MoveRunsXarSource.class);
-
-        private final String _xml;
-        private File _logFile;
-        private File _logFileDir;
-
-        private final String _uploadTime;
-
-        private String _experimentName;
-        private final String _root;
-        private final Container _sourceContainer;
-
-        public MoveRunsXarSource(String xml, Path root, MoveRunsPipelineJob job) throws ExperimentException
-        {
-            super(job);
-            _xml = xml;
-            if (null == root)
-                throw new ExperimentException("File path root is null");
-
-            _root = FileUtil.getAbsolutePath(job.getSourceContainer(), root);
-            if (null == _root)
-                throw new ExperimentException("Unable to create absolute file path for root");
-
-            _sourceContainer = job.getSourceContainer();
-
-            int retry = 0;
-            while (_logFileDir == null)
-            {
-                try
-                {
-                    _logFileDir = FileUtil.createTempFile("xarupload", "");
-                }
-                catch (IOException e)
-                {
-                    if (++retry > 10)
-                    {
-                        throw new ExperimentException("Unable to create a log file", e);
-                    }
-                    _log.warn("Failed to create log file, retrying...", e);
-                }
-            }
-
-            _logFileDir.delete();
-            try
-            {
-                FileUtil.mkdir(_logFileDir);
-            }
-            catch (IOException e)
-            {
-                throw new ExperimentException("Unable to create log file directory", e);
-            }
-            _logFileDir.deleteOnExit();
-            _logFile = FileUtil.appendName(_logFileDir, "upload.xar.log");
-            _logFile.deleteOnExit();
-            _uploadTime = DateUtil.formatDateTime(job.getContainer());
-        }
-
-        @Override
-        public ExperimentArchiveDocument getDocument() throws XmlException
-        {
-            ExperimentArchiveDocument doc = ExperimentArchiveDocument.Factory.parse(_xml, XmlBeansUtil.getDefaultParseOptions());
-            ExperimentArchiveType ea = doc.getExperimentArchive();
-            if (ea != null)
-            {
-                if (ea.getExperimentArray() != null && ea.getExperimentArray().length > 0)
-                {
-                    _experimentName = ea.getExperimentArray()[0].getName();
-                }
-            }
-            return doc;
-        }
-
-        @Override
-        public Path getRootPath()
-        {
-            return FileUtil.stringToPath(_sourceContainer, _root);
-        }
-
-        @Override
-        public Path getJobRootPath()
-        {
-            var pipelineJob = getXarContext().getJob();
-            return pipelineJob != null
-                    ? pipelineJob.getPipeRoot().getRootFileLike().toNioPathForRead()
-                    : super.getJobRootPath();
-        }
-
-        @Override
-        public boolean shouldIgnoreDataFiles()
-        {
-            return true;
-        }
-
-        @Override
-        public String canonicalizeDataFileURL(String dataFileURL)
-        {
-            URI uri = FileUtil.createUri(dataFileURL);
-            Path dataFilePath;
-            if (!uri.isAbsolute())
-            {
-                dataFilePath = getRootPath().resolve(dataFileURL);
-            }
-            else
-            {
-                dataFilePath = FileUtil.getPath(_sourceContainer, uri);
-            }
-            return FileUtil.getAbsoluteCaseSensitivePathString(_sourceContainer, dataFilePath.toUri());
-        }
-
-        @Override
-        public Path getLogFilePath()
-        {
-            return _logFile.toPath();
-        }
-
-        public String toString()
-        {
-            String result = "Uploaded file: " + _uploadTime;
-            if (_experimentName != null)
-            {
-                result += _experimentName;
-            }
-            return result;
-        }
-
-        public void cleanup()
-        {
-            if (_logFile != null)
-            {
-                _logFile.delete();
-                _logFile = null;
-            }
-            if (_logFileDir != null)
-            {
-                _logFileDir.delete();
-                _logFileDir = null;
-            }
-        }
-    }
-}
+/*
+ * Copyright (c) 2008-2018 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.experiment.pipeline;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.xmlbeans.XmlException;
+import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument;
+import org.fhcrc.cpas.exp.xml.ExperimentArchiveType;
+import org.jetbrains.annotations.NotNull;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.exp.ExperimentDataHandler;
+import org.labkey.api.exp.ExperimentException;
+import org.labkey.api.exp.XarSource;
+import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.pipeline.PipelineJob;
+import org.labkey.api.pipeline.RecordedActionSet;
+import org.labkey.api.util.DateUtil;
+import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.XmlBeansUtil;
+import org.labkey.experiment.DataURLRelativizer;
+import org.labkey.api.exp.xar.LSIDRelativizer;
+import org.labkey.experiment.XarExporter;
+import org.labkey.experiment.XarReader;
+import org.labkey.experiment.api.ExpRunImpl;
+import org.labkey.experiment.api.ExperimentServiceImpl;
+
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.nio.file.Path;
+import java.sql.BatchUpdateException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * User: jeckels
+ * Date: Sep 8, 2008
+ */
+public class MoveRunsTask extends PipelineJob.Task<MoveRunsTaskFactory>
+{
+    public MoveRunsTask(MoveRunsTaskFactory factory, PipelineJob job)
+    {
+        super(factory, job);
+    }
+
+    @Override
+    @NotNull
+    public RecordedActionSet run()
+    {
+        MoveRunsPipelineJob job = (MoveRunsPipelineJob)getJob();
+
+        try
+        {
+            for (long runId : job.getRunIds())
+            {
+                ExpRunImpl experimentRun = ExperimentServiceImpl.get().getExpRun(runId);
+                if (experimentRun != null)
+                {
+                    moveRun(job, experimentRun);
+                }
+                else
+                {
+                    job.info("Run with id " + runId + " is no longer available in the system");
+                }
+            }
+        }
+        catch (Throwable t)
+        {
+            job.error("Exception during move", t);
+            job.error("Move FAILED");
+            if (t instanceof BatchUpdateException)
+            {
+                job.error("Underlying exception", ((BatchUpdateException)t).getNextException());
+            }
+        }
+        return new RecordedActionSet();
+    }
+
+    private void moveRun(MoveRunsPipelineJob job, ExpRunImpl experimentRun) throws ExperimentException, IOException
+    {
+        XarExporter exporter = new XarExporter(LSIDRelativizer.PARTIAL_FOLDER_RELATIVE, DataURLRelativizer.ORIGINAL_FILE_LOCATION.createURLRewriter(), getJob().getUser(), getJob().getContainer());
+        exporter.addExperimentRun(experimentRun);
+
+        ByteArrayOutputStream bOut = new ByteArrayOutputStream();
+        exporter.dumpXML(bOut);
+
+        try (DbScope.Transaction transaction = ExperimentService.get().getSchema().getScope().ensureTransaction())
+        {
+            Map<String,Long> dataFiles = new HashMap<>();
+
+            for (ExpData oldData : experimentRun.getAllDataUsedByRun())
+            {
+                ExperimentDataHandler handler = oldData.findDataHandler();
+                handler.beforeMove(oldData, experimentRun.getContainer(), job.getUser());
+            }
+
+            for (ExpData data : ExperimentService.get().deleteExperimentRunForMove(experimentRun.getRowId(), job.getUser()))
+            {
+                if (data.getDataFileUrl() != null)
+                {
+                    dataFiles.put(data.getDataFileUrl(), data.getRowId());
+                }
+            }
+
+            MoveRunsXarSource xarSource = new MoveRunsXarSource(bOut.toString(), experimentRun.getFilePathRootPath(), job);
+            XarReader reader = new XarReader(xarSource, job);
+            reader.parseAndLoad(false, null);
+
+            List<String> runLSIDs = reader.getProcessedRunsLSIDs();
+            assert runLSIDs.size() == 1 : "Expected a single run to be loaded";
+
+            for (String dataURL : dataFiles.keySet())
+            {
+                ExpData newData = ExperimentService.get().getExpDataByURL(xarSource.getCanonicalDataFileURL(dataURL), job.getSourceContainer());
+                if (newData != null)
+                {
+                    ExperimentDataHandler handler = newData.findDataHandler();
+                    handler.runMoved(newData, experimentRun.getContainer(), job.getContainer(), experimentRun.getLSID(), runLSIDs.get(0), job.getUser(), dataFiles.get(dataURL));
+                }
+            }
+            transaction.commit();
+        }
+    }
+
+    public static class MoveRunsXarSource extends XarSource
+    {
+        private static final Logger _log = LogManager.getLogger(MoveRunsXarSource.class);
+
+        private final String _xml;
+        private File _logFile;
+        private File _logFileDir;
+
+        private final String _uploadTime;
+
+        private String _experimentName;
+        private final String _root;
+        private final Container _sourceContainer;
+
+        public MoveRunsXarSource(String xml, Path root, MoveRunsPipelineJob job) throws ExperimentException
+        {
+            super(job);
+            _xml = xml;
+            if (null == root)
+                throw new ExperimentException("File path root is null");
+
+            _root = FileUtil.getAbsolutePath(job.getSourceContainer(), root);
+            if (null == _root)
+                throw new ExperimentException("Unable to create absolute file path for root");
+
+            _sourceContainer = job.getSourceContainer();
+
+            int retry = 0;
+            while (_logFileDir == null)
+            {
+                try
+                {
+                    _logFileDir = FileUtil.createTempFile("xarupload", "");
+                }
+                catch (IOException e)
+                {
+                    if (++retry > 10)
+                    {
+                        throw new ExperimentException("Unable to create a log file", e);
+                    }
+                    _log.warn("Failed to create log file, retrying...", e);
+                }
+            }
+
+            _logFileDir.delete();
+            try
+            {
+                FileUtil.mkdir(_logFileDir);
+            }
+            catch (IOException e)
+            {
+                throw new ExperimentException("Unable to create log file directory", e);
+            }
+            _logFileDir.deleteOnExit();
+            _logFile = FileUtil.appendName(_logFileDir, "upload.xar.log");
+            _logFile.deleteOnExit();
+            _uploadTime = DateUtil.formatDateTime(job.getContainer());
+        }
+
+        @Override
+        public ExperimentArchiveDocument getDocument() throws XmlException
+        {
+            ExperimentArchiveDocument doc = ExperimentArchiveDocument.Factory.parse(_xml, XmlBeansUtil.getDefaultParseOptions());
+            ExperimentArchiveType ea = doc.getExperimentArchive();
+            if (ea != null)
+            {
+                if (ea.getExperimentArray() != null && ea.getExperimentArray().length > 0)
+                {
+                    _experimentName = ea.getExperimentArray()[0].getName();
+                }
+            }
+            return doc;
+        }
+
+        @Override
+        public Path getRootPath()
+        {
+            return FileUtil.stringToPath(_sourceContainer, _root);
+        }
+
+        @Override
+        public Path getJobRootPath()
+        {
+            var pipelineJob = getXarContext().getJob();
+            return pipelineJob != null
+                    ? pipelineJob.getPipeRoot().getRootFileLike().toNioPathForRead()
+                    : super.getJobRootPath();
+        }
+
+        @Override
+        public boolean shouldIgnoreDataFiles()
+        {
+            return true;
+        }
+
+        @Override
+        public String canonicalizeDataFileURL(String dataFileURL)
+        {
+            URI uri = FileUtil.createUri(dataFileURL);
+            Path dataFilePath;
+            if (!uri.isAbsolute())
+            {
+                dataFilePath = getRootPath().resolve(dataFileURL);
+            }
+            else
+            {
+                dataFilePath = FileUtil.getPath(_sourceContainer, uri);
+            }
+            return FileUtil.getAbsoluteCaseSensitivePathString(_sourceContainer, dataFilePath.toUri());
+        }
+
+        @Override
+        public Path getLogFilePath()
+        {
+            return _logFile.toPath();
+        }
+
+        public String toString()
+        {
+            String result = "Uploaded file: " + _uploadTime;
+            if (_experimentName != null)
+            {
+                result += _experimentName;
+            }
+            return result;
+        }
+
+        public void cleanup()
+        {
+            if (_logFile != null)
+            {
+                _logFile.delete();
+                _logFile = null;
+            }
+            if (_logFileDir != null)
+            {
+                _logFileDir.delete();
+                _logFileDir = null;
+            }
+        }
+    }
+}

From e106166570ceee3ac25607d74cb36cd1d06ffe11 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Fri, 10 Oct 2025 17:31:17 -0700
Subject: [PATCH 13/15] More FileLike in assay

---
 .../api/assay/AbstractAssayProvider.java      |  1 -
 .../labkey/api/assay/AssayDataCollector.java  |  3 +-
 .../org/labkey/api/assay/AssayFileWriter.java | 15 ++--
 .../api/assay/AssayRunDatabaseContext.java    |  4 +-
 .../api/assay/AssayRunUploadContext.java      |  2 +-
 .../api/assay/PipelineDataCollector.java      | 48 +++++------
 .../api/assay/actions/AssayRunUploadForm.java |  4 +-
 .../assay/pipeline/AssayRunAsyncContext.java  |  5 +-
 .../labkey/api/exp/api/ExperimentService.java |  9 ++-
 api/src/org/labkey/api/pipeline/PipeRoot.java |  1 +
 .../labkey/api/qc/TsvDataExchangeHandler.java | 17 ++--
 .../labkey/assay/AssayIntegrationTestCase.jsp |  3 +-
 .../PipelineDataCollectorRedirectAction.java  | 23 +++---
 .../experiment/XarExportPipelineJob.java      |  7 +-
 .../experiment/api/ExperimentServiceImpl.java | 79 ++-----------------
 .../org/labkey/pipeline/api/PipeRootImpl.java |  6 ++
 16 files changed, 77 insertions(+), 150 deletions(-)

diff --git a/api/src/org/labkey/api/assay/AbstractAssayProvider.java b/api/src/org/labkey/api/assay/AbstractAssayProvider.java
index b54000c8f56..666153638d5 100644
--- a/api/src/org/labkey/api/assay/AbstractAssayProvider.java
+++ b/api/src/org/labkey/api/assay/AbstractAssayProvider.java
@@ -637,7 +637,6 @@ public List<AssayDataCollector> getDataCollectors(@Nullable Map<String, org.labk
             {
                 // In the re-run scenario, figure out what files to offer up for reuse
 
-//                Map<String, File> reusableFiles = new HashMap<>();
                 Map<String, org.labkey.vfs.FileLike> reusableFiles = new HashMap<>();
                 // Include any files that were uploaded as part of this request
                 if (uploadedFiles != null && !uploadedFiles.isEmpty())
diff --git a/api/src/org/labkey/api/assay/AssayDataCollector.java b/api/src/org/labkey/api/assay/AssayDataCollector.java
index 36774c90c65..90027eb4baa 100644
--- a/api/src/org/labkey/api/assay/AssayDataCollector.java
+++ b/api/src/org/labkey/api/assay/AssayDataCollector.java
@@ -23,7 +23,6 @@
 import org.labkey.api.view.HttpView;
 import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.Map;
 
@@ -81,5 +80,5 @@ default void initDir(ContextType context) throws ExperimentException {}
      * @return null if the file was uploaded as part of the import
      */
     @Nullable
-    default File getOriginalFileLocation() { return null; }
+    default FileLike getOriginalFileLocation() { return null; }
 }
diff --git a/api/src/org/labkey/api/assay/AssayFileWriter.java b/api/src/org/labkey/api/assay/AssayFileWriter.java
index d2130887aaa..5164c5689e3 100644
--- a/api/src/org/labkey/api/assay/AssayFileWriter.java
+++ b/api/src/org/labkey/api/assay/AssayFileWriter.java
@@ -33,7 +33,6 @@
 import org.labkey.api.util.NetworkDrive;
 import org.labkey.api.view.ViewContext;
 import org.labkey.vfs.FileLike;
-import org.labkey.vfs.FileSystemLike;
 import org.springframework.web.multipart.MultipartFile;
 import org.springframework.web.multipart.MultipartHttpServletRequest;
 
@@ -189,8 +188,7 @@ protected FileLike getFileTargetDir(ContextType context) throws ExperimentExcept
         return ensureUploadDirectory(context.getContainer());
     }
 
-    /* TODO: this is a really awkward transition between File->FileLike (files come from FileQueue) */
-    public Map<String, FileLike> savePipelineFiles(ContextType context, Map<String, File> files) throws ExperimentException, IOException
+    public Map<String, FileLike> savePipelineFiles(ContextType context, Map<String, FileLike> files) throws ExperimentException, IOException
     {
         Map<String, FileLike> savedFiles = CollectionUtils.enforceValueClass(new TreeMap<>(), FileLike.class);
         if (context.getRequest() instanceof MultipartHttpServletRequest)
@@ -201,27 +199,24 @@ public Map<String, FileLike> savePipelineFiles(ContextType context, Map<String,
             for (String key : files.keySet())
             {
                 // Copy the user uploaded files not already under the pipeline root to the temp directory.
-                File file = files.get(key);
+                FileLike file = files.get(key);
                 if (!root.isUnderRoot(file))
                 {
                     FileLike savedFile = dir.resolveChild(file.getName());
                     LOG.debug("savePipelineFiles: file '" + file + "' is not under pipeline root. copying to savedFile=" + savedFile);
-                    FileUtils.copyFile(file, toFileForWrite(savedFile));
+                    FileUtils.copyFile(toFileForRead(file), toFileForWrite(savedFile));
                     savedFiles.put(key, savedFile);
                 }
                 else
                 {
-                    savedFiles.put(key, FileSystemLike.wrapFile(file));
+                    savedFiles.put(key, file);
                     LOG.debug("savePipelineFiles: file '" + file.getPath() + "' is already under pipeline root. not copying");
                 }
             }
         }
         else
         {
-            for (var entry : files.entrySet())
-            {
-                savedFiles.put(entry.getKey(), FileSystemLike.wrapFile((entry.getValue())));
-            }
+            savedFiles.putAll(files);
         }
 
         return savedFiles;
diff --git a/api/src/org/labkey/api/assay/AssayRunDatabaseContext.java b/api/src/org/labkey/api/assay/AssayRunDatabaseContext.java
index 7be9b1a8e0a..f19138d5369 100644
--- a/api/src/org/labkey/api/assay/AssayRunDatabaseContext.java
+++ b/api/src/org/labkey/api/assay/AssayRunDatabaseContext.java
@@ -182,14 +182,14 @@ public Map<String, FileLike> getUploadedData() throws ExperimentException
 
     @Nullable
     @Override
-    public File getOriginalFileLocation()
+    public FileLike getOriginalFileLocation()
     {
         for (ExpData data : _run.getOutputDatas(_provider.getDataType()))
         {
             File f = data.getFile();
             if (f != null)
             {
-                return f.getParentFile();
+                return FileSystemLike.wrapFile(f.getParentFile());
             }
         }
         return null;
diff --git a/api/src/org/labkey/api/assay/AssayRunUploadContext.java b/api/src/org/labkey/api/assay/AssayRunUploadContext.java
index f2d7a81fc25..4b69318e848 100644
--- a/api/src/org/labkey/api/assay/AssayRunUploadContext.java
+++ b/api/src/org/labkey/api/assay/AssayRunUploadContext.java
@@ -213,7 +213,7 @@ default void init() throws ExperimentException
      * @return null if the file was uploaded as part of the import
      */
     @Nullable
-    default File getOriginalFileLocation()
+    default FileLike getOriginalFileLocation()
     {
         return null;
     }
diff --git a/api/src/org/labkey/api/assay/PipelineDataCollector.java b/api/src/org/labkey/api/assay/PipelineDataCollector.java
index 1db558acd23..2f2eb520491 100644
--- a/api/src/org/labkey/api/assay/PipelineDataCollector.java
+++ b/api/src/org/labkey/api/assay/PipelineDataCollector.java
@@ -31,7 +31,6 @@
 
 import jakarta.servlet.http.HttpSession;
 import org.labkey.vfs.FileLike;
-import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -54,7 +53,7 @@ public PipelineDataCollector()
     {
     }
 
-    private File _originalFileLocation = null;
+    private FileLike _originalFileLocation = null;
 
     @Override
     public HttpView<?> getView(ContextType context) throws ExperimentException
@@ -64,7 +63,7 @@ public HttpView<?> getView(ContextType context) throws ExperimentException
 
     public HtmlString getHTML(ContextType context)
     {
-        Map<String, File> files = getCurrentFilesForDisplay(context);
+        Map<String, FileLike> files = getCurrentFilesForDisplay(context);
         if (files.isEmpty())
         {
             return DOM.createHtml(DOM.DIV(DOM.at(DOM.cl("labkey-error")), "No files have been selected."));
@@ -72,7 +71,7 @@ public HtmlString getHTML(ContextType context)
 
         HtmlStringBuilder html = HtmlStringBuilder.of();
         html.startTag("ul");
-        for (File file : files.values())
+        for (FileLike file : files.values())
         {
             html.startTag("li");
             html.append(file.getName());
@@ -101,9 +100,9 @@ protected int getAdditionalFileSetCount(ContextType context)
     }
 
     /** @return the files to be processed for the current upload attempt */
-    protected Map<String, File> getCurrentFilesForDisplay(ContextType context)
+    protected Map<String, FileLike> getCurrentFilesForDisplay(ContextType context)
     {
-        List<Map<String, File>> files = getFileQueue(context);
+        List<Map<String, FileLike>> files = getFileQueue(context);
         if (files.isEmpty())
         {
             return Collections.emptyMap();
@@ -120,33 +119,32 @@ public String getShortName()
     @Override
     public String getDescription(ContextType context)
     {
-        List<Map<String, File>> allFiles = getFileQueue(context);
+        List<Map<String, FileLike>> allFiles = getFileQueue(context);
         if (allFiles.isEmpty())
         {
             return "";
         }
-        Map<String, File> files = allFiles.get(0);
+        Map<String, FileLike> files = allFiles.get(0);
         return (files.size() > 1 ? files.size() + " files" : "One file ") + " from the Data Pipeline in " + files.values().iterator().next().getParent();
     }
 
-    public static synchronized void setFileCollection(HttpSession session, Container c, ExpProtocol protocol, List<Map<String, File>> files)
+    public static synchronized void setFileCollection(HttpSession session, Container c, ExpProtocol protocol, List<Map<String, FileLike>> files)
     {
-        List<Map<String, File>> existingFiles = getFileQueue(session, c, protocol);
+        List<Map<String, FileLike>> existingFiles = getFileQueue(session, c, protocol);
         existingFiles.clear();
         existingFiles.addAll(files);
     }
 
-    /* TODO File->FileLike convert FileQueue */
-    public static List<Map<String, File>> getFileQueue(AssayRunUploadContext<?> context)
+    public static List<Map<String, FileLike>> getFileQueue(AssayRunUploadContext<?> context)
     {
         return getFileQueue(context.getRequest().getSession(true), context.getContainer(), context.getProtocol());
     }
 
-    private static List<Map<String, File>> getFileQueue(HttpSession session, Container c, ExpProtocol protocol)
+    private static List<Map<String, FileLike>> getFileQueue(HttpSession session, Container c, ExpProtocol protocol)
     {
         // Use the protocol's RowId instead the ExpProtocol itself because it will be serialized as part of the session
         // state when Tomcat is shut down cleanly
-        Map<Pair<Container, Long>, List<Map<String, File>>> collections = (Map<Pair<Container, Long>, List<Map<String, File>>>) session.getAttribute(PipelineDataCollector.class.getName());
+        Map<Pair<Container, Long>, List<Map<String, FileLike>>> collections = (Map<Pair<Container, Long>, List<Map<String, FileLike>>>) session.getAttribute(PipelineDataCollector.class.getName());
         if (collections == null)
         {
             collections = new HashMap<>();
@@ -170,43 +168,37 @@ public static synchronized void clearFileQueue(HttpSession session, Container c,
     @NotNull
     public Map<String, FileLike> createData(ContextType context) throws IOException, ExperimentException
     {
-        List<Map<String, File>> files = getFileQueue(context);
+        List<Map<String, FileLike>> files = getFileQueue(context);
         if (files.isEmpty())
         {
             throw new FileNotFoundException("No files from the pipeline directory have been selected");
         }
 
-        Map<String, File> currentFiles = files.get(0);
+        Map<String, FileLike> currentFiles = files.get(0);
         if (!currentFiles.isEmpty())
         {
-            _originalFileLocation = currentFiles.values().iterator().next().getParentFile();
+            _originalFileLocation = currentFiles.values().iterator().next().getParent();
         }
         return savePipelineFiles(context, currentFiles);
     }
 
     @Nullable
     @Override
-    public File getOriginalFileLocation()
+    public FileLike getOriginalFileLocation()
     {
         return _originalFileLocation;
     }
 
-    @Override
-    public boolean isVisible()
-    {
-        return true;
-    }
-
     // When importing via pipeline, the file is already on the server so return the path of that file
     @Nullable
     @Override
     protected FileLike getFilePath(ContextType context, @Nullable ExpRun run, FileLike tempDirFile)
     {
-        Map<String, File> files = getFileQueue(context).get(0);
-        for (File file : files.values())
+        Map<String, FileLike> files = getFileQueue(context).get(0);
+        for (FileLike file : files.values())
         {
             if (file.getName().equals(tempDirFile.getName()))
-                return FileSystemLike.wrapFile(file);
+                return file;
         }
 
         return null;
@@ -224,7 +216,7 @@ protected void handleTempFile(File tempDirFile, File assayDirFile)
     public Map<String, FileLike> uploadComplete(ContextType context, @Nullable ExpRun run) throws ExperimentException
     {
         Map<String, FileLike> result = super.uploadComplete(context, run);
-        List<Map<String, File>> files = getFileQueue(context);
+        List<Map<String, FileLike>> files = getFileQueue(context);
         if (!files.isEmpty())
         {
             files.remove(0);
diff --git a/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java b/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java
index 88caae0db1d..0d5f0aeeb24 100644
--- a/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java
+++ b/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java
@@ -247,9 +247,9 @@ private List<AssayDataCollector> getDataCollectors()
 
     @Nullable
     @Override
-    public File getOriginalFileLocation()
+    public FileLike getOriginalFileLocation()
     {
-        AssayDataCollector collector = getSelectedDataCollector();
+        AssayDataCollector<?> collector = getSelectedDataCollector();
         if (collector != null)
         {
             return collector.getOriginalFileLocation();
diff --git a/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java b/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java
index eb60cff2dcd..e8b97177c41 100644
--- a/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java
+++ b/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java
@@ -42,7 +42,6 @@
 import jakarta.servlet.http.HttpServletRequest;
 import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.Serializable;
 import java.util.Collections;
 import java.util.HashMap;
@@ -78,7 +77,7 @@ public class AssayRunAsyncContext<ProviderType extends AssayProvider> implements
     private ReImportOption _reImportOption;
     private boolean _allowCrossRunFileInputs;
 
-    private File _originalFileLocation;
+    private FileLike _originalFileLocation;
 
     // Cached values that aren't serializable
     private transient User _user;
@@ -411,7 +410,7 @@ public Logger getLogger()
 
     @Nullable
     @Override
-    public File getOriginalFileLocation()
+    public FileLike getOriginalFileLocation()
     {
         return _originalFileLocation;
     }
diff --git a/api/src/org/labkey/api/exp/api/ExperimentService.java b/api/src/org/labkey/api/exp/api/ExperimentService.java
index 40d9651fd26..9710e23cf79 100644
--- a/api/src/org/labkey/api/exp/api/ExperimentService.java
+++ b/api/src/org/labkey/api/exp/api/ExperimentService.java
@@ -84,6 +84,7 @@
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.api.view.ViewContext;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -709,6 +710,12 @@ static void validateParentAlias(Map<String, String> aliasMap, Set<String> reserv
      */
     ExpData getExpDataByURL(File f, @Nullable Container c);
 
+    /**
+     * Get the <b>most recently</b> created ExpData for the file, if it exists.
+     * @see #getAllExpDataByURL(Path, Container)
+     */
+    ExpData getExpDataByURL(FileLike f, @Nullable Container c);
+
     /**
      * Get the <b>most recently</b> created ExpData for the path, if it exists.
      * @see #getAllExpDataByURL(Path, Container)
@@ -985,8 +992,6 @@ List<? extends ExpProtocol> getExpProtocolsWithParameterValue(
 
     List<ExpRun> importXar(XarSource source, PipelineJob pipelineJob, XarImportOptions options) throws ExperimentException;
 
-    File exportXarForRuns(User user, Set<Long> runIds, Long expRowId, XarExportOptions options) throws NotFoundException, IOException, ExperimentException;
-
     /**
      * Create an experiment run to represent the work that the task's job has done so far.
      * The job's recorded actions will be marked as completed after creating the ExpRun so subsequent
diff --git a/api/src/org/labkey/api/pipeline/PipeRoot.java b/api/src/org/labkey/api/pipeline/PipeRoot.java
index 4996535e3ad..0bbc1b0aea8 100644
--- a/api/src/org/labkey/api/pipeline/PipeRoot.java
+++ b/api/src/org/labkey/api/pipeline/PipeRoot.java
@@ -113,6 +113,7 @@ public interface PipeRoot extends SecurableResource
 
     /** @return whether the file specified is a child of the pipeline root */
     boolean isUnderRoot(File file);
+    boolean isUnderRoot(FileLike file);
     boolean isUnderRoot(Path file);
 
     boolean hasPermission(Container container, User user, Class<? extends Permission> perm);
diff --git a/api/src/org/labkey/api/qc/TsvDataExchangeHandler.java b/api/src/org/labkey/api/qc/TsvDataExchangeHandler.java
index 1c576c17623..552d468f729 100644
--- a/api/src/org/labkey/api/qc/TsvDataExchangeHandler.java
+++ b/api/src/org/labkey/api/qc/TsvDataExchangeHandler.java
@@ -488,9 +488,9 @@ private Map<String, String> getContextProperties(DataTransformService.TransformO
         {
             map.put(Props.assayId.name(), StringUtils.defaultString(context.getName()));
             map.put(Props.runComments.name(), StringUtils.defaultString(context.getComments()));
-            File originalFileLocation = context.getOriginalFileLocation();
+            FileLike originalFileLocation = context.getOriginalFileLocation();
             if (originalFileLocation != null)
-                map.put(Props.originalFileLocation.name(), originalFileLocation.getPath());
+                map.put(Props.originalFileLocation.name(), originalFileLocation.toNioPathForRead().toFile().getPath());
         }
 
         map.put(Props.baseUrl.name(), AppProps.getInstance().getBaseServerUrl() + AppProps.getInstance().getContextPath());
@@ -1200,7 +1200,7 @@ private static class RunInfo
     {
         private File _errorFile;
         private String _warningSevLevel;
-        private File _originalFileLocation;
+        private FileLike _originalFileLocation;
         private ExpProtocol _protocol;
 
         public void setProtocol(ExpProtocol protocol)
@@ -1222,12 +1222,12 @@ public boolean isBackgroundUpload()
 
         // Original file location used to determine if file was already on the server or not. Used for cleanup when
         // there is an error.
-        public File getOriginalFileLocation()
+        public FileLike getOriginalFileLocation()
         {
             return _originalFileLocation;
         }
 
-        public void setOriginalFileLocation(File originalFileLocation)
+        public void setOriginalFileLocation(FileLike originalFileLocation)
         {
             _originalFileLocation = originalFileLocation;
         }
@@ -1399,12 +1399,5 @@ public Logger getLogger()
         {
             return null;
         }
-
-        @Nullable
-        @Override
-        public File getOriginalFileLocation()
-        {
-            return null;
-        }
     }
 }
diff --git a/assay/src/org/labkey/assay/AssayIntegrationTestCase.jsp b/assay/src/org/labkey/assay/AssayIntegrationTestCase.jsp
index 463eb17340d..674ad8d39fd 100644
--- a/assay/src/org/labkey/assay/AssayIntegrationTestCase.jsp
+++ b/assay/src/org/labkey/assay/AssayIntegrationTestCase.jsp
@@ -95,6 +95,7 @@
 <%@ page import="org.jetbrains.annotations.Nullable" %>
 <%@ page import="java.io.IOException" %>
 <%@ page import="org.apache.commons.collections.MapUtils" %>
+<%@ page import="org.labkey.vfs.FileSystemLike" %>
 
 <%@ page extends="org.labkey.api.jsp.JspTest.BVT" %>
 <%!
@@ -259,7 +260,7 @@
         HttpSession session = TestContext.get().getRequest().getSession();
 
         // Use the AssayFileUploadForm and the PipelineDataCollector to simulate the user selecting a file from the file browser.
-        PipelineDataCollector.setFileCollection(session, c, assayProtocol, List.of(Map.of(AssayDataCollector.PRIMARY_FILE, file)));
+        PipelineDataCollector.setFileCollection(session, c, assayProtocol, List.of(Map.of(AssayDataCollector.PRIMARY_FILE, FileSystemLike.wrapFile(file))));
 
         // Use a multipart request to trigger the AssayFileWriter.savePipelineFiles() code path that copies files into the assay upload directory
         var mockRequest = new MockMultipartHttpServletRequest();
diff --git a/assay/src/org/labkey/assay/actions/PipelineDataCollectorRedirectAction.java b/assay/src/org/labkey/assay/actions/PipelineDataCollectorRedirectAction.java
index 4e34a18e500..552c913f6bd 100644
--- a/assay/src/org/labkey/assay/actions/PipelineDataCollectorRedirectAction.java
+++ b/assay/src/org/labkey/assay/actions/PipelineDataCollectorRedirectAction.java
@@ -36,7 +36,6 @@
 import org.labkey.api.security.permissions.InsertPermission;
 import org.labkey.api.usageMetrics.SimpleMetricsService;
 import org.labkey.api.util.DOM;
-import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.NetworkDrive;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.URLHelper;
@@ -48,6 +47,8 @@
 import org.labkey.api.view.RedirectException;
 import org.labkey.api.view.template.PageConfig;
 import org.labkey.assay.AssayModule;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.springframework.beans.MutablePropertyValues;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
@@ -84,7 +85,7 @@ public ModelAndView getView(UploadRedirectForm form, BindException errors)
         // Can't trust the form's getPath() because it translates the empty string into null, and we
         // need to know if the parameter was present
         String path = getViewContext().getRequest().getParameter("path");
-        List<File> files = new ArrayList<>();
+        List<FileLike> files = new ArrayList<>();
         if (path != null)
         {
             PipeRoot root = PipelineService.get().findPipelineRoot(container);
@@ -92,7 +93,7 @@ public ModelAndView getView(UploadRedirectForm form, BindException errors)
             {
                 throw new NotFoundException("No pipeline root is available");
             }
-            File f = root.resolvePath(path);
+            FileLike f = root.resolvePathToFileLike(path);
             if (!NetworkDrive.exists(f))
             {
                 throw new NotFoundException("Unable to find file: " + path);
@@ -104,7 +105,7 @@ public ModelAndView getView(UploadRedirectForm form, BindException errors)
                 {
                     throw new NotFoundException(fileName);
                 }
-                File file = FileUtil.appendName(f, fileName);
+                FileLike file = f.resolveChild(fileName);
                 if (!NetworkDrive.exists(file))
                 {
                     throw new NotFoundException(fileName);
@@ -125,7 +126,7 @@ public ModelAndView getView(UploadRedirectForm form, BindException errors)
                 File f = data.getFile();
                 if (f != null && f.isFile())
                 {
-                    files.add(f);
+                    files.add(FileSystemLike.wrapFile(f));
                 }
             }
         }
@@ -170,8 +171,8 @@ public ModelAndView getView(UploadRedirectForm form, BindException errors)
         }
 
         Collections.sort(files);
-        List<Map<String, File>> maps = new ArrayList<>();
-        for (File file : files)
+        List<Map<String, FileLike>> maps = new ArrayList<>();
+        for (FileLike file : files)
         {
             maps.add(Collections.singletonMap(AssayDataCollector.PRIMARY_FILE, file));
         }
@@ -203,7 +204,7 @@ private static class FakeConfirmAction extends ConfirmAction<Object>
         }
     }
 
-    private ModelAndView getConfirmView(List<File> remaining, Map<ExpData, ExpRun> filesWithRun)
+    private ModelAndView getConfirmView(List<FileLike> remaining, Map<ExpData, ExpRun> filesWithRun)
     {
         List<DOM.Renderable> nodes = new ArrayList<>();
 
@@ -229,11 +230,11 @@ private ModelAndView getConfirmView(List<File> remaining, Map<ExpData, ExpRun> f
     }
 
     // split the files into those that have been created by an run and the rest.
-    protected Pair<List<File>, Map<ExpData, ExpRun>> filesWithExistingRuns(List<File> files)
+    protected Pair<List<FileLike>, Map<ExpData, ExpRun>> filesWithExistingRuns(List<FileLike> files)
     {
-        var unimported = new ArrayList<File>();
+        var unimported = new ArrayList<FileLike>();
         var existing = new LinkedHashMap<ExpData, ExpRun>();
-        for (File file : files)
+        for (FileLike file : files)
         {
             ExpData data = ExperimentService.get().getExpDataByURL(file, getContainer());
             if (data != null)
diff --git a/experiment/src/org/labkey/experiment/XarExportPipelineJob.java b/experiment/src/org/labkey/experiment/XarExportPipelineJob.java
index 53948f809b2..bec82562dfc 100644
--- a/experiment/src/org/labkey/experiment/XarExportPipelineJob.java
+++ b/experiment/src/org/labkey/experiment/XarExportPipelineJob.java
@@ -28,6 +28,7 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.experiment.pipeline.ExperimentPipelineProvider;
 import org.labkey.experiment.xar.XarExportSelection;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -67,12 +68,12 @@ public XarExportPipelineJob(ViewBackgroundInfo info, PipeRoot root, String fileN
         _xarXmlFileName = xarXmlFileName;
         _selection = selection;
 
-        File exportedXarsDir = root.resolvePath("exportedXars");
+        FileLike exportedXarsDir = root.resolvePathToFileLike("exportedXars");
         FileUtil.mkdir(exportedXarsDir);
 
-        _exportFile = new File(exportedXarsDir, _fileName);
+        _exportFile = exportedXarsDir.resolveChild(_fileName).toNioPathForWrite().toFile();
 
-        setLogFile(new File(_exportFile.getPath() + ".log"));
+        setLogFile(exportedXarsDir.resolveChild(fileName + ".log").toNioPathForWrite());
 
         header("Experiment export to " + _exportFile.getName());
     }
diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
index 5d2e5f94876..5b3d5437d4d 100644
--- a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
@@ -254,6 +254,7 @@
 import org.labkey.experiment.pipeline.MoveRunsPipelineJob;
 import org.labkey.experiment.xar.AutoFileLSIDReplacer;
 import org.labkey.experiment.xar.XarExportSelection;
+import org.labkey.vfs.FileLike;
 import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.dao.PessimisticLockingFailureException;
 
@@ -2109,78 +2110,6 @@ public ExperimentRunListView createExperimentRunWebPart(ViewContext context, Exp
         return view;
     }
 
-    /**
-     * export to temp directory
-     */
-    @Override
-    public File exportXarForRuns(
-            User user,
-            Set<Long> runIds,
-            Long expRowId,
-            XarExportOptions options
-    ) throws NotFoundException, IOException, ExperimentException
-    {
-        if (runIds.isEmpty())
-        {
-            throw new NotFoundException();
-        }
-
-        try
-        {
-            List<ExpRun> runs = new ArrayList<>();
-            for (var id : runIds)
-            {
-                ExpRun run = getExpRun(id);
-                if (run == null || !run.getContainer().hasPermission(user, ReadPermission.class))
-                {
-                    throw new NotFoundException("Could not find run " + id);
-                }
-                runs.add(run);
-            }
-
-            XarExportSelection selection = new XarExportSelection();
-            if (expRowId != null)
-            {
-                ExpExperiment experiment = getExpExperiment(expRowId);
-                if (experiment == null || !experiment.getContainer().hasPermission(user, ReadPermission.class))
-                {
-                    throw new NotFoundException("Run group " + expRowId);
-                }
-                selection.addExperimentIds(experiment.getRowId());
-            }
-            selection.addRuns(runs);
-            // NOTE: selection distinguishes between null and empty (careful)
-            // TODO have ArchiveURLRewriter() differentiate between input and output roles
-            // TODO using Set<roles> is adequate for now (as long as the caller knows all the roles of interest)
-            if (options.isFilterDataRoles())
-                selection.addRoles(options.getDataRoles());
-            XarExporter exporter = new XarExporter(
-                    LSIDRelativizer.valueOf(options.getLsidRelativizer()),
-                    selection,
-                    user,
-                    options.getXarXmlFileName(),
-                    options.getLog(),
-                    null
-            );
-            if (options.getExportFile().isDirectory())
-            {
-                exporter.writeAsDirectory(options.getExportFile());
-            }
-            else
-            {
-                try (FileOutputStream fOut = new FileOutputStream(options.getExportFile().getPath()))
-                {
-                    exporter.writeAsArchive(fOut);
-                }
-            }
-            return options.getExportFile();
-        }
-        catch (NumberFormatException e)
-        {
-            throw new NotFoundException(runIds.toString());
-        }
-    }
-
     @Override
     public DbSchema getSchema()
     {
@@ -4171,6 +4100,12 @@ public Map<String, ProtocolParameter> getProtocolParameters(long protocolRowId)
         return result;
     }
 
+    @Override
+    public ExpDataImpl getExpDataByURL(FileLike file, @Nullable Container c)
+    {
+        return getExpDataByURL(file.toNioPathForRead(), c);
+    }
+
     @Override
     public ExpDataImpl getExpDataByURL(File file, @Nullable Container c)
     {
diff --git a/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java b/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java
index 582e17a010d..45bac58115a 100644
--- a/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java
+++ b/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java
@@ -556,6 +556,12 @@ public boolean isUnderRoot(File file)
         return findRootPath(file) != null;
     }
 
+    @Override
+    public boolean isUnderRoot(FileLike file)
+    {
+        return findRootPath(file.toNioPathForRead()) != null;
+    }
+
     @Override
     public boolean isUnderRoot(Path path)
     {

From 4253d736d108a5e8644b6f12bdf9cf0d81c4d749 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Sat, 11 Oct 2025 15:31:48 -0700
Subject: [PATCH 14/15] ExperimentDataHandler File->FileLike

---
 .../assay/AbstractAssayTsvDataHandler.java    | 15 ++----
 .../api/assay/DefaultAssayRunCreator.java     | 10 +++-
 .../org/labkey/api/assay/TsvDataHandler.java  | 17 ++-----
 .../assay/plate/PlateMetadataDataHandler.java | 17 +------
 .../api/assay/transform/AnalysisScript.java   | 20 ++++++--
 .../labkey/api/exp/ExperimentDataHandler.java | 38 +++------------
 .../api/AbstractExperimentDataHandler.java    | 35 ++++----------
 .../exp/api/DefaultExperimentDataHandler.java |  3 +-
 .../AbstractSpecimenTransformTask.java        | 18 --------
 api/src/org/labkey/api/pipeline/PipeRoot.java |  3 ++
 .../labkey/api/reader/DataLoaderService.java  |  4 +-
 .../org/labkey/api/reader/ExcelFactory.java   |  6 +--
 .../org/labkey/api/reader/ExcelLoader.java    |  3 +-
 .../labkey/api/study/SpecimenTransform.java   | 14 +-----
 api/src/org/labkey/api/util/FileUtil.java     |  6 +++
 .../assay/dilution/DilutionDataHandler.java   | 31 ++++++-------
 .../matrix/AbstractMatrixDataHandler.java     | 22 ++-------
 .../org/labkey/api/assay/nab/Luc5Assay.java   |  8 ++--
 .../AbstractPlateBasedAssayProvider.java      |  6 +--
 .../api/assay/plate/AbstractPlateReader.java  |  4 +-
 .../api/assay/plate/ExcelPlateReader.java     | 13 ++++--
 .../assay/plate/PlateBasedAssayProvider.java  |  3 +-
 .../api/assay/plate/PlateBasedRunCreator.java |  3 +-
 .../labkey/api/assay/plate/PlateReader.java   |  6 +--
 .../plate/PlateSampleFilePropertyHelper.java  | 22 ++++-----
 .../labkey/api/assay/plate/PlateUtils.java    |  9 ++--
 .../api/assay/plate/TextPlateReader.java      |  6 +--
 .../assay/FileBasedModuleDataHandler.java     |  5 +-
 .../plate/AssayPlateMetadataServiceImpl.java  |  2 +-
 .../core/reader/DataLoaderServiceImpl.java    | 46 ++++++-------------
 .../org/labkey/experiment/URLRewriter.java    | 26 ++++++-----
 .../labkey/experiment/api/ExpDataImpl.java    |  3 +-
 .../experiment/api/ExperimentServiceImpl.java |  2 +-
 .../controllers/exp/ExperimentController.java | 22 ++++-----
 .../property/PropertyController.java          | 13 ++++--
 .../org/labkey/pipeline/api/PipeRootImpl.java | 23 +++-------
 36 files changed, 187 insertions(+), 297 deletions(-)

diff --git a/api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java b/api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java
index f8f3f3b2158..715ec17b739 100644
--- a/api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java
+++ b/api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java
@@ -143,19 +143,12 @@ public String toString()
     protected abstract boolean allowEmptyData();
 
     @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
+    public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
     {
-        importFile(data, dataFile, info, log, context, true);
+        importFile(data, dataFile, info, log, context, true, false);
     }
 
-    @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context, boolean allowLookupByAlternateKey) throws ExperimentException
-    {
-        importFile(data, dataFile, info, log, context, allowLookupByAlternateKey, false);
-    }
-
-    @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context, boolean allowLookupByAlternateKey, boolean autoFillDefaultResultColumns) throws ExperimentException
+    protected void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context, boolean allowLookupByAlternateKey, boolean autoFillDefaultResultColumns) throws ExperimentException
     {
         ExpProtocolApplication sourceApplication = data.getSourceApplication();
         if (sourceApplication == null)
@@ -175,7 +168,7 @@ public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgr
         // type conversion error).
         settings.setBestEffortConversion(true);
 
-        FileLike fo = FileSystemLike.wrapFile(dataFile);
+        FileLike fo = dataFile;
         Map<DataType, DataIteratorBuilder> rawData = getValidationDataMap(data, fo, info, log, context, settings);
         assert(rawData.size() <= 1);
         try
diff --git a/api/src/org/labkey/api/assay/DefaultAssayRunCreator.java b/api/src/org/labkey/api/assay/DefaultAssayRunCreator.java
index c0896b81cc7..f48283bf482 100644
--- a/api/src/org/labkey/api/assay/DefaultAssayRunCreator.java
+++ b/api/src/org/labkey/api/assay/DefaultAssayRunCreator.java
@@ -607,7 +607,15 @@ protected void importStandardResultData(
             {
                 ExperimentDataHandler dataHandler = insertedData.findDataHandler();
 
-                dataHandler.importFile(insertedData, insertedData.getFile(), info, logger, xarContext, context.isAllowLookupByAlternateKey(), context.shouldAutoFillDefaultResultColumns());
+                FileLike fileLike = FileSystemLike.wrapFile(insertedData.getFile());
+                if (dataHandler instanceof AbstractAssayTsvDataHandler tsvHandler)
+                {
+                    tsvHandler.importFile(insertedData, fileLike, info, logger, xarContext, context.isAllowLookupByAlternateKey(), context.shouldAutoFillDefaultResultColumns());
+                }
+                else
+                {
+                    dataHandler.importFile(insertedData, fileLike, info, logger, xarContext);
+                }
             }
         }
     }
diff --git a/api/src/org/labkey/api/assay/TsvDataHandler.java b/api/src/org/labkey/api/assay/TsvDataHandler.java
index 52bbc6a1b67..d8d88c447d2 100644
--- a/api/src/org/labkey/api/assay/TsvDataHandler.java
+++ b/api/src/org/labkey/api/assay/TsvDataHandler.java
@@ -118,19 +118,13 @@ protected boolean shouldAddInputMaterials()
     }
 
     @Override
-    public boolean hasContentToExport(ExpData data, File file)
-    {
-        return hasContentToExport(data, null != file ? file.toPath() : null);
-    }
-
-    @Override
-    public boolean hasContentToExport(ExpData data, Path file)
+    public boolean hasContentToExport(ExpData data, org.labkey.vfs.FileLike file)
     {
         return data.isFinalRunOutput();
     }
 
     @Override
-    public void exportFile(ExpData data, Path dataFile, String rootFilePath, User user, OutputStream out) throws ExperimentException
+    public void exportFile(ExpData data, org.labkey.vfs.FileLike dataFile, User user, OutputStream out) throws ExperimentException
     {
         if (data.isFinalRunOutput())
         {
@@ -154,7 +148,7 @@ public void exportFile(ExpData data, Path dataFile, String rootFilePath, User us
 
                         try
                         {
-                            File tempFile = FileUtil.createTempFile(FileUtil.getBaseName(FileUtil.getFileName(dataFile)), ".tsv");
+                            File tempFile = FileUtil.createTempFile("assay_export", ".tsv");
 
                             // Figure out the subset of columns to actually export in the TSV, see Issue 36746
                             Set<FieldKey> ignored = Set.of(FieldKey.fromParts("Run"), FieldKey.fromParts("RowId"), FieldKey.fromParts("DataId"), FieldKey.fromParts("Folder"));
@@ -163,10 +157,7 @@ public void exportFile(ExpData data, Path dataFile, String rootFilePath, User us
                             {
                                 if (!ignored.contains(column.getFieldKey()))
                                 {
-                                    if (PropertyType.FILE_LINK == column.getPropertyType() && !StringUtils.isEmpty(rootFilePath))
-                                        displayColumns.add(new TsvDataHandler.ExportFileLinkColumn(column, rootFilePath));
-                                    else
-                                        displayColumns.add(column.getRenderer());
+                                    displayColumns.add(column.getRenderer());
                                 }
                             }
 
diff --git a/api/src/org/labkey/api/assay/plate/PlateMetadataDataHandler.java b/api/src/org/labkey/api/assay/plate/PlateMetadataDataHandler.java
index 5240e686322..b9c26edc22f 100644
--- a/api/src/org/labkey/api/assay/plate/PlateMetadataDataHandler.java
+++ b/api/src/org/labkey/api/assay/plate/PlateMetadataDataHandler.java
@@ -12,8 +12,7 @@
 import org.labkey.api.exp.api.ExpDataRunInput;
 import org.labkey.api.util.FileType;
 import org.labkey.api.view.ViewBackgroundInfo;
-
-import java.io.File;
+import org.labkey.vfs.FileLike;
 
 public class PlateMetadataDataHandler extends AbstractAssayTsvDataHandler
 {
@@ -57,22 +56,10 @@ public Priority getPriority(ExpData data)
     }
 
     @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
+    public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
     {
         // this is just a noop data handler, the actual parsing and importing of the plate metadata needs to happen in
         // AbstractAssayTsvDataHandler.addAssayPlateMetadata because we need to access the inserted result data to get at the
         // lsids.
     }
-
-    @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context, boolean allowLookupByAlternateKey) throws ExperimentException
-    {
-        // see description above
-    }
-
-    @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context, boolean allowLookupByAlternateKey, boolean autoFillDefaultResultColumns) throws ExperimentException
-    {
-        // see description above
-    }
 }
diff --git a/api/src/org/labkey/api/assay/transform/AnalysisScript.java b/api/src/org/labkey/api/assay/transform/AnalysisScript.java
index 308b06ca052..e43020d4cd1 100644
--- a/api/src/org/labkey/api/assay/transform/AnalysisScript.java
+++ b/api/src/org/labkey/api/assay/transform/AnalysisScript.java
@@ -4,10 +4,12 @@
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
+import org.labkey.api.util.UnexpectedException;
 import org.labkey.vfs.FileLike;
 import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -17,18 +19,18 @@
 
 public class AnalysisScript
 {
-    FileLike _script;
+    final FileLike _script;
     Set<DataTransformService.TransformOperation> _operations = new HashSet<>();
 
     public AnalysisScript(File script, Set<DataTransformService.TransformOperation> operations)
     {
-        _script = new FileSystemLike.Builder(script).build().getRoot();
+        this(script);
         _operations = operations;
     }
 
     private AnalysisScript(File script, List<String> operations)
     {
-        _script = new FileSystemLike.Builder(script).build().getRoot();
+        this(script);
         for (String op : operations)
         {
             if (op != null)
@@ -36,6 +38,18 @@ private AnalysisScript(File script, List<String> operations)
         }
     }
 
+    private AnalysisScript(File script)
+    {
+        try
+        {
+            _script = FileSystemLike.wrapFile(script.getParentFile(), script);
+        }
+        catch (IOException e)
+        {
+            throw UnexpectedException.wrap(e);
+        }
+    }
+
     public FileLike getScript()
     {
         return _script;
diff --git a/api/src/org/labkey/api/exp/ExperimentDataHandler.java b/api/src/org/labkey/api/exp/ExperimentDataHandler.java
index 69cd303f9ba..3c7cba267a4 100644
--- a/api/src/org/labkey/api/exp/ExperimentDataHandler.java
+++ b/api/src/org/labkey/api/exp/ExperimentDataHandler.java
@@ -25,14 +25,12 @@
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.security.User;
-import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.OutputStream;
-import java.nio.file.Path;
 import java.util.List;
 
 /**
@@ -56,36 +54,13 @@ default String getFileName(ExpData data, String defaultName)
      * Import whatever content from the file is destined for storage in the database. Typically persisted in a schema
      * owned by the module that holds the implementation of the ExperimentDataHandler.
      */
-    // TODO File->FileLike
-    void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException;
-    default void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context, boolean allowLookupByAlternateKey) throws ExperimentException
-    {
-        importFile(data, dataFile, info, log, context);
-    }
-
-    // TODO File->FileLike
-    default void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context, boolean allowLookupByAlternateKey, boolean autoFillDefaultResultColumns) throws ExperimentException
-    {
-        importFile(data, dataFile, info, log, context);
-    }
-
-    // TODO File->FileLike
-    default void importFile(@NotNull ExpData data, Path dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
-    {
-        if (FileUtil.hasCloudScheme(dataFile))
-            throw new ExperimentException(this.getClass().getName() + " does not support importFile on a cloud path");
-        importFile(data, dataFile.toFile(), info, log, context);
-    }
+    void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException;
 
     /**
      * Stream the content of this data object. Typically, this just streams the bytes of the file from disk, but could
      * create something based exclusively on what's in the database.
      */
-    // TODO File->FileLike
-    void exportFile(ExpData data, File dataFile, User user, OutputStream out) throws ExperimentException;
-    default void exportFile(ExpData data, Path dataFile, String rootFilePath, User user, OutputStream out) throws ExperimentException
-    {
-    }
+    void exportFile(ExpData data, @Nullable FileLike dataFile, User user, OutputStream out) throws ExperimentException;
 
     /** @return URL to the imported version of the data, like a grid view over a database table or a custom details page */
     @Nullable
@@ -106,11 +81,10 @@ default void exportFile(ExpData data, Path dataFile, String rootFilePath, User u
      */
     void deleteData(ExpData data, Container container, User user);
 
-    // TODO File->FileLike
-    boolean hasContentToExport(ExpData data, File file);
-    default boolean hasContentToExport(ExpData data, Path file)
+    // Preferred: use FileLike
+    default boolean hasContentToExport(ExpData data, @Nullable FileLike file)
     {
-        return false;
+        return file != null && file.exists() && file.isFile();
     }
 
     default void runMoved(ExpData newData, Container container, Container targetContainer, String oldRunLSID, String newRunLSID, User user, long oldDataRowID) throws ExperimentException
diff --git a/api/src/org/labkey/api/exp/api/AbstractExperimentDataHandler.java b/api/src/org/labkey/api/exp/api/AbstractExperimentDataHandler.java
index 97e09b9391f..1ca266c0e90 100644
--- a/api/src/org/labkey/api/exp/api/AbstractExperimentDataHandler.java
+++ b/api/src/org/labkey/api/exp/api/AbstractExperimentDataHandler.java
@@ -21,14 +21,11 @@
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.Lsid;
 import org.labkey.api.security.User;
-import org.labkey.api.util.FileUtil;
-import org.labkey.api.util.NetworkDrive;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.OutputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
 import java.util.List;
 
 /**
@@ -46,19 +43,13 @@ public String getFileName(ExpData data, String defaultName)
     }
 
     @Override
-    public void exportFile(ExpData data, File dataFile, User user, OutputStream out) throws ExperimentException
-    {
-        exportFile(data, dataFile.toPath(), null, user, out);
-    }
-
-    @Override
-    public void exportFile(ExpData data, Path dataFile, String rootFilePath, User user, OutputStream out) throws ExperimentException
+    public void exportFile(ExpData data, FileLike dataFile, User user, OutputStream out) throws ExperimentException
     {
         if (dataFile != null)
         {
-            try
+            try (InputStream is = dataFile.openInputStream())
             {
-                Files.copy(dataFile, out);
+                is.transferTo(out);
             }
             catch (IOException e)
             {
@@ -67,26 +58,16 @@ public void exportFile(ExpData data, Path dataFile, String rootFilePath, User us
         }
     }
 
-    @Override
-    public void beforeDeleteData(List<ExpData> data, User user) throws ExperimentException
-    {
-    }
 
     @Override
-    public boolean hasContentToExport(ExpData data, File file)
+    public void beforeDeleteData(List<ExpData> data, User user) throws ExperimentException
     {
-        return hasContentToExport(data, file.toPath());
     }
 
     @Override
-    public boolean hasContentToExport(ExpData data, Path path)
+    public boolean hasContentToExport(ExpData data, FileLike file)
     {
-        if (!FileUtil.hasCloudScheme(path))
-        {
-            File file = path.toFile();
-            return NetworkDrive.exists(file) && file.isFile();
-        }
-        return Files.exists(path) && !Files.isDirectory(path);
+        return file != null && file.exists() && file.isFile();
     }
 
     @Override
diff --git a/api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java b/api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java
index 24ad6f495ab..8c4600200a1 100644
--- a/api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java
+++ b/api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java
@@ -24,6 +24,7 @@
 import org.labkey.api.security.User;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 
@@ -41,7 +42,7 @@ public DataType getDataType()
     }
 
     @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context)
+    public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context)
     {
         log.debug("No ExperimentDataHandler registered for data file " + data.getDataFileURI() + ", no special loading will be done on this file.");
     }
diff --git a/api/src/org/labkey/api/pipeline/AbstractSpecimenTransformTask.java b/api/src/org/labkey/api/pipeline/AbstractSpecimenTransformTask.java
index 0e23dfd2a9f..42d9aa62f8a 100644
--- a/api/src/org/labkey/api/pipeline/AbstractSpecimenTransformTask.java
+++ b/api/src/org/labkey/api/pipeline/AbstractSpecimenTransformTask.java
@@ -55,24 +55,6 @@ public AbstractSpecimenTransformTask(PipelineJob job)
         _job = job;
     }
 
-    @Deprecated
-    public void transform(File input, File output) throws PipelineJobException
-    {
-        throw new UnsupportedOperationException("Use the Path version of the transform method");
-    }
-
-    public void transform(Path input, Path output) throws PipelineJobException
-    {
-        try
-        {
-            transform(input.toFile(), output.toFile());
-        }
-        catch (UnsupportedOperationException e)
-        {
-            throw new PipelineJobException("Error transforming input file.", e);
-        }
-    }
-
     /**
      * Transform a row of data from the parsed input data file the transformed specimen row
      * During the transform, it's expected that any lab, primary, derivative and additive
diff --git a/api/src/org/labkey/api/pipeline/PipeRoot.java b/api/src/org/labkey/api/pipeline/PipeRoot.java
index 0bbc1b0aea8..d71491f9586 100644
--- a/api/src/org/labkey/api/pipeline/PipeRoot.java
+++ b/api/src/org/labkey/api/pipeline/PipeRoot.java
@@ -108,6 +108,9 @@ public interface PipeRoot extends SecurableResource
     /** @return relative path to the file from the root. null if the file isn't under the root. Does not include a leading slash */
     String relativePath(File file);
 
+    /** @return relative path to the file from the root. null if the file isn't under the root. Does not include a leading slash */
+    String relativePath(FileLike file);
+
     /** @return relative path to the file from the root. null if the path isn't under the root. Does not include a leading slash */
     String relativePath(Path file);
 
diff --git a/api/src/org/labkey/api/reader/DataLoaderService.java b/api/src/org/labkey/api/reader/DataLoaderService.java
index 25396ef5585..ac1c63f4312 100644
--- a/api/src/org/labkey/api/reader/DataLoaderService.java
+++ b/api/src/org/labkey/api/reader/DataLoaderService.java
@@ -47,10 +47,10 @@ static void setInstance(DataLoaderService impl)
     void registerFactory(@NotNull DataLoaderFactory factory);
 
     @Nullable
-    DataLoaderFactory findFactory(File file, @Nullable FileType guessFormat);
+    DataLoaderFactory findFactory(FileLike file, @Nullable FileType guessFormat);
 
     @Nullable
-    DataLoaderFactory findFactory(File file, String contentType, @Nullable FileType guessFormat);
+    DataLoaderFactory findFactory(FileLike file, String contentType, @Nullable FileType guessFormat);
 
     @Nullable
     DataLoaderFactory findFactory(String filename, String contentType, InputStream is, @Nullable FileType guessFormat);
diff --git a/api/src/org/labkey/api/reader/ExcelFactory.java b/api/src/org/labkey/api/reader/ExcelFactory.java
index 9bb65e35935..83f1a895978 100644
--- a/api/src/org/labkey/api/reader/ExcelFactory.java
+++ b/api/src/org/labkey/api/reader/ExcelFactory.java
@@ -181,7 +181,7 @@ public static WorkbookMetadata getMetadata(@NotNull File file) throws IOExceptio
         {
             return getMetadata(opc);
         }
-        // might be OLE2 formet
+        // might be OLE2 format
         catch (InvalidFormatException|UnsupportedFileFormatException e)
         {
             Workbook wb = create(file);
@@ -585,11 +585,11 @@ public static Cell getCell(Sheet sheet, int colIdx, int rowIdx)
 
     /** Supports .xls (BIFF8 only), and .xlsx */
     @NotNull
-    public static JSONArray convertExcelToJSON(InputStream in, boolean extended) throws IOException
+    public static JSONArray convertExcelToJSON(InputStream in, boolean extended, int maxRows) throws IOException
     {
         try (Workbook workbook = WorkbookFactory.create(in))
         {
-            return convertExcelToJSON(workbook, extended, -1);
+            return convertExcelToJSON(workbook, extended, maxRows);
         }
     }
 
diff --git a/api/src/org/labkey/api/reader/ExcelLoader.java b/api/src/org/labkey/api/reader/ExcelLoader.java
index 456d4d921b7..de2535a195d 100644
--- a/api/src/org/labkey/api/reader/ExcelLoader.java
+++ b/api/src/org/labkey/api/reader/ExcelLoader.java
@@ -46,6 +46,7 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.JunitUtil;
 import org.labkey.api.util.StringUtilsLabKey;
+import org.labkey.vfs.FileSystemLike;
 import org.xml.sax.Attributes;
 import org.xml.sax.InputSource;
 import org.xml.sax.XMLReader;
@@ -817,7 +818,7 @@ public void detect() throws Exception
             DataLoaderService svc = DataLoaderService.get();
             if (svc != null)
             {
-                DataLoaderFactory factory = svc.findFactory(JunitUtil.getSampleData(null, "Nab/seaman/MS010407"), null);
+                DataLoaderFactory factory = svc.findFactory(FileSystemLike.wrapFile(JunitUtil.getSampleData(null, "Nab/seaman/MS010407")), null);
                 assertTrue(factory instanceof ExcelLoader.Factory);
             }
 
diff --git a/api/src/org/labkey/api/study/SpecimenTransform.java b/api/src/org/labkey/api/study/SpecimenTransform.java
index 5842bfcadc7..d00b7731f19 100644
--- a/api/src/org/labkey/api/study/SpecimenTransform.java
+++ b/api/src/org/labkey/api/study/SpecimenTransform.java
@@ -53,19 +53,7 @@ public interface SpecimenTransform
      */
     FileType getFileType();
 
-    /**
-     * Transform the input file into a specimen archive that a basic specimen import can
-     * process.
-     */
-    @Deprecated
-    void transform(@Nullable PipelineJob job, File input, File outputArchive) throws PipelineJobException;
-
-    default void transform(@Nullable PipelineJob job, Path input, Path outputArchive) throws PipelineJobException
-    {
-        //TODO this should be implemented in the inheriting classes
-        //  defaulting for now to prevent build issues
-        transform(job, input.toFile(), outputArchive.toFile());
-    }
+    void transform(@Nullable PipelineJob job, Path input, Path outputArchive) throws PipelineJobException;
 
     /**
      * An optional post transform step.
diff --git a/api/src/org/labkey/api/util/FileUtil.java b/api/src/org/labkey/api/util/FileUtil.java
index 88753e6b1f2..d7675c3092d 100644
--- a/api/src/org/labkey/api/util/FileUtil.java
+++ b/api/src/org/labkey/api/util/FileUtil.java
@@ -1559,6 +1559,12 @@ else if (ch == '-' &&
      * Returns the absolute path to a file. On Windows and Mac, corrects casing in file paths to match the
      * canonical path.
      */
+    @NotNull
+    public static FileLike getAbsoluteCaseSensitiveFile(@NotNull FileLike file)
+    {
+        return FileSystemLike.wrapFile(getAbsoluteCaseSensitiveFile(file.toNioPathForRead().toFile()));
+    }
+
     @NotNull
     public static File getAbsoluteCaseSensitiveFile(@NotNull File file)
     {
diff --git a/assay/api-src/org/labkey/api/assay/dilution/DilutionDataHandler.java b/assay/api-src/org/labkey/api/assay/dilution/DilutionDataHandler.java
index 43ecb9ee7cc..e4eabafa1ff 100644
--- a/assay/api-src/org/labkey/api/assay/dilution/DilutionDataHandler.java
+++ b/assay/api-src/org/labkey/api/assay/dilution/DilutionDataHandler.java
@@ -111,10 +111,10 @@ public DilutionDataHandler(String dataLsidPrefix)
     protected class DilutionDataFileParser
     {
         private final ExpData _data;
-        private final File _dataFile;
+        private final FileLike _dataFile;
         private final ViewBackgroundInfo _info;
 
-        public DilutionDataFileParser(ExpData data, File dataFile, ViewBackgroundInfo info)
+        public DilutionDataFileParser(ExpData data, FileLike dataFile, ViewBackgroundInfo info)
         {
             _data = data;
             _dataFile = dataFile;
@@ -136,7 +136,7 @@ public List<Map<String, Object>> getResults() throws ExperimentException
      *                         plate data versus the saved table data. If use run for plates is false (use dataFile) then
      *                         stats are always recalculated.
      */
-    public List<Map<String, Object>> calculateDilutionStats(ExpRun run, User user, @Nullable File dataFile, boolean useRunForPlates, boolean recalculateStats) throws ExperimentException
+    public List<Map<String, Object>> calculateDilutionStats(ExpRun run, User user, @Nullable FileLike dataFile, boolean useRunForPlates, boolean recalculateStats) throws ExperimentException
     {
         try {
             DilutionAssayRun assayResults = getAssayResults(run, user, dataFile, null, useRunForPlates, recalculateStats);
@@ -238,12 +238,12 @@ else if (Double.POSITIVE_INFINITY == icValue)
         results.put(name + OORDisplayColumnFactory.OOR_INDICATOR_COLUMN_SUFFIX, outOfRange);
     }
 
-    protected ExperimentException createParseError(File dataFile, String msg)
+    protected ExperimentException createParseError(FileLike dataFile, String msg)
     {
         return createParseError(dataFile, msg, null);
     }
 
-    protected ExperimentException createParseError(File dataFile, String msg, @Nullable Exception cause)
+    protected ExperimentException createParseError(FileLike dataFile, String msg, @Nullable Exception cause)
     {
         StringBuilder fullMessage = new StringBuilder("There was an error parsing ");
         fullMessage.append(dataFile.getName()).append(".\n");
@@ -290,14 +290,14 @@ public DilutionAssayRun getAssayResults(ExpRun run, User user, @Nullable StatsSe
         return getAssayResults(run, user, getDataFile(run), fit, true, false);
     }
 
-    public File getDataFile(ExpRun run)
+    public FileLike getDataFile(ExpRun run)
     {
         if (run == null)
             return null;
         List<? extends ExpData> outputDatas = run.getOutputDatas(getDataType());
         if (outputDatas == null || outputDatas.size() != 1)
             throw new IllegalStateException(getResourceName(run) + " runs should have a single data output.");
-        File dataFile = outputDatas.get(0).getFile();
+        FileLike dataFile = outputDatas.get(0).getFileLike();
         if (!dataFile.exists())
             return null;
         return dataFile;
@@ -312,7 +312,7 @@ public String getResourceName(ExpRun run)
         return provider != null ? provider.getResourceName() : "Assay";
     }
 
-    protected List<Plate> createPlates(File dataFile, Plate template) throws ExperimentException
+    protected List<Plate> createPlates(FileLike dataFile, Plate template) throws ExperimentException
     {
         return Collections.singletonList(PlateService.get().createPlate(template, getCellValues(dataFile, template), null, PlateService.NO_RUNID, 1));
     }
@@ -335,9 +335,9 @@ protected List<Plate> createPlates(ExpRun run, Plate template, boolean recalcSta
         return Collections.singletonList(plate);
     }
 
-    protected abstract double[][] getCellValues(final File dataFile, Plate nabTemplate) throws ExperimentException;
+    protected abstract double[][] getCellValues(final FileLike dataFile, Plate nabTemplate) throws ExperimentException;
 
-    protected DilutionAssayRun getAssayResults(ExpRun run, User user, @Nullable File dataFile, @Nullable StatsService.CurveFitType fit,
+    protected DilutionAssayRun getAssayResults(ExpRun run, User user, @Nullable FileLike dataFile, @Nullable StatsService.CurveFitType fit,
                                                boolean useRunForPlates, boolean recalcStats) throws ExperimentException
     {
         ExpProtocol protocol = ExperimentService.get().getExpProtocol(run.getProtocol().getLSID());
@@ -473,18 +473,13 @@ protected abstract DilutionAssayRun createDilutionAssayRun(DilutionAssayProvider
 
     public abstract Map<DilutionSummary, DilutionAssayRun> getDilutionSummaries(User user, StatsService.CurveFitType fit, long... dataObjectIds) throws ExperimentException, SQLException;
 
-    protected DilutionDataFileParser getDataFileParser(ExpData data, File dataFile, ViewBackgroundInfo info)
-    {
-        return new DilutionDataFileParser(data, dataFile, info);
-    }
-
     final protected DilutionDataFileParser getDataFileParser(ExpData data, FileLike dataFile, ViewBackgroundInfo info)
     {
-        return new DilutionDataFileParser(data, dataFile.toNioPathForRead().toFile(), info);
+        return new DilutionDataFileParser(data, dataFile, info);
     }
 
     @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
+    public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
     {
         ExpRun run = data.getRun();
         ExpProtocol protocol = run.getProtocol();
@@ -807,7 +802,7 @@ private void _populateWellData(ExpProtocol protocol, ExpRun run, User user, Map<
 
             if (populatePlatesFromFile)
             {
-                File dataFile = getDataFile(run);
+                FileLike dataFile = getDataFile(run);
                 if (null == dataFile)
                     throw new MissingDataFileException("Data file not found.");
                 plates = createPlates(dataFile, nabTemplate);
diff --git a/assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java b/assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java
index bfc8e084733..861e0dc834c 100644
--- a/assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java
+++ b/assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java
@@ -51,13 +51,12 @@
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.reader.ColumnDescriptor;
 import org.labkey.api.reader.DataLoader;
-import org.labkey.api.reader.DataLoaderFactory;
 import org.labkey.api.reader.TabLoader;
 import org.labkey.api.security.User;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -113,26 +112,13 @@ public DataType getDataType()
     }
 
     @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
+    public void importFile(@NotNull ExpData data, @NotNull org.labkey.vfs.FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
     {
     }
 
-    public static DataLoader createLoader(File file, String idColumnName) throws IOException, ExperimentException
+    public static TabLoader createTabLoader(FileLike file, String idColumnName, Set<String> aliases) throws IOException, ExperimentException
     {
-        return createLoader(file, idColumnName, Collections.emptySet());
-    }
-
-    public static DataLoader createLoader(File file, String idColumnName, Set<String> aliases) throws IOException, ExperimentException
-    {
-        DataLoaderFactory factory = DataLoader.get().findFactory(file, null);
-        DataLoader loader = factory.createLoader(file, true);
-        ensureColumns(idColumnName, aliases, loader.getColumns());
-        return loader;
-    }
-
-    public static TabLoader createTabLoader(File file, String idColumnName, Set<String> aliases) throws IOException, ExperimentException
-    {
-        TabLoader loader = new TabLoader(file, true);
+        TabLoader loader = new TabLoader(file.openInputStream(), true, null);
         ensureColumns(idColumnName, aliases, loader.getColumns());
         return loader;
     }
diff --git a/assay/api-src/org/labkey/api/assay/nab/Luc5Assay.java b/assay/api-src/org/labkey/api/assay/nab/Luc5Assay.java
index c98fe6e968e..580ee487433 100644
--- a/assay/api-src/org/labkey/api/assay/nab/Luc5Assay.java
+++ b/assay/api-src/org/labkey/api/assay/nab/Luc5Assay.java
@@ -26,8 +26,8 @@
 import org.labkey.api.assay.plate.Plate;
 import org.labkey.api.assay.plate.Position;
 import org.labkey.api.assay.plate.WellData;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.Serializable;
 import java.util.List;
 import java.util.Map;
@@ -42,7 +42,7 @@ public abstract class Luc5Assay implements Serializable, DilutionCurve.PercentCa
     private final Long _runRowId;
     private final int[] _cutoffs;
     private Map<Integer, String> _cutoffFormats;
-    private File _dataFile;
+    private FileLike _dataFile;
     protected StatsService.CurveFitType _renderedCurveFitType;
     private boolean _lockAxes;
 
@@ -191,12 +191,12 @@ public void setCutoffFormats(Map<Integer, String> cutoffFormats)
         _cutoffFormats = cutoffFormats;
     }
 
-    public File getDataFile()
+    public FileLike getDataFile()
     {
         return _dataFile;
     }
 
-    public void setDataFile(File dataFile)
+    public void setDataFile(FileLike dataFile)
     {
         _dataFile = dataFile;
     }
diff --git a/assay/api-src/org/labkey/api/assay/plate/AbstractPlateBasedAssayProvider.java b/assay/api-src/org/labkey/api/assay/plate/AbstractPlateBasedAssayProvider.java
index 17d2bbc2a87..1e97a198f6a 100644
--- a/assay/api-src/org/labkey/api/assay/plate/AbstractPlateBasedAssayProvider.java
+++ b/assay/api-src/org/labkey/api/assay/plate/AbstractPlateBasedAssayProvider.java
@@ -51,8 +51,8 @@
 import org.labkey.api.util.Pair;
 import org.labkey.api.view.HtmlView;
 import org.labkey.api.view.InsertView;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -127,7 +127,7 @@ public AssayRunCreator<?> getRunCreator()
     }
 
     @Override
-    public File getSampleMetadataFile(Container container, int runId)
+    public FileLike getSampleMetadataFile(Container container, int runId)
     {
         ExpRun run = ExperimentService.get().getExpRun(runId);
         if (!run.getContainer().equals(container))
@@ -151,7 +151,7 @@ public File getSampleMetadataFile(Container container, int runId)
         for (Map.Entry<? extends ExpData, String> entry : sampleDerivationInputs.entrySet())
         {
             if (SAMPLE_METADATA_INPUT_ROLE.equals(entry.getValue()))
-                return entry.getKey().getFile();
+                return entry.getKey().getFileLike();
         }
         return null;
     }
diff --git a/assay/api-src/org/labkey/api/assay/plate/AbstractPlateReader.java b/assay/api-src/org/labkey/api/assay/plate/AbstractPlateReader.java
index 180c86276a9..4758e7d7cd0 100644
--- a/assay/api-src/org/labkey/api/assay/plate/AbstractPlateReader.java
+++ b/assay/api-src/org/labkey/api/assay/plate/AbstractPlateReader.java
@@ -18,8 +18,8 @@
 import org.apache.commons.lang3.math.NumberUtils;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.query.ValidationException;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.List;
 
 /**
@@ -51,7 +51,7 @@ else if (dblValue == WELL_OFF_SCALE)
     }
 
     @Override
-    public List<PlateUtils.GridInfo> loadMultiGridFile(Plate template, File dataFile) throws ExperimentException
+    public List<PlateUtils.GridInfo> loadMultiGridFile(Plate template, FileLike dataFile) throws ExperimentException
     {
         throw new UnsupportedOperationException("loading multiple grids for this reader implementation is not supported");
     }
diff --git a/assay/api-src/org/labkey/api/assay/plate/ExcelPlateReader.java b/assay/api-src/org/labkey/api/assay/plate/ExcelPlateReader.java
index 77d72f0eaf4..daf6fb39de9 100644
--- a/assay/api-src/org/labkey/api/assay/plate/ExcelPlateReader.java
+++ b/assay/api-src/org/labkey/api/assay/plate/ExcelPlateReader.java
@@ -24,9 +24,10 @@
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.reader.DataLoader;
 import org.labkey.api.reader.DataLoaderFactory;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.List;
 
 /**
@@ -46,10 +47,11 @@ public String getType()
     }
 
     @Override
-    public double[][] loadFile(Plate template, File dataFile) throws ExperimentException
+    public double[][] loadFile(Plate template, FileLike dataFile) throws ExperimentException
     {
         DataLoaderFactory factory = DataLoader.get().findFactory(dataFile, null);
-        try (DataLoader loader = factory.createLoader(dataFile, false))
+        try (InputStream in = dataFile.openInputStream();
+             DataLoader loader = factory.createLoader(in, false))
         {
             return PlateUtils.parseGrid(dataFile, loader.load(), template.getRows(), template.getColumns(), this);
         }
@@ -60,10 +62,11 @@ public double[][] loadFile(Plate template, File dataFile) throws ExperimentExcep
     }
 
     @Override
-    public List<PlateUtils.GridInfo> loadMultiGridFile(Plate template, File dataFile) throws ExperimentException
+    public List<PlateUtils.GridInfo> loadMultiGridFile(Plate template, FileLike dataFile) throws ExperimentException
     {
         DataLoaderFactory factory = DataLoader.get().findFactory(dataFile, null);
-        try (DataLoader loader = factory.createLoader(dataFile, false))
+        try (InputStream in = dataFile.openInputStream();
+                DataLoader loader = factory.createLoader(in, false))
         {
             return PlateUtils.parseAllGrids(dataFile, loader.load(), template.getRows(), template.getColumns(), this);
         }
diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateBasedAssayProvider.java b/assay/api-src/org/labkey/api/assay/plate/PlateBasedAssayProvider.java
index 853cdb1738d..4c716f2c652 100644
--- a/assay/api-src/org/labkey/api/assay/plate/PlateBasedAssayProvider.java
+++ b/assay/api-src/org/labkey/api/assay/plate/PlateBasedAssayProvider.java
@@ -25,6 +25,7 @@
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.study.assay.ParticipantVisitResolverType;
 import org.labkey.api.study.assay.SampleMetadataInputFormat;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.util.Collection;
@@ -39,7 +40,7 @@ public interface PlateBasedAssayProvider extends AssayProvider
 
     void setPlate(Container container, ExpProtocol protocol, Plate plate);
     @Nullable Plate getPlate(Container container, ExpProtocol protocol);
-    File getSampleMetadataFile(Container container, int runId);
+    FileLike getSampleMetadataFile(Container container, int runId);
     @Nullable PlateReader getPlateReader(String readerName);
     SampleMetadataInputFormat[] getSupportedMetadataInputFormats();
     SampleMetadataInputFormat getMetadataInputFormat(ExpProtocol protocol);
diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateBasedRunCreator.java b/assay/api-src/org/labkey/api/assay/plate/PlateBasedRunCreator.java
index e4f0e634e44..9872724fce5 100644
--- a/assay/api-src/org/labkey/api/assay/plate/PlateBasedRunCreator.java
+++ b/assay/api-src/org/labkey/api/assay/plate/PlateBasedRunCreator.java
@@ -44,6 +44,7 @@
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.util.Arrays;
@@ -189,7 +190,7 @@ private Map<ExpMaterial, String> createDerivedMaterials(AssayRunUploadContext<?>
             if (getProvider().getMetadataInputFormat(context.getProtocol()) == SampleMetadataInputFormat.FILE_BASED)
             {
                 PlateSampleFilePropertyHelper helper = (PlateSampleFilePropertyHelper) getProvider().getSamplePropertyHelper((PlateUploadForm) context, null);
-                File metadataFile = helper.getMetadataFile();
+                FileLike metadataFile = helper.getMetadataFile();
                 sampleMetadataFile = ExperimentService.get().createData(context.getContainer(), SAMPLE_METADATA_FILE_TYPE);
                 sampleMetadataFile.setDataFileURI(FileUtil.getAbsoluteCaseSensitiveFile(metadataFile).toURI());
                 sampleMetadataFile.setName(metadataFile.getName());
diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateReader.java b/assay/api-src/org/labkey/api/assay/plate/PlateReader.java
index 45105ff5e24..fee10c40fc8 100644
--- a/assay/api-src/org/labkey/api/assay/plate/PlateReader.java
+++ b/assay/api-src/org/labkey/api/assay/plate/PlateReader.java
@@ -18,8 +18,8 @@
 
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.query.ValidationException;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.List;
 
 /**
@@ -41,14 +41,14 @@ public interface PlateReader
     /**
      * Parse the specified datafile and populate an array of well values
      */
-    double[][] loadFile(Plate template, File dataFile) throws ExperimentException;
+    double[][] loadFile(Plate template, FileLike dataFile) throws ExperimentException;
 
     /**
      * Parse the specified datafile and populate a map of array of well values. This is designed to process files
      * that have multiple grids of data embedded and the caller is interested in all of the data. The parser will
      * attempt to annotate the grids with metadata that it may discover during parsing.
      */
-    List<PlateUtils.GridInfo> loadMultiGridFile(Plate template, File dataFile) throws ExperimentException;
+    List<PlateUtils.GridInfo> loadMultiGridFile(Plate template, FileLike dataFile) throws ExperimentException;
 
     /**
      * Determines whether the specified well value should be used in any analytical calculations
diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateSampleFilePropertyHelper.java b/assay/api-src/org/labkey/api/assay/plate/PlateSampleFilePropertyHelper.java
index 9afd4f74ade..e749867e848 100644
--- a/assay/api-src/org/labkey/api/assay/plate/PlateSampleFilePropertyHelper.java
+++ b/assay/api-src/org/labkey/api/assay/plate/PlateSampleFilePropertyHelper.java
@@ -55,8 +55,6 @@
 import org.springframework.web.multipart.MultipartHttpServletRequest;
 
 import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.HashMap;
@@ -88,7 +86,7 @@ public class PlateSampleFilePropertyHelper extends PlateSamplePropertyHelper
     protected Map<String, Map<DomainProperty, String>> _sampleProperties;
     protected String _metadataNoun = "Sample";
     protected String _wellGroupColumnName = SAMPLE_WELLGROUP_COLUMN;
-    private File _metadataFile;
+    private FileLike _metadataFile;
 
     public PlateSampleFilePropertyHelper(Container container, ExpProtocol protocol, List<? extends DomainProperty> domainProperties, Plate template, SampleMetadataInputFormat inputFormat)
     {
@@ -137,7 +135,7 @@ public Map<String, Map<DomainProperty, String>> getPostedPropertyValues(HttpServ
         return new HashMap<>(sampleProperties);
     }
 
-    protected File getSampleMetadata(HttpServletRequest request) throws ExperimentException
+    protected FileLike getSampleMetadata(HttpServletRequest request) throws ExperimentException
     {
         if (_metadataFile != null)
             return _metadataFile;
@@ -146,7 +144,7 @@ protected File getSampleMetadata(HttpServletRequest request) throws ExperimentEx
         {
             String relativePath = request.getParameter(METADATA_PREVUPLOAD_LOCATION);
             PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(_container);
-            _metadataFile = pipelineRoot.resolvePath(relativePath);
+            _metadataFile = pipelineRoot.resolvePathToFileLike(relativePath);
             return _metadataFile;
         }
 
@@ -155,7 +153,7 @@ protected File getSampleMetadata(HttpServletRequest request) throws ExperimentEx
         {
             String relativePath = request.getParameter(PRIMARY_PREV_UPLOAD_PATH);
             PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(_container);
-            _metadataFile = pipelineRoot.resolvePath(relativePath);
+            _metadataFile = pipelineRoot.resolvePathToFileLike(relativePath);
             return _metadataFile;
         }
 
@@ -167,15 +165,15 @@ protected File getSampleMetadata(HttpServletRequest request) throws ExperimentEx
         try
         {
             FileLike uploadDirectory = AssayFileWriter.ensureUploadDirectory(_container);
-            _metadataFile = FileUtil.findUniqueFileName(metadata.getOriginalFilename(), uploadDirectory).toNioPathForWrite().toFile();
-            try (BufferedOutputStream fos = new BufferedOutputStream(new FileOutputStream(_metadataFile));
+            _metadataFile = FileUtil.findUniqueFileName(metadata.getOriginalFilename(), uploadDirectory);
+            try (BufferedOutputStream fos = new BufferedOutputStream(_metadataFile.openOutputStream());
                 InputStream is = metadata.getInputStream())
             {
                 IOUtils.copy(is, fos);
                 FileSystemAuditProvider.FileSystemAuditEvent event = new FileSystemAuditProvider.FileSystemAuditEvent(_container, "Adding sample metadata file " + metadata.getOriginalFilename() + ".");
                 event.setProvidedFileName(metadata.getOriginalFilename());
                 event.setFile(_metadataFile.getName());
-                event.setDirectory(_metadataFile.getParent());
+                event.setDirectory(_metadataFile.getParent().toNioPathForRead().toFile().getPath());
                 AuditLogService.get().addEvent(null, event);
             }
         }
@@ -219,7 +217,7 @@ public Map<String, Map<DomainProperty, String>> getSampleProperties(HttpServletR
         if (_sampleProperties != null)
             return _sampleProperties;
 
-        File metadataFile = getSampleMetadata(request);
+        FileLike metadataFile = getSampleMetadata(request);
         if (metadataFile == null)
             return null;
 
@@ -282,7 +280,7 @@ protected void validateMetadataRow(Map<String, Object> row, String wellGroupName
         }
     }
 
-    public File getMetadataFile()
+    public FileLike getMetadataFile()
     {
         return _metadataFile;
     }
@@ -312,7 +310,7 @@ protected Object getValue(Map<String, Object> row, DomainProperty property)
     @Override
     public void addSampleColumns(InsertView view, User user, final AssayRunUploadForm<?> defaultValueContext, final boolean errorReshow)
     {
-        final File reshowFile;
+        final FileLike reshowFile;
         if (errorReshow)
             reshowFile = getMetadataFile();
         else if (defaultValueContext instanceof PlateUploadForm &&
diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateUtils.java b/assay/api-src/org/labkey/api/assay/plate/PlateUtils.java
index 31f306194db..40c0c8ab60a 100644
--- a/assay/api-src/org/labkey/api/assay/plate/PlateUtils.java
+++ b/assay/api-src/org/labkey/api/assay/plate/PlateUtils.java
@@ -23,6 +23,7 @@
 import org.labkey.api.collections.RowMap;
 import org.labkey.api.collections.RowMapFactory;
 import org.labkey.api.query.ValidationException;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -71,7 +72,7 @@ public double[][] getData()
      * Search for a grid of numbers that has the expected number of rows and columns.
      * TODO: Find multiple plates in "RC121306.xls" while ignoring duplicate plate found in "20131218_0004.txt"
      */
-    public static List<GridInfo> parseAllGrids(File dataFile, List<Map<String, Object>> rows, int expectedRows, int expectedCols, PlateReader reader)
+    public static List<GridInfo> parseAllGrids(FileLike dataFile, List<Map<String, Object>> rows, int expectedRows, int expectedCols, PlateReader reader)
     {
         return _parseGrids(dataFile, rows, expectedRows, expectedCols, true, reader);
     }
@@ -80,8 +81,8 @@ public static List<GridInfo> parseAllGrids(File dataFile, List<Map<String, Objec
      * Search for a grid of numbers that has the expected number of rows and columns.
      * TODO: Find multiple plates in "RC121306.xls" while ignoring duplicate plate found in "20131218_0004.txt"
      */
-    @Nullable
-    public static double[][] parseGrid(File dataFile, List<Map<String, Object>> rows, int expectedRows, int expectedCols, @Nullable PlateReader reader)
+
+    public static double @Nullable[][] parseGrid(FileLike dataFile, List<Map<String, Object>> rows, int expectedRows, int expectedCols, @Nullable PlateReader reader)
     {
         List<GridInfo> grids = _parseGrids(dataFile, rows, expectedRows, expectedCols, false, reader);
         if (!grids.isEmpty())
@@ -97,7 +98,7 @@ public static double[][] parseGrid(File dataFile, List<Map<String, Object>> rows
      * TODO: Find multiple plates in "RC121306.xls" while ignoring duplicate plate found in "20131218_0004.txt"
      */
     private static List<GridInfo> _parseGrids(
-            File dataFile,
+            FileLike dataFile,
             List<Map<String, Object>> rows,
             int expectedRows,
             int expectedCols,
diff --git a/assay/api-src/org/labkey/api/assay/plate/TextPlateReader.java b/assay/api-src/org/labkey/api/assay/plate/TextPlateReader.java
index 1e763de3a8e..9257c5b348e 100644
--- a/assay/api-src/org/labkey/api/assay/plate/TextPlateReader.java
+++ b/assay/api-src/org/labkey/api/assay/plate/TextPlateReader.java
@@ -20,8 +20,8 @@
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.reader.Readers;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.io.LineNumberReader;
 import java.util.ArrayList;
@@ -44,13 +44,13 @@ public String getType()
     }
 
     @Override
-    public double[][] loadFile(Plate template, File dataFile) throws ExperimentException
+    public double[][] loadFile(Plate template, FileLike dataFile) throws ExperimentException
     {
         String fileName = dataFile.getName().toLowerCase();
         if (!fileName.endsWith(".txt"))
             throw new ExperimentException("Unable to load data file: Invalid Format");
 
-        try (LineNumberReader reader = new LineNumberReader(Readers.getReader(dataFile)))
+        try (LineNumberReader reader = new LineNumberReader(Readers.getReader(dataFile.openInputStream())))
         {
             List<String> data = new ArrayList<>();
             String line;
diff --git a/assay/src/org/labkey/assay/FileBasedModuleDataHandler.java b/assay/src/org/labkey/assay/FileBasedModuleDataHandler.java
index 203e170897e..ac5e462e9df 100644
--- a/assay/src/org/labkey/assay/FileBasedModuleDataHandler.java
+++ b/assay/src/org/labkey/assay/FileBasedModuleDataHandler.java
@@ -30,8 +30,7 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
-
-import java.io.File;
+import org.labkey.vfs.FileLike;
 
 /**
  * User: jeckels
@@ -68,7 +67,7 @@ public ActionURL getContentURL(ExpData data)
     }
 
     @Override
-    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context)
+    public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context)
     {
     }
 }
diff --git a/assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java b/assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java
index 66f37dc79ca..7a988d5fe0f 100644
--- a/assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java
+++ b/assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java
@@ -757,7 +757,7 @@ private List<Map<String, Object>> parsePlateGrids(
             if (!plateTypeGrids.containsKey(plate.getPlateType()))
             {
                 Plate p = PlateService.get().createPlate(container, TsvPlateLayoutHandler.TYPE, plate.getPlateType());
-                for (PlateUtils.GridInfo gridInfo : plateReader.loadMultiGridFile(p, dataFile.toNioPathForRead().toFile()))
+                for (PlateUtils.GridInfo gridInfo : plateReader.loadMultiGridFile(p, dataFile))
                 {
                     PlateGridInfo plateInfo = new PlateGridInfo(gridInfo, plateSet, measureAliases);
                     plateTypeGrids.put(plate.getPlateType(), plateInfo);
diff --git a/core/src/org/labkey/core/reader/DataLoaderServiceImpl.java b/core/src/org/labkey/core/reader/DataLoaderServiceImpl.java
index e5bf646b7b0..951a98f0b16 100644
--- a/core/src/org/labkey/core/reader/DataLoaderServiceImpl.java
+++ b/core/src/org/labkey/core/reader/DataLoaderServiceImpl.java
@@ -32,12 +32,12 @@
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.webdav.WebdavResource;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.springframework.web.multipart.MultipartFile;
 
 import java.io.BufferedInputStream;
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
@@ -80,8 +80,6 @@ public List<DataLoaderFactory> getFactories()
     public void registerFactory(@NotNull DataLoaderFactory factory)
     {
         FileType fileType = factory.getFileType();
-        if (fileType == null)
-            throw new IllegalArgumentException("FileType must not be null");
 
         for (String s : fileType.getSuffixes())
         {
@@ -92,32 +90,21 @@ public void registerFactory(@NotNull DataLoaderFactory factory)
         _factories.add(factory);
     }
 
-    private static byte[] getHeader(File f, InputStream in)
+    private static byte[] getHeader(@NotNull InputStream in)
     {
         // Can't read header if underlying stream can't be buffered
-        if (in != null && !in.markSupported())
+        if (!in.markSupported())
             return null;
 
-        InputStream is = in;
-
         try
         {
-            if (null == is)
-                is = new BufferedInputStream(new FileInputStream(f));
-
-            is.skip(Long.MIN_VALUE);
-            return FileUtil.readHeader(is, 8*1024);
+            return FileUtil.readHeader(in, 8*1024);
         }
         catch (IOException e)
         {
             throw new RuntimeException("Failed to read file header");
         }
-        finally
-        {
-            // Don't close original InputStream
-            if (is != in)
-                IOUtils.closeQuietly(is);
-        }
+        // Don't close original InputStream
     }
 
     private Collection<DataLoaderFactory> matches(String filename, String contentType, byte[] header, Collection<DataLoaderFactory> factories)
@@ -133,21 +120,21 @@ private Collection<DataLoaderFactory> matches(String filename, String contentTyp
     }
 
     @Override
-    public DataLoaderFactory findFactory(File file, FileType guessFormat)
+    public DataLoaderFactory findFactory(FileLike file, FileType guessFormat)
     {
         return findFactory(file, null, guessFormat);
     }
 
     @Override
-    public DataLoaderFactory findFactory(File file, String contentType, FileType guessFormat)
+    public DataLoaderFactory findFactory(FileLike file, String contentType, FileType guessFormat)
     {
         InputStream is = null;
         try
         {
-            is = new BufferedInputStream(new FileInputStream(file));
+            is = new BufferedInputStream(file.openInputStream());
             return findFactory(file.getName(), contentType, is, guessFormat);
         }
-        catch (FileNotFoundException e)
+        catch (IOException e)
         {
             throw new RuntimeException(e);
         }
@@ -170,7 +157,7 @@ public DataLoaderFactory findFactory(String filename, @Nullable String contentTy
             assert factory != null : "No DataLoaderFactory registered for FileType: " + guessFormat;
             if (factory != null)
             {
-                header = getHeader(null, is);
+                header = getHeader(is);
                 if (guessFormat.isType(filename, contentType, header))
                     return factory;
             }
@@ -193,7 +180,7 @@ public DataLoaderFactory findFactory(String filename, @Nullable String contentTy
                 else
                 {
                     if (header == null)
-                        header = getHeader(null, is);
+                        header = getHeader(is);
                     matches.addAll(matches(filename, contentType, header, factories));
                 }
             }
@@ -212,7 +199,7 @@ public DataLoaderFactory findFactory(String filename, @Nullable String contentTy
         // No file extension or all FileType for that extension didn't match.
         // Fallback to checking all factories for a match based on the file header.
         if (header == null)
-            header = getHeader(null, is);
+            header = getHeader(is);
 
         matches.addAll(matches(null, contentType, header, _factories));
 
@@ -278,15 +265,10 @@ else if (r instanceof WebdavResource)
         return createLoader(filename, null, r.getInputStream(), hasColumnHeaders, mvIndicatorContainer, guessFormat);
     }
 
-    public DataLoader createLoader(File file, boolean hasColumnHeaders) throws IOException
-    {
-        return createLoader(file, null, hasColumnHeaders, null, null);
-    }
-
     @Override
     public DataLoader createLoader(File file, @Nullable String contentType, boolean hasColumnHeaders, Container mvIndicatorContainer, @Nullable FileType guessFormat) throws IOException
     {
-        DataLoaderFactory factory = findFactory(file, contentType, guessFormat);
+        DataLoaderFactory factory = findFactory(FileSystemLike.wrapFile(file), contentType, guessFormat);
 
         // If no factory matched, attempt to use the guessFormat as the default
         if (factory == null && guessFormat != null)
diff --git a/experiment/src/org/labkey/experiment/URLRewriter.java b/experiment/src/org/labkey/experiment/URLRewriter.java
index cfd86092b3f..1ff9b124337 100644
--- a/experiment/src/org/labkey/experiment/URLRewriter.java
+++ b/experiment/src/org/labkey/experiment/URLRewriter.java
@@ -16,6 +16,7 @@
 
 package org.labkey.experiment;
 
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.exp.ExperimentDataHandler;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.ExpData;
@@ -23,8 +24,9 @@
 import org.labkey.api.security.User;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.NetworkDrive;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.nio.file.Files;
@@ -65,18 +67,18 @@ public boolean isIncludeXarXml()
         return _includeXarXml;
     }
 
-    protected static class FileInfo
+    public static class FileInfo
     {
-        private final Path _path;
+        private final FileLike _path;
         private final String _name;
         private final ExperimentDataHandler _handler;
         private final ExpData _data;
         private final User _user;
         private final String _fileRootPath;
 
-        public FileInfo(ExpData data, Path path, String name, ExperimentDataHandler handler, User user, String fileRootPath)
+        protected FileInfo(ExpData data, Path path, String name, ExperimentDataHandler handler, User user, String fileRootPath)
         {
-            _path = path;
+            _path = FileSystemLike.wrapFile(path);
             _name = name;
             _handler = handler;
             _data = data;
@@ -93,7 +95,7 @@ public void writeFile(final OutputStream out) throws ExperimentException, IOExce
         {
             if (_handler != null)
             {
-                _handler.exportFile(_data, _path, _fileRootPath, _user, new OutputStream()
+                _handler.exportFile(_data, _path, _user, new OutputStream()
                 {
                     private boolean _closed = false;
 
@@ -106,14 +108,14 @@ private void checkClosed()
                     }
                     
                     @Override
-                    public void write(byte b[]) throws IOException
+                    public void write(byte @NotNull [] b) throws IOException
                     {
                         checkClosed();
                         out.write(b);
                     }
 
                     @Override
-                    public void write(byte b[], int off, int len) throws IOException
+                    public void write(byte @NotNull [] b, int off, int len) throws IOException
                     {
                         checkClosed();
                         out.write(b, off, len);
@@ -135,7 +137,7 @@ public void close()
             }
             else
             {
-                Files.copy(_path, out);
+                Files.copy(_path.toNioPathForRead(), out);
             }
         }
 
@@ -149,10 +151,10 @@ public boolean hasContentToExport()
             {
                 if (!FileUtil.hasCloudScheme(_path))
                 {
-                    File file = _path.toFile();
-                    return NetworkDrive.exists(file) && file.isFile();
+                    return NetworkDrive.exists(_path) && _path.isFile();
                 }
-                return Files.exists(_path) && !Files.isDirectory(_path);
+                Path path = _path.toNioPathForRead();
+                return Files.exists(path) && !Files.isDirectory(path);
             }
         }
     }
diff --git a/experiment/src/org/labkey/experiment/api/ExpDataImpl.java b/experiment/src/org/labkey/experiment/api/ExpDataImpl.java
index 9c3e297dee1..79de048c200 100644
--- a/experiment/src/org/labkey/experiment/api/ExpDataImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExpDataImpl.java
@@ -79,6 +79,7 @@
 import org.labkey.api.webdav.WebdavResource;
 import org.labkey.experiment.controllers.exp.ExperimentController;
 import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 import java.net.URI;
@@ -476,7 +477,7 @@ public void importDataFile(PipelineJob job, XarSource xarSource) throws Experime
         ExperimentDataHandler handler = findDataHandler();
         try
         {
-            handler.importFile(this, path, job.getInfo(), job.getLogger(), xarSource.getXarContext());
+            handler.importFile(this, FileSystemLike.wrapFile(path), job.getInfo(), job.getLogger(), xarSource.getXarContext());
         }
         catch (ExperimentException e)
         {
diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
index 5b3d5437d4d..002ca2fa01d 100644
--- a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
@@ -6900,7 +6900,7 @@ else if (existingProtApp.getProtocol().equals(outputProtocol) && existingProtApp
         {
             for (ExpData insertedData : insertedDatas)
             {
-                insertedData.findDataHandler().importFile(getExpData(insertedData.getRowId()), insertedData.getFile(), info, log, context);
+                insertedData.findDataHandler().importFile(getExpData(insertedData.getRowId()), insertedData.getFileLike(), info, log, context);
             }
         }
 
diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
index 49d87a94d84..812156e6a9e 100644
--- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
+++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
@@ -298,6 +298,7 @@
 import org.labkey.experiment.types.TypesController;
 import org.labkey.experiment.xar.XarExportSelection;
 import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.springframework.beans.PropertyValue;
 import org.springframework.beans.PropertyValues;
 import org.springframework.validation.BindException;
@@ -2548,7 +2549,7 @@ protected ModelAndView getDataView(DataForm form, BindException errors) throws I
                 if ("jsonTSV".equalsIgnoreCase(form.getFormat()) || extended || ignoreTypes)
                 {
                     if (!FileUtil.hasCloudScheme(realContent))                      // TODO: handle streaming from S3 to JSON
-                        streamToJSON(realContent.toFile(), form.getFormat(), -1, null);
+                        streamToJSON(FileSystemLike.wrapFile(realContent), form.getFormat(), -1, null);
                     return null;
                 }
 
@@ -2617,11 +2618,11 @@ public Object execute(ParseForm form, BindException errors) throws Exception
                 return true;
             }
 
-            File tempFile = null;
+            FileLike tempFile = null;
             try
             {
-                tempFile = FileUtil.createTempFile("parse", formFile.getOriginalFilename());
-                FileUtil.copyData(formFile.getInputStream(), tempFile);
+                tempFile = FileUtil.createTempFileLike("parse", formFile.getOriginalFilename());
+                FileUtil.copyData(formFile.getInputStream(), tempFile.openOutputStream());
                 streamToJSON(tempFile, form.getFormat(), form.getMaxRows(), formFile.getOriginalFilename());
             }
             finally
@@ -2635,7 +2636,7 @@ public Object execute(ParseForm form, BindException errors) throws Exception
 
 
     // SampleTypeTest
-    private void streamToJSON(File realContent, String format, int maxRow, String originalFileName) throws IOException
+    private void streamToJSON(FileLike realContent, String format, int maxRow, String originalFileName) throws IOException
     {
         String lowerCaseFileName = realContent.getName().toLowerCase();
         boolean extended = "jsonTSVExtended".equalsIgnoreCase(format);
@@ -2644,13 +2645,9 @@ private void streamToJSON(File realContent, String format, int maxRow, String or
         JSONArray sheetsArray;
         if (lowerCaseFileName.endsWith(".xls") || lowerCaseFileName.endsWith(".xlsx"))
         {
-            try
-            {
-                sheetsArray = ExcelFactory.convertExcelToJSON(realContent, extended, maxRow);
-            }
-            catch (InvalidFormatException e)
+            try (InputStream in = realContent.openInputStream())
             {
-                throw new NotFoundException("Could not open " + realContent.getName(), e);
+                sheetsArray = ExcelFactory.convertExcelToJSON(in, extended, maxRow);
             }
         }
         else
@@ -2661,7 +2658,8 @@ private void streamToJSON(File realContent, String format, int maxRow, String or
                 throw new ApiUsageException("Unable to parse file " + realContent + ", it is likely of an unsupported file type");
             }
 
-            try (DataLoader tabLoader = dlf.createLoader(realContent, true))
+            try (InputStream in = realContent.openInputStream();
+                DataLoader tabLoader = dlf.createLoader(in, true))
             {
                 tabLoader.setScanAheadLineCount(5000);
                 ColumnDescriptor[] cols = tabLoader.getColumns();
diff --git a/experiment/src/org/labkey/experiment/controllers/property/PropertyController.java b/experiment/src/org/labkey/experiment/controllers/property/PropertyController.java
index a97927de333..9638e420b46 100644
--- a/experiment/src/org/labkey/experiment/controllers/property/PropertyController.java
+++ b/experiment/src/org/labkey/experiment/controllers/property/PropertyController.java
@@ -112,6 +112,8 @@
 import org.labkey.api.view.UnauthorizedException;
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.experiment.api.VocabularyDomainKind;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.multipart.MultipartFile;
@@ -1457,12 +1459,13 @@ private String getDataFromFile(Writer writer) throws IOException
             String suffix = filename.substring(dotIndex).toLowerCase();
             String prefix = filename.substring(0, dotIndex);
 
-            File tempFile = FileUtil.createTempFile(prefix, suffix);
-            tempFile.deleteOnExit();
+            File rawTempFile = FileUtil.createTempFile(prefix, suffix);
+            rawTempFile.deleteOnExit();
+            FileLike tempFile = FileSystemLike.wrapFile(rawTempFile);
 
             try
             {
-                try (InputStream input = file.getInputStream(); OutputStream output = new FileOutputStream(tempFile))
+                try (InputStream input = file.getInputStream(); OutputStream output = tempFile.openOutputStream())
                 {
                     byte[] buffer = new byte[1024];
                     int len;
@@ -1530,13 +1533,13 @@ private String getStringValue(Object o)
             return o.toString();
         }
 
-        private DataLoader getDataLoader(File tempFile) throws IOException
+        private DataLoader getDataLoader(FileLike tempFile) throws IOException
         {
             DataLoaderFactory factory = DataLoader.get().findFactory(tempFile, null);
             if (factory == null)
                 return null;
 
-            return factory.createLoader(tempFile, true);
+            return factory.createLoader(tempFile.openInputStream(), true);
         }
     }
 
diff --git a/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java b/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java
index 45bac58115a..51af9631832 100644
--- a/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java
+++ b/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java
@@ -509,24 +509,15 @@ public Path deleteImportDirectory(@Nullable Logger logger) throws DirectoryNotDe
     }
 
     @Override
-    public String relativePath(File file)
+    public String relativePath(FileLike file)
     {
-        File root = findRootPath(file);
-        if (root == null)
-        {
-            return null;
-        }
-        String strRoot = root.toString();
+        return relativePath(file.toNioPathForRead());
+    }
 
-        String strFile = file.toString();
-        if (!strFile.toLowerCase().startsWith(strRoot.toLowerCase()))
-            return null;
-        String ret = strFile.substring(strRoot.length());
-        if (ret.startsWith(File.separator))
-        {
-            return ret.substring(1);
-        }
-        return ret;
+    @Override
+    public String relativePath(File file)
+    {
+        return relativePath(file.toPath());
     }
 
     @Override

From 588c9891544de293b7ef1c89a7e3787c80e02d8f Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Sun, 12 Oct 2025 08:13:31 -0700
Subject: [PATCH 15/15] Improve error message to troubleshoot failure

---
 api/src/org/labkey/api/util/JunitUtil.java | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/api/src/org/labkey/api/util/JunitUtil.java b/api/src/org/labkey/api/util/JunitUtil.java
index 7ec4478f7da..492c1156d9d 100644
--- a/api/src/org/labkey/api/util/JunitUtil.java
+++ b/api/src/org/labkey/api/util/JunitUtil.java
@@ -233,6 +233,11 @@ public static void createRaces(final Runnable runnable, final int threads, final
                     }
 
                     sampleDataDir = _sampleDataDirectories.get(name);
+
+                    if (sampleDataDir == null)
+                    {
+                        Assert.fail("Sample data directory not found for module: " + name + ". Known directories: " + _sampleDataDirectories);
+                    }
                 }
             }
         }