Continue adopting FileLike instead of File or Path

api/src/org/labkey/api/assay/AbstractAssayProvider.java

@@ -673,7 +673,7 @@ else if (inputDatas.size() > 1)
                 {
                     Map.Entry<String, FileLike> entry = iter.next();
                     // If it's not under the current pipeline root
-                    if (pipeRoot == null || !pipeRoot.isUnderRoot(entry.getValue().toNioPathForRead()))
+                    if (pipeRoot == null || !pipeRoot.isUnderRoot(entry.getValue()))
                     {
                         // Remove it from both collections
                         iter.remove();
@@ -1267,7 +1267,7 @@ public Pair<ValidationException, Pair<String, String>> setValidationAndAnalysisS
 
         for (AnalysisScript script : scripts)
         {
-            File scriptFile = script.getScript().toNioPathForRead().toFile();
+            FileLike scriptFile = script.getScript();
             String ext = FileUtil.getExtension(scriptFile);
             if (scriptFile.isFile() && ext != null)
             {
@@ -1280,7 +1280,7 @@ public Pair<ValidationException, Pair<String, String>> setValidationAndAnalysisS
                         String scriptText;
                         try
                         {
-                            scriptText = Files.readString(scriptFile.toPath(), StringUtilsLabKey.DEFAULT_CHARSET);
+                            scriptText = Files.readString(scriptFile.toNioPathForRead(), StringUtilsLabKey.DEFAULT_CHARSET);
                         }
                         catch (IOException e)
                         {

api/src/org/labkey/api/assay/DefaultAssayRunCreator.java

@@ -229,7 +229,7 @@ private ExpExperiment saveExperimentRunAsync(AssayRunUploadContext<ProviderType>
                 batch,
                 forceSaveBatchProps,
                 PipelineService.get().getPipelineRootSetting(context.getContainer()),
-                primaryFile.toNioPathForRead().toFile()
+                primaryFile
             );
 
             context.setPipelineJobGUID(pipelineJob.getJobGUID());

api/src/org/labkey/api/assay/pipeline/AssayUploadPipelineJob.java

@@ -37,8 +37,8 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -51,7 +51,7 @@ public class AssayUploadPipelineJob<ProviderType extends AssayProvider> extends
     private long _batchId;
     private AssayRunAsyncContext<ProviderType> _context;
 
-    private File _primaryFile;
+    private FileLike _primaryFile;
     private boolean _forceSaveBatchProps;
     private ExpRun _run;
 
@@ -62,7 +62,7 @@ protected AssayUploadPipelineJob()
     /**
      * @param forceSaveBatchProps whether we need to save the batch properties, or if it's already been handled
      */
-    public AssayUploadPipelineJob(AssayRunAsyncContext<ProviderType> context, ViewBackgroundInfo info, @NotNull ExpExperiment batch, boolean forceSaveBatchProps, PipeRoot root, File primaryFile)
+    public AssayUploadPipelineJob(AssayRunAsyncContext<ProviderType> context, ViewBackgroundInfo info, @NotNull ExpExperiment batch, boolean forceSaveBatchProps, PipeRoot root, FileLike primaryFile)
     {
         super(context.getProvider().getName(), info, root);
         String baseName = primaryFile.getName();
@@ -138,7 +138,7 @@ public void doWork()
             }
 
             // Create the basic run
-            _run = AssayService.get().createExperimentRun(_context.getName(), getContainer(), _context.getProtocol(), _primaryFile);
+            _run = AssayService.get().createExperimentRun(_context.getName(), getContainer(), _context.getProtocol(), _primaryFile.toNioPathForRead().toFile());
             _run.setComments(_context.getComments());
             _run.setWorkflowTaskId(_context.getWorkflowTask());
             // remember which job created the run so we can show this run on the job details page
@@ -224,7 +224,7 @@ protected String getJobNotificationProvider()
         return _context._jobNotificationProvider;
     }
 
-    public File getPrimaryFile()
+    public FileLike getPrimaryFile()
     {
         return _primaryFile;
     }

api/src/org/labkey/api/assay/transform/DataTransformService.java

@@ -23,13 +23,11 @@
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.UnexpectedException;
 import org.labkey.vfs.FileLike;
-import org.labkey.vfs.FileSystemLike;
 
 import javax.script.Bindings;
 import javax.script.ScriptContext;
 import javax.script.ScriptEngine;
 import java.io.BufferedReader;
-import java.io.File;
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
@@ -158,13 +156,9 @@ public TransformResult transformAndValidate(
                         Object output = engine.eval(script);
 
                         FileLike rewrittenScriptFile;
-                        if (bindings.get(ExternalScriptEngine.REWRITTEN_SCRIPT_FILE) instanceof File)
+                        if (bindings.get(ExternalScriptEngine.REWRITTEN_SCRIPT_FILE) instanceof FileLike file)
                         {
-                            var rewrittenScriptFileObject = bindings.get(ExternalScriptEngine.REWRITTEN_SCRIPT_FILE);
-                            if (rewrittenScriptFileObject instanceof FileLike fo)
-                                rewrittenScriptFile = fo;
-                            else
-                                rewrittenScriptFile = FileSystemLike.wrapFile((File)rewrittenScriptFileObject);
+                                rewrittenScriptFile = file;
                         }
                         else
                         {

api/src/org/labkey/api/docker/DockerService.java

@@ -22,6 +22,7 @@
 import org.labkey.api.security.UserManager;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.HeartBeat;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.FileFilter;
@@ -484,7 +485,7 @@ public DockerContainer(
 
     boolean isUseDockerVolumes();
 
-    default void executeR(DockerImage dockerImage, File scriptFile, String localWorkingDir, String remoteWorkingDir, FileFilter inputScripts) throws IOException
+    default void executeR(DockerImage dockerImage, FileLike scriptFile, String localWorkingDir, String remoteWorkingDir, FileFilter inputScripts) throws IOException
     {
         throw new UnsupportedOperationException(NO_DOCKER);
     }

api/src/org/labkey/api/exp/api/ExpRun.java

@@ -20,6 +20,8 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.exp.Identifiable;
 import org.labkey.api.security.User;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 import java.nio.file.Path;
@@ -52,7 +54,15 @@ public interface ExpRun extends ExpObject, Identifiable
     List<? extends ExpData> getInputDatas(@Nullable String inputRole, @Nullable ExpProtocol.ApplicationType appType);
     File getFilePathRoot();
     void setFilePathRoot(File filePathRoot);
+    default void setFilePathRoot(FileLike f)
+    {
+        setFilePathRoot(FileSystemLike.toFile(f));
+    }
     Path getFilePathRootPath();
+    default FileLike getFilePathFileLike()
+    {
+        return FileSystemLike.wrapFile(getFilePathRoot());
+    };
     void setFilePathRootPath(Path filePathRoot);
     void setProtocol(ExpProtocol protocol);
     void setJobId(Long jobId);

api/src/org/labkey/api/moduleeditor/api/ModuleEditorService.java

@@ -4,6 +4,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.module.Module;
 import org.labkey.api.services.ServiceRegistry;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.Path;
 import org.labkey.api.view.ActionURL;
 
@@ -63,6 +64,6 @@ default File getFileForModuleResource(Module module, Path path)
         File resources = getUpdatableResourcesRoot(module, null);
         if (null == resources)
             return null;
-        return new File(resources, path.toString("",""));
+        return FileUtil.appendPath(resources, path);
     }
 }

api/src/org/labkey/api/pipeline/AppPipelineJobNotificationProvider.java

@@ -194,15 +194,15 @@ private String getJobSuccessMsg(PipelineJob job, @NotNull ImportType importType,
 
             return successMsg.toString();
         }
-        else if (job instanceof AssayUploadPipelineJob)
+        else if (job instanceof AssayUploadPipelineJob<?> assayJob)
         {
             String successMsg = "Successfully imported assay run";
 
             if (info != null)
             {
                 String assayName = (String) info.get("assayName");
 
-                String filename = ((AssayUploadPipelineJob<?>) job).getPrimaryFile().getName();
+                String filename = assayJob.getPrimaryFile().getName();
                 if (!filename.endsWith(".tmp"))
                 {
                     successMsg += " from " + filename;
@@ -229,10 +229,10 @@ private String getJobErrorMsg(PipelineJob job, String rawErrorMsg)
                     "\n" +
                     rawErrorMsg;// resolveErrorMessage on client
         }
-        else if (job instanceof AssayUploadPipelineJob)
+        else if (job instanceof AssayUploadPipelineJob<?> assayJob)
         {
             return "Failed to import assay run from " +
-                    ((AssayUploadPipelineJob<?>) job).getPrimaryFile().getName() +
+                    assayJob.getPrimaryFile().getName() +
                     "\n" +
                     rawErrorMsg;
         }