Continue adopting FileLike instead of File or Path

api/src/org/labkey/api/action/AbstractFileUploadAction.java

@@ -25,6 +25,7 @@
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.NavTree;
 import org.labkey.api.writer.PrintWriters;
+import org.labkey.vfs.FileLike;
 import org.springframework.beans.MutablePropertyValues;
 import org.springframework.beans.PropertyValues;
 import org.springframework.validation.BindException;
@@ -34,8 +35,6 @@
 import org.springframework.web.servlet.ModelAndView;
 
 import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -196,7 +195,7 @@ private void export(FORM form, HttpServletResponse response) throws Exception
             HttpServletRequest basicRequest = getViewContext().getRequest();
 
             // Parameter name (String) -> File on disk/original file name Pair
-            Map<String, Pair<File, String>> savedFiles = new HashMap<>();
+            Map<String, Pair<FileLike, String>> savedFiles = new HashMap<>();
 
             if (basicRequest instanceof MultipartHttpServletRequest request)
             {
@@ -212,7 +211,7 @@ private void export(FORM form, HttpServletResponse response) throws Exception
                     {
                         if (!file.isEmpty())
                         {
-                            File f = handleFile(filename, input, writer);
+                            FileLike f = handleFile(filename, input, writer);
                             if (f == null)
                             {
                                 return;
@@ -229,7 +228,7 @@ private void export(FORM form, HttpServletResponse response) throws Exception
                 String content = form.getFileContent()[i];
                 if (content != null)
                 {
-                    File f = handleFile(filename, new ByteArrayInputStream(content.getBytes(StandardCharsets.UTF_8)), writer);
+                    FileLike f = handleFile(filename, new ByteArrayInputStream(content.getBytes(StandardCharsets.UTF_8)), writer);
                     if (f != null)
                     {
                         savedFiles.put("FileContent" + (i == 0 ? "" : (i + 1)), new Pair<>(f, filename));
@@ -249,7 +248,7 @@ private void export(FORM form, HttpServletResponse response) throws Exception
         }
     }
 
-    protected File handleFile(String filename, InputStream input, Writer writer) throws IOException
+    protected FileLike handleFile(String filename, InputStream input, Writer writer) throws IOException
     {
         if (filename == null || input == null)
         {
@@ -261,9 +260,9 @@ protected File handleFile(String filename, InputStream input, Writer writer) thr
         String legalName = FileUtil.makeLegalName(filename);
         try
         {
-            File targetFile = getTargetFile(legalName);
+            FileLike targetFile = getTargetFile(legalName);
 
-            try (OutputStream output = new FileOutputStream(targetFile))
+            try (OutputStream output = targetFile.openOutputStream())
             {
                 byte[] buffer = new byte[1024];
                 int len;
@@ -305,15 +304,17 @@ public int getStatusCode()
         }
     }
 
-    /** Figures out where to write the uploaded file */
-    protected abstract File getTargetFile(String filename) throws IOException;
+    /**
+     * Figures out where to write the uploaded file
+     */
+    protected abstract FileLike getTargetFile(String filename) throws IOException;
 
     /**
      * Callback once the file has been written to the server's file system.
      * @param files HTTP parameter name -> [File as saved on disk (potentially renamed to be unique, Original file name in POST]
      * @return a meaningful handle that the client can use to refer to the file
      */
-    public abstract String getResponse(FORM form, Map<String, Pair<File, String>> files) throws UploadException;
+    public abstract String getResponse(FORM form, Map<String, Pair<FileLike, String>> files) throws IOException;
 
     private void error(Writer writer, String message, int statusCode) throws IOException
     {

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

@@ -18,6 +18,7 @@
 
 import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.collections4.MapUtils;
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -125,7 +126,6 @@
 import java.io.IOException;
 import java.net.URI;
 import java.net.URL;
-import java.nio.file.Files;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -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();
@@ -798,11 +798,7 @@ public Set<Container> getAssociatedStudyContainers(ExpProtocol protocol, Collect
                 {
                     // Ignore Results domain TargetStudy for now.
                     // The participant resolver will find the TargetStudy on the row.
-                    ExpObject source = switch (pair.first)
-                    {
-                        case Run -> run;
-                        default -> cache.getBatch(run);
-                    };
+                    ExpObject source = pair.first == ExpProtocol.AssayDomainTypes.Run ? run : cache.getBatch(run);
 
                     if (source != null)
                     {
@@ -1267,7 +1263,7 @@ 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 +1276,7 @@ public Pair<ValidationException, Pair<String, String>> setValidationAndAnalysisS
                         String scriptText;
                         try
                         {
-                            scriptText = Files.readString(scriptFile.toPath(), StringUtilsLabKey.DEFAULT_CHARSET);
+                            scriptText = IOUtils.toString(scriptFile.openInputStream(), StringUtilsLabKey.DEFAULT_CHARSET);
                         }
                         catch (IOException e)
                         {

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

@@ -41,9 +41,9 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.api.view.WebPartView;
 import org.labkey.api.view.template.ClientDependency;
+import org.labkey.vfs.FileLike;
 import org.springframework.validation.BindException;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.List;
@@ -144,7 +144,7 @@ static void setInstance(AssayService impl)
     /**
      * Creates a run, but does not persist it to the database. Creates the run only, no protocol applications, etc.
      */
-    ExpRun createExperimentRun(@Nullable String name, Container container, ExpProtocol protocol, @Nullable File file);
+    ExpRun createExperimentRun(@Nullable String name, Container container, ExpProtocol protocol, @Nullable FileLike file);
 
     /**
      * Returns the list of valid locations an assay design can be created in.

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

@@ -169,7 +169,7 @@ public Pair<ExpExperiment, ExpRun> saveExperimentRun(
                 FileLike primaryFile = context.getUploadedData().get(AssayDataCollector.PRIMARY_FILE);
                 if (primaryFile != null)
                     auditEvent.addDetail(TransactionAuditProvider.TransactionDetail.ImportFileName, primaryFile.getName());
-                run = AssayService.get().createExperimentRun(context.getName(), context.getContainer(), protocol, null == primaryFile ? null : primaryFile.toNioPathForRead().toFile());
+                run = AssayService.get().createExperimentRun(context.getName(), context.getContainer(), protocol, primaryFile);
                 run.setComments(context.getComments());
                 run.setWorkflowTaskId(context.getWorkflowTaskId());
 
@@ -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();
@@ -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/DefaultExperimentSaveHandler.java

@@ -103,7 +103,7 @@ protected ExpRun createRun(String name, Container container, ExpProtocol protoco
         {
             throw new NotFoundException("Pipeline root is not configured for folder " + container);
         }
-        run.setFilePathRoot(pipeRoot.getRootPath());
+        run.setFilePathRoot(pipeRoot.getRootFileLike());
 
         return run;
     }

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;
         }