More FileLike

Author: labkey-jeckels

panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java

@@ -215,6 +215,8 @@
 import org.labkey.panoramapublic.view.expannotations.TargetedMSExperimentWebPart;
 import org.labkey.panoramapublic.view.expannotations.TargetedMSExperimentsWebPart;
 import org.labkey.panoramapublic.view.publish.CatalogEntryWebPart;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -1748,15 +1750,15 @@ private boolean validateAction(CopyExperimentForm form, BindException errors)
             return true;
         }
 
-        private Path getExportFilesDir(Container c)
+        private FileLike getExportFilesDir(Container c)
         {
             FileContentService fcs = FileContentService.get();
             if(fcs != null)
             {
                 Path fileRoot = fcs.getFileRootPath(c, FileContentService.ContentType.files);
                 if (fileRoot != null)
                 {
-                    return fileRoot.resolve(PipelineService.EXPORT_DIR);
+                    return FileSystemLike.wrapFile(fileRoot.resolve(PipelineService.EXPORT_DIR));
                 }
             }
             return null;

panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java

@@ -79,6 +79,7 @@
 import org.labkey.panoramapublic.query.JournalManager;
 import org.labkey.panoramapublic.query.SubmissionManager;
 import org.labkey.panoramapublic.security.PanoramaPublicSubmitterRole;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -254,9 +255,9 @@ private void verifySymlinks(Container source, Container target, boolean matching
         }
     }
 
-    private void cleanupExportDirectory(User user, File directory)
+    private void cleanupExportDirectory(User user, FileLike directory)
     {
-        List<? extends ExpData> datas = ExperimentService.get().getExpDatasUnderPath(directory.toPath(), null, true);
+        List<? extends ExpData> datas = ExperimentService.get().getExpDatasUnderPath(directory.toNioPathForRead(), null, true);
         for (ExpData data : datas)
         {
             data.delete(user);

panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentJobSupport.java

@@ -17,9 +17,7 @@
 
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
 import org.labkey.panoramapublic.model.Journal;
-
-import java.io.File;
-import java.nio.file.Path;
+import org.labkey.vfs.FileLike;
 
 /**
  * User: vsharma
@@ -32,7 +30,7 @@ public interface CopyExperimentJobSupport
 
     Journal getJournal();
 
-    File getExportDir();
+    FileLike getExportDir();
 
     String getReviewerEmailPrefix();
 
@@ -48,5 +46,5 @@ public interface CopyExperimentJobSupport
 
     String getPreviousVersionName();
 
-    void setExportTargetPath(Path exportTargetPath);
+    void setExportTargetPath(FileLike exportTargetPath);
 }

panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java

@@ -33,10 +33,10 @@
 import org.labkey.panoramapublic.PanoramaPublicModule;
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
 import org.labkey.panoramapublic.model.Journal;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.IOException;
-import java.nio.file.Path;
 
 /**
  * User: vsharma
@@ -63,7 +63,7 @@ public class CopyExperimentPipelineJob extends PipelineJob implements CopyExperi
 
     private String _previousVersionName;
 
-    private Path _exportTargetPath;
+    private FileLike _exportTargetPath;
 
     private Container _exportSourceContainer;
 
@@ -160,9 +160,9 @@ public Journal getJournal()
     }
 
     @Override
-    public File getExportDir()
+    public FileLike getExportDir()
     {
-        return _exportTargetPath.toFile();
+        return _exportTargetPath;
     }
 
     @Override
@@ -254,7 +254,7 @@ public void setPreviousVersionName(String previousVersionName)
     }
 
     @Override
-    public void setExportTargetPath(Path exportTargetPath)
+    public void setExportTargetPath(FileLike exportTargetPath)
     {
         _exportTargetPath = exportTargetPath;
     }

panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java

@@ -16,7 +16,6 @@
 package org.labkey.panoramapublic.pipeline;
 
 import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.admin.FolderArchiveDataTypes;
 import org.labkey.api.admin.FolderExportContext;
@@ -36,8 +35,8 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.writer.FileSystemFile;
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.Collections;
 import java.util.List;
 import java.util.Set;
@@ -49,8 +48,6 @@
  */
 public class ExperimentExportTask extends PipelineJob.Task<ExperimentExportTask.Factory>
 {
-    private static final Logger _log = LogManager.getLogger(ExperimentExportTask.class);
-
     private ExperimentExportTask(Factory factory, PipelineJob job)
     {
         super(factory, job);
@@ -117,15 +114,15 @@ public void writeExperiment(CopyExperimentJobSupport support, ExperimentAnnotati
                 false, false, new StaticLoggerGetter(LogManager.getLogger(FolderWriterImpl.class)));
 
 
-        File exportDir = support.getExportDir();
+        FileLike exportDir = support.getExportDir();
         FileUtil.deleteDir(exportDir);
         if(exportDir.exists())
         {
-            throw new Exception("Could not delete already existing export directory " + exportDir.getAbsolutePath());
+            throw new Exception("Could not delete already existing export directory " + exportDir);
         }
-        if(!exportDir.mkdir())
+        if(!FileUtil.mkdir(exportDir))
         {
-            throw new Exception("Could not create directory " + exportDir.getAbsolutePath());
+            throw new Exception("Could not create directory " + exportDir);
         }
 
         FileSystemFile vf = new FileSystemFile(exportDir);
@@ -143,7 +140,7 @@ public Factory()
         }
 
         @Override
-        public PipelineJob.Task createTask(PipelineJob job)
+        public ExperimentExportTask createTask(PipelineJob job)
         {
             return new ExperimentExportTask(this, job);
         }

panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentImportTask.java

@@ -29,6 +29,7 @@
 import org.labkey.api.util.FileType;
 import org.labkey.api.writer.FileSystemFile;
 import org.labkey.api.writer.VirtualFile;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.util.Collections;
@@ -74,23 +75,23 @@ public RecordedActionSet run() throws PipelineJobException
 
     public static void doImport(PipelineJob job, CopyExperimentJobSupport jobSupport) throws Exception
     {
-        File importDir = jobSupport.getExportDir();
+        FileLike importDir = jobSupport.getExportDir();
 
         if (!importDir.exists())
         {
             throw new Exception("TargetedMS experiment import failed: Could not find directory \"" + importDir.getName() + "\"");
         }
 
-        File folderXml = new File(importDir, "folder.xml");
+        FileLike folderXml = importDir.resolveChild("folder.xml");
         if(!folderXml.exists())
         {
-            throw new Exception("This directory doesn't contain an appropriate xml: " + importDir.getAbsolutePath());
+            throw new Exception("This directory doesn't contain an appropriate xml: " + importDir);
         }
 
         User user = job.getUser();
         Container container = job.getContainer();
-        VirtualFile importJobRoot = new FileSystemFile(folderXml.getParentFile());
-        FolderImportContext importCtx = new FolderImportContext(user, container, folderXml.toPath(),
+        VirtualFile importJobRoot = new FileSystemFile(folderXml.getParent());
+        FolderImportContext importCtx = new FolderImportContext(user, container, folderXml,
                 null, new PipelineJobLoggerGetter(job),
                 importJobRoot);
         importCtx.setSkipQueryValidation(true);
@@ -110,7 +111,7 @@ public Factory()
         }
 
         @Override
-        public PipelineJob.Task createTask(PipelineJob job)
+        public ExperimentImportTask createTask(PipelineJob job)
         {
             return new ExperimentImportTask(this, job);
         }