Adopt FileLike for more pipeline APIs

api/src/org/labkey/api/admin/FolderImportContext.java

@@ -29,11 +29,10 @@
 import org.labkey.api.util.XmlValidationException;
 import org.labkey.api.writer.VirtualFile;
 import org.labkey.folder.xml.FolderDocument;
+import org.labkey.vfs.FileLike;
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
@@ -47,7 +46,7 @@
  */
 public class FolderImportContext extends AbstractFolderContext
 {
-    private Path _folderXml;
+    private FileLike _folderXml;
 
     private String _xarJobId;
 
@@ -66,7 +65,7 @@ public FolderImportContext()
         super(null, null, null, null, null, null);
     }
 
-    public FolderImportContext(User user, Container c, Path folderXml, Set<String> dataTypes, LoggerGetter logger, VirtualFile root)
+    public FolderImportContext(User user, Container c, FileLike folderXml, Set<String> dataTypes, LoggerGetter logger, VirtualFile root)
     {
         super(user, c, null, dataTypes, logger, root);
         _folderXml = folderXml;
@@ -112,17 +111,17 @@ public synchronized FolderDocument getDocument() throws ImportException
         return folderDoc;
     }
 
-    private FolderDocument readFolderDocument(Path folderXml) throws ImportException, IOException
+    private FolderDocument readFolderDocument(FileLike folderXml) throws ImportException, IOException
     {
-        if (!Files.exists(folderXml))
-            throw new ImportException(folderXml.getFileName() + " file does not exist.");
+        if (!folderXml.exists())
+            throw new ImportException(folderXml.getName() + " file does not exist.");
 
         FolderDocument folderDoc;
 
-        try (InputStream inputStream = Files.newInputStream(folderXml))
+        try (InputStream inputStream = folderXml.openInputStream())
         {
             folderDoc = FolderDocument.Factory.parse(inputStream, XmlBeansUtil.getDefaultParseOptions());
-            XmlBeansUtil.validateXmlDocument(folderDoc, folderXml.getFileName().toString());
+            XmlBeansUtil.validateXmlDocument(folderDoc, folderXml.getName());
         }
         catch (XmlException | XmlValidationException e)
         {

api/src/org/labkey/api/admin/ImportOptions.java

@@ -19,6 +19,7 @@
 import org.labkey.api.data.Activity;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
+import org.labkey.vfs.FileLike;
 
 import java.nio.file.Path;
 import java.util.Collection;
@@ -42,7 +43,7 @@ public class ImportOptions
     private final Collection<String> _messages = new LinkedList<>();
     private Set<String> _dataTypes;
     private Activity _activity;
-    private Path _analysisDir;
+    private FileLike _analysisDir;
     private String _folderArchiveSourceName = null;
 
     private boolean _isNewFolderImport; // if we know the target folder is empty, can skip certain merge logic
@@ -153,12 +154,12 @@ public void setActivity(Activity activity)
         _activity = activity;
     }
 
-    public Path getAnalysisDir()
+    public FileLike getAnalysisDir()
     {
         return _analysisDir;
     }
 
-    public void setAnalysisDir(Path analysisDir)
+    public void setAnalysisDir(FileLike analysisDir)
     {
         _analysisDir = analysisDir;
     }

api/src/org/labkey/api/admin/InvalidFileException.java

@@ -20,18 +20,19 @@
 import org.apache.xmlbeans.XmlException;
 import org.labkey.api.util.XmlValidationException;
 import org.labkey.api.writer.VirtualFile;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.nio.file.Path;
 
 public class InvalidFileException extends ImportException
 {
-    @Deprecated // prefer the Path version
-    public InvalidFileException(File root, File file, Throwable t)
+    public InvalidFileException(FileLike root, FileLike file, Throwable t)
     {
-        this(root.toPath(), file.toPath(), t);
+        this(root.toNioPathForRead(), file.toNioPathForRead(), t);
     }
 
+    @Deprecated // prefer the FileLike version
     public InvalidFileException(Path root, Path file, Throwable t)
     {
         super(getErrorString(root, file, t.getMessage()));
@@ -42,21 +43,11 @@ public InvalidFileException(VirtualFile root, File file, Throwable t)
         super(getErrorString(root.getRelativePath(file.getName()), t.getMessage()));
     }    
 
-    public InvalidFileException(File root, File file, XmlException e)
-    {
-        super(getErrorString(root, file, e));
-    }
-
     public InvalidFileException(VirtualFile root, File file, XmlException e)
     {
         super(getErrorString(root, file, e));
     }
 
-    public InvalidFileException(File root, File file, XmlValidationException e)
-    {
-        super(getErrorString(root, file, (String)null), e);
-    }
-
     public InvalidFileException(VirtualFile root, File file, XmlValidationException e)
     {
         super(getErrorString(root.getRelativePath(file.getName()), null), e);

api/src/org/labkey/api/cloud/CloudArchiveImporterSupport.java

@@ -26,7 +26,7 @@ public interface CloudArchiveImporterSupport
     default void downloadCloudArchive(@NotNull PipelineJob job, @NotNull Path studyXml, BindException errors) throws UnsupportedOperationException
     {
         //check if cloud based pipeline root, and study xml hasn't been downloaded already
-        if (!studyXml.startsWith(job.getPipeRoot().getImportDirectory().toPath().toAbsolutePath()))
+        if (!studyXml.startsWith(job.getPipeRoot().getImportDirectory().toNioPathForRead().toAbsolutePath()))
         {
             if (CloudStoreService.get() != null)   //proxy of is Cloud Module enabled for the current job/container
             {

api/src/org/labkey/api/cloud/CloudStoreService.java

@@ -23,6 +23,7 @@
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.Pair;
 import org.labkey.api.webdav.WebdavResource;
+import org.labkey.vfs.FileLike;
 
 import java.nio.file.Path;
 import java.util.Collection;
@@ -141,6 +142,12 @@ default Collection<String> getEnabledCloudStores(Container container, boolean ex
     @Nullable
     Path getPath(Container container, String storeName, org.labkey.api.util.Path path);
 
+    /**
+     * Return nio.Path to cloud file/directory
+     */
+    @Nullable
+    FileLike getFileLike(Container container, String storeName, org.labkey.api.util.Path path);
+
     /**
      * Return path relative to cloud store
      */

api/src/org/labkey/api/data/TSVGridWriter.java

@@ -22,10 +22,9 @@
 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 org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -198,7 +197,7 @@ private int writeBody(Results results)
      * @return List of the output Files.
      */
     @NotNull
-    public List<File> writeBatchFiles(@NotNull File outputDir, @NotNull String baseName, @Nullable String extension, int batchSize, @Nullable FieldKey batchColumn)
+    public List<FileLike> writeBatchFiles(@NotNull FileLike outputDir, @NotNull String baseName, @Nullable String extension, int batchSize, @Nullable FieldKey batchColumn)
     {
         extension = StringUtils.trimToEmpty(extension);
         String ext = "".equals(extension) || extension.startsWith(".") ? extension : "." + extension;
@@ -211,13 +210,13 @@ public List<File> writeBatchFiles(@NotNull File outputDir, @NotNull String baseN
     }
 
     @NotNull
-    private List<File> writeResultSetBatches(Results results, File outputDir, String baseName, String extension, int batchSize, @Nullable FieldKey batchColumn) throws IOException
+    private List<FileLike> writeResultSetBatches(Results results, FileLike outputDir, String baseName, String extension, int batchSize, @Nullable FieldKey batchColumn) throws IOException
     {
         int currentBatchSize = 0;
         int totalBatches = 1;
         Object previousBatchColumnValue = null;
         Object newBatchColumnValue;
-        List<File> outputFiles = new ArrayList<>();
+        List<FileLike> outputFiles = new ArrayList<>();
         outputFiles.add(startBatchFile(outputDir, baseName, extension, batchSize, totalBatches));
         RenderContext ctx = getRenderContext();
         ctx.setResults(results);
@@ -264,11 +263,11 @@ private List<File> writeResultSetBatches(Results results, File outputDir, String
     }
 
     @NotNull
-    private File startBatchFile(File outputDir, String baseName, String extension, int batchSize, int totalBatches) throws IOException
+    private FileLike startBatchFile(FileLike outputDir, String baseName, String extension, int batchSize, int totalBatches) throws IOException
     {
         String batchId = batchSize == 0 ? "" : "-" + totalBatches;
-        File file = FileUtil.appendName(outputDir, baseName + batchId + extension);
-        prepare(file);
+        FileLike file = outputDir.resolveChild(baseName + batchId + extension);
+        prepare(file.openOutputStream());
         writeFileHeader();
         if (isHeaderRowVisible())
             writeColumnHeaders();

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

@@ -27,6 +27,7 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.NetworkDrive;
 import org.labkey.api.util.XmlBeansUtil;
+import org.labkey.vfs.FileLike;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -42,9 +43,9 @@
  */
 public abstract class AbstractFileXarSource extends XarSource
 {
-    protected Path _xmlFile;
+    protected FileLike _xmlFile;
 
-    protected Path getXmlFile()
+    protected FileLike getXmlFile()
     {
         return _xmlFile;
     }
@@ -77,7 +78,7 @@ public ExperimentArchiveDocument getDocument() throws XmlException, IOException
         try
         {
             NetworkDrive.exists(getXmlFile());
-            fIn = Files.newInputStream(getXmlFile());
+            fIn = getXmlFile().openInputStream();
             return ExperimentArchiveDocument.Factory.parse(fIn, XmlBeansUtil.getDefaultParseOptions());
         }
         finally
@@ -88,9 +89,7 @@ public ExperimentArchiveDocument getDocument() throws XmlException, IOException
                 {
                     fIn.close();
                 }
-                catch (IOException e)
-                {
-                }
+                catch (IOException ignored) {}
             }
         }
     }
@@ -99,7 +98,7 @@ public ExperimentArchiveDocument getDocument() throws XmlException, IOException
     @Nullable
     public Path getRootPath()
     {
-        return null != getXmlFile()? getXmlFile().getParent(): null;
+        return null != getXmlFile()? getXmlFile().toNioPathForRead().getParent(): null;
     }
 
     @Override
@@ -137,15 +136,15 @@ public String canonicalizeDataFileURL(String dataFileURL)
         }
     }
 
-    public static Path getLogFileFor(Path f) throws IOException
+    public static FileLike getLogFileFor(FileLike f) throws IOException
     {
-        Path xarDirectory = f.getParent();
-        if (!Files.exists(xarDirectory))
+        FileLike xarDirectory = f.getParent();
+        if (!xarDirectory.exists())
         {
             throw new IOException("Xar file parent directory does not exist");
         }
 
-        String xarShortName = f.getFileName().toString();
+        String xarShortName = f.getName();
         int index = xarShortName.toLowerCase().lastIndexOf(".xml");
         if (index == -1)
         {
@@ -157,6 +156,6 @@ public static Path getLogFileFor(Path f) throws IOException
             xarShortName = xarShortName.substring(0, index);
         }
 
-        return xarDirectory.resolve(xarShortName + LOG_FILE_NAME_SUFFIX);
+        return xarDirectory.resolveChild(xarShortName + LOG_FILE_NAME_SUFFIX);
     }
 }

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

@@ -19,6 +19,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.pipeline.PipelineJob;
+import org.labkey.vfs.FileLike;
 
 import java.io.IOException;
 import java.nio.file.Path;
@@ -30,25 +31,25 @@
  */
 public class FileXarSource extends AbstractFileXarSource
 {
-    public FileXarSource(Path file, PipelineJob job)
+    public FileXarSource(FileLike file, PipelineJob job)
     {
         super(job);
-        _xmlFile = file.normalize();
+        _xmlFile = file;
     }
 
-    public FileXarSource(Path file, PipelineJob job, Container targetContainer, @Nullable Map<String, String> substitutions)
+    public FileXarSource(FileLike file, PipelineJob job, Container targetContainer, @Nullable Map<String, String> substitutions)
     {
         super(job.getDescription(), targetContainer, job.getUser(), job, substitutions);
         _xmlFile = file;
     }
 
-    public FileXarSource(Path file, PipelineJob job, Container targetContainer)
+    public FileXarSource(FileLike file, PipelineJob job, Container targetContainer)
     {
         this(file, job, targetContainer, null);
     }
 
     @Override
-    public Path getLogFilePath() throws IOException
+    public FileLike getLogFilePath() throws IOException
     {
         return getLogFileFor(_xmlFile);
     }

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

@@ -29,6 +29,8 @@
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.NetworkDrive;
+import org.labkey.api.util.Path;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.net.URI;

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

@@ -32,6 +32,7 @@
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.security.User;
 import org.labkey.api.util.FileUtil;
+import org.labkey.vfs.FileLike;
 
 import java.io.IOException;
 import java.io.Serializable;
@@ -122,7 +123,7 @@ public final String getCanonicalDataFileURL(String dataFileURL) throws XarFormat
 
     protected abstract String canonicalizeDataFileURL(String dataFileURL) throws XarFormatException;
 
-    public abstract Path getLogFilePath() throws IOException;
+    public abstract FileLike getLogFilePath() throws IOException;
 
     /**
      * Called before trying to import this XAR to let the source set up any resources that are required 

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

@@ -987,7 +987,7 @@ List<? extends ExpProtocol> getExpProtocolsWithParameterValue(
      *
      * @return the job responsible for doing the work
      */
-    PipelineJob importXarAsync(ViewBackgroundInfo info, File file, String description, PipeRoot root) throws IOException;
+    PipelineJob importXarAsync(ViewBackgroundInfo info, FileLike file, String description, PipeRoot root) throws IOException;
 
     /**
      * Loads the xar synchronously, in the context of the pipelineJob

api/src/org/labkey/api/files/FileContentService.java

@@ -30,6 +30,7 @@
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.webdav.WebdavResource;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.net.URI;
@@ -340,6 +341,9 @@ enum PathType { full, serverRelative, folderRelative }
     @Nullable
     URI getWebDavUrl(@NotNull Path path, @NotNull Container container, @NotNull PathType type);
 
+    @Nullable
+    URI getWebDavUrl(@NotNull FileLike path, @NotNull Container container, @NotNull PathType type);
+
     /**
      * Ensure an entry in the exp.data table exists for all files in the container's file root.
      */