Merge pull request #409 from dominikl/use_gateway_download

Use Gateway method for downloading image

Author: jburel

src/main/java/org/openmicroscopy/shoola/agents/metadata/editor/EditorModel.java

@@ -3166,7 +3166,6 @@ else if (!filesetIds.contains(id)) {
             p = new DownloadArchivedActivityParam(new File(path), images, icon);
             p.setOverride(override);
             p.setZip(false);
-            p.setKeepOriginalPaths(true);
             un.notifyActivity(ctx, p);
         }
     }

src/main/java/org/openmicroscopy/shoola/agents/treeviewer/view/TreeViewerComponent.java

@@ -3709,7 +3709,6 @@ else if (!filesetIds.contains(id)) {
                     folder, archived, icon);
             p.setOverride(override);
             p.setZip(false);
-            p.setKeepOriginalPaths(true);
             un.notifyActivity(ctx, p);
 	    }
 	}

src/main/java/org/openmicroscopy/shoola/env/data/OMEROGateway.java

@@ -43,6 +43,7 @@
 import java.util.concurrent.ExecutionException;
 
 import omero.gateway.facility.RawDataFacility;
+import omero.gateway.facility.TransferFacility;
 import omero.gateway.model.FolderData;
 import omero.gateway.model.PixelsData;
 import org.apache.commons.collections4.CollectionUtils;
@@ -172,7 +173,6 @@
 import omero.model.ExperimenterGroupI;
 import omero.model.FileAnnotation;
 import omero.model.Fileset;
-import omero.model.FilesetEntry;
 import omero.model.GroupExperimenterMap;
 import omero.model.IObject;
 import omero.model.Image;
@@ -3042,177 +3042,25 @@ Set<GroupData> getAvailableGroups(SecurityContext ctx,
 	/**
 	 * Retrieves the archived files if any for the specified set of pixels.
 	 *
-	 * @param ctx The security context.
-	 * @param file The location where to save the files.
-	 * @param image The image to retrieve.
-	 * @param keepOriginalPaths Pass <code>true</code> to preserve the original folder structure
-	 * @return See above.
-	 * @throws DSOutOfServiceException If the connection is broken, or not logged in
-	 * @throws DSAccessException If an error occurred while trying to
-	 * retrieve data from OMERO service.
-	 */
-	Map<Boolean, Object> getArchivedFiles(
-			SecurityContext ctx, File file, ImageData image, boolean keepOriginalPaths)
-		throws DSAccessException, DSOutOfServiceException
-	{
-		return retrieveArchivedFiles(ctx, file, image);
-	}
-
-	/**
-	 * Retrieves the archived files if any for the specified set of pixels.
-	 *
-	 * @param ctx The security context.
-	 * @param dir The location where to save the files.
+	 * @param ctx   The security context.
+	 * @param dir   The location where to save the files.
 	 * @param image The image to retrieve.
 	 * @return See above.
 	 * @throws DSAccessException If an error occurred while trying to
-	 * retrieve data from OMERO service.
+	 *                           retrieve data from OMERO service.
 	 */
-	private Map<Boolean, Object> retrieveArchivedFiles(
+	public List<File> getArchivedFiles(
 			SecurityContext ctx, File dir, ImageData image)
-			throws DSAccessException
-	{
-		List<?> files = null;
-		String query;
+			throws DSAccessException, DSOutOfServiceException {
+		TransferFacility fc = null;
 		try {
-			IQueryPrx service = gw.getQueryService(ctx);
-			ParametersI param = new ParametersI();
-			long id;
-			if (image.isFSImage()) {
-				id = image.getId();
-				List<RType> l = new ArrayList<RType>();
-				l.add(omero.rtypes.rlong(id));
-				param.add("imageIds", omero.rtypes.rlist(l));
-				query = createFileSetQuery();
-			} else { //Prior to FS
-				if (image.isArchived()) {
-					StringBuffer buffer = new StringBuffer();
-					id = image.getDefaultPixels().getId();
-					buffer.append("select ofile from OriginalFile as ofile ");
-					buffer.append("join fetch ofile.hasher ");
-					buffer.append("left join ofile.pixelsFileMaps as pfm ");
-					buffer.append("left join pfm.child as child ");
-					buffer.append("where child.id = :id");
-					param.map.put("id", omero.rtypes.rlong(id));
-					query = buffer.toString();
-				} else return null;
-			}
-			files = service.findAllByQuery(query, param);
-		} catch (Exception e) {
-			handleConnectionException(e);
-			throw new DSAccessException("Cannot retrieve original file", e);
-		}
-
-		Map<Boolean, Object> result = new HashMap<Boolean, Object>();
-		if (CollectionUtils.isEmpty(files)) return result;
-		List<File> downloaded = new ArrayList<File>();
-		List<String> notDownloaded = new ArrayList<String>();
-		result.put(Boolean.valueOf(true), downloaded);
-		result.put(Boolean.valueOf(false), notDownloaded);
-
-		if (image.isFSImage()) {
-			for (Object tmp : files) {
-				Fileset fs = (Fileset) tmp;
-				File filesetDir = new File(dir.getAbsolutePath()+File.separator+"Fileset_"+fs.getId().getValue());
-				filesetDir.mkdir();
-				String repoPath = fs.getTemplatePrefix().getValue();
-				for (FilesetEntry fse: fs.copyUsedFiles()) {
-					OriginalFile of = fse.getOriginalFile();
-					String ofDir = of.getPath().getValue().replace(repoPath, "");
-					File outDir = new File(filesetDir.getAbsolutePath()+File.separator+ofDir);
-					outDir.mkdirs();
-					File saved = saveOriginalFile(ctx, of, outDir);
-					if (saved != null)
-						downloaded.add(saved);
-					else
-						notDownloaded.add(of.getName().getValue());
-				}
-			}
-		}
-		else { //Prior to FS
-			for (Object tmp : files) {
-				OriginalFile of = (OriginalFile) tmp;
-				File outDir = new File(dir.getAbsolutePath());
-				File saved = saveOriginalFile(ctx, of, outDir);
-				if (saved != null)
-					downloaded.add(saved);
-				else
-					notDownloaded.add(of.getName().getValue());
-			}
+			fc = gw.getFacility(TransferFacility.class);
+		} catch (ExecutionException e) {
+			throw new DSOutOfServiceException(e.getMessage());
 		}
-
-		return result;
+		return fc.downloadImage(ctx, dir.getAbsolutePath(), image.getId());
 	}
 
-	/**
-	 * Save an OriginalFile of into directory dir
-	 * @param ctx The SecurityContext
-	 * @param of The OriginalFile
-	 * @param dir The output directory
-	 * @return The File if the operation was successfull, null if it wasn't.
-	 */
-	private File saveOriginalFile(SecurityContext ctx, OriginalFile of, File dir) {
-		File out = new File(dir, of.getName().getValue());
-		if (out.exists()) {
-			log(out.getAbsolutePath()+" already exists.");
-			return null;
-		}
-
-		try {
-			RawFileStorePrx store = gw.getRawFileService(ctx);
-			store.setFileId(of.getId().getValue());
-
-			long size = of.getSize().getValue();
-			long offset = 0;
-			try (FileOutputStream stream = new FileOutputStream(out))
-			{
-				for (offset = 0; (offset+INC) < size;) {
-					stream.write(store.read(offset, INC));
-					offset += INC;
-				}
-				stream.write(store.read(offset, (int) (size-offset)));
-			}
-		} catch (Exception e) {
-			handleConnectionException(e);
-			return null;
-		}
-		return out;
-	}
-
-    /**
-     * Checks if the given path already exists and if so, generates a new path
-     * name path(N), where N is a consecutive number
-     * 
-     * @param path
-     *            The path name to check
-     * @param isFile
-     *            Pass <code>true</code> if the path name represents a file
-     * @return A unique path name based on the given path or the path itself if
-     *         it doesn't exist yet
-     */
-    private String generateUniquePathname(String path, boolean isFile) {
-        File tmp = new File(path);
-        if (tmp.exists()) {
-            String fileExt = null;
-            if (isFile && path.matches(".+\\..+")) {
-                fileExt = path.substring(path.lastIndexOf('.'), path.length());
-                path = path.substring(0, path.lastIndexOf('.'));
-            }
-            if (path.matches(".+\\(\\d+\\)")) {
-                int n = Integer.parseInt(path.substring(
-                        path.lastIndexOf('(') + 1, path.lastIndexOf(')')));
-                n++;
-                path = path.substring(0, path.lastIndexOf('(')) + "(" + n + ")";
-            } else {
-                path += "(1)";
-            }
-            if (fileExt != null)
-                path += fileExt;
-            return generateUniquePathname(path, isFile);
-        }
-        return path;
-    }
-
 	/**
 	 * Downloads a file previously uploaded to the server.
 	 *

src/main/java/org/openmicroscopy/shoola/env/data/OmeroDataService.java

@@ -25,15 +25,13 @@
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 import java.util.concurrent.ExecutionException;
 
 import omero.api.StatefulServiceInterfacePrx;
 
 import omero.gateway.model.FolderData;
 import org.openmicroscopy.shoola.env.data.model.DeletableObject;
 
-import omero.gateway.Gateway;
 import omero.gateway.SecurityContext;
 import omero.gateway.exception.DSAccessException;
 import omero.gateway.exception.DSOutOfServiceException;
@@ -282,20 +280,18 @@ public void cutAndPaste(SecurityContext ctx, Map toPaste, Map toCut)
 		throws DSOutOfServiceException, DSAccessException;
 
 	/**
-	 * Retrieves and saves locally the archived files.
-	 *
-	 * @param ctx The security context.
-	 * @param location The location where to save the files.
-	 * @param imageID The ID of the image.
-	 * @param keepOriginalPath Pass <code>true</code> to preserve the original 
-	 *         path structure
-	 * @return See above.
-	 * @throws DSOutOfServiceException If the connection is broken, or not logged in
-	 * @throws DSAccessException If an error occurred while trying to
-	 * retrieve data from OMERO service.
-	 */
-	public Map<Boolean, Object> getArchivedImage(SecurityContext ctx,
-			File location, long imageID, boolean keepOriginalPath)
+     * Retrieves and saves locally the archived files.
+     *
+     * @param ctx              The security context.
+     * @param location         The location where to save the files.
+     * @param imageID          The ID of the image.
+     * @return See above.
+     * @throws DSOutOfServiceException If the connection is broken, or not logged in
+     * @throws DSAccessException       If an error occurred while trying to
+     *                                 retrieve data from OMERO service.
+     */
+	public List<File> getArchivedImage(SecurityContext ctx,
+                                       File location, long imageID)
 		throws DSOutOfServiceException, DSAccessException;
 
 	/**

src/main/java/org/openmicroscopy/shoola/env/data/OmeroDataServiceImpl.java

@@ -31,11 +31,9 @@
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
-import java.util.concurrent.ExecutionException;
 
 import omero.cmd.Request;
 import omero.cmd.graphs.ChildOption;
-import omero.gateway.facility.DataManagerFacility;
 import omero.gateway.model.FolderData;
 import omero.model.Annotation;
 import omero.model.AnnotationAnnotationLink;
@@ -72,9 +70,6 @@
 
 import omero.gateway.util.PojoMapper;
 
-import org.openmicroscopy.shoola.env.data.util.SearchDataContext;
-
-import omero.gateway.Gateway;
 import omero.gateway.SecurityContext;
 import omero.gateway.exception.DSAccessException;
 import omero.gateway.exception.DSOutOfServiceException;
@@ -495,14 +490,14 @@ public void cutAndPaste(SecurityContext ctx, Map toPaste, Map toCut)
 	/**
 	 * Implemented as specified by {@link OmeroDataService}.
 	 */
-	public Map<Boolean, Object> getArchivedImage(SecurityContext ctx,
-			File file, long imageID, boolean keepOriginalPath)
+	public List<File> getArchivedImage(SecurityContext ctx,
+									   File file, long imageID)
 		throws DSOutOfServiceException, DSAccessException
 	{
 		context.getLogger().debug(this, file.getAbsolutePath());
 		//Check the image is archived.
 		ImageData image = gateway.getImage(ctx, imageID, null);
-		return gateway.getArchivedFiles(ctx, file, image, keepOriginalPath);
+		return gateway.getArchivedFiles(ctx, file, image);
 	}
 
 	/**

src/main/java/org/openmicroscopy/shoola/env/data/model/DownloadArchivedActivityParam.java

@@ -54,9 +54,6 @@ public class DownloadArchivedActivityParam
     /** Flag for zipping the downloaded images */
     private boolean zip = false;
 
-    /** Flag for preserving the original folder structure */
-    private boolean keepOriginalPaths = true;
-    
     /**
      * Creates a new instance.
      * 
@@ -130,24 +127,4 @@ public void setZip(boolean zip) {
         this.zip = zip;
     }
 
-    /**
-     * Returns if the original folder structure should be preserved
-     * 
-     * @return See above
-     */
-    public boolean isKeepOriginalPaths() {
-        return keepOriginalPaths;
-    }
-
-    /**
-     * Sets the keepOriginalPaths flag
-     * 
-     * @param keepOriginalPaths
-     *            Pass <code>true</code> to preserve the original folder
-     *            structure
-     */
-    public void setKeepOriginalPaths(boolean keepOriginalPaths) {
-        this.keepOriginalPaths = keepOriginalPaths;
-    }
-
 }

src/main/java/org/openmicroscopy/shoola/env/data/views/MetadataHandlerView.java

@@ -302,12 +302,11 @@ public CallHandle loadOriginalFiles(SecurityContext ctx,
 	 * @param override Flag indicating to override the existing file if it
 	 *                 exists, <code>false</code> otherwise.
 	 * @param zip Pass <code>true</code> to create a zip file
-	 * @param keepOriginalPaths Pass <code>true</code> to preserve the original folder structure
 	 * @param observer Call-back handler.
 	 * @return A handle that can be used to cancel the call.
 	 */
 	public CallHandle loadArchivedImage(SecurityContext ctx, List<DataObject> objects,
-		File location, boolean override, boolean zip, boolean keepOriginalPaths,
+		File location, boolean override, boolean zip,
 		AgentEventListener observer);
 
 	/**

src/main/java/org/openmicroscopy/shoola/env/data/views/MetadataHandlerViewImpl.java

@@ -251,10 +251,10 @@ public CallHandle loadOriginalFiles(SecurityContext ctx,
      */
     public CallHandle loadArchivedImage(SecurityContext ctx,
             List<DataObject> objects, File location,
-            boolean override, boolean zip, boolean keepOriginalPaths,
+            boolean override, boolean zip,
             AgentEventListener observer) {
         BatchCallTree cmd = new ArchivedImageLoader(ctx, objects, location,
-                override, zip, keepOriginalPaths);
+                override, zip);
         return cmd.exec(observer);
     }