Merge pull request #305 from dominikl/connection_issues

Move gateway calls to OMEROGateway

src/main/java/org/openmicroscopy/shoola/agents/measurement/view/MeasurementViewerModel.java

@@ -1309,9 +1309,6 @@ void deleteFolders(Collection<FolderData> folders) {
 
     /**
      * Add ROIs to Folders
-     * 
-     * @param selectedObjects
-     *            The ROIs
      * @param folders
      *            The Folders
      * @param async
@@ -1337,16 +1334,7 @@ Collection<FolderData> saveROIFolders(Collection<FolderData> folders,
             try {
                 Registry reg = MetadataViewerAgent.getRegistry();
                 OmeroDataService ods = reg.getDataService();
-                Gateway gw = ods.getGateway();
-                DataManagerFacility dm = gw
-                        .getFacility(DataManagerFacility.class);
-                List<IObject> objs = new ArrayList<IObject>(folders.size());
-                for (FolderData f : folders)
-                    objs.add(f.asIObject());
-                objs = dm.saveAndReturnObject(getSecurityContext(), objs, null,
-                        null);
-                Collection<FolderData> result = PojoMapper
-                        .asCastedDataObjects(objs);
+                Collection<FolderData> result = ods.saveROIFolders(getSecurityContext(), folders);
                 Collection<Long> ids = Pojos.extractIds(this.folders);
                 for (FolderData f : result) {
                     if (!ids.contains(f.getId()))

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

@@ -144,9 +144,6 @@ public static DataServicesFactory getInstance(Container c)
 	/** The Administration service adapter. */
 	private AdminService				admin;
 
-    /** Flag indicating that we try to re-establish the connection.*/
-    private final AtomicBoolean reconnecting = new AtomicBoolean(false);
-
 	/**
 	 * Attempts to create a new instance.
      * 
@@ -262,15 +259,13 @@ public void propertyChange(PropertyChangeEvent evt) {
                 String name = evt.getPropertyName();
                 if (NotificationDialog.CLOSE_NOTIFICATION_PROPERTY.equals(name))
                 {
-                    reconnecting.set(false);
                     connectionDialog = null;
                     exitApplication(true, true);
                 } else if (
                     NotificationDialog.CANCEL_NOTIFICATION_PROPERTY.equals(
                             name))
                 {
                     connectionDialog = null;
-                    reconnecting.set(false);
                     int index = (Integer) evt.getNewValue();
                     if (index == ConnectionExceptionHandler.LOST_CONNECTION)
                         reconnect();
@@ -335,7 +330,6 @@ private void reconnect()
             connectionDialog.setVisible(false);
             connectionDialog.dispose();
             connectionDialog = null;
-            reconnecting.set(false);
         } else {
             //connectionDialog.setVisible(false);
             message = "A failure occurred while attempting to " +
@@ -368,8 +362,8 @@ int runAsPlugin()
 	 */
 	public void sessionExpiredExit(int index, Throwable exc)
 	{
-	    if (reconnecting.get()) return;
-		reconnecting.set(true);
+        if (connectionDialog != null && connectionDialog.isVisible())
+            return;
 		String message;
 		if (exc != null) {
 			LogMessage msg = new LogMessage();

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

@@ -26,9 +26,11 @@
 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;
@@ -58,12 +60,6 @@ public interface OmeroDataService
 	 */
 	public static final String IMAGES_PROPERTY = "images";
 
-	/**
-	 * Get a reference to the {@link Gateway}
-	 * @return See above
-	 */
-	public Gateway getGateway();
-
 	/**
 	 * Retrieves hierarchy trees rooted by a given node.
 	 * i.e. the requested node as root and all of its descendants.
@@ -506,5 +502,11 @@ public Map<Long, Map<Boolean, List<ImageData>>> getImagesBySplitFilesets(
 	 * @throws DSAccessException If an error occurred while trying to
 	 * retrieve data from OMERO service.
 	*/
-	public Map<Long, List<DatasetData>> findDatasetsByImageId(SecurityContext ctx, List<Long> imgIds) throws DSOutOfServiceException, DSAccessException;
+	public Map<Long, List<DatasetData>> findDatasetsByImageId(SecurityContext ctx, List<Long> imgIds)
+			throws DSOutOfServiceException, DSAccessException;
+
+	public Collection<FolderData> saveROIFolders(SecurityContext ctx, Collection<FolderData> folders)
+			throws ExecutionException, DSOutOfServiceException, DSAccessException;
+
+	public int getROICount(SecurityContext ctx, long imageId) throws DSOutOfServiceException, DSAccessException;
 }

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

@@ -31,9 +31,12 @@
 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;
 import omero.model.Dataset;
@@ -115,11 +118,6 @@ class OmeroDataServiceImpl
 	/** Reference to the entry point to access the <i>OMERO</i> services. */
 	private OMEROGateway gateway;
 
-	@Override
-	public Gateway getGateway() {
-	    return gateway.getGateway();
-	}
-
 	/**
 	 * Unlinks the collection of children from the specified parent.
 	 *
@@ -494,7 +492,6 @@ public void cutAndPaste(SecurityContext ctx, Map toPaste, Map toCut)
 
 	/**
 	 * Implemented as specified by {@link OmeroDataService}.
-	 * @see OmeroDataService#getArchivedFiles(SecurityContext, File, long, boolean)
 	 */
 	public Map<Boolean, Object> getArchivedImage(SecurityContext ctx,
 			File file, long imageID, boolean keepOriginalPath)
@@ -508,7 +505,6 @@ public Map<Boolean, Object> getArchivedImage(SecurityContext ctx,
 
 	/**
 	 * Implemented as specified by {@link OmeroDataService}.
-	 * @see OmeroDataService#updateExperimenter(SecurityContext, ExperimenterData, GroupData)
 	 */
 	public ExperimenterData updateExperimenter(SecurityContext ctx,
 			ExperimenterData exp, GroupData group)
@@ -589,7 +585,6 @@ public List getImagesAllPeriodCount(SecurityContext ctx,
 
 	/**
 	 * Implemented as specified by {@link OmeroDataService}.
-	 * @see OmeroDataService#advancedSearchFor(List, SearchDataContext)
 	 */
 	public SearchResultCollection search(SecurityContext ctx,
 	        SearchParameters context)
@@ -730,7 +725,7 @@ private void initializeImages(SearchResultCollection results) {
 
         /**
          * Tries to convert all search terms into ids;
-         * @param terms
+         * @param query terms
          * @return The ids or null if one or multiple terms contain non numeric characters
          */
         private long[] convertSearchTermsToIds(String query) {
@@ -1148,7 +1143,6 @@ public Map<Long, Map<Boolean, List<ImageData>>> getImagesBySplitFilesets(
 
 	/**
 	 * Implemented as specified by {@link OmeroDataService}.
-	 * @see OmeroDataService#findDatasetsByImageId(SecurityContext ctx, imgId)
 	 */
 	public Map<Long, List<DatasetData>> findDatasetsByImageId(SecurityContext ctx, List<Long> imgIds) throws DSOutOfServiceException, DSAccessException
 		{
@@ -1173,4 +1167,12 @@ public Map<Long, List<DatasetData>> findDatasetsByImageId(SecurityContext ctx, L
 		return result;
 	}
 
+	public Collection<FolderData> saveROIFolders(SecurityContext ctx, Collection<FolderData> folders)
+			throws DSOutOfServiceException, DSAccessException {
+		return gateway.saveROIFolders(ctx, folders);
+	}
+
+	public int getROICount(SecurityContext ctx, long imageId) throws DSOutOfServiceException, DSAccessException {
+		return gateway.getROICount(ctx, imageId);
+	}
 }

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

@@ -862,4 +862,9 @@ RndProxyDef getSettings(SecurityContext ctx, long rndID)
      */
 	RawPixelsStorePrx createPixelsStore(SecurityContext ctx)
             throws DSAccessException, DSOutOfServiceException;
+
+	public Map<Integer, int[]> getHistogram(SecurityContext ctx,
+											PixelsData pixels,
+											int[] channels, int z, int t) throws DSAccessException,
+			DSOutOfServiceException;
 }

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

@@ -214,10 +214,8 @@ private int getNumberOfRenderingEngines(SecurityContext ctx, long pixelsID)
 	 * Imports the specified candidates.
 	 *
 	 * @param ctx The security context.
-	 * @param candidates The file to import.
 	 * @param status The original status.
 	 * @param object The object hosting information about the import.
-	 * @param ioList The containers where to import the files.
 	 * @param list   The list of annotations.
 	 * @param userID The identifier of the user.
 	 * @param hcs Value returns by the import containers.
@@ -327,9 +325,9 @@ private BufferedImage createImage(byte[] values)
 	}
 
 	/**
-	 * Creates a <code>BufferedImage</code> from the passed array of bytes.
+	 * Creates a <code>BufferedImage</code> from the passed path.
 	 *
-	 * @param values    The array of bytes.
+	 * @param path    The path,
 	 * @return See above.
 	 * @throws RenderingServiceException If we cannot create an image.
 	 */
@@ -570,8 +568,7 @@ private Collection<String> getLookupTables(SecurityContext ctx) {
             return OmeroImageServiceImpl.LOOKUP_TABLES;
 
         try {
-            OmeroImageServiceImpl.LOOKUP_TABLES = gateway.getGateway()
-                    .getFacility(BrowseFacility.class).getLookupTables(ctx);
+            OmeroImageServiceImpl.LOOKUP_TABLES = gateway.getLookupTables(ctx);
             return OmeroImageServiceImpl.LOOKUP_TABLES;
         } catch (Exception e) {
             context.getLogger().warn(this, e.getMessage());
@@ -644,7 +641,6 @@ public BufferedImage getThumbnail(SecurityContext ctx,long pixID, int sizeX,
 
 	/**
 	 * Implemented as specified by {@link OmeroImageService}.
-	 * @see OmeroImageService#getThumbnailSet(SecurityContext, List, int)
 	 */
 	public Map<Long, BufferedImage> getThumbnailSet(SecurityContext ctx,
 		Collection<Long> pixelsID, int max)
@@ -839,7 +835,6 @@ public Map pasteRenderingSettings(SecurityContext ctx, long pixelsID,
 
 	/**
 	 * Implemented as specified by {@link OmeroImageService}.
-	 * @see OmeroImageService#resetRenderingSettings(Class, List)
 	 */
 	public Map resetRenderingSettings(SecurityContext ctx, Class rootNodeType,
 		List nodesID)
@@ -879,7 +874,6 @@ public Map setOwnerRenderingSettings(SecurityContext ctx,
 
 	/**
 	 * Implemented as specified by {@link OmeroImageService}.
-	 * @see OmeroImageService#getRenderingSettings(ctx, long, long)
 	 */
 	public Map<DataObject, Collection<RndProxyDef>> getRenderingSettings(
 	        SecurityContext ctx, long pixelsID, long userID)
@@ -890,7 +884,6 @@ public Map<DataObject, Collection<RndProxyDef>> getRenderingSettings(
 
 	/**
 	 * Implemented as specified by {@link OmeroImageService}.
-	 * @see OmeroImageService#getRenderingSettingsFor(long, long)
 	 */
 	public List<RndProxyDef> getRenderingSettingsFor(SecurityContext ctx,
 		long pixelsID, long userID)
@@ -1026,8 +1019,6 @@ private boolean isHCS(List<ImportContainer> containers)
 
 	/**
 	 * Implemented as specified by {@link OmeroImageService}.
-	 * @see OmeroImageService#importFile(ImportableObject,
-	 * ImportableFile, long, long, boolean)
 	 */
 	public Object importFile(ImportableObject object,
 							 ImportableFile importable, boolean close)
@@ -1595,8 +1586,6 @@ private File applyTransforms(File inputXML, List<InputStream> transforms,
 
 	/**
 	 * Implemented as specified by {@link OmeroImageService}.
-	 * @see OmeroImageService#exportImageAsOMEObject(SecurityContext, int, long,
-	 * File, Target)
 	 */
 	public Object exportImageAsOMEFormat(SecurityContext ctx, int index,
 			long imageID, File file, Target target)
@@ -1797,7 +1786,6 @@ public Object uploadScript(SecurityContext ctx, ScriptObject script)
 
 	/**
 	 * Implemented as specified by {@link OmeroDataService}.
-	 * @see OmeroImageService#loadRatings(SecurityContext, Class, long, long)
 	 */
 	public Collection loadROIMeasurements(SecurityContext ctx, Class type,
 		long id, long userID)
@@ -2022,7 +2010,6 @@ public Long getRenderingDef(SecurityContext ctx, long pixelsID,
 
 	/**
 	 * Implemented as specified by {@link OmeroDataService}.
-	 * @see OmeroImageService#getRenderingDef(SecurityContext, long)
 	 */
 	public RndProxyDef getSettings(SecurityContext ctx, long rndID)
         throws DSOutOfServiceException, DSAccessException
@@ -2045,4 +2032,10 @@ public RawPixelsStorePrx createPixelsStore(SecurityContext ctx)
         return null;
     }
 
+	public Map<Integer, int[]> getHistogram(SecurityContext ctx,
+											PixelsData pixels,
+											int[] channels, int z, int t) throws DSOutOfServiceException,
+			DSAccessException {
+		return gateway.getHistogram(ctx, pixels, channels, z, t);
+	}
 }

src/main/java/org/openmicroscopy/shoola/env/data/views/calls/HistogramLoader.java

@@ -23,7 +23,6 @@
 import java.util.Map;
 
 import omero.gateway.SecurityContext;
-import omero.gateway.facility.RawDataFacility;
 import omero.gateway.model.ImageData;
 
 import org.openmicroscopy.shoola.env.data.views.BatchCall;
@@ -61,11 +60,8 @@ public HistogramLoader(final SecurityContext ctx, final ImageData img, final int
             final int z, final int t) {
         loadCall = new BatchCall("Loading Histogram data") {
             public void doCall() throws Exception {
-                try (RawDataFacility f = context.getGateway().getFacility(
-                        RawDataFacility.class)) {
-                    result = f.getHistogram(ctx, img.getDefaultPixels(),
-                            channels, z, t);
-                }
+                result = context.getImageService().getHistogram(ctx, img.getDefaultPixels(),
+                        channels, z, t);
             }
         };
     }

src/main/java/org/openmicroscopy/shoola/env/data/views/calls/ROICountLoader.java

@@ -23,7 +23,6 @@
 package org.openmicroscopy.shoola.env.data.views.calls;
 
 import omero.gateway.SecurityContext;
-import omero.gateway.facility.ROIFacility;
 
 import org.openmicroscopy.shoola.env.data.views.BatchCall;
 import org.openmicroscopy.shoola.env.data.views.BatchCallTree;
@@ -46,8 +45,7 @@ private BatchCall makeLoadCalls(final SecurityContext ctx,
             final long imageID) {
         return new BatchCall("Load ROI count from Server") {
             public void doCall() throws Exception {
-                results = context.getGateway().getFacility(ROIFacility.class)
-                        .getROICount(ctx, imageID);
+                results = context.getDataService().getROICount(ctx, imageID);
             }
         };
     }

src/test/java/org/openmicroscopy/shoola/env/data/NullOmeroPojoService.java

@@ -27,9 +27,11 @@
 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 org.openmicroscopy.shoola.env.data.util.SearchDataContext;
 
@@ -464,7 +466,17 @@ public Map<Long, List<DatasetData>> findDatasetsByImageId(SecurityContext ctx,
             return null;
         }
 
-        /**
+	@Override
+	public Collection<FolderData> saveROIFolders(SecurityContext ctx, Collection<FolderData> folders) throws ExecutionException, DSOutOfServiceException, DSAccessException {
+		return null;
+	}
+
+	@Override
+	public int getROICount(SecurityContext ctx, long imageId) throws DSOutOfServiceException, DSAccessException {
+		return 0;
+	}
+
+	/**
          * No-operation implementation
          * @see OmeroDataService#search(SecurityContext, SearchParameters)
          */
@@ -484,9 +496,7 @@ public SearchResultCollection search(SecurityContext ctx,
             return null;
         }
 
-        @Override
         public Gateway getGateway() {
-            // TODO Auto-generated method stub
             return null;
         }
 }