Large overhaul for Plate name and description manipulation via ImportCandidates configuration (Fixes #2648)

 * ImportContainer is now much more flexible and as of 4.2.1 will be the primary way to configure an import
 * Deprecated old importImage() methods
 * Added --plate_name and --plate_description to the command line options
 * Removed un-used FileInfo interactions with the ImportContainer
 * ImportCandidates is now much more through in populating ImportContainer fields
 * Cleaned up extra System.err.println of logging levels in command line importer


git-svn-id: file:///home/svn/omero/trunk@8169 05709c45-44f0-0310-885b-81a1db45b4a6

Author: cxallan

components/tools/OmeroImporter/src/ome/formats/OMEROMetadataStoreClient.java

@@ -276,13 +276,19 @@ public class OMEROMetadataStoreClient
 
     /** Annotations from the user for use by model processors. */
     private List<Annotation> userSpecifiedAnnotations;
-    
+  
     /** Image name the user specified for use by model processors. */
     private String userSpecifiedImageName;
-    
+
     /** Image description the user specified for use by model processors. */
     private String userSpecifiedImageDescription;
-    
+
+    /** Plate name the user specified for use by model processors. */
+    private String userSpecifiedPlateName;
+
+    /** Plate description the user specified for use by model processors. */
+    private String userSpecifiedPlateDescription;
+
     /** Linkage target for all Images/Plates for use by model processors. */
     private IObject userSpecifiedTarget;
 
@@ -1024,7 +1030,47 @@ public void setUserSpecifiedAnnotations(List<Annotation> annotations)
     {
     	this.userSpecifiedAnnotations = annotations;
     }
-    
+
+    /* (non-Javadoc)
+     * @see ome.formats.model.IObjectContainerStore#getUserSpecifiedPlateName()
+     */
+    public String getUserSpecifiedPlateName()
+    {
+        return userSpecifiedPlateName;
+    }
+
+    /* (non-Javadoc)
+     * @see ome.formats.model.IObjectContainerStore#setUserSpecifiedPlateName(java.lang.String)
+     */
+    public void setUserSpecifiedPlateName(String name)
+    {
+        if (log.isDebugEnabled())
+        {
+            log.debug("Using user specified plate name: " + name);
+        }
+        userSpecifiedPlateName = name;
+    }
+
+    /* (non-Javadoc)
+     * @see ome.formats.model.IObjectContainerStore#getUserSpecifiedPlateDescription()
+     */
+    public String getUserSpecifiedPlateDescription()
+    {
+        return userSpecifiedPlateDescription;
+    }
+
+    /* (non-Javadoc)
+     * @see ome.formats.model.IObjectContainerStore#setUserSpecifiedPlateDescription(java.lang.String)
+     */
+    public void setUserSpecifiedPlateDescription(String description)
+    {
+        if (log.isDebugEnabled())
+        {
+            log.debug("Using user specified plate description: " + description);
+        }
+        userSpecifiedPlateDescription = description;
+    }
+
     /* (non-Javadoc)
      * @see ome.formats.model.IObjectContainerStore#getUserSpecifiedImageName()
      */
@@ -1038,6 +1084,10 @@ public String getUserSpecifiedImageName()
      */
     public void setUserSpecifiedImageName(String name)
     {
+        if (log.isDebugEnabled())
+        {
+            log.debug("Using user specified image name: " + name);
+        }
         this.userSpecifiedImageName = name;
     }
 
@@ -1054,9 +1104,13 @@ public String getUserSpecifiedImageDescription()
      */
     public void setUserSpecifiedImageDescription(String description)
     {
+        if (log.isDebugEnabled())
+        {
+            log.debug("Using user specified image description: " + description);
+        }
         this.userSpecifiedImageDescription = description;
     }
-    
+
     /* (non-Javadoc)
      * @see ome.formats.model.IObjectContainerStore#getUserSpecifiedTarget()
      */

components/tools/OmeroImporter/src/ome/formats/importer/ImportCandidates.java

@@ -414,7 +414,13 @@ protected ImportContainer singleFile(File file, ImportConfig config)
                 ic.setBfImageCount(reader.getSeriesCount());
                 ic.setBfPixels(getPixelsWithDimensions());
                 ic.setBfImageNames(getImageNames());
+                ic.setCustomImageName(config.imageName.get());
+                ic.setCustomImageDescription(config.imageDescription.get());
+                ic.setCustomPlateName(config.plateName.get());
+                ic.setCustomPlateDescription(config.plateDescription.get());
                 ic.setArchive(config.archiveImage.get());
+                ic.setCustomAnnotationList(config.annotations.get());
+                ic.setUseMetadataFile(config.companionFile.get());
                 return ic;
             } finally 
             {

components/tools/OmeroImporter/src/ome/formats/importer/ImportConfig.java

@@ -106,6 +106,8 @@ public class ImportConfig {
     public final StrValue serverList;
     public final StrValue imageName;
     public final StrValue imageDescription;
+    public final StrValue plateName;
+    public final StrValue plateDescription;
     public final StrValue targetClass;
     public final LongValue targetId;
 
@@ -123,10 +125,11 @@ public class ImportConfig {
 
     public final FileValue savedDirectory;
     public final StrValue readersPath;
-    
+
     public final BoolValue encryptedConnection;
-    
+
     public final AnnotationListValue annotations;
+    public final DoubleArrayValue userPixels;
 
     /**
      * Static method for creating {@link Preferences} during construction if
@@ -211,6 +214,8 @@ public synchronized void load() {
         serverList   = new StrValue("serverList", this);
         imageName    = new StrValue("imageName", this);
         imageDescription  = new StrValue("imageDescription", this);
+        plateName    = new StrValue("plateName", this);
+        plateDescription  = new StrValue("plateDescription", this);
         targetClass  = new StrValue("targetClass", this);
         targetId     = new LongValue("targetId", this, 0);
 
@@ -230,11 +235,13 @@ public synchronized void load() {
         useCustomImageNaming = new BoolValue("overrideImageName", this, true);
         numOfDirectories = new IntValue("numOfDirectories", this, 0);
         savedDirectory = new FileValue("savedDirectory", this);
-        
+
         encryptedConnection = new BoolValue("ecryptedConnection", this, true);
-        
+
         annotations = new AnnotationListValue(
-        		"annotations", this, new ArrayList<Annotation>());
+                "annotations", this, new ArrayList<Annotation>());
+        userPixels = new DoubleArrayValue(
+                "userPixels", this, null);
 
         readersPath = new StrValue("readersPath", this);
     }
@@ -844,18 +851,31 @@ public boolean empty() {
             return s == null || s.length() == 0;
         }
     }
-    
+
     public static class AnnotationListValue extends Value<List<Annotation>> {
-    	
-    	public AnnotationListValue(String key, ImportConfig config, 
-    			                   List<Annotation> defValue) {
-    		super(key, config, defValue);
-    	}
-
-		@Override
-		protected List<Annotation> fromString(String string) {
-			throw new RuntimeException("Not implemented.");
-		}
+
+        public AnnotationListValue(String key, ImportConfig config, 
+                                   List<Annotation> defValue) {
+            super(key, config, defValue);
+        }
+
+        @Override
+        protected List<Annotation> fromString(String string) {
+            throw new RuntimeException("Not implemented.");
+        }
+    }
+
+    public static class DoubleArrayValue extends Value<Double[]> {
+
+        public DoubleArrayValue(String key, ImportConfig config, 
+                                Double[] defValue) {
+            super(key, config, defValue);
+        }
+
+        @Override
+        protected Double[] fromString(String string) {
+            throw new RuntimeException("Not implemented.");
+        }
     }
 
     public static class PassValue extends StrValue {