Changeset 5662

Timestamp:

10/09/08 11:32:19 (6 weeks ago)

Author:

jburel

Message:

Fixed filtering bug

Location:

trunk/SRC/org/openmicroscopy/shoola

Files:

• agents/dataBrowser/DataBrowserTranslator.java (modified) (5 diffs)
• agents/dataBrowser/view/DataBrowserToolBar.java (modified) (2 diffs)
• agents/treeviewer/browser/BrowserUI.java (modified) (1 diff)
• env/data/OMEROGateway.java (modified) (7 diffs)
• env/data/OmeroMetadataService.java (modified) (1 diff)
• env/data/OmeroMetadataServiceImpl.java (modified) (4 diffs)
• env/data/views/calls/DataFilter.java (modified) (3 diffs)

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/DataBrowserTranslator.java

@@ -41 +41 @@
 import org.openmicroscopy.shoola.agents.dataBrowser.browser.WellSampleNode;
 import org.openmicroscopy.shoola.util.ui.UIUtilities;
-import pojos.CategoryData;
-import pojos.CategoryGroupData;
 import pojos.DataObject;
 import pojos.DatasetData;
@@ -192 +190 @@
             formatToolTipFor(node);
             linkImagesTo(images, node, userID, groupID);
-        } else if (uo instanceof CategoryData) {
-            CategoryData data = (CategoryData) uo;
-            String note = "";
-            images = data.getImages();
-            if (images != null) note = LEFT+images.size()+RIGHT;
-            node = new ImageSet(data.getName(), note, data);
-            formatToolTipFor(node);
-            linkImagesTo(images, node, userID, groupID);
-        } 
+        }
         return node;
     }
@@ -221 +211 @@
         Set children;
         Iterator i, j;
-        CategoryData c;
         DatasetData d;
-        if (uo instanceof CategoryData) {
-                c = (CategoryData) uo;
-                images = transformImages(c.getImages(), userID, groupID);
-        } else if (uo instanceof CategoryGroupData) {
-                CategoryGroupData cg = (CategoryGroupData) uo;
-                children = cg.getCategories();
-                if (children != null) {
-                        i = children.iterator();
-                        images = new HashSet();
-                        while (i.hasNext()) {
-                                        c = (CategoryData) i.next();
-                                        images.addAll(transformImages(c.getImages(), 
-                                                                userID, groupID));
-                                }
-                }
-        } else if (uo instanceof DatasetData) {
+        if (uo instanceof DatasetData) {
                 d = (DatasetData) uo;
                 images = transformImages(d.getImages(), userID, groupID);
@@ -485 +459 @@
     }
     
-    /**
-     * Transforms a CategoryGroup/Category/Images hierarchy into a visualisation
-     * tree. 
-     * 
-     * @param groups    Collection of {@link CategoryGroupData}s to transform.
-     *                  Mustn't be <code>null</code>.
-     * @param userID    The id of the current user.
-     * @param groupID   The id of the group the current user selects when 
-     *                  retrieving the data.                
-     * @return Collection of corresponding {@link ImageDisplay}s.
-     */
-    private static Set transformCategoryGroups(Set groups, long userID,
-                                            long groupID)
-    {
-        if (groups == null) throw new IllegalArgumentException("No groups.");
-        Set results = new HashSet();
-        Iterator i = groups.iterator(), j;
-        //DataObject
-        CategoryGroupData  cgData;
-        DataObject child;
-        //Visualisation object.
-        ImageSet group;  
-        Set categories;
-        String note = "";
-        while (i.hasNext()) {
-            cgData = (CategoryGroupData) i.next();
-            categories = cgData.getCategories();
-            if (categories != null) note = LEFT+categories.size()+RIGHT;
-            group = new ImageSet(cgData.getName(), note, cgData);
-            formatToolTipFor(group);
-            
-            if (categories != null) {
-                j = categories.iterator();
-                while (j.hasNext()) {
-                    child = (DataObject) j.next();
-                    if (isReadable(child, userID, groupID))
-                        group.addChildDisplay(linkImages(child, userID, 
-                                                groupID));
-                }     
-            }
-            results.add(group); //add the group ImageSet 
-        }
-        return results;
-    }
-    
-    /** 
-     * Transforms the specified {@link CategoryGroupData} into its corresponding 
-     * visualisation element.
-     * 
-     * @param data      The {@link CategoryGroupData} to transform.
-     * @param userID    The id of the current user.
-     * @param groupID   The id of the group the current user selects when 
-     *                  retrieving the data. 
-     * @return See below.
-     */
-    private static Set transformCategoryGroup(CategoryGroupData data, 
-                                        long userID, long groupID)
-    {
-        Set set = new HashSet(1);
-        set.add(data);
-        return transformCategoryGroups(set, userID, groupID);
-    }
-    
-    /**
-     * Transforms a Category/Images hierarchy into a visualisation tree. 
-     * 
-     * @param categories    Collection of {@link CategoryData}s to transform.
-     * @param userID        The id of the current user.
-     * @param groupID       The id of the group the current user selects when 
-     *                      retrieving the data. 
-     * @return Set of corresponding {@link ImageDisplay}s.
-     */
-    private static Set transformCategories(Set categories, long userID, 
-                                            long groupID)
-    {
-        if (categories == null) 
-            throw new IllegalArgumentException("No categories.");
-        Set results = new HashSet();
-        Iterator i = categories.iterator();
-        CategoryData data;
-        ImageSet parent;
-        Set images;
-        String note = "";
-        while (i.hasNext()) {
-            data = (CategoryData) i.next();
-            if (isReadable(data, userID, groupID)) {
-                images = data.getImages();
-                if (images != null) note = LEFT+images.size()+RIGHT;
-                parent = new ImageSet(data.getName(), note, data);
-                formatToolTipFor(parent);
-                linkImagesTo(images, parent, userID, groupID);
-                results.add(parent);
-            } 
-        }
-        return results;
-    }
-    
-    /** 
-     * Transforms the specified {@link CategoryData} into its corresponding 
-     * visualisation element.
-     * 
-     * @param data      The {@link CategoryData} to transform.
-     * @param userID    The id of the current user.
-     * @param groupID   The id of the group the current user selects when 
-     *                      retrieving the data. 
-     * @return See below.
-     */
-    private static Set transformCategory(CategoryData data, long userID, 
-                                        long groupID)
-    {
-        Set set = new HashSet(1);
-        set.add(data);
-        return transformCategories(set, userID, groupID);
-    }
-    
     /** 
      * Transforms a set of {@link DataObject}s into their corresponding 
@@ -631 +490 @@
             else if (ho instanceof DatasetData)
                 results.add(getFirstElement(transformDataset(ho, userID, 
-                                            groupID)));
-            else if (ho instanceof CategoryGroupData)
-                results.add(getFirstElement(
-                        transformCategoryGroup((CategoryGroupData) ho, userID, 
-                                                groupID)));
-            else if (ho instanceof CategoryData)
-                results.add(getFirstElement(
-                        transformCategory((CategoryData) ho, userID, 
                                             groupID)));
             else if (ho instanceof ImageData) {

trunk/SRC/org/openmicroscopy/shoola/agents/dataBrowser/view/DataBrowserToolBar.java

@@ -34 +34 @@
 import java.util.Collection;
 import java.util.List;
-
 import javax.swing.Box;
 import javax.swing.BoxLayout;
@@ -66 +65 @@
 import org.openmicroscopy.shoola.util.ui.search.SearchComponent;
 import org.openmicroscopy.shoola.util.ui.search.SearchObject;
-
 import pojos.TagAnnotationData;
 import pojos.TextualAnnotationData;

trunk/SRC/org/openmicroscopy/shoola/agents/treeviewer/browser/BrowserUI.java

@@ -1131 +1131 @@
         parent.removeAllChildren();
         parent.setChildrenLoaded(Boolean.TRUE);
-        System.err.println(parent.getNodeText());
         if (nodes.size() != 0) {
             Iterator i = nodes.iterator();

trunk/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

@@ -81 +81 @@
 import omero.model.AnnotationAnnotationLink;
 import omero.model.BooleanAnnotation;
+import omero.model.BooleanAnnotationI;
 import omero.model.Dataset;
 import omero.model.Details;
@@ -86 +87 @@
 import omero.model.ExperimenterGroup;
 import omero.model.FileAnnotation;
+import omero.model.FileAnnotationI;
 import omero.model.Format;
 import omero.model.IObject;
@@ -102 +104 @@
 import omero.model.ScreenPlateLink;
 import omero.model.TagAnnotation;
+import omero.model.TagAnnotationI;
 import omero.model.TextAnnotation;
+import omero.model.TextAnnotationI;
+import omero.model.TimestampAnnotation;
+import omero.model.TimestampAnnotationI;
 import omero.model.UrlAnnotation;
+import omero.model.UrlAnnotationI;
 import omero.model.Well;
 import omero.model.WellSample;
@@ -126 +133 @@
 import pojos.TagAnnotationData;
 import pojos.TextualAnnotationData;
+import pojos.TimeAnnotationData;
 import pojos.URLAnnotationData;
 import pojos.WellData;
@@ -880 +888 @@
                         return WellSample.class.getName();
                 throw new IllegalArgumentException("NodeType not supported");
+        }
+        
+        /**
+         * Converts the specified type to its corresponding type for search.
+         * 
+         * @param nodeType The type to convert.
+         * @return See above.
+         */
+        private String convertTypeForSearch(Class nodeType)
+        {
+                if (nodeType.equals(Image.class))
+                        return ImageI.class.getName();
+                else if (nodeType.equals(TagAnnotation.class) ||
+                                nodeType.equals(TagAnnotationData.class))
+                        return TagAnnotationI.class.getName();
+                else if (nodeType.equals(BooleanAnnotation.class) ||
+                                nodeType.equals(BooleanAnnotationData.class))
+                        return BooleanAnnotationI.class.getName();
+                else if (nodeType.equals(UrlAnnotation.class) ||
+                                nodeType.equals(URLAnnotationData.class))
+                        return UrlAnnotationI.class.getName();
+                else if (nodeType.equals(FileAnnotation.class) ||
+                                nodeType.equals(FileAnnotationData.class))
+                        return FileAnnotationI.class.getName();
+                else if (nodeType.equals(TextAnnotation.class) ||
+                                nodeType.equals(TextualAnnotationData.class))
+                        return TextAnnotationI.class.getName();
+                else if (nodeType.equals(TimestampAnnotation.class) ||
+                                nodeType.equals(TimeAnnotationData.class))
+                        return TimestampAnnotationI.class.getName();
+                throw new IllegalArgumentException("type not supported");
         }
         
@@ -3025 +3064 @@
                                                 service.onlyOwnedBy(d);
                                                 service.bySomeMustNone(fSome, fMust, fNone);
-                                                size = handleSearchResult(ImageI.class.getName(), rType, 
+                                                size = handleSearchResult(
+                                                                convertTypeForSearch(Image.class), rType, 
                                                                 service);
                                                 if (size instanceof Integer)
@@ -3082 +3122 @@
                         }
                         List<String> t = prepareTextSearch(terms, service);
-                        
-                        
-                        String k = convertPojos(annotationType);
-                        service.onlyType(k);
+
+                        service.onlyType(convertPojos(annotationType));
                         Set rType = new HashSet();
                         service.bySomeMustNone(t, null, null);
-                        Object size = handleSearchResult(k, rType, service);
+                        Object size = handleSearchResult(
+                                        convertTypeForSearch(annotationType), rType, service);
                         if (size instanceof Integer) new HashSet();
                         return rType;

trunk/SRC/org/openmicroscopy/shoola/env/data/OmeroMetadataService.java

@@ -74 +74 @@
          *                                      specified. 
          * @return See above.
-         * @throws DSOutOfServiceException
-         * @throws DSAccessException
+         * @throws DSOutOfServiceException  If the connection is broken, or logged
+         *                                  in.
+         * @throws DSAccessException        If an error occured while trying to 
+         *                                  retrieve data from OMEDS service.
          */
         public Collection loadTextualAnnotations(Class type, long id, long userID)

trunk/SRC/org/openmicroscopy/shoola/env/data/OmeroMetadataServiceImpl.java

@@ -38 +38 @@
 
 //Third-party libraries
+import org.apache.commons.collections.ListUtils;
+
+//Application-internal dependencies
 import omero.RString;
 import omero.model.Annotation;
@@ -46 +49 @@
 import omero.model.ImageAnnotationLink;
 import omero.model.OriginalFile;
-import omero.model.Project;
-import omero.model.ProjectAnnotationLink;
 import omero.model.TagAnnotation;
 import omero.model.TagAnnotationI;
 import omero.util.PojoOptionsI;
-
-import org.apache.commons.collections.ListUtils;
-
-//Application-internal dependencies
 import org.openmicroscopy.shoola.env.LookupNames;
 import org.openmicroscopy.shoola.env.config.Registry;
@@ -101 +98 @@
 
 
+        /**
+         * Loads the description of the passed tag for the specified user.
+         * 
+         * @param tag    The tag to handle.
+         * @param userID The id of the user.
+         * @return See above.
+         * @throws DSOutOfServiceException  If the connection is broken, or logged
+         *                                  in.
+         * @throws DSAccessException        If an error occured while trying to 
+         *                                  retrieve data from OMEDS service.
+         */
         private TagAnnotationData loadTagDescription(TagAnnotationData tag, 
                                                             long userID)
@@ -159 +167 @@
                                         of = gateway.uploadFile(fileAnn.getAttachedFile(), 
                                                         fileAnn.getServerFileFormat());
-                                        //tmp
                                         fa = new FileAnnotationI();
-                                        //tmp
                                         fa.setFile(of);
-                                        /*
-                                        fa.setFile(
-                                                        (OriginalFile)
-                                                        gateway.findIObject(OriginalFile.class.getName(), 
-                                                                        of.getId().val));
-                                                                        */
                                         iobject = fa;
                                 } else {

trunk/SRC/org/openmicroscopy/shoola/env/data/views/calls/DataFilter.java

@@ -164 +164 @@
                                 boolean annotated, long userID)
     {
+        if (annotationType == null)
+                throw new IllegalArgumentException("Annotation type not valid.");
+        if (nodeType == null)
+                throw new IllegalArgumentException("Node type not valid.");
         loadCall = filterBy(annotationType, nodeType, nodeIds, annotated, 
                                   userID);
@@ -183 +187 @@
                                 List<String> terms, long userID)
     {
+        if (annotationType == null)
+                throw new IllegalArgumentException("Annotation type not valid.");
+        if (nodeType == null)
+                throw new IllegalArgumentException("Node type not valid.");
         loadCall = filterBy(annotationType, nodeType, nodeIds, terms, userID);
     }
@@ -200 +208 @@
                                         long userID)
     {
+        if (nodeType == null)
+                throw new IllegalArgumentException("Node type not valid.");
         loadCall = filterBy(nodeType, nodeIds, context, userID);
     }