Merge pull request #85 from GReD-Clermont/small-fixes

Small fixes
GReD-Clermont · Feb 23, 2024 · adb96cc · adb96cc
2 parents 892500a + 97806f9
commit adb96cc
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Showing 7 changed files with 19 additions and 30 deletions.
diff --git a/src/main/java/fr/igred/omero/AnnotatableWrapper.java b/src/main/java/fr/igred/omero/AnnotatableWrapper.java
@@ -552,19 +552,21 @@ public void addMapAnnotation(Client client, MapAnnotationWrapper mapAnnotation)
      */
     public void addTable(Client client, TableWrapper table)
     throws ServiceException, AccessException, ExecutionException {
+        String error = "Cannot add table to " + this;
+
         TablesFacility tablesFacility = client.getTablesFacility();
         TableData tableData = ExceptionHandler.of(tablesFacility,
                                                   tf -> tf.addTable(client.getCtx(),
                                                                     data,
                                                                     table.getName(),
                                                                     table.createTable()))
-                                              .handleOMEROException("Cannot add table to " + this)
+                                              .handleOMEROException(error)
                                               .get();
 
         Collection<FileAnnotationData> tables = ExceptionHandler.of(tablesFacility,
                                                                     tf -> tf.getAvailableTables(client.getCtx(),
                                                                                                 data))
-                                                                .handleOMEROException("Cannot add table to " + this)
+                                                                .handleOMEROException(error)
                                                                 .get();
         long fileId = tableData.getOriginalFileId();
 
@@ -590,17 +592,18 @@ public void addTable(Client client, TableWrapper table)
      */
     public void addAndReplaceTable(Client client, TableWrapper table, ReplacePolicy policy)
     throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
+        String error = "Cannot add table to " + this;
+
         Collection<FileAnnotationWrapper> tables = wrap(ExceptionHandler.of(client.getTablesFacility(),
                                                                             t -> t.getAvailableTables(
                                                                                     client.getCtx(), data))
-                                                                        .handleOMEROException("Cannot get tables from "
-                                                                                              + this)
+                                                                        .handleOMEROException(error)
                                                                         .get(),
                                                         FileAnnotationWrapper::new);
         addTable(client, table);
         tables.removeIf(t -> !t.getDescription().equals(table.getName()));
+        this.unlink(client, tables);
         for (FileAnnotationWrapper fileAnnotation : tables) {
-            this.unlink(client, fileAnnotation);
             if (policy == ReplacePolicy.DELETE ||
                 policy == ReplacePolicy.DELETE_ORPHANED && fileAnnotation.countAnnotationLinks(client) == 0) {
                 client.deleteFile(fileAnnotation.getId());

diff --git a/src/main/java/fr/igred/omero/Browser.java b/src/main/java/fr/igred/omero/Browser.java
@@ -434,6 +434,8 @@ public List<ImageWrapper> getImages(String name)
     /**
      * Gets all orphaned images owned by the specified user.
      *
+     * @param experimenter The user.
+     *
      * @return See above.
      *
      * @throws ServiceException   Cannot connect to OMERO.

diff --git a/src/main/java/fr/igred/omero/GenericObjectWrapper.java b/src/main/java/fr/igred/omero/GenericObjectWrapper.java
@@ -20,7 +20,6 @@
 
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
-import fr.igred.omero.exception.OMEROServerError;
 import fr.igred.omero.exception.ServiceException;
 import fr.igred.omero.meta.ExperimenterWrapper;
 import omero.gateway.model.DataObject;
@@ -93,24 +92,6 @@ protected GenericObjectWrapper(T o) {
     }
 
 
-    /**
-     * Deletes an object from OMERO.
-     *
-     * @param client The client handling the connection.
-     * @param object The OMERO object.
-     *
-     * @throws ServiceException     Cannot connect to OMERO.
-     * @throws AccessException      Cannot access data.
-     * @throws ExecutionException   A Facility can't be retrieved or instantiated.
-     * @throws OMEROServerError     Server error.
-     * @throws InterruptedException If block(long) does not return.
-     */
-    protected static void delete(Client client, IObject object)
-    throws ServiceException, AccessException, ExecutionException, OMEROServerError, InterruptedException {
-        client.delete(object);
-    }
-
-
     /**
      * Only keeps objects with different IDs in a collection.
      *

diff --git a/src/main/java/fr/igred/omero/repository/ImageWrapper.java b/src/main/java/fr/igred/omero/repository/ImageWrapper.java
@@ -85,6 +85,9 @@ public class ImageWrapper extends GenericRepositoryObjectWrapper<ImageData> {
     /** Annotation link name for this type of object */
     public static final String ANNOTATION_LINK = "ImageAnnotationLink";
 
+    /** Default IJ property to store image ID. */
+    public static final String IJ_ID_PROPERTY = "IMAGE_ID";
+
 
     /**
      * Constructor of the class ImageWrapper
@@ -771,7 +774,7 @@ public ImagePlus toImagePlus(Client client,
         }
         imp.setPosition(1);
         if (IJ.getVersion().compareTo("1.53a") >= 0) {
-            imp.setProp("IMAGE_ID", getId());
+            imp.setProp(IJ_ID_PROPERTY, getId());
         }
         return imp;
     }

diff --git a/src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java b/src/main/java/fr/igred/omero/roi/GenericShapeWrapper.java
@@ -64,7 +64,7 @@ public abstract class GenericShapeWrapper<T extends ShapeData> extends Annotatab
     public static final String ANNOTATION_LINK = "ShapeAnnotationLink";
 
     /** Default IJ property to store shape ID. */
-    public static final String IJ_IDPROPERTY = "SHAPE_ID";
+    public static final String IJ_ID_PROPERTY = "SHAPE_ID";
 
     /** Transparent color */
     private static final Color TRANSPARENT = new Color(0, 0, 0, 0);
@@ -272,7 +272,7 @@ protected void copyToIJRoi(ij.gui.Roi ijRoi) {
         if (ijRoi instanceof TextRoi) {
             copyToIJTextRoi((TextRoi) ijRoi);
         }
-        ijRoi.setProperty(IJ_IDPROPERTY, String.valueOf(data.getId()));
+        ijRoi.setProperty(IJ_ID_PROPERTY, String.valueOf(data.getId()));
     }
 
 

diff --git a/src/main/java/fr/igred/omero/roi/ROIWrapper.java b/src/main/java/fr/igred/omero/roi/ROIWrapper.java
@@ -286,7 +286,7 @@ public static List<ij.gui.Roi> toImageJ(Collection<? extends ROIWrapper> rois, S
      * @return See above.
      */
     private static ij.gui.Roi xor(Collection<? extends ij.gui.Roi> rois) {
-        String idProperty = GenericShapeWrapper.IJ_IDPROPERTY;
+        String idProperty = GenericShapeWrapper.IJ_ID_PROPERTY;
         String shapeIDs = rois.stream()
                               .map(r -> r.getProperty(idProperty))
                               .collect(Collectors.joining(","));
@@ -317,7 +317,7 @@ private static ij.gui.Roi xor(Collection<? extends ij.gui.Roi> rois) {
      * @return See above.
      */
     private static PointRoi combine(Collection<? extends PointRoi> points) {
-        String idProperty = GenericShapeWrapper.IJ_IDPROPERTY;
+        String idProperty = GenericShapeWrapper.IJ_ID_PROPERTY;
         String shapeIDs = points.stream()
                                 .map(p -> p.getProperty(idProperty))
                                 .collect(Collectors.joining(","));

diff --git a/src/test/java/fr/igred/omero/repository/ImageTest.java b/src/test/java/fr/igred/omero/repository/ImageTest.java
@@ -376,7 +376,7 @@ void testToImagePlus() throws Exception {
         ImageStatistics stats      = difference.getStatistics();
 
         assertEquals(0, (int) stats.max);
-        assertEquals(String.valueOf(IMAGE2.id), imp.getProp("IMAGE_ID"));
+        assertEquals(String.valueOf(IMAGE2.id), imp.getProp(ImageWrapper.IJ_ID_PROPERTY));
     }