Refactor packages

GReD-Clermont · Nov 19, 2024 · 03e6e6a · 03e6e6a
1 parent 431275d
commit 03e6e6a
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Showing 59 changed files with 261 additions and 170 deletions.
diff --git a/src/main/java/fr/igred/omero/AnnotatableWrapper.java b/src/main/java/fr/igred/omero/AnnotatableWrapper.java
@@ -25,9 +25,10 @@
 import fr.igred.omero.annotations.RatingAnnotationWrapper;
 import fr.igred.omero.annotations.TableWrapper;
 import fr.igred.omero.annotations.TagAnnotationWrapper;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.repository.RepositoryObjectWrapper.ReplacePolicy;
+import fr.igred.omero.RepositoryObjectWrapper.ReplacePolicy;
 import omero.gateway.facility.TablesFacility;
 import omero.gateway.model.AnnotationData;
 import omero.gateway.model.DataObject;

diff --git a/src/main/java/fr/igred/omero/ObjectWrapper.java b/src/main/java/fr/igred/omero/ObjectWrapper.java
@@ -18,6 +18,7 @@
 package fr.igred.omero;
 
 
+import fr.igred.omero.client.Client;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
 import fr.igred.omero.meta.ExperimenterWrapper;
@@ -88,7 +89,7 @@ protected ObjectWrapper(T o) {
      *
      * @return See above.
      */
-    protected static <U extends DataObject, V extends ObjectWrapper<U>> List<V>
+    public static <U extends DataObject, V extends ObjectWrapper<U>> List<V>
     wrap(Collection<U> objects, Function<? super U, ? extends V> mapper) {
         return wrap(objects, mapper, ObjectWrapper::getId);
     }
@@ -142,16 +143,6 @@ public T asDataObject() {
     }
 
 
-    /**
-     * Returns the contained DataObject as IObject.
-     *
-     * @return See above.
-     */
-    IObject asIObject() {
-        return data.asIObject();
-    }
-
-
     /**
      * Gets the object id
      *

diff --git a/...o/repository/RepositoryObjectWrapper.java → .../igred/omero/RepositoryObjectWrapper.java b/...o/repository/RepositoryObjectWrapper.java → .../igred/omero/RepositoryObjectWrapper.java
@@ -15,13 +15,12 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero.repository;
+package fr.igred.omero;
 
 
-import fr.igred.omero.AnnotatableWrapper;
-import fr.igred.omero.Browser;
-import fr.igred.omero.Client;
-import fr.igred.omero.GatewayWrapper;
+import fr.igred.omero.client.Browser;
+import fr.igred.omero.client.Client;
+import fr.igred.omero.client.GatewayWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
 import fr.igred.omero.exception.ServiceException;

diff --git a/src/main/java/fr/igred/omero/annotations/AnnotationWrapper.java b/src/main/java/fr/igred/omero/annotations/AnnotationWrapper.java
@@ -18,18 +18,18 @@
 package fr.igred.omero.annotations;
 
 
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.repository.DatasetWrapper;
-import fr.igred.omero.repository.FolderWrapper;
-import fr.igred.omero.repository.ImageWrapper;
-import fr.igred.omero.repository.PlateAcquisitionWrapper;
-import fr.igred.omero.repository.PlateWrapper;
-import fr.igred.omero.repository.ProjectWrapper;
-import fr.igred.omero.repository.ScreenWrapper;
-import fr.igred.omero.repository.WellWrapper;
+import fr.igred.omero.containers.DatasetWrapper;
+import fr.igred.omero.containers.FolderWrapper;
+import fr.igred.omero.core.ImageWrapper;
+import fr.igred.omero.screen.PlateAcquisitionWrapper;
+import fr.igred.omero.screen.PlateWrapper;
+import fr.igred.omero.containers.ProjectWrapper;
+import fr.igred.omero.screen.ScreenWrapper;
+import fr.igred.omero.screen.WellWrapper;
 import omero.RLong;
 import omero.gateway.model.AnnotationData;
 import omero.gateway.model.PlateAcquisitionData;

diff --git a/src/main/java/fr/igred/omero/annotations/FileAnnotationWrapper.java b/src/main/java/fr/igred/omero/annotations/FileAnnotationWrapper.java
@@ -18,7 +18,7 @@
 package fr.igred.omero.annotations;
 
 
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
 import fr.igred.omero.exception.ServiceException;

diff --git a/src/main/java/fr/igred/omero/annotations/TableWrapper.java b/src/main/java/fr/igred/omero/annotations/TableWrapper.java
@@ -18,11 +18,11 @@
 package fr.igred.omero.annotations;
 
 
-import fr.igred.omero.Client;
 import fr.igred.omero.ObjectWrapper;
+import fr.igred.omero.client.Client;
+import fr.igred.omero.core.ImageWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.repository.ImageWrapper;
 import fr.igred.omero.roi.ROIWrapper;
 import ij.gui.Roi;
 import ij.macro.Variable;

diff --git a/src/main/java/fr/igred/omero/annotations/TagAnnotationWrapper.java b/src/main/java/fr/igred/omero/annotations/TagAnnotationWrapper.java
@@ -18,7 +18,7 @@
 package fr.igred.omero.annotations;
 
 
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
 import omero.gateway.model.TagAnnotationData;

diff --git a/src/main/java/fr/igred/omero/annotations/TagSetWrapper.java b/src/main/java/fr/igred/omero/annotations/TagSetWrapper.java
@@ -18,8 +18,8 @@
 package fr.igred.omero.annotations;
 
 
-import fr.igred.omero.Browser;
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Browser;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
 import omero.gateway.model.TagAnnotationData;

diff --git a/src/main/java/fr/igred/omero/Browser.java → ...n/java/fr/igred/omero/client/Browser.java b/src/main/java/fr/igred/omero/Browser.java → ...n/java/fr/igred/omero/client/Browser.java
@@ -15,22 +15,23 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero;
+package fr.igred.omero.client;
 
 
+import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.annotations.AnnotationWrapper;
 import fr.igred.omero.annotations.MapAnnotationWrapper;
 import fr.igred.omero.annotations.TagAnnotationWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
 import fr.igred.omero.meta.ExperimenterWrapper;
-import fr.igred.omero.repository.DatasetWrapper;
-import fr.igred.omero.repository.FolderWrapper;
-import fr.igred.omero.repository.ImageWrapper;
-import fr.igred.omero.repository.PlateWrapper;
-import fr.igred.omero.repository.ProjectWrapper;
-import fr.igred.omero.repository.ScreenWrapper;
-import fr.igred.omero.repository.WellWrapper;
+import fr.igred.omero.containers.DatasetWrapper;
+import fr.igred.omero.containers.FolderWrapper;
+import fr.igred.omero.core.ImageWrapper;
+import fr.igred.omero.screen.PlateWrapper;
+import fr.igred.omero.containers.ProjectWrapper;
+import fr.igred.omero.screen.ScreenWrapper;
+import fr.igred.omero.screen.WellWrapper;
 import omero.RLong;
 import omero.gateway.Gateway;
 import omero.gateway.SecurityContext;

diff --git a/src/main/java/fr/igred/omero/Client.java → ...in/java/fr/igred/omero/client/Client.java b/src/main/java/fr/igred/omero/Client.java → ...in/java/fr/igred/omero/client/Client.java
@@ -15,19 +15,20 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero;
+package fr.igred.omero.client;
 
 
+import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.annotations.AnnotationWrapper;
 import fr.igred.omero.annotations.TableWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
 import fr.igred.omero.exception.ServiceException;
 import fr.igred.omero.meta.ExperimenterWrapper;
 import fr.igred.omero.meta.GroupWrapper;
-import fr.igred.omero.repository.FolderWrapper;
-import fr.igred.omero.repository.ImageWrapper;
-import fr.igred.omero.repository.ProjectWrapper;
+import fr.igred.omero.containers.FolderWrapper;
+import fr.igred.omero.core.ImageWrapper;
+import fr.igred.omero.containers.ProjectWrapper;
 import omero.ApiUsageException;
 import omero.gateway.Gateway;
 import omero.gateway.SecurityContext;
@@ -140,7 +141,7 @@ public void delete(Collection<? extends ObjectWrapper<?>> objects)
         }
         if (!objects.isEmpty()) {
             delete(objects.stream()
-                          .map(ObjectWrapper::asIObject)
+                          .map(o -> o.asDataObject().asIObject())
                           .collect(Collectors.toList()));
         }
     }
@@ -162,7 +163,7 @@ public void delete(ObjectWrapper<?> object)
         if (object instanceof FolderWrapper) {
             ((FolderWrapper) object).unlinkAllROIs(this);
         }
-        delete(object.asIObject());
+        delete(object.asDataObject().asIObject());
     }
 
 

diff --git a/...n/java/fr/igred/omero/GatewayWrapper.java → ...fr/igred/omero/client/GatewayWrapper.java b/...n/java/fr/igred/omero/GatewayWrapper.java → ...fr/igred/omero/client/GatewayWrapper.java
@@ -15,7 +15,7 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero;
+package fr.igred.omero.client;
 
 
 import fr.igred.omero.exception.AccessException;
@@ -475,7 +475,7 @@ public IObject save(IObject object)
      * @throws ExecutionException   A Facility can't be retrieved or instantiated.
      * @throws InterruptedException If block(long) does not return.
      */
-    void delete(IObject object)
+    public void delete(IObject object)
     throws ServiceException, AccessException, ExecutionException, InterruptedException {
         final long wait = 500L;
         ExceptionHandler.ofConsumer(getDm(),
@@ -496,7 +496,7 @@ void delete(IObject object)
      * @throws ExecutionException   A Facility can't be retrieved or instantiated.
      * @throws InterruptedException If block(long) does not return.
      */
-    void delete(List<IObject> objects)
+    public void delete(List<IObject> objects)
     throws ServiceException, AccessException, ExecutionException, InterruptedException {
         final long wait = 500L;
         ExceptionHandler.ofConsumer(getDm(),

diff --git a/src/main/java/fr/igred/omero/client/package-info.java b/src/main/java/fr/igred/omero/client/package-info.java
@@ -0,0 +1,20 @@
+/*
+ *  Copyright (C) 2020-2023 GReD
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU General Public License as published by the Free Software
+ * Foundation; either version 2 of the License, or (at your option) any later
+ * version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+ * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with
+ * this program; if not, write to the Free Software Foundation, Inc., 51 Franklin
+ * Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ */
+/**
+ * This package contains the client classes used to interact with an OMERO server.
+ */
+package fr.igred.omero.client;
diff --git a/...gred/omero/repository/DatasetWrapper.java → ...gred/omero/containers/DatasetWrapper.java b/...gred/omero/repository/DatasetWrapper.java → ...gred/omero/containers/DatasetWrapper.java
@@ -15,15 +15,17 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero.repository;
+package fr.igred.omero.containers;
 
 
-import fr.igred.omero.Browser;
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Browser;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.annotations.TagAnnotationWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
+import fr.igred.omero.core.ImageWrapper;
+import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.roi.ROIWrapper;
 import omero.RLong;
 import omero.gateway.model.DatasetData;

diff --git a/...igred/omero/repository/FolderWrapper.java → ...igred/omero/containers/FolderWrapper.java b/...igred/omero/repository/FolderWrapper.java → ...igred/omero/containers/FolderWrapper.java
@@ -15,15 +15,17 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero.repository;
+package fr.igred.omero.containers;
 
 
-import fr.igred.omero.Browser;
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Browser;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
 import fr.igred.omero.exception.ServiceException;
+import fr.igred.omero.core.ImageWrapper;
+import fr.igred.omero.RepositoryObjectWrapper;
 import fr.igred.omero.roi.ROIWrapper;
 import omero.gateway.facility.ROIFacility;
 import omero.gateway.model.AnnotationData;

diff --git a/...gred/omero/repository/ProjectWrapper.java → ...gred/omero/containers/ProjectWrapper.java b/...gred/omero/repository/ProjectWrapper.java → ...gred/omero/containers/ProjectWrapper.java
@@ -15,15 +15,17 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero.repository;
+package fr.igred.omero.containers;
 
 
-import fr.igred.omero.Browser;
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Browser;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.annotations.TagAnnotationWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
+import fr.igred.omero.core.ImageWrapper;
+import fr.igred.omero.RepositoryObjectWrapper;
 import omero.gateway.model.ImageData;
 import omero.gateway.model.ProjectData;
 import omero.model.ProjectDatasetLink;

diff --git a/.../igred/omero/repository/package-info.java → .../igred/omero/containers/package-info.java b/.../igred/omero/repository/package-info.java → .../igred/omero/containers/package-info.java
@@ -19,4 +19,4 @@
  * <p> This includes containers (such as screens or projects for example), as well as data contained within images
  * (e.g. pixels and channels).
  */
-package fr.igred.omero.repository;
+package fr.igred.omero.containers;
diff --git a/...gred/omero/repository/ChannelWrapper.java → ...a/fr/igred/omero/core/ChannelWrapper.java b/...gred/omero/repository/ChannelWrapper.java → ...a/fr/igred/omero/core/ChannelWrapper.java
@@ -15,7 +15,7 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero.repository;
+package fr.igred.omero.core;
 
 
 import fr.igred.omero.ObjectWrapper;

diff --git a/.../igred/omero/repository/ImageWrapper.java → ...ava/fr/igred/omero/core/ImageWrapper.java b/.../igred/omero/repository/ImageWrapper.java → ...ava/fr/igred/omero/core/ImageWrapper.java
@@ -15,16 +15,25 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero.repository;
+package fr.igred.omero.core;
 
 
-import fr.igred.omero.Browser;
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Browser;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
+import fr.igred.omero.containers.DatasetWrapper;
+import fr.igred.omero.containers.FolderWrapper;
+import fr.igred.omero.containers.ProjectWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.repository.PixelsWrapper.Bounds;
-import fr.igred.omero.repository.PixelsWrapper.Coordinates;
+import fr.igred.omero.core.PixelsWrapper.Bounds;
+import fr.igred.omero.core.PixelsWrapper.Coordinates;
+import fr.igred.omero.screen.PlateAcquisitionWrapper;
+import fr.igred.omero.screen.PlateWrapper;
+import fr.igred.omero.RepositoryObjectWrapper;
+import fr.igred.omero.screen.ScreenWrapper;
+import fr.igred.omero.screen.WellSampleWrapper;
+import fr.igred.omero.screen.WellWrapper;
 import fr.igred.omero.roi.ROIWrapper;
 import ij.CompositeImage;
 import ij.IJ;

diff --git a/...igred/omero/repository/PixelsWrapper.java → ...va/fr/igred/omero/core/PixelsWrapper.java b/...igred/omero/repository/PixelsWrapper.java → ...va/fr/igred/omero/core/PixelsWrapper.java
@@ -15,15 +15,14 @@
  * Street, Fifth Floor, Boston, MA 02110-1301, USA.
  */
 
-package fr.igred.omero.repository;
+package fr.igred.omero.core;
 
 
-import fr.igred.omero.Client;
+import fr.igred.omero.client.Client;
 import fr.igred.omero.ObjectWrapper;
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.ExceptionHandler;
 import fr.igred.omero.exception.ServiceException;
-import fr.igred.omero.meta.PlaneInfoWrapper;
 import ome.units.unit.Unit;
 import omero.gateway.exception.DataSourceException;
 import omero.gateway.facility.RawDataFacility;
@@ -40,7 +39,7 @@
 import java.util.concurrent.ExecutionException;
 
 import static fr.igred.omero.exception.ExceptionHandler.call;
-import static fr.igred.omero.meta.PlaneInfoWrapper.getMinPosition;
+import static fr.igred.omero.core.PlaneInfoWrapper.getMinPosition;
 import static ome.formats.model.UnitsFactory.convertLength;