Solve #24 and #25 (#26)

* Bump version
* Add methods to retrieve/add/copy annotations from/to a repository object
* Add method to retrieve images from project, dataset and image name (see #24)
* Add method to import file and replace images in dataset (see #25)
* Add tests
* Fix table name missing from getTable
* Fix default namespace for MapAnnotations
* Fix redundant annotations being copied

.omeroci/test-data

@@ -81,7 +81,7 @@ omero login testUser@localhost -w password -g testGroup
 
 # create a simple project/dataset/image hierarchy
 PROJECT1=$(omero obj new Project name=TestProject description=description)
-PROJECT2=$(omero obj new Project name=TestProject)
+PROJECT2=$(omero obj new Project name=TestProject2)
 
 DATASET1=$(omero obj new Dataset name=TestDataset description=description)
 DATASET2=$(omero obj new Dataset name=TestDatasetImport)

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>fr.igred</groupId>
     <artifactId>simple-omero-client</artifactId>
-    <version>5.9.0</version>
+    <version>5.9.1</version>
     <packaging>jar</packaging>
 
     <name>Simple OMERO Client</name>

src/main/java/fr/igred/omero/Client.java

@@ -361,6 +361,33 @@ public List<ImageWrapper> getImages(String name) throws ServiceException, Access
     }
 
 
+    /**
+     * Gets all images with the name specified inside projects and datasets with the given names.
+     *
+     * @param projectName Expected project name.
+     * @param datasetName Expected dataset name.
+     * @param imageName   Expected image name.
+     *
+     * @return ImageWrapper list.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    public List<ImageWrapper> getImages(String projectName, String datasetName, String imageName)
+    throws ServiceException, AccessException, ExecutionException {
+        List<ImageWrapper>   images   = new ArrayList<>();
+        List<ProjectWrapper> projects = getProjects(projectName);
+        for (ProjectWrapper project : projects) {
+            List<DatasetWrapper> datasets = project.getDatasets(datasetName);
+            for (DatasetWrapper dataset : datasets) {
+                images.addAll(dataset.getImages(this, imageName));
+            }
+        }
+        return images;
+    }
+
+
     /**
      * Gets all images with a certain motif in their name from OMERO.
      *

src/main/java/fr/igred/omero/annotations/FileAnnotationWrapper.java

@@ -130,4 +130,14 @@ public boolean isMovieFile() {
         return data.isMovieFile();
     }
 
+
+    /**
+     * Gets the FileAnnotationData contained.
+     *
+     * @return the {@link FileAnnotationData} contained.
+     */
+    public FileAnnotationData asFileAnnotationData() {
+        return data;
+    }
+
 }

src/main/java/fr/igred/omero/repository/DatasetWrapper.java

@@ -24,6 +24,7 @@
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.OMEROServerError;
 import fr.igred.omero.exception.ServiceException;
+import fr.igred.omero.roi.ROIWrapper;
 import loci.formats.in.DefaultMetadataOptions;
 import loci.formats.in.MetadataLevel;
 import ome.formats.OMEROMetadataStoreClient;
@@ -69,6 +70,8 @@ public class DatasetWrapper extends GenericRepositoryObjectWrapper<DatasetData>
 
     public static final String ANNOTATION_LINK = "DatasetAnnotationLink";
 
+    private static final Long[] LONGS = new Long[0];
+
 
     /**
      * Constructor of the DatasetWrapper class
@@ -410,7 +413,7 @@ public void removeImage(Client client, ImageWrapper image)
      * Imports all images candidates in the paths to the dataset in OMERO.
      *
      * @param client The client handling the connection.
-     * @param paths  Paths to the image on your computer.
+     * @param paths  Paths to the image files on the computer.
      *
      * @return If the import did not exit because of an error.
      *
@@ -453,10 +456,10 @@ public boolean importImages(Client client, String... paths)
 
 
     /**
-     * Imports one image candidate in the paths to the dataset in OMERO.
+     * Imports one image file to the dataset in OMERO.
      *
      * @param client The client handling the connection.
-     * @param path   Path to the image on your computer.
+     * @param path   Path to the image file on the computer.
      *
      * @return The list of IDs of the newly imported images.
      *
@@ -511,6 +514,50 @@ public List<Long> importImage(Client client, String path)
     }
 
 
+    /**
+     * Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their
+     * annotations and ROIs, and concatenating the descriptions (on new lines).
+     *
+     * @param client The client handling the connection.
+     * @param path   Path to the image on the computer.
+     *
+     * @return The list of IDs of the newly imported images.
+     *
+     * @throws ServiceException     Cannot connect to OMERO.
+     * @throws AccessException      Cannot access data.
+     * @throws OMEROServerError     Server error.
+     * @throws ExecutionException   A Facility can't be retrieved or instantiated.
+     * @throws InterruptedException If block(long) does not return.
+     */
+    public List<Long> importAndReplaceImages(Client client, String path)
+    throws ServiceException, AccessException, OMEROServerError, ExecutionException, InterruptedException {
+        List<Long> ids    = importImage(client, path);
+        Long[]     newIds = ids.toArray(LONGS);
+
+        List<ImageWrapper> newImages = client.getImages(newIds);
+        for (ImageWrapper image : newImages) {
+            List<ImageWrapper> oldImages = getImages(client, image.getName());
+            oldImages.removeIf(i -> ids.contains(i.getId()));
+            ArrayList<String> descriptions = new ArrayList<>(oldImages.size() + 1);
+            descriptions.add(image.getDescription());
+            for (ImageWrapper oldImage : oldImages) {
+                descriptions.add(oldImage.getDescription());
+                image.copyAnnotations(client, oldImage);
+                List<ROIWrapper> rois = oldImage.getROIs(client);
+                for (ROIWrapper roi : rois) {
+                    roi.setImage(image);
+                    image.saveROI(client, roi);
+                }
+                client.delete(oldImage);
+            }
+            descriptions.removeIf(s -> s == null || s.trim().isEmpty());
+            image.setDescription(String.join("\n", descriptions));
+            image.saveAndUpdate(client);
+        }
+        return ids;
+    }
+
+
     /**
      * Refreshes the wrapped dataset.
      *

src/main/java/fr/igred/omero/repository/GenericRepositoryObjectWrapper.java

@@ -26,6 +26,7 @@
 import fr.igred.omero.exception.AccessException;
 import fr.igred.omero.exception.OMEROServerError;
 import fr.igred.omero.exception.ServiceException;
+import omero.constants.metadata.NSCLIENTMAPANNOTATION;
 import omero.gateway.exception.DSAccessException;
 import omero.gateway.exception.DSOutOfServiceException;
 import omero.gateway.model.AnnotationData;
@@ -204,11 +205,11 @@ public void addTags(Client client, Long... ids)
 
 
     /**
-     * Gets all tag linked to an object in OMERO, if possible.
+     * Gets all tags linked to an object in OMERO, if possible.
      *
      * @param client The client handling the connection.
      *
-     * @return Collection of TagAnnotationWrapper each containing a tag linked to the object.
+     * @return List of TagAnnotationWrappers each containing a tag linked to the object.
      *
      * @throws ServiceException   Cannot connect to OMERO.
      * @throws AccessException    Cannot access data.
@@ -234,6 +235,37 @@ public List<TagAnnotationWrapper> getTags(Client client)
     }
 
 
+    /**
+     * Gets all map annotations linked to an object in OMERO, if possible.
+     *
+     * @param client The client handling the connection.
+     *
+     * @return List of MapAnnotationWrappers.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    public List<MapAnnotationWrapper> getMapAnnotations(Client client)
+    throws ServiceException, AccessException, ExecutionException {
+        List<Class<? extends AnnotationData>> types = Collections.singletonList(MapAnnotationData.class);
+
+        List<AnnotationData> annotations = new ArrayList<>(0);
+        try {
+            annotations = client.getMetadata().getAnnotations(client.getCtx(), data, types, null);
+        } catch (DSOutOfServiceException | DSAccessException e) {
+            handleServiceOrAccess(e, "Cannot get tags for " + this);
+        }
+
+        return annotations.stream()
+                          .filter(MapAnnotationData.class::isInstance)
+                          .map(MapAnnotationData.class::cast)
+                          .map(MapAnnotationWrapper::new)
+                          .sorted(Comparator.comparing(MapAnnotationWrapper::getId))
+                          .collect(Collectors.toList());
+    }
+
+
     /**
      * Adds a single Key-Value pair to the object.
      *
@@ -247,8 +279,10 @@ public List<TagAnnotationWrapper> getTags(Client client)
      */
     public void addPairKeyValue(Client client, String key, String value)
     throws ServiceException, AccessException, ExecutionException {
-        List<NamedValue> kv = Collections.singletonList(new NamedValue(key, value));
-        addMapAnnotation(client, new MapAnnotationWrapper(kv));
+        List<NamedValue>     kv  = Collections.singletonList(new NamedValue(key, value));
+        MapAnnotationWrapper pkv = new MapAnnotationWrapper(kv);
+        pkv.setNameSpace(NSCLIENTMAPANNOTATION.value);
+        addMapAnnotation(client, pkv);
     }
 
 
@@ -377,12 +411,20 @@ public void addTable(Client client, TableWrapper table)
     public TableWrapper getTable(Client client, Long fileId)
     throws ServiceException, AccessException, ExecutionException {
         TableData table = null;
+        String    name  = null;
         try {
             table = client.getTablesFacility().getTable(client.getCtx(), fileId);
+            name = client.getTablesFacility()
+                         .getAvailableTables(client.getCtx(), data)
+                         .stream().filter(t -> t.getFileID() == fileId)
+                         .map(FileAnnotationData::getDescription)
+                         .findFirst().orElse(null);
         } catch (DSOutOfServiceException | DSAccessException e) {
             handleServiceOrAccess(e, "Cannot get table from " + this);
         }
-        return new TableWrapper(Objects.requireNonNull(table));
+        TableWrapper result = new TableWrapper(Objects.requireNonNull(table));
+        result.setName(name);
+        return result;
     }
 
 
@@ -438,6 +480,26 @@ public long addFile(Client client, File file) throws ExecutionException, Interru
     }
 
 
+    /**
+     * Links a file annotation to the object
+     *
+     * @param client     The client handling the connection.
+     * @param annotation FileAnnotationWrapper to link.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    public void addFileAnnotation(Client client, FileAnnotationWrapper annotation)
+    throws AccessException, ServiceException, ExecutionException {
+        try {
+            client.getDm().attachAnnotation(client.getCtx(), annotation.asFileAnnotationData(), this.data);
+        } catch (DSOutOfServiceException | DSAccessException e) {
+            handleServiceOrAccess(e, "Cannot link file annotation to " + this);
+        }
+    }
+
+
     /**
      * Returns the file annotations
      *
@@ -509,4 +571,54 @@ protected void removeLink(Client client, String linkType, long childId)
     }
 
 
+    /**
+     * Retrieves annotations linked to the object.
+     *
+     * @param client The client handling the connection.
+     *
+     * @return A list of annotations, as AnnotationData.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    private List<AnnotationData> getAnnotations(Client client)
+    throws AccessException, ServiceException, ExecutionException {
+        List<AnnotationData> annotations = new ArrayList<>(0);
+        try {
+            annotations = client.getMetadata().getAnnotations(client.getCtx(), data);
+        } catch (DSOutOfServiceException | DSAccessException e) {
+            handleServiceOrAccess(e, "Cannot get annotations from " + this);
+        }
+        return annotations;
+    }
+
+
+    /**
+     * Copies annotations from some other object to this one
+     *
+     * @param client The client handling the connection.
+     * @param object Other repository object to copy annotations from.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    public void copyAnnotations(Client client, GenericRepositoryObjectWrapper<?> object)
+    throws AccessException, ServiceException, ExecutionException {
+        List<AnnotationData> newAnnotations = object.getAnnotations(client);
+        List<AnnotationData> oldAnnotations = this.getAnnotations(client);
+        for (AnnotationData annotation : oldAnnotations) {
+            newAnnotations.removeIf(a -> a.getId() == annotation.getId());
+        }
+        try {
+            for (AnnotationData annotation : newAnnotations) {
+                client.getDm().attachAnnotation(client.getCtx(), annotation, this.data);
+            }
+        } catch (DSOutOfServiceException | DSAccessException e) {
+            handleServiceOrAccess(e, "Cannot link annotations to " + this);
+        }
+    }
+
+
 }

src/test/java/fr/igred/omero/ClientTest.java

@@ -71,7 +71,7 @@ public void testGetProjectByName() throws Exception {
                 differences++;
         }
 
-        assertEquals(2, projects.size());
+        assertEquals(1, projects.size());
         assertEquals(0, differences);
     }
 
@@ -175,6 +175,13 @@ public void testGetImagesKeyValue() throws Exception {
     }
 
 
+    @Test
+    public void testGetImagesFromNames() throws Exception {
+        List<ImageWrapper> images = client.getImages(PROJECT1.name, DATASET1.name, IMAGE1.name);
+        assertEquals(2, images.size());
+    }
+
+
     @Test
     public void testGetImagesCond() throws Exception {
         String key = "testKey2";