Fix API retro-compatibility (#23)

Also update README

Author: ppouchin

README.md

@@ -22,7 +22,7 @@ Client client = new Client();
 client.connect("host", 4064, "username", password, groupId);
 ```
 
-### Repository objects (projects, datasets, images)
+### Repository objects (projects, datasets, images, screens, wells, plates)
 
 It can then be used to retrieve all the repository objects the user has access to, like projects or datasets:
 

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

@@ -130,7 +130,7 @@ public TableWrapper(TableData table) {
      * @throws AccessException    Cannot access data.
      * @throws ExecutionException A Facility can't be retrieved or instantiated.
      */
-    public TableWrapper(Client client, ResultsTable results, Long imageId, Collection<Roi> ijRois)
+    public TableWrapper(Client client, ResultsTable results, Long imageId, List<Roi> ijRois)
     throws ServiceException, AccessException, ExecutionException {
         this(client, results, imageId, ijRois, ROIWrapper.IJ_PROPERTY);
     }
@@ -150,7 +150,7 @@ public TableWrapper(Client client, ResultsTable results, Long imageId, Collectio
      * @throws AccessException    Cannot access data.
      * @throws ExecutionException A Facility can't be retrieved or instantiated.
      */
-    public TableWrapper(Client client, ResultsTable results, Long imageId, Collection<Roi> ijRois, String roiProperty)
+    public TableWrapper(Client client, ResultsTable results, Long imageId, List<Roi> ijRois, String roiProperty)
     throws ServiceException, AccessException, ExecutionException {
         roiProperty = ROIWrapper.checkProperty(roiProperty);
 
@@ -395,7 +395,7 @@ public String toString() {
      * @throws AccessException    Cannot access data.
      * @throws ExecutionException A Facility can't be retrieved or instantiated.
      */
-    public void addRows(Client client, ResultsTable results, Long imageId, Collection<? extends Roi> ijRois)
+    public void addRows(Client client, ResultsTable results, Long imageId, List<Roi> ijRois)
     throws ServiceException, AccessException, ExecutionException {
         this.addRows(client, results, imageId, ijRois, ROIWrapper.IJ_PROPERTY);
     }
@@ -415,7 +415,7 @@ public void addRows(Client client, ResultsTable results, Long imageId, Collectio
      * @throws AccessException    Cannot access data.
      * @throws ExecutionException A Facility can't be retrieved or instantiated.
      */
-    public void addRows(Client client, ResultsTable results, Long imageId, Collection<? extends Roi> ijRois,
+    public void addRows(Client client, ResultsTable results, Long imageId, List<Roi> ijRois,
                         String roiProperty)
     throws ServiceException, AccessException, ExecutionException {
         roiProperty = ROIWrapper.checkProperty(roiProperty);

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

@@ -359,7 +359,7 @@ public List<ImageWrapper> getImagesPairKeyValue(Client client, String key, Strin
      * @throws AccessException    Cannot access data.
      * @throws ExecutionException A Facility can't be retrieved or instantiated.
      */
-    public void addImages(Client client, Iterable<? extends ImageWrapper> images)
+    public void addImages(Client client, List<? extends ImageWrapper> images)
     throws ServiceException, AccessException, ExecutionException {
         for (ImageWrapper image : images) {
             addImage(client, image);

src/main/java/fr/igred/omero/roi/ROIWrapper.java

@@ -31,7 +31,6 @@
 import omero.model.Roi;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Comparator;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -170,7 +169,7 @@ public static List<ROIWrapper> fromImageJ(List<? extends ij.gui.Roi> ijRois, Str
      *
      * @return The converted list of ImageJ ROIs.
      */
-    public static List<ij.gui.Roi> toImageJ(Collection<? extends ROIWrapper> rois) {
+    public static List<ij.gui.Roi> toImageJ(List<? extends ROIWrapper> rois) {
         return toImageJ(rois, IJ_PROPERTY);
     }
 
@@ -184,7 +183,7 @@ public static List<ij.gui.Roi> toImageJ(Collection<? extends ROIWrapper> rois) {
      *
      * @return The converted list of ImageJ ROIs.
      */
-    public static List<ij.gui.Roi> toImageJ(Collection<? extends ROIWrapper> rois, String property) {
+    public static List<ij.gui.Roi> toImageJ(List<? extends ROIWrapper> rois, String property) {
         property = checkProperty(property);
         final int maxGroups = 255;
 
@@ -223,7 +222,7 @@ public void setData(ROIData data) {
      *
      * @param shapes List of GenericShapeWrapper.
      */
-    public void addShapes(Iterable<? extends GenericShapeWrapper<?>> shapes) {
+    public void addShapes(List<? extends GenericShapeWrapper<?>> shapes) {
         shapes.forEach(this::addShape);
     }
 

src/test/java/fr/igred/omero/roi/ROITest.java

@@ -101,7 +101,7 @@ public void testROI2() throws Exception {
     public void testRoiAddShapeAndDeleteIt() throws Exception {
         ImageWrapper image = client.getImage(IMAGE1.id);
 
-        Collection<GenericShapeWrapper<?>> shapes = new ArrayList<>(4);
+        List<GenericShapeWrapper<?>> shapes = new ArrayList<>(4);
         for (int i = 0; i < 4; i++) {
             RectangleWrapper rectangle = new RectangleWrapper();
             rectangle.setCoordinates(i * 2, i * 2, 10, 10);