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* Copyright (C) 2015 University of Dundee. All rights reserved.
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*
* 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.
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* 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.
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package integration.gateway;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import java.util.concurrent.ExecutionException;
import ome.model.units.BigResult;
import omero.api.IPixelsPrx;
import omero.gateway.exception.DSAccessException;
import omero.gateway.exception.DSOutOfServiceException;
import omero.gateway.facility.BrowseFacility;
import omero.gateway.facility.DataManagerFacility;
import omero.gateway.facility.MetadataFacility;
import omero.model.IObject;
import omero.model.ImagingEnvironment;
import omero.model.ImagingEnvironmentI;
import omero.model.PixelsType;
import omero.model.Temperature;
import omero.model.TemperatureI;
import omero.model.enums.UnitsTemperature;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import omero.gateway.model.AnnotationData;
import omero.gateway.model.ChannelData;
import omero.gateway.model.DataObject;
import omero.gateway.model.ImageAcquisitionData;
import omero.gateway.model.ImageData;
import omero.gateway.model.ProjectData;
import omero.gateway.model.TagAnnotationData;
import omero.gateway.model.TextualAnnotationData;
/**
*
* @author Dominik Lindner <a
* href="mailto:d.lindner@dundee.ac.uk">d.lindner@dundee.ac.uk</a>
* @since 5.1
*/
public class MetadataFacilityTest extends GatewayTest {
private ImageData img;
private Temperature temp;
private TagAnnotationData tag;
private TextualAnnotationData comment;
@Override
@BeforeClass(alwaysRun = true)
protected void setUp() throws Exception {
super.setUp();
initData();
}
@Test
public void testGetImageAcquisitionData() throws ExecutionException,
BigResult, DSOutOfServiceException, DSAccessException {
MetadataFacility mdf = gw.getFacility(MetadataFacility.class);
ImageAcquisitionData d = mdf.getImageAcquisitionData(rootCtx,
img.getId());
Assert.assertEquals(d.getTemperature(UnitsTemperature.CELSIUS), temp);
}
@Test
public void testgetChannelData() throws ExecutionException,
DSOutOfServiceException, DSAccessException {
MetadataFacility mdf = gw.getFacility(MetadataFacility.class);
List<ChannelData> channels = mdf.getChannelData(rootCtx, img.getId());
Assert.assertEquals(channels.size(), 3);
}
private void initData() throws Exception {
String name = UUID.randomUUID().toString();
IPixelsPrx svc = gw.getPixelsService(rootCtx);
List<IObject> types = svc
.getAllEnumerations(PixelsType.class.getName());
List<Integer> channels = new ArrayList<Integer>();
for (int i = 0; i < 3; i++) {
channels.add(i);
}
long imgId = svc.createImage(100, 100, 1, 1, channels,
(PixelsType) types.get(1), name, "").getValue();
img = gw.getFacility(BrowseFacility.class).getImage(rootCtx, imgId);
temp = new TemperatureI(20, UnitsTemperature.CELSIUS);
ImagingEnvironment env = new ImagingEnvironmentI();
env.setTemperature(temp);
img.asImage().setImagingEnvironment(env);
img = (ImageData) gw.getFacility(DataManagerFacility.class).saveAndReturnObject(rootCtx,
img);
DataManagerFacility dm = gw.getFacility(DataManagerFacility.class);
tag = dm.attachAnnotation(rootCtx, new TagAnnotationData("tag1", "test"), img);
comment = dm.attachAnnotation(rootCtx, new TextualAnnotationData("bla bla"), img);
}
@Test
public void testGetAnnotations() throws ExecutionException,
DSOutOfServiceException, DSAccessException {
MetadataFacility mdf = gw.getFacility(MetadataFacility.class);
List<AnnotationData> annos = mdf.getAnnotations(rootCtx, img);
Assert.assertEquals(annos.size(), 2);
int found = 0;
for (AnnotationData anno : annos) {
if (anno instanceof TagAnnotationData
&& anno.getId() == tag.getId())
found++;
if (anno instanceof TextualAnnotationData
&& anno.getId() == comment.getId())
found++;
}
Assert.assertEquals(found, 2);
}
@Test
public void testGetSpecificAnnotations() throws ExecutionException,
DSOutOfServiceException, DSAccessException {
final MetadataFacility mdf = gw.getFacility(MetadataFacility.class);
final List<DataObject> objs = new ArrayList<DataObject>();
objs.add(img);
final List<Class<? extends AnnotationData>> types = new ArrayList<Class<? extends AnnotationData>>();
types.add(TagAnnotationData.class);
Map<DataObject, List<AnnotationData>> annoMap = mdf.getAnnotations(
rootCtx, objs, types, null);
Assert.assertEquals(1, annoMap.size());
List<AnnotationData> annos = annoMap.get(img);
Assert.assertEquals(annos.size(), 1);
Assert.assertEquals(tag.getId(), annos.get(0).getId());
}
@Test(expectedExceptions = IllegalArgumentException.class)
public void testGetSpecificAnnotationsException()
throws ExecutionException, DSOutOfServiceException,
DSAccessException {
final MetadataFacility mdf = gw.getFacility(MetadataFacility.class);
// Test if exception is thrown when types are mixed.
final List<DataObject> objs = new ArrayList<DataObject>();
objs.add(img);
objs.add(new ProjectData());
final List<Class<? extends AnnotationData>> types = new ArrayList<Class<? extends AnnotationData>>();
types.add(TagAnnotationData.class);
mdf.getAnnotations(rootCtx, objs, types, null);
}
}