From f79880b7ac59f9a4721c3deaa8c2e527724e92dd Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 15 Feb 2011 12:58:47 +0000
Subject: [PATCH] LMS-2040 bug fixing
HCSImageDatasetLoader.getSegmentationImageDatasets. Tests written for loading
child data sets like segmentation images and feature vectors.
SVN: 19976
---
.../api/v1/ScreeningClientApiTester.java | 40 +++++
.../logic/FeatureVectorDatasetLoader.java | 80 +---------
.../server/logic/HCSImageDatasetLoader.java | 103 ++++++++++--
.../logic/FeatureVectorDatasetLoaderTest.java | 125 +++++++++++++++
.../logic/HCSImageDatasetLoaderTest.java | 148 ++++++++++++++++++
5 files changed, 403 insertions(+), 93 deletions(-)
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoaderTest.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoaderTest.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
index 135f28e0036..371787ab23d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTester.java
@@ -46,6 +46,7 @@ import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPasswordField;
import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.text.JTextComponent;
@@ -153,6 +154,15 @@ public class ScreeningClientApiTester
loadImagesByDataSetCode();
}
});
+ JMenuItem overlayItem = new JMenuItem("List Overlay Data Sets");
+ callApiMenu.add(overlayItem);
+ overlayItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ loadOverlays();
+ }
+ });
}
void setUp(String[] args)
@@ -180,6 +190,36 @@ public class ScreeningClientApiTester
}
}
+ private void loadOverlays()
+ {
+ content.removeAll();
+ final JPanel panel = new JPanel();
+ panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
+ content.add(panel, BorderLayout.NORTH);
+ JTextArea textArea = new JTextArea();
+ textArea.setEditable(false);
+ content.add(textArea, BorderLayout.CENTER);
+ List<Plate> plates = facade.listPlates();
+ panel.add(new JLabel(plates.size() + " plates", JLabel.LEFT));
+ validate(panel);
+ List<ImageDatasetReference> rawImageDatasets = facade.listRawImageDatasets(plates);
+ panel.add(new JLabel(rawImageDatasets.size() + " raw image data sets", JLabel.LEFT));
+ validate(panel);
+ List<ImageDatasetReference> overlays = facade.listSegmentationImageDatasets(plates);
+ panel.add(new JLabel(overlays.size() + " overlay data sets:", JLabel.LEFT));
+ StringBuilder builder = new StringBuilder();
+ for (ImageDatasetReference overlay : overlays)
+ {
+ builder.append(overlay).append('\n');
+ ImageDatasetReference parent = overlay.getParentImageDatasetReference();
+ if (parent != null)
+ {
+ builder.append(" overlay data set of ").append(parent).append('\n');
+ }
+ }
+ textArea.setText(builder.toString());
+ }
+
private void loadPlates()
{
content.removeAll();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
index cc4381c9cfa..af7ae73c799 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
@@ -21,10 +21,7 @@ import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -103,7 +100,6 @@ class FeatureVectorDatasetLoader extends HCSImageDatasetLoader
private void loadFeatureVectorDatasets()
{
final Map<Long, ExternalData> featureVectorDatasetSet = new HashMap<Long, ExternalData>();
- IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
List<ExternalData> imageDatasets = new ArrayList<ExternalData>();
for (ExternalData dataset : getDatasets())
@@ -118,83 +114,11 @@ class FeatureVectorDatasetLoader extends HCSImageDatasetLoader
imageDatasets.add(dataset);
}
}
-
- List<ExternalData> connectedFeatureVectorDatasets =
- listChildrenFeatureVectorDatasets(datasetLister, extractIds(imageDatasets));
- Map<Long, Set<Long>> featureVectorToImageDatasetIdsMap =
- datasetLister.listParentIds(extractIds(connectedFeatureVectorDatasets));
- Map<Long, List<ExternalData>> featureVectorToImageDatasetsMap =
- createFeatureVectorToImageDatasetsMap(featureVectorToImageDatasetIdsMap,
- imageDatasets);
- // Implementation note: some data sets in this loop may overwrite data from the first loop.
- // This is intended as we want to keep the parent relationship of the feature vector data
- // sets, if they exist.
- for (ExternalData fv : connectedFeatureVectorDatasets)
- {
- List<ExternalData> parentImageDatasets =
- featureVectorToImageDatasetsMap.get(fv.getId());
- if (parentImageDatasets != null)
- {
- fv.setParents(parentImageDatasets);
- }
- featureVectorDatasetSet.put(fv.getId(), fv);
- }
+
+ gatherChildrenDataSets(featureVectorDatasetSet, imageDatasets, featureVectorDatasetTypeCode);
featureVectorDatasets = featureVectorDatasetSet.values();
}
- private List<ExternalData> listChildrenFeatureVectorDatasets(IDatasetLister datasetLister,
- Collection<Long> imageDatasetIds)
- {
- List<ExternalData> datasets = datasetLister.listByParentTechIds(imageDatasetIds);
- return ScreeningUtils.filterExternalDataByTypePattern(datasets,
- featureVectorDatasetTypeCode);
- }
-
- private static Map<Long/* feature vector dataset id */, List<ExternalData/* image dataset */>> createFeatureVectorToImageDatasetsMap(
- Map<Long, Set<Long>> featureVectorToImageDatasetsMap, List<ExternalData> imageDatasets)
- {
- Map<Long, List<ExternalData>> featureVectorToImageDatasetMap =
- new HashMap<Long, List<ExternalData>>();
- for (Entry<Long, Set<Long>> entry : featureVectorToImageDatasetsMap.entrySet())
- {
- List<ExternalData> parentImageDatasets =
- findDatasetsWithIds(entry.getValue(), imageDatasets);
- // NOTE: if a feature vector dataset has more than one image dataset parent, all the
- // parents will be ignored.
- if (parentImageDatasets.size() == 1)
- {
- Long featureVectorDatasetId = entry.getKey();
- featureVectorToImageDatasetMap.put(featureVectorDatasetId, parentImageDatasets);
- }
- }
- return featureVectorToImageDatasetMap;
- }
-
- // returns all dataset which have an id contained in the specified id set
- private static List<ExternalData> findDatasetsWithIds(Set<Long> datasetIds,
- List<ExternalData> datasets)
- {
- List<ExternalData> found = new ArrayList<ExternalData>();
- for (ExternalData dataset : datasets)
- {
- if (datasetIds.contains(dataset.getId()))
- {
- found.add(dataset);
- }
- }
- return found;
- }
-
- private static Collection<Long> extractIds(List<ExternalData> datasets)
- {
- List<Long> ids = new ArrayList<Long>();
- for (ExternalData dataset : datasets)
- {
- ids.add(dataset.getId());
- }
- return ids;
- }
-
private List<FeatureVectorDatasetReference> asFeatureVectorDatasetReferences()
{
List<FeatureVectorDatasetReference> result = new ArrayList<FeatureVectorDatasetReference>();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
index 98810053aa9..625579a46b1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoader.java
@@ -18,8 +18,13 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -37,6 +42,49 @@ class HCSImageDatasetLoader extends PlateDatasetLoader
{
// TODO 2010-05-27, CR : See PlateDatasetLoader todo comment
+ protected static Collection<Long> extractIds(List<ExternalData> datasets)
+ {
+ List<Long> ids = new ArrayList<Long>();
+ for (ExternalData dataset : datasets)
+ {
+ ids.add(dataset.getId());
+ }
+ return ids;
+ }
+
+ private static Map<Long/* child data set id */, List<ExternalData/* parent data sets */>> createChildDataSetToParentDataSetsMap(
+ Map<Long, Set<Long>> childIdToParentIdsMap, List<ExternalData> parentDatasets)
+ {
+ Map<Long, List<ExternalData>> childDataSetToParentDataSetsMap =
+ new HashMap<Long, List<ExternalData>>();
+ for (Entry<Long, Set<Long>> entry : childIdToParentIdsMap.entrySet())
+ {
+ List<ExternalData> parents =
+ findDatasetsWithIds(entry.getValue(), parentDatasets);
+ // NOTE: if a child data set has more than one parent data set, all the
+ // parents will be ignored.
+ if (parents.size() == 1)
+ {
+ Long childId = entry.getKey();
+ childDataSetToParentDataSetsMap.put(childId, parents);
+ }
+ }
+ return childDataSetToParentDataSetsMap;
+ }
+
+ private static List<ExternalData> findDatasetsWithIds(Set<Long> datasetIds, List<ExternalData> datasets)
+ {
+ List<ExternalData> found = new ArrayList<ExternalData>();
+ for (ExternalData dataset : datasets)
+ {
+ if (datasetIds.contains(dataset.getId()))
+ {
+ found.add(dataset);
+ }
+ }
+ return found;
+ }
+
HCSImageDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
String homeSpaceOrNull, Collection<? extends PlateIdentifier> plates,
String... datasetTypeCodes)
@@ -70,9 +118,20 @@ class HCSImageDatasetLoader extends PlateDatasetLoader
private List<ExternalData> getSegmentationImageDatasets()
{
load();
- return filterSegmententationImageDatasets();
+ List<ExternalData> imageDatasets = new ArrayList<ExternalData>();
+ for (ExternalData dataset : getDatasets())
+ {
+ if (ScreeningUtils.isBasicHcsImageDataset(dataset))
+ {
+ imageDatasets.add(dataset);
+ }
+ }
+ Map<Long, ExternalData> segmentationImageDataSets = new HashMap<Long, ExternalData>();
+ gatherChildrenDataSets(segmentationImageDataSets, imageDatasets,
+ ScreeningConstants.HCS_SEGMENTATION_IMAGE_DATASET_TYPE_PATTERN);
+ return new ArrayList<ExternalData>(segmentationImageDataSets.values());
}
-
+
/**
* Return the image datasets references for the specified plates.
*/
@@ -123,19 +182,6 @@ class HCSImageDatasetLoader extends PlateDatasetLoader
return result;
}
- private List<ExternalData> filterSegmententationImageDatasets()
- {
- List<ExternalData> result = new ArrayList<ExternalData>();
- for (ExternalData externalData : getDatasets())
- {
- if (ScreeningUtils.isSegmentationHcsImageDataset(externalData))
- {
- result.add(externalData);
- }
- }
- return result;
- }
-
private List<ImageDatasetReference> asImageDatasetReferences(List<ExternalData> imageDatasets)
{
List<ImageDatasetReference> references = new ArrayList<ImageDatasetReference>();
@@ -150,6 +196,33 @@ class HCSImageDatasetLoader extends PlateDatasetLoader
return references;
}
+ protected void gatherChildrenDataSets(final Map<Long, ExternalData> childrenDataSets,
+ List<ExternalData> parentDataSets, String childTypePattern)
+ {
+ IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
+ List<ExternalData> filteredChildrenDataSets =
+ ScreeningUtils.filterExternalDataByTypePattern(
+ datasetLister.listByParentTechIds(extractIds(parentDataSets)),
+ childTypePattern);
+ Map<Long, Set<Long>> childIdToParentIdsMap =
+ datasetLister.listParentIds(extractIds(filteredChildrenDataSets));
+ Map<Long, List<ExternalData>> childIdToParentDataSetsMap =
+ createChildDataSetToParentDataSetsMap(childIdToParentIdsMap, parentDataSets);
+ // Implementation note: some data sets in this loop may overwrite data from the first loop.
+ // This is intended as we want to keep the parent relationship of the feature vector data
+ // sets, if they exist.
+ for (ExternalData child : filteredChildrenDataSets)
+ {
+ List<ExternalData> parentImageDatasets =
+ childIdToParentDataSetsMap.get(child.getId());
+ if (parentImageDatasets != null)
+ {
+ child.setParents(parentImageDatasets);
+ }
+ childrenDataSets.put(child.getId(), child);
+ }
+ }
+
private ExternalData tryGetParent(ExternalData externalData)
{
if (externalData.getParents() != null && externalData.getParents().size() == 1)
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoaderTest.java
new file mode 100644
index 00000000000..99b15b63391
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoaderTest.java
@@ -0,0 +1,125 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Set;
+
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
+import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FeatureVectorDatasetLoaderTest extends AbstractServerTestCase
+{
+ private IScreeningBusinessObjectFactory screeningBOFactory;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ screeningBOFactory = context.mock(IScreeningBusinessObjectFactory.class);
+ }
+
+ @Test
+ public void testGetFeatureVectorDatasets()
+ {
+ final RecordingMatcher<ListOrSearchSampleCriteria> recordingCriteriaMatcher =
+ new RecordingMatcher<ListOrSearchSampleCriteria>();
+ final ExternalData ids1 = new DataSetBuilder(1l).code("ids1").type("HCS_IMAGE").getDataSet();
+ final ExternalData fds1 = new DataSetBuilder(11l).code("fds1").type("HCS_ANALYSIS_WELL_FEATURES").getDataSet();
+ final ExternalData fds2 = new DataSetBuilder(12l).code("fds2").type("HCS_ANALYSIS_WELL_FEATURES").getDataSet();
+ final ExternalData ids2 = new DataSetBuilder(2l).code("ids2").type("HCS_IMAGE").getDataSet();
+ final ExternalData fds3 = new DataSetBuilder(21l).code("fds3").type("HCS_ANALYSIS_WELL_FEATURES").getDataSet();
+ final ExternalData fds4 = new DataSetBuilder(100l).code("fds4").type("HCS_ANALYSIS_WELL_FEATURES").getDataSet();
+ final ExternalData ds1 = new DataSetBuilder(101l).code("ds1").type("BLABLA").getDataSet();
+ context.checking(new Expectations()
+ {
+ {
+ one(screeningBOFactory).createSampleLister(SESSION);
+ will(returnValue(sampleLister));
+ allowing(screeningBOFactory).createDatasetLister(SESSION);
+ will(returnValue(datasetLister));
+
+ one(sampleLister).list(with(recordingCriteriaMatcher));
+ ArrayList<Sample> samples = new ArrayList<Sample>();
+ samples.add(new SampleBuilder("/S/P1").id(42l).permID("s-1").getSample());
+ will(returnValue(samples));
+
+ one(datasetLister).listBySampleIds(Arrays.asList(42l));
+ will(returnValue(Arrays.asList(ids1, fds1, fds2, ids2, fds3, fds4, ds1)));
+
+ one(datasetLister).listByParentTechIds(Arrays.asList(1l, 2l));
+ will(returnValue(Arrays.asList(fds1, fds2, fds3, ds1)));
+
+ one(datasetLister).listParentIds(Arrays.asList(11l, 12l, 21l));
+ HashMap<Long, Set<Long>> map = new HashMap<Long, Set<Long>>();
+ map.put(11l, Collections.singleton(1l));
+ map.put(12l, Collections.singleton(1l));
+ map.put(21l, Collections.singleton(2l));
+ will(returnValue(map));
+ }
+ });
+ List<PlateIdentifier> plateIdentifiers =
+ Arrays.<PlateIdentifier> asList(new PlateIdentifier("P1", "S", "s-1"));
+ FeatureVectorDatasetLoader loader =
+ new FeatureVectorDatasetLoader(SESSION, screeningBOFactory, null, plateIdentifiers);
+
+ List<ExternalData> datasets = new ArrayList<ExternalData>(loader.getFeatureVectorDatasets());
+
+ assertEquals("[]", Arrays.asList(recordingCriteriaMatcher.recordedObject().trySampleCodes()).toString());
+ assertEquals("[s-1]", Arrays.asList(recordingCriteriaMatcher.recordedObject().trySamplePermIds()).toString());
+ Collections.sort(datasets, new Comparator<ExternalData>()
+ {
+ public int compare(ExternalData o1, ExternalData o2)
+ {
+ return o1.getCode().compareTo(o2.getCode());
+ }
+ });
+ assertSame(fds1, datasets.get(0));
+ assertSame(ids1, datasets.get(0).getParents().iterator().next());
+ assertEquals(1, datasets.get(0).getParents().size());
+ assertSame(fds2, datasets.get(1));
+ assertSame(ids1, datasets.get(1).getParents().iterator().next());
+ assertEquals(1, datasets.get(1).getParents().size());
+ assertSame(fds3, datasets.get(2));
+ assertSame(ids2, datasets.get(2).getParents().iterator().next());
+ assertEquals(1, datasets.get(2).getParents().size());
+ assertSame(fds4, datasets.get(3));
+ assertEquals(null, datasets.get(3).getParents());
+ assertEquals(4, datasets.size());
+ context.assertIsSatisfied();
+ }
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoaderTest.java
new file mode 100644
index 00000000000..8ad5b2c618a
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoaderTest.java
@@ -0,0 +1,148 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Set;
+
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataStoreBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
+import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class HCSImageDatasetLoaderTest extends AbstractServerTestCase
+{
+ private static final String STORE_CODE = "store-1";
+ private static final String DOWNLOAD_URL = "http://download";
+ private static final String HOST_URL = "http://host";
+
+ private IScreeningBusinessObjectFactory screeningBOFactory;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ screeningBOFactory = context.mock(IScreeningBusinessObjectFactory.class);
+ }
+
+ private DataSetBuilder dataSet(long id)
+ {
+ DataStoreBuilder dataStoreBuilder = new DataStoreBuilder(STORE_CODE);
+ dataStoreBuilder.hostUrl(HOST_URL).downloadUrl(DOWNLOAD_URL);
+ Experiment experiment = new ExperimentBuilder().identifier("/S/P/E1").getExperiment();
+ return new DataSetBuilder(id).store(dataStoreBuilder.getStore()).experiment(experiment);
+ }
+
+ @Test
+ public void testGetSegmentationImageDatasetReferences()
+ {
+ final RecordingMatcher<ListOrSearchSampleCriteria> recordingCriteriaMatcher =
+ new RecordingMatcher<ListOrSearchSampleCriteria>();
+ SampleBuilder sampleBuilder = new SampleBuilder("/S/P1").id(42l).permID("s-1");
+ VocabularyTerm value = new VocabularyTerm();
+ value.setCode("96_WELLS_8X12");
+ sampleBuilder.property(ScreeningConstants.PLATE_GEOMETRY).value(value);
+ final Sample sample = sampleBuilder.getSample();
+ final ExternalData ids1 = dataSet(1l).code("ids1").type("HCS_IMAGE").sample(sample).getDataSet();
+ final ExternalData sds1 = dataSet(11l).code("sds1").type("HCS_IMAGE_SEGMENTATION").sample(sample).getDataSet();
+ final ExternalData sds2 = dataSet(12l).code("sds2").type("HCS_IMAGE_SEGMENTATION").sample(sample).getDataSet();
+ final ExternalData ids2 = dataSet(2l).code("ids2").type("HCS_IMAGE").sample(sample).getDataSet();
+ final ExternalData sds3 = dataSet(21l).code("sds3").type("HCS_IMAGE_SEGMENTATION").sample(sample).getDataSet();
+ final ExternalData sds4 = dataSet(100l).code("sds4").type("HCS_IMAGE_SEGMENTATION").getDataSet();
+ final ExternalData ds1 = dataSet(101l).code("ds1").type("BLABLA").sample(sample).getDataSet();
+ context.checking(new Expectations()
+ {
+ {
+ one(screeningBOFactory).createSampleLister(SESSION);
+ will(returnValue(sampleLister));
+ allowing(screeningBOFactory).createDatasetLister(SESSION);
+ will(returnValue(datasetLister));
+
+ one(sampleLister).list(with(recordingCriteriaMatcher));
+ ArrayList<Sample> samples = new ArrayList<Sample>();
+ samples.add(sample);
+ will(returnValue(samples));
+
+ one(datasetLister).listBySampleIds(Arrays.asList(42l));
+ will(returnValue(Arrays.asList(ids1, sds1, sds2, ids2, sds3, sds4, ds1)));
+
+ one(datasetLister).listByParentTechIds(Arrays.asList(1l, 2l));
+ will(returnValue(Arrays.asList(sds1, sds2, sds3, ds1)));
+
+ one(datasetLister).listParentIds(Arrays.asList(11l, 12l, 21l));
+ HashMap<Long, Set<Long>> map = new HashMap<Long, Set<Long>>();
+ map.put(11l, Collections.singleton(1l));
+ map.put(12l, Collections.singleton(1l));
+ map.put(21l, Collections.singleton(2l));
+ will(returnValue(map));
+ }
+ });
+ List<PlateIdentifier> plateIdentifiers =
+ Arrays.<PlateIdentifier> asList(new PlateIdentifier("P1", "S", "s-1"));
+ HCSImageDatasetLoader loader =
+ new HCSImageDatasetLoader(SESSION, screeningBOFactory, null, plateIdentifiers);
+
+ List<ImageDatasetReference> references = loader.getSegmentationImageDatasetReferences();
+
+ assertEquals("[]", Arrays
+ .asList(recordingCriteriaMatcher.recordedObject().trySampleCodes()).toString());
+ assertEquals("[s-1]",
+ Arrays.asList(recordingCriteriaMatcher.recordedObject().trySamplePermIds())
+ .toString());
+ Collections.sort(references, new Comparator<ImageDatasetReference>()
+ {
+ public int compare(ImageDatasetReference o1, ImageDatasetReference o2)
+ {
+ return o1.getDatasetCode().compareTo(o2.getDatasetCode());
+ }
+ });
+ assertEquals("sds1 (plate: /S/P1 [s-1])", references.get(0).toString());
+ assertEquals("ids1 (plate: /S/P1 [s-1])", references.get(0).getParentImageDatasetReference().toString());
+ assertEquals("sds2 (plate: /S/P1 [s-1])", references.get(1).toString());
+ assertEquals("ids1 (plate: /S/P1 [s-1])", references.get(1).getParentImageDatasetReference().toString());
+ assertEquals("sds3 (plate: /S/P1 [s-1])", references.get(2).toString());
+ assertEquals("ids2 (plate: /S/P1 [s-1])", references.get(2).getParentImageDatasetReference().toString());
+ assertEquals(3, references.size());
+ context.assertIsSatisfied();
+
+ }
+
+}
--
GitLab