diff --git a/screening/.classpath b/screening/.classpath
index 2fa42baa063251bf399987b76769420827521cf4..b64b10e9876dfea4a6b87782256a4fee07766ad4 100644
--- a/screening/.classpath
+++ b/screening/.classpath
@@ -42,5 +42,6 @@
<classpathentry kind="lib" path="/libraries/jhdf5/cisd-jhdf5-batteries_included_lin_win_mac.jar"/>
<classpathentry kind="lib" path="/libraries/hdf5"/>
<classpathentry kind="lib" path="/libraries/nativedata"/>
+ <classpathentry kind="lib" path="/libraries/fastutil/fastutil.jar" sourcepath="/libraries/fastutil/fastutil-src.zip"/>
<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
</classpath>
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 63b64f1093a158586aaaff1c320c8e421c15218a..0ed55be5b6d4e0742e74b25461976a19c74387c2 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
@@ -16,7 +16,12 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+import it.unimi.dsi.fastutil.longs.Long2ObjectLinkedOpenHashMap;
+import it.unimi.dsi.fastutil.longs.Long2ObjectSortedMap;
+
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
@@ -44,7 +49,7 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
FeatureVectorDatasetLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, String dataStoreBaseURL,
- List<? extends PlateIdentifier> plates)
+ Collection<? extends PlateIdentifier> plates)
{
super(session, businessObjectFactory, dataStoreBaseURL, plates,
ScreeningConstants.IMAGE_DATASET_TYPE,
@@ -62,10 +67,8 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
private void loadFeatureVectorDatasets()
{
- // TODO 2010-05-26, CR, : This is slow if there are a large number of image data sets
- // Need to add a query to the dataset lister that returns, for a collection of tech ids, a
- // child datasets and their parents.
- featureVectorDatasets = new ArrayList<ExternalData>();
+ final Long2ObjectSortedMap<ExternalData> featureVectorDatasetSet =
+ new Long2ObjectLinkedOpenHashMap<ExternalData>();
IDatasetLister datasetLister =
businessObjectFactory.createDatasetLister(session, dataStoreBaseURL);
@@ -73,23 +76,33 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
{
if (ScreeningUtils.isTypeEqual(data, ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE))
{
- featureVectorDatasets.add(data);
- } else
+ featureVectorDatasetSet.put(data.getId(), data);
+ }
+ }
+
+ // 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 data : getDatasets())
+ {
+ if (ScreeningUtils.isTypeEqual(data, ScreeningConstants.IMAGE_DATASET_TYPE))
{
- List<ExternalData> children =
+ // TODO 2010-05-26, CR, : This way to access the database one by one is slow if
+ // there are a large number of image data sets
+ // Need to add a query to the dataset lister that returns, for a collection of tech
+ // ids, a child datasets and their parents.
+ final List<ExternalData> children =
datasetLister.listByParentTechId(new TechId(data.getId()));
- ArrayList<ExternalData> parentList = new ArrayList<ExternalData>();
- parentList.add(data);
for (ExternalData child : children)
{
- child.setParents(parentList);
+ child.setParents(Collections.singleton(data));
+ featureVectorDatasetSet.put(child.getId(), child);
}
- featureVectorDatasets.addAll(children);
}
}
featureVectorDatasets =
- ScreeningUtils.filterExternalDataByType(featureVectorDatasets,
+ ScreeningUtils.filterExternalDataByType(featureVectorDatasetSet.values(),
featureVectorDatasetTypeCode);
}
@@ -106,22 +119,21 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
protected FeatureVectorDatasetReference asFeatureVectorDataset(ExternalData externalData)
{
DataStore dataStore = externalData.getDataStore();
- if (externalData.getParents() == null || externalData.getParents().size() == 0)
+ if (externalData.getParents() == null || externalData.getParents().isEmpty())
{
return new FeatureVectorDatasetReference(externalData.getCode(),
getDataStoreUrlFromDataStore(dataStore), createPlateIdentifier(externalData),
- extractPlateGeometry(externalData), externalData.getRegistrationDate(),
- null);
+ extractPlateGeometry(externalData), externalData.getRegistrationDate(), null);
} else
{
- // Note: this only works reliably because this class sets the parents of the feature
+ // Note: this only works reliably because this class sets the parents of the feature
// vector data sets itself and sets it to a list with exactly one entry!
// (see loadFeatureVectorDatasets() above)
final ExternalData parentDataset = externalData.getParents().iterator().next();
return new FeatureVectorDatasetReference(externalData.getCode(),
getDataStoreUrlFromDataStore(dataStore), createPlateIdentifier(parentDataset),
- extractPlateGeometry(parentDataset), externalData.getRegistrationDate(),
- asImageDataset(parentDataset));
+ extractPlateGeometry(parentDataset), externalData.getRegistrationDate(),
+ asImageDataset(parentDataset));
}
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
index b6e1f5684224f4079b23e751d898fbd68832241e..fedb87144b078c9e511744a8ef907c6894858276 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
@@ -37,7 +38,7 @@ class ImageDatasetLoader extends PlateDatasetLoader
// TODO 2010-05-27, CR : See PlateDatasetLoader todo comment
ImageDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
- String dataStoreBaseURL, List<? extends PlateIdentifier> plates,
+ String dataStoreBaseURL, Collection<? extends PlateIdentifier> plates,
String... datasetTypeCodes)
{
super(session, businessObjectFactory, dataStoreBaseURL, plates,
@@ -51,15 +52,18 @@ class ImageDatasetLoader extends PlateDatasetLoader
public List<ImageDatasetReference> getImageDatasets()
{
load();
- return asImageDatasets();
+ return filterImageDatasets();
}
- private List<ImageDatasetReference> asImageDatasets()
+ private List<ImageDatasetReference> filterImageDatasets()
{
List<ImageDatasetReference> result = new ArrayList<ImageDatasetReference>();
for (ExternalData externalData : getDatasets())
{
- result.add(asImageDataset(externalData));
+ if (ScreeningUtils.isTypeEqual(externalData, ScreeningConstants.IMAGE_DATASET_TYPE))
+ {
+ result.add(asImageDataset(externalData));
+ }
}
return result;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java
index 6e604cc9dcc4ac5c0ff0274f40dd67d42061aa85..7b10358d884a39779307d9a44e644704bf4bfa7e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java
@@ -3,9 +3,12 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import static ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants.DATA_STORE_SERVER_WEB_APPLICATION_NAME;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
+import org.apache.commons.lang.StringUtils;
+
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
@@ -44,7 +47,7 @@ class PlateDatasetLoader
protected final String dataStoreBaseURL;
// Parameter state
- private final List<? extends PlateIdentifier> plates;
+ private final Collection<? extends PlateIdentifier> plates;
private final String[] datasetTypeCodes;
@@ -58,7 +61,7 @@ class PlateDatasetLoader
private HashMap<Long, Sample> samplesById;
PlateDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
- String dataStoreBaseURL, List<? extends PlateIdentifier> plates,
+ String dataStoreBaseURL, Collection<? extends PlateIdentifier> plates,
String... datasetTypeCodes)
{
this.session = session;
@@ -122,7 +125,9 @@ class PlateDatasetLoader
{
for (PlateIdentifier plate : plates)
{
- Sample sample = samplesByIdentifier.get(createSampleIdentifier(plate));
+ Sample sample =
+ samplesByIdentifier.get(createSampleIdentifier(plate, session
+ .tryGetHomeGroupCode()));
// Make sure the sample and plate have the same *identifier* not just code
String plateSpaceCodeOrNull = plate.tryGetSpaceCode();
Space sampleSpaceOrNull = sample.getSpace();
@@ -180,7 +185,7 @@ class PlateDatasetLoader
}
}
- throw new UserFailureException("Sample " + sample.getIdentifier() + " has no property "
+ throw new UserFailureException("Sample '" + sample.getIdentifier() + "' has no property "
+ ScreeningConstants.PLATE_GEOMETRY);
}
@@ -210,7 +215,7 @@ class PlateDatasetLoader
private List<Long> extractSampleIds()
{
- ArrayList<Long> sampleIds = new ArrayList<Long>();
+ ArrayList<Long> sampleIds = new ArrayList<Long>(samples.size());
for (Sample sample : samples)
{
sampleIds.add(sample.getId());
@@ -237,17 +242,31 @@ class PlateDatasetLoader
return datastoreUrl;
}
- protected static SampleIdentifier createSampleIdentifier(PlateIdentifier plate)
+ protected static SampleIdentifier createSampleIdentifier(PlateIdentifier plate,
+ String homeSpaceCodeOrNull)
{
SampleOwnerIdentifier owner;
String spaceCode = plate.tryGetSpaceCode();
- if (spaceCode != null)
+ if (StringUtils.isNotBlank(spaceCode))
{
- SpaceIdentifier space = new SpaceIdentifier(DatabaseInstanceIdentifier.HOME, spaceCode);
+ final SpaceIdentifier space =
+ new SpaceIdentifier(DatabaseInstanceIdentifier.HOME, spaceCode);
owner = new SampleOwnerIdentifier(space);
} else
{
- owner = new SampleOwnerIdentifier(DatabaseInstanceIdentifier.createHome());
+ if (spaceCode == null)
+ {
+ owner = new SampleOwnerIdentifier(DatabaseInstanceIdentifier.createHome());
+ } else
+ {
+ if (homeSpaceCodeOrNull == null)
+ {
+ throw new UserFailureException("No space given and user has no home space.");
+ }
+ final SpaceIdentifier space =
+ new SpaceIdentifier(DatabaseInstanceIdentifier.HOME, homeSpaceCodeOrNull);
+ owner = new SampleOwnerIdentifier(space);
+ }
}
return SampleIdentifier.createOwnedBy(owner, plate.getPlateCode());
}