diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index 6023113ff5b52bad79616de1417c671cb83afd9b..829933ec0f7b8e430dd9a8fcb610a323b088960a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -19,8 +19,6 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
-import java.util.LinkedList;
import java.util.List;
import javax.servlet.http.HttpServletRequest;
@@ -28,12 +26,10 @@ import javax.servlet.http.HttpServletRequest;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ITabularData;
+import ch.systemsx.cisd.openbis.dss.screening.server.util.FeatureVectorLoaderMetadataProviderFactory;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
@@ -209,34 +205,7 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
private static IMetadataProvider createFeatureVectorsMetadataProvider()
{
final IEncapsulatedOpenBISService openBISService = ServiceProvider.getOpenBISService();
- return new IMetadataProvider()
- {
- @Override
- public SampleIdentifier tryGetSampleIdentifier(String samplePermId)
- {
- return openBISService.tryGetSampleIdentifier(samplePermId);
- }
-
- @Override
- public List<String> tryGetContainedDatasets(String datasetCode)
- {
- AbstractExternalData ds = openBISService.tryGetDataSet(datasetCode);
- ContainerDataSet container = ds.tryGetAsContainerDataSet();
- if (container != null)
- {
- List<String> list = new LinkedList<String>();
- for (AbstractExternalData contained : container.getContainedDataSets())
- {
- list.add(contained.getCode());
- }
- return list;
- } else
- {
- return Collections.emptyList();
- }
- }
-
- };
+ return FeatureVectorLoaderMetadataProviderFactory.createMetadataProvider(openBISService);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
index dbeeed4ee4e2cdb8429304e94cc2c7b0054c0555..62db47b673a8d3d8146cf7ade3a36131e249a4ab 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
@@ -18,27 +18,22 @@ package ch.systemsx.cisd.openbis.dss.generic.server.plugins;
import java.io.File;
import java.util.ArrayList;
-import java.util.Collections;
-import java.util.LinkedList;
import java.util.List;
import java.util.Properties;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractTableModelReportingPlugin;
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.screening.server.util.FeatureVectorLoaderMetadataProviderFactory;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
@@ -94,7 +89,7 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractTableModelRe
ArrayList<String> featureCodes = new ArrayList<String>(); // fetch all
WellFeatureCollection<FeatureTableRow> featuresCollection =
FeatureVectorLoader.fetchDatasetFeatures(datasetCodes, featureCodes, getDAO(),
- getMetadataProvider());
+ getMetadataProvider(datasetCodes));
List<CodeAndLabel> codeAndLabels = featuresCollection.getFeatureCodesAndLabels();
List<FeatureTableRow> rows = featuresCollection.getFeatures();
@@ -177,47 +172,17 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractTableModelRe
return dao;
}
- private IMetadataProvider getMetadataProvider()
+ private IMetadataProvider getMetadataProvider(final List<String> datasetCodes)
{
synchronized (this)
{
if (metadataProvider == null)
{
- metadataProvider = createFeatureVectorsMetadataProvider();
+ metadataProvider =
+ FeatureVectorLoaderMetadataProviderFactory.createMetadataProvider(
+ ServiceProvider.getOpenBISService(), datasetCodes);
}
}
return metadataProvider;
}
-
- private static IMetadataProvider createFeatureVectorsMetadataProvider()
- {
- final IEncapsulatedOpenBISService openBISService = ServiceProvider.getOpenBISService();
- return new IMetadataProvider()
- {
- @Override
- public SampleIdentifier tryGetSampleIdentifier(String samplePermId)
- {
- return openBISService.tryGetSampleIdentifier(samplePermId);
- }
-
- @Override
- public List<String> tryGetContainedDatasets(String datasetCode)
- {
- AbstractExternalData ds = openBISService.tryGetDataSet(datasetCode);
- ContainerDataSet container = ds.tryGetAsContainerDataSet();
- if (container != null)
- {
- List<String> list = new LinkedList<String>();
- for (AbstractExternalData contained : container.getContainedDataSets())
- {
- list.add(contained.getCode());
- }
- return list;
- } else
- {
- return Collections.emptyList();
- }
- }
- };
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 062a0c6e2db7d22148577a1850df24bfe844ad57..61603a40255cbf86cbf23100344896c27af02305 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -27,7 +27,6 @@ import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -66,12 +65,11 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.screening.server.logic.ImageRepresentationFormatFinder;
+import ch.systemsx.cisd.openbis.dss.screening.server.util.FeatureVectorLoaderMetadataProviderFactory;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.AbstractFormatSelectionCriterion;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImageRepresentationFormats;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
@@ -482,19 +480,26 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
{
List<String> codes = normalize(featureNames);
List<FeatureVectorDataset> result = new ArrayList<FeatureVectorDataset>();
+
+ IMetadataProvider metadataProvider =
+ FeatureVectorLoaderMetadataProviderFactory
+ .createMetadataProviderFromFeatureVectors(getOpenBISService(),
+ featureDatasets);
+
for (FeatureVectorDatasetReference dataset : featureDatasets)
{
- result.add(createFeatureVectorDataset(sessionToken, dataset, codes));
+ result.add(createFeatureVectorDataset(sessionToken, dataset, codes, metadataProvider));
}
return result;
}
private FeatureVectorDataset createFeatureVectorDataset(String sessionToken,
- FeatureVectorDatasetReference dataset, List<String> featureCodes)
+ FeatureVectorDatasetReference dataset, List<String> featureCodes,
+ IMetadataProvider metadataProvider)
{
WellFeatureCollection<FeatureTableRow> datasetFeatures =
FeatureVectorLoader.fetchDatasetFeatures(Arrays.asList(dataset.getDatasetCode()),
- featureCodes, getDAO(), createMetadataProvider());
+ featureCodes, getDAO(), metadataProvider);
List<FeatureVector> featureVectors = new ArrayList<FeatureVector>();
for (FeatureTableRow featureTableRow : datasetFeatures.getFeatures())
{
@@ -548,42 +553,12 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
{
WellFeatureCollection<FeatureTableRow> features =
FeatureVectorLoader.fetchWellFeatures(datasetWellReferences, featureNames, dao,
- createMetadataProvider());
+ FeatureVectorLoaderMetadataProviderFactory
+ .createMetadataProviderFromFeatureVectors(getOpenBISService(),
+ datasetWellReferences));
return createFeatureVectorList(features);
}
- private IMetadataProvider createMetadataProvider()
- {
- final IEncapsulatedOpenBISService openBISService = getOpenBISService();
- return new IMetadataProvider()
- {
- @Override
- public SampleIdentifier tryGetSampleIdentifier(String samplePermId)
- {
- return openBISService.tryGetSampleIdentifier(samplePermId);
- }
-
- @Override
- public List<String> tryGetContainedDatasets(String datasetCode)
- {
- AbstractExternalData ds = openBISService.tryGetDataSet(datasetCode);
- ContainerDataSet container = ds.tryGetAsContainerDataSet();
- if (container != null)
- {
- List<String> list = new LinkedList<String>();
- for (AbstractExternalData contained : container.getContainedDataSets())
- {
- list.add(contained.getCode());
- }
- return list;
- } else
- {
- return Collections.emptyList();
- }
- }
- };
- }
-
private List<FeatureVectorWithDescription> createFeatureVectorList(
final WellFeatureCollection<FeatureTableRow> features)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/util/FeatureVectorLoaderMetadataProviderFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/util/FeatureVectorLoaderMetadataProviderFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..e7473530085a8e3e83d0302a69fc012123d4ba3d
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/util/FeatureVectorLoaderMetadataProviderFactory.java
@@ -0,0 +1,164 @@
+/*
+ * Copyright 2013 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.dss.screening.server.util;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.IMetadataProvider;
+
+/**
+ * Creates a metadata provider for feature data set loader based on the IEncapsulatedOpenBISService
+ *
+ * @author Jakub Straszewski
+ */
+public class FeatureVectorLoaderMetadataProviderFactory
+{
+
+ private static HashMap<String, List<String>> createContainedDatasetMapFromFeatureVectors(
+ IEncapsulatedOpenBISService service,
+ List<? extends FeatureVectorDatasetReference> featureDatasets)
+ {
+
+ List<String> dsCodes = new LinkedList<String>();
+
+ for (FeatureVectorDatasetReference ds : featureDatasets)
+ {
+ dsCodes.add(ds.getDatasetCode());
+ }
+
+ return createContainedDatasetMap(service, dsCodes);
+ }
+
+ private static HashMap<String, List<String>> createContainedDatasetMap(
+ IEncapsulatedOpenBISService service, List<String> dsCodes)
+ {
+ List<AbstractExternalData> dataSets = service.listDataSetsByCode(dsCodes);
+
+ HashMap<String, List<String>> containedDataSetsMap = new HashMap<String, List<String>>();
+
+ for (AbstractExternalData dataSet : dataSets)
+ {
+ List<String> list = getContainedDatasets(dataSet);
+ containedDataSetsMap.put(dataSet.getCode(), list);
+ }
+ return containedDataSetsMap;
+ }
+
+ private static List<String> getContainedDatasets(AbstractExternalData dataSet)
+ {
+ List<String> list;
+ ContainerDataSet container = dataSet.tryGetAsContainerDataSet();
+ if (container != null)
+ {
+ list = new LinkedList<String>();
+ for (AbstractExternalData contained : container.getContainedDataSets())
+ {
+ list.add(contained.getCode());
+ }
+ } else
+ {
+ list = Collections.<String> emptyList();
+ }
+ return list;
+ }
+
+ /**
+ * Metadata provider that get's the request for dataset only once for all datasets at the moment
+ * of creation.
+ */
+ public static IMetadataProvider createMetadataProvider(
+ final IEncapsulatedOpenBISService openBISService, final List<String> dataSetCodes)
+ {
+
+ return createMetadataProvider(openBISService,
+ createContainedDatasetMap(openBISService, dataSetCodes));
+ }
+
+ /**
+ * Creates a metadata provider that will always ask openbis service about the required
+ * information
+ */
+ public static IMetadataProvider createMetadataProvider(
+ final IEncapsulatedOpenBISService openBISService)
+ {
+ return new IMetadataProvider()
+ {
+
+ @Override
+ public SampleIdentifier tryGetSampleIdentifier(String samplePermId)
+ {
+ return openBISService.tryGetSampleIdentifier(samplePermId);
+ }
+
+ @Override
+ public List<String> tryGetContainedDatasets(String datasetCode)
+ {
+ AbstractExternalData dataSet = openBISService.tryGetDataSet(datasetCode);
+ return getContainedDatasets(dataSet);
+ }
+ };
+ }
+
+ /**
+ * Metadata provider that get's the request for dataset only once for all datasets at the moment
+ * of creation
+ */
+ public static IMetadataProvider createMetadataProviderFromFeatureVectors(
+ final IEncapsulatedOpenBISService openBISService,
+ final List<? extends FeatureVectorDatasetReference> featureDatasets)
+ {
+
+ return createMetadataProvider(openBISService,
+ createContainedDatasetMapFromFeatureVectors(openBISService, featureDatasets));
+ }
+
+ private static IMetadataProvider createMetadataProvider(
+ final IEncapsulatedOpenBISService openBISService,
+ final HashMap<String, List<String>> containedDataSetsMap)
+ {
+
+ return new IMetadataProvider()
+ {
+ @Override
+ public SampleIdentifier tryGetSampleIdentifier(String samplePermId)
+ {
+ return openBISService.tryGetSampleIdentifier(samplePermId);
+ }
+
+ @Override
+ public List<String> tryGetContainedDatasets(String datasetCode)
+ {
+ if (containedDataSetsMap.containsKey(datasetCode))
+ {
+ return containedDataSetsMap.get(datasetCode);
+ } else
+ {
+ throw new IllegalArgumentException(
+ "Data set code unknown to the provider. " + datasetCode);
+ }
+ }
+ };
+ }
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index d13e877cc867f0b0b42691fc0257ce545aafc7a9..f6e57d93178496f316ceae350537d908c822b516 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -23,6 +23,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.LinkedList;
import java.util.List;
import org.aopalliance.intercept.MethodInterceptor;
@@ -72,9 +73,9 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.Ds
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtilTest;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -339,10 +340,14 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
@Test
public void testLoadFeatures()
{
+ prepareFeatureVectorContainedDatasets(new long[]
+ { 1, 2 });
+
prepareAssetDataSetsAreAccessible();
prepareLockDataSet("ds1", DATASET_CODE2);
FeatureVectorDatasetReference r1 = createFeatureVectorDatasetReference(DATASET_CODE);
FeatureVectorDatasetReference r2 = createFeatureVectorDatasetReference(DATASET_CODE2);
+
String[][] featureCodesPerDataset = new String[][]
{
{ "F1", "F2" } };
@@ -378,7 +383,6 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
private void prepareLoadFeatures(long[] dataSetIDs, String[][] featureCodesPerDataset)
{
- prepareFeatureVectorContainedDatasets(dataSetIDs);
prepareListAnalysisDatasets(dataSetIDs);
prepareListContainers(dataSetIDs);
prepareGetFeatureDefinitions(dataSetIDs, featureCodesPerDataset);
@@ -928,16 +932,20 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
{
String[] permIDs = new String[dataSetIDs.length];
+ List<AbstractExternalData> result = new LinkedList<AbstractExternalData>();
for (int i = 0; i < dataSetIDs.length; i++)
{
long id = dataSetIDs[i];
permIDs[i] = "ds" + id;
- AbstractExternalData d = new PhysicalDataSet(); // this dataset is only asked if it is a
- // container
- one(service).tryGetDataSet(permIDs[i]);
- will(returnValue(d));
+ PhysicalDataSet dataSet = new PhysicalDataSet();
+ dataSet.setCode(permIDs[i]);
+
+ result.add(dataSet);
+
}
+ one(service).listDataSetsByCode(with(equal(Arrays.asList(permIDs))));
+ will(returnValue(result));
}
});
}