diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index bcc608330bbebe39e73caaa34b581a20bcf5662d..5f750f4ca1fcd476b279bf813027aa3555439f7d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -118,6 +118,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleAssignment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
@@ -126,7 +127,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.UpdatedSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTermReplacement;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentHolderPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
@@ -169,6 +169,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.DataTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.DtoConverters;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.GridCustomExpressionTranslator.GridCustomFilterTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.GroupTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.PersonTranslator;
@@ -179,7 +180,6 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.TypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTermTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.GridCustomExpressionTranslator.GridCustomFilterTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
@@ -402,8 +402,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
{
IHibernateSearchDAO searchDAO = getDAOFactory().getHibernateSearchDAO();
final Collection<Long> sampleIds =
- searchDAO.searchForEntityIds(criteria, DtoConverters
- .convertEntityKind(EntityKind.SAMPLE));
+ searchDAO.searchForEntityIds(criteria,
+ DtoConverters.convertEntityKind(EntityKind.SAMPLE));
final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
return sampleLister.list(new ListOrSearchSampleCriteria(sampleIds));
} catch (final DataAccessException ex)
@@ -447,7 +447,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
datasets = datasetLister.listByChildTechId(datasetId);
break;
case PARENT:
- datasets = datasetLister.listByParentTechId(datasetId);
+ datasets = datasetLister.listByParentTechIds(Arrays.asList(datasetId.getId()));
break;
}
Collections.sort(datasets);
@@ -617,8 +617,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
Session session = getSession(sessionToken);
IEntityTypePropertyTypeBO etptBO =
- businessObjectFactory.createEntityTypePropertyTypeBO(session, DtoConverters
- .convertEntityKind(entityKind));
+ businessObjectFactory.createEntityTypePropertyTypeBO(session,
+ DtoConverters.convertEntityKind(entityKind));
etptBO.loadAssignment(propertyTypeCode, entityTypeCode);
etptBO.updateLoadedAssignment(isMandatory, defaultValue, section, previousETPTOrdinal);
}
@@ -630,8 +630,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
Session session = getSession(sessionToken);
IEntityTypePropertyTypeBO etptBO =
- businessObjectFactory.createEntityTypePropertyTypeBO(session, DtoConverters
- .convertEntityKind(entityKind));
+ businessObjectFactory.createEntityTypePropertyTypeBO(session,
+ DtoConverters.convertEntityKind(entityKind));
etptBO.loadAssignment(propertyTypeCode, entityTypeCode);
etptBO.deleteLoadedAssignment();
}
@@ -643,8 +643,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
Session session = getSession(sessionToken);
IEntityTypePropertyTypeBO etptBO =
- businessObjectFactory.createEntityTypePropertyTypeBO(session, DtoConverters
- .convertEntityKind(entityKind));
+ businessObjectFactory.createEntityTypePropertyTypeBO(session,
+ DtoConverters.convertEntityKind(entityKind));
return etptBO.countAssignmentValues(propertyTypeCode, entityTypeCode);
}
@@ -756,8 +756,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
IHibernateSearchDAO searchDAO = getDAOFactory().getHibernateSearchDAO();
final Collection<Long> datasetIds =
- searchDAO.searchForEntityIds(criteria, DtoConverters
- .convertEntityKind(EntityKind.DATA_SET));
+ searchDAO.searchForEntityIds(criteria,
+ DtoConverters.convertEntityKind(EntityKind.DATA_SET));
final IDatasetLister datasetLister = createDatasetLister(session);
return datasetLister.listByDatasetIds(datasetIds);
} catch (final DataAccessException ex)
@@ -903,8 +903,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
getDAOFactory().getFileFormatTypeDAO().createOrUpdate(fileFormatType);
} catch (final DataAccessException ex)
{
- DataAccessExceptionTranslator.throwException(ex, String.format(
- "File format type '%s' ", fileFormatType.getCode()), null);
+ DataAccessExceptionTranslator.throwException(ex,
+ String.format("File format type '%s' ", fileFormatType.getCode()), null);
}
}
@@ -1172,8 +1172,9 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
{
IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
experimentBO.loadDataByTechId(experimentId);
- return AttachmentTranslator.translate(listHolderAttachments(session, experimentBO
- .getExperiment()), session.getBaseIndexURL());
+ return AttachmentTranslator.translate(
+ listHolderAttachments(session, experimentBO.getExperiment()),
+ session.getBaseIndexURL());
} catch (final DataAccessException ex)
{
throw createUserFailureException(ex);
@@ -1187,8 +1188,9 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
{
ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
sampleBO.loadDataByTechId(sampleId);
- return AttachmentTranslator.translate(listHolderAttachments(session, sampleBO
- .getSample()), session.getBaseIndexURL());
+ return AttachmentTranslator
+ .translate(listHolderAttachments(session, sampleBO.getSample()),
+ session.getBaseIndexURL());
} catch (final DataAccessException ex)
{
throw createUserFailureException(ex);
@@ -1202,8 +1204,9 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
{
IProjectBO projectBO = businessObjectFactory.createProjectBO(session);
projectBO.loadDataByTechId(projectId);
- return AttachmentTranslator.translate(listHolderAttachments(session, projectBO
- .getProject()), session.getBaseIndexURL());
+ return AttachmentTranslator.translate(
+ listHolderAttachments(session, projectBO.getProject()),
+ session.getBaseIndexURL());
} catch (final DataAccessException ex)
{
throw createUserFailureException(ex);
@@ -1346,8 +1349,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
{
if (entityOrNull == null)
{
- throw UserFailureException.fromTemplate("There is no %s with permId '%s'.", kind
- .getDescription(), permId);
+ throw UserFailureException.fromTemplate("There is no %s with permId '%s'.",
+ kind.getDescription(), permId);
}
return createInformationHolder(kind, entityOrNull);
}
@@ -1450,10 +1453,9 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
} catch (DataIntegrityViolationException ex)
{
throw new UserFailureException(
- String
- .format(
- "File format type '%s' is being used. Use 'Data Set Search' to find all connected data sets.",
- code));
+ String.format(
+ "File format type '%s' is being used. Use 'Data Set Search' to find all connected data sets.",
+ code));
}
}
}
@@ -1482,12 +1484,11 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
if (types.size() != 1)
{
section =
- String
- .format(
- "[%s]\n%s%s\n",
- entityType.getCode(),
- firstSection ? "# Comments must be located after the type declaration ('[TYPE]').\n"
- : "", section);
+ String.format(
+ "[%s]\n%s%s\n",
+ entityType.getCode(),
+ firstSection ? "# Comments must be located after the type declaration ('[TYPE]').\n"
+ : "", section);
}
sb.append(section);
firstSection = false;
@@ -1674,8 +1675,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServer> impl
IExternalDataTable externalDataTable =
businessObjectFactory.createExternalDataTable(session);
Map<String, String> parameterBindings = new HashMap<String, String>();
- externalDataTable.processDatasets(serviceDescription.getKey(), serviceDescription
- .getDatastoreCode(), datasetCodes, parameterBindings);
+ externalDataTable.processDatasets(serviceDescription.getKey(),
+ serviceDescription.getDatastoreCode(), datasetCodes, parameterBindings);
}
public void registerAuthorizationGroup(String sessionToken,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
index fef98587ae91649d944fff3cdd7fe0e941224a9f..437a7d4e4001009b543d3b81fa7fc24293df2797 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
@@ -30,8 +30,8 @@ import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import java.util.Map.Entry;
+import java.util.Set;
import net.lemnik.eodsql.DataIterator;
@@ -210,9 +210,10 @@ public class DatasetLister implements IDatasetLister
return enrichDatasets(query.getParentDatasetsForChild(childDatasetId.getId()));
}
- public List<ExternalData> listByParentTechId(TechId parentDatasetId)
+ public List<ExternalData> listByParentTechIds(Collection<Long> parentDatasetIds)
{
- return enrichDatasets(query.getChildDatasetsForParent(parentDatasetId.getId()));
+ return enrichDatasets(query
+ .getChildDatasetsForParents(new LongOpenHashSet(parentDatasetIds)));
}
public List<ExternalData> listByDatasetIds(Collection<Long> datasetIds)
@@ -225,8 +226,8 @@ public class DatasetLister implements IDatasetLister
Long sampleTypeId =
referencedEntityDAO.getSampleTypeIdForSampleTypeCode(criteria
.getConnectedSampleTypeCode());
- return enrichDatasets(query.getNewDataSetsForSampleType(sampleTypeId, criteria
- .getLastSeenDataSetId()));
+ return enrichDatasets(query.getNewDataSetsForSampleType(sampleTypeId,
+ criteria.getLastSeenDataSetId()));
}
public List<ExternalData> listByArchiverCriteria(String dataStoreCode,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
index 14a4b92c080db269f146d9c670019bcc12f6e01e..02de40f08c6ca7dc66ccb53e43a46047fd22d47f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
@@ -46,8 +46,8 @@ public interface IDatasetLister
/** @return datasets that are parents of a dataset with the specified id */
List<ExternalData> listByChildTechId(TechId childDatasetId);
- /** @return datasets that are children of a dataset with the specified id */
- List<ExternalData> listByParentTechId(TechId parentDatasetId);
+ /** @return all datasets that are children of any specified dataset id */
+ List<ExternalData> listByParentTechIds(Collection<Long> parentDatasetIds);
/**
* Returns a map with all parent data set IDs of specified data set IDs. The keys of the map are
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
index 8b1baed17367118c994bc441ba358a16d69f6118..e2263f2d02321ce6d519855891a1f2e496ff0325 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
@@ -110,11 +110,12 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
public DataIterator<DatasetRelationRecord> listParentDataSetIds(LongSet ids);
/**
- * Returns the datasets that are children of a dataset with given id.
+ * Returns all datasets that are children of any specified dataset id.
*/
@Select(sql = "SELECT * FROM data JOIN external_data ON data.id = external_data.data_id"
- + " WHERE data.id IN (SELECT data_id_child FROM data_set_relationships r WHERE r.data_id_parent=?{1})", fetchSize = FETCH_SIZE)
- public DataIterator<DatasetRecord> getChildDatasetsForParent(long parentDatasetId);
+ + " WHERE data.id IN (SELECT data_id_child FROM data_set_relationships r WHERE r.data_id_parent = any(?{1}))", parameterBindings =
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public DataIterator<DatasetRecord> getChildDatasetsForParents(LongSet parentDatasetIds);
/**
* Returns the datasets that are parents of a dataset with given id.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
index 4d18229b6dd1b8458ca4e4c2e2a47c89604ba185..d296588591a828c802b29adecf5d7d568d2f9d1c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
@@ -22,6 +22,8 @@ import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import it.unimi.dsi.fastutil.longs.LongArraySet;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import it.unimi.dsi.fastutil.longs.LongSet;
import java.sql.SQLException;
import java.util.Arrays;
@@ -132,7 +134,7 @@ public class DatasetListingQueryTest extends AbstractDAOTest
ExperimentPE experiment1 =
getExperiment(dbInstance.getCode(), "CISD", "NEMO", "EXP-TEST-1", daoFactory);
ExperimentPE experiment2 =
- getExperiment(dbInstance.getCode(), "CISD", "NEMO", "EXP-TEST-2", daoFactory);
+ getExperiment(dbInstance.getCode(), "CISD", "NEMO", "EXP-TEST-2", daoFactory);
experimentIds.add((long) experiment1.getId());
experimentIds.add((long) experiment2.getId());
List<DatasetRecord> datasets = asList(query.getDatasetsForExperiment(experimentIds));
@@ -144,7 +146,7 @@ public class DatasetListingQueryTest extends AbstractDAOTest
assertEqualWithFetchedById(record);
counters.count(record.expe_id);
}
-
+
assertEquals(1, counters.getCountOf(experiment1.getId()));
assertEquals(1, counters.getCountOf(experiment2.getId()));
assertEquals(2, counters.getNumberOfDifferentObjectsCounted());
@@ -210,8 +212,9 @@ public class DatasetListingQueryTest extends AbstractDAOTest
@Test
public void testChildDatasetsForParent()
{
- long datasetId = 2;
- List<DatasetRecord> children = asList(query.getChildDatasetsForParent(datasetId));
+ LongSet datasetIds = new LongOpenHashSet(new long[]
+ { 2 });
+ List<DatasetRecord> children = asList(query.getChildDatasetsForParents(datasetIds));
assertEquals(2, children.size());
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
index 469d37836cc7b16649188c9d82bc5242ea8fbf85..6b438b328347c02f149bf0dc24af817ea779664c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
@@ -28,6 +29,9 @@ import java.util.Map.Entry;
import java.util.Set;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.featurevectors.FeatureTableRow;
+import ch.systemsx.cisd.openbis.dss.generic.server.featurevectors.FeatureVectorValues;
+import ch.systemsx.cisd.openbis.dss.generic.server.featurevectors.WellFeatureVectorReference;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -70,7 +74,7 @@ public class FeatureTableBuilder
private final boolean useAllFeatures;
/** fetches all features of specified wells */
- public static WellFeatureCollection fetchWellFeatures(
+ public static WellFeatureCollection<FeatureTableRow> fetchWellFeatures(
List<FeatureVectorDatasetWellReference> references, IImagingReadonlyQueryDAO dao,
IEncapsulatedOpenBISService service)
{
@@ -82,18 +86,30 @@ public class FeatureTableBuilder
*
* @param featureCodes empty list means no filtering.
*/
- public static WellFeatureCollection fetchWellFeatures(
+ public static WellFeatureCollection<FeatureTableRow> fetchWellFeatures(
List<FeatureVectorDatasetWellReference> references, List<String> featureCodes,
IImagingReadonlyQueryDAO dao, IEncapsulatedOpenBISService service)
{
FeatureTableBuilder builder = new FeatureTableBuilder(featureCodes, dao, service);
Set<String> datasetCodes = extractDatasetCodes(references);
- for (String datasetCode : datasetCodes)
- {
- builder.addFeatureVectorsOfDataSet(datasetCode);
- }
+ addFeatureVectorsOfDataSets(builder, datasetCodes);
List<FeatureTableRow> features = builder.createFeatureTableRows(references);
- return new WellFeatureCollection(features, builder.getCodesAndLabels());
+ return new WellFeatureCollection<FeatureTableRow>(features, builder.getCodesAndLabels());
+ }
+
+ /**
+ * fetches all features of specified wells, used basic data types
+ */
+ public static WellFeatureCollection<FeatureVectorValues> fetchWellFeatureValues(
+ List<WellFeatureVectorReference> references, IImagingReadonlyQueryDAO dao,
+ IEncapsulatedOpenBISService service)
+ {
+ FeatureTableBuilder builder =
+ new FeatureTableBuilder(new ArrayList<String>(), dao, service);
+ Set<String> datasetCodes = extractDatasetCodesFromSimpleReferences(references);
+ addFeatureVectorsOfDataSets(builder, datasetCodes);
+ List<FeatureVectorValues> features = builder.createFeatureVectorValues(references);
+ return new WellFeatureCollection<FeatureVectorValues>(features, builder.getCodesAndLabels());
}
/**
@@ -101,33 +117,30 @@ public class FeatureTableBuilder
*
* @param featureCodes empty list means no filtering.
*/
- public static WellFeatureCollection fetchDatasetFeatures(List<String> datasetCodes,
- List<String> featureCodes, IImagingReadonlyQueryDAO dao,
+ public static WellFeatureCollection<FeatureTableRow> fetchDatasetFeatures(
+ List<String> datasetCodes, List<String> featureCodes, IImagingReadonlyQueryDAO dao,
IEncapsulatedOpenBISService service)
{
FeatureTableBuilder builder = new FeatureTableBuilder(featureCodes, dao, service);
- for (String datasetCode : datasetCodes)
- {
- builder.addFeatureVectorsOfDataSet(datasetCode);
- }
+ addFeatureVectorsOfDataSets(builder, datasetCodes);
List<FeatureTableRow> features = builder.createFeatureTableRows();
- return new WellFeatureCollection(features, builder.getCodesAndLabels());
+ return new WellFeatureCollection<FeatureTableRow>(features, builder.getCodesAndLabels());
}
/** stores feature vectors for a set of wells */
- public static class WellFeatureCollection
+ public static class WellFeatureCollection<T extends FeatureVectorValues>
{
- private final List<FeatureTableRow> features;
+ private final List<T> features;
private final List<CodeAndLabel> featureNames;
- public WellFeatureCollection(List<FeatureTableRow> features, List<CodeAndLabel> featureNames)
+ public WellFeatureCollection(List<T> features, List<CodeAndLabel> featureNames)
{
this.features = features;
this.featureNames = featureNames;
}
- public List<FeatureTableRow> getFeatures()
+ public List<T> getFeatures()
{
return features;
}
@@ -159,6 +172,26 @@ public class FeatureTableBuilder
}
}
+ private static void addFeatureVectorsOfDataSets(FeatureTableBuilder builder,
+ Collection<String> datasetCodes)
+ {
+ for (String datasetCode : datasetCodes)
+ {
+ builder.addFeatureVectorsOfDataSet(datasetCode);
+ }
+ }
+
+ private static Set<String> extractDatasetCodesFromSimpleReferences(
+ List<WellFeatureVectorReference> references)
+ {
+ Set<String> datasetCodes = new HashSet<String>();
+ for (WellFeatureVectorReference ref : references)
+ {
+ datasetCodes.add(ref.getDatasetCode());
+ }
+ return datasetCodes;
+ }
+
private static Set<String> extractDatasetCodes(
List<FeatureVectorDatasetWellReference> references)
{
@@ -262,7 +295,6 @@ public class FeatureTableBuilder
List<FeatureTableRow> rows = new ArrayList<FeatureTableRow>();
for (DatasetFeaturesBundle bundle : bundles)
{
- String dataSetCode = bundle.dataSet.getPermId();
ImgContainerDTO container = dao.getContainerById(bundle.dataSet.getContainerId());
SampleIdentifier identifier = service.tryToGetSampleIdentifier(container.getPermId());
for (int rowIndex = 1; rowIndex <= container.getNumberOfRows(); rowIndex++)
@@ -270,8 +302,8 @@ public class FeatureTableBuilder
for (int colIndex = 1; colIndex <= container.getNumberOfColumns(); colIndex++)
{
final FeatureTableRow row =
- createFeatureTableRow(bundle.featureDefToValuesMap, dataSetCode,
- identifier, null, new WellPosition(rowIndex, colIndex));
+ createFeatureTableRow(bundle, identifier, null, new WellPosition(
+ rowIndex, colIndex));
rows.add(row);
}
}
@@ -279,6 +311,26 @@ public class FeatureTableBuilder
return rows;
}
+ /**
+ * Returns all features for the specified wells in previously loaded datasets. Operates on very
+ * basic data types.
+ */
+ private List<FeatureVectorValues> createFeatureVectorValues(
+ List<WellFeatureVectorReference> references)
+ {
+ Map<String/* dataset code */, DatasetFeaturesBundle> bundleMap = createBundleMap(bundles);
+ List<FeatureVectorValues> featureVectors = new ArrayList<FeatureVectorValues>();
+ for (WellFeatureVectorReference reference : references)
+ {
+ String dataSetCode = reference.getDatasetCode();
+ DatasetFeaturesBundle bundle = getDatasetFeaturesBundleOrDie(bundleMap, dataSetCode);
+ FeatureVectorValues featureVector =
+ createFeatureVector(bundle, reference.getWellPosition());
+ featureVectors.add(featureVector);
+ }
+ return featureVectors;
+ }
+
/**
* Returns all features for the specified wells in previously loaded datasets.
*/
@@ -290,21 +342,28 @@ public class FeatureTableBuilder
for (FeatureVectorDatasetWellReference reference : references)
{
String dataSetCode = reference.getDatasetCode();
- DatasetFeaturesBundle bundle = bundleMap.get(dataSetCode);
- if (bundle == null)
- {
- throw new IllegalStateException("Dataset has not been loaded: " + dataSetCode);
- }
+ DatasetFeaturesBundle bundle = getDatasetFeaturesBundleOrDie(bundleMap, dataSetCode);
ImgContainerDTO container = dao.getContainerById(bundle.dataSet.getContainerId());
SampleIdentifier identifier = service.tryToGetSampleIdentifier(container.getPermId());
final FeatureTableRow row =
- createFeatureTableRow(bundle.featureDefToValuesMap, dataSetCode, identifier,
- reference, reference.getWellPosition());
+ createFeatureTableRow(bundle, identifier, reference,
+ reference.getWellPosition());
rows.add(row);
}
return rows;
}
+ private DatasetFeaturesBundle getDatasetFeaturesBundleOrDie(
+ Map<String, DatasetFeaturesBundle> bundleMap, String dataSetCode)
+ {
+ DatasetFeaturesBundle bundle = bundleMap.get(dataSetCode);
+ if (bundle == null)
+ {
+ throw new IllegalStateException("Dataset has not been loaded: " + dataSetCode);
+ }
+ return bundle;
+ }
+
private static HashMap<String, DatasetFeaturesBundle> createBundleMap(
List<DatasetFeaturesBundle> bundles)
{
@@ -316,16 +375,32 @@ public class FeatureTableBuilder
return map;
}
- private FeatureTableRow createFeatureTableRow(
- Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> featureDefToValuesMap,
- String dataSetCode, SampleIdentifier identifier,
- FeatureVectorDatasetWellReference reference, WellPosition wellPosition)
+ private FeatureTableRow createFeatureTableRow(DatasetFeaturesBundle bundle,
+ SampleIdentifier identifier, FeatureVectorDatasetWellReference reference,
+ WellPosition wellPosition)
{
- FeatureTableRow row = new FeatureTableRow();
- row.setDataSetCode(dataSetCode);
+ FeatureVectorValues featureVector = createFeatureVector(bundle, wellPosition);
+ FeatureTableRow row = new FeatureTableRow(featureVector);
row.setPlateIdentifier(identifier);
row.setReference(reference);
- row.setWellPosition(wellPosition);
+ return row;
+ }
+
+ private FeatureVectorValues createFeatureVector(DatasetFeaturesBundle bundle,
+ WellPosition wellPosition)
+ {
+ FeatureVectorValues fv = new FeatureVectorValues();
+ fv.setDataSetCode(bundle.dataSet.getPermId());
+ fv.setWellPosition(wellPosition);
+ float[] valueArray = createFeatureValueArray(bundle.featureDefToValuesMap, wellPosition);
+ fv.setFeatureValues(valueArray);
+ return fv;
+ }
+
+ private float[] createFeatureValueArray(
+ Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> featureDefToValuesMap,
+ WellPosition wellPosition)
+ {
float[] valueArray = new float[featureCodeLabelToIndexMap.size()];
Arrays.fill(valueArray, Float.NaN);
for (Entry<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> entry : featureDefToValuesMap
@@ -348,8 +423,7 @@ public class FeatureTableBuilder
featureValues.getForWellLocation(wellPosition.getWellRow(),
wellPosition.getWellColumn());
}
- row.setFeatureValues(valueArray);
- return row;
+ return valueArray;
}
private CodeAndLabel getCodeAndLabel(final ImgFeatureDefDTO featureDefinition)
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 2cb872ff7e233cd4d192a27b0af6a54e05205fb1..c8870edea08fa37d304c427d660f269705880986 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
@@ -22,6 +22,7 @@ import java.util.Arrays;
import java.util.List;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder.WellFeatureCollection;
+import ch.systemsx.cisd.openbis.dss.generic.server.featurevectors.FeatureTableRow;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
@@ -85,7 +86,7 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
private void initialize()
{
- WellFeatureCollection featureCollection =
+ WellFeatureCollection<FeatureTableRow> featureCollection =
FeatureTableBuilder.fetchDatasetFeatures(Arrays.asList(dataSetCode),
new ArrayList<String>(), dao, service);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableRow.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/FeatureTableRow.java
similarity index 53%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableRow.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/FeatureTableRow.java
index 010240425d8da34539f2427fdc8d1a7075eb3324..aed3481b0be4e5cd3fc49e42e9021a1fe15877bb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableRow.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/FeatureTableRow.java
@@ -14,39 +14,28 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.generic.server;
+package ch.systemsx.cisd.openbis.dss.generic.server.featurevectors;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
* Bean for a row in a table of feature vectors. Each row is specified by data set code, plate
- * identifier, well position and and array of feature values. Double.NaN is used for unknown
- * feature value in this array.
+ * identifier, well position and and array of feature values.
*
* @author Franz-Josef Elmer
*/
-public class FeatureTableRow
+public class FeatureTableRow extends FeatureVectorValues
{
- private String dataSetCode;
-
private FeatureVectorDatasetWellReference reference;
private SampleIdentifier plateIdentifier;
- private WellPosition wellPosition;
-
- private float[] featureValues;
-
- public final String getDataSetCode()
+ public FeatureTableRow(FeatureVectorValues featureVector)
{
- return dataSetCode;
- }
-
- public final void setDataSetCode(String dataSetCode)
- {
- this.dataSetCode = dataSetCode;
+ setDataSetCode(featureVector.getDataSetCode());
+ setFeatureValues(featureVector.getFeatureValues());
+ setWellPosition(featureVector.getWellPosition());
}
public FeatureVectorDatasetWellReference getReference()
@@ -68,34 +57,4 @@ public class FeatureTableRow
{
this.plateIdentifier = plateIdentifier;
}
-
- public void setWellPosition(WellPosition wellPosition)
- {
- this.wellPosition = wellPosition;
- }
-
- public final WellPosition getWellPosition()
- {
- return wellPosition;
- }
-
- public final float[] getFeatureValues()
- {
- return featureValues;
- }
-
- public final double[] getFeatureValuesAsDouble()
- {
- final double[] doubleValues = new double[featureValues.length];
- for (int i = 0; i < featureValues.length; ++i)
- {
- doubleValues[i] = featureValues[i];
- }
- return doubleValues;
- }
-
- public final void setFeatureValues(float[] featureValues)
- {
- this.featureValues = featureValues;
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/FeatureVectorValues.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/FeatureVectorValues.java
new file mode 100644
index 0000000000000000000000000000000000000000..d454894c077766d057dcb99bbb8bc00950aa988b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/FeatureVectorValues.java
@@ -0,0 +1,73 @@
+/*
+ * Copyright 2010 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.generic.server.featurevectors;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+
+/**
+ * Bean for one feature vector of the well. Contains data set code, well position and and array of
+ * feature values. Double.NaN is used for unknown feature value in this array.
+ *
+ * @author Tomasz Pylak
+ */
+public class FeatureVectorValues
+{
+ private WellFeatureVectorReference featureVectorReference = new WellFeatureVectorReference();
+
+ private float[] featureValues;
+
+ public float[] getFeatureValues()
+ {
+ return featureValues;
+ }
+
+ public double[] getFeatureValuesAsDouble()
+ {
+ double[] doubleValues = new double[featureValues.length];
+ for (int i = 0; i < featureValues.length; ++i)
+ {
+ doubleValues[i] = featureValues[i];
+ }
+ return doubleValues;
+ }
+
+ public void setFeatureValues(float[] featureValues)
+ {
+ this.featureValues = featureValues;
+ }
+
+ public String getDataSetCode()
+ {
+ return featureVectorReference.getDatasetCode();
+ }
+
+ public void setDataSetCode(String dataSetCode)
+ {
+ featureVectorReference.setDatasetCode(dataSetCode);
+ }
+
+ public void setWellPosition(WellPosition wellPosition)
+ {
+ featureVectorReference.setWellPosition(wellPosition);
+ }
+
+ public WellPosition getWellPosition()
+ {
+ return featureVectorReference.getWellPosition();
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/WellFeatureVectorReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/WellFeatureVectorReference.java
new file mode 100644
index 0000000000000000000000000000000000000000..0922c9eb36ca7d080e392c50f11861255924ee1e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/featurevectors/WellFeatureVectorReference.java
@@ -0,0 +1,51 @@
+/*
+ * Copyright 2010 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.generic.server.featurevectors;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+
+/**
+ * References a feature vector of one well
+ *
+ * @author Tomasz Pylak
+ */
+public class WellFeatureVectorReference
+{
+ private String dataSetCode; // dataset with feature vectors
+
+ private WellPosition wellPosition;
+
+ public final String getDatasetCode()
+ {
+ return dataSetCode;
+ }
+
+ public final void setDatasetCode(String dataSetCode)
+ {
+ this.dataSetCode = dataSetCode;
+ }
+
+ public void setWellPosition(WellPosition wellPosition)
+ {
+ this.wellPosition = wellPosition;
+ }
+
+ public final WellPosition getWellPosition()
+ {
+ return wellPosition;
+ }
+}
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 93e70cbc3ca6f0e1ed10465ef92b9700136b6750..fa937cfa5099d03032e32b1f392fe148cf9722fd 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
@@ -23,7 +23,7 @@ import java.util.Properties;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder.WellFeatureCollection;
-import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableRow;
+import ch.systemsx.cisd.openbis.dss.generic.server.featurevectors.FeatureTableRow;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
@@ -82,7 +82,7 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
{
List<String> datasetCodes = extractDatasetCodes(datasets);
ArrayList<String> featureCodes = new ArrayList<String>(); // fetch all
- WellFeatureCollection featuresCollection =
+ WellFeatureCollection<FeatureTableRow> featuresCollection =
FeatureTableBuilder.fetchDatasetFeatures(datasetCodes, featureCodes, getDAO(),
getService());
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 f0b29b0f271e046633ba7e96746ac2fec4629311..0ee7ce3f30d9a306f27d60c5e6f98d441ed92763 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
@@ -42,7 +42,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServle
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDssServiceRpc;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder;
import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder.WellFeatureCollection;
-import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableRow;
+import ch.systemsx.cisd.openbis.dss.generic.server.featurevectors.FeatureTableRow;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -238,7 +238,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private FeatureVectorDataset createFeatureVectorDataset(String sessionToken,
FeatureVectorDatasetReference dataset, List<String> featureCodes)
{
- WellFeatureCollection datasetFeatures =
+ WellFeatureCollection<FeatureTableRow> datasetFeatures =
FeatureTableBuilder.fetchDatasetFeatures(Arrays.asList(dataset.getDatasetCode()),
featureCodes, getDAO(), getOpenBISService());
List<FeatureVector> featureVectors = new ArrayList<FeatureVector>();
@@ -267,14 +267,14 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
List<String> featureNames)
{
checkDatasetsAuthorizationForIDatasetIdentifier(sessionToken, datasetWellReferences);
- WellFeatureCollection features =
+ WellFeatureCollection<FeatureTableRow> features =
FeatureTableBuilder.fetchWellFeatures(datasetWellReferences, featureNames, dao,
getOpenBISService());
return createFeatureVectorList(features);
}
private List<FeatureVectorWithDescription> createFeatureVectorList(
- final WellFeatureCollection features)
+ final WellFeatureCollection<FeatureTableRow> features)
{
final List<String> featureCodes = features.getFeatureCodes();
final List<FeatureTableRow> featureTableRows = features.getFeatures();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 4990d245edbeaa1be13199b4ee2a68fac1a63df0..c5cf8db77c3bbc8dc3f0cb531b9d8f8e95b2b08b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -156,7 +156,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
{
Session session = getSession(sessionToken);
return PlateMaterialLocationsLoader.load(session, businessObjectFactory, getDAOFactory(),
- materialCriteria, true);
+ materialCriteria);
}
public List<WellImageChannelStack> listImageChannelStacks(String sessionToken,
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 169eafcace92cbee64086c3d76f74d4401d04e55..1e36639bc00c7f76aa89d5887c36e31f972164dd 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
@@ -16,16 +16,15 @@
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.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.TechId;
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;
@@ -45,7 +44,7 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
private final String featureVectorDatasetTypeCode;
// Running state
- private List<ExternalData> featureVectorDatasets;
+ private Collection<ExternalData> featureVectorDatasets;
FeatureVectorDatasetLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, String homeSpaceOrNull,
@@ -57,55 +56,143 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
featureVectorDatasetTypeCode = ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE;
}
- public List<FeatureVectorDatasetReference> getFeatureVectorDatasets()
+ public static class FeatureVectorExternalData
+ {
+ private final ExternalData featureVectorDataset;
+
+ private final ExternalData imageDatasetOrNull;
+
+ public FeatureVectorExternalData(ExternalData featureVectorDataset,
+ ExternalData imageDatasetOrNull)
+ {
+ this.featureVectorDataset = featureVectorDataset;
+ this.imageDatasetOrNull = imageDatasetOrNull;
+ }
+
+ public ExternalData getFeatureVectorDataset()
+ {
+ return featureVectorDataset;
+ }
+
+ public ExternalData tryGetImageDataset()
+ {
+ return imageDatasetOrNull;
+ }
+ }
+
+ /** enriched with image dataset parents */
+ public Collection<ExternalData> getFeatureVectorDatasets()
+ {
+ loadAll();
+ return featureVectorDatasets;
+ }
+
+ public List<FeatureVectorDatasetReference> getFeatureVectorDatasetReferences()
+ {
+ loadAll();
+ return asFeatureVectorDatasetReferences();
+ }
+
+ private void loadAll()
{
// Load the image data sets
load();
loadFeatureVectorDatasets();
- return asFeatureVectorDatasets();
}
private void loadFeatureVectorDatasets()
{
- final Long2ObjectSortedMap<ExternalData> featureVectorDatasetSet =
- new Long2ObjectLinkedOpenHashMap<ExternalData>();
+ final Map<Long, ExternalData> featureVectorDatasetSet = new HashMap<Long, ExternalData>();
IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
- for (ExternalData data : getDatasets())
+ List<ExternalData> imageDatasets = new ArrayList<ExternalData>();
+ for (ExternalData dataset : getDatasets())
{
- if (ScreeningUtils.isTypeEqual(data, ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE))
+ if (ScreeningUtils.isTypeEqual(dataset, ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE))
+ {
+ featureVectorDatasetSet.put(dataset.getId(), dataset);
+ } else if (ScreeningUtils.isTypeEqual(dataset, ScreeningConstants.IMAGE_DATASET_TYPE))
{
- featureVectorDatasetSet.put(data.getId(), data);
+ 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 data : getDatasets())
+ for (ExternalData fv : connectedFeatureVectorDatasets)
{
- if (ScreeningUtils.isTypeEqual(data, ScreeningConstants.IMAGE_DATASET_TYPE))
+ List<ExternalData> parentImageDatasets =
+ featureVectorToImageDatasetsMap.get(fv.getId());
+ if (parentImageDatasets != null)
{
- // 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()));
- for (ExternalData child : children)
- {
- child.setParents(Collections.singleton(data));
- featureVectorDatasetSet.put(child.getId(), child);
- }
+ fv.setParents(parentImageDatasets);
}
+ featureVectorDatasetSet.put(fv.getId(), fv);
}
+ featureVectorDatasets = featureVectorDatasetSet.values();
+ }
- featureVectorDatasets =
- ScreeningUtils.filterExternalDataByType(featureVectorDatasetSet.values(),
- featureVectorDatasetTypeCode);
+ private List<ExternalData> listChildrenFeatureVectorDatasets(IDatasetLister datasetLister,
+ Collection<Long> imageDatasetIds)
+ {
+ List<ExternalData> datasets = datasetLister.listByParentTechIds(imageDatasetIds);
+ return ScreeningUtils.filterExternalDataByType(datasets, featureVectorDatasetTypeCode);
}
- private List<FeatureVectorDatasetReference> asFeatureVectorDatasets()
+ 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>();
for (ExternalData externalData : featureVectorDatasets)
@@ -115,10 +202,24 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
return result;
}
+ private static ExternalData tryGetOneParent(ExternalData externalData)
+ {
+ Collection<ExternalData> parents = externalData.getParents();
+ if (parents != null && parents.size() == 1)
+ {
+ return parents.iterator().next();
+ } else
+ {
+ return null;
+ }
+ }
+
protected FeatureVectorDatasetReference asFeatureVectorDataset(ExternalData externalData)
{
DataStore dataStore = externalData.getDataStore();
- if (externalData.getParents() == null || externalData.getParents().isEmpty())
+ // there should be no more parents than one, we ensure about that earlier
+ ExternalData parentDataset = tryGetOneParent(externalData);
+ if (parentDataset == null)
{
return new FeatureVectorDatasetReference(externalData.getCode(),
getDataStoreUrlFromDataStore(dataStore), createPlateIdentifier(externalData),
@@ -129,7 +230,6 @@ class FeatureVectorDatasetLoader extends ImageDatasetLoader
// 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),
createExperimentIdentifier(externalData), extractPlateGeometry(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 374225ae738437608c76d697ec20c484dbf4b188..119d9ace0666bd0ea76fea538a1fff93b0d00454 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
@@ -49,25 +49,43 @@ class ImageDatasetLoader extends PlateDatasetLoader
/**
* Return the image datasets for the specified plates.
*/
- public List<ImageDatasetReference> getImageDatasets()
+ public List<ExternalData> getImageDatasets()
{
load();
return filterImageDatasets();
}
- private List<ImageDatasetReference> filterImageDatasets()
+ /**
+ * Return the image datasets references for the specified plates.
+ */
+ public List<ImageDatasetReference> getImageDatasetReferences()
+ {
+ return asImageDatasetReferences(getImageDatasets());
+ }
+
+ private List<ExternalData> filterImageDatasets()
{
- List<ImageDatasetReference> result = new ArrayList<ImageDatasetReference>();
+ List<ExternalData> result = new ArrayList<ExternalData>();
for (ExternalData externalData : getDatasets())
{
if (ScreeningUtils.isTypeEqual(externalData, ScreeningConstants.IMAGE_DATASET_TYPE))
{
- result.add(asImageDataset(externalData));
+ result.add(externalData);
}
}
return result;
}
+ private List<ImageDatasetReference> asImageDatasetReferences(List<ExternalData> imageDatasets)
+ {
+ List<ImageDatasetReference> references = new ArrayList<ImageDatasetReference>();
+ for (ExternalData imageDataset : imageDatasets)
+ {
+ references.add(asImageDataset(imageDataset));
+ }
+ return references;
+ }
+
protected ImageDatasetReference asImageDataset(ExternalData externalData)
{
DataStore dataStore = externalData.getDataStore();
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 31de9e17692dab1add7ab93341e3c9cdc803d778..776e7ad244bb3d8dc203264cb521612d53dcfb24 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
@@ -190,7 +190,7 @@ class PlateDatasetLoader
return new PlateIdentifier(plateCode, spaceCodeOrNull, sample.getPermId());
}
- protected ExperimentIdentifier createExperimentIdentifier(ExternalData parentDataset)
+ protected static ExperimentIdentifier createExperimentIdentifier(ExternalData parentDataset)
{
return asExperimentIdentifier(parentDataset.getExperiment());
}
@@ -282,7 +282,7 @@ class PlateDatasetLoader
return sampleIds;
}
- protected String getDataStoreUrlFromDataStore(DataStore dataStore)
+ protected static String getDataStoreUrlFromDataStore(DataStore dataStore)
{
String datastoreUrl = dataStore.getDownloadUrl();
// The url objained form a DataStore object is the *download* url. Convert this to the
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateMaterialLocationsLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateMaterialLocationsLoader.java
index 9c8850e2c7ed364f646c109ad847405304f99904..cd88d1cb6c18a104ffa87e23218b41ae157c61cb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateMaterialLocationsLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateMaterialLocationsLoader.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.sql.Connection;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
@@ -31,11 +32,13 @@ import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.QueryTool;
import org.apache.commons.lang.ArrayUtils;
+import org.apache.log4j.Logger;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
@@ -56,18 +59,18 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria.ExperimentSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria.MaterialSearchCodesCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria.MaterialSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria.SingleExperimentSearchCriteria;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
/**
* Loades selected wells content: metadata and (if available) image dataset and feature vectors.
@@ -77,6 +80,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterials
@Friend(toClasses = IScreeningQuery.class)
public class PlateMaterialLocationsLoader
{
+ private final static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ PlateMaterialLocationsLoader.class);
+
/**
* Finds wells containing the specified material and belonging to the specified experiment.
* Loads wells content: metadata and (if available) image dataset and feature vectors.
@@ -91,10 +97,10 @@ public class PlateMaterialLocationsLoader
public static List<WellContent> load(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- PlateMaterialsSearchCriteria materialCriteria, boolean enrichWithImages)
+ PlateMaterialsSearchCriteria materialCriteria)
{
return new PlateMaterialLocationsLoader(session, businessObjectFactory, daoFactory)
- .getPlateLocations(materialCriteria, enrichWithImages);
+ .getPlateLocations(materialCriteria, true);
}
/** loads wells metadata, but no information about image or image analysis datasets */
@@ -153,52 +159,186 @@ public class PlateMaterialLocationsLoader
private List<WellContent> enrichWithDatasets(List<WellContent> locations)
{
- List<ExternalData> imageDatasets = loadImageDatasets(locations);
- Map<Long/* plate id */, List<ExternalData>> plateToDatasetMap =
- createPlateToDatasetMap(imageDatasets);
+ Collection<PlateIdentifier> plates = extractPlates(locations);
+ FeatureVectorDatasetLoader datasetsRetriever =
+ new FeatureVectorDatasetLoader(session, businessObjectFactory, null, plates);
+ Collection<ExternalData> imageDatasets = datasetsRetriever.getImageDatasets();
Map<String, PlateImageParameters> imageParams = loadImagesReport(imageDatasets);
- return enrichWithImages(locations, plateToDatasetMap, imageParams);
+
+ // TODO 2010-09-07, Tomasz Pylak: uncomment this when showing fetures in Reviewing Panel is
+ // implemented
+ // Collection<ExternalData> featureVectorDatasets =
+ // datasetsRetriever.getFeatureVectorDatasets();
+ // Collection<ExternalData> childlessImageDatasets =
+ // selectChildlessImageDatasets(imageDatasets, featureVectorDatasets);
+ //
+ // Map<Long/* plate id */, List<ExternalData>> plateToChildlessImageDatasetMap =
+ // createPlateToDatasetMap(childlessImageDatasets);
+ // Map<Long/* plate id */, List<ExternalData>> plateToFeatureVectoreDatasetMap =
+ // createPlateToDatasetMap(featureVectorDatasets);
+ //
+ // return enrichWithDatasets(locations, plateToChildlessImageDatasetMap,
+ // plateToFeatureVectoreDatasetMap, imageParams);
+
+ return enrichWithDatasets(locations, createPlateToDatasetMap(imageDatasets),
+ new HashMap<Long, List<ExternalData>>(), imageParams);
}
- private static List<WellContent> enrichWithImages(List<WellContent> wellContents,
- Map<Long/* plate id */, List<ExternalData>> plateToDatasetMap,
- Map<String, PlateImageParameters> imageParams)
+ @SuppressWarnings("unused")
+ private static Collection<ExternalData> selectChildlessImageDatasets(
+ Collection<ExternalData> imageDatasets, Collection<ExternalData> featureVectorDatasets)
{
- List<WellContent> wellsWithImages = new ArrayList<WellContent>();
- for (WellContent wellContent : wellContents)
+ Collection<ExternalData> childlessImageDatasets = new ArrayList<ExternalData>();
+ Set<String> parentImageDatasetCodes = extractParentDatasetCodes(featureVectorDatasets);
+ for (ExternalData imageDataset : imageDatasets)
{
- List<ExternalData> datasets = plateToDatasetMap.get(wellContent.getPlate().getId());
- boolean imagesExist = false;
- // there can be more than one dataset with images for each well - in such a case we will
- // have one well content duplicated for each dataset
- if (datasets != null)
+ if (parentImageDatasetCodes.contains(imageDataset.getCode()) == false)
{
- for (ExternalData dataset : datasets)
+ childlessImageDatasets.add(imageDataset);
+ }
+ }
+ return childlessImageDatasets;
+ }
+
+ private static Set<String> extractParentDatasetCodes(Collection<ExternalData> datasets)
+ {
+ Set<String> codes = new HashSet<String>();
+ for (ExternalData dataset : datasets)
+ {
+ Collection<ExternalData> parents = dataset.getParents();
+ if (parents != null)
+ {
+ for (ExternalData parent : parents)
{
- PlateImageParameters imageParameters = imageParams.get(dataset.getCode());
- if (imageParameters != null)
- {
- DatasetReference datasetReference =
- ScreeningUtils.createDatasetReference(dataset);
- DatasetImagesReference wellImages =
- DatasetImagesReference.create(datasetReference, imageParameters);
- WellContent wellWithImages = wellContent.cloneWithImages(wellImages);
- wellsWithImages.add(wellWithImages);
- imagesExist = true;
- }
+ codes.add(parent.getCode());
}
}
+ }
+ return codes;
+ }
+
+ private static Collection<PlateIdentifier> extractPlates(List<WellContent> locations)
+ {
+ Collection<PlateIdentifier> plates = new ArrayList<PlateIdentifier>();
+ for (WellContent location : locations)
+ {
+ plates.add(PlateIdentifier.createFromPermId(location.getPlate().getPermId()));
+ }
+ return plates;
+ }
+
+ /**
+ * Connects wells with datasets.
+ */
+ private static List<WellContent> enrichWithDatasets(List<WellContent> wellContents,
+ Map<Long/* plate id */, List<ExternalData>> plateToChildlessImageDatasetMap,
+ Map<Long/* plate id */, List<ExternalData>> plateToFeatureVectoreDatasetMap,
+ Map<String, PlateImageParameters> imageParams)
+ {
+ List<WellContent> wellsWithDatasets = new ArrayList<WellContent>();
+ for (WellContent wellContent : wellContents)
+ {
+ List<WellContent> clonedWellContents =
+ enrichWithDatasetReferences(wellContent, plateToChildlessImageDatasetMap,
+ plateToFeatureVectoreDatasetMap, imageParams);
// if there are no datasets for the well content, we add it without images
- if (imagesExist == false)
+ if (clonedWellContents.isEmpty())
+ {
+ wellsWithDatasets.add(wellContent);
+ } else
{
- wellsWithImages.add(wellContent);
+ wellsWithDatasets.addAll(clonedWellContents);
}
}
- return wellsWithImages;
+ wellsWithDatasets = enrichWithFeatureVectors(wellsWithDatasets);
+ return wellsWithDatasets;
+ }
+
+ private static List<WellContent> enrichWithFeatureVectors(List<WellContent> wellsWithDatasets)
+ {
+ // TODO 2010-09-07, Tomasz Pylak: Enrich each WellContent with feature values.
+ // WellFeatureCollection<FeatureVectorValues> featureVectors =
+ // FeatureTableBuilder.fetchWellFeatureValues(references, dao, service);
+ // return enrichWithFeatureVectors(wellsWithDatasets, featureVectors);
+ return wellsWithDatasets;
+ }
+
+ /**
+ * Connects one WellContent with dataset references.<br>
+ * We want to present all the data to the user, so if a well has several feature vector
+ * datasets, it will be cloned several times. By connecting to feature vector datasets we are
+ * possibly connecting to image datasets as well.<br>
+ * Additionally a join with childless image datasets has to be performed.
+ */
+ private static List<WellContent> enrichWithDatasetReferences(WellContent wellContent,
+ Map<Long, List<ExternalData>> plateToChildlessImageDatasetMap,
+ Map<Long, List<ExternalData>> plateToFeatureVectoreDatasetMap,
+ Map<String, PlateImageParameters> imageParams)
+ {
+ Long plateId = wellContent.getPlate().getId();
+ List<WellContent> clonedWellContents = new ArrayList<WellContent>();
+
+ List<ExternalData> featureVectoreDatasets = plateToFeatureVectoreDatasetMap.get(plateId);
+ if (featureVectoreDatasets != null)
+ {
+ for (ExternalData featureVectoreDataset : featureVectoreDatasets)
+ {
+ DatasetReference featureVectoreDatasetReference =
+ ScreeningUtils.createDatasetReference(featureVectoreDataset);
+ DatasetImagesReference imagesDatasetReference =
+ tryGetImageDatasetReference(featureVectoreDataset, imageParams);
+ clonedWellContents.add(wellContent.cloneWithDatasets(imagesDatasetReference,
+ featureVectoreDatasetReference));
+ }
+ }
+
+ // there can be more than one dataset with images for each well - in such a case we will
+ // have one well content duplicated for each dataset
+ List<ExternalData> childlessImageDatasets = plateToChildlessImageDatasetMap.get(plateId);
+ if (childlessImageDatasets != null)
+ {
+ for (ExternalData childlessImageDataset : childlessImageDatasets)
+ {
+ DatasetImagesReference imagesDatasetReference =
+ createDatasetImagesReference(childlessImageDataset, imageParams);
+ clonedWellContents.add(wellContent.cloneWithDatasets(imagesDatasetReference, null));
+ }
+ }
+ return clonedWellContents;
+ }
+
+ private static DatasetImagesReference tryGetImageDatasetReference(
+ ExternalData featureVectoreDataset, Map<String, PlateImageParameters> imageParams)
+ {
+ Collection<ExternalData> parents = featureVectoreDataset.getParents();
+ if (parents != null && parents.size() == 1)
+ {
+ ExternalData imageDataset = parents.iterator().next();
+ return createDatasetImagesReference(imageDataset, imageParams);
+ } else
+ {
+ return null;
+ }
+ }
+
+ private static DatasetImagesReference createDatasetImagesReference(ExternalData imageDataset,
+ Map<String, PlateImageParameters> imageParams)
+ {
+ PlateImageParameters imageParameters = imageParams.get(imageDataset.getCode());
+ if (imageParameters != null)
+ {
+ return DatasetImagesReference.create(
+ ScreeningUtils.createDatasetReference(imageDataset), imageParameters);
+ } else
+ {
+ operationLog.error("Cannot find image parameters for dataset: "
+ + imageDataset.getCode() + ". It will not be displayed");
+ return null;
+ }
}
private static Map<Long/* sample id */, List<ExternalData>> createPlateToDatasetMap(
- List<ExternalData> datasets)
+ Collection<ExternalData> datasets)
{
Map<Long, List<ExternalData>> map = new HashMap<Long, List<ExternalData>>();
for (ExternalData dataset : datasets)
@@ -221,7 +361,7 @@ public class PlateMaterialLocationsLoader
}
private Map<String/* dataset code */, PlateImageParameters> loadImagesReport(
- List<ExternalData> imageDatasets)
+ Collection<ExternalData> imageDatasets)
{
List<PlateImageParameters> imageParameters = new ArrayList<PlateImageParameters>();
for (ExternalData dataSet : imageDatasets)
@@ -242,28 +382,6 @@ public class PlateMaterialLocationsLoader
return map;
}
- private List<ExternalData> loadImageDatasets(List<WellContent> locations)
- {
- Set<Long> plateIds = extractPlateIds(locations);
-
- IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
- List<ExternalData> imageDatasets = datasetLister.listBySampleIds(plateIds);
- imageDatasets =
- ScreeningUtils.filterExternalDataByType(imageDatasets,
- ScreeningConstants.IMAGE_DATASET_TYPE);
- return imageDatasets;
- }
-
- private static Set<Long> extractPlateIds(List<WellContent> locations)
- {
- Set<Long> ids = new HashSet<Long>();
- for (WellContent loc : locations)
- {
- ids.add(loc.getPlate().getId());
- }
- return ids;
- }
-
private List<WellContent> loadLocations(PlateMaterialsSearchCriteria materialCriteria)
{
DataIterator<ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContent> locations;
@@ -403,7 +521,7 @@ public class PlateMaterialLocationsLoader
return wellLocations;
}
- private List<Material> getMaterials(List<WellContent> wellLocations)
+ private static List<Material> getMaterials(List<WellContent> wellLocations)
{
List<Material> materials = new ArrayList<Material>();
for (WellContent wc : wellLocations)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index 2d7102f23a45c158a52d8a72a9e39f6796f6a976..808cbd9d69fba9c9660b187d5623670822476af0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -102,9 +102,9 @@ public class ScreeningApiImpl
List<? extends PlateIdentifier> plates)
{
FeatureVectorDatasetLoader datasetRetriever =
- new FeatureVectorDatasetLoader(session, businessObjectFactory, session
- .tryGetHomeGroupCode(), plates);
- List<FeatureVectorDatasetReference> result = datasetRetriever.getFeatureVectorDatasets();
+ new FeatureVectorDatasetLoader(session, businessObjectFactory,
+ session.tryGetHomeGroupCode(), plates);
+ List<FeatureVectorDatasetReference> result = datasetRetriever.getFeatureVectorDatasetReferences();
return result;
}
@@ -112,7 +112,7 @@ public class ScreeningApiImpl
public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates)
{
return new ImageDatasetLoader(session, businessObjectFactory,
- session.tryGetHomeGroupCode(), plates).getImageDatasets();
+ session.tryGetHomeGroupCode(), plates).getImageDatasetReferences();
}
public List<Plate> listPlates()
@@ -154,8 +154,8 @@ public class ScreeningApiImpl
final String sampleSpaceCode = (sampleSpace != null) ? sampleSpace.getCode() : null;
final Space experimentSpace = project.getSpace();
final ExperimentIdentifier experimentId =
- new ExperimentIdentifier(experiment.getCode(), project.getCode(), experimentSpace
- .getCode(), experiment.getPermId());
+ new ExperimentIdentifier(experiment.getCode(), project.getCode(),
+ experimentSpace.getCode(), experiment.getPermId());
return new Plate(sample.getCode(), sampleSpaceCode, sample.getPermId(), experimentId);
}
@@ -250,34 +250,41 @@ public class ScreeningApiImpl
throw UserFailureException.fromTemplate("Material '%s' does not exist",
materialIdentifier.getAugmentedCode());
}
- final List<WellContent> wellContent;
+ final List<WellContent> wellContents;
final ExperimentIdentifier fullExperimentIdentifier =
getExperimentIdentifierFromDB(experimentIdentifier);
- wellContent =
+ wellContents =
PlateMaterialLocationsLoader.load(session, businessObjectFactory, daoFactory,
new TechId(materialOrNull.getId()), fullExperimentIdentifier.getPermId(),
false);
if (findDatasets)
{
- final Set<Plate> plates = new HashSet<Plate>(wellContent.size());
- for (WellContent w : wellContent)
- {
- plates.add(asPlate(fullExperimentIdentifier, w));
- }
+ final Set<Plate> plates = extractPlates(wellContents, fullExperimentIdentifier);
final FeatureVectorDatasetLoader datasetRetriever =
- new FeatureVectorDatasetLoader(session, businessObjectFactory, session
- .tryGetHomeGroupCode(), plates);
- final List<ImageDatasetReference> imageDatasets = datasetRetriever.getImageDatasets();
+ new FeatureVectorDatasetLoader(session, businessObjectFactory,
+ session.tryGetHomeGroupCode(), plates);
+ final List<ImageDatasetReference> imageDatasets = datasetRetriever.getImageDatasetReferences();
final List<FeatureVectorDatasetReference> featureVectorDatasets =
- datasetRetriever.getFeatureVectorDatasets();
+ datasetRetriever.getFeatureVectorDatasetReferences();
- return asPlateWellReferences(fullExperimentIdentifier, wellContent,
+ return asPlateWellReferences(fullExperimentIdentifier, wellContents,
createPlateToDatasetsMap(imageDatasets, featureVectorDatasets));
} else
{
- return asPlateWellReferences(fullExperimentIdentifier, wellContent, Collections
- .<String, DatasetReferenceHolder> emptyMap());
+ return asPlateWellReferences(fullExperimentIdentifier, wellContents,
+ Collections.<String, DatasetReferenceHolder> emptyMap());
+ }
+ }
+
+ private static Set<Plate> extractPlates(final List<WellContent> wellContents,
+ final ExperimentIdentifier fullExperimentIdentifier)
+ {
+ final Set<Plate> plates = new HashSet<Plate>(wellContents.size());
+ for (WellContent wellContent : wellContents)
+ {
+ plates.add(asPlate(fullExperimentIdentifier, wellContent));
}
+ return plates;
}
public List<PlateWellReferenceWithDatasets> listPlateWells(
@@ -294,8 +301,8 @@ public class ScreeningApiImpl
materialIdentifier.getAugmentedCode());
}
final List<WellContent> wellContent =
- PlateMaterialLocationsLoader.loadOnlyMetadata(session, businessObjectFactory, daoFactory,
- new TechId(materialOrNull.getId()));
+ PlateMaterialLocationsLoader.loadOnlyMetadata(session, businessObjectFactory,
+ daoFactory, new TechId(materialOrNull.getId()));
if (findDatasets)
{
@@ -305,18 +312,18 @@ public class ScreeningApiImpl
plates.add(asPlate(w));
}
final FeatureVectorDatasetLoader datasetRetriever =
- new FeatureVectorDatasetLoader(session, businessObjectFactory, session
- .tryGetHomeGroupCode(), plates);
- final List<ImageDatasetReference> imageDatasets = datasetRetriever.getImageDatasets();
+ new FeatureVectorDatasetLoader(session, businessObjectFactory,
+ session.tryGetHomeGroupCode(), plates);
+ final List<ImageDatasetReference> imageDatasets = datasetRetriever.getImageDatasetReferences();
final List<FeatureVectorDatasetReference> featureVectorDatasets =
- datasetRetriever.getFeatureVectorDatasets();
+ datasetRetriever.getFeatureVectorDatasetReferences();
- return asPlateWellReferences(wellContent, createPlateToDatasetsMap(imageDatasets,
- featureVectorDatasets));
+ return asPlateWellReferences(wellContent,
+ createPlateToDatasetsMap(imageDatasets, featureVectorDatasets));
} else
{
- return asPlateWellReferences(wellContent, Collections
- .<String, DatasetReferenceHolder> emptyMap());
+ return asPlateWellReferences(wellContent,
+ Collections.<String, DatasetReferenceHolder> emptyMap());
}
}
@@ -330,8 +337,8 @@ public class ScreeningApiImpl
for (PlateIdentifier plate : plates)
{
result.add(toPlateWellMaterialMapping(plate, materialTypeIdentifierOrNull,
- getPlateGeometry(query, plate), getPlateMapping(query, plate,
- materialTypeIdentifierOrNull)));
+ getPlateGeometry(query, plate),
+ getPlateMapping(query, plate, materialTypeIdentifierOrNull)));
}
return result;
}
@@ -416,8 +423,8 @@ public class ScreeningApiImpl
{
if (plate.getPermId() == null)
{
- return query.getPlateMappingForMaterialType(plate.tryGetSpaceCode(), plate
- .getPlateCode(), materialTypeIdentifierOrNull.getMaterialTypeCode());
+ return query.getPlateMappingForMaterialType(plate.tryGetSpaceCode(),
+ plate.getPlateCode(), materialTypeIdentifierOrNull.getMaterialTypeCode());
} else
{
return query.getPlateMappingForMaterialType(plate.getPermId(),
@@ -575,8 +582,7 @@ public class ScreeningApiImpl
{
return (o1.getExperimentPlateIdentifier().getAugmentedCode() + ":" + o1
.getWellPosition()).compareTo(o2.getExperimentPlateIdentifier()
- .getAugmentedCode()
- + ":" + o2.getWellPosition());
+ .getAugmentedCode() + ":" + o2.getWellPosition());
}
});
return plateWellReferences;
@@ -599,8 +605,7 @@ public class ScreeningApiImpl
{
return (o1.getExperimentPlateIdentifier().getAugmentedCode() + ":" + o1
.getWellPosition()).compareTo(o2.getExperimentPlateIdentifier()
- .getAugmentedCode()
- + ":" + o2.getWellPosition());
+ .getAugmentedCode() + ":" + o2.getWellPosition());
}
});
return plateWellReferences;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetWellReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetWellReference.java
index 4237ba47b38de4bc6160c425df529a9c2abc3c58..123aff3186c66ad00c1991903c7f754b0fa14c25 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetWellReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetWellReference.java
@@ -39,6 +39,14 @@ public class FeatureVectorDatasetWellReference extends FeatureVectorDatasetRefer
this.wellPosition = wellPosition;
}
+ public FeatureVectorDatasetWellReference(FeatureVectorDatasetReference fvdr,
+ WellPosition wellPosition)
+ {
+ this(fvdr.getDatasetCode(), fvdr.getDatastoreServerUrl(), fvdr.getPlate(), fvdr
+ .getExperimentIdentifier(), fvdr.getPlateGeometry(), fvdr.getRegistrationDate(),
+ fvdr.getParentImageDataset(), wellPosition);
+ }
+
public FeatureVectorDatasetWellReference(String datasetCode, String datastoreServerUrl,
PlateIdentifier plate, ExperimentIdentifier experimentIdentifier,
Geometry plateGeometry, Date registrationDate,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellContent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellContent.java
index d5ae969848daf776b3671f8adfb7843d84cdc2e2..adee923c87ab85ee8fe0b944f1cb36a37a83d9b1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellContent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellContent.java
@@ -37,11 +37,20 @@ public class WellContent implements IsSerializable
private ExperimentReference experiment;
- // a pointer to a material which was being searched for inside a well
+ // Material which was being searched for inside a well. Enriched with properties.
private Material materialContent;
- // contains only images for this well, null if no images have been acquired
- private DatasetImagesReference imagesOrNull;
+ // dataset which contains images for this well, null if no images have been acquired
+ private DatasetImagesReference imagesDatasetOrNull;
+
+ // dataset which contains feature vectors for this well, null if images have not been analyzed
+ private DatasetReference featureVectorDatasetOrNull;
+
+ // Feature vector values, null if images have not been analyzed.
+ // Some features may not be available, then the value is Float.NaN.
+ // External data structure should be used to figure out which value corresponds to which
+ // feature.
+ private float[] featureVectorValuesOrNull;
// GWT only
@SuppressWarnings("unused")
@@ -81,7 +90,17 @@ public class WellContent implements IsSerializable
public DatasetImagesReference tryGetImageDataset()
{
- return imagesOrNull;
+ return imagesDatasetOrNull;
+ }
+
+ public DatasetReference tryGetFeatureVectorDataset()
+ {
+ return featureVectorDatasetOrNull;
+ }
+
+ public float[] tryGetFeatureVectorValues()
+ {
+ return featureVectorValuesOrNull;
}
public ExperimentReference getExperiment()
@@ -89,11 +108,23 @@ public class WellContent implements IsSerializable
return experiment;
}
- public WellContent cloneWithImages(DatasetImagesReference images)
+ public WellContent cloneWithDatasets(DatasetImagesReference imagesOrNull,
+ DatasetReference featureVectorOrNull)
+ {
+ WellContent clone =
+ new WellContent(locationOrNull, well, plate, experiment, materialContent);
+ clone.imagesDatasetOrNull = imagesOrNull;
+ clone.featureVectorDatasetOrNull = featureVectorOrNull;
+ return clone;
+ }
+
+ public WellContent cloneWithDatasets(float[] values)
{
WellContent clone =
new WellContent(locationOrNull, well, plate, experiment, materialContent);
- clone.imagesOrNull = images;
+ clone.imagesDatasetOrNull = imagesDatasetOrNull;
+ clone.featureVectorDatasetOrNull = featureVectorDatasetOrNull;
+ clone.featureVectorValuesOrNull = values;
return clone;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
index 06aeb1158b05a5a2d69735be0aa9597ffce1a38e..0fa3a7a720dcbbc7996e665e5277ad73ff055c3b 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
@@ -27,6 +27,7 @@ import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.openbis.dss.generic.server.featurevectors.FeatureTableRow;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
index c7d94e81902798a8405450fc5b5ede6c7a667b6d..c3d42709a24ce5489adbef95871c5ac66ba9ed13 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
@@ -19,7 +19,11 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
@@ -27,7 +31,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
@@ -81,8 +84,8 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
one(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
- will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1), imageAnalysisDataSet(
- p1, "2", 2))));
+ will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1),
+ imageAnalysisDataSet(p1, "2", 2))));
}
});
@@ -129,8 +132,8 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
- assertEquals("Sample '/p1' has no property " + ScreeningConstants.PLATE_GEOMETRY, ex
- .getMessage());
+ assertEquals("Sample '/p1' has no property " + ScreeningConstants.PLATE_GEOMETRY,
+ ex.getMessage());
}
context.assertIsSatisfied();
}
@@ -178,12 +181,22 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
exactly(2).of(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
- one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
- will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1), imageAnalysisDataSet(
- p1, "2", 2))));
-
- one(datasetLister).listByParentTechId(new TechId(1));
- will(returnValue(Arrays.asList(imageAnalysisDataSet(null, "3", 3))));
+ long imageDatasetId = 1;
+ one(datasetLister).listBySampleIds(with(Arrays.asList(imageDatasetId)));
+ will(returnValue(Arrays.asList(
+ imageDataSet(p1, "" + imageDatasetId, imageDatasetId),
+ imageAnalysisDataSet(p1, "2", 2))));
+
+ one(datasetLister).listByParentTechIds(Arrays.asList(imageDatasetId));
+ long analysisDatasetId = 3;
+ will(returnValue(Arrays.asList(imageAnalysisDataSet(null, ""
+ + analysisDatasetId, analysisDatasetId))));
+
+ one(datasetLister).listParentIds(Arrays.asList(analysisDatasetId));
+ Map<Long, Set<Long>> parentToChildrenMap = new HashMap<Long, Set<Long>>();
+ parentToChildrenMap.put(analysisDatasetId,
+ new HashSet<Long>(Arrays.asList(imageDatasetId)));
+ will(returnValue(parentToChildrenMap));
}
});