From fb783bf9a2b32c22f86f8266539d80d36b0c7f89 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 23 Jun 2010 14:07:54 +0000
Subject: [PATCH] LMS-1584 Added code to find out which sample a data set is
associated with, even if this association is indirect.
SVN: 16699
---
.../business/bo/SimpleDataSetHelper.java | 11 +++++++
.../dto/SimpleDataSetInformationDTO.java | 29 ++++++++++++++-----
.../AbstractFeatureVectorMigrator.java | 13 +++++----
3 files changed, 39 insertions(+), 14 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SimpleDataSetHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SimpleDataSetHelper.java
index 1085a2fe73c..3e097579e7a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SimpleDataSetHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SimpleDataSetHelper.java
@@ -17,8 +17,10 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.List;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
@@ -58,6 +60,15 @@ public class SimpleDataSetHelper
SamplePE sampleOrNull = data.tryGetSample();
result.setSampleCode(sampleOrNull == null ? null : sampleOrNull.getCode());
result.setDataSetType(data.getDataSetType().getCode());
+
+ HashSet<String> parentCodes = new HashSet<String>();
+ for (DataPE parent : data.getParents())
+ {
+ parentCodes.add(parent.getCode());
+ }
+
+ result.setParentDataSetCodes(parentCodes);
+
return result;
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SimpleDataSetInformationDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SimpleDataSetInformationDTO.java
index 2bec7fdd5e0..76c9d83cf0b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SimpleDataSetInformationDTO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SimpleDataSetInformationDTO.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.dto;
import java.io.Serializable;
+import java.util.Collection;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
@@ -29,21 +30,23 @@ public class SimpleDataSetInformationDTO implements Serializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
- String dataSetCode;
+ private String dataSetCode;
- String dataSetLocation;
+ private String dataSetLocation;
- String dataSetType;
+ private String dataSetType;
- String sampleCode;
+ private String sampleCode;
- String groupCode;
+ private String groupCode;
- String experimentCode;
+ private String experimentCode;
- String projectCode;
+ private String projectCode;
- String databaseInstanceCode;
+ private String databaseInstanceCode;
+
+ private Collection<String> parentDataSetCodes;
public String getDataSetType()
{
@@ -126,4 +129,14 @@ public class SimpleDataSetInformationDTO implements Serializable
this.databaseInstanceCode = dbInstanceCode;
}
+ public Collection<String> getParentDataSetCodes()
+ {
+ return parentDataSetCodes;
+ }
+
+ public void setParentDataSetCodes(Collection<String> parentDataSetCodes)
+ {
+ this.parentDataSetCodes = parentDataSetCodes;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java
index 22d4236cc83..ce06b80ce70 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java
@@ -37,6 +37,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -134,7 +135,7 @@ public abstract class AbstractFeatureVectorMigrator implements IMigrator
private Sample findSampleCodeForDataSet(SimpleDataSetInformationDTO dataSetInfo)
{
String sampleCodeOrNull = dataSetInfo.getSampleCode();
- Sample sample = null;
+ SampleIdentifier sampleId = null;
if (null == sampleCodeOrNull)
{
// check the parent data sets for a sample
@@ -142,20 +143,20 @@ public abstract class AbstractFeatureVectorMigrator implements IMigrator
for (String dataSetCode : parentDataSetCodes)
{
ExternalData externalData = openBisService.tryGetDataSetForServer(dataSetCode);
- if (externalData.getSample() != null)
+ if (externalData != null && externalData.getSample() != null)
{
- sample = externalData.getSample();
+ sampleId = SampleIdentifierFactory.parse(externalData.getSampleIdentifier());
break;
}
}
} else
{
- SampleIdentifier sampleId =
+ sampleId =
new SampleIdentifier(new SpaceIdentifier(dataSetInfo.getDatabaseInstanceCode(),
dataSetInfo.getGroupCode()), dataSetInfo.getSampleCode());
- sample = openBisService.tryGetSampleWithExperiment(sampleId);
}
- return sample;
+
+ return openBisService.tryGetSampleWithExperiment(sampleId);
}
public void close()
--
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