From 10e83effa95e4ceede975e49b86258be1c27b60e Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 15 Feb 2011 19:57:25 +0000
Subject: [PATCH] LMS-1988 Fixed some small bugs in the entity registration
code. Removed not-yet-implemented method from interface.
SVN: 19990
---
.../v1/IDataSetRegistrationTransaction.java | 13 +++++++------
.../registrator/api/v1/impl/DataSet.java | 16 ++++++++++++----
.../impl/DataSetRegistrationTransaction.java | 10 ++++++----
.../api/v1/impl/ExperimentImmutable.java | 2 +-
.../registrator/api/v1/impl/Sample.java | 19 +++++++++----------
.../api/v1/impl/SampleImmutable.java | 11 ++++++++++-
6 files changed, 45 insertions(+), 26 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
index 47ffafc5381..d2df83a95ee 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
@@ -39,12 +39,17 @@ public interface IDataSetRegistrationTransaction
IDataSet createNewDataSet();
/**
- * Get a sample from the openBIS AS.
+ * Get a sample from the openBIS AS. Returns null if the sample does not exist.
+ *
+ * @return A sample or null
*/
ISampleImmutable getSample(String sampleIdentifierString);
/**
- * Get a sample from the openBIS AS for the purpose of modifying it.
+ * Get a sample from the openBIS AS for the purpose of modifying it. Returns null if the sample
+ * does not exist.
+ *
+ * @return A sample or null
*/
ISample getSampleForUpdate(String sampleIdentifierString);
@@ -114,8 +119,4 @@ public interface IDataSetRegistrationTransaction
*/
String createNewFile(IDataSet dst, String dstInDataset, String fileName);
- /**
- * Delete a file a the given path.
- */
- void deleteFile(String src);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
index 2c5449dd903..3de83b0cbab 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
@@ -26,6 +26,7 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.ISampleImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
@@ -103,15 +104,22 @@ public class DataSet<T extends DataSetInformation> implements IDataSet
{
this.sampleOrNull = sampleOrNull;
+ DataSetInformation dataSetInformation = registrationDetails.getDataSetInformation();
if (sampleOrNull == null)
{
- registrationDetails.getDataSetInformation().setSample(null);
- registrationDetails.getDataSetInformation().setSampleCode(null);
+ dataSetInformation.setSample(null);
+ dataSetInformation.setSampleCode(null);
} else
{
Sample sample = (Sample) sampleOrNull;
- registrationDetails.getDataSetInformation().setSample(sample.getSample());
- registrationDetails.getDataSetInformation().setSampleCode(sample.getSample().getCode());
+
+ dataSetInformation.setSample(sample.getSample());
+ dataSetInformation.setSampleCode(sample.getSample().getCode());
+ Space space = sample.getSample().getSpace();
+ if (null != space)
+ {
+ dataSetInformation.setSpaceCode(space.getCode());
+ }
setExperiment(sample.getSample().getExperiment());
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
index 4ead56eec83..72d776bc074 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
@@ -179,7 +179,9 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
{
SampleIdentifier sampleIdentifier =
new SampleIdentifierFactory(sampleIdentifierString).createIdentifier();
- return new SampleImmutable(openBisService.tryGetSampleWithExperiment(sampleIdentifier));
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sampleOrNull =
+ openBisService.tryGetSampleWithExperiment(sampleIdentifier);
+ return (null == sampleOrNull) ? null : new SampleImmutable(sampleOrNull);
}
public ISample getSampleForUpdate(String sampleIdentifierString)
@@ -196,9 +198,9 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
{
ExperimentIdentifier experimentIdentifier =
new ExperimentIdentifierFactory(experimentIdentifierString).createIdentifier();
- ExperimentImmutable experiment =
- new ExperimentImmutable(openBisService.tryToGetExperiment(experimentIdentifier));
- return experiment;
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experimentOrNull =
+ openBisService.tryToGetExperiment(experimentIdentifier);
+ return (null == experimentOrNull) ? null : new ExperimentImmutable(experimentOrNull);
}
public IExperiment createNewExperiment(String experimentIdentifierString)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
index 9a101208e37..e13407c4112 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
@@ -40,7 +40,7 @@ class ExperimentImmutable implements IExperimentImmutable
public boolean isExistingExperiment()
{
- return null != experiment;
+ return true;
}
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
index 2f035ce2602..f7b1af97493 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
@@ -16,13 +16,10 @@
package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
-import java.util.ArrayList;
-import java.util.List;
-
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
@@ -31,6 +28,13 @@ import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
public class Sample extends SampleImmutable implements ISample
{
+ private static ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample buildSampleWithIdentifier(
+ String identifier)
+ {
+ SampleBuilder builder = new SampleBuilder(identifier);
+ return builder.getSample();
+ }
+
public Sample(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
{
super(sample);
@@ -38,15 +42,10 @@ public class Sample extends SampleImmutable implements ISample
public Sample(String sampleIdentifier, String permId)
{
- super(new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample());
- getSample().setIdentifier(sampleIdentifier);
+ super(buildSampleWithIdentifier(sampleIdentifier), false);
getSample().setPermId(permId);
-
- List<IEntityProperty> properties = new ArrayList<IEntityProperty>();
- getSample().setProperties(properties);
}
-
public void setExperiment(IExperimentImmutable experiment)
{
ExperimentImmutable exp = (ExperimentImmutable) experiment;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
index b69116947b5..2e73374363c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
@@ -28,9 +28,18 @@ public class SampleImmutable implements ISampleImmutable
{
private final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample;
+ private final boolean existingSample;
+
public SampleImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
+ {
+ this(sample, true);
+ }
+
+ public SampleImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample,
+ boolean existingSample)
{
this.sample = sample;
+ this.existingSample = existingSample;
}
public IExperimentImmutable getExperiment()
@@ -52,7 +61,7 @@ public class SampleImmutable implements ISampleImmutable
public boolean isExistingSample()
{
- return null != sample;
+ return existingSample;
}
/**
--
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