From d9ef3cf1f56aa6793335ac500842b35d26c4723c Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Tue, 26 Jun 2012 15:09:11 +0000
Subject: [PATCH] SP-169 BIS-90 propagate link data set information through
some dss dataSet classes
SVN: 25871
---
.../registrator/api/v1/IDataSetUpdatable.java | 5 +++
.../registrator/api/v1/impl/DataSet.java | 33 +++++++++++++++++--
.../api/v1/impl/DataSetImmutable.java | 22 +++++++++++++
.../api/v1/impl/DataSetUpdatable.java | 14 ++++++++
.../api/internal/v1/IDataSetImmutable.java | 9 +++--
.../shared/dto/DataSetInformation.java | 19 ++++++++++-
6 files changed, 97 insertions(+), 5 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetUpdatable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetUpdatable.java
index ab51cd279c3..c06b321684f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetUpdatable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetUpdatable.java
@@ -20,6 +20,7 @@ import java.util.List;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExternalDataManagementSystemImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
@@ -65,4 +66,8 @@ public interface IDataSetUpdatable extends IDataSetImmutable
/** Set the codes for contained data sets. */
public void setContainedDataSetCodes(List<String> containedDataSetCodes);
+
+ /** Set the external data management system */
+ public void setExternalDataManagementSystem(
+ IExternalDataManagementSystemImmutable externalDataManagementSystem);
}
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 1b41d0094bd..3a43eece4d5 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
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExternalDataManagementSystemImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
@@ -44,7 +45,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
*
* @author Chandrasekhar Ramakrishnan
*/
-public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmutable implements IDataSet
+public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmutable implements
+ IDataSet
{
private final DataSetRegistrationDetails<? extends T> registrationDetails;
@@ -55,6 +57,8 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
private ISampleImmutable sampleOrNull;
+ private IExternalDataManagementSystemImmutable externalDataManagementSystemOrNull;
+
public DataSet(DataSetRegistrationDetails<? extends T> registrationDetails, File dataSetFolder,
IEncapsulatedOpenBISService service)
{
@@ -301,7 +305,7 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
+ "sets not existing prior the transaction start.");
}
- //the dataset cannot be contained before it is created
+ // the dataset cannot be contained before it is created
@Override
public boolean isContainedDataSet()
{
@@ -313,4 +317,29 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
{
return null;
}
+
+ @Override
+ public void setExternalDataManagementSystem(
+ IExternalDataManagementSystemImmutable externalDataManagementSystem)
+ {
+ this.externalDataManagementSystemOrNull = externalDataManagementSystem;
+ String codeToSet =
+ (externalDataManagementSystem != null) ? externalDataManagementSystem.getCode()
+ : null;
+
+ this.registrationDetails.getDataSetInformation().setExternalDataManagementSystem(codeToSet);
+ }
+
+ @Override
+ public boolean isLinkDataSet()
+ {
+ return this.externalDataManagementSystemOrNull != null;
+ }
+
+ @Override
+ public IExternalDataManagementSystemImmutable getExternalDataManagementSystem()
+ {
+ return externalDataManagementSystemOrNull;
+ }
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
index b6fdf509986..1569192b93e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
@@ -23,11 +23,13 @@ import java.util.List;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExternalDataManagementSystemImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalDataManagementSystem;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
@@ -188,4 +190,24 @@ public class DataSetImmutable extends AbstractDataSetImmutable
}
return result;
}
+
+ @Override
+ public boolean isLinkDataSet()
+ {
+ return dataSet.tryGetAsLinkDataSet() != null;
+ }
+
+ @Override
+ public IExternalDataManagementSystemImmutable getExternalDataManagementSystem()
+ {
+ ExternalDataManagementSystem externalDMS =
+ dataSet.tryGetAsLinkDataSet().getExternalDataManagementSystem();
+ if (externalDMS != null)
+ {
+ return new ExternalDataManagementSystemImmutable(externalDMS);
+ } else
+ {
+ return null;
+ }
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java
index 8d7005b3d96..22fa2059c0b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java
@@ -25,10 +25,12 @@ import java.util.Set;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExternalDataManagementSystemImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetBatchUpdateDetails;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalDataManagementSystem;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PlaceholderDataSet;
@@ -202,4 +204,16 @@ public class DataSetUpdatable extends DataSetImmutable implements IDataSetUpdata
return updates;
}
+ @Override
+ public void setExternalDataManagementSystem(
+ IExternalDataManagementSystemImmutable externalDataManagementSystem)
+ {
+
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalDataManagementSystem dummy =
+ new ExternalDataManagementSystem();
+ dummy.setCode(externalDataManagementSystem.getCode());
+
+ dataSet.tryGetAsLinkDataSet().setExternalDataManagementSystem(dummy);
+ }
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IDataSetImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IDataSetImmutable.java
index cbab00ee1b3..8b17efb3d67 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IDataSetImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/IDataSetImmutable.java
@@ -73,7 +73,7 @@ public interface IDataSetImmutable
* data set.
*/
public String getDataSetType();
-
+
/**
* Returns data set type with property types and vocabulary terms for all property types with
* vocabulary data type.
@@ -127,5 +127,10 @@ public interface IDataSetImmutable
* Return the code of the container in which this data set is contained
*/
public String getContainerDataSet();
-
+
+ /** @return true if this is a data set, that links to external data management system */
+ public boolean isLinkDataSet();
+
+ /** Get the external data management system */
+ public IExternalDataManagementSystemImmutable getExternalDataManagementSystem();
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetInformation.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetInformation.java
index 68d51bb95b5..2b2d28ae020 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetInformation.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetInformation.java
@@ -78,7 +78,7 @@ public class DataSetInformation implements Serializable
/** sample with properties, enriched with connected experiment with properties. */
private transient Sample sample;
-
+
private transient boolean linkSample = true;
private transient Experiment experiment;
@@ -87,6 +87,8 @@ public class DataSetInformation implements Serializable
private List<String> containedDataSetCodes = new ArrayList<String>();
+ private String externalDataManagementSystem;
+
/**
* A subset of {@link NewExternalData} which gets set by the code extractor.
* <p>
@@ -385,6 +387,21 @@ public class DataSetInformation implements Serializable
return false == containedDataSetCodes.isEmpty();
}
+ public void setExternalDataManagementSystem(final String code)
+ {
+ this.externalDataManagementSystem = code;
+ }
+
+ public String getExternalDataManagementSystem()
+ {
+ return this.externalDataManagementSystem;
+ }
+
+ public boolean isLinkDataSet()
+ {
+ return this.externalDataManagementSystem != null;
+ }
+
public final String describe()
{
if (experimentIdentifier == null)
--
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