From e34aa703c36d8efb53a81d9c0434a870243dc6a7 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 16 May 2011 13:33:53 +0000
Subject: [PATCH] LMS-2250 extending IDatasetLister, using data set lister for
listing share IDs and data sets.
SVN: 21320
---
.../path/PathInfoDatabaseFeedingTask.java | 1 -
.../openbis/generic/server/ETLService.java | 27 +++++----
.../bo/datasetlister/DatasetLister.java | 16 +++--
.../bo/datasetlister/IDatasetLister.java | 5 ++
.../datasetlister/IDatasetListingQuery.java | 3 +
.../generic/shared/basic/dto/DataSet.java | 12 ++++
.../dto/SimpleDataSetInformationDTO.java | 13 ----
.../translator/SimpleDataSetHelper.java | 33 ++++-------
.../translator/SimpleDataSetHelperTest.java | 59 +++++++++----------
9 files changed, 88 insertions(+), 81 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseFeedingTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseFeedingTask.java
index 06084e7ee2e..71f648a36a7 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseFeedingTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/path/PathInfoDatabaseFeedingTask.java
@@ -111,7 +111,6 @@ public class PathInfoDatabaseFeedingTask implements IMaintenanceTask, IPostRegis
public void execute()
{
- // TODO don't load virtual data sets here or filter them out
List<SimpleDataSetInformationDTO> dataSets = service.listDataSets();
for (SimpleDataSetInformationDTO dataSet : dataSets)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index 9051857dde9..4afaad4d9b7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -37,7 +37,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObject
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGroupBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IRoleAssignmentTable;
@@ -57,6 +56,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ArchiverDataSetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
@@ -800,14 +800,18 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
public List<DataSetShareId> listShareIds(String sessionToken, String dataStore)
throws UserFailureException
{
- List<ExternalDataPE> dataSets = loadDataSets(sessionToken, dataStore);
+ List<ExternalData> dataSets = loadDataSets(sessionToken, dataStore);
ArrayList<DataSetShareId> shareIds = new ArrayList<DataSetShareId>();
- for (ExternalDataPE dataSet : dataSets)
+ for (ExternalData dataSet : dataSets)
{
- DataSetShareId dataSetShareId = new DataSetShareId();
- dataSetShareId.setDataSetCode(dataSet.getCode());
- dataSetShareId.setShareId(dataSet.getShareId());
- shareIds.add(dataSetShareId);
+ if (dataSet instanceof DataSet)
+ {
+ DataSet ds = (DataSet) dataSet;
+ DataSetShareId dataSetShareId = new DataSetShareId();
+ dataSetShareId.setDataSetCode(ds.getCode());
+ dataSetShareId.setShareId(ds.getShareId());
+ shareIds.add(dataSetShareId);
+ }
}
return shareIds;
}
@@ -815,7 +819,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
public List<SimpleDataSetInformationDTO> listDataSets(String sessionToken, String dataStoreCode)
throws UserFailureException
{
- List<ExternalDataPE> dataSets = loadDataSets(sessionToken, dataStoreCode);
+ List<ExternalData> dataSets = loadDataSets(sessionToken, dataStoreCode);
return SimpleDataSetHelper.translate(dataSets);
}
@@ -851,18 +855,17 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return result;
}
- private List<ExternalDataPE> loadDataSets(String sessionToken, String dataStoreCode)
+ private List<ExternalData> loadDataSets(String sessionToken, String dataStoreCode)
{
Session session = getSession(sessionToken);
+ IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
DataStorePE dataStore =
getDAOFactory().getDataStoreDAO().tryToFindDataStoreByCode(dataStoreCode);
if (dataStore == null)
{
throw new UserFailureException(String.format("Unknown data store '%s'", dataStoreCode));
}
- IExternalDataTable dataSetTable = businessObjectFactory.createExternalDataTable(session);
- dataSetTable.loadByDataStore(dataStore);
- return dataSetTable.getExternalData();
+ return datasetLister.listByDataStore(dataStore.getId());
}
public List<DeletedDataSet> listDeletedDataSets(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 137c09868e9..562a285f0fd 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
@@ -343,6 +343,11 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
return asList(createPrimaryDatasets(asList(datasets)));
}
+ public List<ExternalData> listByDataStore(long dataStoreID)
+ {
+ return enrichDatasets(query.getDatasetsByDataStoreId(dataStoreID));
+ }
+
public List<ExternalData> listByTrackingCriteria(TrackingDataSetCriteria criteria)
{
DataIterator<DatasetRecord> dataSets;
@@ -645,7 +650,7 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
for (DatasetRecord record : records)
{
DataSetType dsType = dataSetTypes.get(record.dsty_id);
- if (record.is_placeholder)
+ if (record.is_placeholder || record.location == null)
{
// placeholder data sets are filtered out
} else if (dsType.isContainerType())
@@ -665,13 +670,16 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
convertStandardProperties(dataSet, record);
dataSet.setComplete(resolve(record.is_complete));
- dataSet.setStatus(DataSetArchivingStatus.valueOf(record.status));
+ dataSet.setStatus(record.status == null ? null : DataSetArchivingStatus
+ .valueOf(record.status));
dataSet.setSpeedHint(record.speed_hint == null ? Constants.DEFAULT_SPEED_HINT
: record.speed_hint);
- dataSet.setFileFormatType(fileFormatTypes.get(record.ffty_id));
+ dataSet.setShareId(record.share_id);
+ dataSet.setFileFormatType(record.ffty_id == null ? null : fileFormatTypes
+ .get(record.ffty_id));
dataSet.setLocation(record.location);
dataSet.setSize(record.size);
- dataSet.setLocatorType(locatorTypes.get(record.loty_id));
+ dataSet.setLocatorType(record.loty_id == null ? null : locatorTypes.get(record.loty_id));
return dataSet;
}
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 3ef3183b414..c22dde3e489 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
@@ -76,6 +76,11 @@ public interface IDatasetLister
* Lists all data sets with specified codes. Unenriched data sets will be returned.
*/
List<ExternalData> listByDatasetCode(Collection<String> datasetCodes);
+
+ /**
+ * Lists all data sets of specified data store. Unenriched data sets will be returned.
+ */
+ List<ExternalData> listByDataStore(long dataStoreID);
/** @return datasets with given ids */
List<ExternalData> listByDatasetIds(Collection<Long> datasetIds);
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 62319fb0fb6..e7816b22d05 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
@@ -195,6 +195,9 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
{ StringArrayMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<DatasetRecord> getDatasets(String[] datasetCodes);
+ @Select(sql = SELECT_ALL + " where data.dast_id = ?{1}", fetchSize = FETCH_SIZE)
+ public DataIterator<DatasetRecord> getDatasetsByDataStoreId(long dataStoreId);
+
/**
* Returns the children dataset ids of the specified datasets.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSet.java
index 6201dff3dea..d690ac0cfbe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DataSet.java
@@ -28,6 +28,8 @@ public class DataSet extends ExternalData implements IDatasetLocation
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private Boolean complete;
+
+ private String shareId;
private String location;
@@ -51,6 +53,16 @@ public class DataSet extends ExternalData implements IDatasetLocation
this.complete = complete;
}
+ public void setShareId(String shareId)
+ {
+ this.shareId = shareId;
+ }
+
+ public String getShareId()
+ {
+ return shareId;
+ }
+
@Override
public String getLocation()
{
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 151f99b3386..5da76b66351 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
@@ -17,7 +17,6 @@
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.IDatasetLocation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
@@ -55,8 +54,6 @@ public class SimpleDataSetInformationDTO implements Serializable, IDatasetLocati
private String databaseInstanceCode;
- private Collection<String> parentDataSetCodes;
-
public void setDataStoreCode(String dataStoreCode)
{
this.dataStoreCode = dataStoreCode;
@@ -178,14 +175,4 @@ public class SimpleDataSetInformationDTO implements Serializable, IDatasetLocati
this.databaseInstanceCode = dbInstanceCode;
}
- public Collection<String> getParentDataSetCodes()
- {
- return parentDataSetCodes;
- }
-
- public void setParentDataSetCodes(Collection<String> parentDataSetCodes)
- {
- this.parentDataSetCodes = parentDataSetCodes;
- }
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelper.java
index 9cfc5f5545b..9300849d6d3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelper.java
@@ -17,13 +17,11 @@
package ch.systemsx.cisd.openbis.generic.shared.translator;
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.basic.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-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;
/**
@@ -33,23 +31,25 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
*/
public class SimpleDataSetHelper
{
- public static final List<SimpleDataSetInformationDTO> translate(
- List<ExternalDataPE> externalData)
+ public static final List<SimpleDataSetInformationDTO> translate(List<ExternalData> externalData)
{
if (externalData == null)
{
return null;
}
List<SimpleDataSetInformationDTO> result = new ArrayList<SimpleDataSetInformationDTO>();
- for (ExternalDataPE ed : externalData)
+ for (ExternalData ed : externalData)
{
- result.add(translate(ed));
+ if (ed instanceof DataSet)
+ {
+ DataSet dataSet = (DataSet) ed;
+ result.add(translate(dataSet));
+ }
}
return result;
}
- // TODO KE: use DataPE ?
- private static SimpleDataSetInformationDTO translate(ExternalDataPE data)
+ private static SimpleDataSetInformationDTO translate(DataSet data)
{
SimpleDataSetInformationDTO result = new SimpleDataSetInformationDTO();
result.setDataStoreCode(data.getDataStore().getCode());
@@ -59,22 +59,13 @@ public class SimpleDataSetHelper
result.setDataSetLocation(data.getLocation());
result.setDataSetSize(data.getSize());
result.setDatabaseInstanceCode(data.getExperiment().getProject().getSpace()
- .getDatabaseInstance().getCode());
+ .getInstance().getCode());
result.setExperimentCode(data.getExperiment().getCode());
result.setProjectCode(data.getExperiment().getProject().getCode());
result.setGroupCode(data.getExperiment().getProject().getSpace().getCode());
- SamplePE sampleOrNull = data.tryGetSample();
- result.setSampleCode(sampleOrNull == null ? null : sampleOrNull.getCode());
+ result.setSampleCode(data.getSampleCode());
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/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelperTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelperTest.java
index 56e837cf447..2f17ab45700 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelperTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelperTest.java
@@ -22,21 +22,21 @@ import java.util.List;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.common.types.BooleanOrUnknown;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
+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.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
*
@@ -48,10 +48,11 @@ public class SimpleDataSetHelperTest extends AssertJUnit
@Test
public void testTranslateList()
{
- ExternalDataPE ds1 = create(1);
- ExternalDataPE ds2 = create(2);
+ ExternalData ds1 = create(1);
+ ExternalData ds2 = create(2);
+ ExternalData ds3 = new ContainerDataSet();
- List<SimpleDataSetInformationDTO> list = SimpleDataSetHelper.translate(Arrays.asList(ds1, ds2));
+ List<SimpleDataSetInformationDTO> list = SimpleDataSetHelper.translate(Arrays.asList(ds1, ds2, ds3));
check(1, list.get(0));
check(2, list.get(1));
@@ -62,49 +63,47 @@ public class SimpleDataSetHelperTest extends AssertJUnit
@Test
public void testTranslateDescription()
{
- ExternalData ds = ExternalDataTranslator.translate(create(1), "", false);
- DatasetDescription description = ExternalDataTranslator.translateToDescription(ds);
+ DatasetDescription description = ExternalDataTranslator.translateToDescription(create(1));
SimpleDataSetInformationDTO result = SimpleDataSetHelper.translate(description);
check(1, result);
}
- private ExternalDataPE create(long id)
+ private ExternalData create(long id)
{
- ExternalDataPE dataSet = new ExternalDataPE();
+ DataSet dataSet = new DataSet();
dataSet.setId(id);
dataSet.setCode("ds-" + id);
- dataSet.setComplete(BooleanOrUnknown.T);
+ dataSet.setComplete(true);
dataSet.setDataProducerCode("producer");
- DataSetTypePE dataSetType = new DataSetTypePE();
+ DataSetType dataSetType = new DataSetType();
dataSetType.setCode("MY-TYPE");
dataSet.setDataSetType(dataSetType);
- DataStorePE store = new DataStorePE();
+ DataStore store = new DataStore();
store.setCode("MY-STORE");
dataSet.setDataStore(store);
dataSet.setDerived(true);
- ExperimentPE experiment = new ExperimentPE();
+ Experiment experiment = new Experiment();
experiment.setCode("MY-EXPERIMENT");
- ExperimentTypePE experimentType = new ExperimentTypePE();
+ ExperimentType experimentType = new ExperimentType();
experimentType.setCode("MY-EXPERIMENT-TYPE");
experiment.setExperimentType(experimentType);
- ProjectPE project = new ProjectPE();
+ Project project = new Project();
project.setCode("MY-PROJECT");
- SpacePE space = new SpacePE();
+ Space space = new Space();
space.setCode("MY-SPACE");
- DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
+ DatabaseInstance databaseInstance = new DatabaseInstance();
databaseInstance.setCode("MY-DB");
- space.setDatabaseInstance(databaseInstance);
+ space.setInstance(databaseInstance);
project.setSpace(space);
experiment.setProject(project);
dataSet.setExperiment(experiment);
- FileFormatTypePE fileFormatType = new FileFormatTypePE();
+ FileFormatType fileFormatType = new FileFormatType();
fileFormatType.setCode("MY_FILE_FORMAT");
dataSet.setFileFormatType(fileFormatType);
dataSet.setLocation("my-location");
- dataSet.setPresentInArchive(true);
- SamplePE sample = new SamplePE();
+ Sample sample = new Sample();
sample.setCode("MY-SAMPLE");
dataSet.setSample(sample);
dataSet.setShareId("42");
--
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