diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
index 4a90ae1cc1ed599e7434f9c67d7aa2e3ceec035b..20484481b65ead60cf8989906ac27082db527416 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataSetCommandExecutor.java
@@ -28,9 +28,9 @@ import ch.systemsx.cisd.common.collections.IExtendedBlockingQueue;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* @author Franz-Josef Elmer
@@ -108,7 +108,7 @@ class DataSetCommandExecutor implements IDataSetCommandExecutor
}
public void scheduleUploadingDataSetsToCIFEX(ICIFEXRPCServiceFactory cifexServiceFactory,
- MailClientParameters mailClientParameters, List<ExternalDataPE> dataSets,
+ MailClientParameters mailClientParameters, List<ExternalData> dataSets,
DataSetUploadContext uploadContext)
{
scheduleCommand(new UploadingCommand(cifexServiceFactory, mailClientParameters, dataSets,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
index b85b732d1ed3e86ab8fdc55e590ca2036e9af3a6..69c27cde5aab34c293aad8d2d1f577b45553f173 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
@@ -33,10 +33,10 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPlugi
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProvider;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProviders;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* Implementation of {@link IDataStoreService} which will be accessed remotely by the opneBIS
@@ -151,7 +151,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
commandExecuter.scheduleDeletionOfDataSets(dataSetLocations);
}
- public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalDataPE> dataSets,
+ public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalData> dataSets,
DataSetUploadContext context) throws InvalidAuthenticationException
{
sessionTokenManager.assertValidSessionToken(sessionToken);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
index 6d296f946decbc4fad7b62b85fac87721152c1b1..75ad05a1d93b55f6188c17c54574a0d5b00ff7e1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceLogger.java
@@ -22,10 +22,10 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.exceptions.InvalidAuthenticationException;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* @author Franz-Josef Elmer
@@ -91,11 +91,11 @@ class DataStoreServiceLogger implements IDataStoreService
log("deleteDataSets", "LOCATIONS(%s)", dataSetLocations);
}
- public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalDataPE> dataSets,
+ public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalData> dataSets,
DataSetUploadContext context) throws InvalidAuthenticationException
{
StringBuilder builder = new StringBuilder();
- for (ExternalDataPE externalDataPE : dataSets)
+ for (ExternalData externalDataPE : dataSets)
{
builder.append(' ').append(externalDataPE.getCode());
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/IDataSetCommandExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/IDataSetCommandExecutor.java
index 6973fd21a7f3957aca59eb329f031654135ffe91..d1df9bf0f14b6c0d611ecec7b4f48f1fd107f3ef 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/IDataSetCommandExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/IDataSetCommandExecutor.java
@@ -19,9 +19,9 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.util.List;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* Executor of commands operating on data sets in a data store. Commands are expected to be executed
@@ -49,7 +49,7 @@ interface IDataSetCommandExecutor
* failed.
*/
void scheduleUploadingDataSetsToCIFEX(ICIFEXRPCServiceFactory cifexServiceFactory,
- MailClientParameters mailClientParameters, List<ExternalDataPE> dataSets,
+ MailClientParameters mailClientParameters, List<ExternalData> dataSets,
DataSetUploadContext uploadContext);
/** Schedules the specified processing task for provided datasets */
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
index ac808681abfa112f740cb29a1f1bd986dc3ed9d1..6b4132e21c4c9ab8600460f14797f6071891d788 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommand.java
@@ -26,9 +26,9 @@ import java.io.OutputStream;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Date;
import java.util.List;
-import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
@@ -47,14 +47,13 @@ import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.mail.MailClient;
import ch.systemsx.cisd.common.types.BooleanOrUnknown;
import ch.systemsx.cisd.common.utilities.TokenGenerator;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
+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.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
* A command which zips the given data sets and uploads the ZIP file to CIFEX.
@@ -150,7 +149,7 @@ class UploadingCommand implements IDataSetCommand
addRow("sample", key, value);
}
- void sample(String key, PersonPE person)
+ void sample(String key, Person person)
{
addRow("sample", key, person);
}
@@ -165,7 +164,7 @@ class UploadingCommand implements IDataSetCommand
addRow("experiment", key, value);
}
- void experiment(String key, PersonPE person)
+ void experiment(String key, Person person)
{
addRow("experiment", key, person);
}
@@ -175,7 +174,7 @@ class UploadingCommand implements IDataSetCommand
addRow("experiment", key, date);
}
- private void addRow(String category, String key, PersonPE person)
+ private void addRow(String category, String key, Person person)
{
StringBuilder stringBuilder = new StringBuilder();
if (person != null)
@@ -223,7 +222,7 @@ class UploadingCommand implements IDataSetCommand
private final ICIFEXRPCServiceFactory cifexServiceFactory;
- private final List<ExternalDataPE> dataSets;
+ private final List<ExternalData> dataSets;
private final String fileName;
@@ -243,7 +242,7 @@ class UploadingCommand implements IDataSetCommand
boolean deleteAfterUploading = true;
UploadingCommand(ICIFEXRPCServiceFactory cifexServiceFactory,
- MailClientParameters mailClientParameters, List<ExternalDataPE> dataSets,
+ MailClientParameters mailClientParameters, List<ExternalData> dataSets,
DataSetUploadContext context)
{
this.cifexServiceFactory = cifexServiceFactory;
@@ -302,7 +301,7 @@ class UploadingCommand implements IDataSetCommand
{
outputStream = new FileOutputStream(zipFile);
zipOutputStream = new ZipOutputStream(outputStream);
- for (ExternalDataPE dataSet : dataSets)
+ for (ExternalData dataSet : dataSets)
{
String location = dataSet.getLocation();
File dataSetFile = new File(store, location);
@@ -354,21 +353,21 @@ class UploadingCommand implements IDataSetCommand
}
}
- private String createMetaData(ExternalDataPE dataSet)
+ private String createMetaData(ExternalData dataSet)
{
MetaDataBuilder builder = new MetaDataBuilder();
builder.dataSet("code", dataSet.getCode());
builder.dataSet("production_timestamp", dataSet.getProductionDate());
builder.dataSet("producer_code", dataSet.getDataProducerCode());
builder.dataSet("data_set_type", dataSet.getDataSetType().getCode());
- builder.dataSet("is_measured", dataSet.isMeasured());
+ builder.dataSet("is_measured", dataSet.isDerived() == false);
builder.dataSet("is_complete", BooleanOrUnknown.T.equals(dataSet.getComplete()));
StringBuilder stringBuilder = new StringBuilder();
- Set<DataPE> parents = dataSet.getParents();
+ Collection<ExternalData> parents = dataSet.getParents();
if (parents.isEmpty() == false)
{
- for (DataPE parent : parents)
+ for (ExternalData parent : parents)
{
if (stringBuilder.length() > 0)
{
@@ -378,18 +377,18 @@ class UploadingCommand implements IDataSetCommand
}
}
builder.dataSet("parent_codes", stringBuilder.toString());
- SamplePE sample = dataSet.getSample();
+ Sample sample = dataSet.getSample();
if (sample != null)
{
builder.sample("type_code", sample.getSampleType().getCode());
builder.sample("code", sample.getCode());
- GroupPE group = sample.getGroup();
+ Group group = sample.getGroup();
builder.sample("group_code", group == null ? "(shared)" : group.getCode());
builder.sample("registration_timestamp", sample.getRegistrationDate());
builder.sample("registrator", sample.getRegistrator());
}
- ExperimentPE experiment = dataSet.getExperiment();
- ProjectPE project = experiment.getProject();
+ Experiment experiment = dataSet.getExperiment();
+ Project project = experiment.getProject();
builder.experiment("group_code", project.getGroup().getCode());
builder.experiment("project_code", project.getCode());
builder.experiment("experiment_code", experiment.getCode());
@@ -399,11 +398,11 @@ class UploadingCommand implements IDataSetCommand
return builder.toString();
}
- private String createRootPath(ExternalDataPE dataSet)
+ private String createRootPath(ExternalData dataSet)
{
- SamplePE sample = dataSet.getSample();
- ExperimentPE experiment = sample == null ? dataSet.getExperiment() : sample.getExperiment();
- ProjectPE project = experiment.getProject();
+ Sample sample = dataSet.getSample();
+ Experiment experiment = sample == null ? dataSet.getExperiment() : sample.getExperiment();
+ Project project = experiment.getProject();
project.getGroup().getCode();
return project.getGroup().getCode() + "/" + project.getCode() + "/" + experiment.getCode()
+ "/" + (sample == null ? "" : sample.getCode() + "/") + dataSet.getCode();
@@ -463,7 +462,7 @@ class UploadingCommand implements IDataSetCommand
{
final StringBuilder b = new StringBuilder();
b.append("Upload data sets to CIFEX: ");
- for (ExternalDataPE dataset : dataSets)
+ for (ExternalData dataset : dataSets)
{
b.append(dataset.getCode());
b.append(',');
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
index 1d6fe1bb8c96826a075aac66c9ec043da77b1612..877426063f7b0a932edf120be1cbeadaa4c8706e 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
@@ -36,8 +36,8 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProviders;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PluginUtilTest;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* @author Franz-Josef Elmer
@@ -223,7 +223,7 @@ public class DataStoreServiceTest extends AssertJUnit
@Test
public void testUploadDataSetsForInvalidPassword()
{
- final List<ExternalDataPE> dataSets = new ArrayList<ExternalDataPE>();
+ final List<ExternalData> dataSets = new ArrayList<ExternalData>();
final DataSetUploadContext uploadContext = new DataSetUploadContext();
uploadContext.setCifexURL(CIFEX_URL);
uploadContext.setUserID("user");
@@ -254,7 +254,7 @@ public class DataStoreServiceTest extends AssertJUnit
@Test
public void testUploadDataSets()
{
- final List<ExternalDataPE> dataSets = new ArrayList<ExternalDataPE>();
+ final List<ExternalData> dataSets = new ArrayList<ExternalData>();
final DataSetUploadContext uploadContext = new DataSetUploadContext();
uploadContext.setCifexURL(CIFEX_URL);
uploadContext.setUserID("user");
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
index ca2a223cd32432c4ed96441d5fc3d6adcd47eeb4..aa6fa5172932f5b25ae85dd4c4f6020a834318f7 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
@@ -46,15 +46,19 @@ import ch.systemsx.cisd.cifex.rpc.UploadState;
import ch.systemsx.cisd.cifex.rpc.UploadStatus;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.logging.BufferedAppender;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
+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.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.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
/**
* @author Franz-Josef Elmer
@@ -147,9 +151,11 @@ public class UploadingCommandTest extends AssertJUnit
uploadContext.setFileName(ZIP_FILENAME);
createTestData(LOCATION1);
ds2 = createTestData(LOCATION2);
- ExternalDataPE dataSet1 = createDataSet("1", LOCATION1);
- ExternalDataPE dataSet2 = createDataSet("2", LOCATION2);
- List<ExternalDataPE> dataSets = Arrays.<ExternalDataPE> asList(dataSet1, dataSet2);
+ ExternalData dataSet1 =
+ ExternalDataTranslator.translate(createDataSet("1", LOCATION1), "?", "?");
+ ExternalData dataSet2 =
+ ExternalDataTranslator.translate(createDataSet("2", LOCATION2), "?", "?");
+ List<ExternalData> dataSets = Arrays.<ExternalData> asList(dataSet1, dataSet2);
command = new UploadingCommand(factory, mailClientParameters, dataSets, uploadContext);
command.deleteAfterUploading = false;
}
@@ -165,6 +171,7 @@ public class UploadingCommandTest extends AssertJUnit
externalData.setDataSetType(dataSetTypePE);
externalData.setExperiment(createExperiment());
externalData.setParent(createParent("parent"));
+ externalData.setDataStore(new DataStorePE());
return externalData;
}
@@ -192,6 +199,10 @@ public class UploadingCommandTest extends AssertJUnit
project.setCode("p1");
GroupPE group = new GroupPE();
group.setCode("g1");
+ DatabaseInstancePE instance = new DatabaseInstancePE();
+ instance.setCode("instance");
+ instance.setOriginalSource(true);
+ group.setDatabaseInstance(instance);
project.setGroup(group);
experiment.setProject(project);
return experiment;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
index 816aba87e6dcb7a26264df84cb354859ab9ff16c..98d5ee95b23b12c8238e691329ba3e1729caf831 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
@@ -38,6 +38,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
@@ -51,6 +52,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
/**
@@ -320,8 +322,9 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
{
IDataStoreService service = dssFactory.create(dataStore.getRemoteUrl());
String sessionToken = dataStore.getSessionToken();
- List<ExternalDataPE> cleanDataSets =
- HibernateTransformer.HIBERNATE_BEAN_REPLICATOR.get().copy(dataSets);
+ List<ExternalData> cleanDataSets =
+ ExternalDataTranslator.translate(HibernateTransformer.HIBERNATE_BEAN_REPLICATOR
+ .get().copy(dataSets), "?", "?");
service.uploadDataSetsToCIFEX(sessionToken, cleanDataSets, context);
}
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 99e6ae42ec23401cf6f7ea5f5c26d3ee3abc5d20..e0320633ecf1113c3d72f503b5e2399ada137f81 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
@@ -24,7 +24,9 @@ import it.unimi.dsi.fastutil.longs.LongSet;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.types.BooleanOrUnknown;
@@ -222,11 +224,11 @@ public class DatasetLister implements IDatasetLister
private void enrichWithParents(final Long2ObjectMap<ExternalData> datasetMap)
{
LongSet datasetIds = extractIds(datasetMap);
- Long2ObjectMap<ExternalData> parentsMap = resolveParents(datasetIds, datasetMap);
+ Long2ObjectMap<Set<ExternalData>> parentsMap = resolveParents(datasetIds, datasetMap);
for (ExternalData dataset : datasetMap.values())
{
- ExternalData parent = parentsMap.get(dataset.getId());
- dataset.setParent(parent);
+ final Set<ExternalData> parent = parentsMap.get(dataset.getId());
+ dataset.setParents(parent);
}
}
@@ -244,20 +246,27 @@ public class DatasetLister implements IDatasetLister
* Returns a map from a child id to its parent dataset for the specified dataset ids.<br>
* Uses datasetCache not to resolve datasets which have already been resolved.
*/
- private Long2ObjectMap<ExternalData> resolveParents(LongSet datasetIds,
+ private Long2ObjectMap<Set<ExternalData>> resolveParents(LongSet datasetIds,
Long2ObjectMap<ExternalData> datasetCache)
{
- List<DatasetRelationRecord> datasetParents = asList(setQuery.getDatasetParents(datasetIds));
- Long2ObjectMap<ExternalData> parentsMap =
+ final List<DatasetRelationRecord> datasetParents = asList(setQuery.getDatasetParents(datasetIds));
+ final Long2ObjectMap<ExternalData> parentsMap =
fetchUnknownDatasetParents(datasetParents, datasetCache);
- Long2ObjectMap<ExternalData> childToParentMap = new Long2ObjectOpenHashMap<ExternalData>();
+ final Long2ObjectMap<Set<ExternalData>> childToParentMap =
+ new Long2ObjectOpenHashMap<Set<ExternalData>>();
for (DatasetRelationRecord relation : datasetParents)
{
long parentId = relation.data_id_parent;
ExternalData parentDataset = getCachedItem(parentId, parentsMap, datasetCache);
assert parentDataset != null : "inconsistent parent dataset " + parentId;
- childToParentMap.put(relation.data_id_child, parentDataset);
+ Set<ExternalData> parents = childToParentMap.get(relation.data_id_child);
+ if (parents == null)
+ {
+ parents = new HashSet<ExternalData>();
+ childToParentMap.put(relation.data_id_child, parents);
+ }
+ parents.add(parentDataset);
}
return childToParentMap;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
index 9d1d090ba911512805a274df944132bd1aea8000..bb84d03d79e3faecc77dc3997cef2a6c655fdaa8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
@@ -19,10 +19,10 @@ package ch.systemsx.cisd.openbis.generic.shared;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.InvalidAuthenticationException;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
* Service interface of Data Store Server.
@@ -35,7 +35,7 @@ public interface IDataStoreService
/**
* Every time this interface and related DTO's are changed, we should increment this number.
*/
- public static final int VERSION = 3; // for release S61
+ public static final int VERSION = 4; // for release S64
/**
* Returns the version of this service.
@@ -71,7 +71,7 @@ public interface IDataStoreService
* @param context Context data needed for uploading.
* @throws InvalidAuthenticationException if <code>sessionToken</code> is invalid.
*/
- public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalDataPE> dataSets,
+ public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalData> dataSets,
DataSetUploadContext context) throws InvalidAuthenticationException;
/** Runs the reporting task with the specified id for provided datasets */
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
index 2acdf91c015459453c60db9cdcc4c3301eb503dd..7b7cf0816f4c673b01f5f3323dccdfa1986120c5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
@@ -17,7 +17,9 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Date;
+import java.util.Iterator;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
@@ -54,9 +56,7 @@ public class ExternalData extends CodeWithRegistration<ExternalData> implements
private String producerCode;
- private ExternalData parent;
-
- private String parentCode;
+ private Collection<ExternalData> parents;
private String location;
@@ -208,26 +208,34 @@ public class ExternalData extends CodeWithRegistration<ExternalData> implements
public ExternalData getParent()
{
- return parent;
+ if (parents == null)
+ {
+ return null;
+ }
+ final Iterator<ExternalData> it = parents.iterator();
+ if (it.hasNext())
+ {
+ return parents.iterator().next();
+ } else
+ {
+ return null;
+ }
}
- public void setParent(ExternalData parent)
+ public Collection<ExternalData> getParents()
{
- this.parent = parent;
- if (parent != null)
- {
- setParentCode(parent.getCode());
- }
+ return parents;
}
- public final String getParentCode()
+ public void setParents(Collection<ExternalData> parents)
{
- return parentCode;
+ this.parents = parents;
}
- public final void setParentCode(final String parentCode)
+ public final String getParentCode()
{
- this.parentCode = parentCode;
+ final ExternalData parent = getParent();
+ return (parent == null) ? null : parent.getCode();
}
public final String getLocation()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
index 0bf9e18a2a4b8085221a204c11e3b703a4665e6f..5471f8f9490cf77efe38181e413aa60a29d644f1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
@@ -17,7 +17,9 @@
package ch.systemsx.cisd.openbis.generic.shared.translator;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import org.apache.commons.lang.StringEscapeUtils;
@@ -74,7 +76,6 @@ public class ExternalDataTranslator
final LoadableFields... withExperimentFields)
{
SamplePE sample = externalDataPE.getSample();
- DataPE parent = externalDataPE.tryGetParent();
ExternalData externalData = new ExternalData();
externalData.setId(HibernateUtils.getId(externalDataPE));
externalData.setCode(StringEscapeUtils.escapeHtml(externalDataPE.getCode()));
@@ -89,8 +90,12 @@ public class ExternalDataTranslator
externalData.setInvalidation(tryToGetInvalidation(sample));
externalData.setLocation(StringEscapeUtils.escapeHtml(externalDataPE.getLocation()));
externalData.setLocatorType(TypeTranslator.translate(externalDataPE.getLocatorType()));
- externalData
- .setParent(parent == null ? null : fillExternalData(new ExternalData(), parent));
+ final Collection<ExternalData> parents = new HashSet<ExternalData>();
+ externalData.setParents(parents);
+ for (DataPE parentPE : externalDataPE.getParents())
+ {
+ parents.add(fillExternalData(new ExternalData(), parentPE));
+ }
setChildren(externalDataPE, externalData);
externalData.setProductionDate(externalDataPE.getProductionDate());
externalData.setModificationDate(externalDataPE.getModificationDate());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
index fc80bf487b996ad20e9fe4e2947e94069eb43f1f..b14970ad9bedd4e3db964d29608b5d7ebbda0891 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
@@ -23,6 +23,8 @@ import java.util.Arrays;
import java.util.List;
import org.apache.commons.lang.StringUtils;
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -35,11 +37,14 @@ import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+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.DataSetUploadContext;
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.dto.EventPE;
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.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
@@ -279,34 +284,51 @@ public final class ExternalDataTableTest extends AbstractBOTest
return ExternalDataTable.createDeletionEvent(dataset, person, reason);
}
+ @SuppressWarnings("unchecked")
@Test
public void testUploadDataSets()
{
- final ExternalDataPE d1 = createDataSet("d1", dss1);
- final ExternalDataPE d2 = createDataSet("d2", dss2);
+ final ExternalDataPE d1PE = createDataSet("d1", dss1);
+ final ExternalDataPE d2PE = createDataSet("d2", dss2);
final DataSetUploadContext uploadContext = new DataSetUploadContext();
uploadContext.setCifexURL("cifexURL");
uploadContext.setUserID(EXAMPLE_SESSION.getUserName());
uploadContext.setPassword("pwd");
uploadContext.setUserEMail(EXAMPLE_SESSION.getPrincipal().getEmail());
- uploadContext.setComment(ExternalDataTable.createUploadComment(Arrays.asList(d1, d2)));
+ uploadContext.setComment(ExternalDataTable.createUploadComment(Arrays.asList(d1PE, d2PE)));
context.checking(new Expectations()
{
{
- prepareFindFullDatasets(d1, true);
- prepareFindFullDatasets(d2, true);
+ prepareFindFullDatasets(d1PE, true);
+ prepareFindFullDatasets(d2PE, true);
- List<String> d2Locations = Arrays.asList(d2.getLocation());
+ List<String> d2Locations = Arrays.asList(d2PE.getLocation());
one(dataStoreService2).getKnownDataSets(dss2.getSessionToken(), d2Locations);
will(returnValue(d2Locations));
- one(dataStoreService2).uploadDataSetsToCIFEX(dss2.getSessionToken(),
- Arrays.asList(d2), uploadContext);
+ one(dataStoreService2).uploadDataSetsToCIFEX(with(equal(dss2.getSessionToken())),
+ with(new BaseMatcher<List>() {
+
+ public boolean matches(Object item)
+ {
+ List<ExternalData> list = (List<ExternalData>) item;
+ if (list.size() != 1)
+ {
+ return false;
+ }
+ ExternalData data = list.get(0);
+ return d2PE.getCode().equals(data.getCode());
+ }
+
+ public void describeTo(Description description)
+ {
+ description.appendText("Data set d2");
+ }}), with(same(uploadContext)));
}
});
ExternalDataTable externalDataTable = createExternalDataTable();
- externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode(), d2.getCode()));
+ externalDataTable.loadByDataSetCodes(Arrays.asList(d1PE.getCode(), d2PE.getCode()));
String message = externalDataTable.uploadLoadedDataSetsToCIFEX(uploadContext);
assertEquals(
@@ -373,10 +395,15 @@ public final class ExternalDataTableTest extends AbstractBOTest
data.setLocation("here/" + code);
ExperimentPE experiment = new ExperimentPE();
experiment.setCode("exp1");
+ experiment.setExperimentType(new ExperimentTypePE());
ProjectPE project = new ProjectPE();
project.setCode("p1");
GroupPE group = new GroupPE();
group.setCode("g1");
+ DatabaseInstancePE instance = new DatabaseInstancePE();
+ instance.setCode("instance");
+ instance.setOriginalSource(true);
+ group.setDatabaseInstance(instance);
project.setGroup(group);
experiment.setProject(project);
data.setExperiment(experiment);