diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java
index 488263f931512c8947c88fddb76c473115788521..ccd950e0f6947ba6e1adf1617453b2fbc26e2bf3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java
@@ -82,7 +82,7 @@ public abstract class AbstractStrorageProcessorWithUploader extends
uploader.rollback();
}
logDataSetFileError(incomingDataSetDirectory, exception);
- return UnstoreDataAction.LEAVE_UNTOUCHED;
+ return UnstoreDataAction.MOVE_TO_ERROR;
}
@Override
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
index d51c91f3a817f02a793a4e16b193cf417565a799..c37da5887dc1e53ef4e57e84342caffb62e571a5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
@@ -40,6 +40,7 @@ import ch.systemsx.cisd.common.types.BooleanOrUnknown;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.etlserver.IStorageProcessor.UnstoreDataAction;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
+import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
@@ -300,6 +301,8 @@ public class DataSetRegistrationAlgorithm
public final File createBaseDirectory(final IDataStoreStrategy strategy, final File baseDir,
final DataSetInformation dataSetInfo)
{
+ // TODO replace by mapping
+ dataSetInfo.setShareId(DataStoreService.DEFAULT_SHARE_ID);
final File baseDirectory =
strategy.getBaseDirectory(baseDir, dataSetInfo, state.dataSetType);
baseDirectory.mkdirs();
@@ -451,6 +454,7 @@ public class DataSetRegistrationAlgorithm
data.setUserId(dataSetInformation.getUploadingUserIdOrNull());
data.setUserEMail(dataSetInformation.tryGetUploadingUserEmail());
data.setExtractableData(dataSetInformation.getExtractableData());
+ data.setShareId(dataSetInformation.getShareId());
data.setLocatorType(getTypeExtractor().getLocatorType(incomingDataSetFile));
data.setDataSetType(getTypeExtractor().getDataSetType(incomingDataSetFile));
data.setFileFormatType(getTypeExtractor().getFileFormatType(incomingDataSetFile));
@@ -564,7 +568,7 @@ public class DataSetRegistrationAlgorithm
final BooleanOrUnknown isCompleteFlag)
{
data.setComplete(isCompleteFlag);
- data.setLocation(relativePath);
+ data.setLocation(relativePath.substring(data.getShareId().length() + 1));
data.setStorageFormat(storageFormat);
return data;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
index a46fccb117c16410180c4b413af4e880aa5fccb6..e748ef2b729db8ec2355016b41ba49461ad85299 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
@@ -63,8 +63,10 @@ public final class IdentifiedDataStrategy implements IDataStoreStrategy
static File createBaseDirectory(final File baseDir, final DataSetInformation dataSetInfo)
{
String dataSetCode = dataSetInfo.getDataSetCode();
+ String shareId = dataSetInfo.getShareId();
final String instanceUUID = dataSetInfo.getInstanceUUID();
- return DatasetLocationUtil.getDatasetLocationPath(baseDir, dataSetCode, instanceUUID);
+ return DatasetLocationUtil.getDatasetLocationPath(baseDir, dataSetCode, shareId,
+ instanceUUID);
}
//
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/NamedDataStrategy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/NamedDataStrategy.java
index 5278c9f4d1940282617b6f78e198677c843f94b4..3e6bc69db8d84ac02b22e138974bfc20edfc07e9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/NamedDataStrategy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/NamedDataStrategy.java
@@ -82,7 +82,8 @@ final class NamedDataStrategy implements IDataStoreStrategy
{
assertBaseDirectory(baseDirectory);
assert dataSetType != null : "Missing data set type.";
- return new File(new File(baseDirectory, getDirectoryName()), IdentifiedDataStrategy
+ File share = new File(baseDirectory, dataSetInfo.getShareId());
+ return new File(new File(share, getDirectoryName()), IdentifiedDataStrategy
.createDataSetTypeDirectory(dataSetType));
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
index de57e604fb1d7631498a7a2be19a14017a946002..c7fcac1d6f9f9cfc3c8fd26679f230425c3e7276 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
@@ -222,7 +222,8 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
public File getFileForExternalData(ExternalData externalData)
{
- File dataSetFile = new File(service.getStoreRootDirectory(), externalData.getLocation());
+ File share = new File(service.getStoreRootDirectory(), externalData.getShareId());
+ File dataSetFile = new File(share, externalData.getLocation());
return DefaultStorageProcessor.getOriginalDirectory(dataSetFile);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
index 48d4f7bca7f4b9564f892448cf359f283c56ce56..2fba03b0ec6f2fa9e1fc826caa39d8be7e7cc4ae 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDatasetDownloadServlet.java
@@ -21,8 +21,10 @@ import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import javax.activation.MimetypesFileTypeMap;
@@ -313,8 +315,15 @@ abstract public class AbstractDatasetDownloadServlet extends HttpServlet
protected final File createDataSetRootDirectory(String dataSetCode, HttpSession session)
{
+ List<ExternalData> list =
+ applicationContext.getDataSetService().listDataSetsByCode(
+ Arrays.asList(dataSetCode));
+ if (list.isEmpty())
+ {
+ throw new IllegalArgumentException("Unknown data set " + dataSetCode);
+ }
return DatasetLocationUtil.getDatasetLocationPathCheckingIfExists(dataSetCode,
- getDatabaseInstance(session), getStoreRootPath());
+ list.get(0).getShareId(), getDatabaseInstance(session), getStoreRootPath());
}
protected final File getStoreRootPath()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
index c3ccf5fe0c5ca5c047b36107c40d71cda29c981b..88a486953fafb855bef8fe1514cf8c52405471bb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractDssServiceRpc.java
@@ -19,12 +19,16 @@ package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
+import ch.systemsx.cisd.common.collections.IKeyExtractor;
+import ch.systemsx.cisd.common.collections.TableMap;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
@@ -206,14 +210,24 @@ public abstract class AbstractDssServiceRpc<T> extends AbstractServiceWithLogger
return access;
}
+
+ protected File getRootDirectory(String datasetCode)
+ {
+ List<ExternalData> list = getOpenBISService().listDataSetsByCode(Arrays.asList(datasetCode));
+ if (list.isEmpty())
+ {
+ throw new IllegalArgumentException("Unknown data set " + datasetCode);
+ }
+ return getRootDirectoryForDataSet(datasetCode, list.get(0).getShareId());
+ }
/**
* Get the top level of the folder for the data set.
*/
- protected File getRootDirectoryForDataSet(String code)
+ protected File getRootDirectoryForDataSet(String code, String shareId)
{
File dataSetRootDirectory =
- DatasetLocationUtil.getDatasetLocationPath(getStoreDirectory(), code,
+ DatasetLocationUtil.getDatasetLocationPath(getStoreDirectory(), code, shareId,
getHomeDatabaseInstance().getUuid());
return dataSetRootDirectory;
}
@@ -240,16 +254,32 @@ public abstract class AbstractDssServiceRpc<T> extends AbstractServiceWithLogger
}
HashMap<String, File> rootDirectories = new HashMap<String, File>();
+ List<ExternalData> dataSets =
+ openBISService.listDataSetsByCode(new ArrayList<String>(dataSetCodes));
+ TableMap<String, ExternalData> tableMap =
+ new TableMap<String, ExternalData>(dataSets,
+ new IKeyExtractor<String, ExternalData>()
+ {
+ public String getKey(ExternalData e)
+ {
+ return e.getCode();
+ }
+ });
for (String datasetCode : dataSetCodes)
{
- rootDirectories.put(datasetCode, getRootDirectory(datasetCode));
+ ExternalData dataSet = tableMap.tryGet(datasetCode);
+ if (dataSet == null)
+ {
+ throw new IllegalArgumentException("Unknown data set " + datasetCode);
+ }
+ rootDirectories.put(datasetCode, getRootDirectory(datasetCode, dataSet.getShareId()));
}
return rootDirectories;
}
- private File getRootDirectory(String dataSetCode)
+ private File getRootDirectory(String dataSetCode, String shareId)
{
- File dataSetRootDirectory = getRootDirectoryForDataSet(dataSetCode);
+ File dataSetRootDirectory = getRootDirectoryForDataSet(dataSetCode, shareId);
if (dataSetRootDirectory.exists() == false)
{
throw new IllegalArgumentException("Path does not exist: " + dataSetRootDirectory);
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 034358e63441a39073cb891a9240726430991a6a..c729cde167b56a82d6bc9fac596659b66a19f841 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
@@ -110,9 +110,9 @@ class DataSetCommandExecutor implements IDataSetCommandExecutor
thread.start();
}
- public void scheduleDeletionOfDataSets(List<String> locations)
+ public void scheduleDeletionOfDataSets(List<DatasetDescription> dataSets)
{
- scheduleCommand(new DeletionCommand(locations));
+ scheduleCommand(new DeletionCommand(dataSets));
}
public void scheduleUploadingDataSetsToCIFEX(ICIFEXRPCServiceFactory cifexServiceFactory,
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 ae3c228c512e3dfb8e5f1ab6b9098cfc92281f8d..044e5a1400dbb1a96ed641ff866f201221af03a1 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
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
import java.io.File;
+import java.io.FilenameFilter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
@@ -49,6 +50,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkModel;
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.util.UuidUtil;
/**
* Implementation of {@link IDataStoreService} which will be accessed remotely by the opneBIS
@@ -59,6 +61,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
public class DataStoreService extends AbstractServiceWithLogger<IDataStoreService> implements
IDataStoreService, InitializingBean
{
+ public static final String DEFAULT_SHARE_ID = "1";
+
private final SessionTokenManager sessionTokenManager;
private final IDataSetCommandExecutorFactory commandExecutorFactory;
@@ -67,6 +71,8 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
private final PluginTaskProviders pluginTaskParameters;
+ private final String defaultShareId;
+
private String cifexAdminUserOrNull;
private String cifexAdminPasswordOrNull;
@@ -78,7 +84,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
private IDataSetCommandExecutor commandExecutor;
public DataStoreService(SessionTokenManager sessionTokenManager,
- MailClientParameters mailClientParameters, PluginTaskProviders pluginTaskParameters)
+ MailClientParameters mailClientParameters, PluginTaskProviders pluginTaskParameters, String defaultShareId)
{
this(sessionTokenManager, new IDataSetCommandExecutorFactory()
{
@@ -86,17 +92,18 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
{
return new DataSetCommandExecutor(store, queueDir);
}
- }, mailClientParameters, pluginTaskParameters);
+ }, mailClientParameters, pluginTaskParameters, defaultShareId);
}
DataStoreService(SessionTokenManager sessionTokenManager,
IDataSetCommandExecutorFactory commandExecutorFactory,
- MailClientParameters mailClientParameters, PluginTaskProviders pluginTaskParameters)
+ MailClientParameters mailClientParameters, PluginTaskProviders pluginTaskParameters, String defaultShareId)
{
this.sessionTokenManager = sessionTokenManager;
this.commandExecutorFactory = commandExecutorFactory;
this.mailClientParameters = mailClientParameters;
this.pluginTaskParameters = pluginTaskParameters;
+ this.defaultShareId = defaultShareId.startsWith("$") ? DEFAULT_SHARE_ID : defaultShareId;
storeRoot = pluginTaskParameters.getStoreRoot();
}
@@ -152,6 +159,37 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
}
commandExecutor = commandExecutorFactory.create(storeRoot, commandQueueDirOrNull);
commandExecutor.start();
+ migrateStore();
+ }
+
+ private void migrateStore()
+ {
+ File defaultShare = new File(storeRoot, defaultShareId);
+ if (defaultShare.exists() == false)
+ {
+ if (defaultShare.mkdirs() == false)
+ {
+ throw new IOExceptionUnchecked(new IOException(
+ "Couldn't create default share in data store: " + defaultShare));
+ }
+ File[] stores = storeRoot.listFiles(new FilenameFilter()
+ {
+
+ public boolean accept(File dir, String name)
+ {
+ return UuidUtil.isValidUUID(name);
+ }
+ });
+ for (File file : stores)
+ {
+ if (file.renameTo(new File(defaultShare, file.getName())) == false)
+ {
+ throw new IOExceptionUnchecked(new IOException("Couldn't move '" + file
+ + "' into default share '" + defaultShare + "'."));
+ }
+ }
+ operationLog.info("Store migrated to default share");
+ }
}
public IDataStoreService createLogger(IInvocationLoggerContext context)
@@ -166,15 +204,17 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
return IDataStoreService.VERSION;
}
- public List<String> getKnownDataSets(String sessionToken, List<String> dataSetLocations)
+ public List<String> getKnownDataSets(String sessionToken, List<DatasetDescription> dataSets)
throws InvalidAuthenticationException
{
sessionTokenManager.assertValidSessionToken(sessionToken);
+ injectDefaultShareId(dataSets);
List<String> knownLocations = new ArrayList<String>();
- for (String location : dataSetLocations)
+ for (DatasetDescription dataSet : dataSets)
{
- if (new File(storeRoot, location).exists())
+ String location = dataSet.getDataSetLocation();
+ if (new File(new File(storeRoot, dataSet.getDataSetShareId()), location).exists())
{
knownLocations.add(location);
}
@@ -182,18 +222,26 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
return knownLocations;
}
- public void deleteDataSets(String sessionToken, final List<String> dataSetLocations)
+ public void deleteDataSets(String sessionToken, final List<DatasetDescription> dataSets)
throws InvalidAuthenticationException
{
sessionTokenManager.assertValidSessionToken(sessionToken);
+ injectDefaultShareId(dataSets);
- commandExecutor.scheduleDeletionOfDataSets(dataSetLocations);
+ commandExecutor.scheduleDeletionOfDataSets(dataSets);
}
public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalData> dataSets,
DataSetUploadContext context) throws InvalidAuthenticationException
{
sessionTokenManager.assertValidSessionToken(sessionToken);
+ for (ExternalData dataSet : dataSets)
+ {
+ if (dataSet.getShareId() == null)
+ {
+ dataSet.setShareId(defaultShareId);
+ }
+ }
if (context.getCifexURL() == null)
{
@@ -223,6 +271,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
List<DatasetDescription> datasets)
{
sessionTokenManager.assertValidSessionToken(sessionToken);
+ injectDefaultShareId(datasets);
PluginTaskProvider<IReportingPluginTask> reportingPlugins =
pluginTaskParameters.getReportingPluginsProvider();
@@ -235,6 +284,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
String userEmailOrNull)
{
sessionTokenManager.assertValidSessionToken(sessionToken);
+ injectDefaultShareId(datasets);
PluginTaskProvider<IProcessingPluginTask> plugins =
pluginTaskParameters.getProcessingPluginsProvider();
@@ -261,6 +311,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
String userEmailOrNull, boolean archive)
{
sessionTokenManager.assertValidSessionToken(sessionToken);
+ injectDefaultShareId(datasets);
String description = archive ? "Archiving" : "Unarchiving";
ArchiverTaskFactory factory = pluginTaskParameters.getArchiverTaskFactory();
@@ -305,11 +356,28 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
DatasetDescription dataSet)
{
sessionTokenManager.assertValidSessionToken(sessionToken);
+ injectDefaultShareId(dataSet);
PluginTaskProvider<IReportingPluginTask> reportingPlugins =
pluginTaskParameters.getReportingPluginsProvider();
IReportingPluginTask task = reportingPlugins.getPluginInstance(serviceKey);
return task.createLink(dataSet);
}
+
+ private void injectDefaultShareId(List<DatasetDescription> dataSets)
+ {
+ for (DatasetDescription dataSet : dataSets)
+ {
+ injectDefaultShareId(dataSet);
+ }
+ }
+
+ private void injectDefaultShareId(DatasetDescription dataSetOrNull)
+ {
+ if (dataSetOrNull != null && dataSetOrNull.getDataSetShareId() == null)
+ {
+ dataSetOrNull.setDataSetShareId(defaultShareId);
+ }
+ }
}
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 6ad513f02477ba7a5b01fa848c11dbc9242f4f50..a13f931b506a10b85baabca25df5068970d04eea 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
@@ -78,17 +78,17 @@ class DataStoreServiceLogger implements IDataStoreService
return 0;
}
- public List<String> getKnownDataSets(String sessionToken, List<String> dataSetLocations)
+ public List<String> getKnownDataSets(String sessionToken, List<DatasetDescription> dataSetLocations)
throws InvalidAuthenticationException
{
- log("getKnownDataSets", "LOCATIONS(%s)", dataSetLocations);
+ log("getKnownDataSets", "DATA_SETS(%s)", dataSetLocations);
return null;
}
- public void deleteDataSets(String sessionToken, List<String> dataSetLocations)
+ public void deleteDataSets(String sessionToken, List<DatasetDescription> dataSets)
throws InvalidAuthenticationException
{
- log("deleteDataSets", "LOCATIONS(%s)", dataSetLocations);
+ log("deleteDataSets", "DATA_SETS(%s)", dataSets);
}
public void uploadDataSetsToCIFEX(String sessionToken, List<ExternalData> dataSets,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DeletionCommand.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DeletionCommand.java
index ff4611bd15a8033775d833ad05588ef1cbd20e64..5abeb92395ee7fd39db3e3e592076f4a84dc0f54 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DeletionCommand.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DeletionCommand.java
@@ -20,6 +20,7 @@ import java.io.File;
import java.util.List;
import ch.systemsx.cisd.common.filesystem.QueueingPathRemoverService;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
* A command for deleting data sets, based on their location relative to the data store root.
@@ -30,18 +31,19 @@ class DeletionCommand implements IDataSetCommand
{
private static final long serialVersionUID = 1L;
- private final List<String> dataSetLocations;
+ private final List<DatasetDescription> dataSets;
- DeletionCommand(List<String> dataSetLocations)
+ DeletionCommand(List<DatasetDescription> dataSets)
{
- this.dataSetLocations = dataSetLocations;
+ this.dataSets = dataSets;
}
public void execute(File store)
{
- for (String location : dataSetLocations)
+ for (DatasetDescription dataSet : dataSets)
{
- QueueingPathRemoverService.removeRecursively(new File(store, location));
+ File share = new File(store, dataSet.getDataSetShareId());
+ QueueingPathRemoverService.removeRecursively(new File(share, dataSet.getDataSetLocation()));
}
}
@@ -49,9 +51,9 @@ class DeletionCommand implements IDataSetCommand
{
final StringBuilder b = new StringBuilder();
b.append("Delete data set paths: ");
- for (String dataset : dataSetLocations)
+ for (DatasetDescription dataset : dataSets)
{
- b.append(dataset);
+ b.append(dataset.getDataSetShareId()).append('/').append(dataset.getDataSetLocation());
b.append(',');
}
b.setLength(b.length() - 1);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index a976e50b814658c8706517f9098df0ca39a9b138..5be821b47f4044e14a5e6bf3b12c47dbe6670ba1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -79,17 +79,21 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
// this session object is automatically kept up-to-date by an aspect
private OpenBISSessionHolder session;
+ private final String defaultShareId;
+
public static IETLLIMSService createOpenBisService(String openBISURL)
{
return new OpenBisServiceFactory(openBISURL, ResourceNames.ETL_SERVICE_URL).createService();
}
- public EncapsulatedOpenBISService(IETLLIMSService service, OpenBISSessionHolder sessionHolder)
+ public EncapsulatedOpenBISService(IETLLIMSService service, OpenBISSessionHolder sessionHolder, String defaultShareId)
{
assert service != null : "Given IETLLIMSService implementation can not be null.";
assert sessionHolder != null : "Given OpenBISSessionHolder can not be null.";
this.service = service;
this.session = sessionHolder;
+ this.defaultShareId =
+ defaultShareId.startsWith("$") ? DataStoreService.DEFAULT_SHARE_ID : defaultShareId;
}
@@ -112,7 +116,7 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
//
// IEncapsulatedOpenBISService
//
-
+
public Experiment tryToGetExperiment(ExperimentIdentifier experimentIdentifier)
{
assert experimentIdentifier != null : " Unspecified experiment identifier.";
@@ -164,14 +168,27 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
throws UserFailureException
{
TechId id = new TechId(experimentID);
- return service.listDataSetsByExperimentID(session.getToken(), id);
+ List<ExternalData> result = service.listDataSetsByExperimentID(session.getToken(), id);
+ injectDefaultShareId(result);
+ return result;
}
-
+
public List<ExternalData> listDataSetsBySampleID(long sampleID,
boolean showOnlyDirectlyConnected)
{
TechId id = new TechId(sampleID);
- return service.listDataSetsBySampleID(session.getToken(), id, showOnlyDirectlyConnected);
+ List<ExternalData> result =
+ service.listDataSetsBySampleID(session.getToken(), id, showOnlyDirectlyConnected);
+ injectDefaultShareId(result);
+ return result;
+ }
+
+ public List<ExternalData> listDataSetsByCode(List<String> dataSetCodes)
+ throws UserFailureException
+ {
+ List<ExternalData> dataSets = service.listDataSetsByCode(session.getToken(), dataSetCodes);
+ injectDefaultShareId(dataSets);
+ return dataSets;
}
public long registerExperiment(NewExperiment experiment) throws UserFailureException
@@ -309,13 +326,17 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
public ExternalData tryGetDataSet(String dataSetCode) throws UserFailureException
{
- return service.tryGetDataSet(session.getToken(), dataSetCode);
+ ExternalData dataSet = service.tryGetDataSet(session.getToken(), dataSetCode);
+ injectDefaultShareId(dataSet);
+ return dataSet;
}
public ExternalData tryGetDataSet(String sToken, String dataSetCode)
throws UserFailureException
{
- return service.tryGetDataSet(sToken, dataSetCode);
+ ExternalData dataSet = service.tryGetDataSet(sToken, dataSetCode);
+ injectDefaultShareId(dataSet);
+ return dataSet;
}
public void checkInstanceAdminAuthorization(String sToken)
@@ -350,8 +371,11 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
public List<ExternalData> listAvailableDataSets(ArchiverDataSetCriteria criteria)
throws UserFailureException
{
- return service.listAvailableDataSets(session.getToken(), session.getDataStoreCode(),
- criteria);
+ List<ExternalData> result =
+ service.listAvailableDataSets(session.getToken(), session.getDataStoreCode(),
+ criteria);
+ injectDefaultShareId(result);
+ return result;
}
public List<DeletedDataSet> listDeletedDataSets(Long lastSeenDeletionEventIdOrNull)
@@ -376,7 +400,9 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
public ExternalData tryGetDataSetForServer(String dataSetCode) throws UserFailureException
{
- return service.tryGetDataSetForServer(session.getToken(), dataSetCode);
+ ExternalData dataSet = service.tryGetDataSetForServer(session.getToken(), dataSetCode);
+ injectDefaultShareId(dataSet);
+ return dataSet;
}
public List<String> generateCodes(String prefix, int size)
@@ -407,4 +433,20 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.updateSampleAndRegisterDataSet(session.getToken(), newSample, externalData);
}
+ private void injectDefaultShareId(List<ExternalData> dataSets)
+ {
+ for (ExternalData dataSet : dataSets)
+ {
+ injectDefaultShareId(dataSet);
+ }
+ }
+
+ private void injectDefaultShareId(ExternalData dataSetOrNull)
+ {
+ if (dataSetOrNull != null && dataSetOrNull.getShareId() == null)
+ {
+ dataSetOrNull.setShareId(defaultShareId);
+ }
+ }
+
}
\ No newline at end of file
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 ef31862005f813a5ae0e7982245e1fead09e098a..ee1f5954291c254a6a219a3c13553c5e48256112 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
@@ -41,9 +41,9 @@ interface IDataSetCommandExecutor
void start();
/**
- * Schedules deletion of all data sets at specified locations.
+ * Schedules deletion of all specified data sets.
*/
- void scheduleDeletionOfDataSets(List<String> locations);
+ void scheduleDeletionOfDataSets(List<DatasetDescription> dataSets);
/**
* Schedules uploading of all data sets to CIFEX using the specified upload context.
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 43e7456204e6628518bbcb22fa7b485b64fe7fbc..64edaaa8506cc8c744beb435366c428123a6f65f 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
@@ -397,10 +397,11 @@ class UploadingCommand implements IDataSetCommand
for (ExternalData dataSet : dataSets)
{
String location = dataSet.getLocation();
- File dataSetFile = new File(store, location);
+ String path = dataSet.getShareId() + "/" + location;
+ File dataSetFile = new File(new File(store, dataSet.getShareId()), location);
if (dataSetFile.exists() == false)
{
- notificationLog.error("Data set '" + location + "' does not exist.");
+ notificationLog.error("Data set '" + path + "' does not exist.");
return false;
}
String newRootPath = createRootPath(dataSet);
@@ -421,7 +422,7 @@ class UploadingCommand implements IDataSetCommand
dataSetFile);
} catch (IOException ex)
{
- notificationLog.error("Couldn't add data set '" + location + "' to zip file.",
+ notificationLog.error("Couldn't add data set '" + path + "' to zip file.",
ex);
return false;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index d3e14d58f48842791bd33967a3b534d37ef3a5e0..cc079a441fa13618a95ed4c35dbbbbe65d965de8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -168,6 +168,14 @@ public interface IEncapsulatedOpenBISService
@ManagedAuthentication
public List<ExternalData> listDataSetsBySampleID(long sampleID,
boolean showOnlyDirectlyConnected) throws UserFailureException;
+
+ /**
+ * Returns all data sets found for specified data set codes.
+ *
+ * @return plain data sets without properties, samples, and experiments.
+ */
+ @ManagedAuthentication
+ public List<ExternalData> listDataSetsByCode(List<String> dataSetCodes) throws UserFailureException;
/**
* Registers the specified experiment.
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 978d3d3ff110c5b12a9e9364aedafb7cd13273c9..06b3963273fabc34d867b1290f786ea1460738d7 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
@@ -53,6 +53,8 @@ public class DataSetInformation implements Serializable
private IEntityProperty[] properties = IEntityProperty.EMPTY_ARRAY;
private DataSetType dataSetType;
+
+ private String shareId;
/**
* The database instance <i>UUID</i>.
@@ -96,6 +98,16 @@ public class DataSetInformation implements Serializable
{
}
+ public String getShareId()
+ {
+ return shareId;
+ }
+
+ public void setShareId(String shareId)
+ {
+ this.shareId = shareId;
+ }
+
public String tryGetUploadingUserEmail()
{
return uploadingUserEmailOrNull;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetLocationUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetLocationUtil.java
index 068d3a73392c8f883ba1f074405244d8b72ff64c..a925b91d98929d05c5814e54a6a2a426c2540754 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetLocationUtil.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetLocationUtil.java
@@ -32,13 +32,13 @@ public class DatasetLocationUtil
*
* @throws UserFailureException if the dataset directory does not exist.
*/
- public static File getDatasetLocationPathCheckingIfExists(String dataSetCode,
+ public static File getDatasetLocationPathCheckingIfExists(String dataSetCode, String shareId,
DatabaseInstance databaseInstance, File storeDir)
{
String databaseUuid = databaseInstance.getUuid();
File dataSetRootDirectory =
- DatasetLocationUtil.getDatasetLocationPath(storeDir, dataSetCode, databaseUuid);
+ DatasetLocationUtil.getDatasetLocationPath(storeDir, dataSetCode, shareId, databaseUuid);
if (dataSetRootDirectory.exists() == false)
{
throw new UserFailureException("Data set '" + dataSetCode + "' not found in the store.");
@@ -47,17 +47,17 @@ public class DatasetLocationUtil
}
/** Creates a location where a dataset can be found in a specified base directory. */
- public static File getDatasetLocationPath(final File baseDir, String dataSetCode,
+ public static File getDatasetLocationPath(final File baseDir, String dataSetCode, String shareId,
final String instanceUUID)
{
- return new File(baseDir, getDatasetRelativeLocationPath(dataSetCode, instanceUUID));
+ return new File(baseDir, getDatasetRelativeLocationPath(dataSetCode, shareId, instanceUUID));
}
/** returns path relative to the store */
- public static String getDatasetRelativeLocationPath(String dataSetCode,
+ public static String getDatasetRelativeLocationPath(String dataSetCode, String shareId,
final String instanceUUID)
{
- final File instanceDir = new File(instanceUUID);
+ final File instanceDir = new File(new File(shareId), instanceUUID);
final File shardingDir = createShardingDir(instanceDir, dataSetCode);
final File datasetDir = new File(shardingDir, dataSetCode);
return datasetDir.getPath();
diff --git a/datastore_server/source/java/dssApplicationContext.xml b/datastore_server/source/java/dssApplicationContext.xml
index 3f1e65f2a68489f80023f163fa0137594e746206..8407ce5ff24e148fece4be79bf0a6537e799933c 100644
--- a/datastore_server/source/java/dssApplicationContext.xml
+++ b/datastore_server/source/java/dssApplicationContext.xml
@@ -49,6 +49,7 @@
<bean id="openBIS-service" class="ch.systemsx.cisd.openbis.dss.generic.server.EncapsulatedOpenBISService">
<constructor-arg ref="etl-lims-service"/>
<constructor-arg ref="sessionHolder"/>
+ <constructor-arg value="${default-share-id}" />
</bean>
<bean id="data-store-server"
@@ -65,6 +66,7 @@
</bean>
</constructor-arg>
<constructor-arg ref="plugin-tasks" />
+ <constructor-arg value="${default-share-id}" />
<property name="cifexAdminUserOrNull" value="${cifex-admin-username}" />
<property name="cifexAdminPasswordOrNull" value="${cifex-admin-password}" />
<property name="commandQueueDir" value="${commandqueue-dir}"/>
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategyTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategyTest.java
index eebf650342bccd3daf1afa967cbd13277926bfec..f7630fa1ceb4f388088693f14f6572b7514b92b0 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategyTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategyTest.java
@@ -37,6 +37,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.types.DataSetTypeCode;
*/
public class IdentifiedDataStrategyTest extends AbstractFileSystemTestCase
{
+ private static final String SHARE_ID = "share-1";
+
private static final String DATA_SET_CODE = "data-set-code";
private static final String EXAMPLE_PROJECT_CODE = "P";
@@ -64,6 +66,7 @@ public class IdentifiedDataStrategyTest extends AbstractFileSystemTestCase
dataSetInfo.setInstanceCode("my-instance");
dataSetInfo.setInstanceUUID("1111-2222");
dataSetInfo.setDataSetCode(DATA_SET_CODE);
+ dataSetInfo.setShareId(SHARE_ID);
return dataSetInfo;
}
@@ -92,7 +95,7 @@ public class IdentifiedDataStrategyTest extends AbstractFileSystemTestCase
assertTrue("Null values not permited here", exceptionThrown);
final DataSetInformation dataSetInfo = createDataSetInfo();
File baseDirectory = strategy.getBaseDirectory(workingDirectory, dataSetInfo, dataSetType);
- final File file = new File(workingDirectory, "1111-2222/27/35/33/data-set-code");
+ final File file = new File(new File(workingDirectory, SHARE_ID), "1111-2222/27/35/33/data-set-code");
assertEquals(file, baseDirectory);
assertTrue(baseDirectory.exists() == false);
// Create a file instead of a directory
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/NamedDataStrategyTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/NamedDataStrategyTest.java
index b30d402ff5f3ef884f03c1498f131cba9dbacddf..fe8379f9f8e2a79e871575b982d66b46b2598b53 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/NamedDataStrategyTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/NamedDataStrategyTest.java
@@ -23,6 +23,7 @@ import org.apache.commons.io.FileUtils;
import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
/**
@@ -32,6 +33,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
*/
public final class NamedDataStrategyTest extends AbstractFileSystemTestCase
{
+ private static final String SHARE_ID = "share-1";
+
private static final DataStoreStrategyKey UNIDENTIFIED = DataStoreStrategyKey.UNIDENTIFIED;
private final static String FILE_NAME = "AX14";
@@ -95,9 +98,11 @@ public final class NamedDataStrategyTest extends AbstractFileSystemTestCase
}
assertTrue("Base directory can not be null", exceptionThrown);
final DataSetType dataSetType = new DataSetType("DataSet");
+ DataSetInformation dataSetInfo = new DataSetInformation();
+ dataSetInfo.setShareId(SHARE_ID);
final File baseDirectory =
- strategy.getBaseDirectory(workingDirectory, null, dataSetType);
- assertEquals(new File(new File(workingDirectory, NamedDataStrategy
+ strategy.getBaseDirectory(workingDirectory, dataSetInfo, dataSetType);
+ assertEquals(new File(new File(new File(workingDirectory, SHARE_ID), NamedDataStrategy
.getDirectoryName(UNIDENTIFIED)), IdentifiedDataStrategy
.createDataSetTypeDirectory(dataSetType)), baseDirectory);
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
index 3774fbd7191e452b303ec99f594ecbcc22d27a42..6b6ab2937ed2e7039f108810a750c87fb5b32347 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -52,6 +52,7 @@ import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.test.LogMonitoringAppender;
import ch.systemsx.cisd.etlserver.IStorageProcessor.UnstoreDataAction;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
+import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreService;
import ch.systemsx.cisd.openbis.dss.generic.server.EncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.server.openbisauth.OpenBISSessionHolder;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProviders;
@@ -85,6 +86,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestCase
{
+ private static final String SHARE_ID = DataStoreService.DEFAULT_SHARE_ID;
+
private static final String SAMPLE_CODE = "sample1";
private static final String FOLDER_NAME = "folder";
@@ -135,6 +138,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
assertEquals(expectedData.getCode(), data.getCode());
assertEquals(expectedData.getDataProducerCode(), data.getDataProducerCode());
assertEquals(expectedData.getLocation(), data.getLocation());
+ assertEquals(expectedData.getShareId(), data.getShareId());
assertEquals(expectedData.getLocatorType(), data.getLocatorType());
assertEquals(expectedData.getFileFormatType(), data.getFileFormatType());
assertEquals(expectedData.getDataSetType(), data.getDataSetType());
@@ -261,7 +265,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
OpenBISSessionHolder sessionHolder = new OpenBISSessionHolder();
sessionHolder.setToken(SESSION_TOKEN);
authorizedLimsService =
- new EncapsulatedOpenBISService(limsService, sessionHolder);
+ new EncapsulatedOpenBISService(limsService, sessionHolder, "share-id");
dataSetValidator = context.mock(IDataSetValidator.class);
Properties threadProperties = new Properties();
@@ -304,6 +308,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
dataSetInformation.setProductionDate(DATA_PRODUCTION_DATE);
dataSetInformation.setDataSetCode(DATA_SET_CODE);
dataSetInformation.setParentDataSetCodes(Collections.singletonList(PARENT_DATA_SET_CODE));
+ dataSetInformation.setShareId(SHARE_ID);
targetFolder =
IdentifiedDataStrategy.createBaseDirectory(workingDirectory, dataSetInformation);
targetData1 = createTargetData(data1);
@@ -344,6 +349,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
data.setDataProducerCode(DATA_PRODUCER_CODE);
data.setProductionDate(DATA_PRODUCTION_DATE);
data.setCode(DATA_SET_CODE);
+ data.setShareId(SHARE_ID);
data.setParentDataSetCodes(Collections.singletonList(PARENT_DATA_SET_CODE));
return data;
}
@@ -351,7 +357,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
private String getRelativeTargetFolder()
{
String absoluteTarget = targetFolder.getAbsolutePath();
- return absoluteTarget.substring(workingDirectory.getAbsolutePath().length() + 1);
+ return absoluteTarget.substring(workingDirectory.getAbsolutePath().length() + 1 + SHARE_ID.length() + 1);
}
// crates sample connected to an experiment
@@ -624,7 +630,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
+ "but according to the openBIS server there is no such sample for this experiment "
+ "(it has maybe been invalidated?). We thus consider it invalid."
+ OSUtilities.LINE_SEPARATOR + "INFO OPERATION.FileRenamer - "
- + "Moving file 'data1' from '<wd>' to '<wd>/invalid/DataSetType_O1'.");
+ + "Moving file 'data1' from '<wd>' to '<wd>/1/invalid/DataSetType_O1'.");
context.assertIsSatisfied();
}
@@ -637,7 +643,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
assert data1.exists() && data2.exists();
prepareForStrategy(data1, null);
final File toDir =
- new File(new File(workingDirectory,
+ new File(new File(new File(workingDirectory, SHARE_ID),
NamedDataStrategy.getDirectoryName(DataStoreStrategyKey.UNIDENTIFIED)),
IdentifiedDataStrategy.createDataSetTypeDirectory(DATA_SET_TYPE));
@@ -702,7 +708,8 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
final File dataSet)
{
final File strategyDirectory =
- new File(workingDirectory, NamedDataStrategy.getDirectoryName(key));
+ new File(new File(workingDirectory, SHARE_ID),
+ NamedDataStrategy.getDirectoryName(key));
assertEquals(true, strategyDirectory.exists());
final File dataSetTypeDir =
new File(strategyDirectory,
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
index 105950899be40ef0caec826317bbcd8cae266a96..8fb1ecb334c927d002263a09322acc66e1e305f5 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
@@ -131,8 +131,8 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
String logText =
"Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "Encountered errors in the following lines:\n"
+ "# Illegal empty identifier\n"
+ "\t/MYSPACE/MYPROJ/EXP2\tVAL11\tVAL21\tVAL31\tFILE_TYPE\tVAL41\tVAL51\tds2/\n\n"
@@ -171,7 +171,7 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
String logText =
"Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ "The following subfolders were in the uploaded folder, but were not mentioned in the control file:\n"
+ "ds2,ds3\n"
+ "The following lines were successfully processed:\n"
@@ -209,9 +209,9 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
String logText =
"Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
@@ -244,9 +244,9 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
String logText =
"Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
@@ -280,9 +280,9 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
String logText =
"Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
- + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
+ + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
@@ -319,9 +319,9 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
String logText =
"Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
- + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP1,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL40}, NewProperty{property=prop2,value=VAL50}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP2,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL41}, NewProperty{property=prop2,value=VAL51}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=DataSetInformation{sampleCode=<null>,properties={},dataSetType=MY_DATA_SET_TYPE,shareId=<null>,instanceUUID=<null>,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/MYSPACE/MYPROJ/EXP3,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[],dataSetProperties=[NewProperty{property=prop1,value=VAL42}, NewProperty{property=prop2,value=VAL52}],code=<null>},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=test}]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
index 2cf1d798ce72782fb7e3e965ed3aa0696414f842..a9ef583ccaed649008b334aeffbb7bf3975ab77a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
@@ -53,6 +53,7 @@ import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.ThreadParameters;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
+import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
@@ -175,9 +176,11 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertEquals(DATA_SET_TYPE, dataSet.recordedObject().getDataSetType());
File datasetLocation =
DatasetLocationUtil.getDatasetLocationPath(workingDirectory, DATA_SET_CODE,
+ DataStoreService.DEFAULT_SHARE_ID,
DATABASE_INSTANCE_UUID);
- assertEquals(FileUtilities.getRelativeFile(workingDirectory, datasetLocation), dataSet
- .recordedObject().getLocation());
+ assertEquals(FileUtilities.getRelativeFile(new File(workingDirectory,
+ DataStoreService.DEFAULT_SHARE_ID), datasetLocation), dataSet.recordedObject()
+ .getLocation());
assertEquals(1, MockStorageProcessor.instance.calledCommitCount);
assertEquals(datasetLocation, MockStorageProcessor.instance.rootDirs.get(0));
File incomingDir = MockStorageProcessor.instance.incomingDirs.get(0);
@@ -288,9 +291,10 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertEquals(DATA_SET_TYPE, dataSet1.recordedObject().getDataSetType());
File datasetLocation1 =
DatasetLocationUtil.getDatasetLocationPath(workingDirectory, DATA_SET_CODE + 1,
- DATABASE_INSTANCE_UUID);
- assertEquals(FileUtilities.getRelativeFile(workingDirectory, datasetLocation1), dataSet1
- .recordedObject().getLocation());
+ DataStoreService.DEFAULT_SHARE_ID, DATABASE_INSTANCE_UUID);
+ assertEquals(FileUtilities.getRelativeFile(new File(workingDirectory,
+ DataStoreService.DEFAULT_SHARE_ID), datasetLocation1), dataSet1.recordedObject()
+ .getLocation());
assertEquals(datasetLocation1, MockStorageProcessor.instance.rootDirs.get(0));
File incomingDir1 = MockStorageProcessor.instance.incomingDirs.get(0);
assertEquals(new File(new File(stagingDir, DATA_SET_CODE + 1), "sub_data_set_1"),
@@ -305,9 +309,10 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertEquals(DATA_SET_TYPE, dataSet2.recordedObject().getDataSetType());
File datasetLocation2 =
DatasetLocationUtil.getDatasetLocationPath(workingDirectory, DATA_SET_CODE + 2,
- DATABASE_INSTANCE_UUID);
- assertEquals(FileUtilities.getRelativeFile(workingDirectory, datasetLocation2), dataSet2
- .recordedObject().getLocation());
+ DataStoreService.DEFAULT_SHARE_ID, DATABASE_INSTANCE_UUID);
+ assertEquals(FileUtilities.getRelativeFile(new File(workingDirectory,
+ DataStoreService.DEFAULT_SHARE_ID), datasetLocation2), dataSet2.recordedObject()
+ .getLocation());
assertEquals(datasetLocation2, MockStorageProcessor.instance.rootDirs.get(1));
File incomingDir2 = MockStorageProcessor.instance.incomingDirs.get(1);
assertEquals(new File(new File(stagingDir, DATA_SET_CODE + 2), "sub_data_set_2"),
@@ -339,7 +344,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertEquals(2, MockStorageProcessor.instance.incomingDirs.size());
assertEquals(2, MockStorageProcessor.instance.calledCommitCount);
assertEquals(
- "DataSetInformation{sampleCode=<null>,properties={},dataSetType=O1,instanceUUID=db-uuid,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/SPACE/PROJECT/EXP-CODE,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[data-set-code1],dataSetProperties=[],code=data-set-code2},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=<null>}",
+ "DataSetInformation{sampleCode=<null>,properties={},dataSetType=O1,shareId=1,instanceUUID=db-uuid,instanceCode=<null>,spaceCode=<null>,experimentIdentifier=/SPACE/PROJECT/EXP-CODE,isCompleteFlag=U,extractableData=ExtractableData{productionDate=<null>,dataProducerCode=<null>,parentDataSetCodes=[data-set-code1],dataSetProperties=[],code=data-set-code2},uploadingUserEmailOrNull=<null>,uploadingUserIdOrNull=<null>}",
MockStorageProcessor.instance.dataSetInfoString);
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/DssComponentTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/DssComponentTest.java
index 62e5510a485ee079e17fe87a169b8fb6d9b7b2b3..9245dddf2636630bf1f7fedc4a65b277c932466c 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/DssComponentTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/DssComponentTest.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.openbis.dss.client.api.v1.DssComponentFactory;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent;
+import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssBuilder;
@@ -119,7 +120,9 @@ public class DssComponentTest extends SystemTestCase
{
SimpleDataSetInformationDTO dataSetInfo = getCodeOfLatestDataSet();
String code = dataSetInfo.getDataSetCode();
- File fileIntoStore = new File(new File(rootDir, "store"), dataSetInfo.getDataSetLocation());
+ File fileIntoStore =
+ new File(new File(new File(rootDir, "store"), DataStoreService.DEFAULT_SHARE_ID),
+ dataSetInfo.getDataSetLocation());
IDataSetDss ds = dss.getDataSet(code);
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 32dc33cc3b40489703d6eebde1c920365365833b..774beed590a4dbaae6ce7f1a5dee2388be998da0 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
@@ -39,6 +39,8 @@ 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.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.dto.builders.DatasetDescriptionBuilder;
/**
* @author Franz-Josef Elmer
@@ -53,6 +55,8 @@ public class DataStoreServiceTest extends AssertJUnit
private static final File TEST_STORE = new File(TEST_FOLDER, "store");
+ private static final String SHARE_ID = "share-id";
+
private static final class MockDataStoreService extends DataStoreService
{
private final ICIFEXRPCServiceFactory cifexServiceFactory;
@@ -66,7 +70,7 @@ public class DataStoreServiceTest extends AssertJUnit
PluginTaskProviders pluginTaskParameters)
{
super(sessionTokenManager, commandExecutorFactory, mailClientParameters,
- pluginTaskParameters);
+ pluginTaskParameters, SHARE_ID);
this.cifexServiceFactory = cifexServiceFactory;
this.expectedCIFEXURL = expectedCIFEXURL;
}
@@ -164,18 +168,46 @@ public class DataStoreServiceTest extends AssertJUnit
@Test
public void testGetKnownDataSets() throws IOException
{
+ String shareId = "share-1";
String location = "ds1";
- new File(TEST_STORE, location).createNewFile();
+ DatasetDescriptionBuilder ds1 =
+ new DatasetDescriptionBuilder("ds1").shareId(shareId).location(location);
+ DatasetDescriptionBuilder ds2 = new DatasetDescriptionBuilder("ds2").location(location);
+ File share = new File(TEST_STORE, shareId);
+ share.mkdirs();
+ new File(share, location).createNewFile();
IDataStoreService service = createService();
List<String> knownDataSets =
- service.getKnownDataSets(sessionToken, Arrays.asList(location, "ds2"));
+ service.getKnownDataSets(sessionToken,
+ Arrays.asList(ds1.getDatasetDescription(), ds2.getDatasetDescription()));
assertEquals(1, knownDataSets.size());
assertSame(location, knownDataSets.get(0));
context.assertIsSatisfied();
}
+ @Test
+ public void testGetKnownDataSetsForDefaultShareId() throws IOException
+ {
+ String location = "ds1";
+ DatasetDescriptionBuilder ds1 =
+ new DatasetDescriptionBuilder("ds1").location(location);
+ DatasetDescriptionBuilder ds2 = new DatasetDescriptionBuilder("ds2").location("unknown");
+ File share = new File(TEST_STORE, SHARE_ID);
+ share.mkdirs();
+ new File(share, location).createNewFile();
+
+ IDataStoreService service = createService();
+ List<String> knownDataSets =
+ service.getKnownDataSets(sessionToken,
+ Arrays.asList(ds1.getDatasetDescription(), ds2.getDatasetDescription()));
+
+ assertEquals(1, knownDataSets.size());
+ assertSame(location, knownDataSets.get(0));
+ context.assertIsSatisfied();
+ }
+
@Test
public void testDeleteDataSetsForInvalidSessionToken()
{
@@ -194,15 +226,17 @@ public class DataStoreServiceTest extends AssertJUnit
@Test
public void testDeleteDataSets()
{
- final List<String> locations = Arrays.asList("d1", "d2");
+ DatasetDescription d1 = new DatasetDescription();
+ final List<DatasetDescription> dataSets = Arrays.asList(d1);
context.checking(new Expectations()
{
{
- one(commandExecutor).scheduleDeletionOfDataSets(locations);
+ one(commandExecutor).scheduleDeletionOfDataSets(dataSets);
}
});
- createService().deleteDataSets(sessionToken, locations);
-
+
+ createService().deleteDataSets(sessionToken, dataSets);
+ assertEquals(SHARE_ID, d1.getDataSetShareId());
context.assertIsSatisfied();
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
index afa5e609507e0010da48c5000bed4d900b2e8598..6b45d0cf57168b100be05e278ee3d71d8a305e23 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DatasetDownloadServletTest.java
@@ -29,6 +29,7 @@ import java.io.PrintWriter;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.util.Properties;
@@ -60,6 +61,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
/**
@@ -185,6 +187,7 @@ public class DatasetDownloadServletTest
prepareForObtainingDataSetFromServer(externalData);
prepareForGettingDataSetFromSession(externalData, "");
prepareForCreatingHTML(writer);
+ prepareListDataSetsByCode();
DatasetDownloadServlet servlet = createServlet();
servlet.doGet(request, response);
@@ -220,7 +223,7 @@ public class DatasetDownloadServletTest
assertContains(getSessionCreationLogMessage() + OSUtilities.LINE_SEPARATOR + LOG_INFO
+ "Data set '1234-1' obtained from openBIS server.", normalizedLogContent);
assertContains(OSUtilities.LINE_SEPARATOR + LOG_INFO
- + "For data set '1234-1' show directory <wd>/db-uuid/0a/28/59/1234-1",
+ + "For data set '1234-1' show directory <wd>/1/db-uuid/0a/28/59/1234-1",
normalizedLogContent);
context.assertIsSatisfied();
@@ -259,6 +262,7 @@ public class DatasetDownloadServletTest
final ExternalData externalData = createExternalData();
prepareParseRequestURL();
prepareCreateSession();
+ prepareListDataSetsByCode();
context.checking(new Expectations()
{
{
@@ -296,12 +300,13 @@ public class DatasetDownloadServletTest
prepareParseRequestURL();
prepareCreateSession();
prepareTryGetDataset(null);
+ prepareListDataSetsByCode();
context.checking(new Expectations()
{
{
one(request).getRequestURI();
will(returnValue(REQUEST_URI_PREFIX + EXAMPLE_DATA_SET_CODE));
-
+
one(response).setContentType("text/html");
one(response).getWriter();
will(returnValue(new PrintWriter(writer)));
@@ -332,6 +337,7 @@ public class DatasetDownloadServletTest
{
final StringWriter writer = new StringWriter();
final ExternalData externalData = createExternalData();
+ prepareListDataSetsByCode();
context.checking(new Expectations()
{
{
@@ -361,7 +367,7 @@ public class DatasetDownloadServletTest
+ "</table> </div> </body></html>"
+ OSUtilities.LINE_SEPARATOR, writer.toString());
assertContains(LOG_INFO
- + "For data set '1234-1' show directory <wd>/db-uuid/0a/28/59/1234-1/"
+ + "For data set '1234-1' show directory <wd>/1/db-uuid/0a/28/59/1234-1/"
+ EXAMPLE_DATA_SET_SUB_FOLDER_NAME, getNormalizedLogContent());
context.assertIsSatisfied();
@@ -376,6 +382,7 @@ public class DatasetDownloadServletTest
prepareCreateSession();
prepareCheckDatasetAccess();
prepareParseRequestURL();
+ prepareListDataSetsByCode();
context.checking(new Expectations()
{
{
@@ -406,7 +413,7 @@ public class DatasetDownloadServletTest
+ "Check access to the data set '1234-1' at openBIS server.", normalizedLogContent);
assertContains(OSUtilities.LINE_SEPARATOR + LOG_INFO
+ "For data set '1234-1' deliver file "
- + "<wd>/db-uuid/0a/28/59/1234-1/read me @home.txt (12 bytes).",
+ + "<wd>/1/db-uuid/0a/28/59/1234-1/read me @home.txt (12 bytes).",
normalizedLogContent);
context.assertIsSatisfied();
@@ -420,6 +427,7 @@ public class DatasetDownloadServletTest
prepareParseRequestURLForThumbnail(100, 50);
prepareCreateSession();
prepareCheckDatasetAccess();
+ prepareListDataSetsByCode();
final ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
context.checking(new Expectations()
{
@@ -457,7 +465,7 @@ public class DatasetDownloadServletTest
AssertionUtil
.assertContains(
LOG_INFO
- + "For data set '1234-1' deliver file <wd>/db-uuid/0a/28/59/1234-1/read me @home.txt "
+ + "For data set '1234-1' deliver file <wd>/1/db-uuid/0a/28/59/1234-1/read me @home.txt "
+ "(84 bytes) as a thumbnail.", normalizedLogContent);
context.assertIsSatisfied();
@@ -470,6 +478,7 @@ public class DatasetDownloadServletTest
final ExternalData externalData = createExternalData();
prepareParseRequestURL();
prepareCreateSession();
+ prepareListDataSetsByCode();
context.checking(new Expectations()
{
{
@@ -704,6 +713,18 @@ public class DatasetDownloadServletTest
}
});
}
+
+ private void prepareListDataSetsByCode()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dataSetService).listDataSetsByCode(Arrays.asList(EXAMPLE_DATA_SET_CODE));
+ will(returnValue(Arrays.asList(new DataSetBuilder().code(EXAMPLE_DATA_SET_CODE)
+ .shareId(DataStoreService.DEFAULT_SHARE_ID).getDataSet())));
+ }
+ });
+ }
private void prepareCheckDatasetAccess()
{
@@ -768,14 +789,14 @@ public class DatasetDownloadServletTest
locatorType.setCode(LocatorType.DEFAULT_LOCATOR_TYPE_CODE);
externalData.setLocatorType(locatorType);
externalData.setLocation(DatasetLocationUtil.getDatasetRelativeLocationPath(
- EXAMPLE_DATA_SET_CODE, DATABASE_INSTANCE_UUID));
+ EXAMPLE_DATA_SET_CODE, DataStoreService.DEFAULT_SHARE_ID, DATABASE_INSTANCE_UUID));
return externalData;
}
private static File getDatasetDirectoryLocation(final File baseDir, String dataSetCode)
{
return DatasetLocationUtil.getDatasetLocationPath(baseDir, dataSetCode,
- DATABASE_INSTANCE_UUID);
+ DataStoreService.DEFAULT_SHARE_ID, DATABASE_INSTANCE_UUID);
}
private DatasetDownloadServlet createServlet()
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcV1Test.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcV1Test.java
index 51d40902d0266cee211218cbddfc7311bda13f91..cda5e6076e1b72fbe341352434cb56247570ad09 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcV1Test.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DssServiceRpcV1Test.java
@@ -23,6 +23,7 @@ import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Properties;
@@ -74,6 +75,7 @@ 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.basic.dto.Space;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
@@ -86,6 +88,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
*/
public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
{
+ private static final String SHARE_ID = "share-1";
+
private static final String NEW_DATA_SET_EXP = "E1";
private static final String NEW_DATA_SET_OWNER_ID = "/TEST-SPACE/S1";
@@ -165,7 +169,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
private void initializeDirectories(File storeDir, File incomingDir) throws IOException
{
File location =
- DatasetLocationUtil.getDatasetLocationPath(storeDir, DATA_SET_CODE,
+ DatasetLocationUtil.getDatasetLocationPath(storeDir, DATA_SET_CODE, SHARE_ID,
DB_INSTANCE_UUID);
if (!location.mkdirs())
return;
@@ -273,6 +277,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testDataSetListingNonRecursive()
{
+ prepareListDataSetsByCode();
FileInfoDssDTO[] fileInfos =
rpcService.listFilesForDataSet(SESSION_TOKEN, DATA_SET_CODE, "/", false);
assertEquals(2, fileInfos.length);
@@ -302,6 +307,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testDataSetListingRecursive()
{
+ prepareListDataSetsByCode();
FileInfoDssDTO[] fileInfos =
rpcService.listFilesForDataSet(SESSION_TOKEN, DATA_SET_CODE, "/", true);
assertEquals(3, fileInfos.length);
@@ -344,6 +350,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testDataSetListingOfChild()
{
+ prepareListDataSetsByCode();
FileInfoDssDTO[] fileInfos =
rpcService.listFilesForDataSet(SESSION_TOKEN, DATA_SET_CODE, "/stuff/", false);
assertEquals(1, fileInfos.length);
@@ -373,6 +380,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testDataSetListingOfRelativeChild()
{
+ prepareListDataSetsByCode();
FileInfoDssDTO[] fileInfos =
rpcService.listFilesForDataSet(SESSION_TOKEN, DATA_SET_CODE, "stuff/", false);
assertEquals(1, fileInfos.length);
@@ -386,6 +394,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testDataSetListingOfFile()
{
+ prepareListDataSetsByCode();
FileInfoDssDTO[] fileInfos =
rpcService
.listFilesForDataSet(SESSION_TOKEN, DATA_SET_CODE, "stuff/bar.txt", false);
@@ -424,6 +433,8 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testDataSetListingWithSneakyPath()
{
+ prepareListDataSetsByCode();
+ prepareListDataSetsByCode();
try
{
rpcService.listFilesForDataSet(SESSION_TOKEN, DATA_SET_CODE, "../", true);
@@ -448,6 +459,8 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testDataSetFileRetrieval() throws IOException
{
+ prepareListDataSetsByCode();
+ prepareListDataSetsByCode();
FileInfoDssDTO[] fileInfos =
rpcService
.listFilesForDataSet(SESSION_TOKEN, DATA_SET_CODE, "stuff/bar.txt", false);
@@ -524,6 +537,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testAuthorizationForStringCode()
{
+ prepareListDataSetsByCode();
TestMethodInterceptor testMethodInterceptor = new TestMethodInterceptor();
IDssServiceRpcGenericInternal service = getAdvisedService(testMethodInterceptor);
service.listFilesForDataSet(SESSION_TOKEN, DATA_SET_CODE, "/", false);
@@ -533,6 +547,7 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
@Test
public void testAuthorizationDataSetFile()
{
+ prepareListDataSetsByCode();
TestMethodInterceptor testMethodInterceptor = new TestMethodInterceptor();
IDssServiceRpcGenericInternal service = getAdvisedService(testMethodInterceptor);
DataSetFileDTO dataSetFile = new DataSetFileDTO(DATA_SET_CODE, "/", false);
@@ -605,4 +620,17 @@ public class DssServiceRpcV1Test extends AbstractFileSystemTestCase
builder.appendFileInfosForFile(file, fileInfos, true);
return fileInfos;
}
+
+ private void prepareListDataSetsByCode()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(openBisService).listDataSetsByCode(Arrays.asList(DATA_SET_CODE));
+ will(returnValue(Arrays.asList(new DataSetBuilder().code(DATA_SET_CODE)
+ .shareId(SHARE_ID).getDataSet())));
+ }
+ });
+ }
+
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
index 99de18820783cf51f50380f7e6c3ce4eb9a477ce..e255205ddd0a87794e4304ffc843c55abdbe23ad 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
@@ -35,6 +35,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
*/
public class EncapsulatedOpenBISServiceTest
{
+ private static final String DEFAULT_SHARE_ID = "share-id";
+
private static final String SESSION_TOKEN = "session-token";
private Mockery context;
@@ -52,7 +54,7 @@ public class EncapsulatedOpenBISServiceTest
limsService = context.mock(IETLLIMSService.class);
session = new OpenBISSessionHolder();
session.setToken(SESSION_TOKEN);
- encapsulatedLimsService = new EncapsulatedOpenBISService(limsService, session);
+ encapsulatedLimsService = new EncapsulatedOpenBISService(limsService, session, DEFAULT_SHARE_ID);
}
@AfterMethod
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 c5ce5b43d1abfb1c00c261a1d5be460d16b57adc..39e57cde043d4096193b906d9037d8cfc497b504 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
@@ -71,6 +71,8 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator
@Friend(toClasses = UploadingCommand.class)
public class UploadingCommandTest extends AssertJUnit
{
+ private static final String SHARE_ID = "share-id";
+
private static final String ZIP_FILENAME = "myData";
private static final String INFO_UPLOAD_PREFIX = "INFO OPERATION.UploadingCommand - ";
@@ -182,6 +184,7 @@ public class UploadingCommandTest extends AssertJUnit
{
ExternalDataPE externalData = new ExternalDataPE();
externalData.setCode(code);
+ externalData.setShareId(SHARE_ID);
externalData.setLocation(location);
externalData.setDerived(true); // measured == (derived == false)
DataSetTypePE dataSetTypePE = new DataSetTypePE();
@@ -233,8 +236,8 @@ public class UploadingCommandTest extends AssertJUnit
private File createTestData(String location)
{
- File dataSet = new File(STORE, location);
- dataSet.mkdir();
+ File dataSet = new File(new File(STORE, SHARE_ID), location);
+ dataSet.mkdirs();
FileUtilities.writeToFile(new File(dataSet, "README.TXT"), "Data set " + location);
File dataFolder = new File(dataSet, "data");
dataFolder.mkdir();
@@ -411,7 +414,7 @@ public class UploadingCommandTest extends AssertJUnit
command.execute(STORE);
checkEmail("Couldn't create zip file");
- assertEquals("ERROR NOTIFY.UploadingCommand - Data set 'ds2' does not exist."
+ assertEquals("ERROR NOTIFY.UploadingCommand - Data set 'share-id/ds2' does not exist."
+ OSUtilities.LINE_SEPARATOR + INFO_MAIL_PREFIX
+ "Sending message from 'a@bc.de' to recipients '[user@bc.de]'",
getNormalizedLogContent());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericTest.java
index 4cc02c1392455efa3b5659b0d731b5687dc7d46c..09237fd339bdea5432dd239c04660388aeb09a0b 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v1/DssServiceRpcGenericTest.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.dss.generic.server.api.v1;
import java.io.File;
+import java.util.Arrays;
import org.jmock.Expectations;
import org.jmock.Mockery;
@@ -26,12 +27,14 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.openbis.dss.generic.server.DataStoreService;
import ch.systemsx.cisd.openbis.dss.generic.server.DssServiceRpcAuthorizationAdvisor;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
/**
@@ -88,7 +91,10 @@ public class DssServiceRpcGenericTest extends AbstractFileSystemTestCase
final String dataSetCode = "ds-1";
prepareCheckDataSetAccess(dataSetCode);
prepareCheckDataSetAccess(dataSetCode);
- File location = DatasetLocationUtil.getDatasetLocationPath(store, dataSetCode, DB_UUID);
+ prepareListDataSetsByCode(dataSetCode);
+ File location =
+ DatasetLocationUtil.getDatasetLocationPath(store, dataSetCode,
+ DataStoreService.DEFAULT_SHARE_ID, DB_UUID);
location.mkdirs();
FileInfoDssDTO[] dataSets = dssService.listFilesForDataSet(SESSION_TOKEN, dataSetCode, "abc/de", true);
@@ -98,6 +104,18 @@ public class DssServiceRpcGenericTest extends AbstractFileSystemTestCase
context.assertIsSatisfied();
}
+ private void prepareListDataSetsByCode(final String dataSetCode)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).listDataSetsByCode(Arrays.asList(dataSetCode));
+ will(returnValue(Arrays.asList(new DataSetBuilder().code(dataSetCode)
+ .shareId(DataStoreService.DEFAULT_SHARE_ID).getDataSet())));
+ }
+ });
+ }
+
private void prepareCheckDataSetAccess(final String dataSetCode)
{
context.checking(new Expectations()
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 43ef9fe50dd9c083e9e5aac5cb1ad57ce7427405..8e1d24f2caec897605239d1e807d75bdb75915a9 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
@@ -485,6 +485,13 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
Collections.sort(datasets);
return datasets;
}
+
+ public List<ExternalData> listDataSetsByCode(String sessionToken, List<String> dataSetCodes)
+ {
+ final Session session = getSession(sessionToken);
+ final IDatasetLister datasetLister = createDatasetLister(session);
+ return datasetLister.listByDatasetCode(dataSetCodes);
+ }
public IEntityProperty[] tryToGetPropertiesOfTopSampleRegisteredFor(String sessionToken,
SampleIdentifier sampleIdentifier) throws UserFailureException
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
index fa5be84bea1d506a441ed3a53c5d4d426a33cc85..23be394552a9fdd755011ac23a34384fef71df3c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
@@ -212,6 +212,13 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
return null;
}
+ public List<ExternalData> listDataSetsByCode(String sessionToken, List<String> dataSetCodes)
+ throws UserFailureException
+ {
+ logAccess(sessionToken, "listDataSetsByCode", "DATA_SETS(%s)", dataSetCodes);
+ return null;
+ }
+
public IEntityProperty[] tryToGetPropertiesOfTopSampleRegisteredFor(String sessionToken,
SampleIdentifier sampleIdentifier) throws UserFailureException
{
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 00b7ee038a4d9ae5da2e789516b02549cd2aa7f9..4fb80952c16c6146c5eb723ed2efbe3fdd200487 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
@@ -63,11 +63,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventType;
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.SpacePE;
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;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
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;
@@ -218,7 +218,7 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
deleteDataSetLocally(dataSet, reason);
}
// delete remotely from Data Store
- deleteDataSets(dataStore, getLocations(dataSets));
+ deleteDataSets(dataStore, createDatasetDescriptions(dataSets));
}
}
@@ -318,8 +318,8 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : map.entrySet())
{
DataStorePE dataStore = entry.getKey();
- List<String> locations = getLocations(entry.getValue());
- knownLocations.addAll(getKnownDataSets(dataStore, locations));
+ List<ExternalDataPE> dataSets = entry.getValue();
+ knownLocations.addAll(getKnownDataSets(dataStore, createDatasetDescriptions(dataSets)));
}
List<String> unknownDataSets = new ArrayList<String>();
for (ExternalDataPE dataSet : externalData)
@@ -356,16 +356,6 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
return map;
}
- private List<String> getLocations(List<ExternalDataPE> dataSets)
- {
- List<String> locations = new ArrayList<String>();
- for (ExternalDataPE dataSet : dataSets)
- {
- locations.add(dataSet.getLocation());
- }
- return locations;
- }
-
private void uploadDataSetsToCIFEX(DataStorePE dataStore, List<ExternalDataPE> dataSets,
DataSetUploadContext context)
{
@@ -375,7 +365,7 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
service.uploadDataSetsToCIFEX(sessionToken, cleanDataSets, context);
}
- private void deleteDataSets(DataStorePE dataStore, List<String> locations)
+ private void deleteDataSets(DataStorePE dataStore, List<DatasetDescription> list)
{
IDataStoreService service = tryGetDataStoreService(dataStore);
if (service == null)
@@ -384,7 +374,7 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
return;
}
String sessionToken = dataStore.getSessionToken();
- service.deleteDataSets(sessionToken, locations);
+ service.deleteDataSets(sessionToken, list);
}
// null if DSS URL has not been specified
@@ -398,17 +388,22 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
return dssFactory.create(remoteURL);
}
- private List<String> getKnownDataSets(DataStorePE dataStore, List<String> locations)
+ private List<String> getKnownDataSets(DataStorePE dataStore, List<DatasetDescription> dataSets)
{
String remoteURL = dataStore.getRemoteUrl();
if (StringUtils.isBlank(remoteURL))
{
// Assuming dummy data store "knows" all locations
+ List<String> locations = new ArrayList<String>();
+ for (DatasetDescription dataSet : dataSets)
+ {
+ locations.add(dataSet.getDataSetLocation());
+ }
return locations;
}
IDataStoreService service = dssFactory.create(remoteURL);
String sessionToken = dataStore.getSessionToken();
- return service.getKnownDataSets(sessionToken, locations);
+ return service.getKnownDataSets(sessionToken, dataSets);
}
public void processDatasets(String datastoreServiceKey, String datastoreCode,
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 36e1c6c7d9e118309a979194deba2359812b7b2a..0d2d597e9b5b87d02e87c1bc87b06af6b1f29207 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
@@ -325,7 +325,7 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
return enrichDatasets(query.getDatasets(new LongOpenHashSet(datasetIds)));
}
- public List<ExternalData> listByDatasetCodes(Collection<String> datasetCodes)
+ public List<ExternalData> listByDatasetCode(Collection<String> datasetCodes)
{
String[] codes = datasetCodes.toArray(new String[datasetCodes.size()]);
DataIterator<DatasetRecord> datasets = query.getDatasets(codes);
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 9a9c2c22aaa322899f409d2b21541d6c49f0ad34..2f760abfbc48c89b4775473e18c698a89bcf9630 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
@@ -73,7 +73,7 @@ public interface IDatasetLister
/**
* Lists all data sets with specified codes. Unenriched data sets will be returned.
*/
- List<ExternalData> listByDatasetCodes(Collection<String> datasetCodes);
+ List<ExternalData> listByDatasetCode(Collection<String> datasetCodes);
/** @return datasets with given ids */
List<ExternalData> listByDatasetIds(Collection<Long> datasetIds);
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 3e0ce3eefdd176998a3d790cdbabf5563c47a0c1..7cefba2da43268de1d4295f085dc98587796b2da 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
@@ -49,12 +49,13 @@ public interface IDataStoreService
public int getVersion(String sessionToken) throws InvalidAuthenticationException;
/**
- * Returns from the specified data set locations those locations known by the Data Store Server.
+ * Returns from the specified data sets those known by the Data Store Server.
*
* @param sessionToken Valid token to identify authorised access.
+ * @return locations of known data sets
* @throws InvalidAuthenticationException if <code>sessionToken</code> is invalid.
*/
- public List<String> getKnownDataSets(String sessionToken, List<String> dataSetLocations)
+ public List<String> getKnownDataSets(String sessionToken, List<DatasetDescription> dataSets)
throws InvalidAuthenticationException;
/**
@@ -63,7 +64,7 @@ public interface IDataStoreService
* @param sessionToken Valid token to identify authorised access.
* @throws InvalidAuthenticationException if <code>sessionToken</code> is invalid.
*/
- public void deleteDataSets(String sessionToken, List<String> dataSetLocations)
+ public void deleteDataSets(String sessionToken, List<DatasetDescription> dataSets)
throws InvalidAuthenticationException;
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
index 8fcb7e8576be03a26136d95c7008ac1a86457bf2..0c7a98577cf4086d61ba5c40d5db7696a26bbf20 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
@@ -188,6 +188,18 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class) final TechId sampleId,
final boolean showOnlyDirectlyConnected) throws UserFailureException;
+ /**
+ * Returns all data sets found for specified data set codes.
+ *
+ * @return plain data sets without properties, samples, and experiments.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<ExternalData> listDataSetsByCode(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes)
+ throws UserFailureException;
+
/**
* Lists samples using given configuration.
*
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 d753de49e72ba00566e5e8aee18feb649c433453..67d525597763599975022b15befb266d56066fe1 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
@@ -54,10 +54,10 @@ 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.SpacePE;
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;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
@@ -245,8 +245,8 @@ public final class ExternalDataTableTest extends AbstractBOTest
prepareFindFullDatasets(new ExternalDataPE[]
{ d1, d2 }, false, false);
- one(dataStoreService2).getKnownDataSets(dss2.getSessionToken(),
- Arrays.asList(d2.getLocation()));
+ one(dataStoreService2).getKnownDataSets(with(dss2.getSessionToken()),
+ with(createDatasetDescriptionsMatcher(d2)));
will(returnValue(Arrays.asList()));
}
});
@@ -316,9 +316,9 @@ public final class ExternalDataTableTest extends AbstractBOTest
prepareFindFullDatasets(new ExternalDataPE[]
{ d1, d2 }, false, false);
- List<String> d2Locations = Arrays.asList(d2.getLocation());
- one(dataStoreService2).getKnownDataSets(dss2.getSessionToken(), d2Locations);
- will(returnValue(d2Locations));
+ BaseMatcher<List<DatasetDescription>> dataSets = createDatasetDescriptionsMatcher(d2);
+ one(dataStoreService2).getKnownDataSets(with(dss2.getSessionToken()), with(dataSets));
+ will(returnValue(Arrays.asList(d2.getLocation())));
PersonPE person = EXAMPLE_SESSION.tryGetPerson();
one(eventDAO).persist(createDeletionEvent(d1, person, reason));
@@ -326,7 +326,7 @@ public final class ExternalDataTableTest extends AbstractBOTest
one(eventDAO).persist(createDeletionEvent(d2, person, reason));
one(externalDataDAO).delete(d2);
- one(dataStoreService2).deleteDataSets(dss2.getSessionToken(), d2Locations);
+ one(dataStoreService2).deleteDataSets(with(dss2.getSessionToken()), with(dataSets));
}
});
@@ -361,12 +361,12 @@ public final class ExternalDataTableTest extends AbstractBOTest
prepareFindFullDatasets(new ExternalDataPE[]
{ d1PE, d2PE }, true, false);
- List<String> d2Locations = Arrays.asList(d2PE.getLocation());
- one(dataStoreService2).getKnownDataSets(dss2.getSessionToken(), d2Locations);
- will(returnValue(d2Locations));
+ one(dataStoreService2).getKnownDataSets(with(dss2.getSessionToken()),
+ with(createDatasetDescriptionsMatcher(d2PE)));
+ will(returnValue(Arrays.asList(d2PE.getLocation())));
one(dataStoreService2).uploadDataSetsToCIFEX(
- with(equal(dss2.getSessionToken())), with(new BaseMatcher<List>()
+ with(equal(dss2.getSessionToken())), with(new BaseMatcher<List<ExternalData>>()
{
public boolean matches(Object item)
@@ -621,7 +621,6 @@ public final class ExternalDataTableTest extends AbstractBOTest
});
}
- @SuppressWarnings("unchecked")
private void prepareArchiving(final IDataStoreService service, final DataStorePE store,
final ExternalDataPE... dataSets)
{
@@ -635,7 +634,6 @@ public final class ExternalDataTableTest extends AbstractBOTest
});
}
- @SuppressWarnings("unchecked")
private void prepareUnarchiving(final IDataStoreService service, final DataStorePE store,
final ExternalDataPE... dataSets)
{
@@ -650,24 +648,18 @@ public final class ExternalDataTableTest extends AbstractBOTest
}
@SuppressWarnings("unchecked")
- private BaseMatcher<List> createDatasetDescriptionsMatcher(final ExternalDataPE... dataSets)
+ private BaseMatcher<List<DatasetDescription>> createDatasetDescriptionsMatcher(final ExternalDataPE... dataSets)
{
- return new BaseMatcher<List>()
+ return new BaseMatcher<List<DatasetDescription>>()
{
public boolean matches(Object item)
{
List<DatasetDescription> list = (List<DatasetDescription>) item;
- if (list.size() != dataSets.length)
- {
- return false;
- }
+ assertEquals(dataSets.length, list.size());
for (int i = 0; i < list.size(); i++)
{
- if (false == list.get(i).getDatasetCode().equals(dataSets[i].getCode()))
- {
- return false;
- }
+ assertEquals("data set " + i, dataSets[i].getCode(), list.get(i).getDatasetCode());
}
return true;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
index 9332ce7a94e1adcc5c26e58d9e98122b919592e7..b3083fa9b98e02fa2873646a3ffce0fb52017477 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
@@ -171,7 +171,7 @@ public class DatasetListerTest extends AbstractDAOTest
public void testListDataSetsByCode()
{
List<ExternalData> dataSets =
- lister.listByDatasetCodes(Arrays.asList("20081105092158673-1", "blabla",
+ lister.listByDatasetCode(Arrays.asList("20081105092158673-1", "blabla",
"20081105092159188-3"));
Collections.sort(dataSets, new Comparator<ExternalData>()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
index 8fcb7e8576be03a26136d95c7008ac1a86457bf2..0c7a98577cf4086d61ba5c40d5db7696a26bbf20 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
@@ -188,6 +188,18 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class) final TechId sampleId,
final boolean showOnlyDirectlyConnected) throws UserFailureException;
+ /**
+ * Returns all data sets found for specified data set codes.
+ *
+ * @return plain data sets without properties, samples, and experiments.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<ExternalData> listDataSetsByCode(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> dataSetCodes)
+ throws UserFailureException;
+
/**
* Lists samples using given configuration.
*
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataSetBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataSetBuilder.java
index 4f0b48ad95d02fc2b36baae997b771773d28da32..ac6d7e320684c8fe9580b3ad1c966dc489ddf82a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataSetBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/builders/DataSetBuilder.java
@@ -51,6 +51,12 @@ public class DataSetBuilder
return this;
}
+ public DataSetBuilder shareId(String shareId)
+ {
+ dataSet.setShareId(shareId);
+ return this;
+ }
+
public DataSetBuilder type(String dataSetTypeCode)
{
dataSet.setDataSetType(new DataSetType(dataSetTypeCode));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/DatasetDescriptionBuilder.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/DatasetDescriptionBuilder.java
index f4db74cad72b7dc499bc731db72f598684e95844..9f02cc9ee3b67337e3766ddd478958ca6ca48114 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/DatasetDescriptionBuilder.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/dto/builders/DatasetDescriptionBuilder.java
@@ -45,6 +45,12 @@ public class DatasetDescriptionBuilder
return this;
}
+ public DatasetDescriptionBuilder shareId(String shareId)
+ {
+ datasetDescription.setDataSetShareId(shareId);
+ return this;
+ }
+
public DatasetDescriptionBuilder sample(String sampleCode)
{
datasetDescription.setSampleCode(sampleCode);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/migration/MigrationStepFrom003To004.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/migration/MigrationStepFrom003To004.java
index cbf15c27fd201d39438001bc396ff4a68ffd213c..0e5e35f54f6b7ab9565c8cb7da418bc69d85d20e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/migration/MigrationStepFrom003To004.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/migration/MigrationStepFrom003To004.java
@@ -266,7 +266,7 @@ public class MigrationStepFrom003To004 implements IMigrationStep
{
String permId = dataset.getPermId();
File datasetDir =
- DatasetLocationUtil.getDatasetLocationPath(storeRootDir, permId, dbUUID);
+ DatasetLocationUtil.getDatasetLocationPath(storeRootDir, permId, "1", dbUUID);
DatasetFileLines featureVectorLines = tryFindFeatureVectorsFile(datasetDir);
if (featureVectorLines != null)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
index a43036a74fe69367d09ff3431e41f55f50f1732e..6e83afff6d324d6a934f1bcce99f818563110283 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
@@ -29,8 +29,6 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils.IDatasetDirectoryProvider;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.DatasetAcquiredImagesReference;
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageGenerationDescription;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
/**
* ABstract class for servlets which allow to download screening images in a chosen size for a
@@ -100,16 +98,13 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
writeResponseContent(responseStream, response);
}
- private IDatasetDirectoryProvider createDatasetDirectoryProvider(HttpSession session)
+ private IDatasetDirectoryProvider createDatasetDirectoryProvider(final HttpSession session)
{
- final DatabaseInstance databaseInstance = getDatabaseInstance(session);
- final File storeRootPath = getStoreRootPath();
return new IDatasetDirectoryProvider()
{
public File getDatasetRoot(String datasetCode)
{
- return DatasetLocationUtil.getDatasetLocationPathCheckingIfExists(datasetCode,
- databaseInstance, storeRootPath);
+ return createDataSetRootDirectory(datasetCode, session);
}
};
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index cdb0d996a08dad5d808850b1daf8f2ddf5546f90..dae229d8667501f5502b49d00908b9292ed04a10 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -640,7 +640,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
private IImagingDatasetLoader createImageLoader(IDatasetIdentifier dataSetIdentifier)
{
String datasetCode = dataSetIdentifier.getDatasetCode();
- File rootDir = getRootDirectoryForDataSet(datasetCode);
+ File rootDir = getRootDirectory(datasetCode);
IImagingDatasetLoader imageAccessor = createImageLoader(datasetCode, rootDir);
return imageAccessor;
}
@@ -965,7 +965,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
private IImagingDatasetLoader createImageLoader(String datasetCode)
{
- File datasetRoot = getRootDirectoryForDataSet(datasetCode);
+ File datasetRoot = getRootDirectory(datasetCode);
return createImageLoader(datasetCode, datasetRoot);
}