diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessor.java
index 9251d252912645cdc9729ad63342116cc1f46fc0..498d563d2ad89b104d7f77fc0d9a564421e99d20 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessor.java
@@ -30,7 +30,6 @@ import ch.systemsx.cisd.common.utilities.ClassUtils;
import ch.systemsx.cisd.common.utilities.ExtendedProperties;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
/**
@@ -93,12 +92,12 @@ abstract public class AbstractDelegatingStorageProcessor implements IStorageProc
// delegation
//
- public File storeData(final Sample sample, final DataSetInformation dataSetInformation,
- final ITypeExtractor typeExtractor, final IMailClient mailClient,
- final File incomingDataSetDirectory, final File rootDir)
+ public File storeData(final DataSetInformation dataSetInformation, final ITypeExtractor typeExtractor,
+ final IMailClient mailClient, final File incomingDataSetDirectory,
+ final File rootDir)
{
- return delegate.storeData(sample, dataSetInformation, typeExtractor, mailClient,
- incomingDataSetDirectory, rootDir);
+ return delegate.storeData(dataSetInformation, typeExtractor, mailClient, incomingDataSetDirectory,
+ rootDir);
}
public UnstoreDataAction unstoreData(final File incomingDataSetDirectory,
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessorWithDropbox.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessorWithDropbox.java
index 43eb99d2900495985f6e9eb9454a76fe5bc4ecbd..fe985f40af098a27ca395d947d42933ed4ceab20 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessorWithDropbox.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractDelegatingStorageProcessorWithDropbox.java
@@ -25,7 +25,6 @@ import ch.systemsx.cisd.common.filesystem.IFileOperations;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.AbstractDatasetDropboxHandler;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
* Storage processor which is able to create a copy of incoming data for additional processing.
@@ -66,13 +65,13 @@ abstract public class AbstractDelegatingStorageProcessorWithDropbox extends
//
@Override
- public final File storeData(final Sample sample, final DataSetInformation dataSetInformation,
- final ITypeExtractor typeExtractor, final IMailClient mailClient,
- final File incomingDataSetDirectory, final File rootDir)
+ public final File storeData(final DataSetInformation dataSetInformation, final ITypeExtractor typeExtractor,
+ final IMailClient mailClient, final File incomingDataSetDirectory,
+ final File rootDir)
{
File storeData =
- super.storeData(sample, dataSetInformation, typeExtractor, mailClient,
- incomingDataSetDirectory, rootDir);
+ super.storeData(dataSetInformation, typeExtractor, mailClient, incomingDataSetDirectory,
+ rootDir);
File originalData = super.tryGetProprietaryData(storeData);
dropboxHandler.handle(originalData, dataSetInformation);
return storeData;
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 3a91aa377edafca40b44e9db708b3510f5fbb456..1a2d01888c6afdbffd2afb0e6ebdbc1da9d1bee1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractStrorageProcessorWithUploader.java
@@ -21,7 +21,6 @@ import java.util.Properties;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
* Storage processor which uses an {@link IDataSetUploader} after data set has been stored by
@@ -50,13 +49,13 @@ public abstract class AbstractStrorageProcessorWithUploader extends AbstractDele
}
@Override
- public File storeData(final Sample sample, final DataSetInformation dataSetInformation,
- final ITypeExtractor typeExtractor, final IMailClient mailClient,
- final File incomingDataSetDirectory, final File rootDir)
+ public File storeData(final DataSetInformation dataSetInformation, final ITypeExtractor typeExtractor,
+ final IMailClient mailClient, final File incomingDataSetDirectory,
+ final File rootDir)
{
File storeData =
- super.storeData(sample, dataSetInformation, typeExtractor, mailClient,
- incomingDataSetDirectory, rootDir);
+ super.storeData(dataSetInformation, typeExtractor, mailClient, incomingDataSetDirectory,
+ rootDir);
File originalData = super.tryGetProprietaryData(storeData);
uploader.upload(originalData, dataSetInformation);
return storeData;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
index 6f9072ecb7c3e201da09b903bf4b5dee58c80362..cd70428da46805d030cf49278707c797dbef8c3e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
@@ -401,10 +401,9 @@ public final class BDSStorageProcessor extends AbstractStorageProcessor implemen
//
public final File storeData(
- final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample,
- final DataSetInformation dataSetInformation, final ITypeExtractor typeExtractor,
- final IMailClient mailClient, final File incomingDataSetDirectory,
- final File rootDirectory)
+ final DataSetInformation dataSetInformation,
+ final ITypeExtractor typeExtractor, final IMailClient mailClient,
+ final File incomingDataSetDirectory, final File rootDirectory)
{
checkDataSetInformation(dataSetInformation);
assert rootDirectory != null : "Root directory can not be null.";
@@ -414,7 +413,8 @@ public final class BDSStorageProcessor extends AbstractStorageProcessor implemen
dataStructureDir = rootDirectory;
dataStructureDir.mkdirs();
dataStructure =
- createDataStructure(sample.getExperiment(), dataSetInformation, typeExtractor,
+ createDataStructure(dataSetInformation.tryToGetExperiment(),
+ dataSetInformation, typeExtractor,
incomingDataSetDirectory, dataStructureDir);
final IFormattedData formattedData = dataStructure.getFormattedData();
if (formattedData instanceof IHCSImageFormattedData)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
index c6ab6ca3180a333db6b5817c8f4dfadf1983f588..ffafcc2df4cea2dbf117a51059c1f0e38f13ee63 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/CifexStorageProcessor.java
@@ -35,7 +35,6 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
/**
@@ -85,13 +84,12 @@ public class CifexStorageProcessor extends AbstractStorageProcessor
return StorageFormat.PROPRIETARY;
}
- public File storeData(Sample sample, DataSetInformation dataSetInformation,
- ITypeExtractor typeExtractor, IMailClient mailClient, File incomingDataSetDirectory,
- File rootDir)
+ public File storeData(DataSetInformation dataSetInformation, ITypeExtractor typeExtractor,
+ IMailClient mailClient, File incomingDataSetDirectory, File rootDir)
{
File result =
- delegate.storeData(sample, dataSetInformation, typeExtractor, mailClient,
- incomingDataSetDirectory, rootDir);
+ delegate.storeData(dataSetInformation, typeExtractor, mailClient, incomingDataSetDirectory,
+ rootDir);
if (StringUtils.isBlank(keppFileRegex) == false)
{
clean(delegate.tryGetProprietaryData(rootDir), keppFileRegex);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java
index 2bd210effbc5851597c0417ead94c5fafe2c8690..601609a3c022ca40ecc613ce1dd10a066d513243 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java
@@ -129,54 +129,68 @@ final class DataStrategyStore implements IDataStrategyStore
{
return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
}
+ ExperimentIdentifier experimentIdentifier = dataSetInfo.getExperimentIdentifier();
final SampleIdentifier sampleIdentifier = dataSetInfo.getSampleIdentifier();
- final Sample sample = tryGetSample(sampleIdentifier);
- final Experiment experiment = (sample == null) ? null : sample.getExperiment();
- if (experiment == null)
+ if (experimentIdentifier != null)
{
- notificationLog.error(createNotificationMessage(dataSetInfo, incomingDataSetPath));
- return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
- } else if (experiment.getInvalidation() != null)
- {
- notificationLog.error("Data set for sample '" + sampleIdentifier
- + "' can not be registered because experiment '" + experiment.getCode()
- + "' has been invalidated.");
- return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
- }
- dataSetInfo.setSample(sample);
- final ExperimentIdentifier experimentIdentifier = createExperimentIdentifier(experiment);
- dataSetInfo.setExperimentIdentifier(experimentIdentifier);
-
- final IEntityProperty[] properties =
- limsService.getPropertiesOfTopSampleRegisteredFor(sampleIdentifier);
- if (properties == null)
+ Experiment experiment = limsService.tryToGetExperiment(experimentIdentifier);
+ if (experiment == null)
+ {
+ notificationLog.error("Unknown experiment identifier '" + experimentIdentifier + "'.");
+ return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
+ }
+ dataSetInfo.setExperiment(experiment);
+ } else
{
- final Person registrator = experiment.getRegistrator();
- assert registrator != null : "Registrator must be known";
- final String message = createInvalidSampleCodeMessage(dataSetInfo);
- final String recipientMail = registrator.getEmail();
- if (StringUtils.isNotBlank(recipientMail))
+ final Sample sample = tryGetSample(sampleIdentifier);
+ final Experiment experiment = (sample == null) ? null : sample.getExperiment();
+ if (experiment == null)
+ {
+ notificationLog.error(createNotificationMessage(dataSetInfo, incomingDataSetPath));
+ return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
+ } else if (experiment.getInvalidation() != null)
{
- sendEmail(message, experimentIdentifier, recipientMail);
- } else
+ notificationLog.error("Data set for sample '" + sampleIdentifier
+ + "' can not be registered because experiment '" + experiment.getCode()
+ + "' has been invalidated.");
+ return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
+ }
+ dataSetInfo.setSample(sample);
+ experimentIdentifier = createExperimentIdentifier(experiment);
+ dataSetInfo.setExperimentIdentifier(experimentIdentifier);
+
+ final IEntityProperty[] properties =
+ limsService.getPropertiesOfTopSampleRegisteredFor(sampleIdentifier);
+ if (properties == null)
{
- notificationLog.error("The registrator '" + registrator
- + "' has a blank email, sending the following email failed:\n" + message);
+ final Person registrator = experiment.getRegistrator();
+ assert registrator != null : "Registrator must be known";
+ final String message = createInvalidSampleCodeMessage(dataSetInfo);
+ final String recipientMail = registrator.getEmail();
+ if (StringUtils.isNotBlank(recipientMail))
+ {
+ sendEmail(message, experimentIdentifier, recipientMail);
+ } else
+ {
+ notificationLog.error("The registrator '" + registrator
+ + "' has a blank email, sending the following email failed:\n" + message);
+ }
+ operationLog.error(String.format("Incoming data set '%s' claims to "
+ + "belong to experiment '%s' and sample"
+ + " identifier '%s', but according to the openBIS server "
+ + "there is no such sample for this "
+ + "experiment (it has maybe been invalidated?). We thus consider it invalid.",
+ incomingDataSetPath, experimentIdentifier, sampleIdentifier));
+ return dataStoreStrategies.get(DataStoreStrategyKey.INVALID);
}
- operationLog.error(String.format("Incoming data set '%s' claims to "
- + "belong to experiment '%s' and sample"
- + " identifier '%s', but according to the openBIS server "
- + "there is no such sample for this "
- + "experiment (it has maybe been invalidated?). We thus consider it invalid.",
- incomingDataSetPath, experimentIdentifier, sampleIdentifier));
- return dataStoreStrategies.get(DataStoreStrategyKey.INVALID);
+ dataSetInfo.setProperties(properties);
}
- dataSetInfo.setProperties(properties);
if (operationLog.isInfoEnabled())
{
- operationLog.info("Identified that database knows experiment '" + experimentIdentifier
- + "' and sample '" + sampleIdentifier + "'.");
+ operationLog.info("Identified that database knows experiment '"
+ + experimentIdentifier + "'"
+ + (sampleIdentifier == null ? "." : " and sample '" + sampleIdentifier + "'."));
}
return dataStoreStrategies.get(DataStoreStrategyKey.IDENTIFIED);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
index c0ef00e1b171054cc641fefb189f1767797d9c37..cde68a619e58ca1374c35dd7b5f4e2e9a324db13 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessor.java
@@ -24,7 +24,6 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
/**
@@ -48,9 +47,9 @@ public class DefaultStorageProcessor extends AbstractStorageProcessor
// AbstractStorageProcessor
//
- public final File storeData(final Sample sample, final DataSetInformation dataSetInformation,
- final ITypeExtractor typeExtractor, final IMailClient mailClient,
- final File incomingDataSetDirectory, final File rootDir)
+ public final File storeData(final DataSetInformation dataSetInformation, final ITypeExtractor typeExtractor,
+ final IMailClient mailClient, final File incomingDataSetDirectory,
+ final File rootDir)
{
checkParameters(incomingDataSetDirectory, rootDir);
File originalDir = getOriginalDirectory(rootDir);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IStorageProcessor.java
index d92ed351ec5bd33107c5ba496da83f6c490cfb96..9f21908172836de255b63f786e7eb1eed86f1a13 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IStorageProcessor.java
@@ -21,7 +21,6 @@ import java.util.Properties;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
/**
@@ -45,22 +44,20 @@ public interface IStorageProcessor extends IStoreRootDirectoryHolder
* Do not try/catch exceptions that could occur here. Preferably let the upper layer handle
* them.
* </p>
- *
- * @param sample Sample connected to a dataset, enriched with properties, connected experiment
- * and its properties.
* @param dataSetInformation Information about the data set.
* @param typeExtractor the {@link ITypeExtractor} implementation.
* @param mailClient mail client.
* @param incomingDataSetDirectory folder to store. Do not remove it after the implementation
* has finished processing. {@link TransferredDataSetHandler} takes care of this.
* @param rootDir directory to whom the data will be stored.
+ *
* @return folder which contains the stored data. This folder <i>must</i> be below the
* <var>rootDir</var>. Never returns <code>null</code> but prefers to throw an exception
* in case of unexpected behavior.
*/
- public File storeData(final Sample sample, final DataSetInformation dataSetInformation,
- final ITypeExtractor typeExtractor, final IMailClient mailClient,
- final File incomingDataSetDirectory, final File rootDir);
+ public File storeData(final DataSetInformation dataSetInformation, final ITypeExtractor typeExtractor,
+ final IMailClient mailClient, final File incomingDataSetDirectory,
+ final File rootDir);
/**
* Instructs the dataset handler what to do with the data in incoming directory if there was an
@@ -80,7 +77,7 @@ public interface IStorageProcessor extends IStoreRootDirectoryHolder
/**
* Performs a rollback of
- * {@link #storeData(Sample, DataSetInformation, ITypeExtractor, IMailClient, File, File)} The
+ * {@link #storeData(DataSetInformation, ITypeExtractor, IMailClient, File, File)} The
* data created in <code>directory</code> will also be removed.
* <p>
* Call to this method is safe as implementations should try/catch exceptions that could occur
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
index 543016e76b4cfc8c28d74baba61eae5baaefdc6d..2e7f006dcb42efe3de5817e974cca560896c2228 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
@@ -59,7 +59,6 @@ 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;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExtractableData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
@@ -415,12 +414,11 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
*/
final List<DataSetInformation> registerDataSet()
{
- final Sample sample = dataSetInformation.getSample();
String processorID = typeExtractor.getProcessorType(incomingDataSetFile);
try
{
- registerDataSetAndInitiateProcessing(sample, processorID);
- logAndNotifySuccessfulRegistration(sample.getExperiment().getRegistrator()
+ registerDataSetAndInitiateProcessing(processorID);
+ logAndNotifySuccessfulRegistration(dataSetInformation.tryToGetExperiment().getRegistrator()
.getEmail());
if (fileOperations.exists(incomingDataSetFile)
&& fileOperations.removeRecursivelyQueueing(incomingDataSetFile) == false)
@@ -481,8 +479,7 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
/**
* Registers the data set.
*/
- private void registerDataSetAndInitiateProcessing(final Sample sample,
- final String procedureTypeCode)
+ private void registerDataSetAndInitiateProcessing(final String procedureTypeCode)
{
final File markerFile = createProcessingMarkerFile();
try
@@ -496,8 +493,8 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
watch.start();
NewExternalData data = createExternalData();
File dataFile =
- storageProcessor.storeData(sample, dataSetInformation, typeExtractor,
- mailClient, incomingDataSetFile, baseDirectoryHolder
+ storageProcessor.storeData(dataSetInformation, typeExtractor, mailClient,
+ incomingDataSetFile, baseDirectoryHolder
.getBaseDirectory());
if (operationLog.isInfoEnabled())
{
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 d6cc2dc12d4bada41ecf2eed7ba4c4c44d64e10c..dc74a12dc6e344c6d55f767ab88a18f60d53016b 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
@@ -33,6 +33,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -42,6 +43,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
@@ -175,6 +177,11 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
authenticate();
}
}
+
+ private Experiment primTryToGetExperiment(ExperimentIdentifier experimentIdentifier)
+ {
+ return service.tryToGetExperiment(sessionToken, experimentIdentifier);
+ }
private final Sample primTryGetSampleWithExperiment(final SampleIdentifier sampleIdentifier)
{
@@ -184,7 +191,15 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
private final void primRegisterDataSet(final DataSetInformation dataSetInformation,
final NewExternalData data)
{
- service.registerDataSet(sessionToken, dataSetInformation.getSampleIdentifier(), data);
+ ExperimentIdentifier experimentIdentifier = dataSetInformation.getExperimentIdentifier();
+ if (experimentIdentifier != null)
+ {
+ service.registerDataSet(sessionToken, experimentIdentifier, data);
+ } else
+ {
+ SampleIdentifier sampleIdentifier = dataSetInformation.getSampleIdentifier();
+ service.registerDataSet(sessionToken, sampleIdentifier, data);
+ }
}
private final IEntityProperty[] primGetPropertiesOfSampleRegisteredFor(
@@ -208,6 +223,21 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
// IEncapsulatedOpenBISService
//
+ synchronized public Experiment tryToGetExperiment(ExperimentIdentifier experimentIdentifier)
+ {
+ assert experimentIdentifier != null : " Unspecified experiment identifier.";
+
+ checkSessionToken();
+ try
+ {
+ return primTryToGetExperiment(experimentIdentifier);
+ } catch (InvalidSessionException ex)
+ {
+ authenticate();
+ return primTryToGetExperiment(experimentIdentifier);
+ }
+ }
+
synchronized public final Sample tryGetSampleWithExperiment(
final SampleIdentifier sampleIdentifier)
{
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 521f32a7aad267ffe5343be2bd8f29698b9b6381..ba481bd5e46371bf0fd5fbe8f9a56825205a56ba 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
@@ -23,12 +23,14 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
@@ -46,6 +48,12 @@ public interface IEncapsulatedOpenBISService
public ExternalData tryGetDataSet(final String sessionToken, final String dataSetCode)
throws UserFailureException;
+ /**
+ * Tries to get the experiment of specified identifier or <code>null</code> if not found.
+ */
+ public Experiment tryToGetExperiment(ExperimentIdentifier experimentIdentifier)
+ throws UserFailureException;
+
/**
* Gets a sample with the specified identifier. Sample is enriched with properties and the
* experiment with properties.
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 ca6db23c3f2c08ca7a70c686cadc0202f85b110f..d193444f46cb1af7d0a9ae12bedcecf1820513fb 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
@@ -71,6 +71,8 @@ public class DataSetInformation implements Serializable
/** sample with properties, enriched with connected experiment with properties. */
private transient Sample sample;
+
+ private transient Experiment experiment;
private BooleanOrUnknown isCompleteFlag = BooleanOrUnknown.U;
@@ -119,7 +121,7 @@ public class DataSetInformation implements Serializable
*/
public final IEntityProperty[] getProperties()
{
- return properties;
+ return properties == null ? new IEntityProperty[0] : properties;
}
public final void setProperties(final IEntityProperty[] properties)
@@ -166,18 +168,17 @@ public class DataSetInformation implements Serializable
/**
* Returns the basic information about the experiment.
*/
- public Experiment getExperiment()
+ public Experiment tryToGetExperiment()
{
- return sample == null ? null : sample.getExperiment();
+ return experiment == null ? (sample == null ? null : sample.getExperiment()) : experiment;
+ }
+
+ public void setExperiment(Experiment experiment)
+ {
+ this.experiment = experiment;
}
- /**
- * NOTE: may be NULL
- *
- * @deprecated remove deprecation when all use cases are rewritten in a NULL safe way
- */
- @Deprecated
- public Sample getSample()
+ public Sample tryToGetSample()
{
return sample;
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorWithDropboxTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorWithDropboxTest.java
index ab3006e0b64c426c5c3bcb6c053befc366b10413..440a20b8f359aabcb66c08e26bca32238e052131 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorWithDropboxTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/AbstractStorageProcessorWithDropboxTest.java
@@ -53,8 +53,8 @@ public class AbstractStorageProcessorWithDropboxTest extends AbstractFileSystemT
context.checking(new Expectations()
{
{
- one(delegateStorageProcessor).storeData(null, dataSetInfo, null, null,
- incomingDirectory, null);
+ one(delegateStorageProcessor).storeData(dataSetInfo, null, null, incomingDirectory,
+ null);
will(returnValue(incomingDirectory));
File dropboxIncomingDir = new File(dropboxIncomingDirName);
@@ -77,7 +77,7 @@ public class AbstractStorageProcessorWithDropboxTest extends AbstractFileSystemT
AbstractDelegatingStorageProcessorWithDropbox storageProcessor =
new StorageProcessorWithDropboxTest(props, delegateStorageProcessor, fileOperations);
- storageProcessor.storeData(null, dataSetInfo, null, null, incomingDirectory, null);
+ storageProcessor.storeData(dataSetInfo, null, null, incomingDirectory, null);
context.assertIsSatisfied();
}
@@ -195,7 +195,7 @@ public class AbstractStorageProcessorWithDropboxTest extends AbstractFileSystemT
File store = new File(workingDirectory, "store");
store.mkdirs();
- processor.storeData(null, dataSetInfo, null, null, dataSetFile, store);
+ processor.storeData(dataSetInfo, null, null, dataSetFile, store);
File storeData = new File(store, "original/data.txt");
assertEquals(true, storeData.exists());
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
index 04b417dd60c4bae731642e60c3d873460c4ca5b0..1b272f635f00853f3d4ce585a9f3338693c2838f 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
@@ -354,8 +354,8 @@ public final class BDSStorageProcessorTest extends AbstractFileSystemTestCase
final DataSetInformation dataSetInformation = createDataSetInformation();
prepareMailClient(format);
final File dataFile =
- storageProcessor.storeData(baseSample, dataSetInformation, TYPE_EXTRACTOR,
- mailClient, incomingDataSetDirectory, new File(workingDirectory,
+ storageProcessor.storeData(dataSetInformation, TYPE_EXTRACTOR, mailClient,
+ incomingDataSetDirectory, new File(workingDirectory,
STORE_ROOT_DIR));
assertEquals(new File(workingDirectory, STORE_ROOT_DIR).getAbsolutePath(), dataFile
.getAbsolutePath());
@@ -412,8 +412,8 @@ public final class BDSStorageProcessorTest extends AbstractFileSystemTestCase
prepareMailClient(format);
final File storeRootDir = new File(workingDirectory, STORE_ROOT_DIR);
final File dataStore =
- storageAdapter.storeData(baseSample, dataSetInformation, TYPE_EXTRACTOR,
- mailClient, incomingDirectoryData, storeRootDir);
+ storageAdapter.storeData(dataSetInformation, TYPE_EXTRACTOR, mailClient,
+ incomingDirectoryData, storeRootDir);
assertEquals(true, dataStore.isDirectory());
assertEquals(false, incomingDirectoryData.exists());
storageAdapter.unstoreData(incomingDirectoryData, storeRootDir, null);
@@ -433,8 +433,8 @@ public final class BDSStorageProcessorTest extends AbstractFileSystemTestCase
final DataSetInformation dataSetInformation = createDataSetInformation();
prepareMailClient(format);
final File storeData =
- storageProcessor.storeData(baseSample, dataSetInformation, TYPE_EXTRACTOR,
- mailClient, incomingDirectoryData, workingDirectory);
+ storageProcessor.storeData(dataSetInformation, TYPE_EXTRACTOR, mailClient,
+ incomingDirectoryData, workingDirectory);
final File originalDataSet = storageProcessor.tryGetProprietaryData(storeData);
assertNotNull(originalDataSet);
assertEquals(INCOMING_DATA_SET_DIR, originalDataSet.getName());
@@ -462,8 +462,8 @@ public final class BDSStorageProcessorTest extends AbstractFileSystemTestCase
final DataSetInformation dataSetInformation = createDataSetInformation();
prepareMailClient(HCSImageFormatV1_0.HCS_IMAGE_1_0);
final File storeData =
- storageProcessor.storeData(baseSample, dataSetInformation, TYPE_EXTRACTOR,
- mailClient, incomingDirectoryData, workingDirectory);
+ storageProcessor.storeData(dataSetInformation, TYPE_EXTRACTOR, mailClient,
+ incomingDirectoryData, workingDirectory);
logRecorder.resetLogContent();
final File originalDataSet = storageProcessor.tryGetProprietaryData(storeData);
assertEquals(null, originalDataSet);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/CifexStorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/CifexStorageProcessorTest.java
index 0b57f1aac6083224ce1fff368a553d6e38e9cf2b..700569e9887ba5c40f82715fad3d1787732ef81c 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/CifexStorageProcessorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/CifexStorageProcessorTest.java
@@ -68,8 +68,8 @@ public class CifexStorageProcessorTest extends AbstractFileSystemTestCase
FileUtilities.writeToFile(new File(incomingDataSetDirectory, "read.me"), "hello world");
final File rootDir = createDirectory("root");
final File storeData =
- storageProcessor.storeData(null, null, TYPE_EXTRACTOR, null,
- incomingDataSetDirectory, rootDir);
+ storageProcessor.storeData(null, TYPE_EXTRACTOR, null, incomingDataSetDirectory,
+ rootDir);
assertEquals(false, incomingDataSetDirectory.exists());
assertEquals(true, storeData.isDirectory());
assertEquals(rootDir.getAbsolutePath(), storeData.getAbsolutePath());
@@ -87,7 +87,7 @@ public class CifexStorageProcessorTest extends AbstractFileSystemTestCase
FileUtilities.writeToFile(incoming, "hello world");
final File rootDir = createDirectory("root");
final File storeData =
- storageProcessor.storeData(null, null, TYPE_EXTRACTOR, null, incoming, rootDir);
+ storageProcessor.storeData(null, TYPE_EXTRACTOR, null, incoming, rootDir);
assertEquals(false, incoming.exists());
assertEquals(true, storeData.isDirectory());
File fileName = new File(rootDir, DefaultStorageProcessor.ORIGINAL_DIR + "/read.me");
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessorTest.java
index 796dd33234f661a72504c1a1cdb181934794e084..324630df94ae51b0a6325542bf0d5d7267e2e854 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultStorageProcessorTest.java
@@ -63,7 +63,7 @@ public final class DefaultStorageProcessorTest extends AbstractFileSystemTestCas
final DefaultStorageProcessor storageProcessor = createStorageProcessor();
try
{
- storageProcessor.storeData(null, null, null, null, null, null);
+ storageProcessor.storeData(null, null, null, null, null);
fail("Null values not accepted");
} catch (final AssertionError e)
{
@@ -73,8 +73,8 @@ public final class DefaultStorageProcessorTest extends AbstractFileSystemTestCas
FileUtilities.writeToFile(new File(incomingDataSetDirectory, "read.me"), "hello world");
final File rootDir = createDirectory("root");
final File storeData =
- storageProcessor.storeData(null, null, TYPE_EXTRACTOR, null,
- incomingDataSetDirectory, rootDir);
+ storageProcessor.storeData(null, TYPE_EXTRACTOR, null, incomingDataSetDirectory,
+ rootDir);
assertEquals(false, incomingDataSetDirectory.exists());
assertEquals(true, storeData.isDirectory());
assertEquals(rootDir.getAbsolutePath(), storeData.getAbsolutePath());
@@ -108,8 +108,8 @@ public final class DefaultStorageProcessorTest extends AbstractFileSystemTestCas
File readMeFile = new File(incomingDataSetDirectory, "read.me");
FileUtilities.writeToFile(readMeFile, "hi");
final File storeData =
- storageProcessor.storeData(null, null, TYPE_EXTRACTOR, null,
- incomingDataSetDirectory, root);
+ storageProcessor.storeData(null, TYPE_EXTRACTOR, null, incomingDataSetDirectory,
+ root);
assertEquals(true, storeData.exists());
assertEquals(false, incomingDataSetDirectory.exists());
storageProcessor.unstoreData(incomingDataSetDirectory, root, null);
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 51ec503c86e44efab0f8bcb203b9029b0b93c61f..c7677e1f263853a722b7418f3220a64c9d56cd6a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -560,8 +560,8 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
allowing(storageProcessor).getStorageFormat();
will(returnValue(StorageFormat.BDS_DIRECTORY));
- one(storageProcessor).storeData(baseSample, dataSetInformation, typeExtractor,
- mailClient, data1, baseDir);
+ one(storageProcessor).storeData(dataSetInformation, typeExtractor, mailClient,
+ data1, baseDir);
final File finalDataSetPath = new File(baseDir, DATA1_NAME);
will(returnValue(finalDataSetPath));
}
@@ -602,8 +602,8 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
allowing(storageProcessor).getStorageFormat();
will(returnValue(StorageFormat.BDS_DIRECTORY));
- one(storageProcessor).storeData(baseSample, dataSetInformation, typeExtractor,
- mailClient, data1, baseDir);
+ one(storageProcessor).storeData(dataSetInformation, typeExtractor, mailClient,
+ data1, baseDir);
final File finalDataSetPath = new File(baseDir, DATA1_NAME);
will(returnValue(finalDataSetPath));
}
@@ -696,8 +696,8 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
one(typeExtractor).getProcessorType(folder);
will(returnValue(EXAMPLE_PROCESSOR_ID));
- one(storageProcessor).storeData(baseSample, dataSetInformation, typeExtractor,
- mailClient, folder, baseDir);
+ one(storageProcessor).storeData(dataSetInformation, typeExtractor, mailClient,
+ folder, baseDir);
UserFailureException exception =
new UserFailureException("Could store data by storage processor");
will(throwException(exception));
@@ -755,8 +755,8 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
context.checking(new Expectations()
{
{
- one(storageProcessor).storeData(baseSample, dataSetInformation, typeExtractor,
- mailClient, folder, baseDir);
+ one(storageProcessor).storeData(dataSetInformation, typeExtractor, mailClient,
+ folder, baseDir);
will(returnValue(new File(baseDir, DATA1_NAME)));
one(limsService).registerDataSet(with(equal(SESSION_TOKEN)),