From 9def66150b21799e96cf394ab240fd550db25435 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 5 Mar 2015 10:59:35 +0000
Subject: [PATCH] SSDM-1366: datastore_server: merge feature branch
'data-set-sample' with trunk.
SVN: 33561
---
.../DataSetRegistrationAlgorithm.java | 27 +--
.../cisd/etlserver/DataStrategyStore.java | 168 +++++++++++-------
.../SampleAndDataSetRegistrator.java | 6 +-
.../TemplateBasedLinkNamingStrategy.java | 16 +-
.../etlserver/plugins/grouping/Grouping.java | 8 +-
.../Hdf5CompressingPostRegistrationTask.java | 4 +-
.../api/v1/impl/DataSetImmutable.java | 63 +++++--
.../api/v2/impl/DataSetImmutable.java | 61 ++++++-
.../dss/generic/server/MetaDataBuilder.java | 19 +-
.../dss/generic/server/UploadingCommand.java | 12 +-
.../AbstractDropboxProcessingPlugin.java | 30 +++-
.../AbstractDataSetFileOperationsManager.java | 5 +-
.../shared/ExperimentBasedShareFinder.java | 17 +-
.../IdentifierAttributeMappingManager.java | 8 +
.../TransferredDataSetHandlerTest.java | 13 +-
15 files changed, 318 insertions(+), 139 deletions(-)
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 9e91c50cc81..cbfb5cff099 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithm.java
@@ -51,6 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
@@ -123,8 +124,6 @@ public class DataSetRegistrationAlgorithm
private final String defaultErrorMessageTemplate;
- private final String emailSubjectTemplate;
-
public DataSetRegistrationAlgorithmState(File incomingDataSetFile,
IEncapsulatedOpenBISService openBisService,
IDelegatedActionWithResult<Boolean> cleanAfterwardsAction,
@@ -164,7 +163,6 @@ public class DataSetRegistrationAlgorithm
dataSetInformation.setDataSetType(dataSetType);
this.storeRoot = storageProcessor.getStoreRootDirectory();
this.defaultErrorMessageTemplate = DATA_SET_STORAGE_FAILURE_TEMPLATE;
- this.emailSubjectTemplate = EMAIL_SUBJECT_TEMPLATE;
}
public File getIncomingDataSetFile()
@@ -179,7 +177,7 @@ public class DataSetRegistrationAlgorithm
static private final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
DataSetRegistrationAlgorithm.class);
- public static final String EMAIL_SUBJECT_TEMPLATE = "Success: data set for experiment '%s";
+ public static final String EMAIL_SUBJECT_TEMPLATE = "Success: data set for sample or experiment '%s";
public static final String DATA_SET_REGISTRATION_FAILURE_TEMPLATE =
"Registration of data set '%s' failed.";
@@ -264,12 +262,9 @@ public class DataSetRegistrationAlgorithm
boolean deleted = false;
if (userEmailOrNull != null)
{
- final String errorMessage =
- "Error when trying to register data set '" + incomingDataSetFile.getName()
- + "'.";
- state.mailClient.sendMessage(String.format(errorMessage, dataSetInformation
- .getExperimentIdentifier().getExperimentCode()), ex.getMessage(), null,
- null, userEmailOrNull);
+ final String errorMessage = "Error when trying to register data set '"
+ + incomingDataSetFile.getName() + "'.";
+ state.mailClient.sendMessage(errorMessage, ex.getMessage(), null, null, userEmailOrNull);
if (state.shouldDeleteUnidentified)
{
deleted = removeAndLog(errorMessage + " [" + ex.getMessage() + "]");
@@ -498,8 +493,16 @@ public class DataSetRegistrationAlgorithm
}
if (StringUtils.isBlank(email) == false)
{
- state.mailClient.sendMessage(String.format(state.emailSubjectTemplate,
- dataSetInformation.getExperimentIdentifier().getExperimentCode()), msg,
+ String code = dataSetInformation.getSampleCode();
+ if (code == null)
+ {
+ ExperimentIdentifier experimentIdentifier = dataSetInformation.getExperimentIdentifier();
+ if (experimentIdentifier != null)
+ {
+ code = experimentIdentifier.getExperimentCode();
+ }
+ }
+ state.mailClient.sendMessage(String.format(EMAIL_SUBJECT_TEMPLATE, code), msg,
null, null, email);
}
}
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 55dacbe72fe..00d503a1dcf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DataStrategyStore.java
@@ -36,6 +36,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -50,6 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
public class DataStrategyStore implements IDataStrategyStore
{
static final String SUBJECT_FORMAT = "ATTENTION: experiment '%s'";
+ static final String SUBJECT_SAMPLE_FORMAT = "ATTENTION: sample '%s'";
private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY,
DataStrategyStore.class);
@@ -137,100 +139,65 @@ public class DataStrategyStore implements IDataStrategyStore
return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
}
- if (dataSetInfo.isNoFileDataSet())
- {
- assert incomingDataSetPath == null : "Incoming data set path for a no-file data set must be null";
- } else
- {
- assert incomingDataSetPath != null : "Incoming data set path for a normal data set can not be null.";
- }
-
- String containerDatasetPermId = dataSetInfo.tryGetContainerDatasetPermId();
- if (containerDatasetPermId != null)
- {
- AbstractExternalData container =
- openbisServiceWrapper.tryGetDataSet(containerDatasetPermId);
- if (container != null)
- {
- dataSetInfo.setContainerDataSet(container);
- }
- }
+ assertIncomingDataSetPath(incomingDataSetPath, dataSetInfo);
+ injectContainerDataSet(dataSetInfo);
String emailOrNull = dataSetInfo.tryGetUploadingUserEmail();
- ExperimentIdentifier experimentIdentifier;
+ ExperimentIdentifier experimentIdentifier = dataSetInfo.getExperimentIdentifier();
final SampleIdentifier sampleIdentifier = dataSetInfo.getSampleIdentifier();
if (sampleIdentifier == null)
{
- experimentIdentifier = dataSetInfo.getExperimentIdentifier();
- Experiment experiment = dataSetInfo.tryToGetExperiment();
- if (experiment == null)
- {
- experiment = openbisServiceWrapper.tryGetExperiment(experimentIdentifier);
- }
+ Experiment experiment = tryGetExperiment(dataSetInfo);
if (experiment == null)
{
error(emailOrNull, "Unknown experiment identifier '" + experimentIdentifier + "'.");
return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
}
- if (experiment.getDeletion() != null)
- {
- error(emailOrNull, "Experiment '" + experimentIdentifier + "' has been deleted.");
- return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
- }
dataSetInfo.setExperiment(experiment);
} else
{
- Sample sample = dataSetInfo.tryToGetSample();
- if (sample == null)
- {
- sample = openbisServiceWrapper.tryGetSample(sampleIdentifier);
- }
-
+ Sample sample = tryGetSample(dataSetInfo);
if (sample == null)
{
error(emailOrNull, createNotificationMessage(dataSetInfo, incomingDataSetPath));
return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
}
+ dataSetInfo.setSample(sample);
final Experiment experiment = sample.getExperiment();
if (experiment == null)
{
- error(emailOrNull, String.format("Data set for sample '%s' can not be registered "
- + "because the sample is not attached to an experiment.", sampleIdentifier));
- return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
- } else if (experiment.getDeletion() != null)
+ if (sample.getSpace() == null)
+ {
+ error(emailOrNull, String.format("Data set for sample '%s' can not be registered "
+ + "because the sample is a shared sample not assigned to a particular space.",
+ sampleIdentifier));
+ return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
+ }
+ } else
{
- error(emailOrNull, String.format("Data set for sample '%s' can not be registered "
- + "because experiment '%s' has been deleted.", sampleIdentifier,
- experiment.getCode()));
- return dataStoreStrategies.get(DataStoreStrategyKey.UNIDENTIFIED);
+ experimentIdentifier = new ExperimentIdentifier(experiment);
+ dataSetInfo.setExperimentIdentifier(experimentIdentifier);
}
- dataSetInfo.setSample(sample);
- experimentIdentifier = new ExperimentIdentifier(experiment);
- dataSetInfo.setExperimentIdentifier(experimentIdentifier);
final IEntityProperty[] properties =
openbisServiceWrapper.tryGetPropertiesOfSample(sampleIdentifier);
if (properties == null)
{
- final Person registrator = experiment.getRegistrator();
+ final Person registrator = experiment == null ? sample.getRegistrator() : 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);
+ sendEmail(message, experimentIdentifier, sampleIdentifier, recipientMail);
} else
{
error(emailOrNull, "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 (maybe it has been deleted?). We thus consider it invalid.",
- incomingDataSetPath, experimentIdentifier, sampleIdentifier));
+ operationLog.error(createLogMessageForMissingSampleProperties(incomingDataSetPath,
+ experimentIdentifier, sampleIdentifier));
return dataStoreStrategies.get(DataStoreStrategyKey.INVALID);
}
dataSetInfo.setSampleProperties(properties);
@@ -238,13 +205,87 @@ public class DataStrategyStore implements IDataStrategyStore
if (operationLog.isInfoEnabled())
{
- operationLog.info("Identified that database knows experiment '" + experimentIdentifier
- + "'"
- + (sampleIdentifier == null ? "." : " and sample '" + sampleIdentifier + "'."));
+ operationLog.info(createLogMessageForIdentified(experimentIdentifier, sampleIdentifier));
}
return dataStoreStrategies.get(DataStoreStrategyKey.IDENTIFIED);
}
+ private String createLogMessageForIdentified(ExperimentIdentifier experimentIdentifier,
+ SampleIdentifier sampleIdentifier)
+ {
+ String prefix = "Identified that database knows ";
+ if (sampleIdentifier == null)
+ {
+ return prefix + "experiment '" + experimentIdentifier + "'.";
+ } else if (experimentIdentifier == null)
+ {
+ return prefix + "sample '" + sampleIdentifier + "'.";
+ }
+ return prefix + "experiment '" + experimentIdentifier + "' and sample '" + sampleIdentifier + "'.";
+ }
+
+ private String createLogMessageForMissingSampleProperties(final File incomingDataSetPath,
+ ExperimentIdentifier experimentIdentifier, final SampleIdentifier sampleIdentifier)
+ {
+ String claimedOwner;
+ if (experimentIdentifier == null)
+ {
+ claimedOwner = String.format("sample '%s'", sampleIdentifier);
+ } else
+ {
+ claimedOwner = String.format("experiment '%s' and sample '%s'",
+ experimentIdentifier, sampleIdentifier);
+ }
+ return String.format("Incoming data set '%s' claims to belong to %s, but according to the openBIS server "
+ + "there is no such sample (maybe it has been deleted?). We thus consider it invalid.",
+ incomingDataSetPath, claimedOwner);
+ }
+
+ public Sample tryGetSample(final DataSetInformation dataSetInfo)
+ {
+ Sample sample = dataSetInfo.tryToGetSample();
+ if (sample == null)
+ {
+ sample = openbisServiceWrapper.tryGetSample(dataSetInfo.getSampleIdentifier());
+ }
+ return sample;
+ }
+
+ public Experiment tryGetExperiment(final DataSetInformation dataSetInfo)
+ {
+ Experiment experiment = dataSetInfo.tryToGetExperiment();
+ if (experiment == null)
+ {
+ experiment = openbisServiceWrapper.tryGetExperiment(dataSetInfo.getExperimentIdentifier());
+ }
+ return experiment;
+ }
+
+ public void injectContainerDataSet(final DataSetInformation dataSetInfo)
+ {
+ String containerDatasetPermId = dataSetInfo.tryGetContainerDatasetPermId();
+ if (containerDatasetPermId != null)
+ {
+ AbstractExternalData container =
+ openbisServiceWrapper.tryGetDataSet(containerDatasetPermId);
+ if (container != null)
+ {
+ dataSetInfo.setContainerDataSet(container);
+ }
+ }
+ }
+
+ public void assertIncomingDataSetPath(final File incomingDataSetPath, final DataSetInformation dataSetInfo)
+ {
+ if (dataSetInfo.isNoFileDataSet())
+ {
+ assert incomingDataSetPath == null : "Incoming data set path for a no-file data set must be null";
+ } else
+ {
+ assert incomingDataSetPath != null : "Incoming data set path for a normal data set can not be null.";
+ }
+ }
+
private void error(String emailOrNull, String message)
{
if (emailOrNull == null)
@@ -259,9 +300,16 @@ public class DataStrategyStore implements IDataStrategyStore
}
private void sendEmail(final String message, final ExperimentIdentifier experimentIdentifier,
- final String recipientMail)
+ SampleIdentifier sampleIdentifier, final String recipientMail)
{
- final String subject = String.format(SUBJECT_FORMAT, experimentIdentifier);
+ final String subject;
+ if (experimentIdentifier == null)
+ {
+ subject = String.format(SUBJECT_SAMPLE_FORMAT, sampleIdentifier);
+ } else
+ {
+ subject = String.format(SUBJECT_FORMAT, experimentIdentifier);
+ }
try
{
mailClient.sendMessage(subject, message, null, null, recipientMail);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
index 097138a8e77..e82a3f93fa3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
@@ -79,7 +79,7 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
try
{
checkDataSetFileNotEmpty();
- checkExperimentExists();
+ injectExperiment();
retrieveSampleOrNull();
} catch (UserFailureException ex)
{
@@ -188,13 +188,13 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
sampleOrNull = globalState.getOpenbisService().tryGetSampleWithExperiment(sampleIdentifier);
}
- private void checkExperimentExists()
+ private void injectExperiment()
{
ExperimentIdentifier experimentId =
sampleDataSetPair.getDataSetInformation().getExperimentIdentifier();
if (null == experimentId)
{
- throw new UserFailureException("An experiment identifier must be specified");
+ return;
}
Experiment experiment = globalState.getOpenbisService().tryGetExperiment(experimentId);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/TemplateBasedLinkNamingStrategy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/TemplateBasedLinkNamingStrategy.java
index e88e246064d..9660f7d14e0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/TemplateBasedLinkNamingStrategy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/TemplateBasedLinkNamingStrategy.java
@@ -154,12 +154,7 @@ public class TemplateBasedLinkNamingStrategy implements IHierarchicalStorageLink
@Override
String extractValueFromData(SimpleDataSetInformationDTO data)
{
- String samplePathElement = data.getSampleCode();
- if (samplePathElement == null)
- {
- samplePathElement = NOT_DIRECTLY_CONNECTED;
- }
- return samplePathElement;
+ return getPathElement(data.getSampleCode());
}
},
@@ -170,7 +165,7 @@ public class TemplateBasedLinkNamingStrategy implements IHierarchicalStorageLink
@Override
String extractValueFromData(SimpleDataSetInformationDTO data)
{
- return data.getExperimentCode();
+ return getPathElement(data.getExperimentCode());
}
},
@@ -180,7 +175,7 @@ public class TemplateBasedLinkNamingStrategy implements IHierarchicalStorageLink
@Override
String extractValueFromData(SimpleDataSetInformationDTO data)
{
- return data.getProjectCode();
+ return getPathElement(data.getProjectCode());
}
},
@@ -208,5 +203,10 @@ public class TemplateBasedLinkNamingStrategy implements IHierarchicalStorageLink
abstract String extractValueFromData(SimpleDataSetInformationDTO data);
+ private static String getPathElement(String pathElement)
+ {
+ return pathElement == null ? NOT_DIRECTLY_CONNECTED : pathElement;
+ }
+
}
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/grouping/Grouping.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/grouping/Grouping.java
index fd15217a20a..3be39aa57b5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/grouping/Grouping.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/grouping/Grouping.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.etlserver.plugins.grouping;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
@@ -37,7 +38,7 @@ public enum Grouping implements IGroupKeyProvider
@Override
public String getGroupKey(AbstractExternalData dataset)
{
- return dataset.getExperiment().getProject().getSpace().getCode();
+ return dataset.getSpace().getCode();
}
},
Project
@@ -53,7 +54,8 @@ public enum Grouping implements IGroupKeyProvider
@Override
public String getGroupKey(AbstractExternalData dataset)
{
- return dataset.getExperiment().getIdentifier();
+ Experiment experiment = dataset.getExperiment();
+ return experiment != null ? experiment.getIdentifier() : "no_experiment";
}
},
@@ -87,7 +89,7 @@ public enum Grouping implements IGroupKeyProvider
@Override
public String getGroupKey(AbstractExternalData dataset)
{
- return dataset.getExperiment().getIdentifier() + "#" + dataset.getDataSetType().getCode();
+ return Experiment.getGroupKey(dataset) + "#" + DataSetType.getGroupKey(dataset);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/Hdf5CompressingPostRegistrationTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/Hdf5CompressingPostRegistrationTask.java
index 4308ea02a0b..629be03cead 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/Hdf5CompressingPostRegistrationTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/Hdf5CompressingPostRegistrationTask.java
@@ -46,6 +46,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
@@ -433,7 +434,8 @@ public class Hdf5CompressingPostRegistrationTask extends AbstractPostRegistratio
private ExperimentIdentifier extractExperimentIdentifier(AbstractExternalData data)
{
- return ExperimentIdentifierFactory.parse(data.getExperiment().getIdentifier());
+ Experiment experiment = data.getExperiment();
+ return experiment == null ? null : ExperimentIdentifierFactory.parse(experiment.getIdentifier());
}
private SampleIdentifier extractSampleIdentifier(AbstractExternalData data)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
index 612d4945cac..921f79397b3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
@@ -29,11 +29,13 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmuta
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.IObjectId;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCodeId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalDataManagementSystem;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
@@ -43,6 +45,52 @@ import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
*/
public class DataSetImmutable extends AbstractDataSetImmutable
{
+ private static final class NullExperiment implements IExperimentImmutable
+ {
+ private String message;
+
+ NullExperiment(String dataSetCode)
+ {
+ message = "No experiment defined for data set '" + dataSetCode + "'.";
+ }
+
+ @Override
+ public IObjectId getEntityId()
+ {
+ throw new UnsupportedOperationException(message);
+ }
+
+ @Override
+ public String getExperimentIdentifier()
+ {
+ throw new UnsupportedOperationException(message);
+ }
+
+ @Override
+ public boolean isExistingExperiment()
+ {
+ return false;
+ }
+
+ @Override
+ public String getExperimentType()
+ {
+ return null;
+ }
+
+ @Override
+ public String getPropertyValue(String propertyCode)
+ {
+ return null;
+ }
+
+ @Override
+ public String getPermId()
+ {
+ throw new UnsupportedOperationException(message);
+ }
+ }
+
protected final AbstractExternalData dataSet;
public DataSetImmutable(AbstractExternalData dataSet, IEncapsulatedBasicOpenBISService service)
@@ -66,20 +114,15 @@ public class DataSetImmutable extends AbstractDataSetImmutable
@Override
public IExperimentImmutable getExperiment()
{
- return new ExperimentImmutable(dataSet.getExperiment());
+ Experiment experiment = dataSet.getExperiment();
+ return experiment == null ? new NullExperiment(getDataSetCode()) : new ExperimentImmutable(experiment);
}
@Override
public ISampleImmutable getSample()
{
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample = dataSet.getSample();
- if (sample == null)
- {
- return null;
- } else
- {
- return new SampleImmutable(sample);
- }
+ Sample sample = dataSet.getSample();
+ return sample == null ? null : new SampleImmutable(sample);
}
@Override
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSetImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSetImmutable.java
index 2da13d1f84f..40e83d1c231 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSetImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSetImmutable.java
@@ -32,8 +32,10 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCode
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalDataManagementSystem;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
@@ -43,6 +45,52 @@ import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
*/
public class DataSetImmutable extends AbstractDataSetImmutable
{
+ private static final class NullExperiment implements IExperimentImmutable
+ {
+ private String message;
+
+ NullExperiment(String dataSetCode)
+ {
+ message = "No experiment defined for data set '" + dataSetCode + "'.";
+ }
+
+ @Override
+ public IObjectId getEntityId()
+ {
+ throw new UnsupportedOperationException(message);
+ }
+
+ @Override
+ public String getExperimentIdentifier()
+ {
+ throw new UnsupportedOperationException(message);
+ }
+
+ @Override
+ public boolean isExistingExperiment()
+ {
+ return false;
+ }
+
+ @Override
+ public String getExperimentType()
+ {
+ return null;
+ }
+
+ @Override
+ public String getPropertyValue(String propertyCode)
+ {
+ return null;
+ }
+
+ @Override
+ public String getPermId()
+ {
+ throw new UnsupportedOperationException(message);
+ }
+ }
+
protected final AbstractExternalData dataSet;
public DataSetImmutable(AbstractExternalData dataSet, IEncapsulatedBasicOpenBISService service)
@@ -66,20 +114,15 @@ public class DataSetImmutable extends AbstractDataSetImmutable
@Override
public IExperimentImmutable getExperiment()
{
- return new ExperimentImmutable(dataSet.getExperiment());
+ Experiment experiment = dataSet.getExperiment();
+ return experiment == null ? new NullExperiment(getDataSetCode()) : new ExperimentImmutable(experiment);
}
@Override
public ISampleImmutable getSample()
{
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample = dataSet.getSample();
- if (sample == null)
- {
- return null;
- } else
- {
- return new SampleImmutable(sample);
- }
+ Sample sample = dataSet.getSample();
+ return sample == null ? null : new SampleImmutable(sample);
}
@Override
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MetaDataBuilder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MetaDataBuilder.java
index fc8934a5f12..ee9363997cf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MetaDataBuilder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MetaDataBuilder.java
@@ -130,14 +130,17 @@ public class MetaDataBuilder
builder.sampleProperties(sample.getProperties());
}
Experiment experiment = dataSet.getExperiment();
- Project project = experiment.getProject();
- builder.experiment("space_code", project.getSpace().getCode());
- builder.experiment("project_code", project.getCode());
- builder.experiment("experiment_code", experiment.getCode());
- builder.experiment("experiment_type_code", experiment.getExperimentType().getCode());
- builder.experiment("registration_timestamp", experiment.getRegistrationDate());
- builder.experiment("registrator", experiment.getRegistrator());
- builder.experimentProperties(experiment.getProperties());
+ if (experiment != null)
+ {
+ Project project = experiment.getProject();
+ builder.experiment("space_code", project.getSpace().getCode());
+ builder.experiment("project_code", project.getCode());
+ builder.experiment("experiment_code", experiment.getCode());
+ builder.experiment("experiment_type_code", experiment.getExperimentType().getCode());
+ builder.experiment("registration_timestamp", experiment.getRegistrationDate());
+ builder.experiment("registrator", experiment.getRegistrator());
+ builder.experimentProperties(experiment.getProperties());
+ }
return builder.getRenderedMetaData();
}
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 0adce36e2a7..ea9c31dc70f 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
@@ -326,9 +326,15 @@ class UploadingCommand implements IDataSetCommand
{
Sample sample = dataSet.getSample();
Experiment experiment = dataSet.getExperiment();
- Project project = experiment.getProject();
- return project.getSpace().getCode() + "/" + project.getCode() + "/" + experiment.getCode()
- + "/" + (sample == null ? "" : sample.getCode() + "/") + dataSet.getCode();
+ if (experiment != null)
+ {
+ Project project = experiment.getProject();
+ return project.getSpace().getCode() + "/" + project.getCode() + "/" + experiment.getCode()
+ + "/" + (sample == null ? "" : sample.getCode() + "/") + dataSet.getCode();
+ } else
+ {
+ return sample.getSpace().getCode() + "/" + sample.getCode() + "/" + dataSet.getCode();
+ }
}
private void sendEMail(String message)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
index 3bfae5ee1c3..057e02fb439 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
@@ -40,6 +40,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
* The base class for processing plugins that employ a {@link IPostRegistrationDatasetHandler}.
@@ -116,9 +118,10 @@ abstract public class AbstractDropboxProcessingPlugin extends AbstractDatastoreP
render(dataSetDescription.getSampleIdentifier(),
dataSetDescription.getSampleTypeCode());
boolean withSample = sampleOrNull != null;
+ boolean withExperiment = experiment != null;
boolean processingFailed = status.isError();
String processingDescription = getProcessingDescription(dataSetDescription, context);
- Template template = getEMailMessageTemplate(processingFailed, withSample).createFreshCopy();
+ Template template = getEMailMessageTemplate(processingFailed, withSample, withExperiment).createFreshCopy();
String subject;
if (processingFailed)
{
@@ -130,7 +133,10 @@ abstract public class AbstractDropboxProcessingPlugin extends AbstractDatastoreP
}
template.bind("processing-description", processingDescription);
template.bind("data-set", dataSet);
- template.bind("experiment", experiment);
+ if (withExperiment)
+ {
+ template.bind("experiment", experiment);
+ }
if (withSample)
{
template.bind("sample", sampleOrNull);
@@ -144,14 +150,14 @@ abstract public class AbstractDropboxProcessingPlugin extends AbstractDatastoreP
mailClient.sendEmailMessage(subject, template.createText(), null, null, eMailAddress);
}
- private Template getEMailMessageTemplate(boolean withError, boolean withSample)
+ private Template getEMailMessageTemplate(boolean withError, boolean withSample, boolean withExperiment)
{
return new Template(
(withError ? "Processing of data set ${data-set} failed.\nReason: ${error}"
: "Successfully processed data set ${data-set}.")
+ "\n\nProcessing details:\n"
+ "Description: ${processing-description}\n"
- + "Experiment: ${experiment}\n"
+ + (withExperiment ? "Experiment: ${experiment}\n" : "")
+ (withSample ? "Sample: ${sample}\n" : "")
+ "Started: ${start-time}.\n" + "Finished: ${end-time}.");
}
@@ -201,10 +207,18 @@ abstract public class AbstractDropboxProcessingPlugin extends AbstractDatastoreP
datasetInfo.setSampleCode(dataset.getSampleCode());
datasetInfo.setSpaceCode(dataset.getSpaceCode());
datasetInfo.setDataSetCode(dataset.getDataSetCode());
- ExperimentIdentifier expIdent =
- new ExperimentIdentifier(null, dataset.getSpaceCode(), dataset.getProjectCode(),
- dataset.getExperimentCode());
- datasetInfo.setExperimentIdentifier(expIdent);
+ if (dataset.getExperimentCode() != null)
+ {
+ ExperimentIdentifier expIdent =
+ new ExperimentIdentifier(null, dataset.getSpaceCode(), dataset.getProjectCode(),
+ dataset.getExperimentCode());
+ datasetInfo.setExperimentIdentifier(expIdent);
+ }
+ if (dataset.getSampleCode() != null)
+ {
+ SpaceIdentifier spaceIdentifier = new SpaceIdentifier(dataset.getSpaceCode());
+ datasetInfo.setSampleIdentifier(new SampleIdentifier(spaceIdentifier, dataset.getSampleCode()));
+ }
return datasetInfo;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/archiver/AbstractDataSetFileOperationsManager.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/archiver/AbstractDataSetFileOperationsManager.java
index 5d6187ea24c..1f4d65d59ba 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/archiver/AbstractDataSetFileOperationsManager.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/archiver/AbstractDataSetFileOperationsManager.java
@@ -91,7 +91,10 @@ public abstract class AbstractDataSetFileOperationsManager
{
AbstractExternalData dataSet = getService().tryGetDataSet(datasetDescription.getDataSetCode());
String experimentIdentifier = datasetDescription.getExperimentIdentifier();
- dataSet.setExperiment(getService().tryGetExperiment(ExperimentIdentifierFactory.parse(experimentIdentifier)));
+ if (experimentIdentifier != null)
+ {
+ dataSet.setExperiment(getService().tryGetExperiment(ExperimentIdentifierFactory.parse(experimentIdentifier)));
+ }
String sampleIdentifier = datasetDescription.getSampleIdentifier();
if (sampleIdentifier != null)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ExperimentBasedShareFinder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ExperimentBasedShareFinder.java
index da9b9daf483..64f5c0875b3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ExperimentBasedShareFinder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/ExperimentBasedShareFinder.java
@@ -42,15 +42,18 @@ public class ExperimentBasedShareFinder implements IShareFinder
@Override
public Share tryToFindShare(SimpleDataSetInformationDTO dataSet, List<Share> shares)
{
- String experimentIdentifier =
- new ExperimentIdentifier(null, dataSet.getSpaceCode(), dataSet.getProjectCode(),
- dataSet.getExperimentCode()).toString();
- for (Share share : shares)
+ if (dataSet.getExperimentCode() != null)
{
- if (share.getExperimentIdentifiers().contains(experimentIdentifier)
- && share.calculateFreeSpace() > dataSet.getDataSetSize())
+ String experimentIdentifier =
+ new ExperimentIdentifier(null, dataSet.getSpaceCode(), dataSet.getProjectCode(),
+ dataSet.getExperimentCode()).toString();
+ for (Share share : shares)
{
- return share;
+ if (share.getExperimentIdentifiers().contains(experimentIdentifier)
+ && share.calculateFreeSpace() > dataSet.getDataSetSize())
+ {
+ return share;
+ }
}
}
return null;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IdentifierAttributeMappingManager.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IdentifierAttributeMappingManager.java
index d0feefffc9a..e12b21f2652 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IdentifierAttributeMappingManager.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IdentifierAttributeMappingManager.java
@@ -270,12 +270,20 @@ public class IdentifierAttributeMappingManager
private Attributes tryGetExperimentAttributes(String spaceCode, String projectCode, String experimentCode)
{
+ if (experimentCode == null)
+ {
+ return null;
+ }
String identifier = new ExperimentIdentifier(null, spaceCode, projectCode, experimentCode).toString();
return getAttributesMap().get(identifier);
}
private Attributes tryGetProjectAttributes(String spaceCode, String projectCode)
{
+ if (projectCode == null)
+ {
+ return null;
+ }
String identifier = new ProjectIdentifier(null, spaceCode, projectCode).toString();
return getAttributesMap().get(identifier);
}
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 044e6ced80c..3e4b4c97aab 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -77,6 +77,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.OpenBISSessionHolder;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.util.LogRecordingUtils;
/**
@@ -486,9 +487,11 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
private final void checkSuccessEmailNotification(final Expectations expectations,
final DataSetInformation dataSet, final String dataSetCode, final String recipient)
{
+ SampleIdentifier sampleIdentifier = dataSet.getSampleIdentifier();
+ String code = sampleIdentifier != null ? sampleIdentifier.getSampleCode() :
+ dataSet.getExperimentIdentifier().getExperimentCode();
expectations.one(mailClient).sendMessage(
- String.format(DataSetRegistrationHelper.EMAIL_SUBJECT_TEMPLATE, dataSet
- .getExperimentIdentifier().getExperimentCode()),
+ String.format(DataSetRegistrationHelper.EMAIL_SUBJECT_TEMPLATE, code),
getNotificationEmailContent(dataSet, dataSetCode), null, null, recipient);
}
@@ -662,10 +665,8 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
assertEquals(false, isFinishedData1.exists());
assertLog("ERROR OPERATION.DataStrategyStore - "
+ "Incoming data set '<wd>/data1' claims to belong to experiment "
- + "'/GROUP1/PROJECT1/EXPERIMENT1' and sample identifier '/"
- + SAMPLE_CODE
- + "', "
- + "but according to the openBIS server there is no such sample for this experiment "
+ + "'/GROUP1/PROJECT1/EXPERIMENT1' and sample '/" + SAMPLE_CODE + "', "
+ + "but according to the openBIS server there is no such sample "
+ "(maybe it has been deleted?). We thus consider it invalid."
+ OSUtilities.LINE_SEPARATOR + "INFO OPERATION.FileRenamer - "
+ "Moving file 'data1' from '<wd>' to '<wd>/1/invalid/DataSetType_O1'.");
--
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