diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
index 3bec4d7aea7ca604af0dc1b84cba666e97d688b7..9188f312dd57ce6fc80b5256537d4db943fcc83c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
@@ -77,8 +78,9 @@ public class DefaultEntityOperationService<T extends DataSetInformation> impleme
List<NewExperiment> experimentRegistrations = details.getExperimentRegistrations();
List<SampleUpdatesDTO> sampleUpdates = details.getSampleUpdates();
List<NewSample> sampleRegistrations = details.getSampleRegistrations();
- List<NewExternalData> dataSetRegistrations = new ArrayList<NewExternalData>();
+ List<DataSetUpdatesDTO> dataSetUpdates = details.getDataSetUpdates();
+ List<NewExternalData> dataSetRegistrations = new ArrayList<NewExternalData>();
for (DataSetRegistrationInformation<?> dsRegistration : details.getDataSetRegistrations())
{
NewExternalData newExternalData = dsRegistration.getExternalData();
@@ -87,8 +89,8 @@ public class DefaultEntityOperationService<T extends DataSetInformation> impleme
return new ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails(
details.tryUserIdOrNull(), spaceRegistrations, projectRegistrations,
- experimentRegistrations, sampleUpdates,
- sampleRegistrations, dataSetRegistrations);
+ experimentRegistrations, sampleUpdates, sampleRegistrations, dataSetRegistrations,
+ dataSetUpdates);
}
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSet.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSet.java
index edc65c817ee6f8a3b7ba043c5f679f7a37558049..080a01a5fcaa33955f488d4a21fe6bf5d961293d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSet.java
@@ -16,105 +16,24 @@
package ch.systemsx.cisd.etlserver.registrator.api.v1;
-import java.util.List;
-
import ch.systemsx.cisd.openbis.generic.shared.Constants;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public interface IDataSet
+public interface IDataSet extends IDataSetUpdatable
{
- /**
- * Get the data set code of the data set
- *
- * @return The code of this data set.
- */
- public String getDataSetCode();
-
- /**
- * Get the experiment for this data set. This can only be null at initialization time, and will
- * be non-null for a valid data set.
- *
- * @return The experiment for this data set (will be non-null for a valid data set)
- */
- IExperimentImmutable getExperiment();
-
- /**
- * Set the experiment for this data set. The experiment may also be set by setting the sample.
- *
- * @param experiment The experiment for this data set. Need not actually be immutable, but the
- * immutable one is the supertype.
- */
- void setExperiment(IExperimentImmutable experiment);
-
- /**
- * Get the sample for this data set, if there is one.
- *
- * @return A sample or null.
- */
- ISampleImmutable getSample();
-
- /**
- * Set the sample for this data set. Will also set the experiment, since the sample must have an
- * experiment.
- *
- * @param sampleOrNull The sample to use. Need not actually be immutable, but the immutable one
- * is the supertype.
- */
- void setSample(ISampleImmutable sampleOrNull);
-
- /**
- * The file format type of the data set. Defaults to the default specified in
- * {@link FileFormatType}.
- * <p>
- * This property is undefined for container data sets.
- *
- * @return The code of the {@link FileFormatType} for this data set.
- */
- public String getFileFormatType();
-
- /**
- * Set the file format type.
- * <p>
- * This property is undefined for container data sets.
- *
- * @param fileFormatTypeCode The code of the desired {@link FileFormatType}.
- */
- public void setFileFormatType(String fileFormatTypeCode);
-
- /**
- * Return true if the data set is measured data. Defaults to true.
- *
- * @return True if the data set is measured data, false otherwise.
- */
- public boolean isMeasuredData();
/**
* Set whether the data is measured or not.
*/
public void setMeasuredData(boolean measuredData);
- /**
- * Get the data set type. This is only null during initialization and is non-null for a valid
- * data set.
- */
- public String getDataSetType();
-
/**
* Set the data set type.
*/
public void setDataSetType(String dataSetTypeCode);
- /**
- * Returns the speed hint. If it hasn't been set by {@link #setSpeedHint(int)} the default value
- * {@link Constants#DEFAULT_SPEED_HINT} will be returned.
- * <p>
- * This property is undefined for container data sets.
- */
- public int getSpeedHint();
-
/**
* Sets the speed hint for the data set. The speed hint is a negative or positive number with an
* absolute value less than or equal {@link Constants#MAX_SPEED}.
@@ -123,36 +42,11 @@ public interface IDataSet
* <code>speedHint</code>. A negative value means that the data set should be stored in a
* storage with speed <= <code>abs(speedHint)</code>. The speed hint might be ignored.
* <p>
+ * If no speed hint has been set the default value {@link Constants#DEFAULT_SPEED_HINT} is
+ * assumed.
+ * <p>
* This property is undefined for container data sets.
*/
public void setSpeedHint(int speedHint);
- /**
- * Get the value for a property.
- */
- public String getPropertyValue(String propertyCode);
-
- /**
- * Set the value for a property.
- */
- public void setPropertyValue(String propertyCode, String propertyValue);
-
- /** Sets the parents of the dataset. */
- public void setParentDatasets(List<String> parentDatasetCodes);
-
- /** Gets the parents of the dataset. */
- public List<String> getParentDatasets();
-
- // Methods relating to container data sets which contain other data sets
- /** Return true if this data set contains other data sets. */
- public boolean isContainerDataSet();
-
- /**
- * Get the codes for contained data sets. This is empty if {@link #isContainerDataSet()} returns
- * false.
- */
- public List<String> getContainedDataSetCodes();
-
- /** Set the codes for contained data sets. */
- public void setContainedDataSetCodes(List<String> containedDataSetCodes);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetImmutable.java
new file mode 100644
index 0000000000000000000000000000000000000000..259acceccd6d86bbd9cae2364ae0e2e7fbf6518c
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetImmutable.java
@@ -0,0 +1,99 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.etlserver.registrator.api.v1;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
+
+/**
+ * A data set that has already been stored in openBIS.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public interface IDataSetImmutable
+{
+ /**
+ * Get the data set code of the data set
+ *
+ * @return The code of this data set.
+ */
+ public String getDataSetCode();
+
+ /**
+ * Get the experiment for this data set. This can only be null at initialization time, and will
+ * be non-null for a valid data set.
+ *
+ * @return The experiment for this data set (will be non-null for a valid data set)
+ */
+ IExperimentImmutable getExperiment();
+
+ /**
+ * Get the sample for this data set, if there is one.
+ *
+ * @return A sample or null.
+ */
+ ISampleImmutable getSample();
+
+ /**
+ * The file format type of the data set. Defaults to the default specified in
+ * {@link FileFormatType}.
+ * <p>
+ * This property is undefined for container data sets.
+ *
+ * @return The code of the {@link FileFormatType} for this data set.
+ */
+ public String getFileFormatType();
+
+ /**
+ * Return true if the data set is measured data. Defaults to true.
+ *
+ * @return True if the data set is measured data, false otherwise.
+ */
+ public boolean isMeasuredData();
+
+ /**
+ * Get the data set type. This is only null during initialization and is non-null for a valid
+ * data set.
+ */
+ public String getDataSetType();
+
+ /**
+ * Returns the speed hint.
+ * <p>
+ * This property is undefined for container data sets.
+ */
+ public int getSpeedHint();
+
+ /**
+ * Get the value for a property.
+ */
+ public String getPropertyValue(String propertyCode);
+
+ /** Gets the parents of the dataset. */
+ public List<String> getParentDatasets();
+
+ /** Return true if this data set contains other data sets. */
+ public boolean isContainerDataSet();
+
+ /**
+ * Get the codes for contained data sets. This is empty if {@link #isContainerDataSet()} returns
+ * false.
+ */
+ public List<String> getContainedDataSetCodes();
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
index 6d5a2c885e6832baf29fb927a53fb179219ff822..59002bd77077012eb323a57a5c3c0d089bf7db03 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
@@ -39,7 +39,7 @@ public interface IDataSetRegistrationTransaction
IDataSet createNewDataSet();
/**
- * Create a new data set with the specified type.
+ * Create a new data set with the specified code.
*/
IDataSet createNewDataSet(String dataSetType);
@@ -47,6 +47,21 @@ public interface IDataSetRegistrationTransaction
* Create a new data set with the specified type and code.
*/
IDataSet createNewDataSet(String dataSetType, String dataSetCode);
+
+ /**
+ * Get a data set from the openBIS AS. Returns null if the data set does not exist.
+ *
+ * @return A data set or null
+ */
+ IDataSetImmutable getDataSet(String dataSetCode);
+
+ /**
+ * Get a data set from the openBIS AS for the purpose of modifying it. Returns null if the data
+ * set does not exist.
+ *
+ * @return A data set or null
+ */
+ IDataSetUpdatable getDataSetForUpdate(String dataSetCode);
/**
* Get a sample from the openBIS AS. Returns null if the sample does not exist.
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetUpdatable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetUpdatable.java
new file mode 100644
index 0000000000000000000000000000000000000000..509d323c239db160381956c0f02b7dd288c18af4
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetUpdatable.java
@@ -0,0 +1,65 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.etlserver.registrator.api.v1;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public interface IDataSetUpdatable extends IDataSetImmutable
+{
+
+ /**
+ * Set the experiment for this data set. The experiment may also be set by setting the sample.
+ *
+ * @param experiment The experiment for this data set. Need not actually be immutable, but the
+ * immutable one is the supertype.
+ */
+ void setExperiment(IExperimentImmutable experiment);
+
+ /**
+ * Set the sample for this data set. Will also set the experiment, since the sample must have an
+ * experiment.
+ *
+ * @param sampleOrNull The sample to use. Need not actually be immutable, but the immutable one
+ * is the supertype.
+ */
+ void setSample(ISampleImmutable sampleOrNull);
+
+ /**
+ * Set the file format type.
+ * <p>
+ * This property is undefined for container data sets.
+ *
+ * @param fileFormatTypeCode The code of the desired {@link FileFormatType}.
+ */
+ public void setFileFormatType(String fileFormatTypeCode);
+
+ /**
+ * Set the value for a property.
+ */
+ public void setPropertyValue(String propertyCode, String propertyValue);
+
+ /** Sets the parents of the dataset. */
+ public void setParentDatasets(List<String> parentDatasetCodes);
+
+ /** Set the codes for contained data sets. */
+ public void setContainedDataSetCodes(List<String> containedDataSetCodes);
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
index c572f792f8dddf166dde74d190055cbde7b65791..d2fdff508001368a2243d390bb02c94ef4a1deed 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
@@ -28,6 +28,8 @@ import ch.systemsx.cisd.etlserver.registrator.DataSetStorageAlgorithm;
import ch.systemsx.cisd.etlserver.registrator.DataSetStorageAlgorithmRunner;
import ch.systemsx.cisd.etlserver.registrator.IDataSetRegistrationDetailsFactory;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetImmutable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperiment;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
@@ -38,10 +40,12 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
@@ -92,7 +96,11 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
private final IDataSetRegistrationDetailsFactory<T> registrationDetailsFactory;
- private final ArrayList<DataSet<T>> registeredDataSets = new ArrayList<DataSet<T>>();
+ private final List<DataSet<T>> registeredDataSets =
+ new ArrayList<DataSet<T>>();
+
+ private final List<DataSetUpdatable> dataSetsToBeUpdated =
+ new ArrayList<DataSetUpdatable>();
private final List<Experiment> experimentsToBeRegistered = new ArrayList<Experiment>();
@@ -212,6 +220,32 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
return dataSet;
}
+ public IDataSetImmutable getDataSet(String dataSetCode)
+ {
+ ExternalData dataSet = openBisService.tryGetDataSet(dataSetCode);
+ if (dataSet == null)
+ {
+ return null;
+ } else
+ {
+ return new DataSetImmutable(dataSet);
+ }
+ }
+
+ public IDataSetUpdatable getDataSetForUpdate(String dataSetCode)
+ {
+ ExternalData dataSet = openBisService.tryGetDataSet(dataSetCode);
+ if (dataSet == null)
+ {
+ return null;
+ } else
+ {
+ DataSetUpdatable result = new DataSetUpdatable(dataSet);
+ dataSetsToBeUpdated.add(result);
+ return result;
+ }
+ }
+
public ISample getSampleForUpdate(String sampleIdentifierString)
{
SampleIdentifier sampleIdentifier =
@@ -402,6 +436,7 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
List<NewExperiment> experimentRegistrations = convertExperimentsToBeRegistered();
List<SampleUpdatesDTO> sampleUpdates = convertSamplesToBeUpdated();
List<NewSample> sampleRegistrations = convertSamplesToBeRegistered();
+ List<DataSetUpdatesDTO> dataSetUpdates = convertDataSetsToBeUpdated();
// experiment updates not yet supported
List<ExperimentUpdatesDTO> experimentUpdates = new ArrayList<ExperimentUpdatesDTO>();
@@ -409,7 +444,8 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
AtomicEntityOperationDetails<T> registrationDetails =
new AtomicEntityOperationDetails<T>(getUserId(), spaceRegistrations,
projectRegistrations, experimentUpdates, experimentRegistrations,
- sampleUpdates, sampleRegistrations, dataSetRegistrations);
+ sampleUpdates, sampleRegistrations, dataSetRegistrations,
+ dataSetUpdates);
return registrationDetails;
}
@@ -463,6 +499,16 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
return result;
}
+ private List<DataSetUpdatesDTO> convertDataSetsToBeUpdated()
+ {
+ List<DataSetUpdatesDTO> result = new ArrayList<DataSetUpdatesDTO>();
+ for (DataSetUpdatable dataSet : dataSetsToBeUpdated)
+ {
+ result.add(ConversionUtils.convertToDataSetUpdatesDTO(dataSet));
+ }
+ return result;
+ }
+
@Override
public boolean isCommitted()
{
@@ -474,6 +520,7 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
{
return false;
}
+
}
private static abstract class TerminalTransactionState<T extends DataSetInformation> extends
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ConversionUtils.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ConversionUtils.java
index baf34e3093f169e84b629f64abe74a3474b0112a..d2920bbd4b573b7ae03f58c78c8717f7ea1ef50a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ConversionUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ConversionUtils.java
@@ -29,6 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewContainerDataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewDataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
@@ -178,4 +179,10 @@ public class ConversionUtils
return new NewProject(apiProject.getProjectIdentifier(), apiProject.getDescription());
}
+ public static DataSetUpdatesDTO convertToDataSetUpdatesDTO(DataSetUpdatable dataSet)
+ {
+ // TODO KE: implement
+ return null;
+ }
+
}
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
new file mode 100644
index 0000000000000000000000000000000000000000..44a19dab346afa924c6462f6e3354a0514d0cb50
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetImmutable.java
@@ -0,0 +1,122 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
+
+import java.util.Collections;
+import java.util.List;
+
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetImmutable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.ISampleImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
+
+/**
+ * A data set that has already been stored in openBIS.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class DataSetImmutable implements IDataSetImmutable
+{
+ protected final ExternalData dataSet;
+
+ public DataSetImmutable(ExternalData dataSet)
+ {
+ this.dataSet = dataSet;
+ }
+
+ public String getDataSetCode()
+ {
+ return dataSet.getCode();
+ }
+
+ public IExperimentImmutable getExperiment()
+ {
+ return new ExperimentImmutable(dataSet.getExperiment());
+ }
+
+ 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);
+ }
+ }
+
+ public String getFileFormatType()
+ {
+ if (isContainerDataSet())
+ {
+ return null;
+ } else
+ {
+ return dataSet.tryGetAsDataSet().getFileFormatType().getCode();
+ }
+ }
+
+ public boolean isMeasuredData()
+ {
+ return dataSet.isDerived() == false;
+ }
+
+ public int getSpeedHint()
+ {
+ if (isContainerDataSet())
+ {
+ return Integer.MIN_VALUE;
+ } else
+ {
+ return dataSet.tryGetAsDataSet().getSpeedHint();
+ }
+ }
+
+ public String getDataSetType()
+ {
+ return dataSet.getDataSetType().getCode();
+ }
+
+ public String getPropertyValue(String propertyCode)
+ {
+ return EntityHelper.tryFindPropertyValue(dataSet, propertyCode);
+ }
+
+ public List<String> getParentDatasets()
+ {
+ return Code.extractCodes(dataSet.getParents());
+ }
+
+ public boolean isContainerDataSet()
+ {
+ return dataSet.isContainer();
+ }
+
+ public List<String> getContainedDataSetCodes()
+ {
+ if (isContainerDataSet())
+ {
+ return Code.extractCodes(dataSet.tryGetAsContainerDataSet().getContainedDataSets());
+ } else
+ {
+ return Collections.emptyList();
+ }
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
index e31481806c8ff08ba9766612746066b255ddedee..fecbacdba6f6ce22ec81725fdd7e3cc4c9b14a72 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
@@ -34,7 +34,9 @@ import ch.systemsx.cisd.etlserver.registrator.IDataSetOnErrorActionDecision.Erro
import ch.systemsx.cisd.etlserver.registrator.IDataSetRegistrationDetailsFactory;
import ch.systemsx.cisd.etlserver.registrator.IEntityOperationService;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetImmutable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransaction;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperiment;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
@@ -202,6 +204,17 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
return getStateAsLiveState().createNewDataSet(registrationDetails);
}
+ public IDataSetImmutable getDataSet(String dataSetCode)
+ {
+ return getStateAsLiveState().getDataSet(dataSetCode);
+ }
+
+ public IDataSetUpdatable getDataSetForUpdate(String dataSetCode)
+ {
+ return getStateAsLiveState().getDataSetForUpdate(dataSetCode);
+ }
+
+
public ISampleImmutable getSample(String sampleIdentifierString)
{
SampleIdentifier sampleIdentifier =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java
new file mode 100644
index 0000000000000000000000000000000000000000..a4eaa09b69902573608df0f628e2ad89596ab052
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetUpdatable.java
@@ -0,0 +1,126 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.ISampleImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
+
+/**
+ * A data set already existing in the openBIS database, that is changed as part of the registration
+ * process of another data set.
+ *
+ * @author Kaloyan Enimanev
+ */
+public class DataSetUpdatable extends DataSetImmutable implements IDataSetUpdatable
+{
+ public DataSetUpdatable(ExternalData dataSet)
+ {
+ super(dataSet);
+ }
+
+ public void setExperiment(IExperimentImmutable experiment)
+ {
+ if (experiment == null)
+ {
+ dataSet.setExperiment(null);
+ } else
+ {
+ ExperimentImmutable exp = (ExperimentImmutable) experiment;
+ dataSet.setExperiment(exp.getExperiment());
+ }
+ }
+
+ public void setSample(ISampleImmutable sampleOrNull)
+ {
+ if (sampleOrNull == null)
+ {
+ dataSet.setSample(null);
+ } else
+ {
+ SampleImmutable samp = (SampleImmutable) sampleOrNull;
+ dataSet.setSample(samp.getSample());
+ setExperiment(sampleOrNull.getExperiment());
+ }
+ }
+
+ public void setFileFormatType(String fileFormatTypeCode)
+ {
+ if (isContainerDataSet())
+ {
+ // ignore
+ } else
+ {
+ FileFormatType fileFormatType = new FileFormatType();
+ fileFormatType.setCode(fileFormatTypeCode);
+ dataSet.tryGetAsDataSet().setFileFormatType(fileFormatType);
+ }
+ }
+
+ public void setPropertyValue(String propertyCode, String propertyValue)
+ {
+ EntityHelper.createOrUpdateProperty(dataSet, propertyCode, propertyValue);
+ }
+
+ public void setParentDatasets(List<String> parentDatasetCodes)
+ {
+ List<ExternalData> dummyParents = createDummyDataSetsFromCodes(parentDatasetCodes);
+ dataSet.setParents(dummyParents);
+ }
+
+ public void setContainedDataSetCodes(List<String> containedDataSetCodes)
+ {
+ if (isContainerDataSet())
+ {
+ List<ExternalData> dummyDataSets = createDummyDataSetsFromCodes(containedDataSetCodes);
+ dataSet.tryGetAsContainerDataSet().setContainedDataSets(dummyDataSets);
+ } else
+ {
+ // ignored
+ }
+ }
+
+ private List<ExternalData> createDummyDataSetsFromCodes(List<String> containedDataSetCodes)
+ {
+ List<ExternalData> dummies = new ArrayList<ExternalData>();
+ if (containedDataSetCodes != null)
+ {
+ for (String code : containedDataSetCodes)
+ {
+ ExternalData dummy = new ExternalData();
+ dummy.setCode(code);
+ dummies.add(dummy);
+ }
+ }
+ return dummies;
+ }
+
+ /**
+ * Only visible to internal implementation classes. Not part of the public interface.
+ */
+ public ExternalData getExternalData()
+ {
+ return dataSet;
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/AtomicEntityOperationDetails.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/AtomicEntityOperationDetails.java
index 97a3896011ceccc3c116252806ae018bb12e6683..218a7ae9dc7dbebad8d4a307acc779b1917f31ba 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/AtomicEntityOperationDetails.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/AtomicEntityOperationDetails.java
@@ -24,6 +24,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
@@ -40,26 +41,29 @@ public class AtomicEntityOperationDetails<T extends DataSetInformation> implemen
// The userid on whose behalf the operations are done.
private final String userIdOrNull;
- private final ArrayList<NewSpace> spaceRegistrations;
+ private final List<NewSpace> spaceRegistrations;
- private final ArrayList<NewProject> projectRegistrations;
+ private final List<NewProject> projectRegistrations;
- private final ArrayList<ExperimentUpdatesDTO> experimentUpdates;
+ private final List<ExperimentUpdatesDTO> experimentUpdates;
- private final ArrayList<NewExperiment> experimentRegistrations;
+ private final List<NewExperiment> experimentRegistrations;
- private final ArrayList<SampleUpdatesDTO> sampleUpdates;
+ private final List<SampleUpdatesDTO> sampleUpdates;
- private final ArrayList<NewSample> sampleRegistrations;
+ private final List<NewSample> sampleRegistrations;
- private final ArrayList<DataSetRegistrationInformation<T>> dataSetRegistrations;
+ private final List<DataSetRegistrationInformation<T>> dataSetRegistrations;
+
+ private final List<DataSetUpdatesDTO> dataSetUpdates;
public AtomicEntityOperationDetails(String userIdOrNull, List<NewSpace> spaceRegistrations,
List<NewProject> projectRegistrations,
List<ExperimentUpdatesDTO> experimentUpdates,
List<NewExperiment> experimentRegistrations, List<SampleUpdatesDTO> sampleUpdates,
List<NewSample> sampleRegistrations,
- List<DataSetRegistrationInformation<T>> dataSetRegistrations)
+ List<DataSetRegistrationInformation<T>> dataSetRegistrations,
+ List<DataSetUpdatesDTO> dataSetUpdates)
{
this.userIdOrNull = userIdOrNull;
this.spaceRegistrations = new ArrayList<NewSpace>(spaceRegistrations);
@@ -70,6 +74,7 @@ public class AtomicEntityOperationDetails<T extends DataSetInformation> implemen
this.sampleRegistrations = new ArrayList<NewSample>(sampleRegistrations);
this.dataSetRegistrations =
new ArrayList<DataSetRegistrationInformation<T>>(dataSetRegistrations);
+ this.dataSetUpdates = new ArrayList<DataSetUpdatesDTO>(dataSetUpdates);
}
public String tryUserIdOrNull()
@@ -77,37 +82,42 @@ public class AtomicEntityOperationDetails<T extends DataSetInformation> implemen
return userIdOrNull;
}
- public ArrayList<ExperimentUpdatesDTO> getExperimentUpdates()
+ public List<ExperimentUpdatesDTO> getExperimentUpdates()
{
return experimentUpdates;
}
- public ArrayList<NewExperiment> getExperimentRegistrations()
+ public List<NewExperiment> getExperimentRegistrations()
{
return experimentRegistrations;
}
- public ArrayList<SampleUpdatesDTO> getSampleUpdates()
+ public List<SampleUpdatesDTO> getSampleUpdates()
{
return sampleUpdates;
}
- public ArrayList<NewSample> getSampleRegistrations()
+ public List<NewSample> getSampleRegistrations()
{
return sampleRegistrations;
}
- public ArrayList<DataSetRegistrationInformation<T>> getDataSetRegistrations()
+ public List<DataSetRegistrationInformation<T>> getDataSetRegistrations()
{
return dataSetRegistrations;
}
- public ArrayList<NewSpace> getSpaceRegistrations()
+ public List<DataSetUpdatesDTO> getDataSetUpdates()
+ {
+ return dataSetUpdates;
+ }
+
+ public List<NewSpace> getSpaceRegistrations()
{
return spaceRegistrations;
}
- public ArrayList<NewProject> getProjectRegistrations()
+ public List<NewProject> getProjectRegistrations()
{
return projectRegistrations;
}
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 4c77907a26804576db5c71b4111150648ad45841..6d86c4aaccf6dfa79a31634cfbdf63d5a612bb36 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
@@ -37,6 +37,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSpace;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -160,7 +161,7 @@ public class EncapsulatedOpenBISServiceTest
new AtomicEntityOperationDetails(null, Arrays.<NewSpace> asList(),
Arrays.<NewProject> asList(), Arrays.<NewExperiment> asList(),
Arrays.<SampleUpdatesDTO> asList(), Arrays.<NewSample> asList(),
- Arrays.asList(data));
+ Arrays.asList(data), Arrays.<DataSetUpdatesDTO> asList());
context.checking(new Expectations()
{
{
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploader.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploader.java
index 3648117dea1aacba62da7945989e43fc334abe42..01743c09a6609c4a1a5972bd79286d3bc3f12cd8 100644
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploader.java
+++ b/eu_basysbio/source/java/eu/basysbio/cisd/dss/IDataSetUploader.java
@@ -21,8 +21,6 @@ import java.io.File;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
- * TODO KE : How is this different from ch.systemsx.cisd.etlserver.IDataSetUploader ?
- *
* @author Franz-Josef Elmer
*/
interface IDataSetUploader
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 9e1c73081edab38945bcb49923edd2049a2e8a7e..7fc6b6cadd29e5b8d97700f9038bdb427590f444 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
@@ -93,6 +93,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetShareId;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
@@ -632,7 +633,8 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
assert sessionToken != null : "Unspecified session token.";
assert newSample != null : "Unspecified new sample.";
- SamplePE samplePE = registerSampleInternal(sessionToken, newSample, userIDOrNull);
+ final Session session = getSession(sessionToken);
+ SamplePE samplePE = registerSampleInternal(session, newSample, userIDOrNull);
return samplePE.getId();
}
@@ -963,12 +965,11 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
assert newSample != null : "Unspecified new sample.";
// Register the Sample
- SamplePE samplePE = registerSampleInternal(sessionToken, newSample, userIdOrNull);
+ final Session session = getSession(sessionToken);
+ SamplePE samplePE = registerSampleInternal(session, newSample, userIdOrNull);
// Register the data set
registerDataSetInternal(sessionToken, externalData, samplePE);
-
- final Session session = getSession(sessionToken);
Sample result =
SampleTranslator.translate(Collections.singletonList(samplePE),
session.getBaseIndexURL()).get(0);
@@ -1030,15 +1031,15 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
assert dataSetCode != null : "Data set code not specified.";
}
- private SamplePE registerSampleInternal(String sessionToken, NewSample newSample,
+ private SamplePE registerSampleInternal(Session session, NewSample newSample,
String userIdOrNull)
{
- final Session session = getSession(sessionToken);
final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
sampleBO.define(newSample);
if (userIdOrNull != null)
{
- sampleBO.getSample().setRegistrator(getOrCreatePerson(sessionToken, userIdOrNull));
+ sampleBO.getSample().setRegistrator(
+ getOrCreatePerson(session.getSessionToken(), userIdOrNull));
}
sampleBO.save();
SamplePE samplePE = sampleBO.getSample();
@@ -1084,24 +1085,27 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
public AtomicEntityOperationResult performEntityOperations(String sessionToken,
AtomicEntityOperationDetails operationDetails)
{
+ final Session session = getSession(sessionToken);
- List<Space> spacesCreated = createSpaces(sessionToken, operationDetails);
+ List<Space> spacesCreated = createSpaces(session, operationDetails);
- List<Project> projectsCreated = createProjects(sessionToken, operationDetails);
+ List<Project> projectsCreated = createProjects(session, operationDetails);
- List<Experiment> experimentsCreated = createExperiments(sessionToken, operationDetails);
+ List<Experiment> experimentsCreated = createExperiments(session, operationDetails);
- List<Sample> samplesCreated = createSamples(sessionToken, operationDetails);
+ List<Sample> samplesCreated = createSamples(session, operationDetails);
- List<Sample> samplesUpdated = updateSamples(sessionToken, operationDetails);
+ List<Sample> samplesUpdated = updateSamples(session, operationDetails);
- List<ExternalData> dataSetsCreated = createDataSets(sessionToken, operationDetails);
+ List<ExternalData> dataSetsCreated = createDataSets(session, operationDetails);
+
+ List<ExternalData> dataSetsUpdated = updateDataSets(session, operationDetails);
return new AtomicEntityOperationResult(spacesCreated, projectsCreated, experimentsCreated,
- samplesUpdated, samplesCreated, dataSetsCreated);
+ samplesUpdated, samplesCreated, dataSetsCreated, dataSetsUpdated);
}
- private List<Space> createSpaces(String sessionToken,
+ private List<Space> createSpaces(Session session,
AtomicEntityOperationDetails operationDetails)
{
ArrayList<SpacePE> spacePEsCreated = new ArrayList<SpacePE>();
@@ -1109,24 +1113,23 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
for (NewSpace newSpace : newSpaces)
{
SpacePE spacePE =
- registerSpaceInternal(sessionToken, newSpace,
+ registerSpaceInternal(session, newSpace,
operationDetails.tryUserIdOrNull());
spacePEsCreated.add(spacePE);
}
return GroupTranslator.translate(spacePEsCreated);
}
- private SpacePE registerSpaceInternal(String sessionToken, NewSpace newSpace,
+ private SpacePE registerSpaceInternal(Session session, NewSpace newSpace,
String registratorUserIdOrNull)
{
// create space
- Session session = getSession(sessionToken);
IGroupBO groupBO = businessObjectFactory.createGroupBO(session);
groupBO.define(newSpace.getCode(), newSpace.getDescription());
if (registratorUserIdOrNull != null)
{
groupBO.getGroup().setRegistrator(
- getOrCreatePerson(sessionToken, registratorUserIdOrNull));
+ getOrCreatePerson(session.getSessionToken(), registratorUserIdOrNull));
}
groupBO.save();
@@ -1149,7 +1152,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
}
- private List<Project> createProjects(String sessionToken,
+ private List<Project> createProjects(Session session,
AtomicEntityOperationDetails operationDetails)
{
ArrayList<ProjectPE> projectPEsCreated = new ArrayList<ProjectPE>();
@@ -1157,17 +1160,16 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
for (NewProject newProject : newProjects)
{
ProjectPE projectPE =
- registerProjectInternal(sessionToken, newProject,
+ registerProjectInternal(session, newProject,
operationDetails.tryUserIdOrNull());
projectPEsCreated.add(projectPE);
}
return ProjectTranslator.translate(projectPEsCreated);
}
- private ProjectPE registerProjectInternal(String sessionToken, NewProject newProject,
+ private ProjectPE registerProjectInternal(Session session, NewProject newProject,
String registratorUserIdOrNull)
{
- Session session = getSession(sessionToken);
IProjectBO projectBO = businessObjectFactory.createProjectBO(session);
ProjectIdentifier identifier =
new ProjectIdentifierFactory(newProject.getIdentifier()).createIdentifier();
@@ -1175,14 +1177,14 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
if (registratorUserIdOrNull != null)
{
projectBO.getProject().setRegistrator(
- getOrCreatePerson(sessionToken, registratorUserIdOrNull));
+ getOrCreatePerson(session.getSessionToken(), registratorUserIdOrNull));
}
projectBO.save();
return projectBO.getProject();
}
- private List<Sample> createSamples(String sessionToken,
+ private List<Sample> createSamples(Session session,
AtomicEntityOperationDetails operationDetails)
{
ArrayList<SamplePE> samplePEsCreated = new ArrayList<SamplePE>();
@@ -1190,18 +1192,16 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
for (NewSample newSample : newSamples)
{
SamplePE samplePE =
- registerSampleInternal(sessionToken, newSample,
+ registerSampleInternal(session, newSample,
operationDetails.tryUserIdOrNull());
samplePEsCreated.add(samplePE);
}
- final Session session = getSession(sessionToken);
return SampleTranslator.translate(samplePEsCreated, session.getBaseIndexURL());
}
- private List<Sample> updateSamples(String sessionToken,
+ private List<Sample> updateSamples(Session session,
AtomicEntityOperationDetails operationDetails)
{
- final Session session = getSession(sessionToken);
ArrayList<SamplePE> samplePEsUpdated = new ArrayList<SamplePE>();
List<SampleUpdatesDTO> sampleUpdates = operationDetails.getSampleUpdates();
for (SampleUpdatesDTO sampleUpdate : sampleUpdates)
@@ -1212,12 +1212,11 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return SampleTranslator.translate(samplePEsUpdated, session.getBaseIndexURL());
}
- private List<ExternalData> createDataSets(String sessionToken,
+ private List<ExternalData> createDataSets(Session session,
AtomicEntityOperationDetails operationDetails)
{
- final Session session = getSession(sessionToken);
ArrayList<DataPE> dataSetsCreated = new ArrayList<DataPE>();
- ArrayList<? extends NewExternalData> dataSetRegistrations =
+ List<? extends NewExternalData> dataSetRegistrations =
operationDetails.getDataSetRegistrations();
ArrayList<NewContainerDataSet> containerRegistrations =
@@ -1242,6 +1241,25 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return DataSetTranslator.translate(dataSetsCreated, "", session.getBaseIndexURL());
}
+ private List<ExternalData> updateDataSets(Session session,
+ AtomicEntityOperationDetails operationDetails)
+ {
+ List<DataPE> dataSetsUpdated = new ArrayList<DataPE>();
+ for (DataSetUpdatesDTO dataSet : operationDetails.getDataSetUpdates())
+ {
+ DataPE updatedDataSet = updateDataSetInternal(session, dataSet);
+ dataSetsUpdated.add(updatedDataSet);
+ }
+ return DataSetTranslator.translate(dataSetsUpdated, "", session.getBaseIndexURL());
+ }
+
+ private DataPE updateDataSetInternal(Session session, DataSetUpdatesDTO dataSet)
+ {
+ IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.update(dataSet);
+ return dataBO.getData();
+ }
+
private void registerDatasetInternal(final Session session, ArrayList<DataPE> dataSetsCreated,
NewExternalData dataSet)
{
@@ -1258,17 +1276,18 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
dataSetsCreated.add(dataBO.getData());
}
- private ArrayList<Experiment> createExperiments(String sessionToken,
+ private ArrayList<Experiment> createExperiments(Session session,
AtomicEntityOperationDetails operationDetails)
{
ArrayList<Experiment> experimentsCreated = new ArrayList<Experiment>();
List<NewExperiment> experimentRegistrations = operationDetails.getExperimentRegistrations();
for (NewExperiment experiment : experimentRegistrations)
{
- registerExperiment(sessionToken, experiment);
+ registerExperiment(session.getSessionToken(), experiment);
ExperimentIdentifier experimentIdentifier =
new ExperimentIdentifierFactory(experiment.getIdentifier()).createIdentifier();
- experimentsCreated.add(tryToGetExperiment(sessionToken, experimentIdentifier));
+ experimentsCreated.add(tryToGetExperiment(session.getSessionToken(),
+ experimentIdentifier));
}
return experimentsCreated;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
index 64d2c7fd338a5477437815fe82e45375edb646d3..ab5f5ede932a0ef5b554b39d92b46005144835ac 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
@@ -43,24 +43,27 @@ public class AtomicEntityOperationDetails implements Serializable
// This is always an empty list, since it is not currently possible to update experiments from
// the DSS
- private final ArrayList<ExperimentUpdatesDTO> experimentUpdates;
+ private final List<ExperimentUpdatesDTO> experimentUpdates;
- private final ArrayList<NewSpace> spaceRegistrations;
+ private final List<NewSpace> spaceRegistrations;
- private final ArrayList<NewProject> projectRegistrations;
+ private final List<NewProject> projectRegistrations;
- private final ArrayList<NewExperiment> experimentRegistrations;
+ private final List<NewExperiment> experimentRegistrations;
- private final ArrayList<SampleUpdatesDTO> sampleUpdates;
+ private final List<SampleUpdatesDTO> sampleUpdates;
- private final ArrayList<NewSample> sampleRegistrations;
+ private final List<NewSample> sampleRegistrations;
- private final ArrayList<? extends NewExternalData> dataSetRegistrations;
+ private final List<? extends NewExternalData> dataSetRegistrations;
+ private final List<DataSetUpdatesDTO> dataSetUpdates;
+
public AtomicEntityOperationDetails(String userIdOrNull, List<NewSpace> spaceRegistrations,
List<NewProject> projectRegistrations, List<NewExperiment> experimentRegistrations,
List<SampleUpdatesDTO> sampleUpdates, List<NewSample> sampleRegistrations,
- List<? extends NewExternalData> dataSetRegistrations)
+ List<? extends NewExternalData> dataSetRegistrations,
+ List<DataSetUpdatesDTO> dataSetUpdates)
{
this.userIdOrNull = userIdOrNull;
this.spaceRegistrations = new ArrayList<NewSpace>(spaceRegistrations);
@@ -70,6 +73,7 @@ public class AtomicEntityOperationDetails implements Serializable
this.sampleUpdates = new ArrayList<SampleUpdatesDTO>(sampleUpdates);
this.sampleRegistrations = new ArrayList<NewSample>(sampleRegistrations);
this.dataSetRegistrations = new ArrayList<NewExternalData>(dataSetRegistrations);
+ this.dataSetUpdates = new ArrayList<DataSetUpdatesDTO>(dataSetUpdates);
}
public String tryUserIdOrNull()
@@ -77,37 +81,42 @@ public class AtomicEntityOperationDetails implements Serializable
return userIdOrNull;
}
- public ArrayList<ExperimentUpdatesDTO> getExperimentUpdates()
+ public List<ExperimentUpdatesDTO> getExperimentUpdates()
{
return experimentUpdates;
}
- public ArrayList<NewExperiment> getExperimentRegistrations()
+ public List<NewExperiment> getExperimentRegistrations()
{
return experimentRegistrations;
}
- public ArrayList<SampleUpdatesDTO> getSampleUpdates()
+ public List<SampleUpdatesDTO> getSampleUpdates()
{
return sampleUpdates;
}
- public ArrayList<NewSample> getSampleRegistrations()
+ public List<NewSample> getSampleRegistrations()
{
return sampleRegistrations;
}
- public ArrayList<? extends NewExternalData> getDataSetRegistrations()
+ public List<? extends NewExternalData> getDataSetRegistrations()
{
return dataSetRegistrations;
}
- public ArrayList<NewSpace> getSpaceRegistrations()
+ public List<DataSetUpdatesDTO> getDataSetUpdates()
+ {
+ return dataSetUpdates;
+ }
+
+ public List<NewSpace> getSpaceRegistrations()
{
return spaceRegistrations;
}
- public ArrayList<NewProject> getProjectRegistrations()
+ public List<NewProject> getProjectRegistrations()
{
return projectRegistrations;
}
@@ -124,7 +133,7 @@ public class AtomicEntityOperationDetails implements Serializable
sb.append("sampleUpdates", sampleUpdates);
sb.append("sampleRegistrations", sampleRegistrations);
sb.append("dataSetRegistrations", dataSetRegistrations);
+ sb.append("dataSetUpdates", dataSetUpdates);
return sb.toString();
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationResult.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationResult.java
index af90e30306ac0349b1a93d669b5470847809b5c4..1e7bf47897ec11a350db9853d6d76e6507979251 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationResult.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationResult.java
@@ -50,17 +50,20 @@ public class AtomicEntityOperationResult implements Serializable
private final ArrayList<ExternalData> dataSetsCreated;
+ private final ArrayList<ExternalData> dataSetsUpdated;
+
public AtomicEntityOperationResult()
{
this(Collections.<Space> emptyList(), Collections.<Project> emptyList(),
Collections.<Experiment> emptyList(), Collections.<Sample> emptyList(), Collections
- .<Sample> emptyList(), Collections.<ExternalData> emptyList());
+ .<Sample> emptyList(), Collections.<ExternalData> emptyList(), Collections
+ .<ExternalData> emptyList());
}
public AtomicEntityOperationResult(List<Space> spacesCreated, List<Project> projectsCreated,
- List<Experiment> experimentsCreated,
- List<Sample> samplesUpdated, List<Sample> samplesCreated,
- List<ExternalData> dataSetsCreated)
+ List<Experiment> experimentsCreated, List<Sample> samplesUpdated,
+ List<Sample> samplesCreated, List<ExternalData> dataSetsCreated,
+ List<ExternalData> dataSetsUpdated)
{
this.spacesCreated = new ArrayList<Space>(spacesCreated);
this.projectsCreated = new ArrayList<Project>(projectsCreated);
@@ -69,6 +72,7 @@ public class AtomicEntityOperationResult implements Serializable
this.samplesUpdated = new ArrayList<Sample>(samplesUpdated);
this.samplesCreated = new ArrayList<Sample>(samplesCreated);
this.dataSetsCreated = new ArrayList<ExternalData>(dataSetsCreated);
+ this.dataSetsUpdated = new ArrayList<ExternalData>(dataSetsUpdated);
}
public ArrayList<Experiment> getExperimentsUpdated()
@@ -96,6 +100,11 @@ public class AtomicEntityOperationResult implements Serializable
return dataSetsCreated;
}
+ public ArrayList<ExternalData> getDataSetsUpdated()
+ {
+ return dataSetsUpdated;
+ }
+
public ArrayList<Space> getSpacesCreated()
{
return spacesCreated;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUpdatesDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUpdatesDTO.java
index 448978744a695b2072617efab552dd67adaad24b..b12fc1907881aeccde85ca1d1d2e602c17ac0c5c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUpdatesDTO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUpdatesDTO.java
@@ -52,4 +52,9 @@ public class DataSetUpdatesDTO extends BasicDataSetUpdates
this.experimentIdentifierOrNull = experimentIdentifierOrNull;
}
+ @Override
+ public String toString()
+ {
+ return getDatasetId().toString();
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewDataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewDataSet.java
index 74d11fba1a0201388d628cbc11c7a59f5aa819b7..8563ca095b40ad5622c4bc95cef6961af2aac022 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewDataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewDataSet.java
@@ -23,6 +23,7 @@ public class NewDataSet extends NewExternalData
{
private static final long serialVersionUID = 1L;
+ // TODO KE: Sekhar, should we delete the dead code ?!
// The following fields and methods should eventually be moved here, but it's too difficult to
// do this now.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
index d77ba062187297e2e31426b2d308016fa7ae9201..818cbfb4b9502a148505bcc76e61e54e6e166c15 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
@@ -1373,17 +1373,6 @@ public final class CommonServerTest extends AbstractServerTestCase
context.assertIsSatisfied();
}
- private ExternalDataPE createDataSet(String code, String type)
- {
- ExternalDataPE externalData = new ExternalDataPE();
- externalData.setCode(code);
- DataSetTypePE dataSetType = new DataSetTypePE();
- dataSetType.setCode(type);
- dataSetType.setDatabaseInstance(homeDatabaseInstance);
- externalData.setDataSetType(dataSetType);
- return externalData;
- }
-
@Test
public void testUploadDataSets()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
index f8aa3466495fdd32041fa3ce52012f0ca62c969d..62e2d313715d917ddaabd33084cca89ede988cf4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
@@ -64,7 +64,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataStoreBuild
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
@@ -912,6 +914,13 @@ public class ETLServiceTest extends AbstractServerTestCase
externalData.setMeasured(true);
externalData.setSampleIdentifierOrNull(newSampleIdentifier);
+ final String updatedDataSetCode = "updateDataSetCode";
+ final DataSetUpdatesDTO dataSetUpdate = new DataSetUpdatesDTO();
+ dataSetUpdate.setDatasetId(CommonTestUtils.TECH_ID);
+ dataSetUpdate.setFileFormatTypeCode("new-file-format");
+ dataSetUpdate.setModifiedContainedDatasetCodesOrNull(new String[]
+ { "c1", "c2" });
+
context.checking(new Expectations()
{
{
@@ -961,12 +970,26 @@ public class ETLServiceTest extends AbstractServerTestCase
}
});
+ context.checking(new Expectations()
+ {
+ {
+ exactly(1).of(boFactory).createDataBO(SESSION);
+ will(returnValue(dataBO));
+
+ one(dataBO).update(dataSetUpdate);
+ one(dataBO).getData();
+ final DataPE updatedDataSet = createDataSet(updatedDataSetCode, "type");
+ will(returnValue(updatedDataSet));
+ }
+ });
+
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(null, new ArrayList<NewSpace>(),
new ArrayList<NewProject>(), new ArrayList<NewExperiment>(),
Collections.singletonList(sampleUpdate),
Collections.singletonList(newSample),
- Collections.singletonList(externalData));
+ Collections.singletonList(externalData),
+ Collections.singletonList(dataSetUpdate));
AtomicEntityOperationResult result =
createService().performEntityOperations(SESSION_TOKEN, details);
@@ -979,6 +1002,7 @@ public class ETLServiceTest extends AbstractServerTestCase
assertEquals(newSample.getIdentifier(), result.getSamplesCreated().get(0).getIdentifier());
assertEquals(experiment.getIdentifier(), result.getSamplesCreated().get(0).getExperiment()
.getIdentifier());
+ assertEquals(updatedDataSetCode, result.getDataSetsUpdated().get(0).getCode());
context.assertIsSatisfied();
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
index 073a00327261dea55bff7440825536fb6c36007b..190fac09602cf2fea4c71f646597dfbe1e1c9f3b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
@@ -70,9 +70,12 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IVocabularyDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.IPermIdDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DisplaySettings;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.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.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -368,4 +371,17 @@ public abstract class AbstractServerTestCase extends AssertJUnit
newExperiment.setSamples(samples);
return newExperiment;
}
+
+ protected ExternalDataPE createDataSet(String code, String type)
+ {
+ ExternalDataPE externalData = new ExternalDataPE();
+ externalData.setCode(code);
+ DataSetTypePE dataSetType = new DataSetTypePE();
+ dataSetType.setCode(type);
+ dataSetType.setDatabaseInstance(homeDatabaseInstance);
+ externalData.setDataSetType(dataSetType);
+ externalData.setDataStore(new DataStorePE());
+ return externalData;
+ }
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
index f2a31cf8099ff0d6a04696d818a2965d5e310ecd..bcde99654f13964f64dc0927e77910b53c7b71ad 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationDetailsTest.java
@@ -17,11 +17,14 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.util.ArrayList;
+import java.util.List;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
@@ -62,10 +65,15 @@ public class AtomicEntityOperationDetailsTest extends AssertJUnit
.createIdentifier());
dataSetRegistrations.add(newExternalData);
+ List<DataSetUpdatesDTO> dataSetUpdates = new ArrayList<DataSetUpdatesDTO>();
+ DataSetUpdatesDTO dataSetUpdate = new DataSetUpdatesDTO();
+ dataSetUpdate.setDatasetId(new TechId(1L));
+ dataSetUpdates.add(dataSetUpdate);
+
AtomicEntityOperationDetails details =
new AtomicEntityOperationDetails(null, spaceRegistrations, projectRegistrations,
experimentRegistrations, sampleUpdates, sampleRegistrations,
- dataSetRegistrations);
+ dataSetRegistrations, dataSetUpdates);
assertEquals(
"AtomicEntityOperationDetails[userIdOrNull=<null>"
@@ -75,7 +83,8 @@ public class AtomicEntityOperationDetailsTest extends AssertJUnit
+ ",experimentRegistrations=[/SPACE/PROJECT/EXP-ID1, /SPACE/PROJECT/EXP-ID2]"
+ ",sampleUpdates=[]"
+ ",sampleRegistrations=[/SPACE/SAMPLE-ID1, /SPACE/SAMPLE-ID2]"
- + ",dataSetRegistrations=[NewExternalData[code=DATA-SET-CODE,type=<null>,fileFormat=<null>,properties=[]]]]",
+ + ",dataSetRegistrations=[NewExternalData[code=DATA-SET-CODE,type=<null>,fileFormat=<null>,properties=[]]]"
+ + ",dataSetUpdates=[1]]",
details.toString());
}