From 28af1bf5fcf0adbe1d19dac5c255959ecae6e9e0 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Wed, 18 May 2011 08:14:14 +0000
Subject: [PATCH] [LMS-2104] fixed translation of virtual data sets and got rid
of ExternalDataTranslator (DataSetTranslator is used instead)
SVN: 21356
---
.../ArchivingPostRegistrationTask.java | 29 +-
.../dss/generic/server/UploadingCommand.java | 31 +-
.../generic/server/UploadingCommandTest.java | 6 +-
.../openbis/generic/server/ETLService.java | 1 +
.../shared/translator/DataSetTranslator.java | 24 +-
.../translator/ExternalDataTranslator.java | 322 ------------------
.../web/server/CommonClientServiceTest.java | 4 +-
.../generic/server/CommonServerTest.java | 6 +-
...orTest.java => DataSetTranslatorTest.java} | 12 +-
.../translator/SimpleDataSetHelperTest.java | 21 +-
.../server/logic/PlateContentLoader.java | 4 +-
11 files changed, 76 insertions(+), 384 deletions(-)
delete mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
rename openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/{ExternalDataTranslatorTest.java => DataSetTranslatorTest.java} (95%)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/ArchivingPostRegistrationTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/ArchivingPostRegistrationTask.java
index c4073b06168..328725e8fdc 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/ArchivingPostRegistrationTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/postregistration/ArchivingPostRegistrationTask.java
@@ -39,7 +39,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatasetLocation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
/**
* A post-registration task that archives datasets.
@@ -71,7 +71,7 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
{
return new Executor(dataSetCode);
}
-
+
private final class Executor implements IPostRegistrationTaskExecutor
{
private final String dataSetCode;
@@ -129,7 +129,8 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
String failedMessage =
String.format("Eager archiving of dataset '%s' has failed. \n", dataSetCode);
message.append(failedMessage);
- for (Status status : processingStatus.getErrorStatuses()) {
+ for (Status status : processingStatus.getErrorStatuses())
+ {
if (status.tryGetErrorMessage() != null)
{
message.append("Error encountered : " + status.tryGetErrorMessage());
@@ -140,7 +141,7 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
String.format("If you wish to archive the dataset in the future, "
+ "you can configure an '%s'.", AutoArchiverTask.class.getSimpleName());
message.append(footer);
-
+
notificationLog.error(message);
}
@@ -161,13 +162,13 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
}
ExternalData data = dataList.get(0);
- return ExternalDataTranslator.translateToDescription(data);
+ return DataSetTranslator.translateToDescription(data);
}
-
private static ArchiverTaskContext createArchiverContext()
{
- return new ArchiverTaskContext(ServiceProvider.getDataStoreService().getDataSetDirectoryProvider());
+ return new ArchiverTaskContext(ServiceProvider.getDataStoreService()
+ .getDataSetDirectoryProvider());
}
private static class ArchivingCleanupTask implements ICleanupTask
@@ -184,14 +185,16 @@ public class ArchivingPostRegistrationTask extends AbstractPostRegistrationTask
public void cleanup(ISimpleLogger logger)
{
IEncapsulatedOpenBISService openBISService = ServiceProvider.getOpenBISService();
- boolean statusUpdated = openBISService
- .compareAndSetDataSetStatus(dataSetCode, BACKUP_PENDING, AVAILABLE, false);
-
- if (statusUpdated == false) {
- // invalid data set status, do not continue
+ boolean statusUpdated =
+ openBISService.compareAndSetDataSetStatus(dataSetCode, BACKUP_PENDING,
+ AVAILABLE, false);
+
+ if (statusUpdated == false)
+ {
+ // invalid data set status, do not continue
return;
}
-
+
IArchiverPlugin archiver = ServiceProvider.getDataStoreService().getArchiverPlugin();
DatasetDescription dataSet = tryGetDatasetDescription(dataSetCode, openBISService);
if (archiver != null && dataSet != null)
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 107a12581a4..fdf4ebceba0 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
@@ -58,7 +58,7 @@ 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.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
import de.schlichtherle.util.zip.ZipEntry;
import de.schlichtherle.util.zip.ZipOutputStream;
@@ -72,11 +72,11 @@ class UploadingCommand implements IDataSetCommand
{
private static final long serialVersionUID = 1L;
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, UploadingCommand.class);
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ UploadingCommand.class);
- private static final Logger notificationLog =
- LogFactory.getLogger(LogCategory.NOTIFY, UploadingCommand.class);
+ private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY,
+ UploadingCommand.class);
private final class ProgressListener implements IProgressListener
{
@@ -139,8 +139,8 @@ class UploadingCommand implements IDataSetCommand
private static final char DELIM = '\t';
- private static final DateFormat DATE_FORMAT_PATTERN =
- new SimpleDateFormat("yyyy-MM-dd HH:mm:ss Z");
+ private static final DateFormat DATE_FORMAT_PATTERN = new SimpleDateFormat(
+ "yyyy-MM-dd HH:mm:ss Z");
private final StringBuilder builder = new StringBuilder();
@@ -416,7 +416,7 @@ class UploadingCommand implements IDataSetCommand
assert dataSet != null : "container datasets are currently not supported by DSS client";
DatasetDescription dataSetDescription =
- ExternalDataTranslator.translateToDescription(dataSet);
+ DataSetTranslator.translateToDescription(dataSet);
File dataSetFile = dataSetDirectoryProvider.getDataSetDirectory(dataSetDescription);
if (dataSetFile.exists() == false)
{
@@ -426,13 +426,14 @@ class UploadingCommand implements IDataSetCommand
String newRootPath = createRootPath(dataSet);
try
{
- addEntry(zipOutputStream, newRootPath + "/meta-data.tsv", System
- .currentTimeMillis(), new ByteArrayInputStream(createMetaData(dataSet)
- .getBytes()));
+ addEntry(zipOutputStream, newRootPath + "/meta-data.tsv",
+ System.currentTimeMillis(),
+ new ByteArrayInputStream(createMetaData(dataSet).getBytes()));
} catch (IOException ex)
{
- notificationLog.error("Couldn't add meta date for data set '"
- + dataSet.getCode() + "' to zip file.", ex);
+ notificationLog.error(
+ "Couldn't add meta date for data set '" + dataSet.getCode()
+ + "' to zip file.", ex);
return false;
}
try
@@ -441,8 +442,8 @@ class UploadingCommand implements IDataSetCommand
dataSetFile);
} catch (IOException ex)
{
- notificationLog.error("Couldn't add data set '" + dataSetFile + "' to zip file.",
- ex);
+ notificationLog.error("Couldn't add data set '" + dataSetFile
+ + "' to zip file.", ex);
return false;
}
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
index 075387fd602..3be648335bc 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
@@ -65,8 +65,8 @@ 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.SpacePE;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
/**
* @author Franz-Josef Elmer
@@ -183,11 +183,11 @@ public class UploadingCommandTest extends AssertJUnit
createTestData(LOCATION1);
ds2 = createTestData(LOCATION2);
ExternalData dataSet1 =
- ExternalDataTranslator.translate(createDataSet("1", LOCATION1), "?",
+ DataSetTranslator.translate(createDataSet("1", LOCATION1), "?",
ExperimentTranslator.LoadableFields.PROPERTIES);
System.out.println("ds1:" + dataSet1.getExperiment().getProperties());
ExternalData dataSet2 =
- ExternalDataTranslator.translate(createDataSet("2", LOCATION2), "?",
+ DataSetTranslator.translate(createDataSet("2", LOCATION2), "?",
ExperimentTranslator.LoadableFields.PROPERTIES);
dataSets = Arrays.<ExternalData> asList(dataSet1, dataSet2);
command =
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 4b6832c2363..7fefd401cec 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
@@ -752,6 +752,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
dataBO.loadByCode(dataSetCode);
dataBO.enrichWithParentsAndExperiment();
dataBO.enrichWithProperties();
+ dataBO.enrichWithContainedDataSets();
DataPE dataPE = dataBO.tryGetData();
if (null == dataPE)
return null;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
index 6e0e1cb9179..5af3d6c1832 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
@@ -142,7 +142,7 @@ public class DataSetTranslator
ExternalData externalData = null;
if (dataPE.isContainer())
{
- externalData = translateContainerDataSetProperties(dataPE, withDetails);
+ externalData = translateContainerDataSetProperties(dataPE, baseIndexURL, withDetails);
} else
{
externalData = translateDataSetProperties(dataPE);
@@ -189,12 +189,12 @@ public class DataSetTranslator
}
private static ExternalData translateContainerDataSetProperties(DataPE dataPE,
- boolean withComponents)
+ String baseIndexURL, boolean withComponents)
{
ContainerDataSet containerDataSet = new ContainerDataSet();
if (withComponents)
{
- setContainedDataSets(dataPE, containerDataSet);
+ setContainedDataSets(dataPE, containerDataSet, baseIndexURL);
}
return containerDataSet;
}
@@ -307,14 +307,15 @@ public class DataSetTranslator
externalData.setChildren(children);
}
- private static void setContainedDataSets(DataPE dataPE, ContainerDataSet containerDataSet)
+ private static void setContainedDataSets(DataPE dataPE, ContainerDataSet containerDataSet,
+ String baseIndexURL)
{
List<ExternalData> containedDataSets = new ArrayList<ExternalData>();
if (HibernateUtils.isInitialized(dataPE.getContainedDataSets()))
{
for (DataPE childPE : dataPE.getContainedDataSets())
{
- containedDataSets.add(translateBasicProperties(childPE));
+ containedDataSets.add(translate(childPE, baseIndexURL));
}
}
containerDataSet.setContainedDataSets(containedDataSets);
@@ -326,7 +327,18 @@ public class DataSetTranslator
*/
private static ExternalData translateBasicProperties(DataPE dataPE)
{
- ExternalData result = new ExternalData();
+ ExternalData result = null;
+ if (dataPE.isContainer())
+ {
+ result = new ContainerDataSet();
+ } else if (dataPE.isExternalData())
+ {
+ result = new DataSet();
+ } else
+ {
+ assert dataPE.isPlaceholder() == true;
+ result = new ExternalData();
+ }
result.setId(HibernateUtils.getId(dataPE));
result.setCode(dataPE.getCode());
result.setDataSetType(DataSetTypeTranslator.translate(dataPE.getDataSetType(),
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
deleted file mode 100644
index c1a589d54ba..00000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
+++ /dev/null
@@ -1,322 +0,0 @@
-/*
- * Copyright 2009 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.openbis.generic.shared.translator;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-
-import ch.systemsx.cisd.common.types.BooleanOrUnknown;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Invalidation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.InvalidationPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
-import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class ExternalDataTranslator
-{
- private ExternalDataTranslator()
- {
- }
-
- public static DatasetDescription translateToDescription(ExternalData data)
- {
- DatasetDescription description = new DatasetDescription();
- description.setDatasetCode(data.getCode());
-
- DataSet dataSet = data.tryGetAsDataSet();
- if (dataSet != null)
- {
- description.setDataSetLocation(dataSet.getLocation());
- description.setSpeedHint(dataSet.getSpeedHint());
- }
- description.setDataSetSize(data.getSize());
- DataSetType dataSetType = data.getDataSetType();
- if (dataSetType != null)
- {
- description.setDatasetTypeCode(dataSetType.getCode());
- }
- Experiment experiment = data.getExperiment();
- if (experiment != null)
- {
- description.setExperimentCode(experiment.getCode());
- description.setExperimentIdentifier(experiment.getIdentifier());
- Project project = experiment.getProject();
- if (project != null)
- {
- description.setProjectCode(project.getCode());
- Space space = project.getSpace();
- if (space != null)
- {
- description.setSpaceCode(space.getCode());
- DatabaseInstance instance = space.getInstance();
- if (instance != null)
- {
- description.setDatabaseInstanceCode(instance.getCode());
- }
- }
- }
- ExperimentType experimentType = experiment.getExperimentType();
- if (experimentType != null)
- {
- description.setExperimentTypeCode(experimentType.getCode());
- }
- }
- Sample sample = data.getSample();
- if (sample != null)
- {
- description.setSampleCode(sample.getCode());
- description.setSampleIdentifier(sample.getIdentifier());
- SampleType sampleType = sample.getSampleType();
- if (sampleType != null)
- {
- description.setSampleTypeCode(sampleType.getCode());
- }
- }
- return description;
- }
-
- public static List<ExternalData> translate(List<ExternalDataPE> list,
- String defaultDataStoreBaseURL, String baseIndexURL)
- {
- ArrayList<ExternalData> result = new ArrayList<ExternalData>(list.size());
- for (ExternalDataPE externalDataPE : list)
- {
- ExternalData data =
- translate(externalDataPE, baseIndexURL, true,
- ExperimentTranslator.LoadableFields.PROPERTIES);
- result.add(data);
- }
- return result;
- }
-
- public static ExternalData translate(ExternalDataPE externalDataPE, String baseIndexURL,
- final LoadableFields... withExperimentFields)
- {
- return translate(externalDataPE, baseIndexURL, true, withExperimentFields);
- }
-
- public static ExternalData translate(ExternalDataPE externalDataPE, String baseIndexURL,
- boolean loadSampleProperties, final LoadableFields... withExperimentFields)
- {
- ExternalData externalData = null;
- if (externalDataPE.isContainer())
- {
- externalData = translateContainerDataSetProperties(externalDataPE);
- } else
- {
- externalData = translateDataSetProperties(externalDataPE);
- }
-
- SamplePE sampleOrNull = externalDataPE.tryGetSample();
- ExperimentPE experiment = externalDataPE.getExperiment();
- externalData.setId(HibernateUtils.getId(externalDataPE));
- externalData.setCode(externalDataPE.getCode());
- externalData.setDataProducerCode(externalDataPE.getDataProducerCode());
- externalData.setDataSetType(DataSetTypeTranslator.translate(
- externalDataPE.getDataSetType(), new HashMap<PropertyTypePE, PropertyType>()));
- externalData.setDerived(externalDataPE.isDerived());
- externalData.setInvalidation(tryToGetInvalidation(sampleOrNull, experiment));
- externalData.setSize(externalDataPE.getSize());
- final Collection<ExternalData> parents = new HashSet<ExternalData>();
- externalData.setParents(parents);
- for (DataPE parentPE : externalDataPE.getParents())
- {
- parents.add(translateBasicProperties(parentPE));
- }
- setChildren(externalDataPE, externalData);
- externalData.setProductionDate(externalDataPE.getProductionDate());
- externalData.setModificationDate(externalDataPE.getModificationDate());
- externalData.setRegistrator(PersonTranslator.translate(externalDataPE.getRegistrator()));
- externalData.setRegistrationDate(externalDataPE.getRegistrationDate());
- externalData.setSample(sampleOrNull == null ? null : fillSample(new Sample(), sampleOrNull,
- loadSampleProperties));
- externalData.setDataStore(DataStoreTranslator.translate(externalDataPE.getDataStore()));
- externalData.setPermlink(PermlinkUtilities.createPermlinkURL(baseIndexURL,
- EntityKind.DATA_SET, externalData.getIdentifier()));
- setProperties(externalDataPE, externalData);
- externalData.setExperiment(ExperimentTranslator.translate(experiment, baseIndexURL,
- withExperimentFields));
-
- return externalData;
- }
-
- private static ExternalData translateContainerDataSetProperties(ExternalDataPE externalDataPE)
- {
- ContainerDataSet containerDataSet = new ContainerDataSet();
- setContainedDataSets(externalDataPE, containerDataSet);
- return containerDataSet;
- }
-
- private static ExternalData translateDataSetProperties(ExternalDataPE externalDataPE)
- {
- DataSet dataSet = new DataSet();
- dataSet.setComplete(BooleanOrUnknown.tryToResolve(externalDataPE.getComplete()));
- dataSet.setStatus(externalDataPE.getStatus());
- dataSet.setSpeedHint(externalDataPE.getSpeedHint());
- dataSet.setFileFormatType(TypeTranslator.translate(externalDataPE.getFileFormatType()));
- dataSet.setLocation(externalDataPE.getLocation());
- dataSet.setLocatorType(TypeTranslator.translate(externalDataPE.getLocatorType()));
- return dataSet;
- }
-
- private static void setProperties(ExternalDataPE externalDataPE, ExternalData externalData)
- {
- if (HibernateUtils.isInitialized(externalDataPE.getProperties()))
- {
- externalData.setDataSetProperties(EntityPropertyTranslator.translate(
- externalDataPE.getProperties(), new HashMap<PropertyTypePE, PropertyType>()));
- } else
- {
- externalData.setDataSetProperties(new ArrayList<IEntityProperty>());
- }
- }
-
- private static Invalidation tryToGetInvalidation(SamplePE sampleOrNull, ExperimentPE experiment)
- {
- InvalidationPE invalidationOrNull;
- if (sampleOrNull != null)
- {
- invalidationOrNull = tryToGetInvalidationPE(sampleOrNull);
- } else
- {
- invalidationOrNull = tryToGetInvalidationPE(experiment);
- }
- return translateInvalidation(invalidationOrNull);
- }
-
- private static InvalidationPE tryToGetInvalidationPE(SamplePE sampleOrNull)
- {
- if (sampleOrNull != null)
- {
- return sampleOrNull.getInvalidation();
- } else
- {
- return null;
- }
- }
-
- private static InvalidationPE tryToGetInvalidationPE(ExperimentPE experiment)
- {
- if (experiment != null)
- {
- return experiment.getInvalidation();
- } else
- {
- return null;
- }
- }
-
- private static Invalidation translateInvalidation(InvalidationPE invalidationPE)
- {
- if (invalidationPE == null)
- {
- return null;
- }
- Invalidation result = new Invalidation();
- result.setReason(invalidationPE.getReason());
- result.setRegistrationDate(invalidationPE.getRegistrationDate());
- result.setRegistrator(PersonTranslator.translate(invalidationPE.getRegistrator()));
- return result;
- }
-
- private static Sample fillSample(Sample sample, SamplePE samplePE, boolean loadSampleProperties)
- {
- sample.setId(HibernateUtils.getId(samplePE));
- sample.setPermId(samplePE.getPermId());
- SampleTranslator.setCodes(sample, samplePE);
- sample.setInvalidation(translateInvalidation(samplePE.getInvalidation()));
- sample.setSampleType(TypeTranslator.translate(samplePE.getSampleType()));
- sample.setIdentifier(samplePE.getSampleIdentifier().toString());
- sample.setRegistrationDate(samplePE.getRegistrationDate());
- sample.setRegistrator(PersonTranslator.translate(samplePE.getRegistrator()));
- sample.setSpace(GroupTranslator.translate(samplePE.getSpace()));
- if (loadSampleProperties)
- {
- sample.setProperties(EntityPropertyTranslator.translate(samplePE.getProperties(),
- new HashMap<PropertyTypePE, PropertyType>()));
- }
- return sample;
- }
-
- private static void setChildren(ExternalDataPE externalDataPE, ExternalData externalData)
- {
- List<ExternalData> children = new ArrayList<ExternalData>();
- if (HibernateUtils.isInitialized(externalDataPE.getChildren()))
- {
- for (DataPE childPE : externalDataPE.getChildren())
- {
- children.add(translateBasicProperties(childPE));
- }
- }
- externalData.setChildren(children);
- }
-
- private static void setContainedDataSets(DataPE externalDataPE,
- ContainerDataSet containerDataSet)
- {
- List<ExternalData> containedDataSets = new ArrayList<ExternalData>();
- if (HibernateUtils.isInitialized(externalDataPE.getContainedDataSets()))
- {
- for (DataPE childPE : externalDataPE.getContainedDataSets())
- {
- containedDataSets.add(translateBasicProperties(childPE));
- }
- }
- containerDataSet.setContainedDataSets(containedDataSets);
- }
-
- /**
- * Creates an <var>externalData</var> from <var>dataPE</vra> an fills it with all data needed by
- * {@link IEntityInformationHolder}.
- */
- private static ExternalData translateBasicProperties(DataPE dataPE)
- {
- ExternalData result = new ExternalData();
- result.setId(HibernateUtils.getId(dataPE));
- result.setCode(dataPE.getCode());
- result.setDataSetType(DataSetTypeTranslator.translate(dataPE.getDataSetType(),
- new HashMap<PropertyTypePE, PropertyType>()));
- return result;
- }
-}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
index 7eaab9e4fd0..13f04c7e468 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
@@ -78,7 +78,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
/**
@@ -503,7 +503,7 @@ public final class CommonClientServiceTest extends AbstractClientServiceTest
locatorTypePE.setCode("LOCATOR");
externalDataPE.setLocatorType(locatorTypePE);
final ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL, false);
+ DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL, false);
context.checking(new Expectations()
{
{
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 7b2ef980948..d77ba062187 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
@@ -92,9 +92,9 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.builders.ExperimentTypePEBuil
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.DtoConverters;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.GroupTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.PersonTranslator;
@@ -566,7 +566,7 @@ public final class CommonServerTest extends AbstractServerTestCase
dataStorePE.setCode("DST");
externalDataPE.setDataStore(dataStorePE);
final ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
prepareGetSession();
final boolean showOnlyDirectlyConnected = true;
context.checking(new Expectations()
@@ -605,7 +605,7 @@ public final class CommonServerTest extends AbstractServerTestCase
dataStorePE.setCode("DST");
externalDataPE.setDataStore(dataStorePE);
final ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
prepareGetSession();
context.checking(new Expectations()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslatorTest.java
similarity index 95%
rename from openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java
rename to openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslatorTest.java
index 99f5402e31d..df264d94afa 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslatorTest.java
@@ -47,7 +47,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
* @author Franz-Josef Elmer
*/
-public class ExternalDataTranslatorTest extends AssertJUnit
+// TODO write test with translation of components
+public class DataSetTranslatorTest extends AssertJUnit
{
private static final String DOWNLOAD_URL = "url";
@@ -58,8 +59,7 @@ public class ExternalDataTranslatorTest extends AssertJUnit
{
ExternalDataPE externalDataPE = new ExternalDataPE();
externalDataPE.setDataStore(createStore());
- ExternalData data =
- ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ ExternalData data = DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
DataSet translated = data.tryGetAsDataSet();
@@ -124,8 +124,7 @@ public class ExternalDataTranslatorTest extends AssertJUnit
samplePE.setInvalidation(invalidationPE);
externalDataPE.setSampleAcquiredFrom(samplePE);
- ExternalData data =
- ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ ExternalData data = DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
DataSet translated = data.tryGetAsDataSet();
@@ -180,8 +179,7 @@ public class ExternalDataTranslatorTest extends AssertJUnit
externalDataPE.addParent(createParent("parent-1"));
externalDataPE.addParent(createParent("parent-2"));
- ExternalData externalData =
- ExternalDataTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ ExternalData externalData = DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
assertEquals("my-experiment", externalData.getExperiment().getCode());
assertEquals(2, externalData.getParents().size());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelperTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelperTest.java
index 2f17ab45700..151eedb87c4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelperTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/SimpleDataSetHelperTest.java
@@ -39,8 +39,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class SimpleDataSetHelperTest extends AssertJUnit
@@ -52,24 +50,25 @@ public class SimpleDataSetHelperTest extends AssertJUnit
ExternalData ds2 = create(2);
ExternalData ds3 = new ContainerDataSet();
- List<SimpleDataSetInformationDTO> list = SimpleDataSetHelper.translate(Arrays.asList(ds1, ds2, ds3));
-
+ List<SimpleDataSetInformationDTO> list =
+ SimpleDataSetHelper.translate(Arrays.asList(ds1, ds2, ds3));
+
check(1, list.get(0));
check(2, list.get(1));
assertEquals("42", list.get(1).getDataSetShareId());
assertEquals(2, list.size());
}
-
- @Test
+
+ @Test
public void testTranslateDescription()
{
- DatasetDescription description = ExternalDataTranslator.translateToDescription(create(1));
-
+ DatasetDescription description = DataSetTranslator.translateToDescription(create(1));
+
SimpleDataSetInformationDTO result = SimpleDataSetHelper.translate(description);
-
+
check(1, result);
}
-
+
private ExternalData create(long id)
{
DataSet dataSet = new DataSet();
@@ -112,7 +111,7 @@ public class SimpleDataSetHelperTest extends AssertJUnit
dataSet.setStatus(DataSetArchivingStatus.ARCHIVED);
return dataSet;
}
-
+
public void check(long expectedID, SimpleDataSetInformationDTO dataSet)
{
assertEquals("ds-" + expectedID, dataSet.getDataSetCode());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index 749c2dd0722..e1e09851b7f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -39,8 +39,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.EntityPropertyTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
@@ -163,7 +163,7 @@ public class PlateContentLoader
private ExternalData translate(ExternalDataPE externalData)
{
- return ExternalDataTranslator.translate(externalData, session.getBaseIndexURL());
+ return DataSetTranslator.translate(externalData, session.getBaseIndexURL());
}
private PlateContent getPlateContent(TechId plateId)
--
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