From 4091804b3e2e4110862893876eb8fd16eefa66b6 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 14 Jun 2012 11:29:28 +0000
Subject: [PATCH] BIS-41 SP-57 Use the DataSetBatchUpdatesDTO in
performEntityOperations
SVN: 25701
---
...ProteinResultDataSetParentLinkingTask.java | 15 +++++++---
...einResultDataSetParentLinkingTaskTest.java | 29 +++++++++----------
2 files changed, 24 insertions(+), 20 deletions(-)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTask.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTask.java
index cb236acd8b2..98ff871ae1a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTask.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTask.java
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetBatchUpdateDetails;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
@@ -42,7 +43,7 @@ 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.basic.dto.Project;
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.DataSetBatchUpdatesDTO;
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.ExperimentIdentifierFactory;
@@ -83,7 +84,7 @@ public class ProteinResultDataSetParentLinkingTask implements IMaintenanceTask
@Override
public void execute()
{
- List<DataSetUpdatesDTO> dataSetUpdates = new ArrayList<DataSetUpdatesDTO>();
+ List<DataSetBatchUpdatesDTO> dataSetUpdates = new ArrayList<DataSetBatchUpdatesDTO>();
List<Project> projects = service.listProjects();
for (Project project : projects)
{
@@ -118,14 +119,20 @@ public class ProteinResultDataSetParentLinkingTask implements IMaintenanceTask
continue;
}
DataSet dataSet = (DataSet) ds;
- DataSetUpdatesDTO update = new DataSetUpdatesDTO();
+ DataSetBatchUpdatesDTO update = new DataSetBatchUpdatesDTO();
update.setDatasetId(new TechId(dataSet.getId()));
update.setVersion(dataSet.getModificationDate());
update.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(dataSet
.getExperiment().getIdentifier()));
- update.setModifiedParentDatasetCodesOrNull(codes.toArray(new String[0]));
update.setFileFormatTypeCode(dataSet.getFileFormatType().getCode());
update.setProperties(dataSet.getProperties());
+
+ // All we want to do is update the parents
+ update.setDatasetCode(dataSet.getCode());
+ update.setModifiedParentDatasetCodesOrNull(codes.toArray(new String[0]));
+ DataSetBatchUpdateDetails details = new DataSetBatchUpdateDetails();
+ details.setParentsUpdateRequested(true);
+
operationLog.info("Parent data set links of data set " + dataSet.getCode()
+ " from experiment " + experiment.getIdentifier()
+ " will be updated.");
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTaskTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTaskTest.java
index 3d3ee39f777..3b28178dc39 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTaskTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProteinResultDataSetParentLinkingTaskTest.java
@@ -31,14 +31,12 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.test.RecordingMatcher;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.ProteinResultDataSetParentLinkingTask;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
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.DataSetUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
@@ -95,15 +93,14 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
new ExperimentBuilder().id(4).identifier("/S/P1/E4")
.property(BASE_EXPERIMENT_KEY, "/S/P1/E1").getExperiment();
final DataSet ds1 =
- new DataSetBuilder(1).code("ds1").fileFormat("A")
- .experiment(e1).modificationDate(new Date(11)).getDataSet();
+ new DataSetBuilder(1).code("ds1").fileFormat("A").experiment(e1)
+ .modificationDate(new Date(11)).getDataSet();
final DataSet ds2 =
- new DataSetBuilder(2).code("ds2").fileFormat("B")
- .experiment(e4).modificationDate(new Date(22)).getDataSet();
+ new DataSetBuilder(2).code("ds2").fileFormat("B").experiment(e4)
+ .modificationDate(new Date(22)).getDataSet();
final DataSet ds3 =
- new DataSetBuilder(3).code("ds3").fileFormat("C")
- .experiment(e3).modificationDate(new Date(33)).property("ALPHA", "3.1")
- .getDataSet();
+ new DataSetBuilder(3).code("ds3").fileFormat("C").experiment(e3)
+ .modificationDate(new Date(33)).property("ALPHA", "3.1").getDataSet();
final RecordingMatcher<AtomicEntityOperationDetails> operationRecorder =
new RecordingMatcher<AtomicEntityOperationDetails>();
context.checking(new Expectations()
@@ -120,16 +117,16 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
one(service).tryToGetExperiment(ExperimentIdentifierFactory.parse("/S/P1/E1"));
will(returnValue(e1));
-
+
one(service).tryGetDataSet("non-sense2");
will(returnValue(null));
-
+
one(service).tryGetDataSet("ds1");
will(returnValue(ds1));
-
+
one(service).tryGetDataSet("ds3");
will(returnValue(ds3));
-
+
one(service).listDataSetsByExperimentID(e1.getId());
will(returnValue(Arrays.asList(ds1)));
@@ -142,7 +139,7 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
one(service).performEntityOperations(with(operationRecorder));
}
});
-
+
task.execute();
assertEquals("INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
@@ -154,7 +151,7 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
+ "INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
+ "Parent data set links for 2 data sets have been updated.",
logRecorder.getLogContent());
- List<DataSetUpdatesDTO> dataSetUpdates =
+ List<DataSetBatchUpdatesDTO> dataSetUpdates =
operationRecorder.recordedObject().getDataSetUpdates();
assertEquals(2L, dataSetUpdates.get(0).getDatasetId().getId().longValue());
assertEquals(22L, dataSetUpdates.get(0).getVersion().getTime());
--
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