From 2d93ccf9433fda47a7fc0166e01ca6dd9e0fd28d Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 25 Nov 2010 09:51:58 +0000
Subject: [PATCH] LMS-1886 Changes to make the sample listing functionality
useful.
SVN: 18895
---
.../registrators/ReplicaRegistrator.java | 62 +++++++++++++-
.../constants/BundleStructureConstants.java | 4 +
.../cina/shared/constants/CinaConstants.java | 4 +
.../metadata/ReplicaMetadataExtractor.java | 28 +++++++
.../bundle/CinaBundleDataSetHandlerTest.java | 1 -
.../CinaBundleRegistrationTest.java | 83 ++++++++++++++++++-
.../GridPreparationRegistratorTest.java | 1 -
7 files changed, 177 insertions(+), 6 deletions(-)
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
index c3aa29a4cb0..2009d5f3a23 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
@@ -17,14 +17,25 @@
package ch.systemsx.cisd.cina.dss.bundle.registrators;
import java.io.File;
+import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.cina.shared.constants.BundleStructureConstants;
+import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
import ch.systemsx.cisd.cina.shared.metadata.ImageMetadataExtractor;
import ch.systemsx.cisd.cina.shared.metadata.ReplicaMetadataExtractor;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+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.dto.SampleUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
@@ -92,20 +103,54 @@ public class ReplicaRegistrator extends BundleDataSetHelper
replicaSample = getOpenbisService().tryGetSampleWithExperiment(replicaSampleId);
didCreateSample = false;
- // Sample doesn't exist, create it
+ // Get the relevant metadata from the file
+ String sampleDescriptionOrNull = replicaMetadataExtractor.tryReplicaSampleDescription();
+ String sampleCreatorOrNull = replicaMetadataExtractor.tryReplicaSampleCreatorName();
+
+ ArrayList<IEntityProperty> properties = new ArrayList<IEntityProperty>();
+ if (null != sampleDescriptionOrNull)
+ {
+ EntityProperty prop = createProperty(CinaConstants.DESCRIPTION_PROPERTY_CODE);
+ prop.setValue(sampleDescriptionOrNull);
+ properties.add(prop);
+ }
+
+ if (null != sampleCreatorOrNull)
+ {
+ EntityProperty prop = createProperty(CinaConstants.CREATOR_EMAIL_PROPERTY_CODE);
+ prop.setValue(sampleCreatorOrNull);
+ properties.add(prop);
+ }
+
if (replicaSample == null)
{
+ // Sample doesn't exist, create it
NewSample newSample =
NewSample.createWithParent(replicaSampleId.toString(),
globalState.getReplicaSampleType(), null, gridPrepSampleId.toString());
newSample.setExperimentIdentifier(gridPrepSample.getExperiment().getIdentifier());
+ newSample.setProperties(properties.toArray(IEntityProperty.EMPTY_ARRAY));
String userId = getSessionContext().getUserName();
getOpenbisService().registerSample(newSample, userId);
- replicaSample = getOpenbisService().tryGetSampleWithExperiment(replicaSampleId);
didCreateSample = true;
+ } else
+ {
+ ExperimentIdentifier experimentId =
+ new ExperimentIdentifier(replicaSample.getExperiment());
+ experimentId.setDatabaseInstanceCode(replicaSample.getExperiment().getProject()
+ .getSpace().getInstance().getCode());
+ // Sample does exist, update the metadata
+ SampleUpdatesDTO sampleUpdate =
+ new SampleUpdatesDTO(TechId.create(replicaSample), properties, experimentId,
+ new ArrayList<NewAttachment>(), replicaSample.getModificationDate(),
+ replicaSampleId, null, null);
+ getOpenbisService().updateSample(sampleUpdate);
+ didCreateSample = false;
}
+ replicaSample = getOpenbisService().tryGetSampleWithExperiment(replicaSampleId);
+
assert replicaSample != null;
}
@@ -154,4 +199,17 @@ public class ReplicaRegistrator extends BundleDataSetHelper
getDataSetInformation().addAll(registeredDataSetInfos);
}
}
+
+ private EntityProperty createProperty(String propertyTypeCode)
+ {
+ PropertyType propertyType = new PropertyType();
+ DataType dataType = new DataType();
+ dataType.setCode(DataTypeCode.VARCHAR);
+ propertyType.setCode(propertyTypeCode);
+ propertyType.setDataType(dataType);
+
+ EntityProperty property = new EntityProperty();
+ property.setPropertyType(propertyType);
+ return property;
+ }
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
index 2715427c755..4d88ad52219 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/BundleStructureConstants.java
@@ -59,6 +59,10 @@ public class BundleStructureConstants
public static final String REPLICA_SAMPLE_CODE_KEY = "database id (replica)";
+ public static final String REPLICA_SAMPLE_DESCRIPTION_KEY = "description";
+
+ public static final String REPLICA_SAMPLE_CREATOR_NAME = "creator name (e-mail)";
+
/**
* No reason to instantiate this class.
*/
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
index 1c64a8a40f3..d2a4f9416dc 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/constants/CinaConstants.java
@@ -37,6 +37,10 @@ public class CinaConstants
public static final String SIZE_PREFIX = "Size";
+ public static final String DESCRIPTION_PROPERTY_CODE = "Description";
+
+ public static final String CREATOR_EMAIL_PROPERTY_CODE = "CREATOR_EMAIL";
+
// No need to instantiate this class
private CinaConstants()
{
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.java
index e5fc1856808..fec9ace0bc7 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.java
@@ -37,6 +37,12 @@ public class ReplicaMetadataExtractor implements IMetadataExtractor
private static final String REPLICA_SAMPLE_CODE_KEY =
BundleStructureConstants.REPLICA_SAMPLE_CODE_KEY;
+ private static final String REPLICA_SAMPLE_DESCRIPTION_KEY =
+ BundleStructureConstants.REPLICA_SAMPLE_DESCRIPTION_KEY;
+
+ private static final String REPLICA_SAMPLE_CREATOR_NAME =
+ BundleStructureConstants.REPLICA_SAMPLE_CREATOR_NAME;
+
private final ArrayList<ImageMetadataExtractor> metadataExtractors;
private final File folder;
@@ -124,6 +130,28 @@ public class ReplicaMetadataExtractor implements IMetadataExtractor
return metadataMap.get(REPLICA_SAMPLE_CODE_KEY);
}
+ /**
+ * Return the description for the replica sample.
+ *
+ * @return Return the code, or null if none was found
+ */
+ public String tryReplicaSampleDescription()
+ {
+ checkPrepared();
+ return metadataMap.get(REPLICA_SAMPLE_DESCRIPTION_KEY);
+ }
+
+ /**
+ * Return the creator name for the replica sample.
+ *
+ * @return Return the code, or null if none was found
+ */
+ public String tryReplicaSampleCreatorName()
+ {
+ checkPrepared();
+ return metadataMap.get(REPLICA_SAMPLE_CREATOR_NAME);
+ }
+
public File getFolder()
{
return folder;
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
index af8432098a5..7e4b5e3386a 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/CinaBundleDataSetHandlerTest.java
@@ -47,7 +47,6 @@ public class CinaBundleDataSetHandlerTest extends CinaBundleRegistrationTest
setupNewEntititesExpectations();
setupExistingGridPrepExpectations();
- setupExistingReplicaExpectations();
setupHandleRawDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/RawData/ReplicTest");
setupHandleReplicaMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/ReplicTest");
setupHandleBundleMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/BundleMetadata.xml");
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
index 71255cd6f58..05c4838d849 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.cina.dss.bundle.registrators;
import java.io.File;
import java.io.IOException;
import java.util.Collections;
+import java.util.List;
import org.hamcrest.BaseMatcher;
import org.hamcrest.Description;
@@ -34,11 +35,16 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
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.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
@@ -61,8 +67,12 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
private static final String SPACE_CODE = "SPACE";
- protected static final String EXPERIMENT_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE
- + "/PROJECT/EXP-1";
+ private static final String PROJECT_CODE = "PROJECT";
+
+ private static final String EXPERIMENT_CODE = "EXP-1";
+
+ protected static final String EXPERIMENT_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE + "/"
+ + PROJECT_CODE + "/" + EXPERIMENT_CODE;
private static final String GRID_SAMPLE_CODE = "GRID-CODE";
@@ -206,6 +216,17 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
final Sample sample = new Sample();
Experiment exp = new Experiment();
exp.setIdentifier(EXPERIMENT_IDENTIFIER);
+ exp.setCode(EXPERIMENT_CODE);
+ Project project = new Project();
+ project.setCode(PROJECT_CODE);
+ Space space = new Space();
+ space.setCode(SPACE_CODE);
+ DatabaseInstance dbInstance = new DatabaseInstance();
+ dbInstance.setCode(DB_CODE);
+ space.setInstance(dbInstance);
+ project.setSpace(space);
+ exp.setProject(project);
+ sample.setId((long) 1);
sample.setExperiment(exp);
sample.setIdentifier(REPLICA_SAMPLE_IDENTIFIER);
@@ -213,6 +234,53 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
context.checking(new Expectations()
{
{
+ // Get the sample
+ one(openbisService).tryGetSampleWithExperiment(
+ with(new SampleIdentifierFactory(REPLICA_SAMPLE_IDENTIFIER)
+ .createIdentifier()));
+ will(returnValue(sample));
+
+ // Update it with new data
+ one(openbisService).updateSample(with(new MatcherNoDesc<SampleUpdatesDTO>()
+ {
+ public boolean matches(Object item)
+ {
+ if (item instanceof SampleUpdatesDTO)
+ {
+ SampleUpdatesDTO sampleUpdatesDto = (SampleUpdatesDTO) item;
+ assertEquals(REPLICA_SAMPLE_IDENTIFIER, sampleUpdatesDto
+ .getSampleIdentifier().toString());
+ assertEquals(EXPERIMENT_IDENTIFIER, sampleUpdatesDto
+ .getExperimentIdentifierOrNull().toString());
+ List<IEntityProperty> properties =
+ sampleUpdatesDto.getProperties();
+
+ assertTrue("The update should include properties.",
+ properties.size() > 0);
+ for (IEntityProperty property : properties)
+ {
+ if (property.getPropertyType().getCode()
+ .equals(CinaConstants.DESCRIPTION_PROPERTY_CODE))
+ {
+ assertEquals(
+ "This replica is a test for imported MRC files",
+ property.getValue());
+ }
+
+ if (property.getPropertyType().getCode()
+ .equals(CinaConstants.CREATOR_EMAIL_PROPERTY_CODE))
+ {
+ assertEquals("thomas.braun@bsse.ethz.ch",
+ property.getValue());
+ }
+ }
+ return true;
+ }
+ return false;
+ }
+ }));
+
+ // Return the sample
one(openbisService).tryGetSampleWithExperiment(
with(new SampleIdentifierFactory(REPLICA_SAMPLE_IDENTIFIER)
.createIdentifier()));
@@ -474,6 +542,17 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
}
}), with(TEST_USER_NAME));
will(returnValue(new Long(2)));
+
+ Sample sample = new Sample();
+ Experiment exp = new Experiment();
+ exp.setIdentifier(EXPERIMENT_IDENTIFIER);
+ sample.setId((long) 1);
+ sample.setExperiment(exp);
+ sample.setIdentifier(REPLICA_SAMPLE_IDENTIFIER);
+ one(openbisService).tryGetSampleWithExperiment(
+ with(new SampleIdentifierFactory(REPLICA_SAMPLE_IDENTIFIER)
+ .createIdentifier()));
+ will(returnValue(sample));
}
});
}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
index 408e41bc896..fea5db79363 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistratorTest.java
@@ -73,7 +73,6 @@ public class GridPreparationRegistratorTest extends CinaBundleRegistrationTest
setupNewEntititesExpectations();
setupExistingGridPrepExpectations();
- setupExistingReplicaExpectations();
setupHandleRawDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/RawData/ReplicTest");
setupHandleReplicaMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/Annotations/ReplicTest");
setupHandleBundleMetadataDataSetExpectations("sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Test.bundle/BundleMetadata.xml");
--
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