From b3e5cee6900caca043ffcf7976b1f3051ee26df4 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 6 Aug 2010 14:41:41 +0000
Subject: [PATCH] [LMS-1676] initial changes in sample update; small
refactoring
SVN: 17355
---
.../bo/AbstractSampleBusinessObject.java | 76 +++++++++++++++----
.../server/business/bo/ExperimentBO.java | 15 +---
.../generic/server/business/bo/SampleBO.java | 58 ++++++++++++++
.../shared/basic/dto/BasicSampleUpdates.java | 19 +++++
.../generic/shared/basic/dto/Code.java | 5 ++
.../DataStoreServiceTranslator.java | 21 +----
.../ExperimentPlateLocationsSection.java | 13 +---
.../server/logic/PlateContentLoader.java | 13 +---
8 files changed, 153 insertions(+), 67 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
index 291ba705c57..f7f40c9d9d7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
@@ -192,28 +192,76 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
protected void setGeneratedFrom(final SampleIdentifier sampleIdentifier,
final SamplePE samplePE, String parentIdentifier)
{
- for (SampleRelationshipPE r : samplePE.getParentRelationships())
+ removeParents(samplePE);
+ final SamplePE parentPE = tryGetValidSample(parentIdentifier, sampleIdentifier);
+ if (parentPE != null)
+ {
+ RelationshipTypePE relationship = tryFindParentChildRelationshipType();
+ samplePE.addParentRelationship(new SampleRelationshipPE(parentPE, samplePE,
+ relationship));
+ }
+ }
+
+ protected void setParents(SamplePE child, List<SamplePE> parents)
+ {
+ removeParents(child);
+ RelationshipTypePE relationshipType = tryFindParentChildRelationshipType();
+ for (SamplePE parent : parents)
+ {
+ addParentRelationship(child, parent, relationshipType);
+ }
+ }
+
+ private void removeParents(SamplePE child)
+ {
+ for (SampleRelationshipPE r : child.getParentRelationships())
{
if (r.getRelationship().getCode().equals(
BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP))
{
- samplePE.removeParentRelationship(r);
+ child.removeParentRelationship(r);
}
}
- final SamplePE parentPE = tryGetValidSample(parentIdentifier, sampleIdentifier);
- if (parentPE != null)
+ }
+
+ // ineffective for adding a collection of parents
+ protected void addParent(SamplePE child, SamplePE parent)
+ {
+ RelationshipTypePE relationshipType = tryFindParentChildRelationshipType();
+ addParentRelationship(child, parent, relationshipType);
+ }
+
+ protected void addParents(SamplePE child, List<SamplePE> parents)
+ {
+ RelationshipTypePE relationshipType = tryFindParentChildRelationshipType();
+ for (SamplePE parent : parents)
{
- RelationshipTypePE relationship =
- getRelationshipTypeDAO().tryFindRelationshipTypeByCode(
- BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP);
- if (relationship == null)
- {
- throw new UserFailureException(
- "'Parent - Child' relationship definition could not be found.");
- }
- samplePE.addParentRelationship(new SampleRelationshipPE(parentPE, samplePE,
- relationship));
+ addParentRelationship(child, parent, relationshipType);
+ }
+ }
+
+ private void addParentRelationship(SamplePE child, SamplePE parent,
+ RelationshipTypePE relationshipType)
+ {
+ final SampleRelationshipPE relationship =
+ new SampleRelationshipPE(child, parent, relationshipType);
+ child.addParentRelationship(relationship);
+ }
+
+ protected RelationshipTypePE tryFindParentChildRelationshipType()
+ {
+ return tryFindRelationshipTypeByCode(BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP);
+ }
+
+ protected RelationshipTypePE tryFindRelationshipTypeByCode(String code)
+ {
+ RelationshipTypePE result = getRelationshipTypeDAO().tryFindRelationshipTypeByCode(code);
+ if (result == null)
+ {
+ throw UserFailureException.fromTemplate(
+ "'%s' relationship definition could not be found.", code);
}
+ return result;
}
private SamplePE tryGetValidSample(final String parentIdentifierOrNull,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
index c5c92256fdc..5c2d9d823da 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAttachmentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
@@ -443,7 +444,7 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
void setExperimentSamples(String[] sampleCodes)
{
List<SamplePE> samples = experiment.getSamples();
- String[] currentSampleCodes = extractCodes(samples);
+ String[] currentSampleCodes = Code.extractCodesToArray(samples);
Set<String> currentSampleCodesSet = asSet(currentSampleCodes);
Set<String> codesToAdd = asSet(sampleCodes);
codesToAdd.removeAll(currentSampleCodesSet);
@@ -537,18 +538,6 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
return new HashSet<String>(Arrays.asList(objects));
}
- private static String[] extractCodes(List<SamplePE> samples)
- {
- String[] codes = new String[samples.size()];
- int i = 0;
- for (SamplePE sample : samples)
- {
- codes[i] = sample.getCode();
- i++;
- }
- return codes;
- }
-
@Private
void updateProject(ProjectIdentifier newProjectIdentifier)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
index 2448908f521..7bcf3e78466 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
@@ -17,16 +17,20 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.springframework.dao.DataAccessException;
import org.springframework.dao.DataIntegrityViolationException;
+import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.util.SampleUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAttachmentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
@@ -34,6 +38,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
@@ -238,12 +243,14 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
updateProperties(updates.getProperties());
updateGroup(sample, updates.getSampleIdentifier(), null);
updateExperiment(sample, updates.getExperimentIdentifierOrNull(), null);
+ // TODO 2010-08-06, Piotr Buczek: get rid of this
setGeneratedFrom(updates.getSampleIdentifier(), sample, updates.getParentIdentifierOrNull());
setContainer(updates.getSampleIdentifier(), sample, updates.getContainerIdentifierOrNull());
for (NewAttachment attachment : updates.getAttachments())
{
addAttachment(AttachmentTranslator.translate(attachment));
}
+ updateParents(updates);
dataChanged = true;
}
@@ -256,6 +263,56 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
properties, registrator));
}
+ private void updateParents(SampleUpdatesDTO updates)
+ {
+ String[] parentCodes = updates.getModifiedParentCodesOrNull();
+ if (parentCodes != null)
+ {
+ attachParents(parentCodes);
+ }
+ }
+
+ // attaches specified existing samples to the sample as parents
+ private void attachParents(String[] parentCodes)
+ {
+ List<SamplePE> parents =
+ findSamplesByCodes(getSampleDAO(), asSet(parentCodes), sample.getGroup());
+ setParents(sample, parents);
+ }
+
+ // Finds samples in the specified group. Throws exception if some samples do not exist.
+ private static List<SamplePE> findSamplesByCodes(ISampleDAO sampleDAO, Set<String> sampleCodes,
+ GroupPE group)
+ {
+ List<SamplePE> samples = new ArrayList<SamplePE>();
+ List<String> missingSamples = new ArrayList<String>();
+ for (String code : sampleCodes)
+ {
+ SamplePE sample = sampleDAO.tryFindByCodeAndGroup(code, group);
+ if (sample == null)
+ {
+ missingSamples.add(code);
+ } else
+ {
+ samples.add(sample);
+ }
+ }
+ if (missingSamples.size() > 0)
+ {
+ throw UserFailureException.fromTemplate(
+ "Samples with following codes do not exist in the space '%s': '%s'.", group
+ .getCode(), CollectionUtils.abbreviate(missingSamples, 10));
+ } else
+ {
+ return samples;
+ }
+ }
+
+ private static Set<String> asSet(String[] objects)
+ {
+ return new HashSet<String>(Arrays.asList(objects));
+ }
+
public void setGeneratedCode()
{
final String code = createCode(EntityKind.SAMPLE);
@@ -327,4 +384,5 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
HibernateUtils.initialize(sample.getProperties());
}
}
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicSampleUpdates.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicSampleUpdates.java
index 142d32a5697..84552fab3aa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicSampleUpdates.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicSampleUpdates.java
@@ -39,10 +39,18 @@ public class BasicSampleUpdates implements IsSerializable, Serializable
private Date version;
+ // TODO 2010-08-06, Piotr Buczek: get rid of this
private String parentIdentifierOrNull;
private String containerIdentifierOrNull;
+ // New set of parent sample codes which will replace the old ones. In this way some
+ // parent samples can be unassigned and some assigned as a result. It will be assumed that
+ // all the samples belong to the same group as the child sample.
+ // If equals to null nothing should be changed.
+ // If some previously assigned parent sample is missing on this list, it will be unassigned.
+ private String[] modifiedParentCodesOrNull;
+
public String getParentIdentifierOrNull()
{
return parentIdentifierOrNull;
@@ -107,4 +115,15 @@ public class BasicSampleUpdates implements IsSerializable, Serializable
this.version = version;
}
+ // if null nothing should be changed
+ public String[] getModifiedParentCodesOrNull()
+ {
+ return modifiedParentCodesOrNull;
+ }
+
+ public void setModifiedParentCodesOrNull(String[] modifiedParentCodesOrNull)
+ {
+ this.modifiedParentCodesOrNull = modifiedParentCodesOrNull;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Code.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Code.java
index db5d97ccdf6..56ae7fd4190 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Code.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Code.java
@@ -113,6 +113,11 @@ public class Code<T extends Code<T>> implements IsSerializable, ICodeHolder, Com
return codes;
}
+ public final static String[] extractCodesToArray(Collection<? extends ICodeHolder> codeProviders)
+ {
+ return extractCodes(codeProviders).toArray(new String[codeProviders.size()]);
+ }
+
public final static class CodeProviderComparator implements Comparator<ICodeHolder>,
Serializable
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataStoreServiceTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataStoreServiceTranslator.java
index cac64364708..5c63c1f09f1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataStoreServiceTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataStoreServiceTranslator.java
@@ -16,22 +16,20 @@
package ch.systemsx.cisd.openbis.generic.shared.translator;
-import java.util.Set;
-
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
/**
* Translator for {@link DataStoreServicePE} into {@link DatastoreServiceDescription}.
- *
+ *
* @author Franz-Josef Elmer
*/
public class DataStoreServiceTranslator
{
public static DatastoreServiceDescription translate(DataStoreServicePE service)
{
- String[] datasetTypeCodes = extractCodes(service.getDatasetTypes());
+ String[] datasetTypeCodes = Code.extractCodesToArray(service.getDatasetTypes());
String dssCode = service.getDataStore().getCode();
DatastoreServiceDescription dssDescription =
new DatastoreServiceDescription(service.getKey(), service.getLabel(),
@@ -40,19 +38,6 @@ public class DataStoreServiceTranslator
return dssDescription;
}
- private static String[] extractCodes(Set<DataSetTypePE> datasetTypes)
- {
- String[] codes = new String[datasetTypes.size()];
- int i = 0;
- for (DataSetTypePE datasetType : datasetTypes)
- {
- codes[i] = datasetType.getCode();
- i++;
- }
- return codes;
- }
-
-
private DataStoreServiceTranslator()
{
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentPlateLocationsSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentPlateLocationsSection.java
index a1e9f20ace3..cbf96f2508b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentPlateLocationsSection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentPlateLocationsSection.java
@@ -1,6 +1,5 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
-import java.util.ArrayList;
import java.util.Date;
import java.util.List;
@@ -26,6 +25,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpP
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.MultilineVarcharField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
@@ -152,18 +152,9 @@ public class ExperimentPlateLocationsSection extends SingleSectionPanel
{
return null;
}
- String[] materialTypeCodes = extractCodes(materialTypesOrNull);
+ String[] materialTypeCodes = Code.extractCodesToArray(materialTypesOrNull);
return PlateMaterialReviewer.create(screeningViewContext, experiment, materialItemList,
materialTypeCodes);
}
- private static String[] extractCodes(List<MaterialType> materialTypes)
- {
- List<String> codes = new ArrayList<String>();
- for (MaterialType type : materialTypes)
- {
- codes.add(type.getCode());
- }
- return codes.toArray(new String[0]);
- }
}
\ No newline at end of file
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 150adfba1f4..f96eda9cfd6 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
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -151,7 +152,7 @@ public class PlateContentLoader
{
List<ExternalDataPE> analysisDatasets =
ScreeningUtils.filterImageAnalysisDatasets(datasets);
- List<String> datasetCodes = extractCodes(analysisDatasets);
+ List<String> datasetCodes = Code.extractCodes(analysisDatasets);
String dataStoreCode = extractDataStoreCode(analysisDatasets);
return DatasetReportsLoader.loadAnalysisResults(datasetCodes, dataStoreCode,
externalDataTable);
@@ -165,16 +166,6 @@ public class PlateContentLoader
return dataStoreCode;
}
- private List<String> extractCodes(List<ExternalDataPE> datasets)
- {
- List<String> datasetCodes = new ArrayList<String>();
- for (ExternalDataPE dataset : datasets)
- {
- datasetCodes.add(dataset.getCode());
- }
- return datasetCodes;
- }
-
private String extractDataStoreCode(ExternalDataPE imageDataset)
{
return imageDataset.getDataStore().getCode();
--
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