From 07a51ab6c05d216b2345a6e8e06df2c1caff2f57 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Fri, 17 Sep 2010 11:13:28 +0000
Subject: [PATCH] [LMS-1761] changed comment in templates used for batch
update; use '<DELETE>' to mark deletion of value in sample batch update (not
working for properties yet)
SVN: 17889
---
.../openbis/generic/server/CommonServer.java | 107 ++++++++++--------
.../UpdatedSampleParserObjectFactory.java | 68 ++++++++++-
.../UpdatedSampleParserObjectFactoryTest.java | 3 +-
3 files changed, 125 insertions(+), 53 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index 7464d42f06b..0b18247b6b7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -186,7 +186,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
public final class CommonServer extends AbstractCommonServer<ICommonServerForInternalUse> implements
- ICommonServerForInternalUse
+ ICommonServerForInternalUse
{
private final LastModificationState lastModificationState;
@@ -220,7 +220,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
return new CommonServerLogger(getSessionManager(), context);
}
-
+
//
// ISystemAuthenticator
//
@@ -233,19 +233,20 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
role.setDatabaseInstance(getDAOFactory().getHomeDatabaseInstance());
role.setRole(RoleCode.ADMIN);
systemUser.addRoleAssignment(role);
- String sessionToken = sessionManager.tryToOpenSession(systemUser.getUserId(), new IPrincipalProvider()
- {
- public Principal tryToGetPrincipal(String userID)
- {
- return new Principal(systemUser.getUserId(), systemUser.getFirstName(),
- systemUser.getLastName(), systemUser.getEmail(), true);
- }
- });
+ String sessionToken =
+ sessionManager.tryToOpenSession(systemUser.getUserId(), new IPrincipalProvider()
+ {
+ public Principal tryToGetPrincipal(String userID)
+ {
+ return new Principal(systemUser.getUserId(), systemUser.getFirstName(),
+ systemUser.getLastName(), systemUser.getEmail(), true);
+ }
+ });
Session session = sessionManager.getSession(sessionToken);
session.setPerson(systemUser);
return tryGetSession(sessionToken);
}
-
+
//
// IGenericServer
//
@@ -429,8 +430,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
IHibernateSearchDAO searchDAO = getDAOFactory().getHibernateSearchDAO();
final Collection<Long> sampleIds =
- searchDAO.searchForEntityIds(criteria,
- DtoConverters.convertEntityKind(EntityKind.SAMPLE));
+ searchDAO.searchForEntityIds(criteria, DtoConverters
+ .convertEntityKind(EntityKind.SAMPLE));
final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
return sampleLister.list(new ListOrSearchSampleCriteria(sampleIds));
} catch (final DataAccessException ex)
@@ -644,8 +645,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
Session session = getSession(sessionToken);
IEntityTypePropertyTypeBO etptBO =
- businessObjectFactory.createEntityTypePropertyTypeBO(session,
- DtoConverters.convertEntityKind(entityKind));
+ businessObjectFactory.createEntityTypePropertyTypeBO(session, DtoConverters
+ .convertEntityKind(entityKind));
etptBO.loadAssignment(propertyTypeCode, entityTypeCode);
etptBO.updateLoadedAssignment(isMandatory, defaultValue, section, previousETPTOrdinal);
}
@@ -657,8 +658,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
Session session = getSession(sessionToken);
IEntityTypePropertyTypeBO etptBO =
- businessObjectFactory.createEntityTypePropertyTypeBO(session,
- DtoConverters.convertEntityKind(entityKind));
+ businessObjectFactory.createEntityTypePropertyTypeBO(session, DtoConverters
+ .convertEntityKind(entityKind));
etptBO.loadAssignment(propertyTypeCode, entityTypeCode);
etptBO.deleteLoadedAssignment();
}
@@ -670,8 +671,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
Session session = getSession(sessionToken);
IEntityTypePropertyTypeBO etptBO =
- businessObjectFactory.createEntityTypePropertyTypeBO(session,
- DtoConverters.convertEntityKind(entityKind));
+ businessObjectFactory.createEntityTypePropertyTypeBO(session, DtoConverters
+ .convertEntityKind(entityKind));
return etptBO.countAssignmentValues(propertyTypeCode, entityTypeCode);
}
@@ -783,8 +784,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
IHibernateSearchDAO searchDAO = getDAOFactory().getHibernateSearchDAO();
final Collection<Long> datasetIds =
- searchDAO.searchForEntityIds(criteria,
- DtoConverters.convertEntityKind(EntityKind.DATA_SET));
+ searchDAO.searchForEntityIds(criteria, DtoConverters
+ .convertEntityKind(EntityKind.DATA_SET));
final IDatasetLister datasetLister = createDatasetLister(session);
return datasetLister.listByDatasetIds(datasetIds);
} catch (final DataAccessException ex)
@@ -930,8 +931,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
getDAOFactory().getFileFormatTypeDAO().createOrUpdate(fileFormatType);
} catch (final DataAccessException ex)
{
- DataAccessExceptionTranslator.throwException(ex,
- String.format("File format type '%s' ", fileFormatType.getCode()), null);
+ DataAccessExceptionTranslator.throwException(ex, String.format(
+ "File format type '%s' ", fileFormatType.getCode()), null);
}
}
@@ -1199,9 +1200,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
experimentBO.loadDataByTechId(experimentId);
- return AttachmentTranslator.translate(
- listHolderAttachments(session, experimentBO.getExperiment()),
- session.getBaseIndexURL());
+ return AttachmentTranslator.translate(listHolderAttachments(session, experimentBO
+ .getExperiment()), session.getBaseIndexURL());
} catch (final DataAccessException ex)
{
throw createUserFailureException(ex);
@@ -1215,9 +1215,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
sampleBO.loadDataByTechId(sampleId);
- return AttachmentTranslator
- .translate(listHolderAttachments(session, sampleBO.getSample()),
- session.getBaseIndexURL());
+ return AttachmentTranslator.translate(listHolderAttachments(session, sampleBO
+ .getSample()), session.getBaseIndexURL());
} catch (final DataAccessException ex)
{
throw createUserFailureException(ex);
@@ -1231,9 +1230,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
IProjectBO projectBO = businessObjectFactory.createProjectBO(session);
projectBO.loadDataByTechId(projectId);
- return AttachmentTranslator.translate(
- listHolderAttachments(session, projectBO.getProject()),
- session.getBaseIndexURL());
+ return AttachmentTranslator.translate(listHolderAttachments(session, projectBO
+ .getProject()), session.getBaseIndexURL());
} catch (final DataAccessException ex)
{
throw createUserFailureException(ex);
@@ -1376,8 +1374,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
{
if (entityOrNull == null)
{
- throw UserFailureException.fromTemplate("There is no %s with permId '%s'.",
- kind.getDescription(), permId);
+ throw UserFailureException.fromTemplate("There is no %s with permId '%s'.", kind
+ .getDescription(), permId);
}
return createInformationHolder(kind, entityOrNull);
}
@@ -1480,9 +1478,10 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
} catch (DataIntegrityViolationException ex)
{
throw new UserFailureException(
- String.format(
- "File format type '%s' is being used. Use 'Data Set Search' to find all connected data sets.",
- code));
+ String
+ .format(
+ "File format type '%s' is being used. Use 'Data Set Search' to find all connected data sets.",
+ code));
}
}
}
@@ -1511,11 +1510,12 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
if (types.size() != 1)
{
section =
- String.format(
- "[%s]\n%s%s\n",
- entityType.getCode(),
- firstSection ? "# Comments must be located after the type declaration ('[TYPE]').\n"
- : "", section);
+ String
+ .format(
+ "[%s]\n%s%s\n",
+ entityType.getCode(),
+ firstSection ? "# Comments must be located after the type declaration ('[TYPE]').\n"
+ : "", section);
}
sb.append(section);
firstSection = false;
@@ -1523,6 +1523,11 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
return sb.toString();
}
+ private static final String UPDATE_TEMPLATE_COMMENT =
+ "# If one doesn't want to modify values in a column the column can be removed completely from the file.\n"
+ + "# Empty value in a column also means that the value stored in openBIS shouldn't be changed.\n "
+ + "# To delete a value/connection from openBIS one needs to put '<DELETE>' into the corresponding cell.\n";
+
private String createTemplateForType(EntityKind entityKind, boolean autoGenerate,
EntityTypePE entityType, boolean addComments, boolean withExperiments,
BatchOperationKind operationKind)
@@ -1561,16 +1566,22 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
}
sb.append(column);
}
- if (entityKind.equals(EntityKind.SAMPLE) && addComments)
+ if (addComments)
{
-
switch (operationKind)
{
case REGISTRATION:
- sb.insert(0, NewSample.SAMPLE_REGISTRATION_TEMPLATE_COMMENT);
+ if (entityKind.equals(EntityKind.SAMPLE))
+ {
+ sb.insert(0, NewSample.SAMPLE_REGISTRATION_TEMPLATE_COMMENT);
+ }
break;
case UPDATE:
- sb.insert(0, UpdatedSample.SAMPLE_UPDATE_TEMPLATE_COMMENT);
+ sb.insert(0, UPDATE_TEMPLATE_COMMENT);
+ if (entityKind.equals(EntityKind.SAMPLE))
+ {
+ sb.insert(0, UpdatedSample.SAMPLE_UPDATE_TEMPLATE_COMMENT);
+ }
break;
}
}
@@ -1702,8 +1713,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
IExternalDataTable externalDataTable =
businessObjectFactory.createExternalDataTable(session);
Map<String, String> parameterBindings = new HashMap<String, String>();
- externalDataTable.processDatasets(serviceDescription.getKey(),
- serviceDescription.getDatastoreCode(), datasetCodes, parameterBindings);
+ externalDataTable.processDatasets(serviceDescription.getKey(), serviceDescription
+ .getDatastoreCode(), datasetCodes, parameterBindings);
}
public void registerAuthorizationGroup(String sessionToken,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
index a9fa808590c..e19e568b759 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
+import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleBatchUpdateDetails;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@@ -30,17 +31,21 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.UpdatedSample;
*/
final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactory
{
- private final SampleBatchUpdateDetails batchUpdateDetails;
+ private final SampleBatchUpdateDetails basicBatchUpdateDetails;
UpdatedSampleParserObjectFactory(final SampleType sampleType,
final IPropertyMapper propertyMapper, boolean identifierExpectedInFile,
boolean allowExperiments)
{
super(sampleType, propertyMapper, identifierExpectedInFile, allowExperiments);
- this.batchUpdateDetails = createBatchUpdateDetails();
+ this.basicBatchUpdateDetails = createBasicBatchUpdateDetails();
}
- private SampleBatchUpdateDetails createBatchUpdateDetails()
+ /**
+ * Prepares details about which values should be updated in general taking into account only the
+ * information about availability of columns in the file.
+ */
+ private SampleBatchUpdateDetails createBasicBatchUpdateDetails()
{
boolean updateExperiment = isColumnAvailable(UpdatedSample.EXPERIMENT);
boolean updateParent = isColumnAvailable(UpdatedSample.PARENT);
@@ -57,6 +62,61 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
public NewSample createObject(final String[] lineTokens) throws ParserException
{
final NewSample newSample = super.createObject(lineTokens);
- return new UpdatedSample(newSample, batchUpdateDetails);
+ final SampleBatchUpdateDetails updateDetails = createBatchUpdateDetails(newSample);
+ cleanUp(newSample);
+ return new UpdatedSample(newSample, updateDetails);
}
+
+ //
+
+ /**
+ * Returns details about which values should be updated for the specified sample. If a cell was
+ * left empty in the file the corresponding value will not be modified.
+ */
+ private SampleBatchUpdateDetails createBatchUpdateDetails(NewSample newSample)
+ {
+ boolean updateExperiment =
+ basicBatchUpdateDetails.isExperimentUpdateRequested()
+ && isNotEmpty(newSample.getExperimentIdentifier());
+ boolean updateParent =
+ basicBatchUpdateDetails.isParentUpdateRequested()
+ && isNotEmpty(newSample.getParentIdentifier());
+ boolean updateContainer =
+ basicBatchUpdateDetails.isContainerUpdateRequested()
+ && isNotEmpty(newSample.getContainerIdentifier());
+
+ // TODO 2010-09-17, Piotr Buczek: properties
+ return new SampleBatchUpdateDetails(updateExperiment, updateParent, updateContainer,
+ basicBatchUpdateDetails.getPropertiesToUpdate());
+ }
+
+ /** Cleans the placeholders used to mark deletion of values in the specified sample. */
+ private void cleanUp(NewSample newSample)
+ {
+ if (shouldDelete(newSample.getExperimentIdentifier()))
+ {
+ newSample.setExperimentIdentifier(null);
+ }
+ if (shouldDelete(newSample.getParentIdentifier()))
+ {
+ newSample.setParentIdentifier(null);
+ }
+ if (shouldDelete(newSample.getContainerIdentifier()))
+ {
+ newSample.setContainerIdentifier(null);
+ }
+ }
+
+ private static final String DELETE = "<DELETE>";
+
+ private static boolean isNotEmpty(String value)
+ {
+ return StringUtils.isBlank(value) == false;
+ }
+
+ private static boolean shouldDelete(String value)
+ {
+ return DELETE.equals(value);
+ }
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java
index 96165eecf65..13da86e57eb 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java
@@ -100,7 +100,8 @@ public final class UpdatedSampleParserObjectFactoryTest
assertEquals(2, propertiesToUpdate.size());
assertTrue(propertiesToUpdate.contains(PROPERTY_1));
assertTrue(propertiesToUpdate.contains(PROPERTY_2));
- assertTrue(batchUpdateDetails.isContainerUpdateRequested());
+ assertEquals(StringUtils.isBlank(lineTokens[2]) == false, batchUpdateDetails
+ .isContainerUpdateRequested());
assertFalse(batchUpdateDetails.isParentUpdateRequested());
assertFalse(batchUpdateDetails.isExperimentUpdateRequested());
}
--
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