From 2de7df481aad4d24026075e41a957b89dc144930 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Thu, 16 Jun 2011 13:04:22 +0000
Subject: [PATCH] [LMS-2209] logical deletion of samples (1 level, no cascade)
SVN: 21723
---
.../web/client/ICommonClientService.java | 17 +++---
.../web/client/ICommonClientServiceAsync.java | 31 +++++-----
.../client/web/client/application/Dict.java | 44 +++++++-------
.../SampleListDeletionConfirmationDialog.java | 7 ++-
...actDataListDeletionConfirmationDialog.java | 57 +++++++++++++++++--
.../web/server/CommonClientService.java | 14 +++--
.../openbis/generic/server/CommonServer.java | 14 ++++-
.../generic/server/CommonServerLogger.java | 8 ++-
.../server/business/bo/ISampleTable.java | 9 +++
.../server/business/bo/SampleTable.java | 14 +++++
.../generic/server/dataaccess/ISampleDAO.java | 8 ++-
.../db/AbstractGenericEntityDAO.java | 8 ++-
.../server/dataaccess/db/SampleDAO.java | 21 +++++++
.../openbis/generic/shared/ICommonServer.java | 3 +-
.../shared/basic/IInvalidationProvider.java | 5 +-
.../shared/basic/dto/DeletionType.java | 29 ++++++++++
.../generic/shared/dto/InvalidationPE.java | 4 +-
.../sample/GenericSampleViewer.java | 2 +-
.../cisd/openbis/public/common-dictionary.js | 22 ++++---
.../systemtest/ExperimentBrowsingTest.java | 11 ++--
.../DynamicPropertiesEvaluationTest.java | 4 +-
21 files changed, 247 insertions(+), 85 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DeletionType.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
index 41a9e1661db..ed9a85ce0dc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
@@ -60,6 +60,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DynamicPropertyEvaluationInfo;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
@@ -644,17 +645,19 @@ public interface ICommonClientService extends IClientService
public void deleteDataSet(String singleData, String reason) throws UserFailureException;
/**
- * Deletes the specified samples. NOTE: this is a stale version used only for samples with
- * abundance.
+ * Deletes/Invalidates the specified samples. NOTE: this is a stale version used only for
+ * samples with abundance.
*/
- public void deleteSamples(List<TechId> sampleIds, String reason) throws UserFailureException;
+ public void deleteSamples(List<TechId> sampleIds, String reason, DeletionType deletionType)
+ throws UserFailureException;
- /** Deletes the specified samples. */
+ /** Deletes/Invalidates the specified samples. */
public void deleteSamples(DisplayedOrSelectedIdHolderCriteria<? extends IIdHolder> criteria,
- String reason) throws UserFailureException;
+ String reason, DeletionType deletionType) throws UserFailureException;
- /** Deletes the specified sample. */
- public void deleteSample(TechId sampleId, String reason) throws UserFailureException;
+ /** Deletes/Invalidates the specified sample. */
+ public void deleteSample(TechId sampleId, String reason, DeletionType deletionType)
+ throws UserFailureException;
/** Deletes the specified experiments. */
public void deleteExperiments(
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
index 80be7c17bea..72fb1f7f88d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
@@ -62,6 +62,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DynamicPropertyEvaluationInfo;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
@@ -548,42 +549,46 @@ public interface ICommonClientServiceAsync extends IClientServiceAsync
/** @see ICommonClientService#deleteDataSet(String, String) */
public void deleteDataSet(String singleData, String reason, AsyncCallback<Void> asyncCallback);
- /** @see ICommonClientService#deleteSamples(List, String) */
- public void deleteSamples(List<TechId> sampleIds, String value,
+ /** @see ICommonClientService#deleteSamples(List, String, DeletionType) */
+ public void deleteSamples(List<TechId> sampleIds, String reason, DeletionType type,
AsyncCallback<Void> asyncCallback);
- /** @see ICommonClientService#deleteSamples(DisplayedOrSelectedIdHolderCriteria, String) */
+ /**
+ * @see ICommonClientService#deleteSamples(DisplayedOrSelectedIdHolderCriteria, String,
+ * DeletionType)
+ */
public void deleteSamples(DisplayedOrSelectedIdHolderCriteria<? extends IIdHolder> criteria,
- String value, AsyncCallback<Void> asyncCallback);
+ String reason, DeletionType type, AsyncCallback<Void> asyncCallback);
- /** @see ICommonClientService#deleteSample(TechId, String) */
- public void deleteSample(TechId sampleIs, String value, AsyncCallback<Void> asyncCallback);
+ /** @see ICommonClientService#deleteSample(TechId, String, DeletionType) */
+ public void deleteSample(TechId sampleIs, String reason, DeletionType type,
+ AsyncCallback<Void> asyncCallback);
/** @see ICommonClientService#deleteExperiments(DisplayedOrSelectedIdHolderCriteria, String) */
public void deleteExperiments(
DisplayedOrSelectedIdHolderCriteria<TableModelRowWithObject<Experiment>> criteria,
- String value, AsyncCallback<Void> asyncCallback);
+ String reason, AsyncCallback<Void> asyncCallback);
/** @see ICommonClientService#deleteExperiment(TechId, String) */
- public void deleteExperiment(TechId experimentId, String value,
+ public void deleteExperiment(TechId experimentId, String reason,
AsyncCallback<Void> asyncCallback);
/** @see ICommonClientService#deleteProjects(List, String) */
- public void deleteProjects(List<TechId> projectIds, String value,
+ public void deleteProjects(List<TechId> projectIds, String reason,
AsyncCallback<Void> asyncCallback);
/** @see ICommonClientService#deleteGroups(List, String) */
- public void deleteGroups(List<TechId> groupIds, String value, AsyncCallback<Void> asyncCallback);
+ public void deleteGroups(List<TechId> groupIds, String reason, AsyncCallback<Void> asyncCallback);
/** @see ICommonClientService#deleteScripts(List) */
public void deleteScripts(List<TechId> scriptIds, AsyncCallback<Void> asyncCallback);
/** @see ICommonClientService#deleteVocabularies(List, String) */
- public void deleteVocabularies(List<TechId> vocabularyIds, String value,
+ public void deleteVocabularies(List<TechId> vocabularyIds, String reason,
AsyncCallback<Void> asyncCallback);
/** @see ICommonClientService#deletePropertyTypes(List, String) */
- public void deletePropertyTypes(List<TechId> propertyTypeIds, String value,
+ public void deletePropertyTypes(List<TechId> propertyTypeIds, String reason,
AsyncCallback<Void> asyncCallback);
/** @see ICommonClientService#deleteAttachments(TechId, AttachmentHolderKind, List, String) */
@@ -898,7 +903,7 @@ public interface ICommonClientServiceAsync extends IClientServiceAsync
/** @see ICommonClientService#deleteMaterials(DisplayedOrSelectedIdHolderCriteria, String) */
public void deleteMaterials(DisplayedOrSelectedIdHolderCriteria<Material> uploadCriteria,
- String value, AsyncCallback<Void> callback);
+ String reason, AsyncCallback<Void> callback);
/**
* @see ICommonClientService#lockDatasets(DisplayedOrSelectedDatasetCriteria)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
index 66c66880a48..840b00f5415 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
@@ -476,6 +476,29 @@ public abstract class Dict
// -------- generic plugin dictionary -------------------
+ //
+ // Deletion
+ //
+
+ public static final String INVALIDATE = "invalidate";
+
+ public static final String INVALIDATION = "invalidation";
+
+ public static final String INVALIDATION_TEMPLATE = "invalidation_template";
+
+ public static final String PERMANENT = "permanent";
+
+ public static final String DELETE_CONFIRMATION_TITLE = "delete_confirmation_title";
+
+ public static final String DELETE_CONFIRMATION_MESSAGE = "delete_confirmation_message";
+
+ public static final String DELETE_CONFIRMATION_MESSAGE_WITH_REASON =
+ "delete_confirmation_message_with_reason";
+
+ public static final String DELETE_PROGRESS_MESSAGE = "delete_progress_message";
+
+ public static final String INVALIDATE_PROGRESS_MESSAGE = "invalidate_progress_message";
+
//
// Sample Viewer
//
@@ -492,10 +515,6 @@ public abstract class Dict
public static final String EXTERNAL_DATA_HEADING = "external_data_heading";
- public static final String INVALIDATION = "invalidation";
-
- public static final String INVALIDATION_TEMPLATE = "invalidation_template";
-
public static final String SHOW_ONLY_DIRECTLY_CONNECTED = "show_only_directly_connected";
//
@@ -950,23 +969,6 @@ public abstract class Dict
public static final String BUTTON_DELETE = "button_delete";
- public static final String DELETE_CONFIRMATION_TITLE = "delete_confirmation_title";
-
- public static final String DELETE_CONFIRMATION_MESSAGE = "delete_confirmation_message";
-
- public static final String DELETE_CONFIRMATION_MESSAGE_WITH_REASON =
- "delete_confirmation_message_with_reason";
-
- public static final String DELETE_PROGRESS_MESSAGE = "delete_progress_message";
-
- public static final String DELETE_CONFIRMATION_WARNING = "delete_confirmation_warning";
-
- public static final String DELETE_CONFIRMATION_WARNING_PART_FOR_EXPERIMENT =
- "delete_confirmation_warning_part_for_experiment";
-
- public static final String DELETE_CONFIRMATION_WARNING_PART_FOR_SAMPLE =
- "delete_confirmation_warning_part_for_sample";
-
public static final String BUTTON_CONFIGURE = "button_configure";
public static final String BUTTON_FILTERS = "button_filters";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/SampleListDeletionConfirmationDialog.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/SampleListDeletionConfirmationDialog.java
index a47523b484e..6cf83bc5a7e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/SampleListDeletionConfirmationDialog.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/SampleListDeletionConfirmationDialog.java
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.Widge
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DisplayedOrSelectedIdHolderCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
public final class SampleListDeletionConfirmationDialog<T extends IIdHolder> extends
@@ -68,16 +69,18 @@ public final class SampleListDeletionConfirmationDialog<T extends IIdHolder> ext
@Override
protected void executeDeletion(AsyncCallback<Void> deletionCallback)
{
+ DeletionType deletionType =
+ isPermanentDeletion() ? DeletionType.PERMANENT : DeletionType.INVALIDATION;
if (selectedAndDisplayedItemsOrNull != null)
{
final DisplayedOrSelectedIdHolderCriteria<T> uploadCriteria =
selectedAndDisplayedItemsOrNull.createCriteria(isOnlySelected());
viewContext.getCommonService().deleteSamples(uploadCriteria, reason.getValue(),
- deletionCallback);
+ deletionType, deletionCallback);
} else
{
viewContext.getCommonService().deleteSample(TechId.create(singleDataOrNull),
- reason.getValue(), deletionCallback);
+ reason.getValue(), deletionType, deletionCallback);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/AbstractDataListDeletionConfirmationDialog.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/AbstractDataListDeletionConfirmationDialog.java
index 512e1166d04..a81e00fa1f4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/AbstractDataListDeletionConfirmationDialog.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/AbstractDataListDeletionConfirmationDialog.java
@@ -18,6 +18,9 @@ package ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget
import java.util.List;
+import com.extjs.gxt.ui.client.event.Events;
+import com.extjs.gxt.ui.client.event.FieldEvent;
+import com.extjs.gxt.ui.client.event.Listener;
import com.extjs.gxt.ui.client.widget.form.Radio;
import com.extjs.gxt.ui.client.widget.form.RadioGroup;
import com.google.gwt.user.client.rpc.AsyncCallback;
@@ -25,6 +28,7 @@ import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AsyncCallbackWithProgressBar;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.CheckBoxField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ReasonField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.WidgetUtils;
@@ -46,27 +50,44 @@ public abstract class AbstractDataListDeletionConfirmationDialog<T> extends
private static final String SELECTED = " selected ";
+ private static final String TEMPORARILY = "temporarily";
+
+ private static final String PERMANENTLY_EMPHASIZED = "<b>permanently</b>";
+
private final AbstractAsyncCallback<Void> callback;
private final boolean withRadio;
+ private final boolean withInvalidateOption;
+
protected Radio onlySelectedRadioOrNull;
+ protected CheckBoxField permanentCheckBoxOrNull;
+
protected ReasonField reason;
public AbstractDataListDeletionConfirmationDialog(IMessageProvider messageProvider,
- List<T> data, AbstractAsyncCallback<Void> callback, boolean withRadio)
+ List<T> data, AbstractAsyncCallback<Void> callback, boolean withRadio,
+ boolean withInvalidateOption)
{
super(messageProvider, data, messageProvider.getMessage(Dict.DELETE_CONFIRMATION_TITLE));
this.callback = callback;
this.withRadio = withRadio;
+ this.withInvalidateOption = withInvalidateOption;
+ }
+
+ // maybe with radio & temporarily
+ public AbstractDataListDeletionConfirmationDialog(IMessageProvider messageProvider,
+ List<T> data, AbstractAsyncCallback<Void> callback, boolean withRadio)
+ {
+ this(messageProvider, data, callback, withRadio, true);
}
- // without radio
+ // without radio & permanently
public AbstractDataListDeletionConfirmationDialog(IMessageProvider messageProvider,
List<T> data, AbstractAsyncCallback<Void> callback)
{
- this(messageProvider, data, callback, false);
+ this(messageProvider, data, callback, false, false);
}
@Override
@@ -78,6 +99,10 @@ public abstract class AbstractDataListDeletionConfirmationDialog<T> extends
reason = new ReasonField(messageProvider, true);
reason.focus();
reason.addKeyListener(keyListener);
+ if (withInvalidateOption)
+ {
+ formPanel.add(permanentCheckBoxOrNull = createDeletePermanentlyCheckBox());
+ }
if (withRadio)
{
formPanel.add(createRadio());
@@ -98,7 +123,7 @@ public abstract class AbstractDataListDeletionConfirmationDialog<T> extends
(isOnlySelected() ? data.size() + SELECTED : ALL_EMPHASIZED) + getEntityName();
}
return messageProvider.getMessage(Dict.DELETE_CONFIRMATION_MESSAGE_WITH_REASON,
- deletedObjects);
+ isPermanentDeletion() ? PERMANENTLY_EMPHASIZED : TEMPORARILY, deletedObjects);
}
protected abstract String getEntityName();
@@ -120,18 +145,38 @@ public abstract class AbstractDataListDeletionConfirmationDialog<T> extends
return null;
}
+ private CheckBoxField createDeletePermanentlyCheckBox()
+ {
+ CheckBoxField result = new CheckBoxField(messageProvider.getMessage(Dict.PERMANENT), false);
+ result.setValue(true);
+ result.addListener(Events.Change, new Listener<FieldEvent>()
+ {
+ public void handleEvent(FieldEvent fe)
+ {
+ refreshMessage();
+ }
+ });
+ return result;
+ }
+
protected final boolean isOnlySelected()
{
return WidgetUtils.isSelected(onlySelectedRadioOrNull);
}
+ protected final boolean isPermanentDeletion()
+ {
+ return permanentCheckBoxOrNull == null || permanentCheckBoxOrNull.getValue();
+ }
+
/**
* Returns deletion callback and shows a progress bar that will be hidden when the callback is
* finished.
*/
private AsyncCallback<Void> getCallbackWithProgressBar()
{
- return AsyncCallbackWithProgressBar.decorate(callback,
- messageProvider.getMessage(Dict.DELETE_PROGRESS_MESSAGE, getEntityName()));
+ return AsyncCallbackWithProgressBar.decorate(callback, messageProvider.getMessage(
+ isPermanentDeletion() ? Dict.DELETE_PROGRESS_MESSAGE
+ : Dict.INVALIDATE_PROGRESS_MESSAGE, getEntityName()));
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
index 6d4a4f88713..e392b983a7b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
@@ -115,6 +115,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypePropertyType
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DynamicPropertyEvaluationInfo;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
@@ -1577,26 +1578,27 @@ public final class CommonClientService extends AbstractClientService implements
}
}
- public void deleteSamples(List<TechId> sampleIds, String reason)
+ public void deleteSamples(List<TechId> sampleIds, String reason, DeletionType deletionType)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
try
{
final String sessionToken = getSessionToken();
- commonServer.deleteSamples(sessionToken, sampleIds, reason);
+ commonServer.deleteSamples(sessionToken, sampleIds, reason, deletionType);
} catch (final UserFailureException e)
{
throw UserFailureExceptionTranslator.translate(e);
}
}
- public void deleteSample(TechId sampleId, String reason)
+ public void deleteSample(TechId sampleId, String reason, DeletionType deletionType)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
try
{
final String sessionToken = getSessionToken();
- commonServer.deleteSamples(sessionToken, Collections.singletonList(sampleId), reason);
+ commonServer.deleteSamples(sessionToken, Collections.singletonList(sampleId), reason,
+ deletionType);
} catch (final UserFailureException e)
{
throw UserFailureExceptionTranslator.translate(e);
@@ -1604,14 +1606,14 @@ public final class CommonClientService extends AbstractClientService implements
}
public void deleteSamples(DisplayedOrSelectedIdHolderCriteria<? extends IIdHolder> criteria,
- String reason)
+ String reason, DeletionType deletionType)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
try
{
final String sessionToken = getSessionToken();
List<TechId> sampleIds = extractTechIds(criteria);
- commonServer.deleteSamples(sessionToken, sampleIds, reason);
+ commonServer.deleteSamples(sessionToken, sampleIds, reason, deletionType);
} catch (final UserFailureException e)
{
throw UserFailureExceptionTranslator.translate(e);
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 17eafa058b1..b58ea493799 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
@@ -102,6 +102,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DynamicPropertyEvaluationInfo;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
@@ -1166,13 +1167,22 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
}
}
- public void deleteSamples(String sessionToken, List<TechId> sampleIds, String reason)
+ public void deleteSamples(String sessionToken, List<TechId> sampleIds, String reason,
+ DeletionType deletionType)
{
Session session = getSession(sessionToken);
try
{
ISampleTable sampleTableBO = businessObjectFactory.createSampleTable(session);
- sampleTableBO.deleteByTechIds(sampleIds, reason);
+ switch (deletionType)
+ {
+ case PERMANENT:
+ sampleTableBO.deleteByTechIds(sampleIds, reason);
+ break;
+ case INVALIDATION:
+ sampleTableBO.invalidateByTechIds(sampleIds, reason);
+ break;
+ }
} catch (final DataAccessException ex)
{
throw createUserFailureException(ex);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
index 2a913397bce..bc09b0c62b1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchSubCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DynamicPropertyEvaluationInfo;
@@ -581,10 +582,11 @@ final class CommonServerLogger extends AbstractServerLogger implements ICommonSe
abbreviate(dataSetCodes), reason);
}
- public void deleteSamples(String sessionToken, List<TechId> sampleIds, String reason)
+ public void deleteSamples(String sessionToken, List<TechId> sampleIds, String reason,
+ DeletionType deletionType)
{
- logTracking(sessionToken, "delete_samples", "IDS(%s) REASON(%s)", abbreviate(sampleIds),
- reason);
+ logTracking(sessionToken, "delete_samples", "TYPE(%s) IDS(%s) REASON(%s)", deletionType,
+ abbreviate(sampleIds), reason);
}
public void deleteExperiments(String sessionToken, List<TechId> experimentIds, String reason)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
index edf03ef6e9e..b2aeda9c6da 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
@@ -71,4 +71,13 @@ public interface ISampleTable
*/
public void deleteByTechIds(List<TechId> sampleIds, String reason) throws UserFailureException;
+ /**
+ * Invalidates samples for specified reason.
+ *
+ * @param sampleIds sample technical identifiers
+ * @throws UserFailureException if one of the samples can not be invalidated.
+ */
+ public void invalidateByTechIds(List<TechId> sampleIds, String reason)
+ throws UserFailureException;
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
index 42c245bbe3f..b78e338a97c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
@@ -340,4 +340,18 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
}
}
+ public void invalidateByTechIds(List<TechId> sampleIds, String reason)
+ throws UserFailureException
+ {
+ try
+ {
+ getSessionFactory().getCurrentSession().flush();
+ getSessionFactory().getCurrentSession().clear();
+ getSampleDAO().invalidate(sampleIds, session.tryGetPerson(), reason);
+ } catch (final DataAccessException ex)
+ {
+ throwException(ex, "Sample", EntityKind.SAMPLE);
+ }
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
index c6eeea87ef2..ca4d43c8a9e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
@@ -117,8 +117,14 @@ public interface ISampleDAO extends IGenericDAO<SamplePE>
List<SamplePE> listByPermID(Set<String> values);
/**
- * Delete samples with given by specified registrator with specified reason.
+ * Delete samples with given ids by specified registrator with specified reason.
*/
void delete(List<TechId> sampleIds, PersonPE registrator, String reason)
throws DataAccessException;
+
+ /**
+ * Invalidate samples with given ids by specified registrator with specified reason.
+ */
+ void invalidate(List<TechId> sampleIds, PersonPE registrator, String reason)
+ throws DataAccessException;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityDAO.java
index 9bffc9c7566..3063b7767a8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityDAO.java
@@ -72,7 +72,7 @@ public abstract class AbstractGenericEntityDAO<T extends IIdHolder> extends Abst
+ techId.getId() + " does not exist. Maybe someone has just deleted it.");
} else
{
- result = getEntity(getHibernateTemplate().get(getEntityClass(), techId.getId()));
+ result = getEntity(entity);
}
if (operationLog.isDebugEnabled())
{
@@ -82,6 +82,12 @@ public abstract class AbstractGenericEntityDAO<T extends IIdHolder> extends Abst
return result;
}
+ public final T loadByTechId(final TechId techId) throws DataAccessException
+ {
+ assert techId != null : "Technical identifier unspecified.";
+ return getEntity(getHibernateTemplate().load(getEntityClass(), techId.getId()));
+ }
+
private String getEntityDescription()
{
String nameWithoutPE = getEntityClass().getSimpleName().replace("PE", "");
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
index fe9291cfe13..9dcd63bf55e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
@@ -45,6 +45,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.InvalidationPE;
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;
@@ -439,6 +440,26 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
scheduleRemoveFromFullTextIndex(ids);
}
+ public void invalidate(final List<TechId> sampleIds, final PersonPE registrator,
+ final String reason) throws DataAccessException
+ {
+ // TODO 2011-06-16, Piotr Buczek: move when cascade invalidation is implemented
+ InvalidationPE invalidation = new InvalidationPE();
+ invalidation.setReason(reason);
+ invalidation.setRegistrator(registrator);
+ getHibernateTemplate().save(invalidation);
+
+ // TODO 2011-06-16, Piotr Buczek: could be done faster with bulk update
+ for (TechId sampleId : sampleIds)
+ {
+ SamplePE sample = loadByTechId(sampleId);
+ sample.setInvalidation(invalidation);
+ getHibernateTemplate().update(sample);
+ }
+
+ getHibernateTemplate().flush();
+ }
+
@SuppressWarnings("unchecked")
public Set<TechId> listParents(final Collection<TechId> children, final TechId relationship)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
index 066f0ce4c48..520b457b666 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
@@ -68,6 +68,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DynamicPropertyEvaluationInfo;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
@@ -756,7 +757,7 @@ public interface ICommonServer extends IServer
public void deleteSamples(
String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdCollectionPredicate.class) List<TechId> sampleIds,
- String reason);
+ String reason, DeletionType type);
/**
* Deletes specified experiments.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IInvalidationProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IInvalidationProvider.java
index 06c013e36f1..68d815bcd68 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IInvalidationProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/IInvalidationProvider.java
@@ -19,12 +19,9 @@ package ch.systemsx.cisd.openbis.generic.shared.basic;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Invalidation;
/**
- *
- *
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
public interface IInvalidationProvider
{
public Invalidation getInvalidation();
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DeletionType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DeletionType.java
new file mode 100644
index 00000000000..39c93cbbfc9
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DeletionType.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright 2007 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.basic.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
+
+/**
+ * Types of deletion operations.
+ *
+ * @author Piotr Buczek
+ */
+public enum DeletionType implements ISerializable
+{
+ PERMANENT, INVALIDATION
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/InvalidationPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/InvalidationPE.java
index 3648115ab56..8a25039fb90 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/InvalidationPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/InvalidationPE.java
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
/**
* Class representing invalidation.
*
- * @author Franz-Josef Elmer
+ * @author Franz-Josef Elmer
*/
@Entity
@Table(name = TableNames.INVALIDATION_TABLE)
@@ -47,7 +47,7 @@ public class InvalidationPE extends HibernateAbstractRegistrationHolder implemen
{
private static final long serialVersionUID = IServer.VERSION;
- private transient Long id;
+ private Long id;
private String reason;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewer.java
index 7f2ea5c3a03..37a3b196ca1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleViewer.java
@@ -265,7 +265,6 @@ abstract public class GenericSampleViewer extends AbstractViewerWithVerticalSpli
final Map<String, Object> properties = new LinkedHashMap<String, Object>();
final Sample sample = sampleGeneration.getParent();
final SampleType sampleType = sample.getSampleType();
- final Invalidation invalidation = sample.getInvalidation();
final Sample[] generated = sampleGeneration.getDerived();
properties.put(viewContext.getMessage(Dict.SAMPLE_PROPERTIES_PANEL_SAMPLE_IDENTIFIER),
sample.getIdentifier());
@@ -275,6 +274,7 @@ abstract public class GenericSampleViewer extends AbstractViewerWithVerticalSpli
properties.put(viewContext.getMessage(Dict.REGISTRATOR), sample.getRegistrator());
properties
.put(viewContext.getMessage(Dict.REGISTRATION_DATE), sample.getRegistrationDate());
+ final Invalidation invalidation = sample.getInvalidation();
if (invalidation != null)
{
properties.put(viewContext.getMessage(Dict.INVALIDATION), invalidation);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
index b79e7b58f57..bd3afded33a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
@@ -41,9 +41,6 @@ var common = {
entity_operations: "Entity:",
url: "URL",
is_official: "Approved?",
- reason: "Reason",
- delete_confirmation_message_with_reason: "You are deleting {0}(s).<br><br>Please enter a reason or cancel deletion.",
- delete_progress_message: "Deleting {0}(s)...",
add_attachment: "Add attachment...",
data_view: "Data View",
container_type: "Container",
@@ -59,6 +56,21 @@ var common = {
explore_label: "Explore:",
add_unofficial_vocabulary_term_dialog_title: "Add Ad Hoc Term",
breadcrumbs_separator: "»",
+
+ //
+ // Deletion
+ //
+
+ invalidate: "Invalidate",
+ invalidation: "Invalidation",
+ invalidation_template: "Invalidated by: {0}<br>date: {1}<br>reason: {2}",
+ permanent: "Permanent",
+ reason: "Reason",
+ delete_confirmation_title: "Confirm Deletion",
+ delete_confirmation_message: "Are you sure you want to delete [{0}]?",
+ delete_confirmation_message_with_reason: "You are {0} deleting {1}(s).<br><br>Please enter a reason or cancel deletion.",
+ delete_progress_message: "Deleting {0}(s)...",
+ delete_progress_message: "Invalidating {0}(s)...",
//
// Table Modifications
@@ -203,8 +215,6 @@ var common = {
part_of: "Container",
generatedfromparent: "Parents",
containerparent: "Container",
- invalidation: "Invalidation",
- invalidation_template: "Invalidated by: {0}<br>Invalidation Date: {1}<br>Invalidation Reason: {2}",
//
// Experiment Browser
@@ -244,8 +254,6 @@ var common = {
edit_type_button: "Edit",
add_type_title_template: "Add a new {0} Type",
edit_type_title_template: "Edit {0} Type {1}",
- delete_confirmation_title: "Confirm Deletion",
- delete_confirmation_message: "Are you sure you want to delete [{0}]?",
//
// Sample Type Browser
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/ExperimentBrowsingTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/ExperimentBrowsingTest.java
index 95b02d2b6e4..debf1c9353e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/ExperimentBrowsingTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/ExperimentBrowsingTest.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.systemtest;
-
import static org.testng.AssertJUnit.assertEquals;
import org.testng.annotations.Test;
@@ -31,8 +30,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
/**
- *
- *
* @author Franz-Josef Elmer
*/
@Test(groups = "system test")
@@ -61,7 +58,7 @@ public class ExperimentBrowsingTest extends SystemTestCase
assertEquals(5, resultSet.getResultSet().getTotalLength());
assertEquals(5, resultSet.getResultSet().getList().size());
}
-
+
@Test
public void testListExperiments()
{
@@ -85,7 +82,7 @@ public class ExperimentBrowsingTest extends SystemTestCase
assertEquals(3, resultSet.getResultSet().getTotalLength());
assertEquals(3, resultSet.getResultSet().getList().size());
}
-
+
@Test
public void testListExperimentsPartially()
{
@@ -101,13 +98,13 @@ public class ExperimentBrowsingTest extends SystemTestCase
project.setCode("NEMO");
criteria.setProject(project);
criteria.setLimit(2);
- criteria.setCacheConfig(ResultSetFetchConfig.<String>createComputeAndCache());
+ criteria.setCacheConfig(ResultSetFetchConfig.<String> createComputeAndCache());
TypedTableResultSet<Experiment> resultSet = commonClientService.listExperiments(criteria);
String key = resultSet.getResultSet().getResultSetKey();
assertEquals(true, resultSet.getResultSet().isPartial());
assertEquals(2, resultSet.getResultSet().getTotalLength());
assertEquals(2, resultSet.getResultSet().getList().size());
-
+
criteria.setCacheConfig(ResultSetFetchConfig.createFetchFromCacheAndRecompute(key));
resultSet = commonClientService.listExperiments(criteria);
assertEquals(key, resultSet.getResultSet().getResultSetKey());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/DynamicPropertiesEvaluationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/DynamicPropertiesEvaluationTest.java
index 0e8cf69f580..ca2a5e7da72 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/DynamicPropertiesEvaluationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/DynamicPropertiesEvaluationTest.java
@@ -36,6 +36,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSetWithEntit
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.SampleUpdates;
import ch.systemsx.cisd.openbis.generic.shared.basic.GridRowModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
@@ -362,7 +363,8 @@ public class DynamicPropertiesEvaluationTest extends GenericSystemTestCase
commonClientService.unassignPropertyType(EntityKind.SAMPLE, DESCRIPTION, CELL_PLATE);
if (createdSampleId != null)
{
- commonClientService.deleteSample(createdSampleId, "test cleanup");
+ commonClientService.deleteSample(createdSampleId, "test cleanup",
+ DeletionType.PERMANENT);
}
}
}
--
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