diff --git a/openbis/.classpath b/openbis/.classpath
index 5af6c9a7054f9a91316a6e0fe384155e407bee85..3e4790c9145ae49dc48b00904f1087a74a0e3abc 100644
--- a/openbis/.classpath
+++ b/openbis/.classpath
@@ -61,6 +61,7 @@
<classpathentry kind="lib" path="/libraries/poi/poi-ooxml-3.7-20101029.jar"/>
<classpathentry kind="lib" path="/libraries/poi/poi-ooxml-schemas-3.7-20101029.jar"/>
<classpathentry kind="lib" path="/libraries/gwt-image-loader/gwt-image-loader.jar"/>
+ <classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
<classpathentry kind="lib" path="/libraries/jackson/jackson-core-asl.jar"/>
<classpathentry kind="lib" path="/libraries/jackson/jackson-mapper-asl.jar"/>
<classpathentry kind="lib" path="/libraries/jsonrpc4j/jsonrpc4j.jar"/>
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 6d54a0a50cde0e701da069586e5bd5f987d27fab..bdae38d757459bbd4c06e640d5a214979f40184e 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
@@ -694,6 +694,8 @@ public abstract class Dict
public static final String MENU_ARCHIVING = "menu_archiving";
+ public static final String MENU_GENERAL_IMPORT = "menu_general_import";
+
//
// Tab Titles
//
@@ -734,6 +736,8 @@ public abstract class Dict
public static final String CONFIRM_CLOSE_MSG = "confirm_close_msg";
+ public static final String GENERAL_IMPORT = "general_import";
+
//
// Role View
//
@@ -1056,7 +1060,7 @@ public abstract class Dict
public static final String FILE_TEMPLATE_LABEL = "file_template_label";
public static final String UPDATE_EXISTING_ENTITIES_LABEL = "update_existing_entities_label";
-
+
public static final String URL = "url";
public static final String REASON = "reason";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/ComponentProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/ComponentProvider.java
index 326ca8e8905d2655d9f5fa18795f01599f36d6de..adc2bb9cebb88002d85bd4d88453537d5d826039 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/ComponentProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/ComponentProvider.java
@@ -22,10 +22,12 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAs
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ActionContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.TabContent;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier.HelpPageAction;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier.HelpPageDomain;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AuthorizationGroupGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.GeneralImportComponent;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.PersonGrid;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.RoleAssignmentGrid;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.SpaceGrid;
@@ -1517,6 +1519,45 @@ public final class ComponentProvider
};
}
+ public AbstractTabItemFactory createGeneralImport()
+ {
+ return new AbstractTabItemFactory()
+ {
+ @Override
+ public ITabItem create()
+ {
+ TabContent libraryImportTab = new GeneralImportComponent(viewContext);
+ return createRegistrationTab(getTabTitle(),
+ DatabaseModificationAwareComponent.wrapUnaware(libraryImportTab));
+ }
+
+ @Override
+ public String getId()
+ {
+ return GeneralImportComponent.createId();
+ }
+
+ @Override
+ public HelpPageIdentifier getHelpPageIdentifier()
+ {
+ return new HelpPageIdentifier(HelpPageDomain.GENERAL_IMPORT,
+ HelpPageAction.IMPORT);
+ }
+
+ @Override
+ public String getTabTitle()
+ {
+ return GeneralImportComponent.getTabTitle(viewContext);
+ }
+
+ @Override
+ public String tryGetLink()
+ {
+ return null;
+ }
+ };
+ }
+
public IMainPanel tryGetMainTabPanel()
{
return mainTabPanelOrNull;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/help/HelpPageIdentifier.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/help/HelpPageIdentifier.java
index 38306e8634d9aeb89e6e80fa68150341b0a1f237..dcca2a31db4a361f4e7e2df348a00cfe57bc929e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/help/HelpPageIdentifier.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/help/HelpPageIdentifier.java
@@ -62,6 +62,9 @@ public class HelpPageIdentifier
FILE_TYPE(ADMINISTRATION),
AUTHORIZATION(ADMINISTRATION),
+
+ GENERAL_IMPORT(ADMINISTRATION),
+
// authorization subdomains
USERS(AUTHORIZATION), ROLES(AUTHORIZATION), AUTHORIZATION_GROUPS(AUTHORIZATION),
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/TopMenu.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/TopMenu.java
index 1be451d3979869add42b747189ba376e053001c3..109587f6a084910bf7c48331a9812417a2113e7b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/TopMenu.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/TopMenu.java
@@ -79,7 +79,7 @@ public class TopMenu extends LayoutContainer
USER_MENU_CHANGE_SETTINGS, USER_MENU_LOGOUT, USER_MENU_LOGIN,
- VOCABULARY_MENU_BROWSE, VOCABULARY_MENU_NEW;
+ VOCABULARY_MENU_BROWSE, VOCABULARY_MENU_NEW, GENERAL_IMPORT_MENU;
public String getMenuId()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/administration/AdministrationMenu.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/administration/AdministrationMenu.java
index e20df7990c37477cf8dd22212302b62f04f4aeba..c446ead8c9a2e59e35eb3508c105b0b917b13e05 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/administration/AdministrationMenu.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/menu/administration/AdministrationMenu.java
@@ -51,6 +51,8 @@ public class AdministrationMenu extends TopMenuItem
submenu.add(new AuthorizationMenu(messageProvider, componentProvider));
submenu.add(new ActionMenu(TopMenu.ActionMenuKind.DATA_SET_MENU_FILE_FORMATS,
messageProvider, componentProvider.getFileFormatTypeBrowser()));
+ submenu.add(new ActionMenu(TopMenu.ActionMenuKind.GENERAL_IMPORT_MENU, messageProvider,
+ componentProvider.createGeneralImport()));
if (viewContext.isLoggingEnabled())
{
submenu.add(new ActionMenu(TopMenu.ActionMenuKind.LOGGING_CONSOLE, messageProvider,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/GeneralImportComponent.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/GeneralImportComponent.java
new file mode 100644
index 0000000000000000000000000000000000000000..77240e0f69817e445015cf70b5da0e05335ce91f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/GeneralImportComponent.java
@@ -0,0 +1,59 @@
+package ch.systemsx.cisd.openbis.generic.client.web.client.application.ui;
+
+import com.google.gwt.user.client.ui.Widget;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.TabContent;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+
+/**
+ * Allows to specify search criteria for materials contained in wells. Used in experiment section
+ * panel or as a standalone module.
+ *
+ * @author Pawel Glyzewski
+ */
+public class GeneralImportComponent extends TabContent
+{
+ private static final String PREFIX = "general-import";
+
+ public static final String SESSION_KEY = PREFIX;
+
+ public static final String createId()
+ {
+ return GenericConstants.ID_PREFIX + SESSION_KEY;
+ }
+
+ private final Widget genericImportForm;
+
+ public static String getTabTitle(IViewContext<ICommonClientServiceAsync> viewContext)
+ {
+ return viewContext.getMessage(Dict.GENERAL_IMPORT);
+ }
+
+ public GeneralImportComponent(IViewContext<ICommonClientServiceAsync> viewContext)
+ {
+ super(getTabTitle(viewContext), viewContext, null);
+
+ SampleType sampleType = new SampleType();
+ sampleType
+ .setCode(ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType.DEFINED_IN_FILE);
+ this.genericImportForm =
+ viewContext.getClientPluginFactoryProvider()
+ .getClientPluginFactory(EntityKind.SAMPLE, sampleType)
+ .createClientPlugin(null).createBatchRegistrationForEntityType(null);
+
+ setContentVisible(true);
+ }
+
+ @Override
+ protected void showContent()
+ {
+ removeAll();
+ add(genericImportForm);
+ layout();
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
index ca3e2fd60f42650e57cb3317824752faa5361437..a926344e7cafcc51ebc45221ba403fcb412cc290 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
@@ -40,7 +40,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
*/
abstract class AbstractCommonServer<T extends IServer> extends AbstractServer<T>
{
-
private final IAuthenticationService authenticationService;
protected final ICommonBusinessObjectFactory businessObjectFactory;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
index c31acbdb9605c51688b0888a86c06c8124a5e580..11a19af0e2b699ad0a8ec9c69a959630f501317b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
@@ -16,12 +16,17 @@
package ch.systemsx.cisd.openbis.generic.server;
+import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.Date;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
+import java.util.concurrent.LinkedBlockingQueue;
+import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
import javax.annotation.Resource;
@@ -32,6 +37,9 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.authentication.Principal;
import ch.systemsx.cisd.common.exceptions.InvalidSessionException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.mail.MailClient;
+import ch.systemsx.cisd.common.mail.MailClientParameters;
import ch.systemsx.cisd.common.spring.AbstractServiceWithLogger;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.business.PropertiesBatchManager;
@@ -77,6 +85,9 @@ import ch.systemsx.cisd.openbis.generic.shared.util.ServerUtils;
*/
public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> implements IServer
{
+ protected static ThreadPoolExecutor executor = new ThreadPoolExecutor(1, 10, 360,
+ TimeUnit.SECONDS, new LinkedBlockingQueue<Runnable>());
+
private final static String ETL_SERVER_USERNAME_PREFIX = "etlserver";
protected static final class AuthenticatedPersonBasedPrincipalProvider implements
@@ -120,6 +131,9 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
@Resource(name = ComponentNames.REMOTE_HOST_VALIDATOR)
private IRemoteHostValidator remoteHostValidator;
+ @Resource(name = ResourceNames.MAIL_CLIENT_PARAMETERS)
+ protected MailClientParameters mailClientParameters;
+
private IPropertiesBatchManager propertiesBatchManager;
private String userForAnonymousLogin;
@@ -629,4 +643,47 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
}
}
+ protected void executeASync(final String userEmail, final IASyncAction action)
+ {
+ final IMailClient mailClient = new MailClient(mailClientParameters);
+ Runnable task = new Runnable()
+ {
+ public void run()
+ {
+ StringWriter writer = new StringWriter();
+ boolean success = true;
+ Date startDate = new Date();
+ try
+ {
+ success = action.doAction(writer);
+ } catch (RuntimeException e)
+ {
+ operationLog.error("Asynchronous action '" + action.getName()
+ + "' failed. ", e);
+ success = false;
+ } finally
+ {
+ sendEmail(mailClient, writer.toString(),
+ getSubject(action.getName(), startDate, success), userEmail);
+ }
+ }
+ };
+ executor.submit(task);
+ }
+
+ private void sendEmail(IMailClient mailClient, String content, String subject, String recipient)
+ {
+ mailClient.sendMessage(subject, content, null, null, recipient);
+ }
+
+ private static String getSubject(String actionName, Date startDate, boolean success)
+ {
+ return addDate(actionName + " " + (success ? "successfully performed" : "failed"),
+ startDate);
+ }
+
+ private static String addDate(String subject, Date startDate)
+ {
+ return subject + " (initiated at " + startDate + ")";
+ }
}
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 97ddf4e4a61ca353fe79c05efa80391e58c097e8..227092708f6d6fb80bea6b0ed05e9d4b24f834bd 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
@@ -2486,5 +2486,4 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
return UserFailureException.fromTemplate(exception, "%s '%s': %s", entity.getEntityKind()
.getDescription(), entity.getIdentifier(), exception.getMessage());
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/IASyncAction.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/IASyncAction.java
new file mode 100644
index 0000000000000000000000000000000000000000..cdeb8bde40c84f114ec6ebc4c9e112fa33feff75
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/IASyncAction.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright 2011 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.server;
+
+import java.io.Writer;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public interface IASyncAction
+{
+ public boolean doAction(Writer messageWriter);
+
+ public String getName();
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ResourceNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ResourceNames.java
index df5c19a4bdc3dca9d16910423e433d813223b6f9..bdc6e4191ea327a684d7e0666feea10b0c1a9ff9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ResourceNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ResourceNames.java
@@ -47,6 +47,8 @@ public final class ResourceNames
public final static String ENTITY_INFORMATION_PROVIDER = "entity-information-provider";
+ public static final String MAIL_CLIENT_PARAMETERS = "mail-client-parameters";
+
private ResourceNames()
{
// Can not be instantiated.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientService.java
index 5c9215db4546d71c350c9e568531949fbeeac836..1ebf3c689b8848ab83a6dc0845d3ef18c2555996 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientService.java
@@ -178,7 +178,7 @@ public interface IGenericClientService extends IClientService
* Updates samples and materials from excel files which have been previously uploaded.
*/
public List<BatchRegistrationResult> registerOrUpdateSamplesAndMaterials(
- final String sessionKey, final String defaultGroupIdentifier, boolean updateExisting)
- throws UserFailureException;
+ final String sessionKey, final String defaultGroupIdentifier, boolean updateExisting,
+ boolean async, String userEmail) throws UserFailureException;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientServiceAsync.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientServiceAsync.java
index 667c16a8d64bcd60e3d281f00eb9acbf7eb1913a..de524f2dc8f71bcdcc254496a33a2233fcc7d0c3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientServiceAsync.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientServiceAsync.java
@@ -151,10 +151,12 @@ public interface IGenericClientServiceAsync extends IClientServiceAsync
AsyncCallback<List<BatchRegistrationResult>> registerExperimentsCallback);
/**
- * @see IGenericClientService#registerOrUpdateSamplesAndMaterials(String, String, boolean)
+ * @see IGenericClientService#registerOrUpdateSamplesAndMaterials(String, String, boolean,
+ * boolean, String)
*/
public void registerOrUpdateSamplesAndMaterials(final String sessionKey,
- final String defaultGroupIdentifier, boolean updateExisting,
+ final String defaultGroupIdentifier, boolean updateExisting, boolean async,
+ String userEmail,
AsyncCallback<List<BatchRegistrationResult>> registerSamplesAndMaterialsCallback)
throws UserFailureException;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/ClientPluginFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/ClientPluginFactory.java
index fcd6cd75f10c2431e53274cf486879b0782b37f7..05f548c86797ed93e1d397d805d55e0ec3bbbda0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/ClientPluginFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/ClientPluginFactory.java
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.ICl
import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IModule;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractViewer;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.GeneralImportComponent;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.LinkExtractor;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
@@ -98,6 +99,26 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Gener
public final <T extends BasicEntityType, I extends IIdAndCodeHolder> IClientPlugin<T, I> createClientPlugin(
EntityKind entityKind)
{
+ if (entityKind == null)
+ {
+ return new ClientPluginAdapter<T, I>()
+ {
+ @Override
+ public Widget createBatchRegistrationForEntityType(final T entityType)
+ {
+ return createBatchUpdateForEntityType(entityType);
+ }
+
+ @Override
+ public Widget createBatchUpdateForEntityType(T entityType)
+ {
+ return new GeneralImportForm(getViewContext(),
+ GeneralImportComponent.createId(),
+ GeneralImportComponent.SESSION_KEY);
+ }
+
+ };
+ }
if (EntityKind.EXPERIMENT.equals(entityKind))
{
return (IClientPlugin<T, I>) new ExperimentClientPlugin();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/GeneralImportForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/GeneralImportForm.java
new file mode 100644
index 0000000000000000000000000000000000000000..a9e984d0adb347ab3580d365bc946e026fc1eb5d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/GeneralImportForm.java
@@ -0,0 +1,213 @@
+package ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application;
+
+import static ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareField.wrapUnaware;
+
+import java.util.List;
+
+import com.extjs.gxt.ui.client.Style.Scroll;
+import com.extjs.gxt.ui.client.event.BaseEvent;
+import com.extjs.gxt.ui.client.event.ButtonEvent;
+import com.extjs.gxt.ui.client.event.Events;
+import com.extjs.gxt.ui.client.event.Listener;
+import com.extjs.gxt.ui.client.event.SelectionListener;
+import com.extjs.gxt.ui.client.widget.form.CheckBox;
+import com.extjs.gxt.ui.client.widget.form.Field;
+import com.extjs.gxt.ui.client.widget.form.FileUploadField;
+import com.extjs.gxt.ui.client.widget.form.TextField;
+import com.google.gwt.user.client.Element;
+import com.google.gwt.user.client.ui.AbstractImagePrototype;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.FormPanelListener;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.file.BasicFileFieldManager;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
+import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientServiceAsync;
+
+public class GeneralImportForm extends AbstractRegistrationForm
+{
+ protected final class RegisterOrUpdateSamplesAndMaterialsCallback extends
+ AbstractRegistrationForm.AbstractRegistrationCallback<List<BatchRegistrationResult>>
+ {
+ RegisterOrUpdateSamplesAndMaterialsCallback(
+ final IViewContext<IGenericClientServiceAsync> viewContext)
+ {
+ super(viewContext);
+ }
+
+ @Override
+ protected String createSuccessfullRegistrationInfo(
+ final List<BatchRegistrationResult> result)
+ {
+ final StringBuilder builder = new StringBuilder();
+ for (final BatchRegistrationResult batchRegistrationResult : result)
+ {
+ builder.append("<b>" + batchRegistrationResult.getFileName() + "</b>: ");
+ builder.append(batchRegistrationResult.getMessage());
+ builder.append("<br />");
+ }
+ return builder.toString();
+ }
+ }
+
+ private static final String FIELD_LABEL_TEMPLATE = "File";
+
+ private static final int NUMBER_OF_FIELDS = 1;
+
+ private final String sessionKey;
+
+ private final BasicFileFieldManager fileFieldsManager;
+
+ private final TextField<String> emailField;
+
+ private final CheckBox asynchronous;
+
+ private final IViewContext<IGenericClientServiceAsync> genericViewContext;
+
+ /**
+ * @param genericViewContext
+ * @param id
+ */
+ public GeneralImportForm(IViewContext<IGenericClientServiceAsync> genericViewContext,
+ String id, String sessionKey)
+ {
+ super(genericViewContext, id);
+
+ this.sessionKey = sessionKey;
+ this.genericViewContext = genericViewContext;
+ setScrollMode(Scroll.AUTO);
+ asynchronous = createCheckBox();
+ emailField =
+ createEmailField(genericViewContext.getModel().getSessionContext().getUser()
+ .getUserEmail());
+ fileFieldsManager =
+ new BasicFileFieldManager(sessionKey, NUMBER_OF_FIELDS, FIELD_LABEL_TEMPLATE);
+ fileFieldsManager.setMandatory();
+ addUploadFeatures(sessionKey);
+ }
+
+ @Override
+ protected final void onRender(final Element target, final int index)
+ {
+ System.out.println("onRender!");
+ super.onRender(target, index);
+ addFormFields(false);
+ }
+
+ private CheckBox createCheckBox()
+ {
+ final CheckBox checkBox = new CheckBox();
+ checkBox.setFieldLabel("Asynchronous?");
+ checkBox.setBoxLabel("");
+ checkBox.setValue(true);
+ checkBox.addListener(Events.Change, new Listener<BaseEvent>()
+ {
+ public void handleEvent(BaseEvent be)
+ {
+ System.out.println("Event!");
+ if (checkBox.getValue())
+ {
+ formPanel.removeAll();
+ addFormFields(true);
+ } else
+ {
+ formPanel.remove(emailField);
+ }
+ formPanel.layout();
+ }
+ });
+ return checkBox;
+ }
+
+ private TextField<String> createEmailField(String userEmail)
+ {
+ TextField<String> field = new TextField<String>();
+ field.setAllowBlank(false);
+ field.setFieldLabel("Email");
+ FieldUtil.markAsMandatory(field);
+ field.setValue(userEmail);
+ field.setValidateOnBlur(true);
+ field.setRegex(GenericConstants.EMAIL_REGEX);
+ field.getMessages().setRegexText("Expected email address format: user@domain.com");
+ AbstractImagePrototype infoIcon =
+ AbstractImagePrototype.create(genericViewContext.getImageBundle().getInfoIcon());
+ FieldUtil.addInfoIcon(field,
+ "All relevant notifications will be send to this email address",
+ infoIcon.createImage());
+ return field;
+ }
+
+ @Override
+ protected void submitValidForm()
+ {
+ }
+
+ @Override
+ protected void resetFieldsAfterSave()
+ {
+ for (FileUploadField attachmentField : fileFieldsManager.getFields())
+ {
+ attachmentField.reset();
+ }
+ }
+
+ private final void addFormFields(boolean forceAddEmailField)
+ {
+ formPanel.add(asynchronous);
+ if (forceAddEmailField || asynchronous.getValue())
+ {
+ formPanel.add(emailField);
+ }
+ for (FileUploadField attachmentField : fileFieldsManager.getFields())
+ {
+ formPanel.add(wrapUnaware((Field<?>) attachmentField).get());
+ }
+ formPanel.addListener(Events.Submit, new FormPanelListener(infoBox)
+ {
+ @Override
+ protected void onSuccessfullUpload()
+ {
+ save();
+ }
+
+ @Override
+ protected void setUploadEnabled()
+ {
+ GeneralImportForm.this.setUploadEnabled(true);
+ }
+ });
+ redefineSaveListeners();
+ }
+
+ void redefineSaveListeners()
+ {
+ saveButton.removeAllListeners();
+ saveButton.addSelectionListener(new SelectionListener<ButtonEvent>()
+ {
+ @Override
+ public final void componentSelected(final ButtonEvent ce)
+ {
+ if (formPanel.isValid())
+ {
+ if (fileFieldsManager.filesDefined() > 0)
+ {
+ setUploadEnabled(false);
+ formPanel.submit();
+ } else
+ {
+ save();
+ }
+ }
+ }
+ });
+ }
+
+ protected void save()
+ {
+ genericViewContext.getService().registerOrUpdateSamplesAndMaterials(sessionKey, null, true,
+ asynchronous.getValue(), emailField.getValue(),
+ new RegisterOrUpdateSamplesAndMaterialsCallback(genericViewContext));
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
index fd80dc542a2200e9508fda1b513e3293c06eb9d0..2517a8f801f4214197ac50f6ea532b2acee5edfe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
@@ -173,8 +173,8 @@ public class GenericClientService extends AbstractClientService implements IGene
}
public final List<BatchRegistrationResult> registerOrUpdateSamplesAndMaterials(
- final String sessionKey, final String defaultGroupIdentifier, boolean updateExisting)
- throws UserFailureException
+ final String sessionKey, final String defaultGroupIdentifier, boolean updateExisting,
+ boolean async, String userEmail) throws UserFailureException
{
BatchOperationKind operationKind =
updateExisting ? BatchOperationKind.UPDATE : BatchOperationKind.REGISTRATION;
@@ -197,13 +197,27 @@ public class GenericClientService extends AbstractClientService implements IGene
parseMaterials(session, uploadedFiles, materialType, "MATERIALS",
updateExisting);
final String sessionToken = getSessionToken();
- genericServer.registerOrUpdateSamplesAndMaterials(sessionToken,
- samplesInfo.getSamples(), materialsInfo.getMaterials());
- List<BatchRegistrationResult> results = new ArrayList<BatchRegistrationResult>();
- results.addAll(materialsInfo.getResultList());
- results.addAll(samplesInfo.getResultList());
- return results;
+ if (async)
+ {
+ genericServer.registerOrUpdateSamplesAndMaterialsAsync(sessionToken,
+ samplesInfo.getSamples(), materialsInfo.getMaterials(), userEmail);
+
+ List<BatchRegistrationResult> results = new ArrayList<BatchRegistrationResult>();
+ results.add(new BatchRegistrationResult(uploadedFiles.iterable().iterator().next()
+ .getOriginalFilename(), "File will be processed asynchronously."));
+
+ return results;
+ } else
+ {
+ genericServer.registerOrUpdateSamplesAndMaterials(sessionToken,
+ samplesInfo.getSamples(), materialsInfo.getMaterials());
+
+ List<BatchRegistrationResult> results = new ArrayList<BatchRegistrationResult>();
+ results.addAll(materialsInfo.getResultList());
+ results.addAll(samplesInfo.getResultList());
+ return results;
+ }
} catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
{
throw UserFailureExceptionTranslator.translate(e);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index df37d8bb7b707f10dc84f3ce392fb6fdbc449c5c..dafb53f7661730c3cb7b884af189052af5c2590f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.plugin.generic.server;
+import java.io.Writer;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
@@ -33,6 +34,7 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
+import ch.systemsx.cisd.openbis.generic.server.IASyncAction;
import ch.systemsx.cisd.openbis.generic.server.MaterialHelper;
import ch.systemsx.cisd.openbis.generic.server.batch.BatchOperationExecutor;
import ch.systemsx.cisd.openbis.generic.server.batch.IBatchOperation;
@@ -114,6 +116,9 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
@Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
protected ICommonServer commonServer;
+ @Resource(name = ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER)
+ private IGenericServer genericServer;
+
public GenericServer()
{
}
@@ -779,9 +784,31 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
public void registerOrUpdateSamplesAndMaterials(final String sessionToken,
final List<NewSamplesWithTypes> newSamplesWithType,
- List<NewMaterialsWithTypes> newMaterialsWithType) throws UserFailureException
+ final List<NewMaterialsWithTypes> newMaterialsWithType) throws UserFailureException
{
registerOrUpdateMaterials(sessionToken, newMaterialsWithType);
registerOrUpdateSamples(sessionToken, newSamplesWithType);
}
+
+ public void registerOrUpdateSamplesAndMaterialsAsync(final String sessionToken,
+ final List<NewSamplesWithTypes> newSamplesWithType,
+ final List<NewMaterialsWithTypes> newMaterialsWithType, String userEmail)
+ throws UserFailureException
+ {
+ executeASync(userEmail, new IASyncAction()
+ {
+ public String getName()
+ {
+ return "General Import";
+ }
+
+ public boolean doAction(Writer messageWriter)
+ {
+ genericServer.registerOrUpdateSamplesAndMaterials(sessionToken,
+ newSamplesWithType, newMaterialsWithType);
+ return true;
+ }
+ });
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
index 9c1a2f1d88e26e2dde4e17bbcd70b252e0107ee9..46ea258776fee4e9ac1eacbbfbc3c0c9771fc61b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
@@ -107,31 +107,13 @@ final class GenericServerLogger extends AbstractServerLogger implements IGeneric
public void registerMaterials(String sessionToken, List<NewMaterialsWithTypes> newMaterials)
{
- StringBuilder sb = new StringBuilder();
- for (NewMaterialsWithTypes s : newMaterials)
- {
- if (sb.length() > 0)
- {
- sb.append(",");
- }
- sb.append(s.getEntityType().getCode() + ":" + s.getNewEntities().size());
- }
- logTracking(sessionToken, "register_materials", sb.toString());
+ logTracking(sessionToken, "register_materials", getMaterials(newMaterials));
}
public int updateMaterials(String sessionToken, List<NewMaterialsWithTypes> newMaterials,
boolean ignoreUnregisteredMaterials) throws UserFailureException
{
- StringBuilder sb = new StringBuilder();
- for (NewMaterialsWithTypes s : newMaterials)
- {
- if (sb.length() > 0)
- {
- sb.append(",");
- }
- sb.append(s.getEntityType().getCode() + ":" + s.getNewEntities().size());
- }
- logTracking(sessionToken, "update_materials", sb.toString());
+ logTracking(sessionToken, "update_materials", getMaterials(newMaterials));
return 0;
}
@@ -202,31 +184,13 @@ final class GenericServerLogger extends AbstractServerLogger implements IGeneric
public void registerSamples(String sessionToken, List<NewSamplesWithTypes> newSamplesWithType)
throws UserFailureException
{
- StringBuilder sb = new StringBuilder();
- for (NewSamplesWithTypes s : newSamplesWithType)
- {
- if (sb.length() > 0)
- {
- sb.append(",");
- }
- sb.append(s.getEntityType().getCode() + ":" + s.getNewEntities().size());
- }
- logTracking(sessionToken, "register_samples", sb.toString());
+ logTracking(sessionToken, "register_samples", getSamples(newSamplesWithType));
}
public void updateSamples(String sessionToken, List<NewSamplesWithTypes> updatedSamplesWithType)
throws UserFailureException
{
- StringBuilder sb = new StringBuilder();
- for (NewSamplesWithTypes s : updatedSamplesWithType)
- {
- if (sb.length() > 0)
- {
- sb.append(",");
- }
- sb.append(s.getEntityType().getCode() + ":" + s.getNewEntities().size());
- }
- logTracking(sessionToken, "update_samples", sb.toString());
+ logTracking(sessionToken, "update_samples", getSamples(updatedSamplesWithType));
}
public void registerOrUpdateMaterials(String sessionToken, List<NewMaterialsWithTypes> materials)
@@ -242,16 +206,7 @@ final class GenericServerLogger extends AbstractServerLogger implements IGeneric
public void registerOrUpdateSamples(String sessionToken,
List<NewSamplesWithTypes> newSamplesWithType) throws UserFailureException
{
- StringBuilder sb = new StringBuilder();
- for (NewSamplesWithTypes s : newSamplesWithType)
- {
- if (sb.length() > 0)
- {
- sb.append(",");
- }
- sb.append(s.getEntityType().getCode() + ":" + s.getNewEntities().size());
- }
- logTracking(sessionToken, "register_or_update_samples", sb.toString());
+ logTracking(sessionToken, "register_or_update_samples", getSamples(newSamplesWithType));
}
public void updateDataSets(String sessionToken, NewDataSetsWithTypes dataSets)
@@ -277,7 +232,25 @@ final class GenericServerLogger extends AbstractServerLogger implements IGeneric
public void registerOrUpdateSamplesAndMaterials(final String sessionToken,
final List<NewSamplesWithTypes> newSamplesWithType,
- List<NewMaterialsWithTypes> newMaterialsWithType) throws UserFailureException
+ final List<NewMaterialsWithTypes> newMaterialsWithType) throws UserFailureException
+ {
+
+ logTracking(sessionToken, "register_or_update_samples_and_materials",
+ "SAMPLES(%s) MATERIALS(%s)", getSamples(newSamplesWithType),
+ getMaterials(newMaterialsWithType));
+ }
+
+ public void registerOrUpdateSamplesAndMaterialsAsync(final String sessionToken,
+ final List<NewSamplesWithTypes> newSamplesWithType,
+ final List<NewMaterialsWithTypes> newMaterialsWithType, String userEmail)
+ throws UserFailureException
+ {
+ logTracking(sessionToken, "register_or_update_samples_and_materials_async",
+ "SAMPLES(%s) MATERIALS(%s) EMAIL(%s)", getSamples(newSamplesWithType),
+ getMaterials(newMaterialsWithType), userEmail);
+ }
+
+ private static String getSamples(final List<NewSamplesWithTypes> newSamplesWithType)
{
StringBuilder samples = new StringBuilder();
for (NewSamplesWithTypes s : newSamplesWithType)
@@ -289,6 +262,11 @@ final class GenericServerLogger extends AbstractServerLogger implements IGeneric
samples.append(s.getEntityType().getCode() + ":" + s.getNewEntities().size());
}
+ return samples.toString();
+ }
+
+ private static String getMaterials(final List<NewMaterialsWithTypes> newMaterialsWithType)
+ {
StringBuilder materials = new StringBuilder();
for (NewMaterialsWithTypes s : newMaterialsWithType)
{
@@ -298,7 +276,7 @@ final class GenericServerLogger extends AbstractServerLogger implements IGeneric
}
materials.append(s.getEntityType().getCode() + ":" + s.getNewEntities().size());
}
- logTracking(sessionToken, "register_or_update_samples_and_materials",
- "SAMPLES(%s) MATERIALS(%s)", samples.toString(), materials.toString());
+
+ return materials.toString();
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java
index 7507775d932599857f3da6a517e52d68dcf62b3f..367e42198ebd0d6b06446a0a632465eafe9d2006 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java
@@ -150,6 +150,18 @@ public interface IGenericServer extends IServer
final List<NewSamplesWithTypes> newSamplesWithType,
List<NewMaterialsWithTypes> newMaterialsWithType) throws UserFailureException;
+ /**
+ * Asynchronously registers or updates samples and materials of different types in batches.
+ */
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_ADMIN)
+ @DatabaseCreateOrDeleteModification(value =
+ { ObjectKind.SAMPLE, ObjectKind.MATERIAL })
+ public void registerOrUpdateSamplesAndMaterialsAsync(final String sessionToken,
+ final List<NewSamplesWithTypes> newSamplesWithType,
+ final List<NewMaterialsWithTypes> newMaterialsWithType, String userEmail)
+ throws UserFailureException;
+
/**
* Updates samples of different types in batches.
*/
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 63e8b045cc0894d632ea920b32a967fb2ef79429..204366730d2a06930e1174e1c8d3405054477d23 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
@@ -448,7 +448,9 @@ var common = {
ARCHIVING_MENU_UNARCHIVE: "Unarchive",
ARCHIVING_MENU_LOCK: "Disable",
ARCHIVING_MENU_UNLOCK: "Enable",
-
+
+ GENERAL_IMPORT_MENU: "General Import",
+
menu_modules: "Utilities",
//
@@ -475,7 +477,7 @@ var common = {
list_groups: "Spaces Browser",
confirm_title: "Confirmation",
confirm_close_msg: "All unsaved changes will be lost. Are you sure?",
-
+ general_import: "General Import",
//
// Help Page Titles
diff --git a/openbis/source/java/genericApplicationContext.xml b/openbis/source/java/genericApplicationContext.xml
index 672df3f473020d91bcc96c1f985924d7011a1a47..2a68174d1627c700e55ea1488114ed3e6d669774 100644
--- a/openbis/source/java/genericApplicationContext.xml
+++ b/openbis/source/java/genericApplicationContext.xml
@@ -221,6 +221,18 @@
<bean class="ch.systemsx.cisd.common.spring.LogAdvisor" />
<bean class="ch.systemsx.cisd.common.spring.MarkerLogApplicationListener"/>
+
+ <!--
+ //Mail Client Parameters
+ -->
+ <bean id="mail-client-parameters" class="ch.systemsx.cisd.common.mail.MailClientParameters">
+ <property name="from" value="${mail.from}"/>
+ <property name="smtpHost" value="${mail.smtp.host}"/>
+ <property name="smtpUser" value="${mail.smtp.user}"/>
+ <property name="smtpPassword" value="${mail.smtp.password}"/>
+ </bean>
+
+
<!--
// Plugins
-->
@@ -231,5 +243,4 @@
<plugins:exclude-filter type="annotation"
expression="org.springframework.stereotype.Controller" />
</plugins:component-scan>
-
</beans>
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java.expected
index 7507775d932599857f3da6a517e52d68dcf62b3f..367e42198ebd0d6b06446a0a632465eafe9d2006 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java.expected
@@ -150,6 +150,18 @@ public interface IGenericServer extends IServer
final List<NewSamplesWithTypes> newSamplesWithType,
List<NewMaterialsWithTypes> newMaterialsWithType) throws UserFailureException;
+ /**
+ * Asynchronously registers or updates samples and materials of different types in batches.
+ */
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_ADMIN)
+ @DatabaseCreateOrDeleteModification(value =
+ { ObjectKind.SAMPLE, ObjectKind.MATERIAL })
+ public void registerOrUpdateSamplesAndMaterialsAsync(final String sessionToken,
+ final List<NewSamplesWithTypes> newSamplesWithType,
+ final List<NewMaterialsWithTypes> newMaterialsWithType, String userEmail)
+ throws UserFailureException;
+
/**
* Updates samples of different types in batches.
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningModule.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningModule.java
index bdd80dece9a79b70f929df1bad74035cceebdd34..37640f70b8107dfab62fec758214addf968f9c40 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningModule.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningModule.java
@@ -37,7 +37,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ExperimentAnalysisSummarySection;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ExperimentWellMaterialsSection;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.LibraryImportComponent;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.WellSearchComponent;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.GlobalWellSearchLocatorResolver;
@@ -63,9 +62,7 @@ public class ScreeningModule implements IModule
ActionMenu globalWellSearch =
TabActionMenuItemFactory
.createActionMenu(viewContext, ID, createGlobalWellSearch());
- ActionMenu globalLibraryImport =
- TabActionMenuItemFactory.createActionMenu(viewContext, ID, createLibraryImport());
- return Arrays.asList(globalWellSearch, globalLibraryImport);
+ return Arrays.asList(globalWellSearch);
}
private ITabActionMenuItemDefinition<IScreeningClientServiceAsync> createGlobalWellSearch()
@@ -98,35 +95,6 @@ public class ScreeningModule implements IModule
};
}
- private ITabActionMenuItemDefinition<IScreeningClientServiceAsync> createLibraryImport()
- {
- return new ITabActionMenuItemDefinition<IScreeningClientServiceAsync>()
- {
-
- public String getName()
- {
- return Dict.LIBRARY_IMPORT_MENU_ITEM;
- }
-
- public String getHelpPageTitle()
- {
- return "Global Library Import";
- }
-
- public String tryGetLink()
- {
- return null;
- }
-
- public DatabaseModificationAwareComponent createComponent(
- @SuppressWarnings("hiding") IViewContext<IScreeningClientServiceAsync> viewContext)
- {
- TabContent libraryImportTab = new LibraryImportComponent(viewContext);
- return DatabaseModificationAwareComponent.wrapUnaware(libraryImportTab);
- }
- };
- }
-
public String getName()
{
return viewContext.getMessage(Dict.SCREENING_MODULE_TITLE);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LibraryImportComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LibraryImportComponent.java
deleted file mode 100644
index cc7cf5a40878f9bed3d8f5aad762229ca2dde617..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LibraryImportComponent.java
+++ /dev/null
@@ -1,199 +0,0 @@
-package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
-
-import static ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareField.wrapUnaware;
-
-import java.util.List;
-
-import com.extjs.gxt.ui.client.Style.Scroll;
-import com.extjs.gxt.ui.client.event.ButtonEvent;
-import com.extjs.gxt.ui.client.event.Events;
-import com.extjs.gxt.ui.client.event.SelectionListener;
-import com.extjs.gxt.ui.client.widget.form.Field;
-import com.extjs.gxt.ui.client.widget.form.FileUploadField;
-import com.google.gwt.user.client.Element;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.FormPanelListener;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.TabContent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.file.BasicFileFieldManager;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.GenericViewContext;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningModule;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
-
-/**
- * Allows to specify search criteria for materials contained in wells. Used in experiment section
- * panel or as a standalone module.
- *
- * @author Tomasz Pylak
- */
-public class LibraryImportComponent extends TabContent
-{
-
- private static class LibraryImportForm extends AbstractRegistrationForm
- {
- protected final class RegisterOrUpdateSamplesAndMaterialsCallback
- extends
- AbstractRegistrationForm.AbstractRegistrationCallback<List<BatchRegistrationResult>>
- {
- RegisterOrUpdateSamplesAndMaterialsCallback(
- final IViewContext<IGenericClientServiceAsync> viewContext)
- {
- super(viewContext);
- }
-
- @Override
- protected String createSuccessfullRegistrationInfo(
- final List<BatchRegistrationResult> result)
- {
- final StringBuilder builder = new StringBuilder();
- for (final BatchRegistrationResult batchRegistrationResult : result)
- {
- builder.append("<b>" + batchRegistrationResult.getFileName() + "</b>: ");
- builder.append(batchRegistrationResult.getMessage());
- builder.append("<br />");
- }
- return builder.toString();
- }
- }
-
- private static final String PREFIX = "library-import";
-
- private static final String SESSION_KEY = PREFIX;
-
- private static final String FIELD_LABEL_TEMPLATE = "File";
-
- private static final int NUMBER_OF_FIELDS = 1;
-
- private final BasicFileFieldManager fileFieldsManager;
-
- private final IViewContext<IGenericClientServiceAsync> genericViewContext;
-
- private static String createId(String sessionKey)
- {
- return ScreeningModule.ID + sessionKey;
- }
-
- /**
- * @param viewContext
- */
- protected LibraryImportForm(IViewContext<IGenericClientServiceAsync> viewContext)
- {
- super(viewContext, createId(SESSION_KEY));
-
- this.genericViewContext = viewContext;
- setScrollMode(Scroll.AUTO);
- fileFieldsManager =
- new BasicFileFieldManager(SESSION_KEY, NUMBER_OF_FIELDS, FIELD_LABEL_TEMPLATE);
- fileFieldsManager.setMandatory();
- addUploadFeatures(SESSION_KEY);
- }
-
- @Override
- protected final void onRender(final Element target, final int index)
- {
- super.onRender(target, index);
- addFormFields();
- }
-
- @Override
- protected void submitValidForm()
- {
- }
-
- @Override
- protected void resetFieldsAfterSave()
- {
- for (FileUploadField attachmentField : fileFieldsManager.getFields())
- {
- attachmentField.reset();
- }
- }
-
- private final void addFormFields()
- {
- for (FileUploadField attachmentField : fileFieldsManager.getFields())
- {
- formPanel.add(wrapUnaware((Field<?>) attachmentField).get());
- }
- formPanel.addListener(Events.Submit, new FormPanelListener(infoBox)
- {
- @Override
- protected void onSuccessfullUpload()
- {
- save();
- }
-
- @Override
- protected void setUploadEnabled()
- {
- LibraryImportForm.this.setUploadEnabled(true);
- }
- });
- redefineSaveListeners();
- }
-
- void redefineSaveListeners()
- {
- saveButton.removeAllListeners();
- saveButton.addSelectionListener(new SelectionListener<ButtonEvent>()
- {
- @Override
- public final void componentSelected(final ButtonEvent ce)
- {
- if (formPanel.isValid())
- {
- if (fileFieldsManager.filesDefined() > 0)
- {
- setUploadEnabled(false);
- formPanel.submit();
- } else
- {
- save();
- }
- }
- }
- });
- }
-
- protected void save()
- {
- genericViewContext.getService().registerOrUpdateSamplesAndMaterials(SESSION_KEY, null,
- true, new RegisterOrUpdateSamplesAndMaterialsCallback(genericViewContext));
- }
- }
-
- private final IViewContext<IGenericClientServiceAsync> genericViewContext;
-
- public static String getTabTitle(IViewContext<IScreeningClientServiceAsync> viewContext)
- {
- return viewContext.getMessage(Dict.LIBRARY_IMPORT_TAB_TITLE);
- }
-
- public LibraryImportComponent(IViewContext<IScreeningClientServiceAsync> screeningViewContext)
- {
- this(screeningViewContext, ExperimentSearchCriteria.createAllExperiments());
-
- setContentVisible(true);
- }
-
- public LibraryImportComponent(IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- ExperimentSearchCriteria experimentSearchCriteria)
- {
- super(getTabTitle(screeningViewContext), screeningViewContext, null);
- this.genericViewContext =
- new GenericViewContext(screeningViewContext.getCommonViewContext());
- }
-
- @Override
- protected void showContent()
- {
- removeAll();
- add(new LibraryImportForm(genericViewContext));
- layout();
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
index 687ce99d83d7ac6dbfd3e17da7e0654da94797e0..6f765573fdb9e8dff0023f8cfb4e0f435d9deb10 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTask.java
@@ -1,13 +1,15 @@
package ch.systemsx.cisd.openbis.plugin.screening.server;
+import java.io.IOException;
+import java.io.Writer;
import java.util.Arrays;
-import java.util.Date;
import java.util.List;
import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.common.collections.TableMap;
-import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
+import ch.systemsx.cisd.openbis.generic.server.IASyncAction;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.util.KeyExtractorFactory;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
@@ -30,21 +32,13 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst
*
* @author Izabela Adamczyk
*/
-class LibraryRegistrationTask implements Runnable
+class LibraryRegistrationTask implements IASyncAction
{
- private static final String SUCCESSFUL_LIBRARY_REGISTARION_STATUS =
- "Library successfully registered";
-
- private static final String UNSUCCESSFUL_LIBRARY_REGISTARION_STATUS =
- "Library registration failed";
-
private static final String DELIM = " ";
private final String sessionToken;
- private final String email;
-
private final List<NewMaterial> newGenesOrNull;
private final List<NewMaterial> newOligosOrNull;
@@ -57,45 +51,20 @@ class LibraryRegistrationTask implements Runnable
private final IDAOFactory daoFactory;
- private final IMailClient mailClient;
-
- public LibraryRegistrationTask(String sessionToken, String email,
- List<NewMaterial> newGenesOrNull, List<NewMaterial> newOligosOrNull,
- List<NewSamplesWithTypes> newSamplesWithType, ICommonServer commonServer,
- IGenericServer server, IDAOFactory daoFactory, IMailClient mailClient)
+ public LibraryRegistrationTask(String sessionToken, List<NewMaterial> newGenesOrNull,
+ List<NewMaterial> newOligosOrNull, List<NewSamplesWithTypes> newSamplesWithType,
+ ICommonServer commonServer, IGenericServer server, IDAOFactory daoFactory)
{
this.sessionToken = sessionToken;
- this.email = email;
this.newGenesOrNull = newGenesOrNull;
this.newOligosOrNull = newOligosOrNull;
this.newSamplesWithType = newSamplesWithType;
this.commonServer = commonServer;
this.genericServer = server;
this.daoFactory = daoFactory;
- this.mailClient = mailClient;
}
- public void run()
- {
- boolean success = true;
- Date startDate = new Date();
- StringBuilder message = new StringBuilder();
-
- try
- {
- // when one of these methods fails it will throw an unchecked exception
- registerOrUpdateGenes(message);
- registerOrUpdateOligos(message);
- registerOrUpdateSamples(message);
- } catch (RuntimeException rex)
- {
- success = false;
- }
-
- sendEmail(message.toString(), startDate, email, success);
- }
-
- private void registerOrUpdateSamples(StringBuilder message)
+ private void registerOrUpdateSamples(Writer message) throws IOException
{
try
{
@@ -104,14 +73,14 @@ class LibraryRegistrationTask implements Runnable
genericServer.registerOrUpdateSamples(sessionToken, newSamplesWithType);
for (NewSamplesWithTypes s : newSamplesWithType)
{
- message.append("Successfuly saved " + s.getNewEntities().size()
+ message.write("Successfuly saved " + s.getNewEntities().size()
+ " samples of type " + s.getEntityType() + ".\n");
}
}
} catch (RuntimeException ex)
{
- message.append("ERROR: Plates and wells could not be saved!\n");
- message.append(ex.getMessage());
+ message.write("ERROR: Plates and wells could not be saved!\n");
+ message.write(ex.getMessage());
throw ex;
}
}
@@ -136,7 +105,7 @@ class LibraryRegistrationTask implements Runnable
return materialsWithTypes;
}
- private void registerOrUpdateOligos(StringBuilder message)
+ private void registerOrUpdateOligos(Writer message) throws IOException
{
try
{
@@ -144,17 +113,17 @@ class LibraryRegistrationTask implements Runnable
{
registerOrUpdateMaterials(ScreeningConstants.SIRNA_PLUGIN_TYPE_NAME,
newOligosOrNull);
- message.append("Successfuly saved " + newOligosOrNull.size() + " siRNAs.\n");
+ message.write("Successfuly saved " + newOligosOrNull.size() + " siRNAs.\n");
}
} catch (RuntimeException ex)
{
- message.append("ERROR: siRNAs could not be saved!\n");
- message.append(ex.getMessage());
+ message.write("ERROR: siRNAs could not be saved!\n");
+ message.write(ex.getMessage());
throw ex;
}
}
- private void registerOrUpdateGenes(StringBuilder message)
+ private void registerOrUpdateGenes(Writer message) throws IOException
{
try
{
@@ -171,13 +140,13 @@ class LibraryRegistrationTask implements Runnable
}
registerOrUpdateMaterials(ScreeningConstants.GENE_PLUGIN_TYPE_CODE, newGenesOrNull);
- message.append("Successfuly saved properties of " + newGenesOrNull.size()
+ message.write("Successfuly saved properties of " + newGenesOrNull.size()
+ " genes.\n");
}
} catch (RuntimeException ex)
{
- message.append("ERROR: Genes could not be saved!\n");
- message.append(ex.getMessage());
+ message.write("ERROR: Genes could not be saved!\n");
+ message.write(ex.getMessage());
throw ex;
}
}
@@ -247,19 +216,24 @@ class LibraryRegistrationTask implements Runnable
}
}
- private void sendEmail(String content, Date startDate, String recipient, boolean successful)
+ public boolean doAction(Writer messageWriter)
{
- String status =
- successful ? SUCCESSFUL_LIBRARY_REGISTARION_STATUS
- : UNSUCCESSFUL_LIBRARY_REGISTARION_STATUS;
+ try
+ {
+ registerOrUpdateGenes(messageWriter);
+ registerOrUpdateOligos(messageWriter);
+ registerOrUpdateSamples(messageWriter);
- String subject = addDate(status, startDate);
- mailClient.sendMessage(subject, content, null, null, recipient);
+ return true;
+ } catch (IOException ex)
+ {
+ throw new IOExceptionUnchecked(ex);
+ }
}
- private static String addDate(String subject, Date startDate)
+ public String getName()
{
- return subject + " (initiated at " + startDate + ")";
+ return "Library registration";
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 958ddbff4d91baf0fffde16006e855791f9d41af..24596df1974e710424b315b3e2d3bfff6581af1f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -20,9 +20,6 @@ import java.sql.Connection;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.ThreadPoolExecutor;
-import java.util.concurrent.TimeUnit;
import javax.annotation.Resource;
@@ -34,9 +31,6 @@ import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.mail.MailClient;
-import ch.systemsx.cisd.common.mail.MailClientParameters;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
@@ -132,21 +126,16 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
*/
public static final int MINOR_VERSION = 7;
- private static ThreadPoolExecutor executor = new ThreadPoolExecutor(1, 10, 360,
- TimeUnit.SECONDS, new LinkedBlockingQueue<Runnable>());
-
@Resource(name = ResourceNames.SCREENING_BUSINESS_OBJECT_FACTORY)
private IScreeningBusinessObjectFactory businessObjectFactory;
@Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
private ICommonServer commonServer;
+ // necessary to make it possible to run asynchronous actions
@Resource(name = ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER)
private IGenericServer genericServer;
- @Resource(name = ResourceNames.MAIL_CLIENT_PARAMETERS)
- private MailClientParameters mailClientParameters;
-
public ScreeningServer()
{
}
@@ -287,10 +276,8 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
List<NewMaterial> newGenesOrNull, List<NewMaterial> newOligosOrNull,
List<NewSamplesWithTypes> newSamplesWithType)
{
- IMailClient mailClient = new MailClient(mailClientParameters);
- executor.submit(new LibraryRegistrationTask(sessionToken, userEmail, newGenesOrNull,
- newOligosOrNull, newSamplesWithType, commonServer, genericServer, getDAOFactory(),
- mailClient));
+ executeASync(userEmail, new LibraryRegistrationTask(sessionToken, newGenesOrNull,
+ newOligosOrNull, newSamplesWithType, commonServer, genericServer, getDAOFactory()));
}
public List<Material> listExperimentMaterials(String sessionToken, TechId experimentId,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
index cba01cf953cd84f0a8a859b60ffd4159388ba05f..3cb3884ff6afb6d7c13804871fa22c745f920dc1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
@@ -42,6 +42,4 @@ public final class ResourceNames
public final static String SCREENING_DAO_FACTORY = "screening-dao-factory";
public final static String SCREENING_SAMPLE_SERVER_PLUGIN = "screening-sample-server-plugin";
-
- public static final String MAIL_CLIENT_PARAMETERS = "mail-client-parameters";
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
index 149b6f297d4108cd118ceeab771e708cec9b1f9c..03d4609f20a4edacf29658dfba28750deb6a6314 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/LibraryRegistrationTaskTest.java
@@ -16,8 +16,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.server;
-import static org.hamcrest.text.StringContains.containsString;
-
+import java.io.StringWriter;
import java.util.Arrays;
import java.util.List;
@@ -29,8 +28,6 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.common.mail.From;
-import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.test.RecordingMatcher;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
@@ -59,8 +56,6 @@ public class LibraryRegistrationTaskTest extends AssertJUnit
{
private static final String SESSION_TOKEN = "session";
- private static final String USER_EMAIL = "micky.mouse@acme.org";
-
private Mockery context;
private ICommonServer commonServer;
@@ -71,8 +66,6 @@ public class LibraryRegistrationTaskTest extends AssertJUnit
private IEntityTypeDAO entityTypeDAO;
- private IMailClient mailClient;
-
private LibraryRegistrationTask task;
@BeforeMethod
@@ -83,7 +76,6 @@ public class LibraryRegistrationTaskTest extends AssertJUnit
genericServer = context.mock(IGenericServer.class);
daoFactory = context.mock(IDAOFactory.class);
entityTypeDAO = context.mock(IEntityTypeDAO.class);
- mailClient = context.mock(IMailClient.class);
}
@AfterMethod
@@ -110,8 +102,8 @@ public class LibraryRegistrationTaskTest extends AssertJUnit
new RecordingMatcher<List<NewMaterialsWithTypes>>();
task =
- new LibraryRegistrationTask(SESSION_TOKEN, USER_EMAIL, newGenes, null, null,
- commonServer, genericServer, daoFactory, mailClient);
+ new LibraryRegistrationTask(SESSION_TOKEN, newGenes, null, null, commonServer,
+ genericServer, daoFactory);
context.checking(new Expectations()
{
@@ -129,16 +121,10 @@ public class LibraryRegistrationTaskTest extends AssertJUnit
one(genericServer).registerOrUpdateMaterials(with(SESSION_TOKEN),
with(materialsWithTypesMatcher));
-
- String[] emailTo = new String[]
- { USER_EMAIL };
- one(mailClient).sendMessage(with(containsString("success")),
- with(any(String.class)), with(aNull(String.class)),
- with(aNull(From.class)), with(emailTo));
}
});
- task.run();
+ task.doAction(new StringWriter());
assertEquals("ABC A AB", extractGeneSymbol(g1));
assertEquals("AB", extractGeneSymbol(g2));