diff --git a/openbis/dist/server/service.properties b/openbis/dist/server/service.properties
index a8107147edbea5d16925a5925874f0058baa2676..f8c3d9e88b0ca0e3c26cd587f140000132c1cb41 100644
--- a/openbis/dist/server/service.properties
+++ b/openbis/dist/server/service.properties
@@ -33,6 +33,9 @@ database-instance = TEST
# Base URL of the Data Store Server
data-store-server-base-url = https://localhost:8444
+# The URL of the CIFEX server
+cifex-url = https://cifex.ethz.ch:443
+
# Hibernate Search
# The working directory.
hibernate.search.index-base = ./indices
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 807c9bac0b5544581fd59c554262dd11580dfaa1..9ce4d92410bf1a3b88b2952d93f6b4a5b98d801f 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
@@ -433,4 +433,8 @@ public interface ICommonClientService extends IClientService {
*/
public List<DataSetType> listDataSetTypes() throws UserFailureException;
+ /** Uploads the specified data sets to the specified CIFEX server using the specified password. */
+ public void uploadDataSets(List<String> dataSetCodes, String cifexURL, String password)
+ throws UserFailureException;
+
}
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 412354b5d668eb557c58c3d0698935539aea60cf..219c0b3a621f692916e00432ef5fd5ebba50dbef 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
@@ -373,4 +373,8 @@ public interface ICommonClientServiceAsync extends IClientServiceAsync {
/** @see ICommonClientService#listDataSetTypes() */
public void listDataSetTypes(AsyncCallback<List<DataSetType>> callback);
+
+ /** @see ICommonClientService#uploadDataSets(List, String, String) */
+ public void uploadDataSets(List<String> dataSetCodes, String cifexURL, String password,
+ AsyncCallback<Void> abstractAsyncCallback);
}
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 126b776587c9a7f457f45a217372a637359c5905..2b04cf16b6fce44ddead2a9d65404543d0dd37e5 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
@@ -310,10 +310,16 @@ public abstract class Dict {
public static final String CONFIRM_DATASET_DELETION_MSG = "confirm_dataset_deletion_msg";
- //
- // Sample Registration
- //
-
+ public static final String BUTTON_UPLOAD_DATASETS = "button_upload_datasets";
+
+ public static final String CONFIRM_DATASET_UPLOAD_TITLE = "confirm_dataset_upload_title";
+
+ public static final String CONFIRM_DATASET_UPLOAD_MSG = "confirm_dataset_upload_msg";
+
+ //
+ // Sample Registration
+ //
+
public static final String INSTANCE_SAMPLE = "instance_sample";
public static final String GENERATED_FROM_SAMPLE = "generated_from_sample";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/AbstractExternalDataGrid.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/AbstractExternalDataGrid.java
index eb275269f49ad3909ca57e6a9dc7f642ccbe22f5..77c754e90b045bf8266dc5011996e5b7ef7a9b94 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/AbstractExternalDataGrid.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/data/AbstractExternalDataGrid.java
@@ -53,6 +53,31 @@ public abstract class AbstractExternalDataGrid extends AbstractSimpleBrowserGrid
{
public static final String GRID_POSTFIX = "-grid";
+ private static abstract class AbstractConfirmationDialog extends Dialog
+ {
+ protected final IViewContext<?> viewContext;
+
+ protected final List<String> dataSetCodes;
+
+ protected final IBrowserGridActionInvoker invoker;
+
+ AbstractConfirmationDialog(IViewContext<?> viewContext, List<ExternalData> dataSets,
+ IBrowserGridActionInvoker invoker, String titleKey)
+ {
+ this.viewContext = viewContext;
+ this.invoker = invoker;
+ dataSetCodes = new ArrayList<String>();
+ for (ExternalData externalData : dataSets)
+ {
+ dataSetCodes.add(externalData.getCode());
+ }
+ setHeading(viewContext.getMessage(titleKey));
+ setButtons(Dialog.OKCANCEL);
+ setHideOnButtonClick(true);
+ setModal(true);
+ }
+ }
+
static final class DeletionCallback extends AbstractAsyncCallback<Void>
{
private final IBrowserGridActionInvoker invoker;
@@ -70,28 +95,14 @@ public abstract class AbstractExternalDataGrid extends AbstractSimpleBrowserGrid
}
}
- private static final class DeletionConfirmationDialog extends Dialog
+ private static final class DeletionConfirmationDialog extends AbstractConfirmationDialog
{
- private final IViewContext<?> viewContext;
-
- private final List<String> dataSetCodes;
-
- private final IBrowserGridActionInvoker invoker;
-
private final TextField<String> reason;
public DeletionConfirmationDialog(IViewContext<?> viewContext, List<ExternalData> dataSets,
IBrowserGridActionInvoker invoker)
{
- this.viewContext = viewContext;
- this.invoker = invoker;
- dataSetCodes = new ArrayList<String>();
- for (ExternalData externalData : dataSets)
- {
- dataSetCodes.add(externalData.getCode());
- }
- setHeading(viewContext.getMessage(Dict.CONFIRM_DATASET_DELETION_TITLE));
- setButtons(Dialog.OKCANCEL);
+ super(viewContext, dataSets, invoker, Dict.CONFIRM_DATASET_DELETION_TITLE);
addText(viewContext.getMessage(Dict.CONFIRM_DATASET_DELETION_MSG, dataSets.size()));
reason = new TextField<String>();
reason.setSelectOnFocus(true);
@@ -107,8 +118,6 @@ public abstract class AbstractExternalDataGrid extends AbstractSimpleBrowserGrid
}
});
add(reason);
- setHideOnButtonClick(true);
- setModal(true);
}
@Override
@@ -123,6 +132,73 @@ public abstract class AbstractExternalDataGrid extends AbstractSimpleBrowserGrid
}
}
+ static final class UploadCallback extends AbstractAsyncCallback<Void>
+ {
+ private UploadCallback(IViewContext<?> viewContext)
+ {
+ super(viewContext);
+ }
+
+ @Override
+ protected void process(Void result)
+ {
+ }
+ }
+
+ private static final class UploadConfirmationDialog extends AbstractConfirmationDialog
+ {
+ private final String cifexURL;
+ private final TextField<String> password;
+
+ public UploadConfirmationDialog(IViewContext<?> viewContext, List<ExternalData> dataSets,
+ IBrowserGridActionInvoker invoker)
+ {
+ super(viewContext, dataSets, invoker, Dict.CONFIRM_DATASET_UPLOAD_TITLE);
+ cifexURL = viewContext.getModel().getApplicationInfo().getCIFEXURL();
+ addText(viewContext.getMessage(Dict.CONFIRM_DATASET_UPLOAD_MSG, dataSets.size(), cifexURL));
+ password = new TextField<String>();
+ password.setPassword(true);
+ password.setSelectOnFocus(true);
+ password.setHideLabel(true);
+ password.setWidth("100%");
+ password.setMaxLength(50);
+ add(password);
+ }
+
+ @Override
+ protected void onButtonPressed(Button button)
+ {
+ super.onButtonPressed(button);
+ if (button.getItemId().equals(Dialog.OK))
+ {
+ viewContext.getCommonService().uploadDataSets(dataSetCodes, cifexURL, password.getValue(),
+ new UploadCallback(viewContext));
+ }
+ }
+ }
+
+ private abstract class AbstractDataSetAction extends SelectionListener<ButtonEvent>
+ {
+ @Override
+ public void componentSelected(ButtonEvent ce)
+ {
+ List<BaseEntityModel<ExternalData>> items = getSelectedItems();
+ if (items.isEmpty() == false)
+ {
+ List<ExternalData> dataSets = new ArrayList<ExternalData>();
+ for (BaseEntityModel<ExternalData> item : items)
+ {
+ dataSets.add(item.getBaseObject());
+ }
+ IBrowserGridActionInvoker invoker = asActionInvoker();
+ createDialog(dataSets, invoker).show();
+ }
+ }
+
+ protected abstract Dialog createDialog(List<ExternalData> dataSets,
+ IBrowserGridActionInvoker invoker);
+ }
+
protected AbstractExternalDataGrid(final IViewContext<ICommonClientServiceAsync> viewContext,
String browserId)
{
@@ -135,29 +211,33 @@ public abstract class AbstractExternalDataGrid extends AbstractSimpleBrowserGrid
DataSetUtils.showDataSet(rowItem, viewContext.getModel());
}
});
- Button deleteButton = new Button(viewContext.getMessage(Dict.BUTTON_DELETE_DATASETS));
- deleteButton.addSelectionListener(new SelectionListener<ButtonEvent>()
+ addButton(Dict.BUTTON_DELETE_DATASETS, new AbstractDataSetAction()
{
@Override
- public void componentSelected(ButtonEvent ce)
+ protected Dialog createDialog(List<ExternalData> dataSets,
+ IBrowserGridActionInvoker invoker)
{
- List<BaseEntityModel<ExternalData>> items = getSelectedItems();
- if (items.isEmpty() == false)
- {
- List<ExternalData> dataSets = new ArrayList<ExternalData>();
- for (BaseEntityModel<ExternalData> item : items)
- {
- dataSets.add(item.getBaseObject());
- }
- IBrowserGridActionInvoker invoker = asActionInvoker();
- new DeletionConfirmationDialog(viewContext, dataSets, invoker).show();
- }
-
+ return new DeletionConfirmationDialog(viewContext, dataSets, invoker);
+ }
+ });
+ addButton(Dict.BUTTON_UPLOAD_DATASETS, new AbstractDataSetAction()
+ {
+ @Override
+ protected Dialog createDialog(List<ExternalData> dataSets,
+ IBrowserGridActionInvoker invoker)
+ {
+ return new UploadConfirmationDialog(viewContext, dataSets, invoker);
}
});
- pagingToolbar.add(new AdapterToolItem(deleteButton));
allowMultipleSelection();
}
+
+ private void addButton(String labelKey, SelectionListener<ButtonEvent> action)
+ {
+ Button button = new Button(viewContext.getMessage(labelKey));
+ button.addSelectionListener(action);
+ pagingToolbar.add(new AdapterToolItem(button));
+ }
@Override
protected IColumnDefinitionKind<ExternalData>[] getStaticColumnsDefinition()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/ApplicationInfo.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/ApplicationInfo.java
index fa9a03d106753889393651deddf31d310ef3486f..900357ba2fe4bda92fe24dec64505dc5298d35b1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/ApplicationInfo.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/ApplicationInfo.java
@@ -26,6 +26,7 @@ import com.google.gwt.user.client.rpc.IsSerializable;
public final class ApplicationInfo implements IsSerializable
{
private String version;
+ private String cifexURL;
public final String getVersion()
{
@@ -37,4 +38,14 @@ public final class ApplicationInfo implements IsSerializable
this.version = version;
}
+ public void setCIFEXURL(String cifexURL)
+ {
+ this.cifexURL = cifexURL;
+ }
+
+ public final String getCIFEXURL()
+ {
+ return cifexURL;
+ }
+
}
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 35bd0fe7844f4eb455a007dd06ff0d34c8278172..186683f5550b459f903e636a94d0553712138255 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
@@ -125,16 +125,19 @@ public final class CommonClientService extends AbstractClientService implements
ICommonClientService {
private final ICommonServer commonServer;
- private final String dataStoreBaseURL;
+ private String dataStoreBaseURL;
- public CommonClientService(final ICommonServer commonServer,
- final IRequestContextProvider requestContextProvider,
- String dataStoreBaseURL) {
- super(requestContextProvider);
- this.commonServer = commonServer;
- this.dataStoreBaseURL = dataStoreBaseURL + "/"
- + DATA_STORE_SERVER_WEB_APPLICATION_NAME;
- }
+ public CommonClientService(final ICommonServer commonServer,
+ final IRequestContextProvider requestContextProvider)
+ {
+ super(requestContextProvider);
+ this.commonServer = commonServer;
+ }
+
+ public final void setDataStoreBaseURL(String dataStoreBaseURL)
+ {
+ this.dataStoreBaseURL = dataStoreBaseURL + "/" + DATA_STORE_SERVER_WEB_APPLICATION_NAME;
+ }
@Override
protected final IServer getServer() {
@@ -946,6 +949,35 @@ public final class CommonClientService extends AbstractClientService implements
}
+ public void uploadDataSets(List<String> dataSetCodes, String cifexURL, String password)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ commonServer.uploadDataSets(sessionToken, dataSetCodes, cifexURL, password);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
+ public void updateMaterial(String materialIdentifier, List<MaterialProperty> properties,
+ Date version)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ try
+ {
+ final String sessionToken = getSessionToken();
+ final MaterialIdentifier identifier =
+ MaterialIdentifier.tryParseIdentifier(materialIdentifier);
+ commonServer.editMaterial(sessionToken, identifier, properties, version);
+ } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
public void deleteDataSets(List<String> dataSetCodes, String reason)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
try {
@@ -955,22 +987,7 @@ public final class CommonClientService extends AbstractClientService implements
throw UserFailureExceptionTranslator.translate(e);
}
}
-
- public void updateMaterial(String materialIdentifier,
- List<MaterialProperty> properties, Date version)
- throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException {
- try {
- final String sessionToken = getSessionToken();
- final MaterialIdentifier identifier = MaterialIdentifier
- .tryParseIdentifier(materialIdentifier);
- commonServer.editMaterial(sessionToken, identifier, properties,
- version);
- } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e) {
- throw UserFailureExceptionTranslator.translate(e);
- }
-
- }
-
+
public void updateSample(
String sampleIdentifier,
List<SampleProperty> properties,
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 01fcb06ebe57e72252ef29e8a8e76a89539c3511..fba8b36a1ab34e3986b429bd3ab34764ca8d8aa3 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
@@ -17,16 +17,12 @@
package ch.systemsx.cisd.openbis.generic.server;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.Collections;
import java.util.Date;
-import java.util.LinkedHashSet;
import java.util.List;
-import java.util.Set;
import org.springframework.dao.DataAccessException;
-import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.IAuthenticationService;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.authentication.Principal;
@@ -49,12 +45,10 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IVocabularyBO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IRoleAssignmentDAO;
import ch.systemsx.cisd.openbis.generic.server.util.GroupIdentifierHelper;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
-import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
@@ -67,7 +61,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
@@ -104,11 +97,8 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
*
* @author Franz-Josef Elmer
*/
-public final class CommonServer extends AbstractServer<ICommonServer> implements
- ICommonServer {
- @Private
- static final String DELETION_DESCRIPTION = "single deletion";
-
+public final class CommonServer extends AbstractServer<ICommonServer> implements ICommonServer
+{
private final IAuthenticationService authenticationService;
private final ICommonBusinessObjectFactory businessObjectFactory;
@@ -577,59 +567,37 @@ public final class CommonServer extends AbstractServer<ICommonServer> implements
}
}
- public void deleteDataSets(String sessionToken, List<String> dataSetCodes,
- String reason) {
- Session session = getSessionManager().getSession(sessionToken);
- IExternalDataDAO externalDataDAO = getDAOFactory().getExternalDataDAO();
- List<ExternalDataPE> dataSets = new ArrayList<ExternalDataPE>();
- List<String> locations = new ArrayList<String>();
- for (String dataSetCode : dataSetCodes) {
- ExternalDataPE dataSet = externalDataDAO
- .tryToFindFullDataSetByCode(dataSetCode);
- if (dataSet != null) {
- dataSets.add(dataSet);
- locations.add(dataSet.getLocation());
- }
- }
- assertDataSetsAreKnown(dataSets, locations);
-
- for (ExternalDataPE dataSet : dataSets) {
- externalDataDAO.markAsDeleted(dataSet, session.tryGetPerson(),
- DELETION_DESCRIPTION, reason);
- }
- Collection<DataStoreServerSession> sessions = dssSessionManager
- .getSessions();
- for (DataStoreServerSession dssSession : sessions) {
- dssSession.getService().deleteDataSets(
- dssSession.getSessionToken(), locations);
- }
- }
-
- private void assertDataSetsAreKnown(List<ExternalDataPE> dataSets,
- List<String> locations) {
- Set<String> knownLocations = new LinkedHashSet<String>();
- Collection<DataStoreServerSession> sessions = dssSessionManager
- .getSessions();
- for (DataStoreServerSession session : sessions) {
- IDataStoreService service = session.getService();
- String dssSessionToken = session.getSessionToken();
- knownLocations.addAll(service.getKnownDataSets(dssSessionToken,
- locations));
- }
- List<String> unknownDataSets = new ArrayList<String>();
- for (ExternalDataPE dataSet : dataSets) {
- if (knownLocations.contains(dataSet.getLocation()) == false) {
- unknownDataSets.add(dataSet.getCode());
- }
- }
- if (unknownDataSets.isEmpty() == false) {
- throw new UserFailureException(
- "The following data sets are unknown by any registered Data Store Server. "
- + "May be the responsible Data Store Server is not running.\n"
- + unknownDataSets);
- }
- }
-
+ public void deleteDataSets(String sessionToken, List<String> dataSetCodes, String reason)
+ {
+ Session session = getSessionManager().getSession(sessionToken);
+ try
+ {
+ IExternalDataTable externalDataTable =
+ businessObjectFactory.createExternalDataTable(session);
+ externalDataTable.loadByDataSetCodes(dataSetCodes);
+ externalDataTable.deleteLoadedDataSets(dssSessionManager, reason);
+ } catch (final DataAccessException ex)
+ {
+ throw createUserFailureException(ex);
+ }
+ }
+
+ public void uploadDataSets(String sessionToken, List<String> dataSetCodes, String cifexURL,
+ String password)
+ {
+ Session session = getSessionManager().getSession(sessionToken);
+ try
+ {
+ IExternalDataTable externalDataTable =
+ businessObjectFactory.createExternalDataTable(session);
+ externalDataTable.loadByDataSetCodes(dataSetCodes);
+ externalDataTable.uploadLoadedDataSetsToCIFEX(dssSessionManager, cifexURL, password);
+ } catch (final DataAccessException ex)
+ {
+ throw createUserFailureException(ex);
+ }
+ }
+
public void editExperiment(String sessionToken,
ExperimentIdentifier identifier,
List<ExperimentProperty> properties,
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 915965eb48eb9cf835bdc14dc58aaf3f23eda8d6..ef782cd1d0c2e608a91739f7c878f92b5f9dd3b0 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
@@ -325,11 +325,16 @@ final class CommonServerLogger extends AbstractServerLogger implements
dataSetCodes, reason);
}
- public void editMaterial(String sessionToken,
- MaterialIdentifier identifier, List<MaterialProperty> properties,
- Date version) {
- logTracking(sessionToken, "edit_material", "MATERIAL(%s)", identifier);
-
+ public void uploadDataSets(String sessionToken, List<String> dataSetCodes, String cifexURL,
+ String password)
+ {
+ logTracking(sessionToken, "upload_data_sets", "CODES(%s) CIFEX-URL(%s)", dataSetCodes, cifexURL);
+ }
+
+ public void editMaterial(String sessionToken, MaterialIdentifier identifier,
+ List<MaterialProperty> properties, Date version)
+ {
+ logTracking(sessionToken, "edit_material", "MATERIAL(%s)", identifier);
}
public void editSample(String sessionToken, SampleIdentifier identifier,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
index 02dbcaf7ceb42e0358435e4dba25ffc8995c38c8..813b02203151ebac5c8548edf9d68087c743e662 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
@@ -17,11 +17,20 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProcedurePE;
@@ -44,6 +53,11 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
public final class ExternalDataTable extends AbstractExternalDataBusinessObject implements
IExternalDataTable
{
+ private static final String NEW_LINE = "\n";
+ private static final int MAX_LENGTH_OF_CIFEX_COMMENT = 1000;
+ private static final String AND_MORE_TEMPLATE = "and %d more.";
+ @Private static final String DELETION_DESCRIPTION = "single deletion";
+
private List<ExternalDataPE> externalData;
public ExternalDataTable(final IDAOFactory daoFactory, final Session session)
@@ -61,6 +75,20 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
return externalData;
}
+ public void loadByDataSetCodes(List<String> dataSetCodes)
+ {
+ IExternalDataDAO externalDataDAO = getExternalDataDAO();
+ externalData = new ArrayList<ExternalDataPE>();
+ for (String dataSetCode : dataSetCodes)
+ {
+ ExternalDataPE dataSet = externalDataDAO.tryToFindFullDataSetByCode(dataSetCode);
+ if (dataSet != null)
+ {
+ externalData.add(dataSet);
+ }
+ }
+ }
+
public final void loadBySampleIdentifier(final SampleIdentifier sampleIdentifier)
{
assert sampleIdentifier != null : "Unspecified sample identifier";
@@ -101,4 +129,100 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
}
}
}
+
+ public void deleteLoadedDataSets(DataStoreServerSessionManager dssSessionManager, String reason)
+ {
+ assertDataSetsAreKnown(dssSessionManager);
+ for (ExternalDataPE dataSet : externalData)
+ {
+ IExternalDataDAO externalDataDAO = getExternalDataDAO();
+ externalDataDAO.markAsDeleted(dataSet, session.tryGetPerson(), DELETION_DESCRIPTION, reason);
+ }
+ Collection<DataStoreServerSession> sessions = dssSessionManager.getSessions();
+ List<String> locations = getLocations();
+ for (DataStoreServerSession dssSession : sessions)
+ {
+ dssSession.getService().deleteDataSets(dssSession.getSessionToken(), locations);
+ }
+ }
+
+ public void uploadLoadedDataSetsToCIFEX(DataStoreServerSessionManager dssSessionManager,
+ String cifexURL, String password)
+ {
+ assertDataSetsAreKnown(dssSessionManager);
+ Collection<DataStoreServerSession> sessions = dssSessionManager.getSessions();
+ List<String> locations = getLocations();
+ DataSetUploadContext uploadContext = new DataSetUploadContext();
+ uploadContext.setCifexURL(cifexURL);
+ uploadContext.setUserID(session.getUserName());
+ uploadContext.setPassword(password);
+ uploadContext.setComment(createUploadComment());
+ for (DataStoreServerSession dssSession : sessions)
+ {
+ dssSession.getService().uploadDataSetsToCIFEX(dssSession.getSessionToken(), locations,
+ uploadContext);
+ }
+ }
+
+ private String createUploadComment()
+ {
+ StringBuilder builder = new StringBuilder();
+ builder.append("Uploaded zip file contains the following data sets:");
+ for (int i = 0, n = externalData.size(); i < n; i++)
+ {
+ builder.append(NEW_LINE);
+ String code = externalData.get(i).getCode();
+ int length = builder.length() + code.length();
+ if (i < n - 1)
+ {
+ length += NEW_LINE.length() + String.format(AND_MORE_TEMPLATE, n - i - 1).length();
+ }
+ if (length < MAX_LENGTH_OF_CIFEX_COMMENT)
+ {
+ builder.append(code);
+ } else
+ {
+ builder.append(String.format(AND_MORE_TEMPLATE, n - i));
+ }
+ }
+ return builder.toString();
+ }
+
+ private void assertDataSetsAreKnown(DataStoreServerSessionManager dssSessionManager)
+ {
+ List<String> locations = getLocations();
+ Set<String> knownLocations = new LinkedHashSet<String>();
+ Collection<DataStoreServerSession> sessions = dssSessionManager.getSessions();
+ for (DataStoreServerSession dssSession : sessions)
+ {
+ IDataStoreService service = dssSession.getService();
+ String dssSessionToken = dssSession.getSessionToken();
+ knownLocations.addAll(service.getKnownDataSets(dssSessionToken, locations));
+ }
+ List<String> unknownDataSets = new ArrayList<String>();
+ for (ExternalDataPE dataSet : externalData)
+ {
+ if (knownLocations.contains(dataSet.getLocation()) == false)
+ {
+ unknownDataSets.add(dataSet.getCode());
+ }
+ }
+ if (unknownDataSets.isEmpty() == false)
+ {
+ throw new UserFailureException(
+ "The following data sets are unknown by any registered Data Store Server. "
+ + "May be the responsible Data Store Server is not running.\n"
+ + unknownDataSets);
+ }
+ }
+
+ private List<String> getLocations()
+ {
+ List<String> locations = new ArrayList<String>();
+ for (ExternalDataPE dataSet : externalData)
+ {
+ locations.add(dataSet.getLocation());
+ }
+ return locations;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
index 8c4f278b537d829bd6464385d7b6326d229271f4..89452baaf84bdcc25e3b3b71b6e606fb7beb69ff 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.List;
+import ch.systemsx.cisd.openbis.generic.server.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -29,7 +30,12 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
*/
public interface IExternalDataTable
{
-
+ /**
+ * Loads data sets specified by their codes. Data set codes will be ignored if no
+ * {@link ExternalDataPE} could be found.
+ */
+ void loadByDataSetCodes(List<String> dataSetCodes);
+
/**
* Loads the internal {@link ExternalDataPE} for given <var>identifier</var>.
*/
@@ -45,5 +51,9 @@ public interface IExternalDataTable
* Returns the loaded {@link ExternalDataPE}.
*/
List<ExternalDataPE> getExternalData();
+
+ void deleteLoadedDataSets(DataStoreServerSessionManager dssSessionManager, String reason);
+
+ void uploadLoadedDataSetsToCIFEX(DataStoreServerSessionManager dssSessionManager, String cifexURL, String password);
}
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 2f64236ae77a43fcc218ea71b93503d39b6aa47a..b083f232e16a325cb1d1dd0b8bc2d8d3223c84af 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
@@ -366,18 +366,25 @@ public interface ICommonServer extends IServer {
@AuthorizationGuard(guardClass = DataSetCodePredicate.class) List<String> dataSetCodes,
String reason);
- /**
- * Saves changed experiment.
- */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public void editExperiment(
- String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier,
- List<ExperimentProperty> properties,
- List<AttachmentPE> attachments,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier newProjectIdentifier,
- Date version);
+ /**
+ * Uploads specified data sets to CIFEX server of specified URL with specified password.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.OBSERVER)
+ public void uploadDataSets(String sessionToken, List<String> dataSetCodes, String cifexURL,
+ String password);
+
+ /**
+ * Saves changed experiment.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public void editExperiment(String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
+ ExperimentIdentifier experimentIdentifier, List<ExperimentProperty> properties,
+ List<AttachmentPE> attachments,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
+ ProjectIdentifier newProjectIdentifier, Date version);
/**
* Saves changed material.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
index 844f1795c03824d2c2d9ba8eba74dac6a8b0adb1..ca85adb3529aba37ccd8f42847e7e15873e58a63 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IDataStoreService.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.InvalidAuthenticationException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
/**
* Service interface of Data Store Server.
@@ -63,12 +64,12 @@ public interface IDataStoreService
throws InvalidAuthenticationException;
/**
- * Uploads the specified data sets to CIFEX for the specified user (id and password) and with
- * specified comment.
+ * Uploads the specified data sets to CIFEX.
*
* @param sessionToken Valid token to identify authorised access.
+ * @param context Context data needed for uploading.
* @throws InvalidAuthenticationException if <code>sessionToken</code> is invalid.
*/
public void uploadDataSetsToCIFEX(String sessionToken, List<String> dataSetLocations,
- String comment, String userID, String password) throws InvalidAuthenticationException;
+ DataSetUploadContext context) throws InvalidAuthenticationException;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUploadContext.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUploadContext.java
new file mode 100644
index 0000000000000000000000000000000000000000..019d96db8859b19ab91c15e0ec501de7b40029ca
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetUploadContext.java
@@ -0,0 +1,79 @@
+/*
+ * Copyright 2009 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.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataSetUploadContext implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private String cifexURL;
+
+ private String userID;
+
+ private String password;
+
+ private String comment;
+
+ public final String getCifexURL()
+ {
+ return cifexURL;
+ }
+
+ public final void setCifexURL(String cifexURL)
+ {
+ this.cifexURL = cifexURL;
+ }
+
+ public final String getUserID()
+ {
+ return userID;
+ }
+
+ public final void setUserID(String userID)
+ {
+ this.userID = userID;
+ }
+
+ public final String getPassword()
+ {
+ return password;
+ }
+
+ public final void setPassword(String password)
+ {
+ this.password = password;
+ }
+
+ public final String getComment()
+ {
+ return comment;
+ }
+
+ public final void setComment(String comment)
+ {
+ this.comment = comment;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractClientService.java
index 771c18e7639c6fc5a803752c8442295a4a24cff5..9588c01ed24c89b751d13f35a03725eaaa5fc264 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/AbstractClientService.java
@@ -54,6 +54,8 @@ public abstract class AbstractClientService implements IClientService
@Resource(name = "request-context-provider")
private IRequestContextProvider requestContextProvider;
+ private String cifexURL;
+
protected AbstractClientService()
{
}
@@ -63,6 +65,11 @@ public abstract class AbstractClientService implements IClientService
this.requestContextProvider = requestContextProvider;
}
+ public final void setCifexURL(String cifexURL)
+ {
+ this.cifexURL = cifexURL;
+ }
+
private final SessionContext createSessionContext(final Session session)
{
final SessionContext sessionContext = new SessionContext();
@@ -144,6 +151,7 @@ public abstract class AbstractClientService implements IClientService
{
final ApplicationInfo applicationInfo = new ApplicationInfo();
applicationInfo.setVersion(BuildAndEnvironmentInfo.INSTANCE.getFullVersion());
+ applicationInfo.setCIFEXURL(cifexURL);
return applicationInfo;
}
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 204534a0113a06b4449a1aaa960a8c3aee066dba..da4e551e22f8da43a1edd4828c7926ac593399c1 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
@@ -278,7 +278,10 @@ var common = {
data_producer_code: "Producer",
button_delete_datasets: "Delete",
confirm_dataset_deletion_title: "Data Sets Deletion Confirmation",
- confirm_dataset_deletion_msg: "You are deleting {0} data set(s). Please enter a reason:",
+ confirm_dataset_deletion_msg: "You are deleting {0} data set(s). Please, enter a reason:",
+ button_upload_datasets: "Upload to CIFEX",
+ confirm_dataset_upload_title: "Uploading Confirmation and Authentication",
+ confirm_dataset_upload_msg: "You are uploading {0} data set(s) to CIFEX ({1}). Please, enter your CIFEX password:",
//
diff --git a/openbis/source/java/genericApplicationContext.xml b/openbis/source/java/genericApplicationContext.xml
index f2c99099d3c169e149b87527fde82cbafa7b2f63..2b6c496e7f05be0c9bebb42badb15e9ae36aec13 100644
--- a/openbis/source/java/genericApplicationContext.xml
+++ b/openbis/source/java/genericApplicationContext.xml
@@ -79,7 +79,8 @@
<bean id="common-service" class="ch.systemsx.cisd.openbis.generic.client.web.server.CommonClientService">
<constructor-arg ref="common-server" />
<constructor-arg ref="request-context-provider" />
- <constructor-arg value="${data-store-server-base-url}"/>
+ <property name="dataStoreBaseURL" value="${data-store-server-base-url}"/>
+ <property name="cifexURL" value="${cifex-url}"/>
</bean>
<!--
diff --git a/openbis/source/java/service.properties b/openbis/source/java/service.properties
index d1d62a51c650db46e6fbb9b3453463a98943b1e4..cb65b4ea8d1a3cc22f054378577eb58d9580e933 100644
--- a/openbis/source/java/service.properties
+++ b/openbis/source/java/service.properties
@@ -36,6 +36,9 @@ database-instance = CISD
# Base URL of the Data Store Server
data-store-server-base-url = https://localhost:8889
+# The URL of the CIFEX server
+cifex-url = https://cifex.ethz.ch:443
+
# Hibernate Search
# The working directory.
hibernate.search.index-base = ./targets/indices
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
index 3fb9cf11420f70428830768f6c8c565b61b64397..efbe36a83d2b691c6aec7753a5d9f65ff4bbe273 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientServiceTest.java
@@ -64,6 +64,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityDataType;
public final class CommonClientServiceTest extends AbstractClientServiceTest
{
private static final String DATA_STORE_BASE_URL = "baseURL";
+ private static final String CIFEX_URL = "cifexURL";
private CommonClientService commonClientService;
@@ -123,7 +124,9 @@ public final class CommonClientServiceTest extends AbstractClientServiceTest
{
super.setUp();
commonServer = context.mock(ICommonServer.class);
- commonClientService = new CommonClientService(commonServer, requestContextProvider, DATA_STORE_BASE_URL);
+ commonClientService = new CommonClientService(commonServer, requestContextProvider);
+ commonClientService.setDataStoreBaseURL(DATA_STORE_BASE_URL);
+ commonClientService.setCifexURL(CIFEX_URL);
}
@Test
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
index 3b561de87186a187b38358662f7f7b0dd81ab29a..c36dfe32535d3960d0ec62f82f4a73d4813cdcd4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server;
-import static ch.systemsx.cisd.openbis.generic.server.CommonServer.DELETION_DESCRIPTION;
-
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
@@ -28,13 +26,11 @@ import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
-import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialProperty;
@@ -42,7 +38,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
@@ -70,7 +65,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
*
* @author Franz-Josef Elmer
*/
-@Friend(toClasses=CommonServer.class)
public final class CommonServerTest extends AbstractServerTestCase
{
private static final String MATERIAL_TYPE_1 = "MATERIAL-TYPE-1";
@@ -91,8 +85,6 @@ public final class CommonServerTest extends AbstractServerTestCase
private DataStoreServerSessionManager dssSessionManager;
- private IDataStoreService dataStoreService;
-
private final ICommonServer createServer()
{
return new CommonServer(authenticationService, sessionManager, dssSessionManager,
@@ -116,7 +108,6 @@ public final class CommonServerTest extends AbstractServerTestCase
{
super.setUp();
dssSessionManager = new DataStoreServerSessionManager();
- dataStoreService = context.mock(IDataStoreService.class);
commonBusinessObjectFactory = context.mock(ICommonBusinessObjectFactory.class);
}
@@ -724,75 +715,6 @@ public final class CommonServerTest extends AbstractServerTestCase
context.assertIsSatisfied();
}
- @Test
- public void testDeleteDataSetButDataStoreServerIsDown()
- {
- prepareGetSession();
- final ExternalDataPE d1 = createDataSet("d1");
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
- will(returnValue(d1));
- }
- });
-
- try
- {
- createServer().deleteDataSets(SESSION_TOKEN, Arrays.asList(d1.getCode()), "");
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals(
- "The following data sets are unknown by any registered Data Store Server. "
- + "May be the responsible Data Store Server is not running.\n[d1]", e
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDeleteDataSetsButOneDataSetIsUnknown()
- {
- prepareGetSession();
- dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
- dataStoreService));
- final ExternalDataPE d1 = createDataSet("d1");
- final ExternalDataPE d2 = createDataSet("d2");
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
- will(returnValue(d1));
-
- one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
- will(returnValue(d2));
-
- List<String> locations = Arrays.asList(d1.getLocation(), d2.getLocation());
- one(dataStoreService).getKnownDataSets(with(any(String.class)),
- with(equal(locations)));
- will(returnValue(Arrays.asList(d1.getLocation())));
-
- }
- });
-
- try
- {
- createServer().deleteDataSets(SESSION_TOKEN, Arrays.asList(d1.getCode(), d2.getCode()),
- "");
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals(
- "The following data sets are unknown by any registered Data Store Server. "
- + "May be the responsible Data Store Server is not running.\n[d2]", e
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
@Test
public void testEditMaterialNothingChanged() throws Exception
{
@@ -871,42 +793,42 @@ public final class CommonServerTest extends AbstractServerTestCase
public void testDeleteDataSets()
{
prepareGetSession();
- dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
- dataStoreService));
- final ExternalDataPE d1 = createDataSet("d1");
- final ExternalDataPE d2 = createDataSet("d2");
+ final List<String> dataSetCodes = Arrays.asList("a", "b");
context.checking(new Expectations()
{
{
- one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
- will(returnValue(d1));
-
- one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
- will(returnValue(d2));
-
- List<String> locations = Arrays.asList(d1.getLocation(), d2.getLocation());
- one(dataStoreService).getKnownDataSets(with(any(String.class)),
- with(equal(locations)));
- will(returnValue(locations));
-
- one(externalDataDAO).markAsDeleted(d1, SESSION.tryGetPerson(), DELETION_DESCRIPTION, "reason");
- one(externalDataDAO).markAsDeleted(d2, SESSION.tryGetPerson(), DELETION_DESCRIPTION, "reason");
- one(dataStoreService).deleteDataSets(with(any(String.class)),
- with(equal(locations)));
+ one(commonBusinessObjectFactory).createExternalDataTable(SESSION);
+ will(returnValue(externalDataTable));
+
+ one(externalDataTable).loadByDataSetCodes(dataSetCodes);
+ one(externalDataTable).deleteLoadedDataSets(dssSessionManager, "reason");
}
});
- createServer().deleteDataSets(SESSION_TOKEN, Arrays.asList(d1.getCode(), d2.getCode()),
- "reason");
+ createServer().deleteDataSets(SESSION_TOKEN, dataSetCodes, "reason");
context.assertIsSatisfied();
}
-
- private ExternalDataPE createDataSet(String code)
+
+ @Test
+ public void testUploadDataSets()
{
- ExternalDataPE data = new ExternalDataPE();
- data.setCode(code);
- data.setLocation("here/" + code);
- return data;
+ prepareGetSession();
+ final List<String> dataSetCodes = Arrays.asList("a", "b");
+ context.checking(new Expectations()
+ {
+ {
+ one(commonBusinessObjectFactory).createExternalDataTable(SESSION);
+ will(returnValue(externalDataTable));
+
+ one(externalDataTable).loadByDataSetCodes(dataSetCodes);
+ one(externalDataTable).uploadLoadedDataSetsToCIFEX(dssSessionManager, "cifexURL", "pwd");
+ }
+ });
+
+ createServer().uploadDataSets(SESSION_TOKEN, dataSetCodes, "cifexURL", "pwd");
+
+ context.assertIsSatisfied();
}
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
index 4617845e5f59c6d7df0ef30676ae0049e8b42ab4..414b7ff748ffe50bfaf36166a8be6f29a85d85d6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
@@ -16,21 +16,29 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
+import static ch.systemsx.cisd.openbis.generic.server.business.bo.ExternalDataTable.DELETION_DESCRIPTION;
+
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.server.business.ManagerTestTool;
+import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.HierarchyType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProcedurePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -45,14 +53,26 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
*
* @author Christian Ribeaud
*/
+@Friend(toClasses=ExternalDataTable.class)
public final class ExternalDataTableTest extends AbstractBOTest
{
+ private DataStoreServerSessionManager dssSessionManager;
+ private IDataStoreService dataStoreService;
private final ExternalDataTable createExternalDataTable()
{
return new ExternalDataTable(daoFactory, ManagerTestTool.EXAMPLE_SESSION);
}
+ @BeforeMethod
+ @Override
+ public void beforeMethod()
+ {
+ super.beforeMethod();
+ dssSessionManager = new DataStoreServerSessionManager();
+ dataStoreService = context.mock(IDataStoreService.class);
+ }
+
@Test
public final void testLoadBySampleIdentifierWithNullSampleIdentifier()
{
@@ -193,4 +213,143 @@ public final class ExternalDataTableTest extends AbstractBOTest
context.assertIsSatisfied();
}
+
+ @Test
+ public void testDeleteLoadedDataSetsButDataStoreServerIsDown()
+ {
+ final ExternalDataPE d1 = createDataSet("d1");
+ context.checking(new Expectations()
+ {
+ {
+ one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
+ will(returnValue(d1));
+ }
+ });
+
+ ExternalDataTable externalDataTable = createExternalDataTable();
+ externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode()));
+ try
+ {
+ externalDataTable.deleteLoadedDataSets(dssSessionManager, "");
+ fail("UserFailureException expected");
+ } catch (UserFailureException e)
+ {
+ assertEquals(
+ "The following data sets are unknown by any registered Data Store Server. "
+ + "May be the responsible Data Store Server is not running.\n[d1]", e
+ .getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadByDataSetCodes()
+ {
+ final ExternalDataPE d1 = createDataSet("d1");
+ final ExternalDataPE d2 = createDataSet("d2");
+ context.checking(new Expectations()
+ {
+ {
+ one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
+ will(returnValue(d1));
+
+ one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
+ will(returnValue(null));
+ }
+ });
+
+ ExternalDataTable externalDataTable = createExternalDataTable();
+ externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode(), d2.getCode()));
+
+ assertEquals(1, externalDataTable.getExternalData().size());
+ assertSame(d1, externalDataTable.getExternalData().get(0));
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testDeleteLoadedDataSetsButOneDataSetIsUnknown()
+ {
+ dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
+ dataStoreService));
+ final ExternalDataPE d1 = createDataSet("d1");
+ final ExternalDataPE d2 = createDataSet("d2");
+ context.checking(new Expectations()
+ {
+ {
+ one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
+ will(returnValue(d1));
+
+ one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
+ will(returnValue(d2));
+
+ List<String> locations = Arrays.asList(d1.getLocation(), d2.getLocation());
+ one(dataStoreService).getKnownDataSets(with(any(String.class)),
+ with(equal(locations)));
+ will(returnValue(Arrays.asList(d1.getLocation())));
+
+ }
+ });
+
+ ExternalDataTable externalDataTable = createExternalDataTable();
+ externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode(), d2.getCode()));
+ try
+ {
+ externalDataTable.deleteLoadedDataSets(dssSessionManager, "");
+ fail("UserFailureException expected");
+ } catch (UserFailureException e)
+ {
+ assertEquals(
+ "The following data sets are unknown by any registered Data Store Server. "
+ + "May be the responsible Data Store Server is not running.\n[d2]", e
+ .getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testDeleteLoadedDataSets()
+ {
+ dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
+ dataStoreService));
+ final ExternalDataPE d1 = createDataSet("d1");
+ final ExternalDataPE d2 = createDataSet("d2");
+ context.checking(new Expectations()
+ {
+ {
+ one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
+ will(returnValue(d1));
+
+ one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
+ will(returnValue(d2));
+
+ List<String> locations = Arrays.asList(d1.getLocation(), d2.getLocation());
+ one(dataStoreService).getKnownDataSets(with(any(String.class)),
+ with(equal(locations)));
+ will(returnValue(locations));
+
+ PersonPE person = ManagerTestTool.EXAMPLE_SESSION.tryGetPerson();
+ one(externalDataDAO).markAsDeleted(d1, person, DELETION_DESCRIPTION, "reason");
+ one(externalDataDAO).markAsDeleted(d2, person, DELETION_DESCRIPTION, "reason");
+ one(dataStoreService).deleteDataSets(with(any(String.class)),
+ with(equal(locations)));
+ }
+ });
+
+ ExternalDataTable externalDataTable = createExternalDataTable();
+ externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode(), d2.getCode()));
+ externalDataTable.deleteLoadedDataSets(dssSessionManager, "reason");
+
+ context.assertIsSatisfied();
+ }
+
+ private ExternalDataPE createDataSet(String code)
+ {
+ ExternalDataPE data = new ExternalDataPE();
+ data.setCode(code);
+ data.setLocation("here/" + code);
+ return data;
+ }
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java.expected
index b81a82be2b514c863f1f54cd9391b5e990715afd..a02048f244eb353fba6e800db9ea54805ed0f51f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java.expected
@@ -77,345 +77,352 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
* @author Franz-Josef Elmer
*/
public interface ICommonServer extends IServer {
- /**
- * Returns all groups which belong to the specified database instance. *
- *
- * @return a sorted list of {@link GroupPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = GroupValidator.class)
- public List<GroupPE> listGroups(String sessionToken,
- DatabaseInstanceIdentifier identifier);
-
- /**
- * Registers a new group with specified code and optional description and
- * group leader ID.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerGroup(String sessionToken, String groupCode,
- String descriptionOrNull, String groupLeaderOrNull);
-
- /**
- * Returns all persons from current instance.
- *
- * @return a sorted list of {@link PersonPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<PersonPE> listPersons(String sessionToken);
-
- /**
- * Returns all projects.
- *
- * @return a sorted list of {@link ProjectPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = ProjectValidator.class)
- public List<ProjectPE> listProjects(String sessionToken);
-
- /**
- * Registers a new person.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerPerson(String sessionToken, String userID);
-
- /**
- * Returns a list of all roles.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public List<RoleAssignmentPE> listRoles(String sessionToken);
-
- /**
- * Registers a new group role.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void registerGroupRole(
- String sessionToken,
- RoleCode roleCode,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) GroupIdentifier identifier,
- String person);
-
- /**
- * Registers a new instance role.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerInstanceRole(String sessionToken, RoleCode roleCode,
- String person);
-
- /**
- * Deletes role described by given role code, group identifier and user id.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void deleteGroupRole(
- String sessionToken,
- RoleCode roleCode,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) GroupIdentifier groupIdentifier,
- String person);
-
- /**
- * Deletes role described by given role code and user id.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void deleteInstanceRole(String sessionToken, RoleCode roleCode,
- String person);
-
- /**
- * Lists sample types which are appropriate for listing.
- *
- * @return a sorted list of {@link SampleTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<SampleTypePE> listSampleTypes(String sessionToken);
-
- /**
- * Lists samples using given configuration.
- *
- * @return a sorted list of {@link SamplePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<SamplePE> listSamples(final String sessionToken,
- final ListSampleCriteriaDTO criteria);
-
- /**
- * Lists experiments.
- *
- * @return a sorted list of {@link ExperimentPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExperimentPE> listExperiments(
- final String sessionToken,
- ExperimentTypePE experimentType,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier project);
-
- /**
- * For given {@link SampleIdentifier} returns the corresponding list of
- * {@link ExternalDataPE}.
- *
- * @return a sorted list of {@link ExternalDataPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExternalDataPE> listExternalData(
- final String sessionToken,
- @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) final SampleIdentifier identifier);
-
- /**
- * For given {@link ExperimentIdentifier} returns the corresponding list of
- * {@link ExternalDataPE}.
- *
- * @return a sorted list of {@link ExternalDataPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExternalDataPE> listExternalData(
- final String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) final ExperimentIdentifier identifier);
-
- /**
- * Performs an <i>Hibernate Search</i> based on given parameters.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = MatchingEntityValidator.class)
- public List<SearchHit> listMatchingEntities(final String sessionToken,
- final SearchableEntity[] searchableEntities, final String queryText);
-
- /**
- * List experiment types.
- *
- * @return a sorted list of {@link ExperimentTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<ExperimentTypePE> listExperimentTypes(String sessionToken);
-
- /**
- * List property types.
- *
- * @return a sorted list of {@link PropertyTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<PropertyTypePE> listPropertyTypes(final String sessionToken);
-
- /**
- * Lists data types.
- *
- * @return a sorted list of {@link DataTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<DataTypePE> listDataTypes(final String sessionToken);
-
- /**
- * Lists vocabularies.
- *
- * @return a sorted list of {@link VocabularyPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<VocabularyPE> listVocabularies(final String sessionToken,
- final boolean withTerms, boolean excludeInternal);
-
- /**
- * Registers given {@link PropertyType}.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerPropertyType(final String sessionToken,
- final PropertyType propertyType);
-
- /**
- * Assigns property type to entity type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public String assignPropertyType(final String sessionToken,
- final EntityKind entityKind, final String propertyTypeCode,
- final String entityTypeCode, final boolean isMandatory,
- final String defaultValue);
-
- /**
- * Registers given {@link Vocabulary}.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerVocabulary(final String sessionToken,
- final Vocabulary vocabulary);
-
- /**
- * Registers new project.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void registerProject(
- String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier projectIdentifier,
- String description, String leaderId);
-
- /**
- * Performs an <i>Hibernate Search</i> based on given parameters.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- @ReturnValueFilter(validatorClass = ExternalDataValidator.class)
- public List<ExternalDataPE> searchForDataSets(String sessionToken,
- DataSetSearchCriteria criteria);
-
- /**
- * List material types.
- *
- * @return a sorted list of {@link MaterialTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<MaterialTypePE> listMaterialTypes(String sessionToken);
-
- /**
- * Lists materials.
- *
- * @return a sorted list of {@link MaterialPE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<MaterialPE> listMaterials(String sessionToken,
- MaterialTypePE materialType);
-
- /**
- * Creates a new material type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerMaterialType(String sessionToken,
- MaterialType entityType);
-
- /**
- * Creates a new sample type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerSampleType(String sessionToken, SampleType entityType);
-
- /**
- * Creates a new experiment type.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void registerExperimentType(String sessionToken,
- ExperimentType entityType);
-
- /**
- * Deletes specified data sets.
- */
- @Transactional
- @RolesAllowed(RoleSet.GROUP_ADMIN)
- public void deleteDataSets(
- String sessionToken,
- @AuthorizationGuard(guardClass = DataSetCodePredicate.class) List<String> dataSetCodes,
- String reason);
-
- /**
- * Saves changed experiment.
- */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public void editExperiment(
- String sessionToken,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ExperimentIdentifier experimentIdentifier,
- List<ExperimentProperty> properties,
- List<AttachmentPE> attachments,
- @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier newProjectIdentifier,
- Date version);
-
- /**
- * Saves changed material.
- */
- @Transactional
- @RolesAllowed(RoleSet.INSTANCE_ADMIN)
- public void editMaterial(String sessionToken,
- MaterialIdentifier identifier, List<MaterialProperty> properties,
- Date version);
-
- /**
- * Saves changed sample.
- */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public void editSample(
- String sessionToken,
- @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) SampleIdentifier identifier,
- List<SampleProperty> properties,
- @AuthorizationGuard(guardClass = NullableGroupIdentifierPredicate.class) ExperimentIdentifier experimentIdentifierOrNull,
- Date version);
-
- /**
- * Lists vocabulary terms of a given vocabulary. Includes terms usage
- * statistics.
- */
- @Transactional
- @RolesAllowed(RoleSet.USER)
- public List<VocabularyTermWithStats> listVocabularyTerms(
- String sessionToken, Vocabulary vocabulary);
-
- /**
- * List data set types.
- *
- * @return a sorted list of {@link DataSetTypePE}.
- */
- @Transactional(readOnly = true)
- @RolesAllowed(RoleSet.OBSERVER)
- public List<DataSetTypePE> listDataSetTypes(String sessionToken);
+ /**
+ * Returns all groups which belong to the specified database instance. *
+ *
+ * @return a sorted list of {@link GroupPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = GroupValidator.class)
+ public List<GroupPE> listGroups(String sessionToken,
+ DatabaseInstanceIdentifier identifier);
+
+ /**
+ * Registers a new group with specified code and optional description and
+ * group leader ID.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerGroup(String sessionToken, String groupCode,
+ String descriptionOrNull, String groupLeaderOrNull);
+
+ /**
+ * Returns all persons from current instance.
+ *
+ * @return a sorted list of {@link PersonPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<PersonPE> listPersons(String sessionToken);
+
+ /**
+ * Returns all projects.
+ *
+ * @return a sorted list of {@link ProjectPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = ProjectValidator.class)
+ public List<ProjectPE> listProjects(String sessionToken);
+
+ /**
+ * Registers a new person.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerPerson(String sessionToken, String userID);
+
+ /**
+ * Returns a list of all roles.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public List<RoleAssignmentPE> listRoles(String sessionToken);
+
+ /**
+ * Registers a new group role.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void registerGroupRole(
+ String sessionToken,
+ RoleCode roleCode,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) GroupIdentifier identifier,
+ String person);
+
+ /**
+ * Registers a new instance role.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerInstanceRole(String sessionToken, RoleCode roleCode,
+ String person);
+
+ /**
+ * Deletes role described by given role code, group identifier and user id.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void deleteGroupRole(
+ String sessionToken,
+ RoleCode roleCode,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) GroupIdentifier groupIdentifier,
+ String person);
+
+ /**
+ * Deletes role described by given role code and user id.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void deleteInstanceRole(String sessionToken, RoleCode roleCode,
+ String person);
+
+ /**
+ * Lists sample types which are appropriate for listing.
+ *
+ * @return a sorted list of {@link SampleTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<SampleTypePE> listSampleTypes(String sessionToken);
+
+ /**
+ * Lists samples using given configuration.
+ *
+ * @return a sorted list of {@link SamplePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<SamplePE> listSamples(final String sessionToken,
+ final ListSampleCriteriaDTO criteria);
+
+ /**
+ * Lists experiments.
+ *
+ * @return a sorted list of {@link ExperimentPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExperimentPE> listExperiments(
+ final String sessionToken,
+ ExperimentTypePE experimentType,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier project);
+
+ /**
+ * For given {@link SampleIdentifier} returns the corresponding list of
+ * {@link ExternalDataPE}.
+ *
+ * @return a sorted list of {@link ExternalDataPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExternalDataPE> listExternalData(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) final SampleIdentifier identifier);
+
+ /**
+ * For given {@link ExperimentIdentifier} returns the corresponding list of
+ * {@link ExternalDataPE}.
+ *
+ * @return a sorted list of {@link ExternalDataPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExternalDataPE> listExternalData(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) final ExperimentIdentifier identifier);
+
+ /**
+ * Performs an <i>Hibernate Search</i> based on given parameters.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = MatchingEntityValidator.class)
+ public List<SearchHit> listMatchingEntities(final String sessionToken,
+ final SearchableEntity[] searchableEntities, final String queryText);
+
+ /**
+ * List experiment types.
+ *
+ * @return a sorted list of {@link ExperimentTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ExperimentTypePE> listExperimentTypes(String sessionToken);
+
+ /**
+ * List property types.
+ *
+ * @return a sorted list of {@link PropertyTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<PropertyTypePE> listPropertyTypes(final String sessionToken);
+
+ /**
+ * Lists data types.
+ *
+ * @return a sorted list of {@link DataTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<DataTypePE> listDataTypes(final String sessionToken);
+
+ /**
+ * Lists vocabularies.
+ *
+ * @return a sorted list of {@link VocabularyPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<VocabularyPE> listVocabularies(final String sessionToken,
+ final boolean withTerms, boolean excludeInternal);
+
+ /**
+ * Registers given {@link PropertyType}.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerPropertyType(final String sessionToken,
+ final PropertyType propertyType);
+
+ /**
+ * Assigns property type to entity type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public String assignPropertyType(final String sessionToken,
+ final EntityKind entityKind, final String propertyTypeCode,
+ final String entityTypeCode, final boolean isMandatory,
+ final String defaultValue);
+
+ /**
+ * Registers given {@link Vocabulary}.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerVocabulary(final String sessionToken,
+ final Vocabulary vocabulary);
+
+ /**
+ * Registers new project.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void registerProject(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class) ProjectIdentifier projectIdentifier,
+ String description, String leaderId);
+
+ /**
+ * Performs an <i>Hibernate Search</i> based on given parameters.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ @ReturnValueFilter(validatorClass = ExternalDataValidator.class)
+ public List<ExternalDataPE> searchForDataSets(String sessionToken,
+ DataSetSearchCriteria criteria);
+
+ /**
+ * List material types.
+ *
+ * @return a sorted list of {@link MaterialTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<MaterialTypePE> listMaterialTypes(String sessionToken);
+
+ /**
+ * Lists materials.
+ *
+ * @return a sorted list of {@link MaterialPE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<MaterialPE> listMaterials(String sessionToken,
+ MaterialTypePE materialType);
+
+ /**
+ * Creates a new material type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerMaterialType(String sessionToken,
+ MaterialType entityType);
+
+ /**
+ * Creates a new sample type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerSampleType(String sessionToken, SampleType entityType);
+
+ /**
+ * Creates a new experiment type.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void registerExperimentType(String sessionToken,
+ ExperimentType entityType);
+
+ /**
+ * Deletes specified data sets.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.GROUP_ADMIN)
+ public void deleteDataSets(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class) List<String> dataSetCodes,
+ String reason);
+
+ /**
+ * Uploads specified data sets to CIFEX server of specified URL with specified password.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.OBSERVER)
+ public void uploadDataSets(String sessionToken, List<String> dataSetCodes, String cifexURL,
+ String password);
+
+ /**
+ * Saves changed experiment.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public void editExperiment(String sessionToken,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
+ ExperimentIdentifier experimentIdentifier, List<ExperimentProperty> properties,
+ List<AttachmentPE> attachments,
+ @AuthorizationGuard(guardClass = GroupIdentifierPredicate.class)
+ ProjectIdentifier newProjectIdentifier, Date version);
+
+ /**
+ * Saves changed material.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+ public void editMaterial(String sessionToken,
+ MaterialIdentifier identifier, List<MaterialProperty> properties,
+ Date version);
+
+ /**
+ * Saves changed sample.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public void editSample(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class) SampleIdentifier identifier,
+ List<SampleProperty> properties,
+ @AuthorizationGuard(guardClass = NullableGroupIdentifierPredicate.class) ExperimentIdentifier experimentIdentifierOrNull,
+ Date version);
+
+ /**
+ * Lists vocabulary terms of a given vocabulary. Includes terms usage
+ * statistics.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ public List<VocabularyTermWithStats> listVocabularyTerms(
+ String sessionToken, Vocabulary vocabulary);
+
+ /**
+ * List data set types.
+ *
+ * @return a sorted list of {@link DataSetTypePE}.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<DataSetTypePE> listDataSetTypes(String sessionToken);
}