diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
index 4e55fc527f67ee85a900bb8044edfe8d693cfd40..583ae2548833d1eefe2d574e82e96362e1d84e7d 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
@@ -92,6 +92,7 @@ public interface IPhosphoNetXClientService extends IClientService
public String prepareExportRawDataSamples(TableExportCriteria<GenericTableRow> exportCriteria)
throws UserFailureException;
- public void copyRawData(long[] rawDataSampleIDs) throws UserFailureException;
+ public void processRawData(String dataSetProcessingKey, long[] rawDataSampleIDs)
+ throws UserFailureException;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
index 6d522eb5d2d2fd679a04bcd9553b3af32f4fe404..7d43422e11260cf5b7e5b01d4a57296b73830a1b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
@@ -111,6 +111,6 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
public void prepareExportRawDataSamples(TableExportCriteria<GenericTableRow> exportCriteria,
AsyncCallback<String> callback);
- /** @see IPhosphoNetXClientService#copyRawData(long[]) */
- public void copyRawData(long[] rawDataSampleIDs, AsyncCallback<Void> callback);
+ /** @see IPhosphoNetXClientService#processRawData(String, long[]) */
+ public void processRawData(String dataSetProcessingKey, long[] rawDataSampleIDs, AsyncCallback<Void> callback);
}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataProcessingMenu.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataProcessingMenu.java
new file mode 100644
index 0000000000000000000000000000000000000000..ad1192bce24dddee4ceff505e3daddafbd94e01b
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataProcessingMenu.java
@@ -0,0 +1,167 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.client.web.client.application;
+
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.COPY_DATA_SETS_MESSAGE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.COPY_DATA_SETS_TITLE;
+
+import java.util.List;
+
+import com.extjs.gxt.ui.client.widget.menu.Menu;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.VoidAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.ActionMenu;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.IActionMenuItem;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.AbstractDataConfirmationDialog;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedAction;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedActionWithResult;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.TextToolItem;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SerializableComparableIDDecorator;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class RawDataProcessingMenu extends TextToolItem
+{
+ private static final class CopyConfirmationDialog extends
+ AbstractDataConfirmationDialog<List<GenericTableRow>>
+ {
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+
+ private final List<GenericTableRow> samples;
+
+ private final DatastoreServiceDescription datastoreServiceDescription;
+
+ private CopyConfirmationDialog(
+ IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext,
+ DatastoreServiceDescription datastoreServiceDescription,
+ List<GenericTableRow> samples, String title)
+ {
+ super(specificViewContext, samples, title);
+ this.specificViewContext = specificViewContext;
+ this.datastoreServiceDescription = datastoreServiceDescription;
+ this.samples = samples;
+ }
+
+ @Override
+ protected String createMessage()
+ {
+ String list = "[";
+ String delim = "";
+ for (GenericTableRow sample : samples)
+ {
+ list += delim + sample.tryToGetValue(0);
+ delim = ", ";
+ }
+ list += "]";
+ String label = datastoreServiceDescription.getLabel();
+ return specificViewContext.getMessage(COPY_DATA_SETS_MESSAGE, label, list);
+ }
+
+ @Override
+ protected void executeConfirmedAction()
+ {
+ long[] rawDataSampleIDs = new long[samples.size()];
+ for (int i = 0; i < samples.size(); i++)
+ {
+ GenericTableRow row = samples.get(i);
+ ISerializableComparable c = row.tryToGetValue(0);
+ if (c instanceof SerializableComparableIDDecorator == false)
+ {
+ throw new IllegalArgumentException("Missing id: " + c);
+ }
+ rawDataSampleIDs[i] = ((SerializableComparableIDDecorator) c).getID();
+ }
+ specificViewContext.getService().processRawData(datastoreServiceDescription.getKey(),
+ rawDataSampleIDs, new VoidAsyncCallback<Void>(specificViewContext));
+ }
+
+ @Override
+ protected void extendForm()
+ {
+ }
+ }
+
+ private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+ private final IDelegatedActionWithResult<List<GenericTableRow>> selectedDataProvider;
+
+ public RawDataProcessingMenu(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ IDelegatedActionWithResult<List<GenericTableRow>> selectedDataProvider)
+ {
+ super(viewContext.getMessage(Dict.COPY_DATA_SETS_BUTTON_LABEL));
+ this.viewContext = viewContext;
+ this.selectedDataProvider = selectedDataProvider;
+ IViewContext<ICommonClientServiceAsync> commonViewContext =
+ viewContext.getCommonViewContext();
+ viewContext.getCommonService().listDataStoreServices(DataStoreServiceKind.PROCESSING,
+ new AbstractAsyncCallback<List<DatastoreServiceDescription>>(commonViewContext)
+ {
+ @Override
+ public final void process(List<DatastoreServiceDescription> plugins)
+ {
+ createMenu(plugins);
+ }
+ });
+ }
+
+ private void createMenu(List<DatastoreServiceDescription> plugins)
+ {
+ Menu subMenu = new Menu();
+
+ for (final DatastoreServiceDescription datastoreServiceDescription : plugins)
+ {
+ IActionMenuItem actionMenuItem = new IActionMenuItem()
+ {
+
+ public String getMenuText(IMessageProvider messageProvider)
+ {
+ return datastoreServiceDescription.getLabel();
+ }
+
+ public String getMenuId()
+ {
+ return datastoreServiceDescription.getKey();
+ }
+ };
+ IDelegatedAction action = new IDelegatedAction()
+ {
+
+ public void execute()
+ {
+ String title = viewContext.getMessage(COPY_DATA_SETS_TITLE);
+ List<GenericTableRow> selectedSamples = selectedDataProvider.execute();
+ new CopyConfirmationDialog(viewContext, datastoreServiceDescription,
+ selectedSamples, title).show();
+ }
+ };
+ subMenu.add(new ActionMenu(actionMenuItem, viewContext, action));
+ }
+ setMenu(subMenu);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java
index 22364c4a78c37c54c6b0304c7728425956cf4afa..b50779972b68e6c3128e47bed06cb75951dae242 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RawDataSampleGrid.java
@@ -18,25 +18,18 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.applicatio
import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.createOrDelete;
import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.edit;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.COPY_DATA_SETS_BUTTON_LABEL;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.COPY_DATA_SETS_MESSAGE;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict.COPY_DATA_SETS_TITLE;
import java.util.List;
-import com.extjs.gxt.ui.client.widget.Dialog;
-import com.extjs.gxt.ui.client.widget.button.Button;
import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.VoidAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.GenericTableBrowserGrid;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IBrowserGridActionInvoker;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ICellListener;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.AbstractDataConfirmationDialog;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedActionWithResult;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GenericTableResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
@@ -45,7 +38,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SerializableComparableIDDecorator;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
@@ -66,59 +58,6 @@ class RawDataSampleGrid extends GenericTableBrowserGrid
return grid.asDisposableWithoutToolbar();
}
- private static final class CopyConfirmationDialog extends
- AbstractDataConfirmationDialog<List<GenericTableRow>>
- {
- private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
-
- private final List<GenericTableRow> samples;
-
- private CopyConfirmationDialog(
- IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext,
- List<GenericTableRow> samples, String title)
- {
- super(specificViewContext, samples, title);
- this.specificViewContext = specificViewContext;
- this.samples = samples;
- }
-
- @Override
- protected String createMessage()
- {
- String list = "[";
- String delim = "";
- for (GenericTableRow sample : samples)
- {
- list += delim + sample.tryToGetValue(0);
- delim = ", ";
- }
- list += "]";
- return specificViewContext.getMessage(COPY_DATA_SETS_MESSAGE, list);
- }
-
- @Override
- protected void executeConfirmedAction()
- {
- long[] rawDataSampleIDs = new long[samples.size()];
- for (int i = 0; i < samples.size(); i++)
- {
- GenericTableRow row = samples.get(i);
- ISerializableComparable c = row.tryToGetValue(0);
- if (c instanceof SerializableComparableIDDecorator == false)
- {
- throw new IllegalArgumentException("Missing id: " + c);
- }
- rawDataSampleIDs[i] = ((SerializableComparableIDDecorator) c).getID();
- }
- specificViewContext.getService().copyRawData(rawDataSampleIDs,
- new VoidAsyncCallback<Void>(specificViewContext));
- }
-
- @Override
- protected void extendForm()
- {
- }
- }
private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
@@ -136,20 +75,16 @@ class RawDataSampleGrid extends GenericTableBrowserGrid
});
allowMultipleSelection();
addEntityOperationsLabel();
- Button uploadButton =
- new Button(viewContext.getMessage(COPY_DATA_SETS_BUTTON_LABEL),
- new AbstractCreateDialogListener()
- {
- @Override
- protected Dialog createDialog(List<GenericTableRow> samples,
- IBrowserGridActionInvoker invoker)
- {
- return new CopyConfirmationDialog(specificViewContext, samples,
- specificViewContext.getMessage(COPY_DATA_SETS_TITLE));
- }
- });
- addButton(uploadButton);
-
+ RawDataProcessingMenu button = new RawDataProcessingMenu(viewContext,
+ new IDelegatedActionWithResult<List<GenericTableRow>>()
+ {
+ public List<GenericTableRow> execute()
+ {
+ return getSelectedBaseObjects();
+ }
+ });
+ enableButtonOnSelectedItems(button);
+ addButton(button);
}
@Override
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
index 0faaf75d392e33ddbe4ddfb119a3e906418b43eb..6f307d795b6df3b2b91c8290a6ad991a25318663 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
@@ -42,11 +42,11 @@ var phosphonetx = {
ALL_RAW_DATA_SAMPLES_menu_item: "All MS INJECTION Samples",
ALL_RAW_DATA_SAMPLES_tab_label: "MS INJECTION Samples and Related Biological Samples",
openbis_raw_data_sample_browser_CODE: "MS INJECTION Sample",
- openbis_raw_data_sample_browser_REGISTRATION_DATE: "Regustration Date",
+ openbis_raw_data_sample_browser_REGISTRATION_DATE: "Registration Date",
openbis_raw_data_sample_browser_PARENT: "Biological Sample",
- copy_data_sets_button_label: "Copy Data Sets",
- copy_data_sets_title: "Copy Data Sets Confirmation",
- copy_data_sets_message: "Do you want to make the data sets of the samples {0} available for processing?",
+ copy_data_sets_button_label: "Process Data Sets",
+ copy_data_sets_title: "Process Data Sets Confirmation",
+ copy_data_sets_message: "Do you want to process '{0}' for the data sets of the samples {1}?",
// LAST LINE: KEEP IT AT THE END
lastline: "" // we need a line without a comma
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
index a78874bc47f07f5d537ab00f9df64a79ba66ad7c..74852de88f0af8bb63afda6f816b48b66f43c2c1 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
@@ -201,10 +201,10 @@ public class PhosphoNetXClientService extends AbstractClientService implements
return prepareExportEntities(exportCriteria);
}
- public void copyRawData(long[] rawDataSampleIDs)
+ public void processRawData(String dataSetProcessingKey, long[] rawDataSampleIDs)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
- rawDataService.copyRawData(getSessionToken(), rawDataSampleIDs);
+ rawDataService.processRawData(getSessionToken(), dataSetProcessingKey, rawDataSampleIDs);
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataService.java
index 3fd32b1a160d8c63a705f4730ab625fea03e96ef..cb6a0c32bb1cb826ec79035b9a371ac095a5ca8b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataService.java
@@ -67,13 +67,15 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
}
}
- public void copyRawData(String sessionToken, String userID, long[] rawDataSampleIDs)
+ public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
+ long[] rawDataSampleIDs)
{
checkSession(sessionToken);
SessionContextDTO session = login(userID);
try
{
- service.copyRawData(session.getSessionToken(), rawDataSampleIDs);
+ service.processRawData(session.getSessionToken(), dataSetProcessingKey,
+ rawDataSampleIDs);
} finally
{
service.logout(session.getSessionToken());
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
index 9dbaf9c9ddd93aa7ccf688846c32433eb826a856..228dc07ebd73f6c8b515d1837d0b67895e55ce0f 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java
@@ -56,9 +56,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validato
*/
public class RawDataServiceInternal extends AbstractServer<IRawDataServiceInternal> implements IRawDataServiceInternal
{
- @Private static final String COPY_PROCESSING_KEY = "copy-data-sets";
-
- @Private static final String GROUP_CODE = "MS_DATA";
+ @Private static final String GROUP_CODE = "MS_DATA";
@Private static final String RAW_DATA_SAMPLE_TYPE = "MS_INJECTION";
@@ -95,11 +93,12 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
return loadAllRawDataSamples(getSession(sessionToken));
}
- public void copyRawData(String sessionToken, long[] rawDataSampleIDs)
+ public void processRawData(String sessionToken, String dataSetProcessingKey,
+ long[] rawDataSampleIDs)
{
Session session = getSession(sessionToken);
PersonPE person = session.tryGetPerson();
-
+
List<Sample> samples = loadAllRawDataSamples(session);
Set<Long> sampleIDs = new HashSet<Long>();
for (Sample sample : samples)
@@ -109,7 +108,7 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
sampleIDs.add(sample.getId());
}
}
-
+
ISampleDAO sampleDAO = getDAOFactory().getSampleDAO();
IExternalDataDAO externalDataDAO = getDAOFactory().getExternalDataDAO();
List<String> dataSetCodes = new ArrayList<String>();
@@ -127,10 +126,10 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
dataSetCodes.add(dataSet.getCode());
}
}
- String dataStoreServerCode = findDataStoreServer();
+ String dataStoreServerCode = findDataStoreServer(dataSetProcessingKey);
IExternalDataTable externalDataTable =
businessObjectFactory.createExternalDataTable(session);
- externalDataTable.processDatasets(COPY_PROCESSING_KEY, dataStoreServerCode, dataSetCodes);
+ externalDataTable.processDatasets(dataSetProcessingKey, dataStoreServerCode, dataSetCodes);
}
private List<Sample> loadAllRawDataSamples(Session session)
@@ -147,7 +146,7 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
return sampleLister.list(criteria2);
}
- private String findDataStoreServer()
+ private String findDataStoreServer(String dataSetProcessingKey)
{
List<DataStorePE> dataStores = getDAOFactory().getDataStoreDAO().listDataStores();
for (DataStorePE dataStore : dataStores)
@@ -156,13 +155,13 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
for (DataStoreServicePE dataStoreService : services)
{
if (DataStoreServiceKind.PROCESSING.equals(dataStoreService.getKind())
- && COPY_PROCESSING_KEY.equals(dataStoreService.getKey()))
+ && dataSetProcessingKey.equals(dataStoreService.getKey()))
{
return dataStore.getCode();
}
}
}
throw new EnvironmentFailureException("No data store processing service with key '"
- + COPY_PROCESSING_KEY + "' found.");
+ + dataSetProcessingKey + "' found.");
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalLogger.java
index 98fbf7a477259a4542975b59d461cbab124e98f2..824c9dc0f08bcb3da655d2c907ea89595153cd65 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalLogger.java
@@ -44,7 +44,7 @@ class RawDataServiceInternalLogger extends AbstractServerLogger implements IRawD
return null;
}
- public void copyRawData(String sessionToken, long[] rawDataSampleIDs)
+ public void processRawData(String sessionToken, String dataSetProcessingKey, long[] rawDataSampleIDs)
{
int numberOfDataSets = rawDataSampleIDs == null ? 0 : rawDataSampleIDs.length;
logAccess(sessionToken, "copy_raw_data", "NUMBER_OF_DATA_SETS(%s)", numberOfDataSets);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceLogger.java
index 32d98dff7e08d92f3c549f3de83f87794d3589e0..7af4229bcacbda8c8b47f5273e27b371174e39f5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceLogger.java
@@ -44,11 +44,13 @@ class RawDataServiceLogger extends AbstractServerLogger implements IRawDataServi
return null;
}
- public void copyRawData(String sessionToken, String userID, long[] rawDataSampleIDs)
+ public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
+ long[] rawDataSampleIDs)
{
int numberOfDataSets = rawDataSampleIDs == null ? 0 : rawDataSampleIDs.length;
- logAccess(sessionToken, "copy_raw_data", "USER_ID(%s) NUMBER_OF_DATA_SETS(%s)", userID,
- numberOfDataSets);
+ logAccess(sessionToken, "copy_raw_data",
+ "USER_ID(%s) DSS_PROCESSING_PLUGIN(%s) NUMBER_OF_DATA_SETS(%s)", userID,
+ dataSetProcessingKey, numberOfDataSets);
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataService.java
index 542e60a5b70c42a76f6b2a90f95832a312073afe..9160444ef8c306c1016e0273a8e441bebf5fc9c7 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataService.java
@@ -39,8 +39,14 @@ public interface IRawDataService extends IServer
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.INSTANCE_ADMIN_OBSERVER)
public List<Sample> listRawDataSamples(String sessionToken, String userID);
-
+
+ /**
+ * Processes the data sets of specified samples by the DSS processing plug-in of specified key
+ * for the specified user. Implementations should check that the specified user is allowed
+ * to read specified samples.
+ */
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.INSTANCE_ADMIN_OBSERVER)
- public void copyRawData(String sessionToken, String userID, long[] rawDataSampleIDs);
+ public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
+ long[] rawDataSampleIDs);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
index f0b3483c468d880bcf06393f08ba2fcf71361d55..d782ccf07da5eaebfa5a434b81970711ff464901 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
@@ -45,5 +45,5 @@ public interface IRawDataServiceInternal extends IServer
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.USER)
- public void copyRawData(String sessionToken, long[] rawDataSampleIDs);
+ public void processRawData(String sessionToken, String dataSetProcessingKey, long[] rawDataSampleIDs);
}
\ No newline at end of file
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
index 392f06676b380f8031d7c18c15ad6be3b68c6bfb..6b4ef6d7726ebf821ffa70c80991e25921b46f49 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
@@ -67,6 +67,6 @@ public class RawDataTestClient
Sample sample = samples.get(i);
ids[i] = sample.getId();
}
- service.copyRawData(sessionToken, "test_a", ids);
+ service.processingRawData(sessionToken, "test_a", "copy-data-sets", ids);
}
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
index 866bfec3698d73568aa435d204cbc646341b3922..6b4074dee2a4038555c81c85419a2959b6cf1dc9 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind.PROCESSING;
import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind.QUERIES;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal.COPY_PROCESSING_KEY;
import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal.GROUP_CODE;
import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.RawDataServiceInternal.RAW_DATA_SAMPLE_TYPE;
@@ -57,6 +56,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInterna
@Friend(toClasses=RawDataServiceInternal.class)
public class RawDataServiceInternalTest extends AbstractServerTestCase
{
+ private static final String COPY_PROCESSING_KEY = "copy-data-sets";
private IRawDataServiceInternal service;
private ICommonBusinessObjectFactory boFactory;
private ISampleLister sampleLister;
@@ -126,7 +126,7 @@ public class RawDataServiceInternalTest extends AbstractServerTestCase
});
- service.copyRawData(SESSION_TOKEN, ids);
+ service.processRawData(SESSION_TOKEN, COPY_PROCESSING_KEY, ids);
context.assertIsSatisfied();
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
index 0424cfea03e47b8e14b97a38f1e8d41e1b2347a3..af5128232cd6c5a9b2f2c098e6ca1e79a171aa8e 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
@@ -99,7 +99,7 @@ public class RawDataServiceTest extends AbstractServerTestCase
try
{
- service.copyRawData(SESSION_TOKEN, "abc", new long[0]);
+ service.processingRawData(SESSION_TOKEN, "abc", null, new long[0]);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
@@ -118,11 +118,11 @@ public class RawDataServiceTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(internalService).copyRawData(session2.getSessionToken(), ids);
+ one(internalService).processRawData(session2.getSessionToken(), null, ids);
}
});
- service.copyRawData(SESSION_TOKEN, "abc", ids);
+ service.processingRawData(SESSION_TOKEN, "abc", null, ids);
context.assertIsSatisfied();
}