diff --git a/rtd_phosphonetx/.classpath b/rtd_phosphonetx/.classpath
index 605f3fd7c87f711e4ccce4d71bb026910ee1e47d..efc56346735878751c8c2a0b1a7f889b73e3c206 100644
--- a/rtd_phosphonetx/.classpath
+++ b/rtd_phosphonetx/.classpath
@@ -24,5 +24,7 @@
</classpathentry>
<classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
<classpathentry kind="lib" path="/libraries/spring/spring.jar" sourcepath="/libraries/spring/src.jar"/>
+ <classpathentry kind="lib" path="/libraries/spring/webmvc/spring-webmvc.jar" sourcepath="/libraries/spring/webmvc/src.jar"/>
+ <classpathentry kind="lib" path="/libraries/hibernate-search/jms.jar"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
index 174e75a036f2e8689f1bf551e81e5ef780731941..f2ecde6ff4c6531f7d1f509910b53a6320db5caf 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
@@ -42,7 +42,7 @@ public interface IProtDAO extends BaseQuery
+ "values (?{1.sequence}, ?{1.checksum}) returning id")
public long createSequence(Sequence sequence);
- @Select("insert into proteins (data_set_code) values (?{1}) returning id")
+ @Select("insert into proteins (data_set_perm_id) values (?{1}) returning id")
public long createProtein(String dataSetCode);
@Select("insert into peptides (prot_id, sequ_id) values (?{1}, ?{2}) returning id")
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/OpenBIS.gwt.xml b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/OpenBIS.gwt.xml
index 11c365c365e0733939759e1f1f68cf130b8911fc..7fcaef8e692abf8a83915a497f848510aa3b8dca 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/OpenBIS.gwt.xml
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/OpenBIS.gwt.xml
@@ -9,5 +9,6 @@
<script src="phosphonetx-dictionary.js"/>
<public path="client/web/public"/>
<source path="client/web/client"/>
+ <source path="shared/basic" />
</module>
\ No newline at end of file
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 cb66b9cf333f6922116b3b0c611ef8f85e20d503..8812bbc90e452dda3c55362b2d20b7c5842a0ffa 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
@@ -17,6 +17,11 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client;
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientService;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
+import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
/**
*
@@ -25,5 +30,10 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.IClientService;
*/
public interface IPhosphoNetXClientService extends IClientService
{
+ public ResultSet<Protein> listProteinsByExperiment(ListProteinByExperimentCriteria criteria)
+ throws UserFailureException;
+
+ public String prepareExportProteins(TableExportCriteria<Protein> exportCriteria)
+ 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 0127ad07f7b032f8c3bf47a9d48ff287b90898df..ce9dc0e0a575e38bd2210b9b76ff7d3a92ee2eae 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
@@ -16,7 +16,13 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client;
+import com.google.gwt.user.client.rpc.AsyncCallback;
+
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
/**
*
@@ -25,5 +31,13 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
*/
public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
{
+ /** @see IPhosphoNetXClientService#listProteinsByExperiment(ListProteinByExperimentCriteria) */
+ public void listProteinsByExperiment(ListProteinByExperimentCriteria criteria,
+ AsyncCallback<ResultSet<Protein>> callback);
+
+
+ /** @see IPhosphoNetXClientService#prepareExportProteins(TableExportCriteria) */
+ public void prepareExportProteins(TableExportCriteria<Protein> exportCriteria,
+ AsyncCallback<String> callback);
-}
+}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ClientPluginFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ClientPluginFactory.java
index 7ceb5f04edd35ec0018dbaf0ae31852c5a29844d..b4872352c9dba8324ad6eec6298791f587da2eff 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ClientPluginFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ClientPluginFactory.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItemFactory;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IClientPlugin;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IModule;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentifiable;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
@@ -48,15 +49,19 @@ public class ClientPluginFactory extends AbstractClientPluginFactory<IPhosphoNet
public ClientPluginFactory(IViewContext<ICommonClientServiceAsync> originalViewContext)
{
super(originalViewContext);
- // TODO Auto-generated constructor stub
}
@Override
protected IViewContext<IPhosphoNetXClientServiceAsync> createViewContext(
IViewContext<ICommonClientServiceAsync> originalViewContext)
{
- // TODO Auto-generated method stub
- return null;
+ return new ViewContext(originalViewContext);
+ }
+
+ @Override
+ public IModule tryGetModule()
+ {
+ return new PhosphoNetXModule(getViewContext());
}
public Set<String> getEntityTypeCodes(EntityKind entityKind)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java
new file mode 100644
index 0000000000000000000000000000000000000000..c198f91a739640e42886496db6f0242d60fc857a
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java
@@ -0,0 +1,31 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class Dict
+{
+ public static final String QUERY_MENU_TITLE = "query_menu_title";
+ public static final String QUERY_ALL_PROTEINS_BY_EXPERIMENT = "query_all_proteins_by_experiment";
+ public static final String SELECTED_EXPERIMENT_LABEL = "selected_experiment_label";
+ public static final String PROTEIN_DESCRIPTION = "protein_name";
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
new file mode 100644
index 0000000000000000000000000000000000000000..435fa39e2a9c0e0f9f79b523a249af85dfbf3432
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
@@ -0,0 +1,54 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public enum PhosphoNetXDisplayTypeIDGenerator implements IDisplayTypeIDGenerator
+{
+ PROTEIN_BY_EXPERIMENT_BROWSER_GRID("protein-by-experiment-browser-grid"),
+ ;
+
+ private final String genericNameOrPrefix;
+
+ private PhosphoNetXDisplayTypeIDGenerator(String genericNameOrPrefix)
+ {
+ this.genericNameOrPrefix = genericNameOrPrefix;
+ }
+
+ public String createID(EntityKind entityKindOrNull, EntityType entityTypeOrNull)
+ {
+ String id = genericNameOrPrefix;
+ if (entityKindOrNull != null)
+ {
+ id += "-" + entityKindOrNull.toString();
+ }
+ if (entityTypeOrNull != null)
+ {
+ id += "-" + entityTypeOrNull.getCode();
+ }
+ return id;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXModule.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXModule.java
new file mode 100644
index 0000000000000000000000000000000000000000..33a9f6bab5abaf823b2d5e79bda967443301ba60
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXModule.java
@@ -0,0 +1,44 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import com.google.gwt.user.client.ui.Widget;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IModule;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class PhosphoNetXModule implements IModule
+{
+ private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+
+ public PhosphoNetXModule(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ this.viewContext = viewContext;
+ }
+
+ public Widget getMenu()
+ {
+ return new QueryMenu(viewContext);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
new file mode 100644
index 0000000000000000000000000000000000000000..172faa9f79a7f7394b545b6ac670969074bec336
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
@@ -0,0 +1,70 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import com.extjs.gxt.ui.client.Events;
+import com.extjs.gxt.ui.client.event.BaseEvent;
+import com.extjs.gxt.ui.client.event.Listener;
+import com.extjs.gxt.ui.client.widget.form.TextField;
+import com.extjs.gxt.ui.client.widget.toolbar.AdapterToolItem;
+import com.extjs.gxt.ui.client.widget.toolbar.LabelToolItem;
+import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField.ExperimentChooserFieldAdaptor;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+class ProteinByExperimentBrowerToolBar extends ToolBar
+{
+ private ProteinByExperimentBrowserGrid browserGrid;
+
+ ProteinByExperimentBrowerToolBar(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ setBorders(true);
+ add(new LabelToolItem(viewContext.getMessage(Dict.SELECTED_EXPERIMENT_LABEL)
+ + GenericConstants.LABEL_SEPARATOR));
+ final ExperimentChooserFieldAdaptor chooser =
+ ExperimentChooserField.create("", false, null, viewContext.getCommonViewContext());
+ TextField<String> textField = chooser.getTextField();
+ textField.setReadOnly(true);
+ textField.addListener(Events.Valid, new Listener<BaseEvent>()
+ {
+ public void handleEvent(BaseEvent be)
+ {
+ ExperimentIdentifier identifier = chooser.getValue();
+ if (identifier != null)
+ {
+ System.out.println("Experiment:" + identifier.getIdentifier());
+ browserGrid.update(identifier);
+ }
+ }
+ });
+ add(new AdapterToolItem(textField));
+ add(new AdapterToolItem(chooser.getChooseButton()));
+ }
+
+ void setBrowserGrid(ProteinByExperimentBrowserGrid browserGrid)
+ {
+ this.browserGrid = browserGrid;
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
new file mode 100644
index 0000000000000000000000000000000000000000..50a3b400f8bcf7cb3aea74ab9828c24485827745
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
@@ -0,0 +1,116 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import java.util.List;
+
+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.ui.columns.framework.IColumnDefinitionKind;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.AbstractSimpleBrowserGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IColumnDefinition;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<Protein>
+{
+ private static final String PREFIX = GenericConstants.ID_PREFIX + "protein-by-experiment-browser";
+
+ // browser consists of the grid and additional toolbars (paging, filtering)
+ public static final String BROWSER_ID = PREFIX + "_main";
+
+ public static final String GRID_ID = PREFIX + "_grid";
+
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+
+ private ListProteinByExperimentCriteria criteria;
+
+ static IDisposableComponent create(
+ final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ final ProteinByExperimentBrowerToolBar toolbar =
+ new ProteinByExperimentBrowerToolBar(viewContext);
+ final ProteinByExperimentBrowserGrid browserGrid =
+ new ProteinByExperimentBrowserGrid(viewContext);
+ toolbar.setBrowserGrid(browserGrid);
+ return browserGrid.asDisposableWithToolbar(toolbar);
+ }
+
+ private ProteinByExperimentBrowserGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID);
+ specificViewContext = viewContext;
+ setDisplayTypeIDGenerator(PhosphoNetXDisplayTypeIDGenerator.PROTEIN_BY_EXPERIMENT_BROWSER_GRID);
+ }
+
+ void update(ExperimentIdentifier identifier)
+ {
+ criteria = new ListProteinByExperimentCriteria();
+ criteria.setExperimentID(identifier.getTechID());
+ refresh();
+ }
+
+ @Override
+ protected IColumnDefinitionKind<Protein>[] getStaticColumnsDefinition()
+ {
+ return ProteinColDefKind.values();
+ }
+
+ @Override
+ protected List<IColumnDefinition<Protein>> getInitialFilters()
+ {
+ return asColumnFilters(new ProteinColDefKind[] {ProteinColDefKind.DESCRIPTION});
+ }
+
+ @Override
+ protected void listEntities(DefaultResultSetConfig<String, Protein> resultSetConfig,
+ AbstractAsyncCallback<ResultSet<Protein>> callback)
+ {
+ if (criteria != null)
+ {
+ specificViewContext.getService().listProteinsByExperiment(criteria, callback);
+ }
+ }
+
+ @Override
+ protected void prepareExportEntities(TableExportCriteria<Protein> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ specificViewContext.getService().prepareExportProteins(exportCriteria, callback);
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return new DatabaseModificationKind[]
+ { DatabaseModificationKind.createOrDelete(ObjectKind.DATA_SET) };
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserWidget.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserWidget.java
new file mode 100644
index 0000000000000000000000000000000000000000..bc80b993ff5848cfbd64797a770f0aecffb5bb5a
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserWidget.java
@@ -0,0 +1,55 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import java.util.Set;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ProteinByExperimentBrowserWidget extends QueryWidget
+{
+
+ private IDisposableComponent disposableComponent;
+
+ ProteinByExperimentBrowserWidget(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ super(viewContext);
+ disposableComponent = ProteinByExperimentBrowserGrid.create(viewContext);
+ add(disposableComponent.getComponent());
+ }
+
+ @Override
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return disposableComponent.getRelevantModifications();
+ }
+
+ @Override
+ public void update(Set<DatabaseModificationKind> observedModifications)
+ {
+ disposableComponent.update(observedModifications);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinColDefKind.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinColDefKind.java
new file mode 100644
index 0000000000000000000000000000000000000000..546cfef4c8170d37fde397379c42e8b58551a0a4
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinColDefKind.java
@@ -0,0 +1,54 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.AbstractColumnDefinitionKind;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public enum ProteinColDefKind implements IColumnDefinitionKind<Protein>
+{
+ DESCRIPTION(new AbstractColumnDefinitionKind<Protein>(Dict.PROTEIN_DESCRIPTION, true)
+ {
+ @Override
+ public String tryGetValue(Protein entity)
+ {
+ return entity.getDescription();
+ }
+ }),
+ ;
+
+ private final AbstractColumnDefinitionKind<Protein> columnDefinitionKind;
+
+ private ProteinColDefKind(AbstractColumnDefinitionKind<Protein> columnDefinitionKind)
+ {
+ this.columnDefinitionKind = columnDefinitionKind;
+ }
+
+ public String id()
+ {
+ return name();
+ }
+
+ public AbstractColumnDefinitionKind<Protein> getDescriptor()
+ {
+ return columnDefinitionKind;
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryMenu.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryMenu.java
new file mode 100644
index 0000000000000000000000000000000000000000..a3e23d7b016f1597c15b0558987874c22b51f3e6
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryMenu.java
@@ -0,0 +1,102 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import com.extjs.gxt.ui.client.widget.menu.Menu;
+
+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.framework.DatabaseModificationAwareComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DefaultTabItem;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItemFactory;
+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.menu.TopMenu;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.TopMenuItem;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class QueryMenu extends TopMenuItem
+{
+ public static final String ID = GenericConstants.ID_PREFIX + "-phosphonetx-";
+
+ private static enum ActionMenuKind implements IActionMenuItem
+ {
+ ALL_PROTEINS_OF_AN_EXPERIMENT;
+
+ public String getMenuId()
+ {
+ return ID + "_" + this.name();
+ }
+
+ public String getMenuText(IMessageProvider messageProvider)
+ {
+ return messageProvider.getMessage(this.name());
+ }
+ }
+
+ private static final class TabItemFactory implements ITabItemFactory
+ {
+ protected final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+ private final String id;
+ private final String tabLabelKey;
+ private final QueryWidget widget;
+
+ TabItemFactory(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ String tabLabelKey, QueryWidget widget)
+ {
+ this.viewContext = viewContext;
+ this.tabLabelKey = tabLabelKey;
+ this.widget = widget;
+ this.id = ID + tabLabelKey;
+ }
+
+ public String getId()
+ {
+ return id;
+ }
+
+ public ITabItem create()
+ {
+ String menuItemText = viewContext.getMessage(tabLabelKey);
+ DatabaseModificationAwareComponent component =
+ new DatabaseModificationAwareComponent(widget, widget);
+ return DefaultTabItem.create(menuItemText, component, viewContext, false);
+ }
+ }
+
+ public QueryMenu(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ super(viewContext.getMessage(Dict.QUERY_MENU_TITLE));
+ setIconStyle(TopMenu.ICON_STYLE);
+
+ Menu menu = new Menu();
+ QueryWidget widget = new ProteinByExperimentBrowserWidget(viewContext);
+ TabItemFactory factory =
+ new TabItemFactory(viewContext, Dict.QUERY_ALL_PROTEINS_BY_EXPERIMENT, widget);
+ ActionMenu actionMenu =
+ new ActionMenu(ActionMenuKind.ALL_PROTEINS_OF_AN_EXPERIMENT, viewContext, factory);
+ menu.add(actionMenu);
+ setMenu(menu);
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryWidget.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryWidget.java
new file mode 100644
index 0000000000000000000000000000000000000000..9aff082bf8acf1ea14f358002ae37b8dc3519234
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/QueryWidget.java
@@ -0,0 +1,51 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import java.util.Set;
+
+import com.extjs.gxt.ui.client.widget.ContentPanel;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class QueryWidget extends ContentPanel implements IDatabaseModificationObserver
+{
+ protected final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+
+ public QueryWidget(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ this.viewContext = viewContext;
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return new DatabaseModificationKind[] {};
+ }
+
+ public void update(Set<DatabaseModificationKind> observedModifications)
+ {
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ViewContext.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ViewContext.java
new file mode 100644
index 0000000000000000000000000000000000000000..0fe66f33095a688a1727429f8a0253c322dfd20b
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ViewContext.java
@@ -0,0 +1,54 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application;
+
+import com.google.gwt.core.client.GWT;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractPluginViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ViewContext extends AbstractPluginViewContext<IPhosphoNetXClientServiceAsync>
+{
+ private static final String TECHNOLOGY_NAME = "phosphonetx";
+
+ public ViewContext(IViewContext<ICommonClientServiceAsync> commonViewContext)
+ {
+ super(commonViewContext);
+ }
+
+ @Override
+ protected String getTechnology()
+ {
+ return TECHNOLOGY_NAME;
+ }
+
+
+ @Override
+ protected IPhosphoNetXClientServiceAsync createClientServiceAsync()
+ {
+ return GWT.create(IPhosphoNetXClientService.class);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinByExperimentCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinByExperimentCriteria.java
new file mode 100644
index 0000000000000000000000000000000000000000..55a91b822857a8bf385917c3385fd65e8b804d13
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinByExperimentCriteria.java
@@ -0,0 +1,45 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.dto;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ListProteinByExperimentCriteria extends DefaultResultSetConfig<String, Protein> implements IsSerializable
+{
+ private TechId experimentID;
+
+ public final TechId getExperimentID()
+ {
+ return experimentID;
+ }
+
+ public final void setExperimentID(TechId experimentID)
+ {
+ this.experimentID = experimentID;
+ }
+
+
+}
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 26406c3600d49f9e719b40581ed7c8726dddc8ab..19e63043a9bb3d5c71232d661ab69509fd4843a3 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
@@ -1,6 +1,9 @@
// PhosphoNetX dictionary
-var phospohonetx = {
-
+var phosphonetx = {
+ query_menu_title: "Queries",
+ ALL_PROTEINS_OF_AN_EXPERIMENT: "All Proteins of an Experiment",
+ query_all_proteins_by_experiment: "Proteins of an Experiment",
+ selected_experiment_label: "Experiment",
// 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/ListProteinOriginalDataProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java
new file mode 100644
index 0000000000000000000000000000000000000000..b8ee1e75b71e7e112a6b7a07f323b72d9ab491a0
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java
@@ -0,0 +1,50 @@
+/*
+ * 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.plugin.phosphonetx.client.web.server;
+
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDataProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ListProteinOriginalDataProvider implements IOriginalDataProvider<Protein>
+{
+ private final IPhosphoNetXServer server;
+ private final String sessionToken;
+ private final TechId experimentID;
+
+ ListProteinOriginalDataProvider(IPhosphoNetXServer server, String sessionToken, TechId experimentID)
+ {
+ this.server = server;
+ this.sessionToken = sessionToken;
+ this.experimentID = experimentID;
+ }
+
+ public List<Protein> getOriginalData() throws UserFailureException
+ {
+ return server.listProteinsByExperiment(sessionToken, experimentID);
+ }
+
+}
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
new file mode 100644
index 0000000000000000000000000000000000000000..2d94bd83e2132ee79b6dd6a724765a8175cc892c
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
@@ -0,0 +1,76 @@
+/*
+ * 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.plugin.phosphonetx.client.web.server;
+
+import javax.annotation.Resource;
+
+import org.springframework.stereotype.Component;
+
+import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
+import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractClientService;
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Component(value = ResourceNames.PHOSPHONETX_PLUGIN_SERVICE)
+public class PhosphoNetXClientService extends AbstractClientService implements IPhosphoNetXClientService
+{
+ @Resource(name = ResourceNames.PHOSPHONETX_PLUGIN_SERVER)
+ private IPhosphoNetXServer server;
+
+ public PhosphoNetXClientService()
+ {
+ super();
+ }
+
+ public PhosphoNetXClientService(IRequestContextProvider requestContextProvider)
+ {
+ super(requestContextProvider);
+ }
+
+ @Override
+ protected IServer getServer()
+ {
+ return server;
+ }
+
+ public ResultSet<Protein> listProteinsByExperiment(ListProteinByExperimentCriteria criteria) throws UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(criteria, new ListProteinOriginalDataProvider(server,
+ sessionToken, criteria.getExperimentID()));
+ }
+
+ public String prepareExportProteins(TableExportCriteria<Protein> exportCriteria)
+ throws UserFailureException
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientServiceServlet.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientServiceServlet.java
new file mode 100644
index 0000000000000000000000000000000000000000..2f979d6021b90492396339a5f97e2a21c278b844
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientServiceServlet.java
@@ -0,0 +1,48 @@
+/*
+ * 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.plugin.phosphonetx.client.web.server;
+
+import javax.annotation.Resource;
+
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.RequestMapping;
+
+import ch.systemsx.cisd.common.servlet.GWTRPCServiceExporter;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Controller
+@RequestMapping({"/phosphonetx", "/openbis/phosphonetx"})
+public class PhosphoNetXClientServiceServlet extends GWTRPCServiceExporter
+{
+ private static final long serialVersionUID = 1L;
+
+ @Resource(name = ResourceNames.PHOSPHONETX_PLUGIN_SERVICE)
+ private IPhosphoNetXClientService service;
+
+ @Override
+ protected Object getService()
+ {
+ return service;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
index 96e5fb1c2dc2a302cbbfe3b00fe9be5975ef96e7..28f67d912b3ef8309b4ad5fdfb50b915b33704dd 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
@@ -16,17 +16,23 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
+import java.util.ArrayList;
+import java.util.List;
+
import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
/**
* @author Franz-Josef Elmer
@@ -58,5 +64,12 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
{
return new PhosphoNetXServerLogger(getSessionManager(), invocationSuccessful);
}
+
+ public List<Protein> listProteinsByExperiment(String sessionToken, TechId experimentId)
+ throws UserFailureException
+ {
+ ArrayList<Protein> proteins = new ArrayList<Protein>();
+ return proteins;
+ }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
index c6e8456d40074e3b7063e7865787328a078b47d4..8b4f7ddb9ece61a6631807c7845f38b58cad0de4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleGenerationDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
/**
*
@@ -63,4 +64,11 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
newSample.getSampleType(), newSample.getIdentifier(), attachments.size());
}
+ public List<Protein> listProteinsByExperiment(String sessionToken, TechId experimentId)
+ throws UserFailureException
+ {
+ logAccess(sessionToken, "list_proteins_by_experiment", "ID(%s)", experimentId);
+ return null;
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
index e72021c36f86393203d6ec0ae44981fbe61a5352..6b01c312183e48ee3d3aba9422319ae6ca6fd023 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
@@ -16,7 +16,18 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared;
+import java.util.List;
+
+import org.springframework.transaction.annotation.Transactional;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Protein;
/**
*
@@ -25,5 +36,9 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*/
public interface IPhosphoNetXServer extends IServer
{
-
+ @Transactional
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<Protein> listProteinsByExperiment(String sessionToken,
+ @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
+ TechId experimentId) throws UserFailureException;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AccessionNumberType.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AccessionNumberType.java
new file mode 100644
index 0000000000000000000000000000000000000000..208316f717c5ae58b1b6f9d84b5021aa9408d6d9
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/AccessionNumberType.java
@@ -0,0 +1,30 @@
+/*
+ * 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.plugin.phosphonetx.shared.basic.dto;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public enum AccessionNumberType implements IsSerializable
+{
+ IPI, REF_SEQ, SWISS_PROT, ENSEMBL, TREMBL, LOCUS_LINK, FLYBASE;
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Protein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Protein.java
new file mode 100644
index 0000000000000000000000000000000000000000..c6390c9aae0902f3de59f11ba5442059f9312239
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/Protein.java
@@ -0,0 +1,64 @@
+/*
+ * 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.plugin.phosphonetx.shared.basic.dto;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class Protein implements IsSerializable
+{
+ private AccessionNumberType accessionNumberType;
+
+ private String accessionNumber;
+
+ private String description;
+
+ public final AccessionNumberType getAccessionNumberType()
+ {
+ return accessionNumberType;
+ }
+
+ public final void setAccessionNumberType(AccessionNumberType accessionNumberType)
+ {
+ this.accessionNumberType = accessionNumberType;
+ }
+
+ public final String getAccessionNumber()
+ {
+ return accessionNumber;
+ }
+
+ public final void setAccessionNumber(String accessionNumber)
+ {
+ this.accessionNumber = accessionNumber;
+ }
+
+ public final String getDescription()
+ {
+ return description;
+ }
+
+ public final void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
index 62979f8b28b2fada328cbb552035c2c90985b7f7..223c86cff06e3f7018a186073a6243255bd0b6c8 100644
--- a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
+++ b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
@@ -189,8 +189,7 @@ ALTER TABLE PROTEIN_STATISTICS ADD CONSTRAINT PRST_PK PRIMARY KEY (ID)
CREATE TABLE PROTEINS(
ID BIGSERIAL NOT NULL,
- DATA_SET_CODE CODE NOT NULL,
- SEQU_ID TECH_ID,
+ DATA_SET_PERM_ID CODE NOT NULL,
ABUN_ID TECH_ID,
PRST_ID TECH_ID
)