From bac2fb852e570d2b317751a6d54d7bb3dafe3e3a Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 14 Jul 2009 09:14:05 +0000
Subject: [PATCH] LMS-1028 ProteinViewer: DataSetProteinGrid added
SVN: 11738
---
.../web/client/IPhosphoNetXClientService.java | 8 ++
.../IPhosphoNetXClientServiceAsync.java | 10 ++
.../application/DataSetProteinGrid.java | 117 ++++++++++++++++++
.../client/web/client/application/Dict.java | 4 +
.../PhosphoNetXDisplayTypeIDGenerator.java | 1 +
.../web/client/application/ProteinViewer.java | 18 +--
.../columns/DataSetProteinColDefKind.java | 77 ++++++++++++
...oteinByExperimentAndReferenceCriteria.java | 56 +++++++++
.../web/public/phosphonetx-dictionary.js | 4 +
.../ListDataSetProteinDataProvider.java | 55 ++++++++
.../web/server/PhosphoNetXClientService.java | 17 +++
.../phosphonetx/server/PhosphoNetXServer.java | 56 ++++-----
.../server/PhosphoNetXServerLogger.java | 9 ++
.../business/BusinessObjectFactory.java | 10 ++
.../server/business/DataSetProteinTable.java | 76 ++++++++++++
.../business/IBusinessObjectFactory.java | 4 +
.../server/business/IDataSetProteinTable.java | 36 ++++++
.../business/IProteinSequenceTable.java | 37 ++++++
.../server/business/ProteinSequenceTable.java | 109 ++++++++++++++++
.../server/dataaccess/IProteinQueryDAO.java | 13 +-
.../shared/IPhosphoNetXServer.java | 8 ++
.../shared/basic/dto/DataSetProtein.java | 107 ++++++++++++++++
.../shared/basic/dto/ProteinByExperiment.java | 15 ---
.../shared/basic/dto/ProteinSequence.java | 12 ++
.../shared/dto/IdentifiedProtein.java | 12 +-
.../phosphonetx/shared/dto/Sequence.java | 13 ++
26 files changed, 818 insertions(+), 66 deletions(-)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/DataSetProteinGrid.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/DataSetProteinColDefKind.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinByExperimentAndReferenceCriteria.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListDataSetProteinDataProvider.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetProteinTable.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IDataSetProteinTable.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinSequenceTable.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSequenceTable.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/DataSetProtein.java
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 027f27bf771..0c11144c580 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
@@ -21,9 +21,11 @@ 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.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
@@ -49,4 +51,10 @@ public interface IPhosphoNetXClientService extends IClientService
public String prepareExportProteinSequences(TableExportCriteria<ProteinSequence> exportCriteria)
throws UserFailureException;
+ public ResultSet<DataSetProtein> listProteinsByExperimentAndReference(
+ ListProteinByExperimentAndReferenceCriteria criteria) throws UserFailureException;
+
+ public String prepareExportDataSetProteins(TableExportCriteria<DataSetProtein> 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 a876608648f..2baa98ab4fd 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
@@ -22,9 +22,11 @@ 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.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
@@ -55,4 +57,12 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
public void prepareExportProteinSequences(TableExportCriteria<ProteinSequence> exportCriteria,
AsyncCallback<String> callback);
+ /** @see IPhosphoNetXClientService#listProteinsByExperimentAndReference(ListProteinByExperimentAndReferenceCriteria) */
+ public void listProteinsByExperimentAndReference(
+ ListProteinByExperimentAndReferenceCriteria criteria,
+ AsyncCallback<ResultSet<DataSetProtein>> callback);
+
+ /** @see IPhosphoNetXClientService#prepareExportDataSetProteins(TableExportCriteria) */
+ public void prepareExportDataSetProteins(TableExportCriteria<DataSetProtein> 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/DataSetProteinGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/DataSetProteinGrid.java
new file mode 100644
index 00000000000..52eb6a92aac
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/DataSetProteinGrid.java
@@ -0,0 +1,117 @@
+/*
+ * 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.Experiment;
+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.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.DataSetProteinColDefKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class DataSetProteinGrid extends AbstractSimpleBrowserGrid<DataSetProtein>
+{
+ private static final String PREFIX = GenericConstants.ID_PREFIX + "data-set-protein-browser";
+
+ public static final String BROWSER_ID = PREFIX + "_main";
+
+ public static final String GRID_ID = PREFIX + "_grid";
+
+ static IDisposableComponent create(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ Experiment experimentOrNull, TechId proteinReferenceID)
+ {
+ return new DataSetProteinGrid(viewContext, experimentOrNull, proteinReferenceID)
+ .asDisposableWithoutToolbar();
+ }
+
+ private static String createWidgetID(Experiment experimentOrNull, TechId proteinReferenceID)
+ {
+ return "-" + (experimentOrNull == null ? "" : experimentOrNull.getIdentifier() + "-")
+ + proteinReferenceID;
+ }
+
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+
+ private ListProteinByExperimentAndReferenceCriteria criteria;
+
+ private DataSetProteinGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ Experiment experimentOrNull, TechId proteinReferenceID)
+ {
+ super(viewContext.getCommonViewContext(), BROWSER_ID
+ + createWidgetID(experimentOrNull, proteinReferenceID), GRID_ID
+ + createWidgetID(experimentOrNull, proteinReferenceID), true);
+ specificViewContext = viewContext;
+ criteria = new ListProteinByExperimentAndReferenceCriteria();
+ if (experimentOrNull != null)
+ {
+ criteria.setExperimentID(new TechId(experimentOrNull.getId()));
+ }
+ criteria.setProteinReferenceID(proteinReferenceID);
+ setDisplayTypeIDGenerator(PhosphoNetXDisplayTypeIDGenerator.DATA_SET_PROTEIN_BROWSER_GRID);
+ }
+
+ @Override
+ protected IColumnDefinitionKind<DataSetProtein>[] getStaticColumnsDefinition()
+ {
+ return DataSetProteinColDefKind.values();
+ }
+
+ @Override
+ protected List<IColumnDefinition<DataSetProtein>> getInitialFilters()
+ {
+ return asColumnFilters(new DataSetProteinColDefKind[] {});
+ }
+
+ @Override
+ protected void listEntities(DefaultResultSetConfig<String, DataSetProtein> resultSetConfig,
+ AbstractAsyncCallback<ResultSet<DataSetProtein>> callback)
+ {
+ criteria.copyPagingConfig(resultSetConfig);
+ specificViewContext.getService().listProteinsByExperimentAndReference(criteria, callback);
+ }
+
+ @Override
+ protected void prepareExportEntities(TableExportCriteria<DataSetProtein> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ specificViewContext.getService().prepareExportDataSetProteins(exportCriteria, callback);
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return new DatabaseModificationKind[0];
+ }
+
+}
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
index d6cfad93f96..ee7668f7ee6 100644
--- 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
@@ -39,6 +39,10 @@ public class Dict
public static final String DATABASE_NAME_AND_VERSION = "database_name_and_version";
public static final String SEQUENCE = "sequence";
public static final String SEQUENCES = "sequences";
+ public static final String DATA_SET_PROTEINS = "data_set_proteins";
+ public static final String DATA_SET_PERM_ID = "data_set_perm_id";
+ public static final String PEPTIDE_COUNT = "peptide_count";
+ public static final String SEQUENCE_NAME = "sequence_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
index 3c94d22a076..731e37132f6 100644
--- 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
@@ -29,6 +29,7 @@ public enum PhosphoNetXDisplayTypeIDGenerator implements IDisplayTypeIDGenerator
{
PROTEIN_BY_EXPERIMENT_BROWSER_GRID("protein-by-experiment-browser-grid"),
PROTEIN_SEQUENCE_BROWSER_GRID("protein-sequence-browser-grid"),
+ DATA_SET_PROTEIN_BROWSER_GRID("data-set-protein-browser-grid"),
;
private final String genericNameOrPrefix;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
index 1d5b16eb297..1a11f8861bf 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
@@ -93,8 +93,7 @@ public class ProteinViewer extends
private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
private final Experiment experimentOrNull;
- private final TechId experimentID;
- private final TechId proteinreferenceID;
+ private final TechId proteinReferenceID;
private ProteinViewer(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
Experiment experimentOrNull, TechId proteinReferenceID)
@@ -102,15 +101,17 @@ public class ProteinViewer extends
super(viewContext, "", createWidgetID(proteinReferenceID), false);
this.viewContext = viewContext;
this.experimentOrNull = experimentOrNull;
- this.experimentID = TechId.create(experimentOrNull);
- this.proteinreferenceID = proteinReferenceID;
+ this.proteinReferenceID = proteinReferenceID;
reloadAllData();
}
private void reloadAllData()
{
- viewContext.getService().getProteinByExperiment(experimentID, proteinreferenceID,
- new ProteinByExperimentCallback(viewContext, this));
+ if (experimentOrNull != null)
+ {
+ viewContext.getService().getProteinByExperiment(new TechId(experimentOrNull.getId()),
+ proteinReferenceID, new ProteinByExperimentCallback(viewContext, this));
+ }
}
private void recreateUI(ProteinByExperiment protein)
@@ -134,7 +135,10 @@ public class ProteinViewer extends
layoutData.setSize(400);
add(contentPanel, layoutData);
add(new BrowserSectionPanel(viewContext.getMessage(Dict.SEQUENCES), ProteinSequenceGrid
- .create(viewContext, proteinreferenceID)), createRightBorderLayoutData());
+ .create(viewContext, proteinReferenceID)), createRightBorderLayoutData());
+ add(new BrowserSectionPanel(viewContext.getMessage(Dict.DATA_SET_PROTEINS),
+ DataSetProteinGrid.create(viewContext, experimentOrNull, proteinReferenceID)),
+ createBorderLayoutData(LayoutRegion.SOUTH));
layout();
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/DataSetProteinColDefKind.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/DataSetProteinColDefKind.java
new file mode 100644
index 00000000000..9617da5e34c
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/DataSetProteinColDefKind.java
@@ -0,0 +1,77 @@
+/*
+ * 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.columns;
+
+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.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public enum DataSetProteinColDefKind implements IColumnDefinitionKind<DataSetProtein>
+{
+ DATA_SET_PERM_ID(new AbstractColumnDefinitionKind<DataSetProtein>(Dict.DATA_SET_PERM_ID, 200)
+ {
+ @Override
+ public String tryGetValue(DataSetProtein entity)
+ {
+ return entity.getDataSetPermID();
+ }
+ }),
+ SEQUENCE_NAME(new AbstractColumnDefinitionKind<DataSetProtein>(Dict.SEQUENCE_NAME, 80)
+ {
+ @Override
+ public String tryGetValue(DataSetProtein entity)
+ {
+ return entity.getSequenceName();
+ }
+ }),
+
+ PEPTIDE_COUNT(new AbstractColumnDefinitionKind<DataSetProtein>(Dict.PEPTIDE_COUNT, 80)
+ {
+ @Override
+ public String tryGetValue(DataSetProtein entity)
+ {
+ return Integer.toString(entity.getPeptideCount());
+ }
+ }),
+
+ ;
+
+ private final AbstractColumnDefinitionKind<DataSetProtein> columnDefinitionKind;
+
+ private DataSetProteinColDefKind(AbstractColumnDefinitionKind<DataSetProtein> columnDefinitionKind)
+ {
+ this.columnDefinitionKind = columnDefinitionKind;
+ }
+
+ public String id()
+ {
+ return name();
+ }
+
+ public AbstractColumnDefinitionKind<DataSetProtein> getDescriptor()
+ {
+ return columnDefinitionKind;
+ }
+
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinByExperimentAndReferenceCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinByExperimentAndReferenceCriteria.java
new file mode 100644
index 00000000000..e297544d3df
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinByExperimentAndReferenceCriteria.java
@@ -0,0 +1,56 @@
+/*
+ * 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.DataSetProtein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ListProteinByExperimentAndReferenceCriteria extends
+ DefaultResultSetConfig<String, DataSetProtein> implements IsSerializable
+{
+ private TechId experimentID;
+ private TechId proteinReferenceID;
+
+ public final TechId getExperimentID()
+ {
+ return experimentID;
+ }
+
+ public final void setExperimentID(TechId experimentID)
+ {
+ this.experimentID = experimentID;
+ }
+
+ public final TechId getProteinReferenceID()
+ {
+ return proteinReferenceID;
+ }
+
+ public final void setProteinReferenceID(TechId proteinReferenceID)
+ {
+ this.proteinReferenceID = proteinReferenceID;
+ }
+
+}
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 94845f627aa..50a8a9454f4 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
@@ -18,6 +18,10 @@ var phosphonetx = {
database_name_and_version: "Database",
sequence: "Amino Acid Sequence",
sequences: "Amino Acid Sequences",
+ data_set_proteins: "Data Sets",
+ data_set_perm_id: "Data Set",
+ peptide_count: "Peptides",
+ sequence_name: "Sequence",
// 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/ListDataSetProteinDataProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListDataSetProteinDataProvider.java
new file mode 100644
index 00000000000..7a32cc17440
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListDataSetProteinDataProvider.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.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.DataSetProtein;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class ListDataSetProteinDataProvider implements IOriginalDataProvider<DataSetProtein>
+{
+ private final IPhosphoNetXServer server;
+
+ private final String sessionToken;
+
+ private final TechId experimentID;
+
+ private final TechId proteinReferenceID;
+
+ ListDataSetProteinDataProvider(IPhosphoNetXServer server, String sessionToken,
+ TechId experimentID, TechId proteinReferenceID)
+ {
+ this.server = server;
+ this.sessionToken = sessionToken;
+ this.experimentID = experimentID;
+ this.proteinReferenceID = proteinReferenceID;
+ }
+
+ public List<DataSetProtein> getOriginalData() throws UserFailureException
+ {
+ return server.listProteinsByExperimentAndReference(sessionToken, experimentID,
+ proteinReferenceID);
+ }
+
+}
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 a471a9c70ba..cb81bab75a8 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
@@ -29,11 +29,13 @@ import ch.systemsx.cisd.openbis.generic.client.web.server.translator.UserFailure
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
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.DataSetProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
@@ -105,4 +107,19 @@ public class PhosphoNetXClientService extends AbstractClientService implements
return prepareExportEntities(exportCriteria);
}
+ public ResultSet<DataSetProtein> listProteinsByExperimentAndReference(
+ ListProteinByExperimentAndReferenceCriteria criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(criteria, new ListDataSetProteinDataProvider(server, sessionToken,
+ criteria.getExperimentID(), criteria.getProteinReferenceID()));
+ }
+
+ public String prepareExportDataSetProteins(TableExportCriteria<DataSetProtein> exportCriteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(exportCriteria);
+ }
+
}
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 2c9241cdb80..4ad9017a45a 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
@@ -16,13 +16,10 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
-import java.util.ArrayList;
import java.util.List;
import javax.annotation.Resource;
-import net.lemnik.eodsql.DataSet;
-
import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
@@ -36,15 +33,17 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IDataSetProteinTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinReferenceTable;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinSequenceTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
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.DataSetProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
/**
* @author Franz-Josef Elmer
@@ -92,8 +91,8 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
{
final Session session = getSessionManager().getSession(sessionToken);
IProteinReferenceTable table = specificBOFactory.createProteinReferenceTable(session);
- ExperimentPE experiment = getDAOFactory().getExperimentDAO().getByTechId(experimentId);
- table.load(experiment.getPermId(), falseDiscoveryRate);
+ String experimentPermId = getExperimentPermIDFor(experimentId);
+ table.load(experimentPermId, falseDiscoveryRate);
return table.getProteinReferences();
}
@@ -117,35 +116,28 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
TechId proteinReferenceID) throws UserFailureException
{
- IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO();
- DataSet<Sequence> sequences =
- proteinQueryDAO.listProteinSequencesByProteinReference(proteinReferenceID.getId());
- ArrayList<ProteinSequence> proteinSequences =
- new ArrayList<ProteinSequence>(sequences.size());
- int number = 0;
- for (Sequence sequence : sequences)
- {
- ProteinSequence proteinSequence = new ProteinSequence();
- proteinSequence.setId(new TechId(sequence.getId()));
- proteinSequence.setShortName(createShortName(number++));
- proteinSequence.setSequence(sequence.getSequence());
- proteinSequence.setDatabaseNameAndVersion(sequence.getDatabaseNameAndVersion());
- proteinSequences.add(proteinSequence);
- }
- sequences.close();
- return proteinSequences;
+ final Session session = getSessionManager().getSession(sessionToken);
+ IProteinSequenceTable sequenceTable = specificBOFactory.createProteinSequenceTable(session);
+ sequenceTable.loadByReference(proteinReferenceID);
+ return sequenceTable.getSequences();
}
- private String createShortName(int number)
+ public List<DataSetProtein> listProteinsByExperimentAndReference(String sessionToken,
+ TechId experimentId, TechId proteinReferenceID) throws UserFailureException
{
- StringBuilder builder = new StringBuilder();
- int n = number;
- while (n > 0)
- {
- builder.insert(0, "ABCEDEFGHIJKLMNOPQRSTUVWXYZ".charAt(n % 26));
- n /= 26;
- }
- return builder.toString();
+ final Session session = getSessionManager().getSession(sessionToken);
+ IProteinSequenceTable sequenceTable = specificBOFactory.createProteinSequenceTable(session);
+ sequenceTable.loadByReference(proteinReferenceID);
+ IDataSetProteinTable dataSetProteinTable = specificBOFactory.createDataSetProteinTable(session);
+ dataSetProteinTable.load(getExperimentPermIDFor(experimentId), proteinReferenceID, sequenceTable);
+ return dataSetProteinTable.getDataSetProteins();
}
+ private String getExperimentPermIDFor(TechId experimentId)
+ {
+ ExperimentPE experiment = getDAOFactory().getExperimentDAO().getByTechId(experimentId);
+ String experimentPermId = experiment.getPermId();
+ return experimentPermId;
+ }
+
}
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 8f97366476e..3eb3726b782 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
@@ -24,6 +24,7 @@ import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
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.basic.dto.DataSetProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
@@ -63,4 +64,12 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
return null;
}
+ public List<DataSetProtein> listProteinsByExperimentAndReference(String sessionToken,
+ TechId experimentId, TechId proteinReferenceID) throws UserFailureException
+ {
+ logAccess(sessionToken, "list_proteins_by_experiment_and_reference",
+ "EXPERIMENT_ID(%s) PROTEIN_REFERENCE_ID(%s)", experimentId, proteinReferenceID);
+ return null;
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
index 7c13a6e6c2b..c2e2d5cc4c9 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
@@ -41,4 +41,14 @@ public class BusinessObjectFactory implements IBusinessObjectFactory
return new ProteinReferenceTable(daoFactory, specificDAOFactory, session);
}
+ public IProteinSequenceTable createProteinSequenceTable(Session session)
+ {
+ return new ProteinSequenceTable(daoFactory, specificDAOFactory, session);
+ }
+
+ public IDataSetProteinTable createDataSetProteinTable(Session session)
+ {
+ return new DataSetProteinTable(daoFactory, specificDAOFactory, session);
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetProteinTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetProteinTable.java
new file mode 100644
index 00000000000..d04928a610b
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetProteinTable.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.server.business;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import net.lemnik.eodsql.DataSet;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+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.server.dataaccess.IPhosphoNetXDAOFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class DataSetProteinTable extends AbstractBusinessObject implements IDataSetProteinTable
+{
+ private List<DataSetProtein> dataSetProteins;
+
+ DataSetProteinTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
+ Session session)
+ {
+ super(daoFactory, specificDAOFactory, session);
+ }
+
+ public List<DataSetProtein> getDataSetProteins()
+ {
+ return dataSetProteins;
+ }
+
+ public void load(String experimentPermID, TechId proteinReferenceID,
+ IProteinSequenceTable sequenceTable)
+ {
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ DataSet<IdentifiedProtein> proteins =
+ proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
+ proteinReferenceID.getId());
+ dataSetProteins = new ArrayList<DataSetProtein>();
+ for (IdentifiedProtein protein : proteins)
+ {
+ errorModel.setFalseDiscoveryRateFor(protein);
+ DataSetProtein dataSetProtein = new DataSetProtein();
+ dataSetProtein.setDataSetID(new TechId(protein.getDataSetID()));
+ dataSetProtein.setDataSetPermID(protein.getDataSetPermID());
+ dataSetProtein.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
+ dataSetProtein.setPeptideCount(protein.getPeptideCount());
+ dataSetProtein.setProteinID(new TechId(protein.getProteinID()));
+ dataSetProtein.setSequenceName(sequenceTable.getShortName(protein.getDatabaseID()));
+ dataSetProteins.add(dataSetProtein);
+ }
+ proteins.close();
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
index 059dc69b358..47e2d166ed8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
@@ -26,4 +26,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
public interface IBusinessObjectFactory
{
public IProteinReferenceTable createProteinReferenceTable(Session session);
+
+ public IProteinSequenceTable createProteinSequenceTable(Session session);
+
+ public IDataSetProteinTable createDataSetProteinTable(Session session);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IDataSetProteinTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IDataSetProteinTable.java
new file mode 100644
index 00000000000..d655b3398ac
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IDataSetProteinTable.java
@@ -0,0 +1,36 @@
+/*
+ * 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.server.business;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IDataSetProteinTable
+{
+ public List<DataSetProtein> getDataSetProteins();
+
+ public void load(String experimentPermID, TechId proteinReferenceID,
+ IProteinSequenceTable sequenceTable);
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinSequenceTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinSequenceTable.java
new file mode 100644
index 00000000000..4ee2cfed228
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinSequenceTable.java
@@ -0,0 +1,37 @@
+/*
+ * 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.server.business;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IProteinSequenceTable
+{
+
+ public void loadByReference(TechId proteinReferenceID);
+
+ public List<ProteinSequence> getSequences();
+
+ public String getShortName(long databaseID);
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSequenceTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSequenceTable.java
new file mode 100644
index 00000000000..ffd31325cb7
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSequenceTable.java
@@ -0,0 +1,109 @@
+/*
+ * 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.server.business;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import net.lemnik.eodsql.DataSet;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+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.server.dataaccess.IPhosphoNetXDAOFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ProteinSequenceTable extends AbstractBusinessObject implements IProteinSequenceTable
+{
+ private List<ProteinSequence> proteinSequences;
+ private Map<Long, String> databaseIDToShortNameMap;
+
+ ProteinSequenceTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
+ Session session)
+ {
+ super(daoFactory, specificDAOFactory, session);
+ }
+
+ public List<ProteinSequence> getSequences()
+ {
+ if (proteinSequences == null)
+ {
+ throw new IllegalStateException("Sequences not loaded.");
+ }
+ return proteinSequences;
+ }
+
+ public String getShortName(long databaseID)
+ {
+ if (databaseIDToShortNameMap == null)
+ {
+ throw new IllegalStateException("Sequences not loaded.");
+ }
+ String shortName = databaseIDToShortNameMap.get(databaseID);
+ if (shortName == null)
+ {
+ throw new IllegalArgumentException("No sequence found for databaseID " + databaseID);
+ }
+ return shortName;
+ }
+
+ public void loadByReference(TechId proteinReferenceID)
+ {
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ DataSet<Sequence> sequences =
+ proteinQueryDAO.listProteinSequencesByProteinReference(proteinReferenceID.getId());
+ proteinSequences = new ArrayList<ProteinSequence>(sequences.size());
+ databaseIDToShortNameMap = new HashMap<Long, String>();
+ int number = 0;
+ for (Sequence sequence : sequences)
+ {
+ ProteinSequence proteinSequence = new ProteinSequence();
+ proteinSequence.setId(new TechId(sequence.getId()));
+ String shortName = createShortName(number++);
+ proteinSequence.setShortName(shortName);
+ proteinSequence.setSequence(sequence.getSequence());
+ long databaseID = sequence.getDatabaseID();
+ proteinSequence.setDatabaseID(new TechId(databaseID));
+ proteinSequence.setDatabaseNameAndVersion(sequence.getDatabaseNameAndVersion());
+ proteinSequences.add(proteinSequence);
+ databaseIDToShortNameMap.put(databaseID, shortName);
+ }
+ sequences.close();
+ }
+
+ private String createShortName(int number)
+ {
+ StringBuilder builder = new StringBuilder();
+ int n = number;
+ while (n > 0 || builder.length() == 0)
+ {
+ builder.insert(0, "ABCEDEFGHIJKLMNOPQRSTUVWXYZ".charAt(n % 26));
+ n /= 26;
+ }
+ return builder.toString();
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
index a0df8f0b13f..1f57e069096 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
@@ -47,21 +47,22 @@ public interface IProteinQueryDAO extends BaseQuery
@Select("select * from protein_references where id = ?{1}")
public ProteinReference tryToGetProteinReference(long proteinReferenceID);
- @Select("select s.id, amino_acid_sequence, name_and_version "
+ @Select("select s.id, db_id, amino_acid_sequence, name_and_version "
+ "from sequences as s join databases as d on s.db_id = d.id "
+ "where s.prre_id = ?{1} order by name_and_version")
public DataSet<Sequence> listProteinSequencesByProteinReference(long proteinReferenceID);
@Select("select ds.id as data_set_id, ds.perm_id as data_set_perm_id, p.id as protein_id, "
- + "probability, count(pe.id) as peptide_count, amino_acid_sequence, name_and_version "
- + "from data_sets as ds join proteins as p on p.dase_id = ds.id "
+ + "probability, count(pe.id) as peptide_count, amino_acid_sequence, s.db_id "
+ + "from data_sets as ds join experiments as e on ds.expe_id = e.id "
+ + " join proteins as p on p.dase_id = ds.id "
+ " join identified_proteins as i on i.prot_id = p.id "
+ " join sequences as s on i.sequ_id = s.id "
+ " join databases as db on s.db_id = db.id "
+ " left join peptides as pe on pe.prot_id = p.id "
- + "where s.prre_id = ?{2} and ds.expe_id = ?{1} "
+ + "where s.prre_id = ?{2} and e.perm_id = ?{1} "
+ "group by data_set_id, data_set_perm_id, protein_id, probability, "
- + " amino_acid_sequence, name_and_version order by data_set_perm_id")
+ + " amino_acid_sequence, s.db_id order by data_set_perm_id")
public DataSet<IdentifiedProtein> listProteinsByProteinReferenceAndExperiment(
- long experimentID, long proteinReferenceID);
+ String experimentPermID, long proteinReferenceID);
}
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 61b936b02f1..95e8184589d 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
@@ -27,6 +27,7 @@ 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.DataSetProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
@@ -54,4 +55,11 @@ public interface IPhosphoNetXServer extends IServer
@RolesAllowed(RoleSet.OBSERVER)
public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
TechId proteinReferenceID) throws UserFailureException;
+
+ @Transactional
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<DataSetProtein> listProteinsByExperimentAndReference(String sessionToken,
+ @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
+ TechId experimentId, TechId proteinReferenceID) throws UserFailureException;
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/DataSetProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/DataSetProtein.java
new file mode 100644
index 00000000000..79ac33495e1
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/DataSetProtein.java
@@ -0,0 +1,107 @@
+/*
+ * 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 java.io.Serializable;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataSetProtein implements IsSerializable, Serializable
+{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+ private String dataSetPermID;
+
+ private TechId dataSetID;
+
+ private TechId proteinID;
+
+ private String sequenceName;
+
+ private int peptideCount;
+
+ private double falseDiscoveryRate;
+
+ public final String getDataSetPermID()
+ {
+ return dataSetPermID;
+ }
+
+ public final void setDataSetPermID(String dataSetPermID)
+ {
+ this.dataSetPermID = dataSetPermID;
+ }
+
+ public final TechId getDataSetID()
+ {
+ return dataSetID;
+ }
+
+ public final void setDataSetID(TechId dataSetID)
+ {
+ this.dataSetID = dataSetID;
+ }
+
+ public final TechId getProteinID()
+ {
+ return proteinID;
+ }
+
+ public final void setProteinID(TechId proteinID)
+ {
+ this.proteinID = proteinID;
+ }
+
+ public final String getSequenceName()
+ {
+ return sequenceName;
+ }
+
+ public final void setSequenceName(String sequenceName)
+ {
+ this.sequenceName = sequenceName;
+ }
+
+ public final int getPeptideCount()
+ {
+ return peptideCount;
+ }
+
+ public final void setPeptideCount(int peptideCount)
+ {
+ this.peptideCount = peptideCount;
+ }
+
+ public final double getFalseDiscoveryRate()
+ {
+ return falseDiscoveryRate;
+ }
+
+ public final void setFalseDiscoveryRate(double falseDiscoveryRate)
+ {
+ this.falseDiscoveryRate = falseDiscoveryRate;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinByExperiment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinByExperiment.java
index 3d9ee897f48..b83d457d22c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinByExperiment.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinByExperiment.java
@@ -17,8 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
import com.google.gwt.user.client.rpc.IsSerializable;
@@ -38,8 +36,6 @@ public class ProteinByExperiment implements IsSerializable, Serializable
private String description;
- private List<ProteinSequence> sequences = new ArrayList<ProteinSequence>();
-
public final String getUniprotID()
{
return uniprotID;
@@ -60,15 +56,4 @@ public class ProteinByExperiment implements IsSerializable, Serializable
this.description = description;
}
- public final List<ProteinSequence> getSequences()
- {
- return sequences;
- }
-
- public final void addSequence(ProteinSequence proteinSequence)
- {
- this.sequences.add(proteinSequence);
- }
-
-
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
index e8a00621c49..188adbd03d7 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
@@ -36,6 +36,8 @@ public class ProteinSequence implements IsSerializable, Serializable
private TechId id;
+ private TechId databaseID;
+
private String sequence;
private String databaseNameAndVersion;
@@ -60,6 +62,16 @@ public class ProteinSequence implements IsSerializable, Serializable
this.id = id;
}
+ public final TechId getDatabaseID()
+ {
+ return databaseID;
+ }
+
+ public final void setDatabaseID(TechId databaseID)
+ {
+ this.databaseID = databaseID;
+ }
+
public final String getSequence()
{
return sequence;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
index 7f78dcd9148..52b08cecea8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
@@ -40,8 +40,8 @@ public class IdentifiedProtein extends AbstractDTOWithID
@ResultColumn("amino_acid_sequence")
private String sequence;
- @ResultColumn("name_and_version")
- private String database;
+ @ResultColumn("db_id")
+ private long databaseID;
@ResultColumn("probability")
private double probability;
@@ -118,14 +118,14 @@ public class IdentifiedProtein extends AbstractDTOWithID
this.falseDiscoveryRate = falseDiscoveryRate;
}
- public final String getDatabase()
+ public final long getDatabaseID()
{
- return database;
+ return databaseID;
}
- public final void setDatabase(String database)
+ public final void setDatabase(long databaseID)
{
- this.database = database;
+ this.databaseID = databaseID;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/Sequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/Sequence.java
index 10fa8f96222..f05316ea8bd 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/Sequence.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/Sequence.java
@@ -29,6 +29,9 @@ public class Sequence extends AbstractDTOWithID
@ResultColumn("amino_acid_sequence")
private String sequence;
+ @ResultColumn("db_id")
+ private long databaseID;
+
@ResultColumn("name_and_version")
private String databaseNameAndVersion;
@@ -42,6 +45,16 @@ public class Sequence extends AbstractDTOWithID
this.sequence = sequence;
}
+ public final long getDatabaseID()
+ {
+ return databaseID;
+ }
+
+ public final void setDatabaseID(long databaseID)
+ {
+ this.databaseID = databaseID;
+ }
+
public final String getDatabaseNameAndVersion()
{
return databaseNameAndVersion;
--
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