From ba297fb2fa765dc8bf30fa01b55edd7ddf6a733b Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Mon, 23 May 2011 13:17:15 +0000
Subject: [PATCH] [LMS-2253] Ability to extend vocabularies by 'ad hoc' terms
SVN: 21439
---
.../dss/client/api/gui/AbstractSwingGUI.java | 21 ++
.../api/gui/AddVocabularyTermDialog.java | 246 ++++++++++++++++++
.../api/gui/DataSetPropertiesPanel.java | 48 +---
.../api/gui/DataSetUploadClientModel.java | 51 +++-
.../api/gui/VocabularyTermsComboBoxPanel.java | 205 +++++++++++++++
...bularDataGraphCollectionConfiguration.java | 17 +-
.../shared/utils/CodeAndLabelUtil.java | 24 +-
.../shared/utils/DatasetFileLines.java | 5 +-
.../shared/utils/CodeAndLabelTest.java | 5 +-
.../web/client/ICommonClientService.java | 4 +-
.../web/client/ICommonClientServiceAsync.java | 6 +-
.../client/web/client/application/Dict.java | 3 -
.../field/VocabularyTermSelectionWidget.java | 239 +++++++++++------
.../application/ui/widget/DropDownList.java | 92 ++++++-
.../web/server/CommonClientService.java | 21 +-
.../openbis/generic/server/CommonServer.java | 7 +-
.../generic/server/CommonServerLogger.java | 16 +-
.../v1/GeneralInformationChangingService.java | 20 +-
...neralInformationChangingServiceLogger.java | 13 +-
.../api/v1/GeneralInformationService.java | 2 +-
.../v1/GeneralInformationServiceLogger.java | 9 +
.../generic/server/api/v1/Translator.java | 16 +-
.../server/business/bo/IVocabularyBO.java | 8 +-
.../server/business/bo/VocabularyBO.java | 17 +-
.../datasetlister/IDatasetListingQuery.java | 4 +-
.../materiallister/IMaterialListingQuery.java | 2 +-
.../bo/samplelister/ISampleListingQuery.java | 2 +-
...eUnusedUnofficialTermsMaintenanceTask.java | 115 ++++++++
.../openbis/generic/shared/ICommonServer.java | 4 +-
.../IGeneralInformationChangingService.java | 19 +-
.../api/v1/IGeneralInformationService.java | 12 +
.../dto/ControlledVocabularyPropertyType.java | 35 ++-
.../generic/shared/basic/CodeNormalizer.java | 47 ++++
.../cisd/openbis/public/common-dictionary.js | 15 +-
.../cisd/openbis/public/css/openbis.css | 11 +-
screening/.settings/.gitignore | 0
.../dss/etl/HCSImageFileExtractor.java | 4 +-
.../dss/etl/MicroscopyImageFileExtractor.java | 4 +-
...enedataFormatToCanonicalFeatureVector.java | 4 +-
.../server/TabularDataGraphServlet.java | 8 +-
...mageAnalysisMergedRowsReportingPlugin.java | 12 +-
.../server/DssServiceRpcScreening.java | 4 +-
.../etl/dataaccess/FeatureVectorDAOTest.java | 6 +-
.../graph/TabularDataScatterplotTest.java | 19 +-
44 files changed, 1162 insertions(+), 260 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AddVocabularyTermDialog.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/VocabularyTermsComboBoxPanel.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/RemoveUnusedUnofficialTermsMaintenanceTask.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeNormalizer.java
create mode 100644 screening/.settings/.gitignore
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractSwingGUI.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractSwingGUI.java
index 7bdb9ff5223..4c09fccb81c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractSwingGUI.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractSwingGUI.java
@@ -40,6 +40,7 @@ import ch.systemsx.cisd.common.exceptions.InvalidSessionException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.client.api.v1.DssComponentFactory;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
/**
@@ -366,6 +367,8 @@ class DssCommunicationState
private final IGeneralInformationService generalInformationService;
+ private final IGeneralInformationChangingService generalInformationChangingService;
+
private final boolean logoutOnClose;
private static final long CONNECTION_TIMEOUT_MILLIS = 15 * DateUtils.MILLIS_PER_SECOND;
@@ -380,6 +383,18 @@ class DssCommunicationState
return service;
}
+ private static IGeneralInformationChangingService createGeneralInformationChangingService(
+ String openBISURL)
+ {
+ ServiceFinder generalInformationServiceFinder =
+ new ServiceFinder("openbis", IGeneralInformationChangingService.SERVICE_URL);
+ IGeneralInformationChangingService service =
+ generalInformationServiceFinder.createService(
+ IGeneralInformationChangingService.class, openBISURL);
+ return service;
+
+ }
+
/**
* Create a new instance of the DssCommunicationState based info in the arguments. Throws an
* exception if it could not be created.
@@ -424,6 +439,7 @@ class DssCommunicationState
}
generalInformationService = createGeneralInformationService(openBisUrl);
+ generalInformationChangingService = createGeneralInformationChangingService(openBisUrl);
}
IDssComponent getDssComponent()
@@ -436,6 +452,11 @@ class DssCommunicationState
return generalInformationService;
}
+ public IGeneralInformationChangingService getGeneralInformationChangingService()
+ {
+ return generalInformationChangingService;
+ }
+
public boolean isLogoutOnClose()
{
return logoutOnClose;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AddVocabularyTermDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AddVocabularyTermDialog.java
new file mode 100644
index 00000000000..8d1c527285c
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AddVocabularyTermDialog.java
@@ -0,0 +1,246 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.client.api.gui;
+
+import java.awt.BorderLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.Insets;
+import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+
+import javax.swing.ComboBoxModel;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+
+import ch.systemsx.cisd.openbis.dss.client.api.gui.VocabularyTermsComboBoxPanel.VocabularyTermAdaptor;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class AddVocabularyTermDialog extends JDialog
+{
+ private static final long serialVersionUID = 1L;
+
+ private JPanel mainPanel;
+
+ private JPanel gridPanel;
+
+ private final JTextField codeField = new JTextField();
+
+ private final JTextField labelField = new JTextField();
+
+ private JTextArea descriptionField = new JTextArea();
+
+ private JComboBox vocabularyTermsField = new JComboBox();
+
+ private final Vocabulary vocabulary;
+
+ private final DataSetUploadClientModel clientModel;
+
+ public AddVocabularyTermDialog(JFrame mainWindow, ComboBoxModel comboBoxModel,
+ Vocabulary vocabulary, DataSetUploadClientModel clientModel)
+ {
+ super(mainWindow, "Add Ad Hoc vocabulary term", true);
+
+ this.vocabulary = vocabulary;
+ this.clientModel = clientModel;
+ mainPanel = new JPanel(new BorderLayout());
+
+ this.gridPanel = createMainPanel(comboBoxModel);
+ mainPanel.add(gridPanel, BorderLayout.CENTER);
+
+ mainPanel.add(createButtonsPanel(), BorderLayout.SOUTH);
+
+ this.setContentPane(mainPanel);
+
+ this.setSize(500, 300);
+
+ Point mwLocation = mainWindow.getLocationOnScreen();
+ int x = mwLocation.x + (mainWindow.getWidth() / 2) - (this.getWidth() / 2);
+ int y = mwLocation.y + (mainWindow.getHeight() / 2) - (this.getHeight() / 2);
+
+ this.setLocation(x > 0 ? x : 0, y > 0 ? y : 0);
+ }
+
+ private JPanel createButtonsPanel()
+ {
+ JPanel buttonsPanel = new JPanel();
+ JButton addButton = new JButton("Add");
+ addButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clientModel.addUnofficialVocabularyTerm(vocabulary, codeField.getText(),
+ labelField.getText().trim(), descriptionField.getText(),
+ extractPreviousTermOrdinal());
+ AddVocabularyTermDialog.this.dispose();
+ }
+ });
+ buttonsPanel.add(addButton);
+
+ JButton cancelButton = new JButton("Cancel");
+ cancelButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AddVocabularyTermDialog.this.dispose();
+ }
+ });
+ buttonsPanel.add(cancelButton);
+
+ return buttonsPanel;
+ }
+
+ private Long extractPreviousTermOrdinal()
+ {
+ // - 0 if nothing is selected (move to the beginning),
+ // - (otherwise) selected term's ordinal
+ VocabularyTermAdaptor selectedItem =
+ (VocabularyTermAdaptor) vocabularyTermsField.getSelectedItem();
+ return selectedItem != null ? selectedItem.getOrdinal() : 0;
+ }
+
+ private JPanel createMainPanel(ComboBoxModel comboBoxModel)
+ {
+ JPanel panel = new JPanel(new GridBagLayout());
+
+ codeField.setEnabled(false);
+ labelField.requestFocus();
+ labelField.addKeyListener(new KeyListener()
+ {
+ public void keyPressed(KeyEvent arg0)
+ {
+ handleEvent();
+ }
+
+ public void keyReleased(KeyEvent arg0)
+ {
+ handleEvent();
+ }
+
+ public void keyTyped(KeyEvent arg0)
+ {
+ handleEvent();
+ }
+
+ private void handleEvent()
+ {
+ codeField.setText(CodeNormalizer.normalize(labelField.getText()));
+ }
+ });
+ for (int i = 0; i < comboBoxModel.getSize(); i++)
+ {
+ vocabularyTermsField.addItem(comboBoxModel.getElementAt(i));
+ }
+ selectMaxOrdinal(vocabularyTermsField);
+
+ GridBagConstraints c = new GridBagConstraints();
+ c.gridy = 0;
+ c.gridx = 0;
+ c.weightx = 0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(5, 5, 5, 5);
+ panel.add(new JLabel("Code:"), c);
+
+ c.gridy = 0;
+ c.gridx = 1;
+ c.weightx = 1;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(5, 5, 5, 5);
+ panel.add(codeField, c);
+
+ c.gridy = 1;
+ c.gridx = 0;
+ c.weightx = 0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(5, 5, 5, 5);
+ panel.add(new JLabel("Label:"), c);
+
+ c.gridy = 1;
+ c.gridx = 1;
+ c.weightx = 1;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(5, 5, 5, 5);
+ panel.add(labelField, c);
+
+ c.gridy = 2;
+ c.gridx = 0;
+ c.weightx = 0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(5, 5, 5, 5);
+ panel.add(new JLabel("Description:"), c);
+
+ c.gridy = 2;
+ c.gridx = 1;
+ c.weightx = 1;
+ c.weighty = 1;
+ c.fill = GridBagConstraints.BOTH;
+ c.insets = new Insets(5, 5, 5, 5);
+ panel.add(new JScrollPane(descriptionField), c);
+
+ c.gridy = 3;
+ c.gridx = 0;
+ c.weightx = 0;
+ c.weighty = 0;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(5, 5, 5, 5);
+ panel.add(new JLabel("Position after:"), c);
+
+ c.gridy = 3;
+ c.gridx = 1;
+ c.weightx = 1;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.insets = new Insets(5, 5, 5, 5);
+ panel.add(vocabularyTermsField, c);
+
+ return panel;
+ }
+
+ private static void selectMaxOrdinal(JComboBox comboBox)
+ {
+ ComboBoxModel model = comboBox.getModel();
+ long maxOrdinal = Long.MIN_VALUE;
+ int maxItemIndex = -1;
+ for (int i = 0; i < model.getSize(); i++)
+ {
+ Long ordinal = ((VocabularyTermAdaptor) model.getElementAt(i)).getOrdinal();
+ if (maxOrdinal < ordinal)
+ {
+ maxOrdinal = ordinal;
+ maxItemIndex = i;
+ }
+ }
+ if (maxItemIndex > -1)
+ {
+ comboBox.setSelectedIndex(maxItemIndex);
+ }
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
index c2ee87197a9..d367f3a41c0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPropertiesPanel.java
@@ -38,7 +38,6 @@ import java.util.List;
import java.util.Map;
import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JPanel;
@@ -63,27 +62,6 @@ public class DataSetPropertiesPanel extends JPanel
{
private static final long serialVersionUID = 1L;
- /**
- * An adaptor to convert VocabularyTerms into something that can be put into combo boxes.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- private static final class VocabularyTermAdaptor
- {
- private final VocabularyTerm term;
-
- private VocabularyTermAdaptor(VocabularyTerm term)
- {
- this.term = term;
- }
-
- @Override
- public String toString()
- {
- return term.getLabel();
- }
- }
-
private final DataSetType dataSetType;
private final DataSetUploadClientModel clientModel;
@@ -200,22 +178,22 @@ public class DataSetPropertiesPanel extends JPanel
return textField;
}
- private JComboBox createComboBox(final ControlledVocabularyPropertyType propertyType)
+ private VocabularyTermsComboBoxPanel createComboBox(
+ final ControlledVocabularyPropertyType propertyType)
{
- final JComboBox comboBox = new JComboBox();
- for (VocabularyTerm term : propertyType.getTerms())
- {
- comboBox.addItem(new VocabularyTermAdaptor(term));
- }
+ final VocabularyTermsComboBoxPanel comboBox =
+ new VocabularyTermsComboBoxPanel(propertyType, clientModel);
+
+ clientModel.registerObserver(comboBox);
+
comboBox.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
- setPropertyValue(propertyType,
- ((VocabularyTermAdaptor) e.getItem()).term.getCode());
+ setPropertyValue(propertyType, ((VocabularyTerm) e.getItem()).getCode());
}
-
});
+
return comboBox;
}
@@ -302,13 +280,13 @@ public class DataSetPropertiesPanel extends JPanel
{
JTextField textField = (JTextField) formField;
textField.setText(propertyValue);
- } else if (formField instanceof JComboBox)
+ } else if (formField instanceof VocabularyTermsComboBoxPanel)
{
- JComboBox comboBox = (JComboBox) formField;
+ VocabularyTermsComboBoxPanel comboBox = (VocabularyTermsComboBoxPanel) formField;
for (int i = 0; i < comboBox.getItemCount(); ++i)
{
- VocabularyTermAdaptor adaptor = (VocabularyTermAdaptor) comboBox.getItemAt(i);
- if (adaptor.term.getCode().equals(propertyValue))
+ VocabularyTerm term = comboBox.getItemAt(i);
+ if (term.getCode().equals(propertyValue))
{
comboBox.setSelectedIndex(i);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClientModel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClientModel.java
index 1861daaa54a..d1715e125aa 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClientModel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClientModel.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.dss.client.api.gui;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
@@ -38,11 +39,15 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.VocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.util.SimplePropertyValidator;
/**
@@ -50,6 +55,11 @@ import ch.systemsx.cisd.openbis.generic.shared.util.SimplePropertyValidator;
*/
public class DataSetUploadClientModel
{
+ public static interface Observer
+ {
+ public void update(Vocabulary vocabulary, String code);
+ }
+
private static ExecutorService executor = new NamingThreadPoolExecutor("Data Set Upload", 1, 1,
0, TimeUnit.SECONDS, new LinkedBlockingQueue<Runnable>()).daemonize();
@@ -57,9 +67,11 @@ public class DataSetUploadClientModel
private final IGeneralInformationService generalInformationService;
+ private final IGeneralInformationChangingService generalInformationChangingService;
+
private final ITimeProvider timeProvider;
- private final List<DataSetType> dataSetTypes;
+ private List<DataSetType> dataSetTypes;
private final ArrayList<NewDataSetInfo> newDataSetInfos = new ArrayList<NewDataSetInfo>();
@@ -75,12 +87,19 @@ public class DataSetUploadClientModel
// observer.
private DataSetUploadTableModel tableModel;
+ private final List<Observer> observers = new LinkedList<DataSetUploadClientModel.Observer>();
+
+ private HashMap<Vocabulary, List<VocabularyTerm>> vocabularyTerms;
+
public DataSetUploadClientModel(DssCommunicationState commState, ITimeProvider timeProvider)
{
this.dssComponent = commState.getDssComponent();
this.generalInformationService = commState.getGeneralInformationService();
+ this.generalInformationChangingService = commState.getGeneralInformationChangingService();
this.timeProvider = timeProvider;
dataSetTypes = generalInformationService.listDataSetTypes(dssComponent.getSessionToken());
+ vocabularyTerms =
+ generalInformationService.getVocabularyTermsMap(dssComponent.getSessionToken());
}
/**
@@ -499,6 +518,36 @@ public class DataSetUploadClientModel
errors.add(ValidationError.createPropertyValidationError(propertyType.getCode(),
e.getMessage()));
}
+ }
+ public void addUnofficialVocabularyTerm(Vocabulary vocabulary, String code, String label,
+ String description, Long previousTermOrdinal)
+ {
+ generalInformationChangingService.addUnofficialVocabularyTerm(
+ dssComponent.getSessionToken(), TechId.create(vocabulary), code, label,
+ description, previousTermOrdinal);
+ dataSetTypes = generalInformationService.listDataSetTypes(dssComponent.getSessionToken());
+ vocabularyTerms =
+ generalInformationService.getVocabularyTermsMap(dssComponent.getSessionToken());
+
+ notifyObservers(vocabulary, code);
+ }
+
+ public void registerObserver(Observer observer)
+ {
+ observers.add(observer);
+ }
+
+ public void notifyObservers(Vocabulary vocabulary, String code)
+ {
+ for (Observer observer : observers)
+ {
+ observer.update(vocabulary, code);
+ }
+ }
+
+ public List<VocabularyTerm> getVocabularyTerms(Vocabulary vocabulary)
+ {
+ return vocabularyTerms.get(vocabulary);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/VocabularyTermsComboBoxPanel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/VocabularyTermsComboBoxPanel.java
new file mode 100644
index 00000000000..a00e78d2ddc
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/VocabularyTermsComboBoxPanel.java
@@ -0,0 +1,205 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.client.api.gui;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Font;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.plaf.basic.BasicComboBoxRenderer;
+
+import ch.systemsx.cisd.openbis.dss.client.api.gui.DataSetUploadClientModel.Observer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+
+/**
+ * The class creates a ComboBox together with button which makes it possible to add new Vocabulary
+ * Term.
+ *
+ * @author Pawel Glyzewski
+ */
+public class VocabularyTermsComboBoxPanel extends JPanel implements Observer
+{
+
+ /**
+ * An adaptor to convert VocabularyTerms into something that can be put into combo boxes.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ protected static final class VocabularyTermAdaptor
+ {
+ private final VocabularyTerm term;
+
+ private VocabularyTermAdaptor(VocabularyTerm term)
+ {
+ this.term = term;
+ }
+
+ @Override
+ public String toString()
+ {
+ return term.getLabel();
+ }
+
+ public Long getOrdinal()
+ {
+ return term.getOrdinal();
+ }
+ }
+
+ /**
+ * A renderer which renders 'unofficial' vocabulary terms as grey and italic
+ *
+ * @author Pawel Glyzewski
+ */
+ private static final class VocabularyTermsRenderer extends BasicComboBoxRenderer
+ {
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ public Component getListCellRendererComponent(JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus)
+ {
+ Component result =
+ super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+
+ if (value != null && value instanceof VocabularyTermAdaptor)
+ {
+ VocabularyTermAdaptor termAdaptor = (VocabularyTermAdaptor) value;
+ if (termAdaptor.term != null && termAdaptor.term.isOfficial() == false)
+ {
+ result.setForeground(Color.GRAY);
+ Font font =
+ new Font(result.getFont().getName(), Font.ITALIC, result.getFont()
+ .getSize());
+ result.setFont(font);
+ }
+ }
+
+ return result;
+ }
+ }
+
+ private static final long serialVersionUID = 1L;
+
+ private final JComboBox comboBox;
+
+ private final JButton button;
+
+ private final Vocabulary vocabulary;
+
+ private final DataSetUploadClientModel clientModel;
+
+ public VocabularyTermsComboBoxPanel(final ControlledVocabularyPropertyType propertyType,
+ final DataSetUploadClientModel clientModel)
+ {
+ super(new BorderLayout());
+
+ this.clientModel = clientModel;
+ this.button = new JButton("+");
+ button.setMargin(new Insets(button.getMargin().top, 2, button.getMargin().bottom, 2));
+ this.add(button, BorderLayout.EAST);
+
+ this.comboBox = new JComboBox();
+ this.add(comboBox, BorderLayout.CENTER);
+ this.vocabulary = propertyType.getVocabulary();
+ fillComboBoxWithTerms(propertyType.getTerms(), null);
+ comboBox.setRenderer(new VocabularyTermsRenderer());
+
+ button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AddVocabularyTermDialog dialog =
+ new AddVocabularyTermDialog((JFrame) SwingUtilities
+ .getRoot(VocabularyTermsComboBoxPanel.this), comboBox
+ .getModel(), vocabulary, clientModel);
+
+ dialog.setVisible(true);
+ }
+ });
+ }
+
+ private void fillComboBoxWithTerms(List<VocabularyTerm> terms, String selectedCodeOrNull)
+ {
+ comboBox.removeAllItems();
+ for (VocabularyTerm term : terms)
+ {
+ VocabularyTermAdaptor adaptor = new VocabularyTermAdaptor(term);
+ comboBox.addItem(adaptor);
+ if (adaptor.term.getCode().equals(selectedCodeOrNull))
+ {
+ comboBox.setSelectedItem(adaptor);
+ }
+ }
+ }
+
+ public int getItemCount()
+ {
+ return comboBox.getItemCount();
+ }
+
+ public VocabularyTerm getItemAt(int i)
+ {
+ return ((VocabularyTermAdaptor) comboBox.getItemAt(i)).term;
+ }
+
+ public void setSelectedIndex(int i)
+ {
+ comboBox.setSelectedIndex(i);
+ }
+
+ public void addItemListener(final ItemListener itemListener)
+ {
+ comboBox.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ itemListener.itemStateChanged(new ItemEvent(e.getItemSelectable(), e.getID(),
+ ((VocabularyTermAdaptor) e.getItem()).term, e.getStateChange()));
+ }
+ });
+ }
+
+ @Override
+ public void setToolTipText(String text)
+ {
+ comboBox.setToolTipText(text);
+ }
+
+ public void update(@SuppressWarnings("hiding") Vocabulary vocabulary, String code)
+ {
+ String selectedCode =
+ vocabulary.getId() != this.vocabulary.getId() ? ((VocabularyTermAdaptor) comboBox
+ .getSelectedItem()).term.getCode() : code;
+ fillComboBoxWithTerms(clientModel.getVocabularyTerms(vocabulary), selectedCode);
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
index 81993b87cfd..1a14af3891c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
@@ -32,8 +32,9 @@ import ch.systemsx.cisd.common.utilities.PropertyParametersUtil.SectionPropertie
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphConfiguration.GraphType;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ITabularData;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper.ICsvFileReaderConfiguration;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ITabularData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
/**
@@ -180,12 +181,8 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
case HEATMAP:
// Default the Row and Column header names to the standard ones if no override is
// specified.
- CodeAndLabel xAxis =
- getCodeAndLabelWithDefault(props, X_AXIS_KEY,
- "Row");
- CodeAndLabel yAxis =
- getCodeAndLabelWithDefault(props, Y_AXIS_KEY,
- "Column");
+ CodeAndLabel xAxis = getCodeAndLabelWithDefault(props, X_AXIS_KEY, "Row");
+ CodeAndLabel yAxis = getCodeAndLabelWithDefault(props, Y_AXIS_KEY, "Column");
CodeAndLabel zAxis = getCodeAndLabel(props, COLUMN_KEY);
if (xAxis.equals(yAxis))
{
@@ -231,7 +228,7 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
{
return CodeAndLabelUtil.create(label);
}
- return CodeAndLabelUtil.create(code, label);
+ return CodeNormalizer.create(code, label);
}
private CodeAndLabel getCodeAndLabelWithDefault(Properties properties, String key,
@@ -249,13 +246,13 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
if (label == null && code == null)
{
label = defaultLabel;
- code = CodeAndLabelUtil.normalize(label);
+ code = CodeNormalizer.normalize(label);
}
if (code == null)
{
return CodeAndLabelUtil.create(label);
}
- return CodeAndLabelUtil.create(code, label);
+ return CodeNormalizer.create(code, label);
}
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CodeAndLabelUtil.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CodeAndLabelUtil.java
index 623d708be2e..b9b33512eb1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CodeAndLabelUtil.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CodeAndLabelUtil.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.generic.shared.utils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
/**
@@ -25,11 +26,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
*/
public class CodeAndLabelUtil
{
- public static CodeAndLabel create(String code, String label)
- {
- return new CodeAndLabel(normalize(code), label);
- }
-
/**
* Creates an instance from specified label with optional code prefix in form of
* <code><code></code>. The code will be normalized.
@@ -47,26 +43,10 @@ public class CodeAndLabelUtil
t = labelWithOptionalCode.substring(indexOfClosing + 1).trim();
}
}
- String code = normalize(c);
+ String code = CodeNormalizer.normalize(c);
String rest = t.trim();
String label = rest.length() == 0 ? code : rest;
return new CodeAndLabel(code, label);
}
- /**
- * Normalizes the specified code. That is lower-case characters are turned to upper case and any
- * symbol which isn't from A-Z, 0-9 or '-' is replaced by an underscore character.
- */
- public static String normalize(String code)
- {
- StringBuilder builder = new StringBuilder(code.toUpperCase().trim());
- for (int i = 0, n = builder.length(); i < n; i++)
- {
- if ("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789-".indexOf(builder.charAt(i)) < 0)
- {
- builder.setCharAt(i, '_');
- }
- }
- return builder.toString();
- }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetFileLines.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetFileLines.java
index 2cc92c0d8b7..5f57f581282 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetFileLines.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/DatasetFileLines.java
@@ -23,6 +23,7 @@ import java.util.List;
import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
@@ -64,7 +65,7 @@ public class DatasetFileLines implements ITabularData
headerCodes = new String[headerTokens.length];
for (int i = 0; i < headerCodes.length; i++)
{
- headerCodes[i] = CodeAndLabelUtil.normalize(headerTokens[i]);
+ headerCodes[i] = CodeNormalizer.normalize(headerTokens[i]);
}
dataLines = new ArrayList<String[]>(lines.size());
for (int i = 1; i < lines.size(); i++)
@@ -113,7 +114,7 @@ public class DatasetFileLines implements ITabularData
/**
* Returns the normalized headers. Normalization is done by
- * {@link CodeAndLabelUtil#normalize(String)}.
+ * {@link CodeNormalizer#normalize(String)}.
*/
public String[] getHeaderCodes()
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CodeAndLabelTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CodeAndLabelTest.java
index 8a0f5448581..4f221f62879 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CodeAndLabelTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/CodeAndLabelTest.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.dss.generic.shared.utils;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
/**
@@ -35,9 +36,9 @@ public class CodeAndLabelTest extends AssertJUnit
private void assertNormalized(String expectedNormalizedCode, String code)
{
- assertEquals(expectedNormalizedCode, CodeAndLabelUtil.normalize(code));
+ assertEquals(expectedNormalizedCode, CodeNormalizer.normalize(code));
assertEquals(expectedNormalizedCode,
- CodeAndLabelUtil.normalize(CodeAndLabelUtil.normalize(code)));
+ CodeNormalizer.normalize(CodeNormalizer.normalize(code)));
}
@Test
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
index 7b16b8e39aa..3427cc79dff 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientService.java
@@ -548,8 +548,8 @@ public interface ICommonClientService extends IClientService
* Adds specified unofficial terms to the specified vocabulary after specified ordinal (first
* shift all terms with bigger ordinal).
*/
- public void addUnofficialVocabularyTerms(TechId vocabularyId, List<String> vocabularyTerms,
- Long previousTermOrdinal) throws UserFailureException;
+ public void addUnofficialVocabularyTerm(TechId vocabularyId, String code, String label,
+ String description, Long previousTermOrdinal) throws UserFailureException;
/**
* Updates vocabulary term.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
index e538b8617aa..8a8356bc19d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/ICommonClientServiceAsync.java
@@ -458,9 +458,9 @@ public interface ICommonClientServiceAsync extends IClientServiceAsync
public void addVocabularyTerms(TechId vocabularyId, List<String> vocabularyTerms,
Long previousTermOrdinal, AsyncCallback<Void> callback);
- /** @see ICommonClientService#addUnofficialVocabularyTerms(TechId, List, Long) */
- public void addUnofficialVocabularyTerms(TechId vocabularyId, List<String> vocabularyTerms,
- Long previousTermOrdinal, AsyncCallback<Void> callback);
+ /** @see ICommonClientService#addUnofficialVocabularyTerm(TechId, String, String, String, Long) */
+ public void addUnofficialVocabularyTerm(TechId vocabularyId, String code, String label,
+ String description, Long previousTermOrdinal, AsyncCallback<Void> callback);
/** @see ICommonClientService#updateVocabularyTerm(IVocabularyTermUpdates) */
public void updateVocabularyTerm(final IVocabularyTermUpdates updates,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
index 7a5fe71dc8c..0c1036c5f28 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/Dict.java
@@ -1105,9 +1105,6 @@ public abstract class Dict
public static final String ADD_UNOFFICIAL_VOCABULARY_TERM_DIALOG_TITLE =
"add_unofficial_vocabulary_term_dialog_title";
- public static final String ADD_UNOFFICIAL_VOCABULARY_TERM_DIALOG_MESSAGE =
- "add_unofficial_vocabulary_term_dialog_message";
-
// Material Viewer
public static final String MATERIAL_PROPERTIES_HEADING = "material_properties_heading";
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/field/VocabularyTermSelectionWidget.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/field/VocabularyTermSelectionWidget.java
index f948b9450f1..35905212c5e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/field/VocabularyTermSelectionWidget.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/field/VocabularyTermSelectionWidget.java
@@ -17,21 +17,21 @@
package ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import com.extjs.gxt.ui.client.event.BaseEvent;
+import com.extjs.gxt.ui.client.event.ComponentEvent;
+import com.extjs.gxt.ui.client.event.EventType;
import com.extjs.gxt.ui.client.event.Events;
+import com.extjs.gxt.ui.client.event.KeyListener;
import com.extjs.gxt.ui.client.event.Listener;
-import com.extjs.gxt.ui.client.widget.Dialog;
-import com.extjs.gxt.ui.client.widget.Label;
-import com.extjs.gxt.ui.client.widget.button.Button;
+import com.extjs.gxt.ui.client.widget.form.TextField;
import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.ModelDataPropertyNames;
@@ -42,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.GWTUtils;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedAction;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
@@ -55,52 +56,148 @@ public class VocabularyTermSelectionWidget extends
DropDownList<VocabularyTermModel, VocabularyTerm>
{
- private class UnofficialTermRegistrationDialog extends AbstractRegistrationDialog
+ private class AddVocabularyTermDialog extends AbstractRegistrationDialog
{
+ private static final int LABEL_WIDTH = 100;
+
+ private static final int FIELD_WIDTH = 300;
+
private final IViewContext<?> viewContext;
- private final String code;
+ private final CodeField codeField;
+
+ private final DescriptionField descriptionField;
+
+ private final TextField<String> labelField;
- private final Vocabulary vocabulary;
+ private final VocabularyTermSelectionWidget termSelectionWidget;
- public UnofficialTermRegistrationDialog(IViewContext<?> viewContext, String code)
+ private RefreshAction refreshAction;
+
+ public AddVocabularyTermDialog(IViewContext<?> viewContext, RefreshAction refreshAction)
{
super(viewContext, viewContext
- .getMessage(Dict.ADD_UNOFFICIAL_VOCABULARY_TERM_DIALOG_TITLE),
- createRefreshAction(code));
+ .getMessage(Dict.ADD_UNOFFICIAL_VOCABULARY_TERM_DIALOG_TITLE), refreshAction);
this.viewContext = viewContext;
- this.code = code;
- this.vocabulary = vocabularyOrNull;
+ this.refreshAction = refreshAction;
+
+ form.setLabelWidth(LABEL_WIDTH);
+ form.setFieldWidth(FIELD_WIDTH);
+ this.setWidth(LABEL_WIDTH + FIELD_WIDTH + 50);
+
+ codeField = new CodeField(viewContext, Dict.CODE, CodeFieldKind.CODE_WITH_COLON);
+ codeField.setMaxLength(GenericConstants.COLUMN_LABEL);
+ codeField.setReadOnly(true);
+ addField(codeField);
+
+ boolean mandatory = false;
+ labelField = createTextField(viewContext.getMessage(Dict.LABEL), mandatory);
+ FieldUtil.setValueWithUnescaping(labelField, refreshAction.code);
+ FieldUtil.setValueWithUnescaping(codeField, labelField.getValue() == null ? ""
+ : CodeNormalizer.normalize(labelField.getValue()));
+ labelField.setMaxLength(GenericConstants.COLUMN_LABEL);
+ labelField.addKeyListener(new KeyListener()
+ {
+ @Override
+ public void handleEvent(ComponentEvent e)
+ {
+ EventType type = e.getType();
+ if (type == Events.KeyPress || type == Events.KeyUp
+ || type == Events.KeyDown)
+ {
+ FieldUtil.setValueWithUnescaping(
+ codeField,
+ labelField.getValue() == null ? "" : CodeNormalizer
+ .normalize(labelField.getValue()));
+ }
+ }
+ });
+ addField(labelField);
+
+ descriptionField = createDescriptionField(viewContext, mandatory);
+ FieldUtil.setValueWithUnescaping(descriptionField, "");
+ addField(descriptionField);
- addField(new Label(viewContext.getMessage(
- Dict.ADD_UNOFFICIAL_VOCABULARY_TERM_DIALOG_MESSAGE, code, vocabulary.getCode())));
+ termSelectionWidget = createTermSelectionWidget();
+ addField(termSelectionWidget);
}
@Override
protected void register(AsyncCallback<Void> registrationCallback)
{
- ICommonClientServiceAsync service = viewContext.getCommonService();
-
- service.addUnofficialVocabularyTerms(TechId.create(vocabulary), Arrays.asList(code),
- getMaxOrdinal(), registrationCallback);
- hide();
+ refreshAction.code = codeField.getValue();
+ viewContext.getCommonService().addUnofficialVocabularyTerm(
+ TechId.create(vocabularyOrNull), refreshAction.code,
+ labelField.getValue().trim(), descriptionField.getValue(),
+ extractPreviousTermOrdinal(), registrationCallback);
}
- private long getMaxOrdinal()
+ private VocabularyTermSelectionWidget createTermSelectionWidget()
{
- long result = 0l;
-
- // WORKAROUND for some strange reason getStore().getModels() returns empty list
- for (VocabularyTermModel term : VocabularyTermSelectionWidget.this.store.getModels())
+ List<VocabularyTerm> allTerms = getAllTerms();
+ String previousTermCodeOrNull = null;
+ long maxOrdinal = Long.MIN_VALUE;
+ for (VocabularyTerm term : allTerms)
{
- if (term.getTerm().getOrdinal() > result)
+ if (term.getOrdinal() >= maxOrdinal)
{
- result = term.getTerm().getOrdinal();
+ previousTermCodeOrNull = term.getCode();
+ maxOrdinal = term.getOrdinal();
}
}
+ boolean mandatory = false;
+ VocabularyTermSelectionWidget result =
+ new VocabularyTermSelectionWidget(getId() + "_edit_pos", "Position after",
+ mandatory, allTerms, previousTermCodeOrNull);
+ result.setEmptyText("empty value == beginning");
return result;
}
+
+ /**
+ * extracts ordinal of a term after which edited terms should be put
+ */
+ private Long extractPreviousTermOrdinal()
+ {
+ // - 0 if nothing is selected (move to the beginning),
+ // - (otherwise) selected term's ordinal
+ VocabularyTermModel selectedItem = termSelectionWidget.getValue();
+ return selectedItem != null ? selectedItem.getTerm().getOrdinal() : 0;
+ }
+ }
+
+ private class RefreshAction implements IDelegatedAction
+ {
+ private String code;
+
+ private RefreshAction(String code)
+ {
+ this.code = code;
+ }
+
+ public void execute()
+ {
+ VocabularyTermSelectionWidget.this.typedValueOrNull = code;
+ refreshStore();
+ clearInvalid();
+ focus();
+ }
+ }
+
+ private abstract class AddNewTermListener implements Listener<BaseEvent>
+ {
+ public void handleEvent(BaseEvent be)
+ {
+ if (VocabularyTermSelectionWidget.this.vocabularyOrNull != null && condition())
+ {
+ AddVocabularyTermDialog d =
+ new AddVocabularyTermDialog(viewContextOrNull, new RefreshAction(
+ getRawValue()));
+ d.show();
+ }
+ }
+
+ public abstract boolean condition();
}
private static final String CHOOSE_MSG = "Choose...";
@@ -146,7 +243,8 @@ public class VocabularyTermSelectionWidget extends
{
super(idSuffix, ModelDataPropertyNames.CODE_WITH_LABEL, label,
allowAddingUnofficialTerms(viewContextOrNull) ? CHOOSE_OR_ADD_MSG : CHOOSE_MSG,
- EMPTY_MSG, VALUE_NOT_IN_LIST_MSG, mandatory, viewContextOrNull, termsOrNull == null);
+ EMPTY_MSG, VALUE_NOT_IN_LIST_MSG, mandatory, viewContextOrNull,
+ termsOrNull == null, allowAddingUnofficialTerms(viewContextOrNull));
this.viewContextOrNull = viewContextOrNull;
this.vocabularyOrNull = vocabularyOrNull;
this.initialTermCodeOrNull = initialTermCodeOrNull;
@@ -163,7 +261,24 @@ public class VocabularyTermSelectionWidget extends
if (allowAddingUnofficialTerms(viewContextOrNull))
{
- this.addListener(Events.Blur, createListenerAddingOnofficialTerms());
+ this.addListener(Events.Blur, new AddNewTermListener()
+ {
+ @Override
+ public boolean condition()
+ {
+ return getSelection().size() != 1
+ && (false == StringUtils.isBlank(VocabularyTermSelectionWidget.this
+ .getRawValue()));
+ }
+ });
+ this.addListener(Events.TwinTriggerClick, new AddNewTermListener()
+ {
+ @Override
+ public boolean condition()
+ {
+ return true;
+ }
+ });
}
}
@@ -174,65 +289,22 @@ public class VocabularyTermSelectionWidget extends
.getAllowAddingUnofficialTerms();
}
- private Listener<BaseEvent> createListenerAddingOnofficialTerms()
+ public void setVocabulary(Vocabulary vocabulary)
{
- return new Listener<BaseEvent>()
- {
- public void handleEvent(BaseEvent be)
- {
- if (VocabularyTermSelectionWidget.this.vocabularyOrNull != null
- && getSelection().size() != 1
- && (false == StringUtils.isBlank(VocabularyTermSelectionWidget.this
- .getRawValue())))
- {
- final String code = getRawValue().toUpperCase();
- if (!code.matches(CodeFieldKind.CODE_WITH_COLON.getPattern()))
- {
- Dialog d = new Dialog()
- {
- @Override
- protected void onButtonPressed(Button button)
- {
- super.onButtonPressed(button);
- VocabularyTermSelectionWidget.this.focus();
- }
- };
- d.setHeading(viewContextOrNull.getMessage(Dict.MESSAGEBOX_ERROR));
- d.addText(viewContextOrNull.getMessage(Dict.INVALID_CODE_MESSAGE,
- CodeFieldKind.CODE_WITH_COLON.getAllowedCharacters()));
- d.setSize(400, 200);
- d.setHideOnButtonClick(true);
- d.setButtons(Dialog.OK);
- d.show();
- } else
- {
- UnofficialTermRegistrationDialog d =
- new UnofficialTermRegistrationDialog(viewContextOrNull, code);
- d.show();
- }
- }
- }
- };
+ vocabularyOrNull = vocabulary;
+ refreshStore();
}
- private IDelegatedAction createRefreshAction(final String _typedValue)
+ private List<VocabularyTerm> getAllTerms()
{
- return new IDelegatedAction()
- {
- public void execute()
- {
- VocabularyTermSelectionWidget.this.typedValueOrNull = _typedValue;
- refreshStore();
- clearInvalid();
- focus();
- }
- };
- }
+ List<VocabularyTerm> terms = new ArrayList<VocabularyTerm>();
- public void setVocabulary(Vocabulary vocabulary)
- {
- vocabularyOrNull = vocabulary;
- refreshStore();
+ for (VocabularyTermModel model : store.getModels())
+ {
+ terms.add(model.getTerm());
+ }
+
+ return terms;
}
private void setTerms(List<VocabularyTerm> terms)
@@ -305,5 +377,4 @@ public class VocabularyTermSelectionWidget extends
selectInitialValue();
}
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/DropDownList.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/DropDownList.java
index 7a8c7c90234..d612e85bbde 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/DropDownList.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/widget/DropDownList.java
@@ -21,14 +21,21 @@ import java.util.Collection;
import java.util.List;
import java.util.Set;
+import com.extjs.gxt.ui.client.GXT;
+import com.extjs.gxt.ui.client.core.El;
import com.extjs.gxt.ui.client.data.ModelData;
+import com.extjs.gxt.ui.client.event.ComponentEvent;
+import com.extjs.gxt.ui.client.event.Events;
import com.extjs.gxt.ui.client.store.ListStore;
import com.extjs.gxt.ui.client.store.Store;
import com.extjs.gxt.ui.client.store.StoreFilter;
+import com.extjs.gxt.ui.client.util.Size;
import com.extjs.gxt.ui.client.widget.Component;
import com.extjs.gxt.ui.client.widget.MessageBox;
import com.extjs.gxt.ui.client.widget.form.ComboBox;
+import com.google.gwt.user.client.DOM;
import com.google.gwt.user.client.Element;
+import com.google.gwt.user.client.Event;
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
@@ -81,6 +88,17 @@ abstract public class DropDownList<M extends ModelData, E> extends ComboBox<M> i
private final List<IDataRefreshCallback> dataRefreshCallbacks;
+ /*
+ * Twin trigger related
+ */
+ private final boolean twinTriggerEnabled;
+
+ protected El twinTrigger;
+
+ private String twinTriggerStyle = "x-form-trigger-add";
+
+ protected El span;
+
public DropDownList(final IViewContext<?> viewContext, String idSuffix, String labelDictCode,
String displayField, String chooseSuffix, String nothingFoundSuffix)
{
@@ -90,11 +108,21 @@ abstract public class DropDownList<M extends ModelData, E> extends ComboBox<M> i
.getMessage(Dict.COMBO_BOX_EXPECTED_VALUE_FROM_THE_LIST), true, viewContext, true);
}
- /** if viewContextOrNull is null the combobox is not able to refresh itself */
public DropDownList(String idSuffix, String displayField, String label, String chooseMsg,
String emptyMsg, String valueNotInListMsg, boolean mandatory,
final IViewContext<?> viewContextOrNull, boolean reloadWhenRendering)
{
+ this(idSuffix, displayField, label, chooseMsg, emptyMsg, valueNotInListMsg, mandatory,
+ viewContextOrNull, reloadWhenRendering, false);
+ }
+
+ /** if viewContextOrNull is null the combobox is not able to refresh itself */
+ protected DropDownList(String idSuffix, String displayField, String label, String chooseMsg,
+ String emptyMsg, String valueNotInListMsg, boolean mandatory,
+ final IViewContext<?> viewContextOrNull, boolean reloadWhenRendering,
+ boolean twinTriggerEnabled)
+ {
+ this.twinTriggerEnabled = twinTriggerEnabled;
this.chooseMsg = chooseMsg;
this.emptyMsg = emptyMsg;
this.valueNotInListMsg = valueNotInListMsg;
@@ -483,15 +511,73 @@ abstract public class DropDownList<M extends ModelData, E> extends ComboBox<M> i
}
@Override
- protected void onRender(final Element parent, final int pos)
+ protected void onRender(final Element target, final int index)
{
- super.onRender(parent, pos);
+ if (this.twinTriggerEnabled)
+ {
+ input = new El(DOM.createInputText());
+ setElement(DOM.createDiv(), target, index);
+ addStyleName("x-form-field-wrap");
+
+ trigger = new El(DOM.createImg());
+ trigger.dom.setClassName("x-form-trigger " + triggerStyle);
+ trigger.dom.setPropertyString("src", GXT.BLANK_IMAGE_URL);
+
+ twinTrigger = new El(DOM.createImg());
+ twinTrigger.dom.setClassName("x-form-trigger " + twinTriggerStyle);
+ twinTrigger.dom.setPropertyString("src", GXT.BLANK_IMAGE_URL);
+
+ span = new El(DOM.createSpan());
+ span.dom.setClassName("x-form-twin-triggers");
+
+ span.appendChild(trigger.dom);
+ span.appendChild(twinTrigger.dom);
+
+ el().appendChild(input.dom);
+ el().appendChild(span.dom);
+
+ if (isHideTrigger())
+ {
+ span.setVisible(false);
+ }
+
+ addStyleOnOver(twinTrigger.dom, "x-form-trigger-over");
+ }
+
+ super.onRender(target, index);
if (reloadWhenRendering)
{
refreshStore();
}
}
+ @Override
+ public void onComponentEvent(ComponentEvent ce)
+ {
+ super.onComponentEvent(ce);
+ if (twinTriggerEnabled)
+ {
+ int type = ce.getEventTypeInt();
+ if (ce.getTarget() == twinTrigger.dom && type == Event.ONCLICK)
+ {
+ onTwinTriggerClick(ce);
+ }
+ }
+ }
+
+ @Override
+ protected Size adjustInputSize()
+ {
+ return twinTriggerEnabled ? new Size(isHideTrigger() ? 0
+ : (trigger.getStyleSize().width + twinTrigger.getStyleSize().width), 0) : super
+ .adjustInputSize();
+ }
+
+ protected void onTwinTriggerClick(ComponentEvent ce)
+ {
+ fireEvent(Events.TwinTriggerClick, ce);
+ }
+
public void addPostRefreshCallback(IDataRefreshCallback callback)
{
dataRefreshCallbacks.add(callback);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
index b393d726f24..5b9be0a09e7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
@@ -1278,23 +1278,20 @@ public final class CommonClientService extends AbstractClientService implements
}
}
- public void addUnofficialVocabularyTerms(TechId vocabularyId, List<String> vocabularyTerms,
- Long previousTermOrdinal)
+ public void addUnofficialVocabularyTerm(TechId vocabularyId, String code, String label,
+ String description, Long previousTermOrdinal)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
assert vocabularyId != null : "Unspecified vocabulary id.";
- if (vocabularyTerms != null && vocabularyTerms.isEmpty() == false)
+ try
{
- try
- {
- final String sessionToken = getSessionToken();
- commonServer.addUnofficialVocabularyTerms(sessionToken, vocabularyId,
- vocabularyTerms, previousTermOrdinal);
- } catch (final UserFailureException e)
- {
- throw UserFailureExceptionTranslator.translate(e);
- }
+ final String sessionToken = getSessionToken();
+ commonServer.addUnofficialVocabularyTerm(sessionToken, vocabularyId, code, label,
+ description, previousTermOrdinal);
+ } catch (final UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index ad33e135d94..8cb8c799976 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -815,17 +815,18 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
vocabularyBO.save();
}
- public void addUnofficialVocabularyTerms(String sessionToken, TechId vocabularyId,
- List<String> vocabularyTerms, Long previousTermOrdinal)
+ public void addUnofficialVocabularyTerm(String sessionToken, TechId vocabularyId, String code,
+ String label, String description, Long previousTermOrdinal)
{
assert sessionToken != null : "Unspecified session token";
assert vocabularyId != null : "Unspecified vocabulary id";
+ assert code != null : "Unspecified code";
assert previousTermOrdinal != null : "Unspecified previous term ordinal";
final Session session = getSession(sessionToken);
final IVocabularyBO vocabularyBO = businessObjectFactory.createVocabularyBO(session);
vocabularyBO.loadDataByTechId(vocabularyId);
- vocabularyBO.addNewUnofficialTerms(vocabularyTerms, previousTermOrdinal);
+ vocabularyBO.addNewUnofficialTerm(code, label, description, previousTermOrdinal);
vocabularyBO.save();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
index 1c9612fea47..371dead6f42 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServerLogger.java
@@ -78,11 +78,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleAssignment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Script;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ScriptType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
@@ -425,12 +425,12 @@ final class CommonServerLogger extends AbstractServerLogger implements ICommonSe
vocabularyId, abbreviate(vocabularyTerms), Long.toString(previousTermOrdinal));
}
- public void addUnofficialVocabularyTerms(String sessionToken, TechId vocabularyId,
- List<String> vocabularyTerms, Long previousTermOrdinal)
+ public void addUnofficialVocabularyTerm(String sessionToken, TechId vocabularyId, String code,
+ String label, String description, Long previousTermOrdinal)
{
logTracking(sessionToken, "add_unofficial_vocabulary_terms",
- "ID(%s) TERMS(%s) PREVIOUS_ORDINAL(%s)", vocabularyId, abbreviate(vocabularyTerms),
- Long.toString(previousTermOrdinal));
+ "ID(%s) CODE(%s), LABEL(%s), DESCRIPTION(%s), PREVIOUS_ORDINAL(%s)", vocabularyId,
+ code, label, description, Long.toString(previousTermOrdinal));
}
public void updateVocabularyTerm(String sessionToken, IVocabularyTermUpdates updates)
@@ -1071,7 +1071,7 @@ final class CommonServerLogger extends AbstractServerLogger implements ICommonSe
String propertyTypeCode, String value)
{
logTracking(sessionToken, "updateProperty",
- "ENTITY_KIND(%s) ID(%s) PROPERTY_COLUMN_NAME(%s) VALUE(%s)", kind, entityId, propertyTypeCode,
- value);
+ "ENTITY_KIND(%s) ID(%s) PROPERTY_COLUMN_NAME(%s) VALUE(%s)", kind, entityId,
+ propertyTypeCode, value);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
index 63e3b315b9c..6eb1099d2d9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
@@ -34,7 +34,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
- *
* @author Franz-Josef Elmer
*/
@Component(ResourceNames.GENERAL_INFORMATION_CHANGING_SERVICE_SERVER)
@@ -50,8 +49,9 @@ public class GeneralInformationChangingService extends
{
}
- GeneralInformationChangingService(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
- IPropertiesBatchManager propertiesBatchManager, ICommonServer server)
+ GeneralInformationChangingService(ISessionManager<Session> sessionManager,
+ IDAOFactory daoFactory, IPropertiesBatchManager propertiesBatchManager,
+ ICommonServer server)
{
super(sessionManager, daoFactory, propertiesBatchManager);
this.server = server;
@@ -61,23 +61,29 @@ public class GeneralInformationChangingService extends
{
return new GeneralInformationChangingServiceLogger(sessionManager, context);
}
-
+
public void updateSampleProperties(String sessionToken, long sampleID,
Map<String, String> properties)
{
checkSession(sessionToken);
-
+
EntityHelper.updateSampleProperties(server, sessionToken, new TechId(sampleID), properties);
}
+ public void addUnofficialVocabularyTerm(String sessionToken, TechId vocabularyId, String code,
+ String label, String description, Long previousTermOrdinal)
+ {
+ server.addUnofficialVocabularyTerm(sessionToken, vocabularyId, code, label, description,
+ previousTermOrdinal);
+ }
+
public int getMajorVersion()
{
return 1;
}
-
+
public int getMinorVersion()
{
return 0;
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
index 0beb69b34ff..6ca08af61d8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
@@ -22,11 +22,10 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
/**
- *
- *
* @author Franz-Josef Elmer
*/
class GeneralInformationChangingServiceLogger extends AbstractServerLogger implements
@@ -44,7 +43,15 @@ class GeneralInformationChangingServiceLogger extends AbstractServerLogger imple
{
logTracking(sessionToken, "update-sample-properties", "SAMPLE(%s)", sampleID);
}
-
+
+ public void addUnofficialVocabularyTerm(String sessionToken, TechId vocabularyId, String code,
+ String label, String description, Long previousTermOrdinal)
+ {
+ logTracking(sessionToken, "add_unofficial_vocabulary_terms",
+ "ID(%s) CODE(%s), LABEL(%s), DESCRIPTION(%s), PREVIOUS_ORDINAL(%s)", vocabularyId,
+ code, label, description, Long.toString(previousTermOrdinal));
+ }
+
public int getMajorVersion()
{
return 0;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
index 4f18ac22ec5..f8661cffc80 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
@@ -374,7 +374,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
return dataSetTypes;
}
- private HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary, List<ControlledVocabularyPropertyType.VocabularyTerm>> getVocabularyTermsMap(
+ public HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary, List<ControlledVocabularyPropertyType.VocabularyTerm>> getVocabularyTermsMap(
String sessionToken)
{
HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary, List<ControlledVocabularyPropertyType.VocabularyTerm>> vocabTerms =
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
index 5a142d637fa..6cdf8fe2988 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.api.v1;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -24,6 +25,7 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.VocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
@@ -32,6 +34,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
/**
@@ -124,4 +127,10 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
return null;
}
+ public HashMap<Vocabulary, List<VocabularyTerm>> getVocabularyTermsMap(String sessionToken)
+ {
+ logAccess(sessionToken, "get-vocabulary-terms-map");
+ return null;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
index e634f79a7d2..7bfd43015f4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
@@ -41,9 +41,9 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializ
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleLevel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
/**
* @author Franz-Josef Elmer
@@ -144,6 +144,7 @@ public class Translator
ControlledVocabularyPropertyTypeInitializer cvptInitializer =
new ControlledVocabularyPropertyTypeInitializer();
+ cvptInitializer.setVocabulary(propertyType.getVocabulary());
cvptInitializer.setTerms(vocabTerms.get(propertyType.getVocabulary()));
ptInitializer = cvptInitializer;
} else
@@ -181,19 +182,24 @@ public class Translator
Collections.sort(sortedTerms,
new Comparator<ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm>()
{
-
public int compare(VocabularyTerm o1, VocabularyTerm o2)
{
- return o1.getOrdinal().compareTo(o2.getOrdinal());
+ if (o1.isOfficial() != o2.isOfficial())
+ {
+ return o1.isOfficial() ? -1 : 1;
+ } else
+ {
+ return o1.getOrdinal().compareTo(o2.getOrdinal());
+ }
}
-
});
ArrayList<ControlledVocabularyPropertyType.VocabularyTerm> terms =
new ArrayList<ControlledVocabularyPropertyType.VocabularyTerm>();
for (ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm privateTerm : sortedTerms)
{
terms.add(new ControlledVocabularyPropertyType.VocabularyTerm(privateTerm.getCode(),
- privateTerm.getCodeOrLabel()));
+ privateTerm.getCodeOrLabel(), privateTerm.getOrdinal(), privateTerm
+ .isOfficial()));
}
return terms;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IVocabularyBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IVocabularyBO.java
index d17fd79d283..84c990a983c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IVocabularyBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IVocabularyBO.java
@@ -76,11 +76,15 @@ public interface IVocabularyBO extends IEntityBusinessObject
void addNewTerms(List<String> newTerms, Long previousTermOrdinal);
/**
- * Add unofficial terms with specified codes to a loaded vocabulary.
+ * Add unofficial terms with specified label and description to a loaded vocabulary.
*
+ * @param code code of the vocabulary term
+ * @param label label of the vocabulary term
+ * @description description of the term
* @param previousTermOrdinal ordinal of term after which new terms should be added
*/
- void addNewUnofficialTerms(List<String> newTerms, Long previousTermOrdinal);
+ void addNewUnofficialTerm(String code, String label, String description,
+ Long previousTermOrdinal);
/**
* Deletes the specified terms from a loaded vocabulary and replaces terms which are used.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/VocabularyBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/VocabularyBO.java
index 63305ae3546..1523bfde6ff 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/VocabularyBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/VocabularyBO.java
@@ -133,9 +133,20 @@ public class VocabularyBO extends AbstractBusinessObject implements IVocabularyB
addNewTerms(newTermCodes, previousTermOrdinal, true);
}
- public void addNewUnofficialTerms(List<String> newTermCodes, Long previousTermOrdinal)
+ public void addNewUnofficialTerm(String code, String label, String description,
+ Long previousTermOrdinal)
{
- addNewTerms(newTermCodes, previousTermOrdinal, false);
+ assert vocabularyPE != null : UNSPECIFIED_VOCABULARY;
+ assert code != null : "Unspecified vocabulary term code";
+ assert previousTermOrdinal != null : "Unspecified previous term ordinal";
+ if (vocabularyPE.isManagedInternally())
+ {
+ throw new UserFailureException(
+ "Not allowed to add terms to an internally managed vocabulary.");
+ }
+
+ increaseVocabularyTermOrdinals(previousTermOrdinal + 1, 1);
+ addTerm(code, description, label, previousTermOrdinal + 1, false);
}
/** shift terms in vocabulary by specified increment starting from term with specified ordinal */
@@ -473,4 +484,4 @@ public class VocabularyBO extends AbstractBusinessObject implements IVocabularyB
}
return list;
}
-}
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
index 6f6f6143b88..1fc6b6a4169 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
@@ -197,7 +197,7 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
@Select(sql = SELECT_ALL + " where data.dast_id = ?{1}", fetchSize = FETCH_SIZE)
public DataIterator<DatasetRecord> getDatasetsByDataStoreId(long dataStoreId);
-
+
/**
* Returns the children dataset ids of the specified datasets.
*/
@@ -232,7 +232,7 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
*
* @param entityIds The set of sample ids to get the property values for.
*/
- @Select(sql = "SELECT pr.ds_id as entity_id, etpt.prty_id, etpt.script_id, cvte.id, cvte.covo_id, cvte.code, cvte.label, cvte.ordinal"
+ @Select(sql = "SELECT pr.ds_id as entity_id, etpt.prty_id, etpt.script_id, cvte.id, cvte.covo_id, cvte.code, cvte.label, cvte.ordinal, cvte.is_official"
+ " FROM data_set_properties pr"
+ " JOIN data_set_type_property_types etpt ON pr.dstpt_id=etpt.id"
+ " JOIN controlled_vocabulary_terms cvte ON pr.cvte_id=cvte.id"
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
index 18bcbe1e3a3..6ccaeb79af4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
@@ -87,7 +87,7 @@ public interface IMaterialListingQuery extends TransactionQuery, IPropertyListin
*
* @param entityIds The set of material ids to get the property values for.
*/
- @Select(sql = "SELECT pr.mate_id as entity_id, etpt.prty_id, etpt.script_id, cvte.id, cvte.covo_id, cvte.code, cvte.label, cvte.ordinal"
+ @Select(sql = "SELECT pr.mate_id as entity_id, etpt.prty_id, etpt.script_id, cvte.id, cvte.covo_id, cvte.code, cvte.label, cvte.ordinal, cvte.is_official"
+ " FROM material_properties pr"
+ " JOIN material_type_property_types etpt ON pr.mtpt_id=etpt.id"
+ " JOIN controlled_vocabulary_terms cvte ON pr.cvte_id=cvte.id"
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
index 7be98320745..beb186f7182 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
@@ -370,7 +370,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
*
* @param sampleIds The set of sample ids to get the property values for.
*/
- @Select(sql = "SELECT sp.samp_id as entity_id, stpt.prty_id, stpt.script_id, cvte.id, cvte.covo_id, cvte.code, cvte.label, cvte.ordinal"
+ @Select(sql = "SELECT sp.samp_id as entity_id, stpt.prty_id, stpt.script_id, cvte.id, cvte.covo_id, cvte.code, cvte.label, cvte.ordinal, cvte.is_official"
+ " FROM sample_properties sp"
+ " JOIN sample_type_property_types stpt ON sp.stpt_id=stpt.id"
+ " JOIN controlled_vocabulary_terms cvte ON sp.cvte_id=cvte.id"
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/RemoveUnusedUnofficialTermsMaintenanceTask.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/RemoveUnusedUnofficialTermsMaintenanceTask.java
new file mode 100644
index 00000000000..279ae9d5fa4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/task/RemoveUnusedUnofficialTermsMaintenanceTask.java
@@ -0,0 +1,115 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.task;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.openbis.generic.server.CommonServiceProvider;
+import ch.systemsx.cisd.openbis.generic.server.ICommonServerForInternalUse;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTermReplacement;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermWithStats;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTermTranslator;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class RemoveUnusedUnofficialTermsMaintenanceTask implements IMaintenanceTask
+{
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ RemoveUnusedUnofficialTermsMaintenanceTask.class);
+
+ private static final String OLDER_THAN_DAYS_PROPERTY_NAME = "older-than-days";
+
+ private static final Double DEFAULT_OLDER_THAN_DAYS = 7.0;
+
+ private long olderThan;
+
+ private final double day = 86400000.0;
+
+ public void setUp(String pluginName, Properties properties)
+ {
+ double olderThanDouble =
+ PropertyUtils.getDouble(properties, OLDER_THAN_DAYS_PROPERTY_NAME,
+ DEFAULT_OLDER_THAN_DAYS);
+ this.olderThan = Math.round(olderThanDouble * day); // in milliseconds
+ operationLog.info("Unused unofficial terms older than " + olderThanDouble + " days ("
+ + olderThan + " milliseconds) will be removed.");
+ }
+
+ public void execute()
+ {
+ ICommonServerForInternalUse server = CommonServiceProvider.getCommonServer();
+ SessionContextDTO contextOrNull = server.tryToAuthenticateAsSystem();
+ if (contextOrNull != null)
+ {
+ final String sessionToken = contextOrNull.getSessionToken();
+ List<Vocabulary> vocabularies = server.listVocabularies(sessionToken, false, true);
+ for (Vocabulary vocabulary : vocabularies)
+ {
+ List<VocabularyTermWithStats> termsWithStats =
+ server.listVocabularyTermsWithStatistics(sessionToken, vocabulary);
+
+ List<VocabularyTerm> termsToBeDeleted = new ArrayList<VocabularyTerm>();
+ for (VocabularyTermWithStats term : termsWithStats)
+ {
+ if (!term.getTerm().isOfficial()
+ && new Date().getTime()
+ - term.getTerm().getRegistrationDate().getTime() > olderThan)
+ {
+ int usage = 0;
+ for (EntityKind entityKind : EntityKind.values())
+ {
+ usage += term.getUsageCounter(entityKind);
+ }
+
+ if (usage == 0)
+ {
+ VocabularyTerm vocabularyTerm =
+ VocabularyTermTranslator.translate(term.getTerm());
+ operationLog.info("Term '" + vocabularyTerm + "' will be deleted.");
+ termsToBeDeleted.add(vocabularyTerm);
+ }
+ }
+ }
+ if (termsToBeDeleted.size() > 0)
+ {
+ server.deleteVocabularyTerms(sessionToken, TechId.create(vocabulary),
+ termsToBeDeleted, new ArrayList<VocabularyTermReplacement>());
+ }
+ }
+ } else
+ {
+ operationLog.error("authentication failed");
+ }
+ operationLog.info("task executed");
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
index b38a3e43863..f9aadb8a6e6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
@@ -541,8 +541,8 @@ public interface ICommonServer extends IServer
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_POWER_USER)
@DatabaseCreateOrDeleteModification(value = ObjectKind.VOCABULARY_TERM)
- public void addUnofficialVocabularyTerms(String sessionToken, TechId vocabularyId,
- List<String> vocabularyTerms, Long previousTermOrdinal);
+ public void addUnofficialVocabularyTerm(String sessionToken, TechId vocabularyId, String code,
+ String label, String description, Long previousTermOrdinal);
/**
* Updates a vocabulary term.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
index ce933733549..7501de1e86d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
@@ -21,12 +21,15 @@ import java.util.Map;
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.api.IRpcService;
+import ch.systemsx.cisd.openbis.generic.shared.DatabaseCreateOrDeleteModification;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
/**
* Service for changing general informations.
- *
+ *
* @author Franz-Josef Elmer
*/
public interface IGeneralInformationChangingService extends IRpcService
@@ -40,8 +43,18 @@ public interface IGeneralInformationChangingService extends IRpcService
* Application part of the URL to access this service remotely.
*/
public static final String SERVICE_URL = "/rmi-" + SERVICE_NAME + "-v1";
-
+
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
- public void updateSampleProperties(String sessionToken, long sampleID, Map<String, String> properties);
+ public void updateSampleProperties(String sessionToken, long sampleID,
+ Map<String, String> properties);
+
+ /**
+ * Adds new unofficial terms to a vocabulary starting from specified ordinal + 1.
+ */
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.SPACE_POWER_USER)
+ @DatabaseCreateOrDeleteModification(value = ObjectKind.VOCABULARY_TERM)
+ public void addUnofficialVocabularyTerm(String sessionToken, TechId vocabularyId, String code,
+ String label, String description, Long previousTermOrdinal);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
index 4f262eb34c3..8dc591fe4d9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.shared.api.v1;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -23,6 +24,7 @@ import java.util.Set;
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.api.IRpcService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
@@ -172,4 +174,14 @@ public interface IGeneralInformationService extends IRpcService
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<DataSetType> listDataSetTypes(String sessionToken);
+ /**
+ * Returns map of avaialable vocabulary terms. Available since minor version 6.
+ *
+ * @since 1.6
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ public HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary, List<ControlledVocabularyPropertyType.VocabularyTerm>> getVocabularyTermsMap(
+ String sessionToken);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ControlledVocabularyPropertyType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ControlledVocabularyPropertyType.java
index 760a96d839e..fba27be2cc3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ControlledVocabularyPropertyType.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ControlledVocabularyPropertyType.java
@@ -25,6 +25,8 @@ import org.apache.commons.lang.builder.HashCodeBuilder;
import org.apache.commons.lang.builder.ToStringBuilder;
import org.apache.commons.lang.builder.ToStringStyle;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+
/**
* @author Chandrasekhar Ramakrishnan
*/
@@ -40,10 +42,16 @@ public class ControlledVocabularyPropertyType extends PropertyType
private final String label;
- public VocabularyTerm(String code, String label)
+ private final Long ordinal;
+
+ private final Boolean isOfficial;
+
+ public VocabularyTerm(String code, String label, Long ordinal, Boolean isOfficial)
{
this.code = code;
this.label = label;
+ this.ordinal = ordinal;
+ this.isOfficial = isOfficial == null ? Boolean.TRUE : isOfficial;
}
public String getCode()
@@ -56,6 +64,16 @@ public class ControlledVocabularyPropertyType extends PropertyType
return label;
}
+ public Long getOrdinal()
+ {
+ return ordinal;
+ }
+
+ public Boolean isOfficial()
+ {
+ return isOfficial;
+ }
+
@Override
public boolean equals(Object obj)
{
@@ -96,15 +114,24 @@ public class ControlledVocabularyPropertyType extends PropertyType
{
private final ArrayList<VocabularyTerm> terms = new ArrayList<VocabularyTerm>();
+ private Vocabulary vocabulary;
+
public void setTerms(List<VocabularyTerm> validValues)
{
this.terms.clear();
this.terms.addAll(validValues);
}
+
+ public void setVocabulary(Vocabulary vocabulary)
+ {
+ this.vocabulary = vocabulary;
+ }
}
private final ArrayList<VocabularyTerm> terms;
+ private final Vocabulary vocabulary;
+
/**
* @param initializer
*/
@@ -112,6 +139,7 @@ public class ControlledVocabularyPropertyType extends PropertyType
{
super(initializer);
terms = initializer.terms;
+ vocabulary = initializer.vocabulary;
if (terms == null || terms.isEmpty())
{
throw new IllegalArgumentException(
@@ -124,6 +152,11 @@ public class ControlledVocabularyPropertyType extends PropertyType
return terms;
}
+ public Vocabulary getVocabulary()
+ {
+ return vocabulary;
+ }
+
@Override
protected void appendFieldsToStringBuilder(ToStringBuilder builder)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeNormalizer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeNormalizer.java
new file mode 100644
index 00000000000..c8823dda016
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/CodeNormalizer.java
@@ -0,0 +1,47 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.basic;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class CodeNormalizer
+{
+ public static CodeAndLabel create(String code, String label)
+ {
+ return new CodeAndLabel(normalize(code), label);
+ }
+
+ /**
+ * Normalizes the specified code. That is lower-case characters are turned to upper case and any
+ * symbol which isn't from A-Z, 0-9 or '-' is replaced by an underscore character.
+ */
+ public static String normalize(String code)
+ {
+ StringBuilder builder = new StringBuilder(code.toUpperCase().trim());
+ for (int i = 0, n = builder.length(); i < n; i++)
+ {
+ if ("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789-".indexOf(builder.charAt(i)) < 0)
+ {
+ builder.setCharAt(i, '_');
+ }
+ }
+ return builder.toString();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
index 78e8191072d..f1905a85ba7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
@@ -40,7 +40,7 @@ var common = {
table_operations: "Table:",
entity_operations: "Entity:",
url: "URL",
- is_official: "Is Official?",
+ is_official: "Approved?",
reason: "Reason",
delete_confirmation_message_with_reason: "You are deleting {0}(s).<br><br>Please enter a reason or cancel deletion.",
delete_progress_message: "Deleting {0}(s)...",
@@ -57,8 +57,7 @@ var common = {
auto_resolve_label: "Smart View",
data_report_label: "Report:",
explore_label: "Explore:",
- add_unofficial_vocabulary_term_dialog_title: "Add unofficial term",
- add_unofficial_vocabulary_term_dialog_message: "Do you want to add new unofficial term '{0}' to dictionary '{1}'?",
+ add_unofficial_vocabulary_term_dialog_title: "Add Ad Hoc term",
//
// Field
@@ -217,7 +216,7 @@ var common = {
//
// DataSet Browser
//
-
+
container_dataset: "Container",
order_in_container: "Order in Container",
children_datasets: "Children",
@@ -564,10 +563,10 @@ var common = {
delete_vocabulary_terms_confirmation_message_no_replacements: "Do you want to delete the {0} selected terms?",
delete_vocabulary_terms_confirmation_message_for_replacements: "{0} terms will be deleted.\n\nThe terms below are used. They have to be replaced by one of the remaining terms.",
edit_vocabulary_term_button: "Edit Term",
- make_official_vocabulary_term_button: "Make Official",
- make_official_vocabulary_terms_confirmation_title: "Making Vocabulary Terms Official",
- make_official_vocabulary_terms_confirmation_message_singular: "Do you want to make the selected term official?",
- make_official_vocabulary_terms_confirmation_message: "Do you want to make the {0} selected terms official?",
+ make_official_vocabulary_term_button: "Approve",
+ make_official_vocabulary_terms_confirmation_title: "Approving Vocabulary Terms",
+ make_official_vocabulary_terms_confirmation_message_singular: "Do you want to approve selected term?",
+ make_official_vocabulary_terms_confirmation_message: "Do you want to approve {0} selected terms?",
//
// Person Browser
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/css/openbis.css b/openbis/source/java/ch/systemsx/cisd/openbis/public/css/openbis.css
index 4e2041944d0..e68d16d4f40 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/css/openbis.css
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/css/openbis.css
@@ -222,6 +222,11 @@ body,div,td {
cursor: pointer;
}
+.x-form-trigger-add {
+ background-image: url(../images/generate-trigger.gif) !important;
+ cursor: pointer;
+}
+
.cisd-visible {
visibility: visible !important;
}
@@ -231,5 +236,9 @@ body,div,td {
}
.hands {
- cursor:hand;
+ cursor:hand;
+}
+
+.cisd-unofficial {
+ color: grey; font-style:italic;
}
diff --git a/screening/.settings/.gitignore b/screening/.settings/.gitignore
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
index d201e501d46..922d29bf3f8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
@@ -26,7 +26,7 @@ import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
@@ -167,7 +167,7 @@ public class HCSImageFileExtractor extends AbstractImageFileExtractor
+ unparsedInfo.getTileLocationToken());
return null;
}
- String channelCode = CodeAndLabelUtil.normalize(unparsedInfo.getChannelToken());
+ String channelCode = CodeNormalizer.normalize(unparsedInfo.getChannelToken());
String imageRelativePath = getRelativeImagePath(incomingDataSetDirectory, imageFile);
ImageFileInfo info =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
index 9da58c57b85..317202990f5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java
@@ -23,7 +23,7 @@ import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
@@ -70,7 +70,7 @@ public class MicroscopyImageFileExtractor extends AbstractImageFileExtractor
return null;
}
- String channelCode = CodeAndLabelUtil.normalize(unparsedInfo.getChannelToken());
+ String channelCode = CodeNormalizer.normalize(unparsedInfo.getChannelToken());
String imageRelativePath = getRelativeImagePath(incomingDataSetDirectory, imageFile);
ImageFileInfo info =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
index 36b09449ef0..9dfb7aafd84 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
@@ -27,7 +27,7 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.utilities.Counters;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
@@ -82,7 +82,7 @@ public class GenedataFormatToCanonicalFeatureVector
CanonicalFeatureVector featureVector = new CanonicalFeatureVector();
String name = feature.name;
- String code = CodeAndLabelUtil.normalize(name);
+ String code = CodeNormalizer.normalize(name);
int count = counters.count(code);
ImgFeatureDefDTO featureDef = new ImgFeatureDefDTO();
featureDef.setCode(count == 1 ? code : code + count);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index eb67d2e6e68..070c188e593 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -23,9 +23,9 @@ import java.util.List;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ITabularData;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
@@ -102,9 +102,9 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
headerLabels[1] = WELL_ROW_COLUMN;
headerLabels[2] = WELL_COLUMN_COLUMN;
headerCodes = new String[headerTokensLength];
- headerCodes[0] = CodeAndLabelUtil.normalize(WELL_NAME_COLUMN);
- headerCodes[1] = CodeAndLabelUtil.normalize(WELL_ROW_COLUMN);
- headerCodes[2] = CodeAndLabelUtil.normalize(WELL_COLUMN_COLUMN);
+ headerCodes[0] = CodeNormalizer.normalize(WELL_NAME_COLUMN);
+ headerCodes[1] = CodeNormalizer.normalize(WELL_ROW_COLUMN);
+ headerCodes[2] = CodeNormalizer.normalize(WELL_COLUMN_COLUMN);
int i = 3;
for (CodeAndLabel featureCodeAndLabel : featureCodeAndLabels)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
index d8f14d0d9f2..4eaaaaabaa0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
@@ -25,14 +25,14 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractTabl
import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.util.SimpleTableModelBuilder;
@@ -94,11 +94,11 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractTableModelRe
List<CodeAndLabel> codeAndLabels = featuresCollection.getFeatureCodesAndLabels();
List<FeatureTableRow> rows = featuresCollection.getFeatures();
SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
- builder.addHeader(DATA_SET_CODE_TITLE, CodeAndLabelUtil.normalize(DATA_SET_CODE_TITLE));
+ builder.addHeader(DATA_SET_CODE_TITLE, CodeNormalizer.normalize(DATA_SET_CODE_TITLE));
builder.addHeader(PLATE_IDENTIFIER_TITLE,
- CodeAndLabelUtil.normalize(PLATE_IDENTIFIER_TITLE));
- builder.addHeader(ROW_TITLE, CodeAndLabelUtil.normalize(ROW_TITLE));
- builder.addHeader(COLUMN_TITLE, CodeAndLabelUtil.normalize(COLUMN_TITLE));
+ CodeNormalizer.normalize(PLATE_IDENTIFIER_TITLE));
+ builder.addHeader(ROW_TITLE, CodeNormalizer.normalize(ROW_TITLE));
+ builder.addHeader(COLUMN_TITLE, CodeNormalizer.normalize(COLUMN_TITLE));
for (CodeAndLabel codeAndLabel : codeAndLabels)
{
builder.addHeader(codeAndLabel.getLabel(), "feature-" + codeAndLabel.getCode());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index e2dfa4c3391..ae13e4df8bf 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -54,9 +54,9 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector;
@@ -351,7 +351,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
ArrayList<String> codes = new ArrayList<String>(names.size());
for (String name : names)
{
- codes.add(CodeAndLabelUtil.normalize(name));
+ codes.add(CodeNormalizer.normalize(name));
}
return codes;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java
index a8312c76655..bc73e2f51ae 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java
@@ -27,7 +27,7 @@ import net.lemnik.eodsql.QueryTool;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.AbstractDBTest;
@@ -105,7 +105,7 @@ public class FeatureVectorDAOTest extends AbstractDBTest
ImgFeatureDefDTO featureDef = featureDefs.get(0);
assertEquals(TEST_FEATURE_LABEL, featureDef.getLabel());
- assertEquals(CodeAndLabelUtil.normalize(TEST_FEATURE_LABEL), featureDef.getCode());
+ assertEquals(CodeNormalizer.normalize(TEST_FEATURE_LABEL), featureDef.getCode());
testCreateAndListFeatureVocabularyValues(featureDef);
@@ -179,7 +179,7 @@ public class FeatureVectorDAOTest extends AbstractDBTest
// Attach a feature def to it
ImgFeatureDefDTO featureDef =
new ImgFeatureDefDTO(TEST_FEATURE_LABEL,
- CodeAndLabelUtil.normalize(TEST_FEATURE_LABEL), "Test", dataSet.getId());
+ CodeNormalizer.normalize(TEST_FEATURE_LABEL), "Test", dataSet.getId());
return dao.addFeatureDef(featureDef);
}
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotTest.java
index ad10a3bdc36..6f211afa12f 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataScatterplotTest.java
@@ -22,6 +22,7 @@ import java.io.IOException;
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
/**
@@ -34,7 +35,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
{
File outputFile = getImageOutputFile();
- CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel xAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("<INFECTEDCELLS> Infected Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Total Cells vs. Infected Cells",
@@ -58,7 +59,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
File outputFile = getImageOutputFile();
CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("BigNumber");
- CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel yAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Big Number vs Total Cells", xAxisColumn,
yAxisColumn, 300, 200);
@@ -81,7 +82,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
File outputFile = getImageOutputFile();
CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("SmallNumbers");
- CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel yAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Small Numbers vs Total Cells",
xAxisColumn, yAxisColumn, 300, 200);
@@ -101,7 +102,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
File outputFile = getImageOutputFile();
CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("Zero");
- CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel yAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Zero vs Total Cells", xAxisColumn,
yAxisColumn, 300, 200);
@@ -121,7 +122,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
File outputFile = getImageOutputFile();
CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("JustNaN");
- CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel yAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Just NaN vs Total Cells", xAxisColumn,
yAxisColumn, 300, 200);
@@ -141,7 +142,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
File outputFile = getImageOutputFile();
CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("SomeNaN");
- CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel yAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Some NaN vs Total Cells", xAxisColumn,
yAxisColumn, 300, 200);
@@ -161,7 +162,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
File outputFile = getImageOutputFile();
CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("JustInf");
- CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel yAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Just Inf vs Total Cells", xAxisColumn,
yAxisColumn, 300, 200);
@@ -181,7 +182,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
File outputFile = getImageOutputFile();
CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("SomeInf");
- CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel yAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Some Inf vs Total Cells", xAxisColumn,
yAxisColumn, 300, 200);
@@ -201,7 +202,7 @@ public class TabularDataScatterplotTest extends AbstractTabularDataGraphTest
File outputFile = getImageOutputFile();
CodeAndLabel xAxisColumn = CodeAndLabelUtil.create("Blanks");
- CodeAndLabel yAxisColumn = CodeAndLabelUtil.create("TotalCells", "Total Cells");
+ CodeAndLabel yAxisColumn = CodeNormalizer.create("TotalCells", "Total Cells");
TabularDataScatterplotConfiguration config =
new TabularDataScatterplotConfiguration("Blanks vs Total Cells", xAxisColumn,
yAxisColumn, 300, 200);
--
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