diff --git a/openbis_knime/.classpath b/openbis_knime/.classpath
index 8e08285d5bf6a384f9958c1b8a6db2a883696592..c3513cd8d96a27277f0a19d100e987639f9a0a06 100644
--- a/openbis_knime/.classpath
+++ b/openbis_knime/.classpath
@@ -2,9 +2,17 @@
<classpath>
<classpathentry kind="src" path="source/java"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
- <classpathentry kind="lib" path="/libraries/knime/knime-base.jar"/>
- <classpathentry kind="lib" path="/libraries/knime/knime-core.jar"/>
+ <classpathentry kind="lib" path="/libraries/knime/knime-base.jar">
+ <attributes>
+ <attribute name="javadoc_location" value="jar:platform:/resource/libraries/knime/knime_2.1.2_API.zip!/"/>
+ </attributes>
+ </classpathentry>
+ <classpathentry kind="lib" path="/libraries/knime/knime-core.jar">
+ <attributes>
+ <attribute name="javadoc_location" value="jar:platform:/resource/libraries/knime/knime_2.1.2_API.zip!/"/>
+ </attributes>
+ </classpathentry>
<classpathentry kind="lib" path="/libraries/openbis-apis/query/openbis-query-api.jar"/>
- <classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/openbis_knime/dist/plugin.xml b/openbis_knime/dist/plugin.xml
index c2ef97692956e37673f7942f14fed7b6d523aa3c..b4a1f0bff8e6ff0a830010ce483e9f0d103d79e2 100644
--- a/openbis_knime/dist/plugin.xml
+++ b/openbis_knime/dist/plugin.xml
@@ -3,12 +3,13 @@
<plugin>
<extension point="org.knime.workbench.repository.nodes">
- <node category-path="/openbis" factory-class="ch.systemsx.cisd.openbis.knime.TestNodeFactory"
- id="ch.systemsx.cisd.openbis.knime.node"/>
+ <node category-path="/openbis/query" factory-class="ch.systemsx.cisd.openbis.knime.query.QueryNodeFactory"
+ id="ch.systemsx.cisd.openbis.knime.query.QueryNodeFactory"/>
</extension>
<extension point="org.knime.workbench.repository.categories">
<category icon="icons/openbis.png" level-id="openbis" name="openBIS" path="/"/>
+ <category icon="icons/openbis.png" level-id="query" name="Query" path="/openbis"/>
</extension>
</plugin>
\ No newline at end of file
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeDialog.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeDialog.java
deleted file mode 100644
index f06e6eeb620c856380872c2910e8fc9cb35e1a99..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeDialog.java
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime;
-
-import java.awt.BorderLayout;
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.List;
-
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JPasswordField;
-import javax.swing.JTextField;
-
-import org.apache.log4j.Logger;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeDialogPane;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-import org.knime.core.node.NotConfigurableException;
-import org.knime.core.node.port.PortObjectSpec;
-
-import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.QueryApiFacade;
-import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-public class TestNodeDialog extends NodeDialogPane
-{
- private JTextField urlField;
- private JTextField userField;
- private JPasswordField passwordField;
- private JComboBox queryComboBox;
-
- TestNodeDialog()
- {
- super();
- addTab("openBIS Settings", createGUI());
- }
-
- private JPanel createGUI()
- {
- JPanel panel = new JPanel(new BorderLayout());
- JPanel form = new JPanel(new GridLayout(0, 2));
- form.add(new JLabel("openBIS URL:"));
- urlField = new JTextField();
- form.add(urlField);
- form.add(new JLabel("User:"));
- userField = new JTextField();
- form.add(userField);
- form.add(new JLabel("Password:"));
- passwordField = new JPasswordField();
- form.add(passwordField);
- form.add(new JLabel("Queries:"));
- queryComboBox = new JComboBox();
- form.add(queryComboBox);
- panel.add(form, BorderLayout.NORTH);
- JButton button = new JButton("connect");
- button.addActionListener(new ActionListener()
- {
-
- public void actionPerformed(ActionEvent e)
- {
- QueryApiFacade facade = QueryApiFacade.create(urlField.getText(), userField.getText(), passwordField.getText());
- List<QueryDescription> queries = facade.listQueries();
- for (QueryDescription queryDescription : queries)
- {
- queryComboBox.addItem(queryDescription.getName());
- }
- // TODO Auto-generated method stub
-
- }
- });
- panel.add(button, BorderLayout.SOUTH);
- return panel;
- }
-
- @Override
- protected void loadSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
- throws NotConfigurableException
- {
- }
-
- @Override
- protected void saveSettingsTo(NodeSettingsWO settings) throws InvalidSettingsException
- {
- // TODO Auto-generated method stub
-
- }
-
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeFactory.xml
deleted file mode 100644
index 8128aed79d12698473e73cc68a9feafe8a046942..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeFactory.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
-<knimeNode icon="./openbis.png" type="Source">
- <name>openBIS Test</name>
-
- <shortDescription>
- openBIS test node
- </shortDescription>
-
- <fullDescription>
- <intro>Just testing a very simple node.
- </intro>
-
-
- <option name="short name of first option (like in the dialog)">has no first option</option>
- <option name="short name of second option (like in the dialog)">has no second option</option>
- </fullDescription>
-
- <ports>
- <inPort index="0" name="First In Port">Actual there are no in ports I guess</inPort>
- <outPort index="0" name="First out Port">A simple table</outPort>
- </ports>
- <views>
- <view index="0" name="name of first view">Description of first view...</view>
- </views>
-</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeModel.java
deleted file mode 100644
index ba1e739538afe25f032883a44f2d00bb14dde98d..0000000000000000000000000000000000000000
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeModel.java
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.knime;
-
-import java.io.File;
-import java.io.IOException;
-
-import org.knime.core.data.DataTableSpec;
-import org.knime.core.data.DataType;
-import org.knime.core.data.def.DefaultRow;
-import org.knime.core.data.def.StringCell;
-import org.knime.core.node.BufferedDataContainer;
-import org.knime.core.node.BufferedDataTable;
-import org.knime.core.node.CanceledExecutionException;
-import org.knime.core.node.ExecutionContext;
-import org.knime.core.node.ExecutionMonitor;
-import org.knime.core.node.InvalidSettingsException;
-import org.knime.core.node.NodeModel;
-import org.knime.core.node.NodeSettingsRO;
-import org.knime.core.node.NodeSettingsWO;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-public class TestNodeModel extends NodeModel
-{
-
- protected TestNodeModel()
- {
- super(0, 1);
- }
-
- @Override
- protected void loadInternals(File arg0, ExecutionMonitor arg1) throws IOException,
- CanceledExecutionException
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- protected void loadValidatedSettingsFrom(NodeSettingsRO arg0) throws InvalidSettingsException
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- protected void reset()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- protected void saveInternals(File arg0, ExecutionMonitor arg1) throws IOException,
- CanceledExecutionException
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- protected void saveSettingsTo(NodeSettingsWO arg0)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- protected void validateSettings(NodeSettingsRO arg0) throws InvalidSettingsException
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec)
- throws Exception
- {
- BufferedDataContainer container = exec.createDataContainer(new DataTableSpec(new String[] {"col1", "col2"},
- new DataType[] {StringCell.TYPE, StringCell.TYPE}));
- for (int i = 0; i < 5; i++)
- {
- container.addRowToTable(new DefaultRow("row-"+i, "a-"+i, "b-"+i));
- }
- container.close();
- return new BufferedDataTable[] {container.getTable()};
- }
-
- @Override
- protected DataTableSpec[] configure(final DataTableSpec[] inSpecs)
- throws InvalidSettingsException
- {
- return new DataTableSpec[0];
- }
-}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ParameterBindings.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ParameterBindings.java
new file mode 100644
index 0000000000000000000000000000000000000000..6616201802297ea3b497bc7677e3d11c31fb69cd
--- /dev/null
+++ b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/ParameterBindings.java
@@ -0,0 +1,96 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.knime.query;
+
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import org.knime.core.node.InvalidSettingsException;
+import org.knime.core.node.NodeSettingsRO;
+import org.knime.core.node.NodeSettingsWO;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ParameterBindings
+{
+ static final String PARAMETER_KEYS_KEY = "query-parameter-keys";
+ static final String PARAMETER_VALUES_KEY = "query-parameter-values";
+
+ private Map<String, String> bindings = new LinkedHashMap<String, String>();
+
+ void removeAllBindings()
+ {
+ bindings.clear();
+ }
+
+ void bind(String parameter, String value)
+ {
+ bindings.put(parameter, value);
+ }
+
+ Map<String, String> getBindings()
+ {
+ return bindings;
+ }
+
+ String tryToGetBinding(String parameter)
+ {
+ return bindings.get(parameter);
+ }
+
+ void loadValidatedSettingsFrom(NodeSettingsRO settings)
+ {
+ String[] parameterKeys;
+ String[] parameterValues;
+ try
+ {
+ parameterKeys = settings.getStringArray(PARAMETER_KEYS_KEY);
+ parameterValues = settings.getStringArray(PARAMETER_VALUES_KEY);
+ } catch (InvalidSettingsException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ bindings.clear();
+ for (int i = 0, n = Math.min(parameterKeys.length, parameterValues.length); i < n; i++)
+ {
+ bindings.put(parameterKeys[i], parameterValues[i]);
+ }
+ }
+
+ void saveSettingsTo(NodeSettingsWO settings)
+ {
+ List<String> parameterKeys = new ArrayList<String>(bindings.size());
+ List<String> parameterValues = new ArrayList<String>(bindings.size());
+ Set<Entry<String, String>> entrySet = bindings.entrySet();
+ for (Entry<String, String> entry : entrySet)
+ {
+ parameterKeys.add(entry.getKey());
+ parameterValues.add(entry.getValue());
+ }
+ settings.addStringArray(PARAMETER_KEYS_KEY, parameterKeys.toArray(new String[0]));
+ settings.addStringArray(PARAMETER_VALUES_KEY, parameterValues.toArray(new String[0]));
+ }
+}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeDialog.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeDialog.java
new file mode 100644
index 0000000000000000000000000000000000000000..91cc59b63409648bafe15d2e517c2f02e8380fd1
--- /dev/null
+++ b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeDialog.java
@@ -0,0 +1,251 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.knime.query;
+
+import static ch.systemsx.cisd.openbis.knime.query.QueryNodeModel.PASSWORD_KEY;
+import static ch.systemsx.cisd.openbis.knime.query.QueryNodeModel.QUERY_DESCRIPTION_KEY;
+import static ch.systemsx.cisd.openbis.knime.query.QueryNodeModel.URL_KEY;
+import static ch.systemsx.cisd.openbis.knime.query.QueryNodeModel.USER_KEY;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.GridLayout;
+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.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JPasswordField;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+
+import org.knime.core.node.InvalidSettingsException;
+import org.knime.core.node.NodeDialogPane;
+import org.knime.core.node.NodeLogger;
+import org.knime.core.node.NodeSettingsRO;
+import org.knime.core.node.NodeSettingsWO;
+import org.knime.core.node.NotConfigurableException;
+import org.knime.core.node.port.PortObjectSpec;
+
+import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.FacadeFactory;
+import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
+import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class QueryNodeDialog extends NodeDialogPane
+{
+ private static final NodeLogger log = NodeLogger.getLogger(QueryNodeDialog.class);
+
+ private JTextField urlField;
+ private JTextField userField;
+ private JPasswordField passwordField;
+ private JComboBox queryComboBox;
+ private JPanel parametersPanel;
+ private ParameterBindings parameterBindings = new ParameterBindings();
+ private Map<String, JTextField> parameterFields = new HashMap<String, JTextField>();
+
+ QueryNodeDialog()
+ {
+ super();
+ addTab("Query Settings", createGUI());
+ }
+
+ private JComponent createGUI()
+ {
+ JPanel panel = new JPanel(new BorderLayout());
+ panel.setPreferredSize(new Dimension(400, 450));
+ JPanel connectionPanel = new JPanel(new GridBagLayout());
+ connectionPanel.setBorder(BorderFactory.createTitledBorder("Connection Parameters"));
+ urlField = addField(connectionPanel, "openBIS URL", new JTextField(20));
+ userField = addField(connectionPanel, "User", new JTextField(20));
+ passwordField = addField(connectionPanel, "Password", new JPasswordField(20));
+ JButton button = new JButton("connect");
+ button.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ connectToOpenBIS();
+ }
+ });
+ connectionPanel.add(button, createLast());
+ panel.add(connectionPanel, BorderLayout.NORTH);
+ JPanel queryPanel = new JPanel(new BorderLayout());
+ panel.add(queryPanel, BorderLayout.CENTER);
+ queryComboBox = new JComboBox();
+ queryComboBox.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ QueryDescription queryDescription = (QueryDescription) e.getItem();
+ updateParametersPanel(queryDescription);
+ log.info(queryDescription);
+ }
+ });
+ JPanel querySelectionPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ querySelectionPanel.add(new JLabel("Query:"));
+ querySelectionPanel.add(queryComboBox);
+ queryPanel.add(querySelectionPanel, BorderLayout.NORTH);
+ parametersPanel = new JPanel(new GridLayout(0, 2));
+ parametersPanel.setBorder(BorderFactory.createTitledBorder("Query Parameters"));
+ JPanel northPanel = new JPanel(new BorderLayout());
+ northPanel.add(parametersPanel, BorderLayout.NORTH);
+ queryPanel.add(northPanel, BorderLayout.CENTER);
+ JScrollPane scrollPane = new JScrollPane(panel);
+ scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
+ return scrollPane;
+ }
+
+ @Override
+ protected void loadSettingsFrom(NodeSettingsRO settings, PortObjectSpec[] specs)
+ throws NotConfigurableException
+ {
+ urlField.setText(settings.getString(URL_KEY, ""));
+ userField.setText(settings.getString(USER_KEY, ""));
+ passwordField.setText(settings.getString(PASSWORD_KEY, ""));
+ byte[] bytes = settings.getByteArray(QUERY_DESCRIPTION_KEY, null);
+ QueryDescription queryDescriptionOrNull = Util.deserializeQueryDescription(bytes);
+ parameterBindings.loadValidatedSettingsFrom(settings);
+ if (queryDescriptionOrNull != null && queryComboBox.getItemCount() == 0)
+ {
+ queryComboBox.addItem(queryDescriptionOrNull);
+ queryComboBox.setSelectedIndex(0);
+ }
+ }
+
+ @Override
+ protected void saveSettingsTo(NodeSettingsWO settings) throws InvalidSettingsException
+ {
+ settings.addString(URL_KEY, urlField.getText().trim());
+ settings.addString(USER_KEY, userField.getText().trim());
+ settings.addString(PASSWORD_KEY, passwordField.getText().trim());
+ byte[] bytes = Util.serializeQueryDescription(getSelectedQueryDescriptionOrNull());
+ settings.addByteArray(QUERY_DESCRIPTION_KEY, bytes);
+ parameterBindings.removeAllBindings();
+ Set<Entry<String, JTextField>> entrySet = parameterFields.entrySet();
+ for (Entry<String, JTextField> entry : entrySet)
+ {
+ parameterBindings.bind(entry.getKey(), entry.getValue().getText());
+ }
+ parameterBindings.saveSettingsTo(settings);
+ }
+
+ private QueryDescription getSelectedQueryDescriptionOrNull()
+ {
+ Object selectedItem = queryComboBox.getSelectedItem();
+ return selectedItem == null ? null : (QueryDescription) selectedItem;
+ }
+
+ private <T extends JComponent> T addField(JPanel panel, String label, T field)
+ {
+ panel.add(new JLabel(label + ":"), createFirst());
+ panel.add(field, createLast());
+ return field;
+ }
+
+ private GridBagConstraints createLast()
+ {
+ GridBagConstraints last = createFirst();
+ last.gridwidth = GridBagConstraints.REMAINDER;
+ return last;
+ }
+
+ private GridBagConstraints createFirst()
+ {
+ GridBagConstraints constraints = new GridBagConstraints();
+ constraints.anchor = GridBagConstraints.WEST;
+ constraints.fill = GridBagConstraints.HORIZONTAL;
+ constraints.insets = new Insets(2, 3, 2, 3);
+ return constraints;
+ }
+
+ private void connectToOpenBIS()
+ {
+ String url = urlField.getText();
+ String userID = userField.getText();
+ String password = passwordField.getText();
+ IQueryApiFacade facade = FacadeFactory.create(url, userID, password);
+ List<QueryDescription> queries = facade.listQueries();
+ Collections.sort(queries, new Comparator<QueryDescription>()
+ {
+ public int compare(QueryDescription d1, QueryDescription d2)
+ {
+ return d1.getName().compareTo(d2.getName());
+ }
+ });
+ QueryDescription selectedQueryDescription = getSelectedQueryDescriptionOrNull();
+ queryComboBox.removeAllItems();
+ for (QueryDescription queryDescription : queries)
+ {
+ queryComboBox.addItem(queryDescription);
+ if (queryDescription.equals(selectedQueryDescription))
+ {
+ queryComboBox.setSelectedItem(queryDescription);
+ }
+ }
+ }
+
+ private void updateParametersPanel(QueryDescription queryDescription)
+ {
+ log.info("update parameters panel for '" + queryDescription + "' which has "
+ + queryDescription.getParameters().size() + " parameters.");
+ parametersPanel.removeAll();
+ parameterFields.clear();
+ List<String> parameters = queryDescription.getParameters();
+ parametersPanel.setVisible(parameters.isEmpty() == false);
+ for (String parameter : parameters)
+ {
+ JTextField field = parameterFields.get(parameter);
+ if (field == null)
+ {
+ field = new JTextField(15);
+ parameterFields.put(parameter, field);
+ }
+ String value = parameterBindings.tryToGetBinding(parameter);
+ if (value != null)
+ {
+ field.setText(value);
+ }
+ addField(parametersPanel, parameter, field);
+ }
+ parametersPanel.invalidate();
+ parametersPanel.getParent().validate();
+ }
+
+
+}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeFactory.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.java
similarity index 77%
rename from openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeFactory.java
rename to openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.java
index daa77002197ca8176aac96c8c8f3bbdda80efc02..d10a56ce721bea47aff9d509c1e5ef2f5e4b547a 100644
--- a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/TestNodeFactory.java
+++ b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.knime;
+package ch.systemsx.cisd.openbis.knime.query;
import org.knime.core.node.NodeDialogPane;
import org.knime.core.node.NodeFactory;
@@ -25,23 +25,23 @@ import org.knime.core.node.NodeView;
*
* @author Franz-Josef Elmer
*/
-public class TestNodeFactory extends NodeFactory<TestNodeModel>
+public class QueryNodeFactory extends NodeFactory<QueryNodeModel>
{
@Override
protected NodeDialogPane createNodeDialogPane()
{
- return new TestNodeDialog();
+ return new QueryNodeDialog();
}
@Override
- public TestNodeModel createNodeModel()
+ public QueryNodeModel createNodeModel()
{
- return new TestNodeModel();
+ return new QueryNodeModel();
}
@Override
- public NodeView<TestNodeModel> createNodeView(int arg0, TestNodeModel arg1)
+ public NodeView<QueryNodeModel> createNodeView(int viewIndex, QueryNodeModel model)
{
return null;
}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.xml b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.xml
new file mode 100644
index 0000000000000000000000000000000000000000..85a654551c6f5d60d5890317be9cc0a1d9e0cfc0
--- /dev/null
+++ b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeFactory.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
+<knimeNode icon="./openbis.png" type="Source">
+ <name>openBIS Query Reader</name>
+
+ <shortDescription>openBIS query node</shortDescription>
+
+ <fullDescription>
+ <intro>Data source node to run a parameterized SQL query on openBIS Application Server
+ </intro>
+ </fullDescription>
+
+ <ports>
+ <outPort index="0" name="Result Set">Table with result set</outPort>
+ </ports>
+</knimeNode>
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeModel.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeModel.java
new file mode 100644
index 0000000000000000000000000000000000000000..bdb3ae5bf7d3a709d09f403d2d2b1244b0f89c4c
--- /dev/null
+++ b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/QueryNodeModel.java
@@ -0,0 +1,169 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.knime.query;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.List;
+
+import org.knime.core.data.DataCell;
+import org.knime.core.data.DataTableSpec;
+import org.knime.core.data.DataType;
+import org.knime.core.data.def.DefaultRow;
+import org.knime.core.data.def.DoubleCell;
+import org.knime.core.data.def.LongCell;
+import org.knime.core.data.def.StringCell;
+import org.knime.core.node.BufferedDataContainer;
+import org.knime.core.node.BufferedDataTable;
+import org.knime.core.node.CanceledExecutionException;
+import org.knime.core.node.ExecutionContext;
+import org.knime.core.node.ExecutionMonitor;
+import org.knime.core.node.InvalidSettingsException;
+import org.knime.core.node.NodeModel;
+import org.knime.core.node.NodeSettingsRO;
+import org.knime.core.node.NodeSettingsWO;
+
+import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.FacadeFactory;
+import ch.systemsx.cisd.openbis.plugin.query.client.api.v1.IQueryApiFacade;
+import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription;
+import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumn;
+import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class QueryNodeModel extends NodeModel
+{
+ static final String URL_KEY = "url";
+ static final String USER_KEY = "user";
+ static final String PASSWORD_KEY = "password";
+ static final String QUERY_DESCRIPTION_KEY = "query-description";
+
+ private String url;
+ private String userID;
+ private String password;
+ private QueryDescription queryDescription;
+ private ParameterBindings parameterBindings = new ParameterBindings();
+
+ protected QueryNodeModel()
+ {
+ super(0, 1);
+ }
+
+ @Override
+ protected DataTableSpec[] configure(final DataTableSpec[] inSpecs)
+ throws InvalidSettingsException
+ {
+ return new DataTableSpec[1];
+ }
+
+ @Override
+ protected void validateSettings(NodeSettingsRO settings) throws InvalidSettingsException
+ {
+ }
+
+ @Override
+ protected void loadValidatedSettingsFrom(NodeSettingsRO settings) throws InvalidSettingsException
+ {
+ url = settings.getString(URL_KEY);
+ userID = settings.getString(USER_KEY);
+ password = settings.getString(PASSWORD_KEY);
+ queryDescription = Util.deserializeQueryDescription(settings.getByteArray(QUERY_DESCRIPTION_KEY));
+ parameterBindings.loadValidatedSettingsFrom(settings);
+ }
+
+ @Override
+ protected void saveSettingsTo(NodeSettingsWO settings)
+ {
+ settings.addString(URL_KEY, url);
+ settings.addString(USER_KEY, userID);
+ settings.addString(PASSWORD_KEY, password);
+ settings.addByteArray(QUERY_DESCRIPTION_KEY, Util
+ .serializeQueryDescription(queryDescription));
+ parameterBindings.saveSettingsTo(settings);
+ }
+
+ @Override
+ protected void reset()
+ {
+ }
+
+ @Override
+ protected void saveInternals(File arg0, ExecutionMonitor arg1) throws IOException,
+ CanceledExecutionException
+ {
+ }
+
+ @Override
+ protected void loadInternals(File arg0, ExecutionMonitor arg1) throws IOException,
+ CanceledExecutionException
+ {
+ }
+
+ @Override
+ protected BufferedDataTable[] execute(BufferedDataTable[] inData, ExecutionContext exec)
+ throws Exception
+ {
+ IQueryApiFacade facade = createFacade(url, userID, password);
+ QueryTableModel result = facade.executeQuery(queryDescription.getId(), parameterBindings.getBindings());
+ List<QueryTableColumn> columns = result.getColumns();
+ String[] columnTitles = new String[columns.size()];
+ DataType[] columnTypes = new DataType[columns.size()];
+ for (int i = 0, n = columns.size(); i < n; i++)
+ {
+ QueryTableColumn column = columns.get(i);
+ columnTitles[i] = column.getTitle();
+ columnTypes[i] = Util.translateDataType(column.getDataType());
+ }
+ DataTableSpec dataTableSpec = new DataTableSpec(columnTitles, columnTypes);
+ BufferedDataContainer container = exec.createDataContainer(dataTableSpec);
+ List<Serializable[]> rows = result.getRows();
+ for (int i = 0, n = rows.size(); i < n; i++)
+ {
+ Serializable[] row = rows.get(i);
+ DataCell[] cells = new DataCell[row.length];
+ for (int c = 0; c < row.length; c++)
+ {
+ Serializable value = row[c];
+ DataCell cell = null;
+ if (value instanceof Double)
+ {
+ cell = new DoubleCell((Double) value);
+ } else if (value instanceof Long)
+ {
+ cell = new LongCell((Long) value);
+ } else
+ {
+ cell = new StringCell(value.toString());
+ }
+ cells[c] = cell;
+ }
+ container.addRowToTable(new DefaultRow(Integer.toString(i), cells));
+ }
+ container.close();
+ return new BufferedDataTable[] {container.getTable()};
+ }
+
+ protected IQueryApiFacade createFacade(String serverURL, String user, String psswrd)
+ {
+ return FacadeFactory.create(serverURL, user, psswrd);
+ }
+
+}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/Util.java b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/Util.java
new file mode 100644
index 0000000000000000000000000000000000000000..02023d45fca50f3b3a3df2dd70a19b0cb1c0b09e
--- /dev/null
+++ b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/Util.java
@@ -0,0 +1,82 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.knime.query;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+import org.knime.core.data.DataType;
+import org.knime.core.data.def.DoubleCell;
+import org.knime.core.data.def.LongCell;
+import org.knime.core.data.def.StringCell;
+
+import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryDescription;
+import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableColumnDataType;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class Util
+{
+ static byte[] serializeQueryDescription(QueryDescription queryDescriptionOrNull)
+ {
+ if (queryDescriptionOrNull == null)
+ {
+ return null;
+ }
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ try
+ {
+ new ObjectOutputStream(baos).writeObject(queryDescriptionOrNull);
+ return baos.toByteArray();
+ } catch (IOException ex)
+ {
+ return null;
+ }
+ }
+
+ static QueryDescription deserializeQueryDescription(byte[] serializeQueryDescriptionOrNull)
+ {
+ if (serializeQueryDescriptionOrNull == null)
+ {
+ return null;
+ }
+ ByteArrayInputStream bais = new ByteArrayInputStream(serializeQueryDescriptionOrNull);
+ try
+ {
+ return (QueryDescription) new ObjectInputStream(bais).readObject();
+ } catch (Exception ex)
+ {
+ return null;
+ }
+ }
+
+ static DataType translateDataType(QueryTableColumnDataType dataType)
+ {
+ switch (dataType)
+ {
+ case DOUBLE: return DoubleCell.TYPE;
+ case LONG: return LongCell.TYPE;
+ default: return StringCell.TYPE;
+ }
+ }
+}
diff --git a/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/openbis.png b/openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/openbis.png
similarity index 100%
rename from openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/openbis.png
rename to openbis_knime/source/java/ch/systemsx/cisd/openbis/knime/query/openbis.png