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 6c4eb40adba0f4c6b334434bd76fa069a3167cb8..27144c051f9c9ebcd406c4d7373d0ce7246545c5 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
@@ -236,9 +236,8 @@ public abstract class AbstractSwingGUI
@Override
public void run()
{
- JOptionPane.showMessageDialog(parentFrame,
- WordUtils.wrap(message, MESSAGE_WRAP_MAX_CHAR), title,
- JOptionPane.ERROR_MESSAGE);
+ UiUtilities.showMessageAndException(parentFrame, throwable,
+ WordUtils.wrap(message, MESSAGE_WRAP_MAX_CHAR), title);
}
});
}
@@ -269,90 +268,4 @@ public abstract class AbstractSwingGUI
}
}
- // -------- errors reporting -----------------
-
- protected static void showErrorsAndWarningsIfAny(JFrame frame, String firstMessageOrNull,
- List<String> warningMessages, List<Throwable> exceptions)
- {
- String message = (firstMessageOrNull == null ? "" : firstMessageOrNull + "\n");
- message += joinMessages(warningMessages, exceptions);
- if (exceptions.size() > 0)
- {
- showErrorMessage(frame, message);
- } else if (warningMessages.size() > 0)
- {
- showWarningMessage(frame, message);
- }
- }
-
- private static void showErrorMessage(JFrame frame, String message)
- {
- showMessageDialog(frame, message, "Error", JOptionPane.ERROR_MESSAGE);
- }
-
- private static void showWarningMessage(JFrame frame, String message)
- {
- showMessageDialog(frame, message, "Warning", JOptionPane.WARNING_MESSAGE);
- }
-
- private static void showMessageDialog(JFrame frame, String message, String title,
- int messageType)
- {
- JOptionPane.showMessageDialog(frame, message, title, messageType);
- }
-
- private static String joinMessages(List<String> warningMessages, List<Throwable> exceptions)
- {
- StringBuffer sb = new StringBuffer();
- addErrorMessages(exceptions, sb);
- addWarningMessages(warningMessages, sb);
- return sb.toString();
- }
-
- private static void addErrorMessages(List<Throwable> exceptions, StringBuffer sb)
- {
- if (exceptions.size() > 0)
- {
- if (exceptions.size() > 1)
- {
- sb.append("Following errors occured: \n");
- }
- for (Throwable exception : exceptions)
- {
- sb.append(getErrorMessage(exception));
- sb.append("\n");
- }
- }
- }
-
- private static void addWarningMessages(List<String> warningMessages, StringBuffer sb)
- {
- if (warningMessages.size() > 0)
- {
- sb.append("Following warnings occured (you can most probably ignore them): \n");
- String lastWarningMessage = "";
- for (String warningMessage : warningMessages)
- {
- if (lastWarningMessage.equals(warningMessage) == false)
- {
- sb.append(warningMessage);
- sb.append("\n");
- lastWarningMessage = warningMessage;
- }
- }
- }
- }
-
- private static String getErrorMessage(Throwable throwable)
- {
- final String message;
- if (throwable instanceof HighLevelException)
- {
- message = throwable.getMessage();
- } else
- {
- message = "ERROR: " + throwable;
- }
- return message;
- }
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractTreeEntityPickerDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractTreeEntityPickerDialog.java
index 25de90dc8cf8bca521f571fa1b3cc1839c11ede6..7e1e9d1d6b523b494a7e70c03022480f3d02d610 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractTreeEntityPickerDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AbstractTreeEntityPickerDialog.java
@@ -26,7 +26,6 @@ import java.util.List;
import javax.swing.JDialog;
import javax.swing.JFrame;
-import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
@@ -49,6 +48,7 @@ import ch.systemsx.cisd.openbis.dss.client.api.gui.model.UploadClientSortingUtil
import ch.systemsx.cisd.openbis.dss.client.api.gui.tree.FilterableMutableTreeNode;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
/**
* Abstract super class of all entity picker dialogs based on {@link JTree}.
@@ -77,6 +77,8 @@ public abstract class AbstractTreeEntityPickerDialog extends AbstractEntityPicke
this.entityKind = entityKind;
tree = new JTree();
tree.setModel(new DefaultTreeModel(null));
+ tree.setRootVisible(false);
+ tree.setShowsRootHandles(true);
tree.addTreeWillExpandListener(this);
tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
addTreeSelectionListener();
@@ -93,7 +95,7 @@ public abstract class AbstractTreeEntityPickerDialog extends AbstractEntityPicke
final JScrollPane scrollPane = new JScrollPane(tree);
List<Object> objectsAsList = new ArrayList<Object>();
- objectsAsList.add("Filter experiments: ");
+ objectsAsList.add("Filter experiments and samples: ");
objectsAsList.add(northPanel);
objectsAsList.add("Select " + entityKind.toString().toLowerCase() + ":");
@@ -159,66 +161,104 @@ public abstract class AbstractTreeEntityPickerDialog extends AbstractEntityPicke
}
}
String label = entityKind.toString();
- JOptionPane.showMessageDialog(this, "No correct " + label.toLowerCase() + " found, " + selected + " is not correct!",
- "No correct " + label.toLowerCase() + " found, " + selected + " is not correct!", JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(this, "Please, select a " + label.toLowerCase() + ".",
+ "No " + label.toLowerCase() + " selected!", JOptionPane.WARNING_MESSAGE);
optionPane.setValue(optionPane.getInitialValue());
}
@Override
public void treeWillExpand(final TreeExpansionEvent event) throws ExpandVetoException
{
- final DefaultMutableTreeNode node =
- (DefaultMutableTreeNode) event.getPath().getLastPathComponent();
+ final FilterableMutableTreeNode node =
+ (FilterableMutableTreeNode) event.getPath().getLastPathComponent();
// if top level, then finish
if (((TreeNode) node).getParent() == null)
{
return;
}
Object userObject = node.getUserObject();
- if (userObject instanceof Identifier)
+ if (UiUtilities.ROOT_EXPERIMENTS.equals(userObject))
+ {
+ expandExperiments(node);
+ } else if (UiUtilities.ROOT_SAMPLES.equals(userObject))
+ {
+ expandSamples(node);
+ } else if (userObject instanceof Identifier)
{
expandNode(node, (Identifier) userObject);
}
}
+
+ private void expandExperiments(final FilterableMutableTreeNode node)
+ {
+ AsyncNodeAction<List<Experiment>> action =
+ new AsyncNodeAction<List<Experiment>>(tree, node, scheduler)
+ {
+ @Override
+ public void handleData(List<Experiment> experiments)
+ {
+ node.removeAllChildren();
+ UploadClientSortingUtils.sortExperimentsByIdentifier(experiments);
+ for (Experiment experiment : experiments)
+ {
+ FilterableMutableTreeNode category =
+ new FilterableMutableTreeNode(Identifier.create(experiment));
+ category.add(UiUtilities.createWaitingNode());
+ node.add(category);
+ }
+ }
+ };
+ clientModel.listExperiments(action);
+ }
+
+ private void expandSamples(final FilterableMutableTreeNode node)
+ {
+ AsyncNodeAction<List<Sample>> action =
+ new AsyncNodeAction<List<Sample>>(tree, node, scheduler)
+ {
+ @Override
+ public void handleData(List<Sample> samples)
+ {
+ node.removeAllChildren();
+ UploadClientSortingUtils.sortSamplesByIdentifier(samples);
+ for (Sample sample : samples)
+ {
+ FilterableMutableTreeNode category =
+ new FilterableMutableTreeNode(Identifier.create(sample));
+ category.add(UiUtilities.createWaitingNode());
+ node.add(category);
+ }
+ }
+ };
+ clientModel.listSamplesWithNoExperiments(action);
+ }
- protected abstract void expandNode(final DefaultMutableTreeNode node, Identifier identifier);
+ protected abstract void expandNode(final FilterableMutableTreeNode node, Identifier identifier);
@Override
public void treeWillCollapse(TreeExpansionEvent event) throws ExpandVetoException
{
- DefaultMutableTreeNode node =
- (DefaultMutableTreeNode) event.getPath().getLastPathComponent();
+ FilterableMutableTreeNode node =
+ (FilterableMutableTreeNode) event.getPath().getLastPathComponent();
if (node.isRoot())
{
throw new ExpandVetoException(event);
}
node.removeAllChildren();
- node.add(new DefaultMutableTreeNode(UiUtilities.WAITING_NODE_LABEL));
- }
-
- protected void createNodes(FilterableMutableTreeNode top, List<Experiment> experiments)
- {
- UploadClientSortingUtils.sortExperimentsByIdentifier(experiments);
- for (Experiment experiment : experiments)
- {
- DefaultMutableTreeNode category =
- new DefaultMutableTreeNode(Identifier.create(experiment), true);
- category.add(new DefaultMutableTreeNode(UiUtilities.WAITING_NODE_LABEL));
- top.add(category);
- }
+ node.add(UiUtilities.createWaitingNode());
}
@Override
protected void setDialogData()
{
- FilterableMutableTreeNode top = new FilterableMutableTreeNode("Experiments");
-
- final List<String> projectIdentifiers = clientModel.getProjectIdentifiers();
- List<Experiment> experiments =
- clientModel.getOpenBISService().listExperimentsHavingSamplesForProjects(
- projectIdentifiers);
- createNodes(top, experiments);
+ FilterableMutableTreeNode top = new FilterableMutableTreeNode(null);
+ FilterableMutableTreeNode experimentsTree = new FilterableMutableTreeNode(UiUtilities.ROOT_EXPERIMENTS);
+ experimentsTree.add(UiUtilities.createWaitingNode());
+ top.add(experimentsTree);
+ FilterableMutableTreeNode samplesTree = new FilterableMutableTreeNode(UiUtilities.ROOT_SAMPLES);
+ samplesTree.add(UiUtilities.createWaitingNode());
+ top.add(samplesTree);
DefaultTreeModel treeModel = (DefaultTreeModel) tree.getModel();
treeModel.setRoot(top);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AsyncNodeAction.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AsyncNodeAction.java
index 1c613630ccc618c1b1f6c92be965bc038f16025f..60027e7e13a0f8306773b5b7d4e8d8fb8845b494 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AsyncNodeAction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/AsyncNodeAction.java
@@ -16,11 +16,20 @@
package ch.systemsx.cisd.openbis.dss.client.api.gui;
+import java.awt.BorderLayout;
import java.awt.EventQueue;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
import java.util.Timer;
import java.util.TimerTask;
+import javax.swing.JButton;
+import javax.swing.JLabel;
import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
import javax.swing.JTree;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.DefaultTreeModel;
@@ -61,9 +70,9 @@ public abstract class AsyncNodeAction<T> implements IAsyncAction<T>
}
@Override
- public void handleException(Throwable throwable)
+ public void handleException(final Throwable throwable)
{
- JOptionPane.showMessageDialog(tree, throwable.toString());
+ UiUtilities.showException(tree, throwable);
}
public abstract void handleData(T data);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerDialog.java
index b1718c5f45aba66c6a75cbf9ca03a265f45cf613..52128a080073aedcc7afa6449d89ddd948ae8561 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetPickerDialog.java
@@ -19,14 +19,11 @@ package ch.systemsx.cisd.openbis.dss.client.api.gui;
import java.util.List;
import javax.swing.JFrame;
-import javax.swing.event.TreeExpansionEvent;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.ExpandVetoException;
-import javax.swing.tree.TreeNode;
import ch.systemsx.cisd.openbis.dss.client.api.gui.model.DataSetUploadClientModel;
import ch.systemsx.cisd.openbis.dss.client.api.gui.model.Identifier;
import ch.systemsx.cisd.openbis.dss.client.api.gui.model.SamplesDataSets;
+import ch.systemsx.cisd.openbis.dss.client.api.gui.tree.FilterableMutableTreeNode;
import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
@@ -48,26 +45,7 @@ public class DataSetPickerDialog extends AbstractTreeEntityPickerDialog
}
@Override
- public void treeWillExpand(final TreeExpansionEvent event) throws ExpandVetoException
- {
- final DefaultMutableTreeNode node =
- (DefaultMutableTreeNode) event.getPath().getLastPathComponent();
- // if top level, then finish
- if (((TreeNode) node).getParent() == null)
- {
- return;
- }
- Object userObject = node.getUserObject();
- if (userObject instanceof Identifier == false)
- {
- return;
- }
- Identifier identifier = (Identifier) userObject;
- expandNode(node, identifier);
- }
-
- @Override
- protected void expandNode(final DefaultMutableTreeNode node, Identifier identifier)
+ protected void expandNode(final FilterableMutableTreeNode node, Identifier identifier)
{
if (identifier.getOwnerType() != DataSetOwnerType.DATA_SET)
{
@@ -82,22 +60,21 @@ public class DataSetPickerDialog extends AbstractTreeEntityPickerDialog
node.removeAllChildren();
if (dataSets.size() > 0)
{
- DefaultMutableTreeNode dataSetsNode =
- new DefaultMutableTreeNode("Data Sets");
+ FilterableMutableTreeNode dataSetsNode =
+ new FilterableMutableTreeNode(UiUtilities.DATA_SETS);
node.add(dataSetsNode);
for (DataSet dataSet : dataSets)
{
- dataSetsNode.add(new DefaultMutableTreeNode(Identifier
+ dataSetsNode.add(new FilterableMutableTreeNode(Identifier
.create(dataSet)));
}
}
for (Sample s : samplesDataSets.getSamples())
{
- DefaultMutableTreeNode sampleNode =
- new DefaultMutableTreeNode(Identifier.create(s));
- sampleNode.add(new DefaultMutableTreeNode(
- UiUtilities.WAITING_NODE_LABEL));
+ FilterableMutableTreeNode sampleNode =
+ new FilterableMutableTreeNode(Identifier.create(s));
+ sampleNode.add(UiUtilities.createWaitingNode());
node.add(sampleNode);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
index ad234da86a5a5d7031ac41918f598b3488907267..eb12cd64169b341049c9076f04c15571120d02b9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/DataSetUploadClient.java
@@ -154,13 +154,7 @@ public class DataSetUploadClient extends AbstractSwingGUI
prefs.flush();
} catch (Exception ex)
{
- final JFrame frame = new JFrame(TITLE);
- String message = ex.getMessage();
- if (null == message || message.length() == 0)
- {
- message = ex.toString();
- }
- JOptionPane.showMessageDialog(frame, message, "Error", JOptionPane.ERROR_MESSAGE);
+ UiUtilities.showException(null, ex);
}
}
@@ -187,14 +181,7 @@ public class DataSetUploadClient extends AbstractSwingGUI
newMe.show();
} catch (RuntimeException ex)
{
- final JFrame frame = new JFrame(TITLE);
- frame.setVisible(true);
- String message = ex.getMessage();
- if (null == message || message.length() == 0)
- {
- message = ex.toString();
- }
- JOptionPane.showMessageDialog(frame, message, "Error", JOptionPane.ERROR_MESSAGE);
+ UiUtilities.showException(null, ex);
System.exit(1);
}
}
@@ -210,14 +197,7 @@ public class DataSetUploadClient extends AbstractSwingGUI
newMe.show();
} catch (RuntimeException ex)
{
- final JFrame frame = new JFrame(TITLE);
- frame.setVisible(true);
- String message = ex.getMessage();
- if (null == message || message.length() == 0)
- {
- message = ex.toString();
- }
- JOptionPane.showMessageDialog(frame, message, "Error", JOptionPane.ERROR_MESSAGE);
+ UiUtilities.showException(null, ex);
System.exit(1);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerDialog.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerDialog.java
index 0f73a69bf2a045fa43c421fde576490a67d94a41..ade5d7ac7a95d389505fb627323a20137fcd8e8c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerDialog.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/SamplePickerDialog.java
@@ -19,10 +19,10 @@ package ch.systemsx.cisd.openbis.dss.client.api.gui;
import java.util.List;
import javax.swing.JFrame;
-import javax.swing.tree.DefaultMutableTreeNode;
import ch.systemsx.cisd.openbis.dss.client.api.gui.model.DataSetUploadClientModel;
import ch.systemsx.cisd.openbis.dss.client.api.gui.model.Identifier;
+import ch.systemsx.cisd.openbis.dss.client.api.gui.tree.FilterableMutableTreeNode;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
@@ -44,7 +44,7 @@ public class SamplePickerDialog extends AbstractTreeEntityPickerDialog
}
@Override
- protected void expandNode(final DefaultMutableTreeNode node, Identifier identifier)
+ protected void expandNode(final FilterableMutableTreeNode node, Identifier identifier)
{
AsyncNodeAction<List<Sample>> action =
new AsyncNodeAction<List<Sample>>(tree, node, scheduler)
@@ -55,10 +55,9 @@ public class SamplePickerDialog extends AbstractTreeEntityPickerDialog
node.removeAllChildren();
for (Sample s : samples)
{
- DefaultMutableTreeNode sampleNode =
- new DefaultMutableTreeNode(Identifier.create(s));
- sampleNode.add(new DefaultMutableTreeNode(
- UiUtilities.WAITING_NODE_LABEL));
+ FilterableMutableTreeNode sampleNode =
+ new FilterableMutableTreeNode(Identifier.create(s));
+ sampleNode.add(UiUtilities.createWaitingNode());
node.add(sampleNode);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UiUtilities.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UiUtilities.java
index d4696e15d1aec55423cc6d9d8f1b9109856219c8..03cfa90eab2fcbb509d36692c89b22fe8a1de4c5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UiUtilities.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/UiUtilities.java
@@ -16,11 +16,26 @@
package ch.systemsx.cisd.openbis.dss.client.api.gui;
+import java.awt.BorderLayout;
import java.awt.Color;
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+import java.util.regex.Pattern;
+import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextArea;
+import javax.swing.SwingUtilities;
+import ch.systemsx.cisd.openbis.dss.client.api.gui.model.Identifier;
+import ch.systemsx.cisd.openbis.dss.client.api.gui.tree.FilterableMutableTreeNode;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationError;
/**
@@ -50,5 +65,74 @@ public class UiUtilities
}
}
- static final String WAITING_NODE_LABEL = "Loading data ...";
+ static final String ROOT_SAMPLES = "Samples";
+ static final String ROOT_EXPERIMENTS = "Experiments";
+ static final String DATA_SETS = "Data Sets";
+ private static final String WAITING_NODE_LABEL = "Loading data ...";
+
+ private static final String[] SPECIAL_NODES = {ROOT_EXPERIMENTS, ROOT_SAMPLES, DATA_SETS, WAITING_NODE_LABEL};
+
+ public static boolean isMatchingNode(Object node, Pattern pattern)
+ {
+ for (String specialNode : SPECIAL_NODES)
+ {
+ if (equals(specialNode, node))
+ {
+ return true;
+ }
+ }
+ if (node instanceof FilterableMutableTreeNode)
+ {
+ Object userObject = ((FilterableMutableTreeNode) node).getUserObject();
+ if (userObject instanceof Identifier)
+ {
+ if (((Identifier) userObject).getOwnerType() == DataSetOwnerType.DATA_SET)
+ {
+ return true;
+ }
+ }
+ }
+ return pattern.matcher(node.toString()).find();
+ }
+
+ private static boolean equals(String label, Object object)
+ {
+ return object.toString().equals(label);
+ }
+
+ public static FilterableMutableTreeNode createWaitingNode()
+ {
+ return new FilterableMutableTreeNode(UiUtilities.WAITING_NODE_LABEL);
+ }
+
+ public static void showException(Component parentComponent, final Throwable throwable)
+ {
+ showMessageAndException(parentComponent, throwable, throwable.toString(), "Error");
+ }
+
+ public static void showMessageAndException(Component parentComponent, final Throwable throwable, String message, String title)
+ {
+ final JPanel panel = new JPanel(new BorderLayout(20, 5));
+ panel.add(new JLabel(message), BorderLayout.WEST);
+ JButton button = new JButton("Show Details");
+ button.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ panel.removeAll();
+ JTextArea textArea = new JTextArea(20, 20);
+ textArea.setEditable(false);
+ ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+ throwable.printStackTrace(new PrintStream(byteArrayOutputStream, true));
+ textArea.setText(byteArrayOutputStream.toString());
+ panel.add(textArea, BorderLayout.CENTER);
+ panel.validate();
+ SwingUtilities.getWindowAncestor(panel).pack();
+ }
+ });
+ panel.add(button, BorderLayout.EAST);
+ JOptionPane.showMessageDialog(parentComponent, panel, title, JOptionPane.ERROR_MESSAGE);
+ }
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/model/DataSetUploadClientModel.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/model/DataSetUploadClientModel.java
index dfcdd86a641cf9bc45772bb03224c816257a2a99..f02564db000ffc35d046038510a3fd2abfa37d69 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/model/DataSetUploadClientModel.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/model/DataSetUploadClientModel.java
@@ -23,10 +23,13 @@ import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
+import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.TimeUnit;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleSearchCriteria;
import ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.io.TransmissionSpeedCalculator;
@@ -34,6 +37,7 @@ import ch.systemsx.cisd.common.utilities.ITimeProvider;
import ch.systemsx.cisd.openbis.dss.client.api.gui.model.DataSetUploadClientModel.NewDataSetInfo.Status;
import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.dss.client.api.v3.IOpenbisServiceFacadeV3;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTOBuilder;
@@ -42,6 +46,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.validation.ValidationE
import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetTypeFilter;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
@@ -69,6 +74,8 @@ public class DataSetUploadClientModel
private final IOpenbisServiceFacade openBISService;
+ private final IOpenbisServiceFacadeV3 serviceFacadeV3;
+
private final ITimeProvider timeProvider;
private List<DataSetType> dataSetTypes;
@@ -104,6 +111,7 @@ public class DataSetUploadClientModel
public DataSetUploadClientModel(DssCommunicationState commState, ITimeProvider timeProvider, IUserNotifier userNotifier)
{
this.openBISService = commState.getOpenBISService();
+ serviceFacadeV3 = commState.getServiceFacadeV3();
this.timeProvider = timeProvider;
this.userNotifier = userNotifier;
@@ -327,41 +335,108 @@ public class DataSetUploadClientModel
{
return !openBISService.getSamples(Arrays.asList(identifier)).isEmpty();
}
-
- public void listSamples(final Identifier identifier,
- final IAsyncAction<List<Sample>> action)
+
+ public void listExperiments(IAsyncAction<List<Experiment>> action)
{
- execute(new Runnable()
+ doAsync(new Callable<List<Experiment>>()
{
@Override
- public void run()
+ public List<Experiment> call() throws Exception
{
- try
+ return getOpenBISService().listExperimentsHavingSamplesForProjects(
+ projectIdentifiers);
+ }
+ }, action);
+ }
+
+ public void listSamplesWithNoExperiments(IAsyncAction<List<Sample>> action)
+ {
+ doAsync(new Callable<List<Sample>>()
+ {
+ @Override
+ public List<Sample> call() throws Exception
+ {
+ SampleSearchCriteria criteria = new SampleSearchCriteria();
+ criteria.withoutExperiment();
+ criteria.withType().withListable().setListable(true);
+ List<Sample> result = new ArrayList<>();
+ for (ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample sample :
+ serviceFacadeV3.searchSamples(criteria, new SampleFetchOptions()).getObjects())
{
- List<Sample> samples = new ArrayList<Sample>();
- String permId = identifier.getPermId();
- switch (identifier.getOwnerType())
- {
- case EXPERIMENT:
- loadListableSamples(samples, permId);
- break;
- case SAMPLE:
- loadSamplesLinkedToAnExperiment(samples, permId);
- break;
- default:
- }
- UploadClientSortingUtils.sortSamplesByIdentifier(samples);
- action.performAction(samples);
- } catch (Throwable throwable)
+ Sample.SampleInitializer initializer = new Sample.SampleInitializer();
+ initializer.setIdentifier(sample.getIdentifier().getIdentifier());
+ initializer.setPermId(sample.getPermId().getPermId());
+ initializer.setId(-1l); // dummy value for validation
+ initializer.setCode(sample.getCode());
+ initializer.setSampleTypeCode("dummy"); // dummy value for validation
+ initializer.setSampleTypeId(-1l); // dummy value for validation
+ EntityRegistrationDetails.EntityRegistrationDetailsInitializer detailsInitializer
+ = new EntityRegistrationDetails.EntityRegistrationDetailsInitializer();
+ initializer.setRegistrationDetails(new EntityRegistrationDetails(detailsInitializer));
+ result.add(new Sample(initializer));
+ }
+ return result;
+ }
+ }, action);
+ }
+
+ public void listSamples(final Identifier identifier, final IAsyncAction<List<Sample>> action)
+ {
+ doAsync(new Callable<List<Sample>>()
+ {
+ @Override
+ public List<Sample> call() throws Exception
+ {
+ List<Sample> samples = new ArrayList<Sample>();
+ String permId = identifier.getPermId();
+ switch (identifier.getOwnerType())
{
- action.handleException(throwable);
+ case EXPERIMENT:
+ loadListableSamples(samples, permId);
+ break;
+ case SAMPLE:
+ loadSamplesLinkedToAnExperiment(samples, permId);
+ break;
+ default:
}
+ UploadClientSortingUtils.sortSamplesByIdentifier(samples);
+ return samples;
}
- });
+ }, action);
}
public void listSamplesDataSets(final Identifier identifier, final IAsyncAction<SamplesDataSets> action)
{
+ doAsync(new Callable<SamplesDataSets>()
+ {
+ @Override
+ public SamplesDataSets call() throws Exception
+ {
+ List<Sample> samples = new ArrayList<Sample>();
+ List<DataSet> dataSets = new ArrayList<DataSet>();
+ String permId = identifier.getPermId();
+ switch (identifier.getOwnerType())
+ {
+ case EXPERIMENT:
+ loadListableSamples(samples, permId);
+ dataSets.addAll(openBISService.listDataSetsForExperiment(permId));
+ break;
+ case SAMPLE:
+ loadSamplesLinkedToAnExperiment(samples, permId);
+ dataSets.addAll(openBISService.listDataSetsForSample(permId));
+ break;
+ default:
+ }
+ UploadClientSortingUtils.sortSamplesByIdentifier(samples);
+ UploadClientSortingUtils.sortDataSetsByCode(dataSets);
+ return new SamplesDataSets(samples, dataSets);
+ }
+ }, action);
+ }
+
+ private <T> void doAsync(final Callable<T> action, final IAsyncAction<T> subsequentAction)
+ {
+
execute(new Runnable()
{
@Override
@@ -369,27 +444,10 @@ public class DataSetUploadClientModel
{
try
{
- List<Sample> samples = new ArrayList<Sample>();
- List<DataSet> dataSets = new ArrayList<DataSet>();
- String permId = identifier.getPermId();
- switch (identifier.getOwnerType())
- {
- case EXPERIMENT:
- loadListableSamples(samples, permId);
- dataSets.addAll(openBISService.listDataSetsForExperiment(permId));
- break;
- case SAMPLE:
- loadSamplesLinkedToAnExperiment(samples, permId);
- dataSets.addAll(openBISService.listDataSetsForSample(permId));
- break;
- default:
- }
- UploadClientSortingUtils.sortSamplesByIdentifier(samples);
- UploadClientSortingUtils.sortDataSetsByCode(dataSets);
- action.performAction(new SamplesDataSets(samples, dataSets));
+ subsequentAction.performAction(action.call());
} catch (Throwable throwable)
{
- action.handleException(throwable);
+ subsequentAction.handleException(throwable);
}
}
});
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/model/DssCommunicationState.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/model/DssCommunicationState.java
index b7eb5db0614996eabc33daa58c5c52eb5e79c19a..b57f568928125885e8c1a8f2276e8d74f20e9e5d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/model/DssCommunicationState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/model/DssCommunicationState.java
@@ -23,11 +23,15 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.client.api.v1.IOpenbisServiceFacade;
import ch.systemsx.cisd.openbis.dss.client.api.v1.OpenbisServiceFacadeFactory;
+import ch.systemsx.cisd.openbis.dss.client.api.v3.IOpenbisServiceFacadeV3;
+import ch.systemsx.cisd.openbis.dss.client.api.v3.OpenbisServiceFacadeV3;
public class DssCommunicationState
{
private final IOpenbisServiceFacade openBISService;
+ private final IOpenbisServiceFacadeV3 serviceFacadeV3;
+
private final boolean logoutOnClose;
private static final long CONNECTION_TIMEOUT_MILLIS = 60 * DateUtils.MILLIS_PER_SECOND;
@@ -48,28 +52,27 @@ public class DssCommunicationState
{
case 2:
String sessionToken = args[1];
- openBISService =
- OpenbisServiceFacadeFactory.tryCreate(sessionToken, openBisUrl,
- CONNECTION_TIMEOUT_MILLIS);
- if (null == openBISService)
+ serviceFacadeV3 = OpenbisServiceFacadeV3.tryCreate(sessionToken, openBisUrl, CONNECTION_TIMEOUT_MILLIS);
+ if (null == serviceFacadeV3)
{
throw new ConfigurationFailureException(
"The openBIS File Upload Client was improperly configured -- the session token is not valid. Please talk to the openBIS administrator.");
}
+ openBISService = OpenbisServiceFacadeFactory.tryCreate(sessionToken, openBisUrl, CONNECTION_TIMEOUT_MILLIS);
// Don't logout -- the user wants to keep his/her session token alive.
logoutOnClose = false;
break;
default:
String userName = args[1];
String passwd = args[2];
- openBISService =
- OpenbisServiceFacadeFactory.tryCreate(userName, passwd, openBisUrl,
- CONNECTION_TIMEOUT_MILLIS);
- if (null == openBISService)
+ serviceFacadeV3 = OpenbisServiceFacadeV3.tryCreate(userName, passwd, openBisUrl, CONNECTION_TIMEOUT_MILLIS);
+ if (null == serviceFacadeV3)
{
throw new ConfigurationFailureException(
"The user name / password combination is incorrect.");
}
+ String token = serviceFacadeV3.getSessionToken();
+ openBISService = OpenbisServiceFacadeFactory.tryCreate(token, openBisUrl, CONNECTION_TIMEOUT_MILLIS);
// Do logout on close
logoutOnClose = true;
}
@@ -80,6 +83,11 @@ public class DssCommunicationState
return openBISService;
}
+ public IOpenbisServiceFacadeV3 getServiceFacadeV3()
+ {
+ return serviceFacadeV3;
+ }
+
public boolean isLogoutOnClose()
{
return logoutOnClose;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/tree/FilterableMutableTreeNode.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/tree/FilterableMutableTreeNode.java
index 5d4219b75102996901a94a6f336fa1809493ee4e..d75b50216882d03a721390ec4da699ae3605edb5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/tree/FilterableMutableTreeNode.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/gui/tree/FilterableMutableTreeNode.java
@@ -24,6 +24,8 @@ import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.MutableTreeNode;
import javax.swing.tree.TreeNode;
+import ch.systemsx.cisd.openbis.dss.client.api.gui.UiUtilities;
+
/**
* @author Pawel Glyzewski
*/
@@ -65,7 +67,7 @@ public class FilterableMutableTreeNode extends DefaultMutableTreeNode
while (enumeration.hasMoreElements())
{
final Object tmp = enumeration.nextElement();
- if (pattern.matcher(tmp.toString()).find())
+ if (UiUtilities.isMatchingNode(tmp, pattern))
{
next = tmp;
break;
@@ -95,6 +97,7 @@ public class FilterableMutableTreeNode extends DefaultMutableTreeNode
private synchronized void setPattern(Pattern pattern)
{
this.pattern = pattern;
+ filter(pattern);
}
private synchronized ArrayList<Object> getFiltered()
@@ -120,11 +123,13 @@ public class FilterableMutableTreeNode extends DefaultMutableTreeNode
pattern = Pattern.compile(".*");
}
setPattern(pattern);
-
- filter(pattern);
+ for (int i = 0, n = getChildCount(); i < n; i++)
+ {
+ ((FilterableMutableTreeNode) getChildAt(i)).setPattern(pattern);
+ }
}
- public void filter(@SuppressWarnings("hiding") Pattern pattern)
+ private void filter(@SuppressWarnings("hiding") Pattern pattern)
{
@SuppressWarnings("hiding")
ArrayList<Object> filtered = new ArrayList<Object>();
@@ -133,14 +138,14 @@ public class FilterableMutableTreeNode extends DefaultMutableTreeNode
while (enumeration.hasMoreElements())
{
Object o = enumeration.nextElement();
- if (pattern.matcher(o.toString()).find())
+ if (UiUtilities.isMatchingNode(o, pattern))
{
filtered.add(o);
}
}
setFiltered(filtered);
}
-
+
@Override
public TreeNode getChildAt(int childIndex)
{
@@ -190,11 +195,25 @@ public class FilterableMutableTreeNode extends DefaultMutableTreeNode
{
return new FilteredEnumerationWrapper(super.children(), getPattern());
}
-
+
@Override
public void add(MutableTreeNode o)
{
super.add(o);
+ if (o instanceof FilterableMutableTreeNode)
+ {
+ FilterableMutableTreeNode filterableMutableTreeNode = (FilterableMutableTreeNode) o;
+ filterableMutableTreeNode.setPattern(getPattern());
+ }
+ filter(getPattern());
+ }
+
+ @Override
+ public void removeAllChildren()
+ {
+ super.removeAllChildren();
filter(getPattern());
}
+
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v3/IOpenbisServiceFacadeV3.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v3/IOpenbisServiceFacadeV3.java
new file mode 100644
index 0000000000000000000000000000000000000000..394d0df88ffeaee455105e08cac8e2810f19a043
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v3/IOpenbisServiceFacadeV3.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright 2017 ETH Zuerich, SIS
+ *
+ * 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.v3;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleSearchCriteria;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IOpenbisServiceFacadeV3
+{
+ public String getSessionToken();
+
+ public SearchResult<Sample> searchSamples(SampleSearchCriteria searchCriteria, SampleFetchOptions fetchOptions);
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v3/OpenbisServiceFacadeV3.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v3/OpenbisServiceFacadeV3.java
new file mode 100644
index 0000000000000000000000000000000000000000..4b25d21161a0652d6b8e500ea5274f498b376481
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/client/api/v3/OpenbisServiceFacadeV3.java
@@ -0,0 +1,94 @@
+/*
+ * Copyright 2017 ETH Zuerich, SIS
+ *
+ * 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.v3;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleSearchCriteria;
+import ch.systemsx.cisd.common.api.retry.RetryCaller;
+import ch.systemsx.cisd.common.api.retry.RetryProxyFactory;
+import ch.systemsx.cisd.openbis.common.api.client.ServiceFinder;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class OpenbisServiceFacadeV3 implements IOpenbisServiceFacadeV3
+{
+ public static IOpenbisServiceFacadeV3 tryCreate(final String username, final String password,
+ final String openbisUrl, final long timeoutInMillis)
+ {
+ RetryCaller<IOpenbisServiceFacadeV3, RuntimeException> caller =
+ new RetryCaller<IOpenbisServiceFacadeV3, RuntimeException>()
+ {
+ @Override
+ protected IOpenbisServiceFacadeV3 call()
+ {
+ IApplicationServerApi service = createService(openbisUrl, timeoutInMillis);
+ String sessionToken = service.login(username, password);
+ OpenbisServiceFacadeV3 facade = new OpenbisServiceFacadeV3(sessionToken, service);
+ return RetryProxyFactory.createProxy(facade);
+ }
+ };
+ return caller.callWithRetry();
+ }
+
+ public static IOpenbisServiceFacadeV3 tryCreate(final String sessionToken,
+ final String openbisUrl, final long timeoutInMillis)
+ {
+ RetryCaller<IOpenbisServiceFacadeV3, RuntimeException> caller =
+ new RetryCaller<IOpenbisServiceFacadeV3, RuntimeException>()
+ {
+ @Override
+ protected IOpenbisServiceFacadeV3 call()
+ {
+ IApplicationServerApi service = createService(openbisUrl, timeoutInMillis);
+ OpenbisServiceFacadeV3 facade = new OpenbisServiceFacadeV3(sessionToken, service);
+ return RetryProxyFactory.createProxy(facade);
+ }
+ };
+ return caller.callWithRetry();
+ }
+
+ private static IApplicationServerApi createService(String openbisUrl, long timeoutInMillis)
+ {
+ ServiceFinder serviceFinder = new ServiceFinder("openbis", IApplicationServerApi.SERVICE_URL);
+ return serviceFinder.createService(IApplicationServerApi.class, openbisUrl, timeoutInMillis);
+ }
+
+ private String sessionToken;
+ private IApplicationServerApi service;
+
+ private OpenbisServiceFacadeV3(String sessionToken, IApplicationServerApi service)
+ {
+ this.sessionToken = sessionToken;
+ this.service = service;
+ }
+
+ @Override
+ public String getSessionToken()
+ {
+ return sessionToken;
+ }
+
+ @Override
+ public SearchResult<Sample> searchSamples(SampleSearchCriteria searchCriteria, SampleFetchOptions fetchOptions)
+ {
+ return service.searchSamples(sessionToken, searchCriteria, fetchOptions);
+ }
+}