Java tutorial
/* * This file is part of ADDIS (Aggregate Data Drug Information System). * ADDIS is distributed from http://drugis.org/. * Copyright 2009 Gert van Valkenhoef, Tommi Tervonen. * Copyright 2010 Gert van Valkenhoef, Tommi Tervonen, Tijs Zwinkels, * Maarten Jacobs, Hanno Koeslag, Florin Schimbinschi, Ahmad Kamal, Daniel * Reid. * Copyright 2011 Gert van Valkenhoef, Ahmad Kamal, Daniel Reid, Florin * Schimbinschi. * Copyright 2012 Gert van Valkenhoef, Daniel Reid, Jol Kuiper, Wouter * Reckman. * Copyright 2013 Gert van Valkenhoef, Jol Kuiper. * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package org.drugis.addis.gui.wizard; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.datatransfer.UnsupportedFlavorException; import java.awt.event.ActionEvent; import java.awt.event.KeyEvent; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.FileNotFoundException; import java.io.IOException; import java.lang.reflect.InvocationTargetException; import java.util.ArrayList; import java.util.Date; import java.util.HashSet; import java.util.LinkedList; import java.util.List; import java.util.Set; import javax.swing.AbstractAction; import javax.swing.BorderFactory; import javax.swing.BoxLayout; import javax.swing.DefaultListCellRenderer; import javax.swing.DropMode; import javax.swing.ImageIcon; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDialog; import javax.swing.JLabel; import javax.swing.JList; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JTable; import javax.swing.JTextField; import javax.swing.JTextPane; import javax.swing.KeyStroke; import javax.swing.ListSelectionModel; import javax.swing.SwingUtilities; import javax.swing.TransferHandler; import javax.swing.border.Border; import javax.swing.event.CaretEvent; import javax.swing.event.CaretListener; import javax.swing.event.ListDataEvent; import javax.swing.event.ListDataListener; import javax.swing.event.ListSelectionEvent; import javax.swing.event.ListSelectionListener; import javax.swing.event.TableModelEvent; import javax.swing.event.TableModelListener; import javax.swing.table.DefaultTableCellRenderer; import javax.swing.table.TableModel; import javax.swing.text.BadLocationException; import javax.swing.text.DefaultFormatter; import javax.swing.text.Style; import javax.swing.text.StyleConstants; import javax.swing.text.StyleContext; import javax.swing.text.StyledDocument; import org.apache.commons.math3.util.Pair; import org.drugis.addis.FileNames; import org.drugis.addis.entities.AdverseEvent; import org.drugis.addis.entities.Arm; import org.drugis.addis.entities.BasicStudyCharacteristic; import org.drugis.addis.entities.Endpoint; import org.drugis.addis.entities.Epoch; import org.drugis.addis.entities.Indication; import org.drugis.addis.entities.Note; import org.drugis.addis.entities.ObjectWithNotes; import org.drugis.addis.entities.PopulationCharacteristic; import org.drugis.addis.entities.PubMedIdList; import org.drugis.addis.entities.Source; import org.drugis.addis.entities.Study; import org.drugis.addis.entities.StudyActivity; import org.drugis.addis.entities.StudyOutcomeMeasure; import org.drugis.addis.entities.TypeWithNotes; import org.drugis.addis.gui.AddisWindow; import org.drugis.addis.gui.AuxComponentFactory; import org.drugis.addis.gui.CategoryKnowledgeFactory; import org.drugis.addis.gui.GUIFactory; import org.drugis.addis.gui.Main; import org.drugis.addis.gui.builder.StudyView; import org.drugis.addis.gui.components.ComboBoxPopupOnFocusListener; import org.drugis.addis.gui.components.MeasurementTable; import org.drugis.addis.gui.components.NotesView; import org.drugis.addis.gui.util.ComboBoxSelectionModel; import org.drugis.addis.gui.util.NonEmptyValueModel; import org.drugis.addis.imports.PubMedIDRetriever; import org.drugis.addis.presentation.AbstractListValidator; import org.drugis.addis.presentation.DurationPresentation; import org.drugis.addis.presentation.ModifiableHolder; import org.drugis.addis.presentation.StudyActivitiesTableModel; import org.drugis.addis.presentation.ValueHolder; import org.drugis.addis.presentation.wizard.AddArmsPresentation; import org.drugis.addis.presentation.wizard.AddEpochsPresentation; import org.drugis.addis.presentation.wizard.AddStudyWizardPresentation; import org.drugis.addis.presentation.wizard.AddStudyWizardPresentation.OutcomeMeasurementsModel; import org.drugis.addis.presentation.wizard.StudyActivityPresentation; import org.drugis.addis.util.PubMedListFormat; import org.drugis.addis.util.RunnableReadyModel; import org.drugis.common.beans.ContentAwareListModel; import org.drugis.common.gui.ErrorDialog; import org.drugis.common.gui.LayoutUtil; import org.drugis.common.gui.TextComponentFactory; import org.drugis.common.validation.BooleanAndModel; import org.drugis.common.validation.BooleanNotModel; import org.pietschy.wizard.AbstractWizardModel; import org.pietschy.wizard.PanelWizardStep; import org.pietschy.wizard.Wizard; import org.pietschy.wizard.WizardEvent; import org.pietschy.wizard.WizardListener; import org.pietschy.wizard.models.StaticModel; import com.jgoodies.binding.PresentationModel; import com.jgoodies.binding.adapter.BasicComponentFactory; import com.jgoodies.binding.adapter.Bindings; import com.jgoodies.binding.beans.PropertyAdapter; import com.jgoodies.binding.beans.PropertyConnector; import com.jgoodies.binding.list.ObservableList; import com.jgoodies.binding.value.AbstractValueModel; import com.jgoodies.binding.value.ValueModel; import com.jgoodies.forms.builder.ButtonBarBuilder2; import com.jgoodies.forms.builder.PanelBuilder; import com.jgoodies.forms.layout.CellConstraints; import com.jgoodies.forms.layout.FormLayout; import com.toedter.calendar.JDateChooser; @SuppressWarnings("serial") public class AddStudyWizard extends Wizard { private static final String EXAMPLE_NCT_ID = "NCT00296517"; public static final String INSERT_EXAMPLE_ID = "control I"; public AddStudyWizard(final AddStudyWizardPresentation pm, final AddisWindow mainWindow, JDialog dialog) { super(buildModel(pm, mainWindow, dialog)); setDefaultExitMode(Wizard.EXIT_ON_FINISH); addWizardListener(new WizardListener() { public void wizardClosed(WizardEvent e) { mainWindow.leftTreeFocus(pm.saveStudy()); } public void wizardCancelled(WizardEvent e) { mainWindow.leftTreeFocus(pm.getOldStudy()); } }); setOverviewVisible(false); } private static AbstractWizardModel buildModel(final AddStudyWizardPresentation pm, AddisWindow mainWindow, JDialog dialog) { StaticModel wizardModel = new StaticModel(); wizardModel.add(new EnterIdTitleWizardStep(dialog, pm)); wizardModel.add(new SelectIndicationWizardStep(pm, mainWindow)); wizardModel.add(new EnterCharacteristicsWizardStep(pm)); wizardModel.add(new AddArmsWizardStep(dialog, pm.getAddArmsModel())); wizardModel.add(new AddEpochsWizardStep(dialog, pm.getAddEpochsModel())); wizardModel.add(new AssignActivitiesWizardStep(dialog, pm, mainWindow)); wizardModel.add(new SelectEndpointWizardStep(dialog, pm)); wizardModel.add(new SetEndpointMeasurementsWizardStep(dialog, pm)); wizardModel.add(new SelectAdverseEventWizardStep(dialog, pm)); wizardModel.add(new SetAdverseEventMeasurementsWizardStep(dialog, pm)); wizardModel.add(new SelectPopulationCharsWizardStep(dialog, pm)); wizardModel.add(new SetPopulationCharMeasurementsWizardStep(dialog, pm)); wizardModel.add(new ReviewStudyStep(dialog, pm, mainWindow)); wizardModel.setLastVisible(false); // The measurements + variable lists are saved on viewing the measurement tables // unless this is changed, skipping steps should be disabled. return wizardModel; } // FIXME: should probably be in presentation private static ObjectWithNotes<?> getCharWithNotes(Study newStudy, BasicStudyCharacteristic schar) { ObjectWithNotes<?> charWithNotes = newStudy.getCharacteristicWithNotes(schar); if (charWithNotes == null) { newStudy.setCharacteristic(schar, null); charWithNotes = newStudy.getCharacteristicWithNotes(schar); } return charWithNotes; } static NotesView buildNotesEditor(TypeWithNotes obj) { return buildNotesEditor(obj.getNotes()); } static NotesView buildNotesEditor(ObservableList<Note> notes) { return new NotesView(notes, true); } // -- Wizard Steps public static class AddArmsWizardStep extends AddListItemsWizardStep<Arm> { public AddArmsWizardStep(JDialog dialog, AddArmsPresentation pm) { super("Add arms", "Enter the arms for this study.", pm, dialog); } @Override protected void addAdditionalFields(PanelBuilder builder, CellConstraints cc, int rows, int idx) { builder.addLabel("Size: ", cc.xy(7, rows)); JTextField sizeField = BasicComponentFactory.createFormattedTextField( new PresentationModel<Arm>(d_pm.getList().get(idx)).getModel(Arm.PROPERTY_SIZE), new DefaultFormatter()); sizeField.setColumns(4); builder.add(sizeField, cc.xy(9, rows)); } } public static class AddEpochsWizardStep extends AddListItemsWizardStep<Epoch> { public AddEpochsWizardStep(JDialog dialog, AddEpochsPresentation pm) { super("Add epochs", "Enter the epochs for this study.", pm, dialog); rebuild(); } @Override protected void addAdditionalFields(PanelBuilder builder, CellConstraints cc, int rows, int idx) { DurationPresentation<Epoch> durationModel = ((AddEpochsPresentation) d_pm).getDurationModel(idx); ValueModel definedModel = new PropertyAdapter<DurationPresentation<Epoch>>(durationModel, DurationPresentation.PROPERTY_DEFINED, true); JPanel panel = new JPanel(); panel.add(new JLabel("Duration: ")); // defined/undefined radio buttons panel.add(BasicComponentFactory.createRadioButton(definedModel, true, "Known")); panel.add(BasicComponentFactory.createRadioButton(definedModel, false, "Unknown")); // duration quantity input final JTextField quantityField = BasicComponentFactory .createFormattedTextField(new PropertyAdapter<DurationPresentation<Epoch>>(durationModel, DurationPresentation.PROPERTY_DURATION_QUANTITY, true), new DefaultFormatter()); quantityField.setColumns(4); Bindings.bind(quantityField, "enabled", definedModel); panel.add(quantityField); // duration units input final JComboBox unitsField = AuxComponentFactory.createBoundComboBox( DurationPresentation.DateUnits.values(), new PropertyAdapter<DurationPresentation<Epoch>>( durationModel, DurationPresentation.PROPERTY_DURATION_UNITS, true)); Bindings.bind(unitsField, "enabled", definedModel); panel.add(unitsField); builder.add(panel, cc.xy(7, rows)); } } public static class AssignActivitiesWizardStep extends PanelWizardStep { public final static class ActivitiesCompleteValidator extends AbstractListValidator<StudyActivity> { public ActivitiesCompleteValidator(ObservableList<StudyActivity> list) { super(new ContentAwareListModel<StudyActivity>(list)); } @Override public boolean validate() { for (StudyActivity act : d_list) { if (!act.isComplete()) { return false; } } return true; } } public final static class AllActivitiesUsedValidator extends AbstractListValidator<StudyActivity> { public AllActivitiesUsedValidator(ObservableList<StudyActivity> list) { super(new ContentAwareListModel<StudyActivity>(list)); } @Override public boolean validate() { for (StudyActivity act : d_list) { if (act.getUsedBy().isEmpty()) { return false; } } return true; } } public final static class TableFilledValidator extends AbstractValueModel implements ValueHolder<Boolean> { private final StudyActivitiesTableModel d_tableModel; private boolean d_value; public TableFilledValidator(StudyActivitiesTableModel table) { d_tableModel = table; d_tableModel.addTableModelListener(new TableModelListener() { @Override public void tableChanged(TableModelEvent e) { update(); } }); update(); } private void update() { boolean oldValue = d_value; d_value = validate(); fireValueChange(oldValue, d_value); } private boolean validate() { for (int row = 0; row < d_tableModel.getRowCount(); ++row) { for (int col = 0; col < d_tableModel.getColumnCount(); ++col) { if (d_tableModel.getValueAt(row, col) == null) { return false; } } } return true; } @Override public Boolean getValue() { return d_value; } @Override public void setValue(Object newValue) { throw new IllegalAccessError("TableFilledFilledValidator is read-only"); } } private PanelBuilder d_builder; private JScrollPane d_scrollPane; private AddStudyWizardPresentation d_pm; private List<Pair<String, ValueModel>> d_validators = new ArrayList<Pair<String, ValueModel>>(); public JTable armsEpochsTable; private final JDialog d_parent; private AddisWindow d_mainWindow; private static DataFlavor s_studyActivityFlavor = createFlavor(); private JList d_activityList; private StudyActivitiesTableModel d_tableModel; private BooleanAndModel d_readyValidator; private static DataFlavor createFlavor() { try { return new DataFlavor( DataFlavor.javaJVMLocalObjectMimeType + ";class=" + StudyActivity.class.getCanonicalName()); } catch (ClassNotFoundException e) { throw new RuntimeException(e); } } public AssignActivitiesWizardStep(JDialog parent, AddStudyWizardPresentation pm, AddisWindow mainWindow) { super("Assign activities", "Drag activities to their proper combination of (arm, epoch). Incomplete activities are shown in red."); d_parent = parent; d_mainWindow = mainWindow; d_pm = pm; } private void addValidator(String warning, ValueModel validator) { d_validators.add(new Pair<String, ValueModel>(warning, validator)); } @Override public void prepare() { this.setVisible(false); d_tableModel = new StudyActivitiesTableModel(d_pm.getNewStudyPM().getBean()); d_validators.clear(); addValidator("Some activities have missing data", new ActivitiesCompleteValidator(d_pm.getNewStudyPM().getBean().getStudyActivities())); addValidator("Not all cells in the table are filled in", new TableFilledValidator(d_tableModel)); addValidator("Not all the activities are used", new AllActivitiesUsedValidator(d_pm.getNewStudyPM().getBean().getStudyActivities())); List<ValueModel> validators = new ArrayList<ValueModel>(); for (Pair<String, ValueModel> validator : d_validators) { validators.add(validator.getValue()); } d_readyValidator = new BooleanAndModel(validators); PropertyConnector.connectAndUpdate(d_readyValidator, this, "complete"); if (d_scrollPane != null) remove(d_scrollPane); buildWizardStep(); this.setVisible(true); repaint(); } private void buildWizardStep() { FormLayout layout = new FormLayout("fill:pref, 7dlu, fill:pref:grow", "p, 3dlu, p, 3dlu, p, 3dlu, p, 3dlu, p, 3dlu, p, 3dlu, p"); d_builder = new PanelBuilder(layout); d_builder.setDefaultDialogBorder(); CellConstraints cc = new CellConstraints(); // add labels d_builder.addLabel("Activities: ", cc.xy(1, 1)); d_builder.addLabel("Arms and Epochs: ", cc.xy(3, 1)); Study study = d_pm.getNewStudyPM().getBean(); ContentAwareListModel<StudyActivity> dataModel = new ContentAwareListModel<StudyActivity>( study.getStudyActivities()); dataModel.addListDataListener(new ListDataListener() { public void intervalRemoved(ListDataEvent e) { d_tableModel.fireTableDataChanged(); revalidate(); } public void intervalAdded(ListDataEvent e) { d_tableModel.fireTableDataChanged(); revalidate(); } public void contentsChanged(ListDataEvent e) { d_tableModel.fireTableDataChanged(); revalidate(); } }); d_activityList = new JList(dataModel); d_activityList.setDragEnabled(true); d_activityList.setTransferHandler(new TransferHandler() { @Override public int getSourceActions(JComponent c) { return COPY; } @Override protected Transferable createTransferable(final JComponent c) { return new Transferable() { private Object d_value = ((JList) c).getSelectedValue(); public boolean isDataFlavorSupported(DataFlavor flavor) { return flavor.equals(s_studyActivityFlavor); } public DataFlavor[] getTransferDataFlavors() { return new DataFlavor[] { s_studyActivityFlavor }; } public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException { if (!isDataFlavorSupported(flavor)) { throw new UnsupportedFlavorException(flavor); } return d_value; } }; } }); d_activityList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); d_activityList.setLayoutOrientation(JList.VERTICAL); d_activityList.setCellRenderer(new DefaultListCellRenderer() { public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) { StudyActivity sa = (StudyActivity) value; JComponent listCellRendererComponent = (JComponent) super.getListCellRendererComponent(list, sa.getName(), index, isSelected, cellHasFocus); if (!sa.isComplete()) { listCellRendererComponent.setBorder(BorderFactory.createLineBorder(Color.RED)); listCellRendererComponent.setForeground(Color.RED); } return listCellRendererComponent; } }); JScrollPane activityScrollPane = new JScrollPane(d_activityList); activityScrollPane.setPreferredSize(new Dimension(200, 300)); d_builder.add(activityScrollPane, cc.xy(1, 3)); createArmsAndEpochsTable(cc); createButtons(cc, d_activityList); this.setLayout(new BorderLayout()); d_scrollPane = new JScrollPane(d_builder.getPanel()); d_scrollPane.getVerticalScrollBar().setUnitIncrement(16); add(d_scrollPane, BorderLayout.CENTER); JPanel validationPanel = new JPanel(); validationPanel.setLayout(new BoxLayout(validationPanel, BoxLayout.Y_AXIS)); for (Pair<String, ValueModel> x : d_validators) { validationPanel.add(createValidationLabel(x.getKey(), x.getValue())); } d_builder.add(validationPanel, cc.xy(3, 11)); JComponent note = buildTip( "The study activities encode precisely what happened in each arm (patient group), during each epoch (phase of the study). " + "To create a valid study design, please add an activity to each cell of the arms and epochs table above." + "You should also make sure that each activity is completely specified and used in the study design."); d_builder.add(note, cc.xyw(1, 13, 3)); } private JComponent createValidationLabel(String message, ValueModel validModel) { JLabel label = new JLabel(message); label.setForeground(Color.RED); label.setFont(label.getFont().deriveFont(Font.BOLD)); Bindings.bind(label, "visible", new BooleanNotModel(validModel)); return label; } private void createArmsAndEpochsTable(CellConstraints cc) { final JTable armsEpochsTable = new JTable(d_tableModel); armsEpochsTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); for (int i = 0; i < armsEpochsTable.getColumnCount(); i++) { armsEpochsTable.getColumnModel().getColumn(i).setMinWidth(100); } armsEpochsTable.getTableHeader().setReorderingAllowed(false); armsEpochsTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); armsEpochsTable.setDropMode(DropMode.ON_OR_INSERT_COLS); TransferHandler transferHandler = new TransferHandler() { public boolean canImport(TransferSupport support) { if (!support.isDrop()) { return false; } if (!support.isDataFlavorSupported(s_studyActivityFlavor)) { return false; } if (support.getDropLocation() instanceof JTable.DropLocation) { // drop to table cell return ((JTable.DropLocation) support.getDropLocation()).getColumn() > 0; } if (support.getDropLocation() instanceof TransferHandler.DropLocation) { // drop to table header return getHeaderColumnIndex(support.getDropLocation()) > 0; } return false; } private int getHeaderColumnIndex(TransferHandler.DropLocation dl) { return armsEpochsTable.getTableHeader().getColumnModel().getColumnIndexAtX(dl.getDropPoint().x); } public boolean importData(TransferSupport support) { if (!canImport(support)) { return false; } StudyActivity data; try { data = (StudyActivity) support.getTransferable().getTransferData(s_studyActivityFlavor); } catch (UnsupportedFlavorException e) { return false; } catch (IOException e) { return false; } if (support.getDropLocation() instanceof JTable.DropLocation) { // drop to table cell JTable.DropLocation dl = (JTable.DropLocation) support.getDropLocation(); d_tableModel.setValueAt(data, dl.getRow(), dl.getColumn()); return true; } else { // drop to table header int columnIndex = getHeaderColumnIndex(support.getDropLocation()); for (int i = 0; i < armsEpochsTable.getRowCount(); i++) { d_tableModel.setValueAt(data, i, columnIndex); } return true; } } }; armsEpochsTable.setTransferHandler(transferHandler); armsEpochsTable.getTableHeader().setTransferHandler(transferHandler); armsEpochsTable.setDefaultRenderer(StudyActivity.class, new DefaultTableCellRenderer() { @Override public Component getTableCellRendererComponent(JTable table, Object value, boolean arg2, boolean arg3, int arg4, int arg5) { String strValue = value == null ? "" : ((StudyActivity) value).getName(); return super.getTableCellRendererComponent(table, strValue, arg2, arg3, arg4, arg5); } }); JScrollPane tableScrollPane = new JScrollPane(armsEpochsTable); d_builder.add(tableScrollPane, cc.xywh(3, 3, 1, 5)); } private void createButtons(CellConstraints cc, JList activities) { final JButton newButton = new JButton("New Activity"); final JButton editButton = new JButton("Edit Activity"); final JButton removeButton = new JButton("Remove Activity"); // make sure edit and remove are only enabled when anything is selected. editButton.setEnabled(activities.getSelectedIndex() >= 0); removeButton.setEnabled(activities.getSelectedIndex() >= 0); activities.addListSelectionListener(new ListSelectionListener() { public void valueChanged(ListSelectionEvent e) { boolean anySelected = ((JList) (e.getSource())).getSelectedIndex() >= 0; editButton.setEnabled(anySelected); removeButton.setEnabled(anySelected); } }); d_builder.add(newButton, cc.xy(1, 5)); newButton.addActionListener(new AbstractAction() { public void actionPerformed(ActionEvent e) { AddStudyActivityDialog addStudyActivityDialog = new AddStudyActivityDialog(d_parent, d_mainWindow, new StudyActivityPresentation(getStudyActivities(), d_pm.getDrugsModel())); addStudyActivityDialog.setLocationRelativeTo(d_parent); addStudyActivityDialog.setVisible(true); } }); d_builder.add(editButton, cc.xy(1, 7)); editButton.addActionListener(new AbstractAction() { public void actionPerformed(ActionEvent e) { AddStudyActivityDialog addStudyActivityDialog = new AddStudyActivityDialog(d_parent, d_mainWindow, new StudyActivityPresentation(getStudyActivities(), d_pm.getDrugsModel(), getStudyActivities().get(d_activityList.getSelectedIndex()))); addStudyActivityDialog.setLocationRelativeTo(d_parent); addStudyActivityDialog.setVisible(true); } }); d_builder.add(removeButton, cc.xy(1, 9)); removeButton.addActionListener(new AbstractAction() { public void actionPerformed(ActionEvent e) { Study study = d_pm.getNewStudyPM().getBean(); StudyActivity studyActivity = d_pm.getNewStudyPM().getBean().getStudyActivities() .get(d_activityList.getSelectedIndex()); StudyActivity activity = study.findStudyActivity(studyActivity.getName()); study.getStudyActivities().remove(activity); } }); } private ObservableList<StudyActivity> getStudyActivities() { return d_pm.getNewStudyPM().getBean().getStudyActivities(); } } public static class ReviewStudyStep extends PanelWizardStep { private final AddStudyWizardPresentation d_pm; private final AddisWindow d_mainwindow; private final JDialog d_dialog; public ReviewStudyStep(JDialog dialog, AddStudyWizardPresentation pm, AddisWindow mainWindow) { super("Review study", "Please review the study to be created. " + "You can go back through the wizard to correct any mistakes, " + "but after the study has been added it cannot be changed."); d_pm = pm; d_mainwindow = mainWindow; d_dialog = dialog; setLayout(new BorderLayout()); setComplete(true); } @Override public void prepare() { StudyView view = new StudyView(d_pm.getNewStudyPM(), d_pm.getDomain(), d_dialog, d_mainwindow.getPresentationModelFactory()); removeAll(); add(view.buildPanel(), BorderLayout.CENTER); this.setVisible(true); } } public static class SetMeasurementsWizardStep extends PanelWizardStep { private JScrollPane d_scrollPane; private OutcomeMeasurementsModel d_model; private JDialog d_dialog; private MeasurementTable d_table; public SetMeasurementsWizardStep(AddStudyWizardPresentation pm, String title, String description, OutcomeMeasurementsModel model, JDialog dialog) { super(title, description); d_model = model; d_dialog = dialog; setComplete(true); } @Override public void prepare() { this.setVisible(false); if (d_scrollPane != null) { remove(d_scrollPane); } buildWizardStep(); this.setVisible(true); repaint(); setComplete(true); } private void buildWizardStep() { this.setLayout(new BorderLayout()); TableModel tableModel = d_model.getMeasurementTableModel(); d_table = new MeasurementTable(tableModel, d_dialog); d_scrollPane = new JScrollPane(d_table); d_scrollPane.getVerticalScrollBar().setUnitIncrement(16); add(d_scrollPane, BorderLayout.CENTER); } } public static class SetEndpointMeasurementsWizardStep extends SetMeasurementsWizardStep { public SetEndpointMeasurementsWizardStep(JDialog dialog, AddStudyWizardPresentation pm) { super(pm, "Set Measurements", "Please enter the measurements for all arm-endpoint combinations.", pm.getEndpointsModel(), dialog); } } public static class SetAdverseEventMeasurementsWizardStep extends SetMeasurementsWizardStep { public SetAdverseEventMeasurementsWizardStep(JDialog dialog, AddStudyWizardPresentation pm) { super(pm, "Input adverse event data", "Please enter the measurements for all arm-event combinations.", pm.getAdverseEventsModel(), dialog); } } public static class SetPopulationCharMeasurementsWizardStep extends SetMeasurementsWizardStep { public SetPopulationCharMeasurementsWizardStep(JDialog dialog, AddStudyWizardPresentation pm) { super(pm, "Input population data", "Please enter the measurements for all population baseline characteristics.", pm.getPopulationCharsModel(), dialog); } } public static class SelectEndpointWizardStep extends SelectFromOutcomeMeasureListWizardStep<Endpoint> { public SelectEndpointWizardStep(JDialog parent, AddStudyWizardPresentation pm) { super(parent, pm.getEndpointSelectModel(), pm.getAddEpochsModel()); } @Override protected int createAdditionalComponents(ModifiableHolder<Endpoint> slot, PanelBuilder builder, FormLayout layout, int row) { row = LayoutUtil.addRow(layout, row); StudyOutcomeMeasure<Endpoint> som = (StudyOutcomeMeasure<Endpoint>) slot; PropertyAdapter<StudyOutcomeMeasure<Endpoint>> primaryModel = new PropertyAdapter<StudyOutcomeMeasure<Endpoint>>( som, StudyOutcomeMeasure.PROPERTY_IS_PRIMARY, true); JCheckBox primaryCB = BasicComponentFactory.createCheckBox(primaryModel, "Primary endpoint"); builder.add(primaryCB, (new CellConstraints()).xy(5, row)); return row; } } public static class SelectPopulationCharsWizardStep extends SelectFromOutcomeMeasureListWizardStep<PopulationCharacteristic> { public SelectPopulationCharsWizardStep(JDialog parent, AddStudyWizardPresentation pm) { super(parent, pm.getPopulationCharSelectModel(), pm.getAddEpochsModel()); } } public static class SelectAdverseEventWizardStep extends SelectFromOutcomeMeasureListWizardStep<AdverseEvent> { protected SelectAdverseEventWizardStep(JDialog parent, AddStudyWizardPresentation pm) { super(parent, pm.getAdverseEventSelectModel(), pm.getAddEpochsModel()); } } public static class EnterCharacteristicsWizardStep extends PanelWizardStep { JPanel d_me = this; private PanelBuilder d_builder; private JScrollPane d_scrollPane; private Set<BasicStudyCharacteristic> excludedChars = new HashSet<BasicStudyCharacteristic>(); private AddStudyWizardPresentation d_pm; public EnterCharacteristicsWizardStep(AddStudyWizardPresentation pm) { super("Enter additional information", "Enter additional information for this study. " + "Fields may be left empty if unknown."); excludedChars.add(BasicStudyCharacteristic.TITLE); excludedChars.add(BasicStudyCharacteristic.CREATION_DATE); excludedChars.add(BasicStudyCharacteristic.SOURCE); d_pm = pm; setComplete(true); } @Override public void prepare() { if (d_scrollPane != null) remove(d_scrollPane); buildWizardStep(); repaint(); } private void buildWizardStep() { FormLayout layout = new FormLayout("right:pref, 3dlu, fill:pref:grow, 3dlu, pref", "p, 3dlu, p"); d_builder = new PanelBuilder(layout); d_builder.setDefaultDialogBorder(); CellConstraints cc = new CellConstraints(); buildCharacteristicsPart(3, d_builder, cc, 1, layout); JPanel panel = d_builder.getPanel(); this.setLayout(new BorderLayout()); d_scrollPane = new JScrollPane(panel); d_scrollPane.getVerticalScrollBar().setUnitIncrement(16); add(d_scrollPane, BorderLayout.CENTER); } private int buildCharacteristicsPart(int fullWidth, PanelBuilder builder, CellConstraints cc, int row, FormLayout layout) { for (BasicStudyCharacteristic c : BasicStudyCharacteristic.values()) { if (!excludedChars.contains(c)) { // add characteristic field builder.addLabel(c.getDescription() + ":", cc.xy(1, row)); builder.add(createCharacteristicComponent(c), cc.xyw(3, row, fullWidth)); // add note field LayoutUtil.addRow(layout); row += 2; builder.add(buildNotesEditor(getCharWithNotes(d_pm.getNewStudyPM().getBean(), c)), cc.xy(3, row)); LayoutUtil.addRow(layout); row += 2; } } return row; } private JComponent createCharacteristicComponent(BasicStudyCharacteristic c) { JComponent component = null; if (c.getValueType() != null) { if (c.getValueType().equals(String.class)) { ValueModel model = d_pm.getCharacteristicModel(c); component = TextComponentFactory.createTextArea(model, true); } else if (c.getValueType().equals(Integer.class)) { component = AuxComponentFactory .createNonNegativeIntegerTextField(d_pm.getCharacteristicModel(c)); } else if (c.getValueType().equals(Date.class)) { ValueModel mvmodel = d_pm.getCharacteristicModel(c); JDateChooser chooser = new JDateChooser(); PropertyConnector.connectAndUpdate(mvmodel, chooser, "date"); component = chooser; } else if (PubMedIdList.class.isAssignableFrom(c.getValueType())) { ValueModel model = d_pm.getCharacteristicModel(c); component = createPubMedIDComponent(model); } else { if (c.getValueType().isEnum()) { try { component = createOptionsComboBox(c, c.getValueType().getEnumConstants()); } catch (Exception e) { component = new JLabel("ILLEGAL CHARACTERISTIC ENUM TYPE"); } } else { throw new RuntimeException("unknown characteristic type"); } } } return component; } private class PubMedIdsRetriever implements Runnable { private final JButton d_importButton; public PubMedIdsRetriever(JButton importButton) { d_importButton = importButton; } public void run() { String studyID = d_pm.getIdModel().getValue().toString().trim(); try { d_importButton.setEnabled(false); PubMedIdList importPubMedID = new PubMedIDRetriever() .importPubMedID(studyID.replace(" ", "%20")); if (!importPubMedID.isEmpty()) { d_pm.getCharacteristicModel(BasicStudyCharacteristic.PUBMED).setValue(importPubMedID); } else { JOptionPane.showMessageDialog(d_me, "The Study ID (" + studyID + ")\nhas no PubMed ID associated", "Warning", JOptionPane.WARNING_MESSAGE); } d_importButton.setEnabled(true); } catch (IOException e) { ErrorDialog.showDialog(e, "Couldn't retrieve PubMed ID", "Error reading from PubMed: " + e.toString(), false); } } } private JComponent createPubMedIDComponent(ValueModel model) { JTextField inputField = BasicComponentFactory.createFormattedTextField(model, new PubMedListFormat()); inputField.setColumns(30); inputField.setToolTipText("You can enter multiple PubMed IDs delimited by comma"); final JButton d_importButton = GUIFactory.createIconButton(FileNames.ICON_SEARCH, "Search PubMed ID based on the trial ID"); d_importButton.setDisabledIcon(Main.IMAGELOADER.getIcon(FileNames.ICON_LOADING)); d_importButton.addActionListener(new AbstractAction() { public void actionPerformed(ActionEvent arg0) { PubMedIdsRetriever pubMedRetriever = new PubMedIdsRetriever(d_importButton); RunnableReadyModel readyModel = new RunnableReadyModel(pubMedRetriever); new Thread(readyModel).start(); } }); PanelBuilder builder = new PanelBuilder(new FormLayout("pref:grow, 3dlu, pref", "p")); CellConstraints cc = new CellConstraints(); builder.add(inputField, cc.xy(1, 1)); builder.add(d_importButton, cc.xy(3, 1)); return builder.getPanel(); } private <E> JComponent createOptionsComboBox(BasicStudyCharacteristic c, E[] options) { ValueModel selectionHolder = d_pm.getCharacteristicModel(c); JComboBox component = AuxComponentFactory.createBoundComboBox(options, selectionHolder); ComboBoxPopupOnFocusListener.add(component); return component; } } public static class SelectIndicationWizardStep extends PanelWizardStep { private PanelBuilder d_builder; private BooleanAndModel d_validator = new BooleanAndModel(); private JScrollPane d_scrollPane; private AddStudyWizardPresentation d_pm; private AddisWindow d_mainWindow; public SelectIndicationWizardStep(AddStudyWizardPresentation pm, AddisWindow mainWindow) { super("Select Indication", "Select the indication for this study. " + "An indication must be selected to continue."); d_pm = pm; d_mainWindow = mainWindow; if (d_pm.isEditing()) setComplete(true); } @Override public void prepare() { this.setVisible(false); PropertyConnector.connectAndUpdate(d_validator, this, "complete"); if (d_scrollPane != null) remove(d_scrollPane); buildWizardStep(); this.setVisible(true); repaint(); } public void buildWizardStep() { FormLayout layout = new FormLayout("right:pref, 3dlu, pref:grow:fill, 3dlu, left:pref", "p, 3dlu, p, 3dlu, p, 3dlu, p, 3dlu, p, 3dlu, p"); d_builder = new PanelBuilder(layout); d_builder.setDefaultDialogBorder(); CellConstraints cc = new CellConstraints(); d_builder.addLabel("Indication", cc.xy(1, 3)); JComboBox indBox = AuxComponentFactory.createBoundComboBox(d_pm.getIndicationsModel(), d_pm.getIndicationModel(), true); if (d_pm.getIndicationsModel().size() == 1 && indBox.getSelectedIndex() < 0) { indBox.setSelectedIndex(0); } d_builder.add(indBox, cc.xyw(3, 3, 2)); d_validator.add(new NonEmptyValueModel(new ComboBoxSelectionModel(indBox))); // (new) '+' button JButton btn = GUIFactory.createPlusButton("Create Indication"); d_builder.add(btn, cc.xy(5, 3)); btn.addActionListener(new AbstractAction() { public void actionPerformed(ActionEvent arg0) { d_mainWindow.showAddDialog(CategoryKnowledgeFactory.getCategoryKnowledge(Indication.class), d_pm.getIndicationModel()); prepare(); } }); // add note d_builder.add(buildNotesEditor(d_pm.getNewStudyPM().getBean().getIndicationWithNotes()), cc.xy(3, 5)); this.setLayout(new BorderLayout()); d_scrollPane = new JScrollPane(d_builder.getPanel()); d_scrollPane.getVerticalScrollBar().setUnitIncrement(16); add(d_scrollPane, BorderLayout.CENTER); } } public static class EnterIdTitleWizardStep extends PanelWizardStep { JPanel d_me = this; private JTextField d_idField; private JComponent d_titleField; private PanelBuilder d_builder; private JButton d_importButton; private List<ValueModel> d_validators = new LinkedList<ValueModel>(); private JScrollPane d_scrollPane; private AddStudyWizardPresentation d_pm; private JCheckBox d_withResultsCheckBox; private class IdStepValidator extends NonEmptyValueModel { public IdStepValidator(ValueModel idModel) { super(idModel); } @Override public Boolean getValue() { return super.getValue() && d_pm.isIdAvailable(); } } public EnterIdTitleWizardStep(JDialog dialog, AddStudyWizardPresentation pm) { super("Select ID and Title", "Set the ID and title of the study. Studies can also be extracted from Clinicaltrials.gov using the NCT-id."); d_pm = pm; } @Override public void prepare() { this.setVisible(false); d_validators.clear(); d_validators.add(new IdStepValidator(d_pm.getIdModel())); d_validators.add(new NonEmptyValueModel(d_pm.getTitleModel())); if (d_scrollPane != null) remove(d_scrollPane); buildWizardStep(); final BooleanAndModel validator = new BooleanAndModel(d_validators); PropertyConnector.connectAndUpdate(validator, this, "complete"); this.setVisible(true); repaint(); } private void buildWizardStep() { FormLayout layout = new FormLayout("right:pref, 3dlu, pref:grow:fill, 3dlu, left:pref, 3dlu, left:pref", "p"); d_builder = new PanelBuilder(layout); d_builder.setDefaultDialogBorder(); CellConstraints cc = new CellConstraints(); // add source fields int row = 1; d_builder.addLabel("Source:", cc.xy(1, row)); JComponent sourceSelecter = AuxComponentFactory.createBoundComboBox(Source.values(), d_pm.getSourceModel()); sourceSelecter.setEnabled(false); d_builder.add(sourceSelecter, cc.xyw(3, row, 2)); // add ID fields row = LayoutUtil.addRow(layout, row); d_builder.addLabel("ID:", cc.xy(1, row)); d_idField = BasicComponentFactory.createTextField(d_pm.getIdModel(), false); d_idField.setColumns(30); bindDefaultId(d_idField); d_builder.add(d_idField, cc.xy(3, row)); final Border border = d_idField.getBorder(); final IdValidModel idValidModel = new IdValidModel(); d_idField.addCaretListener(new CaretListener() { public void caretUpdate(CaretEvent e) { if (!d_pm.isIdAvailable()) { d_idField.setBorder(BorderFactory.createLineBorder(Color.RED, 2)); d_idField.setToolTipText("Study ID already exists, please change it."); d_idField.dispatchEvent(new KeyEvent(d_idField, KeyEvent.KEY_PRESSED, 0, KeyEvent.CTRL_MASK, KeyEvent.VK_F1, KeyEvent.CHAR_UNDEFINED)); } else { d_idField.setToolTipText(""); d_idField.setBorder(border); } idValidModel.update(); } }); // add import button row = LayoutUtil.addRow(layout, row); d_importButton = GUIFactory.createLabeledIconButton("Import from ClinicalTrials.gov", FileNames.ICON_IMPORT); d_importButton.setToolTipText("Enter NCT id above to retrieve study data from ClinicalTrials.gov"); final ModifiableHolder<Boolean> retrieverReady = new ModifiableHolder<Boolean>(true); d_importButton.addActionListener(new AbstractAction() { public void actionPerformed(ActionEvent arg0) { final RunnableReadyModel retriever = new RunnableReadyModel(new CTRetriever()); retrieverReady.setValue(false); retriever.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { retrieverReady.setValue(retriever.getValue()); } }); new Thread(retriever).start(); } }); BooleanAndModel importAvailable = new BooleanAndModel(idValidModel, retrieverReady); d_withResultsCheckBox = BasicComponentFactory.createCheckBox(d_pm.shouldImportCTWithResults(), "import results (experimental)"); Bindings.bind(d_importButton, "enabled", importAvailable); Bindings.bind(d_withResultsCheckBox, "enabled", importAvailable); ButtonBarBuilder2 bb = ButtonBarBuilder2.createLeftToRightBuilder(); bb.addButton(d_importButton); bb.addRelatedGap(); bb.addButton(d_withResultsCheckBox); d_builder.add(bb.getPanel(), cc.xy(3, row)); // add note to ID field row = LayoutUtil.addRow(layout, row); Study newStudy = d_pm.getNewStudyPM().getBean(); d_builder.add(buildNotesEditor(newStudy), cc.xy(3, row)); // add title label row = LayoutUtil.addRow(layout, row); d_builder.addLabel("Title:", cc.xy(1, row)); d_titleField = TextComponentFactory.createTextArea(d_pm.getTitleModel(), true, false); d_builder.add(d_titleField, cc.xy(3, row)); row = LayoutUtil.addRow(layout, row); d_builder.add( buildNotesEditor( (ObjectWithNotes<?>) getCharWithNotes(newStudy, BasicStudyCharacteristic.TITLE)), cc.xy(3, row)); // add clear button row = LayoutUtil.addRow(layout, row); JButton clearButton = new JButton("Clear input"); clearButton.addActionListener(new AbstractAction() { public void actionPerformed(ActionEvent arg0) { d_pm.resetStudy(); prepare(); } }); d_builder.add(clearButton, cc.xy(3, row)); String tip = "You can import studies from ClinicalTrials.gov by entering their NCT-ID, " + "and then pressing the import button next to the ID field. " + "For example, try " + EXAMPLE_NCT_ID + ".\n\n" + "Unfortunately, due to limitations of ClinicalTrials.gov, it is currently not possible to import adverse events or study results."; row = LayoutUtil.addRow(layout, row); d_builder.add(buildTip(tip), cc.xy(3, row)); this.setLayout(new BorderLayout()); d_scrollPane = new JScrollPane(d_builder.getPanel()); d_scrollPane.getVerticalScrollBar().setUnitIncrement(16); add(d_scrollPane, BorderLayout.CENTER); } public class CTRetriever implements Runnable { public void run() { try { setImportDisabledIcon(Main.IMAGELOADER.getIcon(FileNames.ICON_LOADING)); d_pm.importCT(); setImportDisabledIcon(Main.IMAGELOADER.getIcon(FileNames.ICON_IMPORT)); } catch (FileNotFoundException e) { // file not found is expected when user enters "strange" IDs JOptionPane.showMessageDialog(d_me, "Couldn't find NCT ID: " + d_pm.getIdModel().getValue(), "Not Found", JOptionPane.WARNING_MESSAGE); } catch (IOException e) { // IOExceptions are expected when there is a network error -- so report them ErrorDialog.showDialog(e, "Couldn't retrieve study", "Error reading from ClinicalTrials.gov: " + e.toString(), false); } catch (Exception e) { // otherwise throw onwards. throw new RuntimeException("Unexpected error trying to import study from ClinicalTrials.gov", e); } prepare(); } private void setImportDisabledIcon(final ImageIcon icon) throws InterruptedException, InvocationTargetException { SwingUtilities.invokeAndWait(new Runnable() { public void run() { d_importButton.setDisabledIcon(icon); } }); } } private class IdValidModel extends AbstractValueModel implements ValueHolder<Boolean> { Boolean d_valid = false; @Override public Boolean getValue() { return d_valid; } @Override public void setValue(Object newValue) { throw new RuntimeException("Unexpected modification"); } private Boolean isIdValid() { return d_idField.getText().toUpperCase().trim().matches("^NCT[0-9]+$"); } public void update() { Boolean oldVal = d_valid; d_valid = isIdValid(); fireValueChange(oldVal, d_valid); } } public static void bindDefaultId(final JTextField idField) { idField.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(KeyStroke.getKeyStroke(INSERT_EXAMPLE_ID), "insertSample"); idField.getActionMap().put("insertSample", new AbstractAction("insertSample") { public void actionPerformed(ActionEvent evt) { idField.setText(EXAMPLE_NCT_ID); } }); } } private static JComponent buildTip(String tip) { JTextPane area = new JTextPane(); StyledDocument doc = area.getStyledDocument(); addStylesToDoc(doc); area.setBackground(new Color(255, 180, 180)); try { doc.insertString(0, "x", doc.getStyle("tip")); doc.insertString(doc.getLength(), " Tip: \n", doc.getStyle("bold")); doc.insertString(doc.getLength(), tip, doc.getStyle("regular")); } catch (BadLocationException e) { e.printStackTrace(); } area.setEditable(false); JScrollPane pane = new JScrollPane(area); pane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED); pane.setPreferredSize(TextComponentFactory.textPaneDimension(area, 270, 70)); pane.setWheelScrollingEnabled(true); pane.getVerticalScrollBar().setValue(0); return pane; } public static void addStylesToDoc(StyledDocument doc) { //Initialize some styles. Style def = StyleContext.getDefaultStyleContext().getStyle(StyleContext.DEFAULT_STYLE); Style regular = doc.addStyle("regular", def); Style bold = doc.addStyle("bold", regular); StyleConstants.setBold(bold, true); // The image must first be wrapped in a style Style style = doc.addStyle("tip", null); StyleConstants.setIcon(style, Main.IMAGELOADER.getIcon(FileNames.ICON_TIP)); } }