Java tutorial
/* * Copyright (c) 2006-2012 Massachusetts General Hospital * All rights reserved. This program and the accompanying materials * are made available under the terms of the i2b2 Software License v2.1 * which accompanies this distribution. * * Contributors: * * Wensong Pan * */ package edu.harvard.i2b2.explorer.ui; import com.cloudgarden.resource.SWTResourceManager; import java.awt.*; import java.io.File; import java.io.FileInputStream; import java.io.IOException; import java.io.StringReader; import java.io.StringWriter; import java.sql.Connection; import java.util.ArrayList; import java.util.Date; import java.util.LinkedHashMap; import java.util.Iterator; import java.util.List; import java.util.Properties; import java.util.Set; import java.util.Collections; import java.util.Comparator; import javax.swing.JOptionPane; import javax.swing.JRootPane; import javax.swing.JScrollPane; import javax.swing.UIManager; import javax.xml.bind.JAXBContext; import javax.xml.bind.JAXBElement; import javax.xml.bind.Unmarshaller; import javax.xml.datatype.XMLGregorianCalendar; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.eclipse.jface.action.StatusLineManager; import org.eclipse.swt.SWT; import org.eclipse.swt.awt.SWT_AWT; import org.eclipse.swt.custom.CCombo; import org.eclipse.swt.custom.SashForm; import org.eclipse.swt.dnd.DND; import org.eclipse.swt.dnd.DragSource; import org.eclipse.swt.dnd.DragSourceAdapter; import org.eclipse.swt.dnd.DragSourceEvent; import org.eclipse.swt.dnd.DropTarget; import org.eclipse.swt.dnd.DropTargetAdapter; import org.eclipse.swt.dnd.DropTargetEvent; import org.eclipse.swt.dnd.TextTransfer; import org.eclipse.swt.dnd.Transfer; import org.eclipse.swt.events.DragDetectEvent; import org.eclipse.swt.events.DragDetectListener; import org.eclipse.swt.events.MouseEvent; import org.eclipse.swt.events.MouseMoveListener; import org.eclipse.swt.events.MouseTrackListener; import org.eclipse.swt.events.PaintEvent; import org.eclipse.swt.events.PaintListener; import org.eclipse.swt.events.SelectionAdapter; import org.eclipse.swt.events.SelectionEvent; import org.eclipse.swt.events.SelectionListener; import org.eclipse.swt.graphics.RGB; import org.eclipse.swt.graphics.Rectangle; import org.eclipse.swt.layout.FillLayout; import org.eclipse.swt.layout.GridData; import org.eclipse.swt.layout.GridLayout; import org.eclipse.swt.widgets.Button; import org.eclipse.swt.widgets.Composite; import org.eclipse.swt.widgets.Control; import org.eclipse.swt.widgets.Display; import org.eclipse.swt.widgets.Event; import org.eclipse.swt.widgets.Label; import org.eclipse.swt.widgets.Listener; import org.eclipse.swt.widgets.MessageBox; import org.eclipse.swt.widgets.Shell; import org.eclipse.swt.widgets.TabFolder; import org.eclipse.swt.widgets.TabItem; import org.eclipse.swt.widgets.Text; import org.eclipse.swt.widgets.Combo; import org.jdom.Element; import org.jdom.JDOMException; import org.jdom.Namespace; import org.jdom.input.SAXBuilder; import org.jdom.output.XMLOutputter; import edu.harvard.i2b2.common.util.jaxb.JAXBUnWrapHelper; import edu.harvard.i2b2.common.util.jaxb.JAXBUtil; import edu.harvard.i2b2.common.util.jaxb.JAXBUtilException; import edu.harvard.i2b2.crcxmljaxb.datavo.dnd.DndType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.BodyType; import edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ResponseMessageType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.InstanceResponseType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ItemType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.MasterResponseType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.PanelType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.QueryDefinitionType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.QueryInstanceType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.QueryResultInstanceType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.RequestXmlType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ResultResponseType; import edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ItemType.ConstrainByModifier; import edu.harvard.i2b2.eclipse.UserInfoBean; import edu.harvard.i2b2.eclipse.plugins.explorer.utils.StackData; import edu.harvard.i2b2.explorer.data.QueryInstanceData; import edu.harvard.i2b2.explorer.data.QueryMasterData; import edu.harvard.i2b2.explorer.dataModel.ConceptTableModel; import edu.harvard.i2b2.explorer.dataModel.ConceptTableRow; import edu.harvard.i2b2.explorer.dataModel.KTable; import edu.harvard.i2b2.explorer.dataModel.KTableCellResizeListener; import edu.harvard.i2b2.explorer.dataModel.KTableCellSelectionListener; import edu.harvard.i2b2.explorer.dataModel.ModifierData; import edu.harvard.i2b2.explorer.dataModel.QueryModel; import edu.harvard.i2b2.explorer.dataModel.TimelineRow; import edu.harvard.i2b2.explorer.datavo.ExplorerJAXBUtil; import edu.harvard.i2b2.explorer.serviceClient.PDOQueryClient; import edu.harvard.i2b2.smlib.DBLib; import edu.harvard.i2b2.timeline.lifelines.QueryClient; import edu.harvard.i2b2.timeline.lifelines.Record; public class MainComposite extends Composite { { //Register as a resource user - SWTResourceManager will //handle the obtaining and disposing of resources SWTResourceManager.registerResourceUser(this); } public static String noteKey = null; private static final Log log = LogFactory.getLog(MainComposite.class); private static final int MAX_STACK_SIZE = 28; public String msTitle = "I2B2 CRC Navigator in"; public String msUsername = ""; public String msPassword = ""; public boolean bWantStatusLine = false; private Composite oTheParent; private StatusLineManager slm = new StatusLineManager(); private KTable table; private Text patientMinNumText; private Text patientMaxNumText; private Text mrnlistText; private boolean bDisplayAllData = false; private boolean bDisplayDemographics = true; private WaitPanel p = null; private TabFolder tabFolder = null; private Thread visualizationQueryThread = null; private Connection oConnection = null; private LinkedHashMap<String, String> values = null; private String valueType = null; private int curRowNumber = 0; private ArrayList<ArrayList<ConceptTableRow>> rowData = null; private java.awt.Container oAwtContainer; private Button rightArrowButton; private Button leftArrowButton; private Text patientSetText; private boolean isAll = false; private Label queryNamemrnlistText; private Label groupNameText; private Record theRecord = null; private FramedComposite oModelQueryComposite; private FramedComposite oModelGroupComposite; private int returnedNumber = -1; private int currentRGBlistindex = 0; public void returnedNumber(int i) { returnedNumber = i; } private int runMode = 0; public int runMode() { return runMode; } public Record getRecord() { return theRecord; } private String patientRefId = null; public void patientRefId(String str) { patientRefId = new String(str); } private int patientSetSize = 0; private boolean drawLeft = true; public boolean drawLeft() { return drawLeft; } private String lastRequestMessage; public String lastRequestMessage() { return lastRequestMessage; } private List<StackData> xmlStack; public List<StackData> getXmlStack() { return xmlStack; } private String lastResponseMessage; private CCombo filterCCombo; //private Combo combo1; private Label label2; private Combo filterCombo; private Label label1; private String filter = "none"; public void lastRequestMessage(String msg) { lastRequestMessage = msg; if (xmlStack == null) xmlStack = new ArrayList<StackData>(); checkXmlStackSize(); StackData stackData = new StackData(); stackData.setMessage(msg); stackData.setName("Sent" + stackData.getTimestamp()); xmlStack.add(stackData); } public void lastResponseMessage(String msg) { lastResponseMessage = msg; if (xmlStack == null) xmlStack = new ArrayList<StackData>(); checkXmlStackSize(); StackData stackData = new StackData(); stackData.setMessage(msg); stackData.setName("Received" + stackData.getTimestamp()); xmlStack.add(stackData); } private void checkXmlStackSize() { if (xmlStack.size() == MAX_STACK_SIZE) { xmlStack.remove(0); xmlStack = xmlStack.subList(1, MAX_STACK_SIZE - 1); } } public String lastResponseMessage() { return lastResponseMessage; } private ArrayList<RGB> rgbList = null; //new ArrayList(); public MainComposite(Composite parent) { super(parent, SWT.FLAT); oTheParent = parent; values = new LinkedHashMap<String, String>(); rowData = new ArrayList<ArrayList<ConceptTableRow>>(); xmlStack = new ArrayList<StackData>(); createContents(parent); addPaintListener(new PaintListener() { public void paintControl(PaintEvent event) { } }); } public MainComposite(Composite parent, boolean drawleft) { super(parent, SWT.FLAT); oTheParent = parent; values = new LinkedHashMap<String, String>(); rowData = new ArrayList<ArrayList<ConceptTableRow>>(); xmlStack = new ArrayList<StackData>(); rgbList = new ArrayList<RGB>(); createRGBListNew(); drawLeft = drawleft; createContents(parent); } public void setPatientSetText(final String str) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { patientSetText.setText(str); } }); } public void selectTab(final int index) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(index); } }); } public void setPatientMinNumText(final String str) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { patientMinNumText.setText(str); } }); } public void setPatientSetSize(final String str) { patientSetSize = new Integer(str).intValue(); oTheParent.getDisplay().syncExec(new Runnable() { public void run() { int maxPatientNum = new Integer(patientMaxNumText.getText()).intValue(); if (patientSetSize > maxPatientNum) { rightArrowButton.setEnabled(true); patientMaxNumText.setText("10"); } else { rightArrowButton.setEnabled(false); // if(patientSetSize>0) { // patientMaxNumText.setText(setSize); // } } } }); } /** * @param args */ @SuppressWarnings("serial") protected Control createContents(Composite parent) { GridLayout topGridLayout = new GridLayout(1, false); topGridLayout.numColumns = 1; topGridLayout.marginWidth = 2; topGridLayout.marginHeight = 2; setLayout(topGridLayout); Composite oTreeComposite = new Composite(this, SWT.NONE); oTreeComposite.setLayout(new FillLayout(SWT.VERTICAL)); GridData gridData2 = new GridData(); gridData2.horizontalAlignment = GridData.FILL; gridData2.verticalAlignment = GridData.FILL; gridData2.grabExcessHorizontalSpace = true; gridData2.grabExcessVerticalSpace = true; oTreeComposite.setLayoutData(gridData2); // the horizontal sash form SashForm horizontalForm = new SashForm(oTreeComposite, SWT.HORIZONTAL); horizontalForm.setOrientation(SWT.HORIZONTAL); horizontalForm.setLayout(new GridLayout()); if (drawLeft) { // left sash form SashForm leftVerticalForm = new SashForm(horizontalForm, SWT.VERTICAL); leftVerticalForm.setOrientation(SWT.VERTICAL); leftVerticalForm.setLayout(new GridLayout()); if (bWantStatusLine) { slm.createControl(this, SWT.NULL); } slm.setMessage("i2b2 Explorer Version 2.0"); slm.update(true); // Create the tab folder final TabFolder oTabFolder = new TabFolder(leftVerticalForm, SWT.NONE); // Create each tab and set its text, tool tip text, // image, and control TabItem oTreeTab = new TabItem(oTabFolder, SWT.NONE); oTreeTab.setText("Concept trees"); oTreeTab.setToolTipText("Hierarchically organized patient characteristics"); oTreeTab.setControl(getConceptTreeTabControl(oTabFolder)); // Select the first tab (index is zero-based) oTabFolder.setSelection(0); // Create the tab folder final TabFolder queryRunFolder = new TabFolder(leftVerticalForm, SWT.NONE); TabItem previousRunTab = new TabItem(queryRunFolder, SWT.NONE); previousRunTab.setText("Patient Sets and Previous Queries"); previousRunTab.setToolTipText("Patient Sets & Previous Queries"); final Composite runComposite = new Composite(queryRunFolder, SWT.EMBEDDED); previousRunTab.setControl(runComposite); /* Create and setting up frame */ ////for mac fix //if ( System.getProperty("os.name").toLowerCase().startsWith("mac")) //SWT_AWT.embeddedFrameClass = "sun.lwawt.macosx.CViewEmbeddedFrame"; Frame runFrame = SWT_AWT.new_Frame(runComposite); Panel runPanel = new Panel(new BorderLayout()); try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception e) { log.debug("Error setting native LAF: " + e); } runFrame.add(runPanel); JRootPane runRoot = new JRootPane(); runPanel.add(runRoot); // Select the first tab (index is zero-based) queryRunFolder.setSelection(0); } SashForm verticalForm = new SashForm(horizontalForm, SWT.VERTICAL); verticalForm.setOrientation(SWT.VERTICAL); verticalForm.setLayout(new GridLayout()); // put a tab folder in it... tabFolder = new TabFolder(verticalForm, SWT.NONE); Composite patientNumsComposite = new Composite(verticalForm, SWT.NONE); GridData patientNumData = new GridData(GridData.HORIZONTAL_ALIGN_FILL); patientNumData.grabExcessHorizontalSpace = true; patientNumsComposite.setLayoutData(patientNumData); patientNumsComposite.setLayout(null); Label patientset = new Label(patientNumsComposite, SWT.NONE); patientset.setText("Patient Set: "); patientset.setBounds(5, 9, 60, 22); patientSetText = new Text(patientNumsComposite, SWT.SINGLE | SWT.BORDER); patientSetText.setText(""); patientSetText.setEditable(false); patientSetText.setBounds(70, 5, 300, 35); leftArrowButton = new Button(patientNumsComposite, SWT.PUSH); leftArrowButton.setText("<<<"); leftArrowButton.setEnabled(false); leftArrowButton.setBounds(380, 5, 38, 22); leftArrowButton.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent event) { runMode = -1; ConceptTableModel i2b2Model = (ConceptTableModel) table.getModel(); i2b2Model.fillDataFromTable(rowData); if (rowData.size() == 0) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("The set up table is empty."); mBox.open(); return; } String patientSetStr = patientSetText.getText(); if (patientSetStr.equals("") && !isAll) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("Please set a patient set or choose all datamart option."); mBox.open(); return; } if (tabFolder.getSelectionIndex() == 1) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { DestroyMiniVisualization(oAwtContainer); } }); } else if (tabFolder.getSelectionIndex() == 0) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(1); } }); } if (patientSetStr.equalsIgnoreCase("All")) { int minPatient = 0; try { String minText = patientMinNumText.getText(); minPatient = Integer.parseInt(minText); } catch (Exception e1) { minPatient = -1; } int maxPatient = 0; try { maxPatient = Integer.parseInt(patientMaxNumText.getText()); } catch (Exception e2) { maxPatient = -1; } PerformVisualizationQuery(oAwtContainer, "All", minPatient, maxPatient, bDisplayAllData); } else { int min = Integer.parseInt(patientMinNumText.getText()); int max = Integer.parseInt(patientMaxNumText.getText()); int start = new Integer(patientMinNumText.getText()).intValue(); int inc = new Integer(patientMaxNumText.getText()).intValue(); if (start - inc <= 1) { leftArrowButton.setEnabled(false); } if (start <= patientSetSize) { rightArrowButton.setEnabled(true); } else { rightArrowButton.setEnabled(false); } //if ((start - inc) > 1) { //patientMinNumText.setText("" + (start - inc)); //} else { //patientMinNumText.setText("1"); //} PerformVisualizationQuery(oAwtContainer, patientRefId, min - max, max - 1, bDisplayAllData); } } }); final Label patNum1 = new Label(patientNumsComposite, SWT.NONE); patNum1.setText(" start: "); patNum1.setBounds(425, 9, 31, 20); patientMinNumText = new Text(patientNumsComposite, SWT.SINGLE | SWT.BORDER); patientMinNumText.setText("1"); patientMinNumText.setBounds(460, 5, 45, 22); final Label patNum2 = new Label(patientNumsComposite, SWT.NONE); patNum2.setText("increment:"); patNum2.setBounds(515, 9, 57, 20); patientMaxNumText = new Text(patientNumsComposite, SWT.SINGLE | SWT.BORDER); patientMaxNumText.setText("10"); patientMaxNumText.setBounds(572, 5, 45, 22); rightArrowButton = new Button(patientNumsComposite, SWT.PUSH); rightArrowButton.setText(">>>"); rightArrowButton.setEnabled(false); rightArrowButton.setBounds(626, 5, 38, 20); rightArrowButton.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent event) { runMode = 1; ConceptTableModel i2b2Model = (ConceptTableModel) table.getModel(); i2b2Model.fillDataFromTable(rowData); if (rowData.size() == 0) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("The set up table is empty."); mBox.open(); return; } String patientSetStr = patientSetText.getText(); if (patientSetStr.equals("") && !isAll) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("Please set a patient set or choose all datamart option."); mBox.open(); return; } if (tabFolder.getSelectionIndex() == 1) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { DestroyMiniVisualization(oAwtContainer); } }); } else if (tabFolder.getSelectionIndex() == 0) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(1); } }); } if (patientSetStr.equalsIgnoreCase("All")) { int minPatient = 0; try { String minText = patientMinNumText.getText(); minPatient = Integer.parseInt(minText); } catch (Exception e1) { minPatient = -1; } int maxPatient = 0; try { maxPatient = Integer.parseInt(patientMaxNumText.getText()); } catch (Exception e2) { maxPatient = -1; } PerformVisualizationQuery(oAwtContainer, "All", minPatient, maxPatient, bDisplayAllData); } else { int min = Integer.parseInt(patientMinNumText.getText()); int max = Integer.parseInt(patientMaxNumText.getText()); int start = new Integer(patientMinNumText.getText()).intValue(); int inc = new Integer(patientMaxNumText.getText()).intValue(); if (start + inc > patientSetSize) { rightArrowButton.setEnabled(false); } //patientMinNumText.setText("" + (start + inc)); leftArrowButton.setEnabled(true); PerformVisualizationQuery(oAwtContainer, patientRefId, min, max - 1, bDisplayAllData); } // getDisplay().syncExec(new Runnable() { // public void run() { // if(returnedNumber >= 0) { // setIncrementNumber(returnedNumber); // MessageBox mBox = new MessageBox(getShell(), // SWT.ICON_INFORMATION // | SWT.OK); // mBox.setText("Please Note ..."); // mBox.setMessage(/*"Can't return all the requested "+ // requestIndex+" patients, */"Only "+returnedNumber+" patients // returned"); // mBox.open(); // } // } // }); } }); addListener(SWT.Resize, new Listener() { public void handleEvent(Event event) { int w = getBounds().width; patientSetText.setBounds(70, 5, w - 357, 24); leftArrowButton.setBounds(w - 281, 5, 38, 24); patNum1.setBounds(w - 239, 9, 31, 24); patientMinNumText.setBounds(w - 204, 5, 45, 24); patNum2.setBounds(w - 149, 9, 57, 24); patientMaxNumText.setBounds(w - 92, 5, 45, 24); rightArrowButton.setBounds(w - 42, 5, 37, 24); } }); verticalForm.setWeights(new int[] { 25, 3 }); // Item 1: a Text Table TabItem item1 = new TabItem(tabFolder, SWT.NONE); item1.setText("Create model for Timeline"); Composite oModelComposite = new Composite(tabFolder, SWT.NONE); item1.setControl(oModelComposite); GridLayout gridLayout = new GridLayout(2, false); // gridLayout.marginHeight = 0; // gridLayout.marginWidth = 0; // gridLayout.verticalSpacing = 0; // gridLayout.horizontalSpacing = 0; gridLayout.marginTop = 2; gridLayout.marginLeft = 0; gridLayout.marginBottom = 2; gridLayout.verticalSpacing = 1; gridLayout.horizontalSpacing = 1; oModelComposite.setLayout(gridLayout); oModelQueryComposite = new FramedComposite(oModelComposite, SWT.SHADOW_NONE); // GridLayout gLq = new GridLayout(25, false); oModelQueryComposite.setLayout(new GridLayout(25, false)); oModelQueryComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_BLACK)); GridData oModelQueryButtonGridData = new GridData(GridData.FILL_HORIZONTAL); oModelQueryButtonGridData.grabExcessHorizontalSpace = false; oModelQueryButtonGridData.horizontalSpan = 2; oModelQueryButtonGridData.verticalAlignment = SWT.CENTER; oModelQueryButtonGridData.verticalIndent = 5; oModelQueryComposite.setLayoutData(oModelQueryButtonGridData); queryNamemrnlistText = new Label(oModelQueryComposite, SWT.NONE); queryNamemrnlistText.setLayoutData(new GridData(GridData.FILL_HORIZONTAL)); queryNamemrnlistText.setText("Query Name: "); // queryNamemrnlistText.setBounds(5, 4, 600, 20); queryNamemrnlistText.addMouseTrackListener(new MouseTrackListener() { public void mouseEnter(MouseEvent arg0) { oModelQueryComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_YELLOW)); } public void mouseExit(MouseEvent arg0) { oModelQueryComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_BLACK)); } public void mouseHover(MouseEvent arg0) { oModelQueryComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_YELLOW)); } }); oModelQueryComposite.addMouseMoveListener(new MouseMoveListener() { public void mouseMove(MouseEvent arg0) { } }); oModelQueryComposite.addDragDetectListener(new DragDetectListener() { public void dragDetected(DragDetectEvent arg0) { } }); Composite oGroupComposite = new Composite(oModelComposite, SWT.NONE); // GridLayout gLq = new GridLayout(25, false); oGroupComposite.setLayout(gridLayout); GridData oGroupGridData = new GridData(GridData.HORIZONTAL_ALIGN_FILL | GridData.VERTICAL_ALIGN_FILL); oGroupGridData.grabExcessHorizontalSpace = true; oGroupGridData.grabExcessVerticalSpace = true; oGroupGridData.verticalIndent = 1; oGroupGridData.verticalSpan = GridData.VERTICAL_ALIGN_FILL; // oGroupGridData.verticalAlignment = GridData.VERTICAL_ALIGN_FILL; oGroupComposite.setLayoutData(oGroupGridData); oModelGroupComposite = new FramedComposite(oGroupComposite, SWT.SHADOW_NONE); // GridLayout gLq = new GridLayout(25, false); oModelGroupComposite.setLayout(new GridLayout(25, false)); GridData oModelGroupButtonGridData = new GridData(GridData.FILL_HORIZONTAL); oModelGroupButtonGridData.grabExcessHorizontalSpace = false; oModelGroupButtonGridData.horizontalSpan = 2; oModelGroupButtonGridData.verticalAlignment = SWT.CENTER; oModelGroupButtonGridData.verticalIndent = 5; oModelGroupComposite.setLayoutData(oModelGroupButtonGridData); // GridData gdAdd = new GridData(GridData.FILL_HORIZONTAL); GridData gdDel1 = new GridData(GridData.FILL_HORIZONTAL); groupNameText = new Label(oModelGroupComposite, SWT.NONE); gdDel1.horizontalSpan = 4; groupNameText.setLayoutData(gdDel1); groupNameText.setText("Panel Name: "); // groupNameText.setBounds(80, 8, 400, 24); // groupNameText.setAlignment(SWT.CENTER); // createDragSource(queryNamemrnlistText); // createDropTarget(queryNamemrnlistText); groupNameText.addMouseTrackListener(new MouseTrackListener() { public void mouseEnter(MouseEvent arg0) { oModelGroupComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_YELLOW)); } public void mouseExit(MouseEvent arg0) { oModelGroupComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_BLACK)); } public void mouseHover(MouseEvent arg0) { oModelGroupComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_YELLOW)); } }); // put a table in tabItem1... table = new KTable(oGroupComposite, SWT.V_SCROLL | SWT.H_SCROLL | SWT.BORDER); table.setFocus(); table.setBackground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_WHITE)); GridData tableGridData = new GridData(SWT.FILL, SWT.FILL, true, true); tableGridData.verticalIndent = 5; table.setLayoutData(tableGridData); table.setRowSelectionMode(true); // table.setMultiSelectionMode(true); // table.setModel(new KTableForModel()); table.setModel(new ConceptTableModel()); // table.getModel().setColumnWidth(0, oModelComposite.getBounds().width // - 35); table.addCellSelectionListener(new KTableCellSelectionListener() { public void cellSelected(int col, int row, int statemask) { log.debug("Cell [" + col + ";" + row + "] selected."); // System.out.println("Cell [" + col + ";" + row + // "] selected."); table.selectedRow = row; table.selectedColumn = col; } public void fixedCellSelected(int col, int row, int statemask) { log.debug("Header [" + col + ";" + row + "] selected."); // System.out.println("Header [" + col + ";" + row + // "] selected."); } }); Transfer[] types = new Transfer[] { TextTransfer.getInstance() }; // create drag source /* * DragSource source = new DragSource(queryNamemrnlistText, * DND.DROP_COPY); source.setTransfer(types); source.addDragListener(new * DragSourceAdapter() { * * @Override public void dragSetData(DragSourceEvent event) { * //DragSource ds = (DragSource) event.widget; StringWriter strWriter = * new StringWriter(); DndType dndType = new DndType(); * edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory pdoFactory * = new edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory(); * PanelType panelType = new PanelType(); * * //get table rows and fill the panel object for(int i=0; i<3; i++) { * ItemType itemType = new ItemType(); * panelType.getItem().add(itemType); * * dndType.getAny().add(pdoFactory.createPanel(panelType)); * edu.harvard.i2b2.crcxmljaxb.datavo.dnd.ObjectFactory dndFactory = new * edu.harvard.i2b2.crcxmljaxb.datavo.dnd.ObjectFactory(); try { * ExplorerJAXBUtil * .getJAXBUtil().marshaller(dndFactory.createPluginDragDrop(dndType), * strWriter); } catch(JAXBUtilException e) { e.printStackTrace(); } * * //put the data into the event event.data = strWriter.toString(); } * * * }); */ Composite oModelAddDelButtonComposite = new Composite(oModelComposite, SWT.NONE); GridLayout gL = new GridLayout(25, false); oModelAddDelButtonComposite.setLayout(gL); GridData oModelAddDelButtonGridData = new GridData(GridData.FILL_HORIZONTAL);// HORIZONTAL_ALIGN_FILL);// | // GridData.VERTICAL_ALIGN_FILL); oModelAddDelButtonGridData.grabExcessHorizontalSpace = false; oModelAddDelButtonGridData.horizontalSpan = 2; oModelAddDelButtonComposite.setLayoutData(oModelAddDelButtonGridData); // GridData gdAdd = new GridData(GridData.FILL_HORIZONTAL); GridData gdDel = new GridData(GridData.FILL_HORIZONTAL); Button deleteArrowButton = new Button(oModelAddDelButtonComposite, SWT.PUSH); gdDel.horizontalSpan = 4; deleteArrowButton.setLayoutData(gdDel); deleteArrowButton.setText("Delete From List"); deleteArrowButton.addSelectionListener(new SelectionAdapter() { @SuppressWarnings("unchecked") public void widgetSelected(SelectionEvent event) { curRowNumber = 0; ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); int[] selectedRow = table.getRowSelection(); m_Model.fillDataFromTable(rowData); if ((selectedRow != null) && (selectedRow.length > 0)) { String conceptName = (String) m_Model.getContentAt(1, selectedRow[0]); if (conceptName.equals("Encounter Range Line")) { } else if (conceptName.equals("Vital Status Line")) { } int rowNumber = new Integer((String) (m_Model.getContentAt(0, selectedRow[0]))).intValue(); int rid = selectedRow[0]; ArrayList list = (ArrayList) rowData.get(rowNumber - 1); for (int i = 0; i < list.size(); i++) { ConceptTableRow tr = (ConceptTableRow) list.get(i); if (tr.rowId == rid) { list.remove(i); break; } } if (list.size() == 0) { rowData.remove(rowNumber - 1); } curRowNumber = rowData.size(); resetRowNumber(); // m_Model.deleteRow(selectedRow[0]); ((ConceptTableModel) table.getModel()).deleteAllRows(); ((ConceptTableModel) table.getModel()).populateTable(rowData); /* * int newRow = 0; for(int i=0; i<rowData.size(); i++) { * ArrayList alist = (ArrayList) rowData.get(i); for(int * j=0; j<alist.size(); j++) { TableRow r = (TableRow) * alist.get(j); newRow++; r.rowId = newRow; * table.getModel().setContentAt(0, newRow, new * Integer(r.rowNumber).toString()); * table.getModel().setContentAt(1, newRow, r.conceptName); * table.getModel().setContentAt(2, newRow, r.valueType); * table.getModel().setContentAt(3, newRow, r.valueText); * table.getModel().setContentAt(4, newRow, r.height); * table.getModel().setContentAt(5, newRow, r.color); * table.getModel().setContentAt(6, newRow, r.conceptXml); } * } */ table.redraw(); queryNamemrnlistText.setText("Query Name: "); groupNameText.setText("Panel Name: "); } } }); Button deleteAllButton = new Button(oModelAddDelButtonComposite, SWT.PUSH); gdDel = new GridData(GridData.FILL_HORIZONTAL); gdDel.horizontalSpan = 4; deleteAllButton.setLayoutData(gdDel); deleteAllButton.setText("Delete All "); deleteAllButton.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent event) { ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); m_Model.deleteAllRows(); curRowNumber = 0; rowData.clear(); queryNamemrnlistText.setText("Query Name: "); groupNameText.setText("Panel Name: "); table.redraw(); } }); Button putInOrderButton = new Button(oModelAddDelButtonComposite, SWT.PUSH); gdDel = new GridData(GridData.FILL_HORIZONTAL); gdDel.horizontalSpan = 4; putInOrderButton.setLayoutData(gdDel); putInOrderButton.setText("Put In Order "); putInOrderButton.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent event) { ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); curRowNumber = 0; m_Model.fillDataFromTable(rowData); Collections.sort(rowData, new Comparator<Object>() { @SuppressWarnings("unchecked") public int compare(Object o1, Object o2) { int i1 = ((ConceptTableRow) ((ArrayList) o1).get(0)).rowNumber; int i2 = ((ConceptTableRow) ((ArrayList) o2).get(0)).rowNumber; if (i1 > i2) { return 1; } else if (i1 < i2) { return -1; } else { return 0; } } }); m_Model.deleteAllRows(); m_Model.populateTable(rowData); table.redraw(); } }); Button upArrowButton = new Button(oModelAddDelButtonComposite, SWT.PUSH); upArrowButton.setText("Move Up"); upArrowButton.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent event) { ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); int[] selectedRow = table.getRowSelection(); curRowNumber = 0; // KTableI2B2Model m_Model = (KTableI2B2Model) table.getModel(); // int[] selectedRow = table.getRowSelection(); m_Model.fillDataFromTable(rowData); int index = new Integer((String) (m_Model.getContentAt(0, selectedRow[0]))).intValue() - 1; if (index < 1) { return; } if ((selectedRow != null) && (selectedRow.length > 0)) { // m_Model.moveRow(selectedRow[0], selectedRow[0] -1); ArrayList<ConceptTableRow> list = rowData.get(index); rowData.remove(index); rowData.add(index - 1, list); resetRowNumber(); m_Model.populateTable(rowData); } table.setSelection(0, selectedRow[0] - 1, true); table.redraw(); } }); Button downArrowButton = new Button(oModelAddDelButtonComposite, SWT.PUSH); downArrowButton.setText("Move Down"); downArrowButton.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent event) { ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); int[] selectedRow = table.getRowSelection(); curRowNumber = 0; // KTableI2B2Model m_Model = (KTableI2B2Model) table.getModel(); // int[] selectedRow = table.getRowSelection(); m_Model.fillDataFromTable(rowData); int index = new Integer((String) (m_Model.getContentAt(0, selectedRow[0]))).intValue() - 1; if (index == (rowData.size() - 1)) { return; } if ((selectedRow != null) && (selectedRow.length > 0)) { // m_Model.moveRow(selectedRow[0], selectedRow[0] -1); ArrayList<ConceptTableRow> list = rowData.get(index); rowData.remove(index); rowData.add(index + 1, list); resetRowNumber(); m_Model.populateTable(rowData); } table.setSelection(0, selectedRow[0] + 1, true); table.redraw(); } }); Composite oModelCheckButtonComposite = new Composite(oModelComposite, SWT.NONE); GridLayout gL1 = new GridLayout(); gL1.numColumns = 20; oModelCheckButtonComposite.setLayout(gL1); GridData oModelCheckButtonGridData = new GridData(); oModelCheckButtonGridData.horizontalSpan = 4; oModelCheckButtonGridData.verticalAlignment = GridData.FILL; oModelCheckButtonGridData.grabExcessHorizontalSpace = true; oModelCheckButtonGridData.horizontalAlignment = GridData.FILL; oModelCheckButtonComposite.setLayoutData(oModelCheckButtonGridData); Button displayOrNotButton = new Button(oModelCheckButtonComposite, SWT.CHECK); displayOrNotButton.setText("Display concepts with no data"); displayOrNotButton.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent event) { // do something here- return null bDisplayAllData = !bDisplayAllData; } }); Button displayDemographicsOrNotButton = new Button(oModelCheckButtonComposite, SWT.CHECK); displayDemographicsOrNotButton.setText("Display patient demographics"); if ((System.getProperty("applicationName") != null) && System.getProperty("applicationName").equals("BIRN")) { displayDemographicsOrNotButton.setSelection(false); displayDemographicsOrNotButton.setEnabled(false); bDisplayDemographics = false; } else if ((System.getProperty("applicationName") == null) || System.getProperty("applicationName").equals("i2b2")) { displayDemographicsOrNotButton.setSelection(true); } displayDemographicsOrNotButton.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent event) { bDisplayDemographics = !bDisplayDemographics; } }); { label2 = new Label(oModelCheckButtonComposite, SWT.NONE); GridData label2LData = new GridData(); label2LData.horizontalIndent = 10; label2.setLayoutData(label2LData); label2.setText("Filter:"); } { filterCCombo = new CCombo(oModelCheckButtonComposite, SWT.BORDER); filterCCombo.setBackground(SWTResourceManager.getColor(255, 255, 255)); filterCCombo.setEditable(false); filterCCombo.addSelectionListener(new SelectionAdapter() { public void widgetSelected(SelectionEvent evt) { System.out.println("filterCCombo.widgetSelected, event=" + evt); int index = filterCCombo.getSelectionIndex(); if (index == 0) { filter = "none"; } else if (index == 1) { filter = "max"; } else if (index == 2) { filter = "min"; } else if (index == 3) { filter = "first"; } else if (index == 4) { filter = "last"; } } }); filterCCombo.add("none"); filterCCombo.add("max"); filterCCombo.add("min"); filterCCombo.add("first"); filterCCombo.add("last"); filterCCombo.select(0); } { //combo1 = new Combo(oModelCheckButtonComposite, SWT.NONE); } { //label1 = new Label(oModelCheckButtonComposite, SWT.NONE); //label1.setText("Filter: "); } /*{ filterCombo = new Combo(oModelCheckButtonComposite, SWT.NONE); GridData filterComboLData = new GridData(); filterComboLData.widthHint = 28; filterComboLData.heightHint = 21; filterCombo.setLayoutData(filterComboLData); filterCombo.add("max"); filterCombo.add("min"); filterCombo.add("first"); filterCombo.add("last"); filterCombo.select(0); //filterCombo.set; //filterCombo.setText("combo1"); }*/ if (UserInfoBean.getInstance().getCellDataUrl("identity") != null) { Composite oPatientSetComposite = new Composite(oModelComposite, SWT.NONE); GridData patientSetData = new GridData(GridData.HORIZONTAL_ALIGN_FILL); patientSetData.grabExcessHorizontalSpace = true; oPatientSetComposite.setLayoutData(patientSetData); oPatientSetComposite.setLayout(null); Label mrnlabel = new Label(oPatientSetComposite, SWT.NONE); mrnlabel.setText("MRN site:"); mrnlabel.setBounds(5, 9, 50, 20); final Combo siteCombo = new Combo(oPatientSetComposite, SWT.NULL); siteCombo.add("BWH"); siteCombo.add("MGH"); siteCombo.setBounds(57, 5, 60, 20); siteCombo.select(1); Label mrnNumber = new Label(oPatientSetComposite, SWT.NONE); mrnNumber.setText("number:"); mrnNumber.setBounds(121, 9, 40, 20); mrnlistText = new Text(oPatientSetComposite, SWT.SINGLE | SWT.BORDER); mrnlistText.setBounds(164, 5, 150, 20); mrnlistText.setText(""); Button runButton = new Button(oPatientSetComposite, SWT.PUSH); runButton.setText("Search By MRN"); runButton.setBounds(315, 5, 85, 23); runButton.addSelectionListener(new SelectionAdapter() { @SuppressWarnings("unchecked") public void widgetSelected(SelectionEvent event) { String mrns = mrnlistText.getText(); if (mrns.equals("")) { return; } String[] mrnArray = mrns.split(","); int[] idlist = new int[mrnArray.length]; String username = UserInfoBean.getInstance().getUserName(); String password = UserInfoBean.getInstance().getUserPassword(); // log.debug("User name: "+username+" password: "+password); String site = siteCombo.getText(); for (int i = 0; i < mrnArray.length; i++) { // String[] tmps = new String[2]; String tmp = mrnArray[i].replaceAll(" ", ""); // tmps = tmp.split(":"); String queryStr = "<?xml version=\"1.0\" standalone=\"yes\"?>\n" + "<search_by_local>" + "<match_id site=\"" + site.toUpperCase()/* EMPI */ + "\">" + tmp/* 100016900 */ + "</match_id>\n" + "</search_by_local>"; String resultStr = QueryClient.query(queryStr, username, password); log.debug(queryStr); log.debug(resultStr); SAXBuilder parser = new SAXBuilder(); String masterID = null; java.io.StringReader xmlStringReader = new java.io.StringReader(resultStr); try { org.jdom.Document tableDoc = parser.build(xmlStringReader); org.jdom.Element tableXml = tableDoc.getRootElement(); Element responseXml = (Element) tableXml.getChild("person_list"); // Element mrnXml = (Element) // responseXml.getChild("MRN"); java.util.List listChildren = responseXml.getChildren(); if (listChildren.isEmpty()) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("No master id found"); mBox.open(); return; } Element masterXml = (Element) responseXml.getChild("master_record"); masterID = masterXml.getAttributeValue("id"); log.debug("Patient id: " + masterID); idlist[i] = new Integer(masterID).intValue(); log.debug("MRN: " + site + "-" + tmp); } catch (Exception e1) { e1.printStackTrace(); } } if (tabFolder.getSelectionIndex() == 1) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { DestroyMiniVisualization(oAwtContainer); } }); } else if (tabFolder.getSelectionIndex() == 0) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(1); } }); } PerformVisualizationQuery(oAwtContainer, idlist, bDisplayAllData); } }); } DropTarget targetLable = new DropTarget(oModelQueryComposite, DND.DROP_COPY); targetLable.setTransfer(types); targetLable.addDropListener(new DropTargetAdapter() { @Override public void dragLeave(DropTargetEvent event) { super.dragLeave(event); oModelQueryComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_BLACK)); } public void dragEnter(DropTargetEvent event) { event.detail = DND.DROP_COPY; oModelQueryComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_YELLOW)); } @SuppressWarnings("unchecked") public void drop(DropTargetEvent event) { if (event.data == null) { event.detail = DND.DROP_NONE; return; } try { SAXBuilder parser = new SAXBuilder(); String xmlContent = (String) event.data; java.io.StringReader xmlStringReader = new java.io.StringReader(xmlContent); org.jdom.Document tableDoc = parser.build(xmlStringReader); org.jdom.Element tableXml = tableDoc.getRootElement().getChild("concepts", Namespace.getNamespace("http://www.i2b2.org/xsd/cell/ont/1.1/")); if (tableXml != null) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here."); mBox.open(); event.detail = DND.DROP_NONE; return; } boolean isQuery = false; if (tableXml == null) tableXml = tableDoc.getRootElement().getChild("query_master", Namespace.getNamespace("http://www.i2b2.org/xsd/cell/crc/psm/1.1/")); if (tableXml != null) isQuery = true; else { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here."); mBox.open(); event.detail = DND.DROP_NONE; return; } if (isQuery) { ArrayList<QueryModel> nodeXmls = new ArrayList<QueryModel>(); try { JAXBUtil jaxbUtil = ExplorerJAXBUtil.getJAXBUtil(); QueryMasterData ndata = new QueryMasterData(); ndata.name(tableXml.getChildText("name")); queryNamemrnlistText.setText("Query Name: " + ndata.name()); groupNameText.setText("Panel Name: All items of Query " + ndata.name()); ndata.xmlContent(null); ndata.id(tableXml.getChildTextTrim("query_master_id")); ndata.userId(tableXml.getChildTextTrim("user_id")); String xmlcontent = null; String xmlrequest = null; xmlrequest = ndata.writeDefinitionQueryXML(); lastRequestMessage(xmlrequest); if (System.getProperty("webServiceMethod").equals("SOAP")) xmlcontent = PDOQueryClient.sendPDQQueryRequestSOAP(xmlrequest); else xmlcontent = PDOQueryClient.sendPDQQueryRequestREST(xmlrequest); lastResponseMessage(xmlcontent); if (xmlcontent == null) return; else { log.debug("Query content response: " + xmlcontent); ndata.xmlContent(xmlcontent); } JAXBElement jaxbElement = jaxbUtil.unMashallFromString(ndata.xmlContent()); ResponseMessageType messageType = (ResponseMessageType) jaxbElement.getValue(); BodyType bt = messageType.getMessageBody(); MasterResponseType masterResponseType = (MasterResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), MasterResponseType.class); RequestXmlType requestXmlType = masterResponseType.getQueryMaster().get(0) .getRequestXml(); org.w3c.dom.Element element = (org.w3c.dom.Element) requestXmlType.getContent().get(0); if (element != null) log.debug("query definition not null"); else log.error("query definition is null"); String domString = edu.harvard.i2b2.common.util.xml.XMLUtil .convertDOMElementToString(element); log.debug("string output" + domString); JAXBContext jc1 = JAXBContext .newInstance(edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory.class); Unmarshaller unMarshaller = jc1.createUnmarshaller(); JAXBElement queryDefinitionJaxbElement = (JAXBElement) unMarshaller .unmarshal(new StringReader(domString)); QueryDefinitionType queryDefinitionType = (QueryDefinitionType) queryDefinitionJaxbElement .getValue(); int numOfPanels = queryDefinitionType.getPanel().size(); int conceptCount = 0; if (queryDefinitionType.getSubquery().size() == 0) // it's a normal query conceptCount = addQueryModel(queryDefinitionType, nodeXmls, conceptCount); // add concepts to nodeXmls, increment conceptCount else if (queryDefinitionType.getSubquery().size() > 0) // temporal queries have subqueries { conceptCount = addQueryModel(queryDefinitionType, nodeXmls, conceptCount); List<QueryDefinitionType> subqueries = queryDefinitionType.getSubquery(); for (QueryDefinitionType subQuery : subqueries) conceptCount = addQueryModel(subQuery, nodeXmls, conceptCount); // for each subquery, add concepts to nodeXmls, increment conceptCount } if (nodeXmls.size() == 0) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("No valid concept was found."); mBox.open(); event.detail = DND.DROP_NONE; return; } populateTable(nodeXmls); // get query instance String xmlRequest = ndata.writeContentQueryXML(); lastRequestMessage(xmlRequest); String xmlResponse = PDOQueryClient.sendPDQQueryRequestREST(xmlRequest); lastResponseMessage(xmlResponse); jaxbElement = jaxbUtil.unMashallFromString(xmlResponse); messageType = (ResponseMessageType) jaxbElement.getValue(); bt = messageType.getMessageBody(); InstanceResponseType instanceResponseType = (InstanceResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), InstanceResponseType.class); QueryInstanceData instanceData = null; XMLGregorianCalendar startDate = null; for (QueryInstanceType queryInstanceType : instanceResponseType.getQueryInstance()) { QueryInstanceData runData = new QueryInstanceData(); runData.visualAttribute("FA"); runData.tooltip("The results of the query run"); runData.id(new Integer(queryInstanceType.getQueryInstanceId()).toString()); XMLGregorianCalendar cldr = queryInstanceType.getStartDate(); runData.name("Results of " + "[" + cldr.getMonth() + "-" + cldr.getDay() + "-" + cldr.getYear() + " " + cldr.getHour() + ":" + cldr.getMinute() + ":" + cldr.getSecond() + "]"); if (instanceData == null) { startDate = cldr; instanceData = runData; } else { if (cldr.toGregorianCalendar().compareTo(startDate.toGregorianCalendar()) > 0) { startDate = cldr; instanceData = runData; } } } // get patient set if (instanceData == null) { event.detail = DND.DROP_NONE; return; } log.debug("Got query instance: " + instanceData.name()); xmlRequest = instanceData.writeContentQueryXML(); lastRequestMessage(xmlRequest); xmlResponse = PDOQueryClient.sendPDQQueryRequestREST(xmlRequest); lastResponseMessage(xmlResponse); jaxbElement = jaxbUtil.unMashallFromString(xmlResponse); messageType = (ResponseMessageType) jaxbElement.getValue(); bt = messageType.getMessageBody(); ResultResponseType resultResponseType = (ResultResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), ResultResponseType.class); for (QueryResultInstanceType queryResultInstanceType : resultResponseType .getQueryResultInstance()) { if (!(queryResultInstanceType.getQueryResultType().getName() .equalsIgnoreCase("PATIENTSET"))) { continue; } String status = queryResultInstanceType.getQueryStatusType().getName(); if (status.equalsIgnoreCase("FINISHED")) { String setId = new Integer(queryResultInstanceType.getResultInstanceId()) .toString(); String setSize = new Integer(queryResultInstanceType.getSetSize()).toString(); String description = queryResultInstanceType.getDescription(); if (description != null) { patientSetText.setText(description); } else { patientSetText.setText("Patient Set: " + setSize + " patients"); } patientRefId = new String(setId); patientMinNumText.setText("1"); leftArrowButton.setEnabled(false); int maxPatientNum = new Integer(patientMaxNumText.getText()).intValue(); patientSetSize = queryResultInstanceType.getSetSize(); if (patientSetSize > maxPatientNum) { rightArrowButton.setEnabled(true); patientMaxNumText.setText("10"); } else { rightArrowButton.setEnabled(false); if (patientSetSize > 0) { patientMaxNumText.setText(setSize); } } log.debug("Dropped set of: " + setSize + " patients"/* strs[0] */ + " with refId: " + setId/* * strs[ 1 ] */); } else { // message } } } catch (Exception e) { e.printStackTrace(); return; } } /* * else { List conceptChildren = tableXml.getChildren(); * parseDropConcepts(conceptChildren, event); * table.redraw(); } */ event.detail = DND.DROP_NONE; } catch (JDOMException e) { System.err.println(e.getMessage()); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here."); mBox.open(); event.detail = DND.DROP_NONE; e.printStackTrace(); return; } catch (Exception e) { System.err.println(e.getMessage()); event.detail = DND.DROP_NONE; e.printStackTrace(); return; } } }); // create drag source DragSource source1 = new DragSource(groupNameText, DND.DROP_COPY); source1.setTransfer(types); source1.addDragListener(new DragSourceAdapter() { @Override public void dragSetData(DragSourceEvent event) { ConceptTableModel i2b2Model = (ConceptTableModel) table.getModel(); i2b2Model.fillDataFromTable(rowData); if (rowData.size() == 0) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("The set up table is empty."); mBox.open(); return; } StringWriter strWriter = new StringWriter(); DndType dndType = new DndType(); edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory pdoFactory = new edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory(); PanelType panelType = new PanelType(); panelType.setInvert(0); PanelType.TotalItemOccurrences totalOccurrences = new PanelType.TotalItemOccurrences(); totalOccurrences.setValue(1); panelType.setTotalItemOccurrences(totalOccurrences); panelType.setPanelNumber(0 + 1); // panelType.setName(panelData.getItems().get(0).name() + "_" // + generateMessageId().substring(0, 4)); panelType.setName("Panel-1"); // TO DO: get table rows and fill the panel object for (int i = 1; i < i2b2Model.getRowCount(); i++) { QueryModel node = (QueryModel) i2b2Model.getContentAt(7, i); ItemType itemType = new ItemType(); itemType.setItemKey(node.fullname()); itemType.setItemName(node.name()); itemType.setTooltip(node.tooltip()); itemType.setHlevel(Integer.parseInt(node.hlevel())); itemType.setClazz("ENC"); itemType.setItemIcon(node.visualAttribute().trim()); itemType.setItemColor(i2b2Model.getColorString((RGB) i2b2Model.getContentAt(5, i))); itemType.setItemRowNumber((String) i2b2Model.getContentAt(0, i)); itemType.setItemShape((String) i2b2Model.getContentAt(4, i)); itemType.getConstrainByValue().add(node.valueModel().writeValueConstraint()); itemType.getConstrainByDate().add(node.writeTimeConstrain()); panelType.getItem().add(itemType); } dndType.getAny().add(pdoFactory.createPanel(panelType)); edu.harvard.i2b2.crcxmljaxb.datavo.dnd.ObjectFactory dndFactory = new edu.harvard.i2b2.crcxmljaxb.datavo.dnd.ObjectFactory(); try { ExplorerJAXBUtil.getJAXBUtil().marshaller(dndFactory.createPluginDragDrop(dndType), strWriter); } catch (JAXBUtilException e) { e.printStackTrace(); } // put the data into the event event.data = strWriter.toString(); } }); DropTarget nameTarget = new DropTarget(groupNameText, DND.DROP_COPY); nameTarget.setTransfer(types); nameTarget.addDropListener(new DropTargetAdapter() { @Override public void dragLeave(DropTargetEvent event) { super.dragLeave(event); oModelGroupComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_BLACK)); } @SuppressWarnings("unchecked") public void drop(DropTargetEvent event) { if (event.data == null) { event.detail = DND.DROP_NONE; return; } ArrayList<QueryModel> nodeXmls = new ArrayList<QueryModel>(); try { SAXBuilder parser = new SAXBuilder(); String xmlContent = (String) event.data; java.io.StringReader xmlStringReader = new java.io.StringReader(xmlContent); org.jdom.Document panelDoc = parser.build(xmlStringReader); org.jdom.Element panelXml = panelDoc.getRootElement().getChild("panel", Namespace.getNamespace("http://www.i2b2.org/xsd/cell/crc/psm/querydefinition/1.1/")); if (panelXml == null) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here."); mBox.open(); event.detail = DND.DROP_NONE; return; } else { String domString = (new XMLOutputter()).outputString(panelXml); JAXBContext jc1 = JAXBContext .newInstance(edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory.class); Unmarshaller unMarshaller = jc1.createUnmarshaller(); JAXBElement panelJaxbElement = (JAXBElement) unMarshaller .unmarshal(new StringReader(domString)); PanelType panelType = (PanelType) panelJaxbElement.getValue(); String panelname = panelType.getName(); groupNameText.setText("Panel Name: " + panelname); queryNamemrnlistText.setText("Query Name: "); for (int j = 0; j < panelType.getItem().size(); j++) { ItemType itemType = panelType.getItem().get(j); QueryModel nodedata = new QueryModel(); nodedata.name(itemType.getItemName()); nodedata.visualAttribute("FA"); nodedata.tooltip(itemType.getTooltip()); nodedata.fullname(itemType.getItemKey()); nodedata.hlevel(new Integer(itemType.getHlevel()).toString()); // / need to handle query tool generated panels if (itemType.getItemShape() != null) { nodedata.tableRow().height = new String(itemType.getItemShape()); nodedata.tableRow().color = ((ConceptTableModel) table.getModel()) .getColor(itemType.getItemColor()); nodedata.tableRow().rowNumber = Integer.parseInt(itemType.getItemRowNumber()); } else { nodedata.tableRow().height = "Medium"; nodedata.tableRow().color = getRGBfromList(curRowNumber);//new RGB(0, 0, 128); nodedata.tableRow().rowNumber = j + 1; } nodedata.constrainByValue(itemType.getConstrainByValue()); if (itemType.getConstrainByValue().size() > 0) { nodedata.setValueConstrains(itemType.getConstrainByValue()); if (itemType.getConstrainByValue().size() > 0) { nodedata.setValueConstrains(itemType.getConstrainByValue()); if (nodedata.valueModel().hasEnumValue()) { if (nodedata.valueModel().useTextValue()) { ArrayList<String> results = new ArrayList<String>(); results.toArray(nodedata.valueModel().value().split(",")); nodedata.valueModel().selectedValues = results; } } } } // Handle Constrain By Dates for (int u = 0; u < itemType.getConstrainByDate().size(); u++) { nodedata.setTimeConstrain(itemType.getConstrainByDate().get(u).getDateFrom(), itemType.getConstrainByDate().get(u).getDateTo()); } String status = nodedata.setXmlContent(); if (status.equalsIgnoreCase("error")) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage( "Response delivered from the remote server could not be understood,\n" + "you may wish to retry your last action."); mBox.open(); event.detail = DND.DROP_NONE; return; } nodeXmls.add(nodedata); } // event.detail = DND.DROP_NONE; } populateTable(nodeXmls); } catch (JDOMException e) { System.err.println(e.getMessage()); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here."); mBox.open(); event.detail = DND.DROP_NONE; e.printStackTrace(); return; } catch (Exception e) { System.err.println(e.getMessage()); event.detail = DND.DROP_NONE; e.printStackTrace(); return; } } public void dragEnter(DropTargetEvent event) { TextTransfer textTransfer = TextTransfer.getInstance(); if (textTransfer.isSupportedType(event.currentDataType)) { event.detail = DND.DROP_COPY; } oModelGroupComposite.setForeground(oTheParent.getDisplay().getSystemColor(SWT.COLOR_YELLOW)); } }); DropTarget target = new DropTarget(table, DND.DROP_COPY); target.setTransfer(types); target.addDropListener(new DropTargetAdapter() { @SuppressWarnings("unchecked") public void drop(DropTargetEvent event) { if (event.data == null) { event.detail = DND.DROP_NONE; return; } try { SAXBuilder parser = new SAXBuilder(); String xmlContent = (String) event.data; java.io.StringReader xmlStringReader = new java.io.StringReader(xmlContent); org.jdom.Document tableDoc = parser.build(xmlStringReader); org.jdom.Element tableXml = tableDoc.getRootElement().getChild("concepts", Namespace.getNamespace("http://www.i2b2.org/xsd/cell/ont/1.1/")); boolean isQuery = false; if (tableXml == null) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here."); mBox.open(); event.detail = DND.DROP_NONE; return; } if (isQuery) { ArrayList<QueryModel> nodeXmls = new ArrayList<QueryModel>(); try { JAXBUtil jaxbUtil = ExplorerJAXBUtil.getJAXBUtil(); QueryMasterData ndata = new QueryMasterData(); ndata.name(tableXml.getChildText("name")); queryNamemrnlistText.setText(ndata.name()); ndata.xmlContent(null); ndata.id(tableXml.getChildTextTrim("query_master_id")); ndata.userId(tableXml.getChildTextTrim("user_id")); String xmlcontent = null; String xmlrequest = null; xmlrequest = ndata.writeDefinitionQueryXML(); lastRequestMessage(xmlrequest); if (System.getProperty("webServiceMethod").equals("SOAP")) { xmlcontent = PDOQueryClient.sendPDQQueryRequestSOAP(xmlrequest); } else { xmlcontent = PDOQueryClient.sendPDQQueryRequestREST(xmlrequest); } lastResponseMessage(xmlcontent); if (xmlcontent == null) { return; } else { log.debug("Query content response: " + xmlcontent); ndata.xmlContent(xmlcontent); } JAXBElement jaxbElement = jaxbUtil.unMashallFromString(ndata.xmlContent()); ResponseMessageType messageType = (ResponseMessageType) jaxbElement.getValue(); BodyType bt = messageType.getMessageBody(); MasterResponseType masterResponseType = (MasterResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), MasterResponseType.class); RequestXmlType requestXmlType = masterResponseType.getQueryMaster().get(0) .getRequestXml(); org.w3c.dom.Element element = (org.w3c.dom.Element) requestXmlType.getContent().get(0); if (element != null) { log.debug("query definition not null"); } else { log.error("query definition is null"); } String domString = edu.harvard.i2b2.common.util.xml.XMLUtil .convertDOMElementToString(element); log.debug("string output" + domString); JAXBContext jc1 = JAXBContext .newInstance(edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory.class); Unmarshaller unMarshaller = jc1.createUnmarshaller(); JAXBElement queryDefinitionJaxbElement = (JAXBElement) unMarshaller .unmarshal(new StringReader(domString)); QueryDefinitionType queryDefinitionType = (QueryDefinitionType) queryDefinitionJaxbElement .getValue(); int numOfPanels = queryDefinitionType.getPanel().size(); for (int i = 0; i < numOfPanels; i++) { PanelType panelType = queryDefinitionType.getPanel().get(i); for (int j = 0; j < panelType.getItem().size(); j++) { ItemType itemType = panelType.getItem().get(j); QueryModel nodedata = new QueryModel(); nodedata.name(itemType.getItemName()); nodedata.visualAttribute("FA"); nodedata.tooltip(itemType.getTooltip()); nodedata.fullname(itemType.getItemKey()); nodedata.hlevel(new Integer(itemType.getHlevel()).toString()); String status = nodedata.setXmlContent(); if (status.equalsIgnoreCase("error")) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage( "Response delivered from the remote server could not be understood,\n" + "you may wish to retry your last action."); mBox.open(); event.detail = DND.DROP_NONE; return; } nodeXmls.add(nodedata); } } populateTable(nodeXmls); // get query instance String xmlRequest = ndata.writeContentQueryXML(); lastRequestMessage(xmlRequest); // log.debug(xmlRequest); String xmlResponse = PDOQueryClient.sendPDQQueryRequestREST(xmlRequest); lastResponseMessage(xmlResponse); jaxbElement = jaxbUtil.unMashallFromString(xmlResponse); messageType = (ResponseMessageType) jaxbElement.getValue(); bt = messageType.getMessageBody(); InstanceResponseType instanceResponseType = (InstanceResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), InstanceResponseType.class); QueryInstanceData instanceData = null; XMLGregorianCalendar startDate = null; for (QueryInstanceType queryInstanceType : instanceResponseType.getQueryInstance()) { QueryInstanceData runData = new QueryInstanceData(); runData.visualAttribute("FA"); runData.tooltip("The results of the query run"); runData.id(new Integer(queryInstanceType.getQueryInstanceId()).toString()); XMLGregorianCalendar cldr = queryInstanceType.getStartDate(); runData.name("Results of " + "[" + cldr.getMonth() + "-" + cldr.getDay() + "-" + cldr.getYear() + " " + cldr.getHour() + ":" + cldr.getMinute() + ":" + cldr.getSecond() + "]"); if (instanceData == null) { startDate = cldr; instanceData = runData; } else { if (cldr.toGregorianCalendar().compareTo(startDate.toGregorianCalendar()) > 0) { startDate = cldr; instanceData = runData; } } } // get patient set if (instanceData == null) { event.detail = DND.DROP_NONE; return; } log.debug("Got query instance: " + instanceData.name()); xmlRequest = instanceData.writeContentQueryXML(); lastRequestMessage(xmlRequest); xmlResponse = PDOQueryClient.sendPDQQueryRequestREST(xmlRequest); lastResponseMessage(xmlResponse); jaxbElement = jaxbUtil.unMashallFromString(xmlResponse); messageType = (ResponseMessageType) jaxbElement.getValue(); bt = messageType.getMessageBody(); ResultResponseType resultResponseType = (ResultResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), ResultResponseType.class); for (QueryResultInstanceType queryResultInstanceType : resultResponseType .getQueryResultInstance()) { if (!(queryResultInstanceType.getQueryResultType().getName() .equalsIgnoreCase("PATIENTSET"))) { continue; } String status = queryResultInstanceType.getQueryStatusType().getName(); if (status.equalsIgnoreCase("FINISHED")) { // resultData.name("Patient Set - "+resultData // .patientCount()+" Patients"); // QueryResultData resultData = new // QueryResultData(); String setId = new Integer(queryResultInstanceType.getResultInstanceId()) .toString(); String setSize = new Integer(queryResultInstanceType.getSetSize()).toString(); patientSetText.setText("Patient Set: " + setSize + " patients");// strs[0]); patientRefId = new String(setId);// strs[1]); patientMinNumText.setText("1"); leftArrowButton.setEnabled(false); int maxPatientNum = new Integer(patientMaxNumText.getText()).intValue(); patientSetSize = queryResultInstanceType.getSetSize(); if (patientSetSize > maxPatientNum) { rightArrowButton.setEnabled(true); patientMaxNumText.setText("10"); } else { rightArrowButton.setEnabled(false); if (patientSetSize > 0) { patientMaxNumText.setText(setSize); } } log.debug("Dropped set of: " + setSize + " patients"/* strs[0] */ + " with refId: " + setId/* * strs[ 1 ] */); } else { // message } } } catch (Exception e) { e.printStackTrace(); return; } } else { List conceptChildren = tableXml.getChildren(); parseDropConcepts(conceptChildren, event); // System.setProperty("XMLfrommodel",(String) // event.data); table.redraw(); queryNamemrnlistText.setText("Query Name: "); groupNameText.setText("Panel Name: "); } event.detail = DND.DROP_NONE; } catch (JDOMException e) { System.err.println(e.getMessage()); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here."); mBox.open(); event.detail = DND.DROP_NONE; e.printStackTrace(); return; } catch (Exception e) { System.err.println(e.getMessage()); event.detail = DND.DROP_NONE; e.printStackTrace(); return; } } public void dragEnter(DropTargetEvent event) { event.detail = DND.DROP_COPY; } }); DropTarget target1 = new DropTarget(patientSetText, DND.DROP_COPY); target1.setTransfer(types); target1.addDropListener(new DropTargetAdapter() { @SuppressWarnings("unchecked") public void drop(DropTargetEvent event) { if (event.data == null) { event.detail = DND.DROP_NONE; return; } String tmp = patientSetText.getText(); String dragStr = (String) event.data; String[] strs = dragStr.split(":"); if (strs[0].equalsIgnoreCase("logicquery")) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here. It accepts a patient set only."); mBox.open(); event.detail = DND.DROP_NONE; patientSetText.setText(tmp); return; } JAXBUtil jaxbUtil = ExplorerJAXBUtil.getJAXBUtil(); try { JAXBElement jaxbElement = jaxbUtil.unMashallFromString(dragStr); DndType dndType = (DndType) jaxbElement.getValue(); QueryResultInstanceType queryResultInstanceType = (QueryResultInstanceType) new JAXBUnWrapHelper() .getObjectByClass(dndType.getAny(), QueryResultInstanceType.class); if (queryResultInstanceType == null) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here. It accepts a patient set only."); mBox.open(); event.detail = DND.DROP_NONE; patientSetText.setText(tmp); return; } String resultTypeName = queryResultInstanceType.getQueryResultType().getName(); if (resultTypeName == null || !resultTypeName.equalsIgnoreCase("PATIENTSET")) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not drop this item here. It accepts a patient set only."); mBox.open(); event.detail = DND.DROP_NONE; patientSetText.setText(tmp); return; } String setId = queryResultInstanceType.getResultInstanceId(); String setSize = new Integer(queryResultInstanceType.getSetSize()).toString(); patientSetText.setText(queryResultInstanceType.getDescription());// "Patient Set: " + setSize // + " patients");// strs[0]); patientRefId = new String(setId);// strs[1]); patientMinNumText.setText("1"); leftArrowButton.setEnabled(false); queryNamemrnlistText.setText("Query Name: "); // groupNameText.setText("Panel Name: "); int maxPatientNum = new Integer(patientMaxNumText.getText()).intValue(); patientSetSize = queryResultInstanceType.getSetSize(); if (patientSetSize > maxPatientNum) { rightArrowButton.setEnabled(true); patientMaxNumText.setText("10"); } else { rightArrowButton.setEnabled(false); // if(patientSetSize>0) { // patientMaxNumText.setText(setSize); // } } log.debug("Dropped set of: " + setSize + " patients"/* * strs[0 * ] */ + " with refId: " + setId/* strs[1] */); } catch (Exception e) { e.printStackTrace(); event.detail = DND.DROP_NONE; return; } } public void dragEnter(DropTargetEvent event) { event.detail = DND.DROP_COPY; } }); table.addCellResizeListener(new KTableCellResizeListener() { public void columnResized(int col, int newWidth) { log.debug("Column " + col + " resized to " + newWidth); } public void rowResized(int newHeight) { log.debug("Rows resized to " + newHeight); } }); table.addListener(SWT.Resize, new Listener() { public void handleEvent(Event event) { int tableWidth = table.getBounds().width; table.getModel().setColumnWidth(1, tableWidth - 505); } }); table.addMouseTrackListener(new MouseTrackListener() { public void mouseEnter(MouseEvent arg0) { } public void mouseExit(MouseEvent arg0) { } public void mouseHover(MouseEvent arg0) { MouseEvent evt = arg0; Rectangle rect = table.getCellRect(3, getRowNumber()); Rectangle rect1 = table.getCellRect(5, 1); // System.out.println("rect X and width: "+rect.x+","+rect.width) // ; // System.out.println("mouse X and Y: "+evt.x+","+evt.y); if (evt.y < rect.y && evt.x > rect1.x && evt.x < rect1.x + rect1.width) { table.setToolTipText("Double click the cell to change color."); } else { table.setToolTipText(""); } } }); // Item 2: a Color Palette TabItem item2 = new TabItem(tabFolder, SWT.NONE); item2.setText("Render a Timeline"); final Composite comp2 = new Composite(tabFolder, SWT.NONE); item2.setControl(comp2); GridLayout oGridLayout0 = new GridLayout(); oGridLayout0.marginWidth = 1; oGridLayout0.marginHeight = 5; comp2.setLayout(oGridLayout0); if (false) { Composite composite = new Composite(comp2, SWT.NO_BACKGROUND | SWT.EMBEDDED); /* * Set a Windows specific AWT property that prevents heavyweight * components from erasing their background. Note that this is a * global property and cannot be scoped. It might not be suitable * for your application. */ try { // System.setProperty("sun.awt.noerasebackground", "true"); } catch (NoSuchMethodError error) { } /* Create and setting up frame */ ////for mac fix //if ( System.getProperty("os.name").toLowerCase().startsWith("mac")) //SWT_AWT.embeddedFrameClass = "sun.lwawt.macosx.CViewEmbeddedFrame"; Frame frame = SWT_AWT.new_Frame(composite); Panel panel = new Panel(new BorderLayout()) { public void update(java.awt.Graphics g) { /* Do not erase the background */ paint(g); } }; frame.add(panel); JRootPane root = new JRootPane(); panel.add(root); java.awt.Container contentPane = root.getContentPane(); log.debug("got to here"); Record record1 = new Record(); // record1.start(); record1.init(); JScrollPane scrollPane = new JScrollPane(record1); contentPane.setLayout(new BorderLayout()); contentPane.add(scrollPane); } if (true) { Composite composite = new Composite(comp2, SWT.NO_BACKGROUND | SWT.EMBEDDED); GridData gridData3 = new GridData(); gridData3.horizontalIndent = 0; gridData3.verticalIndent = 0; gridData3.horizontalAlignment = GridData.FILL; gridData3.verticalAlignment = GridData.FILL; gridData3.grabExcessHorizontalSpace = true; gridData3.grabExcessVerticalSpace = true; composite.setLayoutData(gridData3); /* Create and setting up frame */ ////for mac fix //if ( System.getProperty("os.name").toLowerCase().startsWith("mac")) //SWT_AWT.embeddedFrameClass = "sun.lwawt.macosx.CViewEmbeddedFrame"; Frame frame = SWT_AWT.new_Frame(composite); Panel panel = new Panel(new BorderLayout());// { try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception e) { log.debug("Error setting native LAF: " + e); } frame.add(panel); JRootPane root = new JRootPane(); panel.add(root); oAwtContainer = root.getContentPane(); log.debug("got to here"); } tabFolder.addSelectionListener(new SelectionListener() { public void widgetSelected(SelectionEvent e) { runMode = 0; ConceptTableModel i2b2Model = (ConceptTableModel) table.getModel(); i2b2Model.fillDataFromTable(rowData); if (rowData.size() == 0) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("The set up table is empty."); mBox.open(); return; } String patientSetStr = patientSetText.getText(); if (patientSetStr.equals("") && !isAll) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("Please set a patient set or choose all datamart option."); mBox.open(); return; } if (tabFolder.getSelectionIndex() == 1) { if (patientSetStr.equalsIgnoreCase("All")) { int minPatient = 0; try { String minText = patientMinNumText.getText(); minPatient = Integer.parseInt(minText); } catch (Exception e1) { minPatient = -1; } int maxPatient = 0; try { maxPatient = Integer.parseInt(patientMaxNumText.getText()); } catch (Exception e2) { maxPatient = -1; } PerformVisualizationQuery(oAwtContainer, "All", minPatient, maxPatient, bDisplayAllData); } else { int min = Integer.parseInt(patientMinNumText.getText()); int max = Integer.parseInt(patientMaxNumText.getText()); int start = new Integer(patientMinNumText.getText()).intValue(); int inc = new Integer(patientMaxNumText.getText()).intValue(); if (start + inc - 1 > patientSetSize) { rightArrowButton.setEnabled(false); } //patientMinNumText.setText("" + (start + inc)); leftArrowButton.setEnabled(true); PerformVisualizationQuery(oAwtContainer, patientRefId, min, max - 1, bDisplayAllData); } // getDisplay().syncExec(new Runnable() { // public void run() { // if(returnedNumber >= 0) { // //setDecreaseNumber(returnedNumber); // MessageBox mBox = new MessageBox(getShell(), // SWT.ICON_INFORMATION // | SWT.OK); // mBox.setText("Please Note ..."); // mBox.setMessage(/*"Can't return all the requested "+ // requestIndex+" patients, */"Only "+returnedNumber+" // patients returned"); // mBox.open(); // } // } // }); } else { patientMinNumText.setText("1"); java.awt.EventQueue.invokeLater(new Runnable() { public void run() { DestroyMiniVisualization(oAwtContainer); } }); } } public void widgetDefaultSelected(SelectionEvent e) { widgetSelected(e); } }); if (drawLeft) { horizontalForm.setWeights(new int[] { 30, 70 }); } return parent; } //============================================================================================================= //============================================================================================================= //============================================================================================================= private int addQueryModel(QueryDefinitionType queryDefinitionType, ArrayList<QueryModel> queryModels, int conceptCount) { for (int i = 0; i < queryDefinitionType.getPanel().size(); i++) { PanelType panelType = queryDefinitionType.getPanel().get(i); for (int j = 0; j < panelType.getItem().size(); j++) { ItemType itemType = panelType.getItem().get(j); QueryModel nodedata = null; ConstrainByModifier md = itemType.getConstrainByModifier(); if (md != null) { nodedata = new ModifierData(); nodedata.isModifier(true); ((ModifierData) nodedata).modifier_key(md.getModifierKey()); ((ModifierData) nodedata).applied_path(md.getAppliedPath()); ((ModifierData) nodedata).modifier_name(md.getModifierName()); ((ModifierData) nodedata).setModifierValueConstraint(md.getConstrainByValue()); } else { nodedata = new QueryModel(); } nodedata.name(itemType.getItemName()); nodedata.visualAttribute("FA"); nodedata.tooltip(itemType.getTooltip()); nodedata.fullname(itemType.getItemKey()); nodedata.hlevel(new Integer(itemType.getHlevel()).toString()); if (itemType.getItemShape() != null) { nodedata.tableRow().height = new String(itemType.getItemShape()); nodedata.tableRow().color = ((ConceptTableModel) table.getModel()) .getColor(itemType.getItemColor()); nodedata.tableRow().rowNumber = conceptCount + 1; } else { nodedata.tableRow().height = "Medium"; nodedata.tableRow().color = getRGBfromList(conceptCount + 1);//new RGB(0, 0, 128); nodedata.tableRow().rowNumber = conceptCount + 1; } nodedata.constrainByValue(itemType.getConstrainByValue()); if (itemType.getConstrainByValue().size() > 0) { nodedata.setValueConstrains(itemType.getConstrainByValue()); if (itemType.getConstrainByValue().size() > 0) { nodedata.setValueConstrains(itemType.getConstrainByValue()); if (nodedata.valueModel().hasEnumValue()) { if (nodedata.valueModel().useTextValue()) { ArrayList<String> results = new ArrayList<String>(); results.toArray(nodedata.valueModel().value().split(",")); nodedata.valueModel().selectedValues = results; } } } } // Handle Constrain By Dates for (int u = 0; u < itemType.getConstrainByDate().size(); u++) nodedata.setTimeConstrain(itemType.getConstrainByDate().get(u).getDateFrom(), itemType.getConstrainByDate().get(u).getDateTo()); String status = nodedata.setXmlContent(); if (status.equalsIgnoreCase("error")) { continue; } else { nodedata.updateNodeMetaDataXML(); queryModels.add(nodedata); conceptCount++; } } } return conceptCount; } //============================================================================================================= //============================================================================================================= //============================================================================================================= @SuppressWarnings("unchecked") private void setTableRowData(QueryModel panelData, boolean isRawData) { try { SAXBuilder parser = new SAXBuilder(); java.io.StringReader xmlStringReader = new java.io.StringReader(panelData.xmlContent()); org.jdom.Document tableDoc = parser.build(xmlStringReader); org.jdom.Element tableXml = tableDoc.getRootElement().getChild("concepts", Namespace.getNamespace("http://www.i2b2.org/xsd/cell/ont/1.1/")); List conceptChildren = tableXml.getChildren(); for (Iterator itr = conceptChildren.iterator(); itr.hasNext();) { Element conceptXml = (org.jdom.Element) itr.next(); Element conTableXml = (Element) conceptXml; Element metadataAttribs = conTableXml.getChild("metadataxml"); Element valuedataAttribs = null; if (metadataAttribs != null) { valuedataAttribs = metadataAttribs.getChild("ValueMetadata"); } String val = null; values.clear(); valueType = null; String tmp = null; double ll = -1.0; double hl = -1.0; double lh = -1.0; double hh = -1.0; boolean hasValueSet = false; if (valuedataAttribs != null) { if ((tmp = valuedataAttribs.getChildTextTrim("Oktousevalues")) != null) { hasValueSet = true; if (tmp.equalsIgnoreCase("Y")) { valueType = "NVAL_NUM"; } else if (tmp.equalsIgnoreCase("N")) { valueType = "TVAL_CHAR"; } } if ((val = valuedataAttribs.getChildTextTrim("LowofLowValue")) != null && !(val.equals(""))) { ll = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("HighofLowValue")) != null && !(val.equals(""))) { hl = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("LowofHighValue")) != null && !(val.equals(""))) { lh = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("HighofHighValue")) != null && !(val.equals(""))) { hh = new Double(val).doubleValue(); val = null; } } if (ll >= 0) { values.put("LL", new Double(ll).toString()); } if (hl > 0 && hl >= ll) { values.put("HL", new Double(hl).toString()); } if (lh > 0 && lh >= hl) { values.put("NM", new Double(lh).toString()); values.put("LH", new Double(lh).toString()); } if (hh > 0 && hh >= lh) { values.put("HH", new Double(hh).toString()); } log.debug("Got values: " + values.size()); for (int i = 0; i < values.size(); i++) { log.debug("Got value: " + values.get(values.keySet().toArray()[i])); } org.jdom.Element nameXml = conTableXml.getChild("name"); String cname = nameXml.getText(); if (cname.toLowerCase().startsWith("zz")) { cname = cname.substring(2).trim(); } curRowNumber = rowData.size() + 1; // ConceptTableRow row = null; ArrayList<ConceptTableRow> alist = new ArrayList<ConceptTableRow>(); XMLOutputter outputter = new XMLOutputter(); String xmlOutput = outputter.outputString(conceptXml); ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); if (!isRawData) { ConceptTableRow row = panelData.tableRow(); // row.rowNumber = curRowNumber; if (panelData.isModifier()) { row.conceptName = new String(cname) + " [" + ((ModifierData) panelData).modifier_name() + "]"; } else { row.conceptName = new String(cname); } row.dateText = ""; row.valueType = ""; row.valueText = "Not Applicable"; row.modifierText = "Not Applicable"; // row.height = "Medium"; // row.color = new RGB(0, 0, 128); row.conceptXml = new String(xmlOutput); //QueryModel data = m_Model.parseXMLData(xmlOutput); //m_Model.parseXMLData(panelData, xmlOutput); panelData.hasValueSet(hasValueSet); row.data(panelData); if ((row.data.isModifier())) { //ModifierData mdata = (ModifierData) panelData; if ((((ModifierData) row.data).hasModifierValue())) { //row.data.setValueConstrains(panelData.constrainByValue); if (((ModifierData) row.data).modifierValuePropertyData().hasEnumValue()) { //((ModifierData)row.data).modifierValuePropertyData().useTextValue( // panelData.valueModel().useTextValue()); if (((ModifierData) row.data).modifierValuePropertyData().useTextValue()) { String tmpStr1 = ((ModifierData) row.data).modifierValuePropertyData().value() .replaceAll("'", ""); String tmpStr = tmpStr1.substring(1, tmpStr1.length() - 1); String pValue[] = tmpStr.split(","); ArrayList<String> results = new ArrayList<String>(); for (String data1 : pValue) { results.add(data1); } //((ModifierData)row.data).modifierValuePropertyData().selectedValues = results; ((ModifierData) row.data).modifier_display_name(((ModifierData) row.data) .modifierValuePropertyData().getDisplayTexts()); } else {//if(((ModifierData)row.data).modifierValuePropertyData().useValueFlag()){ ((ModifierData) row.data).modifier_display_name(" = Abnormal"); } } } if (!((ModifierData) row.data).modifier_display_name().equalsIgnoreCase("")) { row.modifierText = ((ModifierData) row.data).modifier_display_name(); } else { //if (hasValueSet) { row.modifierText = new String("All Values"); //} } if (((ModifierData) row.data).modifier_display_name().equalsIgnoreCase(" H")) { row.valueText = new String(" = HIGH"); } else if (((ModifierData) row.data).modifier_display_name().equalsIgnoreCase(" L")) { row.valueText = new String(" = LOW"); } } if ((panelData.hasValue())) { row.data.setValueConstrains(panelData.constrainByValue); if (row.data.valueModel().hasEnumValue()) { row.data.valueModel().useTextValue(panelData.valueModel().useTextValue()); if (row.data.valueModel().useTextValue()) { String tmpStr1 = panelData.valueModel().value().replaceAll("'", ""); String tmpStr = tmpStr1.substring(1, tmpStr1.length() - 1); String pValue[] = tmpStr.split(","); ArrayList<String> results = new ArrayList<String>(); for (String data1 : pValue) { results.add(data1); } row.data.valueModel().selectedValues = results; row.data.valueName(row.data.valueModel().getSelectedTexts()); } else { row.data.valueName(" = Abnormal"); } } } if (!row.data.valueName().equalsIgnoreCase("")) { row.valueText = row.data.valueName(); } else { if (hasValueSet) { row.valueText = new String("All Values"); } } if (row.data.valueName().equalsIgnoreCase(" H")) { row.valueText = new String(" = HIGH"); } else if (row.data.valueName().equalsIgnoreCase(" L")) { row.valueText = new String(" = LOW"); } String dateConstraint = ""; if (panelData.startTime() != -1) { row.data.startYear(panelData.startYear()); row.data.startMonth(panelData.startMonth()); row.data.startDay(panelData.startDay()); row.data.startTime(panelData.startTime()); dateConstraint = (row.data.startMonth() + 1) + "/" + row.data.startDay() + "/" + (row.data.startYear()) + " -> "; } if (panelData.endTime() != -1) { row.data.endYear(panelData.endYear()); row.data.endMonth(panelData.endMonth()); row.data.endDay(panelData.endDay()); row.data.endTime(panelData.endTime()); if (dateConstraint.equals("")) dateConstraint = " -> "; dateConstraint += (row.data.endMonth() + 1) + "/" + row.data.endDay() + "/" + (row.data.endYear()); } row.dateText = dateConstraint; alist.add(row); } else { if (values.size() == 0) { ConceptTableRow row = panelData.tableRow(); row.rowNumber = curRowNumber; row.valueText = "All Values"; row.height = "Medium"; row.color = getRGBfromList(curRowNumber);//new RGB(0, 0, 128); row.conceptXml = new String(xmlOutput); QueryModel data = m_Model.parseXMLData(xmlOutput); data.hasValueSet(hasValueSet); row.data(data); alist.add(row); } else { Set s = values.keySet(); String op = null; Object[] strs = s.toArray(); for (int n = 0; n < values.size(); n++) { ConceptTableRow row = new ConceptTableRow(); row.rowNumber = curRowNumber; row.conceptName = new String(cname); row.valueType = new String(valueType); QueryModel data = m_Model.parseXMLData(xmlOutput); op = (String) strs[n]; if (op.equalsIgnoreCase("LL")) { row.valueText = new String(" < " + values.get(strs[n])); row.height = "Very Low"; row.color = new RGB(255, 0, 0); data.valueModel().operator("LESS THAN (<)"); data.valueModel().value(values.get(strs[n])); } else if (op.equalsIgnoreCase("HL")) { row.valueText = new String( " between " + values.get(strs[n - 1]) + " and " + values.get(strs[n])); row.height = "Low"; row.color = new RGB(255, 215, 0); data.valueModel().operator("BETWEEN"); data.valueModel().lowValue(values.get(strs[n - 1])); data.valueModel().highValue(values.get(strs[n])); } else if (op.equalsIgnoreCase("NM")) { row.valueText = new String( " between " + values.get(strs[n - 1]) + " and " + values.get(strs[n])); row.height = "Medium"; row.color = new RGB(0, 255, 0); data.valueModel().operator("between"); data.valueModel().lowValue(values.get(strs[n - 1])); data.valueModel().highValue(values.get(strs[n])); } else if (op.equalsIgnoreCase("LH")) { row.valueText = new String( " between " + values.get(strs[n]) + " and " + values.get(strs[n + 1])); row.height = "Tall"; row.color = new RGB(255, 215, 0); data.valueModel().operator("between"); data.valueModel().lowValue(values.get(strs[n])); data.valueModel().highValue(values.get(strs[n + 1])); } else if (op.equalsIgnoreCase("HH")) { row.valueText = new String(" > " + values.get(strs[n])); row.height = "Very Tall"; row.color = new RGB(255, 0, 0); data.valueModel().operator("GREATER THAN (>)"); data.valueModel().value(values.get(strs[n])); } row.conceptXml = new String(xmlOutput); data.hasValueSet(hasValueSet); data.valueModel().useNumericValue(true); row.data(data); alist.add(row); } } } rowData.add(alist); } } catch (JDOMException e) { System.err.println(e.getMessage()); e.printStackTrace(); } catch (IOException e) { System.err.println(e.getMessage()); e.printStackTrace(); } } @SuppressWarnings("unchecked") private void parseListOfConcepts(List conceptChildren) { for (Iterator itr = conceptChildren.iterator(); itr.hasNext();) { Element conceptXml = (org.jdom.Element) itr.next(); Element conTableXml = (Element) conceptXml; Element metadataAttribs = conTableXml.getChild("metadataxml"); Element valuedataAttribs = null; if (metadataAttribs != null) { valuedataAttribs = metadataAttribs.getChild("ValueMetadata"); } String val = null; values.clear(); valueType = null; String tmp = null; double ll = -1.0; double hl = -1.0; double lh = -1.0; double hh = -1.0; if (valuedataAttribs != null) { if ((tmp = valuedataAttribs.getChildTextTrim("Oktousevalues")) != null) { if (tmp.equalsIgnoreCase("Y")) { valueType = ""; } else if (tmp.equalsIgnoreCase("N")) { valueType = ""; } } if ((val = valuedataAttribs.getChildTextTrim("LowofLowValue")) != null && !(val.equals(""))) { ll = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("HighofLowValue")) != null && !(val.equals(""))) { hl = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("LowofHighValue")) != null && !(val.equals(""))) { lh = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("HighofHighValue")) != null && !(val.equals(""))) { hh = new Double(val).doubleValue(); val = null; } } if (ll >= 0) { values.put("LL", new Double(ll).toString()); } if (hl > 0 && hl >= ll) { values.put("HL", new Double(hl).toString()); } if (lh > 0 && lh >= hl) { values.put("NM", new Double(lh).toString()); values.put("LH", new Double(lh).toString()); } if (hh > 0 && hh >= lh) { values.put("HH", new Double(hh).toString()); } log.debug("Got values: " + values.size()); for (int i = 0; i < values.size(); i++) { log.debug("Got value: " + values.get(values.keySet().toArray()[i])); } org.jdom.Element nameXml = conTableXml.getChild("name"); String cname = nameXml.getText(); if (cname.toLowerCase().startsWith("zz")) { cname = cname.substring(2).trim(); } curRowNumber = rowData.size() + 1; ConceptTableRow row = null; ArrayList<ConceptTableRow> alist = new ArrayList<ConceptTableRow>(); XMLOutputter outputter = new XMLOutputter(); String xmlOutput = outputter.outputString(conceptXml); ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); if (values.size() == 0) { row = new ConceptTableRow(); row.rowNumber = curRowNumber; row.conceptName = new String(cname); row.dateText = ""; row.valueType = ""; row.valueText = ""; row.height = "Medium"; row.color = getRGBfromList(curRowNumber);//new RGB(0, 0, 128); row.conceptXml = new String(xmlOutput); row.data(m_Model.parseXMLData(xmlOutput)); alist.add(row); } else { Set s = values.keySet(); String op = null; Object[] strs = s.toArray(); for (int n = 0; n < values.size(); n++) { row = new ConceptTableRow(); row.rowNumber = curRowNumber; row.conceptName = new String(cname); row.valueType = new String(valueType); op = (String) strs[n]; if (op.equalsIgnoreCase("LL")) { row.valueText = new String(" < " + values.get(strs[n])); row.height = "Very Low"; row.color = new RGB(255, 0, 0); } else if (op.equalsIgnoreCase("HL")) { row.valueText = new String( " between " + values.get(strs[n - 1]) + " and " + values.get(strs[n])); row.height = "Low"; row.color = new RGB(255, 215, 0); } else if (op.equalsIgnoreCase("NM")) { row.valueText = new String( " between " + values.get(strs[n - 1]) + " and " + values.get(strs[n])); row.height = "Medium"; row.color = new RGB(0, 255, 0); } else if (op.equalsIgnoreCase("LH")) { row.valueText = new String( " between " + values.get(strs[n]) + " and " + values.get(strs[n + 1])); row.height = "Tall"; row.color = new RGB(255, 215, 0); } else if (op.equalsIgnoreCase("HH")) { row.valueText = new String(" > " + values.get(strs[n])); row.height = "Very Tall"; row.color = new RGB(255, 0, 0); } row.conceptXml = new String(xmlOutput); row.data(m_Model.parseXMLData(xmlOutput)); alist.add(row); } } rowData.add(alist); } } @SuppressWarnings("unchecked") private void setupTable(String xmlContent) { try { SAXBuilder parser = new SAXBuilder(); java.io.StringReader xmlStringReader = new java.io.StringReader(xmlContent); org.jdom.Document tableDoc = parser.build(xmlStringReader); org.jdom.Element tableXml = tableDoc.getRootElement().getChild("concepts", Namespace.getNamespace("http://www.i2b2.org/xsd/cell/ont/1.1/")); List conceptChildren = tableXml.getChildren(); parseListOfConcepts(conceptChildren); } catch (JDOMException e) { System.err.println(e.getMessage()); e.printStackTrace(); } catch (IOException e) { System.err.println(e.getMessage()); e.printStackTrace(); } } public void populateTable(ArrayList<QueryModel> xmlContents) { ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); m_Model.deleteAllRows(); curRowNumber = 0; rowData.clear(); for (int i = 0; i < xmlContents.size(); i++) { setTableRowData(xmlContents.get(i), false); } m_Model.populateTable(rowData); oTheParent.getDisplay().syncExec(new Runnable() { public void run() { table.redraw(); } }); } public void populateTableString(ArrayList<String> xmlContents) { ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); m_Model.deleteAllRows(); curRowNumber = 0; rowData.clear(); for (int i = 0; i < xmlContents.size(); i++) { setupTable(xmlContents.get(i)); // parseListOfConcepts(xmlContents.get(i)); } m_Model.populateTable(rowData); oTheParent.getDisplay().syncExec(new Runnable() { public void run() { table.redraw(); } }); } private void performVisualization() { if (tabFolder.getSelectionIndex() == 1) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { DestroyMiniVisualization(oAwtContainer); } }); } else if (tabFolder.getSelectionIndex() == 0) { tabFolder.setSelection(1); } String patientSetStr = patientSetText.getText(); if (patientSetStr.equalsIgnoreCase("All")) { int minPatient = 0; try { String minText = patientMinNumText.getText(); minPatient = Integer.parseInt(minText); } catch (Exception e1) { minPatient = -1; } int maxPatient = 0; try { maxPatient = Integer.parseInt(patientMaxNumText.getText()); } catch (Exception e2) { maxPatient = -1; } PerformVisualizationQuery(oAwtContainer, "All", minPatient, maxPatient, bDisplayAllData); } else { int min = Integer.parseInt(patientMinNumText.getText()); int max = Integer.parseInt(patientMaxNumText.getText()); PerformVisualizationQuery(oAwtContainer, patientRefId, min, max, bDisplayAllData); } } public void generateTimeLine() { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { performVisualization(); } }); } @SuppressWarnings("unchecked") private void resetRowNumber() { for (int i = 0; i < rowData.size(); i++) { ArrayList list = (ArrayList) rowData.get(i); for (int j = 0; j < list.size(); j++) { ConceptTableRow row = (ConceptTableRow) list.get(j); row.rowNumber = i + 1; } } } @SuppressWarnings("unchecked") private void parseDropConcepts(List conceptChildren, DropTargetEvent event) { for (Iterator itr = conceptChildren.iterator(); itr.hasNext();) { Element conceptXml = (org.jdom.Element) itr.next(); String conceptText = conceptXml.getText().trim(); if (conceptText.equals("null")) // this is root level node { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not use this item in a query, it is only used for organizing the lists."); mBox.open(); event.detail = DND.DROP_NONE; return; } Element conTableXml = (Element) conceptXml; Element visualAttribs = conTableXml.getChild("visualattributes"); String sVisualAttribs = visualAttribs.getText().trim(); if (sVisualAttribs.toUpperCase().startsWith("C")) { MessageBox mBox = new MessageBox(table.getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("You can not use this item in a query, it is only used for organizing the lists."); mBox.open(); event.detail = DND.DROP_NONE; return; } Element metadataAttribs = conTableXml.getChild("metadataxml"); Element valuedataAttribs = null; if (metadataAttribs != null) { valuedataAttribs = metadataAttribs.getChild("ValueMetadata"); } String val = null; values.clear(); valueType = null; String tmp = null; double ll = -1.0; double hl = -1.0; double lh = -1.0; double hh = -1.0; boolean hasValueSet = false; if (valuedataAttribs != null) { if ((tmp = valuedataAttribs.getChildTextTrim("Oktousevalues")) != null) { hasValueSet = true; if (tmp.equalsIgnoreCase("Y")) { valueType = "NVAL_NUM"; } else if (tmp.equalsIgnoreCase("N")) { valueType = "TVAL_CHAR"; } } if ((val = valuedataAttribs.getChildTextTrim("LowofLowValue")) != null && !(val.equals(""))) { ll = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("HighofLowValue")) != null && !(val.equals(""))) { hl = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("LowofHighValue")) != null && !(val.equals(""))) { lh = new Double(val).doubleValue(); val = null; } if ((val = valuedataAttribs.getChildTextTrim("HighofHighValue")) != null && !(val.equals(""))) { hh = new Double(val).doubleValue(); val = null; } } if (ll >= 0) { values.put("LL", new Double(ll).toString()); } if (hl > 0 && hl >= ll) { values.put("HL", new Double(hl).toString()); } if (lh > 0 && lh >= hl) { values.put("NM", new Double(lh).toString()); values.put("LH", new Double(lh).toString()); } if (hh > 0 && hh >= lh) { values.put("HH", new Double(hh).toString()); } log.debug("Got values: " + values.size()); for (int i = 0; i < values.size(); i++) { log.debug("Got value: " + values.get(values.keySet().toArray()[i])); } org.jdom.Element nameXml = conTableXml.getChild("name"); String cname = nameXml.getText(); if (cname.toLowerCase().startsWith("zz")) { cname = cname.substring(2).trim(); } // org.jdom.Element fullnameXml = conTableXml.getChild("key"); // String cfullname = fullnameXml.getText(); curRowNumber = rowData.size(); ConceptTableModel m_Model = (ConceptTableModel) table.getModel(); m_Model.fillDataFromTable(rowData); curRowNumber = rowData.size() + 1; ConceptTableRow row = null; ArrayList<ConceptTableRow> alist = new ArrayList<ConceptTableRow>(); XMLOutputter outputter = new XMLOutputter(); String xmlOutput = outputter.outputString(conceptXml); if (values.size() == 0) { QueryModel data = m_Model.parseXMLData(xmlOutput); row = new ConceptTableRow(); row.rowNumber = curRowNumber; if (data.isModifier()) { row.conceptName = new String(cname + " [" + ((ModifierData) data).modifier_name() + "]"); } else { row.conceptName = new String(cname); } row.dateText = ""; row.valueType = ""; row.valueText = "All Values"; row.modifierText = "Not Applicable"; row.height = "Medium"; row.color = getRGBfromList(curRowNumber);//rgbList.get(curRowNumber);//new RGB(0, 0, 128); //row.setColor(); row.conceptXml = new String(xmlOutput); row.data(data); alist.add(row); } else { Set s = values.keySet(); String op = null; Object[] strs = s.toArray(); for (int n = 0; n < values.size(); n++) { row = new ConceptTableRow(); row.rowNumber = curRowNumber; row.conceptName = new String(cname); row.valueType = new String(valueType); QueryModel data = m_Model.parseXMLData(xmlOutput); op = (String) strs[n]; if (op.equalsIgnoreCase("LL")) { row.valueText = new String(" < " + values.get(strs[n])); row.height = "Very Low"; row.color = new RGB(255, 0, 0); data.valueModel().operator("LESS THAN (<)"); data.valueModel().value(values.get(strs[n])); } else if (op.equalsIgnoreCase("HL")) { row.valueText = new String( " between " + values.get(strs[n - 1]) + " and " + values.get(strs[n])); row.height = "Low"; row.color = new RGB(255, 215, 0); data.valueModel().operator("BETWEEN"); data.valueModel().lowValue(values.get(strs[n - 1])); data.valueModel().highValue(values.get(strs[n])); } else if (op.equalsIgnoreCase("NM")) { row.valueText = new String( " between " + values.get(strs[n - 1]) + " and " + values.get(strs[n])); row.height = "Medium"; row.color = new RGB(0, 255, 0); data.valueModel().operator("between"); data.valueModel().lowValue(values.get(strs[n - 1])); data.valueModel().highValue(values.get(strs[n])); } else if (op.equalsIgnoreCase("LH")) { row.valueText = new String( " between " + values.get(strs[n]) + " and " + values.get(strs[n + 1])); row.height = "Tall"; row.color = new RGB(255, 215, 0); data.valueModel().operator("between"); data.valueModel().lowValue(values.get(strs[n])); data.valueModel().highValue(values.get(strs[n + 1])); } else if (op.equalsIgnoreCase("HH")) { row.valueText = new String(" > " + values.get(strs[n])); row.height = "Very Tall"; row.color = new RGB(255, 0, 0); data.valueModel().operator("GREATER THAN (>)"); data.valueModel().value(values.get(strs[n])); } row.conceptXml = new String(xmlOutput); data.hasValueSet(hasValueSet); data.valueModel().useNumericValue(true); data.valueModel().noValue(false); row.data(data); alist.add(row); } } rowData.add(alist); m_Model.deleteAllRows(); m_Model.populateTable(rowData); } } public boolean PerformVisualizationQuery(final java.awt.Container oAwtContainer, final int minPatient, final int maxPatient, final boolean bDisplayAll) { bStillPerformingVisualizationQuery = true; bNoError = true; p = new WaitPanel((int) (oAwtContainer.getWidth() * 0.40), (int) (oAwtContainer.getHeight() * 0.40), (maxPatient - minPatient)); oAwtContainer.add(p); p.setBounds(0, 0, p.getParent().getWidth(), p.getParent().getHeight()); p.init((int) (p.getParent().getWidth() * 0.40), (int) (p.getParent().getHeight() * 0.40)); p.go(); p.setVisible(true); removelldFile(); visualizationQueryThread = new Thread() { public void run() { log.info("before getResultSetAsi2b2XML: " + new Date()); try { ConceptTableModel i2b2Model = (ConceptTableModel) table.getModel(); String xmlContent = i2b2Model.getContentXml(); oConnection = DBLib.openJDBCConnection(System.getProperty("datamartURL"), System.getProperty("datamartDriver"), System.getProperty("datamartUser"), System.getProperty("datamartPassword")); Properties properties = new Properties(); String writeFileStr = ""; String filename = "crcnavigator.properties"; try { properties.load(new FileInputStream(filename)); writeFileStr = properties.getProperty("writeTimelineFile"); log.debug("Properties writeFile: =" + writeFileStr); } catch (IOException e) { log.error(e.getMessage()); } boolean writeFile = false; if ((writeFileStr != null) && (writeFileStr.equalsIgnoreCase("yes"))) { writeFile = true; } String result = DBLib.getResultSetFromI2B2Xml(xmlContent, minPatient, maxPatient, bDisplayAll, oConnection, writeFile, bDisplayDemographics); DBLib.closeConnection(oConnection); if (result != null) { if (result.equalsIgnoreCase("memory error")) { JOptionPane.showMessageDialog(oAwtContainer, "Running out of memory while loading " + (maxPatient - minPatient) + " patients." + "\nPlease try it again with a smaller number of patients."); bNoError = false; } else { PerformMiniVisualization(oAwtContainer, result, writeFile); } } p.stop(); p.setVisible(false); if (result.equalsIgnoreCase("memory error")) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); } } catch (Exception e) { p.stop(); p.setVisible(false); oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); log.error(e.getMessage()); bNoError = false; } log.info("after getResultSetAsi2b2XML: " + new Date()); } }; try { visualizationQueryThread.start(); } catch (Exception e) { p.stop(); p.setVisible(false); oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); log.error(e.getMessage()); return false; } return bNoError; } public boolean PerformVisualizationQuery(final java.awt.Container oAwtContainer, final int[] patientIds, final boolean bDisplayAll) { bStillPerformingVisualizationQuery = true; bNoError = true; p = new WaitPanel((int) (oAwtContainer.getWidth() * 0.40), (int) (oAwtContainer.getHeight() * 0.40), patientIds.length); oAwtContainer.add(p); p.setBounds(0, 0, p.getParent().getWidth(), p.getParent().getHeight()); p.init((int) (p.getParent().getWidth() * 0.40), (int) (p.getParent().getHeight() * 0.40)); p.go(); p.setVisible(true); removelldFile(); visualizationQueryThread = new Thread() { public void run() { log.info("before getResultSetAsi2b2XML: " + new Date()); try { ConceptTableModel i2b2Model = (ConceptTableModel) table.getModel(); String xmlContent = i2b2Model.getContentXml(); oConnection = DBLib.openJDBCConnection(System.getProperty("datamartURL"), System.getProperty("datamartDriver"), System.getProperty("datamartUser"), System.getProperty("datamartPassword")); Properties properties = new Properties(); String writeFileStr = ""; String filename = "crcnavigator.properties"; try { properties.load(new FileInputStream(filename)); writeFileStr = properties.getProperty("writeTimelineFile"); log.debug("Properties writeFile: =" + writeFileStr); } catch (IOException e) { log.error(e.getMessage()); } boolean writeFile = true; if ((writeFileStr != null) && (writeFileStr.equalsIgnoreCase("no"))) { writeFile = false; } String result = DBLib.getResultSetFromI2B2Xml(xmlContent, patientIds, bDisplayAll, oConnection, writeFile, bDisplayDemographics); DBLib.closeConnection(oConnection); if (result != null) { if (result.equalsIgnoreCase("memory error")) { JOptionPane.showMessageDialog(oAwtContainer, "Running out of memory while loading " + patientIds.length + " patients." + "\nPlease try it again with a smaller number of patients."); bNoError = false; } else { PerformMiniVisualization(oAwtContainer, result, writeFile); } } p.stop(); p.setVisible(false); if (result.equalsIgnoreCase("memory error")) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); } } catch (Exception e) { log.error(e.getMessage()); bNoError = false; } log.info("after getResultSetAsi2b2XML: " + new Date()); } }; try { visualizationQueryThread.start(); } catch (Exception e) { log.error(e.getMessage()); } return bNoError; } public boolean PerformVisualizationQuery(final java.awt.Container oAwtContainer, final String patientRefId, final int minPatient, final int maxPatient, final boolean bDisplayAll) { bStillPerformingVisualizationQuery = true; bNoError = true; p = new WaitPanel((int) (oAwtContainer.getWidth() * 0.40), (int) (oAwtContainer.getHeight() * 0.40), (maxPatient - minPatient)); oAwtContainer.add(p); p.setBounds(0, 0, p.getParent().getWidth(), p.getParent().getHeight()); p.init((int) (p.getParent().getWidth() * 0.40), (int) (p.getParent().getHeight() * 0.40)); p.go(); p.setVisible(true); removelldFile(); final MainComposite explorer = this; visualizationQueryThread = new Thread() { public void run() { log.info("before getResultSetAsi2b2XML: " + new Date()); try { ConceptTableModel i2b2Model = (ConceptTableModel) table.getModel(); i2b2Model.fillDataFromTable(rowData); Properties properties = new Properties(); String writeFileStr = ""; String filename = "i2b2workbench.properties"; try { properties.load(new FileInputStream(filename)); writeFileStr = properties.getProperty("writeTimelineFile"); log.debug("Properties writeFile: =" + writeFileStr); } catch (IOException e) { log.error(e.getMessage()); } boolean writeFile = false; if ((writeFileStr != null) && (writeFileStr.equalsIgnoreCase("yes"))) { writeFile = true; } ArrayList<TimelineRow> tlrows = i2b2Model.getTimelineRows(rowData); String result = PDOQueryClient.getlldString(tlrows, patientRefId, minPatient, minPatient + maxPatient, bDisplayAll, writeFile, bDisplayDemographics, explorer, filter); if (result != null) { if (result.equalsIgnoreCase("memory error")) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(oAwtContainer, "Running out of memory while loading " + (maxPatient - minPatient) + " patients." + "\nPlease try it again with a smaller number of patients."); } }); bNoError = false; } else if (result.equalsIgnoreCase("error")) { java.awt.EventQueue.invokeLater(new Runnable() { public void run() { JOptionPane.showMessageDialog(oAwtContainer, "Response delivered from the remote server could not be " + "understood, you may wish to retry your last action"); } }); bNoError = false; } else { PerformMiniVisualization(oAwtContainer, result, writeFile); } } else { // JOptionPane.showMessageDialog(oAwtContainer, // "Response delivered from the remote server could not be understood, you may wish to retry your last action" // ); bNoError = false; } p.stop(); p.setVisible(false); if (result == null || result.equalsIgnoreCase("memory error") || result.equalsIgnoreCase("error")) { oTheParent.getDisplay().syncExec(new Runnable() { public void run() { tabFolder.setSelection(0); } }); } } catch (Exception e) { log.error(e.getMessage()); bNoError = false; e.printStackTrace(); } log.info("after getResultSetAsi2b2XML: " + new Date()); } }; try { visualizationQueryThread.start(); } catch (Exception e) { log.error(e.getMessage()); } return bNoError; } public void PerformMiniVisualization(java.awt.Container poAwtContainer, String result, boolean writeFile) { try { poAwtContainer.removeAll(); log.info("Got to PerformMiniVisualization"); Record record1 = new Record(); poAwtContainer.add(record1); // record1.start(); if (writeFile) { record1.init(); } else { record1.init(result); } theRecord = record1; if (returnedNumber >= 0) { getDisplay().syncExec(new Runnable() { public void run() { MessageBox mBox = new MessageBox(getShell(), SWT.ICON_INFORMATION | SWT.OK); mBox.setText("Please Note ..."); mBox.setMessage("Only " + (returnedNumber) + " patients returned"); mBox.open(); } }); } } catch (Exception e) { log.error("done"); // } } @SuppressWarnings("deprecation") public void DestroyMiniVisualization(final java.awt.Container poAwtContainer) { try { if (p != null) { p.stop(); p.setVisible(false); p = null; } if (visualizationQueryThread != null) { visualizationQueryThread.stop(); visualizationQueryThread = null; } if (oConnection != null) { oConnection = null; } log.debug("got to destroy"); theRecord.removeAll(); theRecord = null; poAwtContainer.removeAll(); } catch (Exception e) { // log.error("done"); } } protected Control getConceptTreeTabControl(TabFolder tabFolder) { Composite compositeQueryTree = new Composite(tabFolder, SWT.NULL); GridLayout gridLayout = new GridLayout(); gridLayout.numColumns = 1; gridLayout.horizontalSpacing = 1; gridLayout.verticalSpacing = 1; gridLayout.marginHeight = 0; gridLayout.marginWidth = 0; compositeQueryTree.setLayout(gridLayout); // *Group compositeQueryTreeTop = new Group(compositeQueryTree, // SWT.NULL); // *compositeQueryTreeTop.setText("Query Items"); GridLayout gridLayoutTree = new GridLayout(1, false); gridLayoutTree.numColumns = 1; gridLayoutTree.marginHeight = 0; // *compositeQueryTreeTop.setLayout(gridLayoutTree); GridData fromTreeGridData = new GridData(GridData.FILL_BOTH); fromTreeGridData.widthHint = 300; // *compositeQueryTreeTop.setLayoutData(fromTreeGridData); compositeQueryTree.setLayoutData(fromTreeGridData); // TreeComposite dragTree = new TreeComposite(compositeQueryTree, 1, // slm); // TreeComposite dragTree = new TreeComposite(compositeQueryTree, // 1,slm); // dragTree.setLayoutData(new GridData (GridData.FILL_BOTH)); // dragTree.setLayout(gridLayout); return compositeQueryTree; } private void processPanels(PanelType panelType) { //PanelType panelType = queryDefinitionType //.getPanel().get(i); for (int j = 0; j < panelType.getItem().size(); j++) { ItemType itemType = panelType.getItem().get(j); /////////////////////////////////////// QueryModel nodedata = null; if (itemType.getConstrainByModifier() != null) { nodedata = new ModifierData(); //itemType.getConstrainByModifier(). } else { nodedata = new QueryModel(); } nodedata.name(itemType.getItemName()); nodedata.visualAttribute("FA"); nodedata.tooltip(itemType.getTooltip()); nodedata.fullname(itemType.getItemKey()); nodedata.hlevel(new Integer(itemType.getHlevel()).toString()); if (itemType.getItemShape() != null) { nodedata.tableRow().height = new String(itemType.getItemShape()); nodedata.tableRow().color = ((ConceptTableModel) table.getModel()) .getColor(itemType.getItemColor()); // nodedata.tableRow().rowNumber = // Integer // .parseInt(itemType // .getItemRowNumber()); //nodedata.tableRow().rowNumber = conceptCount + 1; } else { nodedata.tableRow().height = "Medium"; nodedata.tableRow().color = new RGB(0, 0, 128); //nodedata.tableRow().rowNumber = conceptCount + 1; } nodedata.constrainByValue(itemType.getConstrainByValue()); if (itemType.getConstrainByValue().size() > 0) { nodedata.setValueConstrains(itemType.getConstrainByValue()); if (itemType.getConstrainByValue().size() > 0) { nodedata.setValueConstrains(itemType.getConstrainByValue()); if (nodedata.valueModel().hasEnumValue()) { if (nodedata.valueModel().useTextValue()) { ArrayList<String> results = new ArrayList<String>(); results.toArray(nodedata.valueModel().value().split(",")); nodedata.valueModel().selectedValues = results; } } } } // Handle Constrain By Dates for (int u = 0; u < itemType.getConstrainByDate().size(); u++) { nodedata.setTimeConstrain(itemType.getConstrainByDate().get(u).getDateFrom(), itemType.getConstrainByDate().get(u).getDateTo()); } String status = nodedata.setXmlContent(); if (status.equalsIgnoreCase("error")) { // MessageBox mBox = new // MessageBox(table // .getShell(), // SWT.ICON_INFORMATION | SWT.OK); // mBox.setText("Please Note ..."); // mBox.setMessage("Response delivered from the remote server could not be understood,\n" // + // "you may wish to retry your last action."); // mBox.open(); // event.detail = DND.DROP_NONE; continue; } else { //nodeXmls.add(nodedata); //conceptCount++; } } } public static void main(String[] args) { final String ssFakeApplicationConfigurationXML = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n" + "<contents>\r\n" + " <table>\r\n" + " <name>Demographics</name>\r\n" + " <tableName>Demographics</tableName>\r\n" + " <status/>\r\n" + " <description/>\r\n" + " <lookupDB>metadata</lookupDB>\r\n" + " <webserviceName>http://phsi2b2appprod1.mgh.harvard.edu:8080/i2b2/services/Select</webserviceName>\r\n" + " </table>\r\n" + " <table>\r\n" + " <name>Diagnoses</name>\r\n" + " <tableName>Diagnoses</tableName>\r\n" + " <status/>\r\n" + " <description/>\r\n" + " <lookupDB>metadata</lookupDB>\r\n" + " <webserviceName>http://phsi2b2appprod1.mgh.harvard.edu:8080/i2b2/services/Select</webserviceName>\r\n" + " </table>\r\n" + " <table>\r\n" + " <name>Medications</name>\r\n" + " <tableName>Medications</tableName>\r\n" + " <status/>\r\n" + " <description/>\r\n" + " <lookupDB>metadata</lookupDB>\r\n" + " <webserviceName>http://phsi2b2appprod1.mgh.harvard.edu:8080/i2b2/services/Select</webserviceName>\r\n" + " </table>\r\n" + " <table>\r\n" + " <name>I2B2</name>\r\n" + " <tableName>i2b2</tableName>\r\n" + " <status/>\r\n" + " <description/>\r\n" + " <lookupDB>metadata</lookupDB>\r\n" + " <webserviceName>http://phsi2b2appprod1.mgh.harvard.edu:8080/i2b2/services/Select</webserviceName>\r\n" + " </table>\r\n" + "</contents>"; System.setProperty("ApplicationConfigurationXML", ssFakeApplicationConfigurationXML); Display display = new Display(); Shell shell = new Shell(display); shell.setLayout(new FillLayout(SWT.HORIZONTAL)); shell.setText("ExplorerC Test"); shell.setSize(1000, 800); // ExplorerC oExplorerC = new ExplorerC(shell); // shell.pack(); shell.open(); // oExplorerC.run(); while (!shell.isDisposed()) { if (!display.readAndDispatch()) { display.sleep(); } } display.dispose(); } boolean bStillPerformingVisualizationQuery; boolean bNoError; private void removelldFile() { try { String datafile = "i2b2xml.lld"; String appDirectory = System.getProperty("user.dir").toString(); datafile = appDirectory + File.separator + datafile; File f = new File(datafile); if (f.exists()) { f.delete(); } log.debug(datafile); } catch (Exception e) { e.printStackTrace(); } } public void processQueryData(QueryMasterData ndata) { ArrayList<QueryModel> nodeXmls = new ArrayList<QueryModel>(); try { JAXBUtil jaxbUtil = ExplorerJAXBUtil.getJAXBUtil(); String xmlcontent = null; String xmlrequest = null; xmlrequest = ndata.writeDefinitionQueryXML(); lastRequestMessage(xmlrequest); if (System.getProperty("webServiceMethod").equals("SOAP")) xmlcontent = PDOQueryClient.sendPDQQueryRequestSOAP(xmlrequest); else xmlcontent = PDOQueryClient.sendPDQQueryRequestREST(xmlrequest); lastResponseMessage(xmlcontent); if (xmlcontent == null) return; else { log.debug("Query content response: " + xmlcontent); ndata.xmlContent(xmlcontent); } JAXBElement jaxbElement = jaxbUtil.unMashallFromString(ndata.xmlContent()); ResponseMessageType messageType = (ResponseMessageType) jaxbElement.getValue(); BodyType bt = messageType.getMessageBody(); MasterResponseType masterResponseType = (MasterResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), MasterResponseType.class); RequestXmlType requestXmlType = masterResponseType.getQueryMaster().get(0).getRequestXml(); org.w3c.dom.Element element = (org.w3c.dom.Element) requestXmlType.getContent().get(0); if (element != null) log.debug("query definition not null"); else log.error("query definition is null"); String domString = edu.harvard.i2b2.common.util.xml.XMLUtil.convertDOMElementToString(element); log.debug("string output" + domString); JAXBContext jc1 = JAXBContext .newInstance(edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory.class); Unmarshaller unMarshaller = jc1.createUnmarshaller(); JAXBElement queryDefinitionJaxbElement = (JAXBElement) unMarshaller .unmarshal(new StringReader(domString)); QueryDefinitionType queryDefinitionType = (QueryDefinitionType) queryDefinitionJaxbElement.getValue(); int numOfPanels = queryDefinitionType.getPanel().size(); int conceptCount = 0; if (queryDefinitionType.getSubquery().size() == 0) // it's a normal query conceptCount = addQueryModel(queryDefinitionType, nodeXmls, conceptCount); // add concepts to nodeXmls, increment conceptCount else if (queryDefinitionType.getSubquery().size() > 0) // temporal queries have subqueries { conceptCount = addQueryModel(queryDefinitionType, nodeXmls, conceptCount); List<QueryDefinitionType> subqueries = queryDefinitionType.getSubquery(); for (QueryDefinitionType subQuery : subqueries) conceptCount = addQueryModel(subQuery, nodeXmls, conceptCount); // for each subquery, add concepts to nodeXmls, increment conceptCount } if (nodeXmls.size() == 0) return; populateTable(nodeXmls); // get query instance String xmlRequest = ndata.writeContentQueryXML(); lastRequestMessage(xmlRequest); String xmlResponse = PDOQueryClient.sendPDQQueryRequestREST(xmlRequest); lastResponseMessage(xmlResponse); jaxbElement = jaxbUtil.unMashallFromString(xmlResponse); messageType = (ResponseMessageType) jaxbElement.getValue(); bt = messageType.getMessageBody(); InstanceResponseType instanceResponseType = (InstanceResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), InstanceResponseType.class); QueryInstanceData instanceData = null; XMLGregorianCalendar startDate = null; for (QueryInstanceType queryInstanceType : instanceResponseType.getQueryInstance()) { QueryInstanceData runData = new QueryInstanceData(); runData.visualAttribute("FA"); runData.tooltip("The results of the query run"); runData.id(new Integer(queryInstanceType.getQueryInstanceId()).toString()); XMLGregorianCalendar cldr = queryInstanceType.getStartDate(); runData.name("Results of " + "[" + cldr.getMonth() + "-" + cldr.getDay() + "-" + cldr.getYear() + " " + cldr.getHour() + ":" + cldr.getMinute() + ":" + cldr.getSecond() + "]"); if (instanceData == null) { startDate = cldr; instanceData = runData; } else { if (cldr.toGregorianCalendar().compareTo(startDate.toGregorianCalendar()) > 0) { startDate = cldr; instanceData = runData; } } } // get patient set if (instanceData == null) return; log.debug("Got query instance: " + instanceData.name()); xmlRequest = instanceData.writeContentQueryXML(); lastRequestMessage(xmlRequest); xmlResponse = PDOQueryClient.sendPDQQueryRequestREST(xmlRequest); lastResponseMessage(xmlResponse); jaxbElement = jaxbUtil.unMashallFromString(xmlResponse); messageType = (ResponseMessageType) jaxbElement.getValue(); bt = messageType.getMessageBody(); ResultResponseType resultResponseType = (ResultResponseType) new JAXBUnWrapHelper() .getObjectByClass(bt.getAny(), ResultResponseType.class); for (QueryResultInstanceType queryResultInstanceType : resultResponseType.getQueryResultInstance()) { if (!(queryResultInstanceType.getQueryResultType().getName().equalsIgnoreCase("PATIENTSET"))) continue; String status = queryResultInstanceType.getQueryStatusType().getName(); if (status.equalsIgnoreCase("FINISHED")) { String setId = new Integer(queryResultInstanceType.getResultInstanceId()).toString(); final String setSize = new Integer(queryResultInstanceType.getSetSize()).toString(); final String description = queryResultInstanceType.getDescription(); patientRefId = new String(setId); patientSetSize = queryResultInstanceType.getSetSize(); Display.getDefault().asyncExec(new Runnable() { public void run() { if (description != null) patientSetText.setText(description); else patientSetText.setText("Patient Set: " + setSize + " patients"); patientMinNumText.setText("1"); leftArrowButton.setEnabled(false); int maxPatientNum = new Integer(patientMaxNumText.getText()).intValue(); if (patientSetSize > maxPatientNum) { rightArrowButton.setEnabled(true); patientMaxNumText.setText("10"); } else { rightArrowButton.setEnabled(false); if (patientSetSize > 0) patientMaxNumText.setText(setSize); } } }); log.debug("Dropped set of: " + setSize + " patients" + " with refId: " + setId); } else { // message } } } catch (Exception e) { e.printStackTrace(); return; } } @SuppressWarnings("unchecked") private int getRowNumber() { int n = 1; for (int i = 0; i < rowData.size(); i++) { ArrayList list = (ArrayList) rowData.get(i); for (int j = 0; j < list.size(); j++) { n++; } } return n; } public void setIncrementNumber(int number) { if (number == -1) { String num = patientMinNumText.getText(); int inc = new Integer(patientMaxNumText.getText()).intValue(); int origin = Integer.parseInt(num) + inc;// - inc; patientMinNumText.setText("" + origin); } else { String num = patientMinNumText.getText(); //int inc = new Integer(patientMaxNumText.getText()).intValue(); int origin = Integer.parseInt(num) + number;// - inc; patientMinNumText.setText("" + origin); } } public void setDecreaseNumber(int number) { if (number == -1) { String num = patientMinNumText.getText(); int inc = new Integer(patientMaxNumText.getText()).intValue(); int origin = Integer.parseInt(num) - inc;// + inc; patientMinNumText.setText("" + origin); } else { String num = patientMinNumText.getText(); //int inc = new Integer(patientMaxNumText.getText()).intValue(); int origin = Integer.parseInt(num) - number;// + inc; patientMinNumText.setText("" + origin); } } private RGB getRGBfromList(int n) { RGB color = new RGB(0, 0, 128); int index = rgbList.size() / 2;// - (currentRGBlistindex/2); currentRGBlistindex = index; //color = rgbList.get(index); if (n % 4 == 2) { color = new RGB(0, 100, 0); } else if (n % 4 == 3) { color = new RGB(178, 34, 34); } else if (n % 4 == 0) { color = new RGB(184, 134, 11); } else { //color = new RGB(0, 0, 128); } return color; } private void createRGBListNew() { rgbList.add(new RGB(255, 255, 255)); rgbList.add(new RGB(255, 250, 250)); rgbList.add(new RGB(248, 248, 255)); rgbList.add(new RGB(255, 255, 240)); rgbList.add(new RGB(245, 255, 250)); rgbList.add(new RGB(240, 255, 255)); rgbList.add(new RGB(255, 250, 240)); rgbList.add(new RGB(240, 248, 255)); rgbList.add(new RGB(255, 240, 245)); rgbList.add(new RGB(255, 245, 238)); rgbList.add(new RGB(245, 245, 245)); rgbList.add(new RGB(240, 255, 240)); rgbList.add(new RGB(255, 255, 224)); rgbList.add(new RGB(224, 255, 255)); rgbList.add(new RGB(253, 245, 230)); rgbList.add(new RGB(255, 248, 220)); rgbList.add(new RGB(250, 240, 230)); rgbList.add(new RGB(255, 250, 205)); rgbList.add(new RGB(250, 250, 210)); rgbList.add(new RGB(245, 245, 220)); rgbList.add(new RGB(230, 230, 250)); rgbList.add(new RGB(255, 228, 225)); rgbList.add(new RGB(255, 239, 213)); rgbList.add(new RGB(255, 245, 200)); rgbList.add(new RGB(250, 235, 215)); rgbList.add(new RGB(255, 235, 205)); rgbList.add(new RGB(255, 228, 196)); rgbList.add(new RGB(255, 236, 175)); rgbList.add(new RGB(255, 228, 181)); rgbList.add(new RGB(220, 220, 220)); rgbList.add(new RGB(255, 218, 185)); rgbList.add(new RGB(175, 238, 238)); rgbList.add(new RGB(255, 222, 173)); rgbList.add(new RGB(255, 192, 203)); rgbList.add(new RGB(245, 222, 179)); rgbList.add(new RGB(238, 232, 170)); rgbList.add(new RGB(211, 211, 211)); // rgbList.add(new RGB(211, 211, 211)); rgbList.add(new RGB(255, 182, 193)); rgbList.add(new RGB(176, 224, 230)); rgbList.add(new RGB(216, 191, 216)); rgbList.add(new RGB(173, 216, 230)); rgbList.add(new RGB(238, 130, 238)); rgbList.add(new RGB(221, 160, 221)); rgbList.add(new RGB(176, 196, 222)); rgbList.add(new RGB(127, 255, 212)); rgbList.add(new RGB(135, 206, 250)); rgbList.add(new RGB(238, 221, 130)); rgbList.add(new RGB(135, 206, 235)); rgbList.add(new RGB(190, 190, 190)); rgbList.add(new RGB(152, 251, 152)); rgbList.add(new RGB(218, 112, 214)); rgbList.add(new RGB(255, 105, 180)); // rgbList.add(new RGB(255, 105, 180)); rgbList.add(new RGB(255, 160, 122)); rgbList.add(new RGB(210, 180, 140)); rgbList.add(new RGB(255, 255, 0)); rgbList.add(new RGB(255, 0, 255)); rgbList.add(new RGB(0, 255, 255)); rgbList.add(new RGB(233, 150, 122)); rgbList.add(new RGB(244, 164, 96)); rgbList.add(new RGB(132, 112, 255)); rgbList.add(new RGB(240, 128, 128)); rgbList.add(new RGB(64, 224, 208)); rgbList.add(new RGB(250, 128, 114)); rgbList.add(new RGB(100, 149, 237)); rgbList.add(new RGB(72, 209, 204)); rgbList.add(new RGB(186, 85, 211)); rgbList.add(new RGB(219, 112, 147)); rgbList.add(new RGB(147, 112, 219)); rgbList.add(new RGB(102, 205, 170)); rgbList.add(new RGB(188, 143, 143)); rgbList.add(new RGB(143, 188, 143)); rgbList.add(new RGB(255, 215, 0)); rgbList.add(new RGB(123, 104, 238)); rgbList.add(new RGB(255, 127, 80)); rgbList.add(new RGB(0, 191, 255)); rgbList.add(new RGB(160, 32, 240)); rgbList.add(new RGB(30, 144, 255)); rgbList.add(new RGB(255, 99, 71)); rgbList.add(new RGB(255, 20, 147)); rgbList.add(new RGB(255, 165, 0)); rgbList.add(new RGB(0, 206, 209)); rgbList.add(new RGB(95, 158, 160)); rgbList.add(new RGB(154, 205, 50)); // rgbList.add(new RGB(119, 136, 153)); rgbList.add(new RGB(119, 136, 153)); rgbList.add(new RGB(138, 43, 226)); rgbList.add(new RGB(0, 250, 154)); rgbList.add(new RGB(205, 133, 63)); rgbList.add(new RGB(106, 90, 205)); rgbList.add(new RGB(255, 140, 0)); rgbList.add(new RGB(65, 105, 225)); rgbList.add(new RGB(205, 92, 92)); rgbList.add(new RGB(208, 32, 144)); // rgbList.add(new RGB(112, 128, 144)); rgbList.add(new RGB(112, 128, 144)); rgbList.add(new RGB(127, 255, 0)); rgbList.add(new RGB(0, 255, 127)); rgbList.add(new RGB(70, 130, 180)); rgbList.add(new RGB(32, 178, 170)); rgbList.add(new RGB(124, 252, 0)); rgbList.add(new RGB(148, 0, 211)); rgbList.add(new RGB(199, 21, 133)); rgbList.add(new RGB(60, 179, 113)); rgbList.add(new RGB(210, 105, 30)); rgbList.add(new RGB(184, 134, 11)); rgbList.add(new RGB(255, 69, 0)); rgbList.add(new RGB(176, 48, 96)); rgbList.add(new RGB(105, 105, 105)); // rgbList.add(new RGB(105, 105, 105)); rgbList.add(new RGB(50, 205, 50)); rgbList.add(new RGB(160, 82, 45)); rgbList.add(new RGB(107, 142, 35)); rgbList.add(new RGB(72, 61, 139)); rgbList.add(new RGB(46, 139, 87)); rgbList.add(new RGB(255, 0, 0)); rgbList.add(new RGB(0, 255, 0)); rgbList.add(new RGB(0, 0, 255)); rgbList.add(new RGB(165, 42, 42)); rgbList.add(new RGB(178, 34, 34)); rgbList.add(new RGB(85, 107, 47)); rgbList.add(new RGB(139, 69, 19)); rgbList.add(new RGB(34, 139, 34)); rgbList.add(new RGB(47, 79, 79)); // rgbList.add(new RGB(47, 79, 79)); rgbList.add(new RGB(0, 0, 205)); rgbList.add(new RGB(25, 25, 112)); rgbList.add(new RGB(0, 0, 128)); // rgbList.add(new RGB(0,0,128)); rgbList.add(new RGB(0, 100, 0)); rgbList.add(new RGB(0, 0, 0)); } }