/** Write file with position and size of the login box */
public static void writePersistence() {
Messages.postDebug("LoginBox", "LoginBox.writePersistence");
// If the panel has not been created, don't try to write a file
if (position == null) return;
String filepath = FileUtil.savePath("USER/PERSISTENCE/LoginPanel");
FileWriter fw;
PrintWriter os;
try {
File file = new File(filepath);
fw = new FileWriter(file);
os = new PrintWriter(fw);
os.println("Login Panel");
os.println(height);
os.println(width);
double xd = position.getX();
int xi = (int) xd;
os.println(xi);
double yd = position.getY();
int yi = (int) yd;
os.println(yi);
os.close();
} catch (Exception er) {
Messages.postError("Problem creating " + filepath);
Messages.writeStackTrace(er);
}
}
public void buildPanel() {
String path = FileUtil.getLayoutPath(layoutDir, fname);
if (path == null) {
Messages.postError("Could not open xml file:" + fname);
return;
}
removeAll();
try {
LayoutBuilder.build(pane, vnmrIf, path);
} catch (Exception e) {
String strError = "Error building file: " + path;
Messages.postError(strError);
Messages.writeStackTrace(e);
return;
}
if (bScrollBar) {
spane =
new JScrollPane(
pane,
JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
add(spane);
} else {
spane = null;
add(pane);
}
paramsLayout.preferredLayoutSize(pane);
}
/** Displays the labels and the values for the panel. */
protected void displayPnlFields(HashMap hmPnl) {
if (hmPnl == null || hmPnl.isEmpty()) return;
Iterator keySetItr = hmPnl.keySet().iterator();
String strLabel = "";
String strValue = "";
// if the file is empty, then create an empty set of textfields.
if (hmPnl == null || hmPnl.isEmpty()) {
displayNewTxf("", "");
return;
}
Container container = getParent();
if (container != null) container.setVisible(false);
try {
// Get each set of label and value, and display them.
while (keySetItr.hasNext()) {
strLabel = (String) keySetItr.next();
strValue = (String) hmPnl.get(strLabel);
displayNewTxf(strLabel, strValue);
}
if (container != null) container.setVisible(true);
revalidate();
repaint();
} catch (Exception e) {
Messages.writeStackTrace(e);
// e.printStackTrace();
Messages.postDebug(e.toString());
}
}
protected String getSampleName(String strDir, String strTray) {
String strSampleName = "";
String strSample;
int nTray = 0;
try {
nTray = Integer.parseInt(strTray);
} catch (Exception e) {
}
if (nTray <= 0) return strSampleName;
String cmd =
"SELECT loc_,studystatus from study WHERE (autodir=\'"
+ strDir
+ "\') AND (hostname=\'"
+ getHost()
+ "\')";
// NB: bArrSample[0] is not used; array implicitly initialized false
boolean[] bArrSample = new boolean[nTray + 1];
m_dbResult = null;
try {
m_dbResult = getdbmanager().executeQuery(cmd);
} catch (Exception e) {
return strSampleName;
}
if (m_dbResult == null) return strSampleName;
try {
while (m_dbResult.next()) {
strSample = m_dbResult.getString(1);
int nSample = 0;
nSample = Integer.parseInt(strSample);
try {
bArrSample[nSample] = true;
} catch (IndexOutOfBoundsException ioobe) {
Messages.postDebug("getSampleName: index out of bounds: " + nSample);
}
}
for (int i = 1; i < bArrSample.length; i++) {
if (!bArrSample[i]) {
strSampleName = String.valueOf(i);
break;
}
}
} catch (Exception e) {
// e.printStackTrace();
Messages.writeStackTrace(e);
}
return strSampleName;
}
protected void writeAuditTrail(String strPath, String strUser, StringBuffer sbValues) {
BufferedReader reader = WFileUtil.openReadFile(strPath);
String strLine;
ArrayList aListData = WUtil.strToAList(sbValues.toString(), false, "\n");
StringBuffer sbData = sbValues;
String strPnl = (this instanceof DisplayTemplate) ? "Data Template " : "Data Dir ";
if (reader == null) {
Messages.postDebug("Error opening file " + strPath);
return;
}
try {
while ((strLine = reader.readLine()) != null) {
// if the line in the file is not in the arraylist,
// then that line has been deleted
if (!aListData.contains(strLine))
WUserUtil.writeAuditTrail(new Date(), strUser, "Deleted " + strPnl + strLine);
// remove the lines that are also in the file or those which
// have been deleted.
aListData.remove(strLine);
}
// Traverse through the remaining new lines in the arraylist,
// and write it to the audit trail
for (int i = 0; i < aListData.size(); i++) {
strLine = (String) aListData.get(i);
WUserUtil.writeAuditTrail(new Date(), strUser, "Added " + strPnl + strLine);
}
reader.close();
} catch (Exception e) {
e.printStackTrace();
}
}
protected String gettitle(String strFreq) {
StringBuffer sbufTitle = new StringBuffer().append("VnmrJ ");
String strPath = FileUtil.openPath(FileUtil.SYS_VNMR + "/vnmrrev");
BufferedReader reader = WFileUtil.openReadFile(strPath);
String strLine;
String strtype = "";
if (reader == null) return sbufTitle.toString();
try {
while ((strLine = reader.readLine()) != null) {
strtype = strLine;
}
strtype = strtype.trim();
if (strtype.equals("merc")) strtype = "Mercury";
else if (strtype.equals("mercvx")) strtype = "Mercury-Vx";
else if (strtype.equals("mercplus")) strtype = "MERCURY plus";
else if (strtype.equals("inova")) strtype = "INOVA";
String strHostName = m_strHostname;
if (strHostName == null) strHostName = "";
sbufTitle.append(" ").append(strHostName);
sbufTitle.append(" ").append(strtype);
sbufTitle.append(" - ").append(strFreq);
reader.close();
} catch (Exception e) {
// e.printStackTrace();
Messages.logError(e.toString());
}
return sbufTitle.toString();
}
public void setVisible(boolean bShow, String title) {
if (bShow) {
String strDir = "";
String strFreq = "";
String strTraynum = "";
m_strHelpFile = getHelpFile(title);
String strSampleName = getSampleName(title);
String frameBounds = getFrameBounds(title);
StringTokenizer tok = new QuotedStringTokenizer(title);
if (tok.hasMoreTokens()) strDir = tok.nextToken();
if (tok.hasMoreTokens()) strFreq = tok.nextToken();
if (tok.hasMoreTokens()) strTraynum = tok.nextToken();
else {
try {
Integer.parseInt(strDir);
// if strdir is number, then strdir is empty, and the
// strfreq is the number
strTraynum = strFreq;
strFreq = strDir;
strDir = "";
} catch (Exception e) {
}
}
try {
setTitle(gettitle(strFreq));
m_lblSampleName.setText("3");
boolean bVast = isVast(strTraynum);
CardLayout layout = (CardLayout) m_pnlSampleName.getLayout();
if (!bVast) {
if (strSampleName == null) {
strSampleName = getSampleName(strDir, strTraynum);
}
m_lblSampleName.setText(strSampleName);
layout.show(m_pnlSampleName, OTHER);
} else {
m_strDir = strDir;
setTrays();
layout.show(m_pnlSampleName, VAST);
m_trayTimer.start();
}
boolean bSample = bVast || !strSampleName.trim().equals("");
m_pnlSampleName.setVisible(bSample);
m_lblLogin.setForeground(getBackground());
m_lblLogin.setVisible(false);
m_passwordField.setText("");
m_passwordField.setCaretPosition(0);
} catch (Exception e) {
Messages.writeStackTrace(e);
}
setBounds(frameBounds);
ExpPanel exp = Util.getActiveView();
if (exp != null) exp.waitLogin(true);
}
writePersistence();
setVisible(bShow);
}
private void addTool(String key, Class tool) {
Class[] constructArgs = null;
if (key.equals("XMLToolPanel")) {
constructArgs = new Class[3];
constructArgs[0] = vnmr.ui.SessionShare.class;
constructArgs[1] = String.class;
constructArgs[2] = String.class;
} else {
constructArgs = new Class[1];
constructArgs[0] = vnmr.ui.SessionShare.class;
}
try {
Constructor c = tool.getConstructor(constructArgs);
vobjs.put(key, c);
} catch (NoSuchMethodException nse) {
Messages.postError("Problem initiating " + key + " area.");
Messages.writeStackTrace(nse, tool + " not found.");
} catch (SecurityException se) {
Messages.postError("Problem initiating " + key + " area.");
Messages.writeStackTrace(se);
}
}
protected void setTrayPresent(String strPath) {
String strzone = "zones";
BufferedReader reader = WFileUtil.openReadFile(strPath);
if (reader == null) return;
String strLine;
try {
// if the zones are set to 0, then there is no tray present
// set rackInfo(1,zones) 3 => tray 1 present
// set rackInfo(2,zones) 0 => tray 2 not present
while ((strLine = reader.readLine()) != null) {
int index = strLine.indexOf(strzone);
if (index < 0) continue;
String strTray = strLine.substring(index - 2, index - 1);
int nTray = 0;
try {
nTray = Integer.parseInt(strTray);
} catch (Exception e) {
}
if (nTray <= 0) continue;
int nZone = 0;
try {
strTray = strLine.substring(index + strzone.length() + 2, strLine.length());
nZone = Integer.parseInt(strTray);
} catch (Exception e) {
}
Color colorbg = Color.white;
String strTooltip = TRAY;
if (nZone <= 0) {
colorbg = Color.black;
strTooltip = NOTRAY;
}
VBox pnlVast = m_pnlVast[nTray - 1];
pnlVast.setbackground(colorbg);
pnlVast.setToolTipText(Util.getTooltipString(strTooltip));
}
reader.close();
} catch (Exception e) {
// e.printStackTrace();
Messages.writeStackTrace(e);
}
}
protected void setTrayActive(String strDir) {
String strTray;
String strStudy;
String strActive = "Active";
String cmd =
"SELECT vrack_,studystatus from study WHERE (autodir=\'"
+ strDir
+ "\') AND (hostname=\'"
+ getHost()
+ "\')";
m_dbResult = null;
try {
m_dbResult = getdbmanager().executeQuery(cmd);
} catch (Exception e) {
return;
}
if (m_dbResult == null) return;
int nTray = 0;
try {
while (m_dbResult.next()) {
strTray = m_dbResult.getString(1);
strStudy = m_dbResult.getString(2);
if (strStudy != null && strStudy.equalsIgnoreCase(strActive)) {
try {
nTray = Integer.parseInt(strTray);
} catch (Exception e) {
}
if (nTray > 0) {
m_pnlVast[nTray - 1].setbackground(Color.blue);
m_pnlVast[nTray - 1].setToolTipText(Util.getTooltipString(TRAYACTIVE));
break;
}
}
}
} catch (Exception e) {
// e.printStackTrace();
Messages.writeStackTrace(e);
}
}
protected static boolean vnmrjPassword(String strUser, char[] password) {
boolean blogin = false;
try {
PasswordService objPassword = PasswordService.getInstance();
String encrPassword = objPassword.encrypt(new String(password));
if (pwprops == null) {
String strPath = FileUtil.openPath(WUserUtil.PASSWORD);
if (strPath == null) return blogin;
pwprops = new Properties();
FileInputStream fis = new FileInputStream(strPath);
pwprops.load(fis);
fis.close();
}
String stoPassword = pwprops.getProperty(strUser);
if (encrPassword.equals(stoPassword)) blogin = true;
} catch (Exception e) {
// e.printStackTrace();
Messages.writeStackTrace(e);
}
return blogin;
}
protected void setVast() {
String strPath = FileUtil.openPath("SYSTEM/asm/gilsonNumber");
if (strPath == null) return;
BufferedReader reader = WFileUtil.openReadFile(strPath);
if (reader == null) return;
String strLine;
int i = 0;
try {
while ((strLine = reader.readLine()) != null) {
strLine = strLine.trim();
if (i == 0 || !m_aStrVast[i - 1].equals(strLine)) {
m_aStrVast[i] = strLine;
i = i + 1;
}
}
reader.close();
} catch (Exception e) {
// e.printStackTrace();
Messages.writeStackTrace(e);
}
}
/** Reads the file, and sets the label and the values in the hashmap. */
protected void setHM(String strPath, HashMap hmPnl) {
BufferedReader reader = WFileUtil.openReadFile(strPath);
boolean bFileEmpty = true;
boolean bPart11Pnl = isPart11Pnl();
boolean bDefaultFile = isDefaultFile();
// if the file is empty, then create an empty set of textfields.
if (reader == null) {
// displayNewTxf("","");
return;
}
String strLine = null;
StringTokenizer strTok;
try {
// read the file, and create a new set of textfields,
// with the values from the file.
while ((strLine = reader.readLine()) != null) {
String strLabel = "";
String strValue = "";
bFileEmpty = false;
if (strLine.startsWith("#")
|| strLine.startsWith("@")
|| strLine.startsWith("%")
|| strLine.startsWith("\"@")) continue;
if (strLine.startsWith("\"")) strTok = new StringTokenizer(strLine, "\"");
else strTok = new StringTokenizer(strLine, File.pathSeparator + ",\n");
if (!strTok.hasMoreTokens()) continue;
strLabel = strTok.nextToken();
// the format for the part11 Default file is a little different
// only parse out the part11Dir, and don't display other defaults
if (bPart11Pnl && bDefaultFile) {
if (!strLabel.equalsIgnoreCase("part11Dir")) continue;
}
if (strTok.hasMoreTokens()) {
while (strTok.hasMoreTokens()) {
strValue += strTok.nextToken();
if (strTok.hasMoreTokens()) strValue += " ";
}
}
// append "/data/$name" to part11Dir
if (bPart11Pnl && bDefaultFile && strLabel.equalsIgnoreCase("part11Dir")) {
StringBuffer sbDir = new StringBuffer(strValue);
if (sbDir.lastIndexOf(File.separator) < sbDir.length() - 1)
sbDir.append(File.separator);
sbDir.append("data" + File.separator + "$");
sbDir.append(WGlobal.NAME);
strValue = sbDir.toString();
}
// displayNewTxf(strLabel, strValue);
if (strLabel != null && strLabel.trim().length() > 0) hmPnl.put(strLabel, strValue);
}
reader.close();
} catch (Exception e) {
Messages.writeStackTrace(e);
// e.printStackTrace();
Messages.postDebug(e.toString());
}
}
/**
* Write the file by writing the values from the labels, and the values list.
*
* @param strFile the file to be written.
* @param aListLabels arraylist of texfields of labels.
* @param aListValues arraylist of texfields of values.
*/
protected void writeFile(
String strUser, String strFile, ArrayList aListLabels, ArrayList aListValues) {
String strPath = FileUtil.openPath(strFile);
String strLabel = "";
String strValue = "";
StringBuffer sbValues = new StringBuffer();
JTextField txfLabel = null;
JTextField txfValue = null;
boolean bNewFile = false;
int nFDAMode = Util.getPart11Mode();
// if it's the part11 pnl and the mode is nonFDA,
// then don't write the file for this panel
// the other way is not true.
if (this instanceof DisplayParentDirectory) {
if ((isPart11Pnl() && nFDAMode == Util.NONFDA)) {
return;
}
}
if (strPath == null) {
strPath = FileUtil.savePath(strFile);
bNewFile = true;
}
if (strPath == null || aListLabels == null) return;
if (aListValues == null) aListValues = new ArrayList();
// Get the list of the textfields for values and labels.
int nLblSize = aListLabels.size();
int nValueSize = aListValues.size();
ArrayList<String> labelList = new ArrayList<String>();
// Get the value from each textfield, and add it to the buffer.
for (int i = 0; i < nLblSize; i++) {
txfLabel = (JTextField) aListLabels.get(i);
txfValue = (i < nValueSize) ? (JTextField) aListValues.get(i) : null;
strLabel = (txfLabel != null) ? txfLabel.getText() : null;
strValue = (txfValue != null) ? txfValue.getText() : "";
// We need to be sure they don't have two data directories with
// the same labels. Save the label list if we are writing to
// the "data" file.
if (strFile.indexOf("data") != -1) {
if (labelList.contains(strLabel)) {
Messages.postError(
"The Data Directory specifications "
+ "must not have duplicate Label names. "
+ "The Label \""
+ strLabel
+ "\" is duplicated. "
+ "Skipping the second instance. Please "
+ "specify a new Label.");
continue;
} else labelList.add(strLabel);
}
if (strLabel == null || strLabel.trim().length() <= 0 || strValue.equals(INFOSTR)) continue;
// for user template tab, don't need to parse the value
if (!(this instanceof DisplayTemplate)) strValue = getValue(strUser, strValue);
strLabel = strLabel.trim();
if (strValue != null) strValue = strValue.trim();
// sbValues.append("\"");
sbValues.append(strLabel);
// sbValues.append("\" ");
sbValues.append(File.pathSeparator);
sbValues.append(strValue);
sbValues.append("\n");
}
if (Util.isPart11Sys()) writeAuditTrail(strPath, strUser, sbValues);
// write the data to the file.
BufferedWriter writer = WFileUtil.openWriteFile(strPath);
WFileUtil.writeAndClose(writer, sbValues);
// if it's a template file, then make it writable for everyone.
if (bNewFile) {
String strCmd = "chmod 755 ";
if (this instanceof DisplayTemplate) strCmd = "chmod 777 ";
if (Util.iswindows()) strPath = UtilB.windowsPathToUnix(strPath);
String[] cmd = {WGlobal.SHTOOLCMD, WGlobal.SHTOOLOPTION, strCmd + strPath};
WUtil.runScriptInThread(cmd);
}
}
/**
* Read position and size of the login box from a given abstract path.
*
* @param abstractPath The path to the file.
*/
public void readPersistence(String abstractPath) {
String filepath = FileUtil.openPath(abstractPath);
if (filepath != null) {
BufferedReader in;
String line;
try {
File file = new File(filepath);
in = new BufferedReader(new FileReader(file));
// File must start with 'Login Panel'
if ((line = in.readLine()) != null) {
if (!line.startsWith("Login Panel")) {
Messages.postWarning("The " + filepath + " file is " + "corrupted and being removed");
// Remove the corrupted file.
file.delete();
// Set the size and position to the full vnmrj frame
setDefaultSizePosition();
return;
}
}
String h = null, w = null, x = null, y = null;
int xi, yi;
if (in.ready()) h = in.readLine().trim();
if (in.ready()) w = in.readLine().trim();
if (in.ready()) x = in.readLine().trim();
if (in.ready()) y = in.readLine().trim();
in.close();
// Save width and height for later use also
height = Integer.decode(h).intValue();
width = Integer.decode(w).intValue();
xi = Integer.decode(x).intValue();
yi = Integer.decode(y).intValue();
// Save point for later use also
position = new Point(xi, yi);
// Set them
setSize(width, height);
setLocation(position);
// If we got what we need and set the size and position,
// just return now.
return;
}
// If an exception, continue below
catch (Exception e) {
}
}
// No file or an excpetion happened, set default size and position
// Be sure the file is gone
try {
if (filepath != null) {
File file = new File(filepath);
if (file != null) file.delete();
}
}
// If an exception, just continue below
catch (Exception e) {
}
// Set the size and position to the full vnmrj frame
setDefaultSizePosition();
}
protected void enterLogin() {
char[] password = m_passwordField.getPassword();
String strUser = (String) m_cmbUser.getSelectedItem();
setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
boolean blogin = WUserUtil.isOperatorNameok(strUser, false);
if (blogin) {
blogin = vnmrjPassword(strUser, password);
if (!blogin) blogin = unixPassword(strUser, password);
}
if (blogin) {
m_lblLogin.setForeground(Color.black);
m_lblLogin.setText("Login Successful");
m_lblLogin.setVisible(true);
// Get the Email column string for access to the operator data
String emStr = vnmr.util.Util.getLabel("_admin_Email");
String stremail = WUserUtil.getOperatordata(strUser, emStr);
// Get the Panel Level column string for access to the operator data
String plStr = vnmr.util.Util.getLabel("_admin_Panel_Level");
String strPanel = WUserUtil.getOperatordata(strUser, plStr);
if (stremail == null || stremail.equals("null")) stremail = "";
try {
Integer.parseInt(strPanel);
} catch (Exception e) {
strPanel = WGlobal.PANELLEVEL;
}
m_trayTimer.stop();
Messages.postDebug(" Login: "******"appdir('reset','")
.append(strUser)
.append("','")
.append(stremail)
.append("',")
.append(strPanel)
.append(")")
.toString());
exp.sendToVnmr("vnmrjcmd('util', 'bgReady')\n");
}
setVisible(false);
// Save the current position and size of this panel in case it
// was changed
Dimension size = getSize();
width = size.width;
height = size.height;
position = getLocation();
writePersistence();
// Call the macro to update this operator's
// ExperimentSelector_operatorName.xml file
// from the protocols themselves. This macro will
// cause an update of the ES when it is finished
// Util.getAppIF().sendToVnmr("updateExpSelector");
// I am not sure why we need to force updates since updateExpSelector
// should have caused an update by writing to ES_op.xml file.
// However, it works better if we do the force update.
// ExpSelector.setForceUpdate(true);
} else {
m_lblLogin.setForeground(DisplayOptions.getColor("Error"));
// m_lblLogin.setText("<HTML>Incorrect username/password <p> Please try again </HTML>");
m_lblLogin.setVisible(true);
}
setCursor(Cursor.getDefaultCursor());
}