protected void runScript(String[] cmd, JTextArea txaMsg) {
String strg = "";
if (cmd == null) return;
Process prcs = null;
try {
Messages.postDebug("Running script: " + cmd[2]);
Runtime rt = Runtime.getRuntime();
prcs = rt.exec(cmd);
if (prcs == null) return;
InputStream istrm = prcs.getInputStream();
if (istrm == null) return;
BufferedReader bfr = new BufferedReader(new InputStreamReader(istrm));
while ((strg = bfr.readLine()) != null) {
// System.out.println(strg);
strg = strg.trim();
// Messages.postDebug(strg);
strg = strg.toLowerCase();
if (txaMsg != null) {
txaMsg.append(strg);
txaMsg.append("\n");
}
}
} catch (Exception e) {
// e.printStackTrace();
Messages.writeStackTrace(e);
Messages.postDebug(e.toString());
} finally {
// It is my understanding that these streams are left
// open sometimes depending on the garbage collector.
// So, close them.
try {
if (prcs != null) {
OutputStream os = prcs.getOutputStream();
if (os != null) os.close();
InputStream is = prcs.getInputStream();
if (is != null) is.close();
is = prcs.getErrorStream();
if (is != null) is.close();
}
} catch (Exception ex) {
Messages.writeStackTrace(ex);
}
}
}
protected void buildPanel(String strPath) {
BufferedReader reader = WFileUtil.openReadFile(strPath);
String strLine;
if (reader == null) return;
try {
while ((strLine = reader.readLine()) != null) {
if (strLine.startsWith("#") || strLine.startsWith("%") || strLine.startsWith("@"))
continue;
StringTokenizer sTokLine = new StringTokenizer(strLine, ":");
// first token is the label e.g. Password Length
if (sTokLine.hasMoreTokens()) {
createLabel(sTokLine.nextToken(), this);
}
// second token is the value
String strValue = sTokLine.hasMoreTokens() ? sTokLine.nextToken() : "";
if (strValue.equalsIgnoreCase("yes") || strValue.equalsIgnoreCase("no"))
createChkBox(strValue, this);
else createTxf(strValue, this);
}
} catch (Exception e) {
Messages.writeStackTrace(e);
// e.printStackTrace();
Messages.postDebug(e.toString());
}
}
public void addEotDatum(int nSteps) {
m_eotCount += nSteps;
Messages.postDebug("AllTuneAlgorithm", "Motor " + m_gmi + " EOT count=" + m_eotCount);
if (Math.abs(m_eotCount) > 5) {
setEot(m_eotCount);
}
}
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();
}
}
/** 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());
}
}
/** 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);
}
}
/**
* Set flag indicating if this motor is at the end of it's travel. Typically called after making a
* motion of "step" motor steps. A positive value of "step" indicates are at the positive EOT. A
* negative value of "step" indicates are at the negative EOT. A zero value for "step" indicates
* are not at EOT.
*
* @param step Flag that we are at EOT for steps in this direction.
*/
public void setEot(int step) {
m_eotStatus = step;
if (step == 0) {
m_eotCount = 0;
} else if (DebugOutput.isSetFor("TuneAlgorithm")) {
Messages.postDebug("Setting EOT=" + step + " on motor " + m_gmi);
}
}
/**
* Update the motor position, based on increment from last position. Also updates the backlash
* tracking.
*
* @param n The number of steps from the previous position.
*/
public void incrementPosition(int n) {
Messages.postDebug("BacklashTracking", "incrementPosition(" + n + ") called");
if (n != 0) {
m_position += n;
if (!isSameDirection(n)) {
m_distanceThisDirection = 0; // Reversed direction
}
m_distanceThisDirection += Math.abs(n);
if (n != 0) {
m_lastStep = n;
}
}
}
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;
}
/** Update state from Infostat. */
public void updateStatus(String msg) {
// Messages.postDebug("VLcStatusChart.updateStatus(" + msg + ")");/*CMP*/
if (msg == null) {
return;
}
StringTokenizer tok = new StringTokenizer(msg);
if (tok.hasMoreTokens()) {
String key = tok.nextToken();
String val = "";
if (tok.hasMoreTokens()) {
val = tok.nextToken("").trim(); // Get remainder of msg
}
if (key.equals(statkey)) {
if (val != null && !val.equals("-")) {
valstr = val;
setState(state);
}
/*System.out.println("Chart: statkey=" + statkey
+ ", val=" + val);/*CMP*/
}
if (key.equals(statpar)) {
if (val != null && !val.equals("-")) {
/*System.out.println("Chart statpar=" + statpar
+ ", value=" + value);/*CMP*/
setState(state);
}
}
if (key.equals(statset)) {
if (val != null && !val.equals("-")) {
setval = val;
try {
String num = val.substring(0, val.indexOf(' '));
setStatusValue(Double.parseDouble(num));
} catch (NumberFormatException nfe) {
Messages.postDebug("VLcStatusChart.updateStatus(): " + "Non-numeric value: " + msg);
} catch (StringIndexOutOfBoundsException sioobe) {
setStatusValue(0); // No value found
}
/*System.out.println("Chart statset=" + statset
+ ", setval=" + setval);/*CMP*/
setState(state);
}
}
}
repaint();
}
/**
* Save the data to the file. Read the data from the file, and copy everything to the
* stringbuffer. The lines in the file are of the form:
* auditDir:system:/vnmr/part11/auditTrails:system file:standard:text:yes Based on these formats,
* get the value of either the directory or the checkbox from the corresponding components, and
* replace that value in the stringbuffer.
*/
protected void saveData() {
BufferedReader reader = WFileUtil.openReadFile(m_strPath);
String strLine = null;
StringBuffer sbData = new StringBuffer();
if (reader == null) return;
int nLineInd = 0;
try {
while ((strLine = reader.readLine()) != null) {
// if the line starts with a comment from sccs, add '#' to it,
// to make it a comment
if (strLine.startsWith("%") || strLine.startsWith("@")) strLine = "# " + strLine;
if (strLine.startsWith("#")) {
sbData.append(strLine + "\n");
continue;
}
StringTokenizer sTok = new StringTokenizer(strLine, File.pathSeparator);
boolean bFile = false;
boolean bLineEnd = false;
boolean bDir = false;
for (int i = 0; sTok.hasMoreTokens(); i++) {
String strValue = sTok.nextToken();
if (i == 0) {
bFile = strValue.equalsIgnoreCase("file") ? true : false;
bDir = false;
if (strValue.equalsIgnoreCase("dir")) bDir = true;
} else {
// Case => file:standard:procpar:yes
// skip over 'standard', 'procpar',
// and get the value 'yes' or 'no' from the checkbox
if (bFile) {
if (i == 3) {
String strNewValue = getValue(nLineInd);
if (strNewValue != null) strValue = strNewValue;
bLineEnd = true;
} else bLineEnd = false;
} else if (bDir) {
bLineEnd = false;
if (i == 3) bLineEnd = true;
}
// Case => part11Dir:/vnmr/part11/data 0r
// Case => dataType:FDA
// skip over 'part11Dir'
// and get the value of the directory from the textfield,
// or from the combobox
else {
if (i == 1) {
String strNewValue = getValue(nLineInd);
if (strNewValue != null) strValue = strNewValue;
bLineEnd = true;
} else bLineEnd = false;
}
}
// copy the value to the stringbuffer
sbData.append(strValue);
if (!bLineEnd) sbData.append(File.pathSeparator);
}
nLineInd++;
sbData.append("\n");
}
// write the data to the file
reader.close();
BufferedWriter writer = WFileUtil.openWriteFile(m_strPath);
WFileUtil.writeAndClose(writer, sbData);
m_objTimer =
new javax.swing.Timer(
200,
new ActionListener() {
public void actionPerformed(ActionEvent e) {
VItemAreaIF.firePropertyChng(Global.PART11_CONFIG_FILE, "all", "");
m_objTimer.stop();
}
});
m_objTimer.start();
} catch (Exception e) {
Messages.writeStackTrace(e);
// e.printStackTrace();
Messages.postDebug(e.toString());
}
}
/** 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());
}
}
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());
}