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MainForm.java
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MainForm.java
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package autoLoad;
import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
import java.awt.AWTException;
import java.awt.Dimension;
import java.awt.HeadlessException;
import java.awt.Robot;
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.UnsupportedFlavorException;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.awt.event.WindowListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.lang.ProcessBuilder.Redirect;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.nio.file.DirectoryStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
import java.io.FileInputStream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import java.util.zip.ZipInputStream;
import java.util.zip.ZipException;
import javax.swing.GroupLayout;
import javax.swing.JButton;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.LayoutStyle;
import modules.Form;
import modules.Params;
import com.sun.jna.platform.win32.WinDef;
import com.sun.jna.platform.win32.User32;
@SuppressWarnings("serial")
public class MainForm extends JFrame implements Form {
private boolean _isBusy=false, _isPaused=false, _quant=true;
private JPanel _mainPanel;
private JTextArea _statusArea;
private JLabel _searchIncoming;
private String _paramFile, _appPath, _sep, _userName, _sample=null, _dataDir, _msMethod, _searchEngine, _instrumentType;
private Params _params;
private java.awt.Color _mainColor;
private int _cores;
private Vector<String> _samplesToRun = new Vector<String>();
public MainForm() {
//GUI Basics
super("AutoLoad");
this.setPreferredSize(new Dimension(525, 375));
this.setSize(this.getPreferredSize());
this.setVisible(true);
//Handles window closing events
//Warns user if a process is running at time of shut-down
WindowListener exitListener = new WindowAdapter() {
public void windowClosing(WindowEvent e) {
if (_isBusy) {
String message = "Are you sure you want to close the application?\n" +
"<html><b>There is currently a process running.</b></html>";
int confirm = JOptionPane.showOptionDialog((MainForm) e.getSource(), message,
"Exit Confirmation", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE, null, null, null);
if (confirm == 0) {
setDefaultCloseOperation(EXIT_ON_CLOSE);
}
else {
setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
}
}
else {
setDefaultCloseOperation(EXIT_ON_CLOSE);
}
}
};
this.addWindowListener(exitListener);
//Main Panel
_mainPanel = new JPanel();
_mainPanel.setPreferredSize(this.getPreferredSize());
GroupLayout mainLayout = new GroupLayout(_mainPanel);
mainLayout.setAutoCreateGaps(true);
mainLayout.setAutoCreateContainerGaps(true);
_mainPanel.setLayout(mainLayout);
_mainColor = _mainPanel.getBackground();
//Status Area
_statusArea = new JTextArea("["+new Date().toString()+"] AutoSearch initializing...");
_statusArea.setFont(new java.awt.Font("MONOSPACED", java.awt.Font.PLAIN, 12));
_statusArea.setEditable(false);
JScrollPane statusScroll = new JScrollPane(_statusArea);
statusScroll.setAutoscrolls(true);
//Pause Button
JButton pauseButton = new JButton("Pause");
pauseButton.addActionListener(new PauseListener());
//Pause Button
JButton quantButton = new JButton("Quant: ON");
quantButton.addActionListener(new QuantListener());
//JLabel for incoming transmissions
_searchIncoming = new JLabel("");
//Add components to Main Panel
mainLayout.setHorizontalGroup(
mainLayout.createParallelGroup()
.addComponent(statusScroll)
.addGroup(mainLayout.createSequentialGroup()
.addComponent(pauseButton)
.addComponent(quantButton)
.addPreferredGap(LayoutStyle.ComponentPlacement.UNRELATED, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(_searchIncoming)));
mainLayout.setVerticalGroup(
mainLayout.createSequentialGroup()
.addComponent(statusScroll)
.addGroup(mainLayout.createParallelGroup()
.addComponent(pauseButton)
.addComponent(quantButton)
.addComponent(_searchIncoming)));
this.add(_mainPanel);
this.pack();
//Get & Set the _appPath
_sep = System.getProperty("file.separator");
_appPath = System.getProperty("java.class.path");
//If .jar is launched from the command line in the autoLoad home directory,
//relative _appPath will not contain a file separator. So check for this case.
if(_appPath.indexOf(_sep) != -1){
_appPath = _appPath.substring(0, _appPath.lastIndexOf(_sep));
} else {
_appPath = "";
}
//Get the number of cores
_cores = Runtime.getRuntime().availableProcessors()-1;
System.out.println("Number of cores: "+_cores);
System.out.println("Default charset: "+Charset.defaultCharset());
this.loadForm();
}
//==================== ACCESSORS AND MUTATORS ====================\\
public void setParamFile(String path) {
_paramFile = path;
}
public String getParamFile() {
return _paramFile;
}
public String getAppPath() {
return _appPath;
}
public String getUserName() {
return _userName;
}
public boolean isBusy() {
Path doneFile = Paths.get(_params.getGlobalParam("LOADER.StatusFolder", "C:\\STATUS"), "LoadDone.txt");
try {
List<String> done = Files.readAllLines(doneFile, Charset.defaultCharset());
if (Integer.parseInt(done.get(0))==0) {
_isBusy = false;
}
else {
_isBusy = true;
}
} catch (IOException e) {
e.printStackTrace();
}
return _isBusy;
}
public void setBusy(boolean busy) {
Path doneFile = Paths.get(_params.getGlobalParam("LOADER.StatusFolder", "C:\\STATUS"), "LoadDone.txt");
try {
OutputStream out = Files.newOutputStream(doneFile);
PrintWriter pout = new PrintWriter(out);
if (busy) {
pout.println("1");
}
else {
pout.println("0");
}
out.flush();
out.close();
} catch (IOException e) {
e.printStackTrace();
} finally {
_isBusy = busy;
}
}
public boolean isPaused() {
return _isPaused;
}
public void setSearchIncoming(String incoming) {
_searchIncoming.setText(incoming);
}
//==================== METHODS ====================\\
/**
* This method logs a message into the status panel.
* It prepends the date and time to the message
*
* @param Stirng message
*/
public void log(String message) {
_statusArea.append("\n["+new Date().toString()+"] "+message);
}
/**
* This method logs a message, appending it to the
* previous message without adding the date or a
* new line.
*
* @param message
*/
public void logNNL(String message) {
_statusArea.append(message);
}
private void loadForm() {
this.setParamFile("HTAPP.Configuration.xml");
System.out.println(this.getParamFile());
_params = new Params(this);
_params.loadParam(this.getParamFile());
this.logNNL("done!");
new ASServerSocket(this, _params).start();
while(true) {
this.checkFinishedSampleList();
if (_samplesToRun.size() > 0) {
_sample = _samplesToRun.remove(0);
this.setBusy(true);
this.loadSample();
}
try {
Thread.sleep(60000);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
}
/**
* This method loads the sample into the database
* by calling all the appropriate methods.
*/
private void loadSample() {
this.log("Processing sample "+_sample);
try {
this.deleteTempFiles();
_dataDir = _params.getGlobalParam("LOADER.BaseFolder", "");
this.log(" Unzipping data...");
this.unzip7zip(Paths.get(_dataDir, _sample+".zip"));
this.log(" Gathering information from text file...");
this.readAndMakeSetupFile();
this.log(" Java .OUT Extraction and Filtering...");
this.extractOut();
this.log(" Logistic model setup...");
this.setupLogisticModel();
this.log(" PhosLocalization...");
this.phosQuant();
this.log(" Beginning FileMaker load...");
this.loadFileMaker();
this.log(" Deleting files...");
this.deleteFiles(Paths.get(_dataDir), _sample);
Paths.get(_dataDir, _sample).toFile().delete();
this.log("Finished loading "+_sample);
this.updateFinishedSampleList("#");
this.setBusy(false);
} catch (Exception e) {
e.printStackTrace();
this.log("Error occurred. Skipping sample "+_sample);
this.updateFinishedSampleList("# An error occurred during processing. Check the log for details ");
this.setBusy(false);
_mainPanel.setBackground(_mainColor);
e.printStackTrace();
}
}
/**
* This method creates the temp folder if it doesn't already exist. It then deletes the temporary files & creates new empty folders
*/
private void deleteTempFiles() {
this.pause("Deleting temporary files");
String tempDir = _params.getGlobalParam("LOADER.TempFolder", "");
try {
Files.createDirectory(Paths.get(tempDir));
} catch (IOException e) {
e.printStackTrace();
}
String[] tempSubDir = {"cleanseq", "dta", "phosloca", "out", "peak", "setup", "LogisticScoreInput", "Validations", "silac", "iTRAQ"};
for (String subDir:tempSubDir) {
try {
Path dir = Paths.get(tempDir, subDir);
if(Files.exists(dir)){
DirectoryStream<Path> files = Files.newDirectoryStream(dir, "*.txt");
for(Path file:files) {
Files.deleteIfExists(file);
}
files.close();
} else {
Files.createDirectory(dir);
}
} catch (IOException e) {
System.out.println("Error: couldn't clear out dir " + subDir);
e.printStackTrace();
} catch (SecurityException e){
System.out.println("Error: could not create temp file");
e.printStackTrace();
}
}
}
//deprecated--check the integrity of the zip file before opening
private boolean isValidZip(File file) {
ZipFile zipfile = null;
ZipInputStream zis = null;
try {
zipfile = new ZipFile(file);
zis = new ZipInputStream(new FileInputStream(file));
ZipEntry ze = zis.getNextEntry();
if(ze == null) {
return false;
}
while(ze != null) {
// if it throws an exception fetching any of the following then the file is corrupt
zipfile.getInputStream(ze);
ze.getCrc();
ze.getCompressedSize();
ze.getName();
ze = zis.getNextEntry();
}
return true;
} catch (ZipException e) {
return false;
} catch (IOException e) {
return false;
} finally {
try {
if (zipfile != null) {
zipfile.close();
zipfile = null;
}
} catch (IOException e) {
return false;
} try {
if (zis != null) {
zis.close();
zis = null;
}
} catch (IOException e) {
return false;
}
}
}
// deprecated--use unzip7zip instead
private void unzip(Path file) throws IOException {
this.pause("Unzipping file");
ZipFile zipFile = new ZipFile(file.toString());
Path targetDir = Paths.get(_dataDir, _sample);
Files.createDirectories(Paths.get(targetDir.toString(), _sample));
@SuppressWarnings("unchecked")
Enumeration<ZipEntry> entries = (Enumeration<ZipEntry>) zipFile.entries();
while(entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
if (entry.isDirectory()) {
Files.deleteIfExists(Paths.get(entry.getName()));
Files.createDirectory(Paths.get(entry.getName()));
continue;
}
InputStream in = zipFile.getInputStream(entry);
Files.deleteIfExists(Paths.get(targetDir.toString(), entry.getName()));
Files.createFile(Paths.get(targetDir.toString(), entry.getName()));
OutputStream out = Files.newOutputStream(Paths.get(targetDir.toString(), entry.getName()));
byte[] buffer = new byte[1024];
int len;
while((len = in.read(buffer)) >= 0) {
out.write(buffer, 0, len);
}
in.close();
out.close();
}
zipFile.close();
}
private void unzip7zip(Path file){
this.pause("Unzipping files");
this.log(" Unzipping files...");
String cmd = null;
Path targetDir = Paths.get(_dataDir, _sample);
//try{
// Files.createDirectories(Paths.get(targetDir.toString(), _sample));
//} catch (IOException e){
// e.printStackTrace();
//}
cmd = "\""+_params.getGlobalParam("LOADER.7ziplocation", "C:\\Program Files\\7zip\\7za.exe")+ "\" x -y " + "\""+ file.toString() + "\"" +" -o" + "\""+ targetDir + "\"";
ProcessBuilder builder = null;
builder = new ProcessBuilder(_params.getGlobalParam("LOADER.7ziplocation", "C:\\Program Files\\7zip\\7za.exe"), "x","-y", "\""+file.toString()+"\"", "-o"+"\""+targetDir.toString()+"\""); //no space between -o switch and outpath. modified to add "-y" switch on 130912 to suppress overwrite prompt
System.out.println("7zip command: "+ builder.command());
this.log("7zip command: "+ builder.command());
List<String> cmdList = builder.command();
String cmdPB="";
this.log(" "+cmdPB);
try {
Process p = builder.redirectOutput(Redirect.INHERIT).start();
//Print any print lines from standard out and error out
BufferedReader bri = new BufferedReader(new InputStreamReader(p.getInputStream()));
BufferedReader bre = new BufferedReader(new InputStreamReader(p.getErrorStream()));
String line;
while ((line = bri.readLine()) != null) {
System.out.println(line);
}
bri.close();
while ((line = bre.readLine()) != null) {
System.err.println(line);
}
bre.close();
p.waitFor(); //Maintain thread synchrony
} catch (IOException e) {
this.log(" ERROR: 7Zip could not unzip file");
System.err.println("Could not create zip file");
e.printStackTrace();
} catch (InterruptedException e) {
this.log(" ERROR: Unzipping was interrupted");
System.err.println("Unzipping file was interrupted");
e.printStackTrace();
}
this.logNNL("done!");
}
private void readAndMakeSetupFile() throws IOException, InterruptedException, AutoLoadException, HeadlessException, AWTException, UnsupportedFlavorException {
this.pause("Making setup file");
//Read the text file
Path txt = Paths.get(_dataDir, _sample+".txt");
List<String> lines = Files.readAllLines(txt, Charset.defaultCharset());
String rawPath = lines.get(1).split("=")[1].trim();
String zipPath = lines.get(2).split("=")[1].trim();
_userName = lines.get(3).split("=")[1].trim();
_msMethod = lines.get(4).split("=")[1].trim();
String sampleQID = "";
String expFolder = "";
String storeLocation = "";
String protocolID = "";
String species = "";
//If the Sample Queue ID is in the list
if (lines.get(5).startsWith("Sample Queue ID")) {
sampleQID = lines.get(5).split("=")[1].trim();
_instrumentType = lines.get(6).split("=")[1].trim();
_searchEngine = lines.get(7).split("=")[1].trim();
}
//Or else there are more parameters to load
else {
expFolder = lines.get(6).split("=")[1].trim();
storeLocation = lines.get(7).split("=")[1].trim();
protocolID = lines.get(8).split("=")[1].trim();
species = lines.get(9).split("=")[1].trim();
_instrumentType = lines.get(10).split("=")[1].trim();
_searchEngine = lines.get(11).split("=")[1].trim();
}
//Create the setup file
Path setupFile = Paths.get(_params.getGlobalParam("LOADER.TempFolder", "C:\\temp"), "setup", "loadParameterSetup.txt");
this.log("Setup file: " + setupFile);
Vector<String> toWrite = new Vector<String>();
toWrite.add("--username--"); toWrite.add(_userName);
toWrite.add("--filename--"); toWrite.add(_sample);
toWrite.add("--A--");
if (sampleQID.equals("")) {
toWrite.add("--expfolder--"); toWrite.add(expFolder);
toWrite.add("--species--"); toWrite.add(species);
toWrite.add("--storeLocation--"); toWrite.add(storeLocation);
toWrite.add("--bioprotocol--"); toWrite.add(protocolID);
}
else {
toWrite.add("--sampleQueueID--"); toWrite.add(sampleQID);
}
toWrite.add("--nPathLtqPro--"); toWrite.add(rawPath);
toWrite.add("--nPathSeqPro--"); toWrite.add(zipPath);
toWrite.add("--searchEngine--"); toWrite.add(_searchEngine);
toWrite.add("--isSILAC--"); toWrite.add(this.getSILAC());
String[] fromRAW = this.getRAWInfo();
for (int i=0; i<fromRAW.length; i++) {
toWrite.add(fromRAW[i]);
}
toWrite.add("--HPLCprotocal--"); toWrite.add(this.getSetupFileData(_sample+".met", "method unknown")); toWrite.add(this.getSetupFileData(_sample+".seq", "sequence unknown"));
toWrite.add("--P1P--"); toWrite.add(this.getSetupFileData(_sample+".p1p", ""));
toWrite.add("--P2P--"); toWrite.add(this.getSetupFileData(_sample+".p2p", ""));
toWrite.add("--P1C--"); toWrite.add(this.getSetupFileData(_sample+".p1c", ""));
toWrite.add("--P2C--"); toWrite.add(this.getSetupFileData(_sample+".p2c", ""));
toWrite.add("--THM--"); toWrite.add(this.getSetupFileData(_sample+".thm", ""));
Files.write(setupFile, toWrite, StandardCharsets.UTF_8);
//Modify the file to have the correct line breaks
// String cmd = Paths.get(_appPath, "LineBreak_Win2Mac.exe").toString() + " " + setupFile.toString();
// String cmd = "cmd /C perl -pi -e 's/\r\n|\n|\r/\n/g' "+setupFile.toString();
// this.log(" "+cmd);
Process p = new ProcessBuilder("cmd", "/C", "perl", "-pi", "-e", "'s/\r\n|\n|\r/\n/g'", setupFile.toString()).start();
p.waitFor();
}
private void extractOut() throws IOException, InterruptedException {
this.pause("Extracting out files");
String massError;
if (_instrumentType.equals("LT")) massError = "N";
else massError = "Y";
String cmd;
ProcessBuilder builder;
if (_searchEngine.equals("S")) {
cmd = "cmd /C java -Xmx128m -jar " + Paths.get(_appPath, "OUTFileSelector.jar").toString() + " -p \"" + Paths.get(_dataDir, _sample, _sample).toString() + "\" -s XCorr -t N -m " + massError + " -c " + _params.getGlobalParam("LOADER.XCorrCutoff", "1.5,2.0,2.5");
builder = new ProcessBuilder("cmd", "/C", "java", "-Xmx128m", "-jar", Paths.get(_appPath, "OUTFileSelector.jar").toString(), "-p", Paths.get(_dataDir, _sample, _sample).toString(), "-s", "XCorr", "-t", "N", "-m", massError, "-c", _params.getGlobalParam("LOADER.XCorrCutoff", "1.5,2.0,2.5"));
}
else if (_searchEngine.equals("M")) {
cmd = "cmd /C java -Xmx128m -jar " + Paths.get(_appPath, "OUTFileSelector.jar").toString() + " -p \"" + Paths.get(_dataDir, _sample, _sample).toString() + "\" -s Mowse_Score -t N -m " + massError + " -c " + _params.getGlobalParam("LOADER.MascotCutoff", "10");
builder = new ProcessBuilder("cmd", "/C", "java", "-Xmx128m", "-jar", Paths.get(_appPath, "OUTFileSelector.jar").toString(), "-p", Paths.get(_dataDir, _sample, _sample).toString(), "-s", "Mowse_Score", "-t", "N", "-m", massError, "-c", _params.getGlobalParam("LOADER.MascotCutoff", "10"));
}
else {
cmd = "cmd /C java -Xmx128m -jar " + Paths.get(_appPath, "OUTFileSelector.jar").toString() + " -p \"" + Paths.get(_dataDir, _sample, _sample).toString() + "\" -s XCorr -t N -m 7000 -c 0";
builder = new ProcessBuilder("cmd", "/C", "java", "-Xmx128m", "-jar", Paths.get(_appPath, "OUTFileSelector.jar").toString(), "-p", Paths.get(_dataDir, _sample, _sample).toString(), "-s", "XCorr", "-t", "N", "-m", "7000", "-c", "0");
}
this.log(" "+cmd);
builder.redirectOutput(new File("C:\\autoLoad\\outfileselectorout.txt"));
builder.redirectError(new File("C:\\autoLoad\\outfileselectorerror.txt"));
Process p = builder.start();
// Process p = Runtime.getRuntime().exec(cmd);
p.waitFor();
p.destroy();
System.out.println("OUTFileSelector exit value: "+p.exitValue());
}
private void setupLogisticModel() {
this.pause("Setting up logistic model");
String model;
if (_searchEngine.equals("M")) model = "mascot";
else model = "seqeust";
Path logisticFile = Paths.get(_params.getGlobalParam("LOADER.LogisticModel", "C:\\temp\\RLogisticScore"), "reduced.RData."+model);
Path target = Paths.get(_params.getGlobalParam("LOADER.LogisticModel", "C:\\temp\\RLogisticScore"), "reduced.RData");
this.log("Moving " + Paths.get(_params.getGlobalParam("LOADER.LogisticModel", "C:\\temp\\RLogisticScore"), "reduced.RData."+model).toString() + " to " + Paths.get(_params.getGlobalParam("LOADER.LogisticModel", "C:\\temp\\RLogisticScore"), "reduced.RData").toString());
try {
Files.copy(logisticFile, target, StandardCopyOption.REPLACE_EXISTING);
} catch (IOException e) {
this.log(" WARNING: Using default logistic model");
System.err.println("Logistic model copy failed. Using default...");
e.printStackTrace();
}
}
private void phosQuant() throws IOException, InterruptedException, AutoLoadException {
this.pause("PhosLocalization");
Path tempDir = Paths.get(_params.getGlobalParam("LOADER.TempFolder", "C:\\temp"));
Path msconv = Paths.get(_params.getGlobalParam("LOADER.msconvert", "C:\\Program Files\\ProteoWizard\\msconvert.exe"));
int numDTA = Paths.get(tempDir.toString(), "dta").toFile().list().length;
this.log("Looking for dtas in " + Paths.get(tempDir.toString(), "dta"));
if (numDTA > 0) {
String cmd = "cmd /C "+Paths.get(_appPath, "PhosLocalization.bat").toString();
System.out.println(" "+cmd);
Process pPhos = new ProcessBuilder("cmd", "/C", Paths.get(_appPath, "PhosLocalization.bat").toString()).start();
Path raw = Paths.get(_dataDir,_sample, _sample+".raw");
Path cfg = Paths.get(_dataDir, _sample, _sample+".cfg");
Path outDir = Paths.get(tempDir.toString(), "out");
// Path[] splitDirs = new Path[_cores];
if (_quant) {
// commented code block below is to move quant input
// files to separate folders for parallel processing
// via the ancient and deprecated VB quant program.
// Path splitOuts = Paths.get(tempDir.toString(), "splitouts");
// this.log("splitOuts " + splitOuts);
// this.deleteFiles(splitOuts);
// for (int i=0; i<_cores; i++) {
// splitDirs[i] = Files.createDirectories(Paths.get(splitOuts.toString(), "outsplit"+(i+1)));
// }
// DirectoryStream<Path> outFiles = Files.newDirectoryStream(outDir);
// int j = 0;
// int k = 0;
// for (Path outFile: outFiles) {
// k = j%_cores;
// Files.copy(outFile, Paths.get(splitDirs[k].toString(), outFile.toString().substring(outFile.toString().lastIndexOf(_sep)))); //add outfile name
// j++; k++;
// }
// outFiles.close(); //jmb
// outFiles = null; //jmb
//Do peak calculations
if (Files.exists(raw)) {
this.log(" Peak Calculations...");
cmd = "Rscript " + Paths.get(_params.getGlobalParam("LOADER.AutoFillFolder", "\\\\proteome\\Filemaker Associated Software\\Quantitation"), "PeakCalcLoader.R").toString() + " " + raw.toString() + " " + Paths.get(tempDir.toString(), "dta") + " " + Paths.get(tempDir.toString(), "out") + " " + Paths.get(tempDir.toString(), "peak") + " " + msconv; //replace with path to mzXML
this.log(" "+cmd);
ProcessBuilder pbPeakCalc = new ProcessBuilder("Rscript", Paths.get(_params.getGlobalParam("LOADER.AutoFillFolder", "\\\\proteome\\Filemaker Associated Software\\Quantitation"), "PeakCalcLoader.R").toString(), raw.toString(), Paths.get(tempDir.toString(), "dta").toString(), Paths.get(tempDir.toString(), "out").toString(), Paths.get(tempDir.toString(), "peak").toString(), msconv.toString());
pbPeakCalc.redirectErrorStream(true);
Process pPeakCalc = pbPeakCalc.inheritIO().start();
pPeakCalc.waitFor();
}
else if (Files.exists(Paths.get(_dataDir,_sample, _sample, _sample+".xml"))) {
Path protqIn = Paths.get(_dataDir, _sample, _sample+".proquant.txt");
Path xmlRaw = Paths.get(_dataDir, _sample, _sample+".xml");
cmd = "cmd /C java -Xmx256m -jar " + Paths.get(_appPath, "ProtQuantInterface.jar").toString() + " before " + protqIn.toString() + " " + outDir.toString() + " " + xmlRaw.toString() + ".rstable";
this.log(" "+cmd);
Process pXMLQuant = new ProcessBuilder("cmd", "/C", "java", "-Xmx256m", "-jar", Paths.get(_appPath, "ProtQuantInterface.jar").toString(), "before", protqIn.toString(), outDir.toString(), xmlRaw.toString()+".rstable").start();
pXMLQuant.waitFor();
//Show messages to alert user
JOptionPane.showMessageDialog(this, "Please start ProtQUant for XML-type MS quantitation (next...)");
JOptionPane.showMessageDialog(this, "MS data file is at: " + xmlRaw.toString() + " (next...)" );
JOptionPane.showMessageDialog(this, "Parser file is at: " + protqIn.toString() + " (next...)");
JOptionPane.showMessageDialog(this, "ProtQuant output file must be saved to the following directory: " + Paths.get(_dataDir, _sample).toString());
cmd = "cmd /C java -Xmx256m -jar " + Paths.get(_appPath, "ProtQuantInterface.jar").toString() + " after " + Paths.get(tempDir.toString(), "peak").toString() + " " + Paths.get(_dataDir, _sample, _sample+".csv").toString();
this.log(" "+cmd);
pXMLQuant = new ProcessBuilder("cmd", "/C", "java", "-Xmx256m", "-jar", Paths.get(_appPath, "ProtQuantInterface.jar").toString(), "after", Paths.get(tempDir.toString(), "peak").toString(), Paths.get(_dataDir, _sample, _sample+".csv").toString()).start();
pXMLQuant.waitFor();
}
}
pPhos.waitFor();
pPhos.destroy();
//SILAC Quant
if (Files.exists(cfg) && Files.exists(raw)) {
if (Integer.parseInt(this.getSILAC()) == 2) {
this.log(" Starting iTRAQ Quant...");
Path csv = Paths.get(_dataDir, _sample, _sample+".csv");
Path iTRAQDir = Paths.get(tempDir.toString(), "iTRAQ");
if (Files.exists(csv)) {
Path tempFile = Paths.get(_dataDir, _sample, _sample+".tmp");
Files.createDirectories(iTRAQDir);
this.deleteFiles(iTRAQDir);
cmd = "cmd /C perl "+Paths.get(_appPath, "MascotCSV2PeptIDsOnlyCSV.pl").toString()+" --in "+csv.toString()+" --out "+tempFile.toString();
this.log(" "+cmd);
Process p = new ProcessBuilder("cmd", "/C", "perl", Paths.get(_appPath, "MascotCSV2PeptIDsOnlyCSV.pl").toString(), "--in", csv.toString(), "--out", tempFile.toString()).start();
p.waitFor();
}
else {
cmd = Paths.get(_appPath, "iTRAQ_Quant.exe").toString()+" $"+cfg.toString()+" $"+raw.toString()+" $"+outDir.toString()+" $"+iTRAQDir.toString();
this.log(" "+cmd);
Process p = new ProcessBuilder(Paths.get(_appPath, "iTRAQ_Quant.exe").toString(), "$"+cfg.toString(), "$"+raw.toString(), "$"+outDir.toString(), "$"+iTRAQDir.toString()).start();
p.waitFor();
}
}
else {
this.log(" Starting SILAC Quant...");
// Path splitOuts = Paths.get(tempDir.toString(), "splitouts");
Path silacDir = Paths.get(tempDir.toString(), "silac");
//Process[] quantPID = new Process[_cores];
//for (int i=0; i<_cores; i++) {
//cmd = Paths.get(_appPath, "AQSILAC.exe").toString()+" $a=TRUE $c="+cfg.toString()+" $r="+raw.toString()+" $s="+splitDirs[i]+" $o="+silacDir.toString()+" $f=off"; // jmb removed 140729 -- VB quant software is deprecated
ProcessBuilder pb = new ProcessBuilder("Rscript", Paths.get(_params.getGlobalParam("LOADER.AutoFillFolder", "\\\\proteome\\Filemaker Associated Software\\Quantitation"), "AQSILAC.R").toString(), cfg.toString(), raw.toString(), outDir.toString(), silacDir.toString(), msconv.toString()); //change raw to mzXML path, splitDirs is outfile directory (E:/Temp/splitouts)
pb.redirectErrorStream(true);
Process p = pb.inheritIO().start();
p.waitFor();
//get Process to string for log
cmd = p.toString();
this.log(" "+cmd);
// quantPID[i] = new ProcessBuilder(Paths.get(_appPath, "AQSILAC.exe").toString(), "$a=TRUE", "$c="+cfg.toString(), "$r="+raw.toString(), "$s="+splitDirs[i], "$o="+silacDir.toString(), "$f=off").start();
//}
//for (int i=0; i<_cores; i++) {
// quantPID[i].waitFor();
//}
}
}
}
else {
String _failFolder = _params.getGlobalParam("LOADER.FailureFolder", "E:\\data\\Failed_Mascot_score_thresholding");
try {
Files.move(Paths.get(_dataDir, _sample+".zip"), Paths.get(_failFolder, _sample+".zip"), REPLACE_EXISTING);
Files.move(Paths.get(_dataDir, _sample+".txt"), Paths.get(_failFolder, _sample+".txt"), REPLACE_EXISTING);
this.deleteFiles(Paths.get(_dataDir), _sample);
} catch (IOException e) {
this.log(" ERROR: Could not move samples to " + _failFolder);
System.err.println( "ERROR: Could not move samples to " + _failFolder);
e.printStackTrace();
}
throw new AutoLoadException("PhosLocalization", "No hits passed criteria");
}
}
private void loadFileMaker() throws IOException, InterruptedException, AutoLoadException, AWTException {
this.pause("Loading into FileMaker");
String cmd = "cmd /C "+Paths.get(_appPath, "startApp.bat").toString();
this.log(" "+cmd);
_mainPanel.setBackground(java.awt.Color.RED);
Thread.sleep(30000);
Process pFileMaker = new ProcessBuilder("cmd", "/C", Paths.get(_appPath, "startApp.bat").toString()).start();
Thread.sleep(10000);
//Robot robot = new Robot();
WinDef.HWND window = null;
/*while (window == null) { jmb
window = User32.INSTANCE.FindWindow(null, "Filemaker Pro Advanced");
} */
User32.INSTANCE.SetForegroundWindow(window);
User32.INSTANCE.SetFocus(window);
Thread.sleep(75000);
//Send ctrl-3 to start the FileMaker loading script jmb deprecated 150413: FM import script should run automatically now
/*robot.keyPress(KeyEvent.VK_CONTROL);
robot.keyPress(KeyEvent.VK_3);
robot.keyRelease(KeyEvent.VK_3);
robot.keyRelease(KeyEvent.VK_CONTROL);*/
pFileMaker.waitFor();
_mainPanel.setBackground(_mainColor);
}
//==================== SAMPLE LIST METHODS ====================\\
/**
* This method checks the sample list to see if any
* new samples need to be loaded.
*/
private void checkFinishedSampleList() {
try {
System.out.println("Checking sample list...");
List<String> samples = Files.readAllLines(Paths.get(_appPath, "finishedSampleList.txt"), Charset.defaultCharset());
for (int i=0; i<= samples.size()-1; i++) {
if (!samples.get(i).startsWith("#")) {
_samplesToRun.add(samples.get(i));
break;
}
else if (samples.get(i).startsWith("##")) {
_samplesToRun.add(samples.get(i).substring(2));
break;
}
}
samples = null;
} catch(IOException e) {
e.printStackTrace();
}
}
/**
* This method updates the sample list with either
* a success or failure tag (# or ##, respectively).
*
* @param status - String indicating success or failure
*/
private void updateFinishedSampleList(String status) {
try {
List<String> samples = Files.readAllLines(Paths.get(_appPath, "finishedSampleList.txt"), Charset.defaultCharset());
int i;
if ((i=samples.lastIndexOf(_sample)) >= 0 || (i=samples.lastIndexOf("##"+_sample)) >= 0) {
samples.set(i, status+_sample);
}
Files.write(Paths.get(_appPath, "finishedSampleList.txt"), samples, Charset.defaultCharset());
} catch (IOException e) {
e.printStackTrace();
}
}
//==================== HELPER METHODS & CLASSES ====================\\
/**
* Convenience method to put the thread to sleep
* if the application is paused.
*
* @param String method - method name for debugging purposes
*/
private void pause(String method) {
int min = 0;
while(this.isPaused()) {
try {
System.out.println("AutoLoad has been paused at "+method+" for "+min+" minutes");
min++;
Thread.sleep(60000);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
}
/**
* Obtains the SILAC value from the cfg file
* for creating the setup file.
*
* @return
* @throws IOException
*/
private String getSILAC() throws IOException {
int silac = 0;
Path cfg = Paths.get(_dataDir, _sample, _sample+".cfg");
if (Files.exists(cfg)) {
silac = 1;
List<String> cfgs = Files.readAllLines(cfg, Charset.defaultCharset());
for (String config:cfgs) {
if (config.startsWith("iTRAQ")) {
silac = 2;
}
}
}
return Integer.toString(silac);
}
private String[] getRAWInfo() throws IOException, AutoLoadException, InterruptedException, AWTException, HeadlessException, UnsupportedFlavorException {
Path rawFile = Paths.get(_dataDir,_sample, _sample+".raw");
String msTune = "";
String msMethod = "";
String[] toReturn = new String[7];
if (Files.exists(rawFile)) {
this.log(" Reading data from RAW file...");
String cmd = _params.getGlobalParam("LOADER.QualBrowswer", "C:\\xcalibur\\system\\programs\\qualbrowser.exe") + " " + rawFile.toString();
this.log(" "+cmd);
_mainPanel.setBackground(java.awt.Color.RED);
Thread.sleep(30000);
Process p = new ProcessBuilder(_params.getGlobalParam("LOADER.QualBrowswer", "C:\\xcalibur\\system\\programs\\qualbrowser.exe"), rawFile.toString()).start();
//Wait for process to start up...
Long tdelay = Long.parseLong(_params.getGlobalParam("LOADER.QbrowserTimeDelay", "10000"));
Thread.sleep(tdelay);
//Start robot for send keys
Robot robot = new Robot();
WinDef.HWND window = null;
int i = 0;
/*while (window == null) { jmb commented out 131008
window = User32.INSTANCE.FindWindow("QualBrowser.exe", "Thermo Xcalibur Qual Browser");
if (i++ == 20) break;
}
User32.INSTANCE.SetForegroundWindow(window);
User32.INSTANCE.SetFocus(window);*/
Thread.sleep(10000);
/*if (!User32.INSTANCE.GetForegroundWindow().equals(window)) { jmb commented out 131008
throw new AutoLoadException("getRAWInfo", "QualBrowser window could not be found");
}*/
this.log(" Retrieving data from Qual Browser");
//Gather information using sendkeys
//Send "alt"
robot.keyPress(KeyEvent.VK_ALT);
robot.keyRelease(KeyEvent.VK_ALT);
Thread.sleep(1000);
//Send "v"
robot.keyPress(KeyEvent.VK_V);
robot.keyRelease(KeyEvent.VK_V);
Thread.sleep(500);
//Send "r"
robot.keyPress(KeyEvent.VK_R);
robot.keyRelease(KeyEvent.VK_R);
Thread.sleep(500);
//Send "t"
robot.keyPress(KeyEvent.VK_T);
robot.keyRelease(KeyEvent.VK_T);
Thread.sleep(1000);
//Copy the MS tune parameter
robot.keyPress(KeyEvent.VK_CONTROL);
robot.keyPress(KeyEvent.VK_C);
robot.keyRelease(KeyEvent.VK_C);
robot.keyRelease(KeyEvent.VK_CONTROL);
msTune = (String) Toolkit.getDefaultToolkit().getSystemClipboard().getData(DataFlavor.stringFlavor);
//Send "alt"
robot.keyPress(KeyEvent.VK_ALT);
robot.keyRelease(KeyEvent.VK_ALT);
Thread.sleep(1000);
//Send "v"
robot.keyPress(KeyEvent.VK_V);
robot.keyRelease(KeyEvent.VK_V);
Thread.sleep(500);
//Send "r"
robot.keyPress(KeyEvent.VK_R);
robot.keyRelease(KeyEvent.VK_R);
Thread.sleep(500);
//Send "t"
robot.keyPress(KeyEvent.VK_M);
robot.keyRelease(KeyEvent.VK_M);
Thread.sleep(1000);
//Copy the MS method parameter
robot.keyPress(KeyEvent.VK_CONTROL);
robot.keyPress(KeyEvent.VK_C);
robot.keyRelease(KeyEvent.VK_C);
robot.keyRelease(KeyEvent.VK_CONTROL);
//Retrieve copied data from clipboard
msMethod = (String) Toolkit.getDefaultToolkit().getSystemClipboard().getData(DataFlavor.stringFlavor);
this.log(" Finished retrieving data from Qual Browser");
//Quit Qual Browser
//Send "alt-f"
robot.keyPress(KeyEvent.VK_ALT);
robot.keyPress(KeyEvent.VK_F);
robot.keyRelease(KeyEvent.VK_F);
robot.keyRelease(KeyEvent.VK_ALT);
Thread.sleep(1000);
//Send "x"
robot.keyPress(KeyEvent.VK_X);
robot.keyRelease(KeyEvent.VK_X);
Thread.sleep(2000);
p.waitFor();
_mainPanel.setBackground(_mainColor);
toReturn[0] = "--MSTune--";
DateFormat dateFormat = new SimpleDateFormat("MM/dd/YYYY HH:mm:ss a");
toReturn[1] = dateFormat.format(new Date());
toReturn[2] = msTune;
toReturn[3] = "--MSMeth--";
dateFormat = new SimpleDateFormat("MM/dd/YYYY");
toReturn[4] = _msMethod + " " + dateFormat.format(new Date());
toReturn[5] = _sample;
toReturn[6] = msMethod;
robot = null;
}
else {
toReturn[0] = "--MSTune--";
DateFormat dateFormat = new SimpleDateFormat("MM/dd/YYYY HH:mm:ss a");
toReturn[1] = dateFormat.format(new Date());
toReturn[2] = "";
toReturn[3] = "--MSMeth--";
dateFormat = new SimpleDateFormat("MM/dd/YYYY");
toReturn[4] = _msMethod + " " + dateFormat.format(new Date());
toReturn[5] = _sample;
toReturn[6] = "";
}
return toReturn;
}
private String getSetupFileData(String fileName, String def) throws IOException {
this.log(" Gathering information from "+fileName);
StringBuilder sb = new StringBuilder();
if (Files.exists(Paths.get(_dataDir, _sample, fileName))) {
List<String> lines = Files.readAllLines(Paths.get(_dataDir, _sample, fileName), Charset.defaultCharset());
if (lines.size() == 0) {
return def;
}
else {
for (String line:lines) {
sb.append(line);
}
return sb.toString();
}
}
return def;
}
private void deleteFiles(Path source, String... filter) {
try {
DirectoryStream<Path> files = Files.newDirectoryStream(source);
if (filter.length > 0) {
for (Path file:files) {
if (file.toString().contains(filter[0])) {
if (Files.isDirectory(file)) {
this.deleteFiles(file, filter[0]);
}
else file.toFile().delete();
}
}
}
else {
for (Path file:files) {
if (Files.isDirectory(file)) {
this.deleteFiles(file);
}
else file.toFile().delete();
}
}
files = null;
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* This class sets the _isPaused boolean to
* either true or false depending on the
* paused state.
*/
private class PauseListener implements ActionListener {
public void actionPerformed(ActionEvent e) {
JButton source = (JButton) e.getSource();
if (source.getText().equals("Pause")) {
source.setText("Resume");
log("AutoSearch is paused...");
_isPaused = true;
}
else {
source.setText("Pause");