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How can I get all errors when executing a command?

I'm developing a java program, at a certain point in the program I need to execute some commands and show all the errors returned by that command. But I can only show the first one.
This is my code:
String[] comando = {mql,"-c",cmd};
File errorsFile = new File("C:\\Users\\Administrator2\\Desktop\\errors.txt");
ProcessBuilder pb = new ProcessBuilder(comando);
pb.redirectError(errorsFile);
Process p = pb.start();
p.waitFor();
String r = errorsFile.getAbsolutePath();
Path ruta = Paths.get(r);
Charset charset = Charset.forName("ISO-8859-1");
List<String> fileContents = Files.readAllLines(ruta,charset);
if (fileContents.size()>0){
int cont = 1;
for(String str : fileContents){
System.out.println("Error"+cont);
System.out.println("\t"+str);
cont++;
}
}
else{
//other code
}
In this case I know that there are more than one errors, so I expect more than one output but as you can see in the photo I get only one.

I think the key here might be that ProcessBuilder's redirectError(File file) is actually redirectError (Redirect.to(file)) .
From Oracle's documentation of ProcessBuilder class:
This is a convenience method. An invocation of the form redirectError(file) behaves in exactly the same way as the invocation redirectError (Redirect.to(file)).
Most example's I have seen use Redirect.appendTo(File file) rather than Redirect.to(file). The documentation may explain why.
From Oracle's documentation of ProcessBuilder.Redirect :
public static ProcessBuilder.Redirect to(File file)
Returns a redirect to write to the specified file. If the specified file exists when the subprocess is started, its previous contents will be discarded.
public static ProcessBuilder.Redirect appendTo(File file)
Returns a redirect to append to the specified file. Each write operation first advances the position to the end of the file and then writes the requested data.
I would try replacing
pb.redirectError(errorsFile)
with
pb.redirectError(Redirect.appendTo(errorsFile))
and see if you get more lines that way.

Have you debugged and checked the contents of fileContents?
EDIT: Sorry, it should be a comment, but can't do it yet :(

Generic DataFlavor for All MIME-Types As InputStream

I'd like to read the clipboard in a console-application and print out the contents of the clipboard. That should happen completely independent of the MIME-type. As far as I can tell in Java it's all done based on the data's MIME-type and I should know what I expect. The default DataFlavors only support text and some binary stuff.
Anyway, I want to cover images, all kinds of text, serialised stuff and any kind of binary data.
The easy part is
Clipboard systemClipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
Looping over systemClipboard.getContents(null).getTransferDataFlavors() doesn't help much. I also tried to create my own DataFlavor, but that doesn't work (from what I analysed in Java's source the sub-type can be "*"):
systemClipboard.getData(new DataFlavor("application/*", "bytes"))
Also I don't know how to figure out what the MIME-type actually is. No UNIX-tool I looked at could tell me that.
My final goal is to write a data generator that does the opposite, meaning create the clipboard data and provide that to the application in question. But, for now I have to figure out the structure I need to create then, which is why I need that parser first.

After deep-diving into the involved objects with Reflection I came up with this. I know that this usually is bad and it actually uses undocumented methods in undocumented classes, which means that this might not work with the next Java-release. Due to that I'm still looking for a nice solution! Don't hesitate to post an answer if you have one!
Anyway:
public static void main(String[] args) throws Exception {
Clipboard systemClipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
System.out.println("systemClipboard: " + systemClipboard.getClass().getName());
Method method = systemClipboard.getClass().getDeclaredMethod("getClipboardFormats");
method.setAccessible(true);
long[] clipboardFormats = (long[]) method.invoke(systemClipboard);
for (long clipboardFormat : clipboardFormats) {
String line = "format " + clipboardFormat + ": ";
try {
method = systemClipboard.getClass().getDeclaredMethod("getClipboardData", long.class);
method.setAccessible(true);
byte[] bytes = (byte[]) method.invoke(systemClipboard, clipboardFormat);
line += "length: " + bytes.length + "\n";
line += DatatypeConverter.printHexBinary(bytes) + "\n";
line += new String(bytes);
} catch (Exception e) {
StringWriter stringWriter = new StringWriter();
e.printStackTrace(new PrintWriter(stringWriter));
line += stringWriter.getBuffer();
}
System.out.println(line);
}
}
For the clipboard I looked at I noticed that it actually contains plain readable XML. However, it's not possible to load that the normal way using the DataFlavors available. I assume that this is due to a possibly missing MIME-type information in the clipboard.
Note that for my system the second line prints out systemClipboard: sun.awt.X11.XClipboard and the two methods I use are protected. I'm trying to say that it may look different on anyone else's machine.
As an additional information who want to use the above code:
The clipboard formats I run in are 589 (the only one that works), 460, 462, 463, 464. According to this 589 (= 0x024D) is a private clipboard format.
What would be interesting to see is where Java maps that clipboardFormat to a MIME-type. Maybe that would explain a few things.

Java 8 Nashorn - capturing engine.eval("print('hello world')) into String object?

Is there a way to capture the result of print('hello world') inside Nashorn and place it in a String object.
I have tried this:
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos, true);
System.setOut(ps);
String result = (String)engine.eval("print('hello world')");
if (result != null) {
System.out.println(result);
} else {
System.out.println(baos.toString());
}
When engine evaluates this javascript it just prints to stdout so I figured I just redirect stdout to my own OutputStream and then convert it to String, but it doesn't work.
Any thoughts?

You are setting the System.out stream after you have created your engine so it’s very likely that the engine’s context has already recorded the value of System.out/System.err at construction time.
Therefore you still see the output of the script on the console. Even worse, you don’t see the output of your own later-on System.out.println anymore as you have redirected System.out to your ByteArrayOutputStream.
So don’t modify System.out, instead change the output in the context of your scripting engine engine.getContext().setWriter(stringWriter).
Complete code:
StringWriter sw=new StringWriter();
engine.getContext().setWriter(sw);
String result = (String)engine.eval("print('hello world')");
System.out.println("Result returned by eval(): "+result);
System.out.println("Captured output: "+sw);

I suspect the problem is with:
if (result != null)
Evaluating the print(...) statement will still give you the return value of print, which is probably undefined. But my guess is that you still have the right stuff in baos, and if you changed your statement to if (false) it would work as expected.
That said, this may not be the best way to do this, depending what you're trying to do.

You don't want to cast the eval result - that would be JS undefined value. After you set Writer instance for the current ScriptContext, you eval code that writes by print. And then pick up accumulated strings from the Writer instance. (StringWriter's toString would give you that String).

Java Apache FileUtils readFileToString and writeStringToFile problems

I need to parse a java file (actually a .pdf) to an String and go back to a file. Between those process I'll apply some patches to the given string, but this is not important in this case.
I've developed the following JUnit test case:
String f1String=FileUtils.readFileToString(f1);
File temp=File.createTempFile("deleteme", "deleteme");
FileUtils.writeStringToFile(temp, f1String);
assertTrue(FileUtils.contentEquals(f1, temp));
This test converts a file to a string and writtes it back. However the test is failing.
I think it may be because of the encodings, but in FileUtils there is no much detailed info about this.
Anyone can help?
Thanks!
Added for further undestanding:
Why I need this?
I have very large pdfs in one machine, that are replicated in another one. The first one is in charge of creating those pdfs. Due to the low connectivity of the second machine and the big size of pdfs, I don't want to synch the whole pdfs, but only the changes done.
To create patches/apply them, I'm using the google library DiffMatchPatch. This library creates patches between two string. So I need to load a pdf to an string, apply a generated patch, and put it back to a file.

A PDF is not a text file. Decoding (into Java characters) and re-encoding of binary files that are not encoded text is asymmetrical. For example, if the input bytestream is invalid for the current encoding, you can be assured that it won't re-encode correctly. In short - don't do that. Use readFileToByteArray and writeByteArrayToFile instead.

Just a few thoughts:
There might actually some BOM (byte order mark) bytes in one of the files that either gets stripped when reading or added during writing. Is there a difference in the file size (if it is the BOM the difference should be 2 or 3 bytes)?
The line breaks might not match, depending which system the files are created on, i.e. one might have CR LF while the other only has LF or CR. (1 byte difference per line break)
According to the JavaDoc both methods should use the default encoding of the JVM, which should be the same for both operations. However, try and test with an explicitly set encoding (JVM's default encoding would be queried using System.getProperty("file.encoding")).

Ed Staub awnser points why my solution is not working and he suggested using bytes instead of Strings. In my case I need an String, so the final working solution I've found is the following:
#Test
public void testFileRWAsArray() throws IOException{
String f1String="";
byte[] bytes=FileUtils.readFileToByteArray(f1);
for(byte b:bytes){
f1String=f1String+((char)b);
}
File temp=File.createTempFile("deleteme", "deleteme");
byte[] newBytes=new byte[f1String.length()];
for(int i=0; i<f1String.length(); ++i){
char c=f1String.charAt(i);
newBytes[i]= (byte)c;
}
FileUtils.writeByteArrayToFile(temp, newBytes);
assertTrue(FileUtils.contentEquals(f1, temp));
}
By using a cast between byte-char, I have the symmetry on conversion.
Thank you all!

Try this code...
public static String fetchBase64binaryEncodedString(String path) {
File inboundDoc = new File(path);
byte[] pdfData;
try {
pdfData = FileUtils.readFileToByteArray(inboundDoc);
} catch (IOException e) {
throw new RuntimeException(e);
}
byte[] encodedPdfData = Base64.encodeBase64(pdfData);
String attachment = new String(encodedPdfData);
return attachment;
}
//How to decode it
public void testConversionPDFtoBase64() throws IOException
{
String path = "C:/Documents and Settings/kantab/Desktop/GTR_SDR/MSDOC.pdf";
File origFile = new File(path);
String encodedString = CreditOneMLParserUtil.fetchBase64binaryEncodedString(path);
//now decode it
byte[] decodeData = Base64.decodeBase64(encodedString.getBytes());
String decodedString = new String(decodeData);
//or actually give the path to pdf file.
File decodedfile = File.createTempFile("DECODED", ".pdf");
FileUtils.writeByteArrayToFile(decodedfile,decodeData);
Assert.assertTrue(FileUtils.contentEquals(origFile, decodedfile));
// Frame frame = new Frame("PDF Viewer");
// frame.setLayout(new BorderLayout());
}

Writing in the beginning of a text file Java

I need to write something into a text file's beginning. I have a text file with content and i want write something before this content. Say i have;
Good afternoon sir,how are you today?
I'm fine,how are you?
Thanks for asking,I'm great
After modifying,I want it to be like this:
Page 1-Scene 59
25.05.2011
Good afternoon sir,how are you today?
I'm fine,how are you?
Thanks for asking,I'm great
Just made up the content :) How can i modify a text file like this way?

You can't really modify it that way - file systems don't generally let you insert data in arbitrary locations - but you can:
Create a new file
Write the prefix to it
Copy the data from the old file to the new file
Move the old file to a backup location
Move the new file to the old file's location
Optionally delete the old backup file

Just in case it will be useful for someone here is full source code of method to prepend lines to a file using Apache Commons IO library. The code does not read whole file into memory, so will work on files of any size.
public static void prependPrefix(File input, String prefix) throws IOException {
LineIterator li = FileUtils.lineIterator(input);
File tempFile = File.createTempFile("prependPrefix", ".tmp");
BufferedWriter w = new BufferedWriter(new FileWriter(tempFile));
try {
w.write(prefix);
while (li.hasNext()) {
w.write(li.next());
w.write("\n");
}
} finally {
IOUtils.closeQuietly(w);
LineIterator.closeQuietly(li);
}
FileUtils.deleteQuietly(input);
FileUtils.moveFile(tempFile, input);
}

I think what you want is random access. Check out the related java tutorial. However, I don't believe you can just insert data at an arbitrary point in the file; If I recall correctly, you'd only overwrite the data. If you wanted to insert, you'd have to have your code
copy a block,
overwrite with your new stuff,
copy the next block,
overwrite with the previously copied block,
return to 3 until no more blocks

As #atk suggested, java.nio.channels.SeekableByteChannel is a good interface. But it is available from 1.7 only.
Update : If you have no issue using FileUtils then use
String fileString = FileUtils.readFileToString(file);

This isn't a direct answer to the question, but often files are accessed via InputStreams. If this is your use case, then you can chain input streams via SequenceInputStream to achieve the same result. E.g.
InputStream inputStream = new SequenceInputStream(new ByteArrayInputStream("my line\n".getBytes()), new FileInputStream(new File("myfile.txt")));

I will leave it here just in case anyone need
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
try (FileInputStream fileInputStream1 = new FileInputStream(fileName1);
FileInputStream fileInputStream2 = new FileInputStream(fileName2)) {
while (fileInputStream2.available() > 0) {
byteArrayOutputStream.write(fileInputStream2.read());
}
while (fileInputStream1.available() > 0) {
byteArrayOutputStream.write(fileInputStream1.read());
}
}
try (FileOutputStream fileOutputStream = new FileOutputStream(fileName1)) {
byteArrayOutputStream.writeTo(fileOutputStream);
}