Package org.apache.pdfbox.pdfwriter

Source Code of org.apache.pdfbox.pdfwriter.COSWriter

/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements.  See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License.  You may obtain a copy of the License at
*
*      http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.pdfbox.pdfwriter;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.Closeable;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.SequenceInputStream;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import org.apache.pdfbox.cos.COSArray;
import org.apache.pdfbox.cos.COSBase;
import org.apache.pdfbox.cos.COSBoolean;
import org.apache.pdfbox.cos.COSDictionary;
import org.apache.pdfbox.cos.COSDocument;
import org.apache.pdfbox.cos.COSFloat;
import org.apache.pdfbox.cos.COSInteger;
import org.apache.pdfbox.cos.COSName;
import org.apache.pdfbox.cos.COSNull;
import org.apache.pdfbox.cos.COSNumber;
import org.apache.pdfbox.cos.COSObject;
import org.apache.pdfbox.cos.COSStream;
import org.apache.pdfbox.cos.COSString;
import org.apache.pdfbox.cos.ICOSVisitor;
import org.apache.pdfbox.io.IOUtils;
import org.apache.pdfbox.pdfparser.PDFXRefStream;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.pdmodel.encryption.SecurityHandler;
import org.apache.pdfbox.pdmodel.interactive.digitalsignature.SignatureInterface;
import org.apache.pdfbox.persistence.util.COSObjectKey;
import org.apache.pdfbox.util.StringUtil;

/**
* this class acts on a in-memory representation of a pdf document.
*
* todo no support for incremental updates
* todo single xref section only
* todo no linearization
*
* @author Michael Traut
* @author <a href="mailto:ben@benlitchfield.com">Ben Litchfield</a>
*
*/
public class COSWriter implements ICOSVisitor, Closeable
{

    /**
     * Log instance.
     */
    private static final Log LOG = LogFactory.getLog(COSWriter.class);

    /**
     * The dictionary open token.
     */
    public static final byte[] DICT_OPEN = StringUtil.getBytes("<<");
    /**
     * The dictionary close token.
     */
    public static final byte[] DICT_CLOSE = StringUtil.getBytes(">>");
    /**
     * space character.
     */
    public static final byte[] SPACE = StringUtil.getBytes(" ");
    /**
     * The start to a PDF comment.
     */
    public static final byte[] COMMENT = StringUtil.getBytes("%");

    /**
     * The output version of the PDF.
     */
    public static final byte[] VERSION = StringUtil.getBytes("PDF-1.4");
    /**
     * Garbage bytes used to create the PDF header.
     */
    public static final byte[] GARBAGE = new byte[] {(byte)0xf6, (byte)0xe4, (byte)0xfc, (byte)0xdf};
    /**
     * The EOF constant.
     */
    public static final byte[] EOF = StringUtil.getBytes("%%EOF");
    // pdf tokens

    /**
     * The reference token.
     */
    public static final byte[] REFERENCE = StringUtil.getBytes("R");
    /**
     * The XREF token.
     */
    public static final byte[] XREF = StringUtil.getBytes("xref");
    /**
     * The xref free token.
     */
    public static final byte[] XREF_FREE = StringUtil.getBytes("f");
    /**
     * The xref used token.
     */
    public static final byte[] XREF_USED = StringUtil.getBytes("n");
    /**
     * The trailer token.
     */
    public static final byte[] TRAILER = StringUtil.getBytes("trailer");
    /**
     * The start xref token.
     */
    public static final byte[] STARTXREF = StringUtil.getBytes("startxref");
    /**
     * The starting object token.
     */
    public static final byte[] OBJ = StringUtil.getBytes("obj");
    /**
     * The end object token.
     */
    public static final byte[] ENDOBJ = StringUtil.getBytes("endobj");
    /**
     * The array open token.
     */
    public static final byte[] ARRAY_OPEN = StringUtil.getBytes("[");
    /**
     * The array close token.
     */
    public static final byte[] ARRAY_CLOSE = StringUtil.getBytes("]");
    /**
     * The open stream token.
     */
    public static final byte[] STREAM = StringUtil.getBytes("stream");
    /**
     * The close stream token.
     */
    public static final byte[] ENDSTREAM = StringUtil.getBytes("endstream");

    private NumberFormat formatXrefOffset = new DecimalFormat("0000000000");

    // the decimal format for the xref object generation number data
    private NumberFormat formatXrefGeneration = new DecimalFormat("00000");

    private NumberFormat formatDecimal = NumberFormat.getNumberInstance( Locale.US );

    // the stream where we create the pdf output
    private OutputStream output;

    // the stream used to write standard cos data
    private COSStandardOutputStream standardOutput;

    // the start position of the x ref section
    private long startxref = 0;

    // the current object number
    private long number = 0;

    // maps the object to the keys generated in the writer
    // these are used for indirect references in other objects
    //A hashtable is used on purpose over a hashmap
    //so that null entries will not get added.
    private Map<COSBase,COSObjectKey> objectKeys = new Hashtable<COSBase,COSObjectKey>();
    private Map<COSObjectKey,COSBase> keyObject = new Hashtable<COSObjectKey,COSBase>();

    // the list of x ref entries to be made so far
    private List<COSWriterXRefEntry> xRefEntries = new ArrayList<COSWriterXRefEntry>();
    private HashSet<COSBase> objectsToWriteSet = new HashSet<COSBase>();

    //A list of objects to write.
    private LinkedList<COSBase> objectsToWrite = new LinkedList<COSBase>();

    //a list of objects already written
    private Set<COSBase> writtenObjects = new HashSet<COSBase>();

    //An 'actual' is any COSBase that is not a COSObject.
    //need to keep a list of the actuals that are added
    //as well as the objects because there is a problem
    //when adding a COSObject and then later adding
    //the actual for that object, so we will track
    //actuals separately.
    private Set<COSBase> actualsAdded = new HashSet<COSBase>();

    private COSObjectKey currentObjectKey = null;
    private PDDocument document = null;
    private boolean willEncrypt = false;

    // signing
    private boolean incrementalUpdate = false;
    private boolean reachedSignature = false;
    private long signatureOffset, signatureLength;
    private long byteRangeOffset, byteRangeLength;
    private InputStream incrementalInput;
    private OutputStream incrementalOutput;

    /**
     * COSWriter constructor comment.
     *
     * @param os The wrapped output stream.
     */
    public COSWriter(OutputStream os)
    {
        super();
        setOutput(os);
        setStandardOutput(new COSStandardOutputStream(output));
        formatDecimal.setMaximumFractionDigits( 10 );
        formatDecimal.setGroupingUsed( false );
    }
   
    /**
     * COSWriter constructor for incremental updates.
     *
     * @param output output stream where the new PDF data will be written
     * @param input input stream containing source PDF data
     */
    public COSWriter(OutputStream output, InputStream input) throws IOException
    {
        super();

        // write to buffer instead of output
        setOutput(new ByteArrayOutputStream());
        setStandardOutput(new COSStandardOutputStream(this.output, input.available()));

        incrementalInput = input;
        incrementalOutput = output;
        incrementalUpdate = true;

        formatDecimal.setMaximumFractionDigits( 10 );
        formatDecimal.setGroupingUsed( false );
    }

    private void prepareIncrement(PDDocument doc)
    {
      try
      {
        if (doc != null)
        {
          COSDocument cosDoc = doc.getDocument();
         
          Map<COSObjectKey, Long> xrefTable = cosDoc.getXrefTable();
          Set<COSObjectKey> keySet = xrefTable.keySet();
          long highestNumber=0;
          for ( COSObjectKey cosObjectKey : keySet )
          {
            COSBase object = cosDoc.getObjectFromPool(cosObjectKey).getObject();
            if (object != null && cosObjectKey!= null && !(object instanceof COSNumber))
            {
            objectKeys.put(object, cosObjectKey);
            keyObject.put(cosObjectKey,object);
            }
           
            long num = cosObjectKey.getNumber();
            if (num > highestNumber)
            {
                highestNumber=num;
            }
          }
          setNumber(highestNumber);
          // xrefTable.clear();

        }
      }
      catch (IOException e)
      {
        LOG.error(e,e);
      }
    }
   
    /**
     * add an entry in the x ref table for later dump.
     *
     * @param entry The new entry to add.
     */
    protected void addXRefEntry(COSWriterXRefEntry entry)
    {
        getXRefEntries().add(entry);
    }

    /**
     * This will close the stream.
     *
     * @throws IOException If the underlying stream throws an exception.
     */
    public void close() throws IOException
    {
        if (getStandardOutput() != null)
        {
            getStandardOutput().close();
        }
        if (getOutput() != null)
        {
            getOutput().close();
        }
        if (incrementalOutput != null)
        {
            incrementalOutput.close();
        }
    }

    /**
     * This will get the current object number.
     *
     * @return The current object number.
     */
    protected long getNumber()
    {
        return number;
    }

    /**
     * This will get all available object keys.
     *
     * @return A map of all object keys.
     */
    public Map<COSBase,COSObjectKey> getObjectKeys()
    {
        return objectKeys;
    }

    /**
     * This will get the output stream.
     *
     * @return The output stream.
     */
    protected java.io.OutputStream getOutput()
    {
        return output;
    }

    /**
     * This will get the standard output stream.
     *
     * @return The standard output stream.
     */
    protected COSStandardOutputStream getStandardOutput()
    {
        return standardOutput;
    }

    /**
     * This will get the current start xref.
     *
     * @return The current start xref.
     */
    protected long getStartxref()
    {
        return startxref;
    }
    /**
     * This will get the xref entries.
     *
     * @return All available xref entries.
     */
    protected List<COSWriterXRefEntry> getXRefEntries()
    {
        return xRefEntries;
    }

    /**
     * This will set the current object number.
     *
     * @param newNumber The new object number.
     */
    protected void setNumber(long newNumber)
    {
        number = newNumber;
    }

    /**
     * This will set the output stream.
     *
     * @param newOutput The new output stream.
     */
    private void setOutput( OutputStream newOutput )
    {
        output = newOutput;
    }

    /**
     * This will set the standard output stream.
     *
     * @param newStandardOutput The new standard output stream.
     */
    private void setStandardOutput(COSStandardOutputStream newStandardOutput)
    {
        standardOutput = newStandardOutput;
    }

    /**
     * This will set the start xref.
     *
     * @param newStartxref The new start xref attribute.
     */
    protected void setStartxref(long newStartxref)
    {
        startxref = newStartxref;
    }

    /**
     * This will write the body of the document.
     *
     * @param doc The document to write the body for.
     *
     * @throws IOException If there is an error writing the data.
     */
    protected void doWriteBody(COSDocument doc) throws IOException
    {
        COSDictionary trailer = doc.getTrailer();
        COSDictionary root = (COSDictionary)trailer.getDictionaryObject( COSName.ROOT );
        COSDictionary info = (COSDictionary)trailer.getDictionaryObject( COSName.INFO );
        COSDictionary encrypt = (COSDictionary)trailer.getDictionaryObject( COSName.ENCRYPT );
          if( root != null )
          {
              addObjectToWrite( root );
          }
          if( info != null )
          {
              addObjectToWrite( info );
          }

        while( objectsToWrite.size() > 0 )
        {
            COSBase nextObject = objectsToWrite.removeFirst();
            objectsToWriteSet.remove(nextObject);
            doWriteObject( nextObject );
        }


        willEncrypt = false;

        if( encrypt != null )
        {
            addObjectToWrite( encrypt );
        }

        while( objectsToWrite.size() > 0 )
        {
            COSBase nextObject = objectsToWrite.removeFirst();
            objectsToWriteSet.remove(nextObject);
            doWriteObject( nextObject );
        }
    }

    private void addObjectToWrite( COSBase object )
    {
        COSBase actual = object;
        if( actual instanceof COSObject )
        {
            actual = ((COSObject)actual).getObject();
        }

        if( !writtenObjects.contains( object ) &&
            !objectsToWriteSet.contains( object ) &&
            !actualsAdded.contains( actual ) )
        {
            COSBase cosBase=null;
            COSObjectKey cosObjectKey = null;
            if(actual != null)
            {
                cosObjectKey= objectKeys.get(actual);
            }
            if(cosObjectKey!=null)
            {
                cosBase = keyObject.get(cosObjectKey);
            }
            if(actual != null && objectKeys.containsKey(actual) &&
                    !object.isNeedToBeUpdate() && (cosBase!= null &&
                    !cosBase.isNeedToBeUpdate()))
            {
                return;
            }
         
            objectsToWrite.add( object );
            objectsToWriteSet.add( object );
            if( actual != null )
            {
                actualsAdded.add( actual );
            }
        }
    }

    /**
     * This will write a COS object.
     *
     * @param obj The object to write.
     *
     * @throws IOException if the output cannot be written
     */
    public void doWriteObject( COSBase obj ) throws IOException
    {
        writtenObjects.add( obj );
        if(obj instanceof COSDictionary)
        {
            COSDictionary dict = (COSDictionary)obj;
            COSBase itemType = dict.getItem(COSName.TYPE);
            if (itemType instanceof COSName)
            {
                COSName item = (COSName) itemType;
                if (COSName.SIG.equals(item) || COSName.DOC_TIME_STAMP.equals(item))
                {
                    reachedSignature = true;
                }
            }
        }

        // find the physical reference
        currentObjectKey = getObjectKey( obj );
        // add a x ref entry
        addXRefEntry( new COSWriterXRefEntry(getStandardOutput().getPos(), obj, currentObjectKey));
        // write the object
        getStandardOutput().write(String.valueOf(currentObjectKey.getNumber()).getBytes("ISO-8859-1"));
        getStandardOutput().write(SPACE);
        getStandardOutput().write(String.valueOf(currentObjectKey.getGeneration()).getBytes("ISO-8859-1"));
        getStandardOutput().write(SPACE);
        getStandardOutput().write(OBJ);
        getStandardOutput().writeEOL();
        obj.accept( this );
        getStandardOutput().writeEOL();
        getStandardOutput().write(ENDOBJ);
        getStandardOutput().writeEOL();
    }

    /**
     * This will write the header to the PDF document.
     *
     * @param doc The document to get the data from.
     *
     * @throws IOException If there is an error writing to the stream.
     */
    protected void doWriteHeader(COSDocument doc) throws IOException
    {
        getStandardOutput().write( doc.getHeaderString().getBytes("ISO-8859-1") );
        getStandardOutput().writeEOL();
        getStandardOutput().write(COMMENT);
        getStandardOutput().write(GARBAGE);
        getStandardOutput().writeEOL();
    }


    /**
     * This will write the trailer to the PDF document.
     *
     * @param doc The document to create the trailer for.
     *
     * @throws IOException If there is an IOError while writing the document.
     */
    protected void doWriteTrailer(COSDocument doc) throws IOException
    {
        getStandardOutput().write(TRAILER);
        getStandardOutput().writeEOL();

        COSDictionary trailer = doc.getTrailer();
        //sort xref, needed only if object keys not regenerated
        Collections.sort(getXRefEntries());
        COSWriterXRefEntry lastEntry = getXRefEntries().get( getXRefEntries().size()-1);
        trailer.setInt(COSName.SIZE, (int)lastEntry.getKey().getNumber()+1);
        // Only need to stay, if an incremental update will be performed
        if (!incrementalUpdate)
        {
          trailer.removeItem( COSName.PREV );
        }
        if (!doc.isXRefStream())
        {
            trailer.removeItem( COSName.XREF_STM );
        }
        // Remove a checksum if present
        trailer.removeItem( COSName.DOC_CHECKSUM );
       
        trailer.accept(this);
    }

    /**
     * write the x ref section for the pdf file
     *
     * currently, the pdf is reconstructed from the scratch, so we write a single section
     *
     * todo support for incremental writing?
     *
     * @param doc The document to write the xref from.
     *
     * @throws IOException If there is an error writing the data to the stream.
     */
    protected void doWriteXRef(COSDocument doc) throws IOException
    {
        if (doc.isXRefStream())
        {
            // sort xref, needed only if object keys not regenerated
            Collections.sort(getXRefEntries());
            COSWriterXRefEntry lastEntry = getXRefEntries().get( getXRefEntries().size()-1 );
   
            // remember the position where x ref is written
            setStartxref(getStandardOutput().getPos());
            //
            getStandardOutput().write(XREF);
            getStandardOutput().writeEOL();
            // write start object number and object count for this x ref section
            // we assume starting from scratch
            writeXrefRange(0, lastEntry.getKey().getNumber() + 1);
            // write initial start object with ref to first deleted object and magic generation number
            writeXrefEntry(COSWriterXRefEntry.getNullEntry());
            // write entry for every object
            long lastObjectNumber = 0;
            for (COSWriterXRefEntry entry : getXRefEntries())
            {
                while( lastObjectNumber<entry.getKey().getNumber()-1 )
                {
                    writeXrefEntry(COSWriterXRefEntry.getNullEntry());
                }
                lastObjectNumber = entry.getKey().getNumber();
                writeXrefEntry(entry);
            }
        }
        else
        {

            COSDictionary trailer = doc.getTrailer();
            trailer.setLong(COSName.PREV, doc.getStartXref());
            addXRefEntry(COSWriterXRefEntry.getNullEntry());

            // sort xref, needed only if object keys not regenerated
            Collections.sort(getXRefEntries());

            // remember the position where x ref was written
            setStartxref(getStandardOutput().getPos());

            getStandardOutput().write(XREF);
            getStandardOutput().writeEOL();
            // write start object number and object count for this x ref section
            // we assume starting from scratch

            Integer[] xRefRanges = getXRefRanges(getXRefEntries());
            int xRefLength = xRefRanges.length;
            int x = 0;
            int j = 0;
            while (x < xRefLength && (xRefLength % 2) == 0)
            {
                writeXrefRange(xRefRanges[x], xRefRanges[x + 1]);

                for ( int i = 0; i < xRefRanges[x + 1]; ++i )
                {
                    writeXrefEntry(xRefEntries.get(j++));
                }
                x += 2;
            }
        }
    }

    private void doWriteXRefInc(COSDocument doc, long hybridPrev) throws IOException
    {
        if (doc.isXRefStream() || hybridPrev != -1)
        {
            // the file uses XrefStreams, so we need to update
            // it with an xref stream. We create a new one and fill it
            // with data available here
            // first set an entry for the null entry in the xref table
            // this is probably not necessary
            // addXRefEntry(COSWriterXRefEntry.getNullEntry());

            // create a new XRefStrema object
            PDFXRefStream pdfxRefStream = new PDFXRefStream();

            // add all entries from the incremental update.
            List<COSWriterXRefEntry> xRefEntries2 = getXRefEntries();
            for ( COSWriterXRefEntry cosWriterXRefEntry : xRefEntries2 )
            {
                pdfxRefStream.addEntry(cosWriterXRefEntry);
            }

            COSDictionary trailer = doc.getTrailer();
            //            trailer.setLong(COSName.PREV, hybridPrev == -1 ? prev : hybridPrev);
            trailer.setLong(COSName.PREV, doc.getStartXref());

            pdfxRefStream.addTrailerInfo(trailer);
            // the size is the highest object number+1. we add one more
            // for the xref stream object we are going to write
            pdfxRefStream.setSize(getNumber() + 2);

            setStartxref(getStandardOutput().getPos());
            COSStream stream2 = pdfxRefStream.getStream();
            doWriteObject(stream2);
        }

        if (!doc.isXRefStream() || hybridPrev != -1)
        {
            COSDictionary trailer = doc.getTrailer();
            trailer.setLong(COSName.PREV, doc.getStartXref());
            if (hybridPrev != -1)
            {
                COSName xrefStm = COSName.XREF_STM;
                trailer.removeItem(xrefStm);
                trailer.setLong(xrefStm, getStartxref());
            }
            addXRefEntry(COSWriterXRefEntry.getNullEntry());
   
            // sort xref, needed only if object keys not regenerated
            Collections.sort(getXRefEntries());
         
            // remember the position where x ref was written
            setStartxref(getStandardOutput().getPos());
   
            getStandardOutput().write(XREF);
            getStandardOutput().writeEOL();
            // write start object number and object count for this x ref section
            // we assume starting from scratch
   
            Integer[] xRefRanges = getXRefRanges(getXRefEntries());
            int xRefLength = xRefRanges.length;
            int x = 0;
            int j = 0;
            while(x < xRefLength && (xRefLength % 2) == 0)
            {
                writeXrefRange(xRefRanges[x], xRefRanges[x + 1]);
   
                for(int i = 0; i < xRefRanges[x + 1]; ++i)
                {
                    writeXrefEntry(xRefEntries.get(j++));
                }
                x += 2;
            }
        }
    }

    private void doWriteSignature(COSDocument doc) throws IOException
    {
        if (signatureOffset == 0 || byteRangeOffset == 0)
        {
            return;
        }

        // calculate the ByteRange values
        long inLength = incrementalInput.available();
        long beforeLength = signatureOffset;
        long afterOffset = signatureOffset + signatureLength;
        long afterLength = getStandardOutput().getPos() - (inLength + signatureLength) - (signatureOffset - inLength);

        String byteRange = "0 " + beforeLength + " " + afterOffset + " " + afterLength + "]";
        if (byteRangeLength - byteRange.length() < 0)
        {
            throw new IOException("Can't write new ByteRange, not enough space");
        }

        // copy the new incremental data into a buffer (e.g. signature dict, trailer)
        ByteArrayOutputStream byteOut = (ByteArrayOutputStream) output;
        byteOut.flush();
        byte[] buffer = byteOut.toByteArray();

        // overwrite the ByteRange in the buffer
        byte[] byteRangeBytes = byteRange.getBytes();
        for (int i = 0; i < byteRangeLength; i++)
        {
            if (i >= byteRangeBytes.length)
            {
                buffer[(int)(byteRangeOffset + i - inLength)] = 0x20; // SPACE
            }
            else
            {
                buffer[(int)(byteRangeOffset + i - inLength)] = byteRangeBytes[i];
            }
        }

        // get the input PDF bytes
        byte[] inputBytes = IOUtils.toByteArray(incrementalInput);

        // get only the incremental bytes to be signed (includes /ByteRange but not /Contents)
        byte[] signBuffer = new byte[buffer.length - (int)signatureLength];
        int bufSignatureOffset = (int)(signatureOffset - inLength);
        System.arraycopy(buffer, 0, signBuffer, 0, bufSignatureOffset);
        System.arraycopy(buffer, bufSignatureOffset + (int)signatureLength,
                         signBuffer, bufSignatureOffset, buffer.length - bufSignatureOffset - (int)signatureLength);

        SequenceInputStream signStream = new SequenceInputStream(new ByteArrayInputStream(inputBytes),
                new ByteArrayInputStream(signBuffer));

        // sign the bytes
        SignatureInterface signatureInterface = doc.getSignatureInterface();
        byte[] sign = signatureInterface.sign(signStream);
        String signature = new COSString(sign).getHexString();
        // substract 2 bytes because of the enclosing "<>"
        if (signature.length() > signatureLength - 2)
        {
            throw new IOException("Can't write signature, not enough space");
        }

        // overwrite the signature Contents in the buffer
        byte[] signatureBytes = signature.getBytes();
        System.arraycopy(signatureBytes, 0, buffer, bufSignatureOffset + 1, signatureBytes.length);

        // write the data to the incremental output stream
        incrementalOutput.write(inputBytes);
        incrementalOutput.write(buffer);
    }
   
    private void writeXrefRange(long x, long y) throws IOException
    {
        getStandardOutput().write(String.valueOf(x).getBytes());
        getStandardOutput().write(SPACE);
        getStandardOutput().write(String.valueOf(y).getBytes());
        getStandardOutput().writeEOL();
    }

    private void writeXrefEntry(COSWriterXRefEntry entry) throws IOException
    {
        String offset = formatXrefOffset.format(entry.getOffset());
        String generation = formatXrefGeneration.format(entry.getKey().getGeneration());
        getStandardOutput().write(offset.getBytes("ISO-8859-1"));
        getStandardOutput().write(SPACE);
        getStandardOutput().write(generation.getBytes("ISO-8859-1"));
        getStandardOutput().write(SPACE);
        getStandardOutput().write(entry.isFree() ? XREF_FREE : XREF_USED);
        getStandardOutput().writeCRLF();
    }

    /**
     * check the xref entries and write out the ranges.  The format of the
     * returned array is exactly the same as the pdf specification.  See section
     * 7.5.4 of ISO32000-1:2008, example 1 (page 40) for reference.
     * <p>
     * example: 0 1 2 5 6 7 8 10
     * <p>
     * will create a array with follow ranges
     * <p>
     * 0 3 5 4 10 1
     * <p>
     * this mean that the element 0 is followed by two other related numbers
     * that represent a cluster of the size 3. 5 is follow by three other
     * related numbers and create a cluster of size 4. etc.
     *
     * @param xRefEntriesList list with the xRef entries that was written
     * @return a integer array with the ranges
     */
    protected Integer[] getXRefRanges(List<COSWriterXRefEntry> xRefEntriesList)
    {
        int nr = 0;
        int last = -2;
        int count = 1;

        ArrayList<Integer> list = new ArrayList<Integer>();
        for( Object object : xRefEntriesList )
        {
            nr = (int)((COSWriterXRefEntry)object).getKey().getNumber();
            if (nr == last + 1)
            {
                ++count;
                last = nr;
            }
            else if (last == -2)
            {
                last = nr;
            }
            else
            {
                list.add(last - count + 1);
                list.add(count);
                last = nr;
                count = 1;
            }
        }
        // If no new entry is found, we need to write out the last result
        if(xRefEntriesList.size() > 0)
        {
            list.add(last - count + 1);
            list.add(count);
        }
        return list.toArray(new Integer[list.size()]);
    }
   
    /**
     * This will get the object key for the object.
     *
     * @param obj The object to get the key for.
     *
     * @return The object key for the object.
     */
    private COSObjectKey getObjectKey( COSBase obj )
    {
        COSBase actual = obj;
        if( actual instanceof COSObject )
        {
            actual = ((COSObject)obj).getObject();
        }
        COSObjectKey key = null;
        if( actual != null )
        {
            key = objectKeys.get(actual);
        }
        if( key == null )
        {
            key = objectKeys.get(obj);
        }
        if (key == null)
        {
            setNumber(getNumber()+1);
            key = new COSObjectKey(getNumber(),0);
            objectKeys.put(obj, key);
            if( actual != null )
            {
                objectKeys.put(actual, key);
            }
        }
        return key;
    }

    @Override
    public Object visitFromArray( COSArray obj ) throws IOException
    {
        int count = 0;
        getStandardOutput().write(ARRAY_OPEN);
        for (Iterator<COSBase> i = obj.iterator(); i.hasNext();)
        {
            COSBase current = i.next();
            if( current instanceof COSDictionary )
            {
                if (current.isDirect())
                {
                    visitFromDictionary((COSDictionary)current);
                }
                else
                {
                    addObjectToWrite( current );
                    writeReference( current );
                }
            }
            else if( current instanceof COSObject )
            {
                COSBase subValue = ((COSObject)current).getObject();
                if( subValue instanceof COSDictionary || subValue == null )
                {
                    addObjectToWrite( current );
                    writeReference( current );
                }
                else
                {
                    subValue.accept( this );
                }
            }
            else if( current == null )
            {
                COSNull.NULL.accept( this );
            }
            else if( current instanceof COSString )
            {
                COSString copy = new COSString();
                copy.append(((COSString)current).getBytes());
                copy.accept(this);
            }
            else
            {
                current.accept(this);
            }
            count++;
            if (i.hasNext())
            {
                if (count % 10 == 0)
                {
                    getStandardOutput().writeEOL();
                }
                else
                {
                    getStandardOutput().write(SPACE);
                }
            }
        }
        getStandardOutput().write(ARRAY_CLOSE);
        getStandardOutput().writeEOL();
        return null;
    }

    @Override
    public Object visitFromBoolean(COSBoolean obj) throws IOException
    {
        obj.writePDF( getStandardOutput() );
        return null;
    }

    @Override
    public Object visitFromDictionary(COSDictionary obj) throws IOException
    {
        getStandardOutput().write(DICT_OPEN);
        getStandardOutput().writeEOL();
        for (Map.Entry<COSName, COSBase> entry : obj.entrySet())
        {
            COSBase value = entry.getValue();
            if (value != null)
            {
                entry.getKey().accept(this);
                getStandardOutput().write(SPACE);
                if( value instanceof COSDictionary )
                {
                    COSDictionary dict = (COSDictionary)value;

                    // write all XObjects as direct objects, this will save some size
                    COSBase item = dict.getItem(COSName.XOBJECT);
                    if(item!=null)
                    {
                        item.setDirect(true);
                    }
                    item = dict.getItem(COSName.RESOURCES);
                    if(item!=null)
                    {
                        item.setDirect(true);
                    }

                    if(dict.isDirect())
                    {
                        // If the object should be written direct, we need
                        // to pass the dictionary to the visitor again.
                        visitFromDictionary(dict);
                    }
                    else
                    {
                        addObjectToWrite( dict );
                        writeReference( dict );
                    }
                }
                else if( value instanceof COSObject )
                {
                    COSBase subValue = ((COSObject)value).getObject();
                    if( subValue instanceof COSDictionary || subValue == null )
                    {
                        addObjectToWrite( value );
                        writeReference( value );
                    }
                    else
                    {
                        subValue.accept( this );
                    }
                }
                else
                {
                    // If we reach the pdf signature, we need to determinate the position of the
                    // content and byterange
                    if(reachedSignature && COSName.CONTENTS.equals(entry.getKey()))
                    {
                        signatureOffset = getStandardOutput().getPos();
                        value.accept(this);
                        signatureLength = getStandardOutput().getPos()- signatureOffset;
                    }
                    else if(reachedSignature && COSName.BYTERANGE.equals(entry.getKey()))
                    {
                        byteRangeOffset = getStandardOutput().getPos() + 1;
                        value.accept(this);
                        byteRangeLength = getStandardOutput().getPos() - 1 - byteRangeOffset;
                        reachedSignature = false;
                    }
                    else
                    {
                        value.accept(this);
                    }
                }
                getStandardOutput().writeEOL();

            }
            else
            {
                //then we won't write anything, there are a couple cases
                //were the value of an entry in the COSDictionary will
                //be a dangling reference that points to nothing
                //so we will just not write out the entry if that is the case
            }
        }
        getStandardOutput().write(DICT_CLOSE);
        getStandardOutput().writeEOL();
        return null;
    }

    @Override
    public Object visitFromDocument(COSDocument doc) throws IOException
    {
        if(!incrementalUpdate)
        {
            doWriteHeader(doc);
        }
        else
        {
            // Sometimes the original file will be missing a newline at the end
            // In order to avoid having %%EOF the first object on the same line
            // as the %%EOF, we put a newline here. If there's already one at
            // the end of the file, an extra one won't hurt. PDFBOX-1051
            getStandardOutput().writeCRLF();
        }

        doWriteBody(doc);

        // get the previous trailer
        COSDictionary trailer = doc.getTrailer();
        long hybridPrev = -1;

        if (trailer != null)
        {
            hybridPrev = trailer.getLong(COSName.XREF_STM);
        }

        if(incrementalUpdate)
        {
            doWriteXRefInc(doc, hybridPrev);
        }
        else
        {
            doWriteXRef(doc);
        }

        // the trailer section should only be used for xref tables not for xref streams
        if (!incrementalUpdate || !doc.isXRefStream() || hybridPrev != -1)
        {
            doWriteTrailer(doc);
        }

        // write endof
        getStandardOutput().write(STARTXREF);
        getStandardOutput().writeEOL();
        getStandardOutput().write(String.valueOf(getStartxref()).getBytes("ISO-8859-1"));
        getStandardOutput().writeEOL();
        getStandardOutput().write(EOF);
        getStandardOutput().writeEOL();

        if(incrementalUpdate)
        {
            doWriteSignature(doc);
        }

        return null;
    }

    @Override
    public Object visitFromFloat(COSFloat obj) throws IOException
    {
        obj.writePDF( getStandardOutput() );
        return null;
    }

    @Override
    public Object visitFromInt(COSInteger obj) throws IOException
    {
        obj.writePDF( getStandardOutput() );
        return null;
    }

    @Override
    public Object visitFromName(COSName obj) throws IOException
    {
        obj.writePDF( getStandardOutput() );
        return null;
    }

    @Override
    public Object visitFromNull(COSNull obj) throws IOException
    {
        obj.writePDF( getStandardOutput() );
        return null;
    }

    /**
     * visitFromObjRef method comment.
     *
     * @param obj The object that is being visited.
     *
     * @throws IOException If there is an exception while visiting this object.
     */
    public void writeReference(COSBase obj) throws IOException
    {
        COSObjectKey key = getObjectKey(obj);
        getStandardOutput().write(String.valueOf(key.getNumber()).getBytes("ISO-8859-1"));
        getStandardOutput().write(SPACE);
        getStandardOutput().write(String.valueOf(key.getGeneration()).getBytes("ISO-8859-1"));
        getStandardOutput().write(SPACE);
        getStandardOutput().write(REFERENCE);
    }

    @Override
    public Object visitFromStream(COSStream obj) throws IOException
    {
        if (willEncrypt)
        {
            document.getEncryption().getSecurityHandler()
                    .encryptStream(obj, currentObjectKey.getNumber(),
                            currentObjectKey.getGeneration());
        }

        COSObject lengthObject = null;
        // check if the length object is required to be direct, like in
        // a cross reference stream dictionary
        COSBase lengthEntry = obj.getDictionaryObject(COSName.LENGTH);
        String type = obj.getNameAsString(COSName.TYPE);
        if (lengthEntry != null && lengthEntry.isDirect() || "XRef".equals(type))
        {
            // the length might be the non encoded length,
            // set the real one as direct object
            COSInteger cosInteger = COSInteger.get(obj.getFilteredLength());
            cosInteger.setDirect(true);
            obj.setItem(COSName.LENGTH, cosInteger);
        }
        else
        {
            // make the length an implicit indirect object
            // set the length of the stream and write stream dictionary
            lengthObject = new COSObject(null);
            obj.setItem(COSName.LENGTH, lengthObject);
        }

        InputStream input = null;
        try
        {
            input = obj.getFilteredStream();
            //obj.accept(this);
            // write the stream content
            visitFromDictionary(obj);
            getStandardOutput().write(STREAM);
            getStandardOutput().writeCRLF();
            byte[] buffer = new byte[1024];
            int amountRead = 0;
            int totalAmountWritten = 0;
            while ((amountRead = input.read(buffer, 0, 1024)) != -1)
            {
                getStandardOutput().write(buffer, 0, amountRead);
                totalAmountWritten += amountRead;
            }
            // set the length as an indirect object
            if (lengthObject != null)
            {
                lengthObject.setObject(COSInteger.get(totalAmountWritten));
            }
            getStandardOutput().writeCRLF();
            getStandardOutput().write(ENDSTREAM);
            getStandardOutput().writeEOL();
            return null;
        }
        finally
        {
            if (input != null)
            {
                input.close();
            }
        }
    }

    @Override
    public Object visitFromString(COSString obj) throws IOException
    {
        if(willEncrypt)
        {
            document.getEncryption().getSecurityHandler().encryptString(
                    obj,
                    currentObjectKey.getNumber(),
                    currentObjectKey.getGeneration());
        }

        obj.writePDF( getStandardOutput() );
        return null;
    }

    /**
     * This will write the pdf document.
     *
     * @throws IOException If an error occurs while generating the data.
     * @param doc The document to write.
     */
    public void write(COSDocument doc) throws IOException
    {
        PDDocument pdDoc = new PDDocument( doc );
        write( pdDoc );
    }

    /**
     * This will write the pdf document.
     *
     * @param doc The document to write.
     *
     * @throws IOException If an error occurs while generating the data.
     */
    public void write(PDDocument doc) throws IOException
    {
        Long idTime = doc.getDocumentId() == null ? System.currentTimeMillis() :
                                                    doc.getDocumentId();

        document = doc;
        if(incrementalUpdate)
        {
            prepareIncrement(doc);
        }
       
        // if the document says we should remove encryption, then we shouldn't encrypt
        if(doc.isAllSecurityToBeRemoved())
        {
            willEncrypt = false;
            // also need to get rid of the "Encrypt" in the trailer so readers
            // don't try to decrypt a document which is not encrypted
            COSDocument cosDoc = doc.getDocument();
            COSDictionary trailer = cosDoc.getTrailer();
            trailer.removeItem(COSName.ENCRYPT);
        }
        else
        {
            if (document.getEncryption() != null)
            {
                SecurityHandler securityHandler = document.getEncryption().getSecurityHandler();
                if(securityHandler != null)
                {
                    securityHandler.prepareDocumentForEncryption(document);
                    willEncrypt = true;
                }
                else
                {
                    willEncrypt = false;
                }
            }
            else
            {
                willEncrypt = false;
            }
        }

        COSDocument cosDoc = document.getDocument();
        COSDictionary trailer = cosDoc.getTrailer();
        COSArray idArray = (COSArray)trailer.getDictionaryObject( COSName.ID );
        boolean missingID = true;
        // check for an existing documentID
        if (idArray != null && idArray.size() == 2)
        {
            missingID = false;
        }
        if( missingID || incrementalUpdate)
        {
            MessageDigest md5;
            try
            {
                md5 = MessageDigest.getInstance("MD5");
            }
            catch (NoSuchAlgorithmException e)
            {
                // should never happen
                throw new RuntimeException(e);
            }

            // algorithm says to use time/path/size/values in doc to generate the id.
            // we don't have path or size, so do the best we can
            md5.update( Long.toString(idTime).getBytes("ISO-8859-1") );

            COSDictionary info = (COSDictionary)trailer.getDictionaryObject( COSName.INFO );
            if( info != null )
            {
                Iterator<COSBase> values = info.getValues().iterator();
                while( values.hasNext() )
                {
                    md5.update( values.next().toString().getBytes("ISO-8859-1") );
                }
            }
            // reuse origin documentID if available as first value
            COSString firstID = missingID ? new COSString( md5.digest() ) : (COSString)idArray.get(0);
            COSString secondID = new COSString( md5.digest() );
            idArray = new COSArray();
            idArray.add( firstID );
            idArray.add( secondID );
            trailer.setItem( COSName.ID, idArray );
        }
        cosDoc.accept(this);
    }
}
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