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This is a libray to digital signing a PDF and a PFX valid certificate. Based in PDFBox official SVN example.
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/*
 * Copyright 2015 The Apache Software Foundation.
 *
 * Licensed 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 com.somospnt.signature;

import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.security.NoSuchAlgorithmException;
import java.util.Arrays;
import java.util.SortedMap;
import java.util.TreeMap;
import org.apache.pdfbox.cos.COSBase;
import org.apache.pdfbox.cos.COSName;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.pdmodel.interactive.digitalsignature.PDSignature;
import org.apache.pdfbox.util.Hex;
import org.bouncycastle.cms.CMSException;
import org.bouncycastle.cms.CMSSignedData;

/**
 * A simple wrapper class for signing PDF files using PDFBOX Example usage:
 *
 *  * {@code
 * FileInputStream inputStream = new FileInputStream(INPUT_FILE);
 * FileOutputStream outputStream = new FileOutputStream(OUTPUT_FILE);
 * Signer signer = new Signer(KEYSTORE_PATH, PASSWORD, LOCATION, REASON);
 * signer.sign(inputStream, outputStream);
 * }
 * 
 *
 * @author SomosPNT
 */
class TimeStamperEmbedder {

    private final String tsaUrl;
    private PDDocument document;
    private PDSignature signature;
    private byte[] changedEncodedSignature;

    public TimeStamperEmbedder(String tsaUrl) {
        this.tsaUrl = tsaUrl;
    }

    /**
     * Embeds signed timestamp(s) into existing signatures of the given document
     *
     * @param inputStream containing the bytes of the input pdf
     * @param outputStream Where the changed document will be saved
     * @throws IOException
     */
    void embedTimeStamp(InputStream inputStream, OutputStream outputStream) throws IOException {
        byte[] inputBytes = inputStream.readAllBytes();
        // sign
        try (PDDocument doc = PDDocument.load(inputBytes)) {
            document = doc;
            processTimeStamping(inputBytes, outputStream);
        }
    }

    /**
     * Processes the time-stamping of the Signature.
     *
     * @param documentBytes of the existing file containing the pdf
     * @param outputStream Where the new file will be written to
     * @throws IOException
     */
    private void processTimeStamping(byte[] documentBytes, OutputStream outputStream) throws IOException {
        try {
            processRelevantSignatures(documentBytes);

            if (changedEncodedSignature != null) {
                embedNewSignatureIntoDocument(documentBytes, outputStream);
            } else {
                throw new IOException("No signatures were found in the document.");
            }
        } catch (IOException | NoSuchAlgorithmException | CMSException e) {
            throw new IOException(e);
        }
    }

    /**
     * Create changed Signature with embedded TimeStamp from TSA
     *
     * @param documentBytes byte[] of the input file
     * @throws IOException
     * @throws CMSException
     * @throws NoSuchAlgorithmException
     */
    private void processRelevantSignatures(byte[] documentBytes)
            throws IOException, CMSException, NoSuchAlgorithmException {
        getRelevantSignature(document);
        if (signature != null) {
            byte[] sigBlock = signature.getContents(documentBytes);
            CMSSignedData signedData = new CMSSignedData(sigBlock);

            System.out.println("INFO: Byte Range: " + Arrays.toString(signature.getByteRange()));

            ValidationTimeStamp validation = new ValidationTimeStamp(tsaUrl);
            signedData = validation.addSignedTimeStamp(signedData);

            byte[] newEncoded = Hex.getBytes(signedData.getEncoded());
            int maxSize = signature.getByteRange()[2] - signature.getByteRange()[1];
            System.out.println(
                    "INFO: New Signature has Size: " + newEncoded.length + " maxSize: " + maxSize);

            if (newEncoded.length > maxSize - 2) {
                throw new IOException(
                        "New Signature is too big for existing Signature-Placeholder. Max Place: "
                        + maxSize);
            } else {
                changedEncodedSignature = newEncoded;
            }
        }
    }

    /**
     * Extracts last Document-Signature from the document. The signature will be
     * set on the signature-field.
     *
     * @param document to get the Signature from
     * @throws IOException
     */
    private void getRelevantSignature(PDDocument document) throws IOException {
        // we can't use getLastSignatureDictionary() because this will fail (see PDFBOX-3978)
        // if a signature is assigned to a pre-defined empty signature field that isn't the last.
        // we get the last in time by looking at the offset in the PDF file.
        SortedMap sortedMap = new TreeMap<>();
        for (PDSignature sig : document.getSignatureDictionaries()) {
            int sigOffset = sig.getByteRange()[1];
            sortedMap.put(sigOffset, sig);
        }
        if (sortedMap.size() > 0) {
            PDSignature lastSignature = sortedMap.get(sortedMap.lastKey());
            COSBase type = lastSignature.getCOSObject().getItem(COSName.TYPE);
            if (type.equals(COSName.SIG)) {
                signature = lastSignature;
            }
        }
    }

    /**
     * Embeds the new signature into the document, by copying the rest of the
     * document
     *
     * @param docBytes byte array of the document
     * @param output target, where the file will be written
     * @throws IOException
     */
    private void embedNewSignatureIntoDocument(byte[] docBytes, OutputStream output)
            throws IOException {
        int[] byteRange = signature.getByteRange();
        output.write(docBytes, byteRange[0], byteRange[1] + 1);
        output.write(changedEncodedSignature);
        int addingLength = byteRange[2] - byteRange[1] - 2 - changedEncodedSignature.length;
        byte[] zeroes = Hex.getBytes(new byte[(addingLength + 1) / 2]);
        output.write(zeroes);
        output.write(docBytes, byteRange[2] - 1, byteRange[3] + 1);
    }
}