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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 org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.pdfbox.cos.COSName;
import org.apache.pdfbox.pdmodel.PDDocument;
import org.apache.pdfbox.pdmodel.interactive.digitalsignature.PDSignature;

/**
 * A simple wrapper class for timestamping PDF files using PDFBOX Example usage:
 *
 *  * {@code
 * FileInputStream inputStream = new FileInputStream(INPUT_FILE);
 * FileOutputStream outputStream = new FileOutputStream(OUTPUT_FILE);
 * TimeStamper timeStamper = new TimeStamper(TSA_URL);
 * timeStamper.addTimeStamp(inputStream, outputStream);
 * timeStamper.embedTimeStamp(inputStream, outputStream);
 * }
 * 
 *
 * @author SomosPNT
 */
public class TimeStamper {

    private static final Log LOG = LogFactory.getLog(TimeStamper.class);
    private final String tsaUrl;
    private final TimeStamperEmbedder timeStamperEmbedder;

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

    /**
     * Signs the given PDF file. Adds timeStamp to the signature.
     *
     * @param inputStream the input stream that contains the PDF file
     * @param outputStream the output stream that contains the PDF signed file
     * @throws IOException if the file could not be read or signed
     */
    public void addTimeStamp(InputStream inputStream, OutputStream outputStream) throws IOException {
        PDDocument document = PDDocument.load(inputStream);
        int accessPermissions = SigUtils.getMDPPermission(document);
        if (accessPermissions == 1) {
            throw new IllegalStateException(
                    "No changes to the document are permitted due to DocMDP transform parameters dictionary");
        }

        // create signature dictionary
        PDSignature signature = new PDSignature();
        signature.setType(COSName.DOC_TIME_STAMP);
        signature.setFilter(PDSignature.FILTER_ADOBE_PPKLITE);
        signature.setSubFilter(COSName.getPDFName("ETSI.RFC3161"));

        // No certification allowed because /Reference not allowed in signature directory
        // see ETSI EN 319 142-1 Part 1 and ETSI TS 102 778-4
        // http://www.etsi.org/deliver/etsi_en%5C319100_319199%5C31914201%5C01.01.00_30%5Cen_31914201v010100v.pdf
        // http://www.etsi.org/deliver/etsi_ts/102700_102799/10277804/01.01.01_60/ts_10277804v010101p.pdf
        // register signature dictionary and sign interface
        document.addSignature(signature, (content) -> {
            ValidationTimeStamp validation;
            try {
                validation = new ValidationTimeStamp(tsaUrl);
                return validation.getTimeStampToken(content);
            } catch (NoSuchAlgorithmException e) {
                LOG.error("Hashing-Algorithm not found for TimeStamping", e);
            }
            return new byte[]{};
        });

        // write incremental (only for signing purpose)
        document.saveIncremental(outputStream);
    }

    /**
     * Add timeStamp to an existing signature.
     *
     * @param inputStream the input stream that contains the PDF file
     * @param outputStream the output stream that contains the PDF signed file
     * @throws IOException if the file could not be read or signed
     */
    public void embedTimeStamp(InputStream inputStream, OutputStream outputStream) throws IOException {
        timeStamperEmbedder.embedTimeStamp(inputStream, outputStream);
    }

}