A static method for extract hash/digest from a pdfbox document object to sign and the static method to "insert" the new hash/digest signed to the pdf box object

ManageHashPdfBox

public static byte[] createHashToSignFromPdfFile(InputStream pdf2sign, OutputStream fos, String sigName, String sigLocation,String sigReason,String contactInfo,Date forcedDate,Long revisionId) throws IOException {
		File pdfFileToSigned = TempFileProvider.createTempFile("chars", ""+Calendar.getInstance().getTimeInMillis());
		File pdfPreparedToBeSigned = TempFileProvider.createTempFile("chars", ""+Calendar.getInstance().getTimeInMillis());
		File pdfHashPreparedToBeSigned = TempFileProvider.createTempFile("chars", ""+Calendar.getInstance().getTimeInMillis());
		try{

			if(fos == null)	fos = new FileOutputStream(pdfPreparedToBeSigned);

			FileUtils.copyInputStreamToFile(pdf2sign,pdfFileToSigned);
			final byte[] signatureBytes = FileUtils.readFileToByteArray(pdfFileToSigned);
			PDDocument doc = PDDocument.load(pdfFileToSigned);
			if(sigName == null)
			{
				sigName = getFirmaSigName(doc);
			}
			// create signature dictionary
			PDSignature signature = new PDSignature();
			signature.setFilter(PDSignature.FILTER_ADOBE_PPKLITE); // default filter
			// subfilter for basic and PAdES Part 2 signatures
			//Utile link https://stackoverflow.com/questions/25957573/unable-to-verify-digital-signature-using-apache-pdfbox
			signature.setSubFilter(PDSignature.SUBFILTER_ADBE_PKCS7_DETACHED);
			//signature.setSubFilter(PDSignature.SUBFILTER_ETSI_CADES_DETACHED);

			if (contactInfo!=null && !contactInfo.isEmpty()) {
				signature.setContactInfo(contactInfo);
			}
			if (sigLocation!= null && !sigLocation.isEmpty()) {
				signature.setLocation(sigLocation);
			}
			if (sigReason!=null && !sigReason.isEmpty()) {
				signature.setReason(sigReason);
			}
			if (sigName!=null && !sigName.isEmpty()) {
				signature.setName(sigName);
			}   
			// the signing date, needed for valid signature
			if(forcedDate != null){
				SimpleDateFormat sdf = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss");
				Calendar cal = Calendar.getInstance();
				cal.setTime(sdf.parse(sdf.format(forcedDate)));
				signature.setSignDate(cal);	
			}		    
			// register signature dictionary and sign interface
			final OutputStream improntaNonFirmata = new FileOutputStream(pdfHashPreparedToBeSigned);
			final MessageDigest digest = MessageDigest.getInstance("SHA-256");		    
			SignatureInterface signatureInterface = new SignatureInterface() {
				@Override
				public byte[] sign(InputStream content) throws IOException {					
					try {
						byte[] imp = getImprontaHash(content,"SHA-256");
						IOUtils.copy(new ByteArrayInputStream(imp), improntaNonFirmata);						
						return new byte[0];
					} catch (NoSuchAlgorithmException e) {						
						e.printStackTrace();
						return new byte[0];
					}
				}
			};
			// register signature dictionary and sign interface
			SignatureOptions signatureOptions = new SignatureOptions();
			// Size can vary, but should be enough for purpose.
			signatureOptions.setPreferredSignatureSize(SignatureOptions.DEFAULT_SIGNATURE_SIZE * 8);  
			doc.addSignature(signature, signatureInterface,signatureOptions);
			//doc.addSignature(signature, signatureInterface);
			if(revisionId !=null){
				doc.setDocumentId(revisionId);		    
			}else{
				doc.setDocumentId(0L);
			}
			// write incremental (only for signing purpose)
			doc.saveIncremental(fos);	
			//return FileUtils.readFileToByteArray(pdfPreparedToBeSigned);
			return IOUtils.toByteArray(new FileInputStream(pdfHashPreparedToBeSigned));//getImprontaHash(pdfPreparedToBeSigned,"SHA-256");
		}
		catch (IOException | SignatureException | ParseException | NoSuchAlgorithmException e)
		{
			throw new IOException(e);
		}finally
		{
			fos.close();		   
			pdf2sign.close();
			FileUtils.deleteQuietly(pdfPreparedToBeSigned);
			FileUtils.deleteQuietly(pdfHashPreparedToBeSigned);
			FileUtils.deleteQuietly(pdfFileToSigned);
		}

	}
  
public static File insertHashSignedToPdfFile(InputStream file, final byte[] signedBytes, OutputStream out,String signerName,String location,String reason,String contactInfo,Date forcedDate,Long forceRevisionId) throws IOException, NoSuchAlgorithmException, ParseException{

		File pdfFileToSigned = TempFileProvider.createTempFile("chars", ""+Calendar.getInstance().getTimeInMillis());		
		FileUtils.writeByteArrayToFile(pdfFileToSigned, IOUtils.toByteArray(file));

		logger.debug("Crea File PDF Firmato");
		//byte[] buffer = new byte[8 * 1024];	  
		// creating output document and prepare the IO streams.
		//String name = pdfFileToSigned.getName();
		//String substring = name.substring(0, name.lastIndexOf("."));

		File outputDocument = TempFileProvider.createTempFile("chars", ""+Calendar.getInstance().getTimeInMillis());	
		//File outputDocument = new File(pdfFileToSigned.getParent(), substring+"_signed.pdf");
		FileInputStream fis = new FileInputStream(pdfFileToSigned);
		FileOutputStream fos = new FileOutputStream(outputDocument);

		// load document
		PDDocument doc = PDDocument.load(fis);
		//https://stackoverflow.com/questions/30549830/attachment-damages-signature-part-2
		doc.getDocument().getTrailer().removeItem(COSName.TYPE); // <<<<<<<<<< Remove misleading entry <<<<<<<<<<
		//final MessageDigest digest = MessageDigest.getInstance("SHA-256");
		//final OutputStream improntaNonFirmata = new FileOutputStream(outputDocument);
		// register signature dictionary and sign interface	

		SignatureInterface signatureInterface = new SignatureInterface() {
			@Override
			public byte[] sign(InputStream content) throws IOException {
				return signedBytes;
			}
		};

		//Filling Image Parameters codice preso da dss
		//https://stackoverflow.com/questions/27926407/visual-signature-with-pdfbox-1-8-8
		/*
		PDVisibleSignDesigner signatureDesigner = new PDVisibleSignDesigner(doc, image, doc.getNumberOfPages());
	    signatureDesigner.xAxis(250).yAxis(60).zoom(-90).signatureFieldName("signature");

	    PDVisibleSigProperties signatureProperties = new PDVisibleSigProperties();
	    signatureProperties
	    .signerName(name).signerLocation(location).signatureReason(reason).preferredSize(0).page(1)
	    .visualSignEnabled(true).setPdVisibleSignature(signatureDesigner)
	    .buildSignature();

		doc.addSignature(pdSignature, signatureInterface, options);
		 options.setVisualSignature(signatureProperties);
		 */
		// create signature dictionary
		PDSignature signature = new PDSignature();
		signature.setFilter(PDSignature.FILTER_ADOBE_PPKLITE); // default filter
		// subfilter for basic and PAdES Part 2 signatures
		//Utile link https://stackoverflow.com/questions/25957573/unable-to-verify-digital-signature-using-apache-pdfbox
		signature.setSubFilter(PDSignature.SUBFILTER_ADBE_PKCS7_DETACHED);
		//signature.setSubFilter(PDSignature.SUBFILTER_ETSI_CADES_DETACHED);

		if (contactInfo!=null && !contactInfo.isEmpty()) {
			signature.setContactInfo(contactInfo);
		}
		if (location!= null && !location.isEmpty()) {
			signature.setLocation(location);
		}
		if (reason!=null && !reason.isEmpty()) {
			signature.setReason(reason);
		}
		if (signerName!=null && !signerName.isEmpty()) {
			signature.setName(signerName);
		}   
		// the signing date, needed for valid signature
		/*
			final Calendar cal = Calendar.getInstance();
			final Date signingDate = new Date();
			cal.setTime(signingDate);
	    signature.setSignDate(cal);
	    signature.setSignDate(Calendar.getInstance());
		 */
		// the signing date, needed for valid signature
		if(forcedDate!=null){
			SimpleDateFormat sdf = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss");
			Calendar cal = Calendar.getInstance();
			cal.setTime(sdf.parse(sdf.format(forcedDate)));
			signature.setSignDate(cal);	
		}
		//signature.setContents(signedBytes);
		boolean isExternalSigning = false;
		if (isExternalSigning)
		{
			//        logger.info("Sign externally...");
			//        doc.addSignature(signature);
			//        ExternalSigningSupport externalSigning = doc.saveIncrementalForExternalSigning(out);
			//        // invoke external signature service
			//        byte[] cmsSignature = null;//sign(externalSigning.getContent());
			//        // set signature bytes received from the service
			//        externalSigning.setSignature(cmsSignature);
		}
		else
		{
			SignatureOptions signatureOptions = new SignatureOptions();
			// Size can vary, but should be enough for purpose.
			signatureOptions.setPreferredSignatureSize(SignatureOptions.DEFAULT_SIGNATURE_SIZE * 8);           
			// register signature dictionary and sign interface
			doc.addSignature(signature,signatureInterface,signatureOptions);
			//doc.setDocumentId(0L);	
			if(forceRevisionId !=null){
				doc.setDocumentId(forceRevisionId);		    
			}else{
				doc.setDocumentId(0L);
			}
			// write incremental (only for signing purpose)
			doc.saveIncremental(fos);
		}

		//doc.addSignature(signature,signatureInterface,options);	      
		//doc.saveIncremental(fos);

		if(fis!=null)fis.close();
		if(fos!=null)fos.close();
		FileUtils.deleteQuietly(pdfFileToSigned);

		IOUtils.copy(FileUtils.openInputStream(outputDocument),out);

		return outputDocument;  
	}