<doc:document 
xmlns:cct="http://emias.mos.ru/simi/cct"      
xmlns:doc="http://emias.mos.ru/simi/document"      
xmlns:ds="http://www.w3.org/2000/09/xmldsig#" 
xmlns:simicore="http://emias.mos.ru/simi/core">
	<doc:metadata>
		<doc:documentId>ecd99ae4-b15c-46f0-a98c-c16aeb7619a2</doc:documentId>
		<doc:documentInfo>
			<simicore:patientId>79812</simicore:patientId>
		</doc:documentInfo>
	</doc:metadata>
	<doc:content mimeClass="APPLICATION" mimeType="application/tdd" valid="true"><doc:data>MDAx</doc:data></doc:content>
	<doc:signature signeeLogin="username" technicalSignature="true"/>
</doc:document>

org.apache.xml.security.Init.init();
JCPXMLDSigInit.init();

Document doc = --указанный выше документ
/*при парсинге документа указано что
factory.setNamespaceAware(true);
*/

String providerName = "ru.CryptoPro.JCPxml.dsig.internal.dom.XMLDSigRI";

final XMLSignatureFactory sigFactory = XMLSignatureFactory.getInstance("DOM",(Provider) Class.forName(providerName).newInstance());

NodeList signNodes = CryptoUtils.xPathToNodeList(doc, "//*[local-name() = 'signature']");

Node sigParent = signNodes.item(0);
String referenceURI = ""; // Пустая строка означает весь документ.
List transforms = new ArrayList<Transform>() {{
            add(sigFactory.newTransform(Transform.XPATH, new XPathFilterParameterSpec(xpathString)));//xpathString = //doc:content
            add(sigFactory.newTransform(Transform.ENVELOPED, (TransformParameterSpec) null));
}};
        
Reference ref = sigFactory.newReference(referenceURI,
                sigFactory.newDigestMethod(Consts.URN_GOST_DIGEST_2012_256, null), transforms, null, null);

SignedInfo signedInfo = sigFactory.newSignedInfo(
                sigFactory.newCanonicalizationMethod(CanonicalizationMethod.EXCLUSIVE, (C14NMethodParameterSpec) null),
                sigFactory.newSignatureMethod(Consts.URN_GOST_SIGN_2012_256, null), Collections.singletonList(ref));

KeyInfoFactory keyInfoFactory = sigFactory.getKeyInfoFactory();
        
X509Data x509d = keyInfoFactory.newX509Data(Collections.singletonList(cert));

KeyInfo keyInfo = keyInfoFactory.newKeyInfo(Collections.singletonList(x509d));

DOMSignContext dsc = new DOMSignContext(privateKey, sigParent);

dsc.setProperty("org.jcp.xml.dsig.internal.dom.SignatureProvider", JCP.PROVIDER_NAME);

XMLSignature signature = sigFactory.newXMLSignature(signedInfo, keyInfo);
        
signature.sign(dsc);

<?xml version="1.0" encoding="UTF-8"?>
<doc:document xmlns:doc="http://emias.mos.ru/simi/document" xmlns:cct="http://emias.mos.ru/simi/cct" xmlns:ds="http://www.w3.org/2000/09/xmldsig#" xmlns:simicore="http://emias.mos.ru/simi/core">
	<doc:metadata>
		<doc:documentId>ecd99ae4-b15c-46f0-a98c-c16aeb7619a2</doc:documentId>
		<doc:documentInfo>
			<simicore:patientId>79812</simicore:patientId>
		</doc:documentInfo>
	</doc:metadata>
	<doc:content mimeClass="APPLICATION" mimeType="application/tdd" valid="true">
		<doc:data>MDAx</doc:data>
	</doc:content>
	<doc:signature signeeLogin="username" technicalSignature="true">
		<Signature xmlns="http://www.w3.org/2000/09/xmldsig#">
			<SignedInfo>
				<CanonicalizationMethod Algorithm="http://www.w3.org/2001/10/xml-exc-c14n#"/>
				<SignatureMethod Algorithm="urn:ietf:params:xml:ns:cpxmlsec:algorithms:gostr34102012-gostr34112012-256"/>
				<Reference URI="">
					<Transforms>
						<Transform Algorithm="http://www.w3.org/TR/1999/REC-xpath-19991116">
							<XPath>//doc:content</XPath>
						</Transform>
						<Transform Algorithm="http://www.w3.org/2000/09/xmldsig#enveloped-signature"/>
					</Transforms>
					<DigestMethod Algorithm="urn:ietf:params:xml:ns:cpxmlsec:algorithms:gostr34112012-256"/>
					<DigestValue>CnP0L9CaumMYIx0wElcSDdW4hvxmnldoZOzhnWKbG/U=</DigestValue>
				</Reference>
			</SignedInfo>
			<SignatureValue>iZiY/wLmBAnXRNLtouqudI+oyLrbuA3Bu+Z6dlqSBKPBsqnO/MnhDNwZCbcA7rzTfUfRf7w991hDlMPFLNTfcg==</SignatureValue>
			<KeyInfo>
				<X509Data>
					<X509Certificate>MIII...</X509Certificate>
				</X509Data>
			</KeyInfo>
		</Signature>
	</doc:signature>
</doc:document>