Convierta una cadena con formato PEM en un certificado java.security.cert.X509

Solución:

Decodifique Base64 a binario, con algún InputStream leyéndolo, luego intente

CertificateFactory cf = CertificateFactory.getInstance("X.509");
Certificate cert = cf.generateCertificate(is);

Tengo un problema similar, estoy pegando también aquí el código java que funcionó para mí en caso de que alguien lo negara:

import java.util.Base64;

public static X509Certificate parseCertificate(String _headerName, HttpServletRequest _request) throws CertificateException {
    String certStr = _request.getHeader("x-clientcert");
    //before decoding we need to get rod off the prefix and suffix
    byte [] decoded = Base64.getDecoder().decode(certStr.replaceAll(X509Factory.BEGIN_CERT, "").replaceAll(X509Factory.END_CERT, ""));

    return (X509Certificate) CertificateFactory.getInstance("X.509").generateCertificate(new ByteArrayInputStream(decoded));
}

Los pasos en la conversión de String con formato PEM son opuestos a cómo se llevó a cabo (x509 -> String).

Ejemplo de cadena con formato PEM:

-----BEGIN CERTIFICATE-----
MIIEczCCA1ugAwIBAgIBADANBgkqhkiG9w0BAQQFAD..AkGA1UEBhMCR0Ix
EzARBgNVBAgTClNvbWUtU3RhdGUxFDASBgNVBAoTC0..0EgTHRkMTcwNQYD
VQQLEy5DbGFzcyAxIFB1YmxpYyBQcmltYXJ5IENlcn..XRpb24gQXV0aG9y
aXR5MRQwEgYDVQQDEwtCZXN0IENBIEx0ZDAeFw0wMD..TUwMTZaFw0wMTAy
MDQxOTUwMTZaMIGHMQswCQYDVQQGEwJHQjETMBEGA1..29tZS1TdGF0ZTEU
MBIGA1UEChMLQmVzdCBDQSBMdGQxNzA1BgNVBAsTLk..DEgUHVibGljIFBy
aW1hcnkgQ2VydGlmaWNhdGlvbiBBdXRob3JpdHkxFD..AMTC0Jlc3QgQ0Eg
THRkMIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCg..Tz2mr7SZiAMfQyu
vBjM9OiJjRazXBZ1BjP5CE/Wm/Rr500PRK+Lh9x5eJ../ANBE0sTK0ZsDGM
ak2m1g7oruI3dY3VHqIxFTz0Ta1d+NAjwnLe4nOb7/..k05ShhBrJGBKKxb
8n104o/5p8HAsZPdzbFMIyNjJzBM2o5y5A13wiLitE..fyYkQzaxCw0Awzl
kVHiIyCuaF4wj571pSzkv6sv+4IDMbT/XpCo8L6wTa..sh+etLD6FtTjYbb
rvZ8RQM1tlKdoMHg2qxraAV++HNBYmNWs0duEdjUbJ..XI9TtnS4o1Ckj7P
OfljiQIDAQABo4HnMIHkMB0GA1UdDgQWBBQ8urMCRL..5AkIp9NJHJw5TCB
tAYDVR0jBIGsMIGpgBQ8urMCRLYYMHUKU5AkIp9NJH..aSBijCBhzELMAkG
A1UEBhMCR0IxEzARBgNVBAgTClNvbWUtU3RhdGUxFD..AoTC0Jlc3QgQ0Eg
THRkMTcwNQYDVQQLEy5DbGFzcyAxIFB1YmxpYyBQcm..ENlcnRpZmljYXRp
b24gQXV0aG9yaXR5MRQwEgYDVQQDEwtCZXN0IENBIE..DAMBgNVHRMEBTAD
AQH/MA0GCSqGSIb3DQEBBAUAA4IBAQC1uYBcsSncwA..DCsQer772C2ucpX
xQUE/C0pWWm6gDkwd5D0DSMDJRqV/weoZ4wC6B73f5..bLhGYHaXJeSD6Kr
XcoOwLdSaGmJYslLKZB3ZIDEp0wYTGhgteb6JFiTtn..sf2xdrYfPCiIB7g
BMAV7Gzdc4VspS6ljrAhbiiawdBiQlQmsBeFz9JkF4..b3l8BoGN+qMa56Y
It8una2gY4l2O//on88r5IWJlm1L0oA8e4fR2yrBHX..adsGeFKkyNrwGi/
7vQMfXdGsRrXNGRGnX+vWDZ3/zWI0joDtCkNnqEpVn..HoX
-----END CERTIFICATE-----

Estos son los pasos:

1. Remove headers from PEM formatted String
Headers are : ---- BEGIN CERTIFICATE ----- and ----- END CERTIFICATE ------
2. Decode the rest of the part using Base64 to byte array
3. Then you can use CertificateFactory to convert byte stream to x509Certificate object

Código de muestra para hacer arriba (con PEM Writer):

  /**
     * Converts a PEM formatted String to a {@link X509Certificate} instance.
     *
     * @param pem PEM formatted String
     * @return a X509Certificate instance
     * @throws CertificateException 
     * @throws IOException
     */
    public X509Certificate convertToX509Certificate(String pem) throws CertificateException, IOException {
        X509Certificate cert = null;
        StringReader reader = new StringReader(pem);
        PEMReader pr = new PEMReader(reader);
        cert = (X509Certificate)pr.readObject();
        return cert;
    }

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