Digests using OpenSSL. Shell and perl editions,

Here's a small snippet that allows one to generate a digest.
Short of it: Perl

my $key_string = read_file("secretkey.pem");
my $key = Crypt::OpenSSL::RSA->new_private_key($key_string);
my $filestring = read_file("somefile");
$key->use_md5_hash();
my $signature = $key->sign($filestring);
print encode_base64($signature)."\n";

Short of it: shell

openssl dgst -md5 -sign secretkey.pem  <  somefile |base64 | tee somefile.sig_from_shell
cat somefile.sig_from_shell | base64 -d > somefile.sig_from_shell.raw
openssl dgst -md5 -verify public.pem  -signature somefile.sig_from_perl.raw <  somefile

In it's goriness:

Apache x509 Client authentication

Say you have a website where you need your clients to authenticate using x509 certificates generated by your CA (memberca) and that you have a verisign issued CA for your server end (HTTPS certificate)
You'd want to configure apache to:

• Accept only certificates issued by memberca.
• Set it's server certificate to be what verisign issued.
• Use a CRL to know which certificates have been revoked.

A sample apache configuration would look like:

# cat /etc/httpd/conf.d/ssl.conf 
#
# This is the Apache server configuration file providing SSL support.
# It contains the configuration directives to instruct the server how to
# serve pages over an https connection. For detailing information about these 
# directives see <URL:http://httpd.apache.org/docs/2.2/mod/mod_ssl.html>
# 
# Do NOT simply read the instructions in here without understanding
# what they do.  They're here only as hints or reminders.  If you are unsure
# consult the online docs. You have been warned.  
#

LoadModule ssl_module modules/mod_ssl.so

#
# When we also provide SSL we have to listen to the 
# the HTTPS port in addition.
#
Listen 443

##
##  SSL Global Context
##
##  All SSL configuration in this context applies both to
##  the main server and all SSL-enabled virtual hosts.
##

#
#   Some MIME-types for downloading Certificates and CRLs
#
AddType application/x-x509-ca-cert .crt
AddType application/x-pkcs7-crl    .crl

#   Pass Phrase Dialog:
#   Configure the pass phrase gathering process.
#   The filtering dialog program (`builtin' is a internal
#   terminal dialog) has to provide the pass phrase on stdout.
SSLPassPhraseDialog  builtin

#   Inter-Process Session Cache:
#   Configure the SSL Session Cache: First the mechanism 
#   to use and second the expiring timeout (in seconds).
#SSLSessionCache        dc:UNIX:/var/cache/mod_ssl/distcache
SSLSessionCache         shmcb:/var/cache/mod_ssl/scache(512000)
SSLSessionCacheTimeout  300

#   Semaphore:
#   Configure the path to the mutual exclusion semaphore the
#   SSL engine uses internally for inter-process synchronization. 
SSLMutex default

#   Pseudo Random Number Generator (PRNG):
#   Configure one or more sources to seed the PRNG of the 
#   SSL library. The seed data should be of good random quality.
#   WARNING! On some platforms /dev/random blocks if not enough entropy
#   is available. This means you then cannot use the /dev/random device
#   because it would lead to very long connection times (as long as
#   it requires to make more entropy available). But usually those
#   platforms additionally provide a /dev/urandom device which doesn't
#   block. So, if available, use this one instead. Read the mod_ssl User
#   Manual for more details.
SSLRandomSeed startup file:/dev/urandom  256
SSLRandomSeed connect builtin
#SSLRandomSeed startup file:/dev/random  512
#SSLRandomSeed connect file:/dev/random  512
#SSLRandomSeed connect file:/dev/urandom 512

#
# Use "SSLCryptoDevice" to enable any supported hardware
# accelerators. Use "openssl engine -v" to list supported
# engine names.  NOTE: If you enable an accelerator and the
# server does not start, consult the error logs and ensure
# your accelerator is functioning properly. 
#
SSLCryptoDevice builtin
#SSLCryptoDevice ubsec

##
## SSL Virtual Host Context
##

<VirtualHost _default_:443>

ServerAdmin admin@example.net
DocumentRoot /var/www/htdocs
ServerName secure.example.net
#ServerName www.example.com:443

# Use separate log files for the SSL virtual host; note that LogLevel
# is not inherited from httpd.conf.
ErrorLog logs/ssl_error_log
TransferLog logs/ssl_access_log
LogLevel warn # debug is useful too

SetEnvIf Request_URI \.(gif|jpg|css|js)$ inc-file

# HTTPS protected site. Client auth not necessary
<Location />
        Options FollowSymLinks +Includes
        # You may add your directives
        Order deny,allow
        Allow from all
</Location>

# Accessible over client auth. May prompt user to select a cert.
# You can use script logic to look into the env vars apache will set
# if it gets a certificate or a None/undef if doesn't
# You can then show a user an error message on missing a cert or display
# supersecret stuff otherwise.
<Location /resources/secure/>
    SSLOptions +StdEnvVars
    SSLVerifyClient optional
</Location>

#   SSL Engine Switch:
#   Enable/Disable SSL for this virtual host.
SSLEngine on

#   SSL Protocol support:
# List the enable protocol levels with which clients will be able to
# connect.  Disable SSLv2 access by default:
SSLProtocol all -SSLv2

#   SSL Cipher Suite:
# List the ciphers that the client is permitted to negotiate.
# See the mod_ssl documentation for a complete list.
SSLCipherSuite ALL:!ADH:!EXPORT:!SSLv2:RC4+RSA:+HIGH:+MEDIUM:+LOW

#   Server Certificate:
# Point SSLCertificateFile at a PEM encoded certificate.  If
# the certificate is encrypted, then you will be prompted for a
# pass phrase.  Note that a kill -HUP will prompt again.  A new
# certificate can be generated using the genkey(1) command.
SSLCertificateFile /etc/httpd/conf/ssl.crt/signed_by_verisign_server_cert.pem 

#   Server Private Key:
#   If the key is not combined with the certificate, use this
#   directive to point at the key file.  Keep in mind that if
#   you've both a RSA and a DSA private key you can configure
#   both in parallel (to also allow the use of DSA ciphers, etc.)
SSLCertificateKeyFile /etc/httpd/conf/ssl.key/key_for_server_certificate.key 

#   Server Certificate Chain:
#   Point SSLCertificateChainFile at a file containing the
#   concatenation of PEM encoded CA certificates which form the
#   certificate chain for the server certificate. Alternatively
#   the referenced file can be the same as SSLCertificateFile
#   when the CA certificates are directly appended to the server
#   certificate for convinience.
#SSLCertificateChainFile /etc/pki/tls/certs/server-chain.crt
SSLCertificateChainFile /etc/httpd/conf/ssl.crt/verisign_chain.crt

#   Certificate Authority (CA):
#   Set the CA certificate verification path where to find CA
#   certificates for client authentication or alternatively one
#   huge file containing all of them (file must be PEM encoded)
SSLCACertificateFile /etc/httpd/conf/ssl.crt/memberca

#   Client Authentication (Type):
#   Client certificate verification type and depth.  Types are
#   none, optional, require and optional_no_ca.  Depth is a
#   number which specifies how deeply to verify the certificate
#   issuer chain before deciding the certificate is not valid.
#SSLVerifyClient require
#SSLVerifyDepth  10

#   Access Control:
#   With SSLRequire you can do per-directory access control based
#   on arbitrary complex boolean expressions containing server
#   variable checks and other lookup directives.  The syntax is a
#   mixture between C and Perl.  See the mod_ssl documentation
#   for more details.
#<Location />
#SSLRequire (    %{SSL_CIPHER} !~ m/^(EXP|NULL)/ \
#            and %{SSL_CLIENT_S_DN_O} eq "Snake Oil, Ltd." \
#            and %{SSL_CLIENT_S_DN_OU} in {"Staff", "CA", "Dev"} \
#            and %{TIME_WDAY} >= 1 and %{TIME_WDAY} <= 5 \
#            and %{TIME_HOUR} >= 8 and %{TIME_HOUR} <= 20       ) \
#           or %{REMOTE_ADDR} =~ m/^192\.76\.162\.[0-9]+$/
#</Location>

#   SSL Engine Options:
#   Set various options for the SSL engine.
#   o FakeBasicAuth:
#     Translate the client X.509 into a Basic Authorisation.  This means that
#     the standard Auth/DBMAuth methods can be used for access control.  The
#     user name is the `one line' version of the client's X.509 certificate.
#     Note that no password is obtained from the user. Every entry in the user
#     file needs this password: `xxj31ZMTZzkVA'.
#   o ExportCertData:
#     This exports two additional environment variables: SSL_CLIENT_CERT and
#     SSL_SERVER_CERT. These contain the PEM-encoded certificates of the
#     server (always existing) and the client (only existing when client
#     authentication is used). This can be used to import the certificates
#     into CGI scripts.
#   o StdEnvVars:
#     This exports the standard SSL/TLS related `SSL_*' environment variables.
#     Per default this exportation is switched off for performance reasons,
#     because the extraction step is an expensive operation and is usually
#     useless for serving static content. So one usually enables the
#     exportation for CGI and SSI requests only.
#   o StrictRequire:
#     This denies access when "SSLRequireSSL" or "SSLRequire" applied even
#     under a "Satisfy any" situation, i.e. when it applies access is denied
#     and no other module can change it.
#   o OptRenegotiate:
#     This enables optimized SSL connection renegotiation handling when SSL
#     directives are used in per-directory context. 
#SSLOptions +FakeBasicAuth +ExportCertData +StrictRequire
<Files ~ "\.(cgi|shtml|phtml|php3?)$">
    SSLOptions +StdEnvVars
</Files>
<Directory "/var/www/cgi-bin">
    SSLOptions +StdEnvVars
</Directory>

#   SSL Protocol Adjustments:
#   The safe and default but still SSL/TLS standard compliant shutdown
#   approach is that mod_ssl sends the close notify alert but doesn't wait for
#   the close notify alert from client. When you need a different shutdown
#   approach you can use one of the following variables:
#   o ssl-unclean-shutdown:
#     This forces an unclean shutdown when the connection is closed, i.e. no
#     SSL close notify alert is send or allowed to received.  This violates
#     the SSL/TLS standard but is needed for some brain-dead browsers. Use
#     this when you receive I/O errors because of the standard approach where
#     mod_ssl sends the close notify alert.
#   o ssl-accurate-shutdown:
#     This forces an accurate shutdown when the connection is closed, i.e. a
#     SSL close notify alert is send and mod_ssl waits for the close notify
#     alert of the client. This is 100% SSL/TLS standard compliant, but in
#     practice often causes hanging connections with brain-dead browsers. Use
#     this only for browsers where you know that their SSL implementation
#     works correctly. 
#   Notice: Most problems of broken clients are also related to the HTTP
#   keep-alive facility, so you usually additionally want to disable
#   keep-alive for those clients, too. Use variable "nokeepalive" for this.
#   Similarly, one has to force some clients to use HTTP/1.0 to workaround
#   their broken HTTP/1.1 implementation. Use variables "downgrade-1.0" and
#   "force-response-1.0" for this.
SetEnvIf User-Agent ".*MSIE.*" \
         nokeepalive ssl-unclean-shutdown \
         downgrade-1.0 force-response-1.0

#   Per-Server Logging:
#   The home of a custom SSL log file. Use this when you want a
#   compact non-error SSL logfile on a virtual host basis.
CustomLog logs/ssl_request_log \
          "%t %h %{SSL_PROTOCOL}x %{SSL_CIPHER}x \"%r\" %b"

</VirtualHost>

And you'd want to test with openSSL

<?php
openssl s_client -connect secure.example.net:443 -CAfile memberca.crt  -cert User-YourCompany.crt  -key User-YourCompany.key  -showcerts -CAfile Verisign-CAca.crt 
CONNECTED(00000003)
depth=1 /CN=Verisign-CA
verify return:1
depth=0 /CN=secure.example.net/O=YourCompany Ltd/C=CC
verify return:1
---
Certificate chain
 0 s:/CN=secure.example.net/O=YourCompany Ltd/C=CC
   i:/CN=Verisign-CA
-----BEGIN CERTIFICATE-----
................................................................
................................................................
.................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
............
-----END CERTIFICATE-----
 1 s:/CN=memberca/DC=YourCompany/DC=net
   i:/CN=memberca/DC=YourCompany/DC=net
-----BEGIN CERTIFICATE-----
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................................................................
................
-----END CERTIFICATE-----
---
Server certificate
subject=/CN=secure.example.net/O=YourCompany Ltd/C=CC
issuer=/CN=Verisign-CA
---
No client certificate CA names sent
---
SSL handshake has read 2418 bytes and written 319 bytes
---
New, TLSv1/SSLv3, Cipher is DHE-RSA-AES256-SHA
Server public key is 1024 bit
Secure Renegotiation IS supported
Compression: NONE
Expansion: NONE
SSL-Session:
    Protocol  : TLSv1
    Cipher    : DHE-RSA-AES256-SHA
    Session-ID: 444444444444444444444444444444444444444444222222222222221
    Session-ID-ctx: 
    Master-Key: 1111111111111111111111111222222222222222222222223333333333
    Key-Arg   : None
    Start Time: 1301664102
    Timeout   : 300 (sec)
    Verify return code: 0 (ok)
---
GET / HTTP/1.1
Host: secure.YourCompany.net:8080
Accept: /sgml, */*;q=0.01
Accept-Language: en
User-Agent: Lynx/2.8.8dev.5 libwww-FM/2.14 SSL-MM/1.4.1 GNUTLS/2.8.6

HTTP/1.1 302 Found
Date: Fri, 01 Apr 2011 13:19:55 GMT
Server: Apache/2.2.3 (CentOS)
X-Catalyst: xxxxxxx
Location: /login
Content-Length: 79
Connection: close
Content-Type: text/html; charset=UTF-8

<html><body><p>This item has moved <a href="/login">here</a>.</p></body></html>closed
?>

and Curl

# Login and dump cookie on a standard https page

$ curl -k  -d "handle=User-YourCompany&user_password=123secure" -c cookie-borg https://secure.example.net/login            
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/TR/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta http-equiv="Pragma" content="no-cache"></meta><meta http-equiv="Expires" content="0">
.....
</body></html>

# Use client auth to access protected areas. Use the cookie from the login session

$ curl   -v --key User-YourCompany.key --cert User-YourCompany.crt --cacert memberca.crt --cacert verisign_ca.crt -b cookie https://secure.example.net/resources/secure/ 
* About to connect() to secure.example.net port 443 (#0)
*   Trying 2001:xxx:xx:xxx::xxx... connected
* Connected to secure.example.net (2001:xxx:xx:xxx::xxx) port 443 (#0)
* successfully set certificate verify locations:
*   CAfile: verisign_ca.crt
  CApath: /etc/ssl/certs
* SSLv3, TLS handshake, Client hello (1):
* SSLv3, TLS handshake, Server hello (2):
* SSLv3, TLS handshake, CERT (11):
* SSLv3, TLS handshake, Server key exchange (12):
* SSLv3, TLS handshake, Server finished (14):
* SSLv3, TLS handshake, Client key exchange (16):
* SSLv3, TLS change cipher, Client hello (1):
* SSLv3, TLS handshake, Finished (20):
* SSLv3, TLS change cipher, Client hello (1):
* SSLv3, TLS handshake, Finished (20):
* SSL connection using DHE-RSA-AES256-SHA
.....

And in your code (Example: perl)

if (! $ENV{SSL_CLIENT_S_DN_CN} || ($session_username ne  $ENV{SSL_CLIENT_S_DN_CN}) )
{           
        echo "Bad user. Go get a  cert"
}else{
#Allow access
}