Bio-Das-ProServer
=================

Bio::Das::ProServer is an implementation of the BioDAS protocol,
http://biodas.org/ for the serving of biological data using XML over
HTTP.

Bio::Das::ProServer is designed as a lightweight alternative to some
other DAS servers. Version 2.0 is a drop-in replacement for previous
versions but has a core based on the POE system which is much better
tested and debugged than the ProServer v1 core. ProServer can be seen
as the server-side complement to the Bio-DasLite client.

More information can be found at the ProServer homepage:

    http://www.sanger.ac.uk/proserver/


INSTALLATION

To install this module type the following:

   perl Build.PL
   ./Build
   ./Build test

You may receive warnings about missing dependencies, note that only
some of these are required (see DEPENDENCIES section).

RUNNING

  There is a command-line executable in the eg directory:
  eg/proserver --help

  To start the server, type:
  eg/proserver

  To stop:
  kill -TERM `cat eg/proserver.myhostname.pid`

  To restart:
  kill -USR1 `cat eg/proserver.myhostname.pid`


DEPENDENCIES

Any missing dependencies will be reported during the build proces. All are
available from CPAN (http://www.cpan.org).

CGI
Compress::Zlib
Config::IniFiles
File::Spec
Getopt::Long
HTML::Entities
HTTP::Request
HTTP::Response
HTTP::Date
POE
POE::Filter::HTTPD
POE::Wheel::ReadWrite
POE::Wheel::SocketFactory
POSIX
Socket
Sys::Hostname


SECURITY

Whilst every attempt is made to keep ProServer free from security
holes we cannot guarantee its safety. As with all daemon services like
this, it is strongly advised to take certain measures to mitigate any
faults which may be present and minimised their consequences.

       1. Run ProServer as a non-privileged user. Usually there is a
          'nobody' user or equivalent. Running daemon services as this
          user means that if compromised the service has minimal
          access to the rest of the host.

       2. Where possible run in a chroot'ed environment. This is more
          complicated than simply using a non-privileged user but is
          safer all-round. Using chroot puts the ProServer processes
          in a jail from which they cannot easily access the rest of
          the filesystem. This may be complex to set up, depending on
          the variety of your source adaptors and the access they
          require to resources outside of your ProServer
          installation. This method also requires a dedicated copy of
          all dependencies such as a perl interpreter and system
          libraries.

       3. Another useful mechanism is to run ProServer behind a
          reverse-proxy. This means ProServer is never in direct
          communication with the client and the reverse-proxy will
          sanitise requests, removing some of the opportunities for
          attack. It also allows services to be moved behind the
          scenes using for example a combination of Apache and
          mod_rewrite on the proxy. One other possibility is to use a
          reverse-proxy to unify services provided by other
          technologies such as LDAS or Dazzle into one consolidated
          namespace.

SCALABILITY

At the Sanger Institute we run ProServer, behind an Apache
reverse-proxy, on 14 2.4GHz blades serving just under 300,000 DAS
requests a week for 220 sources mostly with MySQL databases. ProServer
should scale comfortably being only IO-bound as it's not
computationally intensive. Efficiency of data retrieval is most
important. Ensure database connections and statement handles are
cached and reused wherever possible.

KNOWN PROBLEMS

ProServer depends on source adaptors to provide details of known
segments in order to correctly serve error or unknown segments.
In the absence of this information responses serve empty result sets.

COPYRIGHT AND LICENCE

Copyright (C) 2006 by Roger M Pettett, Genome Research Ltd.
http://www.sanger.ac.uk/

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.7 or,
at your option, any later version of Perl 5 you may have available.