/ 
MOBY-1.16
River stage one • 1 direct dependent • 1 total dependent
/ MOBY

NAME

MOBY - API for hosting and/or communicating with a MOBY Central registry

DESCRIPTION

This module serves 2 purposes:

  • Used to do various transactions with MOBY-Central registry, including registering new Object and Service types, querying for these types, registering new Servers/Services, or queryiong for available services given certain input/output or service type constraints.

  • Aid in the installation of a custom local MOBY-Central registry.

Package Installation

Installation of this perl package is straightforward!

On *nix machines, install as follows:

  • perl Makefile.PL

  • make test

  • make install

On Window machines, substitute nmake for make!

Important if you are upgrading to newer versions, please make sure to remove any files that may be cached by this module! To help you do this, run the script moby-s-caching.pl. For information on using moby-s-caching.pl, use the -h option!

Important II make sure to run moby-s-update-db with the -h option to see if you need to updgrade the db schemas.

Installing A Custom MOBY-Central Registry

Assuming that you have already installed this package, the very first thing that you should do is run the script moby-s-install.pl.

This script will do the following:

  • Check for prerequisite modules and warn you if they are missing

  • Run you through some configuration details

  • Optionally help you mirror an already existing registry

  • Optionally install various scripts used by the registry or its' clients

BioMOBY Client Installation

Once the module has been installed using the command make install, there is nothing further left for you to do. You are free to start using the BioMOBY API.

BioMOBY Server Installation

To set up your own custom registry, you have to ensure that a few things are ready before hand!

  • You have an apache webserver installed/started on your machine

  • You have mysql installed/started on your machine

  • You are aware of the full path to the apache cgi-bin directory

  • You have a mysql username/password with read/write access available to use

  • You have root priviledges on your machine!

Once you are sure that you satisfy the above items, go ahead and run the moby-s-install.pl script, by typing moby-s-install.pl at the command line. This file was installed onto your machine when you did your 'make install'!

What Exactly does moby-s-install.pl do?

Like we said before, the install script helps you install/configure your custom MOBY-Central registry.

First of all, the script ensure that you have all of the proper libraries installed.

The very next thing that the script does is prompt you for some information:

  • What is your base installation path for apache?

  • Where is the conf/cgi-bin directory for apache located?

  • What is the path to your Perl executable?

Once that information is entered, the script prompts you to set up apache.

Apache setup

The following is done when the installation script sets up apache:

  • A mobycentral configuration file is added to your apache conf directory

  • mySQL connection information is obtained from you and inserted into the the configuration file

  • mySQL table names for the registry are chosen

  • Optionally, httpd.conf is edited adding various environment variables necessary for the registry

FAQ

When I run the install script, IO::Prompt complains ...

This could mean that the package IO::Prompt is not installed properly.

What version do you have?

perl -MIO::Prompt -e'print "$IO::Prompt::VERSION\n";'

We have tested version 0.99.2 on both *nix machines and windows. Please make sure that you have that version. If you do not, please remove the one that you have (the cpan module CPAN Plus is very useful here) and install version 0.99.2! Version 0.99.4 doesn't seem to work too well and produces numerous warnings in our module. Other versions have yet to be tested.

How can I make the service tester run every hour?

First of all, the service tester only works on *NIX machines and will not work on Windows. The reason is due to a the module IPC::Shareable which doesn't port to windows.

To set up the service tester simply create a cron job. The following is an illustration of how to do this!

  • Edit your crontab (as root):

    crontab -e

  • Add the following to the top of the crontab

    MOBY_CENTRAL_CONFIG=/etc/apache2/mobycentral.config

  • Add the actual job:

    00 * * * * perl /path/to/the/service_tester.pl

This will set up a cron job to run every start of the hour!

How do I set up the RDF Agent?

Detailed instructions for building, installing and configuring the agent can be found at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ConfigureRDFAgent.html

Missing Features

  • automatic installation of the RDF Agent

Acknowledgement

EXPORT

None by default.

SEE ALSO

For the most up-to-date documentation, visit the BioMOBY website at http://biomoby.org!

If you have questions or comments, please feel free to message us on the following mailing lists:

MOBY discussion list http://www.biomoby.org/mailman/listinfo/moby-l
MOBY Developers List http://www.biomoby.org/mailman/listinfo/moby-dev
MOBY bugs discussion list http://www.biomoby.org/mailman/listinfo/moby-bugs

AUTHORS

COPYRIGHT

Copyright (c) 2007 The Biomoby Consortium.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

This software is provided "as is" without warranty of any kind.

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