[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Thu Mar 20 17:35:43 UTC 2008
kawas
Thu Mar 20 13:35:42 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30839/Perl/MOBY-Server/lib/MOBY
Modified Files:
MOBY.pm
Log Message:
found 2 MOBY.pm modules. cpan ignored the correct one and indexed the wrong one ...
moby-live/Perl/MOBY-Server/lib/MOBY MOBY.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm 2008/03/20 17:35:42 1.2
@@ -1,84 +1,270 @@
package MOBY;
-use 5.008008;
use strict;
use warnings;
-require Exporter;
-our @ISA = qw(Exporter);
-# Items to export into callers namespace by default. Note: do not export
-# names by default without a very good reason. Use EXPORT_OK instead.
-# Do not simply export all your public functions/methods/constants.
+use vars qw{$VERSION @ISA @EXPORT @EXPORT_OK};
+BEGIN {
+ $VERSION = '0.85';
+ @ISA = qw{ Exporter };
+ @EXPORT = qw{};
+ @EXPORT_OK = qw{};
+}
-# This allows declaration use MOBY ':all';
-# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
-# will save memory.
-our %EXPORT_TAGS = ( 'all' => [ qw(
-
-) ] );
-
-our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
-
-our @EXPORT = qw(
-
-);
-
-our $VERSION = '0.01';
# Preloaded methods go here.
1;
__END__
-# Below is stub documentation for your module. You'd better edit it!
=head1 NAME
-MOBY - Perl extension for blah blah blah
+MOBY - API for hosting and/or communicating with a MOBY Central registry
+
+=head1 DESCRIPTION
-=head1 SYNOPSIS
+This module serves 2 purposes:
- use MOBY;
- blah blah blah
+=over 4
-=head1 DESCRIPTION
+=item * 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.
+
+=item * Aid in the installation of a custom local MOBY-Central registry.
+
+=back
+
+=head2 Package Installation
+
+Installation of this perl package is straightforward!
+
+On *nix machines, install as follows:
+
+=over 4
+
+=item * C<perl Makefile.PL>
+
+=item * C<make test>
+
+=item * C<make install>
+
+=back
+
+On Window machines, substitute C<nmake> for C<make>!
+
+B<Important> if you are upgrading to newer versions, please make sure to remove any files that may be cached by this module!
+
+=cut
+
+=head2 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 B<moby-s-install.pl>.
+
+This script will do the following:
+
+=over 4
+
+=item * Check for prerequisite modules and warn you if they are missing
+
+=item * Run you through some configuration details
+
+=item * Optionally help you mirror an already existing registry
+
+=item * Optionally install various scripts used by the registry or its' clients
+
+=back
+
+=cut
+
+=head2 BioMOBY Client Installation
+
+Once the module has been installed using the command B<make install>, there is nothing further left for you to do. You are free to start using the BioMOBY API.
+
+=cut
+
+=head2 BioMOBY Server Installation
+
+To set up your own custom registry, you have to ensure that a few things are ready before hand!
+
+=over 4
+
+=item * You have an apache webserver installed/started on your machine
+
+=item * You have mysql installed/started on your machine
+
+=item * You are aware of the full path to the apache cgi-bin directory
+
+=item * You have a mysql username/password with read/write access available to use
+
+=item * You have root priviledges on your machine!
+
+=back
+
+Once you are sure that you satisfy the above items, go ahead and run the B<moby-s-install.pl> script, by typing C<moby-s-install.pl> at the command line. This file was installed onto your machine when you did your 'make install'!
+
+=head3 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:
+
+=over 4
+
+=item * What is your base installation path for apache?
+
+=item * Where is the conf/cgi-bin directory for apache located?
+
+=item * What is the path to your Perl executable?
+
+=back
+
+Once that information is entered, the script prompts you to set up apache.
+
+=head4 Apache setup
+
+The following is done when the installation script sets up apache:
+
+=over 4
+
+=item * A mobycentral configuration file is added to your apache conf directory
+
+=item * mySQL connection information is obtained from you and inserted into the the configuration file
+
+=item * mySQL table names for the registry are chosen
+
+=item * Optionally, httpd.conf is edited adding various environment variables necessary for the registry
-Stub documentation for MOBY, created by h2xs. It looks like the
-author of the extension was negligent enough to leave the stub
-unedited.
+=back
-Blah blah blah.
+=cut
+
+Once apache has been set up, the installation script prompts you to set up mySQL.
+
+During mySQL setup, you will be prompted to either create a complete clone of an existing registry or to simply add the base tables required for a registry to your database.
+
+The very next thing that will happen, is that you will be prompted to install the RESOURCES script. This script is mandatory for those hosting a registry.
+
+During the installation of the RESOURCES script, you will be prompted for a place to store the RDF cache. This directory needs to read/writable by apache.
+
+After installation of the RESOURCES script, you will be prompted to install the LSID authority script.
+
+The very last thing that the script does is to prompt you install other auxillary scripts. While they are not required, it is recommended to install them.
+
+Please make sure that any file installed into your cgi-bin directory is executable and that you restart apache so that all changes are reflected!
+
+Assuming that you installed the auxillary scripts, from a web browser, browse to the url:
+
+C<http://localhost/cgi-bin/Moby>
+
+B<Note:> Of course, we are assuming that your localhost is your valid hostname and that the cgi-bin directory location is correct.
+
+A helper page with various links should be visible. Go ahead and try them out!
+
+=cut
+
+=cut
+
+=head2 FAQ
+
+=head3 When I run the install script, IO::Prompt complains ...
+
+This could mean that the package C<IO::Prompt> is not installed properly.
+
+What version do you have?
+
+C<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 B<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.
+
+=cut
+
+=head3 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!
+
+=over 4
+
+=item * Edit your crontab (as root):
+
+C<crontab -e>
+
+=item * Add the following to the top of the crontab
+
+C<MOBY_CENTRAL_CONFIG=/etc/apache2/mobycentral.config>
+
+=item * Add the actual job:
+
+C<00 * * * * perl /path/to/the/service_tester.pl>
+
+=back
+
+This will set up a cron job to run every start of the hour!
+
+=cut
+
+=head3 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
+
+=cut
+
+=cut
+
+=head2 Missing Features
+
+=over
+
+=item * automatic installation of the RDF Agent
+
+=back
+
+=cut
+
+=head2 Acknowledgement
+
+
+=cut
=head2 EXPORT
None by default.
-
=head1 SEE ALSO
-Mention other useful documentation such as the documentation of
-related modules or operating system documentation (such as man pages
-in UNIX), or any relevant external documentation such as RFCs or
-standards.
+For the most up-to-date documentation, visit the BioMOBY website at L<http://biomoby.org>!
-If you have a mailing list set up for your module, mention it here.
+If you have questions or comments, please feel free to message us on the following mailing lists:
-If you have a web site set up for your module, mention it here.
+=over
-=head1 AUTHOR
+=item MOBY discussion list L<http://www.biomoby.org/mailman/listinfo/moby-l>
-A. U. Thor, E<lt>a.u.thor at a.galaxy.far.far.awayE<gt>
+=item MOBY Developers List L<http://www.biomoby.org/mailman/listinfo/moby-dev>
-=head1 COPYRIGHT AND LICENSE
+=item MOBY bugs discussion list L<http://www.biomoby.org/mailman/listinfo/moby-bugs>
-Copyright (C) 2007 by A. U. Thor
+=back
-This library is free software; you can redistribute it and/or modify
-it under the same terms as Perl itself, either Perl version 5.8.8 or,
-at your option, any later version of Perl 5 you may have available.
+=head1 AUTHORS
=cut
+
+=head1 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.
+
+=cut
+
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