From pieter at dev.open-bio.org Sun Dec 2 12:15:49 2007
From: pieter at dev.open-bio.org (Pieter Neerincs)
Date: Sun, 2 Dec 2007 12:15:49 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200712021715.lB2HFnaS010440@dev.open-bio.org>
pieter
Sun Dec 2 12:15:49 EST 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl
In directory dev.open-bio.org:/tmp/cvs-serv10387/Perl/MOBY/Adaptor/moby/Impl
Modified Files:
FetaQueryAdaptor.pm
Log Message:
Removed redundancy from Makefile.PL. Fixed small POD errors in FetaQueryAdaptor.pm, MobyException.pm and MobyExceptionCodes.pm
moby-live/Perl/MOBY/Adaptor/moby/Impl FetaQueryAdaptor.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm 2005/08/03 16:33:55 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm 2007/12/02 17:15:49 1.2
@@ -3,6 +3,15 @@
use vars qw(@ISA);
use XML::LibXML;
@ISA = qw{MOBY::Adaptor::moby::DataAdapterI}; # implements the interface
+
+=head1 NAME
+
+MOBY::Adaptor::moby::impl::FetaQueryAdaptor.pm - FetaQueryAdaptor
+
+=head1 DESCRIPTION
+
+Todo
+
=head2 _queryServiceInstanceHash
Title : _queryServiceInstanceHash
@@ -21,6 +30,7 @@
description => String,
signatureURL => String,
lsid => String}
+
=cut
sub queryServiceInstanceHash {
From pieter at dev.open-bio.org Sun Dec 2 12:15:49 2007
From: pieter at dev.open-bio.org (Pieter Neerincs)
Date: Sun, 2 Dec 2007 12:15:49 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200712021715.lB2HFnmg010422@dev.open-bio.org>
pieter
Sun Dec 2 12:15:49 EST 2007
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv10387/Perl
Modified Files:
Makefile.PL
Log Message:
Removed redundancy from Makefile.PL. Fixed small POD errors in FetaQueryAdaptor.pm, MobyException.pm and MobyExceptionCodes.pm
moby-live/Perl Makefile.PL,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/09/24 18:53:32 1.31
+++ /home/repository/moby/moby-live/Perl/Makefile.PL 2007/12/02 17:15:49 1.32
@@ -248,205 +248,3 @@
#
#MAKE_FRAG
#}
-
-use ExtUtils::MakeMaker;
-use FindBin '$Bin';
-use strict;
-my $VERSION = '0.87';
-
-
-sub MY::postamble {
- # Now build documentation.
- use Pod::Find qw(pod_find simplify_name);
- use Cwd;
- my $cur_dir = getcwd();
- # Find the files that contain POD, starting from the top-level build directory, and do it silently.
- my %pods = pod_find({ -verbose => 0},
- File::Spec->catfile($cur_dir, "MOBY") );
- my @PM = sort keys %pods;
- my @MOD_NAMES = map {$pods{$_}} @PM;
- # Make home for all docs
- # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
- # It's more robust to put it directly into the Makefile,
- # so that it can be rebuilt with a simple "make" if needed.
- # But that would require figuring out how to walk a tree from the shell,
- # and I don't have time for that. Maybe some other day.
- my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
- mkdir File::Spec->catfile($cur_dir, "docs")
- unless -e File::Spec->catfile($cur_dir, "docs");
- mkdir $HTML_ROOT unless -e $HTML_ROOT;
- # Create a new directory tree for the documentation, that mirrors the source tree.
- use File::Find;
- my @make_dirs_list;
- sub wanted { # Define nested subroutine, to inherit variable scope
- my $src_dir = $File::Find::dir;
- (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
-# print STDERR "EXamining $doc_dir\n";
- if ( !($doc_dir =~ /CVS$/) ) {
- push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
- unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
- if (!(-e $doc_dir)) {
- my $made_dir = mkdir $doc_dir;
- if (!$made_dir) {
- print STDERR "Couldn't create directory '$doc_dir' because '$!'";
- }
- }
- }
- }
- find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
- # Finally, start writing the rules.
- # Let's make a big rule to build all the docs at once, call it 'html'
- # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
- my @HTML = map { # Edit beginning and end of PM files, to make HTML filenames
- my $x = $_; # Don't want to change the original...
- $x =~ s/\.p[lm]$/\.html/;
- $x =~ s/^$cur_dir/$HTML_ROOT/;
- $x} @PM;
- my $postamble = "# Rules to keep developer docs up-to-date.\n";
- $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML)
- . "\n\nhtml: \$(POD_TO_HTML)\n";
-# $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
-# . "\n\nhtml:\n"; # \$(HTML_DIRS)
-# $postamble .= "\$(HTML_DIRS):\n\tfor file in "
-# . join(" \\\n", @make_dirs_list) .
-# "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
-
- # Now, finally, we build rules for the makefile.
- # The TAB ('\t') characters are essential, otherwise 'make' will silently ignore the rules.
- # Don't be tempted to remove them.
- for (my $i = 0; $i < @PM; $i++) {
- $postamble .= <index.html" or die "Couldn't open index.html ($!)";
- print INDEX <
-
-
-
- MOBY-S Perl Module Documentation
-
-
-
-
MOBY-S Perl Modules Documentation
-
-For an overview of how to do various things in Perl, see the
-Perl Tutorial
-The documents below (including this one) are generated by pod2html from the various perl
-modules and give specific interface information for each of the Perl modules described in the tutorial.
-
-
-HEAD
- for (my $i = 0; $i < @{$pms}; $i++) {
- print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
- }
-print INDEX <
-
-
-FOOT
-}
-
-
-# Override built-in target, by adding the 'html' dependency
-# Now HTML gets updated every time you type "make"
-sub MY::top_targets {
- my $self = shift;
- my $string = $self->MM::top_targets;
- my $add = 'html';
- $string =~ s/\s+(pure_all)/ $add $1/;
- return $string;
-}
-
-#sub MY::install {
-# my $self = shift;
-# my $string = $self->MM::install;
-# my $add = 'html';
-# $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
-# print "INSTALL: $string\n";
-# return $string;
-#}
-
-WriteMakefile(
- NAME => 'MOBY-S',
- VERSION => $VERSION,
- # VERSION_FROM => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
- PMLIBDIRS => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
- # Version numbers specified for prerequiisites are simply "desired" versions,
- # not minimum, or anything else.
- PREREQ_PM => {
- 'SOAP::Lite' => 0.69,
- 'SOAP::MIME' => 0.55,
- 'XML::LibXML' => 1.58,
- 'XML::XPath' => 1.12,
- 'Text::Shellwords' => 1.00,
- 'HTML::Entities' => 0.01,
- 'Test::More' => 0.60,
- # Database stuff required only for local registry, but notify user if missing anyway.
- 'DBI' => 0.01,
- 'DBD::mysql' => 0.01,
- # 'WSRF::Lite' => '0.8.2.1', but it is not declared in the proper way there
- 'WSRF::Lite' => '',
- 'Test::Simple' => 0.44,
- 'XML::DOM' => '',
- 'DateTime::Format::Epoch' => '',
- 'DateTime::Format::W3CDTF' => '',
- 'HTTP::Daemon' => '',
- 'HTTP::Daemon::SSL' => '',
- 'MIME::Base64' => '',
- 'Digest::SHA1' => '',
- 'Crypt::OpenSSL::X509' => '',
- 'Crypt::OpenSSL::RSA' => '',
- 'XML::CanonicalizeXML' => 0.02,
- 'Sys::Hostname::Long' => '',
- 'RDF::Core' => '.51',
- #Sharable only used for isAlive script
- #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
- #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
- #'LS' => 1.1.4,
- }, # e.g., Module::Name => 1.1
- #PM_FILTER => "",
- ($] >= 5.005 ? ## Add these new keywords supported since 5.005
- (ABSTRACT => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
- AUTHOR => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
-);
-
-#
-# Insert additional MOBY specific Makefile targets
-#
-#
-#sub MY::postamble {
-# return <<"MAKE_FRAG";
-#Central:
-# echo 'Make (local) MOBY Central stub'
-#
-#Server:
-# echo 'Make (local) MOBY Server stub'
-#
-#WWWClient:
-# echo 'Setting up MOBY WWW Client'
-# cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
-# chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
-#
-#MAKE_FRAG
-#}
-
From pieter at dev.open-bio.org Sun Dec 2 12:15:50 2007
From: pieter at dev.open-bio.org (Pieter Neerincs)
Date: Sun, 2 Dec 2007 12:15:50 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200712021715.lB2HFonm010462@dev.open-bio.org>
pieter
Sun Dec 2 12:15:49 EST 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client/Exception
In directory dev.open-bio.org:/tmp/cvs-serv10387/Perl/MOBY/Client/Exception
Modified Files:
MobyException.pm MobyExceptionCodes.pm
Log Message:
Removed redundancy from Makefile.PL. Fixed small POD errors in FetaQueryAdaptor.pm, MobyException.pm and MobyExceptionCodes.pm
moby-live/Perl/MOBY/Client/Exception MobyException.pm,1.1,1.2 MobyExceptionCodes.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/MobyException.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/MobyException.pm 2006/08/29 13:41:15 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/MobyException.pm 2007/12/02 17:15:49 1.2
@@ -316,7 +316,7 @@
=head1 NAME
-MOBY::Client::Exception::MobyException
+MOBY::Client::Exception::MobyException - MobyException
=head1 DESCRIPTION
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/MobyExceptionCodes.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/MobyExceptionCodes.pm 2006/08/29 13:41:15 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Exception/MobyExceptionCodes.pm 2007/12/02 17:15:49 1.2
@@ -303,7 +303,7 @@
=head1 NAME
-MOBY::Client::Exception::MobyExceptionCodes
+MOBY::Client::Exception::MobyExceptionCodes - MobyExceptionCodes
=head1 DESCRIPTION
From mwilkinson at dev.open-bio.org Mon Dec 3 17:26:54 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 3 Dec 2007 17:26:54 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200712032226.lB3MQsoO015284@dev.open-bio.org>
mwilkinson
Mon Dec 3 17:26:54 EST 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv15265/MOBY
Modified Files:
Config.pm
Log Message:
adding documentation for the Config module
moby-live/Perl/MOBY Config.pm,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2006/05/04 18:38:15 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2007/12/03 22:26:54 1.11
@@ -1,3 +1,37 @@
+#$Id$
+
+=head1 NAME
+
+MOBY::Config.pm - An object containing information about how to get access to teh Moby databases, resources, etc. from the
+mobycentral.config file
+
+=cut
+
+
+=head2 USAGE
+
+ $CONF = MOBY::Config->new();
+
+ # for fields in the mobycentral.config file, use the section name
+ # as the first object, then the item name as the hash-hey within that
+ # object.
+ # i.e. $CONF->mobycentral returns a MOBY::dbConfig representing the
+ # [mobycentral] part of the mobycentral.config file
+
+ $centraluser = $CONF->mobycentral->{username}
+ $centralpass = $CONF->mobycentral->{password}
+ $objectuser = $CONF->mobyobject->{username}
+
+ $ADAPTOR = $CONF->getDataAdaptor('mobyobject');
+ # $ADAPTOR is probably a MOBY::adaptor::queryapi::mysql object
+
+ my $dbh = $ADAPTOR->dbh();
+ my $sth = $object_dbh->prepare("select description from object where object_type = ?");
+ $sth->execute("GenericSequence");
+
+=cut
+
+
package MOBY::Config;
BEGIN {}
From mwilkinson at dev.open-bio.org Mon Dec 3 17:30:42 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 3 Dec 2007 17:30:42 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200712032230.lB3MUgwj015321@dev.open-bio.org>
mwilkinson
Mon Dec 3 17:30:42 EST 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv15302/MOBY
Modified Files:
Config.pm
Log Message:
adding documentation for the Config module
moby-live/Perl/MOBY Config.pm,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2007/12/03 22:26:54 1.11
+++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2007/12/03 22:30:42 1.12
@@ -22,7 +22,7 @@
$centralpass = $CONF->mobycentral->{password}
$objectuser = $CONF->mobyobject->{username}
- $ADAPTOR = $CONF->getDataAdaptor('mobyobject');
+ $ADAPTOR = $CONF->getDataAdaptor(source => 'mobyobject');
# $ADAPTOR is probably a MOBY::adaptor::queryapi::mysql object
my $dbh = $ADAPTOR->dbh();
From kawas at dev.open-bio.org Tue Dec 4 13:00:47 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 4 Dec 2007 13:00:47 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200712041800.lB4I0lf8017877@dev.open-bio.org>
kawas
Tue Dec 4 13:00:47 EST 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv17842/Docs/MOBY-S_API
Modified Files:
RegistryScripts.html
Log Message:
added documentation about the now existing cgi script 'Moby'
moby-live/Docs/MOBY-S_API RegistryScripts.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2007/12/04 14:54:07 1.2
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RegistryScripts.html 2007/12/04 18:00:47 1.3
@@ -206,20 +206,16 @@
- Copy the following files to your webservers cgi-bin directory
- authority.pl
- ValidateService
- AgentRDFValidator
- RESOURCES
+ authority.pl
+ ValidateService
+ AgentRDFValidator
+ RESOURCES
+ Moby
Copy the following file somewhere other than a web accessible directory (this script will be placed on a cron)
service_tester.pl
- Copy the following file to your webservers' htdocs directory
-
-
-
- moby.html
@@ -421,7 +417,7 @@
Testing Your Scripts
Once you have installed and configured the scripts, you can determine if the install was successful by attempting to resolve the following URL:
- http://your.domain.com:your_port/moby.html
+ http://your.domain.com:your_port/cgi-bin/Moby
where your.domain.com is the domain name of the server that the servlets were installed on and your_port is the server port.
The resulting page will outline those scripts that are included in this distribution and will provide you with links to test them.
From kawas at dev.open-bio.org Tue Dec 4 13:02:30 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 4 Dec 2007 13:02:30 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200712041802.lB4I2Usf017933@dev.open-bio.org>
kawas
Tue Dec 4 13:02:30 EST 2007
Update of /home/repository/moby/moby-live/Perl/scripts
In directory dev.open-bio.org:/tmp/cvs-serv17902/Perl/scripts
Added Files:
Moby
Log Message:
A cgi script that presents a web form that can be used for testing the perl based registry scripts
moby-live/Perl/scripts Moby,NONE,1.1
From kawas at dev.open-bio.org Tue Dec 4 13:03:16 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 4 Dec 2007 13:03:16 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200712041803.lB4I3GYA017991@dev.open-bio.org>
kawas
Tue Dec 4 13:03:16 EST 2007
Update of /home/repository/moby/moby-live/Perl/scripts
In directory dev.open-bio.org:/tmp/cvs-serv17956/Perl/scripts
Modified Files:
AgentRDFValidator
Log Message:
Added a waiting dialog, and cleaned up the code
moby-live/Perl/scripts AgentRDFValidator,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator 2007/08/15 17:39:06 1.2
+++ /home/repository/moby/moby-live/Perl/scripts/AgentRDFValidator 2007/12/04 18:03:16 1.3
@@ -1,157 +1,265 @@
-#!/usr/bin/perl -w
-#-----------------------------------------------------------------
-# ValidateService
-# Author: Edward Kawas
-# Copyright (c) 2007 Edward Kawas. All Rights Reserved.
-#
-# 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.
-#
-# $Id$
-#
-# This script is a web based form for testing the RDF agent
-# on a specified user URL. When the script is called without
-# parameters, a FORM is generated.
-#
-# Parameters understood by this script:
-# url - the remote url of the RDF doc that the agent will fetch
-# NOTES:
-# 1. This script assumes that a BioMOBY registry is properly
-# installed
-# 2. JAVA_HOME is set in the environment or 'java' called
-# at a command prompt actually calls a java runtime.
-# 3. This script attempts to ensure that the arguement passed
-# in is a 'real' url by first calling head on the URL.
-# I am not sure if this will cause problems later on.
-#-----------------------------------------------------------------
-use strict;
-use CGI qw/:standard/;
-use LWP::UserAgent;
-use HTTP::Request::Common;
-use LWP::Simple qw(!head);
-use MOBY::Config;
-
-
-my $form = new CGI;
-use Data::Dumper;
-my $url = param('url') || undef;
-if ($url) {
- print $form->header('text/plain');
- # confirm valid url
- if (!LWP::Simple::head($url)) {
- my $ua = LWP::UserAgent->new;
- my $response = $ua->request(GET, $url);
- print $response->content;
- print "Invalid URL please try again.";
- exit(0);
- }
- # call the agent
- my $JAVA_HOME = $ENV{JAVA_HOME} || "";
- if ($JAVA_HOME) {
- $JAVA_HOME .="/bin/java";
- } else {
- $JAVA_HOME ="java";
- }
- my $CONF = MOBY::Config->new;
- my $agent = $CONF->{mobycentral}->{rdfagent} or do{print "There was a problem calling the agent.\nPlease notify the administrator for this registry."; exit(0);};
- my $text = `$JAVA_HOME -DRDFagent.home=$agent -jar $agent/RDFagent.jar -test $url`;
- print $text;
-} else {
-print $form->header('text/html');
-print generate_page();
-}
-
-sub generate_page {
-
-return <
-
-
-
-
-
-RDF Agent Test Page
-
-
-
-RDF Agent Test Page
-
-
Please enter the url to your RDF document that describes
-one or more moby services. The agent will then attempt to
-resolve and parse that url.
-
-Once the agent is complete, you should see what services were
-considered valid and what errors occurred below.
-
-
-
-
-
-
-
-
-
-
-