From mwilkinson at pub.open-bio.org Sat Nov 1 04:06:15 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:36:50 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311010906.hA196FQA013696@pub.open-bio.org>
mwilkinson
Sat Nov 1 04:06:15 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid
In directory pub.open-bio.org:/tmp/cvs-serv13678/lsid
Log Message:
Directory /home/repository/moby/moby-live/Perl/lsid added to the repository
moby-live/Perl/lsid - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/lsid/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Perl/lsid/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Perl/lsid/RCS/directory,v: No such file or directory
From mwilkinson at pub.open-bio.org Sat Nov 1 04:06:24 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:36:53 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311010906.hA196O9g013750@pub.open-bio.org>
mwilkinson
Sat Nov 1 04:06:24 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv13732/lsid/authority
Log Message:
Directory /home/repository/moby/moby-live/Perl/lsid/authority added to the repository
moby-live/Perl/lsid/authority - New directory
rcsdiff: /home/repository/moby/moby-live/Perl/lsid/authority/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Perl/lsid/authority/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Perl/lsid/authority/RCS/directory,v: No such file or directory
From mwilkinson at pub.open-bio.org Sat Nov 1 04:40:58 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:36:57 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311010940.hA19ewqw015790@pub.open-bio.org>
mwilkinson
Sat Nov 1 04:40:58 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv15771/MOBY
Modified Files:
CommonSubs.pm
Log Message:
Added the beginnings of an LSID resolver. It currently resolves only namespace type LSIDs. Small changes to commonsubs to make it more robust to namespaced XML
moby-live/Perl/MOBY CommonSubs.pm,1.18,1.19
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/10/25 22:20:47 1.18
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 09:40:57 1.19
@@ -234,13 +234,13 @@
if ($articleName) {
return "
- $data
+ $data
";
} elsif($data) {
return "
- $data
+ $data
";
} else {
@@ -276,26 +276,26 @@
foreach (@{$data}){
if($_) {
$content .= "
- $_
+ $_
";
} else {
$content .= "
-
+
";
}
}
if ($articleName) {
return "
-
+
$content
-
+
";
} else {
return "
- $content
+ $content
";
}
@@ -322,7 +322,7 @@
sub responseHeader {
return "
-
+
";
}
@@ -456,7 +456,7 @@
$DOM = $doc->getDocumentElement();
}
$DOM = $DOM->getDocumentElement if ($DOM->isa("XML::DOM::Document"));
- return 1 if ($DOM->getTagName eq "Collection");
+ return 1 if ($DOM->getTagName =~ /Collection/);
return 0;
}
@@ -673,8 +673,8 @@
}
my @xrefs; my @XREFS;
my @simples;
- return @XREFS if $XML->getTagName eq "Collection";
- if ($XML->getTagName eq "Simple"){
+ return @XREFS if ($XML->getTagName =~/Collection/);
+ if ($XML->getTagName =~/Simple/){
foreach my $child ($XML->getChildNodes){
next unless $child->getNodeType == ELEMENT_NODE;
$XML = $child;
@@ -683,16 +683,16 @@
}
foreach ($XML->getChildNodes){
next unless $_->getNodeType == ELEMENT_NODE;
- next unless $_->getTagName eq "CrossReference";
+ next unless $_->getTagName =~/CrossReference/;
foreach my $xref($_->getChildNodes){
next unless $xref->getNodeType == ELEMENT_NODE;
- next unless ($xref->getTagName eq "Xref" || $xref->getTagName eq 'Object');
+ next unless ($xref->getTagName =~/Xref/ || $xref->getTagName =~ /Object/);
push @xrefs, $xref;
}
}
foreach (@xrefs){
- $x = &_makeXrefType($_) if $_->getTagName eq "Xref";
- $x = &_makeObjectType($_) if $_->getTagName eq "Object";
+ $x = &_makeXrefType($_) if $_->getTagName =~/Xref/;
+ $x = &_makeObjectType($_) if $_->getTagName =~ /Object/;
push @XREFS, $x if $x;
}
return @XREFS;
From mwilkinson at pub.open-bio.org Sat Nov 1 04:40:58 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:01 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311010940.hA19ew42015805@pub.open-bio.org>
mwilkinson
Sat Nov 1 04:40:58 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv15771/lsid/authority
Added Files:
RDFConfigure.pm authority.pl dbConfigure.pm.template
metadata.pl
Log Message:
Added the beginnings of an LSID resolver. It currently resolves only namespace type LSIDs. Small changes to commonsubs to make it more robust to namespaced XML
moby-live/Perl/lsid/authority RDFConfigure.pm,NONE,1.1 authority.pl,NONE,1.1 dbConfigure.pm.template,NONE,1.1 metadata.pl,NONE,1.1
From mwilkinson at pub.open-bio.org Sat Nov 1 04:59:04 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:04 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311010959.hA19x4Hn016935@pub.open-bio.org>
mwilkinson
Sat Nov 1 04:59:04 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv16916/MOBY
Modified Files:
CommonSubs.pm
Log Message:
adding debugging info to commonsubs. I broke it with the last commit
moby-live/Perl/MOBY CommonSubs.pm,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 09:40:57 1.19
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 09:59:04 1.20
@@ -603,10 +603,13 @@
my $responses = $moby->getElementsByTagName('moby:queryResponse');
$responses ||= $moby->getElementsByTagName('queryResponse');
foreach my $n(0..($responses->getLength - 1)){
+ print STDERR "***found response # $n\n";
my $resp = $responses->item($n);
foreach my $response_component($resp->getChildNodes){
+ print STDERR "***found child node\n";
next unless $response_component->getNodeType == ELEMENT_NODE;
if (($response_component->getTagName eq "Simple") || ($response_component->getTagName eq "moby:Simple")){
+ print STDERR "***found Simple # $n\n";
my $simples = $resp->getElementsByTagName('Simple');
$simples ||=$resp->getElementsByTagName('moby:Simple');
From mwilkinson at pub.open-bio.org Sat Nov 1 05:02:13 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:08 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011002.hA1A2D9K017009@pub.open-bio.org>
mwilkinson
Sat Nov 1 05:02:13 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv16990/MOBY
Modified Files:
CommonSubs.pm
Log Message:
adding debugging info to commonsubs. I broke it with the last commit
moby-live/Perl/MOBY CommonSubs.pm,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 09:59:04 1.20
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 10:02:13 1.21
@@ -602,6 +602,7 @@
my $success = 0;
my $responses = $moby->getElementsByTagName('moby:queryResponse');
$responses ||= $moby->getElementsByTagName('queryResponse');
+ print STDERR "***checked responses\n";
foreach my $n(0..($responses->getLength - 1)){
print STDERR "***found response # $n\n";
my $resp = $responses->item($n);
From mwilkinson at pub.open-bio.org Sat Nov 1 05:04:13 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:13 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011004.hA1A4DwG017341@pub.open-bio.org>
mwilkinson
Sat Nov 1 05:04:13 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv17322/MOBY
Modified Files:
CommonSubs.pm
Log Message:
adding debugging info to commonsubs. I broke it with the last commit
moby-live/Perl/MOBY CommonSubs.pm,1.21,1.22
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 10:02:13 1.21
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 10:04:13 1.22
@@ -587,7 +587,9 @@
sub extractResponseArticles {
my ($result) = @_;
+ print STDERR "***extracting response articles\n";
return ([], []) unless $result;
+ print STDERR "***extracted response articles\n";
my $moby;
unless (ref($result) =~ /XML\:\:DOM/){
my $parser = new XML::DOM::Parser;
From mwilkinson at pub.open-bio.org Sat Nov 1 05:23:54 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:18 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011023.hA1ANsYP018465@pub.open-bio.org>
mwilkinson
Sat Nov 1 05:23:54 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv18446/MOBY
Modified Files:
CommonSubs.pm
Log Message:
this should fix it.
moby-live/Perl/MOBY CommonSubs.pm,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 10:04:13 1.22
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 10:23:54 1.23
@@ -587,7 +587,6 @@
sub extractResponseArticles {
my ($result) = @_;
- print STDERR "***extracting response articles\n";
return ([], []) unless $result;
print STDERR "***extracted response articles\n";
my $moby;
@@ -614,10 +613,10 @@
if (($response_component->getTagName eq "Simple") || ($response_component->getTagName eq "moby:Simple")){
print STDERR "***found Simple # $n\n";
- my $simples = $resp->getElementsByTagName('Simple');
- $simples ||=$resp->getElementsByTagName('moby:Simple');
- next unless $simples->item(0);
- foreach my $Object($simples->item(0)->getChildNodes) {
+# my $simples = $resp->getElementsByTagName('Simple');
+# $simples ||=$resp->getElementsByTagName('moby:Simple');
+ # next unless $simples->item(0);
+ foreach my $Object($response_component->getChildNodes) {
next unless $Object->getNodeType == ELEMENT_NODE;
$success = 1;
push @objects,$Object;
From mwilkinson at pub.open-bio.org Sat Nov 1 05:35:20 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:23 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011035.hA1AZK5g019193@pub.open-bio.org>
mwilkinson
Sat Nov 1 05:35:20 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv19174/lsid/authority
Modified Files:
metadata.pl
Log Message:
undeclared variables fixed
moby-live/Perl/lsid/authority metadata.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 09:40:58 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 10:35:20 1.2
@@ -12,6 +12,7 @@
$SERVICE_CGI
$RDF_PREFIX
$RDF_SUFFIX);
+
use dbConfigure qw(
$service
$namespace
@@ -169,8 +170,8 @@
my $host = $db->{host};
my $dbname = $db->{dbname};
my $port = $db->{port};
- my ($dsn) = "DBI:mysql:$dbname:$url:$port";
- my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
+ my ($dsn) = "DBI:mysql:$dbname:$host:$port";
+ my $dbh = DBI->connect($dsn, $user, $pass, {RaiseError => 1}) or die "can't connect to database";
return ($dbh);
}
From mwilkinson at pub.open-bio.org Sat Nov 1 05:37:41 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:27 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011037.hA1AbfXc019290@pub.open-bio.org>
mwilkinson
Sat Nov 1 05:37:41 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv19275
Added Files:
Error.pm
Log Message:
this isn't useful yet, but it is used in the code so silence the error message
moby-live/Perl/lsid/authority Error.pm,NONE,1.1
From mwilkinson at pub.open-bio.org Sat Nov 1 05:40:28 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:35 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011040.hA1AeSga019653@pub.open-bio.org>
mwilkinson
Sat Nov 1 05:40:28 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv19634/MOBY
Modified Files:
CommonSubs.pm
Log Message:
fixed. removing debugging messages
moby-live/Perl/MOBY CommonSubs.pm,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 10:23:54 1.23
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/11/01 10:40:28 1.24
@@ -588,7 +588,6 @@
sub extractResponseArticles {
my ($result) = @_;
return ([], []) unless $result;
- print STDERR "***extracted response articles\n";
my $moby;
unless (ref($result) =~ /XML\:\:DOM/){
my $parser = new XML::DOM::Parser;
@@ -603,19 +602,11 @@
my $success = 0;
my $responses = $moby->getElementsByTagName('moby:queryResponse');
$responses ||= $moby->getElementsByTagName('queryResponse');
- print STDERR "***checked responses\n";
foreach my $n(0..($responses->getLength - 1)){
- print STDERR "***found response # $n\n";
my $resp = $responses->item($n);
foreach my $response_component($resp->getChildNodes){
- print STDERR "***found child node\n";
next unless $response_component->getNodeType == ELEMENT_NODE;
if (($response_component->getTagName eq "Simple") || ($response_component->getTagName eq "moby:Simple")){
- print STDERR "***found Simple # $n\n";
-
-# my $simples = $resp->getElementsByTagName('Simple');
-# $simples ||=$resp->getElementsByTagName('moby:Simple');
- # next unless $simples->item(0);
foreach my $Object($response_component->getChildNodes) {
next unless $Object->getNodeType == ELEMENT_NODE;
$success = 1;
From mwilkinson at pub.open-bio.org Sat Nov 1 06:17:24 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:40 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011117.hA1BHOsu021549@pub.open-bio.org>
mwilkinson
Sat Nov 1 06:17:24 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv21514/lsid/authority
Modified Files:
Error.pm RDFConfigure.pm authority.pl dbConfigure.pm.template
metadata.pl
Log Message:
shuffling stuff around to make it available to various modules
moby-live/Perl/lsid/authority Error.pm,1.1,1.2 RDFConfigure.pm,1.1,1.2 authority.pl,1.1,1.2 dbConfigure.pm.template,1.1,1.2 metadata.pl,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/Error.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/Error.pm 2003/11/01 10:37:41 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/Error.pm 2003/11/01 11:17:24 1.2
@@ -1,3 +1,4 @@
+#$Id$
package Error;
sub clientFault {}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 09:40:58 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 11:17:24 1.2
@@ -1,3 +1,4 @@
+#$Id$
package RDFConfigure;
use strict;
@@ -8,11 +9,16 @@
$SERVICE_CGI
$RDF_PREFIX
$RDF_SUFFIX
+ rdfLiteral
+ rdfResource
);
-#our %EXPORT_TAGS =(all => [qw($SERVICE_CGI
-# $RDF_PREFIX
-# $RDF_SUFFIX
-# )]);
+our %EXPORT_TAGS =(all => [qw(
+ $SERVICE_CGI
+ $RDF_PREFIX
+ $RDF_SUFFIX
+ rdfLiteral
+ rdfResource
+ )]);
our $SERVICE_CGI= 'http://localhost:80/cgi-bin/authority/metadata.pl';
@@ -23,4 +29,20 @@
xmlns:i3cp='urn:lsid:i3c.org:predicates:'
xmlns:mobyp='urn:lsid:biomoby.org:rdfpredicates:'>\n\n";
our $RDF_SUFFIX= "";
+
+
+sub rdfLiteral {
+ my ($subj, $pred, $obj)= @_;
+ return "
+\t<$pred>$obj$pred>
+\n";
+}
+
+sub rdfResource {
+ my ($subj, $pred, $obj)= @_;
+ return "
+\t<$pred rdf:resource='$obj'/>
+";
+}
+
1;
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/authority.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/authority.pl 2003/11/01 09:40:58 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/authority.pl 2003/11/01 11:17:24 1.2
@@ -1,12 +1,5 @@
#!/usr/bin/perl -w
-# =====================================================================
-# Copyright (c) 2002,2003 IBM Corporation
-# All rights reserved. This program and the accompanying materials
-# are made available under the terms of the Common Public License v1.0
-# which accompanies this distribution, and is available at
-# http://www.opensource.org/licenses/cpl.php
-#
-# =====================================================================
+#$Id$
use LS::Authority::WSDL::Simple;
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/dbConfigure.pm.template,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/dbConfigure.pm.template 2003/11/01 09:40:58 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/dbConfigure.pm.template 2003/11/01 11:17:24 1.2
@@ -14,22 +14,22 @@
=cut
-
+#$Id$
package dbConfigure;
use strict;
use base 'Exporter';
require Exporter;
our @EXPORT_OK = qw(
- $central
- $namespace
- $object
- $service
- $relationship
+ $centraldb
+ $namespacedb
+ $objectdb
+ $servicedb
+ $relationshipdb
);
# parameters for the mobycentral database
-our $central = {'host' => '',
+our $centraldb = {'host' => '',
'dbname' => '',
'user' => '',
'pass' => '',
@@ -37,7 +37,7 @@
};
# parameters for the namespace database
-our $namespace = {'host' => '',
+our $namespacedb = {'host' => '',
'dbname' => '',
'user' => '',
'pass' => '',
@@ -45,7 +45,7 @@
};
# parameters for the object database
-our $object = { 'host' => '',
+our $objectdb = { 'host' => '',
'dbname' => '',
'user' => '',
'pass' => '',
@@ -53,7 +53,7 @@
};
# parameters for the service database
-our $service = {'host' => '',
+our $servicedb = {'host' => '',
'dbname' => '',
'user' => '',
'pass' => '',
@@ -62,7 +62,7 @@
# parameters for the relationship database
-our $relationship = {'host' => '',
+our $relationshipdb = {'host' => '',
'dbname' => '',
'user' => '',
'pass' => '',
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 10:35:20 1.2
+++ /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 11:17:24 1.3
@@ -1,4 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl -w
+#$Id$
+
use CGI qw/:standard/;
use lib "/usr/local/apache/cgi-bin/lsid/authority";
use strict;
@@ -8,19 +10,17 @@
use LS::Authority::WSDL::Simple;
use Error;
-use RDFConfigure qw(
- $SERVICE_CGI
- $RDF_PREFIX
- $RDF_SUFFIX);
+use RDFConfigure qw(:all);
use dbConfigure qw(
- $service
- $namespace
- $object
- $central
- $relationship
+ $servicedb
+ $namespacedb
+ $objectdb
+ $centraldb
+ $relationshipdb
);
+use NamespaceResolver qw(:all);
my %known_types = ( # switch on/off various LSID resolvers.
'namespacetype' => 1,
@@ -37,15 +37,8 @@
my $lsid = param('lsid');
print header(-type => 'x-application/rdf+xml', -expires => 'now'); # both tags are required by the spec
-
- #my $rdfheader = "\n".
- #"\n";
my $rdf = validate_lsid($lsid);
- #my $rdffooter = '';
_die("RDF creation failed") unless ($rdf);
-# print $rdfheader.$rdf.$rdffooter;
print $rdf;
exit 1;
}
@@ -71,7 +64,7 @@
_die("unknown LSID namespace $1 : $known_types{$1}; known types are ".(keys %known_types)."\n", 404);
}
- return resolve_namespacetype($lsid) if $1 eq "namespacetype";
+ return resolve_namespacetype($namespacedb,$lsid) if $1 eq "namespacetype";
}
@@ -81,98 +74,3 @@
die ($e, $m);
}
-sub resolve_namespacetype {
- my $ls = shift;
- print STDERR "LSID is $ls\n";
- my $lsid= LS::ID->new($ls)->canonical;
- unless ($lsid) {
- _die('Malformed LSID', 200);
- }
-
- my $authority= $lsid->authority;
- my $ns= $lsid->namespace;
- my $obj= $lsid->object;
- my $rev= $lsid->revision;
-
- my $mdata;
- my $dbh = _dbAccess($namespace);
-
- my $sth = $dbh->prepare("select namespace_type, description, authority, contact_email from namespace where namespace_lsid = ?");
- $sth->execute($lsid);
- my ($namespace_type, $description, $authURI, $contact_email) = $sth->fetchrow_array;
- unless ($namespace_type){
- _die('LSID Does not exist', 404);
- }
-
- # SID is now fully validated. Carry on with metadata.
- $RDF_PREFIX?1:1;
- $mdata= $RDF_PREFIX;
- $mdata.= rdfLiteral(
- $lsid->as_string,
- 'dc:title',
- $namespace_type
- );
- $mdata.= rdfLiteral(
- $lsid->as_string,
- 'rdfs:label',
- $namespace_type
- );
- $mdata.= rdfLiteral(
- $lsid->as_string,
- 'dc:description',
- $description
- );
- $mdata.= rdfLiteral(
- $lsid->as_string,
- 'dc:contributor',
- $authURI
- );
- $mdata.= rdfLiteral(
- $lsid->as_string,
- 'dc:type',
- "bioMoby namespace identifier"
- );
- $mdata.= rdfResource(
- $contact_email,
- 'dc:label',
- $contact_email
- );
- $mdata.= $RDF_SUFFIX;
- $RDF_SUFFIX?1:1;
-
- unless ($mdata) {
- die Error::clientFault('Metadata not available', 300);
- }
- return $mdata;
-}
-
-sub rdfLiteral {
- my ($subj, $pred, $obj)= @_;
- return "
-\t<$pred>$obj$pred>
-\n";
-}
-
-sub rdfResource {
- my ($subj, $pred, $obj)= @_;
- return "
-\t<$pred rdf:resource='$obj'/>
-";
-}
-
-
-sub _dbAccess {
- use DBI;
- use DBD::mysql;
- my ($db) = @_;
- my $pass = $db->{pass};
- my $user = $db->{user};
- my $host = $db->{host};
- my $dbname = $db->{dbname};
- my $port = $db->{port};
- my ($dsn) = "DBI:mysql:$dbname:$host:$port";
- my $dbh = DBI->connect($dsn, $user, $pass, {RaiseError => 1}) or die "can't connect to database";
-
- return ($dbh);
-}
-
From mwilkinson at pub.open-bio.org Sat Nov 1 06:26:08 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:44 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011126.hA1BQ8sf022231@pub.open-bio.org>
mwilkinson
Sat Nov 1 06:26:08 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv22216
Added Files:
NamespaceResolver.pm dbConnect.pm
Log Message:
db connection module and namespace resolver RDF meta-data generator
moby-live/Perl/lsid/authority NamespaceResolver.pm,NONE,1.1 dbConnect.pm,NONE,1.1
From mwilkinson at pub.open-bio.org Sat Nov 1 06:37:02 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:47 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011137.hA1Bb2ta022867@pub.open-bio.org>
mwilkinson
Sat Nov 1 06:37:02 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv22848
Modified Files:
NamespaceResolver.pm
Log Message:
debugging changes
moby-live/Perl/lsid/authority NamespaceResolver.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/NamespaceResolver.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/NamespaceResolver.pm 2003/11/01 11:26:08 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/NamespaceResolver.pm 2003/11/01 11:37:02 1.2
@@ -3,7 +3,6 @@
require Exporter;
use XML::DOM;
-use MOBY::CrossReference;
use dbConnect qw(:all);
use RDFConfigure qw(:all);
From mwilkinson at pub.open-bio.org Sat Nov 1 08:28:33 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:37:51 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011328.hA1DSX8e029006@pub.open-bio.org>
mwilkinson
Sat Nov 1 08:28:32 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv28979
Modified Files:
NamespaceResolver.pm RDFConfigure.pm metadata.pl
Added Files:
ClassResolver.pm RelationshipResolver.pm ServiceResolver.pm
Log Message:
added LSID resolvers for the Class and Service and Relationship ontologies.
moby-live/Perl/lsid/authority ClassResolver.pm,NONE,1.1 RelationshipResolver.pm,NONE,1.1 ServiceResolver.pm,NONE,1.1 NamespaceResolver.pm,1.2,1.3 RDFConfigure.pm,1.2,1.3 metadata.pl,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/NamespaceResolver.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/lsid/authority/NamespaceResolver.pm 2003/11/01 11:37:02 1.2
+++ /home/repository/moby/moby-live/Perl/lsid/authority/NamespaceResolver.pm 2003/11/01 13:28:32 1.3
@@ -17,7 +17,7 @@
sub resolve_namespacetype {
my ($namespace_db_params, $ls) = @_;
- print STDERR "LSID is $ls\n";
+ #print STDERR "LSID is $ls\n";
my $lsid= LS::ID->new($ls)->canonical;
unless ($lsid) {
_die('Malformed LSID', 200);
@@ -29,7 +29,7 @@
my $rev= $lsid->revision;
my $mdata;
- my $dbh = dbAccess($namespace_db_params);
+ my $dbh = dbConnect($namespace_db_params);
my $sth = $dbh->prepare("select namespace_type, description, authority, contact_email from namespace where namespace_lsid = ?");
$sth->execute($lsid);
@@ -64,7 +64,7 @@
$mdata.= rdfLiteral(
$lsid->as_string,
'dc:type',
- "bioMoby namespace identifier"
+ "bioMoby Namespace identifier"
);
$mdata.= rdfResource(
$contact_email,
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 11:17:24 1.2
+++ /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 13:28:32 1.3
@@ -11,6 +11,7 @@
$RDF_SUFFIX
rdfLiteral
rdfResource
+ _die
);
our %EXPORT_TAGS =(all => [qw(
$SERVICE_CGI
@@ -18,6 +19,7 @@
$RDF_SUFFIX
rdfLiteral
rdfResource
+ _die
)]);
@@ -45,4 +47,11 @@
";
}
+
+sub _die {
+ my $m = shift;
+ my $e = shift;
+ die ($e, $m);
+}
+
1;
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 11:17:24 1.3
+++ /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 13:28:32 1.4
@@ -21,12 +21,16 @@
);
use NamespaceResolver qw(:all);
+use ClassResolver qw(:all);
+use ServiceResolver qw(:all);
+use RelationshipResolver qw(:all);
-my %known_types = ( # switch on/off various LSID resolvers.
+my %known_types = ( # switch on/off various LSID-namespace resolvers.
'namespacetype' => 1,
- 'objecttype' => 0,
- 'servicetype' => 0,
- 'relationshiptype' => 0,
+ 'objectclass' => 1,
+ 'servicetype' => 1,
+ 'servicerelation' => 1,
+ 'objectrelation' => 1,
'serviceinstance' => 0,
);
@@ -65,12 +69,10 @@
}
return resolve_namespacetype($namespacedb,$lsid) if $1 eq "namespacetype";
+ return resolve_classtype($objectdb,$lsid) if $1 eq "objectclass";
+ return resolve_servicetype($servicedb,$lsid) if $1 eq "objectclass";
+ return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "objectrelation";
+ return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "servicerelation";
}
-sub _die {
- my $m = shift;
- my $e = shift;
- die ($e, $m);
-}
-
From mwilkinson at pub.open-bio.org Sat Nov 1 08:35:12 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:01 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011335.hA1DZCgp029347@pub.open-bio.org>
mwilkinson
Sat Nov 1 08:35:12 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv29328
Modified Files:
metadata.pl
Log Message:
added service LSID's were resolving to the Object ontology. oops.
moby-live/Perl/lsid/authority metadata.pl,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 13:28:32 1.4
+++ /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 13:35:12 1.5
@@ -70,7 +70,7 @@
return resolve_namespacetype($namespacedb,$lsid) if $1 eq "namespacetype";
return resolve_classtype($objectdb,$lsid) if $1 eq "objectclass";
- return resolve_servicetype($servicedb,$lsid) if $1 eq "objectclass";
+ return resolve_servicetype($servicedb,$lsid) if $1 eq "servicetype";
return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "objectrelation";
return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "servicerelation";
From mwilkinson at pub.open-bio.org Sat Nov 1 08:41:46 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:06 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011341.hA1Dfks0029697@pub.open-bio.org>
mwilkinson
Sat Nov 1 08:41:46 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv29678
Modified Files:
RelationshipResolver.pm
Log Message:
bad SQL
moby-live/Perl/lsid/authority RelationshipResolver.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/RelationshipResolver.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/RelationshipResolver.pm 2003/11/01 13:28:32 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/RelationshipResolver.pm 2003/11/01 13:41:46 1.2
@@ -30,7 +30,7 @@
my $mdata;
my $dbh = dbConnect($class_db_params);
# e.g. urn:lsid:biomoby.org:objectrelation:isa
- my $sth = $dbh->prepare("select relationship_type, description, authority, contact_email, ontology from object where object_lsid = ?");
+ my $sth = $dbh->prepare("select relationship_type, description, authority, contact_email, ontology from relationship where relationship_lsid = ?");
$sth->execute($lsid);
my ($relationship_type, $description, $authURI, $contact_email, $ontology) = $sth->fetchrow_array;
unless ($relationship_type){
From mwilkinson at pub.open-bio.org Sat Nov 1 09:00:58 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:10 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011400.hA1E0wMV030851@pub.open-bio.org>
mwilkinson
Sat Nov 1 09:00:58 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv30832
Modified Files:
RelationshipResolver.pm
Added Files:
PredicateResolver.pm
Log Message:
bioMoby predicate resolver to deal with LSID's that reprsent MOBY-project specific RDF predicates
moby-live/Perl/lsid/authority PredicateResolver.pm,NONE,1.1 RelationshipResolver.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/RelationshipResolver.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/lsid/authority/RelationshipResolver.pm 2003/11/01 13:41:46 1.2
+++ /home/repository/moby/moby-live/Perl/lsid/authority/RelationshipResolver.pm 2003/11/01 14:00:58 1.3
@@ -68,7 +68,7 @@
$mdata.= rdfLiteral(
$lsid->as_string,
'mobyp:mobyOntology',
- $ontology
+ uc_first($ontology)
);
$mdata.= rdfResource(
$contact_email,
From mwilkinson at pub.open-bio.org Sat Nov 1 09:06:35 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:18 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011406.hA1E6ZvP031202@pub.open-bio.org>
mwilkinson
Sat Nov 1 09:06:35 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv31179
Modified Files:
PredicateResolver.pm metadata.pl
Log Message:
fixing the class LSID resolver and making more useful error messages
moby-live/Perl/lsid/authority PredicateResolver.pm,1.1,1.2 metadata.pl,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/PredicateResolver.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/PredicateResolver.pm 2003/11/01 14:00:57 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/PredicateResolver.pm 2003/11/01 14:06:35 1.2
@@ -18,7 +18,7 @@
};
sub resolve_mobyPredicate {
- my ($class_db_params, $ls) = @_;
+ my ($ls) = @_;
my $lsid= LS::ID->new($ls)->canonical;
unless ($lsid) {
_die('Malformed LSID', 200);
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 13:35:12 1.5
+++ /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 14:06:35 1.6
@@ -24,6 +24,7 @@
use ClassResolver qw(:all);
use ServiceResolver qw(:all);
use RelationshipResolver qw(:all);
+use PredicateResolver qw(:all);
my %known_types = ( # switch on/off various LSID-namespace resolvers.
'namespacetype' => 1,
@@ -32,6 +33,7 @@
'servicerelation' => 1,
'objectrelation' => 1,
'serviceinstance' => 0,
+ 'rdfpredicates' => 1,
);
MetaData();
@@ -65,7 +67,7 @@
_die('Malformed LSID', 200);
}
unless ($known_types{$1}){
- _die("unknown LSID namespace $1 : $known_types{$1}; known types are ".(keys %known_types)."\n", 404);
+ _die("unknown LSID namespace $1; known types are ".(join ",", (keys %known_types))."\n", 404);
}
return resolve_namespacetype($namespacedb,$lsid) if $1 eq "namespacetype";
@@ -73,6 +75,7 @@
return resolve_servicetype($servicedb,$lsid) if $1 eq "servicetype";
return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "objectrelation";
return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "servicerelation";
+ return resolve_mobyPredicate($lsid) if $1 eq "rdfpredicates";
}
From mwilkinson at pub.open-bio.org Sat Nov 1 09:10:05 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:25 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011410.hA1EA5SL031547@pub.open-bio.org>
mwilkinson
Sat Nov 1 09:10:05 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv31524
Modified Files:
RDFConfigure.pm metadata.pl
Log Message:
changed the predicate namespace from plural to singular... it sounds better that way
moby-live/Perl/lsid/authority RDFConfigure.pm,1.3,1.4 metadata.pl,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 13:28:32 1.3
+++ /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 14:10:05 1.4
@@ -29,7 +29,7 @@
xmlns:rdfs='http://www.w3.org/2000/01/rdf-schema#'
xmlns:dc='http://purl.org/dc/elements/1.1/'
xmlns:i3cp='urn:lsid:i3c.org:predicates:'
-xmlns:mobyp='urn:lsid:biomoby.org:rdfpredicates:'>\n\n";
+xmlns:mobyp='urn:lsid:biomoby.org:rdfpredicate:'>\n\n";
our $RDF_SUFFIX= "";
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 14:06:35 1.6
+++ /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 14:10:05 1.7
@@ -33,7 +33,7 @@
'servicerelation' => 1,
'objectrelation' => 1,
'serviceinstance' => 0,
- 'rdfpredicates' => 1,
+ 'rdfpredicate' => 1,
);
MetaData();
@@ -75,7 +75,7 @@
return resolve_servicetype($servicedb,$lsid) if $1 eq "servicetype";
return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "objectrelation";
return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "servicerelation";
- return resolve_mobyPredicate($lsid) if $1 eq "rdfpredicates";
+ return resolve_mobyPredicate($lsid) if $1 eq "rdfpredicate";
}
From mwilkinson at pub.open-bio.org Sat Nov 1 09:25:15 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:31 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011425.hA1EPFbH032408@pub.open-bio.org>
mwilkinson
Sat Nov 1 09:25:15 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv32389
Modified Files:
PredicateResolver.pm
Log Message:
compensating for ambiguity v.v. whether or not LSID's are case sensitive. Will chose one or the other when I get confirmation from the horses mouth
moby-live/Perl/lsid/authority PredicateResolver.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/PredicateResolver.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/lsid/authority/PredicateResolver.pm 2003/11/01 14:06:35 1.2
+++ /home/repository/moby/moby-live/Perl/lsid/authority/PredicateResolver.pm 2003/11/01 14:25:15 1.3
@@ -15,6 +15,7 @@
my $known_predicates = {
mobyOntology => 'A phrase representing one of the bioMoby ontologies.',
+ mobyontology => 'A phrase representing one of the bioMoby ontologies.',
};
sub resolve_mobyPredicate {
@@ -31,7 +32,7 @@
# e.g. urn:lsid:biomoby.org:rdfpredicates:mobyOntology
unless ($known_predicates->{$obj}){
- _die('LSID '.($lsid->as_string).' Does not exist', 404);
+ _die('LSID '.($lsid->as_string).' ($obj) Does not exist', 404);
}
# LSID is now fully validated. Carry on with metadata.
From mwilkinson at pub.open-bio.org Sat Nov 1 10:24:00 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:36 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011524.hA1FO0XQ003242@pub.open-bio.org>
mwilkinson
Sat Nov 1 10:23:59 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv3223
Modified Files:
Central.pm
Log Message:
screen for illegally formatted authURIs in order to be able to use them in our LSID's
moby-live/Perl/MOBY Central.pm,1.109,1.110
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.109
retrieving revision 1.110
diff -u -r1.109 -r1.110
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/10/22 14:27:45 1.109
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/11/01 15:23:59 1.110
@@ -1014,6 +1014,7 @@
$error .="missing serviceName \n" unless defined $serviceName;
$error .="missing serviceType \n" unless defined $serviceType;
$error .="missing authURI \n" unless defined $AuthURI;
+ $error .="malformed authURI; must be the domain name only with no http prefix or trailing path information \n" if $AuthURI =~ '[/:]';
$error .="missing contactEmail \n" unless defined $contactEmail;
$error .="missing URL \n" unless defined $URL;
$error .="missing description \n" unless defined $desc;
From mwilkinson at pub.open-bio.org Sat Nov 1 10:53:14 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:42 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011553.hA1FrExw004679@pub.open-bio.org>
mwilkinson
Sat Nov 1 10:53:14 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv4633/Client
Modified Files:
Central.pm ServiceInstance.html ServiceInstance.pm
Log Message:
pass the authoritative flag back to a service instance object since it should be there, and now we need it for the LSID resolution service
moby-live/Perl/MOBY/Client Central.pm,1.57,1.58 ServiceInstance.html,1.3,1.4 ServiceInstance.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.57
retrieving revision 1.58
diff -u -r1.57 -r1.58
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/10/22 14:27:46 1.57
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/11/01 15:53:13 1.58
@@ -1438,6 +1438,7 @@
my $AuthURI = $Service->getAttributeNode('authURI')->getValue;
my $servicename = $Service->getAttributeNode('serviceName')->getValue;
my $Type = &_nodeTextContent($Service, 'serviceType');
+ my $authoritative = &_nodeTextContent($Service, 'authoritative');
#my $Output = &_nodeTextContent($Service, 'outputObject');
my $Description = &_nodeTextContent($Service, 'Description');
my $cat = &_nodeTextContent($Service, 'Category');
@@ -1471,6 +1472,7 @@
my $Instance = MOBY::Client::ServiceInstance->new(
authority => $AuthURI,
+ authoritative => $authoritative,
name => $servicename,
type => $Type,
category => $cat,
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/07/01 15:00:47 1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/11/01 15:53:14 1.4
@@ -26,6 +26,7 @@
input
output
description
+ authoritative
registry
@@ -148,6 +149,15 @@
Returns : string
+
+
+ Title : authoritative
+ Usage : $description = $Service->authoritative(1|0)
+ Args : (optional) boolean 1 or 0
+ Function : get/set authoritative flag
+ Returns : current value
+
+
Title : registry
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/07/01 15:00:47 1.5
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 15:53:14 1.6
@@ -129,6 +129,17 @@
=cut
+=head2 authoritative
+
+ Title : authoritative
+ Usage : $description = $Service->authoritative(1|0)
+ Args : (optional) boolean 1 or 0
+ Function : get/set authoritative flag
+ Returns : current value
+
+=cut
+
+
=head2 registry
Title : registry
@@ -155,6 +166,7 @@
description => [undef, 'read/write'],
registry => ['MOBY_Central', 'read/write'],
XML => [undef, 'read/write'],
+ authoritative => [undef, 'read/write'],
);
#_____________________________________________________________
From mwilkinson at pub.open-bio.org Sat Nov 1 11:02:53 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:38:54 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011602.hA1G2rC5005294@pub.open-bio.org>
mwilkinson
Sat Nov 1 11:02:53 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv5271/Client
Modified Files:
Central.pm ServiceInstance.pm
Log Message:
pass the URL back to a service instance object since it should be there, and now we need it for the LSID resolution service
moby-live/Perl/MOBY/Client Central.pm,1.58,1.59 ServiceInstance.pm,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.58
retrieving revision 1.59
diff -u -r1.58 -r1.59
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/11/01 15:53:13 1.58
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/11/01 16:02:52 1.59
@@ -1439,6 +1439,7 @@
my $servicename = $Service->getAttributeNode('serviceName')->getValue;
my $Type = &_nodeTextContent($Service, 'serviceType');
my $authoritative = &_nodeTextContent($Service, 'authoritative');
+ my $URL = &_nodeTextContent($Service, 'URL');
#my $Output = &_nodeTextContent($Service, 'outputObject');
my $Description = &_nodeTextContent($Service, 'Description');
my $cat = &_nodeTextContent($Service, 'Category');
@@ -1473,6 +1474,7 @@
my $Instance = MOBY::Client::ServiceInstance->new(
authority => $AuthURI,
authoritative => $authoritative,
+ URL => $URL,
name => $servicename,
type => $Type,
category => $cat,
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 15:53:14 1.6
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 16:02:52 1.7
@@ -132,7 +132,7 @@
=head2 authoritative
Title : authoritative
- Usage : $description = $Service->authoritative(1|0)
+ Usage : $auth = $Service->authoritative(1|0)
Args : (optional) boolean 1 or 0
Function : get/set authoritative flag
Returns : current value
@@ -140,6 +140,17 @@
=cut
+=head2 URL
+
+ Title : URL
+ Usage : $URL = $Service->URL($url)
+ Args : (optional) string representing a URL
+ Function : get/set service URL endpoint
+ Returns : current value
+
+=cut
+
+
=head2 registry
Title : registry
@@ -167,6 +178,7 @@
registry => ['MOBY_Central', 'read/write'],
XML => [undef, 'read/write'],
authoritative => [undef, 'read/write'],
+ URL => [undef, 'read/write'],
);
#_____________________________________________________________
From mwilkinson at pub.open-bio.org Sat Nov 1 11:03:04 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:00 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011603.hA1G34Sn005339@pub.open-bio.org>
mwilkinson
Sat Nov 1 11:03:04 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv5320/Client
Modified Files:
ServiceInstance.html
Log Message:
pass the URL back to a service instance object since it should be there, and now we need it for the LSID resolution service
moby-live/Perl/MOBY/Client ServiceInstance.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/11/01 15:53:14 1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/11/01 16:03:04 1.5
@@ -27,6 +27,7 @@
output
description
authoritative
+ URL
registry
@@ -152,12 +153,21 @@
Title : authoritative
- Usage : $description = $Service->authoritative(1|0)
+ Usage : $auth = $Service->authoritative(1|0)
Args : (optional) boolean 1 or 0
Function : get/set authoritative flag
Returns : current value
+
+
+ Title : URL
+ Usage : $URL = $Service->URL($url)
+ Args : (optional) string representing a URL
+ Function : get/set service URL endpoint
+ Returns : current value
+
+
Title : registry
From mwilkinson at pub.open-bio.org Sat Nov 1 11:42:14 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:12 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011642.hA1GgERt007577@pub.open-bio.org>
mwilkinson
Sat Nov 1 11:42:14 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv7526/Client
Modified Files:
Central.pm ServiceInstance.html ServiceInstance.pm
Log Message:
changed the output of the findService method to return XML elements for the service endpoint and the contact email address. This should be a backward-compatible change. Updated the client code accordingly. updated the ServiceInstance object to hold this new data. Updated documentation
moby-live/Perl/MOBY/Client Central.pm,1.59,1.60 ServiceInstance.html,1.5,1.6 ServiceInstance.pm,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.59
retrieving revision 1.60
diff -u -r1.59 -r1.60
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/11/01 16:02:52 1.59
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2003/11/01 16:42:14 1.60
@@ -1439,6 +1439,7 @@
my $servicename = $Service->getAttributeNode('serviceName')->getValue;
my $Type = &_nodeTextContent($Service, 'serviceType');
my $authoritative = &_nodeTextContent($Service, 'authoritative');
+ my $contactEmail = &_nodeTextContent($Service, 'contactEmail');
my $URL = &_nodeTextContent($Service, 'URL');
#my $Output = &_nodeTextContent($Service, 'outputObject');
my $Description = &_nodeTextContent($Service, 'Description');
@@ -1475,6 +1476,7 @@
authority => $AuthURI,
authoritative => $authoritative,
URL => $URL,
+ contactEmail => $contactEmail,
name => $servicename,
type => $Type,
category => $cat,
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/11/01 16:03:04 1.5
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/11/01 16:42:14 1.6
@@ -28,6 +28,7 @@
description
authoritative
URL
+ contactEmail
registry
@@ -168,6 +169,15 @@
Returns : current value
+
+
+ Title : contactEmail
+ Usage : $email = $Service->contactEmail($email)
+ Args : (optional) string representing an email address
+ Function : get/set service email address
+ Returns : current value
+
+
Title : registry
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 16:02:52 1.7
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 16:42:14 1.8
@@ -151,6 +151,17 @@
=cut
+=head2 contactEmail
+
+ Title : contactEmail
+ Usage : $email = $Service->contactEmail($email)
+ Args : (optional) string representing an email address
+ Function : get/set service email address
+ Returns : current value
+
+=cut
+
+
=head2 registry
Title : registry
@@ -179,6 +190,7 @@
XML => [undef, 'read/write'],
authoritative => [undef, 'read/write'],
URL => [undef, 'read/write'],
+ contactEmail => [undef, 'read/write'],
);
#_____________________________________________________________
From mwilkinson at pub.open-bio.org Sat Nov 1 12:48:56 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:19 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011748.hA1HmuoI011380@pub.open-bio.org>
mwilkinson
Sat Nov 1 12:48:56 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv11357/lsid/authority
Modified Files:
RDFConfigure.pm metadata.pl
Added Files:
ServiceInstanceResolver.pm
Log Message:
added a prototype service instance LSID resolver. I'm not sure that the RDF graph of this is correct, and it also ignores secondary parameters, so it isn't complete either. It uses the predicate vocabulary that we agreed upon at the I3C meeting in Hinxton, so we should be able to discover both myGrid and MOBY services with identical meta data vocabularies. This will also allow third parties to construct and publish workflows by referring to MOBY and/or myGrid services by their LSID's.
moby-live/Perl/lsid/authority ServiceInstanceResolver.pm,NONE,1.1 RDFConfigure.pm,1.4,1.5 metadata.pl,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 14:10:05 1.4
+++ /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 17:48:56 1.5
@@ -29,7 +29,8 @@
xmlns:rdfs='http://www.w3.org/2000/01/rdf-schema#'
xmlns:dc='http://purl.org/dc/elements/1.1/'
xmlns:i3cp='urn:lsid:i3c.org:predicates:'
-xmlns:mobyp='urn:lsid:biomoby.org:rdfpredicate:'>\n\n";
+xmlns:mobyp='urn:lsid:biomoby.org:rdfpredicate:'
+xmlns:i3csp='urn:lsid:i3c.org:services:'>\n\n";
our $RDF_SUFFIX= "";
@@ -47,6 +48,33 @@
";
}
+sub rdfBnode {
+ my ($subj, $pred, $id)= @_;
+ return "
+\t<$pred rdf:nodeID='$id'/>
+";
+}
+
+sub rdfBnodeResource {
+ my ($subj, $pred, $obj)= @_;
+ return "
+\t<$pred rdf:resource='$obj'/>
+";
+}
+
+sub rdfBnodeLiteral {
+ my ($subj, $pred, $obj)= @_;
+ return "
+\t<$pred>$obj$pred>
+";
+}
+
+sub rdfBnodeBnode {
+ my ($subj, $pred, $id)= @_;
+ return "
+\t<$pred rdf:nodeID='$id'/>
+";
+}
sub _die {
my $m = shift;
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 14:10:05 1.7
+++ /home/repository/moby/moby-live/Perl/lsid/authority/metadata.pl 2003/11/01 17:48:56 1.8
@@ -25,6 +25,7 @@
use ServiceResolver qw(:all);
use RelationshipResolver qw(:all);
use PredicateResolver qw(:all);
+use ServiceInstanceResolver qw(:all);
my %known_types = ( # switch on/off various LSID-namespace resolvers.
'namespacetype' => 1,
@@ -32,7 +33,7 @@
'servicetype' => 1,
'servicerelation' => 1,
'objectrelation' => 1,
- 'serviceinstance' => 0,
+ 'serviceinstance' => 1,
'rdfpredicate' => 1,
);
@@ -76,6 +77,7 @@
return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "objectrelation";
return resolve_relationshiptype($relationshipdb,$lsid) if $1 eq "servicerelation";
return resolve_mobyPredicate($lsid) if $1 eq "rdfpredicate";
+ return resolve_ServiceInstance($lsid) if $1 eq "serviceinstance";
}
From mwilkinson at pub.open-bio.org Sat Nov 1 13:04:44 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:25 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011804.hA1I4inL012219@pub.open-bio.org>
mwilkinson
Sat Nov 1 13:04:44 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12200/MOBY/Client
Modified Files:
ServiceInstance.pm
Log Message:
forgot to export the new RDF graph writing subs
moby-live/Perl/MOBY/Client ServiceInstance.pm,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 16:42:14 1.8
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2003/11/01 18:04:44 1.9
@@ -14,6 +14,9 @@
use MOBY::Client::ServiceInstance;
my $Instance = MOBY::Client::ServieInstance->new(
authority => 'bioinfo.pbi.nrc.ca',
+ authoritative => 0,
+ URL => http://bioinfo.pbi.nrc.ca/runMe.pl,
+ contactEmail => markw@illumin.com,
name => 'marksFabulousService',
type => 'Retrieve',
category => 'moby',
@@ -33,8 +36,7 @@
=head1 AUTHORS
-Mark Wilkinson (mwilkinson@gene.pbi.nrc.ca)
-Plant Biotechnology Institute, National Research Council of Canada.
+Mark Wilkinson (markw at illuminae dot com)
BioMOBY Project: http://www.biomoby.org
From mwilkinson at pub.open-bio.org Sat Nov 1 13:04:44 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:31 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011804.hA1I4iq2012238@pub.open-bio.org>
mwilkinson
Sat Nov 1 13:04:44 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv12200/lsid/authority
Modified Files:
RDFConfigure.pm
Log Message:
forgot to export the new RDF graph writing subs
moby-live/Perl/lsid/authority RDFConfigure.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 17:48:56 1.5
+++ /home/repository/moby/moby-live/Perl/lsid/authority/RDFConfigure.pm 2003/11/01 18:04:44 1.6
@@ -5,24 +5,6 @@
use base 'Exporter';
require Exporter;
-our @EXPORT_OK = qw(
- $SERVICE_CGI
- $RDF_PREFIX
- $RDF_SUFFIX
- rdfLiteral
- rdfResource
- _die
- );
-our %EXPORT_TAGS =(all => [qw(
- $SERVICE_CGI
- $RDF_PREFIX
- $RDF_SUFFIX
- rdfLiteral
- rdfResource
- _die
- )]);
-
-
our $SERVICE_CGI= 'http://localhost:80/cgi-bin/authority/metadata.pl';
our $RDF_PREFIX="
[qw(
+ $SERVICE_CGI
+ $RDF_PREFIX
+ $RDF_SUFFIX
+ rdfLiteral
+ rdfResource
+ rdfBnode
+ rdfBnodeResource
+ rdfBnodeLiteral
+ rdfBnodeBnode
+ _die
+ )]);
+
1;
From mwilkinson at pub.open-bio.org Sat Nov 1 13:05:55 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:34 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011805.hA1I5t0O012289@pub.open-bio.org>
mwilkinson
Sat Nov 1 13:05:55 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12269/MOBY/Client
Modified Files:
ServiceInstance.html
Log Message:
forgot to export the new RDF graph writing subs
moby-live/Perl/MOBY/Client ServiceInstance.html,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/11/01 16:42:14 1.6
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.html 2003/11/01 18:05:55 1.7
@@ -48,6 +48,9 @@
use MOBY::Client::ServiceInstance;
my $Instance = MOBY::Client::ServieInstance->new(
authority => 'bioinfo.pbi.nrc.ca',
+ authoritative => 0,
+ URL => http://bioinfo.pbi.nrc.ca/runMe.pl,
+ contactEmail => markw@illumin.com,
name => 'marksFabulousService',
type => 'Retrieve',
category => 'moby',
@@ -66,8 +69,7 @@
-Mark Wilkinson (mwilkinson@gene.pbi.nrc.ca)
-Plant Biotechnology Institute, National Research Council of Canada.
+Mark Wilkinson (markw at illuminae dot com)
BioMOBY Project: http://www.biomoby.org
From mwilkinson at pub.open-bio.org Sat Nov 1 13:25:03 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:39 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011825.hA1IP31r013429@pub.open-bio.org>
mwilkinson
Sat Nov 1 13:25:03 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv13410
Modified Files:
ServiceInstanceResolver.pm
Log Message:
primary inputs and outputs were referring to the same bnode because the counter was reset. I have re-numbered them to be unique now
moby-live/Perl/lsid/authority ServiceInstanceResolver.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm 2003/11/01 17:48:56 1.1
+++ /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm 2003/11/01 18:25:02 1.2
@@ -158,8 +158,8 @@
'i3csp:primaryOutput', # primaryInput bnode
'primaryOutput'
);
- my $out= 0;
- foreach (@outputs){
+ my $out= $in; # switch for readability
+ foreach (@outputs){
++$out;
$mdata .= rdfBnodeBnode(
'primaryOutput',
From mwilkinson at pub.open-bio.org Sat Nov 1 13:34:52 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:43 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011834.hA1IYqH1014010@pub.open-bio.org>
mwilkinson
Sat Nov 1 13:34:52 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv13991
Modified Files:
ServiceInstanceResolver.pm
Log Message:
primary inputs and outputs articlenames were given same predicate as the service name. bad bad bad. I'm leaving them in there even if they are blank for the moment so that Chris can see how my entire graph is structured. In the future I will not write them out if the value is null.
moby-live/Perl/lsid/authority ServiceInstanceResolver.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm 2003/11/01 18:25:02 1.2
+++ /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm 2003/11/01 18:34:52 1.3
@@ -122,7 +122,7 @@
);
$mdata .= rdfBnodeLiteral(
"primaryParameter$in",
- 'i3csp:name',
+ 'i3csp:parameterName',
$_->articleName
);
if ($_->isSimple){
@@ -168,7 +168,7 @@
);
$mdata .= rdfBnodeLiteral(
"primaryParameter$out",
- 'i3csp:name',
+ 'i3csp:parameterName',
$_->articleName
);
if ($_->isSimple){
From mwilkinson at pub.open-bio.org Sat Nov 1 13:38:22 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 10:39:47 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311011838.hA1IcMuK014093@pub.open-bio.org>
mwilkinson
Sat Nov 1 13:38:22 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv14073
Modified Files:
ServiceInstanceResolver.pm
Log Message:
input and output had different predicates for their simple articles. ick.
moby-live/Perl/lsid/authority ServiceInstanceResolver.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm 2003/11/01 18:34:52 1.3
+++ /home/repository/moby/moby-live/Perl/lsid/authority/ServiceInstanceResolver.pm 2003/11/01 18:38:22 1.4
@@ -175,7 +175,7 @@
$mdata .= rdfBnodeResource(
"primaryParameter$out",
'i3csp:parameterType',
- 'i3csp:simpleType'
+ 'i3csp:mobySimpleType'
);
$mdata .= rdfBnodeResource(
"primaryParameter$out",
@@ -186,7 +186,7 @@
$mdata .= rdfBnodeResource(
"primaryParameter$out",
'i3csp:parameterType',
- 'i3csp:collectionType'
+ 'i3csp:mobyCollectionType'
);
my $simps = $_->Simples;
foreach my $simp(@{$simps}){
From mwilkinson at pub.open-bio.org Mon Nov 3 17:37:34 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 17:30:27 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311032237.hA3MbYT2022781@pub.open-bio.org>
mwilkinson
Mon Nov 3 17:37:34 EST 2003
Update of /home/repository/moby/moby-live/Perl/docs
In directory pub.open-bio.org:/tmp/cvs-serv22765
Removed Files:
INSTALL-Service_Provider.txt
Log Message:
removing deprecated documentation
moby-live/Perl/docs INSTALL-Service_Provider.txt,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Perl/docs/RCS/INSTALL-Service_Provider.txt,v: No such file or directory
From mwilkinson at pub.open-bio.org Mon Nov 3 20:48:10 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon Nov 3 20:41:01 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311040148.hA41mAO5032635@pub.open-bio.org>
mwilkinson
Mon Nov 3 20:48:10 EST 2003
Update of /home/repository/moby/moby-live/Perl/lsid/authority
In directory pub.open-bio.org:/tmp/cvs-serv32616/lsid/authority
Modified Files:
authority.pl
Log Message:
this should make LSID resolution kick into life
moby-live/Perl/lsid/authority authority.pl,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/lsid/authority/authority.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/lsid/authority/authority.pl 2003/11/01 11:17:24 1.2
+++ /home/repository/moby/moby-live/Perl/lsid/authority/authority.pl 2003/11/04 01:48:10 1.3
@@ -34,7 +34,7 @@
type => 'metaDataPortType',
protocol => $LS::Authority::WSDL::HTTP,
method => 'GET',
- location => "localhost",
+ location => "mobycentral.cbr.nrc.ca",
operations => {
getMetaData => "/cgi-bin/authority/metadata.pl?lsid=$lsid"
}
From cherburtner at lauvabrum.hasmoved.com Tue Nov 4 10:59:34 2003
From: cherburtner at lauvabrum.hasmoved.com (Female Update)
Date: Tue Nov 4 11:58:39 2003
Subject: [MOBY-guts] L|ps SO Plump - your friends will be envious!
Message-ID:
An HTML attachment was scrubbed...
URL: http://portal.open-bio.org/pipermail/moby-guts/attachments/20031104/dcbd6e93/attachment.htm
From sixtadenby at prorsus.prospectivebuyers.com Tue Nov 11 06:11:32 2003
From: sixtadenby at prorsus.prospectivebuyers.com (Beauty Secret)
Date: Tue Nov 11 07:15:33 2003
Subject: [MOBY-guts] Get Plumper & Sexier L|ps
Message-ID:
An HTML attachment was scrubbed...
URL: http://portal.open-bio.org/pipermail/moby-guts/attachments/20031111/da65fcc0/attachment.htm
From senger at pub.open-bio.org Sat Nov 8 20:05:02 2003
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Wed Nov 12 15:13:55 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311090105.hA9152W9021554@pub.open-bio.org>
senger
Sat Nov 8 20:05:02 EST 2003
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv21510/docs
Modified Files:
ChangeLog
Log Message:
moby-live/Java/docs ChangeLog,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/docs/ChangeLog 2003/11/08 00:27:24 1.4
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2003/11/09 01:05:02 1.5
@@ -1,3 +1,7 @@
+2003-11-09 Martin Senger
+
+ * Added servlet properties for HTTP proxies and path to 'dot'.
+
2003-11-07 Martin Senger
* Added BioMoby Graphs (command-line client and a servlet-based
From senger at pub.open-bio.org Sat Nov 8 20:52:28 2003
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Wed Nov 12 15:14:11 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311090152.hA91qSQj021795@pub.open-bio.org>
senger
Sat Nov 8 20:52:28 EST 2003
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv21776/src/main/org/biomoby/client
Modified Files:
GraphsServlet.java
Log Message:
moby-live/Java/src/main/org/biomoby/client GraphsServlet.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2003/11/09 01:05:02 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/GraphsServlet.java 2003/11/09 01:52:28 1.3
@@ -667,9 +667,9 @@
// where is the 'dot' program
String dotProg = "dot";
- String dotPath = getString (req, DOT_PATH);
+ String dotPath = (String)initParams.get (DOT_PATH);
if (dotPath != null)
- dotProg = dotPath + System.getProperty ("file.sparator") + dotProg;
+ dotProg = dotPath + System.getProperty ("file.separator") + dotProg;
// depending on the cache implementation we may ask
// 'dot' to produce output to its standard output, or
@@ -742,9 +742,9 @@
// where is the 'dot' program
String dotProg = "dot";
- String dotPath = getString (req, DOT_PATH);
+ String dotPath = (String)initParams.get (DOT_PATH);
if (dotPath != null)
- dotProg = dotPath + System.getProperty ("file.sparator") + dotProg;
+ dotProg = dotPath + System.getProperty ("file.separator") + dotProg;
// depending on the cache implementation we may ask
// 'dot' to produce output to its standard output, or
From senger at pub.open-bio.org Fri Nov 7 19:27:24 2003
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Wed Nov 12 15:14:21 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311080027.hA80ROes017330@pub.open-bio.org>
senger
Fri Nov 7 19:27:24 EST 2003
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory pub.open-bio.org:/tmp/cvs-serv17161/src/Clients/help
Modified Files:
MobyGraphs_usage.txt
Log Message:
added graphs for exploring biomoby registry
moby-live/Java/src/Clients/help MobyGraphs_usage.txt,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2003/10/17 13:13:34 1.1
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2003/11/08 00:27:24 1.2
@@ -1,15 +1,27 @@
Usage:
java MobyGraphs -h[elp]
- java MobyGraphs []
+ java MobyGraphs
-q ... quiet mode
- -debug ... print debug messages
-d ... graph showing data types
-s ... graph showing services
-t ... reserved: for the graph of service types
- outputs:
+ output format:
+ -dot ... (this is default)
+ -rdf ... (this works only for graph of services)
+
+ output filter (what to be included,
+ only used for services):
+ -auth
+ -name
+ -depth ... an integer, how far to go from
+ given services (default is 1)
+ or
+ -path
+
+ output destinations:
-fd ... where to put the data types graph
(makes sense only together with -d)
-fs ... where to put the services graph
From mwilkinson at pub.open-bio.org Wed Nov 12 11:08:52 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Nov 12 15:14:29 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311121608.hACG8qhe011391@pub.open-bio.org>
mwilkinson
Wed Nov 12 11:08:52 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv11376
Added Files:
debug_a_service.pl
Log Message:
added a simple service debugging script
moby-live/Perl/scripts debug_a_service.pl,NONE,1.1
From mwilkinson at pub.open-bio.org Wed Nov 12 11:12:47 2003
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Nov 12 15:14:30 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311121612.hACGCl3K011506@pub.open-bio.org>
mwilkinson
Wed Nov 12 11:12:47 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts
In directory pub.open-bio.org:/tmp/cvs-serv11491
Added Files:
debugYourService
Log Message:
oops. Forgot to set the executable flag. Have to rename the file to get CVS to accept this kind of change
moby-live/Perl/scripts debugYourService,NONE,1.1
From senger at pub.open-bio.org Sat Nov 8 20:05:02 2003
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Wed Nov 12 16:13:52 2003
Subject: [MOBY-guts] biomoby commit
Message-ID: <200311090105.hA9152Df021535@pub.open-bio.org>
senger
Sat Nov 8 20:05:02 EST 2003
Update of /home/repository/moby/moby-live/Java
In directory pub.open-bio.org:/tmp/cvs-serv21510
Modified Files:
build.properties.template build.xml
Log Message:
moby-live/Java build.properties.template,1.1,1.2 build.xml,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.properties.template,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/build.properties.template 2003/11/08 00:27:23 1.1
+++ /home/repository/moby/moby-live/Java/build.properties.template 2003/11/09 01:05:02 1.2
@@ -7,6 +7,11 @@
build.compiler = jikes
+#dot.path = /path/to/dot
+#proxySet = true
+#http.proxyHost = your proxy host
+#http.proxyPort = your proxy port
+
# all other properties are used only if you wish to deploy jMoby
# servlets into your Tomcat - the more verbose description of these
# properties is in the deployment descriptor in
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/build.xml 2003/11/08 21:05:51 1.5
+++ /home/repository/moby/moby-live/Java/build.xml 2003/11/09 01:05:02 1.6
@@ -196,6 +196,18 @@
+
+
+
+
+
+
+
+
+
+
+
+
@@ -380,6 +392,10 @@
+
+
+
+
senger
Sat Nov 8 20:05:02 EST 2003
Update of /home/repository/moby/moby-live/Java/docs/graphs
In directory pub.open-bio.org:/tmp/cvs-serv21510/docs/graphs
Modified Files:
index.html
Log Message:
moby-live/Java/docs/graphs index.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/graphs/index.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/graphs/index.html 2003/11/08 00:27:24 1.1
+++ /home/repository/moby/moby-live/Java/docs/graphs/index.html 2003/11/09 01:05:02 1.2
@@ -27,7 +27,7 @@
The BioMoby Graphs are available: