From mwilkinson at pub.open-bio.org Tue Aug 10 11:57:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 10 11:36:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408101557.i7AFvma0017380@pub.open-bio.org> mwilkinson Tue Aug 10 11:57:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv17357/MOBY/Client Modified Files: OntologyServer.pm Service.pm Log Message: updated documentation and made the environment variables consistent for configuring proxy servers moby-live/Perl/MOBY/Client OntologyServer.pm,1.5,1.6 Service.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm 2004/05/13 17:57:34 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm 2004/08/10 15:57:48 1.6 @@ -39,8 +39,17 @@ what is returned will be an LSID, and skip the checking step yourself. + +=head1 PROXY SERVERS + +If your site uses a proxy server, simply set the environment variable +MOBY_PROXY=http://your.proxy.server/address + +=cut + =head1 AUTHORS + Mark Wilkinson (markw at illuminae.com) Nina Opushneva (opushneva at yahoo.ca) @@ -219,7 +228,7 @@ sub getUserAgent{ my ($self, @args) = @_; my $ua = LWP::UserAgent->new; - my $proxy = $ENV{PROXY} if $ENV{PROXY}; # first check the environment + my $proxy = $ENV{MOBY_PROXY} if $ENV{MOBY_PROXY}; # first check the environment $proxy = $self->proxy if $self->proxy; # but if the object was initialized with a proxy argument then use that instead if($proxy){ $ua->proxy('http', $proxy); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2004/05/19 14:58:36 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2004/08/10 15:57:48 1.12 @@ -31,7 +31,7 @@ Title : new Usage : $Service = MOBY::Client::Service->new(@args) Function : create a service connection - Returns : MOBY::Client::Service object + Returns : MOBY::Client::Service object, undef if no wsdl. Args : service : string ; required a WSDL file defining a MOBY service uri : string ; optional ; default NULL @@ -122,7 +122,7 @@ $self->{$attrname} = $self->_default_for($attrname) } } - my $dir = cwd; + #my $dir = cwd; # seems to be a bug in SOAP::Lite that the WSDL document # fails a parse if it is passed as a scalar rather than a file @@ -133,6 +133,7 @@ # ________________________________________ my $wsdl = URI::Escape::uri_escape($self->service); # this seems to fix the bug + return undef unless $wsdl; my $soap = SOAP::Lite->service("data:,$wsdl"); if ($self->uri){$soap->uri($self->uri)} From mwilkinson at pub.open-bio.org Wed Aug 11 12:27:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Aug 11 12:06:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111627.i7BGRmnm024237@pub.open-bio.org> mwilkinson Wed Aug 11 12:27:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv24218/MOBY/Client Modified Files: Central.pm Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/MOBY/Client Central.pm,1.78,1.79 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.78 retrieving revision 1.79 diff -u -r1.78 -r1.79 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/30 00:16:32 1.78 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/08/11 16:27:48 1.79 @@ -263,10 +263,10 @@ my %reg = %{$self->Registries}; while (my ($name, $acc) = each %reg){ $regno++; # count how many registries we have in total - my $url = $acc->{URL}; - my $uri = $acc->{URI}; - my $type = $acc->{TYPE}; - my $proxy = $acc->{PROXY}; + my $url = $acc->{URL}?$acc->{URL}:$self->default_MOBY_server; + my $uri = $acc->{URI}?$acc->{URI}:$self->default_MOBY_uri; + my $type = $acc->{TYPE}?$acc->{TYPE}:$self->default_MOBY_type; + my $proxy = $acc->{PROXY}?$acc->{PROXY}:$self->default_MOBY_proxy; $type ||='soap'; if (lc($type) eq "get"){ push @{$self->Connections}, [$name, $type, $url]; From mwilkinson at pub.open-bio.org Wed Aug 11 12:27:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Aug 11 12:06:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111627.i7BGRmN6024256@pub.open-bio.org> mwilkinson Wed Aug 11 12:27:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv24218/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.22,1.23 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 01:14:44 1.22 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:27:48 1.23 @@ -24,14 +24,18 @@ } } +my $URL = $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl'; +my $URI = $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'; my $C = MOBY::Client::Central->new( Registries => { - mobycentral => {URL => $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl', - URI => $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'} + mobycentral => {URL => $URL, + URI => $URI} } ); +print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\n"; + #register with two ISA's -> should fail TEST($C->registerObjectClass(objectType => "HypotheticalObject1", From mwilkinson at pub.open-bio.org Wed Aug 11 12:30:57 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Aug 11 12:09:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111630.i7BGUvbK024448@pub.open-bio.org> mwilkinson Wed Aug 11 12:30:57 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv24428/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.23,1.24 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.23 retrieving revision 1.24 diff -u -r1.23 -r1.24 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:27:48 1.23 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:30:57 1.24 @@ -26,6 +26,7 @@ } my $URL = $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl'; my $URI = $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'; +my $PROXY = $ENV{MOBY_PROXY}?$ENV{MOBY_PROXY}:'No Proxy Server'; my $C = MOBY::Client::Central->new( Registries => { @@ -34,7 +35,7 @@ } ); -print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\n"; +print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\tProxy: $PROXY\n\n"; #register with two ISA's -> should fail From mwilkinson at pub.open-bio.org Tue Aug 17 13:15:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 17 12:53:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171715.i7HHFbmd022873@pub.open-bio.org> mwilkinson Tue Aug 17 13:15:36 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv22854/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: added support for secondary parameters to the RDF generation routine moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 23:34:06 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 17:15:36 1.8 @@ -100,6 +100,8 @@ my $outputs = $service->output; + my $secondary = $service->secondary; + my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', @@ -114,6 +116,12 @@ articles => $outputs, ); + my $SecondaryArticles = MOBY::RDF::InOutArticlesRDF->new( + model => $model, + type => 'consumes', + subject => $subject, + articles => $secondary, + ); } From mwilkinson at pub.open-bio.org Tue Aug 17 13:22:45 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 17 13:00:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171722.i7HHMjfF022994@pub.open-bio.org> mwilkinson Tue Aug 17 13:22:45 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv22975/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: enum passes a listref not a list moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 16:11:40 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:22:45 1.8 @@ -192,7 +192,7 @@ _addClassLiteral($model, MP, $article, 'datatype', $ART->datatype) if $ART->datatype; _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; - my @enums = $ART->enum; + my @enums = @{$ART->enum}; foreach (@enums){ _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; } From mwilkinson at pub.open-bio.org Tue Aug 17 13:34:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 17 13:11:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171734.i7HHYIDA023104@pub.open-bio.org> mwilkinson Tue Aug 17 13:34:17 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv23085/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: somehow passing namesppsaces into the enum? moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:22:45 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:34:17 1.9 @@ -193,8 +193,8 @@ _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; my @enums = @{$ART->enum}; - foreach (@enums){ - _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; + foreach my $enum(@enums){ + _addClassLiteral($model, MP, $article, 'enum', $enum) if defined $enum; } } From mwilkinson at pub.open-bio.org Tue Aug 17 13:43:58 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 17 13:21:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171743.i7HHhwMc023216@pub.open-bio.org> mwilkinson Tue Aug 17 13:43:58 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv23197/MOBY/Client Modified Files: SecondaryArticle.pm Log Message: aha. My enum list was a class variable rather than an instance variable. Should be fixed now. moby-live/Perl/MOBY/Client SecondaryArticle.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/06/16 01:15:30 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:43:58 1.3 @@ -156,7 +156,7 @@ default => [undef, 'read/write' ], max => [undef, 'read/write' ], min => [undef, 'read/write' ], - enum => [[], 'read/write' ], + enum => [undef, 'read/write' ], value => [undef, 'read/write'], ); @@ -185,6 +185,7 @@ sub addEnum { my ($self, $enum) = @_; + $self->{enum} = [] unless $self->{enum}; return $self->{enum} unless defined($enum); push @{$self->{enum}}, $enum; return $self->{enum}; From mwilkinson at pub.open-bio.org Tue Aug 17 13:48:10 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 17 13:25:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171748.i7HHmAFr023288@pub.open-bio.org> mwilkinson Tue Aug 17 13:48:10 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv23269/MOBY/Client Modified Files: SecondaryArticle.pm Log Message: aha. My enum list was a class variable rather than an instance variable. Should be fixed now. moby-live/Perl/MOBY/Client SecondaryArticle.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:43:58 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:48:10 1.4 @@ -182,7 +182,6 @@ keys %_attr_data; } - sub addEnum { my ($self, $enum) = @_; $self->{enum} = [] unless $self->{enum}; @@ -211,7 +210,8 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - + $self->{enum} = [] unless $self->enum; + if ($self->XML && ref($self->XML)){ return 0; } elsif ($self->XML_DOM && !(ref($self->XML_DOM) =~ /dom/i)){ From mwilkinson at pub.open-bio.org Tue Aug 17 19:24:32 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 17 19:02:07 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408172324.i7HNOW1P024493@pub.open-bio.org> mwilkinson Tue Aug 17 19:24:32 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv24474/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: both primary and secondary inputs should be part of the same rdf:Bag moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 17:15:36 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 23:24:32 1.9 @@ -97,10 +97,10 @@ _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title my $inputs = $service->input; + push @$inputs, @{$service->secondary}; my $outputs = $service->output; - my $secondary = $service->secondary; my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, @@ -115,13 +115,6 @@ subject => $subject, articles => $outputs, ); - - my $SecondaryArticles = MOBY::RDF::InOutArticlesRDF->new( - model => $model, - type => 'consumes', - subject => $subject, - articles => $secondary, - ); } From mwilkinson at pub.open-bio.org Wed Aug 18 19:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Aug 18 18:43:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63KU029752@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv29714/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 23:24:32 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:06:03 1.10 @@ -96,24 +96,24 @@ _addClassLiteral($model, DC, $subject, 'identifier', $service->URL); # dublin core identifier (this is a stretch!) _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title - my $inputs = $service->input; - push @$inputs, @{$service->secondary}; + my @inputs = @{$service->input}; + push @inputs, @{$service->secondary}; - my $outputs = $service->output; + my @outputs = @{$service->output}; my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', subject => $subject, - articles => $inputs, + articles => \@inputs, ); my $OutputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'produces', subject => $subject, - articles => $outputs, + articles => \@outputs, ); } From mwilkinson at pub.open-bio.org Wed Aug 18 19:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Aug 18 18:43:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63GV029733@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv29714/MOBY/Client Modified Files: ServiceInstance.pm Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/MOBY/Client ServiceInstance.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/04/14 19:56:59 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/08/18 23:06:03 1.12 @@ -184,9 +184,9 @@ authority => [undef, 'read/write'], name => [undef, 'read/write'], type => [undef, 'read/write'], - input => [[], 'read/write'], # listref of Simple and Collection articles - output => [[], 'read/write'], # listref of Simple and Collection articles - secondary => [[], 'read/write'], # listref of SecondaryArticles + input => [undef, 'read/write'], # listref of Simple and Collection articles + output => [undef, 'read/write'], # listref of Simple and Collection articles + secondary => [undef, 'read/write'], # listref of SecondaryArticles category => [undef, 'read/write'], description => [undef, 'read/write'], registry => ['MOBY_Central', 'read/write'], @@ -228,7 +228,7 @@ my $proxy; my $self = bless {}, $class; - + foreach my $attrname ( $self->_standard_keys ) { if (exists $args{$attrname}) { $self->{$attrname} = $args{$attrname} } @@ -238,6 +238,10 @@ $self->{$attrname} = $self->_default_for($attrname) } } + $self->input([]) unless $self->input; + $self->output([]) unless $self->output; + $self->secondary([]) unless $self->secondary; + return $self; } From mwilkinson at pub.open-bio.org Wed Aug 18 19:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Aug 18 18:43:28 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63dR029772@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/t In directory pub.open-bio.org:/tmp/cvs-serv29714/t Modified Files: Client-Central.t Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/t Client-Central.t,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/t/Client-Central.t 2004/06/16 19:08:05 1.5 +++ /home/repository/moby/moby-live/Perl/t/Client-Central.t 2004/08/18 23:06:03 1.6 @@ -5,7 +5,7 @@ # change 'tests => 1' to 'tests => last_test_to_print'; -use Test::More tests => 12; # perldoc Test::More for details +use Test::More tests => 13; # perldoc Test::More for details # Test 1 BEGIN { use_ok('MOBY::Client::Central') }; @@ -37,24 +37,37 @@ HASA => [ ['Object', 'articleName3']]} ); +( ok(!$r->success,"Object registration correctly failed") + or diag("Object registration failure: ".$r->message)); + +# Test 4 +$r = $C->registerObjectClass(objectType => "TotalCrap", + description => "a human-readable description of the object", + contactEmail => 'your@email.address', + authURI => "test.suite.com", + Relationships => { + ISA => [ + ['Object', 'article1']], + HASA => [ + ['Object', 'articleName3']]} + ); ( ok($r->success,"Object registration successful") or diag("Object registration failure: ".$r->message)); -# Test 4 +# Test 5 $r = $C->deregisterObjectClass(objectType => "TotalCrap"); ( ok($r->success,"Object deregistration successful")) or diag("Object deregistration failure: ".$r->message) ; -# Test 5 (identical to #3 +# Test 6 (identical to #4 $r = $C->registerObjectClass(objectType => "TotalCrap", description => "a human-readable description of the object", contactEmail => 'your@email.address', authURI => "test.suite.com", Relationships => { ISA => [ - ['Object', 'article1'], - ['Object', 'articleName2']], + ['Object', 'article1']], HASA => [ ['Object', 'articleName3']]} ); From mwilkinson at pub.open-bio.org Wed Aug 18 19:40:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Aug 18 19:17:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182340.i7INe3U5029944@pub.open-bio.org> mwilkinson Wed Aug 18 19:40:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv29925/MOBY Modified Files: Central.pm Log Message: after noticing a service that had managed to become registered incorrectly, I think I have fixed an error that allowed registration of services that consumed collections of nothing. moby-live/Perl/MOBY Central.pm,1.138,1.139 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.138 retrieving revision 1.139 diff -u -r1.138 -r1.139 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 01:14:44 1.138 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/18 23:40:03 1.139 @@ -1219,6 +1219,7 @@ my $Simples = $node->getElementsByTagName('Simple'); my $length = $Simples->getLength; + unless ($length > 0){return (-1, "Your collection must be a collection of one or more Simple types");} for (my $x=0; $x<$length; ++$x){ my ($success, $message) = &_registerArticles($SVC, $inout, $Simples->item($x),$collection_id); unless ($success == 1){return (-1, $message);} From mwilkinson at pub.open-bio.org Wed Aug 18 19:40:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed Aug 18 19:17:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182340.i7INe3uX029963@pub.open-bio.org> mwilkinson Wed Aug 18 19:40:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv29925/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: after noticing a service that had managed to become registered incorrectly, I think I have fixed an error that allowed registration of services that consumed collections of nothing. moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:06:03 1.10 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:40:03 1.11 @@ -2,6 +2,7 @@ use strict; use MOBY::RDF::InOutArticlesRDF; use RDF::Core::Statement; +use RDF::Core::Model::Serializer; require Exporter; our @ISA = qw(Exporter); From mwilkinson at pub.open-bio.org Thu Aug 19 18:30:52 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Aug 19 18:08:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408192230.i7JMUqJh001192@pub.open-bio.org> mwilkinson Thu Aug 19 18:30:52 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv1173/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: it was getting too painful to parse the RDF (and determine correct vs incorrectc formatting) without any predicates indicating the type of input article, so I added three new predicates: Simple, Collection, Secondary moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:34:17 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/19 22:30:52 1.10 @@ -120,13 +120,29 @@ my @articles = $self->articles; my $Bag = $self->{Bag}; - my $li = 0; +# my $li = 0; foreach my $IN(@articles){ - ++$li; - my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc my $input = &nextsimple; - my $statement = new RDF::Core::Statement($Thingy, $LI, $input); - $model->addStmt($statement); + if ($IN->isSimple){ + my $LI = $Thingy->new(MP, "SimpleArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } elsif ($IN->isCollection){ + my $LI = $Thingy->new(MP, "CollectionArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } elsif ($IN->isSecondary){ + my $LI = $Thingy->new(MP, "SecondaryArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } else { + print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; + return; + } +# ++$li; + #my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc + #my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + #$model->addStmt($statement); # # @@ -153,8 +169,6 @@ } } elsif ($IN->isSecondary) { &_addSecondary($model, $input, $IN); - } else { - print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; } } } From mwilkinson at pub.open-bio.org Mon Aug 23 17:29:58 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon Aug 23 17:06:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408232129.i7NLTwkD022944@pub.open-bio.org> mwilkinson Mon Aug 23 17:29:58 EDT 2004 Update of /home/repository/moby/moby-live/Agents In directory pub.open-bio.org:/tmp/cvs-serv22926/Agents Log Message: Directory /home/repository/moby/moby-live/Agents added to the repository moby-live/Agents - New directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Mon Aug 23 17:30:17 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon Aug 23 17:07:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408232130.i7NLUHPE022993@pub.open-bio.org> mwilkinson Mon Aug 23 17:30:17 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S In directory pub.open-bio.org:/tmp/cvs-serv22975/MOBY-S Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S added to the repository moby-live/Agents/MOBY-S - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Tue Aug 24 16:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 24 16:20:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhXY6027837@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY/Client Modified Files: Registration.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY/Client Registration.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/07/29 21:53:54 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/08/24 20:43:33 1.6 @@ -62,6 +62,10 @@ get/set the value +=head2 RDF + +get/set the value + =cut From mwilkinson at pub.open-bio.org Tue Aug 24 16:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 24 16:20:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhX5V027856@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:40:03 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/24 20:43:33 1.12 @@ -5,9 +5,6 @@ use RDF::Core::Model::Serializer; require Exporter; -our @ISA = qw(Exporter); -our @EXPORT_OK = qw(); - use RDF::Core::Constants qw(:xml :rdf :rdfs); use constant OBJ => 'http://biomoby.org/RESOURCES/MOBY-S/Objects#'; use constant SRV => 'http://biomoby.org/RESOURCES/MOBY-S/Services#'; @@ -16,6 +13,11 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +our @ISA = qw(Exporter); +our @EXPORT = qw(OBJ SRV NS MP SI DC xmlNamespaces serialize); +our @EXPORT_OK = qw(OBJ SRV NS MP SI DC xmlNamespaces serialize); + + sub xmlNamespaces { return { RDF_NS() => 'rdf', From mwilkinson at pub.open-bio.org Tue Aug 24 16:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Aug 24 16:20:28 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhX2i027818@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY Modified Files: Config.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY Config.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/07/09 00:21:53 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/08/24 20:43:33 1.5 @@ -74,11 +74,11 @@ } my $file = $ENV{MOBY_CENTRAL_CONFIG}; - (-e $file) || die "can't open MOBY Configuration file $!\n"; + (-e $file) || die "MOBY Configuration file $file doesn't exist $!\n"; chomp $file; if ((-e $file) && (!(-d $file))){ - open IN, $file || die "can't open MOBY Configuration file $!\n"; + open IN, $file || die "can't open MOBY Configuration file $file for unknown reasons$!\n"; } my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", ; #print STDERR "split into @sections\n"; From nopushneva at pub.open-bio.org Tue Aug 24 16:46:09 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue Aug 24 16:35:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242046.i7OKk9e5027898@pub.open-bio.org> nopushneva Tue Aug 24 16:46:09 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv27873/RDFAgent Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent added to the repository moby-live/Agents/MOBY-S/RDFAgent - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 17:28:43 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue Aug 24 17:05:29 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242128.i7OLSh0Y028019@pub.open-bio.org> nopushneva Tue Aug 24 17:28:43 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf In directory pub.open-bio.org:/tmp/cvs-serv27994/conf Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf added to the repository moby-live/Agents/MOBY-S/RDFAgent/conf - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 17:42:49 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue Aug 24 17:19:32 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242142.i7OLgnCi028080@pub.open-bio.org> nopushneva Tue Aug 24 17:42:48 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv28055/lib Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib added to the repository moby-live/Agents/MOBY-S/RDFAgent/lib - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 17:45:02 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue Aug 24 17:21:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242145.i7OLj2wp028142@pub.open-bio.org> nopushneva Tue Aug 24 17:45:02 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv28118 Added Files: servicevalidation.mysql Log Message: agent for browsing service signature RDF moby-live/Agents/MOBY-S/RDFAgent servicevalidation.mysql,NONE,1.1 From nopushneva at pub.open-bio.org Tue Aug 24 17:45:02 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue Aug 24 17:21:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242145.i7OLj2Mr028160@pub.open-bio.org> nopushneva Tue Aug 24 17:45:02 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv28118/lib Added Files: activation.jar antlr.jar commons-logging.jar concurrent.jar icu4j.jar jakarta-oro-2.0.5.jar jdom.jar jena.jar junit.jar log4j-1.2.7.jar mail.jar rdf-api-2001-01-19.jar xercesImpl.jar xml-apis.jar Log Message: agent for browsing service signature RDF moby-live/Agents/MOBY-S/RDFAgent/lib activation.jar,NONE,1.1 antlr.jar,NONE,1.1 commons-logging.jar,NONE,1.1 concurrent.jar,NONE,1.1 icu4j.jar,NONE,1.1 jakarta-oro-2.0.5.jar,NONE,1.1 jdom.jar,NONE,1.1 jena.jar,NONE,1.1 junit.jar,NONE,1.1 log4j-1.2.7.jar,NONE,1.1 mail.jar,NONE,1.1 rdf-api-2001-01-19.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 xml-apis.jar,NONE,1.1 From ambrose at pub.open-bio.org Thu Aug 26 16:09:22 2004 From: ambrose at pub.open-bio.org (Ambrose Ng) Date: Thu Aug 26 15:45:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408262009.i7QK9MvF004469@pub.open-bio.org> ambrose Thu Aug 26 16:09:22 EDT 2004 Update of //home/repository/moby/moby-live/Perl/Accessories In directory pub.open-bio.org:/tmp/cvs-serv4445 Added Files: frame.cgi namespaceframe.cgi searchframe.cgi Removed Files: NamespaceMaintenance.cgi SearchDatabase.cgi Log Message: Ambrose Ng moby-live/Perl/Accessories frame.cgi,NONE,1.1 namespaceframe.cgi,NONE,1.1 searchframe.cgi,NONE,1.1 NamespaceMaintenance.cgi,1.3,NONE SearchDatabase.cgi,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/Accessories/RCS/NamespaceMaintenance.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/Accessories/RCS/SearchDatabase.cgi,v: No such file or directory From mwilkinson at pub.open-bio.org Thu Aug 26 16:52:28 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Aug 26 16:29:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408262052.i7QKqSk6004646@pub.open-bio.org> mwilkinson Thu Aug 26 16:52:28 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv4627/MOBY Modified Files: Central.pm Log Message: interpret empty XML nodes in the findService message as undef, rather than spaces moby-live/Perl/MOBY Central.pm,1.139,1.140 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.139 retrieving revision 1.140 diff -u -r1.139 -r1.140 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/18 23:40:03 1.139 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/26 20:52:28 1.140 @@ -1597,7 +1597,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if ($findme{serviceType}){ + if ($findme{serviceType}){ # must have something more than empty content my $OS = MOBY::OntologyServer->new(ontology => 'service'); $findme{serviceType} =~ s/^moby\://; my ($exists, $message, $URI) = $OS->serviceExists(term =>$findme{serviceType}); @@ -1899,12 +1899,19 @@ return undef unless ($obj eq 'findService'); my $serviceType = &_nodeTextContent($Object, "serviceType"); + $serviceType && ($serviceType =~ s/\s+//g); my $servicename = &_nodeTextContent($Object, "serviceName"); + $servicename && ($servicename =~ s/\s+//g); my $authoritative = &_nodeTextContent($Object, "authoritative"); + $authoritative && ($authoritative =~ s/\s+//g); my $Category = &_nodeTextContent($Object, "Category"); + $Category && ($Category =~ s/\s+//g); my $AuthURI = &_nodeTextContent($Object, "authURI"); + $AuthURI && ($AuthURI =~ s/\s+//g); my $expandObjects = &_nodeTextContent($Object, "expandObjects"); + $expandObjects && ($expandObjects =~ s/\s+//g); my $expandServices = &_nodeTextContent($Object, "expandServices"); + $expandServices && ($expandServices =~ s/\s+//g); my @kw = &_nodeArrayContent($Object, "keywords"); my $INPUTS = &_nodeRawContent($Object, "Input"); # returns array ref my $OUTPUTS = &_nodeRawContent($Object, "Output"); # returns array ref @@ -2919,13 +2926,14 @@ $sth_simple_in->execute($_); while (my ($objURI, $nsURI, $article) = $sth_simple_in->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\n"; $output .="\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t$NSname\n"; + $output .="\t\t\t$NSname\n" if $NSname; } $output .="\t\t\n"; } @@ -2935,13 +2943,14 @@ $sth_collection_in->execute($collid); while (my ($objURI, $nsURI, $article) = $sth_collection_in->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\t\n"; $output .="\t\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t\t$NSname\n"; + $output .="\t\t\t\t$NSname\n" if $NSname; } $output .="\t\t\t\n"; } @@ -2954,13 +2963,14 @@ $sth_simple_out->execute($_); while (my ($objURI, $nsURI, $article) = $sth_simple_out->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\n"; $output .="\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t$NSname\n"; + $output .="\t\t\t$NSname\n" if $NSname; } $output .="\t\t\n"; } @@ -2970,12 +2980,14 @@ $sth_collection_out->execute($collid); while (my ($objURI, $nsURI, $article) = $sth_collection_out->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); - my @nsURIs = split ",", $nsURI; + $nsURI ||=""; + my @nsURIs = split ",", $nsURI; + $article ||=""; $output .="\t\t\t\n"; $output .="\t\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t\t$NSname\n"; + $output .="\t\t\t\t$NSname\n" if $NSname; } $output .="\t\t\t\n"; } @@ -2986,6 +2998,11 @@ $output .="\t\n"; $sth_secondary_in->execute($_); while (my ($default_value, $maximum_value, $minimum_value, $enum_value, $datatype, $article_name) = $sth_secondary_in->fetchrow_array()){ + $article_name ||=""; + $datatype ||=""; + $default_value ||=""; + $maximum_value ||=""; + $minimum_value ||=""; $output .= "\t\t\t\n"; $output .= "\t\t\t\t$datatype\n"; $output .="\t\t\t\t$default_value\n"; From nopushneva at pub.open-bio.org Fri Aug 27 16:05:29 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Fri Aug 27 15:41:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408272005.i7RK5TA4008730@pub.open-bio.org> nopushneva Fri Aug 27 16:05:29 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv8708 Added Files: RDFAgent.jar Log Message: add the procedure for deletion a set of the services moby-live/Agents/MOBY-S/RDFAgent RDFAgent.jar,NONE,1.1 From nopushneva at pub.open-bio.org Fri Aug 27 16:10:00 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Fri Aug 27 15:46:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200408272010.i7RKA0AE008772@pub.open-bio.org> nopushneva Fri Aug 27 16:10:00 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv8741 Modified Files: servicevalidation.mysql Log Message: change of the structure moby-live/Agents/MOBY-S/RDFAgent servicevalidation.mysql,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql 2004/08/24 21:45:02 1.1 +++ /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql 2004/08/27 20:10:00 1.2 @@ -1,6 +1,6 @@ CREATE TABLE service_validation ( - servicename varchar(255) NOT NULL default '', + signatureURL varchar(255) NOT NULL default '', error_code int(4) NOT NULL, counter int (1) NOT NULL default '0', - PRIMARY KEY (servicename) + PRIMARY KEY (signatureURL) ) TYPE=MyISAM; From mwilkinson at pub.open-bio.org Tue Aug 10 11:57:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 10 Aug 2004 11:57:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408101557.i7AFvma0017380@pub.open-bio.org> mwilkinson Tue Aug 10 11:57:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv17357/MOBY/Client Modified Files: OntologyServer.pm Service.pm Log Message: updated documentation and made the environment variables consistent for configuring proxy servers moby-live/Perl/MOBY/Client OntologyServer.pm,1.5,1.6 Service.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm 2004/05/13 17:57:34 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm 2004/08/10 15:57:48 1.6 @@ -39,8 +39,17 @@ what is returned will be an LSID, and skip the checking step yourself. + +=head1 PROXY SERVERS + +If your site uses a proxy server, simply set the environment variable +MOBY_PROXY=http://your.proxy.server/address + +=cut + =head1 AUTHORS + Mark Wilkinson (markw at illuminae.com) Nina Opushneva (opushneva at yahoo.ca) @@ -219,7 +228,7 @@ sub getUserAgent{ my ($self, @args) = @_; my $ua = LWP::UserAgent->new; - my $proxy = $ENV{PROXY} if $ENV{PROXY}; # first check the environment + my $proxy = $ENV{MOBY_PROXY} if $ENV{MOBY_PROXY}; # first check the environment $proxy = $self->proxy if $self->proxy; # but if the object was initialized with a proxy argument then use that instead if($proxy){ $ua->proxy('http', $proxy); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2004/05/19 14:58:36 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2004/08/10 15:57:48 1.12 @@ -31,7 +31,7 @@ Title : new Usage : $Service = MOBY::Client::Service->new(@args) Function : create a service connection - Returns : MOBY::Client::Service object + Returns : MOBY::Client::Service object, undef if no wsdl. Args : service : string ; required a WSDL file defining a MOBY service uri : string ; optional ; default NULL @@ -122,7 +122,7 @@ $self->{$attrname} = $self->_default_for($attrname) } } - my $dir = cwd; + #my $dir = cwd; # seems to be a bug in SOAP::Lite that the WSDL document # fails a parse if it is passed as a scalar rather than a file @@ -133,6 +133,7 @@ # ________________________________________ my $wsdl = URI::Escape::uri_escape($self->service); # this seems to fix the bug + return undef unless $wsdl; my $soap = SOAP::Lite->service("data:,$wsdl"); if ($self->uri){$soap->uri($self->uri)} From mwilkinson at pub.open-bio.org Wed Aug 11 12:27:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 11 Aug 2004 12:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111627.i7BGRmnm024237@pub.open-bio.org> mwilkinson Wed Aug 11 12:27:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv24218/MOBY/Client Modified Files: Central.pm Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/MOBY/Client Central.pm,1.78,1.79 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.78 retrieving revision 1.79 diff -u -r1.78 -r1.79 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/30 00:16:32 1.78 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/08/11 16:27:48 1.79 @@ -263,10 +263,10 @@ my %reg = %{$self->Registries}; while (my ($name, $acc) = each %reg){ $regno++; # count how many registries we have in total - my $url = $acc->{URL}; - my $uri = $acc->{URI}; - my $type = $acc->{TYPE}; - my $proxy = $acc->{PROXY}; + my $url = $acc->{URL}?$acc->{URL}:$self->default_MOBY_server; + my $uri = $acc->{URI}?$acc->{URI}:$self->default_MOBY_uri; + my $type = $acc->{TYPE}?$acc->{TYPE}:$self->default_MOBY_type; + my $proxy = $acc->{PROXY}?$acc->{PROXY}:$self->default_MOBY_proxy; $type ||='soap'; if (lc($type) eq "get"){ push @{$self->Connections}, [$name, $type, $url]; From mwilkinson at pub.open-bio.org Wed Aug 11 12:27:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 11 Aug 2004 12:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111627.i7BGRmN6024256@pub.open-bio.org> mwilkinson Wed Aug 11 12:27:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv24218/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.22,1.23 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 01:14:44 1.22 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:27:48 1.23 @@ -24,14 +24,18 @@ } } +my $URL = $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl'; +my $URI = $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'; my $C = MOBY::Client::Central->new( Registries => { - mobycentral => {URL => $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl', - URI => $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'} + mobycentral => {URL => $URL, + URI => $URI} } ); +print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\n"; + #register with two ISA's -> should fail TEST($C->registerObjectClass(objectType => "HypotheticalObject1", From mwilkinson at pub.open-bio.org Wed Aug 11 12:30:57 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 11 Aug 2004 12:30:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111630.i7BGUvbK024448@pub.open-bio.org> mwilkinson Wed Aug 11 12:30:57 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv24428/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.23,1.24 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.23 retrieving revision 1.24 diff -u -r1.23 -r1.24 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:27:48 1.23 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:30:57 1.24 @@ -26,6 +26,7 @@ } my $URL = $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl'; my $URI = $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'; +my $PROXY = $ENV{MOBY_PROXY}?$ENV{MOBY_PROXY}:'No Proxy Server'; my $C = MOBY::Client::Central->new( Registries => { @@ -34,7 +35,7 @@ } ); -print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\n"; +print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\tProxy: $PROXY\n\n"; #register with two ISA's -> should fail From mwilkinson at pub.open-bio.org Tue Aug 17 13:15:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:15:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171715.i7HHFbmd022873@pub.open-bio.org> mwilkinson Tue Aug 17 13:15:36 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv22854/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: added support for secondary parameters to the RDF generation routine moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 23:34:06 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 17:15:36 1.8 @@ -100,6 +100,8 @@ my $outputs = $service->output; + my $secondary = $service->secondary; + my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', @@ -114,6 +116,12 @@ articles => $outputs, ); + my $SecondaryArticles = MOBY::RDF::InOutArticlesRDF->new( + model => $model, + type => 'consumes', + subject => $subject, + articles => $secondary, + ); } From mwilkinson at pub.open-bio.org Tue Aug 17 13:22:45 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:22:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171722.i7HHMjfF022994@pub.open-bio.org> mwilkinson Tue Aug 17 13:22:45 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv22975/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: enum passes a listref not a list moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 16:11:40 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:22:45 1.8 @@ -192,7 +192,7 @@ _addClassLiteral($model, MP, $article, 'datatype', $ART->datatype) if $ART->datatype; _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; - my @enums = $ART->enum; + my @enums = @{$ART->enum}; foreach (@enums){ _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; } From mwilkinson at pub.open-bio.org Tue Aug 17 13:34:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:34:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171734.i7HHYIDA023104@pub.open-bio.org> mwilkinson Tue Aug 17 13:34:17 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv23085/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: somehow passing namesppsaces into the enum? moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:22:45 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:34:17 1.9 @@ -193,8 +193,8 @@ _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; my @enums = @{$ART->enum}; - foreach (@enums){ - _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; + foreach my $enum(@enums){ + _addClassLiteral($model, MP, $article, 'enum', $enum) if defined $enum; } } From mwilkinson at pub.open-bio.org Tue Aug 17 13:43:58 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:43:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171743.i7HHhwMc023216@pub.open-bio.org> mwilkinson Tue Aug 17 13:43:58 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv23197/MOBY/Client Modified Files: SecondaryArticle.pm Log Message: aha. My enum list was a class variable rather than an instance variable. Should be fixed now. moby-live/Perl/MOBY/Client SecondaryArticle.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/06/16 01:15:30 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:43:58 1.3 @@ -156,7 +156,7 @@ default => [undef, 'read/write' ], max => [undef, 'read/write' ], min => [undef, 'read/write' ], - enum => [[], 'read/write' ], + enum => [undef, 'read/write' ], value => [undef, 'read/write'], ); @@ -185,6 +185,7 @@ sub addEnum { my ($self, $enum) = @_; + $self->{enum} = [] unless $self->{enum}; return $self->{enum} unless defined($enum); push @{$self->{enum}}, $enum; return $self->{enum}; From mwilkinson at pub.open-bio.org Tue Aug 17 13:48:10 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:48:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171748.i7HHmAFr023288@pub.open-bio.org> mwilkinson Tue Aug 17 13:48:10 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv23269/MOBY/Client Modified Files: SecondaryArticle.pm Log Message: aha. My enum list was a class variable rather than an instance variable. Should be fixed now. moby-live/Perl/MOBY/Client SecondaryArticle.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:43:58 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:48:10 1.4 @@ -182,7 +182,6 @@ keys %_attr_data; } - sub addEnum { my ($self, $enum) = @_; $self->{enum} = [] unless $self->{enum}; @@ -211,7 +210,8 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - + $self->{enum} = [] unless $self->enum; + if ($self->XML && ref($self->XML)){ return 0; } elsif ($self->XML_DOM && !(ref($self->XML_DOM) =~ /dom/i)){ From mwilkinson at pub.open-bio.org Tue Aug 17 19:24:32 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 19:24:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408172324.i7HNOW1P024493@pub.open-bio.org> mwilkinson Tue Aug 17 19:24:32 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv24474/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: both primary and secondary inputs should be part of the same rdf:Bag moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 17:15:36 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 23:24:32 1.9 @@ -97,10 +97,10 @@ _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title my $inputs = $service->input; + push @$inputs, @{$service->secondary}; my $outputs = $service->output; - my $secondary = $service->secondary; my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, @@ -115,13 +115,6 @@ subject => $subject, articles => $outputs, ); - - my $SecondaryArticles = MOBY::RDF::InOutArticlesRDF->new( - model => $model, - type => 'consumes', - subject => $subject, - articles => $secondary, - ); } From mwilkinson at pub.open-bio.org Wed Aug 18 19:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:06:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63KU029752@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv29714/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 23:24:32 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:06:03 1.10 @@ -96,24 +96,24 @@ _addClassLiteral($model, DC, $subject, 'identifier', $service->URL); # dublin core identifier (this is a stretch!) _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title - my $inputs = $service->input; - push @$inputs, @{$service->secondary}; + my @inputs = @{$service->input}; + push @inputs, @{$service->secondary}; - my $outputs = $service->output; + my @outputs = @{$service->output}; my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', subject => $subject, - articles => $inputs, + articles => \@inputs, ); my $OutputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'produces', subject => $subject, - articles => $outputs, + articles => \@outputs, ); } From mwilkinson at pub.open-bio.org Wed Aug 18 19:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:06:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63GV029733@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv29714/MOBY/Client Modified Files: ServiceInstance.pm Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/MOBY/Client ServiceInstance.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/04/14 19:56:59 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/08/18 23:06:03 1.12 @@ -184,9 +184,9 @@ authority => [undef, 'read/write'], name => [undef, 'read/write'], type => [undef, 'read/write'], - input => [[], 'read/write'], # listref of Simple and Collection articles - output => [[], 'read/write'], # listref of Simple and Collection articles - secondary => [[], 'read/write'], # listref of SecondaryArticles + input => [undef, 'read/write'], # listref of Simple and Collection articles + output => [undef, 'read/write'], # listref of Simple and Collection articles + secondary => [undef, 'read/write'], # listref of SecondaryArticles category => [undef, 'read/write'], description => [undef, 'read/write'], registry => ['MOBY_Central', 'read/write'], @@ -228,7 +228,7 @@ my $proxy; my $self = bless {}, $class; - + foreach my $attrname ( $self->_standard_keys ) { if (exists $args{$attrname}) { $self->{$attrname} = $args{$attrname} } @@ -238,6 +238,10 @@ $self->{$attrname} = $self->_default_for($attrname) } } + $self->input([]) unless $self->input; + $self->output([]) unless $self->output; + $self->secondary([]) unless $self->secondary; + return $self; } From mwilkinson at pub.open-bio.org Wed Aug 18 19:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:06:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63dR029772@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/t In directory pub.open-bio.org:/tmp/cvs-serv29714/t Modified Files: Client-Central.t Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/t Client-Central.t,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/t/Client-Central.t 2004/06/16 19:08:05 1.5 +++ /home/repository/moby/moby-live/Perl/t/Client-Central.t 2004/08/18 23:06:03 1.6 @@ -5,7 +5,7 @@ # change 'tests => 1' to 'tests => last_test_to_print'; -use Test::More tests => 12; # perldoc Test::More for details +use Test::More tests => 13; # perldoc Test::More for details # Test 1 BEGIN { use_ok('MOBY::Client::Central') }; @@ -37,24 +37,37 @@ HASA => [ ['Object', 'articleName3']]} ); +( ok(!$r->success,"Object registration correctly failed") + or diag("Object registration failure: ".$r->message)); + +# Test 4 +$r = $C->registerObjectClass(objectType => "TotalCrap", + description => "a human-readable description of the object", + contactEmail => 'your at email.address', + authURI => "test.suite.com", + Relationships => { + ISA => [ + ['Object', 'article1']], + HASA => [ + ['Object', 'articleName3']]} + ); ( ok($r->success,"Object registration successful") or diag("Object registration failure: ".$r->message)); -# Test 4 +# Test 5 $r = $C->deregisterObjectClass(objectType => "TotalCrap"); ( ok($r->success,"Object deregistration successful")) or diag("Object deregistration failure: ".$r->message) ; -# Test 5 (identical to #3 +# Test 6 (identical to #4 $r = $C->registerObjectClass(objectType => "TotalCrap", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "test.suite.com", Relationships => { ISA => [ - ['Object', 'article1'], - ['Object', 'articleName2']], + ['Object', 'article1']], HASA => [ ['Object', 'articleName3']]} ); From mwilkinson at pub.open-bio.org Wed Aug 18 19:40:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:40:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182340.i7INe3U5029944@pub.open-bio.org> mwilkinson Wed Aug 18 19:40:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv29925/MOBY Modified Files: Central.pm Log Message: after noticing a service that had managed to become registered incorrectly, I think I have fixed an error that allowed registration of services that consumed collections of nothing. moby-live/Perl/MOBY Central.pm,1.138,1.139 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.138 retrieving revision 1.139 diff -u -r1.138 -r1.139 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 01:14:44 1.138 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/18 23:40:03 1.139 @@ -1219,6 +1219,7 @@ my $Simples = $node->getElementsByTagName('Simple'); my $length = $Simples->getLength; + unless ($length > 0){return (-1, "Your collection must be a collection of one or more Simple types");} for (my $x=0; $x<$length; ++$x){ my ($success, $message) = &_registerArticles($SVC, $inout, $Simples->item($x),$collection_id); unless ($success == 1){return (-1, $message);} From mwilkinson at pub.open-bio.org Wed Aug 18 19:40:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:40:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182340.i7INe3uX029963@pub.open-bio.org> mwilkinson Wed Aug 18 19:40:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv29925/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: after noticing a service that had managed to become registered incorrectly, I think I have fixed an error that allowed registration of services that consumed collections of nothing. moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:06:03 1.10 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:40:03 1.11 @@ -2,6 +2,7 @@ use strict; use MOBY::RDF::InOutArticlesRDF; use RDF::Core::Statement; +use RDF::Core::Model::Serializer; require Exporter; our @ISA = qw(Exporter); From mwilkinson at pub.open-bio.org Thu Aug 19 18:30:52 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 19 Aug 2004 18:30:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408192230.i7JMUqJh001192@pub.open-bio.org> mwilkinson Thu Aug 19 18:30:52 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv1173/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: it was getting too painful to parse the RDF (and determine correct vs incorrectc formatting) without any predicates indicating the type of input article, so I added three new predicates: Simple, Collection, Secondary moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:34:17 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/19 22:30:52 1.10 @@ -120,13 +120,29 @@ my @articles = $self->articles; my $Bag = $self->{Bag}; - my $li = 0; +# my $li = 0; foreach my $IN(@articles){ - ++$li; - my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc my $input = &nextsimple; - my $statement = new RDF::Core::Statement($Thingy, $LI, $input); - $model->addStmt($statement); + if ($IN->isSimple){ + my $LI = $Thingy->new(MP, "SimpleArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } elsif ($IN->isCollection){ + my $LI = $Thingy->new(MP, "CollectionArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } elsif ($IN->isSecondary){ + my $LI = $Thingy->new(MP, "SecondaryArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } else { + print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; + return; + } +# ++$li; + #my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc + #my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + #$model->addStmt($statement); # # @@ -153,8 +169,6 @@ } } elsif ($IN->isSecondary) { &_addSecondary($model, $input, $IN); - } else { - print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; } } } From mwilkinson at pub.open-bio.org Mon Aug 23 17:29:58 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 23 Aug 2004 17:29:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408232129.i7NLTwkD022944@pub.open-bio.org> mwilkinson Mon Aug 23 17:29:58 EDT 2004 Update of /home/repository/moby/moby-live/Agents In directory pub.open-bio.org:/tmp/cvs-serv22926/Agents Log Message: Directory /home/repository/moby/moby-live/Agents added to the repository moby-live/Agents - New directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Mon Aug 23 17:30:17 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 23 Aug 2004 17:30:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408232130.i7NLUHPE022993@pub.open-bio.org> mwilkinson Mon Aug 23 17:30:17 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S In directory pub.open-bio.org:/tmp/cvs-serv22975/MOBY-S Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S added to the repository moby-live/Agents/MOBY-S - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Tue Aug 24 16:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 24 Aug 2004 16:43:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhXY6027837@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY/Client Modified Files: Registration.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY/Client Registration.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/07/29 21:53:54 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/08/24 20:43:33 1.6 @@ -62,6 +62,10 @@ get/set the value +=head2 RDF + +get/set the value + =cut From mwilkinson at pub.open-bio.org Tue Aug 24 16:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 24 Aug 2004 16:43:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhX5V027856@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:40:03 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/24 20:43:33 1.12 @@ -5,9 +5,6 @@ use RDF::Core::Model::Serializer; require Exporter; -our @ISA = qw(Exporter); -our @EXPORT_OK = qw(); - use RDF::Core::Constants qw(:xml :rdf :rdfs); use constant OBJ => 'http://biomoby.org/RESOURCES/MOBY-S/Objects#'; use constant SRV => 'http://biomoby.org/RESOURCES/MOBY-S/Services#'; @@ -16,6 +13,11 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +our @ISA = qw(Exporter); +our @EXPORT = qw(OBJ SRV NS MP SI DC xmlNamespaces serialize); +our @EXPORT_OK = qw(OBJ SRV NS MP SI DC xmlNamespaces serialize); + + sub xmlNamespaces { return { RDF_NS() => 'rdf', From mwilkinson at pub.open-bio.org Tue Aug 24 16:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 24 Aug 2004 16:43:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhX2i027818@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY Modified Files: Config.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY Config.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/07/09 00:21:53 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/08/24 20:43:33 1.5 @@ -74,11 +74,11 @@ } my $file = $ENV{MOBY_CENTRAL_CONFIG}; - (-e $file) || die "can't open MOBY Configuration file $!\n"; + (-e $file) || die "MOBY Configuration file $file doesn't exist $!\n"; chomp $file; if ((-e $file) && (!(-d $file))){ - open IN, $file || die "can't open MOBY Configuration file $!\n"; + open IN, $file || die "can't open MOBY Configuration file $file for unknown reasons$!\n"; } my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", ; #print STDERR "split into @sections\n"; From nopushneva at pub.open-bio.org Tue Aug 24 16:46:09 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 16:46:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242046.i7OKk9e5027898@pub.open-bio.org> nopushneva Tue Aug 24 16:46:09 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv27873/RDFAgent Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent added to the repository moby-live/Agents/MOBY-S/RDFAgent - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 17:28:43 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 17:28:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242128.i7OLSh0Y028019@pub.open-bio.org> nopushneva Tue Aug 24 17:28:43 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf In directory pub.open-bio.org:/tmp/cvs-serv27994/conf Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf added to the repository moby-live/Agents/MOBY-S/RDFAgent/conf - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 17:42:49 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 17:42:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242142.i7OLgnCi028080@pub.open-bio.org> nopushneva Tue Aug 24 17:42:48 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv28055/lib Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib added to the repository moby-live/Agents/MOBY-S/RDFAgent/lib - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 17:45:02 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 17:45:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242145.i7OLj2wp028142@pub.open-bio.org> nopushneva Tue Aug 24 17:45:02 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv28118 Added Files: servicevalidation.mysql Log Message: agent for browsing service signature RDF moby-live/Agents/MOBY-S/RDFAgent servicevalidation.mysql,NONE,1.1 From nopushneva at pub.open-bio.org Tue Aug 24 17:45:02 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 17:45:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242145.i7OLj2Mr028160@pub.open-bio.org> nopushneva Tue Aug 24 17:45:02 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv28118/lib Added Files: activation.jar antlr.jar commons-logging.jar concurrent.jar icu4j.jar jakarta-oro-2.0.5.jar jdom.jar jena.jar junit.jar log4j-1.2.7.jar mail.jar rdf-api-2001-01-19.jar xercesImpl.jar xml-apis.jar Log Message: agent for browsing service signature RDF moby-live/Agents/MOBY-S/RDFAgent/lib activation.jar,NONE,1.1 antlr.jar,NONE,1.1 commons-logging.jar,NONE,1.1 concurrent.jar,NONE,1.1 icu4j.jar,NONE,1.1 jakarta-oro-2.0.5.jar,NONE,1.1 jdom.jar,NONE,1.1 jena.jar,NONE,1.1 junit.jar,NONE,1.1 log4j-1.2.7.jar,NONE,1.1 mail.jar,NONE,1.1 rdf-api-2001-01-19.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 xml-apis.jar,NONE,1.1 From ambrose at pub.open-bio.org Thu Aug 26 16:09:22 2004 From: ambrose at pub.open-bio.org (Ambrose Ng) Date: Thu, 26 Aug 2004 16:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408262009.i7QK9MvF004469@pub.open-bio.org> ambrose Thu Aug 26 16:09:22 EDT 2004 Update of //home/repository/moby/moby-live/Perl/Accessories In directory pub.open-bio.org:/tmp/cvs-serv4445 Added Files: frame.cgi namespaceframe.cgi searchframe.cgi Removed Files: NamespaceMaintenance.cgi SearchDatabase.cgi Log Message: Ambrose Ng moby-live/Perl/Accessories frame.cgi,NONE,1.1 namespaceframe.cgi,NONE,1.1 searchframe.cgi,NONE,1.1 NamespaceMaintenance.cgi,1.3,NONE SearchDatabase.cgi,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/Accessories/RCS/NamespaceMaintenance.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/Accessories/RCS/SearchDatabase.cgi,v: No such file or directory From mwilkinson at pub.open-bio.org Thu Aug 26 16:52:28 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 26 Aug 2004 16:52:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408262052.i7QKqSk6004646@pub.open-bio.org> mwilkinson Thu Aug 26 16:52:28 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv4627/MOBY Modified Files: Central.pm Log Message: interpret empty XML nodes in the findService message as undef, rather than spaces moby-live/Perl/MOBY Central.pm,1.139,1.140 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.139 retrieving revision 1.140 diff -u -r1.139 -r1.140 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/18 23:40:03 1.139 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/26 20:52:28 1.140 @@ -1597,7 +1597,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if ($findme{serviceType}){ + if ($findme{serviceType}){ # must have something more than empty content my $OS = MOBY::OntologyServer->new(ontology => 'service'); $findme{serviceType} =~ s/^moby\://; my ($exists, $message, $URI) = $OS->serviceExists(term =>$findme{serviceType}); @@ -1899,12 +1899,19 @@ return undef unless ($obj eq 'findService'); my $serviceType = &_nodeTextContent($Object, "serviceType"); + $serviceType && ($serviceType =~ s/\s+//g); my $servicename = &_nodeTextContent($Object, "serviceName"); + $servicename && ($servicename =~ s/\s+//g); my $authoritative = &_nodeTextContent($Object, "authoritative"); + $authoritative && ($authoritative =~ s/\s+//g); my $Category = &_nodeTextContent($Object, "Category"); + $Category && ($Category =~ s/\s+//g); my $AuthURI = &_nodeTextContent($Object, "authURI"); + $AuthURI && ($AuthURI =~ s/\s+//g); my $expandObjects = &_nodeTextContent($Object, "expandObjects"); + $expandObjects && ($expandObjects =~ s/\s+//g); my $expandServices = &_nodeTextContent($Object, "expandServices"); + $expandServices && ($expandServices =~ s/\s+//g); my @kw = &_nodeArrayContent($Object, "keywords"); my $INPUTS = &_nodeRawContent($Object, "Input"); # returns array ref my $OUTPUTS = &_nodeRawContent($Object, "Output"); # returns array ref @@ -2919,13 +2926,14 @@ $sth_simple_in->execute($_); while (my ($objURI, $nsURI, $article) = $sth_simple_in->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\n"; $output .="\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t$NSname\n"; + $output .="\t\t\t$NSname\n" if $NSname; } $output .="\t\t\n"; } @@ -2935,13 +2943,14 @@ $sth_collection_in->execute($collid); while (my ($objURI, $nsURI, $article) = $sth_collection_in->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\t\n"; $output .="\t\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t\t$NSname\n"; + $output .="\t\t\t\t$NSname\n" if $NSname; } $output .="\t\t\t\n"; } @@ -2954,13 +2963,14 @@ $sth_simple_out->execute($_); while (my ($objURI, $nsURI, $article) = $sth_simple_out->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\n"; $output .="\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t$NSname\n"; + $output .="\t\t\t$NSname\n" if $NSname; } $output .="\t\t\n"; } @@ -2970,12 +2980,14 @@ $sth_collection_out->execute($collid); while (my ($objURI, $nsURI, $article) = $sth_collection_out->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); - my @nsURIs = split ",", $nsURI; + $nsURI ||=""; + my @nsURIs = split ",", $nsURI; + $article ||=""; $output .="\t\t\t\n"; $output .="\t\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t\t$NSname\n"; + $output .="\t\t\t\t$NSname\n" if $NSname; } $output .="\t\t\t\n"; } @@ -2986,6 +2998,11 @@ $output .="\t\n"; $sth_secondary_in->execute($_); while (my ($default_value, $maximum_value, $minimum_value, $enum_value, $datatype, $article_name) = $sth_secondary_in->fetchrow_array()){ + $article_name ||=""; + $datatype ||=""; + $default_value ||=""; + $maximum_value ||=""; + $minimum_value ||=""; $output .= "\t\t\t\n"; $output .= "\t\t\t\t$datatype\n"; $output .="\t\t\t\t$default_value\n"; From nopushneva at pub.open-bio.org Fri Aug 27 16:05:29 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Fri, 27 Aug 2004 16:05:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408272005.i7RK5TA4008730@pub.open-bio.org> nopushneva Fri Aug 27 16:05:29 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv8708 Added Files: RDFAgent.jar Log Message: add the procedure for deletion a set of the services moby-live/Agents/MOBY-S/RDFAgent RDFAgent.jar,NONE,1.1 From nopushneva at pub.open-bio.org Fri Aug 27 16:10:00 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Fri, 27 Aug 2004 16:10:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408272010.i7RKA0AE008772@pub.open-bio.org> nopushneva Fri Aug 27 16:10:00 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv8741 Modified Files: servicevalidation.mysql Log Message: change of the structure moby-live/Agents/MOBY-S/RDFAgent servicevalidation.mysql,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql 2004/08/24 21:45:02 1.1 +++ /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql 2004/08/27 20:10:00 1.2 @@ -1,6 +1,6 @@ CREATE TABLE service_validation ( - servicename varchar(255) NOT NULL default '', + signatureURL varchar(255) NOT NULL default '', error_code int(4) NOT NULL, counter int (1) NOT NULL default '0', - PRIMARY KEY (servicename) + PRIMARY KEY (signatureURL) ) TYPE=MyISAM; From mwilkinson at pub.open-bio.org Tue Aug 10 15:57:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 10 Aug 2004 11:57:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408101557.i7AFvma0017380@pub.open-bio.org> mwilkinson Tue Aug 10 11:57:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv17357/MOBY/Client Modified Files: OntologyServer.pm Service.pm Log Message: updated documentation and made the environment variables consistent for configuring proxy servers moby-live/Perl/MOBY/Client OntologyServer.pm,1.5,1.6 Service.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm 2004/05/13 17:57:34 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm 2004/08/10 15:57:48 1.6 @@ -39,8 +39,17 @@ what is returned will be an LSID, and skip the checking step yourself. + +=head1 PROXY SERVERS + +If your site uses a proxy server, simply set the environment variable +MOBY_PROXY=http://your.proxy.server/address + +=cut + =head1 AUTHORS + Mark Wilkinson (markw at illuminae.com) Nina Opushneva (opushneva at yahoo.ca) @@ -219,7 +228,7 @@ sub getUserAgent{ my ($self, @args) = @_; my $ua = LWP::UserAgent->new; - my $proxy = $ENV{PROXY} if $ENV{PROXY}; # first check the environment + my $proxy = $ENV{MOBY_PROXY} if $ENV{MOBY_PROXY}; # first check the environment $proxy = $self->proxy if $self->proxy; # but if the object was initialized with a proxy argument then use that instead if($proxy){ $ua->proxy('http', $proxy); =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2004/05/19 14:58:36 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm 2004/08/10 15:57:48 1.12 @@ -31,7 +31,7 @@ Title : new Usage : $Service = MOBY::Client::Service->new(@args) Function : create a service connection - Returns : MOBY::Client::Service object + Returns : MOBY::Client::Service object, undef if no wsdl. Args : service : string ; required a WSDL file defining a MOBY service uri : string ; optional ; default NULL @@ -122,7 +122,7 @@ $self->{$attrname} = $self->_default_for($attrname) } } - my $dir = cwd; + #my $dir = cwd; # seems to be a bug in SOAP::Lite that the WSDL document # fails a parse if it is passed as a scalar rather than a file @@ -133,6 +133,7 @@ # ________________________________________ my $wsdl = URI::Escape::uri_escape($self->service); # this seems to fix the bug + return undef unless $wsdl; my $soap = SOAP::Lite->service("data:,$wsdl"); if ($self->uri){$soap->uri($self->uri)} From mwilkinson at pub.open-bio.org Wed Aug 11 16:27:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 11 Aug 2004 12:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111627.i7BGRmnm024237@pub.open-bio.org> mwilkinson Wed Aug 11 12:27:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv24218/MOBY/Client Modified Files: Central.pm Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/MOBY/Client Central.pm,1.78,1.79 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.78 retrieving revision 1.79 diff -u -r1.78 -r1.79 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/07/30 00:16:32 1.78 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/08/11 16:27:48 1.79 @@ -263,10 +263,10 @@ my %reg = %{$self->Registries}; while (my ($name, $acc) = each %reg){ $regno++; # count how many registries we have in total - my $url = $acc->{URL}; - my $uri = $acc->{URI}; - my $type = $acc->{TYPE}; - my $proxy = $acc->{PROXY}; + my $url = $acc->{URL}?$acc->{URL}:$self->default_MOBY_server; + my $uri = $acc->{URI}?$acc->{URI}:$self->default_MOBY_uri; + my $type = $acc->{TYPE}?$acc->{TYPE}:$self->default_MOBY_type; + my $proxy = $acc->{PROXY}?$acc->{PROXY}:$self->default_MOBY_proxy; $type ||='soap'; if (lc($type) eq "get"){ push @{$self->Connections}, [$name, $type, $url]; From mwilkinson at pub.open-bio.org Wed Aug 11 16:27:48 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 11 Aug 2004 12:27:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111627.i7BGRmN6024256@pub.open-bio.org> mwilkinson Wed Aug 11 12:27:48 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv24218/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.22,1.23 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/07/30 01:14:44 1.22 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:27:48 1.23 @@ -24,14 +24,18 @@ } } +my $URL = $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl'; +my $URI = $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'; my $C = MOBY::Client::Central->new( Registries => { - mobycentral => {URL => $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl', - URI => $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'} + mobycentral => {URL => $URL, + URI => $URI} } ); +print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\n"; + #register with two ISA's -> should fail TEST($C->registerObjectClass(objectType => "HypotheticalObject1", From mwilkinson at pub.open-bio.org Wed Aug 11 16:30:57 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 11 Aug 2004 12:30:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408111630.i7BGUvbK024448@pub.open-bio.org> mwilkinson Wed Aug 11 12:30:57 EDT 2004 Update of /home/repository/moby/moby-live/Perl/scripts In directory pub.open-bio.org:/tmp/cvs-serv24428/scripts Modified Files: testMOBYClientCentral_v05.pl Log Message: still wasn't handling proxy servers properly. Try this version. moby-live/Perl/scripts testMOBYClientCentral_v05.pl,1.23,1.24 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl,v retrieving revision 1.23 retrieving revision 1.24 diff -u -r1.23 -r1.24 --- /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:27:48 1.23 +++ /home/repository/moby/moby-live/Perl/scripts/testMOBYClientCentral_v05.pl 2004/08/11 16:30:57 1.24 @@ -26,6 +26,7 @@ } my $URL = $ENV{MOBY_SERVER}?$ENV{MOBY_SERVER}:'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl'; my $URI = $ENV{MOBY_URI}?$ENV{MOBY_URI}:'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central'; +my $PROXY = $ENV{MOBY_PROXY}?$ENV{MOBY_PROXY}:'No Proxy Server'; my $C = MOBY::Client::Central->new( Registries => { @@ -34,7 +35,7 @@ } ); -print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\n"; +print "TESTING MOBY CLIENT with\n\tURL: $URL\n\tURI: $URI\n\tProxy: $PROXY\n\n"; #register with two ISA's -> should fail From mwilkinson at pub.open-bio.org Tue Aug 17 17:15:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:15:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171715.i7HHFbmd022873@pub.open-bio.org> mwilkinson Tue Aug 17 13:15:36 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv22854/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: added support for secondary parameters to the RDF generation routine moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/07/29 23:34:06 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 17:15:36 1.8 @@ -100,6 +100,8 @@ my $outputs = $service->output; + my $secondary = $service->secondary; + my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', @@ -114,6 +116,12 @@ articles => $outputs, ); + my $SecondaryArticles = MOBY::RDF::InOutArticlesRDF->new( + model => $model, + type => 'consumes', + subject => $subject, + articles => $secondary, + ); } From mwilkinson at pub.open-bio.org Tue Aug 17 17:22:45 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:22:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171722.i7HHMjfF022994@pub.open-bio.org> mwilkinson Tue Aug 17 13:22:45 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv22975/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: enum passes a listref not a list moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/07/29 16:11:40 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:22:45 1.8 @@ -192,7 +192,7 @@ _addClassLiteral($model, MP, $article, 'datatype', $ART->datatype) if $ART->datatype; _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; - my @enums = $ART->enum; + my @enums = @{$ART->enum}; foreach (@enums){ _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; } From mwilkinson at pub.open-bio.org Tue Aug 17 17:34:18 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:34:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171734.i7HHYIDA023104@pub.open-bio.org> mwilkinson Tue Aug 17 13:34:17 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv23085/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: somehow passing namesppsaces into the enum? moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:22:45 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:34:17 1.9 @@ -193,8 +193,8 @@ _addClassLiteral($model, MP, $article, 'max', $ART->max) if $ART->max; _addClassLiteral($model, MP, $article, 'min', $ART->min) if $ART->min; my @enums = @{$ART->enum}; - foreach (@enums){ - _addClassLiteral($model, MP, $article, 'enum', $_) if defined $_; + foreach my $enum(@enums){ + _addClassLiteral($model, MP, $article, 'enum', $enum) if defined $enum; } } From mwilkinson at pub.open-bio.org Tue Aug 17 17:43:58 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:43:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171743.i7HHhwMc023216@pub.open-bio.org> mwilkinson Tue Aug 17 13:43:58 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv23197/MOBY/Client Modified Files: SecondaryArticle.pm Log Message: aha. My enum list was a class variable rather than an instance variable. Should be fixed now. moby-live/Perl/MOBY/Client SecondaryArticle.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/06/16 01:15:30 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:43:58 1.3 @@ -156,7 +156,7 @@ default => [undef, 'read/write' ], max => [undef, 'read/write' ], min => [undef, 'read/write' ], - enum => [[], 'read/write' ], + enum => [undef, 'read/write' ], value => [undef, 'read/write'], ); @@ -185,6 +185,7 @@ sub addEnum { my ($self, $enum) = @_; + $self->{enum} = [] unless $self->{enum}; return $self->{enum} unless defined($enum); push @{$self->{enum}}, $enum; return $self->{enum}; From mwilkinson at pub.open-bio.org Tue Aug 17 17:48:10 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 13:48:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408171748.i7HHmAFr023288@pub.open-bio.org> mwilkinson Tue Aug 17 13:48:10 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv23269/MOBY/Client Modified Files: SecondaryArticle.pm Log Message: aha. My enum list was a class variable rather than an instance variable. Should be fixed now. moby-live/Perl/MOBY/Client SecondaryArticle.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:43:58 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/SecondaryArticle.pm 2004/08/17 17:48:10 1.4 @@ -182,7 +182,6 @@ keys %_attr_data; } - sub addEnum { my ($self, $enum) = @_; $self->{enum} = [] unless $self->{enum}; @@ -211,7 +210,8 @@ else { $self->{$attrname} = $self->_default_for($attrname) } } - + $self->{enum} = [] unless $self->enum; + if ($self->XML && ref($self->XML)){ return 0; } elsif ($self->XML_DOM && !(ref($self->XML_DOM) =~ /dom/i)){ From mwilkinson at pub.open-bio.org Tue Aug 17 23:24:32 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 17 Aug 2004 19:24:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408172324.i7HNOW1P024493@pub.open-bio.org> mwilkinson Tue Aug 17 19:24:32 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv24474/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: both primary and secondary inputs should be part of the same rdf:Bag moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 17:15:36 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 23:24:32 1.9 @@ -97,10 +97,10 @@ _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title my $inputs = $service->input; + push @$inputs, @{$service->secondary}; my $outputs = $service->output; - my $secondary = $service->secondary; my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, @@ -115,13 +115,6 @@ subject => $subject, articles => $outputs, ); - - my $SecondaryArticles = MOBY::RDF::InOutArticlesRDF->new( - model => $model, - type => 'consumes', - subject => $subject, - articles => $secondary, - ); } From mwilkinson at pub.open-bio.org Wed Aug 18 23:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:06:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63KU029752@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv29714/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/17 23:24:32 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:06:03 1.10 @@ -96,24 +96,24 @@ _addClassLiteral($model, DC, $subject, 'identifier', $service->URL); # dublin core identifier (this is a stretch!) _addResource($model, MP, 'performs_task', $subject, SRV, $service->type); # dublin core title - my $inputs = $service->input; - push @$inputs, @{$service->secondary}; + my @inputs = @{$service->input}; + push @inputs, @{$service->secondary}; - my $outputs = $service->output; + my @outputs = @{$service->output}; my $InputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'consumes', subject => $subject, - articles => $inputs, + articles => \@inputs, ); my $OutputArticles = MOBY::RDF::InOutArticlesRDF->new( model => $model, type => 'produces', subject => $subject, - articles => $outputs, + articles => \@outputs, ); } From mwilkinson at pub.open-bio.org Wed Aug 18 23:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:06:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63GV029733@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv29714/MOBY/Client Modified Files: ServiceInstance.pm Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/MOBY/Client ServiceInstance.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/04/14 19:56:59 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/ServiceInstance.pm 2004/08/18 23:06:03 1.12 @@ -184,9 +184,9 @@ authority => [undef, 'read/write'], name => [undef, 'read/write'], type => [undef, 'read/write'], - input => [[], 'read/write'], # listref of Simple and Collection articles - output => [[], 'read/write'], # listref of Simple and Collection articles - secondary => [[], 'read/write'], # listref of SecondaryArticles + input => [undef, 'read/write'], # listref of Simple and Collection articles + output => [undef, 'read/write'], # listref of Simple and Collection articles + secondary => [undef, 'read/write'], # listref of SecondaryArticles category => [undef, 'read/write'], description => [undef, 'read/write'], registry => ['MOBY_Central', 'read/write'], @@ -228,7 +228,7 @@ my $proxy; my $self = bless {}, $class; - + foreach my $attrname ( $self->_standard_keys ) { if (exists $args{$attrname}) { $self->{$attrname} = $args{$attrname} } @@ -238,6 +238,10 @@ $self->{$attrname} = $self->_default_for($attrname) } } + $self->input([]) unless $self->input; + $self->output([]) unless $self->output; + $self->secondary([]) unless $self->secondary; + return $self; } From mwilkinson at pub.open-bio.org Wed Aug 18 23:06:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:06:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182306.i7IN63dR029772@pub.open-bio.org> mwilkinson Wed Aug 18 19:06:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/t In directory pub.open-bio.org:/tmp/cvs-serv29714/t Modified Files: Client-Central.t Log Message: RDF is still not quite right. Seems to sometimes generate an extra empty input. This might fix it. Also updated test suite so that all tests pass with new tighter rules on ontology registrations moby-live/Perl/t Client-Central.t,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/t/Client-Central.t,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/t/Client-Central.t 2004/06/16 19:08:05 1.5 +++ /home/repository/moby/moby-live/Perl/t/Client-Central.t 2004/08/18 23:06:03 1.6 @@ -5,7 +5,7 @@ # change 'tests => 1' to 'tests => last_test_to_print'; -use Test::More tests => 12; # perldoc Test::More for details +use Test::More tests => 13; # perldoc Test::More for details # Test 1 BEGIN { use_ok('MOBY::Client::Central') }; @@ -37,24 +37,37 @@ HASA => [ ['Object', 'articleName3']]} ); +( ok(!$r->success,"Object registration correctly failed") + or diag("Object registration failure: ".$r->message)); + +# Test 4 +$r = $C->registerObjectClass(objectType => "TotalCrap", + description => "a human-readable description of the object", + contactEmail => 'your at email.address', + authURI => "test.suite.com", + Relationships => { + ISA => [ + ['Object', 'article1']], + HASA => [ + ['Object', 'articleName3']]} + ); ( ok($r->success,"Object registration successful") or diag("Object registration failure: ".$r->message)); -# Test 4 +# Test 5 $r = $C->deregisterObjectClass(objectType => "TotalCrap"); ( ok($r->success,"Object deregistration successful")) or diag("Object deregistration failure: ".$r->message) ; -# Test 5 (identical to #3 +# Test 6 (identical to #4 $r = $C->registerObjectClass(objectType => "TotalCrap", description => "a human-readable description of the object", contactEmail => 'your at email.address', authURI => "test.suite.com", Relationships => { ISA => [ - ['Object', 'article1'], - ['Object', 'articleName2']], + ['Object', 'article1']], HASA => [ ['Object', 'articleName3']]} ); From mwilkinson at pub.open-bio.org Wed Aug 18 23:40:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:40:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182340.i7INe3U5029944@pub.open-bio.org> mwilkinson Wed Aug 18 19:40:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv29925/MOBY Modified Files: Central.pm Log Message: after noticing a service that had managed to become registered incorrectly, I think I have fixed an error that allowed registration of services that consumed collections of nothing. moby-live/Perl/MOBY Central.pm,1.138,1.139 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.138 retrieving revision 1.139 diff -u -r1.138 -r1.139 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/07/30 01:14:44 1.138 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/18 23:40:03 1.139 @@ -1219,6 +1219,7 @@ my $Simples = $node->getElementsByTagName('Simple'); my $length = $Simples->getLength; + unless ($length > 0){return (-1, "Your collection must be a collection of one or more Simple types");} for (my $x=0; $x<$length; ++$x){ my ($success, $message) = &_registerArticles($SVC, $inout, $Simples->item($x),$collection_id); unless ($success == 1){return (-1, $message);} From mwilkinson at pub.open-bio.org Wed Aug 18 23:40:03 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Wed, 18 Aug 2004 19:40:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408182340.i7INe3uX029963@pub.open-bio.org> mwilkinson Wed Aug 18 19:40:03 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv29925/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: after noticing a service that had managed to become registered incorrectly, I think I have fixed an error that allowed registration of services that consumed collections of nothing. moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:06:03 1.10 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:40:03 1.11 @@ -2,6 +2,7 @@ use strict; use MOBY::RDF::InOutArticlesRDF; use RDF::Core::Statement; +use RDF::Core::Model::Serializer; require Exporter; our @ISA = qw(Exporter); From mwilkinson at pub.open-bio.org Thu Aug 19 22:30:52 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 19 Aug 2004 18:30:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408192230.i7JMUqJh001192@pub.open-bio.org> mwilkinson Thu Aug 19 18:30:52 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv1173/MOBY/RDF Modified Files: InOutArticlesRDF.pm Log Message: it was getting too painful to parse the RDF (and determine correct vs incorrectc formatting) without any predicates indicating the type of input article, so I added three new predicates: Simple, Collection, Secondary moby-live/Perl/MOBY/RDF InOutArticlesRDF.pm,1.9,1.10 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/17 17:34:17 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/InOutArticlesRDF.pm 2004/08/19 22:30:52 1.10 @@ -120,13 +120,29 @@ my @articles = $self->articles; my $Bag = $self->{Bag}; - my $li = 0; +# my $li = 0; foreach my $IN(@articles){ - ++$li; - my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc my $input = &nextsimple; - my $statement = new RDF::Core::Statement($Thingy, $LI, $input); - $model->addStmt($statement); + if ($IN->isSimple){ + my $LI = $Thingy->new(MP, "SimpleArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } elsif ($IN->isCollection){ + my $LI = $Thingy->new(MP, "CollectionArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } elsif ($IN->isSecondary){ + my $LI = $Thingy->new(MP, "SecondaryArticle"); # nodes - need to be numbered :_1, :_2, etc + my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + $model->addStmt($statement); + } else { + print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; + return; + } +# ++$li; + #my $LI = $Thingy->new(RDF_NS, "_$li"); # nodes - need to be numbered :_1, :_2, etc + #my $statement = new RDF::Core::Statement($Thingy, $LI, $input); + #$model->addStmt($statement); # # @@ -153,8 +169,6 @@ } } elsif ($IN->isSecondary) { &_addSecondary($model, $input, $IN); - } else { - print STDERR "the InOutArticlesRDF got a service instance input or output that was not a simple, collection, nor secondary???\n"; } } } From mwilkinson at pub.open-bio.org Mon Aug 23 21:29:58 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 23 Aug 2004 17:29:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408232129.i7NLTwkD022944@pub.open-bio.org> mwilkinson Mon Aug 23 17:29:58 EDT 2004 Update of /home/repository/moby/moby-live/Agents In directory pub.open-bio.org:/tmp/cvs-serv22926/Agents Log Message: Directory /home/repository/moby/moby-live/Agents added to the repository moby-live/Agents - New directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Mon Aug 23 21:30:17 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Mon, 23 Aug 2004 17:30:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408232130.i7NLUHPE022993@pub.open-bio.org> mwilkinson Mon Aug 23 17:30:17 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S In directory pub.open-bio.org:/tmp/cvs-serv22975/MOBY-S Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S added to the repository moby-live/Agents/MOBY-S - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RCS/directory,v: No such file or directory From mwilkinson at pub.open-bio.org Tue Aug 24 20:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 24 Aug 2004 16:43:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhXY6027837@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY/Client Modified Files: Registration.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY/Client Registration.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/07/29 21:53:54 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Registration.pm 2004/08/24 20:43:33 1.6 @@ -62,6 +62,10 @@ get/set the value +=head2 RDF + +get/set the value + =cut From mwilkinson at pub.open-bio.org Tue Aug 24 20:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 24 Aug 2004 16:43:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhX5V027856@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/RDF In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY/RDF Modified Files: ServiceInstanceRDF.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY/RDF ServiceInstanceRDF.pm,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/18 23:40:03 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY/RDF/ServiceInstanceRDF.pm 2004/08/24 20:43:33 1.12 @@ -5,9 +5,6 @@ use RDF::Core::Model::Serializer; require Exporter; -our @ISA = qw(Exporter); -our @EXPORT_OK = qw(); - use RDF::Core::Constants qw(:xml :rdf :rdfs); use constant OBJ => 'http://biomoby.org/RESOURCES/MOBY-S/Objects#'; use constant SRV => 'http://biomoby.org/RESOURCES/MOBY-S/Services#'; @@ -16,6 +13,11 @@ use constant SI => 'http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances#'; use constant DC => 'http://purl.org/dc/elements/1.1/'; +our @ISA = qw(Exporter); +our @EXPORT = qw(OBJ SRV NS MP SI DC xmlNamespaces serialize); +our @EXPORT_OK = qw(OBJ SRV NS MP SI DC xmlNamespaces serialize); + + sub xmlNamespaces { return { RDF_NS() => 'rdf', From mwilkinson at pub.open-bio.org Tue Aug 24 20:43:33 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 24 Aug 2004 16:43:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242043.i7OKhX2i027818@pub.open-bio.org> mwilkinson Tue Aug 24 16:43:33 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv27799/MOBY Modified Files: Config.pm Log Message: various small tweaks and doc fixes moby-live/Perl/MOBY Config.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Config.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/07/09 00:21:53 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY/Config.pm 2004/08/24 20:43:33 1.5 @@ -74,11 +74,11 @@ } my $file = $ENV{MOBY_CENTRAL_CONFIG}; - (-e $file) || die "can't open MOBY Configuration file $!\n"; + (-e $file) || die "MOBY Configuration file $file doesn't exist $!\n"; chomp $file; if ((-e $file) && (!(-d $file))){ - open IN, $file || die "can't open MOBY Configuration file $!\n"; + open IN, $file || die "can't open MOBY Configuration file $file for unknown reasons$!\n"; } my @sections = split /(\[\s*\S+\s*\][^\[]*)/s, join "", ; #print STDERR "split into @sections\n"; From nopushneva at pub.open-bio.org Tue Aug 24 20:46:09 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 16:46:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242046.i7OKk9e5027898@pub.open-bio.org> nopushneva Tue Aug 24 16:46:09 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv27873/RDFAgent Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent added to the repository moby-live/Agents/MOBY-S/RDFAgent - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 21:28:43 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 17:28:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242128.i7OLSh0Y028019@pub.open-bio.org> nopushneva Tue Aug 24 17:28:43 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf In directory pub.open-bio.org:/tmp/cvs-serv27994/conf Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf added to the repository moby-live/Agents/MOBY-S/RDFAgent/conf - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/conf/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 21:42:49 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 17:42:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242142.i7OLgnCi028080@pub.open-bio.org> nopushneva Tue Aug 24 17:42:48 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv28055/lib Log Message: Directory /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib added to the repository moby-live/Agents/MOBY-S/RDFAgent/lib - New directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/RCS/directory,v: No such file or directory From nopushneva at pub.open-bio.org Tue Aug 24 21:45:02 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 17:45:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242145.i7OLj2wp028142@pub.open-bio.org> nopushneva Tue Aug 24 17:45:02 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv28118 Added Files: servicevalidation.mysql Log Message: agent for browsing service signature RDF moby-live/Agents/MOBY-S/RDFAgent servicevalidation.mysql,NONE,1.1 From nopushneva at pub.open-bio.org Tue Aug 24 21:45:02 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Tue, 24 Aug 2004 17:45:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408242145.i7OLj2Mr028160@pub.open-bio.org> nopushneva Tue Aug 24 17:45:02 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib In directory pub.open-bio.org:/tmp/cvs-serv28118/lib Added Files: activation.jar antlr.jar commons-logging.jar concurrent.jar icu4j.jar jakarta-oro-2.0.5.jar jdom.jar jena.jar junit.jar log4j-1.2.7.jar mail.jar rdf-api-2001-01-19.jar xercesImpl.jar xml-apis.jar Log Message: agent for browsing service signature RDF moby-live/Agents/MOBY-S/RDFAgent/lib activation.jar,NONE,1.1 antlr.jar,NONE,1.1 commons-logging.jar,NONE,1.1 concurrent.jar,NONE,1.1 icu4j.jar,NONE,1.1 jakarta-oro-2.0.5.jar,NONE,1.1 jdom.jar,NONE,1.1 jena.jar,NONE,1.1 junit.jar,NONE,1.1 log4j-1.2.7.jar,NONE,1.1 mail.jar,NONE,1.1 rdf-api-2001-01-19.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 xml-apis.jar,NONE,1.1 From ambrose at pub.open-bio.org Thu Aug 26 20:09:22 2004 From: ambrose at pub.open-bio.org (Ambrose Ng) Date: Thu, 26 Aug 2004 16:09:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408262009.i7QK9MvF004469@pub.open-bio.org> ambrose Thu Aug 26 16:09:22 EDT 2004 Update of //home/repository/moby/moby-live/Perl/Accessories In directory pub.open-bio.org:/tmp/cvs-serv4445 Added Files: frame.cgi namespaceframe.cgi searchframe.cgi Removed Files: NamespaceMaintenance.cgi SearchDatabase.cgi Log Message: Ambrose Ng moby-live/Perl/Accessories frame.cgi,NONE,1.1 namespaceframe.cgi,NONE,1.1 searchframe.cgi,NONE,1.1 NamespaceMaintenance.cgi,1.3,NONE SearchDatabase.cgi,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Perl/Accessories/RCS/NamespaceMaintenance.cgi,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Perl/Accessories/RCS/SearchDatabase.cgi,v: No such file or directory From mwilkinson at pub.open-bio.org Thu Aug 26 20:52:28 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 26 Aug 2004 16:52:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408262052.i7QKqSk6004646@pub.open-bio.org> mwilkinson Thu Aug 26 16:52:28 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv4627/MOBY Modified Files: Central.pm Log Message: interpret empty XML nodes in the findService message as undef, rather than spaces moby-live/Perl/MOBY Central.pm,1.139,1.140 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.139 retrieving revision 1.140 diff -u -r1.139 -r1.140 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/18 23:40:03 1.139 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/26 20:52:28 1.140 @@ -1597,7 +1597,7 @@ ++$valid_service_ids{$_->[0]}; # increment that particular id's count by one } } - if ($findme{serviceType}){ + if ($findme{serviceType}){ # must have something more than empty content my $OS = MOBY::OntologyServer->new(ontology => 'service'); $findme{serviceType} =~ s/^moby\://; my ($exists, $message, $URI) = $OS->serviceExists(term =>$findme{serviceType}); @@ -1899,12 +1899,19 @@ return undef unless ($obj eq 'findService'); my $serviceType = &_nodeTextContent($Object, "serviceType"); + $serviceType && ($serviceType =~ s/\s+//g); my $servicename = &_nodeTextContent($Object, "serviceName"); + $servicename && ($servicename =~ s/\s+//g); my $authoritative = &_nodeTextContent($Object, "authoritative"); + $authoritative && ($authoritative =~ s/\s+//g); my $Category = &_nodeTextContent($Object, "Category"); + $Category && ($Category =~ s/\s+//g); my $AuthURI = &_nodeTextContent($Object, "authURI"); + $AuthURI && ($AuthURI =~ s/\s+//g); my $expandObjects = &_nodeTextContent($Object, "expandObjects"); + $expandObjects && ($expandObjects =~ s/\s+//g); my $expandServices = &_nodeTextContent($Object, "expandServices"); + $expandServices && ($expandServices =~ s/\s+//g); my @kw = &_nodeArrayContent($Object, "keywords"); my $INPUTS = &_nodeRawContent($Object, "Input"); # returns array ref my $OUTPUTS = &_nodeRawContent($Object, "Output"); # returns array ref @@ -2919,13 +2926,14 @@ $sth_simple_in->execute($_); while (my ($objURI, $nsURI, $article) = $sth_simple_in->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\n"; $output .="\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t$NSname\n"; + $output .="\t\t\t$NSname\n" if $NSname; } $output .="\t\t\n"; } @@ -2935,13 +2943,14 @@ $sth_collection_in->execute($collid); while (my ($objURI, $nsURI, $article) = $sth_collection_in->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\t\n"; $output .="\t\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t\t$NSname\n"; + $output .="\t\t\t\t$NSname\n" if $NSname; } $output .="\t\t\t\n"; } @@ -2954,13 +2963,14 @@ $sth_simple_out->execute($_); while (my ($objURI, $nsURI, $article) = $sth_simple_out->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); + $nsURI ||=""; my @nsURIs = split ",", $nsURI; $article ||=""; $output .="\t\t\n"; $output .="\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t$NSname\n"; + $output .="\t\t\t$NSname\n" if $NSname; } $output .="\t\t\n"; } @@ -2970,12 +2980,14 @@ $sth_collection_out->execute($collid); while (my ($objURI, $nsURI, $article) = $sth_collection_out->fetchrow_array()){ my $objName = $OSobj->getObjectCommonName($objURI); - my @nsURIs = split ",", $nsURI; + $nsURI ||=""; + my @nsURIs = split ",", $nsURI; + $article ||=""; $output .="\t\t\t\n"; $output .="\t\t\t\t$objName\n"; foreach my $ns(@nsURIs){ my $NSname = $OSns->getNamespaceCommonName($ns); - $output .="\t\t\t\t$NSname\n"; + $output .="\t\t\t\t$NSname\n" if $NSname; } $output .="\t\t\t\n"; } @@ -2986,6 +2998,11 @@ $output .="\t\n"; $sth_secondary_in->execute($_); while (my ($default_value, $maximum_value, $minimum_value, $enum_value, $datatype, $article_name) = $sth_secondary_in->fetchrow_array()){ + $article_name ||=""; + $datatype ||=""; + $default_value ||=""; + $maximum_value ||=""; + $minimum_value ||=""; $output .= "\t\t\t\n"; $output .= "\t\t\t\t$datatype\n"; $output .="\t\t\t\t$default_value\n"; From nopushneva at pub.open-bio.org Fri Aug 27 20:05:29 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Fri, 27 Aug 2004 16:05:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408272005.i7RK5TA4008730@pub.open-bio.org> nopushneva Fri Aug 27 16:05:29 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv8708 Added Files: RDFAgent.jar Log Message: add the procedure for deletion a set of the services moby-live/Agents/MOBY-S/RDFAgent RDFAgent.jar,NONE,1.1 From nopushneva at pub.open-bio.org Fri Aug 27 20:10:00 2004 From: nopushneva at pub.open-bio.org (Nina Opushneva) Date: Fri, 27 Aug 2004 16:10:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200408272010.i7RKA0AE008772@pub.open-bio.org> nopushneva Fri Aug 27 16:10:00 EDT 2004 Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent In directory pub.open-bio.org:/tmp/cvs-serv8741 Modified Files: servicevalidation.mysql Log Message: change of the structure moby-live/Agents/MOBY-S/RDFAgent servicevalidation.mysql,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql 2004/08/24 21:45:02 1.1 +++ /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/servicevalidation.mysql 2004/08/27 20:10:00 1.2 @@ -1,6 +1,6 @@ CREATE TABLE service_validation ( - servicename varchar(255) NOT NULL default '', + signatureURL varchar(255) NOT NULL default '', error_code int(4) NOT NULL, counter int (1) NOT NULL default '0', - PRIMARY KEY (servicename) + PRIMARY KEY (signatureURL) ) TYPE=MyISAM;