From jmrc at dev.open-bio.org Mon Sep 1 14:53:57 2008 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Mon, 1 Sep 2008 14:53:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809011853.m81IrvSL019292@dev.open-bio.org> jmrc Mon Sep 1 14:53:57 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv19249 Modified Files: Service.pm SimpleServer.pm WSRF.pm Log Message: * Cosmetic fixes in Service.pm and SimpleServer.pm. * Fixed a bug in WSRF.pm related to temporal file location/creation introduced by a previous commit. moby-live/Perl/MOBY-Server/lib/MOBY/Async Service.pm,1.2,1.3 SimpleServer.pm,1.2,1.3 WSRF.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm 2008/04/23 13:08:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm 2008/09/01 18:53:57 1.3 @@ -18,8 +18,8 @@ =head1 DESCRIPTION It provides a class to invoke asynchronous services. Its use is very similar to -MOBY::Client::Service, but it also provides additional methods in order to -have more control over the asynchronous service execution. +MOBY::Client::Service because it is its super-class. It also provides additional +methods in order to have more control over the asynchronous service execution. =head1 METHODS @@ -27,7 +27,7 @@ Name : new Function : create a service connection. - Usage : $Service = MOBY::Client::Service->new(@args) + Usage : $Service = MOBY::Async::Service->new(@args) Args : service - string with a WSDL defining an asynchronous MOBY service Returns : MOBY::Async::Service object, undef if no wsdl. @@ -135,6 +135,10 @@ use MOBY::Client::Service; use base qw(MOBY::Client::Service); +sub _getPollingTime($$$@); +sub _getServiceEndpoint($); +sub _getPseudoRandomPollingTime($$); +sub _composeResponse(@); sub new { my ($this, %args) = @_; @@ -162,7 +166,7 @@ my $pollingTime; my ($i, $j) = (0, 1); my @status; - while ( $pollingTime = &_getPollingTime($i, $j, $start, @status) ) { + while ( $pollingTime = _getPollingTime($i, $j, $start, @status) ) { ($i, $j) = ($j, $i+$j); print "(next polling in $pollingTime seconds)\n\n" unless ($self->{silent}); @@ -180,7 +184,7 @@ my @responses = $self->result($EPR, @queryIDs); $self->destroy($EPR); - my $response = &_composeResponse(@responses); + my $response = _composeResponse(@responses); print "Finished.\n\n" unless ($self->{silent}); @@ -239,7 +243,7 @@ # Create the resource and submit the batch-call my $func = $self->{serviceName}.'_submit'; my $ans = WSRF::Lite - -> proxy(&_getServiceEndpoint($self->{service})) + -> proxy(_getServiceEndpoint($self->{service})) -> uri($WSRF::Constants::MOBY) -> $func(SOAP::Data->value($data)->type('string')); die "ERROR: ".$ans->faultstring if ($ans->fault); @@ -296,7 +300,7 @@ my $pollingTime; my ($i, $j) = (0, 1); my @status; - while ( $pollingTime = &_getPollingTime($i, $j, $start, @status) ) { + while ( $pollingTime = _getPollingTime($i, $j, $start, @status) ) { ($i, $j) = ($j, $i+$j); print "(next polling in $pollingTime seconds)\n\n" unless ($self->{silent}); @@ -314,7 +318,7 @@ my @responses = $self->result($EPR, @queryIDs); $self->destroy($EPR); - my $response = &_composeResponse(@responses); + my $response = _composeResponse(@responses); print "Finished.\n\n" unless ($self->{silent}); @@ -372,7 +376,7 @@ # Create the resource and submit the batch-call my $func = $self->{serviceName}.'_submit'; my $ans = WSRF::Lite - -> proxy(&_getServiceEndpoint($self->{service})) + -> proxy(_getServiceEndpoint($self->{service})) -> uri($WSRF::Constants::MOBY) -> $func(SOAP::Data->value($data)->type('string')); die "ERROR: ".$ans->faultstring if ($ans->fault); @@ -512,7 +516,7 @@ die "ERROR: ".$ans->faultstring if ($ans->fault); } -sub _getServiceEndpoint { +sub _getServiceEndpoint($) { my ($wsdl) = @_; $wsdl =~ /address location\s*=\s*["|'](.+)["|']/; @@ -521,10 +525,10 @@ return $serviceEndpoint; } -sub _getPollingTime { +sub _getPollingTime($$$@) { my ($i, $j, $start, @status) = @_; - return &_getPseudoRandomPollingTime($i, $j) unless (scalar(@status)); + return _getPseudoRandomPollingTime($i, $j) unless (scalar(@status)); my $pollingTime = 0; foreach my $status (@status) { @@ -558,7 +562,7 @@ ($status->new_state eq "running") || ($status->new_state eq "RUNNING") ) { - $pTime = &_getPseudoRandomPollingTime($i, $j); + $pTime = _getPseudoRandomPollingTime($i, $j); } else { die "ERROR: analysis event block not well formed.\n"; @@ -597,7 +601,7 @@ return $pollingTime; } -sub _getPseudoRandomPollingTime { +sub _getPseudoRandomPollingTime($$) { my ($i, $j) = @_; my $c = 15; my $p = 0.1; @@ -607,7 +611,7 @@ return $delay; } -sub _composeResponse { +sub _composeResponse(@) { my (@datas) = @_; my @authorities; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2008/04/23 13:08:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2008/09/01 18:53:57 1.3 @@ -178,6 +178,7 @@ # Get mobyData and iterate over them in order to run the service for each one my @mobyData = ($moby->getElementsByTagNameNS($WSRF::Constants::MOBY_MESSAGE_NS,'mobyData')); + foreach my $mobyData (@mobyData) { my $queryID = $mobyData->getAttribute('queryID') || $mobyData->getAttributeNS($WSRF::Constants::MOBY_MESSAGE_NS,'queryID'); my $property_pid = "pid_$queryID"; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm 2008/08/29 14:16:02 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm 2008/09/01 18:53:57 1.6 @@ -28,6 +28,7 @@ package MOBY::Async::WSRF; use strict; use WSRF::Lite 0.8.2.2; +use File::Path; use vars qw /$VERSION/; $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; @@ -37,7 +38,9 @@ $WSRF::WSRP::MobyPropertiesPrefixes = ['status', 'result']; $WSRF::Constants::DataDir = (exists($ENV{TMPDIR}) && defined($ENV{TMPDIR}) && $ENV{TMPDIR} ne '')?$ENV{TMPDIR}:'/tmp'; +mkpath($WSRF::Constants::DataDir,1,0777); $WSRF::Constants::DataPrefix = 'moby_'; +$WSRF::Constants::Data = $WSRF::Constants::DataDir .'/'. $WSRF::Constants::DataPrefix; $WSRF::Constants::MOBY = 'http://biomoby.org/'; $WSRF::Constants::MOBY_MESSAGE_NS = 'http://www.biomoby.org/moby'; #$WSRF::Constants::WSA = 'http://www.w3.org/2005/08/addressing'; @@ -324,60 +327,9 @@ ) ) if (scalar(@notfound)); my @resp = $self->SUPER::GetMultipleResourceProperties($envelope); - return @resp; + return @resp; } -#sub GetMultipleResourcePropertiesRequest { -# my $self = shift @_; -# my $envelope = pop @_; -# my $methodname = (caller(0))[3]; -# $methodname = substr($methodname,rindex($methodname,':')+1); -# eval { -# my $parser=XML::LibXML->new(); -# my $envxml = $parser->parse_string($envelope->raw_xml); -# my $context=XML::LibXML::XPathContext->new(); -# $context->registerNs('s11',$SOAP::Constants::NS_ENV); -# $context->registerNs('wsa',$WSRF::Constants::WSA); -# my(@actions)=$context->findnodes('/s11:Envelope/s11:Header/wsa:Action[1]',$envxml); -# if(scalar(@actions)>0) { -# my($action)=$actions[0]; -# my $acturi = $action->textContent(); -# my $newacturi= $acturi; -# $newacturi =~ s/Request$//; -# if( $acturi ne $newacturi) { -# foreach my $child ($action->childNodes) { -# $action->removeChild($child); -# } -# $action->appendChild($envxml->createTextNode($newacturi)); -# -# -# my(@query)=$context->findnodes("/s11:Envelope/s11:Body/wsa:$methodname".'[1]',$envxml); -# if(scalar(@query)>0) { -# my($prefix)=$query[0]->prefix(); -# if(defined($prefix) && $prefix ne '') { -# $prefix.=':'; -# } else { -# $prefix=''; -# } -# $methodname =~ s/Request$//; -# $query[0]->setNodeName($prefix.$methodname); -# } -# -# # Last, craete new SOM object -# my $sparser = WSRF::Deserializer->new(); -# my($manistring)=$envxml->toString(); -# $manistring =~ s/[\r\n]+//g; -# print STDERR "ENVELOPE ",$manistring,"\n"; -# $envelope = $sparser->deserialize($manistring); -# } -# } -# }; -# -# if($@) { -# print STDERR "FALLACANALLA $@\n"; -# } -# return $self->GetMultipleResourceProperties(@_,$envelope); -#} #=============================================================================== # WSRF::FileBasedMobyResourceLifetimes @@ -414,7 +366,7 @@ my $self = shift @_; my $envelope = pop @_; my $lock = WSRF::MobyFile->new($envelope); - my $file = $WSRF::Constants::DataDir . '/' . $WSRF::Constants::DataPrefix.$lock->ID(); + my $file = $WSRF::Constants::Data.$lock->ID(); unlink $file or WSRF::BaseFaults::die_with_fault( $envelope, ( BaseFault => "ResourceNotDestroyedFault", Description => "Could not remove WS-Resource file" @@ -620,7 +572,7 @@ $ID_clipped =~ s/-\w*//o; # File containing resource properties - my $path = $WSRF::Constants::DataDir . '/' . $WSRF::Constants::DataPrefix.$ID_clipped; + my $path = $WSRF::Constants::Data.$ID_clipped; WSRF::BaseFaults::die_with_fault( $envelope, ( BaseFault => "ResourceUnknownFault", Description => "No WS-Resource with Identifer $ID" From jmrc at dev.open-bio.org Mon Sep 1 14:55:20 2008 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Mon, 1 Sep 2008 14:55:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809011855.m81ItKfl019335@dev.open-bio.org> jmrc Mon Sep 1 14:55:20 EDT 2008 Update of /home/repository/moby/moby-live/Docs/asyncDocs In directory dev.open-bio.org:/tmp/cvs-serv19300/asyncDocs Modified Files: README.txt Log Message: * Added more asynchronous client examples. * README has been updated according to the new example. moby-live/Docs/asyncDocs README.txt,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/asyncDocs/README.txt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Docs/asyncDocs/README.txt 2008/08/29 14:03:16 1.2 +++ /home/repository/moby/moby-live/Docs/asyncDocs/README.txt 2008/09/01 18:55:20 1.3 @@ -105,13 +105,10 @@ In the Perl script "running_runAsyncMOBYservice.pl" show us how to call our BioMOBY asynchronous service. In the script "running_runAsyncMOBYservice-StepByStep.pl" show us how to call our BioMOBY asynchronous service - controlling the "polling" calls. - - Note: Be carefull!! These scripts are created to be examples. Some part of them are "hardcore". - - - - + controlling the "polling" calls in a very detailed way. + In the script "running_runAsyncMOBYservice-poll.pl" show us how to call our BioMOBY asynchronous service + controlling the "polling" calls in a "quick&dirty" way. + Note: Be carefull!! These scripts are created to be examples. Some part of them are "hardcoded". From jmrc at dev.open-bio.org Mon Sep 1 14:55:21 2008 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Mon, 1 Sep 2008 14:55:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809011855.m81ItLKu019349@dev.open-bio.org> jmrc Mon Sep 1 14:55:20 EDT 2008 Update of /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test In directory dev.open-bio.org:/tmp/cvs-serv19300/asyncDocs/async-MOBY-test Added Files: running_runAsyncMOBYservice-poll.pl Log Message: * Added more asynchronous client examples. * README has been updated according to the new example. moby-live/Docs/asyncDocs/async-MOBY-test running_runAsyncMOBYservice-poll.pl,NONE,1.1 From jmrc at dev.open-bio.org Mon Sep 1 15:01:49 2008 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Mon, 1 Sep 2008 15:01:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809011901.m81J1nUq019440@dev.open-bio.org> jmrc Mon Sep 1 15:01:49 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv19403/Perl/MOBY-Server/lib/MOBY Modified Files: CommonSubs.pm Log Message: * Fixed the "hideous" bug found by Eddie, related to asynchronous MOBY calls with empty mobyData elements. Although it is a very strange case, there could be a service with no input parameter. MOBY::Async::SimpleServer uses serviceInputParser, which had the bug fixed by this commit. moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/03/05 20:27:11 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/01 19:01:49 1.4 @@ -375,6 +375,10 @@ foreach my $query ( @queries ) { my $queryID = _getQID( $query ); # get the queryID attribute of the mobyData my @input_articles = _getArticlesAsObjects( $query ); + # This is done for empty mobyData. It is a strange case + # but it can happen (a service which is a random answer + # generator, for instance) + $input_parameters{$queryID}={}; foreach my $article ( @input_articles ) { ${$input_parameters{$queryID}}{$article->articleName} = $article; } From kawas at dev.open-bio.org Tue Sep 2 09:09:02 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:09:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021309.m82D92cK021463@dev.open-bio.org> kawas Tue Sep 2 09:09:01 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv21412/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl Modified Files: NamespaceDataAdapter.pm ServiceTypeDataAdapter.pm ServiceInstanceDataAdapter.pm ObjectDataAdapter.pm FetaQueryAdaptor.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl NamespaceDataAdapter.pm,1.2,1.3 ServiceTypeDataAdapter.pm,1.2,1.3 ServiceInstanceDataAdapter.pm,1.2,1.3 ObjectDataAdapter.pm,1.2,1.3 FetaQueryAdaptor.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/NamespaceDataAdapter.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/NamespaceDataAdapter.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/NamespaceDataAdapter.pm 2008/09/02 13:09:01 1.3 @@ -3,6 +3,8 @@ use strict; use Carp; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; =head1 NAME =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceTypeDataAdapter.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceTypeDataAdapter.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceTypeDataAdapter.pm 2008/09/02 13:09:01 1.3 @@ -4,6 +4,10 @@ use Carp; use vars qw(@ISA); @ISA = qw{MOBY::Adaptor::moby::queryapi}; # implements the interface + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::Impl::ServiceTypeDataAdapter - An interface definition for MOBY Central underlying data-stores =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceInstanceDataAdapter.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceInstanceDataAdapter.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceInstanceDataAdapter.pm 2008/09/02 13:09:01 1.3 @@ -5,6 +5,9 @@ use vars qw(@ISA); @ISA = qw{MOBY::Adaptor::moby::DataAdapterI}; # implements the interface +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::impl::ServiceInstanceDataAdapter - An interface definition for MOBY Central underlying data-stores =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ObjectDataAdapter.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ObjectDataAdapter.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ObjectDataAdapter.pm 2008/09/02 13:09:01 1.3 @@ -5,6 +5,9 @@ use vars qw(@ISA); @ISA = qw{MOBY::Adaptor::moby::DataAdapterI}; # implements the interface +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::Impl::ObjectDataAdapter - An interface definition for MOBY Central underlying data-stores =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm 2008/09/02 13:09:01 1.3 @@ -4,6 +4,9 @@ use XML::LibXML; @ISA = qw{MOBY::Adaptor::moby::DataAdapterI}; # implements the interface +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::impl::FetaQueryAdaptor.pm - FetaQueryAdaptor From kawas at dev.open-bio.org Tue Sep 2 09:09:13 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:09:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021309.m82D9DNk021503@dev.open-bio.org> kawas Tue Sep 2 09:09:12 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv21468/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi mysql.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/mysql.pm 2008/02/21 00:21:28 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/mysql.pm 2008/09/02 13:09:12 1.2 @@ -7,6 +7,9 @@ use DBI; use DBD::mysql; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + @ISA = qw{MOBY::Adaptor::moby::queryapi}; # implements the interface { From kawas at dev.open-bio.org Tue Sep 2 09:09:30 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:09:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021309.m82D9UoT021551@dev.open-bio.org> kawas Tue Sep 2 09:09:30 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby In directory dev.open-bio.org:/tmp/cvs-serv21508/Perl/MOBY-Server/lib/MOBY/Adaptor/moby Modified Files: queryapi.pm DataAdapterI.pm DataAccessI.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby queryapi.pm,1.2,1.3 DataAdapterI.pm,1.1,1.2 DataAccessI.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi.pm 2008/02/21 17:15:41 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi.pm 2008/09/02 13:09:30 1.3 @@ -4,6 +4,8 @@ use Carp; use vars qw($AUTOLOAD); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; =head1 NAME =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAdapterI.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAdapterI.pm 2008/02/21 00:21:28 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAdapterI.pm 2008/09/02 13:09:30 1.2 @@ -3,6 +3,9 @@ use strict; use Carp; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::DataAdapterI - An interface definition for MOBY Central underlying data-stores =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAccessI.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAccessI.pm 2008/02/21 17:15:41 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAccessI.pm 2008/09/02 13:09:30 1.3 @@ -4,6 +4,9 @@ use strict; use Carp; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::DataAccessI - This file may need to be renamed and may not make sense as From kawas at dev.open-bio.org Tue Sep 2 09:10:26 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:10:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021310.m82DAQmL021725@dev.open-bio.org> kawas Tue Sep 2 09:10:26 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv21682/Perl/MOBY-Server/lib/MOBY/Async Modified Files: SimpleServer.pm LSAE.pm Service.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Async SimpleServer.pm,1.3,1.4 LSAE.pm,1.2,1.3 Service.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2008/09/01 18:53:57 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2008/09/02 13:10:26 1.4 @@ -99,6 +99,9 @@ use base qw(WSRF::FileBasedMobyResourceLifetimes); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #=============================================================================== # async_create # =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/LSAE.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/LSAE.pm 2008/04/23 13:08:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/LSAE.pm 2008/09/02 13:10:26 1.3 @@ -199,6 +199,9 @@ use XML::LibXML; use Exporter; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use base qw(Exporter); our @EXPORT = qw( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm 2008/09/01 18:53:57 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm 2008/09/02 13:10:26 1.4 @@ -135,6 +135,9 @@ use MOBY::Client::Service; use base qw(MOBY::Client::Service); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + sub _getPollingTime($$$@); sub _getServiceEndpoint($); sub _getPseudoRandomPollingTime($$); From kawas at dev.open-bio.org Tue Sep 2 09:11:25 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:11:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021311.m82DBPs4021769@dev.open-bio.org> kawas Tue Sep 2 09:11:25 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv21730/Perl/MOBY-Server/lib/MOBY/Client/Exception Modified Files: MobyExceptionCodes.pm MobyException.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception MobyExceptionCodes.pm,1.2,1.3 MobyException.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyExceptionCodes.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyExceptionCodes.pm 2008/08/29 16:18:51 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyExceptionCodes.pm 2008/09/02 13:11:25 1.3 @@ -5,6 +5,9 @@ # Name of the package package MOBY::Client::Exception::MobyExceptionCodes; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use strict; ############## =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyException.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyException.pm 2008/08/29 16:18:51 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyException.pm 2008/09/02 13:11:25 1.3 @@ -13,6 +13,9 @@ use Carp qw(croak); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use MOBY::Client::Exception::MobyExceptionCodes; From kawas at dev.open-bio.org Tue Sep 2 09:11:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:11:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021311.m82DBeB3021842@dev.open-bio.org> kawas Tue Sep 2 09:11:40 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv21774/Perl/MOBY-Server/lib/MOBY/Client Modified Files: Service.pm SimpleArticle.pm ServiceInstance.pm SimpleInput.pm Registration.pm OntologyServer.pm SecondaryArticle.pm CollectionArticle.pm Central.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Client Service.pm,1.2,1.3 SimpleArticle.pm,1.2,1.3 ServiceInstance.pm,1.1,1.2 SimpleInput.pm,1.3,1.4 Registration.pm,1.1,1.2 OntologyServer.pm,1.1,1.2 SecondaryArticle.pm,1.3,1.4 CollectionArticle.pm,1.2,1.3 Central.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm 2008/09/02 13:11:40 1.3 @@ -48,6 +48,10 @@ use Cwd; use URI::Escape; use vars qw($AUTOLOAD @ISA); + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + my $debug = 0; if ( $debug ) { open( OUT, ">/tmp/ServiceCallLogOut.txt" ) || die "cant open logfile\n"; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm 2008/09/02 13:11:40 1.3 @@ -5,6 +5,9 @@ use MOBY::MobyXMLConstants; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::SimpleArticle - a small object describing the Simple articles from the findService Response message of MOBY Central =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm 2008/09/02 13:11:40 1.2 @@ -3,6 +3,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::ServiceInstance - a small object describing a MOBY service =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm 2008/02/21 17:42:15 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm 2008/09/02 13:11:40 1.4 @@ -3,6 +3,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::SimpleInput - a small object describing a MOBY service =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Registration.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Registration.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Registration.pm 2008/09/02 13:11:40 1.2 @@ -70,6 +70,10 @@ use strict; use Carp; use vars qw($AUTOLOAD); + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + { #Encapsulated class data =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm 2008/09/02 13:11:40 1.2 @@ -75,6 +75,10 @@ use Carp; use vars qw($AUTOLOAD); use LWP::UserAgent; + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + my $debug = 0; my $user_agent = "MOBY-OntologyServer-Perl"; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm 2008/02/21 17:42:15 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm 2008/09/02 13:11:40 1.4 @@ -5,6 +5,9 @@ use MOBY::MobyXMLConstants; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::SecondaryArticle - a small object describing the Simple articles from the findService Response message of MOBY Central =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm 2008/09/02 13:11:40 1.3 @@ -6,6 +6,9 @@ use vars qw($AUTOLOAD @ISA); use MOBY::Client::SimpleArticle; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::CollectionArticle - a small object describing the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm 2008/05/14 14:04:03 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm 2008/09/02 13:11:40 1.6 @@ -15,6 +15,9 @@ use MOBY::Client::OntologyServer; use vars qw($AUTOLOAD @ISA $MOBY_server $MOBY_uri); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::Central - a client side wrapper for MOBY Central From kawas at dev.open-bio.org Tue Sep 2 09:11:54 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:11:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021311.m82DBsfk021883@dev.open-bio.org> kawas Tue Sep 2 09:11:53 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv21848/Perl/MOBY-Server/lib/MOBY/lsid/authority Modified Files: MobyMetadataResolver.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority MobyMetadataResolver.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/MobyMetadataResolver.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/MobyMetadataResolver.pm 2008/02/21 17:54:56 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/MobyMetadataResolver.pm 2008/09/02 13:11:53 1.3 @@ -18,6 +18,9 @@ use MOBY::RDF::Ontologies::Namespaces; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use base 'LS::Service::Namespace'; =head1 NAME From kawas at dev.open-bio.org Tue Sep 2 09:12:34 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:12:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021312.m82DCYhl021939@dev.open-bio.org> kawas Tue Sep 2 09:12:33 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv21888/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache Modified Files: NamespaceCache.pm CacheUtils.pm ServiceCache.pm ObjectCache.pm ServiceTypeCache.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache NamespaceCache.pm,1.3,1.4 CacheUtils.pm,1.2,1.3 ServiceCache.pm,1.5,1.6 ObjectCache.pm,1.4,1.5 ServiceTypeCache.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/04/30 16:53:19 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/09/02 13:12:33 1.4 @@ -30,6 +30,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::NamespaceCache - Module for creating a cache of namespaces for use when generating RDF =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/09/02 13:12:33 1.3 @@ -23,6 +23,9 @@ use constant NAMESPACES_CACHE => 'namespaces'; use constant SERVICETYPES_CACHE => 'serviceTypes'; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::CacheUtils - Utility module that aids in caching =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/06/19 21:47:35 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/09/02 13:12:33 1.6 @@ -30,6 +30,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::ServiceCache - Module for creating a cache of service instances for use when generating RDF =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/04/30 16:53:26 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/09/02 13:12:33 1.5 @@ -30,6 +30,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::ObjectCache - Module for creating a cache of datatypes for use when generating RDF =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/04/30 16:53:45 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/09/02 13:12:33 1.4 @@ -30,6 +30,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::ServiceTypeCache - Module for creating a cache of service types for use when generating RDF From kawas at dev.open-bio.org Tue Sep 2 09:12:46 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:12:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021312.m82DCk3q021991@dev.open-bio.org> kawas Tue Sep 2 09:12:46 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv21944/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Modified Files: ServiceTypes.pm Objects.pm Services.pm Namespaces.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies ServiceTypes.pm,1.3,1.4 Objects.pm,1.4,1.5 Services.pm,1.6,1.7 Namespaces.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/ServiceTypes.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/ServiceTypes.pm 2008/06/19 21:49:01 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/ServiceTypes.pm 2008/09/02 13:12:46 1.4 @@ -27,6 +27,9 @@ use MOBY::RDF::Utils; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Objects.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Objects.pm 2008/06/19 21:49:01 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Objects.pm 2008/09/02 13:12:46 1.5 @@ -30,6 +30,9 @@ use CGI; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm 2008/06/25 16:13:02 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm 2008/09/02 13:12:46 1.7 @@ -35,6 +35,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm 2008/07/22 15:54:29 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm 2008/09/02 13:12:46 1.7 @@ -27,6 +27,9 @@ use MOBY::RDF::Utils; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- From kawas at dev.open-bio.org Tue Sep 2 09:12:58 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:12:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021312.m82DCwe3022039@dev.open-bio.org> kawas Tue Sep 2 09:12:58 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers In directory dev.open-bio.org:/tmp/cvs-serv21996/Perl/MOBY-Server/lib/MOBY/RDF/Parsers Modified Files: NamespaceParser.pm DatatypeParser.pm ServiceTypeParser.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers NamespaceParser.pm,1.2,1.3 DatatypeParser.pm,1.1,1.2 ServiceTypeParser.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm 2008/03/05 17:43:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm 2008/09/02 13:12:58 1.3 @@ -21,6 +21,9 @@ use MOBY::RDF::Predicates::RDF; use MOBY::RDF::Predicates::RDFS; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME NamespaceParser - An module for obtaining namespaces from the RDF Namespace ontology =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/DatatypeParser.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/DatatypeParser.pm 2008/03/13 19:12:07 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/DatatypeParser.pm 2008/09/02 13:12:58 1.2 @@ -21,6 +21,9 @@ use MOBY::RDF::Predicates::RDF; use MOBY::RDF::Predicates::RDFS; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME DatatypeParser - An module for obtaining datatypes from the RDF Namespace ontology =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm 2008/03/05 17:43:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm 2008/09/02 13:12:58 1.3 @@ -21,6 +21,9 @@ use MOBY::RDF::Predicates::RDF; use MOBY::RDF::Predicates::RDFS; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME ServiceTypeParser - An module for obtaining services from the RDF Service Type ontology From kawas at dev.open-bio.org Tue Sep 2 09:13:10 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:13:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021313.m82DDAsa022103@dev.open-bio.org> kawas Tue Sep 2 09:13:09 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates In directory dev.open-bio.org:/tmp/cvs-serv22044/Perl/MOBY-Server/lib/MOBY/RDF/Predicates Modified Files: MOBY_PREDICATES.pm OWL.pm FETA.pm RDFS.pm RDF.pm OMG_LSID.pm DC_PROTEGE.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates MOBY_PREDICATES.pm,1.1,1.2 OWL.pm,1.1,1.2 FETA.pm,1.1,1.2 RDFS.pm,1.1,1.2 RDF.pm,1.1,1.2 OMG_LSID.pm,1.1,1.2 DC_PROTEGE.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,8 @@ use strict; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant MOBY_PREDICATES_PREFIX => 'moby'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OWL.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OWL.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OWL.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,9 @@ use strict; BEGIN { +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use constant OWL_PREFIX => 'owl'; use constant OWL_URI => 'http://www.w3.org/2002/07/owl#'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/FETA.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/FETA.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/FETA.pm 2008/09/02 13:13:09 1.2 @@ -4,6 +4,8 @@ use warnings; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant FETA_PREFIX => 'myGrid'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDFS.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDFS.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDFS.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,8 @@ use strict; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant RDFS_PREFIX => 'rdfs'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDF.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDF.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDF.pm 2008/09/02 13:13:09 1.2 @@ -2,6 +2,8 @@ use strict; BEGIN { +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant RDF_PREFIX => 'rdf'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OMG_LSID.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OMG_LSID.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OMG_LSID.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,8 @@ use strict; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant OMG_LSID_PREFIX => 'lsid'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/DC_PROTEGE.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/DC_PROTEGE.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/DC_PROTEGE.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,8 @@ use strict; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant DC_PROTEGE_PREFIX => 'protege-dc'; From kawas at dev.open-bio.org Tue Sep 2 09:13:20 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:13:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021313.m82DDKIQ022143@dev.open-bio.org> kawas Tue Sep 2 09:13:20 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv22108/Perl/MOBY-Server/lib/MOBY/RDF Modified Files: Utils.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF Utils.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm 2008/04/30 16:52:25 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm 2008/09/02 13:13:20 1.6 @@ -14,6 +14,9 @@ use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- From kawas at dev.open-bio.org Tue Sep 2 09:13:57 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:13:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021313.m82DDvIJ022183@dev.open-bio.org> kawas Tue Sep 2 09:13:57 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv22148/Perl/MOBY-Server/lib/MOBY Modified Files: Admin.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY Admin.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Admin.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Admin.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Admin.pm 2008/09/02 13:13:57 1.2 @@ -24,6 +24,9 @@ use MOBY::CommonSubs; use MOBY::MobyXMLConstants; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + sub deregisterService { my ( $self, $xml ) = @_; From kawas at dev.open-bio.org Tue Sep 2 09:14:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:14:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021314.m82DEIEY022295@dev.open-bio.org> kawas Tue Sep 2 09:14:18 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv22188/Perl/MOBY-Server/lib/MOBY Modified Files: secondary_input.pm collection_input.pm MobyXMLConstants.pm service_instance.pm central_db_connection.pm OntologyServer.pm dbConfig.pm MOBY.pm MOBYXSLT.pm service_type.pm authority.pm CommonSubs.pm mysql.pm Central.pm Config.pm CrossReference.pm collection_output.pm simple_input.pm simple_output.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY secondary_input.pm,1.2,1.3 collection_input.pm,1.3,1.4 MobyXMLConstants.pm,1.1,1.2 service_instance.pm,1.2,1.3 central_db_connection.pm,1.2,1.3 OntologyServer.pm,1.2,1.3 dbConfig.pm,1.2,1.3 MOBY.pm,1.3,1.4 MOBYXSLT.pm,1.2,1.3 service_type.pm,1.2,1.3 authority.pm,1.2,1.3 CommonSubs.pm,1.4,1.5 mysql.pm,1.2,1.3 Central.pm,1.6,1.7 Config.pm,1.4,1.5 CrossReference.pm,1.2,1.3 collection_output.pm,1.2,1.3 simple_input.pm,1.2,1.3 simple_output.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::secondary_input - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm 2008/07/07 16:50:25 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm 2008/09/02 13:14:18 1.4 @@ -4,6 +4,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::collection_input - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MobyXMLConstants.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MobyXMLConstants.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MobyXMLConstants.pm 2008/09/02 13:14:18 1.2 @@ -2,6 +2,8 @@ use strict; use vars qw( $VERSION @ISA @EXPORT @NodeNames); +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + BEGIN { @ISA = qw( Exporter ); ######################################################### =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_instance.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_instance.pm 2008/02/21 17:58:58 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_instance.pm 2008/09/02 13:14:18 1.3 @@ -8,6 +8,9 @@ use MOBY::authority; use MOBY::Config; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #@ISA = qw(MOBY::central_db_connection); # can't do this yet... =head1 NAME =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/central_db_connection.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/central_db_connection.pm 2008/02/21 17:54:56 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/central_db_connection.pm 2008/09/02 13:14:18 1.3 @@ -4,6 +4,9 @@ use vars qw($AUTOLOAD @ISA); use MOBY::Config; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::central_db_connection - container object for a specific DB connection =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/OntologyServer.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/OntologyServer.pm 2008/08/22 18:30:50 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/OntologyServer.pm 2008/09/02 13:14:18 1.3 @@ -70,6 +70,10 @@ use DBI; use DBD::mysql; use MOBY::Config; + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + my $debug = 0; { =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/dbConfig.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/dbConfig.pm 2008/06/20 19:50:55 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/dbConfig.pm 2008/09/02 13:14:18 1.3 @@ -2,6 +2,10 @@ use strict; use Carp; use vars qw($AUTOLOAD); + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use Text::Shellwords; { =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm 2008/07/07 16:29:19 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm 2008/09/02 13:14:18 1.4 @@ -3,11 +3,10 @@ use strict; use warnings; - - use vars qw{$VERSION @ISA @EXPORT @EXPORT_OK}; +# add versioning to this module BEGIN { - $VERSION = '0.85'; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; @ISA = qw{ Exporter }; @EXPORT = qw{}; @EXPORT_OK = qw{}; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm 2008/09/02 13:14:18 1.3 @@ -4,6 +4,9 @@ my $XSLTPROC = '/usr/bin/xsltproc';#Where your xsltproc binary is located my $XSL_SHEET = 'xsl/parseMobyMessage.xsl';#Where your xsltproc style-sheet is located +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #$Id$ =pod =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm 2008/09/02 13:14:18 1.3 @@ -4,6 +4,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::service_type - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::authority - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/01 19:01:49 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/02 13:14:18 1.5 @@ -239,6 +239,10 @@ use constant BE_STRICT => 0; our @ISA = qw(Exporter); our @EXPORT = qw(COLLECTION SIMPLE SECONDARY PARAMETER BE_NICE BE_STRICT); + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + our %EXPORT_TAGS = ( all => [ qw( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/mysql.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/mysql.pm 2008/02/21 17:58:58 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/mysql.pm 2008/09/02 13:14:18 1.3 @@ -4,6 +4,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::mysql - makes a MYSQL database connection. =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm 2008/08/22 19:12:20 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm 2008/09/02 13:14:18 1.7 @@ -27,6 +27,9 @@ use LWP; use MOBY::CommonSubs; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use Encode; use MOBY::MobyXMLConstants; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/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-Server/lib/MOBY/Config.pm 2008/04/15 00:26:29 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Config.pm 2008/09/02 13:14:18 1.5 @@ -41,6 +41,9 @@ use vars qw($AUTOLOAD); use Text::Shellwords; use vars '$VERSION', '@ISA', '@EXPORT', '$CONFIG'; + +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + @ISA = qw(Exporter); @EXPORT = ('$CONFIG'); { =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::CrossReference - a small object describing a MOBY Simple input/output article =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::collection_output - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::simple_input - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::simple_output - a lightweight connection to the From kawas at dev.open-bio.org Tue Sep 2 09:14:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:14:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021314.m82DEuEG022335@dev.open-bio.org> kawas Tue Sep 2 09:14:56 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv22300/Perl/MOBY-Server Modified Files: Changes Log Message: added all known changes that have been committed to this file moby-live/Perl/MOBY-Server Changes,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2008/07/02 20:51:33 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2008/09/02 13:14:56 1.12 @@ -1,5 +1,24 @@ Revision history for Perl extension MOBY. +1.06 + - Changes to makefile reflecting the cpan addition of wsrf. + - Added Boolean to the data sql dump file for initializing + a new registry. + - Added character encoding checks to the data kept in the + registry. All data used in the register* methods are + checked to be encoded in UTF-8 + - Added $VERSION info for all the modules. Sorry if this + creates some initial confusion; The longer term gains + far exceed any short term disruptions. + - Cosmetic fixes in Service.pm and SimpleServer.pm. + - Fixed a bug in WSRF.pm related to temporal file location/creation + introduced by a previous commit + - Bug fix related to asynchronous MOBY calls with empty mobyData elements. + MOBY::Async::SimpleServer uses serviceInputParser, which had the bug fixed. + - + - + + 1.05 - Multiple bug fixes / additions to installer (thanks to Jason Stewart), From kawas at dev.open-bio.org Tue Sep 2 09:15:34 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:15:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021315.m82DFY1q022411@dev.open-bio.org> kawas Tue Sep 2 09:15:34 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv22376/Perl/MOBY-Server Modified Files: README Log Message: updated the README to reflect the fact that WSRF-lite is now available on cpan moby-live/Perl/MOBY-Server README,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/README 2008/07/07 16:29:39 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/README 2008/09/02 13:15:34 1.3 @@ -25,25 +25,6 @@ each dependency independently and install them as per their installation instructions. -WRSF::Lite - -If module 'WSRF::Lite' is not installed and you are -thinking about developing BioMOBY Asynchronous service, -then following is for you! - -Unfortunately, this module is not available on CPAN -and must be manually installed. Some of the -dependencies are beta and as such, may not be stable. - -Try downloading it from the following link: - -http://www.rcs.manchester.ac.uk/research/projects/wsrflite - -or you can try searching the net with Google using the keywords: - - 'perl WSRF::Lite' - - COPYRIGHT AND LICENCE Copyright (C) 2003 BioMoby Developers Group (www.biomoby.org) From kawas at dev.open-bio.org Tue Sep 2 09:17:25 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:17:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021317.m82DHPIC022487@dev.open-bio.org> kawas Tue Sep 2 09:17:25 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv22452/Perl/MOBY-Server Modified Files: Makefile.PL Log Message: updated the makefile to reflect the fact that wsrf is now in cpan. added some missing requires that other modules that we 'use' dont properly specify in their makefile moby-live/Perl/MOBY-Server Makefile.PL,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/07/02 20:49:44 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/09/02 13:17:25 1.9 @@ -3,7 +3,7 @@ # Define metadata name 'MOBY'; - version '1.05'; + version '1.06'; license 'perl'; abstract 'This distribution is for communicating with or creating your own MOBY Central registry'; @@ -15,6 +15,7 @@ requires 'SOAP::Lite' => '0.69'; requires 'XML::LibXML' => '1.62'; requires 'IO::Stringy' => '2.110'; + requires 'File::HomeDir' => '0.8'; requires 'Unicode::String' => '2.09'; requires 'File::ShareDir' => '0.05'; requires 'Template' => '0'; @@ -27,6 +28,9 @@ requires 'DBI' => '0.01'; requires 'DBD::mysql' => '0.01'; + # MOBY::Async requires + requires 'WSRF::Lite' => '0.8.2.3'; + if ( not( $^O =~ /MSWin32|Windows_NT/i ) ) { # non portable requires @@ -34,49 +38,6 @@ requires 'IO::Prompt' => '0.99.2'; requires 'IPC::Shareable' => '0.6'; - # check for WSRF - eval "require WSRF::Lite"; - if ($@) { - - # WSRF not installed ... tell them where to get it - print STDOUT <<'END_OF_TEXT'; - -################### IMPORTANT ################### - - WSRF lite is not installed on your system. - Unfortunately, at this time, this Makefile - cannot automatically find and install it for - you. You will have to install it manually. - - The last known URL of where you could find - this package is @ - http://www.rcs.manchester.ac.uk/research/wsrflite - - If that url does not exist, please search with - google using the phrase 'WSRF-Lite'. - - Sorry for any inconvenience caused! - -################################################## - -END_OF_TEXT - - } - - # MOBY::Async requires - requires 'WSRF::Lite' => '0.008.2.2'; - requires 'XML::DOM' => ''; - requires 'DateTime::Format::Epoch' => ''; - requires 'DateTime::Format::W3CDTF' => ''; - requires 'HTTP::Daemon' => ''; - requires 'HTTP::Daemon::SSL' => ''; - requires 'MIME::Base64' => ''; - requires 'Digest::SHA1' => ''; - requires 'Crypt::OpenSSL::RSA' => ''; - requires 'XML::CanonicalizeXML' => '0.02'; - requires 'Sys::Hostname::Long' => ''; - requires 'Crypt::OpenSSL::X509' => '0'; - } else { print STDOUT <<'END_OF_TEXT'; @@ -89,8 +50,7 @@ required libraries. The libraries in question are as follows: - IPC::Shareable, IO::Prompt, - WSRF-Lite, & Crypt-OpenSSL-X509. + IPC::Shareable, IO::Prompt. Sorry for any inconvenience caused! From kawas at dev.open-bio.org Tue Sep 2 09:19:14 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:19:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021319.m82DJE3q022563@dev.open-bio.org> kawas Tue Sep 2 09:19:14 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv22528/Perl/MOBY-Server/bin/scripts Modified Files: moby-s-install.pl Log Message: removed a module check that wsrf no longer requires. moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl 2008/07/02 20:49:23 1.12 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl 2008/09/02 13:19:13 1.13 @@ -107,7 +107,6 @@ Crypt::OpenSSL::RSA Sys::Hostname::Long HTTP::Daemon::SSL - XML::CanonicalizeXML / ) { check_module($module); From kawas at dev.open-bio.org Tue Sep 2 12:35:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 12:35:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021635.m82GZW46023012@dev.open-bio.org> kawas Tue Sep 2 12:35:32 EDT 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv22981/Docs/MOBY-S_API/Perl Added Files: construct_moses_async_service.html Log Message: how to use MOSES to create perl asynchronous services **Missing section on testing** - will be completed very shortly! moby-live/Docs/MOBY-S_API/Perl construct_moses_async_service.html,NONE,1.1 From kawas at dev.open-bio.org Tue Sep 2 13:58:02 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 13:58:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021758.m82Hw25r023100@dev.open-bio.org> kawas Tue Sep 2 13:58:02 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv23065/Perl/MOSES-MOBY/bin/scripts Modified Files: moses-testing-service.pl Log Message: service tester script now incorporates the async client code for calling async services. there are no limitations to the number of 'jobs' submitted (can handle 0 or more jobs per message) moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl 2008/05/06 16:52:48 1.6 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl 2008/09/02 17:58:02 1.7 @@ -7,14 +7,15 @@ # ----------------------------------------------------------- BEGIN { - # some command-line options - use Getopt::Std; - use vars qw/ $opt_h $opt_d $opt_v $opt_l $opt_e $opt_c /; - getopts ('hdvl:e:c:'); - - # usage - if ($opt_h or (@ARGV == 0 and (not $opt_c))) { - print STDOUT <<'END_OF_USAGE'; + + # some command-line options + use Getopt::Std; + use vars qw/ $opt_h $opt_d $opt_v $opt_l $opt_e $opt_c $opt_a /; + getopts('hdvl:e:c:a:'); + + # usage + if ( $opt_h or ( @ARGV == 0 and ( not $opt_c ) ) ) { + print STDOUT <<'END_OF_USAGE'; Calling a BioMoby services (without using SOAP, just locally). Usage: # calling a local module representing a service, without using SOAP [-vd] [-l ] [] @@ -31,6 +32,9 @@ # calling a real service, using cgi -c [] + # calling a real service, using SOAP + -a [] + is a full name of a called module (service) e.g. Service::Mabuhay @@ -46,6 +50,10 @@ A cgi biomoby service url (e.g. http://localhost/cgi-bin/HelloBiomobyWorld.cgi) + -a + An asynchronous service url + (e.g. http://localhost/cgi-bin/AsyncMobyServer.cgi) + A BioMoby XML file with input data. Default: an empty BioMoby request @@ -54,38 +62,49 @@ -d ... debug -h ... help END_OF_USAGE - exit (0); - } + exit(0); + } -# use MOSES::MOBY::Base; - # load modules, depending on the mode of calling - if ($opt_e) { - # calling a real service, using SOAP - eval "use SOAP::Lite; 1;" - or die "$@\n"; - - } elsif ($opt_c) { - # calling a real service, using cgi - eval "use HTTP::Request; 1;" - or die "$@\n"; - eval "use LWP::UserAgent; 1;" - or die "$@\n"; - }else { - # calling a local service module, without SOAP - eval "use MOSES::MOBY::Base; 1;"; - # take the lib location from the config file - require lib ; lib->import (MOSES::MOBY::Config->param ("generators.impl.outdir")); - require lib ; lib->import (MOSES::MOBY::Config->param ("generators.outdir")); - unshift (@INC, $opt_l) if $opt_l; - $LOG->level ('INFO') if $opt_v; - $LOG->level ('DEBUG') if $opt_d; - } + # use MOSES::MOBY::Base; + # load modules, depending on the mode of calling + if ($opt_e) { + + # calling a real service, using SOAP + eval "use SOAP::Lite; 1;" + or die "$@\n"; + } elsif ($opt_c) { + + # calling a real service, using cgi + eval "use HTTP::Request; 1;" + or die "$@\n"; + eval "use LWP::UserAgent; 1;" + or die "$@\n"; + } else { + + # calling a local service module, without SOAP + eval "use MOSES::MOBY::Base; 1;"; + + # take the lib location from the config file + require lib; + lib->import( MOSES::MOBY::Config->param("generators.impl.outdir") ); + require lib; + lib->import( MOSES::MOBY::Config->param("generators.outdir") ); + unshift( @INC, $opt_l ) if $opt_l; + $LOG->level('INFO') if $opt_v; + $LOG->level('DEBUG') if $opt_d; + } + # load these modules always to get constants and to avoid warnings + eval "use MOBY::Async::LSAE; 1;" + or die "$@\n"; + eval "use MOBY::Async::WSRF; 1;" + or die "$@\n"; + } use strict; sub _empty_input { - return <<'END_OF_XML'; + return <<'END_OF_XML'; @@ -95,78 +114,286 @@ END_OF_XML } +sub _get_query_ids { + my $input = shift; + my @query_ids = (); + my $parser = XML::LibXML->new(); + my $doc = $parser->parse_string($input); + my $iterator = $doc->getElementsByLocalName("mobyData"); + for ( 1 .. $iterator->size() ) { + my $node = $iterator->get_node($_); + my $id = $node->getAttribute("queryID") + || $node->getAttribute( + $node->lookupNamespacePrefix($WSRF::Constants::MOBY_MESSAGE_NS) + . ":queryID" ); + push @query_ids, $id; + } + return @query_ids; +} + # --- what service to call -my $module = shift unless $opt_c; # eg. Service::Mabuhay, or just Mabuhay +my $module = shift unless $opt_c; # eg. Service::Mabuhay, or just Mabuhay my $service; -($service = $module) =~ s/.*::// unless $opt_c; +( $service = $module ) =~ s/.*::// unless $opt_c; # --- call the service if ($opt_e) { - # calling a real service, using SOAP - my $soap = SOAP::Lite - -> uri ("http://biomoby.org/") - -> proxy ($opt_e) - -> on_fault (sub { - my $soap = shift; - my $res = shift; - my $msg = - ref $res ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring - : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n"; - die $msg; - }); - - my $input = ''; - if (@ARGV > 0) { - my $data = shift; # a file name - open INPUT, "<$data" - or die "Cannot read '$data': $!\n"; - while () { $input .= $_; } - close INPUT; - } else { - $input = _empty_input; - } - - print $soap - -> $service (SOAP::Data->type('string' => "$input")) - -> result; + + # calling a real service, using SOAP + my $soap = SOAP::Lite->uri("http://biomoby.org/")->proxy($opt_e)->on_fault( + sub { + my $soap = shift; + my $res = shift; + my $msg = + ref $res + ? "--- SOAP FAULT ---\n" + . $res->faultcode . " " + . $res->faultstring + : "--- TRANSPORT ERROR ---\n" + . $soap->transport->status + . "\n$res\n"; + die $msg; + } + ); + + my $input = ''; + if ( @ARGV > 0 ) { + my $data = shift; # a file name + open INPUT, "<$data" + or die "Cannot read '$data': $!\n"; + while () { $input .= $_; } + close INPUT; + } else { + $input = _empty_input; + } + + print $soap ->$service( SOAP::Data->type( 'string' => "$input" ) )->result; } elsif ($opt_c) { - # calling a real service, using cgi - my $ua = LWP::UserAgent->new; - - my $input = ''; - if (@ARGV > 0) { - my $data = shift; # a file name - open INPUT, "<$data" - or die "Cannot read '$data': $!\n"; - while () { $input .= $_; } - close INPUT; - } else { - $input = _empty_input; - } - my $req = HTTP::Request->new(POST => $opt_c); + # calling a real service, using cgi + my $ua = LWP::UserAgent->new; + + my $input = ''; + if ( @ARGV > 0 ) { + my $data = shift; # a file name + open INPUT, "<$data" + or die "Cannot read '$data': $!\n"; + while () { $input .= $_; } + close INPUT; + } else { + $input = _empty_input; + } + + my $req = HTTP::Request->new( POST => $opt_c ); $req->content_type('application/x-www-form-urlencoded'); $req->content("data=$input"); print "\n" . $ua->request($req)->as_string . "\n"; +} elsif ($opt_a) { + + # calling a real service, using async soap + # call using async mode for async service ... _submit + $service .= "_submit"; + + # set up the wsrf call + my $soap = WSRF::Lite->proxy($opt_a)->uri($WSRF::Constants::MOBY)->on_fault( + sub { + my $soap = shift; + my $res = shift; + my $msg = + ref $res + ? "--- SOAP FAULT ---\n" + . $res->faultcode . " " + . $res->faultstring + : "--- TRANSPORT ERROR ---\n" + . $soap->transport->status + . "\n$res\n"; + die $msg; + } + ); + + # get the input + my $input = ''; + if ( @ARGV > 0 ) { + my $data = shift; # a file name + open INPUT, "<$data" + or die "Cannot read '$data': $!\n"; + while () { $input .= $_; } + close INPUT; + } else { + $input = _empty_input; + } + + # extract all of the query ids from $input + my @query_ids = _get_query_ids($input); + print "\nSending the following data to $service asynchronously:\n", + $input, "\n" + if $opt_v; + + # submit the job + my $epr = + ( $soap->$service( SOAP::Data->type( 'string' => "$input" ) )->result ); + + # Get address from the returned Endpoint Reference + my $address = $epr->{'EndpointReference'}->{Address}; + + # Get resource identifier from the returned Endpoint Reference + my $identifier = + $epr->{'EndpointReference'}->{ReferenceParameters}->{ServiceInvocationId}; + + # Compose the Endpoint Reference + my $EPR = WSRF::WS_Address->new(); + $EPR->Address($address); + $EPR->ReferenceParameters( '' + . $identifier + . '' ); + my %completed = (); + while (1) { + foreach my $queryID (@query_ids) { + + # skip poll if current job completed + next if $completed{$queryID}; + + # poll the service for given query ID + my $searchTerm = ""; + $searchTerm .= +""; + $searchTerm .= "mobyws:status_" . $queryID; + $searchTerm .= ""; + + $soap = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action( + sub { + sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], + $_[1]; + } + )->wsaddress($EPR) + ->GetMultipleResourceProperties( + SOAP::Data->value($searchTerm)->type('xml') ); + + my $parser = XML::LibXML->new(); + my $xml = $soap->raw_xml; + my $doc = $parser->parse_string($xml); + $soap = $doc->getDocumentElement(); + my $prop_name = "status_" . $queryID; + + my ($prop) = + $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, + $prop_name ) + || $soap->getElementsByTagName($prop_name); + my $event = $prop->getFirstChild->toString + unless ref $prop eq "XML::LibXML::NodeList"; + $event = $prop->pop()->getFirstChild->toString + if ref $prop eq "XML::LibXML::NodeList"; + + my $status = LSAE::AnalysisEventBlock->new($event); + if ( $status->type == LSAE_PERCENT_PROGRESS_EVENT ) { + if ( $status->percentage >= 100 ) { + $completed{$queryID} = 1; + } elsif ( $status->percentage < 100 ) { + print "Current percentage: ", $status->percentage, "\n" if $opt_v; + sleep(20); + } else { + die "ERROR: analysis event block not well formed.\n"; + } + + } elsif ( $status->type == LSAE_STATE_CHANGED_EVENT ) { + if ( ( $status->new_state =~ m"completed"i ) + || ( $status->new_state =~ m"terminated_by_request"i ) + || ( $status->new_state =~ m"terminated_by_error"i ) ) + { + $completed{$queryID} = 1; + } elsif ( ( $status->new_state =~ m"created"i ) + || ( $status->new_state =~ m"running"i ) ) + { + print "Current State: ", $status->new_state, "\n" if $opt_v; + sleep(20); + } else { + die "ERROR: analysis event block not well formed.\n"; + } + + } elsif ( $status->type == LSAE_STEP_PROGRESS_EVENT ) { + if ( $status->steps_completed >= $status->total_steps ) { + $completed{$queryID} = 1; + } elsif ( $status->steps_completed < $status->total_steps ) { + print "Steps completed: ", $status->steps_completed, "\n" if $opt_v; + sleep(20); + } else { + die "ERROR: analysis event block not well formed.\n"; + } + + } elsif ( $status->type == LSAE_TIME_PROGRESS_EVENT ) { + if ( $status->remaining == 0 ) { + $completed{$queryID} = 1; + } elsif ( $status->remaining > 0 ) { + print "Time remaining: ", $status->remaining, "\n" if $opt_v; + sleep(20); + } else { + die "ERROR: analysis event block not well formed.\n"; + } + } + } + last if scalar keys(%completed) == $#query_ids + 1; + } + + foreach my $queryID (@query_ids) { + # get the result + my $searchTerm .= +""; + $searchTerm .= "mobyws:result_" . $queryID; + $searchTerm .= ""; + my $ans = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action( + sub { + sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], + $_[1]; + } + )->wsaddress($EPR) + ->GetMultipleResourceProperties( + SOAP::Data->value($searchTerm)->type('xml') ); + die "ERROR: " . $ans->faultstring if ( $ans->fault ); + + my $parser = XML::LibXML->new(); + my $xml = $ans->raw_xml; + my $doc = $parser->parse_string($xml); + $soap = $doc->getDocumentElement(); + my $prop_name = "result_" . $queryID; + my ($prop) = + $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name ) + || $soap->getElementsByTagName($prop_name); + my $result = $prop->getFirstChild->toString + unless ref $prop eq "XML::LibXML::NodeList"; + $result = $prop->pop()->getFirstChild->toString + if ref $prop eq "XML::LibXML::NodeList"; + print $result; + } + + # destroy the result + my $ans = WSRF::Lite->uri($WSRF::Constants::WSRL)->on_action( + sub { + sprintf '%s/ImmediateResourceTermination/%sRequest', + $WSRF::Constants::WSRLW, $_[1]; + } + )->wsaddress($EPR)->Destroy(); + } else { - # calling a local service module, without SOAP - my $data; - if (@ARGV > 0) { - $data = shift; # a file name - } else { - use File::Temp qw( tempfile ); - my $fh; - ($fh, $data) = tempfile (UNLINK => 1); - print $fh _empty_input(); - close $fh; - } - eval "require $module" or croak $@; - eval { - my $target = new $module; - print $target->$service ($data), "\n"; - } or croak $@; + + # calling a local service module, without SOAP + my $data; + if ( @ARGV > 0 ) { + $data = shift; # a file name + } else { + use File::Temp qw( tempfile ); + my $fh; + ( $fh, $data ) = tempfile( UNLINK => 1 ); + print $fh _empty_input(); + close $fh; + } + eval "require $module" or croak $@; + eval { + my $target = new $module; + print $target->$service($data), "\n"; + } or croak $@; } __END__ From kawas at dev.open-bio.org Tue Sep 2 13:58:54 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 13:58:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021758.m82HwsW6023176@dev.open-bio.org> kawas Tue Sep 2 13:58:54 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv23141/Perl/MOSES-MOBY Modified Files: Makefile.PL Log Message: makefile has been updated to always check for wsrf lite and moby client central code. moby-live/Perl/MOSES-MOBY Makefile.PL,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL 2008/08/25 16:27:28 1.7 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL 2008/09/02 17:58:54 1.8 @@ -33,15 +33,11 @@ requires 'Want' => '0.18'; requires 'IO::Prompt' => '0.99.2'; } - - print STDOUT "Shall I check for async libraries (do you plan on writing async services)? y/n [n] "; - my $tmp = ; - $tmp =~ s/\s//g; - if ($tmp =~ /y/i) { - requires 'MOBY::Client::Central' => 1.03; - requires 'WSRF::Lite' => 0.8.8.2; - } - + + # for async services + requires 'MOBY::Client::Central' => 1.06; + requires 'WSRF::Lite' => '0.8.2.3'; + build_requires 'Test::More' => '0.42'; no_index 'directory' => 'bin/scripts'; From kawas at dev.open-bio.org Tue Sep 2 14:25:37 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 14:25:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021825.m82IPb3t023303@dev.open-bio.org> kawas Tue Sep 2 14:25:37 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv23268/Perl/MOBY-Server/lib/MOBY/Async Modified Files: WSRF.pm Log Message: added no warnings 'redefine'; so that messages like: Subroutine header redefined ../MOBY/Async/WSRF.pm line 474. Subroutine new redefined at ../MOBY/Async/WSRF.pm line 647. Subroutine DESTROY redefined at ... /MOBY/Async/WSRF.pm line 657. are suppressed. moby-live/Perl/MOBY-Server/lib/MOBY/Async WSRF.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm 2008/09/01 18:53:57 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm 2008/09/02 18:25:37 1.7 @@ -470,7 +470,7 @@ $WSRF::Constants::WSRP => [$WSRF::Constants::WSRPW,undef], $WSRF::Constants::WSRL => [$WSRF::Constants::WSRLW,'ImmediateResourceTermination'] ); - +no warnings 'redefine'; sub header { my ($envelope, %args) = @_; my $myHeader; From kawas at dev.open-bio.org Tue Sep 2 14:27:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 14:27:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021827.m82IRFpI023343@dev.open-bio.org> kawas Tue Sep 2 14:27:15 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv23308/Perl/MOBY-Server Modified Files: Changes Log Message: added changes to reflect the addition of code to suppress redefinition warnings for MOBY::Async::WSRF moby-live/Perl/MOBY-Server Changes,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2008/09/02 13:14:56 1.12 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2008/09/02 18:27:15 1.13 @@ -15,7 +15,8 @@ introduced by a previous commit - Bug fix related to asynchronous MOBY calls with empty mobyData elements. MOBY::Async::SimpleServer uses serviceInputParser, which had the bug fixed. - - + - Added "no warnings 'redefine';" to MOBY::Async::WSRF to suppress redefinition + warnings. - From kawas at dev.open-bio.org Tue Sep 2 14:48:23 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 14:48:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021848.m82ImNfP023428@dev.open-bio.org> kawas Tue Sep 2 14:48:23 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv23393/src/main/org/biomoby/service/dashboard Modified Files: PerlMoSeSPanel.java Log Message: added an option to generate async services moby-live/Java/src/main/org/biomoby/service/dashboard PerlMoSeSPanel.java,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java 2008/06/12 16:46:52 1.12 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java 2008/09/02 18:48:23 1.13 @@ -87,6 +87,9 @@ // boolean do we generate soap services static String PM_SOAP = "perl-moses-soap"; + + // boolean do we generate async services + static String PM_ASYNC = "perl-moses-async"; // boolean: are we currently updating the datatype cache static String PM_SYNC_DATATYPES = "perl-moses-sync-datatypes"; @@ -298,6 +301,7 @@ propertyChannel.put(PM_SYNC_DATATYPES, new Boolean(false)); propertyChannel.put(PM_OVERWRITE, new Boolean(false)); propertyChannel.put(PM_CGI, new Boolean(false)); + propertyChannel.put(PM_ASYNC, new Boolean(false)); propertyChannel.put(PM_PERL_INSTALL_DIR, getPrefValue(PM_PERL_INSTALL_DIR, "")); propertyChannel.put(PM_PERL_LIB_1, getPrefValue(PM_PERL_LIB_1, "")); @@ -514,14 +518,16 @@ }); generateBtn.setEnabled(enable_moses_actions); ButtonGroup group = new ButtonGroup(); - JRadioButton genCgi, genSoap; - group.add (genCgi = createHowToButton ("Generate CGI Service", PM_CGI)); + JRadioButton genCgi, genSoap, genAsync; + group.add (genCgi = createHowToButton ("Generate CGI Service", PM_CGI)); group.add (genSoap = createHowToButton ("Generate SOAP Service", PM_SOAP)); + group.add (genAsync = createHowToButton ("Generate ASYNC Service", PM_ASYNC)); SwingUtils.addComponent(bPanel, genOverwrite, 0, 0, 1, 1, NONE, NWEST, 0.0, 0.0); SwingUtils.addComponent(bPanel, genCgi, 0, 1, 2, 1, NONE, NWEST, 0.0, 0.0); SwingUtils.addComponent(bPanel, genSoap, 0, 2, 2, 1, NONE, NWEST, 0.0, 0.0); - SwingUtils.addComponent(bPanel, generateBtn, 0, 3, 2, 1, HORI, NWEST, 0.0, 0.0); + SwingUtils.addComponent(bPanel, genAsync, 0, 3, 2, 1, NONE, NWEST, 0.0, 0.0); + SwingUtils.addComponent(bPanel, generateBtn, 0, 4, 2, 1, HORI, NWEST, 0.0, 0.0); // add to the main panel int count = 0; @@ -816,17 +822,20 @@ JRadioButton radio = new JRadioButton (title); radio.setActionCommand (howTo); radio.addActionListener (howToListener); - if (!howTo.equals(PM_CGI)) { + if (!howTo.equals(PM_CGI) && !howTo.equals(PM_ASYNC)) { radio.setSelected (true); radio.setEnabled (true); + propertyChannel.put (PM_CGI, false); + propertyChannel.put (PM_ASYNC, false); } - propertyChannel.put (PM_CGI, false); return radio; } private ActionListener howToListener = new ActionListener() { public void actionPerformed (ActionEvent e) { String howTo = e.getActionCommand(); propertyChannel.put (PM_CGI, howTo.equals(PM_CGI)); + propertyChannel.put (PM_ASYNC, howTo.equals(PM_ASYNC)); + propertyChannel.put (PM_SOAP, howTo.equals(PM_SOAP)); } }; private JPanel getServicesSelectionPanel() { @@ -1097,7 +1106,10 @@ if (Boolean.parseBoolean(propertyChannel .getString(PM_CGI))){ command.add("-c"); - } + } else if (Boolean.parseBoolean(propertyChannel + .getString(PM_ASYNC))){ + command.add("-A"); + } command.add(authority); // place command into com String[] com = command.toArray(new String[] {}); @@ -1189,6 +1201,9 @@ if (Boolean.parseBoolean(propertyChannel .getString(PM_CGI))){ command.add("-c"); + } else if (Boolean.parseBoolean(propertyChannel + .getString(PM_ASYNC))){ + command.add("-A"); } command.add(auth); command.add(name); From kawas at dev.open-bio.org Tue Sep 2 15:04:36 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 15:04:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021904.m82J4a8r023474@dev.open-bio.org> kawas Tue Sep 2 15:04:36 EDT 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv23438/Docs/MOBY-S_API/Perl Modified Files: construct_moses_async_service.html Log Message: updated the service testing section. this document is now up to date. moby-live/Docs/MOBY-S_API/Perl construct_moses_async_service.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html 2008/09/02 16:35:32 1.1 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html 2008/09/02 19:04:36 1.2 @@ -130,9 +130,9 @@ Done.

If you happen to see redefinition warnings, please just ignore them; The warnings look like the following:

Generating services from samples.jmoby.net:
-Subroutine header redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 521.
+Subroutine header redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 521.
 Subroutine new redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 694.
-Subroutine DESTROY redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 704.
+Subroutine DESTROY redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 704.
 Done.

Basically, we used the script moses-generate-services.pl to:

    @@ -170,6 +170,11 @@ value => "$string", # TO BE EDITED ); +

    Optionally, to test out the asynchronous aspect of our service, feel free to slow your service down. Something like the following would do that for you:

    +
    # this will cause our service to sleep for 60 seconds
    +# as long as data was sent to our service
    +sleep(60) if defined $my_input_string;
    +

    You can add the optional code below the definition of $my_reverse_string.

    That is all there is to it. Now we can test our service!

    Service testing

    To test the service, issue the following command:

    @@ -195,15 +200,23 @@

    You only have to do this once. In other words, all other asynchronous SOAP based services that you construct using MoSeS automatically use that cgi-bin script, because the moses-generate-services.pl script updates the ASYNC_SERVICE_TABLE that we talked about earlier.

    Service testing using SOAP

    Now that the service has been deployed, you can test it using WSRF/SOAP with the following command:

    -
    moses-testing-service.pl -e http://localhost/cgi-bin/MobyServer.cgi getReverseEchoString input.xml
    -

    When we call the script with the -e option, we tell the moses-testing-service.pl script that we would like to call our service using SOAP. We then must provide the script with 2 or 3 parameters:

    +
    moses-testing-service.pl -v -a http://localhost/cgi-bin/AsyncMobyServer.cgi getReverseEchoString input.xml
    +

    The -v option is just a flag that makes the script be verbose, so that you can see what is going on.

    +

    When we call the script with the -a option, we tell the moses-testing-service.pl script that we would like to call our service using Asynchronous SOAP. We then must provide the script with 2 or 3 parameters:

    1. the url to the service
    2. the name of the service that we would like to call
    3. an optional file containing the input to our service

    The expected output should be very similar to the output we saw above when we tested our service:

    -
    <?xml version="1.0"?>
    <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
    <moby:mobyContent moby:authority="samples.jmoby.net">
    <moby:serviceNotes>
    <moby:Notes>Response created at Thu May 1 19:22:00 2008 (GMT), by the service 'getReverseEchoString'.</moby:Notes>
    </moby:serviceNotes>
    <moby:mobyData moby:queryID="job_0">
    <moby:Simple moby:articleName="my_reverse_string">
    <moby:String moby:id="" moby:namespace="">!desrever gnirts siht tnaw I</moby:String>
    </moby:Simple>
    </moby:mobyData>
    </moby:mobyContent>
    </moby:MOBY>
    +
    +Sending the following data to getReverseEchoString_submit asynchronously:
    <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
    <moby:mobyContent>
    <moby:mobyData moby:queryID="job_0">
    <moby:Simple moby:articleName="my_input_string">
    <moby:String moby:id="" moby:namespace="">I want this string reversed!</moby:String>
    </moby:Simple>
    </moby:mobyData>
    </moby:mobyContent>
    </moby:MOBY> + + +Current State: running
    Current State: running
    Current State: running + + +<?xml version="1.0"?>
    <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
    <moby:mobyContent moby:authority="samples.jmoby.net">
    <moby:serviceNotes>
    <moby:Notes>Response created at Thu May 1 19:22:00 2008 (GMT), by the service 'getReverseEchoString'.</moby:Notes>
    </moby:serviceNotes>
    <moby:mobyData moby:queryID="job_0">
    <moby:Simple moby:articleName="my_reverse_string">
    <moby:String moby:id="" moby:namespace="">!desrever gnirts siht tnaw I</moby:String>
    </moby:Simple>
    </moby:mobyData>
    </moby:mobyContent>
    </moby:MOBY>

    That's all there is to constructing asynchronous SOAP based Perl MoSeS services!

    From gordonp at dev.open-bio.org Wed Sep 10 15:36:45 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 10 Sep 2008 15:36:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809101936.m8AJajQc027466@dev.open-bio.org> gordonp Wed Sep 10 15:36:44 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv27430/src/main/org/biomoby/shared/data Modified Files: MobyDataComposite.java Log Message: Added support for put() in datatypes not found in the registry (i.e. the HAS/HAS-A relationship for the member is not validated) moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.26,1.27 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/02/13 09:26:08 1.26 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/09/10 19:36:44 1.27 @@ -418,7 +418,17 @@ MobyRelationship relationship = getDataType().getChild(fieldName); if(relationship == null){ - relationship = MobyDataType.getDataType(getDataType().getName(), getDataType().getRegistry()).getChild(fieldName); + MobyDataType t = MobyDataType.getDataType(getDataType().getName(), getDataType().getRegistry()); + if(t == null){ + System.err.println("Data type " + getDataType().getName() + " is not in the registry: " + + "validity of member put() operation will not be confirmed"); + relationship = new MobyRelationship(fieldName, + value.getDataType().getName(), + members.containsKey(fieldName) ? Central.iHAS : Central.iHASA); + } + else{ + relationship = t.getChild(fieldName); + } if(relationship == null){ String memberNames = ""; for(MobyRelationship rel: getDataType().getChildren()){ From gordonp at dev.open-bio.org Wed Sep 10 16:02:11 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 10 Sep 2008 16:02:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809102002.m8AK2B4E027598@dev.open-bio.org> gordonp Wed Sep 10 16:02:11 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv27562/src/Clients Modified Files: TestClientServiceChain.java Log Message: Updte to reflect MobyRequest's setSecondaries throwing exceptions now moby-live/Java/src/Clients TestClientServiceChain.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestClientServiceChain.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/Clients/TestClientServiceChain.java 2006/12/14 19:37:37 1.1 +++ /home/repository/moby/moby-live/Java/src/Clients/TestClientServiceChain.java 2008/09/10 20:02:11 1.2 @@ -36,7 +36,7 @@ } } - public static void setSecondaries(MobyRequest mr, MobyService service){ + public static void setSecondaries(MobyRequest mr, MobyService service) throws Exception{ MobySecondaryData[] secondaryData = service.getSecondaryInputs(); MobyDataSecondaryInstance[] secondaryInstances = new MobyDataSecondaryInstance[secondaryData.length]; From gordonp at dev.open-bio.org Wed Sep 10 16:02:42 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 10 Sep 2008 16:02:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809102002.m8AK2gwq027642@dev.open-bio.org> gordonp Wed Sep 10 16:02:41 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv27606/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyServicesGUI.java Log Message: Updte to reflect MobyRequest's setSecondaries throwing exceptions now moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java 2008/01/08 15:27:50 1.14 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java 2008/09/10 20:02:41 1.15 @@ -195,11 +195,11 @@ try{ mobyRequest.setInput(castInputs); + mobyRequest.setSecondaryInput(secondaryInputInstances); } catch(MobyException me){ me.printStackTrace(); logger.warn("Error while trying to set service input: " + me); } - mobyRequest.setSecondaryInput(secondaryInputInstances); executeService(handler); } From gordonp at dev.open-bio.org Wed Sep 10 16:04:03 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 10 Sep 2008 16:04:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809102004.m8AK43WO027686@dev.open-bio.org> gordonp Wed Sep 10 16:04:02 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv27650/src/main/org/biomoby/client Modified Files: MobyRequest.java Log Message: MobyRequest's setSecondaries throws exceptions now if the parameters are blank or overwrite primary params with the same name moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.37,1.38 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.37 retrieving revision 1.38 diff -u -r1.37 -r1.38 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2008/01/26 17:54:59 1.37 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2008/09/10 20:04:02 1.38 @@ -230,8 +230,10 @@ * in this object. This is covenient if you are running 100 seqs through BLAST and only want to set * the parameters once. If you instead want to set secondary input differently for all primary inputs, you'll * need to create a custom MobyContentInstance as input to setInput(). + * + * @throws MobyException if a parameter name is blank, or overrides a primary parameter */ - public void setSecondaryInput(MobyDataSecondaryInstance[] secondaryData){ + public void setSecondaryInput(MobyDataSecondaryInstance[] secondaryData) throws MobyException{ Iterator queryNames = inputData.keySet().iterator(); // For each query @@ -239,7 +241,15 @@ MobyDataJob queryParams = inputData.get(queryNames.next()); // Set all the secondary params (overwrites any old ones) for(int i = 0; i < secondaryData.length; i++){ - queryParams.put(secondaryData[i].getName(), secondaryData[i]); + String secName = secondaryData[i].getName(); + if(secName == null || secName.length() == 0){ + throw new MobyException("A secondary parameter cannot have a blank name (array index " + i + ")"); + } + if(queryParams.containsKey(secName) && queryParams.get(secName) instanceof MobyPrimaryData){ + throw new MobyException("A secondary parameter cannot override an existing primary parameter " + + "with the same name (" + secName + ")"); + } + queryParams.put(secName, secondaryData[i]); } } } From kawas at dev.open-bio.org Mon Sep 22 11:42:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 22 Sep 2008 11:42:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809221542.m8MFgSeq013536@dev.open-bio.org> kawas Mon Sep 22 11:42:27 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13501/Perl/MOBY-Server/lib/MOBY Modified Files: CommonSubs.pm Log Message: tried to remove dependency on the 'moby' prefix when resolving attributes. need to do this for elements too. moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/02 13:14:18 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/22 15:42:27 1.6 @@ -1171,7 +1171,7 @@ . "\n called from line $line"; return ''; } - return ( $xref->getAttributeNode($attr) || $xref->getAttributeNode( "moby:$attr" ) ); + return ( $xref->getAttributeNode($attr) || $xref->getAttributeNode( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr" ) ); } sub _moby_getAttribute { @@ -1191,7 +1191,7 @@ . "\n called from line $line"; return ''; } - return ( $xref->getAttribute($attr) || $xref->getAttribute("moby:$attr") ); + return ( $xref->getAttribute($attr) || $xref->getAttribute( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") ); } sub _makeXrefType { From jmrc at dev.open-bio.org Mon Sep 1 18:53:57 2008 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Mon, 1 Sep 2008 14:53:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809011853.m81IrvSL019292@dev.open-bio.org> jmrc Mon Sep 1 14:53:57 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv19249 Modified Files: Service.pm SimpleServer.pm WSRF.pm Log Message: * Cosmetic fixes in Service.pm and SimpleServer.pm. * Fixed a bug in WSRF.pm related to temporal file location/creation introduced by a previous commit. moby-live/Perl/MOBY-Server/lib/MOBY/Async Service.pm,1.2,1.3 SimpleServer.pm,1.2,1.3 WSRF.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm 2008/04/23 13:08:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm 2008/09/01 18:53:57 1.3 @@ -18,8 +18,8 @@ =head1 DESCRIPTION It provides a class to invoke asynchronous services. Its use is very similar to -MOBY::Client::Service, but it also provides additional methods in order to -have more control over the asynchronous service execution. +MOBY::Client::Service because it is its super-class. It also provides additional +methods in order to have more control over the asynchronous service execution. =head1 METHODS @@ -27,7 +27,7 @@ Name : new Function : create a service connection. - Usage : $Service = MOBY::Client::Service->new(@args) + Usage : $Service = MOBY::Async::Service->new(@args) Args : service - string with a WSDL defining an asynchronous MOBY service Returns : MOBY::Async::Service object, undef if no wsdl. @@ -135,6 +135,10 @@ use MOBY::Client::Service; use base qw(MOBY::Client::Service); +sub _getPollingTime($$$@); +sub _getServiceEndpoint($); +sub _getPseudoRandomPollingTime($$); +sub _composeResponse(@); sub new { my ($this, %args) = @_; @@ -162,7 +166,7 @@ my $pollingTime; my ($i, $j) = (0, 1); my @status; - while ( $pollingTime = &_getPollingTime($i, $j, $start, @status) ) { + while ( $pollingTime = _getPollingTime($i, $j, $start, @status) ) { ($i, $j) = ($j, $i+$j); print "(next polling in $pollingTime seconds)\n\n" unless ($self->{silent}); @@ -180,7 +184,7 @@ my @responses = $self->result($EPR, @queryIDs); $self->destroy($EPR); - my $response = &_composeResponse(@responses); + my $response = _composeResponse(@responses); print "Finished.\n\n" unless ($self->{silent}); @@ -239,7 +243,7 @@ # Create the resource and submit the batch-call my $func = $self->{serviceName}.'_submit'; my $ans = WSRF::Lite - -> proxy(&_getServiceEndpoint($self->{service})) + -> proxy(_getServiceEndpoint($self->{service})) -> uri($WSRF::Constants::MOBY) -> $func(SOAP::Data->value($data)->type('string')); die "ERROR: ".$ans->faultstring if ($ans->fault); @@ -296,7 +300,7 @@ my $pollingTime; my ($i, $j) = (0, 1); my @status; - while ( $pollingTime = &_getPollingTime($i, $j, $start, @status) ) { + while ( $pollingTime = _getPollingTime($i, $j, $start, @status) ) { ($i, $j) = ($j, $i+$j); print "(next polling in $pollingTime seconds)\n\n" unless ($self->{silent}); @@ -314,7 +318,7 @@ my @responses = $self->result($EPR, @queryIDs); $self->destroy($EPR); - my $response = &_composeResponse(@responses); + my $response = _composeResponse(@responses); print "Finished.\n\n" unless ($self->{silent}); @@ -372,7 +376,7 @@ # Create the resource and submit the batch-call my $func = $self->{serviceName}.'_submit'; my $ans = WSRF::Lite - -> proxy(&_getServiceEndpoint($self->{service})) + -> proxy(_getServiceEndpoint($self->{service})) -> uri($WSRF::Constants::MOBY) -> $func(SOAP::Data->value($data)->type('string')); die "ERROR: ".$ans->faultstring if ($ans->fault); @@ -512,7 +516,7 @@ die "ERROR: ".$ans->faultstring if ($ans->fault); } -sub _getServiceEndpoint { +sub _getServiceEndpoint($) { my ($wsdl) = @_; $wsdl =~ /address location\s*=\s*["|'](.+)["|']/; @@ -521,10 +525,10 @@ return $serviceEndpoint; } -sub _getPollingTime { +sub _getPollingTime($$$@) { my ($i, $j, $start, @status) = @_; - return &_getPseudoRandomPollingTime($i, $j) unless (scalar(@status)); + return _getPseudoRandomPollingTime($i, $j) unless (scalar(@status)); my $pollingTime = 0; foreach my $status (@status) { @@ -558,7 +562,7 @@ ($status->new_state eq "running") || ($status->new_state eq "RUNNING") ) { - $pTime = &_getPseudoRandomPollingTime($i, $j); + $pTime = _getPseudoRandomPollingTime($i, $j); } else { die "ERROR: analysis event block not well formed.\n"; @@ -597,7 +601,7 @@ return $pollingTime; } -sub _getPseudoRandomPollingTime { +sub _getPseudoRandomPollingTime($$) { my ($i, $j) = @_; my $c = 15; my $p = 0.1; @@ -607,7 +611,7 @@ return $delay; } -sub _composeResponse { +sub _composeResponse(@) { my (@datas) = @_; my @authorities; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2008/04/23 13:08:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2008/09/01 18:53:57 1.3 @@ -178,6 +178,7 @@ # Get mobyData and iterate over them in order to run the service for each one my @mobyData = ($moby->getElementsByTagNameNS($WSRF::Constants::MOBY_MESSAGE_NS,'mobyData')); + foreach my $mobyData (@mobyData) { my $queryID = $mobyData->getAttribute('queryID') || $mobyData->getAttributeNS($WSRF::Constants::MOBY_MESSAGE_NS,'queryID'); my $property_pid = "pid_$queryID"; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm 2008/08/29 14:16:02 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm 2008/09/01 18:53:57 1.6 @@ -28,6 +28,7 @@ package MOBY::Async::WSRF; use strict; use WSRF::Lite 0.8.2.2; +use File::Path; use vars qw /$VERSION/; $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; @@ -37,7 +38,9 @@ $WSRF::WSRP::MobyPropertiesPrefixes = ['status', 'result']; $WSRF::Constants::DataDir = (exists($ENV{TMPDIR}) && defined($ENV{TMPDIR}) && $ENV{TMPDIR} ne '')?$ENV{TMPDIR}:'/tmp'; +mkpath($WSRF::Constants::DataDir,1,0777); $WSRF::Constants::DataPrefix = 'moby_'; +$WSRF::Constants::Data = $WSRF::Constants::DataDir .'/'. $WSRF::Constants::DataPrefix; $WSRF::Constants::MOBY = 'http://biomoby.org/'; $WSRF::Constants::MOBY_MESSAGE_NS = 'http://www.biomoby.org/moby'; #$WSRF::Constants::WSA = 'http://www.w3.org/2005/08/addressing'; @@ -324,60 +327,9 @@ ) ) if (scalar(@notfound)); my @resp = $self->SUPER::GetMultipleResourceProperties($envelope); - return @resp; + return @resp; } -#sub GetMultipleResourcePropertiesRequest { -# my $self = shift @_; -# my $envelope = pop @_; -# my $methodname = (caller(0))[3]; -# $methodname = substr($methodname,rindex($methodname,':')+1); -# eval { -# my $parser=XML::LibXML->new(); -# my $envxml = $parser->parse_string($envelope->raw_xml); -# my $context=XML::LibXML::XPathContext->new(); -# $context->registerNs('s11',$SOAP::Constants::NS_ENV); -# $context->registerNs('wsa',$WSRF::Constants::WSA); -# my(@actions)=$context->findnodes('/s11:Envelope/s11:Header/wsa:Action[1]',$envxml); -# if(scalar(@actions)>0) { -# my($action)=$actions[0]; -# my $acturi = $action->textContent(); -# my $newacturi= $acturi; -# $newacturi =~ s/Request$//; -# if( $acturi ne $newacturi) { -# foreach my $child ($action->childNodes) { -# $action->removeChild($child); -# } -# $action->appendChild($envxml->createTextNode($newacturi)); -# -# -# my(@query)=$context->findnodes("/s11:Envelope/s11:Body/wsa:$methodname".'[1]',$envxml); -# if(scalar(@query)>0) { -# my($prefix)=$query[0]->prefix(); -# if(defined($prefix) && $prefix ne '') { -# $prefix.=':'; -# } else { -# $prefix=''; -# } -# $methodname =~ s/Request$//; -# $query[0]->setNodeName($prefix.$methodname); -# } -# -# # Last, craete new SOM object -# my $sparser = WSRF::Deserializer->new(); -# my($manistring)=$envxml->toString(); -# $manistring =~ s/[\r\n]+//g; -# print STDERR "ENVELOPE ",$manistring,"\n"; -# $envelope = $sparser->deserialize($manistring); -# } -# } -# }; -# -# if($@) { -# print STDERR "FALLACANALLA $@\n"; -# } -# return $self->GetMultipleResourceProperties(@_,$envelope); -#} #=============================================================================== # WSRF::FileBasedMobyResourceLifetimes @@ -414,7 +366,7 @@ my $self = shift @_; my $envelope = pop @_; my $lock = WSRF::MobyFile->new($envelope); - my $file = $WSRF::Constants::DataDir . '/' . $WSRF::Constants::DataPrefix.$lock->ID(); + my $file = $WSRF::Constants::Data.$lock->ID(); unlink $file or WSRF::BaseFaults::die_with_fault( $envelope, ( BaseFault => "ResourceNotDestroyedFault", Description => "Could not remove WS-Resource file" @@ -620,7 +572,7 @@ $ID_clipped =~ s/-\w*//o; # File containing resource properties - my $path = $WSRF::Constants::DataDir . '/' . $WSRF::Constants::DataPrefix.$ID_clipped; + my $path = $WSRF::Constants::Data.$ID_clipped; WSRF::BaseFaults::die_with_fault( $envelope, ( BaseFault => "ResourceUnknownFault", Description => "No WS-Resource with Identifer $ID" From jmrc at dev.open-bio.org Mon Sep 1 18:55:20 2008 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Mon, 1 Sep 2008 14:55:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809011855.m81ItKfl019335@dev.open-bio.org> jmrc Mon Sep 1 14:55:20 EDT 2008 Update of /home/repository/moby/moby-live/Docs/asyncDocs In directory dev.open-bio.org:/tmp/cvs-serv19300/asyncDocs Modified Files: README.txt Log Message: * Added more asynchronous client examples. * README has been updated according to the new example. moby-live/Docs/asyncDocs README.txt,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/asyncDocs/README.txt,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Docs/asyncDocs/README.txt 2008/08/29 14:03:16 1.2 +++ /home/repository/moby/moby-live/Docs/asyncDocs/README.txt 2008/09/01 18:55:20 1.3 @@ -105,13 +105,10 @@ In the Perl script "running_runAsyncMOBYservice.pl" show us how to call our BioMOBY asynchronous service. In the script "running_runAsyncMOBYservice-StepByStep.pl" show us how to call our BioMOBY asynchronous service - controlling the "polling" calls. - - Note: Be carefull!! These scripts are created to be examples. Some part of them are "hardcore". - - - - + controlling the "polling" calls in a very detailed way. + In the script "running_runAsyncMOBYservice-poll.pl" show us how to call our BioMOBY asynchronous service + controlling the "polling" calls in a "quick&dirty" way. + Note: Be carefull!! These scripts are created to be examples. Some part of them are "hardcoded". From jmrc at dev.open-bio.org Mon Sep 1 18:55:21 2008 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Mon, 1 Sep 2008 14:55:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809011855.m81ItLKu019349@dev.open-bio.org> jmrc Mon Sep 1 14:55:20 EDT 2008 Update of /home/repository/moby/moby-live/Docs/asyncDocs/async-MOBY-test In directory dev.open-bio.org:/tmp/cvs-serv19300/asyncDocs/async-MOBY-test Added Files: running_runAsyncMOBYservice-poll.pl Log Message: * Added more asynchronous client examples. * README has been updated according to the new example. moby-live/Docs/asyncDocs/async-MOBY-test running_runAsyncMOBYservice-poll.pl,NONE,1.1 From jmrc at dev.open-bio.org Mon Sep 1 19:01:49 2008 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Mon, 1 Sep 2008 15:01:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809011901.m81J1nUq019440@dev.open-bio.org> jmrc Mon Sep 1 15:01:49 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv19403/Perl/MOBY-Server/lib/MOBY Modified Files: CommonSubs.pm Log Message: * Fixed the "hideous" bug found by Eddie, related to asynchronous MOBY calls with empty mobyData elements. Although it is a very strange case, there could be a service with no input parameter. MOBY::Async::SimpleServer uses serviceInputParser, which had the bug fixed by this commit. moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/03/05 20:27:11 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/01 19:01:49 1.4 @@ -375,6 +375,10 @@ foreach my $query ( @queries ) { my $queryID = _getQID( $query ); # get the queryID attribute of the mobyData my @input_articles = _getArticlesAsObjects( $query ); + # This is done for empty mobyData. It is a strange case + # but it can happen (a service which is a random answer + # generator, for instance) + $input_parameters{$queryID}={}; foreach my $article ( @input_articles ) { ${$input_parameters{$queryID}}{$article->articleName} = $article; } From kawas at dev.open-bio.org Tue Sep 2 13:09:02 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:09:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021309.m82D92cK021463@dev.open-bio.org> kawas Tue Sep 2 09:09:01 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv21412/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl Modified Files: NamespaceDataAdapter.pm ServiceTypeDataAdapter.pm ServiceInstanceDataAdapter.pm ObjectDataAdapter.pm FetaQueryAdaptor.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl NamespaceDataAdapter.pm,1.2,1.3 ServiceTypeDataAdapter.pm,1.2,1.3 ServiceInstanceDataAdapter.pm,1.2,1.3 ObjectDataAdapter.pm,1.2,1.3 FetaQueryAdaptor.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/NamespaceDataAdapter.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/NamespaceDataAdapter.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/NamespaceDataAdapter.pm 2008/09/02 13:09:01 1.3 @@ -3,6 +3,8 @@ use strict; use Carp; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; =head1 NAME =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceTypeDataAdapter.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceTypeDataAdapter.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceTypeDataAdapter.pm 2008/09/02 13:09:01 1.3 @@ -4,6 +4,10 @@ use Carp; use vars qw(@ISA); @ISA = qw{MOBY::Adaptor::moby::queryapi}; # implements the interface + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::Impl::ServiceTypeDataAdapter - An interface definition for MOBY Central underlying data-stores =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceInstanceDataAdapter.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceInstanceDataAdapter.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ServiceInstanceDataAdapter.pm 2008/09/02 13:09:01 1.3 @@ -5,6 +5,9 @@ use vars qw(@ISA); @ISA = qw{MOBY::Adaptor::moby::DataAdapterI}; # implements the interface +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::impl::ServiceInstanceDataAdapter - An interface definition for MOBY Central underlying data-stores =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ObjectDataAdapter.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ObjectDataAdapter.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/ObjectDataAdapter.pm 2008/09/02 13:09:01 1.3 @@ -5,6 +5,9 @@ use vars qw(@ISA); @ISA = qw{MOBY::Adaptor::moby::DataAdapterI}; # implements the interface +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::Impl::ObjectDataAdapter - An interface definition for MOBY Central underlying data-stores =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm 2008/09/02 13:09:01 1.3 @@ -4,6 +4,9 @@ use XML::LibXML; @ISA = qw{MOBY::Adaptor::moby::DataAdapterI}; # implements the interface +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::impl::FetaQueryAdaptor.pm - FetaQueryAdaptor From kawas at dev.open-bio.org Tue Sep 2 13:09:13 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:09:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021309.m82D9DNk021503@dev.open-bio.org> kawas Tue Sep 2 09:09:12 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi In directory dev.open-bio.org:/tmp/cvs-serv21468/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi Modified Files: mysql.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi mysql.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/mysql.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/mysql.pm 2008/02/21 00:21:28 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi/mysql.pm 2008/09/02 13:09:12 1.2 @@ -7,6 +7,9 @@ use DBI; use DBD::mysql; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + @ISA = qw{MOBY::Adaptor::moby::queryapi}; # implements the interface { From kawas at dev.open-bio.org Tue Sep 2 13:09:30 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:09:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021309.m82D9UoT021551@dev.open-bio.org> kawas Tue Sep 2 09:09:30 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby In directory dev.open-bio.org:/tmp/cvs-serv21508/Perl/MOBY-Server/lib/MOBY/Adaptor/moby Modified Files: queryapi.pm DataAdapterI.pm DataAccessI.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby queryapi.pm,1.2,1.3 DataAdapterI.pm,1.1,1.2 DataAccessI.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi.pm 2008/02/21 17:15:41 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/queryapi.pm 2008/09/02 13:09:30 1.3 @@ -4,6 +4,8 @@ use Carp; use vars qw($AUTOLOAD); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; =head1 NAME =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAdapterI.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAdapterI.pm 2008/02/21 00:21:28 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAdapterI.pm 2008/09/02 13:09:30 1.2 @@ -3,6 +3,9 @@ use strict; use Carp; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::DataAdapterI - An interface definition for MOBY Central underlying data-stores =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAccessI.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAccessI.pm 2008/02/21 17:15:41 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Adaptor/moby/DataAccessI.pm 2008/09/02 13:09:30 1.3 @@ -4,6 +4,9 @@ use strict; use Carp; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Adaptor::moby::DataAccessI - This file may need to be renamed and may not make sense as From kawas at dev.open-bio.org Tue Sep 2 13:10:26 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:10:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021310.m82DAQmL021725@dev.open-bio.org> kawas Tue Sep 2 09:10:26 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv21682/Perl/MOBY-Server/lib/MOBY/Async Modified Files: SimpleServer.pm LSAE.pm Service.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Async SimpleServer.pm,1.3,1.4 LSAE.pm,1.2,1.3 Service.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2008/09/01 18:53:57 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2008/09/02 13:10:26 1.4 @@ -99,6 +99,9 @@ use base qw(WSRF::FileBasedMobyResourceLifetimes); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #=============================================================================== # async_create # =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/LSAE.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/LSAE.pm 2008/04/23 13:08:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/LSAE.pm 2008/09/02 13:10:26 1.3 @@ -199,6 +199,9 @@ use XML::LibXML; use Exporter; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use base qw(Exporter); our @EXPORT = qw( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm 2008/09/01 18:53:57 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/Service.pm 2008/09/02 13:10:26 1.4 @@ -135,6 +135,9 @@ use MOBY::Client::Service; use base qw(MOBY::Client::Service); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + sub _getPollingTime($$$@); sub _getServiceEndpoint($); sub _getPseudoRandomPollingTime($$); From kawas at dev.open-bio.org Tue Sep 2 13:11:25 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:11:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021311.m82DBPs4021769@dev.open-bio.org> kawas Tue Sep 2 09:11:25 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception In directory dev.open-bio.org:/tmp/cvs-serv21730/Perl/MOBY-Server/lib/MOBY/Client/Exception Modified Files: MobyExceptionCodes.pm MobyException.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception MobyExceptionCodes.pm,1.2,1.3 MobyException.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyExceptionCodes.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyExceptionCodes.pm 2008/08/29 16:18:51 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyExceptionCodes.pm 2008/09/02 13:11:25 1.3 @@ -5,6 +5,9 @@ # Name of the package package MOBY::Client::Exception::MobyExceptionCodes; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use strict; ############## =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyException.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyException.pm 2008/08/29 16:18:51 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Exception/MobyException.pm 2008/09/02 13:11:25 1.3 @@ -13,6 +13,9 @@ use Carp qw(croak); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use MOBY::Client::Exception::MobyExceptionCodes; From kawas at dev.open-bio.org Tue Sep 2 13:11:40 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:11:40 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021311.m82DBeB3021842@dev.open-bio.org> kawas Tue Sep 2 09:11:40 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client In directory dev.open-bio.org:/tmp/cvs-serv21774/Perl/MOBY-Server/lib/MOBY/Client Modified Files: Service.pm SimpleArticle.pm ServiceInstance.pm SimpleInput.pm Registration.pm OntologyServer.pm SecondaryArticle.pm CollectionArticle.pm Central.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/Client Service.pm,1.2,1.3 SimpleArticle.pm,1.2,1.3 ServiceInstance.pm,1.1,1.2 SimpleInput.pm,1.3,1.4 Registration.pm,1.1,1.2 OntologyServer.pm,1.1,1.2 SecondaryArticle.pm,1.3,1.4 CollectionArticle.pm,1.2,1.3 Central.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Service.pm 2008/09/02 13:11:40 1.3 @@ -48,6 +48,10 @@ use Cwd; use URI::Escape; use vars qw($AUTOLOAD @ISA); + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + my $debug = 0; if ( $debug ) { open( OUT, ">/tmp/ServiceCallLogOut.txt" ) || die "cant open logfile\n"; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleArticle.pm 2008/09/02 13:11:40 1.3 @@ -5,6 +5,9 @@ use MOBY::MobyXMLConstants; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::SimpleArticle - a small object describing the Simple articles from the findService Response message of MOBY Central =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm 2008/09/02 13:11:40 1.2 @@ -3,6 +3,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::ServiceInstance - a small object describing a MOBY service =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm 2008/02/21 17:42:15 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SimpleInput.pm 2008/09/02 13:11:40 1.4 @@ -3,6 +3,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::SimpleInput - a small object describing a MOBY service =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Registration.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Registration.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Registration.pm 2008/09/02 13:11:40 1.2 @@ -70,6 +70,10 @@ use strict; use Carp; use vars qw($AUTOLOAD); + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + { #Encapsulated class data =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/OntologyServer.pm 2008/09/02 13:11:40 1.2 @@ -75,6 +75,10 @@ use Carp; use vars qw($AUTOLOAD); use LWP::UserAgent; + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + my $debug = 0; my $user_agent = "MOBY-OntologyServer-Perl"; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm 2008/02/21 17:42:15 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/SecondaryArticle.pm 2008/09/02 13:11:40 1.4 @@ -5,6 +5,9 @@ use MOBY::MobyXMLConstants; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::SecondaryArticle - a small object describing the Simple articles from the findService Response message of MOBY Central =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/CollectionArticle.pm 2008/09/02 13:11:40 1.3 @@ -6,6 +6,9 @@ use vars qw($AUTOLOAD @ISA); use MOBY::Client::SimpleArticle; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::CollectionArticle - a small object describing the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm 2008/05/14 14:04:03 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/Central.pm 2008/09/02 13:11:40 1.6 @@ -15,6 +15,9 @@ use MOBY::Client::OntologyServer; use vars qw($AUTOLOAD @ISA $MOBY_server $MOBY_uri); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::Central - a client side wrapper for MOBY Central From kawas at dev.open-bio.org Tue Sep 2 13:11:54 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:11:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021311.m82DBsfk021883@dev.open-bio.org> kawas Tue Sep 2 09:11:53 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority In directory dev.open-bio.org:/tmp/cvs-serv21848/Perl/MOBY-Server/lib/MOBY/lsid/authority Modified Files: MobyMetadataResolver.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority MobyMetadataResolver.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/MobyMetadataResolver.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/MobyMetadataResolver.pm 2008/02/21 17:54:56 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/lsid/authority/MobyMetadataResolver.pm 2008/09/02 13:11:53 1.3 @@ -18,6 +18,9 @@ use MOBY::RDF::Ontologies::Namespaces; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use base 'LS::Service::Namespace'; =head1 NAME From kawas at dev.open-bio.org Tue Sep 2 13:12:34 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:12:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021312.m82DCYhl021939@dev.open-bio.org> kawas Tue Sep 2 09:12:33 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache In directory dev.open-bio.org:/tmp/cvs-serv21888/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache Modified Files: NamespaceCache.pm CacheUtils.pm ServiceCache.pm ObjectCache.pm ServiceTypeCache.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache NamespaceCache.pm,1.3,1.4 CacheUtils.pm,1.2,1.3 ServiceCache.pm,1.5,1.6 ObjectCache.pm,1.4,1.5 ServiceTypeCache.pm,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/04/30 16:53:19 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/NamespaceCache.pm 2008/09/02 13:12:33 1.4 @@ -30,6 +30,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::NamespaceCache - Module for creating a cache of namespaces for use when generating RDF =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/CacheUtils.pm 2008/09/02 13:12:33 1.3 @@ -23,6 +23,9 @@ use constant NAMESPACES_CACHE => 'namespaces'; use constant SERVICETYPES_CACHE => 'serviceTypes'; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::CacheUtils - Utility module that aids in caching =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceCache.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/06/19 21:47:35 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceCache.pm 2008/09/02 13:12:33 1.6 @@ -30,6 +30,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::ServiceCache - Module for creating a cache of service instances for use when generating RDF =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/04/30 16:53:26 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ObjectCache.pm 2008/09/02 13:12:33 1.5 @@ -30,6 +30,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::ObjectCache - Module for creating a cache of datatypes for use when generating RDF =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/04/30 16:53:45 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Cache/ServiceTypeCache.pm 2008/09/02 13:12:33 1.4 @@ -30,6 +30,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::RDF::Ontologies::Cache::ServiceTypeCache - Module for creating a cache of service types for use when generating RDF From kawas at dev.open-bio.org Tue Sep 2 13:12:46 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:12:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021312.m82DCk3q021991@dev.open-bio.org> kawas Tue Sep 2 09:12:46 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies In directory dev.open-bio.org:/tmp/cvs-serv21944/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Modified Files: ServiceTypes.pm Objects.pm Services.pm Namespaces.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies ServiceTypes.pm,1.3,1.4 Objects.pm,1.4,1.5 Services.pm,1.6,1.7 Namespaces.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/ServiceTypes.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/ServiceTypes.pm 2008/06/19 21:49:01 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/ServiceTypes.pm 2008/09/02 13:12:46 1.4 @@ -27,6 +27,9 @@ use MOBY::RDF::Utils; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Objects.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Objects.pm 2008/06/19 21:49:01 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Objects.pm 2008/09/02 13:12:46 1.5 @@ -30,6 +30,9 @@ use CGI; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm 2008/06/25 16:13:02 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm 2008/09/02 13:12:46 1.7 @@ -35,6 +35,9 @@ use Data::Dumper; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm 2008/07/22 15:54:29 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Namespaces.pm 2008/09/02 13:12:46 1.7 @@ -27,6 +27,9 @@ use MOBY::RDF::Utils; use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- From kawas at dev.open-bio.org Tue Sep 2 13:12:58 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:12:58 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021312.m82DCwe3022039@dev.open-bio.org> kawas Tue Sep 2 09:12:58 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers In directory dev.open-bio.org:/tmp/cvs-serv21996/Perl/MOBY-Server/lib/MOBY/RDF/Parsers Modified Files: NamespaceParser.pm DatatypeParser.pm ServiceTypeParser.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers NamespaceParser.pm,1.2,1.3 DatatypeParser.pm,1.1,1.2 ServiceTypeParser.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm 2008/03/05 17:43:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/NamespaceParser.pm 2008/09/02 13:12:58 1.3 @@ -21,6 +21,9 @@ use MOBY::RDF::Predicates::RDF; use MOBY::RDF::Predicates::RDFS; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME NamespaceParser - An module for obtaining namespaces from the RDF Namespace ontology =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/DatatypeParser.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/DatatypeParser.pm 2008/03/13 19:12:07 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/DatatypeParser.pm 2008/09/02 13:12:58 1.2 @@ -21,6 +21,9 @@ use MOBY::RDF::Predicates::RDF; use MOBY::RDF::Predicates::RDFS; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME DatatypeParser - An module for obtaining datatypes from the RDF Namespace ontology =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm 2008/03/05 17:43:11 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceTypeParser.pm 2008/09/02 13:12:58 1.3 @@ -21,6 +21,9 @@ use MOBY::RDF::Predicates::RDF; use MOBY::RDF::Predicates::RDFS; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME ServiceTypeParser - An module for obtaining services from the RDF Service Type ontology From kawas at dev.open-bio.org Tue Sep 2 13:13:10 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:13:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021313.m82DDAsa022103@dev.open-bio.org> kawas Tue Sep 2 09:13:09 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates In directory dev.open-bio.org:/tmp/cvs-serv22044/Perl/MOBY-Server/lib/MOBY/RDF/Predicates Modified Files: MOBY_PREDICATES.pm OWL.pm FETA.pm RDFS.pm RDF.pm OMG_LSID.pm DC_PROTEGE.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates MOBY_PREDICATES.pm,1.1,1.2 OWL.pm,1.1,1.2 FETA.pm,1.1,1.2 RDFS.pm,1.1,1.2 RDF.pm,1.1,1.2 OMG_LSID.pm,1.1,1.2 DC_PROTEGE.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/MOBY_PREDICATES.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,8 @@ use strict; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant MOBY_PREDICATES_PREFIX => 'moby'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OWL.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OWL.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OWL.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,9 @@ use strict; BEGIN { +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use constant OWL_PREFIX => 'owl'; use constant OWL_URI => 'http://www.w3.org/2002/07/owl#'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/FETA.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/FETA.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/FETA.pm 2008/09/02 13:13:09 1.2 @@ -4,6 +4,8 @@ use warnings; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant FETA_PREFIX => 'myGrid'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDFS.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDFS.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDFS.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,8 @@ use strict; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant RDFS_PREFIX => 'rdfs'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDF.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDF.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/RDF.pm 2008/09/02 13:13:09 1.2 @@ -2,6 +2,8 @@ use strict; BEGIN { +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant RDF_PREFIX => 'rdf'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OMG_LSID.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OMG_LSID.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/OMG_LSID.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,8 @@ use strict; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant OMG_LSID_PREFIX => 'lsid'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/DC_PROTEGE.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/DC_PROTEGE.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Predicates/DC_PROTEGE.pm 2008/09/02 13:13:09 1.2 @@ -3,6 +3,8 @@ use strict; BEGIN { + use vars qw /$VERSION/; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; use constant DC_PROTEGE_PREFIX => 'protege-dc'; From kawas at dev.open-bio.org Tue Sep 2 13:13:20 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:13:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021313.m82DDKIQ022143@dev.open-bio.org> kawas Tue Sep 2 09:13:20 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF In directory dev.open-bio.org:/tmp/cvs-serv22108/Perl/MOBY-Server/lib/MOBY/RDF Modified Files: Utils.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY/RDF Utils.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm 2008/04/30 16:52:25 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Utils.pm 2008/09/02 13:13:20 1.6 @@ -14,6 +14,9 @@ use strict; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #----------------------------------------------------------------- # load all modules needed for my attributes #----------------------------------------------------------------- From kawas at dev.open-bio.org Tue Sep 2 13:13:57 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:13:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021313.m82DDvIJ022183@dev.open-bio.org> kawas Tue Sep 2 09:13:57 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv22148/Perl/MOBY-Server/lib/MOBY Modified Files: Admin.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY Admin.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Admin.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Admin.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Admin.pm 2008/09/02 13:13:57 1.2 @@ -24,6 +24,9 @@ use MOBY::CommonSubs; use MOBY::MobyXMLConstants; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + sub deregisterService { my ( $self, $xml ) = @_; From kawas at dev.open-bio.org Tue Sep 2 13:14:18 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:14:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021314.m82DEIEY022295@dev.open-bio.org> kawas Tue Sep 2 09:14:18 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv22188/Perl/MOBY-Server/lib/MOBY Modified Files: secondary_input.pm collection_input.pm MobyXMLConstants.pm service_instance.pm central_db_connection.pm OntologyServer.pm dbConfig.pm MOBY.pm MOBYXSLT.pm service_type.pm authority.pm CommonSubs.pm mysql.pm Central.pm Config.pm CrossReference.pm collection_output.pm simple_input.pm simple_output.pm Log Message: added $VERSION numbers to the modules. moby-live/Perl/MOBY-Server/lib/MOBY secondary_input.pm,1.2,1.3 collection_input.pm,1.3,1.4 MobyXMLConstants.pm,1.1,1.2 service_instance.pm,1.2,1.3 central_db_connection.pm,1.2,1.3 OntologyServer.pm,1.2,1.3 dbConfig.pm,1.2,1.3 MOBY.pm,1.3,1.4 MOBYXSLT.pm,1.2,1.3 service_type.pm,1.2,1.3 authority.pm,1.2,1.3 CommonSubs.pm,1.4,1.5 mysql.pm,1.2,1.3 Central.pm,1.6,1.7 Config.pm,1.4,1.5 CrossReference.pm,1.2,1.3 collection_output.pm,1.2,1.3 simple_input.pm,1.2,1.3 simple_output.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::secondary_input - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm 2008/07/07 16:50:25 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm 2008/09/02 13:14:18 1.4 @@ -4,6 +4,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::collection_input - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MobyXMLConstants.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MobyXMLConstants.pm 2008/02/21 00:21:27 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MobyXMLConstants.pm 2008/09/02 13:14:18 1.2 @@ -2,6 +2,8 @@ use strict; use vars qw( $VERSION @ISA @EXPORT @NodeNames); +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + BEGIN { @ISA = qw( Exporter ); ######################################################### =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_instance.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_instance.pm 2008/02/21 17:58:58 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_instance.pm 2008/09/02 13:14:18 1.3 @@ -8,6 +8,9 @@ use MOBY::authority; use MOBY::Config; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #@ISA = qw(MOBY::central_db_connection); # can't do this yet... =head1 NAME =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/central_db_connection.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/central_db_connection.pm 2008/02/21 17:54:56 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/central_db_connection.pm 2008/09/02 13:14:18 1.3 @@ -4,6 +4,9 @@ use vars qw($AUTOLOAD @ISA); use MOBY::Config; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::central_db_connection - container object for a specific DB connection =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/OntologyServer.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/OntologyServer.pm 2008/08/22 18:30:50 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/OntologyServer.pm 2008/09/02 13:14:18 1.3 @@ -70,6 +70,10 @@ use DBI; use DBD::mysql; use MOBY::Config; + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + my $debug = 0; { =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/dbConfig.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/dbConfig.pm 2008/06/20 19:50:55 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/dbConfig.pm 2008/09/02 13:14:18 1.3 @@ -2,6 +2,10 @@ use strict; use Carp; use vars qw($AUTOLOAD); + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use Text::Shellwords; { =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm 2008/07/07 16:29:19 1.3 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm 2008/09/02 13:14:18 1.4 @@ -3,11 +3,10 @@ use strict; use warnings; - - use vars qw{$VERSION @ISA @EXPORT @EXPORT_OK}; +# add versioning to this module BEGIN { - $VERSION = '0.85'; + $VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; @ISA = qw{ Exporter }; @EXPORT = qw{}; @EXPORT_OK = qw{}; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBYXSLT.pm 2008/09/02 13:14:18 1.3 @@ -4,6 +4,9 @@ my $XSLTPROC = '/usr/bin/xsltproc';#Where your xsltproc binary is located my $XSL_SHEET = 'xsl/parseMobyMessage.xsl';#Where your xsltproc style-sheet is located +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + #$Id$ =pod =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm 2008/09/02 13:14:18 1.3 @@ -4,6 +4,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::service_type - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::authority - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/01 19:01:49 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/02 13:14:18 1.5 @@ -239,6 +239,10 @@ use constant BE_STRICT => 0; our @ISA = qw(Exporter); our @EXPORT = qw(COLLECTION SIMPLE SECONDARY PARAMETER BE_NICE BE_STRICT); + +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + our %EXPORT_TAGS = ( all => [ qw( =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/mysql.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/mysql.pm 2008/02/21 17:58:58 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/mysql.pm 2008/09/02 13:14:18 1.3 @@ -4,6 +4,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::mysql - makes a MYSQL database connection. =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm 2008/08/22 19:12:20 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm 2008/09/02 13:14:18 1.7 @@ -27,6 +27,9 @@ use LWP; use MOBY::CommonSubs; +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + use Encode; use MOBY::MobyXMLConstants; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/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-Server/lib/MOBY/Config.pm 2008/04/15 00:26:29 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Config.pm 2008/09/02 13:14:18 1.5 @@ -41,6 +41,9 @@ use vars qw($AUTOLOAD); use Text::Shellwords; use vars '$VERSION', '@ISA', '@EXPORT', '$CONFIG'; + +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + @ISA = qw(Exporter); @EXPORT = ('$CONFIG'); { =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm 2008/02/21 17:15:40 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CrossReference.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use Carp; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::Client::CrossReference - a small object describing a MOBY Simple input/output article =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::collection_output - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::simple_input - a lightweight connection to the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm 2008/07/07 16:50:25 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm 2008/09/02 13:14:18 1.3 @@ -5,6 +5,9 @@ use MOBY::Config; use vars qw($AUTOLOAD @ISA); +use vars qw /$VERSION/; +$VERSION = sprintf "%d.%02d", q$Revision$ =~ /: (\d+)\.(\d+)/; + =head1 NAME MOBY::simple_output - a lightweight connection to the From kawas at dev.open-bio.org Tue Sep 2 13:14:56 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:14:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021314.m82DEuEG022335@dev.open-bio.org> kawas Tue Sep 2 09:14:56 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv22300/Perl/MOBY-Server Modified Files: Changes Log Message: added all known changes that have been committed to this file moby-live/Perl/MOBY-Server Changes,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2008/07/02 20:51:33 1.11 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2008/09/02 13:14:56 1.12 @@ -1,5 +1,24 @@ Revision history for Perl extension MOBY. +1.06 + - Changes to makefile reflecting the cpan addition of wsrf. + - Added Boolean to the data sql dump file for initializing + a new registry. + - Added character encoding checks to the data kept in the + registry. All data used in the register* methods are + checked to be encoded in UTF-8 + - Added $VERSION info for all the modules. Sorry if this + creates some initial confusion; The longer term gains + far exceed any short term disruptions. + - Cosmetic fixes in Service.pm and SimpleServer.pm. + - Fixed a bug in WSRF.pm related to temporal file location/creation + introduced by a previous commit + - Bug fix related to asynchronous MOBY calls with empty mobyData elements. + MOBY::Async::SimpleServer uses serviceInputParser, which had the bug fixed. + - + - + + 1.05 - Multiple bug fixes / additions to installer (thanks to Jason Stewart), From kawas at dev.open-bio.org Tue Sep 2 13:15:34 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:15:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021315.m82DFY1q022411@dev.open-bio.org> kawas Tue Sep 2 09:15:34 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv22376/Perl/MOBY-Server Modified Files: README Log Message: updated the README to reflect the fact that WSRF-lite is now available on cpan moby-live/Perl/MOBY-Server README,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/README,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOBY-Server/README 2008/07/07 16:29:39 1.2 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/README 2008/09/02 13:15:34 1.3 @@ -25,25 +25,6 @@ each dependency independently and install them as per their installation instructions. -WRSF::Lite - -If module 'WSRF::Lite' is not installed and you are -thinking about developing BioMOBY Asynchronous service, -then following is for you! - -Unfortunately, this module is not available on CPAN -and must be manually installed. Some of the -dependencies are beta and as such, may not be stable. - -Try downloading it from the following link: - -http://www.rcs.manchester.ac.uk/research/projects/wsrflite - -or you can try searching the net with Google using the keywords: - - 'perl WSRF::Lite' - - COPYRIGHT AND LICENCE Copyright (C) 2003 BioMoby Developers Group (www.biomoby.org) From kawas at dev.open-bio.org Tue Sep 2 13:17:25 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:17:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021317.m82DHPIC022487@dev.open-bio.org> kawas Tue Sep 2 09:17:25 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv22452/Perl/MOBY-Server Modified Files: Makefile.PL Log Message: updated the makefile to reflect the fact that wsrf is now in cpan. added some missing requires that other modules that we 'use' dont properly specify in their makefile moby-live/Perl/MOBY-Server Makefile.PL,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/07/02 20:49:44 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2008/09/02 13:17:25 1.9 @@ -3,7 +3,7 @@ # Define metadata name 'MOBY'; - version '1.05'; + version '1.06'; license 'perl'; abstract 'This distribution is for communicating with or creating your own MOBY Central registry'; @@ -15,6 +15,7 @@ requires 'SOAP::Lite' => '0.69'; requires 'XML::LibXML' => '1.62'; requires 'IO::Stringy' => '2.110'; + requires 'File::HomeDir' => '0.8'; requires 'Unicode::String' => '2.09'; requires 'File::ShareDir' => '0.05'; requires 'Template' => '0'; @@ -27,6 +28,9 @@ requires 'DBI' => '0.01'; requires 'DBD::mysql' => '0.01'; + # MOBY::Async requires + requires 'WSRF::Lite' => '0.8.2.3'; + if ( not( $^O =~ /MSWin32|Windows_NT/i ) ) { # non portable requires @@ -34,49 +38,6 @@ requires 'IO::Prompt' => '0.99.2'; requires 'IPC::Shareable' => '0.6'; - # check for WSRF - eval "require WSRF::Lite"; - if ($@) { - - # WSRF not installed ... tell them where to get it - print STDOUT <<'END_OF_TEXT'; - -################### IMPORTANT ################### - - WSRF lite is not installed on your system. - Unfortunately, at this time, this Makefile - cannot automatically find and install it for - you. You will have to install it manually. - - The last known URL of where you could find - this package is @ - http://www.rcs.manchester.ac.uk/research/wsrflite - - If that url does not exist, please search with - google using the phrase 'WSRF-Lite'. - - Sorry for any inconvenience caused! - -################################################## - -END_OF_TEXT - - } - - # MOBY::Async requires - requires 'WSRF::Lite' => '0.008.2.2'; - requires 'XML::DOM' => ''; - requires 'DateTime::Format::Epoch' => ''; - requires 'DateTime::Format::W3CDTF' => ''; - requires 'HTTP::Daemon' => ''; - requires 'HTTP::Daemon::SSL' => ''; - requires 'MIME::Base64' => ''; - requires 'Digest::SHA1' => ''; - requires 'Crypt::OpenSSL::RSA' => ''; - requires 'XML::CanonicalizeXML' => '0.02'; - requires 'Sys::Hostname::Long' => ''; - requires 'Crypt::OpenSSL::X509' => '0'; - } else { print STDOUT <<'END_OF_TEXT'; @@ -89,8 +50,7 @@ required libraries. The libraries in question are as follows: - IPC::Shareable, IO::Prompt, - WSRF-Lite, & Crypt-OpenSSL-X509. + IPC::Shareable, IO::Prompt. Sorry for any inconvenience caused! From kawas at dev.open-bio.org Tue Sep 2 13:19:14 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 09:19:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021319.m82DJE3q022563@dev.open-bio.org> kawas Tue Sep 2 09:19:14 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv22528/Perl/MOBY-Server/bin/scripts Modified Files: moby-s-install.pl Log Message: removed a module check that wsrf no longer requires. moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl 2008/07/02 20:49:23 1.12 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl 2008/09/02 13:19:13 1.13 @@ -107,7 +107,6 @@ Crypt::OpenSSL::RSA Sys::Hostname::Long HTTP::Daemon::SSL - XML::CanonicalizeXML / ) { check_module($module); From kawas at dev.open-bio.org Tue Sep 2 16:35:33 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 12:35:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021635.m82GZW46023012@dev.open-bio.org> kawas Tue Sep 2 12:35:32 EDT 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv22981/Docs/MOBY-S_API/Perl Added Files: construct_moses_async_service.html Log Message: how to use MOSES to create perl asynchronous services **Missing section on testing** - will be completed very shortly! moby-live/Docs/MOBY-S_API/Perl construct_moses_async_service.html,NONE,1.1 From kawas at dev.open-bio.org Tue Sep 2 17:58:02 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 13:58:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021758.m82Hw25r023100@dev.open-bio.org> kawas Tue Sep 2 13:58:02 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts In directory dev.open-bio.org:/tmp/cvs-serv23065/Perl/MOSES-MOBY/bin/scripts Modified Files: moses-testing-service.pl Log Message: service tester script now incorporates the async client code for calling async services. there are no limitations to the number of 'jobs' submitted (can handle 0 or more jobs per message) moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl 2008/05/06 16:52:48 1.6 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl 2008/09/02 17:58:02 1.7 @@ -7,14 +7,15 @@ # ----------------------------------------------------------- BEGIN { - # some command-line options - use Getopt::Std; - use vars qw/ $opt_h $opt_d $opt_v $opt_l $opt_e $opt_c /; - getopts ('hdvl:e:c:'); - - # usage - if ($opt_h or (@ARGV == 0 and (not $opt_c))) { - print STDOUT <<'END_OF_USAGE'; + + # some command-line options + use Getopt::Std; + use vars qw/ $opt_h $opt_d $opt_v $opt_l $opt_e $opt_c $opt_a /; + getopts('hdvl:e:c:a:'); + + # usage + if ( $opt_h or ( @ARGV == 0 and ( not $opt_c ) ) ) { + print STDOUT <<'END_OF_USAGE'; Calling a BioMoby services (without using SOAP, just locally). Usage: # calling a local module representing a service, without using SOAP [-vd] [-l ] [] @@ -31,6 +32,9 @@ # calling a real service, using cgi -c [] + # calling a real service, using SOAP + -a [] + is a full name of a called module (service) e.g. Service::Mabuhay @@ -46,6 +50,10 @@ A cgi biomoby service url (e.g. http://localhost/cgi-bin/HelloBiomobyWorld.cgi) + -a + An asynchronous service url + (e.g. http://localhost/cgi-bin/AsyncMobyServer.cgi) + A BioMoby XML file with input data. Default: an empty BioMoby request @@ -54,38 +62,49 @@ -d ... debug -h ... help END_OF_USAGE - exit (0); - } + exit(0); + } -# use MOSES::MOBY::Base; - # load modules, depending on the mode of calling - if ($opt_e) { - # calling a real service, using SOAP - eval "use SOAP::Lite; 1;" - or die "$@\n"; - - } elsif ($opt_c) { - # calling a real service, using cgi - eval "use HTTP::Request; 1;" - or die "$@\n"; - eval "use LWP::UserAgent; 1;" - or die "$@\n"; - }else { - # calling a local service module, without SOAP - eval "use MOSES::MOBY::Base; 1;"; - # take the lib location from the config file - require lib ; lib->import (MOSES::MOBY::Config->param ("generators.impl.outdir")); - require lib ; lib->import (MOSES::MOBY::Config->param ("generators.outdir")); - unshift (@INC, $opt_l) if $opt_l; - $LOG->level ('INFO') if $opt_v; - $LOG->level ('DEBUG') if $opt_d; - } + # use MOSES::MOBY::Base; + # load modules, depending on the mode of calling + if ($opt_e) { + + # calling a real service, using SOAP + eval "use SOAP::Lite; 1;" + or die "$@\n"; + } elsif ($opt_c) { + + # calling a real service, using cgi + eval "use HTTP::Request; 1;" + or die "$@\n"; + eval "use LWP::UserAgent; 1;" + or die "$@\n"; + } else { + + # calling a local service module, without SOAP + eval "use MOSES::MOBY::Base; 1;"; + + # take the lib location from the config file + require lib; + lib->import( MOSES::MOBY::Config->param("generators.impl.outdir") ); + require lib; + lib->import( MOSES::MOBY::Config->param("generators.outdir") ); + unshift( @INC, $opt_l ) if $opt_l; + $LOG->level('INFO') if $opt_v; + $LOG->level('DEBUG') if $opt_d; + } + # load these modules always to get constants and to avoid warnings + eval "use MOBY::Async::LSAE; 1;" + or die "$@\n"; + eval "use MOBY::Async::WSRF; 1;" + or die "$@\n"; + } use strict; sub _empty_input { - return <<'END_OF_XML'; + return <<'END_OF_XML'; @@ -95,78 +114,286 @@ END_OF_XML } +sub _get_query_ids { + my $input = shift; + my @query_ids = (); + my $parser = XML::LibXML->new(); + my $doc = $parser->parse_string($input); + my $iterator = $doc->getElementsByLocalName("mobyData"); + for ( 1 .. $iterator->size() ) { + my $node = $iterator->get_node($_); + my $id = $node->getAttribute("queryID") + || $node->getAttribute( + $node->lookupNamespacePrefix($WSRF::Constants::MOBY_MESSAGE_NS) + . ":queryID" ); + push @query_ids, $id; + } + return @query_ids; +} + # --- what service to call -my $module = shift unless $opt_c; # eg. Service::Mabuhay, or just Mabuhay +my $module = shift unless $opt_c; # eg. Service::Mabuhay, or just Mabuhay my $service; -($service = $module) =~ s/.*::// unless $opt_c; +( $service = $module ) =~ s/.*::// unless $opt_c; # --- call the service if ($opt_e) { - # calling a real service, using SOAP - my $soap = SOAP::Lite - -> uri ("http://biomoby.org/") - -> proxy ($opt_e) - -> on_fault (sub { - my $soap = shift; - my $res = shift; - my $msg = - ref $res ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring - : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n"; - die $msg; - }); - - my $input = ''; - if (@ARGV > 0) { - my $data = shift; # a file name - open INPUT, "<$data" - or die "Cannot read '$data': $!\n"; - while () { $input .= $_; } - close INPUT; - } else { - $input = _empty_input; - } - - print $soap - -> $service (SOAP::Data->type('string' => "$input")) - -> result; + + # calling a real service, using SOAP + my $soap = SOAP::Lite->uri("http://biomoby.org/")->proxy($opt_e)->on_fault( + sub { + my $soap = shift; + my $res = shift; + my $msg = + ref $res + ? "--- SOAP FAULT ---\n" + . $res->faultcode . " " + . $res->faultstring + : "--- TRANSPORT ERROR ---\n" + . $soap->transport->status + . "\n$res\n"; + die $msg; + } + ); + + my $input = ''; + if ( @ARGV > 0 ) { + my $data = shift; # a file name + open INPUT, "<$data" + or die "Cannot read '$data': $!\n"; + while () { $input .= $_; } + close INPUT; + } else { + $input = _empty_input; + } + + print $soap ->$service( SOAP::Data->type( 'string' => "$input" ) )->result; } elsif ($opt_c) { - # calling a real service, using cgi - my $ua = LWP::UserAgent->new; - - my $input = ''; - if (@ARGV > 0) { - my $data = shift; # a file name - open INPUT, "<$data" - or die "Cannot read '$data': $!\n"; - while () { $input .= $_; } - close INPUT; - } else { - $input = _empty_input; - } - my $req = HTTP::Request->new(POST => $opt_c); + # calling a real service, using cgi + my $ua = LWP::UserAgent->new; + + my $input = ''; + if ( @ARGV > 0 ) { + my $data = shift; # a file name + open INPUT, "<$data" + or die "Cannot read '$data': $!\n"; + while () { $input .= $_; } + close INPUT; + } else { + $input = _empty_input; + } + + my $req = HTTP::Request->new( POST => $opt_c ); $req->content_type('application/x-www-form-urlencoded'); $req->content("data=$input"); print "\n" . $ua->request($req)->as_string . "\n"; +} elsif ($opt_a) { + + # calling a real service, using async soap + # call using async mode for async service ... _submit + $service .= "_submit"; + + # set up the wsrf call + my $soap = WSRF::Lite->proxy($opt_a)->uri($WSRF::Constants::MOBY)->on_fault( + sub { + my $soap = shift; + my $res = shift; + my $msg = + ref $res + ? "--- SOAP FAULT ---\n" + . $res->faultcode . " " + . $res->faultstring + : "--- TRANSPORT ERROR ---\n" + . $soap->transport->status + . "\n$res\n"; + die $msg; + } + ); + + # get the input + my $input = ''; + if ( @ARGV > 0 ) { + my $data = shift; # a file name + open INPUT, "<$data" + or die "Cannot read '$data': $!\n"; + while () { $input .= $_; } + close INPUT; + } else { + $input = _empty_input; + } + + # extract all of the query ids from $input + my @query_ids = _get_query_ids($input); + print "\nSending the following data to $service asynchronously:\n", + $input, "\n" + if $opt_v; + + # submit the job + my $epr = + ( $soap->$service( SOAP::Data->type( 'string' => "$input" ) )->result ); + + # Get address from the returned Endpoint Reference + my $address = $epr->{'EndpointReference'}->{Address}; + + # Get resource identifier from the returned Endpoint Reference + my $identifier = + $epr->{'EndpointReference'}->{ReferenceParameters}->{ServiceInvocationId}; + + # Compose the Endpoint Reference + my $EPR = WSRF::WS_Address->new(); + $EPR->Address($address); + $EPR->ReferenceParameters( '' + . $identifier + . '' ); + my %completed = (); + while (1) { + foreach my $queryID (@query_ids) { + + # skip poll if current job completed + next if $completed{$queryID}; + + # poll the service for given query ID + my $searchTerm = ""; + $searchTerm .= +""; + $searchTerm .= "mobyws:status_" . $queryID; + $searchTerm .= ""; + + $soap = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action( + sub { + sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], + $_[1]; + } + )->wsaddress($EPR) + ->GetMultipleResourceProperties( + SOAP::Data->value($searchTerm)->type('xml') ); + + my $parser = XML::LibXML->new(); + my $xml = $soap->raw_xml; + my $doc = $parser->parse_string($xml); + $soap = $doc->getDocumentElement(); + my $prop_name = "status_" . $queryID; + + my ($prop) = + $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, + $prop_name ) + || $soap->getElementsByTagName($prop_name); + my $event = $prop->getFirstChild->toString + unless ref $prop eq "XML::LibXML::NodeList"; + $event = $prop->pop()->getFirstChild->toString + if ref $prop eq "XML::LibXML::NodeList"; + + my $status = LSAE::AnalysisEventBlock->new($event); + if ( $status->type == LSAE_PERCENT_PROGRESS_EVENT ) { + if ( $status->percentage >= 100 ) { + $completed{$queryID} = 1; + } elsif ( $status->percentage < 100 ) { + print "Current percentage: ", $status->percentage, "\n" if $opt_v; + sleep(20); + } else { + die "ERROR: analysis event block not well formed.\n"; + } + + } elsif ( $status->type == LSAE_STATE_CHANGED_EVENT ) { + if ( ( $status->new_state =~ m"completed"i ) + || ( $status->new_state =~ m"terminated_by_request"i ) + || ( $status->new_state =~ m"terminated_by_error"i ) ) + { + $completed{$queryID} = 1; + } elsif ( ( $status->new_state =~ m"created"i ) + || ( $status->new_state =~ m"running"i ) ) + { + print "Current State: ", $status->new_state, "\n" if $opt_v; + sleep(20); + } else { + die "ERROR: analysis event block not well formed.\n"; + } + + } elsif ( $status->type == LSAE_STEP_PROGRESS_EVENT ) { + if ( $status->steps_completed >= $status->total_steps ) { + $completed{$queryID} = 1; + } elsif ( $status->steps_completed < $status->total_steps ) { + print "Steps completed: ", $status->steps_completed, "\n" if $opt_v; + sleep(20); + } else { + die "ERROR: analysis event block not well formed.\n"; + } + + } elsif ( $status->type == LSAE_TIME_PROGRESS_EVENT ) { + if ( $status->remaining == 0 ) { + $completed{$queryID} = 1; + } elsif ( $status->remaining > 0 ) { + print "Time remaining: ", $status->remaining, "\n" if $opt_v; + sleep(20); + } else { + die "ERROR: analysis event block not well formed.\n"; + } + } + } + last if scalar keys(%completed) == $#query_ids + 1; + } + + foreach my $queryID (@query_ids) { + # get the result + my $searchTerm .= +""; + $searchTerm .= "mobyws:result_" . $queryID; + $searchTerm .= ""; + my $ans = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action( + sub { + sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], + $_[1]; + } + )->wsaddress($EPR) + ->GetMultipleResourceProperties( + SOAP::Data->value($searchTerm)->type('xml') ); + die "ERROR: " . $ans->faultstring if ( $ans->fault ); + + my $parser = XML::LibXML->new(); + my $xml = $ans->raw_xml; + my $doc = $parser->parse_string($xml); + $soap = $doc->getDocumentElement(); + my $prop_name = "result_" . $queryID; + my ($prop) = + $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name ) + || $soap->getElementsByTagName($prop_name); + my $result = $prop->getFirstChild->toString + unless ref $prop eq "XML::LibXML::NodeList"; + $result = $prop->pop()->getFirstChild->toString + if ref $prop eq "XML::LibXML::NodeList"; + print $result; + } + + # destroy the result + my $ans = WSRF::Lite->uri($WSRF::Constants::WSRL)->on_action( + sub { + sprintf '%s/ImmediateResourceTermination/%sRequest', + $WSRF::Constants::WSRLW, $_[1]; + } + )->wsaddress($EPR)->Destroy(); + } else { - # calling a local service module, without SOAP - my $data; - if (@ARGV > 0) { - $data = shift; # a file name - } else { - use File::Temp qw( tempfile ); - my $fh; - ($fh, $data) = tempfile (UNLINK => 1); - print $fh _empty_input(); - close $fh; - } - eval "require $module" or croak $@; - eval { - my $target = new $module; - print $target->$service ($data), "\n"; - } or croak $@; + + # calling a local service module, without SOAP + my $data; + if ( @ARGV > 0 ) { + $data = shift; # a file name + } else { + use File::Temp qw( tempfile ); + my $fh; + ( $fh, $data ) = tempfile( UNLINK => 1 ); + print $fh _empty_input(); + close $fh; + } + eval "require $module" or croak $@; + eval { + my $target = new $module; + print $target->$service($data), "\n"; + } or croak $@; } __END__ From kawas at dev.open-bio.org Tue Sep 2 17:58:54 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 13:58:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021758.m82HwsW6023176@dev.open-bio.org> kawas Tue Sep 2 13:58:54 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv23141/Perl/MOSES-MOBY Modified Files: Makefile.PL Log Message: makefile has been updated to always check for wsrf lite and moby client central code. moby-live/Perl/MOSES-MOBY Makefile.PL,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL 2008/08/25 16:27:28 1.7 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL 2008/09/02 17:58:54 1.8 @@ -33,15 +33,11 @@ requires 'Want' => '0.18'; requires 'IO::Prompt' => '0.99.2'; } - - print STDOUT "Shall I check for async libraries (do you plan on writing async services)? y/n [n] "; - my $tmp = ; - $tmp =~ s/\s//g; - if ($tmp =~ /y/i) { - requires 'MOBY::Client::Central' => 1.03; - requires 'WSRF::Lite' => 0.8.8.2; - } - + + # for async services + requires 'MOBY::Client::Central' => 1.06; + requires 'WSRF::Lite' => '0.8.2.3'; + build_requires 'Test::More' => '0.42'; no_index 'directory' => 'bin/scripts'; From kawas at dev.open-bio.org Tue Sep 2 18:25:37 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 14:25:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021825.m82IPb3t023303@dev.open-bio.org> kawas Tue Sep 2 14:25:37 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv23268/Perl/MOBY-Server/lib/MOBY/Async Modified Files: WSRF.pm Log Message: added no warnings 'redefine'; so that messages like: Subroutine header redefined ../MOBY/Async/WSRF.pm line 474. Subroutine new redefined at ../MOBY/Async/WSRF.pm line 647. Subroutine DESTROY redefined at ... /MOBY/Async/WSRF.pm line 657. are suppressed. moby-live/Perl/MOBY-Server/lib/MOBY/Async WSRF.pm,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm 2008/09/01 18:53:57 1.6 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/WSRF.pm 2008/09/02 18:25:37 1.7 @@ -470,7 +470,7 @@ $WSRF::Constants::WSRP => [$WSRF::Constants::WSRPW,undef], $WSRF::Constants::WSRL => [$WSRF::Constants::WSRLW,'ImmediateResourceTermination'] ); - +no warnings 'redefine'; sub header { my ($envelope, %args) = @_; my $myHeader; From kawas at dev.open-bio.org Tue Sep 2 18:27:15 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 14:27:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021827.m82IRFpI023343@dev.open-bio.org> kawas Tue Sep 2 14:27:15 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv23308/Perl/MOBY-Server Modified Files: Changes Log Message: added changes to reflect the addition of code to suppress redefinition warnings for MOBY::Async::WSRF moby-live/Perl/MOBY-Server Changes,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2008/09/02 13:14:56 1.12 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2008/09/02 18:27:15 1.13 @@ -15,7 +15,8 @@ introduced by a previous commit - Bug fix related to asynchronous MOBY calls with empty mobyData elements. MOBY::Async::SimpleServer uses serviceInputParser, which had the bug fixed. - - + - Added "no warnings 'redefine';" to MOBY::Async::WSRF to suppress redefinition + warnings. - From kawas at dev.open-bio.org Tue Sep 2 18:48:23 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 14:48:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021848.m82ImNfP023428@dev.open-bio.org> kawas Tue Sep 2 14:48:23 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv23393/src/main/org/biomoby/service/dashboard Modified Files: PerlMoSeSPanel.java Log Message: added an option to generate async services moby-live/Java/src/main/org/biomoby/service/dashboard PerlMoSeSPanel.java,1.12,1.13 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java 2008/06/12 16:46:52 1.12 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java 2008/09/02 18:48:23 1.13 @@ -87,6 +87,9 @@ // boolean do we generate soap services static String PM_SOAP = "perl-moses-soap"; + + // boolean do we generate async services + static String PM_ASYNC = "perl-moses-async"; // boolean: are we currently updating the datatype cache static String PM_SYNC_DATATYPES = "perl-moses-sync-datatypes"; @@ -298,6 +301,7 @@ propertyChannel.put(PM_SYNC_DATATYPES, new Boolean(false)); propertyChannel.put(PM_OVERWRITE, new Boolean(false)); propertyChannel.put(PM_CGI, new Boolean(false)); + propertyChannel.put(PM_ASYNC, new Boolean(false)); propertyChannel.put(PM_PERL_INSTALL_DIR, getPrefValue(PM_PERL_INSTALL_DIR, "")); propertyChannel.put(PM_PERL_LIB_1, getPrefValue(PM_PERL_LIB_1, "")); @@ -514,14 +518,16 @@ }); generateBtn.setEnabled(enable_moses_actions); ButtonGroup group = new ButtonGroup(); - JRadioButton genCgi, genSoap; - group.add (genCgi = createHowToButton ("Generate CGI Service", PM_CGI)); + JRadioButton genCgi, genSoap, genAsync; + group.add (genCgi = createHowToButton ("Generate CGI Service", PM_CGI)); group.add (genSoap = createHowToButton ("Generate SOAP Service", PM_SOAP)); + group.add (genAsync = createHowToButton ("Generate ASYNC Service", PM_ASYNC)); SwingUtils.addComponent(bPanel, genOverwrite, 0, 0, 1, 1, NONE, NWEST, 0.0, 0.0); SwingUtils.addComponent(bPanel, genCgi, 0, 1, 2, 1, NONE, NWEST, 0.0, 0.0); SwingUtils.addComponent(bPanel, genSoap, 0, 2, 2, 1, NONE, NWEST, 0.0, 0.0); - SwingUtils.addComponent(bPanel, generateBtn, 0, 3, 2, 1, HORI, NWEST, 0.0, 0.0); + SwingUtils.addComponent(bPanel, genAsync, 0, 3, 2, 1, NONE, NWEST, 0.0, 0.0); + SwingUtils.addComponent(bPanel, generateBtn, 0, 4, 2, 1, HORI, NWEST, 0.0, 0.0); // add to the main panel int count = 0; @@ -816,17 +822,20 @@ JRadioButton radio = new JRadioButton (title); radio.setActionCommand (howTo); radio.addActionListener (howToListener); - if (!howTo.equals(PM_CGI)) { + if (!howTo.equals(PM_CGI) && !howTo.equals(PM_ASYNC)) { radio.setSelected (true); radio.setEnabled (true); + propertyChannel.put (PM_CGI, false); + propertyChannel.put (PM_ASYNC, false); } - propertyChannel.put (PM_CGI, false); return radio; } private ActionListener howToListener = new ActionListener() { public void actionPerformed (ActionEvent e) { String howTo = e.getActionCommand(); propertyChannel.put (PM_CGI, howTo.equals(PM_CGI)); + propertyChannel.put (PM_ASYNC, howTo.equals(PM_ASYNC)); + propertyChannel.put (PM_SOAP, howTo.equals(PM_SOAP)); } }; private JPanel getServicesSelectionPanel() { @@ -1097,7 +1106,10 @@ if (Boolean.parseBoolean(propertyChannel .getString(PM_CGI))){ command.add("-c"); - } + } else if (Boolean.parseBoolean(propertyChannel + .getString(PM_ASYNC))){ + command.add("-A"); + } command.add(authority); // place command into com String[] com = command.toArray(new String[] {}); @@ -1189,6 +1201,9 @@ if (Boolean.parseBoolean(propertyChannel .getString(PM_CGI))){ command.add("-c"); + } else if (Boolean.parseBoolean(propertyChannel + .getString(PM_ASYNC))){ + command.add("-A"); } command.add(auth); command.add(name); From kawas at dev.open-bio.org Tue Sep 2 19:04:36 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 2 Sep 2008 15:04:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809021904.m82J4a8r023474@dev.open-bio.org> kawas Tue Sep 2 15:04:36 EDT 2008 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl In directory dev.open-bio.org:/tmp/cvs-serv23438/Docs/MOBY-S_API/Perl Modified Files: construct_moses_async_service.html Log Message: updated the service testing section. this document is now up to date. moby-live/Docs/MOBY-S_API/Perl construct_moses_async_service.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html 2008/09/02 16:35:32 1.1 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html 2008/09/02 19:04:36 1.2 @@ -130,9 +130,9 @@ Done.

    If you happen to see redefinition warnings, please just ignore them; The warnings look like the following:

    Generating services from samples.jmoby.net:
    -Subroutine header redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 521.
    +Subroutine header redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 521.
     Subroutine new redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 694.
    -Subroutine DESTROY redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 704.
    +Subroutine DESTROY redefined at /usr/local/share/perl/5.8.8/MOBY/Async/WSRF.pm line 704.
     Done.

    Basically, we used the script moses-generate-services.pl to:

      @@ -170,6 +170,11 @@ value => "$string", # TO BE EDITED ); +

      Optionally, to test out the asynchronous aspect of our service, feel free to slow your service down. Something like the following would do that for you:

      +
      # this will cause our service to sleep for 60 seconds
      +# as long as data was sent to our service
      +sleep(60) if defined $my_input_string;
      +

      You can add the optional code below the definition of $my_reverse_string.

      That is all there is to it. Now we can test our service!

      Service testing

      To test the service, issue the following command:

      @@ -195,15 +200,23 @@

      You only have to do this once. In other words, all other asynchronous SOAP based services that you construct using MoSeS automatically use that cgi-bin script, because the moses-generate-services.pl script updates the ASYNC_SERVICE_TABLE that we talked about earlier.

      Service testing using SOAP

      Now that the service has been deployed, you can test it using WSRF/SOAP with the following command:

      -
      moses-testing-service.pl -e http://localhost/cgi-bin/MobyServer.cgi getReverseEchoString input.xml
      -

      When we call the script with the -e option, we tell the moses-testing-service.pl script that we would like to call our service using SOAP. We then must provide the script with 2 or 3 parameters:

      +
      moses-testing-service.pl -v -a http://localhost/cgi-bin/AsyncMobyServer.cgi getReverseEchoString input.xml
      +

      The -v option is just a flag that makes the script be verbose, so that you can see what is going on.

      +

      When we call the script with the -a option, we tell the moses-testing-service.pl script that we would like to call our service using Asynchronous SOAP. We then must provide the script with 2 or 3 parameters:

      1. the url to the service
      2. the name of the service that we would like to call
      3. an optional file containing the input to our service

      The expected output should be very similar to the output we saw above when we tested our service:

      -
      <?xml version="1.0"?>
      <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
      <moby:mobyContent moby:authority="samples.jmoby.net">
      <moby:serviceNotes>
      <moby:Notes>Response created at Thu May 1 19:22:00 2008 (GMT), by the service 'getReverseEchoString'.</moby:Notes>
      </moby:serviceNotes>
      <moby:mobyData moby:queryID="job_0">
      <moby:Simple moby:articleName="my_reverse_string">
      <moby:String moby:id="" moby:namespace="">!desrever gnirts siht tnaw I</moby:String>
      </moby:Simple>
      </moby:mobyData>
      </moby:mobyContent>
      </moby:MOBY>
      +
      +Sending the following data to getReverseEchoString_submit asynchronously:
      <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
      <moby:mobyContent>
      <moby:mobyData moby:queryID="job_0">
      <moby:Simple moby:articleName="my_input_string">
      <moby:String moby:id="" moby:namespace="">I want this string reversed!</moby:String>
      </moby:Simple>
      </moby:mobyData>
      </moby:mobyContent>
      </moby:MOBY> + + +Current State: running
      Current State: running
      Current State: running + + +<?xml version="1.0"?>
      <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
      <moby:mobyContent moby:authority="samples.jmoby.net">
      <moby:serviceNotes>
      <moby:Notes>Response created at Thu May 1 19:22:00 2008 (GMT), by the service 'getReverseEchoString'.</moby:Notes>
      </moby:serviceNotes>
      <moby:mobyData moby:queryID="job_0">
      <moby:Simple moby:articleName="my_reverse_string">
      <moby:String moby:id="" moby:namespace="">!desrever gnirts siht tnaw I</moby:String>
      </moby:Simple>
      </moby:mobyData>
      </moby:mobyContent>
      </moby:MOBY>

      That's all there is to constructing asynchronous SOAP based Perl MoSeS services!

      From gordonp at dev.open-bio.org Wed Sep 10 19:36:45 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 10 Sep 2008 15:36:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809101936.m8AJajQc027466@dev.open-bio.org> gordonp Wed Sep 10 15:36:44 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory dev.open-bio.org:/tmp/cvs-serv27430/src/main/org/biomoby/shared/data Modified Files: MobyDataComposite.java Log Message: Added support for put() in datatypes not found in the registry (i.e. the HAS/HAS-A relationship for the member is not validated) moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.26,1.27 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/02/13 09:26:08 1.26 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java 2008/09/10 19:36:44 1.27 @@ -418,7 +418,17 @@ MobyRelationship relationship = getDataType().getChild(fieldName); if(relationship == null){ - relationship = MobyDataType.getDataType(getDataType().getName(), getDataType().getRegistry()).getChild(fieldName); + MobyDataType t = MobyDataType.getDataType(getDataType().getName(), getDataType().getRegistry()); + if(t == null){ + System.err.println("Data type " + getDataType().getName() + " is not in the registry: " + + "validity of member put() operation will not be confirmed"); + relationship = new MobyRelationship(fieldName, + value.getDataType().getName(), + members.containsKey(fieldName) ? Central.iHAS : Central.iHASA); + } + else{ + relationship = t.getChild(fieldName); + } if(relationship == null){ String memberNames = ""; for(MobyRelationship rel: getDataType().getChildren()){ From gordonp at dev.open-bio.org Wed Sep 10 20:02:11 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 10 Sep 2008 16:02:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809102002.m8AK2B4E027598@dev.open-bio.org> gordonp Wed Sep 10 16:02:11 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/Clients In directory dev.open-bio.org:/tmp/cvs-serv27562/src/Clients Modified Files: TestClientServiceChain.java Log Message: Updte to reflect MobyRequest's setSecondaries throwing exceptions now moby-live/Java/src/Clients TestClientServiceChain.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestClientServiceChain.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/Clients/TestClientServiceChain.java 2006/12/14 19:37:37 1.1 +++ /home/repository/moby/moby-live/Java/src/Clients/TestClientServiceChain.java 2008/09/10 20:02:11 1.2 @@ -36,7 +36,7 @@ } } - public static void setSecondaries(MobyRequest mr, MobyService service){ + public static void setSecondaries(MobyRequest mr, MobyService service) throws Exception{ MobySecondaryData[] secondaryData = service.getSecondaryInputs(); MobyDataSecondaryInstance[] secondaryInstances = new MobyDataSecondaryInstance[secondaryData.length]; From gordonp at dev.open-bio.org Wed Sep 10 20:02:42 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 10 Sep 2008 16:02:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809102002.m8AK2gwq027642@dev.open-bio.org> gordonp Wed Sep 10 16:02:41 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv27606/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyServicesGUI.java Log Message: Updte to reflect MobyRequest's setSecondaries throwing exceptions now moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java 2008/01/08 15:27:50 1.14 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java 2008/09/10 20:02:41 1.15 @@ -195,11 +195,11 @@ try{ mobyRequest.setInput(castInputs); + mobyRequest.setSecondaryInput(secondaryInputInstances); } catch(MobyException me){ me.printStackTrace(); logger.warn("Error while trying to set service input: " + me); } - mobyRequest.setSecondaryInput(secondaryInputInstances); executeService(handler); } From gordonp at dev.open-bio.org Wed Sep 10 20:04:03 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 10 Sep 2008 16:04:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809102004.m8AK43WO027686@dev.open-bio.org> gordonp Wed Sep 10 16:04:02 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv27650/src/main/org/biomoby/client Modified Files: MobyRequest.java Log Message: MobyRequest's setSecondaries throws exceptions now if the parameters are blank or overwrite primary params with the same name moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.37,1.38 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.37 retrieving revision 1.38 diff -u -r1.37 -r1.38 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2008/01/26 17:54:59 1.37 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2008/09/10 20:04:02 1.38 @@ -230,8 +230,10 @@ * in this object. This is covenient if you are running 100 seqs through BLAST and only want to set * the parameters once. If you instead want to set secondary input differently for all primary inputs, you'll * need to create a custom MobyContentInstance as input to setInput(). + * + * @throws MobyException if a parameter name is blank, or overrides a primary parameter */ - public void setSecondaryInput(MobyDataSecondaryInstance[] secondaryData){ + public void setSecondaryInput(MobyDataSecondaryInstance[] secondaryData) throws MobyException{ Iterator queryNames = inputData.keySet().iterator(); // For each query @@ -239,7 +241,15 @@ MobyDataJob queryParams = inputData.get(queryNames.next()); // Set all the secondary params (overwrites any old ones) for(int i = 0; i < secondaryData.length; i++){ - queryParams.put(secondaryData[i].getName(), secondaryData[i]); + String secName = secondaryData[i].getName(); + if(secName == null || secName.length() == 0){ + throw new MobyException("A secondary parameter cannot have a blank name (array index " + i + ")"); + } + if(queryParams.containsKey(secName) && queryParams.get(secName) instanceof MobyPrimaryData){ + throw new MobyException("A secondary parameter cannot override an existing primary parameter " + + "with the same name (" + secName + ")"); + } + queryParams.put(secName, secondaryData[i]); } } } From kawas at dev.open-bio.org Mon Sep 22 15:42:28 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Mon, 22 Sep 2008 11:42:28 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200809221542.m8MFgSeq013536@dev.open-bio.org> kawas Mon Sep 22 11:42:27 EDT 2008 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv13501/Perl/MOBY-Server/lib/MOBY Modified Files: CommonSubs.pm Log Message: tried to remove dependency on the 'moby' prefix when resolving attributes. need to do this for elements too. moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/02 13:14:18 1.5 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2008/09/22 15:42:27 1.6 @@ -1171,7 +1171,7 @@ . "\n called from line $line"; return ''; } - return ( $xref->getAttributeNode($attr) || $xref->getAttributeNode( "moby:$attr" ) ); + return ( $xref->getAttributeNode($attr) || $xref->getAttributeNode( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr" ) ); } sub _moby_getAttribute { @@ -1191,7 +1191,7 @@ . "\n called from line $line"; return ''; } - return ( $xref->getAttribute($attr) || $xref->getAttribute("moby:$attr") ); + return ( $xref->getAttribute($attr) || $xref->getAttribute( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") ); } sub _makeXrefType {