From kawas at dev.open-bio.org Tue Sep 1 12:27:05 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 12:27:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909011627.n81GR4dj016422@dev.open-bio.org> kawas Tue Sep 1 12:27:04 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv16387/MOBY-Server/lib/MOBY Modified Files: CommonSubs.pm Log Message: removed the hard coded references to moby: (namespace prefix) in all places that i found it to be hard coded. Instead, i look for any prefix. Moreover, I removed all references to $element->nodeName and replaced them with references to $element->localname so that we can check the element name without worrying about the xml namespace prefix. CommonSubs.t seems to run completely normal after making these changes (all tests pass). moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2009/04/15 17:45:23 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2009/09/01 16:27:04 1.8 @@ -413,19 +413,19 @@ $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; return undef - unless ($moby->nodeName =~ /^(moby:|)mobyData$/); + unless ($moby->localname =~ /^(.*:|)mobyData$/); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace next - unless ( $child->nodeName =~ /^(moby:|)(Simple|Collection|Parameter)$/ ); + unless ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ); my $object; - if ( $child->nodeName =~ /^(moby:|)Simple$/ ) { + if ( $child->localname=~ /^(.*:|)Simple$/ ) { $object = MOBY::Client::SimpleArticle->new( XML_DOM => $child ); - } elsif ( $child->nodeName =~ /^(moby:|)Collection$/ ) { + } elsif ( $child->localname=~ /^(.*:|)Collection$/ ) { $object = MOBY::Client::CollectionArticle->new( XML_DOM => $child ); - } elsif ( $child->nodeName =~ /^(moby:|)Parameter$/ ) { + } elsif ( $child->localname =~ /^(.*:|)Parameter$/ ) { $object = MOBY::Client::SecondaryArticle->new( XML_DOM => $child ); } next unless $object; @@ -438,7 +438,7 @@ sub _getQID { my ( $XML ) = @_; my $moby = _string_to_DOM($XML); - return '' unless ( $moby->nodeName =~ /^(moby:|)mobyData$/ ); + return '' unless ( $moby->localname =~ /^(.*:|)mobyData$/ ); my $qid = _moby_getAttribute($moby, 'queryID' ); $qid ||= _moby_getAttribute($moby, 'moby:queryID' ); return defined( $qid ) ? $qid : ''; @@ -480,7 +480,7 @@ eval { $DOM = _string_to_DOM($DOM) }; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ($DOM->nodeName =~ /^(moby:|)Simple$/) ? 1 : 0; #Optional 'moby:' namespace prefix + return ($DOM->localname =~ /^(.*:|)Simple$/) ? 1 : 0; #Optional 'moby:' namespace prefix } sub isCollectionArticle { @@ -488,7 +488,7 @@ eval {$DOM = _string_to_DOM($DOM) }; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ( $DOM->nodeName =~ /^(moby\:|)Collection$/ ) ? 1 : 0; #Optional 'moby:' prefix + return ( $DOM->localname =~ /^(.*:|)Collection$/ ) ? 1 : 0; #Optional 'moby:' prefix } sub isSecondaryArticle { @@ -497,7 +497,7 @@ eval {$DOM = _string_to_DOM($XML)} ; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ($DOM->nodeName =~ /^(moby\:|)Parameter$/) ? 1 : 0; #Optional 'moby:' prefix + return ($DOM->localname =~ /^(.*:|)Parameter$/) ? 1 : 0; #Optional 'moby:' prefix } @@ -961,8 +961,8 @@ $XML = _string_to_DOM($XML); my @xrefs; my @XREFS; - return () if ( $XML->nodeName =~ /^(moby:|)Collection$/ ); - if ( $XML->nodeName =~ /^(moby:|)Simple$/ ) { + return () if ( $XML->localname =~ /^(.*:|)Collection$/ ); + if ( $XML->localname =~ /^(.*:|)Simple$/ ) { foreach my $child ( $XML->childNodes ) { next unless $child->nodeType == ELEMENT_NODE; $XML = $child; @@ -971,17 +971,17 @@ } foreach ( $XML->childNodes ) { next unless (($_->nodeType == ELEMENT_NODE) - || ($_->nodeName =~ /^(moby:|)CrossReference$/) ); + || ($_->localname && $_->localname =~ /^(.*:|)CrossReference$/) ); foreach my $xref ( $_->childNodes ) { - next unless ( ($xref->nodeType == ELEMENT_NODE) - || ($xref->nodeName =~ /^(moby:|)(Xref|Object)$/) ); + next unless $xref && ( ($xref->nodeType == ELEMENT_NODE) + || ($xref->localname && $xref->localname =~ /^(.*:|)(Xref|Object)$/) ); push @xrefs, $xref; } } foreach ( @xrefs ) { my $x; - if ($_->nodeName =~ /^(moby:|)Xref$/) { $x = _makeXrefType( $_ ) } - elsif ($_->nodeName =~ /^(moby:|)Object$/) { $x = _makeObjectType( $_ ) } + if ($_->localname =~ /^(.*:|)Xref$/) { $x = _makeXrefType( $_ ) } + elsif ($_->localname =~ /^(.*:|)Object$/) { $x = _makeObjectType( $_ ) } push @XREFS, $x if $x; } return @XREFS; @@ -1338,7 +1338,7 @@ sub _getQueryID { my ( $query ) = @_; $query = _string_to_XML($query); - return '' unless ( $query->nodeName =~ /^(moby:|)mobyData$/ ); #Eddie - unsure + return '' unless ( $query->localname =~ /^(.*:|)mobyData$/ ); #Eddie - unsure return _moby_getAttribute($query, 'queryID' ); } @@ -1392,19 +1392,19 @@ my $resp = $responses->get_node( $n ); foreach my $response_component ( $resp->childNodes ) { next unless $response_component->nodeType == ELEMENT_NODE; - if ( $response_component->nodeName =~ /^(moby:|)Simple$/ ) + if ( $response_component->localname =~ /^(.*:|)Simple$/ ) { foreach my $Object ( $response_component->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; push @objects, $Object; } - } elsif ( $response_component->nodeName =~ /^(moby:|)Collection$/ ) + } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ ) { my @objects; foreach my $simple ( $response_component->childNodes ) { next unless $simple->nodeType == ELEMENT_NODE; - next unless ( $simple->nodeName =~ /^(moby:|)Simple$/ ); + next unless ( $simple->localname =~ /^(.*:|)Simple$/ ); foreach my $Object ( $simple->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; @@ -1498,12 +1498,12 @@ $moby = _string_to_DOM($moby); return undef unless ( ($moby->nodeType == ELEMENT_NODE) - && ( $moby->nodeName =~ /^(moby:|)(queryInput|queryResponse|mobyData)$/ ) ); + && ( $moby->localname =~ /^(.*:|)(queryInput|queryResponse|mobyData)$/ ) ); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless ( ($child->nodeType == ELEMENT_NODE) # ignore whitespace - && ( $child->nodeName =~ /^(moby:|)(Simple|Collection|Parameter)$/ ) ); + && ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ) ); my $articleName = _moby_getAttribute($child, 'articleName' ); # push the named child DOM elements (which are or , ) push @articles, [ $articleName, $child ]; @@ -1548,7 +1548,7 @@ foreach my $in ( @input_nodes ) { next unless $in; #$in = "" - next unless $in->nodeName =~ /^(moby:|)Simple$/; # only allow simples + next unless $in->localname =~ /^(.*)Simple$/; # only allow simples my @simples = $in->childNodes; foreach ( @simples ) { # $_ = next unless $_->nodeType == ELEMENT_NODE; @@ -1647,7 +1647,7 @@ print STDERR "getInputID method is now deprecated. Please use serviceInputParser or serviceResponseParser\n"; my ( $XML ) = @_; my $moby = _string_to_DOM($XML); - return '' unless ( $moby->nodeName =~ /^(moby:|)queryInput|mobyData$/ ); + return '' unless ( $moby->localname =~ /^(.*:|)queryInput|mobyData$/ ); my $qid = _moby_getAttribute($moby, 'queryID' ); $qid ||= _moby_getAttribute($moby, 'moby:queryID' ); return defined( $qid ) ? $qid : ''; @@ -1665,19 +1665,19 @@ $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; return undef - unless ($moby->nodeName =~ /^(moby:|)(queryInput|queryResponse|mobyData)$/); + unless ($moby->localname =~ /^(.*:|)(queryInput|queryResponse|mobyData)$/); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace next - unless ( $child->nodeName =~ /^(moby:|)(Simple|Collection|Parameter)$/ ); + unless ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ); my $object; - if ( $child->nodeName =~ /^(moby:|)Simple$/ ) { + if ( $child->localname =~ /^(.*:|)Simple$/ ) { $object = MOBY::Client::SimpleArticle->new( XML_DOM => $child ); - } elsif ( $child->nodeName =~ /^(moby:|)Collection$/ ) { + } elsif ( $child->localname =~ /^(.*:|)Collection$/ ) { $object = MOBY::Client::CollectionArticle->new( XML_DOM => $child ); - } elsif ( $child->nodeName =~ /^(moby:|)Parameter$/ ) { + } elsif ( $child->localname =~ /^(.*:|)Parameter$/ ) { $object = MOBY::Client::SecondaryArticle->new( XML_DOM => $child ); } next unless $object; @@ -1697,12 +1697,12 @@ my ( $moby ) = @_; $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; - return undef unless ( $moby->nodeName =~ /^(moby\:|)Collection$/ ); + return undef unless ( $moby->localname =~ /^(.*:|)Collection$/ ); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace - next unless ( $child->nodeName =~ /^(moby\:|)Simple$/ ); + next unless ( $child->localname =~ /^(.*:|)Simple$/ ); push @articles, $child; # take the child elements, which are or } return @articles; # return them. @@ -1791,19 +1791,19 @@ my $resp = $responses->get_node( $n ); foreach my $response_component ( $resp->childNodes ) { next unless $response_component->nodeType == ELEMENT_NODE; - if ( $response_component->nodeName =~ /^(moby:|)Simple$/ ) + if ( $response_component->localname =~ /^(.*:|)Simple$/ ) { foreach my $Object ( $response_component->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; push @objects, $Object; } - } elsif ( $response_component->nodeName =~ /^(moby:|)Collection$/ ) + } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ ) { my @objects; foreach my $simple ( $response_component->childNodes ) { next unless $simple->nodeType == ELEMENT_NODE; - next unless ( $simple->nodeName =~ /^(moby:|)Simple$/ ); + next unless ( $simple->localname =~ /^(.*:|)Simple$/ ); foreach my $Object ( $simple->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; From kawas at dev.open-bio.org Tue Sep 1 16:13:20 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 16:13:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909012013.n81KDKZq017336@dev.open-bio.org> kawas Tue Sep 1 16:13:20 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/t In directory dev.open-bio.org:/tmp/cvs-serv17301/MOBY-Server/t Modified Files: CommonSubs.t Log Message: modified CommonSubs.t to reflect that one of the tests using an incorrect namespaceURI use to pass when it should have failed. modified CommonSubs.pm: now we compare the actual namespaceURI to http://www.biomoby.org/moby and dont extract content unless the elements and attributes properly resolve. CommonSubs is now more strict w.r.t. biomoby services api moby-live/Perl/MOBY-Server/t CommonSubs.t,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/t/CommonSubs.t,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/t/CommonSubs.t 2008/02/21 00:21:28 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/t/CommonSubs.t 2009/09/01 20:13:20 1.2 @@ -13,6 +13,10 @@ #use SOAP::Lite +trace; use Test::More 'no_plan'; #skip_all => "Turned off for development"; #'no_plan'; use strict; + +use FindBin qw ($Bin); +use lib "$Bin/../lib/"; + use English; use Data::Dumper; #Is the client-code even installed? @@ -138,7 +142,7 @@ # Test getInputArticles with one, and with more than one mobyData block. my $two_mobyDatas = < + @@ -161,6 +165,31 @@ ok ($ids[0] eq "first") or die "serviceResponseParser didn't find the first query id\n"; ok ($ids[1] eq "second") or die "serviceResponseParser didn't find the second query id that included a moby: namespace\n"; +# pass 2 invalid messages ... should not parse +$two_mobyDatas = < + + + + + + + + + + + + + +INP_ART + +$responses = serviceResponseParser($two_mobyDatas); # returns MOBY objects +print Dumper($responses); +isa_ok ($responses, "HASH", "response parser returned a HASH" ) or die "serviceResponseParser didn't return a hashref for multiple input test\n"; + at ids = keys %{$responses}; +ok (scalar(@ids) == 0) or die "serviceResponseParser didn't find right number of invocation messages when two invalid ones were passed\n"; + + my $sequence = "TAGCTGATCGAGCTGATGCTGA"; my $articlename = "SequenceString"; From kawas at dev.open-bio.org Tue Sep 1 16:13:20 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 16:13:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909012013.n81KDKRP017356@dev.open-bio.org> kawas Tue Sep 1 16:13:20 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv17301/MOBY-Server/lib/MOBY Modified Files: CommonSubs.pm Log Message: modified CommonSubs.t to reflect that one of the tests using an incorrect namespaceURI use to pass when it should have failed. modified CommonSubs.pm: now we compare the actual namespaceURI to http://www.biomoby.org/moby and dont extract content unless the elements and attributes properly resolve. CommonSubs is now more strict w.r.t. biomoby services api moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2009/09/01 16:27:04 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2009/09/01 20:13:20 1.9 @@ -221,22 +221,31 @@ =cut package MOBY::CommonSubs; +use strict; +use warnings; + require Exporter; use XML::LibXML; + use MOBY::CrossReference; use MOBY::Client::OntologyServer; -use strict; -use warnings; use MOBY::Client::SimpleArticle; use MOBY::Client::CollectionArticle; use MOBY::Client::SecondaryArticle; use MOBY::MobyXMLConstants; + +# create the namespace URI +# can be modified by clients if they see fit using +# $MOBY::CommonSubs::MOBY_NS +our $MOBY_NS = 'http://www.biomoby.org/moby'; + use constant COLLECTION => 1; use constant SIMPLE => 2; use constant SECONDARY => 3; use constant PARAMETER => 3; # be friendly in case they use this instead use constant BE_NICE => 1; use constant BE_STRICT => 0; + our @ISA = qw(Exporter); our @EXPORT = qw(COLLECTION SIMPLE SECONDARY PARAMETER BE_NICE BE_STRICT); @@ -378,13 +387,14 @@ my %input_parameters; # $input_parameters{$queryID} = [ foreach my $query ( @queries ) { my $queryID = _getQID( $query ); # get the queryID attribute of the mobyData + next unless $queryID; 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; + ${$input_parameters{$queryID}}{$article->articleName} = $article if $article and $article->articleName ne ''; } } return \%input_parameters; @@ -413,19 +423,19 @@ $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; return undef - unless ($moby->localname =~ /^(.*:|)mobyData$/); + unless ($moby->localname =~ /^mobyData$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace next - unless ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ); + unless ( $child->localname =~ /^(Simple|Collection|Parameter)$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my $object; - if ( $child->localname=~ /^(.*:|)Simple$/ ) { + if ( $child->localname=~ /^Simple$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::SimpleArticle->new( XML_DOM => $child ); - } elsif ( $child->localname=~ /^(.*:|)Collection$/ ) { + } elsif ( $child->localname=~ /^Collection$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::CollectionArticle->new( XML_DOM => $child ); - } elsif ( $child->localname =~ /^(.*:|)Parameter$/ ) { + } elsif ( $child->localname =~ /^Parameter$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::SecondaryArticle->new( XML_DOM => $child ); } next unless $object; @@ -438,7 +448,7 @@ sub _getQID { my ( $XML ) = @_; my $moby = _string_to_DOM($XML); - return '' unless ( $moby->localname =~ /^(.*:|)mobyData$/ ); + return '' unless ( $moby->localname =~ /^mobyData$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my $qid = _moby_getAttribute($moby, 'queryID' ); $qid ||= _moby_getAttribute($moby, 'moby:queryID' ); return defined( $qid ) ? $qid : ''; @@ -480,7 +490,7 @@ eval { $DOM = _string_to_DOM($DOM) }; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ($DOM->localname =~ /^(.*:|)Simple$/) ? 1 : 0; #Optional 'moby:' namespace prefix + return ($DOM->localname =~ /^Simple$/ and ($DOM->namespaceURI() ? $DOM->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ? 1 : 0; #Optional 'moby:' namespace prefix } sub isCollectionArticle { @@ -488,7 +498,7 @@ eval {$DOM = _string_to_DOM($DOM) }; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ( $DOM->localname =~ /^(.*:|)Collection$/ ) ? 1 : 0; #Optional 'moby:' prefix + return ( $DOM->localname =~ /^Collection$/ and ($DOM->namespaceURI() ? $DOM->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ? 1 : 0; #Optional 'moby:' prefix } sub isSecondaryArticle { @@ -497,7 +507,7 @@ eval {$DOM = _string_to_DOM($XML)} ; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ($DOM->localname =~ /^(.*:|)Parameter$/) ? 1 : 0; #Optional 'moby:' prefix + return ($DOM->localname =~ /^Parameter$/ and ($DOM->namespaceURI() ? $DOM->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ? 1 : 0; #Optional 'moby:' prefix } @@ -763,7 +773,7 @@ $exception ||=""; my $xml = "" - . "" + . "" . ""; if ($exception) { $xml .= "$exception"; @@ -961,8 +971,8 @@ $XML = _string_to_DOM($XML); my @xrefs; my @XREFS; - return () if ( $XML->localname =~ /^(.*:|)Collection$/ ); - if ( $XML->localname =~ /^(.*:|)Simple$/ ) { + return () if ( $XML->localname =~ /^Collection$/ and ($XML->namespaceURI() ? $XML->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); + if ( $XML->localname =~ /^Simple$/ and ($XML->namespaceURI() ? $XML->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { foreach my $child ( $XML->childNodes ) { next unless $child->nodeType == ELEMENT_NODE; $XML = $child; @@ -971,17 +981,17 @@ } foreach ( $XML->childNodes ) { next unless (($_->nodeType == ELEMENT_NODE) - || ($_->localname && $_->localname =~ /^(.*:|)CrossReference$/) ); + || ($_->localname && $_->localname =~ /^CrossReference$/ and ($_->namespaceURI() ? $_->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ); foreach my $xref ( $_->childNodes ) { next unless $xref && ( ($xref->nodeType == ELEMENT_NODE) - || ($xref->localname && $xref->localname =~ /^(.*:|)(Xref|Object)$/) ); + || ($xref->localname && $xref->localname =~ /^(Xref|Object)$/ and ($xref->namespaceURI() ? $xref->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ); push @xrefs, $xref; } } foreach ( @xrefs ) { my $x; - if ($_->localname =~ /^(.*:|)Xref$/) { $x = _makeXrefType( $_ ) } - elsif ($_->localname =~ /^(.*:|)Object$/) { $x = _makeObjectType( $_ ) } + if ($_->localname =~ /^Xref$/ and ($_->namespaceURI() ? $_->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $x = _makeXrefType( $_ ) } + elsif ($_->localname =~ /^Object$/ and ($_->namespaceURI() ? $_->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $x = _makeObjectType( $_ ) } push @XREFS, $x if $x; } return @XREFS; @@ -1175,11 +1185,11 @@ return $xref->getAttributeNode($attr) if $xref->getAttributeNode($attr); # check for a namespaced attribute by name - return $xref->getAttributeNodeNS('http://www.biomoby.org/moby', $attr) - if $xref->getAttributeNodeNS('http://www.biomoby.org/moby', $attr); + return $xref->getAttributeNodeNS($MOBY_NS, $attr) + if $xref->getAttributeNodeNS($MOBY_NS, $attr); # check for a namespaced attribute with a prefix ... this is probably redundant! - return $xref->getAttributeNode( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") - if $xref->lookupNamespacePrefix('http://www.biomoby.org/moby'); + return $xref->getAttributeNode( $xref->lookupNamespacePrefix($MOBY_NS) . ":$attr") + if $xref->lookupNamespacePrefix($MOBY_NS); # cant find it ... return ''; } @@ -1206,11 +1216,11 @@ return $xref->getAttribute($attr) if $xref->getAttribute($attr); # check for a namespaced attribute by name - return $xref->getAttributeNS('http://www.biomoby.org/moby', $attr) - if $xref->getAttributeNS('http://www.biomoby.org/moby', $attr); + return $xref->getAttributeNS($MOBY_NS, $attr) + if $xref->getAttributeNS($MOBY_NS, $attr); # check for a namespaced attribute with a prefix ... this is probably redundant! - return $xref->getAttribute( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") - if $xref->lookupNamespacePrefix('http://www.biomoby.org/moby'); + return $xref->getAttribute( $xref->lookupNamespacePrefix($MOBY_NS) . ":$attr") + if $xref->lookupNamespacePrefix($MOBY_NS); # cant find it ... return ''; } @@ -1338,7 +1348,7 @@ sub _getQueryID { my ( $query ) = @_; $query = _string_to_XML($query); - return '' unless ( $query->localname =~ /^(.*:|)mobyData$/ ); #Eddie - unsure + return '' unless ( $query->localname =~ /^mobyData$/ and ($query->namespaceURI() ? $query->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); #Eddie - unsure return _moby_getAttribute($query, 'queryID' ); } @@ -1392,19 +1402,19 @@ my $resp = $responses->get_node( $n ); foreach my $response_component ( $resp->childNodes ) { next unless $response_component->nodeType == ELEMENT_NODE; - if ( $response_component->localname =~ /^(.*:|)Simple$/ ) + if ( $response_component->localname =~ /^Simple$/ and ($response_component->namespaceURI() ? $response_component->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { foreach my $Object ( $response_component->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; push @objects, $Object; } - } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ ) + } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ and ($response_component->namespaceURI() ? $response_component->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { my @objects; foreach my $simple ( $response_component->childNodes ) { next unless $simple->nodeType == ELEMENT_NODE; - next unless ( $simple->localname =~ /^(.*:|)Simple$/ ); + next unless ( $simple->localname =~ /^Simple$/ and ($simple->namespaceURI() ? $simple->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); foreach my $Object ( $simple->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; @@ -1498,12 +1508,12 @@ $moby = _string_to_DOM($moby); return undef unless ( ($moby->nodeType == ELEMENT_NODE) - && ( $moby->localname =~ /^(.*:|)(queryInput|queryResponse|mobyData)$/ ) ); + && ( $moby->localname =~ /^(queryInput|queryResponse|mobyData)$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless ( ($child->nodeType == ELEMENT_NODE) # ignore whitespace - && ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ) ); + && ( $child->localname =~ /^(Simple|Collection|Parameter)$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ); my $articleName = _moby_getAttribute($child, 'articleName' ); # push the named child DOM elements (which are or , ) push @articles, [ $articleName, $child ]; @@ -1548,7 +1558,7 @@ foreach my $in ( @input_nodes ) { next unless $in; #$in = "" - next unless $in->localname =~ /^(.*)Simple$/; # only allow simples + next unless $in->localname =~ /^Simple$/ and ($in->namespaceURI() ? $in->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1); # only allow simples my @simples = $in->childNodes; foreach ( @simples ) { # $_ = next unless $_->nodeType == ELEMENT_NODE; @@ -1647,7 +1657,7 @@ print STDERR "getInputID method is now deprecated. Please use serviceInputParser or serviceResponseParser\n"; my ( $XML ) = @_; my $moby = _string_to_DOM($XML); - return '' unless ( $moby->localname =~ /^(.*:|)queryInput|mobyData$/ ); + return '' unless ( $moby->localname =~ /^queryInput|mobyData$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my $qid = _moby_getAttribute($moby, 'queryID' ); $qid ||= _moby_getAttribute($moby, 'moby:queryID' ); return defined( $qid ) ? $qid : ''; @@ -1665,19 +1675,19 @@ $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; return undef - unless ($moby->localname =~ /^(.*:|)(queryInput|queryResponse|mobyData)$/); + unless ($moby->localname =~ /^(queryInput|queryResponse|mobyData)$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace next - unless ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ); + unless ( $child->localname =~ /^(Simple|Collection|Parameter)$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my $object; - if ( $child->localname =~ /^(.*:|)Simple$/ ) { + if ( $child->localname =~ /^Simple$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::SimpleArticle->new( XML_DOM => $child ); - } elsif ( $child->localname =~ /^(.*:|)Collection$/ ) { + } elsif ( $child->localname =~ /^Collection$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::CollectionArticle->new( XML_DOM => $child ); - } elsif ( $child->localname =~ /^(.*:|)Parameter$/ ) { + } elsif ( $child->localname =~ /^Parameter$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::SecondaryArticle->new( XML_DOM => $child ); } next unless $object; @@ -1697,12 +1707,12 @@ my ( $moby ) = @_; $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; - return undef unless ( $moby->localname =~ /^(.*:|)Collection$/ ); + return undef unless ( $moby->localname =~ /^Collection$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace - next unless ( $child->localname =~ /^(.*:|)Simple$/ ); + next unless ( $child->localname =~ /^Simple$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); push @articles, $child; # take the child elements, which are or } return @articles; # return them. @@ -1791,19 +1801,19 @@ my $resp = $responses->get_node( $n ); foreach my $response_component ( $resp->childNodes ) { next unless $response_component->nodeType == ELEMENT_NODE; - if ( $response_component->localname =~ /^(.*:|)Simple$/ ) + if ( $response_component->localname =~ /^Simple$/ and ($response_component->namespaceURI() ? $response_component->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { foreach my $Object ( $response_component->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; push @objects, $Object; } - } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ ) + } elsif ( $response_component->localname =~ /^Collection$/ and ($response_component->namespaceURI() ? $response_component->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { my @objects; foreach my $simple ( $response_component->childNodes ) { next unless $simple->nodeType == ELEMENT_NODE; - next unless ( $simple->localname =~ /^(.*:|)Simple$/ ); + next unless ( $simple->localname =~ /^Simple$/ and ($simple->namespaceURI() ? $simple->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); foreach my $Object ( $simple->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; From kawas at dev.open-bio.org Tue Sep 1 16:13:51 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 16:13:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909012013.n81KDpa5017426@dev.open-bio.org> kawas Tue Sep 1 16:13:51 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv17363/MOBY-Client Modified Files: Changes Makefile.PL Log Message: updated to reflect recent changes to codebase moby-live/Perl/MOBY-Client Changes,1.9,1.10 Makefile.PL,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/05/22 16:38:38 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/09/01 20:13:51 1.10 @@ -2,6 +2,11 @@ 1.05 * Updated the Makefile.PL to handle some missing dependencies. + * Updated CommonSubs to remove all hard coded entries for the + namespace prefix 'moby:'. In addition, all references to + nodeName were replaced with localname so that element namespace + prefixes are ignored since they dont really matter. + Also, the localnames are resolved to check the namespaceURI 1.04 * Fix bug in CollectionArticle, SimpleInput, SecondaryArticle, and =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/05/22 16:38:38 1.13 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/09/01 20:13:51 1.14 @@ -4,7 +4,7 @@ # all_from 'lib/MOBY/Client/Central.pm'; author 'Mark Wilkinson '; -version '1.04'; +version '1.05'; license 'perl'; abstract 'This distribution is for communicating with a MOBY Central registry'; @@ -12,17 +12,17 @@ build_requires 'Test::Pod' => 0; # MOBY::Client::* depends -requires 'SOAP::Lite' => '0.60'; -requires 'XML::LibXML::Common' => '0.13'; +requires 'SOAP::Lite' => 0.60; +requires 'XML::LibXML::Common' => 0.13; requires 'XML::LibXML' => 0; requires 'LWP::UserAgent' => 0; requires 'CGI' => 0; requires 'HTTP::Request::Common' => 0; requires 'URI::Escape' => 0; -requires 'RDF::Core' => '0.51'; +requires 'RDF::Core' => 0.51; # MOBY::Client::MobyUnitTest depends -requires 'XML::Simple' => '2.18'; -requires 'XML::SemanticCompare' => '0.91'; +requires 'XML::Simple' => 2.18; +requires 'XML::SemanticCompare' => 0.91; # MOBY::CommonSubs depends requires 'HTML::Entities' => 0; From kawas at dev.open-bio.org Tue Sep 1 16:13:51 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 16:13:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909012013.n81KDpFC017402@dev.open-bio.org> kawas Tue Sep 1 16:13:51 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv17363/MOBY-Server Modified Files: Makefile.PL Changes Log Message: updated to reflect recent changes to codebase moby-live/Perl/MOBY-Server Makefile.PL,1.20,1.21 Changes,1.30,1.31 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2009/08/28 15:07:18 1.20 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2009/09/01 20:13:51 1.21 @@ -3,7 +3,7 @@ # Define metadata name 'MOBY'; - version '1.11'; + version '1.12'; license 'perl'; abstract 'This distribution is for communicating with or creating your own MOBY Central registry'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2009/08/28 15:03:33 1.30 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2009/09/01 20:13:51 1.31 @@ -1,6 +1,13 @@ Revision history for Perl extension MOBY. +1.12 + - Updated CommonSubs to remove all hard coded entries for the + namespace prefix 'moby:'. In addition, all references to + nodeName were replaced with localname so that element namespace + prefixes are ignored since they dont really matter. + Also, the localnames/prefixes are resolved to check the namespaceURI. + 1.11 - Updated the Makefile.PL to handle some missing dependencies. Changes From drepchevski at dev.open-bio.org Wed Sep 2 14:38:26 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:38:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021838.n82IcQ2F024347@dev.open-bio.org> drepchevski Wed Sep 2 14:38:25 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB In directory dev.open-bio.org:/tmp/cvs-serv24313/INB Log Message: Directory /home/repository/moby/moby-live/Java/src/INB added to the repository moby-live/Java/src/INB - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:39:50 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:39:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021839.n82Idoim024393@dev.open-bio.org> drepchevski Wed Sep 2 14:39:50 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore In directory dev.open-bio.org:/tmp/cvs-serv24359/MobyCore Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore added to the repository moby-live/Java/src/INB/MobyCore - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:41:39 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:41:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021841.n82Ifdfe024437@dev.open-bio.org> drepchevski Wed Sep 2 14:41:38 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src In directory dev.open-bio.org:/tmp/cvs-serv24403/src Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src added to the repository moby-live/Java/src/INB/MobyCore/src - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:42:43 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:42:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021842.n82IghlS024480@dev.open-bio.org> drepchevski Wed Sep 2 14:42:42 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org In directory dev.open-bio.org:/tmp/cvs-serv24446/org Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org added to the repository moby-live/Java/src/INB/MobyCore/src/org - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:42:59 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:42:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021842.n82IgxCB024522@dev.open-bio.org> drepchevski Wed Sep 2 14:42:59 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb In directory dev.open-bio.org:/tmp/cvs-serv24488/inb Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:43:16 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhGcW024564@dev.open-bio.org> drepchevski Wed Sep 2 14:43:16 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv24530/biomoby Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:43:16 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhGqI024600@dev.open-bio.org> drepchevski Wed Sep 2 14:43:16 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf In directory dev.open-bio.org:/tmp/cvs-serv24530/wsrf Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:43:34 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhYJh024666@dev.open-bio.org> drepchevski Wed Sep 2 14:43:34 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv24615/shared Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:43:34 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhYvk024649@dev.open-bio.org> drepchevski Wed Sep 2 14:43:34 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv24615/client Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:43:16 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhGek024581@dev.open-bio.org> drepchevski Wed Sep 2 14:43:16 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae In directory dev.open-bio.org:/tmp/cvs-serv24530/lsae Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/lsae - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:44:03 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:44:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021844.n82Ii3CJ024756@dev.open-bio.org> drepchevski Wed Sep 2 14:44:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message In directory dev.open-bio.org:/tmp/cvs-serv24705/message Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:44:04 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:44:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021844.n82Ii49c024794@dev.open-bio.org> drepchevski Wed Sep 2 14:44:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf In directory dev.open-bio.org:/tmp/cvs-serv24705/wsrf Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:44:03 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:44:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021844.n82Ii3fC024739@dev.open-bio.org> drepchevski Wed Sep 2 14:44:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv24705/datatypes Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:44:03 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:44:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021844.n82Ii3NU024773@dev.open-bio.org> drepchevski Wed Sep 2 14:44:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry In directory dev.open-bio.org:/tmp/cvs-serv24705/registry Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:45:03 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82Ij3Uk024907@dev.open-bio.org> drepchevski Wed Sep 2 14:45:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault In directory dev.open-bio.org:/tmp/cvs-serv24873/fault Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:45:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82Ijj3m024993@dev.open-bio.org> drepchevski Wed Sep 2 14:45:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 In directory dev.open-bio.org:/tmp/cvs-serv24959/bf2 Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:45:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82Ijjji025010@dev.open-bio.org> drepchevski Wed Sep 2 14:45:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 In directory dev.open-bio.org:/tmp/cvs-serv24959/r2 Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:45:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82Ijjmo025050@dev.open-bio.org> drepchevski Wed Sep 2 14:45:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 In directory dev.open-bio.org:/tmp/cvs-serv24959/rp2 Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:45:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82IjjUC025029@dev.open-bio.org> drepchevski Wed Sep 2 14:45:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 In directory dev.open-bio.org:/tmp/cvs-serv24959/rl2 Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:50:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:50:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021850.n82IoWmw025184@dev.open-bio.org> drepchevski Wed Sep 2 14:50:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral In directory dev.open-bio.org:/tmp/cvs-serv25150/MobyCentral Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral added to the repository moby-live/Java/src/INB/MobyCentral - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:50:46 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:50:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021850.n82Iokem025227@dev.open-bio.org> drepchevski Wed Sep 2 14:50:46 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src In directory dev.open-bio.org:/tmp/cvs-serv25193/src Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src added to the repository moby-live/Java/src/INB/MobyCentral/src - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:51:00 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82Ip0RM025269@dev.open-bio.org> drepchevski Wed Sep 2 14:51:00 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF In directory dev.open-bio.org:/tmp/cvs-serv25235/META-INF Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF added to the repository moby-live/Java/src/INB/MobyCentral/src/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:51:01 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82Ip1PG025288@dev.open-bio.org> drepchevski Wed Sep 2 14:51:00 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org In directory dev.open-bio.org:/tmp/cvs-serv25235/org Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org added to the repository moby-live/Java/src/INB/MobyCentral/src/org - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:51:15 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82IpF8C025332@dev.open-bio.org> drepchevski Wed Sep 2 14:51:15 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services In directory dev.open-bio.org:/tmp/cvs-serv25298/services Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services added to the repository moby-live/Java/src/INB/MobyCentral/src/META-INF/services - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:51:43 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82Iph38025398@dev.open-bio.org> drepchevski Wed Sep 2 14:51:42 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb In directory dev.open-bio.org:/tmp/cvs-serv25364/inb Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:51:57 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82Ipvb8025440@dev.open-bio.org> drepchevski Wed Sep 2 14:51:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv25406/biomoby Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:52:10 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:52:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021852.n82IqAAL025482@dev.open-bio.org> drepchevski Wed Sep 2 14:52:09 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv25448/central Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:52:24 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:52:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021852.n82IqOm2025525@dev.open-bio.org> drepchevski Wed Sep 2 14:52:24 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory In directory dev.open-bio.org:/tmp/cvs-serv25491/factory Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:52:41 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:52:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021852.n82Iqfw7025567@dev.open-bio.org> drepchevski Wed Sep 2 14:52:41 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv25533/jaxb Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 14:52:54 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:52:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021852.n82IqsM2025609@dev.open-bio.org> drepchevski Wed Sep 2 14:52:54 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv25575/registry Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 15:24:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 15:24:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021924.n82JOj2D026604@dev.open-bio.org> drepchevski Wed Sep 2 15:24:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore In directory dev.open-bio.org:/tmp/cvs-serv26570 Log Message: INB Client API for BioMoby services Status: Vendor Tag: default_vendor Release Tags: default_release N moby-live/Java/src/INB/MobyCore/build.xml N moby-live/Java/src/INB/MobyCore/.cvsignore N moby-live/Java/src/INB/MobyCore/nbproject/project.properties N moby-live/Java/src/INB/MobyCore/nbproject/genfiles.properties N moby-live/Java/src/INB/MobyCore/nbproject/.cvsignore N moby-live/Java/src/INB/MobyCore/nbproject/project.xml N moby-live/Java/src/INB/MobyCore/nbproject/build-impl.xml N moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/CribTest.java N moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/GetAminoAcidSequence.java N moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/CommonsubsMoby.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/ResourceNotDestroyedFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/ResourceUnavailableFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/ResourceUnknownFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/GetResourcePropertyResponse.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/InvalidResourcePropertyQNameFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/QueryResourcePropertiesResponse.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/QueryEvaluationErrorFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/UnknownQueryExpressionDialectFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/QueryExpressionType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/GetMultipleResourcePropertiesResponse.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/GetMultipleResourceProperties.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/InvalidQueryExpressionFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/QueryResourceProperties.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/BaseFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/MobyClassLoader.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/MobyMessageContext.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/MobyDispatch.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyData.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyMessage.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/AnyMobyObject.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/AbstractMobyElement.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/CrossReference.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyDataElement.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyObject.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobySimple.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyExceptions.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/AbstractMobyObject.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyParameter.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyContent.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyException.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyCollection.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/ServiceNotes.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyDateTime.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyPrimitive.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyString.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyBinary.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyFloat.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyBoolean.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyInteger.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/PropertyResponseWrapper.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/SubmitResponseWrapper.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/MobyEndpointReference.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/QueryEvaluationErrorFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/InvalidResourcePropertyQNameFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/UnknownQueryExpressionDialectFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/ResourceUnavailableFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/ResourceNotDestroyedFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/InvalidQueryExpressionFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/ResourceUnknownFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Registration.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Simple.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Relationship.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Namespace.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Resource.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Collection.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Service.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/ServiceType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Output.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Parameter.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Input.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/ServiceProvider.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/ObjectType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/AbstractTypeEntity.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/AbstractEntity.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Data.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/StepProgress.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/StateChanged.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/Event.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/AnalysisEvent.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/TimeProgress.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/HeartbeatProgress.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/PercentProgress.java No conflicts created by this import moby-live/Java/src/INB/MobyCore - Imported sources rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/Imported,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/sources,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 16:27:01 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 16:27:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022027.n82KR1Fn027774@dev.open-bio.org> drepchevski Wed Sep 2 16:27:01 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject In directory dev.open-bio.org:/tmp/cvs-serv27738 Removed Files: .cvsignore build-impl.xml genfiles.properties project.properties project.xml Log Message: remove all netbeans artefacts moby-live/Java/src/INB/MobyCore/nbproject .cvsignore,1.1.1.1,NONE build-impl.xml,1.1.1.1,NONE genfiles.properties,1.1.1.1,NONE project.properties,1.1.1.1,NONE project.xml,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/build-impl.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/genfiles.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/project.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/project.xml,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 16:31:26 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 16:31:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022031.n82KVQSj027879@dev.open-bio.org> drepchevski Wed Sep 2 16:31:26 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws In directory dev.open-bio.org:/tmp/cvs-serv27845 Removed Files: CommonsubsMoby.java CribTest.java GetAminoAcidSequence.java Log Message: will provide unit tests later moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws CommonsubsMoby.java,1.1.1.1,NONE CribTest.java,1.1.1.1,NONE GetAminoAcidSequence.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/RCS/CommonsubsMoby.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/RCS/CribTest.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/RCS/GetAminoAcidSequence.java,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 16:33:24 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 16:33:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022033.n82KXOrH027962@dev.open-bio.org> drepchevski Wed Sep 2 16:33:24 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore In directory dev.open-bio.org:/tmp/cvs-serv27929 Removed Files: .cvsignore build.xml Log Message: moby-live/Java/src/INB/MobyCore .cvsignore,1.1.1.1,NONE build.xml,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/build.xml,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 16:53:34 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 16:53:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022053.n82KrYaO028075@dev.open-bio.org> drepchevski Wed Sep 2 16:53:33 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv28040 Modified Files: MobyDispatch.java Log Message: test (some comments added) moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client MobyDispatch.java,1.1.1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/MobyDispatch.java,v retrieving revision 1.1.1.1 retrieving revision 1.2 diff -u -r1.1.1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/MobyDispatch.java 2009/09/02 19:24:44 1.1.1.1 +++ /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/MobyDispatch.java 2009/09/02 20:53:33 1.2 @@ -90,7 +90,14 @@ this.service.addPort(sName, SOAPBinding.SOAP11HTTP_MTOM_BINDING, mobyService.getUrl()); } - + + /** + * Method to synchronously invoke BioMoby service (provided in constructor) + * + * @param message - message to be sent. + * @return message sent by the service. + * @throws Exception + */ public MobyMessage invoke(MobyMessage message) throws Exception { CATEGORY category = mobyService.getCategory(); From drepchevski at dev.open-bio.org Wed Sep 2 17:12:19 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:12:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022112.n82LCJFN028675@dev.open-bio.org> drepchevski Wed Sep 2 17:12:19 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral In directory dev.open-bio.org:/tmp/cvs-serv28641 Log Message: INB API to work with BioMoby Registry Status: Vendor Tag: default_vendor Release Tags: default_release N moby-live/Java/src/INB/MobyCentral/build.xml N moby-live/Java/src/INB/MobyCentral/.cvsignore N moby-live/Java/src/INB/MobyCentral/nbproject/project.properties N moby-live/Java/src/INB/MobyCentral/nbproject/genfiles.properties N moby-live/Java/src/INB/MobyCentral/nbproject/.cvsignore N moby-live/Java/src/INB/MobyCentral/nbproject/project.xml N moby-live/Java/src/INB/MobyCentral/nbproject/build-impl.xml N moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test/RegisterServiceFromXMLTest.java N moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test/CentralOperationsTest.java N moby-live/Java/src/INB/MobyCentral/src/META-INF/services/org.inb.biomoby.central.MobyCentralService N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralFactory.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentral.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralOperations.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralService.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/ModelConverter.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/MobyCentralServiceImpl.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/MobyRegistryEndpoint.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RegisterServiceTypeOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveResourceURLsOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RegisterNamespaceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RegisterObjectClassOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/DeregisterNamespaceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RegisterServiceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/jaxb.index N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveObjectNamesOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/DeregisterServiceTypeOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/FindServiceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveObjectDefinitionOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceTypesOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/DeregisterObjectClassOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveObjectOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RelationshipsOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/MobyRegistration.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceNamesOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/package-info.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveNamespacesOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceProvidersOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/DeregisterServiceOperation.java No conflicts created by this import moby-live/Java/src/INB/MobyCentral - Imported sources rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/Imported,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/sources,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 17:18:09 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022118.n82LI9Qt028842@dev.open-bio.org> drepchevski Wed Sep 2 17:18:09 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral In directory dev.open-bio.org:/tmp/cvs-serv28809 Removed Files: .cvsignore build.xml Log Message: remove all netbeans shit moby-live/Java/src/INB/MobyCentral .cvsignore,1.1.1.1,NONE build.xml,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/build.xml,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 17:18:09 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022118.n82LI9pJ028879@dev.open-bio.org> drepchevski Wed Sep 2 17:18:09 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test In directory dev.open-bio.org:/tmp/cvs-serv28809/test/org/biomoby/central/test Removed Files: CentralOperationsTest.java RegisterServiceFromXMLTest.java Log Message: remove all netbeans shit moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test CentralOperationsTest.java,1.1.1.1,NONE RegisterServiceFromXMLTest.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test/RCS/CentralOperationsTest.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test/RCS/RegisterServiceFromXMLTest.java,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 17:18:09 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022118.n82LI9bf028861@dev.open-bio.org> drepchevski Wed Sep 2 17:18:09 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject In directory dev.open-bio.org:/tmp/cvs-serv28809/nbproject Removed Files: .cvsignore build-impl.xml genfiles.properties project.properties project.xml Log Message: remove all netbeans shit moby-live/Java/src/INB/MobyCentral/nbproject .cvsignore,1.1.1.1,NONE build-impl.xml,1.1.1.1,NONE genfiles.properties,1.1.1.1,NONE project.properties,1.1.1.1,NONE project.xml,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/build-impl.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/genfiles.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/project.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/project.xml,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 17:41:36 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:41:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022141.n82LfaQm028994@dev.open-bio.org> drepchevski Wed Sep 2 17:41:36 EDT 2009 Update of /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv28959 Modified Files: MobyCentralOperations.java Log Message: test (some comments added) /moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central MobyCentralOperations.java,1.1.1.1,1.2 =================================================================== RCS file: /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralOperations.java,v retrieving revision 1.1.1.1 retrieving revision 1.2 diff -u -r1.1.1.1 -r1.2 --- /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralOperations.java 2009/09/02 21:12:16 1.1.1.1 +++ /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralOperations.java 2009/09/02 21:41:36 1.2 @@ -11,6 +11,8 @@ import org.inb.biomoby.shared.registry.Relationship.RELATIONSHIP_TYPE; /** + * An interface that defines all standard BioMoby Registry operations. + * * @author Dmitry Repchevsky */ From drepchevski at dev.open-bio.org Wed Sep 2 17:48:09 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:48:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022148.n82Lm9gi029058@dev.open-bio.org> drepchevski Wed Sep 2 17:48:09 EDT 2009 Update of /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv29023 Modified Files: MobyCentralFactory.java Log Message: test /moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central MobyCentralFactory.java,1.1.1.1,1.2 =================================================================== RCS file: /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralFactory.java,v retrieving revision 1.1.1.1 retrieving revision 1.2 diff -u -r1.1.1.1 -r1.2 --- /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralFactory.java 2009/09/02 21:12:16 1.1.1.1 +++ /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralFactory.java 2009/09/02 21:48:09 1.2 @@ -15,7 +15,14 @@ public class MobyCentralFactory { private MobyCentralFactory() {} - + + /** + * Factory method to obtain an implementation of MobyCentralOperations interface + * + * @param central - A MobyCentral object which defines which BioMoby Registry we are connecting. + * + * @return - MobyCentralOperatons interface implementation to connect to the given BioMoby Registry + */ public static MobyCentralOperations getCentralDigest(MobyCentral central) { ServiceLoader loader = java.util.ServiceLoader.load(MobyCentralService.class); From drepchevski at dev.open-bio.org Tue Sep 8 18:30:59 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:30:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082230.n88MUxB9029336@dev.open-bio.org> drepchevski Tue Sep 8 18:30:59 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services In directory dev.open-bio.org:/tmp/cvs-serv29304 Removed Files: org.inb.biomoby.central.MobyCentralService Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCentral/src/META-INF/services org.inb.biomoby.central.MobyCentralService,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services/RCS/org.inb.biomoby.central.MobyCentralService,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:13 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVD6j029522@dev.open-bio.org> drepchevski Tue Sep 8 18:31:13 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/datatypes Removed Files: MobyBinary.java MobyBoolean.java MobyDateTime.java MobyFloat.java MobyInteger.java MobyPrimitive.java MobyString.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes MobyBinary.java,1.1.1.1,NONE MobyBoolean.java,1.1.1.1,NONE MobyDateTime.java,1.1.1.1,NONE MobyFloat.java,1.1.1.1,NONE MobyInteger.java,1.1.1.1,NONE MobyPrimitive.java,1.1.1.1,NONE MobyString.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyBinary.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyBoolean.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyDateTime.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyFloat.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyInteger.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyPrimitive.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyString.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:06 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MV6jR029379@dev.open-bio.org> drepchevski Tue Sep 8 18:31:06 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv29344 Removed Files: MobyCentral.java MobyCentralFactory.java MobyCentralOperations.java MobyCentralService.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central MobyCentral.java,1.1.1.1,NONE MobyCentralFactory.java,1.2,NONE MobyCentralOperations.java,1.2,NONE MobyCentralService.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/MobyCentral.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/MobyCentralFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/MobyCentralOperations.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/MobyCentralService.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVNgC029751@dev.open-bio.org> drepchevski Tue Sep 8 18:31:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 In directory dev.open-bio.org:/tmp/cvs-serv29678/rl2 Removed Files: ResourceNotDestroyedFaultType.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 ResourceNotDestroyedFaultType.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/ResourceNotDestroyedFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVNKn029783@dev.open-bio.org> drepchevski Tue Sep 8 18:31:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 In directory dev.open-bio.org:/tmp/cvs-serv29678/rp2 Removed Files: GetMultipleResourceProperties.java GetMultipleResourcePropertiesResponse.java GetResourcePropertyResponse.java InvalidQueryExpressionFaultType.java InvalidResourcePropertyQNameFaultType.java QueryEvaluationErrorFaultType.java QueryExpressionType.java QueryResourceProperties.java QueryResourcePropertiesResponse.java UnknownQueryExpressionDialectFaultType.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 GetMultipleResourceProperties.java,1.1.1.1,NONE GetMultipleResourcePropertiesResponse.java,1.1.1.1,NONE GetResourcePropertyResponse.java,1.1.1.1,NONE InvalidQueryExpressionFaultType.java,1.1.1.1,NONE InvalidResourcePropertyQNameFaultType.java,1.1.1.1,NONE QueryEvaluationErrorFaultType.java,1.1.1.1,NONE QueryExpressionType.java,1.1.1.1,NONE QueryResourceProperties.java,1.1.1.1,NONE QueryResourcePropertiesResponse.java,1.1.1.1,NONE UnknownQueryExpressionDialectFaultType.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/GetMultipleResourceProperties.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/GetMultipleResourcePropertiesResponse.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/GetResourcePropertyResponse.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/InvalidQueryExpressionFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/InvalidResourcePropertyQNameFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/QueryEvaluationErrorFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/QueryExpressionType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/QueryResourceProperties.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/QueryResourcePropertiesResponse.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/UnknownQueryExpressionDialectFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:06 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MV612029399@dev.open-bio.org> drepchevski Tue Sep 8 18:31:06 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv29344/factory/jaxb Removed Files: JAXBMobyCentralImpl.java MobyCentralServiceImpl.java MobyRegistryEndpoint.java ModelConverter.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb JAXBMobyCentralImpl.java,1.1.1.1,NONE MobyCentralServiceImpl.java,1.1.1.1,NONE MobyRegistryEndpoint.java,1.1.1.1,NONE ModelConverter.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/JAXBMobyCentralImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/MobyCentralServiceImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/MobyRegistryEndpoint.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/ModelConverter.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:06 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MV6Df029439@dev.open-bio.org> drepchevski Tue Sep 8 18:31:06 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv29344/factory/jaxb/registry Removed Files: DeregisterNamespaceOperation.java DeregisterObjectClassOperation.java DeregisterServiceOperation.java DeregisterServiceTypeOperation.java FindServiceOperation.java MobyRegistration.java RegisterNamespaceOperation.java RegisterObjectClassOperation.java RegisterServiceOperation.java RegisterServiceTypeOperation.java RelationshipsOperation.java RetrieveNamespacesOperation.java RetrieveObjectDefinitionOperation.java RetrieveObjectNamesOperation.java RetrieveObjectOperation.java RetrieveResourceURLsOperation.java RetrieveServiceNamesOperation.java RetrieveServiceOperation.java RetrieveServiceProvidersOperation.java RetrieveServiceTypesOperation.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry DeregisterNamespaceOperation.java,1.1.1.1,NONE DeregisterObjectClassOperation.java,1.1.1.1,NONE DeregisterServiceOperation.java,1.1.1.1,NONE DeregisterServiceTypeOperation.java,1.1.1.1,NONE FindServiceOperation.java,1.1.1.1,NONE MobyRegistration.java,1.1.1.1,NONE RegisterNamespaceOperation.java,1.1.1.1,NONE RegisterObjectClassOperation.java,1.1.1.1,NONE RegisterServiceOperation.java,1.1.1.1,NONE RegisterServiceTypeOperation.java,1.1.1.1,NONE RelationshipsOperation.java,1.1.1.1,NONE RetrieveNamespacesOperation.java,1.1.1.1,NONE RetrieveObjectDefinitionOperation.java,1.1.1.1,NONE RetrieveObjectNamesOperation.java,1.1.1.1,NONE RetrieveObjectOperation.java,1.1.1.1,NONE RetrieveResourceURLsOperation.java,1.1.1.1,NONE RetrieveServiceNamesOperation.java,1.1.1.1,NONE RetrieveServiceOperation.java,1.1.1.1,NONE RetrieveServiceProvidersOperation.java,1.1.1.1,NONE RetrieveServiceTypesOperation.java,1.1.! 1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/DeregisterNamespaceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/DeregisterObjectClassOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/DeregisterServiceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/DeregisterServiceTypeOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/FindServiceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/MobyRegistration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RegisterNamespaceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RegisterObjectClassOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RegisterServiceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RegisterServiceTypeOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RelationshipsOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveNamespacesOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveObjectDefinitionOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveObjectNamesOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveObjectOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveResourceURLsOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveServiceNamesOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveServiceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveServiceProvidersOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveServiceTypesOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:13 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVDIM029482@dev.open-bio.org> drepchevski Tue Sep 8 18:31:13 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby Removed Files: MobyClassLoader.java MobyMessageContext.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby MobyClassLoader.java,1.1.1.1,NONE MobyMessageContext.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/MobyClassLoader.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/MobyMessageContext.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVEZ7029611@dev.open-bio.org> drepchevski Tue Sep 8 18:31:14 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/wsrf Removed Files: MobyEndpointReference.java PropertyResponseWrapper.java SubmitResponseWrapper.java jaxb.index Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf MobyEndpointReference.java,1.1.1.1,NONE PropertyResponseWrapper.java,1.1.1.1,NONE SubmitResponseWrapper.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/MobyEndpointReference.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/PropertyResponseWrapper.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/SubmitResponseWrapper.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/jaxb.index,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVEql029593@dev.open-bio.org> drepchevski Tue Sep 8 18:31:14 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/registry Removed Files: AbstractEntity.java AbstractTypeEntity.java Collection.java Data.java Input.java Namespace.java ObjectType.java Output.java Parameter.java Registration.java Relationship.java Resource.java Service.java ServiceProvider.java ServiceType.java Simple.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry AbstractEntity.java,1.1.1.1,NONE AbstractTypeEntity.java,1.1.1.1,NONE Collection.java,1.1.1.1,NONE Data.java,1.1.1.1,NONE Input.java,1.1.1.1,NONE Namespace.java,1.1.1.1,NONE ObjectType.java,1.1.1.1,NONE Output.java,1.1.1.1,NONE Parameter.java,1.1.1.1,NONE Registration.java,1.1.1.1,NONE Relationship.java,1.1.1.1,NONE Resource.java,1.1.1.1,NONE Service.java,1.1.1.1,NONE ServiceProvider.java,1.1.1.1,NONE ServiceType.java,1.1.1.1,NONE Simple.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/AbstractEntity.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/AbstractTypeEntity.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Collection.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Data.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Input.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Namespace.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/ObjectType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Output.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Parameter.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Registration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Relationship.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Resource.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Service.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/ServiceProvider.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/ServiceType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Simple.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVEwE029561@dev.open-bio.org> drepchevski Tue Sep 8 18:31:13 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/message Removed Files: AbstractMobyElement.java AbstractMobyObject.java AnyMobyObject.java CrossReference.java MobyCollection.java MobyContent.java MobyData.java MobyDataElement.java MobyException.java MobyExceptions.java MobyMessage.java MobyObject.java MobyParameter.java MobySimple.java ServiceNotes.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message AbstractMobyElement.java,1.1.1.1,NONE AbstractMobyObject.java,1.1.1.1,NONE AnyMobyObject.java,1.1.1.1,NONE CrossReference.java,1.1.1.1,NONE MobyCollection.java,1.1.1.1,NONE MobyContent.java,1.1.1.1,NONE MobyData.java,1.1.1.1,NONE MobyDataElement.java,1.1.1.1,NONE MobyException.java,1.1.1.1,NONE MobyExceptions.java,1.1.1.1,NONE MobyMessage.java,1.1.1.1,NONE MobyObject.java,1.1.1.1,NONE MobyParameter.java,1.1.1.1,NONE MobySimple.java,1.1.1.1,NONE ServiceNotes.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/AbstractMobyElement.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/AbstractMobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/AnyMobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/CrossReference.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyCollection.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyContent.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyDataElement.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyExceptions.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyMessage.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyParameter.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobySimple.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/ServiceNotes.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:13 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVDCh029497@dev.open-bio.org> drepchevski Tue Sep 8 18:31:13 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/client Removed Files: MobyDispatch.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client MobyDispatch.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/RCS/MobyDispatch.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVNtk029712@dev.open-bio.org> drepchevski Tue Sep 8 18:31:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 In directory dev.open-bio.org:/tmp/cvs-serv29678/bf2 Removed Files: BaseFaultType.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 BaseFaultType.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/BaseFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVNPB029730@dev.open-bio.org> drepchevski Tue Sep 8 18:31:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 In directory dev.open-bio.org:/tmp/cvs-serv29678/r2 Removed Files: ResourceUnavailableFaultType.java ResourceUnknownFaultType.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 ResourceUnavailableFaultType.java,1.1.1.1,NONE ResourceUnknownFaultType.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/ResourceUnavailableFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/ResourceUnknownFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVEZS029668@dev.open-bio.org> drepchevski Tue Sep 8 18:31:14 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae In directory dev.open-bio.org:/tmp/cvs-serv29449/lsae Removed Files: AnalysisEvent.java Event.java HeartbeatProgress.java PercentProgress.java StateChanged.java StepProgress.java TimeProgress.java jaxb.index Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/lsae AnalysisEvent.java,1.1.1.1,NONE Event.java,1.1.1.1,NONE HeartbeatProgress.java,1.1.1.1,NONE PercentProgress.java,1.1.1.1,NONE StateChanged.java,1.1.1.1,NONE StepProgress.java,1.1.1.1,NONE TimeProgress.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/AnalysisEvent.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/Event.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/HeartbeatProgress.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/PercentProgress.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/StateChanged.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/StepProgress.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/TimeProgress.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/jaxb.index,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 18:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVE30029638@dev.open-bio.org> drepchevski Tue Sep 8 18:31:14 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/wsrf/fault Removed Files: InvalidQueryExpressionFault.java InvalidResourcePropertyQNameFault.java QueryEvaluationErrorFault.java ResourceNotDestroyedFault.java ResourceUnavailableFault.java ResourceUnknownFault.java UnknownQueryExpressionDialectFault.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault InvalidQueryExpressionFault.java,1.1.1.1,NONE InvalidResourcePropertyQNameFault.java,1.1.1.1,NONE QueryEvaluationErrorFault.java,1.1.1.1,NONE ResourceNotDestroyedFault.java,1.1.1.1,NONE ResourceUnavailableFault.java,1.1.1.1,NONE ResourceUnknownFault.java,1.1.1.1,NONE UnknownQueryExpressionDialectFault.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/InvalidQueryExpressionFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/InvalidResourcePropertyQNameFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/QueryEvaluationErrorFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/ResourceNotDestroyedFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/ResourceUnavailableFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/ResourceUnknownFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/UnknownQueryExpressionDialectFault.java,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:17:04 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:17:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091917.n89JH4KC003508@dev.open-bio.org> drepchevski Wed Sep 9 15:17:04 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb In directory dev.open-bio.org:/tmp/cvs-serv3474/inb Log Message: Directory /home/repository/moby/moby-live/Java/src/config/inb added to the repository moby-live/Java/src/config/inb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:17:29 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:17:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091917.n89JHTpb003550@dev.open-bio.org> drepchevski Wed Sep 9 15:17:28 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb/mobycentral In directory dev.open-bio.org:/tmp/cvs-serv3516/mobycentral Log Message: Directory /home/repository/moby/moby-live/Java/src/config/inb/mobycentral added to the repository moby-live/Java/src/config/inb/mobycentral - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:17:42 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:17:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091917.n89JHg13003592@dev.open-bio.org> drepchevski Wed Sep 9 15:17:42 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF In directory dev.open-bio.org:/tmp/cvs-serv3558/META-INF Log Message: Directory /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF added to the repository moby-live/Java/src/config/inb/mobycentral/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:17:57 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:17:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091917.n89JHvB9003634@dev.open-bio.org> drepchevski Wed Sep 9 15:17:57 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services In directory dev.open-bio.org:/tmp/cvs-serv3600/services Log Message: Directory /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services added to the repository moby-live/Java/src/config/inb/mobycentral/META-INF/services - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:07 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJ772003717@dev.open-bio.org> drepchevski Wed Sep 9 15:19:06 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb In directory dev.open-bio.org:/tmp/cvs-serv3683/inb Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb added to the repository moby-live/Java/src/main/org/inb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:12 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJCWc003776@dev.open-bio.org> drepchevski Wed Sep 9 15:19:12 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/lsae In directory dev.open-bio.org:/tmp/cvs-serv3725/lsae Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/lsae added to the repository moby-live/Java/src/main/org/inb/lsae - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/lsae/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/lsae/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/lsae/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJNZd003927@dev.open-bio.org> drepchevski Wed Sep 9 15:19:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory In directory dev.open-bio.org:/tmp/cvs-serv3893/factory Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory added to the repository moby-live/Java/src/main/org/inb/biomoby/central/factory - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:29 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJTrv003969@dev.open-bio.org> drepchevski Wed Sep 9 15:19:29 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv3935/jaxb Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb added to the repository moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:12 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJCTN003797@dev.open-bio.org> drepchevski Wed Sep 9 15:19:12 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf In directory dev.open-bio.org:/tmp/cvs-serv3725/wsrf Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf added to the repository moby-live/Java/src/main/org/inb/wsrf - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:12 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJCCb003759@dev.open-bio.org> drepchevski Wed Sep 9 15:19:12 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv3725/biomoby Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby added to the repository moby-live/Java/src/main/org/inb/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:35 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJZAs004011@dev.open-bio.org> drepchevski Wed Sep 9 15:19:35 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv3977/registry Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry added to the repository moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:18 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJISF003881@dev.open-bio.org> drepchevski Wed Sep 9 15:19:18 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv3809/shared Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared added to the repository moby-live/Java/src/main/org/inb/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:18 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJIYi003843@dev.open-bio.org> drepchevski Wed Sep 9 15:19:18 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv3809/central Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central added to the repository moby-live/Java/src/main/org/inb/biomoby/central - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:18 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJImr003862@dev.open-bio.org> drepchevski Wed Sep 9 15:19:18 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv3809/client Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client added to the repository moby-live/Java/src/main/org/inb/biomoby/client - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:52 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJqx7004112@dev.open-bio.org> drepchevski Wed Sep 9 15:19:52 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message In directory dev.open-bio.org:/tmp/cvs-serv4061/message Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/message - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:52 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJqYx004095@dev.open-bio.org> drepchevski Wed Sep 9 15:19:52 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv4061/datatypes Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/datatypes - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:52 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJq4p004154@dev.open-bio.org> drepchevski Wed Sep 9 15:19:52 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf In directory dev.open-bio.org:/tmp/cvs-serv4061/wsrf Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/wsrf - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:19:52 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJqOW004131@dev.open-bio.org> drepchevski Wed Sep 9 15:19:52 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry In directory dev.open-bio.org:/tmp/cvs-serv4061/registry Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/registry - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:20:15 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKFmO004263@dev.open-bio.org> drepchevski Wed Sep 9 15:20:15 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault In directory dev.open-bio.org:/tmp/cvs-serv4229/fault Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:20:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKWAG004347@dev.open-bio.org> drepchevski Wed Sep 9 15:20:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2 In directory dev.open-bio.org:/tmp/cvs-serv4313/bf2 Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2 added to the repository moby-live/Java/src/main/org/inb/wsrf/bf2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:20:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKWFx004366@dev.open-bio.org> drepchevski Wed Sep 9 15:20:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2 In directory dev.open-bio.org:/tmp/cvs-serv4313/r2 Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2 added to the repository moby-live/Java/src/main/org/inb/wsrf/r2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:20:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKWh3004383@dev.open-bio.org> drepchevski Wed Sep 9 15:20:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2 In directory dev.open-bio.org:/tmp/cvs-serv4313/rl2 Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2 added to the repository moby-live/Java/src/main/org/inb/wsrf/rl2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:20:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKWf2004406@dev.open-bio.org> drepchevski Wed Sep 9 15:20:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2 In directory dev.open-bio.org:/tmp/cvs-serv4313/rp2 Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2 added to the repository moby-live/Java/src/main/org/inb/wsrf/rp2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 15:26:47 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091926.n89JQlHr004620@dev.open-bio.org> drepchevski Wed Sep 9 15:26:47 EDT 2009 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv4585 Modified Files: build.xml Log Message: INB MobyCore & MobyCentral libraries added moby-live/Java build.xml,1.76,1.77 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.76 retrieving revision 1.77 diff -u -r1.76 -r1.77 --- /home/repository/moby/moby-live/Java/build.xml 2008/11/26 11:07:57 1.76 +++ /home/repository/moby/moby-live/Java/build.xml 2009/09/09 19:26:47 1.77 @@ -15,6 +15,7 @@ + ]> @@ -64,16 +65,17 @@ - - - - - - - - - - + + + + + + + + + + + @@ -148,6 +150,7 @@ &seahawkBuild; &mobysyncBuild; &featureClientBuild; + &inbMoby; @@ -177,6 +180,8 @@ + + From drepchevski at dev.open-bio.org Wed Sep 9 15:47:38 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlctK005229@dev.open-bio.org> drepchevski Wed Sep 9 15:47:38 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services In directory dev.open-bio.org:/tmp/cvs-serv5198 Added Files: org.inb.biomoby.central.MobyCentralService Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/config/inb/mobycentral/META-INF/services org.inb.biomoby.central.MobyCentralService,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmtO005268@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby Added Files: MobyClassLoader.java MobyMessageContext.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby MobyClassLoader.java,NONE,1.1 MobyMessageContext.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmDN005338@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/client Added Files: MobyDispatch.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/client MobyDispatch.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmTn005284@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/central Added Files: MobyCentral.java MobyCentralFactory.java MobyCentralOperations.java MobyCentralService.java ServiceLoader.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/central MobyCentral.java,NONE,1.1 MobyCentralFactory.java,NONE,1.1 MobyCentralOperations.java,NONE,1.1 MobyCentralService.java,NONE,1.1 ServiceLoader.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:48:00 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:48:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091948.n89Jm0mP005580@dev.open-bio.org> drepchevski Wed Sep 9 15:48:00 EDT 2009 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv5549 Added Files: inbMoby.xml Log Message: MobyCore and MobyCentral source code upload moby-live/Java/xmls inbMoby.xml,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89Jlngl005392@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/registry Added Files: AbstractEntity.java AbstractTypeEntity.java Collection.java Data.java Input.java Namespace.java ObjectType.java Output.java Parameter.java Registration.java Relationship.java Resource.java Service.java ServiceProvider.java ServiceType.java Simple.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/registry AbstractEntity.java,NONE,1.1 AbstractTypeEntity.java,NONE,1.1 Collection.java,NONE,1.1 Data.java,NONE,1.1 Input.java,NONE,1.1 Namespace.java,NONE,1.1 ObjectType.java,NONE,1.1 Output.java,NONE,1.1 Parameter.java,NONE,1.1 Registration.java,NONE,1.1 Relationship.java,NONE,1.1 Resource.java,NONE,1.1 Service.java,NONE,1.1 ServiceProvider.java,NONE,1.1 ServiceType.java,NONE,1.1 Simple.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlnIL005410@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/wsrf Added Files: MobyEndpointReference.java PropertyResponseWrapper.java SubmitResponseWrapper.java jaxb.index Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/wsrf MobyEndpointReference.java,NONE,1.1 PropertyResponseWrapper.java,NONE,1.1 SubmitResponseWrapper.java,NONE,1.1 jaxb.index,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmMN005320@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/central/factory/jaxb/registry Added Files: DeregisterNamespaceOperation.java DeregisterObjectClassOperation.java DeregisterServiceOperation.java DeregisterServiceTypeOperation.java FindServiceOperation.java MobyRegistration.java RegisterNamespaceOperation.java RegisterObjectClassOperation.java RegisterServiceOperation.java RegisterServiceTypeOperation.java RelationshipsOperation.java RetrieveNamespacesOperation.java RetrieveObjectDefinitionOperation.java RetrieveObjectNamesOperation.java RetrieveObjectOperation.java RetrieveResourceURLsOperation.java RetrieveServiceNamesOperation.java RetrieveServiceOperation.java RetrieveServiceProvidersOperation.java RetrieveServiceTypesOperation.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry DeregisterNamespaceOperation.java,NONE,1.1 DeregisterObjectClassOperation.java,NONE,1.1 DeregisterServiceOperation.java,NONE,1.1 DeregisterServiceTypeOperation.java,NONE,1.1 FindServiceOperation.java,NONE,1.1 MobyRegistration.java,NONE,1.1 RegisterNamespaceOperation.java,NONE,1.1 RegisterObjectClassOperation.java,NONE,1.1 RegisterServiceOperation.java,NONE,1.1 RegisterServiceTypeOperation.java,NONE,1.1 RelationshipsOperation.java,NONE,1.1 RetrieveNamespacesOperation.java,NONE,1.1 RetrieveObjectDefinitionOperation.java,NONE,1.1 RetrieveObjectNamesOperation.java,NONE,1.1 RetrieveObjectOperation.java,NONE,1.1 RetrieveResourceURLsOperation.java,NONE,1.1 RetrieveServiceNamesOperation.java,NONE,1.1 RetrieveServiceOperation.java,NONE,1.1 RetrieveServiceProvidersOperation.java,NONE,1.1 RetrieveServiceTypesOperation.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89Jln8b005374@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/message Added Files: AbstractMobyElement.java AbstractMobyObject.java AnyMobyObject.java CrossReference.java MobyCollection.java MobyContent.java MobyData.java MobyDataElement.java MobyException.java MobyExceptions.java MobyMessage.java MobyObject.java MobyParameter.java MobySimple.java ServiceNotes.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/message AbstractMobyElement.java,NONE,1.1 AbstractMobyObject.java,NONE,1.1 AnyMobyObject.java,NONE,1.1 CrossReference.java,NONE,1.1 MobyCollection.java,NONE,1.1 MobyContent.java,NONE,1.1 MobyData.java,NONE,1.1 MobyDataElement.java,NONE,1.1 MobyException.java,NONE,1.1 MobyExceptions.java,NONE,1.1 MobyMessage.java,NONE,1.1 MobyObject.java,NONE,1.1 MobyParameter.java,NONE,1.1 MobySimple.java,NONE,1.1 ServiceNotes.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89Jlmi9005302@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/central/factory/jaxb Added Files: JAXBMobyCentralImpl.java MobyCentralServiceImpl.java MobyRegistryEndpoint.java ModelConverter.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb JAXBMobyCentralImpl.java,NONE,1.1 MobyCentralServiceImpl.java,NONE,1.1 MobyRegistryEndpoint.java,NONE,1.1 ModelConverter.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlneW005424@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/wsrf/fault Added Files: InvalidQueryExpressionFault.java InvalidResourcePropertyQNameFault.java QueryEvaluationErrorFault.java ResourceNotDestroyedFault.java ResourceUnavailableFault.java ResourceUnknownFault.java UnknownQueryExpressionDialectFault.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault InvalidQueryExpressionFault.java,NONE,1.1 InvalidResourcePropertyQNameFault.java,NONE,1.1 QueryEvaluationErrorFault.java,NONE,1.1 ResourceNotDestroyedFault.java,NONE,1.1 ResourceUnavailableFault.java,NONE,1.1 ResourceUnknownFault.java,NONE,1.1 UnknownQueryExpressionDialectFault.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlnNk005444@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/lsae In directory dev.open-bio.org:/tmp/cvs-serv5237/lsae Added Files: AnalysisEvent.java Event.java HeartbeatProgress.java PercentProgress.java StateChanged.java StepProgress.java TimeProgress.java jaxb.index Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/lsae AnalysisEvent.java,NONE,1.1 Event.java,NONE,1.1 HeartbeatProgress.java,NONE,1.1 PercentProgress.java,NONE,1.1 StateChanged.java,NONE,1.1 StepProgress.java,NONE,1.1 TimeProgress.java,NONE,1.1 jaxb.index,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmsE005356@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/datatypes Added Files: MobyBinary.java MobyBoolean.java MobyDateTime.java MobyFloat.java MobyInteger.java MobyPrimitive.java MobyString.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/datatypes MobyBinary.java,NONE,1.1 MobyBoolean.java,NONE,1.1 MobyDateTime.java,NONE,1.1 MobyFloat.java,NONE,1.1 MobyInteger.java,NONE,1.1 MobyPrimitive.java,NONE,1.1 MobyString.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:56 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JluEe005487@dev.open-bio.org> drepchevski Wed Sep 9 15:47:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2 In directory dev.open-bio.org:/tmp/cvs-serv5456/bf2 Added Files: BaseFaultType.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/wsrf/bf2 BaseFaultType.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:56 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89Jluws005519@dev.open-bio.org> drepchevski Wed Sep 9 15:47:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2 In directory dev.open-bio.org:/tmp/cvs-serv5456/rl2 Added Files: ResourceNotDestroyedFaultType.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/wsrf/rl2 ResourceNotDestroyedFaultType.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:56 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JluOg005501@dev.open-bio.org> drepchevski Wed Sep 9 15:47:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2 In directory dev.open-bio.org:/tmp/cvs-serv5456/r2 Added Files: ResourceUnavailableFaultType.java ResourceUnknownFaultType.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/wsrf/r2 ResourceUnavailableFaultType.java,NONE,1.1 ResourceUnknownFaultType.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 15:47:56 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JluaP005535@dev.open-bio.org> drepchevski Wed Sep 9 15:47:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2 In directory dev.open-bio.org:/tmp/cvs-serv5456/rp2 Added Files: GetMultipleResourceProperties.java GetMultipleResourcePropertiesResponse.java GetResourcePropertyResponse.java InvalidQueryExpressionFaultType.java InvalidResourcePropertyQNameFaultType.java QueryEvaluationErrorFaultType.java QueryExpressionType.java QueryResourceProperties.java QueryResourcePropertiesResponse.java UnknownQueryExpressionDialectFaultType.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/wsrf/rp2 GetMultipleResourceProperties.java,NONE,1.1 GetMultipleResourcePropertiesResponse.java,NONE,1.1 GetResourcePropertyResponse.java,NONE,1.1 InvalidQueryExpressionFaultType.java,NONE,1.1 InvalidResourcePropertyQNameFaultType.java,NONE,1.1 QueryEvaluationErrorFaultType.java,NONE,1.1 QueryExpressionType.java,NONE,1.1 QueryResourceProperties.java,NONE,1.1 QueryResourcePropertiesResponse.java,NONE,1.1 UnknownQueryExpressionDialectFaultType.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 17:35:21 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 17:35:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909092135.n89LZLxm006007@dev.open-bio.org> drepchevski Wed Sep 9 17:35:21 EDT 2009 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv5972 Modified Files: inbMoby.xml Log Message: minor modifications... still has issues moby-live/Java/xmls inbMoby.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/inbMoby.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/inbMoby.xml 2009/09/09 19:48:00 1.1 +++ /home/repository/moby/moby-live/Java/xmls/inbMoby.xml 2009/09/09 21:35:21 1.2 @@ -33,7 +33,7 @@ - @@ -85,13 +85,14 @@ + excludes="org/inb/biomoby/shared/*"> From drepchevski at dev.open-bio.org Fri Sep 11 02:55:25 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Fri, 11 Sep 2009 02:55:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909110655.n8B6tPgT017139@dev.open-bio.org> drepchevski Fri Sep 11 02:55:24 EDT 2009 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv17104 Modified Files: inbMoby.xml Log Message: fixed an issue with java6 (javac) moby-live/Java/xmls inbMoby.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/inbMoby.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/inbMoby.xml 2009/09/09 21:35:21 1.2 +++ /home/repository/moby/moby-live/Java/xmls/inbMoby.xml 2009/09/11 06:55:24 1.3 @@ -83,6 +83,7 @@ + + From drepchevski at dev.open-bio.org Tue Sep 15 13:16:51 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 15 Sep 2009 13:16:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909151716.n8FHGphl021278@dev.open-bio.org> drepchevski Tue Sep 15 13:16:50 EDT 2009 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv21247 Added Files: inb_moby.html Log Message: initial INB BioMoby documentation upload moby-live/Java/docs inb_moby.html,NONE,1.1 From drepchevski at dev.open-bio.org Tue Sep 15 13:17:43 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 15 Sep 2009 13:17:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909151717.n8FHHhYf021317@dev.open-bio.org> drepchevski Tue Sep 15 13:17:43 EDT 2009 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv21286 Added Files: inb_moby_core.html Log Message: initial INB BioMoby documentation upload moby-live/Java/docs inb_moby_core.html,NONE,1.1 From drepchevski at dev.open-bio.org Tue Sep 15 13:18:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 15 Sep 2009 13:18:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909151718.n8FHINP4021376@dev.open-bio.org> drepchevski Tue Sep 15 13:18:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv21345 Added Files: inb_moby_central.html Log Message: initial INB BioMoby documentation upload moby-live/Java/docs inb_moby_central.html,NONE,1.1 From drepchevski at dev.open-bio.org Mon Sep 21 12:31:18 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Mon, 21 Sep 2009 12:31:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909211631.n8LGVIsZ019566@dev.open-bio.org> drepchevski Mon Sep 21 12:31:17 EDT 2009 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv19531 Modified Files: inb_moby_core.html Log Message: fixed an error in async example moby-live/Java/docs inb_moby_core.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/inb_moby_core.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/inb_moby_core.html 2009/09/15 17:17:43 1.1 +++ /home/repository/moby/moby-live/Java/docs/inb_moby_core.html 2009/09/21 16:31:17 1.2 @@ -311,7 +311,7 @@ // sequence.setSequenceString(new MobyString("ATCG")): // sequence.setLength(new MobyInteger(4)); -AnyMobyObject sequence = new AnyMobyObject("AminoAcidSequece"); +AnyMobyObject sequence = new AnyMobyObject("AminoAcidSequence"); sequence.putAttribute("SequenceString", new MobyString("ATCG")); sequence.putAttribute("Length", new MobyInteger(4)); From jmrc at dev.open-bio.org Tue Sep 22 11:55:43 2009 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Tue, 22 Sep 2009 11:55:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909221555.n8MFthOf030941@dev.open-bio.org> jmrc Tue Sep 22 11:55:42 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv30812 Modified Files: SimpleServer.pm Log Message: A couple of bugfixes from Dmitry and Romina from INB. * One of the bugs is related to huge input messages, which are inspected in depth where only a one level check is needed. * The second one is a fix to avoid a serialization bug from XML::LibXML, which does not generate serialization for implicit namespace nodes inherited from ancestors. moby-live/Perl/MOBY-Server/lib/MOBY/Async SimpleServer.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.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/Async/SimpleServer.pm 2008/09/02 13:10:26 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2009/09/22 15:55:42 1.5 @@ -180,9 +180,12 @@ my $auth = $mobyContent->getAttribute('authority') || $mobyContent->getAttributeNS($WSRF::Constants::MOBY_MESSAGE_NS,'authority'); # 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')); + my @mobyData = ($mobyContent->getChildrenByTagNameNS($WSRF::Constants::MOBY_MESSAGE_NS,'mobyData')); foreach my $mobyData (@mobyData) { + # This line avoids a serialization bug in XML::LibXML, which probably + # is inherited from libxml2 + $mobyData->setNamespace($WSRF::Constants::MOBY_MESSAGE_NS, $mobyData->prefix(), 0); my $queryID = $mobyData->getAttribute('queryID') || $mobyData->getAttributeNS($WSRF::Constants::MOBY_MESSAGE_NS,'queryID'); my $property_pid = "pid_$queryID"; my $property_input = "input_$queryID"; From kawas at dev.open-bio.org Tue Sep 1 16:27:05 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 12:27:05 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909011627.n81GR4dj016422@dev.open-bio.org> kawas Tue Sep 1 12:27:04 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv16387/MOBY-Server/lib/MOBY Modified Files: CommonSubs.pm Log Message: removed the hard coded references to moby: (namespace prefix) in all places that i found it to be hard coded. Instead, i look for any prefix. Moreover, I removed all references to $element->nodeName and replaced them with references to $element->localname so that we can check the element name without worrying about the xml namespace prefix. CommonSubs.t seems to run completely normal after making these changes (all tests pass). moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2009/04/15 17:45:23 1.7 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2009/09/01 16:27:04 1.8 @@ -413,19 +413,19 @@ $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; return undef - unless ($moby->nodeName =~ /^(moby:|)mobyData$/); + unless ($moby->localname =~ /^(.*:|)mobyData$/); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace next - unless ( $child->nodeName =~ /^(moby:|)(Simple|Collection|Parameter)$/ ); + unless ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ); my $object; - if ( $child->nodeName =~ /^(moby:|)Simple$/ ) { + if ( $child->localname=~ /^(.*:|)Simple$/ ) { $object = MOBY::Client::SimpleArticle->new( XML_DOM => $child ); - } elsif ( $child->nodeName =~ /^(moby:|)Collection$/ ) { + } elsif ( $child->localname=~ /^(.*:|)Collection$/ ) { $object = MOBY::Client::CollectionArticle->new( XML_DOM => $child ); - } elsif ( $child->nodeName =~ /^(moby:|)Parameter$/ ) { + } elsif ( $child->localname =~ /^(.*:|)Parameter$/ ) { $object = MOBY::Client::SecondaryArticle->new( XML_DOM => $child ); } next unless $object; @@ -438,7 +438,7 @@ sub _getQID { my ( $XML ) = @_; my $moby = _string_to_DOM($XML); - return '' unless ( $moby->nodeName =~ /^(moby:|)mobyData$/ ); + return '' unless ( $moby->localname =~ /^(.*:|)mobyData$/ ); my $qid = _moby_getAttribute($moby, 'queryID' ); $qid ||= _moby_getAttribute($moby, 'moby:queryID' ); return defined( $qid ) ? $qid : ''; @@ -480,7 +480,7 @@ eval { $DOM = _string_to_DOM($DOM) }; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ($DOM->nodeName =~ /^(moby:|)Simple$/) ? 1 : 0; #Optional 'moby:' namespace prefix + return ($DOM->localname =~ /^(.*:|)Simple$/) ? 1 : 0; #Optional 'moby:' namespace prefix } sub isCollectionArticle { @@ -488,7 +488,7 @@ eval {$DOM = _string_to_DOM($DOM) }; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ( $DOM->nodeName =~ /^(moby\:|)Collection$/ ) ? 1 : 0; #Optional 'moby:' prefix + return ( $DOM->localname =~ /^(.*:|)Collection$/ ) ? 1 : 0; #Optional 'moby:' prefix } sub isSecondaryArticle { @@ -497,7 +497,7 @@ eval {$DOM = _string_to_DOM($XML)} ; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ($DOM->nodeName =~ /^(moby\:|)Parameter$/) ? 1 : 0; #Optional 'moby:' prefix + return ($DOM->localname =~ /^(.*:|)Parameter$/) ? 1 : 0; #Optional 'moby:' prefix } @@ -961,8 +961,8 @@ $XML = _string_to_DOM($XML); my @xrefs; my @XREFS; - return () if ( $XML->nodeName =~ /^(moby:|)Collection$/ ); - if ( $XML->nodeName =~ /^(moby:|)Simple$/ ) { + return () if ( $XML->localname =~ /^(.*:|)Collection$/ ); + if ( $XML->localname =~ /^(.*:|)Simple$/ ) { foreach my $child ( $XML->childNodes ) { next unless $child->nodeType == ELEMENT_NODE; $XML = $child; @@ -971,17 +971,17 @@ } foreach ( $XML->childNodes ) { next unless (($_->nodeType == ELEMENT_NODE) - || ($_->nodeName =~ /^(moby:|)CrossReference$/) ); + || ($_->localname && $_->localname =~ /^(.*:|)CrossReference$/) ); foreach my $xref ( $_->childNodes ) { - next unless ( ($xref->nodeType == ELEMENT_NODE) - || ($xref->nodeName =~ /^(moby:|)(Xref|Object)$/) ); + next unless $xref && ( ($xref->nodeType == ELEMENT_NODE) + || ($xref->localname && $xref->localname =~ /^(.*:|)(Xref|Object)$/) ); push @xrefs, $xref; } } foreach ( @xrefs ) { my $x; - if ($_->nodeName =~ /^(moby:|)Xref$/) { $x = _makeXrefType( $_ ) } - elsif ($_->nodeName =~ /^(moby:|)Object$/) { $x = _makeObjectType( $_ ) } + if ($_->localname =~ /^(.*:|)Xref$/) { $x = _makeXrefType( $_ ) } + elsif ($_->localname =~ /^(.*:|)Object$/) { $x = _makeObjectType( $_ ) } push @XREFS, $x if $x; } return @XREFS; @@ -1338,7 +1338,7 @@ sub _getQueryID { my ( $query ) = @_; $query = _string_to_XML($query); - return '' unless ( $query->nodeName =~ /^(moby:|)mobyData$/ ); #Eddie - unsure + return '' unless ( $query->localname =~ /^(.*:|)mobyData$/ ); #Eddie - unsure return _moby_getAttribute($query, 'queryID' ); } @@ -1392,19 +1392,19 @@ my $resp = $responses->get_node( $n ); foreach my $response_component ( $resp->childNodes ) { next unless $response_component->nodeType == ELEMENT_NODE; - if ( $response_component->nodeName =~ /^(moby:|)Simple$/ ) + if ( $response_component->localname =~ /^(.*:|)Simple$/ ) { foreach my $Object ( $response_component->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; push @objects, $Object; } - } elsif ( $response_component->nodeName =~ /^(moby:|)Collection$/ ) + } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ ) { my @objects; foreach my $simple ( $response_component->childNodes ) { next unless $simple->nodeType == ELEMENT_NODE; - next unless ( $simple->nodeName =~ /^(moby:|)Simple$/ ); + next unless ( $simple->localname =~ /^(.*:|)Simple$/ ); foreach my $Object ( $simple->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; @@ -1498,12 +1498,12 @@ $moby = _string_to_DOM($moby); return undef unless ( ($moby->nodeType == ELEMENT_NODE) - && ( $moby->nodeName =~ /^(moby:|)(queryInput|queryResponse|mobyData)$/ ) ); + && ( $moby->localname =~ /^(.*:|)(queryInput|queryResponse|mobyData)$/ ) ); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless ( ($child->nodeType == ELEMENT_NODE) # ignore whitespace - && ( $child->nodeName =~ /^(moby:|)(Simple|Collection|Parameter)$/ ) ); + && ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ) ); my $articleName = _moby_getAttribute($child, 'articleName' ); # push the named child DOM elements (which are or , ) push @articles, [ $articleName, $child ]; @@ -1548,7 +1548,7 @@ foreach my $in ( @input_nodes ) { next unless $in; #$in = "" - next unless $in->nodeName =~ /^(moby:|)Simple$/; # only allow simples + next unless $in->localname =~ /^(.*)Simple$/; # only allow simples my @simples = $in->childNodes; foreach ( @simples ) { # $_ = next unless $_->nodeType == ELEMENT_NODE; @@ -1647,7 +1647,7 @@ print STDERR "getInputID method is now deprecated. Please use serviceInputParser or serviceResponseParser\n"; my ( $XML ) = @_; my $moby = _string_to_DOM($XML); - return '' unless ( $moby->nodeName =~ /^(moby:|)queryInput|mobyData$/ ); + return '' unless ( $moby->localname =~ /^(.*:|)queryInput|mobyData$/ ); my $qid = _moby_getAttribute($moby, 'queryID' ); $qid ||= _moby_getAttribute($moby, 'moby:queryID' ); return defined( $qid ) ? $qid : ''; @@ -1665,19 +1665,19 @@ $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; return undef - unless ($moby->nodeName =~ /^(moby:|)(queryInput|queryResponse|mobyData)$/); + unless ($moby->localname =~ /^(.*:|)(queryInput|queryResponse|mobyData)$/); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace next - unless ( $child->nodeName =~ /^(moby:|)(Simple|Collection|Parameter)$/ ); + unless ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ); my $object; - if ( $child->nodeName =~ /^(moby:|)Simple$/ ) { + if ( $child->localname =~ /^(.*:|)Simple$/ ) { $object = MOBY::Client::SimpleArticle->new( XML_DOM => $child ); - } elsif ( $child->nodeName =~ /^(moby:|)Collection$/ ) { + } elsif ( $child->localname =~ /^(.*:|)Collection$/ ) { $object = MOBY::Client::CollectionArticle->new( XML_DOM => $child ); - } elsif ( $child->nodeName =~ /^(moby:|)Parameter$/ ) { + } elsif ( $child->localname =~ /^(.*:|)Parameter$/ ) { $object = MOBY::Client::SecondaryArticle->new( XML_DOM => $child ); } next unless $object; @@ -1697,12 +1697,12 @@ my ( $moby ) = @_; $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; - return undef unless ( $moby->nodeName =~ /^(moby\:|)Collection$/ ); + return undef unless ( $moby->localname =~ /^(.*:|)Collection$/ ); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace - next unless ( $child->nodeName =~ /^(moby\:|)Simple$/ ); + next unless ( $child->localname =~ /^(.*:|)Simple$/ ); push @articles, $child; # take the child elements, which are or } return @articles; # return them. @@ -1791,19 +1791,19 @@ my $resp = $responses->get_node( $n ); foreach my $response_component ( $resp->childNodes ) { next unless $response_component->nodeType == ELEMENT_NODE; - if ( $response_component->nodeName =~ /^(moby:|)Simple$/ ) + if ( $response_component->localname =~ /^(.*:|)Simple$/ ) { foreach my $Object ( $response_component->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; push @objects, $Object; } - } elsif ( $response_component->nodeName =~ /^(moby:|)Collection$/ ) + } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ ) { my @objects; foreach my $simple ( $response_component->childNodes ) { next unless $simple->nodeType == ELEMENT_NODE; - next unless ( $simple->nodeName =~ /^(moby:|)Simple$/ ); + next unless ( $simple->localname =~ /^(.*:|)Simple$/ ); foreach my $Object ( $simple->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; From kawas at dev.open-bio.org Tue Sep 1 20:13:20 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 16:13:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909012013.n81KDKZq017336@dev.open-bio.org> kawas Tue Sep 1 16:13:20 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/t In directory dev.open-bio.org:/tmp/cvs-serv17301/MOBY-Server/t Modified Files: CommonSubs.t Log Message: modified CommonSubs.t to reflect that one of the tests using an incorrect namespaceURI use to pass when it should have failed. modified CommonSubs.pm: now we compare the actual namespaceURI to http://www.biomoby.org/moby and dont extract content unless the elements and attributes properly resolve. CommonSubs is now more strict w.r.t. biomoby services api moby-live/Perl/MOBY-Server/t CommonSubs.t,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/t/CommonSubs.t,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY-Server/t/CommonSubs.t 2008/02/21 00:21:28 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/t/CommonSubs.t 2009/09/01 20:13:20 1.2 @@ -13,6 +13,10 @@ #use SOAP::Lite +trace; use Test::More 'no_plan'; #skip_all => "Turned off for development"; #'no_plan'; use strict; + +use FindBin qw ($Bin); +use lib "$Bin/../lib/"; + use English; use Data::Dumper; #Is the client-code even installed? @@ -138,7 +142,7 @@ # Test getInputArticles with one, and with more than one mobyData block. my $two_mobyDatas = < + @@ -161,6 +165,31 @@ ok ($ids[0] eq "first") or die "serviceResponseParser didn't find the first query id\n"; ok ($ids[1] eq "second") or die "serviceResponseParser didn't find the second query id that included a moby: namespace\n"; +# pass 2 invalid messages ... should not parse +$two_mobyDatas = < + + + + + + + + + + + + + +INP_ART + +$responses = serviceResponseParser($two_mobyDatas); # returns MOBY objects +print Dumper($responses); +isa_ok ($responses, "HASH", "response parser returned a HASH" ) or die "serviceResponseParser didn't return a hashref for multiple input test\n"; + at ids = keys %{$responses}; +ok (scalar(@ids) == 0) or die "serviceResponseParser didn't find right number of invocation messages when two invalid ones were passed\n"; + + my $sequence = "TAGCTGATCGAGCTGATGCTGA"; my $articlename = "SequenceString"; From kawas at dev.open-bio.org Tue Sep 1 20:13:20 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 16:13:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909012013.n81KDKRP017356@dev.open-bio.org> kawas Tue Sep 1 16:13:20 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY In directory dev.open-bio.org:/tmp/cvs-serv17301/MOBY-Server/lib/MOBY Modified Files: CommonSubs.pm Log Message: modified CommonSubs.t to reflect that one of the tests using an incorrect namespaceURI use to pass when it should have failed. modified CommonSubs.pm: now we compare the actual namespaceURI to http://www.biomoby.org/moby and dont extract content unless the elements and attributes properly resolve. CommonSubs is now more strict w.r.t. biomoby services api moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2009/09/01 16:27:04 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm 2009/09/01 20:13:20 1.9 @@ -221,22 +221,31 @@ =cut package MOBY::CommonSubs; +use strict; +use warnings; + require Exporter; use XML::LibXML; + use MOBY::CrossReference; use MOBY::Client::OntologyServer; -use strict; -use warnings; use MOBY::Client::SimpleArticle; use MOBY::Client::CollectionArticle; use MOBY::Client::SecondaryArticle; use MOBY::MobyXMLConstants; + +# create the namespace URI +# can be modified by clients if they see fit using +# $MOBY::CommonSubs::MOBY_NS +our $MOBY_NS = 'http://www.biomoby.org/moby'; + use constant COLLECTION => 1; use constant SIMPLE => 2; use constant SECONDARY => 3; use constant PARAMETER => 3; # be friendly in case they use this instead use constant BE_NICE => 1; use constant BE_STRICT => 0; + our @ISA = qw(Exporter); our @EXPORT = qw(COLLECTION SIMPLE SECONDARY PARAMETER BE_NICE BE_STRICT); @@ -378,13 +387,14 @@ my %input_parameters; # $input_parameters{$queryID} = [ foreach my $query ( @queries ) { my $queryID = _getQID( $query ); # get the queryID attribute of the mobyData + next unless $queryID; 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; + ${$input_parameters{$queryID}}{$article->articleName} = $article if $article and $article->articleName ne ''; } } return \%input_parameters; @@ -413,19 +423,19 @@ $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; return undef - unless ($moby->localname =~ /^(.*:|)mobyData$/); + unless ($moby->localname =~ /^mobyData$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace next - unless ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ); + unless ( $child->localname =~ /^(Simple|Collection|Parameter)$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my $object; - if ( $child->localname=~ /^(.*:|)Simple$/ ) { + if ( $child->localname=~ /^Simple$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::SimpleArticle->new( XML_DOM => $child ); - } elsif ( $child->localname=~ /^(.*:|)Collection$/ ) { + } elsif ( $child->localname=~ /^Collection$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::CollectionArticle->new( XML_DOM => $child ); - } elsif ( $child->localname =~ /^(.*:|)Parameter$/ ) { + } elsif ( $child->localname =~ /^Parameter$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::SecondaryArticle->new( XML_DOM => $child ); } next unless $object; @@ -438,7 +448,7 @@ sub _getQID { my ( $XML ) = @_; my $moby = _string_to_DOM($XML); - return '' unless ( $moby->localname =~ /^(.*:|)mobyData$/ ); + return '' unless ( $moby->localname =~ /^mobyData$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my $qid = _moby_getAttribute($moby, 'queryID' ); $qid ||= _moby_getAttribute($moby, 'moby:queryID' ); return defined( $qid ) ? $qid : ''; @@ -480,7 +490,7 @@ eval { $DOM = _string_to_DOM($DOM) }; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ($DOM->localname =~ /^(.*:|)Simple$/) ? 1 : 0; #Optional 'moby:' namespace prefix + return ($DOM->localname =~ /^Simple$/ and ($DOM->namespaceURI() ? $DOM->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ? 1 : 0; #Optional 'moby:' namespace prefix } sub isCollectionArticle { @@ -488,7 +498,7 @@ eval {$DOM = _string_to_DOM($DOM) }; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ( $DOM->localname =~ /^(.*:|)Collection$/ ) ? 1 : 0; #Optional 'moby:' prefix + return ( $DOM->localname =~ /^Collection$/ and ($DOM->namespaceURI() ? $DOM->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ? 1 : 0; #Optional 'moby:' prefix } sub isSecondaryArticle { @@ -497,7 +507,7 @@ eval {$DOM = _string_to_DOM($XML)} ; return 0 if $@; $DOM = $DOM->getDocumentElement if ( $DOM->isa( "XML::LibXML::Document" ) ); - return ($DOM->localname =~ /^(.*:|)Parameter$/) ? 1 : 0; #Optional 'moby:' prefix + return ($DOM->localname =~ /^Parameter$/ and ($DOM->namespaceURI() ? $DOM->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ? 1 : 0; #Optional 'moby:' prefix } @@ -763,7 +773,7 @@ $exception ||=""; my $xml = "" - . "" + . "" . ""; if ($exception) { $xml .= "$exception"; @@ -961,8 +971,8 @@ $XML = _string_to_DOM($XML); my @xrefs; my @XREFS; - return () if ( $XML->localname =~ /^(.*:|)Collection$/ ); - if ( $XML->localname =~ /^(.*:|)Simple$/ ) { + return () if ( $XML->localname =~ /^Collection$/ and ($XML->namespaceURI() ? $XML->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); + if ( $XML->localname =~ /^Simple$/ and ($XML->namespaceURI() ? $XML->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { foreach my $child ( $XML->childNodes ) { next unless $child->nodeType == ELEMENT_NODE; $XML = $child; @@ -971,17 +981,17 @@ } foreach ( $XML->childNodes ) { next unless (($_->nodeType == ELEMENT_NODE) - || ($_->localname && $_->localname =~ /^(.*:|)CrossReference$/) ); + || ($_->localname && $_->localname =~ /^CrossReference$/ and ($_->namespaceURI() ? $_->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ); foreach my $xref ( $_->childNodes ) { next unless $xref && ( ($xref->nodeType == ELEMENT_NODE) - || ($xref->localname && $xref->localname =~ /^(.*:|)(Xref|Object)$/) ); + || ($xref->localname && $xref->localname =~ /^(Xref|Object)$/ and ($xref->namespaceURI() ? $xref->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ); push @xrefs, $xref; } } foreach ( @xrefs ) { my $x; - if ($_->localname =~ /^(.*:|)Xref$/) { $x = _makeXrefType( $_ ) } - elsif ($_->localname =~ /^(.*:|)Object$/) { $x = _makeObjectType( $_ ) } + if ($_->localname =~ /^Xref$/ and ($_->namespaceURI() ? $_->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $x = _makeXrefType( $_ ) } + elsif ($_->localname =~ /^Object$/ and ($_->namespaceURI() ? $_->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $x = _makeObjectType( $_ ) } push @XREFS, $x if $x; } return @XREFS; @@ -1175,11 +1185,11 @@ return $xref->getAttributeNode($attr) if $xref->getAttributeNode($attr); # check for a namespaced attribute by name - return $xref->getAttributeNodeNS('http://www.biomoby.org/moby', $attr) - if $xref->getAttributeNodeNS('http://www.biomoby.org/moby', $attr); + return $xref->getAttributeNodeNS($MOBY_NS, $attr) + if $xref->getAttributeNodeNS($MOBY_NS, $attr); # check for a namespaced attribute with a prefix ... this is probably redundant! - return $xref->getAttributeNode( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") - if $xref->lookupNamespacePrefix('http://www.biomoby.org/moby'); + return $xref->getAttributeNode( $xref->lookupNamespacePrefix($MOBY_NS) . ":$attr") + if $xref->lookupNamespacePrefix($MOBY_NS); # cant find it ... return ''; } @@ -1206,11 +1216,11 @@ return $xref->getAttribute($attr) if $xref->getAttribute($attr); # check for a namespaced attribute by name - return $xref->getAttributeNS('http://www.biomoby.org/moby', $attr) - if $xref->getAttributeNS('http://www.biomoby.org/moby', $attr); + return $xref->getAttributeNS($MOBY_NS, $attr) + if $xref->getAttributeNS($MOBY_NS, $attr); # check for a namespaced attribute with a prefix ... this is probably redundant! - return $xref->getAttribute( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") - if $xref->lookupNamespacePrefix('http://www.biomoby.org/moby'); + return $xref->getAttribute( $xref->lookupNamespacePrefix($MOBY_NS) . ":$attr") + if $xref->lookupNamespacePrefix($MOBY_NS); # cant find it ... return ''; } @@ -1338,7 +1348,7 @@ sub _getQueryID { my ( $query ) = @_; $query = _string_to_XML($query); - return '' unless ( $query->localname =~ /^(.*:|)mobyData$/ ); #Eddie - unsure + return '' unless ( $query->localname =~ /^mobyData$/ and ($query->namespaceURI() ? $query->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); #Eddie - unsure return _moby_getAttribute($query, 'queryID' ); } @@ -1392,19 +1402,19 @@ my $resp = $responses->get_node( $n ); foreach my $response_component ( $resp->childNodes ) { next unless $response_component->nodeType == ELEMENT_NODE; - if ( $response_component->localname =~ /^(.*:|)Simple$/ ) + if ( $response_component->localname =~ /^Simple$/ and ($response_component->namespaceURI() ? $response_component->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { foreach my $Object ( $response_component->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; push @objects, $Object; } - } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ ) + } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ and ($response_component->namespaceURI() ? $response_component->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { my @objects; foreach my $simple ( $response_component->childNodes ) { next unless $simple->nodeType == ELEMENT_NODE; - next unless ( $simple->localname =~ /^(.*:|)Simple$/ ); + next unless ( $simple->localname =~ /^Simple$/ and ($simple->namespaceURI() ? $simple->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); foreach my $Object ( $simple->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; @@ -1498,12 +1508,12 @@ $moby = _string_to_DOM($moby); return undef unless ( ($moby->nodeType == ELEMENT_NODE) - && ( $moby->localname =~ /^(.*:|)(queryInput|queryResponse|mobyData)$/ ) ); + && ( $moby->localname =~ /^(queryInput|queryResponse|mobyData)$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless ( ($child->nodeType == ELEMENT_NODE) # ignore whitespace - && ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ) ); + && ( $child->localname =~ /^(Simple|Collection|Parameter)$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) ); my $articleName = _moby_getAttribute($child, 'articleName' ); # push the named child DOM elements (which are or , ) push @articles, [ $articleName, $child ]; @@ -1548,7 +1558,7 @@ foreach my $in ( @input_nodes ) { next unless $in; #$in = "" - next unless $in->localname =~ /^(.*)Simple$/; # only allow simples + next unless $in->localname =~ /^Simple$/ and ($in->namespaceURI() ? $in->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1); # only allow simples my @simples = $in->childNodes; foreach ( @simples ) { # $_ = next unless $_->nodeType == ELEMENT_NODE; @@ -1647,7 +1657,7 @@ print STDERR "getInputID method is now deprecated. Please use serviceInputParser or serviceResponseParser\n"; my ( $XML ) = @_; my $moby = _string_to_DOM($XML); - return '' unless ( $moby->localname =~ /^(.*:|)queryInput|mobyData$/ ); + return '' unless ( $moby->localname =~ /^queryInput|mobyData$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my $qid = _moby_getAttribute($moby, 'queryID' ); $qid ||= _moby_getAttribute($moby, 'moby:queryID' ); return defined( $qid ) ? $qid : ''; @@ -1665,19 +1675,19 @@ $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; return undef - unless ($moby->localname =~ /^(.*:|)(queryInput|queryResponse|mobyData)$/); + unless ($moby->localname =~ /^(queryInput|queryResponse|mobyData)$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace next - unless ( $child->localname =~ /^(.*:|)(Simple|Collection|Parameter)$/ ); + unless ( $child->localname =~ /^(Simple|Collection|Parameter)$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my $object; - if ( $child->localname =~ /^(.*:|)Simple$/ ) { + if ( $child->localname =~ /^Simple$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::SimpleArticle->new( XML_DOM => $child ); - } elsif ( $child->localname =~ /^(.*:|)Collection$/ ) { + } elsif ( $child->localname =~ /^Collection$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::CollectionArticle->new( XML_DOM => $child ); - } elsif ( $child->localname =~ /^(.*:|)Parameter$/ ) { + } elsif ( $child->localname =~ /^Parameter$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { $object = MOBY::Client::SecondaryArticle->new( XML_DOM => $child ); } next unless $object; @@ -1697,12 +1707,12 @@ my ( $moby ) = @_; $moby = _string_to_DOM($moby); return undef unless $moby->nodeType == ELEMENT_NODE; - return undef unless ( $moby->localname =~ /^(.*:|)Collection$/ ); + return undef unless ( $moby->localname =~ /^Collection$/ and ($moby->namespaceURI() ? $moby->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); my @articles; foreach my $child ( $moby->childNodes ) { # there may be more than one Simple/Collection per input; iterate over them next unless $child->nodeType == ELEMENT_NODE; # ignore whitespace - next unless ( $child->localname =~ /^(.*:|)Simple$/ ); + next unless ( $child->localname =~ /^Simple$/ and ($child->namespaceURI() ? $child->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); push @articles, $child; # take the child elements, which are or } return @articles; # return them. @@ -1791,19 +1801,19 @@ my $resp = $responses->get_node( $n ); foreach my $response_component ( $resp->childNodes ) { next unless $response_component->nodeType == ELEMENT_NODE; - if ( $response_component->localname =~ /^(.*:|)Simple$/ ) + if ( $response_component->localname =~ /^Simple$/ and ($response_component->namespaceURI() ? $response_component->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { foreach my $Object ( $response_component->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; push @objects, $Object; } - } elsif ( $response_component->localname =~ /^(.*:|)Collection$/ ) + } elsif ( $response_component->localname =~ /^Collection$/ and ($response_component->namespaceURI() ? $response_component->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)) { my @objects; foreach my $simple ( $response_component->childNodes ) { next unless $simple->nodeType == ELEMENT_NODE; - next unless ( $simple->localname =~ /^(.*:|)Simple$/ ); + next unless ( $simple->localname =~ /^Simple$/ and ($simple->namespaceURI() ? $simple->namespaceURI() =~ m/\Q$MOBY_NS\E/i : 1)); foreach my $Object ( $simple->childNodes ) { next unless $Object->nodeType == ELEMENT_NODE; $success = 1; From kawas at dev.open-bio.org Tue Sep 1 20:13:51 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 16:13:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909012013.n81KDpa5017426@dev.open-bio.org> kawas Tue Sep 1 16:13:51 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv17363/MOBY-Client Modified Files: Changes Makefile.PL Log Message: updated to reflect recent changes to codebase moby-live/Perl/MOBY-Client Changes,1.9,1.10 Makefile.PL,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/05/22 16:38:38 1.9 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/09/01 20:13:51 1.10 @@ -2,6 +2,11 @@ 1.05 * Updated the Makefile.PL to handle some missing dependencies. + * Updated CommonSubs to remove all hard coded entries for the + namespace prefix 'moby:'. In addition, all references to + nodeName were replaced with localname so that element namespace + prefixes are ignored since they dont really matter. + Also, the localnames are resolved to check the namespaceURI 1.04 * Fix bug in CollectionArticle, SimpleInput, SecondaryArticle, and =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/05/22 16:38:38 1.13 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/09/01 20:13:51 1.14 @@ -4,7 +4,7 @@ # all_from 'lib/MOBY/Client/Central.pm'; author 'Mark Wilkinson '; -version '1.04'; +version '1.05'; license 'perl'; abstract 'This distribution is for communicating with a MOBY Central registry'; @@ -12,17 +12,17 @@ build_requires 'Test::Pod' => 0; # MOBY::Client::* depends -requires 'SOAP::Lite' => '0.60'; -requires 'XML::LibXML::Common' => '0.13'; +requires 'SOAP::Lite' => 0.60; +requires 'XML::LibXML::Common' => 0.13; requires 'XML::LibXML' => 0; requires 'LWP::UserAgent' => 0; requires 'CGI' => 0; requires 'HTTP::Request::Common' => 0; requires 'URI::Escape' => 0; -requires 'RDF::Core' => '0.51'; +requires 'RDF::Core' => 0.51; # MOBY::Client::MobyUnitTest depends -requires 'XML::Simple' => '2.18'; -requires 'XML::SemanticCompare' => '0.91'; +requires 'XML::Simple' => 2.18; +requires 'XML::SemanticCompare' => 0.91; # MOBY::CommonSubs depends requires 'HTML::Entities' => 0; From kawas at dev.open-bio.org Tue Sep 1 20:13:51 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 1 Sep 2009 16:13:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909012013.n81KDpFC017402@dev.open-bio.org> kawas Tue Sep 1 16:13:51 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv17363/MOBY-Server Modified Files: Makefile.PL Changes Log Message: updated to reflect recent changes to codebase moby-live/Perl/MOBY-Server Makefile.PL,1.20,1.21 Changes,1.30,1.31 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2009/08/28 15:07:18 1.20 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2009/09/01 20:13:51 1.21 @@ -3,7 +3,7 @@ # Define metadata name 'MOBY'; - version '1.11'; + version '1.12'; license 'perl'; abstract 'This distribution is for communicating with or creating your own MOBY Central registry'; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v retrieving revision 1.30 retrieving revision 1.31 diff -u -r1.30 -r1.31 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2009/08/28 15:03:33 1.30 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2009/09/01 20:13:51 1.31 @@ -1,6 +1,13 @@ Revision history for Perl extension MOBY. +1.12 + - Updated CommonSubs to remove all hard coded entries for the + namespace prefix 'moby:'. In addition, all references to + nodeName were replaced with localname so that element namespace + prefixes are ignored since they dont really matter. + Also, the localnames/prefixes are resolved to check the namespaceURI. + 1.11 - Updated the Makefile.PL to handle some missing dependencies. Changes From drepchevski at dev.open-bio.org Wed Sep 2 18:38:26 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:38:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021838.n82IcQ2F024347@dev.open-bio.org> drepchevski Wed Sep 2 14:38:25 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB In directory dev.open-bio.org:/tmp/cvs-serv24313/INB Log Message: Directory /home/repository/moby/moby-live/Java/src/INB added to the repository moby-live/Java/src/INB - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:39:50 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:39:50 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021839.n82Idoim024393@dev.open-bio.org> drepchevski Wed Sep 2 14:39:50 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore In directory dev.open-bio.org:/tmp/cvs-serv24359/MobyCore Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore added to the repository moby-live/Java/src/INB/MobyCore - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:41:39 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:41:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021841.n82Ifdfe024437@dev.open-bio.org> drepchevski Wed Sep 2 14:41:38 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src In directory dev.open-bio.org:/tmp/cvs-serv24403/src Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src added to the repository moby-live/Java/src/INB/MobyCore/src - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:42:43 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:42:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021842.n82IghlS024480@dev.open-bio.org> drepchevski Wed Sep 2 14:42:42 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org In directory dev.open-bio.org:/tmp/cvs-serv24446/org Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org added to the repository moby-live/Java/src/INB/MobyCore/src/org - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:42:59 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:42:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021842.n82IgxCB024522@dev.open-bio.org> drepchevski Wed Sep 2 14:42:59 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb In directory dev.open-bio.org:/tmp/cvs-serv24488/inb Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:43:16 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhGcW024564@dev.open-bio.org> drepchevski Wed Sep 2 14:43:16 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv24530/biomoby Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:43:16 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhGqI024600@dev.open-bio.org> drepchevski Wed Sep 2 14:43:16 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf In directory dev.open-bio.org:/tmp/cvs-serv24530/wsrf Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:43:34 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhYJh024666@dev.open-bio.org> drepchevski Wed Sep 2 14:43:34 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv24615/shared Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:43:34 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhYvk024649@dev.open-bio.org> drepchevski Wed Sep 2 14:43:34 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv24615/client Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:43:16 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:43:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021843.n82IhGek024581@dev.open-bio.org> drepchevski Wed Sep 2 14:43:16 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae In directory dev.open-bio.org:/tmp/cvs-serv24530/lsae Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/lsae - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:44:03 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:44:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021844.n82Ii3CJ024756@dev.open-bio.org> drepchevski Wed Sep 2 14:44:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message In directory dev.open-bio.org:/tmp/cvs-serv24705/message Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:44:04 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:44:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021844.n82Ii49c024794@dev.open-bio.org> drepchevski Wed Sep 2 14:44:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf In directory dev.open-bio.org:/tmp/cvs-serv24705/wsrf Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:44:03 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:44:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021844.n82Ii3fC024739@dev.open-bio.org> drepchevski Wed Sep 2 14:44:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv24705/datatypes Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:44:03 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:44:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021844.n82Ii3NU024773@dev.open-bio.org> drepchevski Wed Sep 2 14:44:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry In directory dev.open-bio.org:/tmp/cvs-serv24705/registry Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:45:03 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82Ij3Uk024907@dev.open-bio.org> drepchevski Wed Sep 2 14:45:03 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault In directory dev.open-bio.org:/tmp/cvs-serv24873/fault Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:45:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82Ijj3m024993@dev.open-bio.org> drepchevski Wed Sep 2 14:45:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 In directory dev.open-bio.org:/tmp/cvs-serv24959/bf2 Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:45:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82Ijjji025010@dev.open-bio.org> drepchevski Wed Sep 2 14:45:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 In directory dev.open-bio.org:/tmp/cvs-serv24959/r2 Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:45:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82Ijjmo025050@dev.open-bio.org> drepchevski Wed Sep 2 14:45:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 In directory dev.open-bio.org:/tmp/cvs-serv24959/rp2 Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:45:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:45:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021845.n82IjjUC025029@dev.open-bio.org> drepchevski Wed Sep 2 14:45:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 In directory dev.open-bio.org:/tmp/cvs-serv24959/rl2 Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 added to the repository moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:50:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:50:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021850.n82IoWmw025184@dev.open-bio.org> drepchevski Wed Sep 2 14:50:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral In directory dev.open-bio.org:/tmp/cvs-serv25150/MobyCentral Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral added to the repository moby-live/Java/src/INB/MobyCentral - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:50:46 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:50:46 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021850.n82Iokem025227@dev.open-bio.org> drepchevski Wed Sep 2 14:50:46 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src In directory dev.open-bio.org:/tmp/cvs-serv25193/src Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src added to the repository moby-live/Java/src/INB/MobyCentral/src - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:51:00 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82Ip0RM025269@dev.open-bio.org> drepchevski Wed Sep 2 14:51:00 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF In directory dev.open-bio.org:/tmp/cvs-serv25235/META-INF Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF added to the repository moby-live/Java/src/INB/MobyCentral/src/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:51:01 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82Ip1PG025288@dev.open-bio.org> drepchevski Wed Sep 2 14:51:00 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org In directory dev.open-bio.org:/tmp/cvs-serv25235/org Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org added to the repository moby-live/Java/src/INB/MobyCentral/src/org - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:51:15 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82IpF8C025332@dev.open-bio.org> drepchevski Wed Sep 2 14:51:15 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services In directory dev.open-bio.org:/tmp/cvs-serv25298/services Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services added to the repository moby-live/Java/src/INB/MobyCentral/src/META-INF/services - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:51:43 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82Iph38025398@dev.open-bio.org> drepchevski Wed Sep 2 14:51:42 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb In directory dev.open-bio.org:/tmp/cvs-serv25364/inb Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:51:57 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:51:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021851.n82Ipvb8025440@dev.open-bio.org> drepchevski Wed Sep 2 14:51:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv25406/biomoby Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:52:10 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:52:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021852.n82IqAAL025482@dev.open-bio.org> drepchevski Wed Sep 2 14:52:09 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv25448/central Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:52:24 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:52:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021852.n82IqOm2025525@dev.open-bio.org> drepchevski Wed Sep 2 14:52:24 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory In directory dev.open-bio.org:/tmp/cvs-serv25491/factory Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:52:41 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:52:41 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021852.n82Iqfw7025567@dev.open-bio.org> drepchevski Wed Sep 2 14:52:41 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv25533/jaxb Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 18:52:54 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 14:52:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021852.n82IqsM2025609@dev.open-bio.org> drepchevski Wed Sep 2 14:52:54 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv25575/registry Log Message: Directory /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry added to the repository moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 19:24:45 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 15:24:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909021924.n82JOj2D026604@dev.open-bio.org> drepchevski Wed Sep 2 15:24:45 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore In directory dev.open-bio.org:/tmp/cvs-serv26570 Log Message: INB Client API for BioMoby services Status: Vendor Tag: default_vendor Release Tags: default_release N moby-live/Java/src/INB/MobyCore/build.xml N moby-live/Java/src/INB/MobyCore/.cvsignore N moby-live/Java/src/INB/MobyCore/nbproject/project.properties N moby-live/Java/src/INB/MobyCore/nbproject/genfiles.properties N moby-live/Java/src/INB/MobyCore/nbproject/.cvsignore N moby-live/Java/src/INB/MobyCore/nbproject/project.xml N moby-live/Java/src/INB/MobyCore/nbproject/build-impl.xml N moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/CribTest.java N moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/GetAminoAcidSequence.java N moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/CommonsubsMoby.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/ResourceNotDestroyedFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/ResourceUnavailableFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/ResourceUnknownFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/GetResourcePropertyResponse.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/InvalidResourcePropertyQNameFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/QueryResourcePropertiesResponse.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/QueryEvaluationErrorFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/UnknownQueryExpressionDialectFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/QueryExpressionType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/GetMultipleResourcePropertiesResponse.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/GetMultipleResourceProperties.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/InvalidQueryExpressionFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/QueryResourceProperties.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/BaseFaultType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/MobyClassLoader.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/MobyMessageContext.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/MobyDispatch.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyData.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyMessage.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/AnyMobyObject.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/AbstractMobyElement.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/CrossReference.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyDataElement.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyObject.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobySimple.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyExceptions.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/AbstractMobyObject.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyParameter.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyContent.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyException.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/MobyCollection.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/ServiceNotes.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyDateTime.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyPrimitive.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyString.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyBinary.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyFloat.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyBoolean.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/MobyInteger.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/package-info.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/PropertyResponseWrapper.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/SubmitResponseWrapper.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/MobyEndpointReference.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/QueryEvaluationErrorFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/InvalidResourcePropertyQNameFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/UnknownQueryExpressionDialectFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/ResourceUnavailableFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/ResourceNotDestroyedFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/InvalidQueryExpressionFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/ResourceUnknownFault.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Registration.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Simple.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Relationship.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Namespace.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Resource.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Collection.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Service.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/ServiceType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Output.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Parameter.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Input.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/ServiceProvider.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/ObjectType.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/AbstractTypeEntity.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/AbstractEntity.java N moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/Data.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/StepProgress.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/jaxb.index N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/StateChanged.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/Event.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/AnalysisEvent.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/TimeProgress.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/HeartbeatProgress.java N moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/PercentProgress.java No conflicts created by this import moby-live/Java/src/INB/MobyCore - Imported sources rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/Imported,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/sources,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 20:27:01 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 16:27:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022027.n82KR1Fn027774@dev.open-bio.org> drepchevski Wed Sep 2 16:27:01 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject In directory dev.open-bio.org:/tmp/cvs-serv27738 Removed Files: .cvsignore build-impl.xml genfiles.properties project.properties project.xml Log Message: remove all netbeans artefacts moby-live/Java/src/INB/MobyCore/nbproject .cvsignore,1.1.1.1,NONE build-impl.xml,1.1.1.1,NONE genfiles.properties,1.1.1.1,NONE project.properties,1.1.1.1,NONE project.xml,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/build-impl.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/genfiles.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/project.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/nbproject/RCS/project.xml,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 20:31:26 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 16:31:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022031.n82KVQSj027879@dev.open-bio.org> drepchevski Wed Sep 2 16:31:26 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws In directory dev.open-bio.org:/tmp/cvs-serv27845 Removed Files: CommonsubsMoby.java CribTest.java GetAminoAcidSequence.java Log Message: will provide unit tests later moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws CommonsubsMoby.java,1.1.1.1,NONE CribTest.java,1.1.1.1,NONE GetAminoAcidSequence.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/RCS/CommonsubsMoby.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/RCS/CribTest.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/test/org/biomoby/shared/jaxws/RCS/GetAminoAcidSequence.java,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 20:33:24 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 16:33:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022033.n82KXOrH027962@dev.open-bio.org> drepchevski Wed Sep 2 16:33:24 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore In directory dev.open-bio.org:/tmp/cvs-serv27929 Removed Files: .cvsignore build.xml Log Message: moby-live/Java/src/INB/MobyCore .cvsignore,1.1.1.1,NONE build.xml,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/RCS/build.xml,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 20:53:34 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 16:53:34 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022053.n82KrYaO028075@dev.open-bio.org> drepchevski Wed Sep 2 16:53:33 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv28040 Modified Files: MobyDispatch.java Log Message: test (some comments added) moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client MobyDispatch.java,1.1.1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/MobyDispatch.java,v retrieving revision 1.1.1.1 retrieving revision 1.2 diff -u -r1.1.1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/MobyDispatch.java 2009/09/02 19:24:44 1.1.1.1 +++ /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/MobyDispatch.java 2009/09/02 20:53:33 1.2 @@ -90,7 +90,14 @@ this.service.addPort(sName, SOAPBinding.SOAP11HTTP_MTOM_BINDING, mobyService.getUrl()); } - + + /** + * Method to synchronously invoke BioMoby service (provided in constructor) + * + * @param message - message to be sent. + * @return message sent by the service. + * @throws Exception + */ public MobyMessage invoke(MobyMessage message) throws Exception { CATEGORY category = mobyService.getCategory(); From drepchevski at dev.open-bio.org Wed Sep 2 21:12:19 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:12:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022112.n82LCJFN028675@dev.open-bio.org> drepchevski Wed Sep 2 17:12:19 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral In directory dev.open-bio.org:/tmp/cvs-serv28641 Log Message: INB API to work with BioMoby Registry Status: Vendor Tag: default_vendor Release Tags: default_release N moby-live/Java/src/INB/MobyCentral/build.xml N moby-live/Java/src/INB/MobyCentral/.cvsignore N moby-live/Java/src/INB/MobyCentral/nbproject/project.properties N moby-live/Java/src/INB/MobyCentral/nbproject/genfiles.properties N moby-live/Java/src/INB/MobyCentral/nbproject/.cvsignore N moby-live/Java/src/INB/MobyCentral/nbproject/project.xml N moby-live/Java/src/INB/MobyCentral/nbproject/build-impl.xml N moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test/RegisterServiceFromXMLTest.java N moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test/CentralOperationsTest.java N moby-live/Java/src/INB/MobyCentral/src/META-INF/services/org.inb.biomoby.central.MobyCentralService N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralFactory.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentral.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralOperations.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralService.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/ModelConverter.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/MobyCentralServiceImpl.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/MobyRegistryEndpoint.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/JAXBMobyCentralImpl.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RegisterServiceTypeOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveResourceURLsOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RegisterNamespaceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RegisterObjectClassOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/DeregisterNamespaceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RegisterServiceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/jaxb.index N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveObjectNamesOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/DeregisterServiceTypeOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/FindServiceOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveObjectDefinitionOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceTypesOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/DeregisterObjectClassOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveObjectOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RelationshipsOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/MobyRegistration.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceNamesOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/package-info.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveNamespacesOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RetrieveServiceProvidersOperation.java N moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/DeregisterServiceOperation.java No conflicts created by this import moby-live/Java/src/INB/MobyCentral - Imported sources rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/Imported,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/sources,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 21:18:09 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022118.n82LI9Qt028842@dev.open-bio.org> drepchevski Wed Sep 2 17:18:09 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral In directory dev.open-bio.org:/tmp/cvs-serv28809 Removed Files: .cvsignore build.xml Log Message: remove all netbeans shit moby-live/Java/src/INB/MobyCentral .cvsignore,1.1.1.1,NONE build.xml,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/RCS/build.xml,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 21:18:09 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022118.n82LI9pJ028879@dev.open-bio.org> drepchevski Wed Sep 2 17:18:09 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test In directory dev.open-bio.org:/tmp/cvs-serv28809/test/org/biomoby/central/test Removed Files: CentralOperationsTest.java RegisterServiceFromXMLTest.java Log Message: remove all netbeans shit moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test CentralOperationsTest.java,1.1.1.1,NONE RegisterServiceFromXMLTest.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test/RCS/CentralOperationsTest.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/test/org/biomoby/central/test/RCS/RegisterServiceFromXMLTest.java,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 21:18:09 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:18:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022118.n82LI9bf028861@dev.open-bio.org> drepchevski Wed Sep 2 17:18:09 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject In directory dev.open-bio.org:/tmp/cvs-serv28809/nbproject Removed Files: .cvsignore build-impl.xml genfiles.properties project.properties project.xml Log Message: remove all netbeans shit moby-live/Java/src/INB/MobyCentral/nbproject .cvsignore,1.1.1.1,NONE build-impl.xml,1.1.1.1,NONE genfiles.properties,1.1.1.1,NONE project.properties,1.1.1.1,NONE project.xml,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/.cvsignore,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/build-impl.xml,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/genfiles.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/project.properties,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/nbproject/RCS/project.xml,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 2 21:41:36 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:41:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022141.n82LfaQm028994@dev.open-bio.org> drepchevski Wed Sep 2 17:41:36 EDT 2009 Update of /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv28959 Modified Files: MobyCentralOperations.java Log Message: test (some comments added) /moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central MobyCentralOperations.java,1.1.1.1,1.2 =================================================================== RCS file: /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralOperations.java,v retrieving revision 1.1.1.1 retrieving revision 1.2 diff -u -r1.1.1.1 -r1.2 --- /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralOperations.java 2009/09/02 21:12:16 1.1.1.1 +++ /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralOperations.java 2009/09/02 21:41:36 1.2 @@ -11,6 +11,8 @@ import org.inb.biomoby.shared.registry.Relationship.RELATIONSHIP_TYPE; /** + * An interface that defines all standard BioMoby Registry operations. + * * @author Dmitry Repchevsky */ From drepchevski at dev.open-bio.org Wed Sep 2 21:48:09 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 2 Sep 2009 17:48:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909022148.n82Lm9gi029058@dev.open-bio.org> drepchevski Wed Sep 2 17:48:09 EDT 2009 Update of /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv29023 Modified Files: MobyCentralFactory.java Log Message: test /moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central MobyCentralFactory.java,1.1.1.1,1.2 =================================================================== RCS file: /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralFactory.java,v retrieving revision 1.1.1.1 retrieving revision 1.2 diff -u -r1.1.1.1 -r1.2 --- /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralFactory.java 2009/09/02 21:12:16 1.1.1.1 +++ /home/repository/moby//moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/MobyCentralFactory.java 2009/09/02 21:48:09 1.2 @@ -15,7 +15,14 @@ public class MobyCentralFactory { private MobyCentralFactory() {} - + + /** + * Factory method to obtain an implementation of MobyCentralOperations interface + * + * @param central - A MobyCentral object which defines which BioMoby Registry we are connecting. + * + * @return - MobyCentralOperatons interface implementation to connect to the given BioMoby Registry + */ public static MobyCentralOperations getCentralDigest(MobyCentral central) { ServiceLoader loader = java.util.ServiceLoader.load(MobyCentralService.class); From drepchevski at dev.open-bio.org Tue Sep 8 22:30:59 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:30:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082230.n88MUxB9029336@dev.open-bio.org> drepchevski Tue Sep 8 18:30:59 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services In directory dev.open-bio.org:/tmp/cvs-serv29304 Removed Files: org.inb.biomoby.central.MobyCentralService Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCentral/src/META-INF/services org.inb.biomoby.central.MobyCentralService,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/META-INF/services/RCS/org.inb.biomoby.central.MobyCentralService,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:13 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVD6j029522@dev.open-bio.org> drepchevski Tue Sep 8 18:31:13 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/datatypes Removed Files: MobyBinary.java MobyBoolean.java MobyDateTime.java MobyFloat.java MobyInteger.java MobyPrimitive.java MobyString.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes MobyBinary.java,1.1.1.1,NONE MobyBoolean.java,1.1.1.1,NONE MobyDateTime.java,1.1.1.1,NONE MobyFloat.java,1.1.1.1,NONE MobyInteger.java,1.1.1.1,NONE MobyPrimitive.java,1.1.1.1,NONE MobyString.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyBinary.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyBoolean.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyDateTime.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyFloat.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyInteger.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyPrimitive.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/MobyString.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/datatypes/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:06 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MV6jR029379@dev.open-bio.org> drepchevski Tue Sep 8 18:31:06 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv29344 Removed Files: MobyCentral.java MobyCentralFactory.java MobyCentralOperations.java MobyCentralService.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central MobyCentral.java,1.1.1.1,NONE MobyCentralFactory.java,1.2,NONE MobyCentralOperations.java,1.2,NONE MobyCentralService.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/MobyCentral.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/MobyCentralFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/MobyCentralOperations.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/RCS/MobyCentralService.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVNgC029751@dev.open-bio.org> drepchevski Tue Sep 8 18:31:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 In directory dev.open-bio.org:/tmp/cvs-serv29678/rl2 Removed Files: ResourceNotDestroyedFaultType.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2 ResourceNotDestroyedFaultType.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/ResourceNotDestroyedFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rl2/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVNKn029783@dev.open-bio.org> drepchevski Tue Sep 8 18:31:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 In directory dev.open-bio.org:/tmp/cvs-serv29678/rp2 Removed Files: GetMultipleResourceProperties.java GetMultipleResourcePropertiesResponse.java GetResourcePropertyResponse.java InvalidQueryExpressionFaultType.java InvalidResourcePropertyQNameFaultType.java QueryEvaluationErrorFaultType.java QueryExpressionType.java QueryResourceProperties.java QueryResourcePropertiesResponse.java UnknownQueryExpressionDialectFaultType.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2 GetMultipleResourceProperties.java,1.1.1.1,NONE GetMultipleResourcePropertiesResponse.java,1.1.1.1,NONE GetResourcePropertyResponse.java,1.1.1.1,NONE InvalidQueryExpressionFaultType.java,1.1.1.1,NONE InvalidResourcePropertyQNameFaultType.java,1.1.1.1,NONE QueryEvaluationErrorFaultType.java,1.1.1.1,NONE QueryExpressionType.java,1.1.1.1,NONE QueryResourceProperties.java,1.1.1.1,NONE QueryResourcePropertiesResponse.java,1.1.1.1,NONE UnknownQueryExpressionDialectFaultType.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/GetMultipleResourceProperties.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/GetMultipleResourcePropertiesResponse.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/GetResourcePropertyResponse.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/InvalidQueryExpressionFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/InvalidResourcePropertyQNameFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/QueryEvaluationErrorFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/QueryExpressionType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/QueryResourceProperties.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/QueryResourcePropertiesResponse.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/UnknownQueryExpressionDialectFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/rp2/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:06 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MV612029399@dev.open-bio.org> drepchevski Tue Sep 8 18:31:06 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv29344/factory/jaxb Removed Files: JAXBMobyCentralImpl.java MobyCentralServiceImpl.java MobyRegistryEndpoint.java ModelConverter.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb JAXBMobyCentralImpl.java,1.1.1.1,NONE MobyCentralServiceImpl.java,1.1.1.1,NONE MobyRegistryEndpoint.java,1.1.1.1,NONE ModelConverter.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/JAXBMobyCentralImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/MobyCentralServiceImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/MobyRegistryEndpoint.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/RCS/ModelConverter.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:06 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MV6Df029439@dev.open-bio.org> drepchevski Tue Sep 8 18:31:06 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv29344/factory/jaxb/registry Removed Files: DeregisterNamespaceOperation.java DeregisterObjectClassOperation.java DeregisterServiceOperation.java DeregisterServiceTypeOperation.java FindServiceOperation.java MobyRegistration.java RegisterNamespaceOperation.java RegisterObjectClassOperation.java RegisterServiceOperation.java RegisterServiceTypeOperation.java RelationshipsOperation.java RetrieveNamespacesOperation.java RetrieveObjectDefinitionOperation.java RetrieveObjectNamesOperation.java RetrieveObjectOperation.java RetrieveResourceURLsOperation.java RetrieveServiceNamesOperation.java RetrieveServiceOperation.java RetrieveServiceProvidersOperation.java RetrieveServiceTypesOperation.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry DeregisterNamespaceOperation.java,1.1.1.1,NONE DeregisterObjectClassOperation.java,1.1.1.1,NONE DeregisterServiceOperation.java,1.1.1.1,NONE DeregisterServiceTypeOperation.java,1.1.1.1,NONE FindServiceOperation.java,1.1.1.1,NONE MobyRegistration.java,1.1.1.1,NONE RegisterNamespaceOperation.java,1.1.1.1,NONE RegisterObjectClassOperation.java,1.1.1.1,NONE RegisterServiceOperation.java,1.1.1.1,NONE RegisterServiceTypeOperation.java,1.1.1.1,NONE RelationshipsOperation.java,1.1.1.1,NONE RetrieveNamespacesOperation.java,1.1.1.1,NONE RetrieveObjectDefinitionOperation.java,1.1.1.1,NONE RetrieveObjectNamesOperation.java,1.1.1.1,NONE RetrieveObjectOperation.java,1.1.1.1,NONE RetrieveResourceURLsOperation.java,1.1.1.1,NONE RetrieveServiceNamesOperation.java,1.1.1.1,NONE RetrieveServiceOperation.java,1.1.1.1,NONE RetrieveServiceProvidersOperation.java,1.1.1.1,NONE RetrieveServiceTypesOperation.java,1.1.! 1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/DeregisterNamespaceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/DeregisterObjectClassOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/DeregisterServiceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/DeregisterServiceTypeOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/FindServiceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/MobyRegistration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RegisterNamespaceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RegisterObjectClassOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RegisterServiceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RegisterServiceTypeOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RelationshipsOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveNamespacesOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveObjectDefinitionOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveObjectNamesOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveObjectOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveResourceURLsOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveServiceNamesOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveServiceOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveServiceProvidersOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/RetrieveServiceTypesOperation.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCentral/src/org/inb/biomoby/central/factory/jaxb/registry/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:13 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVDIM029482@dev.open-bio.org> drepchevski Tue Sep 8 18:31:13 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby Removed Files: MobyClassLoader.java MobyMessageContext.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby MobyClassLoader.java,1.1.1.1,NONE MobyMessageContext.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/MobyClassLoader.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/RCS/MobyMessageContext.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVEZ7029611@dev.open-bio.org> drepchevski Tue Sep 8 18:31:14 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/wsrf Removed Files: MobyEndpointReference.java PropertyResponseWrapper.java SubmitResponseWrapper.java jaxb.index Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf MobyEndpointReference.java,1.1.1.1,NONE PropertyResponseWrapper.java,1.1.1.1,NONE SubmitResponseWrapper.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/MobyEndpointReference.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/PropertyResponseWrapper.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/SubmitResponseWrapper.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/RCS/jaxb.index,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVEql029593@dev.open-bio.org> drepchevski Tue Sep 8 18:31:14 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/registry Removed Files: AbstractEntity.java AbstractTypeEntity.java Collection.java Data.java Input.java Namespace.java ObjectType.java Output.java Parameter.java Registration.java Relationship.java Resource.java Service.java ServiceProvider.java ServiceType.java Simple.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry AbstractEntity.java,1.1.1.1,NONE AbstractTypeEntity.java,1.1.1.1,NONE Collection.java,1.1.1.1,NONE Data.java,1.1.1.1,NONE Input.java,1.1.1.1,NONE Namespace.java,1.1.1.1,NONE ObjectType.java,1.1.1.1,NONE Output.java,1.1.1.1,NONE Parameter.java,1.1.1.1,NONE Registration.java,1.1.1.1,NONE Relationship.java,1.1.1.1,NONE Resource.java,1.1.1.1,NONE Service.java,1.1.1.1,NONE ServiceProvider.java,1.1.1.1,NONE ServiceType.java,1.1.1.1,NONE Simple.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/AbstractEntity.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/AbstractTypeEntity.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Collection.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Data.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Input.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Namespace.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/ObjectType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Output.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Parameter.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Registration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Relationship.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Resource.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Service.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/ServiceProvider.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/ServiceType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/registry/RCS/Simple.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVEwE029561@dev.open-bio.org> drepchevski Tue Sep 8 18:31:13 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/message Removed Files: AbstractMobyElement.java AbstractMobyObject.java AnyMobyObject.java CrossReference.java MobyCollection.java MobyContent.java MobyData.java MobyDataElement.java MobyException.java MobyExceptions.java MobyMessage.java MobyObject.java MobyParameter.java MobySimple.java ServiceNotes.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message AbstractMobyElement.java,1.1.1.1,NONE AbstractMobyObject.java,1.1.1.1,NONE AnyMobyObject.java,1.1.1.1,NONE CrossReference.java,1.1.1.1,NONE MobyCollection.java,1.1.1.1,NONE MobyContent.java,1.1.1.1,NONE MobyData.java,1.1.1.1,NONE MobyDataElement.java,1.1.1.1,NONE MobyException.java,1.1.1.1,NONE MobyExceptions.java,1.1.1.1,NONE MobyMessage.java,1.1.1.1,NONE MobyObject.java,1.1.1.1,NONE MobyParameter.java,1.1.1.1,NONE MobySimple.java,1.1.1.1,NONE ServiceNotes.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/AbstractMobyElement.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/AbstractMobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/AnyMobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/CrossReference.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyCollection.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyContent.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyDataElement.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyExceptions.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyMessage.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobyParameter.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/MobySimple.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/ServiceNotes.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/message/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:13 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVDCh029497@dev.open-bio.org> drepchevski Tue Sep 8 18:31:13 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/client Removed Files: MobyDispatch.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client MobyDispatch.java,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/client/RCS/MobyDispatch.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVNtk029712@dev.open-bio.org> drepchevski Tue Sep 8 18:31:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 In directory dev.open-bio.org:/tmp/cvs-serv29678/bf2 Removed Files: BaseFaultType.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2 BaseFaultType.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/BaseFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/bf2/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVNPB029730@dev.open-bio.org> drepchevski Tue Sep 8 18:31:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 In directory dev.open-bio.org:/tmp/cvs-serv29678/r2 Removed Files: ResourceUnavailableFaultType.java ResourceUnknownFaultType.java jaxb.index package-info.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2 ResourceUnavailableFaultType.java,1.1.1.1,NONE ResourceUnknownFaultType.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE package-info.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/ResourceUnavailableFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/ResourceUnknownFaultType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/jaxb.index,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/wsrf/r2/RCS/package-info.java,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVEZS029668@dev.open-bio.org> drepchevski Tue Sep 8 18:31:14 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae In directory dev.open-bio.org:/tmp/cvs-serv29449/lsae Removed Files: AnalysisEvent.java Event.java HeartbeatProgress.java PercentProgress.java StateChanged.java StepProgress.java TimeProgress.java jaxb.index Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/lsae AnalysisEvent.java,1.1.1.1,NONE Event.java,1.1.1.1,NONE HeartbeatProgress.java,1.1.1.1,NONE PercentProgress.java,1.1.1.1,NONE StateChanged.java,1.1.1.1,NONE StepProgress.java,1.1.1.1,NONE TimeProgress.java,1.1.1.1,NONE jaxb.index,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/AnalysisEvent.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/Event.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/HeartbeatProgress.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/PercentProgress.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/StateChanged.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/StepProgress.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/TimeProgress.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/lsae/RCS/jaxb.index,v: No such file or directory From drepchevski at dev.open-bio.org Tue Sep 8 22:31:14 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 8 Sep 2009 18:31:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909082231.n88MVE30029638@dev.open-bio.org> drepchevski Tue Sep 8 18:31:14 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault In directory dev.open-bio.org:/tmp/cvs-serv29449/biomoby/shared/wsrf/fault Removed Files: InvalidQueryExpressionFault.java InvalidResourcePropertyQNameFault.java QueryEvaluationErrorFault.java ResourceNotDestroyedFault.java ResourceUnavailableFault.java ResourceUnknownFault.java UnknownQueryExpressionDialectFault.java Log Message: will be placed to a main directory moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault InvalidQueryExpressionFault.java,1.1.1.1,NONE InvalidResourcePropertyQNameFault.java,1.1.1.1,NONE QueryEvaluationErrorFault.java,1.1.1.1,NONE ResourceNotDestroyedFault.java,1.1.1.1,NONE ResourceUnavailableFault.java,1.1.1.1,NONE ResourceUnknownFault.java,1.1.1.1,NONE UnknownQueryExpressionDialectFault.java,1.1.1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/InvalidQueryExpressionFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/InvalidResourcePropertyQNameFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/QueryEvaluationErrorFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/ResourceNotDestroyedFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/ResourceUnavailableFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/ResourceUnknownFault.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/INB/MobyCore/src/org/inb/biomoby/shared/wsrf/fault/RCS/UnknownQueryExpressionDialectFault.java,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:17:04 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:17:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091917.n89JH4KC003508@dev.open-bio.org> drepchevski Wed Sep 9 15:17:04 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb In directory dev.open-bio.org:/tmp/cvs-serv3474/inb Log Message: Directory /home/repository/moby/moby-live/Java/src/config/inb added to the repository moby-live/Java/src/config/inb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:17:29 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:17:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091917.n89JHTpb003550@dev.open-bio.org> drepchevski Wed Sep 9 15:17:28 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb/mobycentral In directory dev.open-bio.org:/tmp/cvs-serv3516/mobycentral Log Message: Directory /home/repository/moby/moby-live/Java/src/config/inb/mobycentral added to the repository moby-live/Java/src/config/inb/mobycentral - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:17:42 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:17:42 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091917.n89JHg13003592@dev.open-bio.org> drepchevski Wed Sep 9 15:17:42 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF In directory dev.open-bio.org:/tmp/cvs-serv3558/META-INF Log Message: Directory /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF added to the repository moby-live/Java/src/config/inb/mobycentral/META-INF - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:17:57 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:17:57 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091917.n89JHvB9003634@dev.open-bio.org> drepchevski Wed Sep 9 15:17:57 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services In directory dev.open-bio.org:/tmp/cvs-serv3600/services Log Message: Directory /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services added to the repository moby-live/Java/src/config/inb/mobycentral/META-INF/services - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:07 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:07 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJ772003717@dev.open-bio.org> drepchevski Wed Sep 9 15:19:06 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb In directory dev.open-bio.org:/tmp/cvs-serv3683/inb Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb added to the repository moby-live/Java/src/main/org/inb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:12 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJCWc003776@dev.open-bio.org> drepchevski Wed Sep 9 15:19:12 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/lsae In directory dev.open-bio.org:/tmp/cvs-serv3725/lsae Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/lsae added to the repository moby-live/Java/src/main/org/inb/lsae - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/lsae/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/lsae/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/lsae/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJNZd003927@dev.open-bio.org> drepchevski Wed Sep 9 15:19:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory In directory dev.open-bio.org:/tmp/cvs-serv3893/factory Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory added to the repository moby-live/Java/src/main/org/inb/biomoby/central/factory - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:29 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJTrv003969@dev.open-bio.org> drepchevski Wed Sep 9 15:19:29 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv3935/jaxb Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb added to the repository moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:12 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJCTN003797@dev.open-bio.org> drepchevski Wed Sep 9 15:19:12 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf In directory dev.open-bio.org:/tmp/cvs-serv3725/wsrf Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf added to the repository moby-live/Java/src/main/org/inb/wsrf - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:12 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJCCb003759@dev.open-bio.org> drepchevski Wed Sep 9 15:19:12 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv3725/biomoby Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby added to the repository moby-live/Java/src/main/org/inb/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:35 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJZAs004011@dev.open-bio.org> drepchevski Wed Sep 9 15:19:35 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv3977/registry Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry added to the repository moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:18 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJISF003881@dev.open-bio.org> drepchevski Wed Sep 9 15:19:18 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv3809/shared Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared added to the repository moby-live/Java/src/main/org/inb/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:18 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJIYi003843@dev.open-bio.org> drepchevski Wed Sep 9 15:19:18 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv3809/central Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central added to the repository moby-live/Java/src/main/org/inb/biomoby/central - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:18 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJImr003862@dev.open-bio.org> drepchevski Wed Sep 9 15:19:18 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv3809/client Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client added to the repository moby-live/Java/src/main/org/inb/biomoby/client - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:52 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJqx7004112@dev.open-bio.org> drepchevski Wed Sep 9 15:19:52 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message In directory dev.open-bio.org:/tmp/cvs-serv4061/message Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/message - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:52 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJqYx004095@dev.open-bio.org> drepchevski Wed Sep 9 15:19:52 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv4061/datatypes Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/datatypes - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:52 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJq4p004154@dev.open-bio.org> drepchevski Wed Sep 9 15:19:52 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf In directory dev.open-bio.org:/tmp/cvs-serv4061/wsrf Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/wsrf - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:19:52 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:19:52 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091919.n89JJqOW004131@dev.open-bio.org> drepchevski Wed Sep 9 15:19:52 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry In directory dev.open-bio.org:/tmp/cvs-serv4061/registry Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/registry - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:20:15 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKFmO004263@dev.open-bio.org> drepchevski Wed Sep 9 15:20:15 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault In directory dev.open-bio.org:/tmp/cvs-serv4229/fault Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault added to the repository moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:20:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKWAG004347@dev.open-bio.org> drepchevski Wed Sep 9 15:20:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2 In directory dev.open-bio.org:/tmp/cvs-serv4313/bf2 Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2 added to the repository moby-live/Java/src/main/org/inb/wsrf/bf2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:20:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKWFx004366@dev.open-bio.org> drepchevski Wed Sep 9 15:20:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2 In directory dev.open-bio.org:/tmp/cvs-serv4313/r2 Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2 added to the repository moby-live/Java/src/main/org/inb/wsrf/r2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:20:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKWh3004383@dev.open-bio.org> drepchevski Wed Sep 9 15:20:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2 In directory dev.open-bio.org:/tmp/cvs-serv4313/rl2 Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2 added to the repository moby-live/Java/src/main/org/inb/wsrf/rl2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:20:32 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:20:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091920.n89JKWf2004406@dev.open-bio.org> drepchevski Wed Sep 9 15:20:32 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2 In directory dev.open-bio.org:/tmp/cvs-serv4313/rp2 Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2 added to the repository moby-live/Java/src/main/org/inb/wsrf/rp2 - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2/RCS/directory,v: No such file or directory From drepchevski at dev.open-bio.org Wed Sep 9 19:26:47 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:26:47 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091926.n89JQlHr004620@dev.open-bio.org> drepchevski Wed Sep 9 15:26:47 EDT 2009 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv4585 Modified Files: build.xml Log Message: INB MobyCore & MobyCentral libraries added moby-live/Java build.xml,1.76,1.77 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.76 retrieving revision 1.77 diff -u -r1.76 -r1.77 --- /home/repository/moby/moby-live/Java/build.xml 2008/11/26 11:07:57 1.76 +++ /home/repository/moby/moby-live/Java/build.xml 2009/09/09 19:26:47 1.77 @@ -15,6 +15,7 @@ + ]> @@ -64,16 +65,17 @@ - - - - - - - - - - + + + + + + + + + + + @@ -148,6 +150,7 @@ &seahawkBuild; &mobysyncBuild; &featureClientBuild; + &inbMoby; @@ -177,6 +180,8 @@ + + From drepchevski at dev.open-bio.org Wed Sep 9 19:47:38 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlctK005229@dev.open-bio.org> drepchevski Wed Sep 9 15:47:38 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/config/inb/mobycentral/META-INF/services In directory dev.open-bio.org:/tmp/cvs-serv5198 Added Files: org.inb.biomoby.central.MobyCentralService Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/config/inb/mobycentral/META-INF/services org.inb.biomoby.central.MobyCentralService,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmtO005268@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby Added Files: MobyClassLoader.java MobyMessageContext.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby MobyClassLoader.java,NONE,1.1 MobyMessageContext.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmDN005338@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/client Added Files: MobyDispatch.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/client MobyDispatch.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmTn005284@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/central Added Files: MobyCentral.java MobyCentralFactory.java MobyCentralOperations.java MobyCentralService.java ServiceLoader.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/central MobyCentral.java,NONE,1.1 MobyCentralFactory.java,NONE,1.1 MobyCentralOperations.java,NONE,1.1 MobyCentralService.java,NONE,1.1 ServiceLoader.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:48:00 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:48:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091948.n89Jm0mP005580@dev.open-bio.org> drepchevski Wed Sep 9 15:48:00 EDT 2009 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv5549 Added Files: inbMoby.xml Log Message: MobyCore and MobyCentral source code upload moby-live/Java/xmls inbMoby.xml,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89Jlngl005392@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/registry Added Files: AbstractEntity.java AbstractTypeEntity.java Collection.java Data.java Input.java Namespace.java ObjectType.java Output.java Parameter.java Registration.java Relationship.java Resource.java Service.java ServiceProvider.java ServiceType.java Simple.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/registry AbstractEntity.java,NONE,1.1 AbstractTypeEntity.java,NONE,1.1 Collection.java,NONE,1.1 Data.java,NONE,1.1 Input.java,NONE,1.1 Namespace.java,NONE,1.1 ObjectType.java,NONE,1.1 Output.java,NONE,1.1 Parameter.java,NONE,1.1 Registration.java,NONE,1.1 Relationship.java,NONE,1.1 Resource.java,NONE,1.1 Service.java,NONE,1.1 ServiceProvider.java,NONE,1.1 ServiceType.java,NONE,1.1 Simple.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlnIL005410@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/wsrf Added Files: MobyEndpointReference.java PropertyResponseWrapper.java SubmitResponseWrapper.java jaxb.index Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/wsrf MobyEndpointReference.java,NONE,1.1 PropertyResponseWrapper.java,NONE,1.1 SubmitResponseWrapper.java,NONE,1.1 jaxb.index,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmMN005320@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/central/factory/jaxb/registry Added Files: DeregisterNamespaceOperation.java DeregisterObjectClassOperation.java DeregisterServiceOperation.java DeregisterServiceTypeOperation.java FindServiceOperation.java MobyRegistration.java RegisterNamespaceOperation.java RegisterObjectClassOperation.java RegisterServiceOperation.java RegisterServiceTypeOperation.java RelationshipsOperation.java RetrieveNamespacesOperation.java RetrieveObjectDefinitionOperation.java RetrieveObjectNamesOperation.java RetrieveObjectOperation.java RetrieveResourceURLsOperation.java RetrieveServiceNamesOperation.java RetrieveServiceOperation.java RetrieveServiceProvidersOperation.java RetrieveServiceTypesOperation.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb/registry DeregisterNamespaceOperation.java,NONE,1.1 DeregisterObjectClassOperation.java,NONE,1.1 DeregisterServiceOperation.java,NONE,1.1 DeregisterServiceTypeOperation.java,NONE,1.1 FindServiceOperation.java,NONE,1.1 MobyRegistration.java,NONE,1.1 RegisterNamespaceOperation.java,NONE,1.1 RegisterObjectClassOperation.java,NONE,1.1 RegisterServiceOperation.java,NONE,1.1 RegisterServiceTypeOperation.java,NONE,1.1 RelationshipsOperation.java,NONE,1.1 RetrieveNamespacesOperation.java,NONE,1.1 RetrieveObjectDefinitionOperation.java,NONE,1.1 RetrieveObjectNamesOperation.java,NONE,1.1 RetrieveObjectOperation.java,NONE,1.1 RetrieveResourceURLsOperation.java,NONE,1.1 RetrieveServiceNamesOperation.java,NONE,1.1 RetrieveServiceOperation.java,NONE,1.1 RetrieveServiceProvidersOperation.java,NONE,1.1 RetrieveServiceTypesOperation.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89Jln8b005374@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/message In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/message Added Files: AbstractMobyElement.java AbstractMobyObject.java AnyMobyObject.java CrossReference.java MobyCollection.java MobyContent.java MobyData.java MobyDataElement.java MobyException.java MobyExceptions.java MobyMessage.java MobyObject.java MobyParameter.java MobySimple.java ServiceNotes.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/message AbstractMobyElement.java,NONE,1.1 AbstractMobyObject.java,NONE,1.1 AnyMobyObject.java,NONE,1.1 CrossReference.java,NONE,1.1 MobyCollection.java,NONE,1.1 MobyContent.java,NONE,1.1 MobyData.java,NONE,1.1 MobyDataElement.java,NONE,1.1 MobyException.java,NONE,1.1 MobyExceptions.java,NONE,1.1 MobyMessage.java,NONE,1.1 MobyObject.java,NONE,1.1 MobyParameter.java,NONE,1.1 MobySimple.java,NONE,1.1 ServiceNotes.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89Jlmi9005302@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/central/factory/jaxb Added Files: JAXBMobyCentralImpl.java MobyCentralServiceImpl.java MobyRegistryEndpoint.java ModelConverter.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/central/factory/jaxb JAXBMobyCentralImpl.java,NONE,1.1 MobyCentralServiceImpl.java,NONE,1.1 MobyRegistryEndpoint.java,NONE,1.1 ModelConverter.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlneW005424@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/wsrf/fault Added Files: InvalidQueryExpressionFault.java InvalidResourcePropertyQNameFault.java QueryEvaluationErrorFault.java ResourceNotDestroyedFault.java ResourceUnavailableFault.java ResourceUnknownFault.java UnknownQueryExpressionDialectFault.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/fault InvalidQueryExpressionFault.java,NONE,1.1 InvalidResourcePropertyQNameFault.java,NONE,1.1 QueryEvaluationErrorFault.java,NONE,1.1 ResourceNotDestroyedFault.java,NONE,1.1 ResourceUnavailableFault.java,NONE,1.1 ResourceUnknownFault.java,NONE,1.1 UnknownQueryExpressionDialectFault.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:49 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:49 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlnNk005444@dev.open-bio.org> drepchevski Wed Sep 9 15:47:49 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/lsae In directory dev.open-bio.org:/tmp/cvs-serv5237/lsae Added Files: AnalysisEvent.java Event.java HeartbeatProgress.java PercentProgress.java StateChanged.java StepProgress.java TimeProgress.java jaxb.index Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/lsae AnalysisEvent.java,NONE,1.1 Event.java,NONE,1.1 HeartbeatProgress.java,NONE,1.1 PercentProgress.java,NONE,1.1 StateChanged.java,NONE,1.1 StepProgress.java,NONE,1.1 TimeProgress.java,NONE,1.1 jaxb.index,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:48 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JlmsE005356@dev.open-bio.org> drepchevski Wed Sep 9 15:47:48 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/datatypes In directory dev.open-bio.org:/tmp/cvs-serv5237/biomoby/shared/datatypes Added Files: MobyBinary.java MobyBoolean.java MobyDateTime.java MobyFloat.java MobyInteger.java MobyPrimitive.java MobyString.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/biomoby/shared/datatypes MobyBinary.java,NONE,1.1 MobyBoolean.java,NONE,1.1 MobyDateTime.java,NONE,1.1 MobyFloat.java,NONE,1.1 MobyInteger.java,NONE,1.1 MobyPrimitive.java,NONE,1.1 MobyString.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:56 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JluEe005487@dev.open-bio.org> drepchevski Wed Sep 9 15:47:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/bf2 In directory dev.open-bio.org:/tmp/cvs-serv5456/bf2 Added Files: BaseFaultType.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/wsrf/bf2 BaseFaultType.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:56 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89Jluws005519@dev.open-bio.org> drepchevski Wed Sep 9 15:47:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rl2 In directory dev.open-bio.org:/tmp/cvs-serv5456/rl2 Added Files: ResourceNotDestroyedFaultType.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/wsrf/rl2 ResourceNotDestroyedFaultType.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:56 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JluOg005501@dev.open-bio.org> drepchevski Wed Sep 9 15:47:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/r2 In directory dev.open-bio.org:/tmp/cvs-serv5456/r2 Added Files: ResourceUnavailableFaultType.java ResourceUnknownFaultType.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/wsrf/r2 ResourceUnavailableFaultType.java,NONE,1.1 ResourceUnknownFaultType.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 19:47:56 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 15:47:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909091947.n89JluaP005535@dev.open-bio.org> drepchevski Wed Sep 9 15:47:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/inb/wsrf/rp2 In directory dev.open-bio.org:/tmp/cvs-serv5456/rp2 Added Files: GetMultipleResourceProperties.java GetMultipleResourcePropertiesResponse.java GetResourcePropertyResponse.java InvalidQueryExpressionFaultType.java InvalidResourcePropertyQNameFaultType.java QueryEvaluationErrorFaultType.java QueryExpressionType.java QueryResourceProperties.java QueryResourcePropertiesResponse.java UnknownQueryExpressionDialectFaultType.java jaxb.index package-info.java Log Message: MobyCore and MobyCentral source code upload moby-live/Java/src/main/org/inb/wsrf/rp2 GetMultipleResourceProperties.java,NONE,1.1 GetMultipleResourcePropertiesResponse.java,NONE,1.1 GetResourcePropertyResponse.java,NONE,1.1 InvalidQueryExpressionFaultType.java,NONE,1.1 InvalidResourcePropertyQNameFaultType.java,NONE,1.1 QueryEvaluationErrorFaultType.java,NONE,1.1 QueryExpressionType.java,NONE,1.1 QueryResourceProperties.java,NONE,1.1 QueryResourcePropertiesResponse.java,NONE,1.1 UnknownQueryExpressionDialectFaultType.java,NONE,1.1 jaxb.index,NONE,1.1 package-info.java,NONE,1.1 From drepchevski at dev.open-bio.org Wed Sep 9 21:35:21 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Wed, 9 Sep 2009 17:35:21 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909092135.n89LZLxm006007@dev.open-bio.org> drepchevski Wed Sep 9 17:35:21 EDT 2009 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv5972 Modified Files: inbMoby.xml Log Message: minor modifications... still has issues moby-live/Java/xmls inbMoby.xml,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/inbMoby.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/xmls/inbMoby.xml 2009/09/09 19:48:00 1.1 +++ /home/repository/moby/moby-live/Java/xmls/inbMoby.xml 2009/09/09 21:35:21 1.2 @@ -33,7 +33,7 @@ - @@ -85,13 +85,14 @@ + excludes="org/inb/biomoby/shared/*"> From drepchevski at dev.open-bio.org Fri Sep 11 06:55:25 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Fri, 11 Sep 2009 02:55:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909110655.n8B6tPgT017139@dev.open-bio.org> drepchevski Fri Sep 11 02:55:24 EDT 2009 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv17104 Modified Files: inbMoby.xml Log Message: fixed an issue with java6 (javac) moby-live/Java/xmls inbMoby.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/inbMoby.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/inbMoby.xml 2009/09/09 21:35:21 1.2 +++ /home/repository/moby/moby-live/Java/xmls/inbMoby.xml 2009/09/11 06:55:24 1.3 @@ -83,6 +83,7 @@ + + From drepchevski at dev.open-bio.org Tue Sep 15 17:16:51 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 15 Sep 2009 13:16:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909151716.n8FHGphl021278@dev.open-bio.org> drepchevski Tue Sep 15 13:16:50 EDT 2009 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv21247 Added Files: inb_moby.html Log Message: initial INB BioMoby documentation upload moby-live/Java/docs inb_moby.html,NONE,1.1 From drepchevski at dev.open-bio.org Tue Sep 15 17:17:43 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 15 Sep 2009 13:17:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909151717.n8FHHhYf021317@dev.open-bio.org> drepchevski Tue Sep 15 13:17:43 EDT 2009 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv21286 Added Files: inb_moby_core.html Log Message: initial INB BioMoby documentation upload moby-live/Java/docs inb_moby_core.html,NONE,1.1 From drepchevski at dev.open-bio.org Tue Sep 15 17:18:23 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Tue, 15 Sep 2009 13:18:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909151718.n8FHINP4021376@dev.open-bio.org> drepchevski Tue Sep 15 13:18:23 EDT 2009 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv21345 Added Files: inb_moby_central.html Log Message: initial INB BioMoby documentation upload moby-live/Java/docs inb_moby_central.html,NONE,1.1 From drepchevski at dev.open-bio.org Mon Sep 21 16:31:18 2009 From: drepchevski at dev.open-bio.org (Dmitry Repchevski) Date: Mon, 21 Sep 2009 12:31:18 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909211631.n8LGVIsZ019566@dev.open-bio.org> drepchevski Mon Sep 21 12:31:17 EDT 2009 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv19531 Modified Files: inb_moby_core.html Log Message: fixed an error in async example moby-live/Java/docs inb_moby_core.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/inb_moby_core.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/inb_moby_core.html 2009/09/15 17:17:43 1.1 +++ /home/repository/moby/moby-live/Java/docs/inb_moby_core.html 2009/09/21 16:31:17 1.2 @@ -311,7 +311,7 @@ // sequence.setSequenceString(new MobyString("ATCG")): // sequence.setLength(new MobyInteger(4)); -AnyMobyObject sequence = new AnyMobyObject("AminoAcidSequece"); +AnyMobyObject sequence = new AnyMobyObject("AminoAcidSequence"); sequence.putAttribute("SequenceString", new MobyString("ATCG")); sequence.putAttribute("Length", new MobyInteger(4)); From jmrc at dev.open-bio.org Tue Sep 22 15:55:43 2009 From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco) Date: Tue, 22 Sep 2009 11:55:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200909221555.n8MFthOf030941@dev.open-bio.org> jmrc Tue Sep 22 11:55:42 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async In directory dev.open-bio.org:/tmp/cvs-serv30812 Modified Files: SimpleServer.pm Log Message: A couple of bugfixes from Dmitry and Romina from INB. * One of the bugs is related to huge input messages, which are inspected in depth where only a one level check is needed. * The second one is a fix to avoid a serialization bug from XML::LibXML, which does not generate serialization for implicit namespace nodes inherited from ancestors. moby-live/Perl/MOBY-Server/lib/MOBY/Async SimpleServer.pm,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.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/Async/SimpleServer.pm 2008/09/02 13:10:26 1.4 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Async/SimpleServer.pm 2009/09/22 15:55:42 1.5 @@ -180,9 +180,12 @@ my $auth = $mobyContent->getAttribute('authority') || $mobyContent->getAttributeNS($WSRF::Constants::MOBY_MESSAGE_NS,'authority'); # 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')); + my @mobyData = ($mobyContent->getChildrenByTagNameNS($WSRF::Constants::MOBY_MESSAGE_NS,'mobyData')); foreach my $mobyData (@mobyData) { + # This line avoids a serialization bug in XML::LibXML, which probably + # is inherited from libxml2 + $mobyData->setNamespace($WSRF::Constants::MOBY_MESSAGE_NS, $mobyData->prefix(), 0); my $queryID = $mobyData->getAttribute('queryID') || $mobyData->getAttributeNS($WSRF::Constants::MOBY_MESSAGE_NS,'queryID'); my $property_pid = "pid_$queryID"; my $property_input = "input_$queryID";