From kawas at dev.open-bio.org Wed May 6 09:46:24 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 6 May 2009 09:46:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905061346.n46DkO8I009247@dev.open-bio.org> kawas Wed May 6 09:46:23 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv9211/MOSES-MOBY Modified Files: Changes Log Message: bug fix: datatype names with a dash in them resulted in the incorrect name being used in the messaging XML moby-live/Perl/MOSES-MOBY Changes,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes 2009/04/16 18:18:25 1.14 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes 2009/05/06 13:46:23 1.15 @@ -6,6 +6,9 @@ incoming message. - bug fix: moses-testing-service.pl was truncating the message sent to an async POST service. + - bug fix: when datatypes contained a dash, they + were inadvertently converted to underscore, + resulting in incorrect typing .89 - The tag MOBY was missing in the async cgi From kawas at dev.open-bio.org Wed May 6 09:46:24 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 6 May 2009 09:46:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905061346.n46DkOML009265@dev.open-bio.org> kawas Wed May 6 09:46:23 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv9211/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Modified Files: datatype.tt Log Message: bug fix: datatype names with a dash in them resulted in the incorrect name being used in the messaging XML moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates datatype.tt,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/datatype.tt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/datatype.tt 2008/02/21 00:12:55 1.3 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/datatype.tt 2009/05/06 13:46:23 1.4 @@ -48,6 +48,17 @@ return $self->SUPER::_attr_prop ($attr_name, $prop_name); } } + +# here we ensure that we set the mobyname (used in XML genesis) +sub init { + my ($self) = shift; + $self->SUPER::init(); + [% IF obj.name %] + $self->mobyname('[% obj.name %]'); + [% END %] + +} + [% IF full_source %] 1; __END__ From kawas at dev.open-bio.org Wed May 6 09:47:31 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 6 May 2009 09:47:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905061347.n46DlVoW009399@dev.open-bio.org> kawas Wed May 6 09:47:31 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv9364/MOSES-MOBY/lib/MOSES/MOBY Modified Files: Async.pm Log Message: moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Async.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm 2009/04/08 20:46:23 1.2 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm 2009/05/06 13:47:31 1.3 @@ -454,6 +454,7 @@ my $ans = ''; foreach my $queryID (@ids) { my $property_status = "result_$queryID"; + # TODO - does the property exist? if not throw error so we dont pass invalid XML $ans .= "<" . $WSRF::WSRP::PropertyNamespaceMap->{$property_status}{prefix} . ":$property_status"; @@ -575,6 +576,8 @@ my $ans = ''; foreach my $queryID (@ids) { my $property_status = "status_$queryID"; + # does our property exist? + # TODO - throw error if property doesnt exist so that we dont pass invalid XML $ans .= "<" . $WSRF::WSRP::PropertyNamespaceMap->{$property_status}{prefix} . ":$property_status"; From mwilkinson at dev.open-bio.org Sat May 16 16:14:48 2009 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Sat, 16 May 2009 16:14:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905162014.n4GKEmSe023333@dev.open-bio.org> mwilkinson Sat May 16 16:14:47 EDT 2009 Update of /home/repository/moby/moby-live/Perl/Accessories In directory dev.open-bio.org:/tmp/cvs-serv23318 Added Files: createGadgets.pl Log Message: adding the gadget creator just to make sure we never lose it moby-live/Perl/Accessories createGadgets.pl,NONE,1.1 From kawas at dev.open-bio.org Tue May 19 17:03:56 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 19 May 2009 17:03:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905192103.n4JL3uQK015830@dev.open-bio.org> kawas Tue May 19 17:03:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv15795/src/main/org/biomoby/service/dashboard Modified Files: RegistrationServiceSubPanel.java Log Message: added the CGI/CGI-ASYNC services for a demo later this week. moby-live/Java/src/main/org/biomoby/service/dashboard RegistrationServiceSubPanel.java,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistrationServiceSubPanel.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistrationServiceSubPanel.java 2008/03/02 12:45:26 1.13 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistrationServiceSubPanel.java 2009/05/19 21:03:56 1.14 @@ -111,7 +111,9 @@ MobyService.CATEGORY_MOBY, MobyService.CATEGORY_MOBY_ASYNC, MobyService.CATEGORY_MOBY_DOCLIT, - MobyService.CATEGORY_MOBY_DOCLIT_ASYNC + MobyService.CATEGORY_MOBY_DOCLIT_ASYNC, + MobyService.CATEGORY_CGI, + MobyService.CATEGORY_CGI_ASYNC }); sCategories.setToolTipText ("What kind of BioMoby service you wish to register"); sCategories.setSelectedItem (getPrefValue (DP_REG_S_CATEGORY, From kawas at dev.open-bio.org Tue May 19 17:03:56 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 19 May 2009 17:03:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905192103.n4JL3u3V015850@dev.open-bio.org> kawas Tue May 19 17:03:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv15795/src/main/org/biomoby/shared Modified Files: MobyService.java Log Message: added the CGI/CGI-ASYNC services for a demo later this week. moby-live/Java/src/main/org/biomoby/shared MobyService.java,1.27,1.28 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v retrieving revision 1.27 retrieving revision 1.28 diff -u -r1.27 -r1.28 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2009/01/29 19:12:39 1.27 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2009/05/19 21:03:56 1.28 @@ -68,7 +68,13 @@ /** Name of a category for asynchornous BioMoby services. */ public static final String CATEGORY_MOBY_ASYNC = "moby-async"; - + + /** Name of a category for CGI BioMoby services. */ + public static final String CATEGORY_CGI = "cgi"; + + /** Name of an asynchronous CGI category for BioMoby services. */ + public static final String CATEGORY_CGI_ASYNC = "cgi-async"; + /** Name of a category for document/literal BioMoby services. */ public static final String CATEGORY_MOBY_DOCLIT = "doc-literal"; From kawas at dev.open-bio.org Fri May 22 12:38:39 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 May 2009 12:38:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905221638.n4MGcd8d006751@dev.open-bio.org> kawas Fri May 22 12:38:38 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv6712/MOBY-Client Modified Files: Makefile.PL Changes Log Message: updated dependency versions moby-live/Perl/MOBY-Client Makefile.PL,1.12,1.13 Changes,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/01/28 17:29:19 1.12 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/05/22 16:38:38 1.13 @@ -13,6 +13,7 @@ # MOBY::Client::* depends requires 'SOAP::Lite' => '0.60'; +requires 'XML::LibXML::Common' => '0.13'; requires 'XML::LibXML' => 0; requires 'LWP::UserAgent' => 0; requires 'CGI' => 0; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/04/03 17:01:30 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/05/22 16:38:38 1.9 @@ -1,5 +1,8 @@ Revision history for MOBY-Client +1.05 + * Updated the Makefile.PL to handle some missing dependencies. + 1.04 * Fix bug in CollectionArticle, SimpleInput, SecondaryArticle, and SimpleArticle that caused objects created to have 'memory'. From kawas at dev.open-bio.org Fri May 22 12:38:39 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 May 2009 12:38:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905221638.n4MGcd1o006775@dev.open-bio.org> kawas Fri May 22 12:38:39 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv6712/MOSES-MOBY Modified Files: Changes Makefile.PL Log Message: updated dependency versions moby-live/Perl/MOSES-MOBY Changes,1.15,1.16 Makefile.PL,1.16,1.17 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes 2009/05/06 13:46:23 1.15 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes 2009/05/22 16:38:39 1.16 @@ -1,5 +1,8 @@ Revision history for Perl extension MOSES::MOBY. +0.91 + - Updated the Makefile.PL to handle some missing + dependencies. .90 - bug fix: when sending data with newlines on a WinOS, \r was causing problems with the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL 2009/04/20 14:32:55 1.16 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL 2009/05/22 16:38:39 1.17 @@ -13,21 +13,22 @@ all_from 'lib/MOSES/MOBY.pm'; # Specific dependencies - requires 'Carp' => 0; - requires 'CGI' => 0; - requires 'File::Spec' => 0.80; - requires 'SOAP::Lite' => 0.69; - requires 'XML::LibXML' => 1.62; - requires 'Log::Log4perl' => 1.12; - requires 'Template' => 1.11; - requires 'Config::Simple' => 4.58; - requires 'IO::String' => 1.08; - requires 'Unicode::String' => 2.09; - requires 'File::HomeDir' => 0.65; - requires 'File::ShareDir' => 0.05; - requires 'Class::Inspector' => 1.17; - requires 'Params::Util' => 0.28; - requires 'HTTP::Date' => 5.81; + requires 'Carp' => 0; + requires 'CGI' => 0; + requires 'File::Spec' => 0.80; + requires 'SOAP::Lite' => 0.69; + requires 'XML::LibXML::Common' => '0.13'; + requires 'XML::LibXML' => 1.62; + requires 'Log::Log4perl' => 1.12; + requires 'Template' => 1.11; + requires 'Config::Simple' => 4.58; + requires 'IO::String' => 1.08; + requires 'Unicode::String' => 2.09; + requires 'File::HomeDir' => 0.65; + requires 'File::ShareDir' => 0.05; + requires 'Class::Inspector' => 1.17; + requires 'Params::Util' => 0.38; + requires 'HTTP::Date' => 5.81; # windows doesn't need this if ( not MSWIN ) { From kawas at dev.open-bio.org Fri May 22 12:38:39 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 May 2009 12:38:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905221638.n4MGcddq006801@dev.open-bio.org> kawas Fri May 22 12:38:39 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv6712/MOBY-Server Modified Files: Changes Makefile.PL Log Message: updated dependency versions moby-live/Perl/MOBY-Server Changes,1.27,1.28 Makefile.PL,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v retrieving revision 1.27 retrieving revision 1.28 diff -u -r1.27 -r1.28 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2009/04/15 17:45:23 1.27 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2009/05/22 16:38:39 1.28 @@ -1,5 +1,9 @@ Revision history for Perl extension MOBY. + +1.11 + - Updated the Makefile.PL to handle some missing dependencies. + 1.10 - Added a RESTful WSDL page to the installation. Basically, you do a GET on BioMobyWSDL/authURI/servicename/ and a WSDL for that service =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2009/04/15 16:38:57 1.18 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2009/05/22 16:38:39 1.19 @@ -13,6 +13,7 @@ requires 'Carp' => '0'; requires 'File::Spec' => '0.80'; requires 'SOAP::Lite' => '0.69'; + requires 'XML::LibXML::Common' => '0.13'; requires 'XML::LibXML' => '1.62'; requires 'IO::Stringy' => '2.110'; requires 'File::HomeDir' => '0.8'; From kawas at dev.open-bio.org Wed May 6 13:46:24 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 6 May 2009 09:46:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905061346.n46DkO8I009247@dev.open-bio.org> kawas Wed May 6 09:46:23 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv9211/MOSES-MOBY Modified Files: Changes Log Message: bug fix: datatype names with a dash in them resulted in the incorrect name being used in the messaging XML moby-live/Perl/MOSES-MOBY Changes,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes 2009/04/16 18:18:25 1.14 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes 2009/05/06 13:46:23 1.15 @@ -6,6 +6,9 @@ incoming message. - bug fix: moses-testing-service.pl was truncating the message sent to an async POST service. + - bug fix: when datatypes contained a dash, they + were inadvertently converted to underscore, + resulting in incorrect typing .89 - The tag MOBY was missing in the async cgi From kawas at dev.open-bio.org Wed May 6 13:46:24 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 6 May 2009 09:46:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905061346.n46DkOML009265@dev.open-bio.org> kawas Wed May 6 09:46:23 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates In directory dev.open-bio.org:/tmp/cvs-serv9211/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates Modified Files: datatype.tt Log Message: bug fix: datatype names with a dash in them resulted in the incorrect name being used in the messaging XML moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates datatype.tt,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/datatype.tt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/datatype.tt 2008/02/21 00:12:55 1.3 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/datatype.tt 2009/05/06 13:46:23 1.4 @@ -48,6 +48,17 @@ return $self->SUPER::_attr_prop ($attr_name, $prop_name); } } + +# here we ensure that we set the mobyname (used in XML genesis) +sub init { + my ($self) = shift; + $self->SUPER::init(); + [% IF obj.name %] + $self->mobyname('[% obj.name %]'); + [% END %] + +} + [% IF full_source %] 1; __END__ From kawas at dev.open-bio.org Wed May 6 13:47:31 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Wed, 6 May 2009 09:47:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905061347.n46DlVoW009399@dev.open-bio.org> kawas Wed May 6 09:47:31 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY In directory dev.open-bio.org:/tmp/cvs-serv9364/MOSES-MOBY/lib/MOSES/MOBY Modified Files: Async.pm Log Message: moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Async.pm,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm 2009/04/08 20:46:23 1.2 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm 2009/05/06 13:47:31 1.3 @@ -454,6 +454,7 @@ my $ans = ''; foreach my $queryID (@ids) { my $property_status = "result_$queryID"; + # TODO - does the property exist? if not throw error so we dont pass invalid XML $ans .= "<" . $WSRF::WSRP::PropertyNamespaceMap->{$property_status}{prefix} . ":$property_status"; @@ -575,6 +576,8 @@ my $ans = ''; foreach my $queryID (@ids) { my $property_status = "status_$queryID"; + # does our property exist? + # TODO - throw error if property doesnt exist so that we dont pass invalid XML $ans .= "<" . $WSRF::WSRP::PropertyNamespaceMap->{$property_status}{prefix} . ":$property_status"; From mwilkinson at dev.open-bio.org Sat May 16 20:14:48 2009 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Sat, 16 May 2009 16:14:48 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905162014.n4GKEmSe023333@dev.open-bio.org> mwilkinson Sat May 16 16:14:47 EDT 2009 Update of /home/repository/moby/moby-live/Perl/Accessories In directory dev.open-bio.org:/tmp/cvs-serv23318 Added Files: createGadgets.pl Log Message: adding the gadget creator just to make sure we never lose it moby-live/Perl/Accessories createGadgets.pl,NONE,1.1 From kawas at dev.open-bio.org Tue May 19 21:03:56 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 19 May 2009 17:03:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905192103.n4JL3uQK015830@dev.open-bio.org> kawas Tue May 19 17:03:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory dev.open-bio.org:/tmp/cvs-serv15795/src/main/org/biomoby/service/dashboard Modified Files: RegistrationServiceSubPanel.java Log Message: added the CGI/CGI-ASYNC services for a demo later this week. moby-live/Java/src/main/org/biomoby/service/dashboard RegistrationServiceSubPanel.java,1.13,1.14 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistrationServiceSubPanel.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistrationServiceSubPanel.java 2008/03/02 12:45:26 1.13 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistrationServiceSubPanel.java 2009/05/19 21:03:56 1.14 @@ -111,7 +111,9 @@ MobyService.CATEGORY_MOBY, MobyService.CATEGORY_MOBY_ASYNC, MobyService.CATEGORY_MOBY_DOCLIT, - MobyService.CATEGORY_MOBY_DOCLIT_ASYNC + MobyService.CATEGORY_MOBY_DOCLIT_ASYNC, + MobyService.CATEGORY_CGI, + MobyService.CATEGORY_CGI_ASYNC }); sCategories.setToolTipText ("What kind of BioMoby service you wish to register"); sCategories.setSelectedItem (getPrefValue (DP_REG_S_CATEGORY, From kawas at dev.open-bio.org Tue May 19 21:03:56 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 19 May 2009 17:03:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905192103.n4JL3u3V015850@dev.open-bio.org> kawas Tue May 19 17:03:56 EDT 2009 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv15795/src/main/org/biomoby/shared Modified Files: MobyService.java Log Message: added the CGI/CGI-ASYNC services for a demo later this week. moby-live/Java/src/main/org/biomoby/shared MobyService.java,1.27,1.28 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v retrieving revision 1.27 retrieving revision 1.28 diff -u -r1.27 -r1.28 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2009/01/29 19:12:39 1.27 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2009/05/19 21:03:56 1.28 @@ -68,7 +68,13 @@ /** Name of a category for asynchornous BioMoby services. */ public static final String CATEGORY_MOBY_ASYNC = "moby-async"; - + + /** Name of a category for CGI BioMoby services. */ + public static final String CATEGORY_CGI = "cgi"; + + /** Name of an asynchronous CGI category for BioMoby services. */ + public static final String CATEGORY_CGI_ASYNC = "cgi-async"; + /** Name of a category for document/literal BioMoby services. */ public static final String CATEGORY_MOBY_DOCLIT = "doc-literal"; From kawas at dev.open-bio.org Fri May 22 16:38:39 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 May 2009 12:38:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905221638.n4MGcd8d006751@dev.open-bio.org> kawas Fri May 22 12:38:38 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Client In directory dev.open-bio.org:/tmp/cvs-serv6712/MOBY-Client Modified Files: Makefile.PL Changes Log Message: updated dependency versions moby-live/Perl/MOBY-Client Makefile.PL,1.12,1.13 Changes,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/01/28 17:29:19 1.12 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Makefile.PL 2009/05/22 16:38:38 1.13 @@ -13,6 +13,7 @@ # MOBY::Client::* depends requires 'SOAP::Lite' => '0.60'; +requires 'XML::LibXML::Common' => '0.13'; requires 'XML::LibXML' => 0; requires 'LWP::UserAgent' => 0; requires 'CGI' => 0; =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/04/03 17:01:30 1.8 +++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes 2009/05/22 16:38:38 1.9 @@ -1,5 +1,8 @@ Revision history for MOBY-Client +1.05 + * Updated the Makefile.PL to handle some missing dependencies. + 1.04 * Fix bug in CollectionArticle, SimpleInput, SecondaryArticle, and SimpleArticle that caused objects created to have 'memory'. From kawas at dev.open-bio.org Fri May 22 16:38:39 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 May 2009 12:38:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905221638.n4MGcd1o006775@dev.open-bio.org> kawas Fri May 22 12:38:39 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY In directory dev.open-bio.org:/tmp/cvs-serv6712/MOSES-MOBY Modified Files: Changes Makefile.PL Log Message: updated dependency versions moby-live/Perl/MOSES-MOBY Changes,1.15,1.16 Makefile.PL,1.16,1.17 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes 2009/05/06 13:46:23 1.15 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes 2009/05/22 16:38:39 1.16 @@ -1,5 +1,8 @@ Revision history for Perl extension MOSES::MOBY. +0.91 + - Updated the Makefile.PL to handle some missing + dependencies. .90 - bug fix: when sending data with newlines on a WinOS, \r was causing problems with the =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL 2009/04/20 14:32:55 1.16 +++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL 2009/05/22 16:38:39 1.17 @@ -13,21 +13,22 @@ all_from 'lib/MOSES/MOBY.pm'; # Specific dependencies - requires 'Carp' => 0; - requires 'CGI' => 0; - requires 'File::Spec' => 0.80; - requires 'SOAP::Lite' => 0.69; - requires 'XML::LibXML' => 1.62; - requires 'Log::Log4perl' => 1.12; - requires 'Template' => 1.11; - requires 'Config::Simple' => 4.58; - requires 'IO::String' => 1.08; - requires 'Unicode::String' => 2.09; - requires 'File::HomeDir' => 0.65; - requires 'File::ShareDir' => 0.05; - requires 'Class::Inspector' => 1.17; - requires 'Params::Util' => 0.28; - requires 'HTTP::Date' => 5.81; + requires 'Carp' => 0; + requires 'CGI' => 0; + requires 'File::Spec' => 0.80; + requires 'SOAP::Lite' => 0.69; + requires 'XML::LibXML::Common' => '0.13'; + requires 'XML::LibXML' => 1.62; + requires 'Log::Log4perl' => 1.12; + requires 'Template' => 1.11; + requires 'Config::Simple' => 4.58; + requires 'IO::String' => 1.08; + requires 'Unicode::String' => 2.09; + requires 'File::HomeDir' => 0.65; + requires 'File::ShareDir' => 0.05; + requires 'Class::Inspector' => 1.17; + requires 'Params::Util' => 0.38; + requires 'HTTP::Date' => 5.81; # windows doesn't need this if ( not MSWIN ) { From kawas at dev.open-bio.org Fri May 22 16:38:39 2009 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Fri, 22 May 2009 12:38:39 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200905221638.n4MGcddq006801@dev.open-bio.org> kawas Fri May 22 12:38:39 EDT 2009 Update of /home/repository/moby/moby-live/Perl/MOBY-Server In directory dev.open-bio.org:/tmp/cvs-serv6712/MOBY-Server Modified Files: Changes Makefile.PL Log Message: updated dependency versions moby-live/Perl/MOBY-Server Changes,1.27,1.28 Makefile.PL,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v retrieving revision 1.27 retrieving revision 1.28 diff -u -r1.27 -r1.28 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2009/04/15 17:45:23 1.27 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes 2009/05/22 16:38:39 1.28 @@ -1,5 +1,9 @@ Revision history for Perl extension MOBY. + +1.11 + - Updated the Makefile.PL to handle some missing dependencies. + 1.10 - Added a RESTful WSDL page to the installation. Basically, you do a GET on BioMobyWSDL/authURI/servicename/ and a WSDL for that service =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2009/04/15 16:38:57 1.18 +++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL 2009/05/22 16:38:39 1.19 @@ -13,6 +13,7 @@ requires 'Carp' => '0'; requires 'File::Spec' => '0.80'; requires 'SOAP::Lite' => '0.69'; + requires 'XML::LibXML::Common' => '0.13'; requires 'XML::LibXML' => '1.62'; requires 'IO::Stringy' => '2.110'; requires 'File::HomeDir' => '0.8';