[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Mon Jul 7 16:50:25 UTC 2008
kawas
Mon Jul 7 12:50:25 EDT 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv6721/Perl/MOBY-Server/lib/MOBY
Modified Files:
secondary_input.pm collection_input.pm collection_output.pm
simple_input.pm service_type.pm simple_output.pm authority.pm
Log Message:
fixed the perldoc for the synopsis and in some cases formatted the code.
moby-live/Perl/MOBY-Server/lib/MOBY secondary_input.pm,1.1,1.2 collection_input.pm,1.2,1.3 collection_output.pm,1.1,1.2 simple_input.pm,1.1,1.2 service_type.pm,1.1,1.2 simple_output.pm,1.1,1.2 authority.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/secondary_input.pm 2008/07/07 16:50:25 1.2
@@ -12,14 +12,15 @@
=head1 SYNOPSIS
-NON FUNCTIONAL AT THIS TIME
+ NON FUNCTIONAL AT THIS TIME
+
use MOBY::secondary_input;
- my $Instance = MOBY::secondary_input->new(
- object_type => "Sequence",
- namespaces => ["genbank/gi", "genbank/Acc"],
- article_name => "InputSequenceThingy",
- )
+ my $Instance = MOBY::secondary_input->new(
+ object_type => "Sequence",
+ namespaces => ["genbank/gi", "genbank/Acc"],
+ article_name => "InputSequenceThingy",
+ );
=cut
@@ -42,17 +43,17 @@
#ATTRIBUTES
my %_attr_data = # DEFAULT ACCESSIBILITY
(
- secondary_input_id => [ undef, 'read/write' ],
- default_value => [ undef, 'read/write' ],
- maximum_value => [ undef, 'read/write' ],
- minimum_value => [ undef, 'read/write' ],
- enum_value => [ undef, 'read/write' ],
- datatype => [ undef, 'read/write' ],
- article_name => [ undef, 'read/write' ],
- service_instance_id => [ undef, 'read/write' ],
- service_instance_lsid => [ undef, 'read/write' ],
- dbh => [ undef, 'read/write' ],
- description => [undef, 'read/write'],
+ secondary_input_id => [ undef, 'read/write' ],
+ default_value => [ undef, 'read/write' ],
+ maximum_value => [ undef, 'read/write' ],
+ minimum_value => [ undef, 'read/write' ],
+ enum_value => [ undef, 'read/write' ],
+ datatype => [ undef, 'read/write' ],
+ article_name => [ undef, 'read/write' ],
+ service_instance_id => [ undef, 'read/write' ],
+ service_instance_lsid => [ undef, 'read/write' ],
+ dbh => [ undef, 'read/write' ],
+ description => [ undef, 'read/write' ],
);
#_____________________________________________________________
@@ -118,15 +119,17 @@
$CONFIG ||= MOBY::Config->new; # exported by Config.pm
my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
my $dbh = $self->dbh;
- my $insertid = $adaptor->insert_secondary_input(default_value => $self->default_value,
- maximum_value => $self->maximum_value,
- minimum_value => $self->minimum_value,
- enum_value => $self->enum_value,
- datatype => $self->datatype,
- article_name => $self->article_name,
- service_instance_lsid => $self->service_instance_lsid,
- description => $self->description);
-
+ my $insertid = $adaptor->insert_secondary_input(
+ default_value => $self->default_value,
+ maximum_value => $self->maximum_value,
+ minimum_value => $self->minimum_value,
+ enum_value => $self->enum_value,
+ datatype => $self->datatype,
+ article_name => $self->article_name,
+ service_instance_lsid => $self->service_instance_lsid,
+ description => $self->description
+ );
+
return $insertid;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm 2008/02/21 17:54:56 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_input.pm 2008/07/07 16:50:25 1.3
@@ -11,14 +11,14 @@
=head1 SYNOPSIS
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
use MOBY::collection_input;
my $Instance = MOBY::collection_input->new(
object_type => "Sequence",
namespaces => ["genbank/gi", "genbank/Acc"],
article_name => "InputSequenceThingy",
- )
+ );
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/collection_output.pm 2008/07/07 16:50:25 1.2
@@ -12,13 +12,14 @@
=head1 SYNOPSIS
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
+
use MOBY::collection_output;
my $Instance = MOBY::collection_output->new(
object_type => "Sequence",
namespaces => ["genbank/gi", "genbank/Acc"],
article_name => "InputSequenceThingy",
- )
+ );
=cut
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_input.pm 2008/07/07 16:50:25 1.2
@@ -12,14 +12,14 @@
=head1 SYNOPSIS
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
use MOBY::simple_input;
my $Instance = MOBY::simple_input->new(
object_type => "Sequence",
namespaces => ["genbank/gi", "genbank/Acc"],
article_name => "InputSequenceThingy",
- )
+ );
print $Instance->simple_input_id;
print $Instance->service_instance_id;
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/service_type.pm 2008/07/07 16:50:25 1.2
@@ -15,7 +15,7 @@
my $Instance = MOBY::service_type->new(
rdf_definition => "URI:LSID:www.biomoby.org:services:Blast",
name "Blast",
- )
+ );
print $Instance->service_type_id;
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/simple_output.pm 2008/07/07 16:50:25 1.2
@@ -12,13 +12,14 @@
=head1 SYNOPSIS
-NON FUNCTIONAL AT THIS TIME
+ #NON FUNCTIONAL AT THIS TIME
+
use MOBY::simple_output;
my $Instance = MOBY::simple_output->new(
object_type => "Sequence",
namespaces => ["genbank/gi", "genbank/Acc"],
article_name => "InputSequenceThingy",
- )
+ );
print $Instance->simple_output_id;
print $Instance->service_instance_id;
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm 2008/02/21 00:21:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/authority.pm 2008/07/07 16:50:25 1.2
@@ -18,7 +18,7 @@
authority_uri => "ncbi.nlm.nih.gov",
contact_email => "mr.BIG at ncbi.nlm.nih.gov",
- )
+ );
print $Instance->authority_id;
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