[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Mon Jul 25 17:50:02 UTC 2005
mwilkinson
Mon Jul 25 13:50:02 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv20439/MOBY
Modified Files:
Central.pm collection_input.pm
Log Message:
changing the adaptor API to be more perlish. No longer passing a list of hashes, just a hash
moby-live/Perl/MOBY Central.pm,1.178,1.179 collection_input.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.178
retrieving revision 1.179
diff -u -r1.178 -r1.179
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2005/07/22 23:20:26 1.178
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2005/07/25 17:50:02 1.179
@@ -3100,120 +3100,120 @@
return "<GETstring><![CDATA[$sprintf]]></GETstring>";
}
-=head2 _traverseServiceDAG
-
- Title : _traverseServiceDAG
- Usage : @valid = $MOBY->_traverseServiceDAG($dbh, $serviceType, $sth_hash)
- Function : starting from $serviceType, find all child services non-redundantly
- by traversing the DAG.
- Returns : list of Service.id database entries.
- Args : none
-
-=cut
-
-sub _traverseServiceDAG {
-
- $CONFIG ||= MOBY::Config->new; # exported by Config.pm
- my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
-
- my ( $dbh, $serviceType, $sth_hash ) = @_;
- my %sth = %{$sth_hash};
- my %ServiceIDs;
-
- my $result = $adaptor->general_query({statement => $sth{get_service_type_id}}, {bind_values => [$serviceType]});
- my $row = shift(@$result);
- my ($root_id) = @$row;
- return undef unless $root_id;
-
-# we have to do a traversal of the DAG here to get all child nodes...
-# this is one UGLY piece of code written in a hurry! Please, someone, shoot it and put it out of its misery...
- $ServiceIDs{$root_id} = "untested"; # mark the one in-hand as untested
- while ( grep /untested/, ( values %ServiceIDs ) )
- { # now, while there are untested services in our list...
- foreach my $service ( keys %ServiceIDs )
- { # start parsing through the list
- next
- if ( $ServiceIDs{$service} eq "tested" )
- ; # if it has been tested already then move on
-
- my $result = $adaptor->general_query({statement => $sth{get_service_hierarchy_list}}, {bind_values => [$service]} );
- # execute the query for child nodes
- $ServiceIDs{$service} = "tested"; # mark it as tested
- foreach my $row (@$result)
- { # now get each of the child nodes
- my $new = @$row;
- next
- if ( defined $ServiceIDs{$new} )
- ; # if we have already heard about it then move on
- $ServiceIDs{$new} = "untested"
- ; #otherwise mark it as untested, and start all over again
- }
- }
- }
- return keys %ServiceIDs;
-}
-
-=head2 _traverseObjectDAG
-
- Title : _traverseObjectDAG
- Usage : @valid = $MOBY->_traverseObjectDAG( $dbh, $objectType, $sth_hash, "p|c")
- Function : from $objectType, find all parent/child objects non-redundantly
- by traversing the DAG.
- Returns : list of Object.id database entries.
- Args : objectType (by name), $statement ahngles, "p" parent, or "c" child
-
-=cut
-
-sub _traverseObjectDAG {
- $CONFIG ||= MOBY::Config->new; # exported by Config.pm
- my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
-
- my ( $dbh, $objectType, $sth_hash, $dir ) = @_;
- my %sth = %{$sth_hash};
- my %ObjectIDs;
-
- my $result = $adaptor->general_query({statement => $sth{get_object_type_id}}, {bind_values => [$objectType]});
-
- my $row = shift (@$result);
- my ($root_id) = @$row;
- return undef unless $root_id;
-
-# we have to do a traversal of the DAG here to get all child nodes...
-# this is one UGLY piece of code written in a hurry! Please, someone, shoot it and put it out of its misery...
- $ObjectIDs{$root_id} = "untested"; # mark the one in-hand as untested
- while ( grep /untested/, ( values %ObjectIDs ) )
- { # now, while there are untested services in our list...
- foreach my $object ( keys %ObjectIDs )
- { # start parsing through the list
- next
- if ( $ObjectIDs{$object} eq "tested" )
- ; # if it has been tested already then move on
-
- my $result;
- if ( $dir eq "p" ) {
- $debug && &_LOG("getting parents");
- $result = $adaptor->general_query({statement => $sth{get_object_parent_list}}, {bind_values => [$object]});
- }
- else {
- $debug && &_LOG("getting children");
- $result = $adaptor->general_query({statement => $sth{get_object_child_list}}, {bind_values => [$object]});
- }
- # execute the query for child nodes
+#=head2 _traverseServiceDAG
+#
+# Title : _traverseServiceDAG
+# Usage : @valid = $MOBY->_traverseServiceDAG($dbh, $serviceType, $sth_hash)
+# Function : starting from $serviceType, find all child services non-redundantly
+# by traversing the DAG.
+# Returns : list of Service.id database entries.
+# Args : none
+#
+#=cut
+#
+#sub _traverseServiceDAG {
+#
+# $CONFIG ||= MOBY::Config->new; # exported by Config.pm
+# my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
+#
+# my ( $dbh, $serviceType, $sth_hash ) = @_;
+# my %sth = %{$sth_hash};
+# my %ServiceIDs;
+#
+# my $result = $adaptor->general_query({statement => $sth{get_service_type_id}}, {bind_values => [$serviceType]});
+# my $row = shift(@$result);
+# my ($root_id) = @$row;
+# return undef unless $root_id;
+#
+## we have to do a traversal of the DAG here to get all child nodes...
+## this is one UGLY piece of code written in a hurry! Please, someone, shoot it and put it out of its misery...
+# $ServiceIDs{$root_id} = "untested"; # mark the one in-hand as untested
+# while ( grep /untested/, ( values %ServiceIDs ) )
+# { # now, while there are untested services in our list...
+# foreach my $service ( keys %ServiceIDs )
+# { # start parsing through the list
+# next
+# if ( $ServiceIDs{$service} eq "tested" )
+# ; # if it has been tested already then move on
+#
+# my $result = $adaptor->general_query({statement => $sth{get_service_hierarchy_list}}, {bind_values => [$service]} );
+# # execute the query for child nodes
+# $ServiceIDs{$service} = "tested"; # mark it as tested
+# foreach my $row (@$result)
+# { # now get each of the child nodes
+# my $new = @$row;
+# next
+# if ( defined $ServiceIDs{$new} )
+# ; # if we have already heard about it then move on
+# $ServiceIDs{$new} = "untested"
+# ; #otherwise mark it as untested, and start all over again
+# }
+# }
+# }
+# return keys %ServiceIDs;
+#}
- $ObjectIDs{$object} = "tested"; # mark it as tested
- foreach my $row (@$result)
- { # now get each of the child nodes
- my $new = @$row;
- next
- if ( defined $ObjectIDs{$new} )
- ; # if we have already heard about it then move on
- $ObjectIDs{$new} = "untested"
- ; #otherwise mark it as untested, and start all over again
- }
- }
- }
- return keys %ObjectIDs;
-}
+#=head2 _traverseObjectDAG
+#
+# Title : _traverseObjectDAG
+# Usage : @valid = $MOBY->_traverseObjectDAG( $dbh, $objectType, $sth_hash, "p|c")
+# Function : from $objectType, find all parent/child objects non-redundantly
+# by traversing the DAG.
+# Returns : list of Object.id database entries.
+# Args : objectType (by name), $statement ahngles, "p" parent, or "c" child
+#
+#=cut
+#
+#sub _traverseObjectDAG {
+# $CONFIG ||= MOBY::Config->new; # exported by Config.pm
+# my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
+#
+# my ( $dbh, $objectType, $sth_hash, $dir ) = @_;
+# my %sth = %{$sth_hash};
+# my %ObjectIDs;
+#
+# my $result = $adaptor->general_query({statement => $sth{get_object_type_id}}, {bind_values => [$objectType]});
+#
+# my $row = shift (@$result);
+# my ($root_id) = @$row;
+# return undef unless $root_id;
+#
+## we have to do a traversal of the DAG here to get all child nodes...
+## this is one UGLY piece of code written in a hurry! Please, someone, shoot it and put it out of its misery...
+# $ObjectIDs{$root_id} = "untested"; # mark the one in-hand as untested
+# while ( grep /untested/, ( values %ObjectIDs ) )
+# { # now, while there are untested services in our list...
+# foreach my $object ( keys %ObjectIDs )
+# { # start parsing through the list
+# next
+# if ( $ObjectIDs{$object} eq "tested" )
+# ; # if it has been tested already then move on
+#
+# my $result;
+# if ( $dir eq "p" ) {
+# $debug && &_LOG("getting parents");
+# $result = $adaptor->general_query({statement => $sth{get_object_parent_list}}, {bind_values => [$object]});
+# }
+# else {
+# $debug && &_LOG("getting children");
+# $result = $adaptor->general_query({statement => $sth{get_object_child_list}}, {bind_values => [$object]});
+# }
+# # execute the query for child nodes
+#
+# $ObjectIDs{$object} = "tested"; # mark it as tested
+# foreach my $row (@$result)
+# { # now get each of the child nodes
+# my $new = @$row;
+# next
+# if ( defined $ObjectIDs{$new} )
+# ; # if we have already heard about it then move on
+# $ObjectIDs{$new} = "untested"
+# ; #otherwise mark it as untested, and start all over again
+# }
+# }
+# }
+# return keys %ObjectIDs;
+#}
#Eddie - converted
sub _nodeTextContent {
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm 2005/07/18 16:53:03 1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/collection_input.pm 2005/07/25 17:50:02 1.5
@@ -94,9 +94,8 @@
my ($self) = @_;
$CONFIG ||= MOBY::Config->new; # exported by Config.pm
my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
- my $id = $adaptor->insert_collection_input(
- {service_instance => $self->service_instance_id},
- {article_name => $self->article_name} );
+ my $id = $adaptor->insert_collection_input(service_instance => $self->service_instance_id,
+ article_name => $self->article_name);
return $id;
}
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