[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Mon Jul 25 20:55:35 UTC 2005
mwilkinson
Mon Jul 25 16:55:35 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv21506/MOBY
Modified Files:
OntologyServer.pm secondary_input.pm service_instance.pm
Log Message:
more of the same. Pass hashes instead of hashrefs, and avoid passing database ids
moby-live/Perl/MOBY OntologyServer.pm,1.54,1.55 secondary_input.pm,1.7,1.8 service_instance.pm,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.54
retrieving revision 1.55
diff -u -r1.54 -r1.55
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2005/07/19 23:37:35 1.54
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2005/07/25 20:55:35 1.55
@@ -192,17 +192,10 @@
my $sth;
return ( 0, "WRONG ONTOLOGY!", '' ) unless ( $self->ontology eq 'object' );
-# if ($term =~ /^urn:lsid/ && !($term =~ /^urn:lsid:biomoby.org:objecttype/)){
-# return (1, "external ontology", $term);
-# }
my $result;
- if ( $term =~ /^urn\:lsid/ ) {
- $result = $adaptor->query_object({object_lsid => $term});
-
- } else {
- $result = $adaptor->query_object({object_type => $term});
-
- }
+
+ $result = $adaptor->query_object(type => $term);
+
my $row = shift(@$result);
my $lsid = $row->{object_lsid};
my $type = $row->{object_type};
@@ -271,12 +264,7 @@
: $self->setURI( $args{'node'} );
unless ($LSID) { return ( 0, "Failed during creation of an LSID", '' ) }
my $result;
- if ( $args{'node'} =~ /^urn\:lsid/ ) {
-
- $result = $adaptor->query_object({object_lsid => $term});
- } else {
- $result = $adaptor->query_object({object_type => $term});
- }
+ $result = $adaptor->query_object(type => $term);
my $row = shift(@$result);
my $lsid = $row->{object_lsid};
my $type = $row->{object_type};
@@ -320,7 +308,7 @@
? $args{'node'}
: $self->getObjectURI($term);
unless ($LSID) { return ( 0, "Failed during creation of an LSID", '' ) }
- my $result = $adaptor->query_object({object_lsid => $LSID});
+ my $result = $adaptor->query_object(type => $LSID);
my $row = shift(@$result);
my $id = $row->{object_id};
my $type = $row->{object_type};
@@ -372,7 +360,7 @@
return ( 0, q{Object type $term cannot be resolved to an LSID}, "" )
unless $LSID;
- my $result = $adaptor->query_object({object_lsid => $LSID});
+ my $result = $adaptor->query_object(type => $LSID);
my $row = shift(@$result);
my $id = $row->{object_id};
my $lsid = $row->{object_lsid};
@@ -471,41 +459,20 @@
my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobyobject' );
return ( 0, "WRONG ONTOLOGY!", '' ) unless ( $self->ontology eq 'object' );
+
my ( $subj_id, $subj_lsid, $obj_id, $obj_lsid );
- if ( $args{subject_node} =~ /^urn:lsid/ ) {
-
- my $result = $adaptor->query_object({object_lsid => $args{subject_node}});
- my $row = shift(@$result);
- $subj_id = $row->{object_id};
- $subj_lsid = $row->{object_lsid};
-
- } else {
- my $result = $adaptor->query_object({object_type => $args{subject_node}});
- my $row = shift(@$result);
- $subj_id = $row->{object_id};
- $subj_lsid = $row->{object_lsid};
-
- }
- return ( 0,
- qq{Object type $args{subject_node} does not exist in the ontology},
- '' )
+ my $result = $adaptor->query_object(type => $args{subject_node});
+ my $row = shift(@$result);
+ $subj_id = $row->{object_id};
+ $subj_lsid = $row->{object_lsid};
+ return ( 0, qq{Object type $args{subject_node} does not exist in the ontology}, '' )
unless defined $subj_id;
- if ( $args{object_node} =~ /^urn:lsid/ ) {
-
- my $result = $adaptor->query_object({object_lsid => $args{object_node}});
- my $row = shift(@$result);
- $obj_id = $row->{object_id};
- $obj_lsid = $row->{object_lsid};
-
- } else {
- my $result = $adaptor->query_object({object_type => $args{object_node}});
- my $row = shift(@$result);
- $obj_id = $row->{object_id};
- $obj_lsid = $row->{object_lsid};
- }
- return ( 0,
- qq{Object type $args{object_node} does not exist in the ontology},
- '' )
+
+ $result = $adaptor->query_object(type => $args{object_node});
+ $row = shift(@$result);
+ $obj_id = $row->{object_id};
+ $obj_lsid = $row->{object_lsid};
+ return ( 0,qq{Object type $args{object_node} does not exist in the ontology},'' )
unless defined $obj_id;
my $isa = $adaptor->query_object_term2term({object2_id => $subj_id});
@@ -967,7 +934,7 @@
$CONFIG ||= MOBY::Config->new; # exported by Config.pm
my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobyobject' );
return undef unless $URI =~ /urn\:lsid/;
- my $result = $adaptor->query_object({object_lsid => $URI});
+ my $result = $adaptor->query_object(type => $URI);
my $row = shift(@$result);
my $name = $row->{object_type};
@@ -1033,7 +1000,7 @@
my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobyobject' );
return $term if $term =~ /urn\:lsid/;
- my $result = $adaptor->query_object({object_type => $term});
+ my $result = $adaptor->query_object(type => $term);
my $row = shift(@$result);
my $id = $row->{object_lsid};
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/secondary_input.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY/secondary_input.pm 2005/07/25 19:53:35 1.7
+++ /home/repository/moby/moby-live/Perl/MOBY/secondary_input.pm 2005/07/25 20:55:35 1.8
@@ -115,13 +115,13 @@
$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_id});
+ 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_id);
return $insertid;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2005/07/25 20:14:34 1.26
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm 2005/07/25 20:55:35 1.27
@@ -269,24 +269,24 @@
# by collecion ID... BAD BAD BAD
$adaptor->delete_service_instance({service_instance_lsid => $self->lsid});
$adaptor->delete_simple_input(service_instance_lsid => $self->lsid);
- $adaptor->delete_simple_output({service_instance_lsid => $self->lsid});
+ $adaptor->delete_simple_output(service_instance_lsid => $self->lsid);
my $result = $adaptor->query_collection_input({service_instance_lsid => $self->lsid});
foreach my $row (@$result) {
my $id = $row->{collection_input_id};
- $adaptor->delete_simple_input({collection_input_id => $id});
+ $adaptor->delete_simple_input(collection_input_id => $id);
}
$result = $adaptor->query_collection_output(service_instance_lsid => $self->lsid);
foreach my $row (@$result) {
my $id = $row->{collection_output_id};
- $adaptor->delete_simple_output({collection_output_id => $id});
+ $adaptor->delete_simple_output(collection_output_id => $id);
}
$adaptor->delete_collection_input(service_instance_lsid => $self->lsid);
$adaptor->delete_collection_output(service_instance_lsid => $self->lsid);
- $adaptor->delete_secondary_input({service_instance_lsid => $self->lsid});
+ $adaptor->delete_secondary_input(service_instance_lsid => $self->lsid);
return 1;
}
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