[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Sun Dec 28 20:41:59 UTC 2003
mwilkinson
Sun Dec 28 15:41:59 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv9318/MOBY
Modified Files:
Central.pm CommonSubs.pm OntologyServer.pm simple_input.pm
Log Message:
making MOBY Central case-sensitive for LSIDs. I might have missed a few places. please let me know if you find any.
moby-live/Perl/MOBY Central.pm,1.119,1.120 CommonSubs.pm,1.38,1.39 OntologyServer.pm,1.30,1.31 simple_input.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.119
retrieving revision 1.120
diff -u -r1.119 -r1.120
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/27 15:12:31 1.119
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2003/12/28 20:41:59 1.120
@@ -758,7 +758,7 @@
my $dbh = MOBY::central_db_connection->new->dbh;
- my $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where namespace_type_uris like '%$existingURI%'");
+ my $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where INSTR(namespace_type_uris,'$existingURI')");
$sth->execute;
while (my ($id, $ns) = $sth->fetchrow_array()){
my @nss = split ",", $ns;
@@ -768,7 +768,7 @@
}
}
- $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where namespace_type_uris like '%$existingURI%'");
+ $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where INSTR(namespace_type_uris,'$existingURI')");
$sth->execute;
while (my ($id, $ns) = $sth->fetchrow_array()){
my @nss = split ",", $ns;
@@ -778,7 +778,7 @@
}
}
- $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_input natural join simple_input where namespace_type_uris like '%$existingURI%'");
+ $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_input natural join simple_input where INSTR(namespace_type_uris, '$existingURI')");
$sth->execute;
while (my ($id, $ns) = $sth->fetchrow_array()){
my @nss = split ",", $ns;
@@ -788,7 +788,7 @@
}
}
- $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_output natural join simple_output where namespace_type_uris like '%$existingURI%'");
+ $sth = $dbh->prepare("select service_instance.service_instance_id, namespace_type_uris from service_instance natural join collection_output natural join simple_output where INSTR(namespace_type_uris, '$existingURI')");
$sth->execute;
while (my ($id, $ns) = $sth->fetchrow_array()){
my @nss = split ",", $ns;
@@ -1699,7 +1699,7 @@
my $nsquery;
foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's
- $nsquery .=" OR namespace_type_uris like '%$ns%' ";
+ $nsquery .=" OR INSTR(namespace_type_uris, '$ns') ";
}
if ($nsquery){
$nsquery =~ s/OR//; # just the first
@@ -1754,7 +1754,7 @@
my $nsquery;
foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's
- $nsquery .=" OR namespace_type_uris like '%$ns%' ";
+ $nsquery .=" OR INSTR(namespace_type_uris, '$ns') ";
}
if ($nsquery){
$nsquery =~ s/^\sOR//; # just the first
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.38
retrieving revision 1.39
diff -u -r1.38 -r1.39
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/27 20:24:52 1.38
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/12/28 20:41:59 1.39
@@ -1074,7 +1074,6 @@
}
-
=head2 whichDeepestParentObject
name : whichDeepestParentObject
@@ -1084,8 +1083,12 @@
args : $CENTRAL - your MOBY::Client::Central object
$queryTerm - the object type I am interested in
\@termlist - the list of object types that I know about
- returns : an ontology term as a scalar, or undef if there
- is no parent of this node in the nodelist
+ returns : an ontology term and LSID as a scalar, or undef if there
+ is no parent of this node in the nodelist.
+ (note that it will only return the term if you give it
+ term names in the @termList. If you give it
+ LSID's in the termList, then both the parameters
+ returned will be LSID's - it doesn't back-translate...)
=cut
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/02 00:23:23 1.30
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm 2003/12/28 20:41:59 1.31
@@ -179,7 +179,7 @@
}
if ($term =~ /^urn\:lsid/){
- $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_lsid = ?");
+ $sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where INSTR(object_lsid, ?)");
} else {
$sth = $self->dbh->prepare("select object_lsid, object_type, description, authority, contact_email from object where object_type = ?");
}
@@ -326,7 +326,7 @@
return (0, "requires both term and ontology arguments\n",'') unless (defined($term) && defined($ont));
my $sth;
if ($term =~ /^urn\:lsid/){
- $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where relationship_lsid = ? and ontology=?");
+ $sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where INSTR(relationship_lsid,?) and ontology=?");
} else {
$sth = $self->dbh->prepare("select relationship_lsid, relationship_type, description, authority, contact_email from relationship where relationship_type = ? and ontology=?");
}
@@ -433,7 +433,7 @@
my $sth;
if ($term =~ /^urn\:lsid/){
- $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_lsid = ?");
+ $sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where INSTR(service_lsid, ?)");
} else {
$sth = $self->dbh->prepare("select service_id, service_type, service_lsid, description, authority, contact_email from service where service_type = ?");
}
@@ -545,7 +545,7 @@
}
if ($term =~ /^urn:lsid:biomoby.org:namespacetype/){
- $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid = ?");
+ $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where INSTR(namespace_lsid, ?)");
} else {
$sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_type = ?");
}
@@ -691,7 +691,7 @@
sub getObjectCommonName {
my ($self, $URI) = @_;
return undef unless $URI =~ /urn\:lsid/;
- my ($name) = $self->dbh->selectrow_array(q{select object_type from object where object_id = ?}, undef, $URI);
+ my ($name) = $self->dbh->selectrow_array(q{select object_type from object where object_lsid = ?}, undef, $URI);
return $name?$name:$URI;
}
@@ -702,7 +702,7 @@
sub getNamespaceCommonName {
my ($self, $URI) = @_;
return undef unless $URI =~ /urn\:lsid/;
- my ($name) = $self->dbh->selectrow_array(q{select namespace_type from namespace where namespace_id = ?}, undef, $URI);
+ my ($name) = $self->dbh->selectrow_array(q{select namespace_type from namespace where namespace_lsid = ?}, undef, $URI);
return $name?$name:$URI;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/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/simple_input.pm 2003/05/07 19:20:27 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_input.pm 2003/12/28 20:41:59 1.2
@@ -14,7 +14,7 @@
=head1 SYNOPSIS
- use MOBY::authority;
+ use MOBY::simple_input;
my $Instance = MOBY::simple_input->new(
object_type => "Sequence",
namespaces => ["genbank/gi", "genbank/Acc"],
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