[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/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv21506/MOBY/Adaptor/moby/queryapi
Modified Files:
mysql.pm
Log Message:
more of the same. Pass hashes instead of hashrefs, and avoid passing database ids
moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2005/07/25 20:14:35 1.32
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm 2005/07/25 20:55:35 1.33
@@ -302,9 +302,13 @@
my ($self, %args) = @_;
my $dbh = $self->dbh;
my ($siid) = $self->getSIIDFromLSID($args{service_instance_lsid});
- my $statement = "delete from simple_input where service_instance_lsid = ?";
-
- $dbh->do( $statement, undef,($siid));
+ my ($collid) = $args{collection_input_id};
+ my $statement1; my $statement2;
+ $siid && ($statement1 = "delete from simple_input where service_instance_lsid = ?");
+ $collid && ($statement2 = "delete from simple_input where collection_input_id = ?");
+
+ $siid && ($dbh->do( $statement1, undef,($siid)));
+ $collid && ($dbh->do($statement2, undef,($collid)));
if ($dbh->err){
return (1, $dbh->errstr);
}
@@ -317,7 +321,7 @@
my ($self, %args) = @_;
my $dbh = $self->dbh;
my ($siid) = $self->getSIIDFromLSID($args{service_instance_lsid});
- my $result_ids = $adaptor->query_collection_input(service_instance_lsid => $self->lsid);
+ my $result_ids = $self->query_collection_input(service_instance_lsid => $self->lsid);
my $statement = "delete from simple_input where service_instance_lsid = ?";
@@ -381,86 +385,88 @@
}
+# pass service_instance_id or collection_output_id
sub delete_simple_output{
- my ($self, @args) = @_;
- my $dbh = $self->dbh;
- my $statement = "delete from simple_output ";
- my @bindvalues = ();
- ($statement, @bindvalues) =_add_condition($statement, @args);
- $dbh->do( $statement,
- undef, @bindvalues );
- if ($dbh->err){
- return (1, $dbh->errstr);
- }
- else{
- return 0;
- }
+ my ($self, %args) = @_;
+ my $dbh = $self->dbh;
+ my ($siid) = $self->getSIIDFromLSID($args{service_instance_lsid});
+ my ($collid) = $args{collection_output_id};
+ my $statement1; my $statement2;
+ $siid && ($statement1 = "delete from simple_output where service_instance_lsid = ?");
+ $collid && ($statement2 = "delete from simple_output where collection_input_id = ?");
+
+ $siid && ($dbh->do( $statement1, undef,($siid)));
+ $collid && ($dbh->do($statement2, undef,($collid)));
+ if ($dbh->err){
+ return (1, $dbh->errstr);
+ }
+ else{
+ return 0;
+ }
}
+# pass service_instance_lsid
sub query_secondary_input{
- my ($self, @args) = @_;
- my $dbh = $self->dbh;
-
- my $statement = "select
- secondary_input_id,
- default_value,
- maximum_value,
- minimum_value,
- enum_value,
- datatype,
- article_name,
- service_instance_id
- from secondary_input ";
- my @bindvalues = ();
-
- if (@args > 0)
- {
- ($statement, @bindvalues) =_add_condition($statement, @args);
- }
-
- my $result = do_query($dbh, $statement, @bindvalues);
- return $result;
+ my ($self, %args) = @_;
+ my ($siid) = $self->getSIIDFromLSID($args{service_instance_lsid});
+ my $dbh = $self->dbh;
+
+ my $statement = "select
+ secondary_input_id,
+ default_value,
+ maximum_value,
+ minimum_value,
+ enum_value,
+ datatype,
+ article_name,
+ service_instance_id
+ from secondary_input where service_instance_id = ?";
+ my $result = do_query($dbh, $statement, ($siid));
+ return $result;
}
+# pass default_value, maximum_value minimum_value enum_value datatype article_name service_instance_lsid
sub insert_secondary_input{
- my ($self, @args) = @_;
- my $dbh = $self->dbh;
- $dbh->do(
-q{insert into secondary_input (default_value,maximum_value,minimum_value,enum_value,datatype,article_name,service_instance_id) values (?,?,?,?,?,?,?)},
- undef,
- (
- get_value('default_value', @args), get_value('maximum_value', @args),
- get_value('minimum_value', @args), get_value('enum_value', @args),
- get_value('datatype', @args), get_value('article_name', @args),
- get_value('service_instance_id', @args),
- )
- );
- return $dbh->{mysql_insertid};
+ my ($self, %args) = @_;
+ my ($siid) = $self->getSIIDFromLSID($args{service_instance_lsid});
+ my $dbh = $self->dbh;
+ $dbh->do(q{insert into secondary_input (default_value,maximum_value,minimum_value,enum_value,datatype,article_name,service_instance_id) values (?,?,?,?,?,?,?)},
+ undef,
+ (
+ $args{'default_value'}, $args{'maximum_value'},
+ $args{'minimum_value'}, $args{'enum_value'},
+ $args{'datatype'}, $args{'article_name'},$siid)
+ );
+ return $dbh->{mysql_insertid};
}
+# pass service_instance_lsid
sub delete_secondary_input{
- my ($self, @args) = @_;
- my $dbh = $self->dbh;
- my $statement = "delete from secondary_input ";
- my @bindvalues = ();
- ($statement, @bindvalues) =_add_condition($statement, @args);
- $dbh->do( $statement,
- undef, @bindvalues );
-
- if ($dbh->err){
- return (1, $dbh->errstr);
- }
- else{
- return 0;
- }
+ my ($self, %args) = @_;
+ my ($siid) = $self->getSIIDFromLSID($args{service_instance_lsid});
+ my $dbh = $self->dbh;
+ my $statement = "delete from secondary_input where service_instance_lsid=?";
+
+ $dbh->do( $statement, undef, ($siid));
+ if ($dbh->err){
+ return (1, $dbh->errstr);
+ }
+ else{
+ return 0;
+ }
}
-# query subroutine will selects all rows from object table
-sub query_object
-{
- my ($self, @args) = @_;
- my $dbh = $self->dbh;
-
+
+# receives argument "type", that may be either an LSID or a type term
+sub query_object {
+ my ($self, %args) = @_;
+ my $type = $args{type};
+ my $condition;
+ if ($type =~ /^urn\:lsid/){
+ $condition = "where object_lsid = ?";
+ } else {
+ $condition = "where object_type = ?";
+ }
my $statement = "select
object_id,
object_lsid,
@@ -468,15 +474,10 @@
description,
authority,
contact_email
- from object ";
- my @bindvalues = ();
-
- if (@args > 0)
- {
- ($statement, @bindvalues) =_add_condition($statement, @args);
- }
-
- my $result = do_query($dbh, $statement, @bindvalues);
+ from object $condition";
+
+ my $dbh = $self->dbh;
+ my $result = do_query($dbh, $statement, ($type));
return $result;
}
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