[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Jul 25 13:50:02 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv20439/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.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/Adaptor/moby/queryapi mysql.pm,1.28,1.29
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/22 20:00:10	1.28
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/25 17:50:02	1.29
@@ -75,25 +75,24 @@
     my $driver = $self->driver;  # inherited from the adaptorI (queryapi)
     my $username = $self->username;
     my $password = $self->password;
-	my $port = $self->port;
-	my $url = $self->url;
-	my $dbname = $self->dbname;
-	
-	my ($dsn) = "$driver:$dbname:$url:$port";
-# print STDERR "\n\nconnectiung to $driver:$dbname:$url:$port\n\n";
-	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
+    my $port = $self->port;
+    my $url = $self->url;
+    my $dbname = $self->dbname;
+    
+    my ($dsn) = "$driver:$dbname:$url:$port";
+    my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
 
 
-	##############################################################
-	unless ($dbh) {
-		print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n";
-		return undef;
-	}
-	
+    ##############################################################
+    unless ($dbh) {
+	    print STDERR "Couldn't connect to the datasource \n",($self->_dump()),"\n\n";
+	    return undef;
+    }
+    
     $self->dbh($dbh);
-	#############################################################
+    #############################################################
 
-	return undef unless $self->dbh;
+    return undef unless $self->dbh;
     return $self;
     
 }
@@ -162,29 +161,23 @@
 	    }
 	}
 }
-
-# general query subroutine
-# parameters: 
-# 	statement - a string SQL statement
-#	bind_values - an array of values to be bound to the parameters
-# returns:
-#	resultset - reference to an array containing ARRAY references
-sub general_query{
-	my ($self, @args) = @_;	
-	my $dbh = $self->dbh;
-	my $statement = get_value('statement', @args);
-	my $sth = $dbh->prepare($statement);
-	if (@args > 1)
-	{
-		my $bindvalues = get_value('bind_values', @args);
-		$sth->execute(@$bindvalues);
-	}
-	else {
-		$sth->execute;
-	}
-	my $result = $sth->fetchall_arrayref();
-	return $result;
-}
+#
+#sub general_query{
+#	my ($self, @args) = @_;	
+#	my $dbh = $self->dbh;
+#	my $statement = get_value('statement', @args);
+#	my $sth = $dbh->prepare($statement);
+#	if (@args > 1)
+#	{
+#		my $bindvalues = get_value('bind_values', @args);
+#		$sth->execute(@$bindvalues);
+#	}
+#	else {
+#		$sth->execute;
+#	}
+#	my $result = $sth->fetchall_arrayref();
+#	return $result;
+#}
 	
 sub query_collection_input{
 	my ($self, @args) = @_;	
@@ -207,15 +200,12 @@
 }
 
 sub insert_collection_input {
-	my ($self, @args) = @_;	
+	my ($self, %args) = @_;	
 	my $dbh = $self->dbh;
-#	if ($self->sourcetype eq "MOBY::Adaptor::moby::queryapi::mysql"){
-		# this should be dropped down into the mysql.pm module??  probably...
 		$self->dbh->do("insert into collection_input (service_instance_id, article_name) values (?,?)", 
-		undef, (get_value('service_instance_id', @args), get_value('article_name', @args)));
+		undef, $args{'service_instance_id'},$args{'article_name'});
 		my $id=$self->dbh->{mysql_insertid};
 		return $id;
-#	}
 }
 
 sub delete_collection_input{