[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Jul 25 16:14:35 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv21136/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,1.31,1.32
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -r1.31 -r1.32
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/25 19:53:36	1.31
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/25 20:14:35	1.32
@@ -297,15 +297,14 @@
     return $id;
 }
 
+# pass service_instance_lsid
 sub delete_simple_input{
-    my ($self, @args) = @_;	
+    my ($self, %args) = @_;
     my $dbh = $self->dbh;
     my ($siid) = $self->getSIIDFromLSID($args{service_instance_lsid});
-    my $statement = "delete from simple_input ";
-    my @bindvalues = ();
-    ($statement, @bindvalues) =_add_condition($statement, @args); 
-    $dbh->do( $statement,
-		      undef, @bindvalues );
+    my $statement = "delete from simple_input where service_instance_lsid = ?";
+
+    $dbh->do( $statement, undef,($siid));
     if ($dbh->err){
 	    return (1, $dbh->errstr);
     }
@@ -314,50 +313,71 @@
     }			  
 }
 
+sub delete_inputs {  # this should replace all other delete_*_input
+    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 $statement = "delete from simple_input where service_instance_lsid = ?";
+
+    $dbh->do( $statement, undef,($siid));
+    if ($dbh->err){
+	    return (1, $dbh->errstr);
+    }
+    else{
+	    return 0;
+    }			  
+    
+}
+
+sub delete_output {  # this should replace all other delete_*_output
+    
+}
+
+# UGH this has to know too much bout the underlying database structure e.g. that one is null and other is full
+# this problem is in MOBY::Central line 3321 3346 and 3374
+#****** FIX
+# send service_instance_lsid, collection_input_id
 sub query_simple_output{
-	my ($self, @args) = @_;	
-	my $dbh = $self->dbh;
-	
-	my $statement = "select
-          simple_output_id,
-          object_type_uri,
-          namespace_type_uris,
-          article_name,
-          service_instance_id,
-          collection_output_id
-          from simple_output ";
-    my @bindvalues = (); 
-          
-	if  (@args > 0) 
- 	{
- 		($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 $collid = $args{collection_input_id};
+    my $dbh = $self->dbh;
+    
+    my $statement = "select
+      simple_output_id,
+      object_type_uri,
+      namespace_type_uris,
+      article_name,
+      service_instance_id,
+      collection_output_id
+      from simple_output where service_instance_id = ? and collection_input_id= ?";    
+    my $result = do_query($dbh, $statement, ($siid, $collid));
+    return $result;
 }
 
+# pass args service_instance_id and collection_output_id
 sub insert_simple_output {
-	my ($self, @args) = @_;	
-	my $dbh = $self->dbh;
-	my $si = get_value('collection_output_id', @args)?undef:get_value('service_instance_id', @args);
+    my ($self, %args) = @_;	
+    my ($siid) = $self->getSIIDFromLSID($args{service_instance_lsid});
+    my $dbh = $self->dbh;
 
-	$dbh->do("insert into simple_output
-				 (object_type_uri,
-				  namespace_type_uris,
-				  article_name,
-				  service_instance_id,
-				  collection_output_id)
-				 values (?,?,?,?,?)",
-		undef,
-		(get_value('object_type_uri', @args),
-		get_value('namespace_type_uris', @args),
-		get_value('article_name', @args),
-# and here
-        $si,
-		get_value('collection_output_id', @args)));
-	my $id=$dbh->{mysql_insertid};
-	return $id;
+    $dbh->do("insert into simple_output
+			     (object_type_uri,
+			      namespace_type_uris,
+			      article_name,
+			      service_instance_id,
+			      collection_output_id)
+			     values (?,?,?,?,?)",
+	    undef,(
+	    $args{'object_type_uri'},
+	    $args{'namespace_type_uris'},
+	    $args{'article_name'},
+	    $siid,
+	    $args{'collection_output_id'}));
+    my $id=$dbh->{mysql_insertid};
+    return $id;
 
 }