mysql, duplicate entry error with unknown character: �

pwd_pwd_omg_pwd · 02-06-2009, 09:45 AM

Im running a pipeline (est2uni) which does some analysis and then puts the output into a mysql database. the database structure is already produced from a sql file they supplied, so that is correct but im getting the error:

Quote:

DBD::mysql::st execute failed: Duplicate entry �' for key 1 at /usr/local/bioinf/est2uni/perl/pipe_db.pm line 1153.

I know that duplicate entry would usually be resolved by an auto increment function, but i need the id's that it imports to stay the same, and I have no idea what the � is supposed to represent

Heres the point where its reading in the .pm :

Code:

        #should we clean previous clones?
        my $clean=read_config($config,'do_clean_db','');
        if ($clean){
                #rflp table should be completely cleanned
                my @tables=($table);
                clean_tables($config,@tables) or return 0;
        }

        my $only_clean = read_config($config,'only_clean','');
        if (!$only_clean){
                #we assume that there is no previuos clone info in the database
                my $st="INSERT INTO $table (name,library) VALUES (?,?);";
                $sth=prepare_st($dbh,$st);

                foreach my $clone (keys %clone_info){
                        $sth->bind_param(1,$clone);
                        if ($clone_info{$clone} eq 'none'){
                                $clone_info{$clone}=undef;
                        }
                        $sth->bind_param(2,$clone_info{$clone});
                        $sth->execute or return 0;

with the last line being 1153 which it refers to.

Ill be thankfull for any help. been stuck on this for a while. (and ive just put the RAM up from 1gb to 4gb today so i want to get it whirring!)

Dan

rylan76 · 02-09-2009, 05:31 AM

Hmm doesn't that error mean that somewhere a query like this is trying to execute:

Code:

insert into whatever set id = ,;

??

This is invalid SQL, as far as I know.... what type of column is the ID column?

pwd_pwd_omg_pwd · 02-11-2009, 04:38 AM

Ive figured out the problem now guys. It was a duplication, but it was trying to put in the alphabetic files and the chromatogram (images) files too so it just buggered it up royaly. Now all i have to do is get it to take the files but thats for another day!