my ($self) = @_;


  foreach my $type (qw(gene transcript translation)){
    
    my $sql = "select s.name, count(*) from source s, xref x, ".$type."_direct_xref gdx left join ".$type."_stable_id gsi on gdx.ensembl_stable_id = gsi.stable_id where s.source_id = x.source_id and x.xref_id = gdx.general_xref_id and gsi.stable_id is null group by s.name";
    
    my $sth = $self->xref->dbc->prepare($sql);
    $sth->execute();
    my ($name, $count);
    $sth->bind_columns(\$name,\$count);
    my $total_count=0;
    while($sth->fetch()){
      print STDERR "WARNING $name has $count invalid stable ids in ".$type."_direct_xrefs\n";
      $total_count += $count;
    }	
    $sth->finish;
    if($total_count){
      print STDERR "USEFUL SQL: $sql\n";
    }
  }

}
1;

  my ($self) = @_;
  

# No point doing xrefs object_xrefs are more important and gives a better indication of wether things went okay.

  my %old_object_xref_count;
  my %new_object_xref_count;

  my $sth = $self->xref->dbc->prepare('select s.name, count(*) from xref x, object_xref ox, source s where ox.xref_id = x.xref_id  and x.source_id = s.source_id and ox_status = "DUMP_OUT" and s.name not like "AFFY%"  group by s.name');
  $sth->execute();
  my ($name, $count);
  $sth->bind_columns(\$name,\$count);
  while($sth->fetch()){
    $new_object_xref_count{$name} = $count;
  }
  $sth->finish;

  
 $sth = $self->core->dbc->prepare('select e.db_name, count(*) from xref x, object_xref ox, external_db e where ox.xref_id = x.xref_id and x.external_db_id = e.external_db_id and e.db_name not like "AFFY%" group by e.db_name');

  $sth->execute();
  $sth->bind_columns(\$name,\$count);
  while($sth->fetch()){
    my $change = 0;
    $old_object_xref_count{$name} = $count;
    if(defined($new_object_xref_count{$name})){
      $change = (($new_object_xref_count{$name} - $count)/$new_object_xref_count{$name}) * 100;
      if($change > 5){ # increase of 5%
	print "WARNING: $name has increased by $change\% was $count now ". $new_object_xref_count{$name}. "\n" if($self->mapper->verbose); 
      }
      elsif($change < -5){ # decrease by 5%
	print "WARNING: $name has decreased by $change\% was $count now ". $new_object_xref_count{$name}. "\n" if($self->mapper->verbose); 
      }
    }
    else{
      print "WARNING: xrefs $name are not in the new database but are in the old???\n" if($self->mapper->verbose);
    }
  }
  $sth->finish;
  
  foreach my $key (keys %new_object_xref_count){
    if(!defined($old_object_xref_count{$key})){
      print "WARNING: $key has ".$new_object_xref_count{$key}." xrefs in the new database but NONE in the old\n" if($self->mapper->verbose);
    }
  }
  
  return;

  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_mapper} = $arg );
  return $self->{_mapper};

  my ($self) = @_;

  my %new_name; # $old_name{$gene_id} = HGNC_%name
  my %id_to_stable_id;

  my $official_name = $self->mapper->get_official_name;
  if(!defined($official_name)){
    return;
  }
#  print "Checking names\n";

  my $sql = 'select x.label, gsi.internal_id, gsi.stable_id from object_xref ox, xref x, gene_stable_id gsi, source s  where x.xref_id = ox.xref_id and ox.ensembl_object_type = "Gene" and gsi.internal_id = ox.ensembl_id and x.source_id = s.source_id and s.name like "'.$official_name.'_%"';

  my $sth = $self->xref->dbc->prepare($sql);
  $sth->execute();
  my ($name, $gene_id, $stable_id);
  $sth->bind_columns(\$name,\$gene_id,\$ stable_id);
  my $count = 0;
  while($sth->fetch()){
    $new_name{$gene_id} = $name;
    $id_to_stable_id{$gene_id} = $stable_id;
    $count++;
  }
  $sth->finish;
#  print $sql."\n";
#  print $count." entries found in xref database\n";



  # Use synonyms as well.
  my %alias;
  $sql = 'select x.label, sy.synonym from xref x, synonym sy, source so where x.xref_id = sy.xref_id and so.source_id = x.source_id and so.name like "'.$official_name.'_%" ';
  $sth = $self->xref->dbc->prepare($sql);
  $sth->execute();
  my ($syn);
  $sth->bind_columns(\$name,\$syn);
  $count = 0;
  while($sth->fetch()){
    $alias{$syn} = $name;
  }
  $sth->finish;  

  $sql = 'select x.label, sy.synonym from xref x, synonym sy, source so where x.xref_id = sy.xref_id and so.source_id = x.source_id and so.name like "EntrezGene"';
  $sth = $self->xref->dbc->prepare($sql);
  $sth->execute();
  $sth->bind_columns(\$name,\$syn);
  while($sth->fetch()){
    $alias{$syn} = $name;
  }
  $sth->finish;



  # NOTE ncRNA has higher priority
  $sql = "select x.display_label, g.gene_id from gene g, xref x where g.display_xref_id = x.xref_id and biotype = 'protein_coding'";

  $sth = $self->core->dbc->prepare($sql);
  $sth->execute();
  $sth->bind_columns(\$name,\$gene_id);
  $count =0;
  my $total_count=0;
  while($sth->fetch()){
    if(defined($new_name{$gene_id})){
      $total_count++;
    }	
    if(defined($new_name{$gene_id}) and $new_name{$gene_id} ne $name){
      if(!defined($alias{$name}) or $alias{$name} ne $new_name{$gene_id}){
	print STDERR "WARN: gene_id ($gene_id) ".$id_to_stable_id{$gene_id}." new = ".$new_name{$gene_id}." old = $name\n";
	$count++;
      }
    }	
  }
  if($total_count){
    print STDERR "$count entries with different names out of $total_count protein coding gene comparisons?\n";
  }

  my($class, $mapper) = @_;

  my $self ={};
  bless $self,$class;
  $self->core($mapper->core);
  $self->xref($mapper->xref);
  $self->mapper($mapper);
  return $self;

  my ($self) = @_;
  
  my $failed = 0;

  my $xref_id;
  my $count;

  my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('tests_started',now())");
  $sth_stat->execute();

  #    dependent_xref            and xref
  my $count_sql = "select count(1) from dependent_xref d left join xref x on d.master_xref_id = x.xref_id where x.xref_id is null";
  my $sql = "select distinct(d.master_xref_id) from dependent_xref d left join xref x on d.master_xref_id = x.xref_id where x.xref_id is null limit 10";
  my $sth = $self->xref->dbc->prepare($count_sql);
  $sth->execute();
  $sth->bind_columns(\$count);
  $sth->fetch();
  $sth->finish;
  
  if($count){
    $failed = 1;
    $sth = $self->xref->dbc->prepare($sql);
    $sth->execute();
    $sth->bind_columns(\$xref_id);
    print STDERR "SQL QUERY: $sql\n";
    while($sth->fetch){
      print STDERR "Problem with master xref $xref_id\n";
    }
    $sth->finish;
  }




  $count_sql = "select count(1) from dependent_xref d left join xref x on d.dependent_xref_id = x.xref_id where x.xref_id is null";

  $sql = "select distinct(d.dependent_xref_id) from dependent_xref d left join xref x on d.dependent_xref_id = x.xref_id where x.xref_id is null limit 10";

  $sth = $self->xref->dbc->prepare($count_sql);
  $sth->execute();
  $sth->bind_columns(\$count);
  $sth->fetch();
  $sth->finish;
  
  if($count){
    $failed = 1;
    $sth = $self->xref->dbc->prepare($sql);
    $sth->execute();
    $sth->bind_columns(\$xref_id);
    print STDERR "SQL QUERY: $sql\n";
    while($sth->fetch){
      print STDERR "Problem with dependent xref $xref_id\n";
    }
    $sth->finish;
  }

  $count_sql = "select count(1) from primary_xref d left join xref x on d.xref_id = x.xref_id where x.xref_id is null";

  $sql = "select distinct(d.xref_id) from primary_xref d left join xref x on d.xref_id = x.xref_id where x.xref_id is null limit 10";

  $sth = $self->xref->dbc->prepare($count_sql);
  $sth->execute();
  $sth->bind_columns(\$count);
  $sth->fetch();
  $sth->finish;
  
  if($count){
    $failed = 1;
    $sth = $self->xref->dbc->prepare($sql);
    $sth->execute();
    $sth->bind_columns(\$xref_id);
    print STDERR "SQL QUERY: $sql\n";
    while($sth->fetch){
      print STDERR "Problem with primary xref $xref_id\n";
    }
    $sth->finish;
  }

  foreach my $type (qw(transcript translation gene)){
    $count_sql =      "select count(1) from ".$type."_direct_xref d left join xref x on d.general_xref_id = x.xref_id where x.xref_id is null";
    
    $sql = "select distinct(d.general_xref_id) from ".$type."_direct_xref d left join xref x on d.general_xref_id = x.xref_id where x.xref_id is null limit 10";
    
    $sth = $self->xref->dbc->prepare($count_sql);
    $sth->execute();
    $sth->bind_columns(\$count);
    $sth->fetch();
    $sth->finish;
    
    if($count){
      $failed = 1;
      $sth = $self->xref->dbc->prepare($sql);
      $sth->execute();
      $sth->bind_columns(\$xref_id);
      print STDERR "SQL QUERY: $sql\n";
      while($sth->fetch){
	print STDERR "Problem with ".$type."_direct_xref $xref_id\n";
      }
      $sth->finish;
    }
    
  }


  $count_sql = "select count(1) from synonym d left join xref x on d.xref_id = x.xref_id where x.xref_id is null";

  $sql = "select distinct(d.xref_id) from synonym d left join xref x on d.xref_id = x.xref_id where x.xref_id is null limit 10";

  $sth = $self->xref->dbc->prepare($count_sql);
  $sth->execute();
  $sth->bind_columns(\$count);
  $sth->fetch();
  $sth->finish;
  
  if($count){
    $failed = 1;
    $sth = $self->xref->dbc->prepare($sql);
    $sth->execute();
    $sth->bind_columns(\$xref_id);
    print STDERR "SQL QUERY: $sql\n";
    while($sth->fetch){
      print STDERR "Problem with synonym $xref_id\n";
    }
    $sth->finish;
  }


  $count_sql = "select count(1) from identity_xref d left join object_xref o on d.object_xref_id = o.object_xref_id where o.object_xref_id is null";

  $sql = "select distinct(d.object_xref_id) from identity_xref d left join object_xref o on d.object_xref_id = o.object_xref_id where o.object_xref_id is null limit 10";

  $sth = $self->xref->dbc->prepare($count_sql);
  $sth->execute();
  $sth->bind_columns(\$count);
  $sth->fetch();
  $sth->finish;
  
  if($count){
    $failed = 1;
    $sth = $self->xref->dbc->prepare($sql);
    $sth->execute();
    $sth->bind_columns(\$xref_id);
    print STDERR "SQL QUERY: $sql\n";
    while($sth->fetch){
      print STDERR "Problem with object_xref $xref_id\n";
    }
    $sth->finish;
  }

  $count_sql = "select count(1) from go_xref d left join object_xref o on d.object_xref_id = o.object_xref_id where o.object_xref_id is null";

  $sql = "select distinct(d.object_xref_id) from go_xref d left join object_xref o on d.object_xref_id = o.object_xref_id where o.object_xref_id is null limit 10";

  $sth = $self->xref->dbc->prepare($count_sql);
  $sth->execute();
  $sth->bind_columns(\$count);
  $sth->fetch();
  $sth->finish;
  
  if($count){
    $failed = 1;
    $sth = $self->xref->dbc->prepare($sql);
    $sth->execute();
    $sth->bind_columns(\$xref_id);
    print STDERR "SQL QUERY: $sql\n";
    while($sth->fetch){
      print STDERR "Problem with object_xref $xref_id\n";
    }
    $sth->finish;
  }


  foreach my $type (qw(transcript translation gene)){
    $count_sql = "select count(1) from gene_transcript_translation d left join ".$type."_stable_id x on d.".$type."_id = x.internal_id where x.internal_id is null and d.".$type."_id is not null";
    
    $sql = "select distinct(d.".$type."_id) from gene_transcript_translation d left join  ".$type."_stable_id x on d.".$type."_id = x.internal_id where x.internal_id is null and d.".$type."_id is not null limit 10";
    
    $sth = $self->xref->dbc->prepare($count_sql);
    $sth->execute();
    $sth->bind_columns(\$count);
    $sth->fetch();
    $sth->finish;
    
    if($count){
      $failed = 1;
      $sth = $self->xref->dbc->prepare($sql);
      $sth->execute();
      $sth->bind_columns(\$xref_id);
      print STDERR "SQL QUERY: $sql\n";
      while($sth->fetch){
	print STDERR "Problem with ".$type."_id $xref_id\n";
      }
      $sth->finish;
    }
    
  }


  $count_sql = "select count(1) from xref x, source s, object_xref o left join go_xref g on o.object_xref_id = g.object_xref_id where x.xref_id = o.xref_id and s.source_id = x.source_id and s.name like 'GO' and g.object_xref_id is null";
  $sql = "select distinct(o.object_xref_id) from xref x, source s, object_xref o left join go_xref g on o.object_xref_id = g.object_xref_id where x.xref_id = o.xref_id and s.source_id = x.source_id and s.name like 'GO' and g.object_xref_id is null limit 10";

  $sth = $self->xref->dbc->prepare($count_sql);
  $sth->execute();
  $sth->bind_columns(\$count);
  $sth->fetch();
  $sth->finish;
  
  if($count){
    $failed = 1;
    $sth = $self->xref->dbc->prepare($sql);
    $sth->execute();
    $sth->bind_columns(\$xref_id);
    print STDERR "SQL QUERY: $sql\n";
    while($sth->fetch){
      print STDERR "Problem with object_xref $xref_id which is linked to a GO source but has no go_xref reference\n";
    }
    $sth->finish;
  }

  if(!$failed){
    $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('tests_finished',now())");
    $sth_stat->execute();
  }
  else{
    $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('tests_failed',now())");
    $sth_stat->execute();
  }
  $sth_stat->finish;

  return $failed;