[Gmod-schema-cmts] schema/chado/lib/Bio/GMOD/DB Adapter.pm, 1.38, 1.39

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado/lib/Bio/GMOD/DB
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv28210/lib/Bio/GMOD/DB

Modified Files:
	Adapter.pm 
Log Message:
adding the ability to use the feature_property cv that comes with chado and squashing a bug that caused loads to fail if --recreate is specified on the command line and the cache table doesn't already exist.


Index: Adapter.pm
===================================================================
RCS file: /cvsroot/gmod/schema/chado/lib/Bio/GMOD/DB/Adapter.pm,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** Adapter.pm	15 Dec 2006 22:59:48 -0000	1.38
--- Adapter.pm	20 Dec 2006 15:48:31 -0000	1.39
***************
*** 194,197 ****
--- 194,198 ----
      $self->unique_target(   $arg{unique_target}  );
      $self->dbxref(          $arg{dbxref}         );
+     $self->fp_cv(           $arg{fp_cv}          );
  
      $self->{const}{source_success} = 1; #flag to indicate GFF_source is in db table
***************
*** 873,876 ****
--- 874,910 ----
  }
  
+ =head2 fp_cv
+ 
+ =over
+ 
+ =item Usage
+ 
+   $obj->fp_cv()        #get existing value
+   $obj->fp_cv($newval) #set new value
+ 
+ =item Function
+ 
+ Gets/sets the name of the feature property cv
+ 
+ =item Returns
+ 
+ value of fp_cv (a scalar)
+ 
+ =item Arguments
+ 
+ new value of fp_cv (to set)
+ 
+ =back
+ 
+ =cut
+ 
+ sub fp_cv {
+     my $self = shift;
+     my $fp_cv = shift if defined(@_);
+     return $self->{'fp_cv'} = $fp_cv if defined($fp_cv);
+     return $self->{'fp_cv'};
+ }
+ 
+ 
  =head2 recreate_cache
  
***************
*** 979,983 ****
      if (!$table_exists || $self->recreate_cache() ) {
          print STDERR "(Re)creating the uniquename cache in the database... ";
!         $dbh->do(DROP_CACHE_TABLE) if $self->recreate_cache();
  
          print STDERR "\nCreating table...\n";
--- 1013,1017 ----
      if (!$table_exists || $self->recreate_cache() ) {
          print STDERR "(Re)creating the uniquename cache in the database... ";
!         $dbh->do(DROP_CACHE_TABLE) if ($self->recreate_cache() and $table_exists);
  
          print STDERR "\nCreating table...\n";
***************
*** 2763,2774 ****
  
        unless ($self->{const}{auto_cv_id}){
!         my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='autocreated'");
          $sth->execute;
          ($self->{const}{auto_cv_id}) = $sth->fetchrow_array;
        }
  
        unless ( $self->cache('type',$tag) ) {
!         $self->{queries}{search_cvterm_id}->execute($tag, $self->{const}{auto_cv_id});
          my ($tag_cvterm) = $self->{queries}{search_cvterm_id}->fetchrow_array;
          if ($tag_cvterm) { #good, the term is already there
            $self->cache('type',$tag,$tag_cvterm);
--- 2797,2827 ----
  
        unless ($self->{const}{auto_cv_id}){
!         my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='autocreated' or name='". $self->fp_cv  ."'");
          $sth->execute;
          ($self->{const}{auto_cv_id}) = $sth->fetchrow_array;
        }
  
+       if (!$self->{const}{tried_fp_cv} and !$self->{const}{fp_cv_id}) {
+         my $sth = $self->dbh->prepare("SELECT cv_id FROM cv WHERE name='". $self->fp_cv  ."'");
+         $sth->execute;
+         ($self->{const}{fp_cv_id}) = $sth->fetchrow_array;
+         $self->{const}{tried_fp_cv} = 1;
+       }
+ 
        unless ( $self->cache('type',$tag) ) {
!         #check fp cv first, then autocreated
!         $self->{queries}{search_cvterm_id}->execute(
!                                  $tag, 
!                                  $self->{const}{fp_cv_id})
!                               if $self->{const}{fp_cv_id};
          my ($tag_cvterm) = $self->{queries}{search_cvterm_id}->fetchrow_array;
+ 
+         unless ($tag_cvterm) {
+             $self->{queries}{search_cvterm_id}->execute(
+                                  $tag, 
+                                  $self->{const}{auto_cv_id});
+             ($tag_cvterm) = $self->{queries}{search_cvterm_id}->fetchrow_array;
+         }
+ 
          if ($tag_cvterm) { #good, the term is already there
            $self->cache('type',$tag,$tag_cvterm);