Gene Ontology

Update of /cvsroot/geneontology/go-dev/amigo/amigo/cgi-bin
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv28729/amigo/cgi-bin

Modified Files:
      Tag: amigo_exp_1_5
	term_enrichment 
Log Message:
db filter fixes for wonky GO-TF

Index: term_enrichment
===================================================================
RCS file: /cvsroot/geneontology/go-dev/amigo/amigo/cgi-bin/Attic/term_enrichment,v
retrieving revision 1.1.2.18
retrieving revision 1.1.2.19
diff -C2 -d -r1.1.2.18 -r1.1.2.19
*** term_enrichment	6 Nov 2007 20:02:46 -0000	1.1.2.18
--- term_enrichment	7 Nov 2007 00:09:56 -0000	1.1.2.19
***************
*** 272,276 ****
  my @in_speciesdbs = $query->param('speciesdb');
  my $speciesdbs_cardinality = scalar(keys %{$apph_sd_hash});
! if( @in_speciesdbs && scalar(@in_speciesdbs) == 0 ){
    foreach my $speciesdb (@in_speciesdbs){
      if( $speciesdb ){
--- 272,280 ----
  my @in_speciesdbs = $query->param('speciesdb');
  my $speciesdbs_cardinality = scalar(keys %{$apph_sd_hash});
! #print STDERR "__1" . @in_speciesdbs . "\n";
! #print STDERR "__2" . scalar(@in_speciesdbs) . "\n";
! #my $foo = join ', ', @in_speciesdbs;
! #print STDERR "__3" . $foo . "\n";
! if( @in_speciesdbs && scalar(@in_speciesdbs) != 0 ){
    foreach my $speciesdb (@in_speciesdbs){
      if( $speciesdb ){
***************
*** 283,294 ****
        }
        push @speciesdbs, $speciesdb;
      }
    }
- }else{
-   ## BUG: This gets around a GO::TermFinder bug. Think about how wrong
-   ## this is...
-   #@speciesdbs = ();
-   @speciesdbs = keys %{$apph_sd_hash};
  }
  
  ##
--- 287,307 ----
        }
        push @speciesdbs, $speciesdb;
+       #print STDERR "  _" . $speciesdb . "\n";
      }
+     #else{
+     #print STDERR "  -s-" . $speciesdb . "\n";
+     #}
    }
  }
+ #else{
+ #  ## BUG: This gets around a GO::TermFinder bug. Think about how wrong
+ #  ## this is...
+ #  #@speciesdbs = ();
+ #  #@speciesdbs = keys %{$apph_sd_hash};
+ #}
+ @speciesdbs = keys %{$apph_sd_hash} if ! @speciesdbs;
+ #$foo = join ', ', @speciesdbs;
+ #print STDERR "===" . $foo . "\n";
+ #sleep 1;
  
  ##
***************
*** 383,390 ****
  ## Variables for GUI
  $vars->{AVAILABLE_ONTOLOGIES} = $apph_ontology_hash; # Onts we can choose from.
- $vars->{AVAILABLE_SPECIESDBS} = $apph_sd_hash; # DBs we can choose from.
- #$vars->{AVAILABLE_EVCODES} = $apph_evcode_hash; # evcodes we can choose from.
  %{$vars->{ECHO_ONTOLOGIES}} = map { $_ => 1 } @ontologies;
  
  ## BUG: This is still fallout from the TermFinder argument bug from
  ## above.
--- 396,406 ----
  ## Variables for GUI
  $vars->{AVAILABLE_ONTOLOGIES} = $apph_ontology_hash; # Onts we can choose from.
  %{$vars->{ECHO_ONTOLOGIES}} = map { $_ => 1 } @ontologies;
  
+ #$vars->{AVAILABLE_EVCODES} = $apph_evcode_hash; # evcodes we can choose from.
+ #%{$vars->{ECHO_EVCODES}} = map { $_ => 1 } @evcodes;
+ 
+ $vars->{AVAILABLE_SPECIESDBS} = $apph_sd_hash; # DBs we can choose from.
+ 
  ## BUG: This is still fallout from the TermFinder argument bug from
  ## above.
***************
*** 397,401 ****
  }
  
- #%{$vars->{ECHO_EVCODES}} = map { $_ => 1 } @evcodes;
  $vars->{ECHO_GP_LIST} = $gp_list;
  $vars->{ECHO_BGGP_LIST} = $bggp_list;
--- 413,416 ----
***************
*** 435,439 ****
    $apph->filters({speciesdbs=>\@speciesdbs})
      if @speciesdbs;
!   #$apph->filters({ontology=>\@ontologies}) if @ontologies;
    #$apph->filters({evcodes=>\@evcodes}) if @evcodes;
    #$apph->filters({speciesdb=>\@speciesdbs}) if @speciesdbs;
--- 450,455 ----
    $apph->filters({speciesdbs=>\@speciesdbs})
      if @speciesdbs;
!   #$apph->filters({ontology=>\@ontologies})
!   #  if @ontologies;
    #$apph->filters({evcodes=>\@evcodes}) if @evcodes;
    #$apph->filters({speciesdb=>\@speciesdbs}) if @speciesdbs;