[Gmod-schema-cmts] schema/chado/bin/cxgn load_cvterms.pl,1.4,1.5

[Naama M. <nm...@us...>]

Update of /cvsroot/gmod/schema/chado/bin/cxgn
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv5125/bin/cxgn

Modified Files:
	load_cvterms.pl 
Log Message:
load_cvterms checks first if relationship ontology is loaded.
When inserting a cvterm_relationship will use relationships under RO namespace before looking 
for predicate terms from the loaded ontology name. 



Index: load_cvterms.pl
===================================================================
RCS file: /cvsroot/gmod/schema/chado/bin/cxgn/load_cvterms.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** load_cvterms.pl	10 Mar 2008 17:39:56 -0000	1.4
--- load_cvterms.pl	17 Mar 2008 20:13:46 -0000	1.5
***************
*** 6,10 ****
  =head1 DESCRIPTION
  
! Usage: perl load_cvterms.pl -H dbhost -D dbname [-vDnFo] file
  
  parameters
--- 6,10 ----
  =head1 DESCRIPTION
  
! Usage: perl load_cvterms.pl -H dbhost -D dbname [-vdntuFo] file
  
  parameters
***************
*** 117,121 ****
  =head1 VERSION AND DATE
  
! Version 0.12, February 2007.
  
  =cut
--- 117,121 ----
  =head1 VERSION AND DATE
  
! Version 0.12, February 2008.
  
  =cut
***************
*** 146,150 ****
  
  my $DBPROFILE = $opt_p;
! $DBPROFILE ||= 'default';
  my $gmod_conf = Bio::GMOD::Config->new();
  my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE );
--- 146,150 ----
  
  my $DBPROFILE = $opt_p;
! $DBPROFILE ||= undef;
  my $gmod_conf = Bio::GMOD::Config->new();
  my $db_conf = Bio::GMOD::DB::Config->new( $gmod_conf, $DBPROFILE );
***************
*** 187,191 ****
  my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>$dbhost,
  				      dbname=>$dbname,  
!                                       dbprofile=>$DBPROFILE,
  				   } );
  
--- 187,191 ----
  my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>$dbhost,
  				      dbname=>$dbname,  
!                                       #dbprofile=>$DBPROFILE,
  				   } );
  
***************
*** 204,208 ****
      push @onts, $ont;
  }
! #$new_ont = $onts[-1];
  
  foreach my $new_ont(@onts) {
--- 204,208 ----
      push @onts, $ont;
  }
! 
  
  foreach my $new_ont(@onts) {
***************
*** 212,216 ****
--- 212,231 ----
      if ($opt_n && ( $opt_n ne $new_ont_name) ) { print STDERR "$opt_n: skipping to next ontology..\n"; next (); } 
      
+     #check if relationship ontology is already loaded:
+     if ($new_ont_name ne 'relationship') {
+ 	my $rel_cv= CXGN::Chado::Ontology->new_with_name($dbh, 'relationship');
+ 	my @rel=$rel_cv->get_predicate_terms();
+ 	if (!@rel) {
+ 	    warn "Relationship ontology must be loaded first!!\n" ;
+ 	    exit(0);
+ 	}
+     }
+     
      my $cv = CXGN::Chado::Ontology->new_with_name($dbh, $new_ont->name()); # also get a CXGN::Chado::Ontology object for the cv_id (see later).
+     #store a new cv if the ontology namespace does not exist
+     if (!$cv->get_cv_id() ) { 
+ 	$cv->name($new_ont_name);
+ 	$cv->store();
+     }
      print STDERR "cv_id = ".($cv->get_cv_id())."\n";
      
***************
*** 235,240 ****
  	
  	print STDERR "Retrieved ".(scalar(@all_file_terms))." terms.\n";
! 	print OUT "Retrieved ".(scalar(@all_file_terms))." terms.\n" if $opt_o;
  	
  	#look at all predecate terms (Typedefs)
  	my @all_db_predicate_terms = $db_ont->get_predicate_terms();
--- 250,256 ----
  	
  	print STDERR "Retrieved ".(scalar(@all_file_terms))." terms.\n";
! 	print OUT "Retrieved ".(scalar(@all_file_terms))." terms.\n" if $opt_o;	
  	
+         
  	#look at all predecate terms (Typedefs)
  	my @all_db_predicate_terms = $db_ont->get_predicate_terms();
***************
*** 299,303 ****
  	
  	print STDERR "Determining which terms are new...\n";
! 	
  	
  	foreach my $k (keys(%file_index)) { 
--- 315,319 ----
  	
  	print STDERR "Determining which terms are new...\n";
! 	#exit();
  	
  	foreach my $k (keys(%file_index)) { 
***************
*** 570,582 ****
  		
  		my $predicate_term_name = $file_relationships{$r}->predicate_term()->name();
! 		my $cv_id= CXGN::Chado::CV->new_with_name($dbh, "relationship")->get_cv_id();
! 		if (!$cv_id) { $cv_id= CXGN::Chado::CV->new_with_name($dbh, $db_ont->name)->get_cv_id(); }
  		
! 		my $predicate_term = CXGN::Chado::Cvterm->new_with_term_name($dbh, $predicate_term_name, $cv_id);
! 		if (!$predicate_term->get_cvterm_id()) { 
! 		    die "The predicate term $predicate_term_name does not exist in the database\n"; 
  		}
  		$new_rel->predicate_term($predicate_term);
! 		if ($opt_v) { print STDERR "Storing relationship $r. type cv_id=$cv_id\n"; }
  		if (!$opt_t) { 
  		    $new_rel->store();
--- 586,601 ----
  		
  		my $predicate_term_name = $file_relationships{$r}->predicate_term()->name();
! 		my $rel_cv_id= CXGN::Chado::Ontology->new_with_name($dbh, "relationship")->identifier();
! 		my $cv_id= $db_ont->identifier();
  		
! 		my $predicate_term = CXGN::Chado::Cvterm->new_with_term_name($dbh, $predicate_term_name, $rel_cv_id);
! 		if (!$predicate_term->get_cvterm_id()) {
! 		    $predicate_term=CXGN::Chado::Cvterm->new_with_term_name($dbh, $predicate_term_name, $cv_id);
! 		    if (!$predicate_term->get_cvterm_id()) { 
! 			die "The predicate term $predicate_term_name does not exist in the database\n";  
! 		    }
  		}
  		$new_rel->predicate_term($predicate_term);
! 		if ($opt_v) { print STDERR "Storing relationship $r. type cv_id=" . $predicate_term->get_cv_id() ."\n"; }
  		if (!$opt_t) { 
  		    $new_rel->store();