[Bioperl-guts-l] bioperl-live/t SearchIO.t,1.107,1.108

Christopher John Fields cjfields at dev.open-bio.org
Tue Jan 30 14:30:22 EST 2007


Update of /home/repository/bioperl/bioperl-live/t
In directory dev.open-bio.org:/tmp/cvs-serv3134/t

Modified Files:
	SearchIO.t 
Log Message:
XML::SAX::Expat (v. 0.38) works for XML parsing now; catch fails in testing.

Index: SearchIO.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/SearchIO.t,v
retrieving revision 1.107
retrieving revision 1.108
diff -C2 -d -r1.107 -r1.108
*** SearchIO.t	24 Jan 2007 16:22:06 -0000	1.107
--- SearchIO.t	30 Jan 2007 19:30:20 -0000	1.108
***************
*** 1,2 ****
--- 1,3 ----
+ 
  # -*-Perl-*-
  ## Bioperl Test Harness Script for Modules
***************
*** 54,63 ****
  		# this needs to be eval'd b/c the XML::SAX parser object is
  		# instantiated in the constructor
! 		$searchio = new Bio::SearchIO ('-tempfile' => 1,
  			   '-format' => 'blastxml',
  			   '-file'   => Bio::Root::IO->catfile('t','data','ecoli_domains.rps.xml'),
! 			   '-verbose' => -2);
  		# PurePerl works with these BLAST reports, so removed verbose promotion
  		$result = $searchio->next_result;
  	};
  	if ($@ && $@ =~ m{Handler couldn't resolve external entity}) {
--- 55,65 ----
  		# this needs to be eval'd b/c the XML::SAX parser object is
  		# instantiated in the constructor
! 		$searchio = Bio::SearchIO->new('-tempfile' => 1,
  			   '-format' => 'blastxml',
  			   '-file'   => Bio::Root::IO->catfile('t','data','ecoli_domains.rps.xml'),
! 			   '-verbose' => -1);
  		# PurePerl works with these BLAST reports, so removed verbose promotion
  		$result = $searchio->next_result;
+         die if !defined $result;
  	};
  	if ($@ && $@ =~ m{Handler couldn't resolve external entity}) {
***************
*** 66,70 ****
  		skip("Problem with XML::SAX setup: $@. Check ParserDetails.ini; skipping XML tests",129);
  	}
!     isa_ok($result, 'Bio::Search::Result::ResultI');    
      is($result->database_name, '/data_2/jason/db/cdd/cdd/Pfam', 'database_name()');
      is($result->query_name,'gi|1786182|gb|AAC73112.1|','query_name()');
--- 68,72 ----
  		skip("Problem with XML::SAX setup: $@. Check ParserDetails.ini; skipping XML tests",129);
  	}
!     isa_ok($result, 'Bio::Search::Result::ResultI');
      is($result->database_name, '/data_2/jason/db/cdd/cdd/Pfam', 'database_name()');
      is($result->query_name,'gi|1786182|gb|AAC73112.1|','query_name()');
***************
*** 126,130 ****
  
  
!     $searchio = new Bio::SearchIO(-format => 'blastxml', 
  				  -file => Bio::Root::IO->catfile('t','data','plague_yeast.bls.xml'));
  
--- 128,133 ----
  
  
!     $searchio = new Bio::SearchIO(-format => 'blastxml',
! 								  -verbose => -1,
  				  -file => Bio::Root::IO->catfile('t','data','plague_yeast.bls.xml'));
  
***************
*** 140,144 ****
      ok(! $hit);
  
!     $searchio = new Bio::SearchIO(-format => 'blastxml', 
  				  -file => Bio::Root::IO->catfile('t','data','mus.bls.xml'));
  
--- 143,148 ----
      ok(! $hit);
  
!     $searchio = new Bio::SearchIO(-format => 'blastxml',
! 								  -verbose => -1,
  				  -file => Bio::Root::IO->catfile('t','data','mus.bls.xml'));
  
***************
*** 157,161 ****
      
      # deal with new BLAST XML changes
!     $searchio = new Bio::SearchIO(-format => 'blastxml', 
  				  -file => Bio::Root::IO->catfile('t','data','newblast.xml'));
  
--- 161,166 ----
      
      # deal with new BLAST XML changes
!     $searchio = new Bio::SearchIO(-format => 'blastxml',
! 								  -verbose => -1,
  				  -file => Bio::Root::IO->catfile('t','data','newblast.xml'));
  



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