removed comment and added type check for SP object. Re #26

solgenomics · May 13, 2015 · c9200f4 · c9200f4
1 parent f189681
commit c9200f4
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Showing 2 changed files with 9 additions and 6 deletions.
diff --git a/lib/Bio/GenomeUpdate/SP/SPLine.pm b/lib/Bio/GenomeUpdate/SP/SPLine.pm
@@ -6,8 +6,6 @@ use Moose;
 use MooseX::FollowPBP;
 use Moose::Util::TypeConstraints;
 
-use Data::Dumper;#for debugging
-
 =head1 NAME
 
     SP - Switch point lines for NCBI GRC pipeline with instructions used to generate a Accessioned Golden Path (AGP) file
@@ -38,7 +36,7 @@ Gets the chromosome.
 
 subtype 'SPChromosome', #only works for genomes with 12 chrs or less.
   as 'Str',
-  where { $_ eq '1' || $_ eq '2' || $_ eq '3' || $_ eq '4' || $_ eq '5' || $_ eq '6' || $_ eq '7' || $_ eq '8' || $_ eq '9' || $_ eq '10' || $_ eq '11' || $_ eq '12' || $_ eq "Un" },#does NOT work. need to do -> if int check 1-12, if str check Un
+  where { $_ eq '1' || $_ eq '2' || $_ eq '3' || $_ eq '4' || $_ eq '5' || $_ eq '6' || $_ eq '7' || $_ eq '8' || $_ eq '9' || $_ eq '10' || $_ eq '11' || $_ eq '12' || $_ eq "Un" },
   message { "The string, $_, was not a valid chromosome number.  Valid values for Solanum lycopersicum are 1-12 and Un." };
 has 'chromosome' => ( isa => 'SPChromosome', is => 'rw', required => 1, clearer => 'clear_chromosome' );
 

diff --git a/t/GenomeUpdate/sp.t b/t/GenomeUpdate/sp.t
@@ -25,7 +25,7 @@ use strict;
 use warnings;
 use autodie;
 
-use Test::More tests => 1;
+use Test::More;
 use Test::Exception;
 
 BEGIN {use_ok( 'Bio::GenomeUpdate::SP' ); }
@@ -64,7 +64,7 @@ is($sp_line1->get_accession_prefix_last_base(), 100, 'Got correct accession_pref
 is($sp_line1->get_accession_suffix_first_base(), 200, 'Got correct accession_suffix_first_base from $sp_line1');
 is($sp_line1->get_comment(), 'test line 1 comment some nonsense here and here too', 'Got correct comment from $sp_line1');
 
-#test for type checks
+#test for type checks for SP line
 throws_ok{$sp_line1->set_chromosome(13)} qr/not a valid chromosome number/, "invalid chr exception caught"; 
 throws_ok{$sp_line1->set_accession_prefix_orientation('3')} qr/not a valid orientation type/, "invalid orientation exception caught";
 throws_ok{$sp_line1->set_accession_prefix_last_base(-1)} qr/not a positive coordinate/, "negative coordinate exception caught";
@@ -81,9 +81,11 @@ ok(my $sp = Bio::GenomeUpdate::SP->new(
 ok ($sp->add_line_to_end($sp_line1), 'added $sp_line1');
 ok ($sp->add_line_to_end($sp_line2), 'added $sp_line2');
 
+#test for type checks for SP object
+throws_ok{$sp->set_tpf_type('blah blah')} qr/not a valid TPF type/, "invalid TPF type exception caught";
+
 #print out SP object and compare to string
 ok(my $sp_file_string = $sp->get_formatted_sp(), 'got switch point file content' );
-print $sp_file_string;
 my $expected_sp_file_string = q(001	TGP	Primary	Un	chromosome	accession1	accession2	+	-	100	200	test line 1 comment some nonsense here and here too
 001	TGP	Primary	1	chromosome	accession3	accession4	-	-	300	100	test line 2 comment some nonsense here and here too
 );
@@ -101,3 +103,6 @@ $expected_sp_file_string = q(001	TGP	Primary	Un	chromosome	accession1	accession2
 001	TGP	Primary	Un	chromosome	accession1	accession2	+	-	110	210	test line 1 comment some nonsense here and here too
 ); #$sp_line1 also changes as its a hashref
 ok( $sp_file_string eq $expected_sp_file_string, 'modified switch point file content looks good' );
+
+#no more tests
+done_testing();