[med-svn] [Git][med-team/bioperl-run][master] flag tests needing adaptations

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / bioperl-run


Commits:
86ba0c47 by Étienne Mollier at 2020-12-04T23:57:46+01:00
flag tests needing adaptations

These adaptations are due to the use of a dataset different from
the reference data in use by bioperl-run upstream.

- - - - -


1 changed file:

- debian/patches/alternate-data.patch


Changes:

=====================================
debian/patches/alternate-data.patch
=====================================
@@ -30,3 +30,26 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
          ($gene_bed)    = `find /usr -name 'knownGene.hg18.chr21.bed' 2>/dev/null`;
          ($mm8_genome)  = `find /usr -name 'mouse.mm8.genome' 2>/dev/null`;
          ($mm9_genome)  = `find /usr -name 'mouse.mm9.genome' 2>/dev/null`;
+@@ -326,7 +326,10 @@
+             open (FILE, $file);
+             my $lines =()= <FILE>;
+             close FILE;
++            TODO: {
++            local $TODO = "maybe adapt reference results to Debian specific dataset";
+             is( $lines, $result_lookup{$command}, " - number of lines");
++            }
+         } else {
+             $v && diag(" check can get internal result format matches result file");
+             my $guesser = Bio::Tools::GuessSeqFormat->new( -file => $file );
+@@ -356,8 +359,11 @@
+                 isa_ok( $objres, 'Bio::SeqFeature::Collection',
+                     "returned object is correct for command '$command'" );
+                 $v && diag(" - correct number of features");
++		TODO: {
++		local $TODO = "maybe adapt reference results to Debian specific dataset";
+                 is( scalar $objres->get_all_features, $result_lookup{$command},
+                     "correct number of features for command '$command'" );
++		}
+                 last;
+             };
+             m/^fasta$/ && do {



View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/commit/86ba0c476be5118a5cec3cc3e1c2bb62c6f93ff4

-- 
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/commit/86ba0c476be5118a5cec3cc3e1c2bb62c6f93ff4
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