remove Bio::Root::Test, use Test::Most

bioperl · Jan 17, 2012 · 11d8653 · 11d8653
1 parent b3d48bc
commit 11d8653
Showing 1 changed file with 57 additions and 82 deletions.
diff --git a/xt/release/EUtilities.t b/xt/release/EUtilities.t
@@ -1,94 +1,69 @@
-# -*-Perl-*- Test Harness script for Bioperl
-# $Id: EUtilities.t 15112 2008-12-08 18:12:38Z sendu $
-#
-
 use strict;
-our $NUMTESTS;
-our $DEBUG;
-our %EUTILS;
-
-BEGIN {
-    $NUMTESTS = 5; # base number of tests (those not in blocks)
-
-    # I have set up eutils tests to run in sections for easier test maintenance
-    # and keeping track of problematic tests. The below hash is the list of
-    # tests, with test number and coderef.
-
-    # these now run very simple tests for connectivity and data sampling
-    # main tests now with the parser
-
-    %EUTILS = (
-        'efetch'        => {'tests' => 5,
-                            'sub'   => \&efetch},
-        'epost'         => {'tests' => 11,
-                            'sub'   => \&epost},
-        'esummary'      => {'tests' => 254,
-                            'sub'   => \&esummary},
-        'esearch'       => {'tests' => 13,
-                            'sub'   => \&esearch},
-        'einfo'         => {'tests' => 10,
-                            'sub'   => \&einfo},
-        'elink1'        => {'tests' => 8,
-                            'sub'   => \&elink1},
-        'egquery'       => {'tests' => 4,
-                            'sub'   => \&egquery},
-        );
-    $NUMTESTS += $EUTILS{$_}->{'tests'} for (keys %EUTILS);
-    # this seems to work for perl 5.6 and perl 5.8
+use warnings;
+use Test::Most;
+use Bio::DB::EUtilities; # use_ok tested in 00-compile.t during release
+
+my $test_ct = 1; # base number of tests (those not in blocks)
+
+my %eutils = (
+    'efetch'        => {'tests' => 5,
+                        'sub'   => \&efetch},
+    'epost'         => {'tests' => 11,
+                        'sub'   => \&epost},
+    'esummary'      => {'tests' => 254,
+                        'sub'   => \&esummary},
+    'esearch'       => {'tests' => 13,
+                        'sub'   => \&esearch},
+    'einfo'         => {'tests' => 10,
+                        'sub'   => \&einfo},
+    'elink1'        => {'tests' => 8,
+                        'sub'   => \&elink1},
+    'egquery'       => {'tests' => 4,
+                        'sub'   => \&egquery},
+);
+$test_ct += $eutils{$_}->{'tests'} for (keys %eutils);
+
+plan tests => $test_ct;
+
+my $debug = $ENV{BIOPERLDEBUG} || $ENV{BIOPERL_DEBUG} || 0;
+my $email = $ENV{BIOPERL_EMAIL};
 
-    use Bio::Root::Test;
-    $DEBUG = test_debug() || 0;
+my ($eutil, $response);
 
-    test_begin(-tests               => $NUMTESTS,
-               -requires_modules    => [qw(XML::Simple LWP::UserAgent)],
-               -requires_email      => 1,
-              );
+# NOTE : Bio::DB::EUtilities is just a specialized pipeline to get any
+# data available via NCBI's Entrez interface, with a few convenience methods
+# to get UIDs and other additional information.  All data returned
+# using EFetch is raw (not Bioperl objects) and is meant to be piped into
+# other Bioperl modules at a later point for further processing
 
-    use_ok('Bio::DB::EUtilities');
-    use_ok('LWP::UserAgent');
-    use_ok('Bio::Tools::EUtilities');
-    use_ok('Bio::Tools::EUtilities::EUtilParameters');
-}
+#   protein acc
+my @acc = qw(MUSIGHBA1 P18584 CH402638);
 
-my $email = $ENV{BIOPERL_EMAIL};
+# protein GI
+my @ids = sort qw(1621261 89318838 68536103 20807972 730439);
+
+# test search term
+my $term = 'dihydroorotase AND human';
+
+my %dbs = (taxonomy => 1,
+           nucleotide => 1,
+           pubmed => 1);
+my %links = (protein_taxonomy => 1,
+             protein_nucleotide => 1,
+             protein_nucleotide_wgs => 1,
+             protein_pubmed => 1,
+             protein_pubmed_refseq => 1
+             );
 
 SKIP: {
-    ok($email, 'Make sure email is set (BIOPERL_EMAIL)');
-    skip("Must provide a valid email for tests", $NUMTESTS) if !defined($email);
-    diag("Using $email for tests") if $DEBUG;
-
-    # NOTE : Bio::DB::EUtilities is just a specialized pipeline to get any
-    # data available via NCBI's Entrez interface, with a few convenience methods
-    # to get UIDs and other additional information.  All data returned
-    # using EFetch is raw (not Bioperl objects) and is meant to be piped into
-    # other Bioperl modules at a later point for further processing
-
-    #   protein acc
-    my @acc = qw(MUSIGHBA1 P18584 CH402638);
-
-    # protein GI
-    my @ids = sort qw(1621261 89318838 68536103 20807972 730439);
-
-    # test search term
-    my $term = 'dihydroorotase AND human';
-
-    my ($eutil, $response);
-
-    my %dbs = (taxonomy => 1,
-               nucleotide => 1,
-               pubmed => 1);
-    my %links = (protein_taxonomy => 1,
-                 protein_nucleotide => 1,
-                 protein_nucleotide_wgs => 1,
-                 protein_pubmed => 1,
-                 protein_pubmed_refseq => 1
-                 );
-
+    ok($email, 'Make sure email is set (set BIOPERL_EMAIL)');
+    skip("Must provide a valid email for tests", $test_ct - 1) if !defined($email);
+    diag("Using $email for tests") if $debug;
+
     # this loops through the required tests, only running what is in %EUTILS
-    for my $test (keys %EUTILS) {
-        $EUTILS{$test}->{'sub'}->();
+    for my $test (keys %eutils) {
+        $eutils{$test}->{'sub'}->();
     }
-
 }
 # Simple EFetch