utilsIo.t merged with io.t

modules/t/io.t

-# Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# 
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# 
-#      http://www.apache.org/licenses/LICENSE-2.0
-# 
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-################################################ 
-#                                              #
-# io.t                                         #
-#                                              #
-# A set of tests to verify various subroutines #
-# in the Bio::EnsEMBL::Utils::IO module        #
-#                                              #
-################################################
-
-use strict;
-use warnings;
-
-use Test::More;
-use File::Temp;
-use Bio::EnsEMBL::Utils::IO qw/:all/;
-
-ok(1, 'Module compiles');
-
-my $tmpdir = File::Temp->newdir();
-my $dirname = $tmpdir->dirname;
-
-#
-# test working with bzip2 and zip files
-#
-# create a dummy file
-my $tmpfile = File::Temp->new(DIR => $dirname, SUFFIX => '.txt');
-my $tmpfilename = $tmpfile->filename;
-print $tmpfile "test data\n";
-print $tmpfile "some more data.";
-$tmpfile->close;
-
-my $BZIP2_OK = 0;
-eval {
-  require IO::Compress::Bzip2;
-  require IO::Uncompress::Bunzip2;
-  $BZIP2_OK = 1;
-};
-
-SKIP: {
-  skip "Cannot run Bzip2/Bunzip2 tests, install related IO::[Un]Compress modules first",
-    4 unless $BZIP2_OK;
-
-  # send the content of the tmpfile to another
-  # bzip2 compressed file
-  my $file_content = slurp($tmpfilename);
-  my $bz2tmpfile = File::Temp->new(DIR => $dirname, SUFFIX => '.bz2');
-
-  bz_work_with_file($bz2tmpfile->filename, 'w', sub {
-    my ($fh) = @_;
-    print $fh $file_content;
-    return;
-  });
-
-  # check the content of the compressed file
-  my $content = bz_slurp($bz2tmpfile->filename);
-  like($content, qr/test data/, "Bzip2: correct content");
-  like($content, qr/more data/, "Bzip2: more correct content");
-
-  # test bz_slurp_to_array
-  my $content_array = bz_slurp_to_array($bz2tmpfile->filename, 1);
-  ok($content_array->[0] eq 'test data', "Bzip2 slurped file first element");
-  ok($content_array->[1] eq 'some more data.', "Bzip2 slurped file second element");
-
-}
-
-my $ZIP_OK = 0;
-eval {
-  require IO::Compress::Zip;
-  require IO::Uncompress::Unzip;
-  $ZIP_OK = 1;
-};
-
-SKIP: {
-  skip "Cannot run Zip/Unzip tests, install related IO::[Un]Compress modules first",
-    4 unless $ZIP_OK;
-
-  # send the content of the tmpfile to another
-  # bzip2 compressed file
-  my $file_content = slurp($tmpfilename);
-  my $ziptmpfile = File::Temp->new(DIR => $dirname, SUFFIX => '.zip');
-
-  zip_work_with_file($ziptmpfile->filename, 'w', sub {
-    my ($fh) = @_;
-    print $fh $file_content;
-    return;
-  });
-
-  # check the content of the compressed file
-  my $content = zip_slurp($ziptmpfile->filename);
-  like($content, qr/test data/, "Zip: correct content");
-  like($content, qr/more data/, "Zip: more correct content");
-
-  # test zip_slurp_to_array
-  my $content_array = zip_slurp_to_array($ziptmpfile->filename, 1);
-  ok($content_array->[0] eq 'test data', "Zip slurped file first element");
-  ok($content_array->[1] eq 'some more data.', "Zip slurped file second element");
-
-}
-
-
-#
-# test filtering the content of a directory
-#
-my $perl_tmp_file1 = File::Temp->new(DIR => $dirname, SUFFIX => '.pl');
-my $perl_tmp_file2 = File::Temp->new(DIR => $dirname, SUFFIX => '.pl');
-my $perl_tmp_file3 = File::Temp->new(DIR => $dirname, SUFFIX => '.pl');
-my $other_tmp_file1 = File::Temp->new(DIR => $dirname, SUFFIX => '.dat');
-my $other_tmp_file2 = File::Temp->new(DIR => $dirname, SUFFIX => '.dat');
-
-is(scalar @{Bio::EnsEMBL::Utils::IO::filter_dir($dirname, sub {
-						  my $file = shift;
-						  return $file if $file =~ /\.pl$/;
-						})}, 3, "Number of entries in filtered and sorted dir");
-
-done_testing();

modules/t/utilsIo.t

@@ -17,11 +17,11 @@ use warnings;
 
 use Test::More;
 use Test::Exception;
-use File::Temp qw/tempfile/;
+use File::Temp;
 use Bio::EnsEMBL::Utils::IO qw/:all/;
 use IO::String;
 
-my ($tmp_fh, $file) = tempfile();
+my ($tmp_fh, $file) = File::Temp::tempfile();
 close($tmp_fh);
 unlink $file;
 
@@ -117,4 +117,101 @@ my $expected_array = [qw/>X AAAAGGGTTCCC TTGGCCAAAAAA ATTC/];
   dies_ok { slurp($file) } 'File no longer exists so die';
 }
 
+my $tmpdir = File::Temp->newdir();
+my $dirname = $tmpdir->dirname;
+
+#
+# test working with bzip2 and zip files
+#
+# create a dummy file
+my $tmpfile = File::Temp->new(DIR => $dirname, SUFFIX => '.txt');
+my $tmpfilename = $tmpfile->filename;
+print $tmpfile "test data\n";
+print $tmpfile "some more data.";
+$tmpfile->close;
+
+my $BZIP2_OK = 0;
+eval {
+  require IO::Compress::Bzip2;
+  require IO::Uncompress::Bunzip2;
+  $BZIP2_OK = 1;
+};
+
+SKIP: {
+  skip "Cannot run Bzip2/Bunzip2 tests, install related IO::[Un]Compress modules first",
+    4 unless $BZIP2_OK;
+
+  # send the content of the tmpfile to another
+  # bzip2 compressed file
+  my $file_content = slurp($tmpfilename);
+  my $bz2tmpfile = File::Temp->new(DIR => $dirname, SUFFIX => '.bz2');
+
+  bz_work_with_file($bz2tmpfile->filename, 'w', sub {
+    my ($fh) = @_;
+    print $fh $file_content;
+    return;
+  });
+
+  # check the content of the compressed file
+  my $content = bz_slurp($bz2tmpfile->filename);
+  like($content, qr/test data/, "Bzip2: correct content");
+  like($content, qr/more data/, "Bzip2: more correct content");
+
+  # test bz_slurp_to_array
+  my $content_array = bz_slurp_to_array($bz2tmpfile->filename, 1);
+  ok($content_array->[0] eq 'test data', "Bzip2 slurped file first element");
+  ok($content_array->[1] eq 'some more data.', "Bzip2 slurped file second element");
+
+}
+
+my $ZIP_OK = 0;
+eval {
+  require IO::Compress::Zip;
+  require IO::Uncompress::Unzip;
+  $ZIP_OK = 1;
+};
+
+SKIP: {
+  skip "Cannot run Zip/Unzip tests, install related IO::[Un]Compress modules first",
+    4 unless $ZIP_OK;
+
+  # send the content of the tmpfile to another
+  # bzip2 compressed file
+  my $file_content = slurp($tmpfilename);
+  my $ziptmpfile = File::Temp->new(DIR => $dirname, SUFFIX => '.zip');
+
+  zip_work_with_file($ziptmpfile->filename, 'w', sub {
+    my ($fh) = @_;
+    print $fh $file_content;
+    return;
+  });
+
+  # check the content of the compressed file
+  my $content = zip_slurp($ziptmpfile->filename);
+  like($content, qr/test data/, "Zip: correct content");
+  like($content, qr/more data/, "Zip: more correct content");
+
+  # test zip_slurp_to_array
+  my $content_array = zip_slurp_to_array($ziptmpfile->filename, 1);
+  ok($content_array->[0] eq 'test data', "Zip slurped file first element");
+  ok($content_array->[1] eq 'some more data.', "Zip slurped file second element");
+
+}
+
+
+#
+# test filtering the content of a directory
+#
+my $perl_tmp_file1 = File::Temp->new(DIR => $dirname, SUFFIX => '.pl');
+my $perl_tmp_file2 = File::Temp->new(DIR => $dirname, SUFFIX => '.pl');
+my $perl_tmp_file3 = File::Temp->new(DIR => $dirname, SUFFIX => '.pl');
+my $other_tmp_file1 = File::Temp->new(DIR => $dirname, SUFFIX => '.dat');
+my $other_tmp_file2 = File::Temp->new(DIR => $dirname, SUFFIX => '.dat');
+
+is(scalar @{Bio::EnsEMBL::Utils::IO::filter_dir($dirname, sub {
+						  my $file = shift;
+						  return $file if $file =~ /\.pl$/;
+						})}, 3, "Number of entries in filtered and sorted dir");
+
+
 done_testing();