From 5090e6739b5e5083937831c8c41882ccecd95a96 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Tue, 9 Dec 2014 10:12:48 +0000
Subject: [PATCH] utilsIo.t merged with io.t
---
modules/t/io.t | 129 --------------------------------------------
modules/t/utilsIo.t | 101 +++++++++++++++++++++++++++++++++-
2 files changed, 99 insertions(+), 131 deletions(-)
delete mode 100644 modules/t/io.t
diff --git a/modules/t/io.t b/modules/t/io.t
deleted file mode 100644
index cbc6568758..0000000000
--- a/modules/t/io.t
+++ /dev/null
@@ -1,129 +0,0 @@
-# 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();
diff --git a/modules/t/utilsIo.t b/modules/t/utilsIo.t
index e3c7e81d09..7f7ed10f45 100644
--- a/modules/t/utilsIo.t
+++ b/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();
--
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