Bio::Root::Test(3pm) User Contributed Perl Documentation Bio::Root::Test(3pm)
NAME
Bio::Root::Test - A common base for all Bioperl test scripts.
SYNOPSIS
use lib '.'; # (for core package tests only)
use Bio::Root::Test;
test_begin(-tests => 20,
-requires_modules => [qw(IO::String XML::Parser)],
-requires_networking => 1);
my $do_network_tests = test_network();
my $output_debugging = test_debug();
# carry out tests with Test::More, Test::Exception and Test::Warn syntax
SKIP: {
# these tests need version 2.6 of Optional::Module to work
test_skip(-tests => 10, -requires_module => 'Optional::Module 2.6');
use_ok('Optional::Module');
# 9 other optional tests that need Optional::Module
}
SKIP: {
test_skip(-tests => 10, -requires_networking => 1);
# 10 optional tests that require internet access (only makes sense in the
# context of a script that doesn't use -requires_networking in the call to
# &test_begin)
}
# in unix terms, we want to test with a file t/data/input_file.txt
my $input_file = test_input_file('input_file.txt');
# we want the name of a file we can write to, that will be automatically
# deleted when the test script finishes
my $output_file = test_output_file();
# we want the name of a directory we can store files in, that will be
# automatically deleted when the test script finishes
my $output_dir = test_output_dir();
DESCRIPTION
This provides a common base for all BioPerl test scripts. It safely handles the loading of Test::More, Test::Exception and Test::Warn
(actually, a subclass compatible with Bioperl warnings) prior to tests being run. It also presents an interface to common needs such as
skipping all tests if required modules aren't present or if network tests haven't been enabled. See test_begin().
In the same way, it allows you to skip just a subset of tests for those same reasons, in addition to requiring certain executables and
environment variables. See test_skip().
It also has two further methods that let you decide if network tests should be run, and if debugging information should be printed. See
test_network() and test_debug().
Finally, it presents a consistent way of getting the path to input and output files. See test_input_file(), test_output_file() and
test_output_dir().
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
test_begin
Title : test_begin
Usage : test_begin(-tests => 20);
Function: Begin your test script, setting up the plan (skip all tests, or run
them all)
Returns : True if tests should be run.
Args : -tests => int (REQUIRED, the number of tests that will
be run)
-requires_modules => [] (array ref of module names that are
required; if any don't load, all tests
will be skipped. To specify a required
version of a module, include the version
number after the module name, separated
by a space)
-requires_module => str (as above, but for just one module)
-requires_networking => 1|0 (default 0, if true all tests will be
skipped if network tests haven't been
enabled in Build.PL)
-requires_email => 1 (if true the desired number of tests will
be skipped if either network tests
haven't been enabled in Build.PL or an
email hasn't been entered)
-excludes_os => str (default none, if OS suppied, all tests
will skip if running on that OS (eg.
'mswin'))
-framework => str (default 'Test::More', the Test module
to load. NB: experimental, avoid using)
Note, supplying -tests => 0 is possible, allowing you to skip all
tests in the case that a test script is testing deprecated modules
that have yet to be removed from the distribution
test_skip
Title : test_skip
Usage : SKIP: {
test_skip(-tests => 10,
-requires_module => 'Optional::Module 2.01');
# 10 tests that need v2.01 of Optional::Module
}
Function: Skip a subset of tests for one of several common reasons: missing one
or more optional modules, network tests haven't been enabled, a
required binary isn't present, or an environmental variable isn't set
Returns : n/a
Args : -tests => int (REQUIRED, the number of tests that are
to be skipped in the event one of the
following options isn't satisfied)
-requires_modules => [] (array ref of module names that are
required; if any don't load, the desired
number of tests will be skipped. To
specify a required version of a module,
include the version number after the
module name, separated by a space)
-requires_module => str (as above, but for just one module)
-requires_executable => Bio::Tools::Run::WrapperBase instance
(checks WrapperBase::executable for the
presence of a binary, skips if absent)
-requires_env => str (checks %ENV for a specific env. variable,
skips if absent)
-excludes_os => str (default none, if OS suppied, desired num
of tests will skip if running on that OS
(eg. 'mswin'))
-requires_networking => 1 (if true the desired number of tests will
be skipped if network tests haven't been
enabled in Build.PL)
-requires_email => 1 (if true the desired number of tests will
be skipped if either network tests
haven't been enabled in Build.PL or an
email hasn't been entered)
test_output_file
Title : test_output_file
Usage : my $output_file = test_output_file();
Function: Get the full path of a file suitable for writing to.
When your test script ends, the file will be automatically deleted.
Returns : string (file path)
Args : none
test_output_dir
Title : test_output_dir
Usage : my $output_dir = test_output_dir();
Function: Get the full path of a directory suitable for storing temporary files
in.
When your test script ends, the directory and its contents will be
automatically deleted.
Returns : string (path)
Args : none
test_input_file
Title : test_input_file
Usage : my $input_file = test_input_file();
Function: Get the path of a desired input file stored in the standard location
(currently t/data), but correct for all platforms.
Returns : string (file path)
Args : list of strings (ie. at least the input filename, preceded by the
names of any subdirectories within t/data)
eg. for the file t/data/in.file pass 'in.file', for the file
t/data/subdir/in.file, pass ('subdir', 'in.file')
test_network
Title : test_network
Usage : my $do_network_tests = test_network();
Function: Ask if network tests should be run.
Returns : boolean
Args : none
test_email
Title : test_email
Usage : my $do_network_tests = test_email();
Function: Ask if email address provided
Returns : boolean
Args : none
test_debug
Title : test_debug
Usage : my $output_debugging = test_debug();
Function: Ask if debugging information should be output.
Returns : boolean
Args : none
float_is
Title : float_is
Usage : float_is($val1, $val2);
Function: test two floating point values for equality
Returns : Boolean based on test (can use in combination with diag)
Args : two scalar values (floating point numbers) (required via prototype)
test message (optional)
perl v5.14.2 2012-03-02 Bio::Root::Test(3pm)