Linux Certif

Toute la documentation sur la certification Linux LPI

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:

   http://bugzilla.open-bio.org/
 
 

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)
            -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)
 
 

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_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)