Summary

Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  # do not use this object directly, it provides the following methods
  # for its subclasses

  my $errstr = $obj->error_string();
  my $exe    = $obj->executable();
  $obj->save_tempfiles($booleanflag)
  my $outfile= $obj->outfile_name();
  my $tempdir= $obj->tempdir(); # get a temporary dir for executing
  my $io     = $obj->io;  # Bio::Root::IO object
  my $cleanup= $obj->cleanup(); # remove tempfiles

  $obj->run({-arg1 => $value});

Description

This is a basic module from which to build executable wrapper modules.
It has some basic methods to help when implementing new modules.

Methods

Methods description

 Title   : run
 Usage   : $wrapper->run({ARGS HERE});
 Function: Support generic running with args passed in
           as a hashref
 Returns : Depends on the implementation, status OR data
 Args    : hashref of named arguments

 Title   : error_string
 Usage   : $obj->error_string($newval)
 Function: Where the output from the last analysis run is stored.
 Returns : value of error_string
 Args    : newvalue (optional)

 Title   : arguments
 Usage   : $obj->arguments($newval)
 Function: Commandline parameters 
 Returns : value of arguments
 Args    : newvalue (optional)

 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values
 Returns : value of no_param_checks
 Args    : newvalue (optional)

 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)

 Title   : outfile_name
 Usage   : my $outfile = $wrapper->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to

 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none

 Title   : cleanup
 Usage   : $wrapper->cleanup();
 Function: Will cleanup the tempdir directory
 Returns : none
 Args    : none

 Title   : io
 Usage   : $obj->io($newval)
 Function: Gets a Bio::Root::IO object
 Returns : Bio::Root::IO object
 Args    : none

 Title   : version
 Usage   : $version = $wrapper->version()
 Function: Returns the program version (if available)
 Returns : string representing version of the program 
 Args    : [Optional] value to (re)set version string

 Title   : executable
 Usage   : my $exe = $factory->executable();
 Function: Finds the full path to the executable
 Returns : string representing the full path to the exe
 Args    : [optional] name of executable to set path to
           [optional] boolean flag whether or not warn when exe is not found

 Title   : program_path
 Usage   : my $path = $factory->program_path();
 Function: Builds path for executable 
 Returns : string representing the full path to the exe
 Args    : none

 Title   : program_dir
 Usage   : my $dir = $factory->program_dir();
 Function: Abstract get method for dir of program. To be implemented
           by wrapper.
 Returns : string representing program directory 
 Args    : none

 Title   : program_name
 Usage   : my $name = $factory->program_name();
 Function: Abstract get method for name of program. To be implemented
           by wrapper.
 Returns : string representing program name
 Args    : none

Methods code

sub run {

   my ($self,@args) = @_;
   $self->throw_not_implemented();

}

sub error_string {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_error_string'} = $value;
    }
    return $self->{'_error_string'} || '';

}

sub arguments {

  my ($self,$value) = @_;
  if(defined $value) {
    $self->{'_arguments'} = $value;
  }
  return $self->{'_arguments'} || '';

}

sub no_param_checks {

   my ($self,$value) = @_;
   if( defined $value || ! defined $self->{'no_param_checks'} ) {
       $value = 0 unless defined $value;
      $self->{'no_param_checks'} = $value;
    }
    return $self->{'no_param_checks'};

}

sub save_tempfiles {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'save_tempfiles'} = $value;
    }
    return $self->{'save_tempfiles'};

}

sub outfile_name {

   my ($self,$nm) = @_;
   if( defined $nm || ! defined $self->{'_outfilename'} ) { 
       $nm = 'mlc' unless defined $nm;
       $self->{'_outfilename'} = $nm;
   }
   return $self->{'_outfilename'};

}

sub tempdir {

   my ($self) = shift;

   $self->{'_tmpdir'} = shift if @_;
   unless( $self->{'_tmpdir'} ) {
       $self->{'_tmpdir'} = $self->io->tempdir(CLEANUP => ! $self->save_tempfiles );
   }
   unless( -d $self->{'_tmpdir'} ) {
       mkdir($self->{'_tmpdir'},0777);
   }
   return $self->{'_tmpdir'};

}

sub cleanup {

   my ($self) = @_;
   $self->io->_io_cleanup();
   if( defined $self->{'_tmpdir'} && -d $self->{'_tmpdir'} ) {
       # $self->io->rmtree($self->{'_tmpdir'});
       File::Path->rmtree( $self->{'_tmpdir'} );
   }

}

sub io {

   my ($self) = @_;
   unless( defined $self->{'io'} ) {
       $self->{'io'} = new Bio::Root::IO(-verbose => $self->verbose());
   }
    return $self->{'io'};

}

sub version {

   my ($self,@args) = @_;
   return;

}

sub executable {

   my ($self, $exe,$warn) = @_;

   if( defined $exe ) {
     $self->{'_pathtoexe'} = $exe;
   }
   unless( defined $self->{'_pathtoexe'} ) {
       my $prog_path = $self->program_path;
       if( $prog_path && -e $prog_path && -x $prog_path ) {
           $self->{'_pathtoexe'} = $prog_path;
       } else {
           my $exe;
           if( ( $exe = $self->io->exists_exe($self->program_name) ) &&
               -x $exe ) {
               $self->{'_pathtoexe'} = $exe;
           } else {
               $self->warn("Cannot find executable for ".$self->program_name) if $warn;
               $self->{'_pathtoexe'} = undef;
           }
       }
   }
   $self->{'_pathtoexe'};

}

sub program_path {

    my ($self) = @_;
    my @path;
    push @path, $self->program_dir if $self->program_dir;
    push @path, $self->program_name.($^O =~ /mswin/i ?'.exe':'');

    return File::Spec->catfile(@path);

}

sub program_dir {

    my ($self) = @_;
    $self->throw_not_implemented();

}

sub program_name {

    my ($self) = @_;
    $self->throw_not_implemented();

}

sub DESTROY {

    my $self= shift;
    unless ( $self->save_tempfiles ) {
	$self->cleanup();
    }
    $self->SUPER::DESTROY();

}

General documentation

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

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/

Email jason-at-bioperl.org

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _