Bio::Tools::Run WrapperBase
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Summary
Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables
Package variables
No package variables defined.
Included modules
File::Path qw ( )
File::Spec
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
runDescriptionCode
error_stringDescriptionCode
argumentsDescriptionCode
no_param_checksDescriptionCode
save_tempfilesDescriptionCode
outfile_nameDescriptionCode
tempdirDescriptionCode
cleanupDescriptionCode
ioDescriptionCode
versionDescriptionCode
executableDescriptionCode
program_pathDescriptionCode
program_dirDescriptionCode
program_nameDescriptionCode
quietDescriptionCode
_setparamsDescriptionCode
DESTROY
No description
Code
Methods description
runcode    nextTop
 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
error_stringcodeprevnextTop
 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)
argumentscodeprevnextTop
 Title   : arguments
Usage : $obj->arguments($newval)
Function: Commandline parameters
Returns : value of arguments
Args : newvalue (optional)
no_param_checkscodeprevnextTop
 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)
save_tempfilescodeprevnextTop
 Title   : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function: Get/set the choice of if tempfiles in the temp dir (see tempdir())
are kept or cleaned up. Default is '0', ie. delete temp files.
NB: This must be set to the desired value PRIOR to first creating
a temp dir with tempdir(). Any attempt to set this after tempdir creation will get a warning.
Returns : boolean
Args : none to get, boolean to set
outfile_namecodeprevnextTop
 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
tempdircodeprevnextTop
 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
cleanupcodeprevnextTop
 Title   : cleanup
Usage : $wrapper->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
iocodeprevnextTop
 Title   : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO object
Args : none
versioncodeprevnextTop
 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
executablecodeprevnextTop
 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
program_pathcodeprevnextTop
 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
program_dircodeprevnextTop
 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
program_namecodeprevnextTop
 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
quietcodeprevnextTop
 Title   : quiet
Usage : $factory->quiet(1);
if ($factory->quiet()) { ... }
Function: Get/set the quiet state. Can be used by wrappers to control if
program output is printed to the console or not.
Returns : boolean
Args : none to get, boolean to set
_setparams()codeprevnextTop
 Title   : _setparams
Usage : $params = $self->_setparams(-params => [qw(window evalue_cutoff)])
Function: For internal use by wrapper modules to build parameter strings
suitable for sending to the program being wrapped. For each method
name supplied, calls the method and adds the method name (as modified
by optional things) along with its value (unless a switch) to the
parameter string
Example : $params = $self->_setparams(-params => [qw(window evalue_cutoff)],
-switches => [qw(simple large all)],
-double_dash => 1,
-underscore_to_dash => 1);
If window() and simple() had not been previously called, but
evalue_cutoff(0.5), large(1) and all(0) had been called, $params
would be ' --evalue-cutoff 0.5 --large'
Returns : parameter string
Args : -params => [] or {} # array ref of method names to call,
or hash ref where keys are method names and
values are how those names should be output
in the params string
-switches => [] or {}# as for -params, but no value is printed for
these methods
-join => string # define how parameters and their values are
joined, default ' '. (eg. could be '=' for
param=value)
-lc => boolean # lc() method names prior to output in string
-dash => boolean # prefix all method names with a single dash
-double_dash => bool # prefix all method names with a double dash
-mixed_dash => bool # prefix single-character method names with a
# single dash, and multi-character method names
# with a double-dash
-underscore_to_dash => boolean # convert all underscores in method
names to dashes
Methods code
rundescriptionprevnextTop
sub run {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
error_stringdescriptionprevnextTop
sub error_string {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_error_string'} = $value;
    }
    return $self->{'_error_string'} || '';
}
argumentsdescriptionprevnextTop
sub arguments {
  my ($self,$value) = @_;
  if(defined $value) {
    $self->{'_arguments'} = $value;
  }
  return $self->{'_arguments'} || '';
}
no_param_checksdescriptionprevnextTop
sub no_param_checks {
   my ($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'};
}
save_tempfilesdescriptionprevnextTop
sub save_tempfiles {
    my $self = shift;
    my @args = @_;
    if (($args[0]) && (exists ($self->{'_tmpdir'}))) {
        $self->warn ("Tempdir already created; setting save_tempfiles will not affect cleanup behavior.");
    }
    return $self->io->save_tempfiles(@_);
}
outfile_namedescriptionprevnextTop
sub outfile_name {
   my ($self,$nm) = @_;
   if( defined $nm || ! defined $self->{'_outfilename'} ) {
       $nm = 'mlc' unless defined $nm;
       $self->{'_outfilename'} = $nm;
   }
   return $self->{'_outfilename'};
}
tempdirdescriptionprevnextTop
sub tempdir {
   my ($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 $self->{'_tmpdir'};
}
cleanupdescriptionprevnextTop
sub cleanup {
   my ($self) = @_;
   $self->io->_io_cleanup();
   if( defined $self->{'_tmpdir'} && -d $self->{'_tmpdir'} ) {
      my $verbose = ($self->verbose >= 1) ? 1 : 0;
      File::Path::rmtree( $self->{'_tmpdir'}, $verbose);
   }
}
iodescriptionprevnextTop
sub io {
   my ($self) = @_;
   unless( defined $self->{'io'} ) {
       $self->{'io'} = Bio::Root::IO->new(-verbose => $self->verbose);
   }
    return $self->{'io'};
}
versiondescriptionprevnextTop
sub version {
   my ($self,@args) = @_;
   return;
}
executabledescriptionprevnextTop
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) {
            if (-f $prog_path && -x $prog_path) {
                $self->{'_pathtoexe'} = $prog_path;
            }
            elsif ($self->program_dir) {
                $self->warn("executable not found in $prog_path, trying system path...") if $warn;
            }
        }
        unless ($self->{'_pathtoexe'}) {
            my $exe;
            if ( $exe = $self->io->exists_exe($self->program_name) ) {
                $self->{'_pathtoexe'} = $exe;
            }
            else {
                $self->warn("Cannot find executable for ".$self->program_name) if $warn;
                $self->{'_pathtoexe'} = undef;
            }
        }
    }

    # bail if we never found the executable
unless ( defined $self->{'_pathtoexe'}) { $self->throw("Cannot find executable for ".$self->program_name . ". path=\"".$self->program_path."\""); } return $self->{'_pathtoexe'};
}
program_pathdescriptionprevnextTop
sub program_path {
   my ($self) = @_;
   my @path;
   push @path, $self->program_dir if $self->program_dir;
   push @path, $self->program_name.($^O =~ /mswin/i ? '.exe' : '') if $self->program_name;
   return File::Spec->catfile(@path);
}
program_dirdescriptionprevnextTop
sub program_dir {
    my ($self) = @_;
    $self->throw_not_implemented();
}
program_namedescriptionprevnextTop
sub program_name {
    my ($self) = @_;
    $self->throw_not_implemented();
}
quietdescriptionprevnextTop
sub quiet {
    my $self = shift;
    if (@_) { $self->{quiet} = shift }
    return $self->{quiet} || 0;
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($self, @args) = @_;

    my ($params, $switches, $join, $lc, $d, $dd, $md, $utd) =
        $self->_rearrange([qw(PARAMS
                              SWITCHES
                              JOIN
                              LC
                              DASH
                              DOUBLE_DASH
                              MIXED_DASH
                              UNDERSCORE_TO_DASH)], @args);
    $self->throw('at least one of -params or -switches is required') unless ($params || $switches);
    $self->throw("-dash, -double_dash and -mixed_dash are mutually exclusive") if (defined($d) + defined($dd) + defined($md) > 1);
    $join ||= ' ';

    my %params = ref($params) eq 'HASH' ? %{$params} : map { $_ => $_ } @{$params};
    my %switches = ref($switches) eq 'HASH' ? %{$switches} : map { $_ => $_ } @{$switches};

    my $param_string = '';
    for my $hash_ref (\%params,\% switches) {
        while (my ($method, $method_out) = each %{$hash_ref}) {
            my $value = $self->$method();
            next unless (defined $value);
            next if (exists $switches{$method} && ! $value);

            $method_out = lc($method_out) if $lc;
            my $method_length = length($method_out) if $md;
            $method_out = '-'.$method_out if ($d || ($md && ($method_length == 1)));
            $method_out = '--'.$method_out if ($dd || ($md && ($method_length > 1)));
            $method_out =~ s/_/-/g if $utd;

            if ( exists $params{$method} ) {
              # if value are quoted with " or ', re-quote it
if ( $value =~ m{^[\'\"]+(.+)[\'\"]+$} ) { $value = '"'. $1 . '"'; } # quote values that contain spaces
elsif ( $value =~ m{\s+} ) { $value = '"'. $value . '"'; } } $param_string .= ' '.$method_out.(exists $switches{$method} ? '' : $join.$value); } } return $param_string;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self= shift;
    unless ( $self->save_tempfiles ) {
	$self->cleanup();
    }
    $self->SUPER::DESTROY();
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
SupportTop
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 BugsTop
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 - Jason StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Sendu Bala, bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _